ORCID Profile
0000-0002-8783-1223
Current Organisations
Queensland University of Technology
,
Queensland University of Technology School of Teacher Education and Leadership
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Research Topics
In Research Link Australia (RLA), "Research Topics" refer to ANZSRC FOR and SEO codes. These topics are either sourced from ANZSRC FOR and SEO codes listed in researchers' related grants or generated by a large language model (LLM) based on their publications.
Top 5 Research Topics
ANZSRC Field of Research (FoR)
Water Resources Engineering | Water Quality Engineering | Simulation And Modelling | Colloid And Surface Chemistry | Fluidization And Fluid Mechanics | Physical Geography and Environmental Geoscience | Social And Community Psychology | Physical Chemistry (Incl. Structural) | Environmental Engineering | Environmental Engineering Design | Civil Engineering | Road And Rail Transportation | Environmental Engineering Modelling | Applied Hydrology (Drainage, Flooding, Irrigation, Quality, Etc.) | Groundwater Hydrology | Surfacewater Hydrology | Urban And Regional Planning | Urban and Regional Planning | Interdisciplinary Engineering Not Elsewhere Classified | Water And Sanitary Engineering | Interdisciplinary Engineering | Decision Support And Group Support Systems | Computer Vision
ANZSRC Socio-Economic Objective (SEO)
Land and water management | Management and productivity issues not elsewhere classified | Land and water management | Integrated systems | Air transport | Water Services and Utilities | Ground transport | Climate change | Land and water management | Land and water management | Civil | Water and Waste Services not elsewhere classified | Ground transport not elsewhere classified | Waste management and recycling |
Related Links
Publications
Taxonomy for rainfall events based on pollutant wash-off potential in urban areas
Publisher: Elsevier BV
Date: 10-2012
Monitoring of a mixed land use catchment for pollutant source characterisation
Publisher: Springer Science and Business Media LLC
Date: 13-06-2017
DOI: 10.1007/S10661-017-6047-7
Abstract: Protection of surface water quality is a key driver in catchment management, particularly for areas undergoing land use change. Changing land use can result in the input of a range of pollutants to surface waters, resulting in water quality impairment, leading to eutrophication and the appearance of algae blooms. This study investigated a mixed land use coastal catchment by undertaking extensive field s ling and data analysis for pollutant source characterisation. The objective was to contribute to a greater understanding of pollutant inputs to surface water resources and for effective catchment management. Based on data analysis results, a ersity of pollutant sources was noted, including both natural areas and areas subject to anthropogenic activities such as agriculture and urban developments, with agricultural areas being comparatively more significant in exporting nutrients. Additionally, pollutant inputs into estuarine and freshwater areas were found to have specific characteristics influenced by land use. The pollutant inputs from these sources were found to be significantly affected by seasonal factors, with the dominant pollutant sources differing between the wet and dry seasons. This underlines the importance of taking seasonal factors into account in the development of effective catchment management strategies. Based on the study outcomes, a critical point monitoring program was developed with a focus on preventing algae blooms. This will allow the development of a decentralised catchment management strategy where resource-efficient monitoring of critical pollutant parameters at key locations can be undertaken for minimising the risk from algae blooms, rather than implementing a whole of catchment and resource-demanding large-scale monitoring program.
Author Correction: Divergent mutational processes distinguish hypoxic and normoxic tumours
Publisher: Springer Science and Business Media LLC
Date: 08-12-2022
Inadequacy of land use and impervious area fraction for determining urban stormwater quality
Publisher: Springer Science and Business Media LLC
Date: 13-03-2012
Role of agricultural land practices in the behaviour of nitrates in groundwater
Publisher: Springer Science and Business Media LLC
Date: 28-07-2022
Adsorption and mobility of metals in build-up on road surfaces
Publisher: Elsevier BV
Date: 2015
DOI: 10.1016/J.CHEMOSPHERE.2014.02.048
Abstract: The study investigated the adsorption and bioavailability characteristics of traffic generated metals common to urban land uses, in road deposited solids particles. To validate the outcomes derived from the analysis of field s les, adsorption and desorption experiments were undertaken. The analysis of field s les revealed that metals are selectively adsorbed to different charge sites on solids. Zinc, copper, lead and nickel are adsorbed preferentially to oxides of manganese, iron and aluminium. Lead is adsorbed to organic matter through chemisorption. Cadmium and chromium form weak bonding through cation exchange with most of the particle sizes. Adsorption and desorption experiments revealed that at high metal concentrations, chromium, copper and lead form relatively strong bonds with solids particles while zinc is adsorbed through cation exchange with high likelihood of being released back into solution. Outcomes from this study provide specific guidance for the removal of metals from stormwater based on solids removal.
Distribution of PBDEs, HBCDs and PCBs in the Brisbane River estuary sediment
Publisher: Elsevier BV
Date: 07-2017
DOI: 10.1016/J.MARPOLBUL.2017.05.002
Abstract: To date, very little or no data exist in literature for some brominated flame retardants (BFRs) and polychlorinated biphenyls in Queensland sediments. These pollutants were measured in the sediments along the Brisbane River estuary. The target compounds were regularly detected in measurable concentrations: PBDEs=33.3-97.8% (n=45), PCBs=94.1-100% (n=51) and HBCDs=79-98% (n=48). Consistently, >90% of the observed ∑
Rainfall Simulation to Evaluate Pollutant Build-Up and Wash-Off from Selected Land Uses Within a Port Environment
Publisher: American Society of Civil Engineers
Date: 22-03-2007
DOI: 10.1061/40834(238)29
Rainfall Simulation as a Tool for Urban Water Quality Research
Publisher: Mary Ann Liebert Inc
Date: 05-2005
Primary pancreatic spindle cell sarcoma with a TMEM106B::BRAF gene fusion treated with MEK inhibition
Publisher: Elsevier BV
Date: 02-2023
Sources and transport pathways of common heavy metals to urban road surfaces
Publisher: Elsevier BV
Date: 04-2015
Selecting rainfall events for effective Water Sensitive Urban Design: A case study in Gold Coast City, Australia
Publisher: Elsevier BV
Date: 07-2016
A rare diagnostically challenging case of CIC-DUX4 sarcoma arising in the neck
Publisher: Elsevier BV
Date: 06-2023
Assessing mercury pollution in Amazon River tributaries using a Bayesian Network approach
Publisher: Elsevier BV
Date: 12-2018
DOI: 10.1016/J.ECOENV.2018.09.099
Abstract: Mercury pollution of water bodies exerts significant human and ecosystem health impacts due to high toxicity. Relatively high levels of mercury have been detected in the Amazon River and its tributaries and associated lakes. The study employed a Bayesian Network approach to investigate the contribution from geogenic sources to mercury pollution of lakes in the Madeira River basin, which is the largest tributary of the Amazon River. It was found that the source indicators of naturally occurring mercury have both, positive and negative relationships with mercury in lake sediments. Although the positive relationships indicated the influence of geological and soil formations, the negative relationships implied that the use of mercury amalgam for gold extraction in artisanal and small-scale mining (ASM), which is the primary anthropogenic source of mercury, also contribute to mercury in Amazon tributaries. This was further evident as mercury concentrations in lake sediments were found to be significantly higher than those in the surrounding rocks. However, potential anthropogenic mercury was attributed to historical inputs from gold mining due to the recent decline of ASM mining practice in the region.
Targeting of TP53-independent cell cycle checkpoints overcomes FOLFOX resistance in Metastatic Colorectal Cancer
Publisher: Cold Spring Harbor Laboratory
Date: 05-02-2021
DOI: 10.1101/2021.02.04.429849
Abstract: Patients with colorectal cancer (CRC) frequently develop liver metastases during the course of their disease. A substantial proportion of them receive neoadjuvant FOLFOX (5-Fluorouracil, Oxaliplatin, Leucovorin) prior to surgery in an attempt to enable successful surgical removal of their metastases and to reduce the risk of recurrence. Yet, the majority of patients progress during treatment or recur following surgery, and molecular mechanisms that contribute to FOLFOX resistance remain poorly understood. Here, using a combination of phenotypic, transcriptomic and genomic analyses of both tumor s les derived from patients with metastatic CRC and matching patient-derived tumor organoids (PDTOs), we characterize a novel FOLFOX resistance mechanism and identify inhibitors that target this mechanism to resensitize metastatic organoids to FOLFOX. Resistant PDTOs, identified after in vitro exposure to FOLFOX, exhibited elevated expression of E2F pathway, S phase, G 2 /M and spindle assembly checkpoints (SAC) genes. Similar molecular features were detected in CRLM from patients with progressive disease while under neoadjuvant FOLFOX treatment, highlighting the relevance of this finding. FOLFOX resistant PDTOs displayed inactivating mutations of TP53 and exhibited transcriptional features of P53 pathway downregulation. We found that they accumulated in early S-phase and underwent significant DNA damage during FOLFOX exposure, thereafter arresting in G 2 /M while they repaired their DNA after FOLFOX withdrawal. In parallel, results of a large kinase inhibitor screen indicated that drugs targeting regulators of the DNA damage response, G 2 M checkpoint and SAC had cytotoxic effects on PDTOs generated from patients whose disease progressed during treatment with FOLFOX. Corroborating this finding, CHK1 and WEE1 inhibitors were found to synergize with FOLFOX and sensitize previously resistant PDTOs. Additionally, targeting the SAC master regulator MPS1 using empesertib after exposure to FOLFOX, when cells accumulate in G 2 M, was also very effective to kill FOLFOX-resistant PDTOs. Our results indicate that targeted and timely inhibition of specific cell cycle checkpoints shows great potential to improve response rates to FOLFOX in patients with metastatic CRC, for whom therapeutic alternatives remain extremely limited.
Detection and source identification of faecal pollution in non-sewered catchment by means of host-specific molecular markers
Publisher: IWA Publishing
Date: 08-2008
DOI: 10.2166/WST.2008.436
Abstract: Multiple host-specific molecular markers were used to detect the sources of faecal pollution in a mixed land use non-sewered catchment in Southeast Queensland, Australia. These markers included human-specific Bacteroides (HF183 and HF134), cattle-specific Bacteroides (CF128), dog-specific Bacteroides (BacCan) and human-specific enterococci surface protein (esp) markers. The sensitivity and specificity of these markers were determined by testing 197 faecal s les from 13 host groups. The overall sensitivity and specificity of these markers was high (sensitivity≥85% and specificity≥93%) indicating their suitability for detecting the sources of faecal pollution. Of the 16 s les collected from the study area, 14 (87%) were positive for at least one of the molecular marker tested. Amongst all the markers, cattle-specific CF128 was more prevalent than others, followed by human-specific HF183 which was consistently detected in s les collected from sites within close proximity to urban development. Significant correlations were found between E. coli and enterococci concentrations with the positive/negative results of human-specific Bacteroides HF183 (p& .001, p& .0001) and HF134 (p& .001, p& .004) markers. No correlations were found between faecal indicators (E. coli or enterococci) with the CF128 or BacCan markers. A significant correlation was also found between enterococci concentrations and the presence/absence of the esp marker (p& .02). Based on the results, it appears that the host-specific markers such as HF183 and esp are a sensitive measure of sources of human faecal pollution in surface waters in Southeast Queensland, Australia.
Decision making with uncertainty in stormwater pollutant processes: A perspective on urban stormwater pollution mitigation
Publisher: Springer Singapore
Date: 2019
Determination of surrogate indicators for phosphorus and solids in urban stormwater : application of multivariate data analysis techniques
Publisher: Springer Science and Business Media LLC
Date: 03-01-2007
Influence of the hierarchical structure of land use on metals, nutrients and organochlorine pesticides in urban river sediments
Publisher: Elsevier BV
Date: 2021
Spatial response surface modelling in the presence of data paucity for the evaluation of potential human health risk due to the contamination of potable water resources
Publisher: Elsevier BV
Date: 10-2016
DOI: 10.1016/J.SCITOTENV.2016.05.200
Abstract: Potential human health risk from waterborne diseases arising from unsatisfactory performance of on-site wastewater treatment systems is driven by landscape factors such as topography, soil characteristics, depth to water table, drainage characteristics and the presence of surface water bodies. These factors are present as random variables which are spatially distributed across a region. A methodological framework is presented that can be applied to model and evaluate the influence of various factors on waterborne disease potential. This framework is informed by spatial data and expert knowledge. For prediction at uns led sites, interpolation methods were used to derive a spatially smoothed surface of disease potential which takes into account the uncertainty due to spatial variation at any pre-determined level of significance. This surface was constructed by accounting for the influence of multiple variables which appear to contribute to disease potential. The framework developed in this work strengthens the understanding of the characteristics of disease potential and provides predictions of this potential across a region. The study outcomes presented constitutes an innovative approach to environmental monitoring and management in the face of data paucity.
Source apportionment and risk assessment of PAHs in Brisbane River sediment, Australia
Publisher: Elsevier BV
Date: 02-2017
Potential bioavailability assessment, source apportionment and ecological risk of heavy metals in the sediment of Brisbane River estuary, Australia
Publisher: Elsevier BV
Date: 04-2017
DOI: 10.1016/J.MARPOLBUL.2017.02.017
Abstract: A weak acid extraction was used to mobilize the loosely bound metals in estuary sediment s les. More than 30% of Ag, As, Ca, Cd, Co, Cu, Hg, Mn Ni, Pb and Zn were leached from the sediment showing that these metals are significantly present in the bioavailable form. PCA/APCS identified three sources of the metals, namely: lithogenic accounting for 72%, shipping related contributing 15% and traffic related representing 13% of the total load. Application of pollution index (PI) and modified pollution index (MPI) revealed that the sediment range from unpolluted to heavily polluted while ecological risk index (RI) classifies the sediment as posing low ecological risk modified ecological risk index (MRI) suggests considerable to very high ecological risk. To provide holistic insights into the ecological risks posed by metals, enrichment factor, MPI and MRI are recommended for the assessment of sediment in complex environments such as estuaries.
Comprehensive carbon stock and flow accounting: A national framework to support climate change mitigation policy
Publisher: Elsevier BV
Date: 05-2013
Author Correction: Integrative pathway enrichment analysis of multivariate omics data
Publisher: Springer Science and Business Media LLC
Date: 08-12-2022
Factors influencing organochlorine pesticides distribution in the Brisbane River Estuarine sediment, Australia
Publisher: Elsevier BV
Date: 10-2017
DOI: 10.1016/J.MARPOLBUL.2017.09.022
Abstract: Sediment s les collected from Brisbane River were analysed for organochlorine pesticide residues (OCPs). The factors influencing OCPs distribution in the sediment were investigated using multivariate analytical tools. Thirteen OCPs were detected in the sediment with concentrations ranging between below detection to 83.9ng/g, and detection frequency >90%. With the exception of dieldrin, the OCP inputs appear to be historical and may cause adverse ecological impacts. Multi-criteria ranking of the factors influencing the OCPs (except dieldrin) distribution in the sediment revealed that TOC>silt>intensive urban land use>population>seasons. Dieldrin distribution is significantly influenced by season>TOC>silt>intensive urban land use>population. The study helps to prioritise factors required for managing OCPs contamination in sediments and identification of appropriate mitigation measures.
Health Risk from the Use of Roof-Harvested Rainwater in Southeast Queensland, Australia, as Potable or Nonpotable Water, Determined Using Quantitative Microbial Risk Assessment
Publisher: American Society for Microbiology
Date: 15-11-2010
DOI: 10.1128/AEM.00944-10
Abstract: A total of 214 rainwater s les from 82 tanks were collected in urban Southeast Queensland (SEQ) in Australia and analyzed for the presence and numbers of zoonotic bacterial and protozoal pathogens using binary PCR and quantitative PCR (qPCR). Quantitative microbial risk assessment (QMRA) analysis was used to quantify the risk of infection associated with the exposure to potential pathogens from roof-harvested rainwater used as potable or nonpotable water. Of the 214 s les tested, 10.7%, 9.8%, 5.6%, and 0.4% were positive for the Salmonella invA , Giardia lamblia β-giardin, Legionella pneumophila mip , and C ylobacter jejuni mapA genes, respectively. Cryptosporidium parvum oocyst wall protein (COWP) could not be detected. The estimated numbers of Salmonella , G. lamblia , and L. pneumophila organisms ranged from 6.5 × 10 1 to 3.8 × 10 2 cells, 0.6 × 10° to 3.6 × 10° cysts, and 6.0 × 10 1 to 1.7 × 10 2 cells per 1,000 ml of water, respectively. Six risk scenarios were considered for exposure to Salmonella spp., G. lamblia , and L. pneumophila . For Salmonella spp. and G. lamblia , these scenarios were (i) liquid ingestion due to drinking of rainwater on a daily basis, (ii) accidental liquid ingestion due to hosing twice a week, (iii) aerosol ingestion due to showering on a daily basis, and (iv) aerosol ingestion due to hosing twice a week. For L. pneumophila , these scenarios were (i) aerosol inhalation due to showering on a daily basis and (ii) aerosol inhalation due to hosing twice a week. The risk of infection from Salmonella spp., G. lamblia , and L. pneumophila associated with the use of rainwater for showering and garden hosing was calculated to be well below the threshold value of one extra infection per 10,000 persons per year in urban SEQ. However, the risk of infection from ingesting Salmonella spp. and G. lamblia via drinking exceeded this threshold value and indicated that if undisinfected rainwater is ingested by drinking, then the incidences of the gastrointestinal diseases salmonellosis and giardiasis are expected to range from 9.8 × 10° to 5.4 × 10 1 (with a mean of 1.2 × 10 1 from Monte Carlo analysis) and from 1.0 × 10 1 to 6.5 × 10 1 cases (with a mean of 1.6 × 10 1 from Monte Carlo analysis) per 10,000 persons per year, respectively, in urban SEQ. Since this health risk seems higher than that expected from the reported incidences of gastroenteritis, the assumptions used to estimate these infection risks are critically examined. Nonetheless, it would seem prudent to disinfect rainwater for use as potable water.
Influence of land use class and configuration on water-sediment partitioning of heavy metals
Publisher: Elsevier BV
Date: 2022
Essential Indicators for Measuring Area-Based Conservation Effectiveness in the Post-2020 Global Biodiversity Framework
Publisher: MDPI AG
Date: 25-03-2020
DOI: 10.20944/PREPRINTS202003.0370.V1
Abstract: Work has begun in earnest to formulate a post-2020 Global Bio ersity Framework which will outline the vision and targets for the next decade of bio ersity conservation and beyond. However, the performance of the 2011-2020 Strategic Plan for Bio ersity suggests that even a meaningful target can fail to deliver if not accompanied by fit-for-purpose indicators. Here we provide a review of how & lsquo rotected area& rsquo effectiveness was addressed in the 2011-2020 plan and based on this, provide recommendations for fit-for-purpose indicators that will measure how such efforts contribute to the conservation of bio ersity. Indicators need to be built on quantitative data from site-level bio ersity monitoring of species and ecosystems combined with measurements of the state of nature in near-time, informed by remote-sensed products and other technologies. Additionally, indicators need to capture whether the essential elements of good management are in place including the identification of ecological values, threats, and objectives, equitable governance, and sufficient management resources and capacity. These fit-for-purpose indicators will require multilateral collaboration to galvanize support for, and resources to develop, the necessary infrastructure to collate and store information from countries.
The Diverse Applications of Pancreatic Ductal Adenocarcinoma Organoids
Publisher: MDPI AG
Date: 04-10-2021
Abstract: Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal solid malignancies. While immortalized cancer cell lines and genetically engineered murine models have increased our understanding of PDAC tumorigenesis, they do not recapitulate inter- and intra-patient heterogeneity. PDAC patient derived organoid (PDO) biobanks have overcome this hurdle, and provide an opportunity for the high throughput screening of potential new therapies. This review provides a summary of the PDAC PDO biobanks established to date, and discusses how they have advanced our understanding of PDAC biology. Looking forward, the development of coculturing techniques for specific immune or stromal cell populations will enable a better understanding of the crosstalk that occurs within the tumor microenvironment, and the impact of this crosstalk on treatment response.
Role of Solids in Heavy Metals Buildup on Urban Road Surfaces
Publisher: American Society of Civil Engineers (ASCE)
Date: 04-2012
Treatment technologies for emerging contaminants in water: A review
Publisher: Elsevier BV
Date: 09-2017
Impact of global warming on urban stormwater quality: From the perspective of an alternative water resource
Publisher: Elsevier BV
Date: 07-2020
Microorganisms and heavy metals associated with atmospheric deposition in a congested urban environment of a developing country: Sri Lanka
Publisher: Elsevier BV
Date: 04-2017
DOI: 10.1016/J.SCITOTENV.2017.01.121
Abstract: The presence of bacteria and heavy metals in atmospheric deposition were investigated in Kandy, Sri Lanka, which is a typical city in the developing world with significant traffic congestion. Atmospheric deposition s les were analyzed for Al, Cr, Mn, Fe, Ni, Cu, Zn, Cd and Pb which are heavy metals common to urban environments. Al and Fe were found in high concentrations due to the presence of natural sources, but may also be re-suspended by vehicular traffic. Relatively high concentrations of toxic metals such as Cr and Pb in dissolved form were also found. High Zn loads can be attributed to vehicular emissions and the wide use of Zn coated roofing materials. The metal loads in wet deposition showed higher concentrations compared to dry deposition. The metal concentrations among the different s ling sites significantly differ from each other depending on the traffic conditions. Industrial activities are not significant in Kandy City. Consequently, the traffic exerts high influence on heavy metal loadings. As part of the bacterial investigations, nine species of culturable bacteria, namely Sphingomonas sp., Pseudomonas aeruginosa, Pseudomonas monteilii, Klebsiella pneumonia, Ochrobactrum intermedium, Leclercia adecarboxylata, Exiguobacterium sp., Bacillus pumilus and Kocuria kristinae, which are opportunistic pathogens, were identified. This is the first time Pseudomonas monteilii and Ochrobactrum intermedium has been reported from a country in Asia. The culturable fraction constituted ~0.01 to 10%. Pigmented bacteria and endospore forming bacteria were copious in the atmospheric depositions due to their capability to withstand harsh environmental conditions. The presence of pathogenic bacteria and heavy metals creates potential human and ecosystem health risk.
Enhancer retargeting of CDX2 and UBTF::ATXN7L3 define a subtype of high-risk B-progenitor acute lymphoblastic leukemia
Publisher: American Society of Hematology
Date: 16-06-2022
Abstract: Transcriptome sequencing has identified multiple subtypes of B-progenitor acute lymphoblastic leukemia (B-ALL) of prognostic significance, but a minority of cases lack a known genetic driver. Here, we used integrated whole-genome (WGS) and -transcriptome sequencing (RNA-seq), enhancer mapping, and chromatin topology analysis to identify previously unrecognized genomic drivers in B-ALL. Newly diagnosed (n = 3221) and relapsed (n = 177) B-ALL cases with tumor RNA-seq were studied. WGS was performed to detect mutations, structural variants, and copy number alterations. Integrated analysis of histone 3 lysine 27 acetylation and chromatin looping was performed using HiChIP. We identified a subset of 17 newly diagnosed and 5 relapsed B-ALL cases with a distinct gene expression profile and 2 universal and unique genomic alterations resulting from aberrant recombination-activating gene activation: a focal deletion downstream of PAN3 at 13q12.2 resulting in CDX2 deregulation by the PAN3 enhancer and a focal deletion of exons 18-21 of UBTF at 17q21.31 resulting in a chimeric fusion, UBTF::ATXN7L3. A subset of cases also had rearrangement and increased expression of the PAX5 gene, which is otherwise uncommon in B-ALL. Patients were more commonly female and young adult with median age 35 (range,12-70 years). The immunophenotype was characterized by CD10 negativity and immunoglobulin M positivity. Among 16 patients with known clinical response, 9 (56.3%) had high-risk features including relapse (n = 4) or minimal residual disease & % at the end of remission induction (n = 5). CDX2-deregulated, UBTF::ATXN7L3 rearranged (CDX2/UBTF) B-ALL is a high-risk subtype of leukemia in young adults for which novel therapeutic approaches are required.
Linking source characterisation and human health risk assessment of metals to rainfall characteristics
Publisher: Elsevier BV
Date: 07-2018
DOI: 10.1016/J.ENVPOL.2018.03.077
Abstract: Metals deposited on urban road surfaces and incorporated in stormwater runoff are discharged into receiving waters, influencing their quality and can pose human health risks. Effective design of stormwater treatment measures is closely dependent on the in-depth understanding of stormwater pollutant sources and the associated health risks. The study discussed in this paper has linked the sources of metals in stormwater runoff and the accompanying human health risk to rainfall characteristics. The study outcomes confirmed that the metal contributions to stormwater runoff from the primary sources were in the order of sea salt > soil > traffic. Although traffic contributes a relatively lower percentage to wash-off, the human health risks posed by traffic sourced metals were relatively much higher. This implies that traffic sources should receive particular attention in treating stormwater. These outcomes have the potential to contribute to enhancing effective source control measures in order to safeguard natural waterways from polluted road wash-off.
Influence of landscape patterns on nitrate and particulate organic nitrogen inputs to urban stormwater runoff
Publisher: Elsevier BV
Date: 12-2023
Removal of heavy metals from water using engineered hydrochar: Kinetics and mechanistic approach
Publisher: Elsevier BV
Date: 04-2021
Exploring the Properties and Potential Uses of Biocarbon from Spent Coffee Grounds: A Comparative Look at Dry and Wet Processing Methods
Publisher: MDPI AG
Date: 13-07-2023
DOI: 10.3390/PR11072099
Abstract: Coffee is among the most widely consumed beverages worldwide, leading to the annual generation of substantial quantities of spent coffee grounds (SCGs). This study explored the influence of fabrication methods on the properties and potential applications of the resulting biocarbon materials. Dry methods (torrefaction at 270 °C and slow pyrolysis at 500 °C) and wet methods (hydrothermal carbonization HTC at 210 °C and hydrothermal liquefaction HTL at 270 °C) were employed to fabricate SCG-based biochar and hydrochar, respectively. The carbonization degree followed the order of slow pyrolysis HTL HTC ≈ torrefaction, yielding significant differences in energy properties, elemental composition, morphology, and surface functionality. Slow pyrolysis biochar was suitable for energy applications due to a similar fuel ratio as and higher heating value than semianthracite coal. For agricultural applications, SCG biochar produced through dry methods could be utilized to mitigate acidic soil conditions, whereas HTC hydrochar, with its elevated surface area and porosity, could enhance soil microbiological ersity and water-holding capacity, as well as benefit environmental applications such as wastewater remediation. In summary, the findings of this study are anticipated to inform decision-making processes concerning sustainable waste management of SCGs and the exploration of carbon-based materials applications across erse sectors.
Comparison of pollution indices for the assessment of heavy metal in Brisbane River sediment
Publisher: Elsevier BV
Date: 12-2016
DOI: 10.1016/J.ENVPOL.2016.09.008
Abstract: Estuarine environment is complex and receives different contaminants from numerous sources that are persistent, bioaccumulative and toxic. The distribution, source, contamination and ecological risk status of heavy metals in sediment of Brisbane River, Australia were investigated. Sediment s les were analysed for major and minor elements using LA-ICP-MS. Principal component analysis and cluster analysis identified three main sources of metals in the s les: marine sand intrusion, mixed lithogenic and sand intrusion as well as transport related. To overcome inherent deficiencies in using a single index, a range of sediment quality indices, including contamination factor, enrichment factor, index of geo-accumulation, modified degree of contamination, pollution index and modified pollution index were utilised to ascertain the sediment quality. Generally, the sediment is deemed to be "slightly" to "heavily" polluted. A further comparison with the Australian Sediment Quality Guidelines indicated that Ag, Cr, Cu, Ni, Pb and Zn had the potential to rarely cause biological effects while Hg could frequently cause biological effects. Application of potential ecological risk index (RI) revealed that the sediment poses moderate to considerable ecological risk. However, RI could not account for the complex sediment behaviour because it uses a simple contamination factor. Consequently, a modified ecological risk index (MRI) employing enrichment factor is proposed. This provides a more reliable understanding of whole sediment behaviour and classified the ecological risk of the sediment as moderate to very high. The results demonstrate the need for further investigation into heavy metal speciation and bioavailability in the sediment to ascertain the degree of toxicity.
Assessment via discriminant analysis of soil suitability for effluent renovation using undisturbed soil columns
Publisher: Elsevier BV
Date: 03-2006
Climate change adaptation in the management of public buildings: an Indonesian context
Publisher: Emerald
Date: 08-04-2019
DOI: 10.1108/IJBPA-02-2018-0019
Abstract: The purpose of this paper is to provide a strategy to integrate climate change adaptation (CCA) in public asset management (PAM) in Indonesia. This paper focusses on public buildings as part of a public asset. As an archipelagic country, Indonesia is very vulnerable to sea-level rise as a result of climate change. The outcomes of a qualitative analysis of interviews with relevant stakeholders were used for the development of the CCA framework in an Indonesian context. The study identified that the integration of CCA in PAM in Indonesia requires the incorporation of nine key elements. These are as follows: recognition of climate change risk management and insurance schemes for assets integrated asset management and planning asset use and knowledge reliable, accessible and understandable data set on climate change leadership, government commitment and incentives involvement of research and private entities community engagement and coordination of relevant agencies. This paper informed only the key elements required on the development of framework which integrate CCA in PAM. The integration of CCA to a PAM framework will support the development of policies and procedures for better-informed decisions. The framework increases opportunities for stakeholders and community engagement in policy development and decision making in relation to CCA for public assets. This paper synthesises CCA and PAM using knowledge from the three levels of governments in Australia and Indonesia. CCA and PAM groups work separately in Indonesia and integration will reduce climate change risks and improve decision making in PAM.
Analysis of the build-up of semi and non volatile organic compounds on urban roads
Publisher: Elsevier BV
Date: 04-2011
DOI: 10.1016/J.WATRES.2011.02.033
Abstract: Vehicular traffic in urban areas may adversely affect urban water quality through the build-up of traffic generated semi and non volatile organic compounds (SVOCs and NVOCs) on road surfaces. The characterisation of the build-up processes is the key to developing mitigation measures for the removal of such pollutants from urban stormwater. An in-depth analysis of the build-up of SVOCs and NVOCs was undertaken in the Gold Coast region in Australia. Principal Component Analysis (PCA) and Multicriteria Decision tools such as PROMETHEE and GAIA were employed to understand the SVOC and NVOC build-up under combined traffic scenarios of low, moderate, and high traffic in different land uses. It was found that congestion in the commercial areas and use of lubricants and motor oils in the industrial areas were the main sources of SVOCs and NVOCs on urban roads, respectively. The contribution from residential areas to the build-up of such pollutants was hardly noticeable. It was also revealed through this investigation that the target SVOCs and NVOCs were mainly attached to particulate fractions of 75-300 μm whilst the redistribution of coarse fractions due to vehicle activity mainly occurred in the >300 μm size range. Lastly, under combined traffic scenario, moderate traffic with average daily traffic ranging from 2300 to 5900 and average congestion of 0.47 were found to dominate SVOC and NVOC build-up on roads.
Impacts of traffic and rainfall characteristics on heavy metals build-up and wash-off from urban roads
Publisher: American Chemical Society (ACS)
Date: 21-10-2010
DOI: 10.1021/ES1012565
Abstract: An investigation into the effects of changes in urban traffic characteristics due to rapid urbanisation and the predicted changes in rainfall characteristics due to climate change on the build-up and wash-off of heavy metals was carried out in Gold Coast, Australia. The study sites encompassed three different urban land uses. Nine heavy metals commonly associated with traffic emissions were selected. The results were interpreted using multivariate data analysis and decision making tools, such as principal component analysis (PCA), fuzzy clustering (FC), PROMETHEE, and GAIA. Initial analyses established high, low, and moderate traffic scenarios as well as low, low to moderate, moderate, high, and extreme rainfall scenarios for build-up and wash-off investigations. GAIA analyses established that moderate to high traffic scenarios could affect the build-up, while moderate to high rainfall scenarios could affect the wash-off of heavy metals under changed conditions. However, in wash-off, metal concentrations in 1-75 μm fraction were found to be independent of the changes to rainfall characteristics. In build-up, high traffic activities in commercial and industrial areas influenced the accumulation of heavy metal concentrations in particulate size range from 75 - >300 μm, whereas metal concentrations in finer size range of <1-75 μm were not affected. As practical implications, solids 300 μm can be targeted for removal of Ni, Cu, Pb, Cd, Cr, and Zn from build-up, while organic matter from 300 μm can be targeted for removal of Cd, Cr, Pb, and Ni from wash-off. Cu and Zn need to be removed as free ions from most fractions in wash-off.
Understanding nutrient dynamics for effective stormwater treatment design
Publisher: Elsevier BV
Date: 12-2022
DOI: 10.1016/J.SCITOTENV.2022.157962
Abstract: Current stormwater quality modelling tools lack robust mathematical replication of nutrient entrainment in runoff. This makes it challenging to design effective stormwater treatment systems such as nature based solutions with adequate resilience to future changes in nutrient inputs in urban environments. Consequently, poorly treated stormwater can be discharged into receiving waters, leading to nutrient enrichment and in turn, environmental and human health impacts. This study integrated empirically based with statistical modelling techniques to incorporate nutrient dynamics into commonly used Intensity-Frequency-Duration (IFD) distributions of design rainfall. Field based nutrient wash-off experiments were conducted to understand nutrient behaviour during a runoff event. New mathematical formulations were derived to describe the decay (wash-off) of nutrients. Rainfall intensity, duration and initially accumulated pollutant load exert positive influence on the decay of nitrogen and phosphorous, while organic carbon has a negative impact on phosphorus decay. It was also evident that nitrogen species would decay at a similar rate, while phosphorus species may decay at different rates. Compared to nitrogen species, phosphorous species were found more likely to be washed-off during a rainfall event. Using the mathematical formulations developed, wash-off of nitrogen and phosphorous was simulated for 435 very frequent and frequent/infrequent design rainfall events leading to the creation of Intensity-Frequency-Duration-Wash-off (IFDW) curves. Analysis of uncertainty associated with IFDW indicated that total phosphorous could be completely washed-off during most of the design rainfall events, while total nitrogen would only be completely washed-off by very few events that are rarer than 10 % AEP (annual exceedance probability). IFDW can act as a tool for supporting effective stormwater treatment design in order to promote sustainable stormwater management and reuse.
Influence of physical and chemical parameters on the treatment of heavy metals in polluted stormwater using zeolite : A review
Publisher: Scientific Research Publishing, Inc.
Date: 2011
Evaluating Sewage‐Associated JCV and BKV Polyomaviruses for Sourcing Human Fecal Pollution in a Coastal River in Southeast Queensland, Australia
Publisher: Wiley
Date: 09-2010
DOI: 10.2134/JEQ2010.0062
Abstract: In this study, the host-sensitivity and host-specificity of JC virus (JCV) and BK virus (BKV) polyomaviruses were evaluated by testing wastewater and fecal s les from nine host groups in Southeast Queensland, Australia. The JCV and BKV polyomaviruses were detected in 63 human wastewater s les collected from primary and secondary effluent, suggesting high sensitivity of these viruses in human wastewater. In the 81 animal wastewater and fecal s les tested, 80 were polymerase chain reaction (PCR) negative for the JCV and BKV markers. Only one s le (out of 81 animal wastewater and fecal s les) from pig wastewater was positive. Nonetheless, the overall host-specificity of these viruses to differentiate between human and animal wastewater and fecal s les was 0.99. To our knowledge, this is the first study in Australia that reports on the high specificity of JCV and BKV polyomaviruses. To evaluate the field application of these viral markers for detecting human fecal pollution, 20 environmental s les were collected from a coastal river. In the 20 s les tested, 15% (3/20) and 70% (14/20) s les exceeded the regulatory guidelines for Escherichia coli and enterococci levels for marine waters. In all, five (25%) s les were PCR positive for JCV and BKV, indicating the presence of human fecal pollution in the coastal river investigated. The results suggest that JCV and BKV detection using PCR could be a useful tool for identifying human-sourced fecal pollution in coastal waters.
Reply to comment on Characterising metal build-up on urban road surfaces by Egodawatta et al. (2013). Environmental Pollution, 176, 87-91
Publisher: Elsevier BV
Date: 11-2013
Whole-genome landscapes of major melanoma subtypes
Publisher: Springer Science and Business Media LLC
Date: 05-2017
DOI: 10.1038/NATURE22071
Abstract: Melanoma of the skin is a common cancer only in Europeans, whereas it arises in internal body surfaces (mucosal sites) and on the hands and feet (acral sites) in people throughout the world. Here we report analysis of whole-genome sequences from cutaneous, acral and mucosal subtypes of melanoma. The heavily mutated landscape of coding and non-coding mutations in cutaneous melanoma resolved novel signatures of mutagenesis attributable to ultraviolet radiation. However, acral and mucosal melanomas were dominated by structural changes and mutation signatures of unknown aetiology, not previously identified in melanoma. The number of genes affected by recurrent mutations disrupting non-coding sequences was similar to that affected by recurrent mutations to coding sequences. Significantly mutated genes included BRAF, CDKN2A, NRAS and TP53 in cutaneous melanoma, BRAF, NRAS and NF1 in acral melanoma and SF3B1 in mucosal melanoma. Mutations affecting the TERT promoter were the most frequent of all however, neither they nor ATRX mutations, which correlate with alternative telomere lengthening, were associated with greater telomere length. Most melanomas had potentially actionable mutations, most in components of the mitogen-activated protein kinase and phosphoinositol kinase pathways. The whole-genome mutation landscape of melanoma reveals erse carcinogenic processes across its subtypes, some unrelated to sun exposure, and extends potential involvement of the non-coding genome in its pathogenesis.
A Bayesian approach to model the trends and variability in urban stormwater quality associated with catchment and hydrologic parameters
Publisher: Elsevier BV
Date: 06-2021
How engaging are disaster management related social media channels? The case of Australian state emergency organisations
Publisher: Elsevier BV
Date: 09-2020
Description of a novel subtype of acute myeloid leukemia defined by recurrent CBFB insertions.
Publisher: American Society of Hematology
Date: 16-02-2022
Investigating low-carbon pathways for hydrocarbon-dependent rentier states: Economic transition in Qatar
Publisher: Elsevier BV
Date: 12-2022
Occurrence and risk associated with urban road-deposited microplastics
Publisher: Elsevier BV
Date: 10-2023
Pharmaceuticals, personal care products, food additive and pesticides in surface waters from three Australian east coast estuaries (Sydney, Yarra and Brisbane)
Publisher: Elsevier BV
Date: 04-2020
Spatial conservation prioritization inclusive of wilderness quality: A case study of Australia's biodiversity
Publisher: Elsevier BV
Date: 07-2009
Ranking the factors influencing polycyclic aromatic hydrocarbons (PAHs) build-up on urban roads
Publisher: Elsevier BV
Date: 05-2017
DOI: 10.1016/J.ECOENV.2017.02.011
Abstract: An in-depth understanding of polycyclic aromatic hydrocarbons (PAHs) build-up on urban roads is essential for effective stormwater treatment design. Past research studies have pointed out the relationship between influential factors and PAHs build-up in idually. However, these studies do not provide a comprehensive analysis of the relationships and the hierarchy of factors in terms of their importance in influencing PAHs build-up. This paper presents the outcomes of an in-depth investigation into the range of influential factors, including traffic volume, land use, distance to highway and roughness of road surfaces by ranking them in terms of their influence on PAHs build-up. A number of data analysis techniques including forward stepwise linear regression (FSWLR), principal component analysis (PCA) and multiple linear regression (MLR) were employed for the analyses undertaken. The outcomes confirmed that traffic volume is ranked first while land use and roughness of road surfaces are second and the third, respectively. Distance to highway did not show a significant influence on PAHs build-up. Additionally, it was noted that a high traffic volume tended to produce high loads of PAHs with more than 4 rings and the spatial variability of PAHs build-up were relatively higher in high traffic volume areas. These outcomes contributed to the formulation of a robust stormwater treatment strategy and generation of priority area maps focusing on the removal of PAHs.
Impacts of COVID-19 pandemic on the wastewater pathway into surface water: A review
Publisher: Elsevier BV
Date: 06-2021
The role of different governance regimes in reducing native vegetation conversion and promoting regrowth in the Brazilian Amazon
Publisher: Elsevier BV
Date: 03-2022
Comprehensive molecular characterization of mitochondrial genomes in human cancers
Publisher: Springer Science and Business Media LLC
Date: 05-02-2020
DOI: 10.1038/S41588-019-0557-X
Abstract: Mitochondria are essential cellular organelles that play critical roles in cancer. Here, as part of the International Cancer Genome Consortium/The Cancer Genome Atlas Pan-Cancer Analysis of Whole Genomes Consortium, which aggregated whole-genome sequencing data from 2,658 cancers across 38 tumor types, we performed a multidimensional, integrated characterization of mitochondrial genomes and related RNA sequencing data. Our analysis presents the most definitive mutational landscape of mitochondrial genomes and identifies several hypermutated cases. Truncating mutations are markedly enriched in kidney, colorectal and thyroid cancers, suggesting oncogenic effects with the activation of signaling pathways. We find frequent somatic nuclear transfers of mitochondrial DNA, some of which disrupt therapeutic target genes. Mitochondrial copy number varies greatly within and across cancers and correlates with clinical variables. Co-expression analysis highlights the function of mitochondrial genes in oxidative phosphorylation, DNA repair and the cell cycle, and shows their connections with clinically actionable genes. Our study lays a foundation for translating mitochondrial biology into clinical applications.
Role of organic matter in framboidal pyrite oxidation
Publisher: Elsevier BV
Date: 08-2006
DOI: 10.1016/J.SCITOTENV.2004.10.011
Abstract: An experimental system has been set up to investigate the reaction kinetics of framboidal pyrite oxidation in real, reactive acid sulfate soil assemblages. This study was undertaken to determine the degree to which pyrite oxidation rates are reduced by bacteriological reactions and organic matter, which both modify the net reaction mechanisms and compete for available oxygen. The results from these experimental runs not only confirm the role of organic matter in mitigating pyrite oxidation but indicate that at least initially, the acidity produced is consumed or otherwise ameliorated by parallel reactions. Tracking pH or [H+] in both a reactor and in soil does not accurately reflect reaction progress and may not correctly indicate the true level of risk. In comparison, the tracking of pyrite oxidation with the concentration of sulfate in solution is not affected by side reactions or precipitation and is therefore a better indicator for the rate of pyrite destruction.
Real-Time PCR Detection of Pathogenic Microorganisms in Roof-Harvested Rainwater in Southeast Queensland, Australia
Publisher: American Society for Microbiology
Date: 09-2008
DOI: 10.1128/AEM.00331-08
Abstract: In this study, the microbiological quality of roof-harvested rainwater was assessed by monitoring the concentrations of Escherichia coli , enterococci, Clostridium perfringens , and Bacteroides spp. in rainwater obtained from tanks in Southeast Queensland, Australia. S les were also tested using real-time PCR (with SYBR Green I dye) for the presence of potential pathogenic microorganisms. Of the 27 rainwater s les tested, 17 (63%), 21 (78%), 13 (48%), and 24 (89%) were positive for E. coli , enterococci, C. perfringens , and Bacteroides spp., respectively. Of the 27 s les, 11 (41%), 7 (26%), 4 (15%), 3 (11%), and 1 (4%) were PCR positive for the C ylobacter coli ceuE gene, the Legionella pneumophila mip gene, the Aeromonas hydrophila lip gene, the Salmonella invA gene, and the C ylobacter jejuni mapA gene. Of the 21 s les tested, 4 (19%) were positive for the Giardia lamblia β-giardin gene. The binary logistic regression model indicated a positive correlation ( P 0.02) between the presence/absence of enterococci and A. hydrophila . In contrast, the presence/absence of the remaining potential pathogens did not correlate with traditional fecal indicators. The poor correlation between fecal indicators and potential pathogens suggested that fecal indicators may not be adequate to assess the microbiological quality of rainwater and consequent health risk.
Implications of faecal indicator bacteria for the microbiological assessment of roof-harvested rainwater quality in southeast Queensland, Australia
Publisher: Canadian Science Publishing
Date: 06-2010
DOI: 10.1139/W10-037
Abstract: The study aimed to evaluate the suitability of Escherichia coli , enterococci, and Clostridium perfringens for assessing the microbiological quality of roof-harvested rainwater and assessing whether the concentrations of these faecal indicators can be used to predict the presence or absence of specific zoonotic bacterial or protozoan pathogens. From a total of 100 s les tested, 58%, 83%, and 46% of s les were found to be positive for, respectively, E. coli, enterococci, and Clostridium perfringens spores, as determined by traditional culture-based methods. Additionally, in the s les tested, 7%, 19%, 1%, 8%, 17%, and 15% were PCR positive for Aeromonas hydrophila lip, C ylobacter coli ceuE, C ylobacter jejuni mapA, Legionella pneumophila mip, Salmonella invA, and Giardia lamblia β-giardin genes, respectively. However, none of the s les was positive for E. coli O157 lipopolysaccharide, verocytotoxin 1, and verocytotoxin 2 and Cryptosporidium parvum oocyst wall protein genes. The presence or absence of these potential pathogens did not correlate with any of the faecal indicator bacterial concentrations as determined by a binary logistic regression model. The roof-harvested rainwater s les tested in this study appeared to be of poor microbiological quality, and no significant correlation was found between the concentration of faecal indicators and pathogenic microorganisms. The use of faecal indicator bacteria raises questions regarding their reliability in assessing the microbiological quality of water and particularly their poor correlation with pathogenic microorganisms. The presence of one or more zoonotic pathogens suggests that the microbiological analysis of water should be performed and that appropriate treatment measures should be undertaken, especially in tanks where the water is used for drinking.
Influence of microplastics on nutrients and metal concentrations in river sediments
Publisher: Elsevier BV
Date: 08-2020
Narrative futures of a low carbon transition for hydrocarbon rentier states: Case of Qatar
Publisher: Elsevier BV
Date: 10-2022
Distribution of polycyclic aromatic hydrocarbons in urban stormwater in Queensland, Australia
Publisher: Elsevier BV
Date: 09-2010
DOI: 10.1016/J.ENVPOL.2010.06.015
Abstract: This paper reports the distribution of Polycyclic Aromatic Hydrocarbons (PAHs) in wash-off in urban stormwater in Gold Coast, Australia. Runoff s les collected from residential, industrial and commercial sites were separated into a dissolved fraction ( 150 microm). Patterns in the distribution of PAHs in the fractions were investigated using Principal Component Analysis. Regardless of the land use and particle size fraction characteristics, the presence of organic carbon plays a dominant role in the distribution of PAHs. The PAHs concentrations were also found to decrease with rainfall duration. Generally, the 1- and 2-year average recurrence interval rainfall events were associated with the majority of the PAHs and the wash-off was a source limiting process. In the context of stormwater quality mitigation, targeting the initial part of the rainfall event is the most effective treatment strategy. The implications of the study results for urban stormwater quality management are also discussed.
Role of Land Use and Seasonal Factors in Water Quality Degradations
Publisher: Springer Science and Business Media LLC
Date: 05-2013
Traffic and climate change impacts on water quality : measuring build-up and wash-off of heavy metals and petroleum hydrocarbons
Publisher: IGI Global
Date: 2010
DOI: 10.4018/978-1-61692-022-7.CH011
Abstract: Understanding the impacts of traffic and climate change on water quality helps decision makers to develop better policy and plans for dealing with unsustainable urban and transport development. This chapter presents detailed methodologies developed for s le collection and testing for heavy metals and total petroleum hydrocarbons, as part of a research study to investigate the impacts of climate change and changes to urban traffic characteristics on pollutant build-up and wash-off from urban road surfaces. Cadmium, chromium, nickel, copper, lead, iron, aluminium, manganese and zinc were the target heavy metals, and selected gasoline and diesel range organics were the target total petroleum hydrocarbons for this study. The study sites were selected to encompass the urban traffic characteristics of the Gold Coast region, Australia. An improved s le collection method referred to as ‘the wet and dry vacuum system’ for the pollutant build-up, and an effective wash-off plan to incorporate predicted changes to rainfall characteristics due to climate change, were implemented. The novel approach to s le collection for pollutant build-up helped to maintain the integrity of collection efficiency. The wash-off plan helped to incorporate the predicted impacts of climate change in the Gold Coast region. The robust experimental methods developed will help in field s le collection and chemical testing of different stormwater pollutants in build-up and wash-off.& nbsp
Application of landscape epidemiology to assess potential public health risk due to poor sanitation
Publisher: Elsevier BV
Date: 05-2017
DOI: 10.1016/J.JENVMAN.2017.01.051
Abstract: Clear identification of areas vulnerable to waterborne diseases is essential for protecting community health. This is particularly important in developing countries where unsafe disposal of domestic wastewater and limited potable water supply pose potential public health risks. However, data paucity can be a compounding issue. Under these circumstances, landscape epidemiology can be applied as a resource efficient approach for mapping potential disease risk areas associated with poor sanitation. However, in order to realise the full potential offered by this approach, an in-depth understanding of the impact of different classes of an explanatory variable on a target disease and the validity of hotspot analysis using limited datasets is needed. Accordingly, this research study focused on typhoid and diarrhoea incidence with respect to different classes of elevation, flood inundation, land use, soil permeability, population density and rainfall as explanatory variables. An integrated methodology consisting of hot spot analysis and Poisson regression was employed to map potential disease risk areas. The study findings confirmed the significant differences in the influence exerted by the various classes of an explanatory variable in relation to a target disease. The results also confirmed the feasibility of the hotspot analysis for identifying areas vulnerable to the target diseases using a limited dataset. The study outcomes are expected to contribute to creating an in-depth understanding of the relationship between disease prevalence and associated landscape factors for the delineation of disease risk zones in the context of data paucity.
Quantitative assessment of resilience of a water supply system under rainfall reduction due to climate change
Publisher: Elsevier BV
Date: 09-2016
Catchment scale assessment of risk posed by traffic generated heavy metals and polycyclic aromatic hydrocarbons
Publisher: Elsevier BV
Date: 10-2017
DOI: 10.1016/J.ECOENV.2017.06.073
Abstract: Heavy metals (HMs) and polycyclic aromatic hydrocarbons (PAHs) are among the most toxic chemical pollutants present in urban stormwater. Consequently, urban stormwater reuse is constrained due to the human health risk posed by these pollutants. This study developed a scientifically robust approach to assess the risk to human health posed by HMs and PAHs in urban stormwater in order to enhance its reuse. Accordingly, an innovative methodology was created consisting of four stages: quantification of traffic and land use parameters estimation of pollutant concentrations for model development risk assessment, and risk map presentation. This methodology will contribute to catchment scale assessment of the risk associated with urban stormwater and for risk mitigation. The risk map developed provides a simple and efficient approach to identify the critical areas within a large catchment. The study also found that heavy molecular weight PAHs (PAHs with 5-6 benzene rings) in urban stormwater pose higher risk to human health compared to light molecular PAHs (PAHs with 2-4 benzene rings). These outcomes will facilitate the development of practical approaches for applying appropriate mitigation measures for the safe management of urban stormwater pollution and for the identification of enhanced reuse opportunities.
Transformation Processes of Metals in Urban Road Dust
Publisher: Springer Singapore
Date: 2020
Platypus Induced Pluripotent Stem Cells: the Unique Pluripotency Signature of a Monotreme
Publisher: Cold Spring Harbor Laboratory
Date: 25-07-2018
DOI: 10.1101/377010
Abstract: The generation and transcriptome analysis of the first induced pluripotent stem cells from the platypus reveals SOX2 has been a key driver of the expanded pluripotency regulatory network in placental mammals. The mechanisms by which pluripotency has evolved remain unclear. To gain insight into the evolution of mammalian pluripotency we have generated induced pluripotent stem cells (piPSCs) from the platypus. Deep sequencing of the piPSC transcriptome revealed that piPSCs robustly express the core eutherian pluripotency factors OCT4, SOX2 and NANOG . Given the more extensive role of SOX3 over SOX2 in avian pluripotency, our data indicate that between 315 million years and 166 million years ago primitive mammals replaced the role of SOX3 in the vertebrate pluripotency network with SOX2. DAX1/NR0B1 is not expressed in piPSCs and an analysis of the platypus DAX1 promoter revealed the absence of a proximal SOX2-binding DNA motif known to be critical for DAX1 expression in eutherian pluripotent stem cells, suggesting that the acquisition of SOX2 responsiveness by DAX1 has facilitated its recruitment into the pluripotency network of eutherians. We further show that the expression ratio of X chromosomes to autosomes (X 1-5 X 1-5 :AA) is approximately equal to 1 indicating that there is no upregulation of X-linked genes and that there is no preference for silencing of maternal or paternal alleles (ie imprinting).
Catastrophic Declines in Wilderness Areas Undermine Global Environment Targets
Publisher: Elsevier BV
Date: 11-2016
DOI: 10.1016/J.CUB.2016.08.049
Abstract: Humans have altered terrestrial ecosystems for millennia [1], yet wilderness areas still remain as vital refugia where natural ecological and evolutionary processes operate with minimal human disturbance [2-4], underpinning key regional- and planetary-scale functions [5, 6]. Despite the myriad values of wilderness areas-as critical strongholds for endangered bio ersity [7], for carbon storage and sequestration [8], for buffering and regulating local climates [9], and for supporting many of the world's most politically and economically marginalized communities [10]-they are almost entirely ignored in multilateral environmental agreements. This is because they are assumed to be relatively free from threatening processes and therefore are not a priority for conservation efforts [11, 12]. Here we challenge this assertion using new comparable maps of global wilderness following methods established in the original "last of the wild" analysis [13] to examine the change in extent since the early 1990s. We demonstrate alarming losses comprising one-tenth (3.3 million km
Influence of rainfall and catchment characteristics on urban stormwater quality
Publisher: Elsevier BV
Date: 02-2013
DOI: 10.1016/J.SCITOTENV.2012.11.053
Abstract: The accuracy and reliability of urban stormwater quality modelling outcomes are important for stormwater management decision making. The commonly adopted approach where only a limited number of factors are used to predict urban stormwater quality may not adequately represent the complexity of the quality response to a rainfall event or site-to-site differences to support efficient treatment design. This paper discusses an investigation into the influence of rainfall and catchment characteristics on urban stormwater quality in order to investigate the potential areas for errors in current stormwater quality modelling practices. It was found that the influence of rainfall characteristics on pollutant wash-off is step-wise based on specific thresholds. This means that a modelling approach where the wash-off process is predicted as a continuous function of rainfall intensity and duration is not appropriate. Additionally, other than conventional catchment characteristics, namely, land use and impervious surface fraction, other catchment characteristics such as impervious area layout, urban form and site specific characteristics have an important influence on both, pollutant build-up and wash-off processes. Finally, the use of solids as a surrogate to estimate other pollutant species was found to be inappropriate. In idually considering build-up and wash-off processes for each pollutant species should be the preferred option.
Assessing the effect of surface hydrophobicity/hydrophilicity on pollutant leaching potential of biochar in water treatment
Publisher: Elsevier BV
Date: 09-2020
Author Correction: Genomic footprints of activated telomere maintenance mechanisms in cancer
Publisher: Springer Science and Business Media LLC
Date: 08-12-2022
Treatment technologies for stormwater reuse
Publisher: Elsevier
Date: 2021
The In Planta Gene Expression of Austropuccinia psidii in Resistant and Susceptible Eucalyptus grandis
Publisher: Scientific Societies
Date: 06-2023
DOI: 10.1094/PHYTO-07-22-0257-R
Abstract: Austropuccinia psidii, commonly known as myrtle rust, is an obligate, biotrophic rust pathogen that causes rust disease in a broad host range of Myrtaceae species. Eucalyptus grandis, a widely cultivated hardwood Myrtaceae species, is susceptible to A. psidii infection, with this pathogen threatening both their natural range and various forest plantations across the world. This study aimed to investigate the A. psidii transcriptomic responses in resistant and susceptible E. grandis at four time points. RNA-seq reads were mapped to the A. psidii reference genome to quantify expressed genes at 12 h postinoculation and 1, 2, and 5 days postinoculation (dpi). A total of eight hundred and ninety expressed genes were found, of which 43 were candidate effector protein genes. These included rust transferred protein 1 ( RTP1), expressed in susceptible hosts at 5 dpi, and a hydrolase protein gene expressed in both resistant and susceptible hosts over time. Functional categorization of expressed genes revealed processes enriched in susceptible hosts, including malate metabolic and malate dehydrogenase activity, implicating oxalic acid in disease susceptibility. These results highlight putative virulence or pathogenicity mechanisms employed by A. psidii to cause disease, and they provide the first insight into the molecular responses of A. psidii in E. grandis over time.
PRMT5: An Emerging Target for Pancreatic Adenocarcinoma
Publisher: MDPI AG
Date: 13-10-2021
Abstract: The overall survival of pancreatic ductal adenocarcinoma (PDAC) remains poor and its incidence is rising. Targetable mutations in PDAC are rare, thus novel therapeutic approaches are needed. Protein arginine methyltransferase 5 (PRMT5) overexpression is associated with worse survival and inhibition of PRMT5 results in decreased cancer growth across multiple cancers, including PDAC. Emerging evidence also suggests that altered RNA processing is a driver in PDAC tumorigenesis and creates a partial dependency on this process. PRMT5 inhibition induces altered splicing and this vulnerability can be exploited as a novel therapeutic approach. Three possible biological pathways underpinning the action of PRMT5 inhibitors are discussed c-Myc regulation appears central to its action in the PDAC setting. Whilst homozygous MTAP deletion and symmetrical dimethylation levels are associated with increased sensitivity to PRMT5 inhibition, neither measure robustly predicts its growth inhibitory response. The immunomodulatory effect of PRMT5 inhibitors on the tumour microenvironment will also be discussed, based on emerging evidence that PDAC stroma has a significant bearing on disease behaviour and response to therapy. Lastly, with the above caveats in mind, current knowledge gaps and the implications and rationales for PRMT5 inhibitor development in PDAC will be explored.
Author Correction: Combined burden and functional impact tests for cancer driver discovery using DriverPower
Publisher: Springer Science and Business Media LLC
Date: 08-12-2022
Integrating Tank Model and adsorption/desorption characteristics of filter media to simulate outflow water quantity and quality of a bioretention basin: A case study of biochar-based bioretention basi
Publisher: Elsevier BV
Date: 02-2022
DOI: 10.1016/J.JENVMAN.2021.114282
Abstract: Reliable approaches for accurately assessing the performance of stormwater treatment systems is essential for their effective design, including filter media selection which can be a significant constituent in stormwater treatment systems. This study presents an innovative modelling approach integrating the Tank Model with the adsorption-desorption characteristics of the filter media. The resulting modelling approach was applied to simulate a field-scale bioretention basin where biochar was used as filter media with over ten years of rainfall records. The resulting outflow and overflow volumes were compared with observed data for calibration. The Stormwater Treatment Tank Model (STTM) was validated using the Leave-One-Out-Cross-Validation (LOOCV) method. The simulation outcomes include water outflow and overflow (quantity) from the bioretention basin as well as outflow water quality represented by three heavy metals (Pb, Cu, and Zn). The modelling approach developed was found to be capable of accurately simulating outflow and overflow volumes, with outlet water quantity being significantly influenced by the total rainfall depth. The modeling results also suggested that a sole treatment system would not be adequate, particularly for large rainfall events (>100 mm) and a treatment train would be more effective. Simulating long-term (over ten years) pollutant removal performance in the bioretention basin indicated that heavy metals outflow event mean concentration (EMCs) values calculated using simulated results of 30% biochar application rate generated the best pollutant removal with consistent values (2.7 μg/L, 3.0 μg/L, 17.2 μg/L for Pb, Cu, and Zn, respectively). These results confirm that the modelling approach is reliable for assessing long-term treatment performance, as well as a robust tool able to contribute to more effective treatment system design, particularly filter media selection and evaluation.
Managing floods in Chennai City as part of situation understanding and improvement project
Publisher: Wiley
Date: 27-07-2023
DOI: 10.1002/WWP2.12119
Abstract: Transdisciplinary approaches in water are important to ensure water security to everyone around the world. Recently, Young Water Professionals (YWPs) training was carried out to impart learning in transdisciplinary approaches. Besides online workshops and lectures, the training program included the Situation Understanding and Improvement Project (SUIP). Through SUIP, YWPs were able to implement the transdisciplinary approaches learnt during lectures and workshops. The SUIP selected by one of the groups of YWPs was related to the flooding experienced by the residents of Chennai, India. Flooding is a very common phenomenon having its occurrence across the world with varying severity and magnitude because of changes to the use of river floodplains, changing the land use pattern, encroachment of waterbodies, and the impact of climate change on water resources. Chennai City in Tamil Nadu, India, with a population of about 6.5 million is facing frequent flooding because of extreme rainfall events and the presence of three rivers within the city and is also facing an acute shortage of water which also needs to be addressed for its sustainable development. This study used transdisciplinary approach to understand 2015 flooding in Chennai and made several recommendations to improve the flood management in Chennai including an early warning system. The YWP training and the concept of SUIP significantly enhanced the outcomes from this study.
Factors influencing volatile hydrocarbon pollution in urban areas
Publisher: Elsevier BV
Date: 2019
Can volunteer crowdsourcing reduce disaster risk? A systematic review of the literature
Publisher: Elsevier BV
Date: 04-2019
A new fuzzy multicriteria evaluation method for group site selection in GIS
Publisher: Wiley
Date: 11-2003
DOI: 10.1002/MCDA.365
A critical review of social resilience assessment frameworks in disaster management
Publisher: Elsevier BV
Date: 04-2019
Stormwater reuse, a viable option: Fact or fiction?
Publisher: Elsevier BV
Date: 12-2017
Author Correction: Genomic basis for RNA alterations in cancer
Publisher: Springer Science and Business Media LLC
Date: 25-01-2023
Urbanisation and Stormwater Quality
Publisher: Springer Singapore
Date: 2015
Divergent mutational processes distinguish hypoxic and normoxic tumours
Publisher: Springer Science and Business Media LLC
Date: 05-02-2020
DOI: 10.1038/S41467-019-14052-X
Abstract: Many primary tumours have low levels of molecular oxygen (hypoxia), and hypoxic tumours respond poorly to therapy. Pan-cancer molecular hallmarks of tumour hypoxia remain poorly understood, with limited comprehension of its associations with specific mutational processes, non-coding driver genes and evolutionary features. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2658 cancers across 38 tumour types, we quantify hypoxia in 1188 tumours spanning 27 cancer types. Elevated hypoxia associates with increased mutational load across cancer types, irrespective of underlying mutational class. The proportion of mutations attributed to several mutational signatures of unknown aetiology directly associates with the level of hypoxia, suggesting underlying mutational processes for these signatures. At the gene level, driver mutations in TP53 , MYC and PTEN are enriched in hypoxic tumours, and mutations in PTEN interact with hypoxia to direct tumour evolutionary trajectories. Overall, hypoxia plays a critical role in shaping the genomic and evolutionary landscapes of cancer.
HNF4A and GATA6 Loss Reveals Therapeutically Actionable Subtypes in Pancreatic Cancer
Publisher: Elsevier BV
Date: 05-2020
Heavy metals transport pathways: The importance of atmospheric pollution contributing to stormwater pollution
Publisher: Elsevier BV
Date: 11-2018
DOI: 10.1016/J.ECOENV.2018.08.072
Abstract: Pollution has become a serious issue in the urban water environment as stormwater runoff transports a range of pollutants to receiving water bodies, undermining water quality and posing human and ecosystem health risks. Commonly, the primary focus of stormwater quality research is on the role of pollutants directly accumulating at the ground phase. However, atmospheric phase can also exert a significant impact on stormwater quality through atmospheric deposition. Unfortunately, only limited research has focused on the linkage between atmospheric and ground phases in relation to urban stormwater quality. The study discussed in this paper characterised the four primary transport pathways, atmospheric build-up (AB), atmospheric deposition (AD) and road surface build-up (BU) and wash-off (WO) in relation to heavy metals, which is a key urban stormwater pollutant. The research outcomes confirmed the direct linkage between atmospheric phase and ground phase and in turn the significance of atmospheric heavy metals as a contributing source to stormwater runoff pollution. Zn was the most dominant heavy metal in all four pathways. For the AB pathway, atmospheric heavy metal pollution on weekdays is more serious than weekends. For the AD pathway, dry atmospheric deposition of heavy metals is positively correlated to dry days, whilst wet (bulk) deposition is related to rainfall depth. For the BU pathway, heavy-duty vehicle traffic volume was found to be the most important source. For the WO pathway, industrial and commercial areas tend to produce higher heavy metal concentrations in stormwater runoff than residential areas. The study results will contribute to the creation of effective urban stormwater pollution mitigation strategies and thereby enhancing the quality of the urban water environment.
Comparison of molecular markers to detect fresh sewage in environmental waters
Publisher: Elsevier BV
Date: 11-2009
DOI: 10.1016/J.WATRES.2009.09.047
Abstract: Human-specific Bacteroides HF183 (HS-HF183), human-specific Enterococci faecium esp (HS-esp), human-specific adenoviruses (HS-AVs) and human-specific polyomaviruses (HS-PVs) assays were evaluated in freshwater, seawater and distilled water to detect fresh sewage. The sewage spiked water s les were also tested for the concentrations of traditional fecal indicators (i.e., Escherichia coli, enterococci and Clostridium perfringens) and enteric viruses such as enteroviruses (EVs), sapoviruses (SVs), and torquetenoviruses (TVs). The overall host-specificity of the HS-HF183 marker to differentiate between humans and other animals was 98%. However, the HS-esp, HS-AVs and HS-PVs showed 100% host-specificity. All the human-specific markers showed >97% sensitivity to detect human fecal pollution. E. coli, enterococci and, C. perfringens were detected up to dilutions of sewage 10(-5), 10(-4) and 10(-3) respectively. HS-esp, HS-AVs, HS-PVs, SVs and TVs were detected up to dilution of sewage 10(-4) whilst EVs were detected up to dilution 10(-5). The ability of the HS-HF183 marker to detect fresh sewage was 3-4 orders of magnitude higher than that of the HS-esp and viral markers. The ability to detect fresh sewage in freshwater, seawater and distilled water matrices was similar for human-specific bacterial and viral marker. Based on our data, it appears that human-specific molecular markers are sensitive measures of fresh sewage pollution, and the HS-HF183 marker appears to be the most sensitive among these markers in terms of detecting fresh sewage. However, the presence of the HS-HF183 marker in environmental waters may not necessarily indicate the presence of enteric viruses due to their high abundance in sewage compared to enteric viruses. More research is required on the persistency of these markers in environmental water s les in relation to traditional fecal indicators and enteric pathogens.
Lost in translation: Returning germline genetic results in genome-scale cancer research
Publisher: Springer Science and Business Media LLC
Date: 28-04-2017
Essential indicators for measuring site‐based conservation effectiveness in the post‐2020 global biodiversity framework
Publisher: Wiley
Date: 04-02-2021
DOI: 10.1111/CONL.12792
Abstract: Work on the post‐2020 global bio ersity framework is now well advanced and will outline a vision, goals, and targets for the next decade of bio ersity conservation and beyond. For the effectiveness of Protected areas and Other Effective area‐based Conservation Measures, an indicator has been proposed for “areas meeting their documented ecological objectives.” However, the Convention on Biological Diversity (CBD) has not identified or agreed on what data should inform this indicator. Here we draw on experiences from the assessment of protected area effectiveness in the CBD's previous strategic plan to provide recommendations on the essential elements related to bio ersity outcomes and management that need to be captured in this updated indicator as well as how this could be done. Our proposed protected area effectiveness indicators include a combination of remotely derived products for all protected areas, combined with data from monitoring of both protected area management and trends in species and ecosystems based on field observations. Additionally, we highlight the need for creating a digital infrastructure to operationalize national‐level data‐capture. We believe these steps are critical and urge the adoption of suitable protected area effectiveness indicators before the post‐2020 framework is agreed in 2021.
Understanding re-distribution of road deposited particle-bound pollutants using a Bayesian Network (BN) approach
Publisher: Elsevier BV
Date: 08-2018
DOI: 10.1016/J.JHAZMAT.2018.05.012
Abstract: Road deposited pollutants (build-up) are continuously re-distributed by external factors such as traffic and wind turbulence, influencing stormwater runoff quality. However, current stormwater quality modelling approaches do not account for the re-distribution of pollutants. This undermines the accuracy of stormwater quality predictions, constraining the design of effective stormwater treatment measures. This study, using over 1000 data points, developed a Bayesian Network modelling approach to investigate the re-distribution of pollutant build-up on urban road surfaces. BTEX, which are a group of highly toxic pollutants, was the case study pollutants. Build-up s ling was undertaken in Shenzhen, China, using a dry and wet vacuuming method. The research outcomes confirmed that the vehicle type and particle size significantly influence the re-distribution of particle-bound BTEX. Compared to heavy-duty traffic in commercial areas, light-duty traffic dominates the re-distribution of particles of all size ranges. In industrial areas, heavy-duty traffic re-distributes particles >75 μm, and light-duty traffic re-distributes particles 300 μm and <75 μm and heavy-duty traffic re-distributes particles in the 300-150 μm range. The study results provide important insights to improve stormwater quality modelling and the interpretation of modelling outcomes, contributing to safeguard the urban water environment.
Prevalence and occurrence of zoonotic bacterial pathogens in surface waters determined by quantitative PCR
Publisher: Elsevier BV
Date: 11-2009
DOI: 10.1016/J.WATRES.2009.03.041
Abstract: The prevalence and concentrations of C ylobacter jejuni, Salmonella spp. and enterohaemorrhagic Escherichia coli (EHEC) were investigated in surface waters in Brisbane, Australia using quantitative PCR (qPCR) based methodologies. Water s les were collected from Brisbane City Botanic Gardens (CBG) Pond, and two urban tidal creeks (i.e., Oxley Creek and Blunder Creek). Of the 32 water s les collected, 8 (25%), 1 (3%), 9 (28%), 14 (44%), and 15 (47%) were positive for C. jejuni mapA, Salmonella invA, EHEC O157 LPS, EHEC VT1, and EHEC VT2 genes, respectively. The presence/absence of the potential pathogens did not correlate with either E. coli or enterococci concentrations as determined by binary logistic regression. In conclusion, the high prevalence, and concentrations of potential zoonotic pathogens along with the concentrations of one or more fecal indicators in surface water s les indicate a poor level of microbial quality of surface water, and could represent a significant health risk to users. The results from the current study would provide valuable information to the water quality managers in terms of minimizing the risk from pathogens in surface waters.
Water resources management: Innovation and challenges in a changing world
Publisher: MDPI AG
Date: 17-04-2017
DOI: 10.3390/W9040281
Build-up of toxic metals on the impervious surfaces of a commercial seaport
Publisher: Elsevier BV
Date: 05-2016
DOI: 10.1016/J.ECOENV.2016.01.027
Abstract: In the context of increasing threats to the sensitive marine ecosystem by toxic metals, this study investigated the metal build-up on impervious surfaces specific to commercial seaports. The knowledge generated from this study will contribute to managing toxic metal pollution of the marine ecosystem. The study found that inter-modal operations and main access roadway had the highest loads followed by container storage and vehicle marshalling sites, while the quay line and short term storage areas had the lowest. Additionally, it was found that Cr, Al, Pb, Cu and Zn were predominantly attached to solids, while significant amount of Cu, Pb and Zn were found as nutrient complexes. As such, treatment options based on solids retention can be effective for some metal species, while ineffective for other species. Furthermore, Cu and Zn are more likely to become bioavailable in seawater due to their strong association with nutrients. Mathematical models to replicate the metal build-up process were also developed using experimental design approach and partial least squares regression. The models for Cr and Pb were found to be reliable, while those for Al, Zn and Cu were relatively less reliable, but could be employed for preliminary investigations.
A Wilderness Approach under the World Heritage Convention
Publisher: Wiley
Date: 02-11-2015
DOI: 10.1111/CONL.12205
A Framework for Stormwater Quality Modelling under the Effects of Climate Change to Enhance Reuse
Publisher: MDPI AG
Date: 14-12-1970
DOI: 10.3390/SU122410463
Abstract: Water scarcity, which is exacerbated by climate change, is a major challenge to ensure human well-being. Therefore, it is equally important to protect conventional water resources from degradation and at the same time to identify cost-effective alternatives with a low carbon footprint. In this regard, stormwater plays a key role as it is a largely under-utilised resource for both, potable and non-potable use. However, stormwater carries substantial loads of pollutants to receiving waters such as rivers. Unfortunately, the lack of comprehensive stormwater quality modelling strategies, which account for the effects of climate change, constrains the formulation of effective measures to improve the quality of stormwater. Currently, there is a significant knowledge gap in the merging of stormwater quality modelling and climate modelling. This paper critically reviews current stormwater quality modelling approaches (quantity and quality) and the role of climate modelling outputs in stormwater quality modelling. This is followed by the presentation of a robust framework to integrate the impacts of climate change with stormwater quality models.
Human health risk assessment of heavy metals in urban stormwater
Publisher: Elsevier BV
Date: 07-2016
DOI: 10.1016/J.SCITOTENV.2016.03.067
Abstract: Toxic chemical pollutants such as heavy metals (HMs) are commonly present in urban stormwater. These pollutants can pose a significant risk to human health and hence a significant barrier for urban stormwater reuse. The primary aim of this study was to develop an approach for quantitatively assessing the risk to human health due to the presence of HMs in stormwater. This approach will lead to informed decision making in relation to risk management of urban stormwater reuse, enabling efficient implementation of appropriate treatment strategies. In this study, risks to human health from heavy metals were assessed as hazard index (HI) and quantified as a function of traffic and land use related parameters. Traffic and land use are the primary factors influencing heavy metal loads in the urban environment. The risks posed by heavy metals associated with total solids and fine solids (<150μm) were considered to represent the maximum and minimum risk levels, respectively. The study outcomes confirmed that Cr, Mn and Pb pose the highest risks, although these elements are generally present in low concentrations. The study also found that even though the presence of a single heavy metal does not pose a significant risk, the presence of multiple heavy metals could be detrimental to human health. These findings suggest that stormwater guidelines should consider the combined risk from multiple heavy metals rather than the threshold concentration of an in idual species. Furthermore, it was found that risk to human health from heavy metals in stormwater is significantly influenced by traffic volume and the risk associated with stormwater from industrial areas is generally higher than that from commercial and residential areas.
Selection of surrogates to assess social resilience in disaster management using multi-criteria decision analysis
Publisher: Emerald
Date: 26-02-2020
DOI: 10.1108/IJDRBE-07-2019-0045
Abstract: The purpose of this paper is to present a framework for evaluation and ranking of potential surrogates to select the optimum surrogates and test it for five selected social resilience indicators in a disaster context. Innovative resilience assessment approaches are required to capture key facets of resilience indicators to deepen the understanding of social resilience. Surrogates can adequately represent the target indicator that is difficult to measure, as surrogates are defined as key facets of a target indicator. To optimize the selection of surrogates, five key evaluation criteria were used. Disaster management experts completed an online survey questionnaire and evaluated three potential surrogate options. Surrogates were then ranked using PROMETHEE, a multi-experts multi-criteria group decision analysis technique. A framework was devised to evaluate and rank potential surrogates to assess social resilience in a disaster context. The findings revealed that the first ranked surrogate can be the most critical facet of a resilience indicator of measure. In most instances, highly experienced cohort of practitioners and policy makers have aligned their preferences of surrogates with the overall ranking of surrogates obtained in this study. The surrogate approach can also be tested in different disaster and geographic contexts. The resilience indicators used in this study to explore surrogates are largely applicable in all contexts. However, the preference of surrogates may also vary in different contexts. Once the surrogate is selected through an evaluation process proposed in this paper, the resilience status can be updated regularly with the help of the selected surrogate. The first ranked surrogate for each of the social resilience indicator can be applied, since the findings revealed that the first ranked surrogate can be the most critical facet in the context of the social resilience indicator being measured. The framework and the selection of optimal surrogates will assist to overcome the conceptual and methodical challenges of social resilience assessment. The applicability of selected surrogates by practitioners and policymakers in disaster management will play a vital role in resilience investment decision-making at the community level. The surrogate approach has been used in the fields of ecology and clinical medicine to overcome the challenges in measuring difficult to measure indicators. The use of surrogates in this study to measure social resilience indicators in a disaster context is innovative, which was not yet explored in resilience measurement in disaster management.
Public Perceptions on Artificial Intelligence Driven Disaster Management: Evidence from Sydney, Melbourne and Brisbane
Publisher: Elsevier BV
Date: 12-2021
Integrative pathway enrichment analysis of multivariate omics data
Publisher: Springer Science and Business Media LLC
Date: 05-02-2020
DOI: 10.1038/S41467-019-13983-9
Abstract: Multi-omics datasets represent distinct aspects of the central dogma of molecular biology. Such high-dimensional molecular profiles pose challenges to data interpretation and hypothesis generation. ActivePathways is an integrative method that discovers significantly enriched pathways across multiple datasets using statistical data fusion, rationalizes contributing evidence and highlights associated genes. As part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2658 cancers across 38 tumor types, we integrated genes with coding and non-coding mutations and revealed frequently mutated pathways and additional cancer genes with infrequent mutations. We also analyzed prognostic molecular pathways by integrating genomic and transcriptomic features of 1780 breast cancers and highlighted associations with immune response and anti-apoptotic signaling. Integration of ChIP-seq and RNA-seq data for master regulators of the Hippo pathway across normal human tissues identified processes of tissue regeneration and stem cell regulation. ActivePathways is a versatile method that improves systems-level understanding of cellular organization in health and disease through integration of multiple molecular datasets and pathway annotations.
Genomic and Molecular Analyses Identify Molecular Subtypes of Pancreatic Cancer Recurrence
Publisher: Elsevier BV
Date: 2022
Evaluation of multiple sewage-associated Bacteroides PCR markers for sewage pollution tracking
Publisher: Elsevier BV
Date: 11-2009
DOI: 10.1016/J.WATRES.2009.08.042
Abstract: The host specificity of the five published sewage-associated Bacteroides markers (i.e., HF183, BacHum, HuBac, BacH and Human-Bac) was evaluated in Southeast Queensland, Australia by testing fecal DNA s les (n=186) from 11 animal species including human fecal s les collected via influent to a sewage treatment plant (STP). All human fecal s les (n=50) were positive for all five markers indicating 100% sensitivity of these markers. The overall specificity of the HF183 markers to differentiate between humans and animals was 99%. The specificities of the BacHum and BacH markers were>94%, suggesting that these markers are suitable for the detection of sewage pollution in environmental waters in Australia. The HuBac (i.e., 63%) and Human-Bac (i.e., 79% specificity) markers performed poorly in distinguishing between the sources of human and animal fecal s les. It is recommended that the specificity of the sewage-associated markers must be rigorously tested prior to its application to identify the sources of fecal pollution in environmental waters.
Patterns of somatic structural variation in human cancer genomes
Publisher: Springer Science and Business Media LLC
Date: 05-02-2020
DOI: 10.1038/S41586-019-1913-9
Abstract: A key mutational process in cancer is structural variation, in which rearrangements delete, lify or reorder genomic segments that range in size from kilobases to whole chromosomes 1–7 . Here we develop methods to group, classify and describe somatic structural variants, using data from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA), which aggregated whole-genome sequencing data from 2,658 cancers across 38 tumour types 8 . Sixteen signatures of structural variation emerged. Deletions have a multimodal size distribution, assort unevenly across tumour types and patients, are enriched in late-replicating regions and correlate with inversions. Tandem duplications also have a multimodal size distribution, but are enriched in early-replicating regions—as are unbalanced translocations. Replication-based mechanisms of rearrangement generate varied chromosomal structures with low-level copy-number gains and frequent inverted rearrangements. One prominent structure consists of 2–7 templates copied from distinct regions of the genome strung together within one locus. Such cycles of templated insertions correlate with tandem duplications, and—in liver cancer—frequently activate the telomerase gene TERT . A wide variety of rearrangement processes are active in cancer, which generate complex configurations of the genome upon which selection can act.
How can gamification be incorporated into disaster emergency planning? A systematic review of the literature
Publisher: Emerald
Date: 20-04-2020
DOI: 10.1108/IJDRBE-08-2019-0054
Abstract: The purpose of this paper is to investigate the role of gamification as a novel technique in motivating community engagement in disaster-related activities in order to address the question of how gamification can be incorporated into disaster emergency planning. This study conducts a systematic literature review and explores available gamified applications for disaster emergency planning and their purpose of use. In total, 51 scholarly articles on the topic and 35 disaster-related gamified applications are reviewed. The findings reveal the following: (a) gamified applications ( n = 35) are used for education, research and intervention purposes (b) gamified applications create new opportunities for community engagement and raise disaster awareness among the community in virtual environments and (c) gamified applications help shape a new culture – i.e. gamified culture – that supports smart disaster emergency planning practice. During the recent years, utilisation of game elements in non-game contexts – i.e., gamification – has become a popular approach in motivating people in various actions. Increasing research highlighted the benefits of gamification in enhancing community engagement, creating interactive environments, providing better behavioural outcomes and influencing democratic processes. Despite some of the applications indicating the potential of gamification in disaster emergency planning, the use of gamification technique in this discipline is an understudied area. This study reveals gamification can be incorporated into disaster emergency planning.
Optimized simultaneous pressurized fluid extraction and in-cell clean-up, and analysis of polycyclic aromatic hydrocarbons (PAHs), and nitro-, carbonyl-, hydroxy -PAHs in solid particles
Publisher: Elsevier BV
Date: 08-2020
Sustainable water provision: challenges, alternative strategies and sources in the era of climate change
Publisher: IGI Global
Date: 2010
DOI: 10.4018/978-1-61520-775-6.CH002
Abstract: As a result of rapid urbanisation, population growth, changes in lifestyle, pollution and the impacts of climate change, water provision has become a critical challenge for planners and policy-makers. In the wake of increasingly difficult water provision and drought, the notion that freshwater is a finite and vulnerable resource is increasingly being realised. Many city administrations around the world are struggling to provide water security for their residents to maintain lifestyle and economic growth. This chapter reviews the global challenge of providing freshwater to sustain lifestyles and economic growth, and the contributing challenges of climate change, urbanisation, population growth and problems in rainfall distribution. The chapter proceeds to evaluate major alternatives to current water sources such as conservation, recycling and reclamation, and desalination. Integrated water resource management is briefly looked at to explore its role in complementing water provision. A comparative study on alternative resources is undertaken to evaluate their strengths, weaknesses, opportunities and constraints, and the results are discussed.
Exome-Wide Association Study of Pancreatic Cancer Risk
Publisher: Elsevier BV
Date: 02-2018
Application of quantitative structure-activity relationship (QSAR) model in comprehensive human health risk assessment of PAHs, and alkyl-, nitro-, carbonyl-, and hydroxyl-PAHs laden in urban road dust
Publisher: Elsevier BV
Date: 02-2020
DOI: 10.1016/J.JHAZMAT.2019.121154
Abstract: The carcinogenic human health risks (CHHR) posed by the exposure to PAHs and transformed PAH products (TPPs) are currently inconclusive due to the lack of toxicity equivalency factors (TEFs) for most TPPs although some of these pollutants are more potent carcinogens. The applicability of quantitative structure-activity relationship (QSAR) model in predicting TEF of PAHs and TPPs to holistically evaluate the CHHR posed by the exposure to these pollutants in road dust from Gold Coast, Australia was examined. Statistical evaluation via ten metrics shows that partial least-squares regression (PLSR1) model has more statistical power in predicting TEF than multiple linear regression (MLR) within relevant applicability domain. For instance, the predicted residual sum of squares (PRESS) and standard deviation of error of prediction (SDEP) for PLSR is closer to zero than that of MLR. The total cancer risk estimated using the QSAR model derived TEFs and original TEFs for outliers gives a more holistic incremental lifetime cancer risk in relation to children and adults. Potential cancer risk exists for adults with this approach whereas reliance on only the originally available TEFs lead to a negligible risk diagnosis. The application of QSAR model in assessing CHHR due to PAHs and TPPs exposures is very viable.
Source characterisation of road dust based on chemical and mineralogical composition
Publisher: Elsevier BV
Date: 04-2012
DOI: 10.1016/J.CHEMOSPHERE.2011.12.012
Abstract: Road dust contain potentially toxic pollutants originating from a range of anthropogenic sources common to urban land uses and soil inputs from surrounding areas. The research study analysed the mineralogy and morphology of dust s les from road surfaces from different land uses and background soil s les to characterise the relative source contributions to road dust. The road dust consist primarily of soil derived minerals (60%) with quartz averaging 40-50% and remainder being clay forming minerals of albite, microcline, chlorite and muscovite originating from surrounding soils. About 2% was organic matter primarily originating from plant matter. Potentially toxic pollutants represented about 30% of the build-up. These pollutants consist of brake and tire wear, combustion emissions and fly ash from asphalt. Heavy metals such as Zn, Cu, Pb, Ni, Cr and Cd primarily originate from vehicular traffic while Fe, Al and Mn primarily originate from surrounding soils. The research study confirmed the significant contribution of vehicular traffic to dust deposited on urban road surfaces.
Optimization of in-cell accelerated solvent extraction technique for the determination of organochlorine pesticides in river sediments
Publisher: Elsevier BV
Date: 04-2016
DOI: 10.1016/J.TALANTA.2015.12.049
Abstract: Organochlorine pesticides (OCPs) are ubiquitous environmental contaminants with adverse impacts on aquatic biota, wildlife and human health even at low concentrations. However, conventional methods for their determination in river sediments are resource intensive. This paper presents an approach that is rapid and also reliable for the detection of OCPs. Accelerated Solvent Extraction (ASE) with in-cell silica gel clean-up followed by Triple Quadrupole Gas Chromatograph Mass Spectrometry (GCMS/MS) was used to recover OCPs from sediment s les. Variables such as temperature, solvent ratio, adsorbent mass and extraction cycle were evaluated and optimized for the extraction. With the exception of Aldrin, which was unaffected by any of the variables evaluated, the recovery of OCPs from sediment s les was largely influenced by solvent ratio and adsorbent mass and, to some extent, the number of cycles and temperature. The optimized conditions for OCPs extraction in sediment with good recoveries were determined to be 4 cycles, 4.5 g of silica gel, 105 °C, and 4:3 v/v DCM: hexane mixture. With the exception of two compounds (α-BHC and Aldrin) whose recoveries were low (59.73 and 47.66% respectively), the recovery of the other pesticides were in the range 85.35-117.97% with precision <10% RSD. The method developed significantly reduces s le preparation time, the amount of solvent used, matrix interference, and is highly sensitive and selective.
Distribution and variation of metals in urban river sediments in response to microplastics presence, catchment characteristics and sediment properties
Publisher: Elsevier BV
Date: 2023
DOI: 10.1016/J.SCITOTENV.2022.159139
Abstract: Despite well documented studies on metal pollutants in aquatic ecosystems, knowledge on the combined effects of catchment characteristics, sediment properties, and emerging pollutants, such as microplastics (MPs) on the presence of metals in urban river sediments is still limited. In this study, the synergistic influence of MPs type and hazard indices, catchment characteristics and sediment properties on the variability of metals present in sediments was investigated based on a typical urban river, Brisbane River, Australia. It was noted that the mean concentrations of metals in Brisbane River decreases in the order of Al (94,142 ± 12,194 μg/g) > Fe (62,970 ± 8104 μg/g) > Mn (746 ± 258 μg/g) > Zn (196 ± 29 μg/g) > Cu (50 ± 19 μg/g) > Pb (47 ± 25 μg/g) > Ni (25 ± 3 μg/g) while the variability of metals decreases in the order of Pb > Cu > Mn > Al > Ni > Zn > Fe along the river. According to enrichment factor (Ef) contamination categories, Mn, Cu and Zn exert a moderate level of contamination (Ef > 2), while Fe, Ni, and Zn show slight sediment pollution (1 <Ef 3) was found at s ling locations having a high urbanisation level and traffic related activities. Crustal metal elements (namely, Al, Fe, Mn) were found to be statistically significantly correlated with sediment properties (P < 0.05). Anthropogenic source metals (namely, Cu, Ni, Pb, Zn) were observed to be highly correlated with catchment characteristics. Additionally, the presence of metals in sediments were positively correlated with MPs concentration, and negatively correlated with MPs hazard indices. The outcomes of this study provide new insights for understanding the relationships among metals and various influential factors in the context of urban river sediment pollution, which will benefit the formulation of risk assessment and regulatory measures for protecting urban waterways.
Urban Water Quality
Publisher: Springer International Publishing
Date: 2019
Use of surrogate indicators for the evaluation of potential health risks due to poor urban water quality: A Bayesian Network approach
Publisher: Elsevier BV
Date: 02-2018
DOI: 10.1016/J.ENVPOL.2017.10.076
Abstract: Urban water pollution poses risks of waterborne infectious diseases. Therefore, in order to improve urban liveability, effective pollution mitigation strategies are required underpinned by predictions generated using water quality models. However, the lack of reliability in current modelling practices detrimentally impacts planning and management decision making. This research study adopted a novel approach in the form of Bayesian Networks to model urban water quality to better investigate the factors that influence risks to human health. The application of Bayesian Networks was found to enhance the integration of quantitative and qualitative spatially distributed data for analysing the influence of environmental and anthropogenic factors using three surrogate indicators of human health risk, namely, turbidity, total nitrogen and fats/oils. Expert knowledge was found to be of critical importance in assessing the interdependent relationships between health risk indicators and influential factors. The spatial variability maps of health risk indicators developed enabled the initial identification of high risk areas in which flooding was found to be the most significant influential factor in relation to human health risk. Surprisingly, population density was found to be less significant in influencing health risk indicators. These high risk areas in turn can be subjected to more in-depth investigations instead of the entire region, saving time and resources. It was evident that decision making in relation to the design of pollution mitigation strategies needs to account for the impact of landscape characteristics on water quality, which can be related to risk to human health.
Major Conservation Policy Issues for Biodiversity in Oceania
Publisher: Wiley
Date: 13-07-2009
DOI: 10.1111/J.1523-1739.2009.01287.X
Abstract: Oceania is a erse region encompassing Australia, Melanesia, Micronesia, New Zealand, and Polynesia, and it contains six of the world's 39 hotspots of ersity. It has a poor record for extinctions, particularly for birds on islands and mammals. Major causes include habitat loss and degradation, invasive species, and overexploitation. We identified six major threatening processes (habitat loss and degradation, invasive species, climate change, overexploitation, pollution, and disease) based on a comprehensive review of the literature and for each developed a set of conservation policies. Many policies reflect the urgent need to deal with the effects of burgeoning human populations (expected to increase significantly in the region) on bio ersity. There is considerable difference in resources for conservation, including people and available scientific information, which are heavily biased toward more developed countries in Oceania. Most scientific publications analyzed for four threats (habitat loss, invasive species, overexploitation, and pollution) are from developed countries: 88.6% of Web of Science publications were from Australia (53.7%), New Zealand (24.3%), and Hawaiian Islands (10.5%). Many island states have limited resources or expertise. Even countries that do (e.g., Australia, New Zealand) have ongoing and emerging significant challenges, particularly with the interactive effects of climate change. Oceania will require the implementation of effective policies for conservation if the region's poor record on extinctions is not to continue.
A deep learning system accurately classifies primary and metastatic cancers using passenger mutation patterns
Publisher: Springer Science and Business Media LLC
Date: 05-02-2020
DOI: 10.1038/S41467-019-13825-8
Abstract: In cancer, the primary tumour’s organ of origin and histopathology are the strongest determinants of its clinical behaviour, but in 3% of cases a patient presents with a metastatic tumour and no obvious primary. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium , we train a deep learning classifier to predict cancer type based on patterns of somatic passenger mutations detected in whole genome sequencing (WGS) of 2606 tumours representing 24 common cancer types produced by the PCAWG Consortium. Our classifier achieves an accuracy of 91% on held-out tumor s les and 88% and 83% respectively on independent primary and metastatic s les, roughly double the accuracy of trained pathologists when presented with a metastatic tumour without knowledge of the primary. Surprisingly, adding information on driver mutations reduced accuracy. Our results have clinical applicability, underscore how patterns of somatic passenger mutations encode the state of the cell of origin, and can inform future strategies to detect the source of circulating tumour DNA.
ROR1 and ROR2 expression in pancreatic cancer
Publisher: Springer Science and Business Media LLC
Date: 11-11-2021
DOI: 10.1186/S12885-021-08952-9
Abstract: The Wnt receptors ROR1 and ROR2 are generating increased interest as cancer therapeutic targets but remain understudied in pancreatic ductal adenocarcinoma (PDAC). Compared to canonical Wnt/ β-catenin signalling, the role of noncanonical Wnt signalling in PDAC remains largely unknown. Only one study has investigated the prognostic significance of the noncanonical Wnt signalling receptor, ROR2 in PDAC. No studies have investigated the prognostic role of ROR1 in PDAC. Here, we performed analysis of ROR1 and ROR2 mRNA expression in three publicly available datasets ICGC-PACA-AU ( n = 81), TCGA-PAAD ( n = 150) and CPTAC-PDAC ( n = 137). ROR1 and ROR2 protein expression from the CPTAC-PDAC discovery cohort were also analysed. Immunohistochemistry (IHC) using the validated anti ROR1 monoclonal antibody (4A5) was performed on the Australian Pancreatic Cancer Genome Initiative (APGI) cohort of PDAC s les ( n = 152). Association between ROR1 cytoplasmic staining intensity and clinicopathological parameters including stage, grade and overall survival (OS) was investigated. High ROR1 mRNA expression levels correlated with a favourable OS outcome in all of the ICGC-PACA-AU, TCGA-PAAD and CPTAC-PDAC cohorts. ROR1 protein expression was not associated with stage, grade or OS in the APGI cohort. ROR1 and ROR2 have potential as prognostic markers when measured at the mRNA level in PDAC. Our IHC cohort did not support ROR1 protein expression in predicting OS, and highlighted the discrepancy of prognostic biomarkers when measured by MS, IHC and RNAseq.
Clinical interpretation of whole-genome and whole-transcriptome sequencing for precision oncology
Publisher: Elsevier BV
Date: 09-2022
DOI: 10.1016/J.SEMCANCER.2021.07.003
Abstract: Whole-genome sequencing either alone or in combination with whole-transcriptome sequencing has started to be used to analyze clinical tumor s les to improve diagnosis, provide risk stratification, and select patient-specific therapies. Compared with current genomic testing strategies, largely focused on small number of genes tested in idually or targeted panels, whole-genome and transcriptome sequencing (WGTS) provides novel opportunities to identify and report a potentially much larger number of actionable alterations with diagnostic, prognostic, and/or predictive impact. Such alterations include point mutations, indels, copy- number aberrations and structural variants, but also germline variants, fusion genes, noncoding alterations and mutational signatures. Nevertheless, these comprehensive tests are accompanied by many challenges ranging from the extent and ersity of sequence alterations detected by these methods to the complexity and limited existing standardization in interpreting them. We describe the challenges of WGTS interpretation and the opportunities with comprehensive genomic testing.
Analysis of build-up of heavy metals and volatile organics on urban roads in gold coast, Australia
Publisher: IWA Publishing
Date: 05-2011
DOI: 10.2166/WST.2011.151
Abstract: Urban water quality can be significantly impaired by the build-up of pollutants such as heavy metals and volatile organics on urban road surfaces due to vehicular traffic. Any control strategy for the mitigation of traffic related build-up of heavy metals and volatile organic pollutants should be based on the knowledge of their build-up processes. In the study discussed in this paper, the outcomes of a detailed experimental investigation into build-up processes of heavy metals and volatile organics are presented. It was found that traffic parameters such as average daily traffic, volume over capacity ratio and surface texture depth had similar strong correlations with the build-up of heavy metals and volatile organics. Multicriteria decision analyses revealed that that the 1–74 μm particulate fraction of total suspended solids (TSS) could be regarded as a surrogate indicator for particulate heavy metals in build-up and this same fraction of total organic carbon could be regarded as a surrogate indicator for particulate volatile organics build-up. In terms of pollutants affinity, TSS was found to be the predominant parameter for particulate heavy metals build-up and total dissolved solids was found to be the predominant parameter for the potential dissolved particulate fraction in heavy metals buildup. It was also found that land use did not play a significant role in the build-up of traffic generated heavy metals and volatile organics.
TiO2-biochar composites as alternative photocatalyst for stormwater disinfection
Publisher: Elsevier BV
Date: 08-2022
Effective degradation of polychlorinated biphenyls by a facultative anaerobic bacterial consortium using alternating anaerobic aerobic treatments
Publisher: Elsevier BV
Date: 04-2009
DOI: 10.1016/J.SCITOTENV.2018.12.385
Abstract: Polychlorinated biphenyls (PCBs) are synthetic mixtures of chlorinated hydrocarbon compounds that were widely used in the past and still found in the environment due to their highly recalcitrant nature. A combination of anaerobic dechlorination and aerobic oxidation is essential to degrade these PCB mixtures into less toxic products. It was hypothesized that due to the complexity of PCB mixtures, a consortium of carefully selected suitable microbial species will perform better than the application of in idual microbes. In the present study, biodegradation of the commercial PCB mixture, Aroclor 1260, was studied under two different combined anaerobic-aerobic conditions, namely, alternating (AN) and two stage (TS). The facultative anaerobic bacterial consortium consisted of naturally occurring Achromobacter sp. NP03, Ochrobactrum sp. NP04 and Lysinibacillus sp. NP05. These bacteria were found capable as in iduals of solubilizing and degrading PCBs under both anaerobic and aerobic conditions. 49.2 ± 2.5% total reduction of the original 50 mg/L Aroclor 1260 mixture was achieved after 2 weeks in AN treatment whereas the reduction was only 24.44 ± 2.46% in TS treatment. At the end of week 6, a yield of 17.63 ± 0.91 mg/L chloride released was measured under AN condition compared to 11.79 ± 1.28 mg/L measured under TS condition. The overall results suggested that the microbial consortia capable of degrading and utilizing PCBs under both, anaerobic and aerobic conditions achieved better PCB degradation by repeated exposure to short periods of anaerobic and aerobic conditions alternatingly rather than the conventional two stage anaerobic-aerobic conditions.
Intravital imaging technology guides FAK-mediated priming in pancreatic cancer precision medicine according to Merlin status
Publisher: American Association for the Advancement of Science (AAAS)
Date: 10-2021
Abstract: Intravital imaging guides a personalized medicine approach to target mechanoreciprocity in pancreatic cancer.
Identification of unique neoantigen qualities in long-term survivors of pancreatic cancer
Publisher: Springer Science and Business Media LLC
Date: 11-2017
DOI: 10.1038/NATURE24462
Filling in biodiversity threat gaps: Only 5% of global threat data sets meet a gold standard
Publisher: American Association for the Advancement of Science (AAAS)
Date: 22-04-2016
Abstract: Only 5% of global threat data sets meet a “gold standard”
Inotuzumab ozogamicin resistance associated with a novel CD22 truncating mutation in a case of B‐acute lymphoblastic leukaemia
Publisher: Wiley
Date: 09-07-2020
DOI: 10.1111/BJH.16949
Inherent and external factors influencing the distribution of PAHs, hydroxy-PAHs, carbonyl-PAHs and nitro-PAHs in urban road dust
Publisher: Elsevier BV
Date: 09-2022
DOI: 10.1016/J.ENVPOL.2022.119705
Abstract: The distribution and fate of hazardous polycyclic aromatic hydrocarbons (PAHs) and their associated transformed PAHs products (TPPs) notably carbonyl-PAHs (CPAHs), hydroxy-PAHs (HoPAHs), and nitro-PAHs (NPAHs) on urban road surfaces are influenced by erse factors to varying extent. The pollutants are eventually transported to urban receiving waters via stormwater runoff posing risks to human and ecosystem health. In order to formulate an effective mitigation strategy, it is essential to comprehensively examine the role of both inherent and external factors in the distribution and fate of these hazardous pollutants, and thus, the need for this study. The research study showed that commercial land use has the highest cumulative concentration of PAHs and TPPs. Antecedent dry days (ADDs) has an inverse influence on the distribution of the total concentrations of low-molecular weight PAHs (LMW-PAHs), PAHs, and (PAHs + TPPs) irrespective of the type of land use, whilst there was no major influence on the total concentrations of high molecular weight PAHs (HMW-PAHs), and TPPs. The high volatility of LMW-PAHs compared to HMW-PAHs is considered to account for the decreasing concentration of LMW-PAH with increasing ADD. Particle size range has significant inverse influence on the cumulative concentration of pollutants across all land uses, since smaller particles are characteristically associated with larger surface area leading to the higher sorption of pollutants. Multivariate analysis of the influential factors indicated that two particle size ranges (0.45-150 μm and 150-425 μm) constitute the major influential factors on the distribution and fate of PAHs and TPPs in urban road dust. Greater quantum of pollutants are sorbed to the 0.45-150 μm particles due to the relatively higher specific surface area (SSA), concentration of total organic carbon (TOC) and total suspended solids (TSS) concentration. Therefore, it is critical to effectively remove finer particles from road surfaces in order to reduce exposure to hazardous pollutants.
Author Correction: Patterns of somatic structural variation in human cancer genomes
Publisher: Springer Science and Business Media LLC
Date: 25-01-2023
Prediction model of the buildup of volatile organic compounds on urban roads
Publisher: American Chemical Society (ACS)
Date: 22-04-2011
DOI: 10.1021/ES200307X
Abstract: A model to predict the buildup of mainly traffic-generated volatile organic compounds or VOCs (toluene, ethylbenzene, ortho-xylene, meta-xylene, and para-xylene) on urban road surfaces is presented. The model required three traffic parameters, namely average daily traffic (ADT), volume to capacity ratio (V/C), and surface texture depth (STD), and two chemical parameters, namely total suspended solid (TSS) and total organic carbon (TOC), as predictor variables. Principal component analysis and two phase factor analysis were performed to characterize the model calibration parameters. Traffic congestion was found to be the underlying cause of traffic-related VOC buildup on urban roads. The model calibration was optimized using orthogonal experimental design. Partial least squares regression was used for model prediction. It was found that a better optimized orthogonal design could be achieved by including the latent factors of the data matrix into the design. The model performed fairly accurately for three different land uses as well as five different particle size fractions. The relative prediction errors were 10-40% for the different size fractions and 28-40% for the different land uses while the coefficients of variation of the predicted intersite VOC concentrations were in the range of 25-45% for the different size fractions. Considering the sizes of the data matrices, these coefficients of variation were within the acceptable interlaboratory range for analytes at ppb concentration levels.
Comparison of partial extraction reagents for assessing potential bioavailability of heavy metals in sediments
Publisher: Elsevier BV
Date: 05-2016
DOI: 10.1016/J.MARPOLBUL.2016.03.029
Abstract: Assessment of heavy metal bioavailability in sediments is complex because of the number of partial extraction methods available for the assessment and the general lack of certified reference materials. This study evaluates five different extraction methodologies to ascertain the relative strengths and weaknesses of each method. The results are then compared to previously published work to ascertain the most effective partial extraction technique, which was established to dilute (0.75-1M) nitric acid solutions. These results imply that single reagent weak acid extractions provide a better assessment of potentially bioavailable metals than the chelating agents used in sequential extraction methods.
Clinical utility of whole-genome sequencing in precision oncology
Publisher: Elsevier BV
Date: 09-2022
DOI: 10.1016/J.SEMCANCER.2021.06.018
Abstract: Precision diagnostics is one of the two pillars of precision medicine. Sequencing efforts in the past decade have firmly established cancer as a primarily genetically driven disease. This concept is supported by therapeutic successes aimed at particular pathways that are perturbed by specific driver mutations in protein-coding domains and reflected in three recent FDA tissue agnostic cancer drug approvals. In addition, there is increasing evidence from studies that interrogate the entire genome by whole-genome sequencing that acquired global and complex genomic aberrations including those in non-coding regions of the genome might also reflect clinical outcome. After addressing technical, logistical, financial and ethical challenges, national initiatives now aim to introduce clinical whole-genome sequencing into real-world diagnostics as a rational and potentially cost-effective tool for response prediction in cancer and to identify patients who would benefit most from 'expensive' targeted therapies and recruitment into clinical trials. However, so far, this has not been accompanied by a systematic and prospective evaluation of the clinical utility of whole-genome sequencing within clinical trials of uniformly treated patients of defined clinical outcome. This approach would also greatly facilitate novel predictive biomarker discovery and validation, ultimately reducing size and duration of clinical trials and cost of drug development. This manuscript is the third in a series of three to review and critically appraise the potential and challenges of clinical whole-genome sequencing in solid tumors and hematological malignancies.
Sustainable water provision : challenges, alternative strategies and sources in the ERA of climate change
Publisher: IGI Global
Date: 2011
DOI: 10.4018/978-1-60960-472-1.CH714
Abstract: As a result of rapid urbanisation, population growth, changes in lifestyle, pollution and the impacts of climate change, water provision has become a critical challenge for planners and policy-makers. In the wake of increasingly difficult water provision and drought, the notion that freshwater is a finite and vulnerable resource is increasingly being realised. Many city administrations around the world are struggling to provide water security for their residents to maintain lifestyle and economic growth. This chapter reviews the global challenge of providing freshwater to sustain lifestyles and economic growth, and the contributing challenges of climate change, urbanisation, population growth and problems in rainfall distribution. The chapter proceeds to evaluate major alternatives to current water sources such as conservation, recycling and reclamation, and desalination. Integrated water resource management is briefly looked at to explore its role in complementing water provision. A comparative study on alternative resources is undertaken to evaluate their strengths, weaknesses, opportunities and constraints, and the results are discussed.
Engineered technologies for the separation and degradation of microplastics in water: A review
Publisher: Elsevier BV
Date: 06-2021
Population similarity analysis of indicator bacteria for source prediction of faecal pollution in a coastal lake
Publisher: Elsevier BV
Date: 08-2008
DOI: 10.1016/J.MARPOLBUL.2008.04.043
Abstract: Biochemical fingerprinting (BF) databases of 524 enterococci and 571 Escherichia coli isolates and an antibiotic resistance analysis (ARA) database comprising of 380 E. coli isolates from four suspected sources (i.e. dogs, chickens, waterfowls, and human sewage) were developed to predict the sources of faecal pollution in a recreational coastal lake. Twenty water s les representing four s ling episodes were collected from five sites and the enterococci and E. coli population from each site were compared with those of the databases. The degree of similarity between bacterial populations was measured as population similarity (Sp) coefficient. Using the BF-database, bacterial populations of waterfowls showed the highest similarity with the water s les followed by a sewage treatment plant (STP). Higher population similarities were found between s les from STP and water s les especially at two sites (T2 and T3) which were located near the sewerage pipes collecting wastewater from the study area. When using the ARA-database, the highest similarity was found between E. coli populations from STP and water s les at sites T2 and T4. Both faecal indicators and as well as methods predicted human faecal pollution, possibly through leakage from submerged sewerage pipes. The results indicated that the Sp-analysis of faecal indicator bacterial populations from suspected sources and water s les can be used as a simple tool to predict the source(s) of faecal pollution in surface waters.
Influence of physicochemical properties of road dust on the build-up of hydrocarbons
Publisher: Elsevier BV
Date: 12-2019
DOI: 10.1016/J.SCITOTENV.2019.133812
Abstract: Understanding the factors influencing the build-up behaviour of different pollutants accumulated on urban roads is essential for the implementation of effective stormwater pollution mitigation strategies. Even though a significant knowledge base exists on different factors influencing hydrocarbon build-up, there is a dearth of evidence on how physicochemical properties of road dust influence hydrocarbon build-up. Accordingly, this study investigated the relationships between physicochemical properties of road dust and hydrocarbons associated with different particle size fractions of road dust. Hydrocarbons with different sources of origin in all size fractions showed a significant correlation with different soil constituents of road dust, predominantly with organic matter, amorphous matter, clay minerals and clay forming minerals of feldspars. However, the physicochemical properties influencing the hydrocarbon build-up is different among different particle size fractions. The interactions identified between hydrocarbon compounds and different minerals associated with road dust will contribute to the development of effective stormwater pollution mitigation strategies.
The repertoire of mutational signatures in human cancer
Publisher: Springer Science and Business Media LLC
Date: 05-02-2020
DOI: 10.1038/S41586-020-1943-3
Abstract: Somatic mutations in cancer genomes are caused by multiple mutational processes, each of which generates a characteristic mutational signature 1 . Here, as part of the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium 2 of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA), we characterized mutational signatures using 84,729,690 somatic mutations from 4,645 whole-genome and 19,184 exome sequences that encompass most types of cancer. We identified 49 single-base-substitution, 11 doublet-base-substitution, 4 clustered-base-substitution and 17 small insertion-and-deletion signatures. The substantial size of our dataset, compared with previous analyses 3–15 , enabled the discovery of new signatures, the separation of overlapping signatures and the decomposition of signatures into components that may represent associated—but distinct—DNA damage, repair and/or replication mechanisms. By estimating the contribution of each signature to the mutational catalogues of in idual cancer genomes, we revealed associations of signatures to exogenous or endogenous exposures, as well as to defective DNA-maintenance processes. However, many signatures are of unknown cause. This analysis provides a systematic perspective on the repertoire of mutational processes that contribute to the development of human cancer.
Risk associated with microplastics in urban aquatic environments: A critical review
Publisher: Elsevier BV
Date: 10-2022
DOI: 10.1016/J.JHAZMAT.2022.129587
Abstract: The presence of microplastics (MPs) has been recognized as a significant environmental threat due to adverse effects spanning from molecular level, organism health, ecosystem services to human health and well-being. MPs are complex environmental contaminants as they bind to a wide range of other contaminants. MPs associated contaminants include toxic chemical substances that are used as additives during the plastic manufacturing process and adsorbed contaminants that co-exist with MPs in aquatic environments. With the transfer between the water column and sediments, and the migration within aquatic systems, such contaminants associated MPs potentially pose high risk to aquatic systems. However, only limited research has been undertaken currently to link the environmental risk associated with MPs occurrence and movement behaviour in aquatic systems. Given the significant environmental risk and current knowledge gaps, this review focuses on the role played by the abundance of different MP species in water and sediment compartments as well as provides the context for assessing and quantifying the multiple risks associated with the occurrence and movement behaviour of different MP types. Based on the review of past literature, it is found that the physicochemical properties of MPs influence the release/sorption of other contaminants and current MPs transport modelling studies have primarily focused on virgin plastics rather than aged plastics. Additionally, risk assessment of contaminants-associated MPs needs significantly more research. This paper consolidates the current state-of-the art knowledge on the source to sink movement behaviour of MPs and methodologies for assessing the risk of different MP species. Moreover, knowledge gaps and emerging trends in the field are also identified for future research endeavours.
Traffic and climate change impacts on water quality : measuring build-up and wash-off of heavy metals and petroleum hydrocarbons
Publisher: IGI Global
Date: 2011
DOI: 10.4018/978-1-60960-472-1.CH716
Abstract: Understanding the impacts of traffic and climate change on water quality helps decision makers to develop better policy and plans for dealing with unsustainable urban and transport development. This chapter presents detailed methodologies developed for s le collection and testing for heavy metals and total petroleum hydrocarbons, as part of a research study to investigate the impacts of climate change and changes to urban traffic characteristics on pollutant build-up and wash-off from urban road surfaces. Cadmium, chromium, nickel, copper, lead, iron, aluminium, manganese and zinc were the target heavy metals, and selected gasoline and diesel range organics were the target total petroleum hydrocarbons for this study. The study sites were selected to encompass the urban traffic characteristics of the Gold Coast region, Australia. An improved s le collection method referred to as ‘the wet and dry vacuum system’ for the pollutant build-up, and an effective wash-off plan to incorporate predicted changes to rainfall characteristics due to climate change, were implemented. The novel approach to s le collection for pollutant build-up helped to maintain the integrity of collection efficiency. The wash-off plan helped to incorporate the predicted impacts of climate change in the Gold Coast region. The robust experimental methods developed will help in field s le collection and chemical testing of different stormwater pollutants in build-up and wash-off.& nbsp
Abundance, distribution patterns, and identification of microplastics in Brisbane River sediments, Australia
Publisher: Elsevier BV
Date: 2020
DOI: 10.1016/J.SCITOTENV.2019.134467
Abstract: Plastic pollutants in aquatic ecosystems have received wide attention and research endeavours since early 1970s. However, in comparison to marine environments, the occurrence of microplastics in a tidal river system remains largely unknown, especially in river sediments. Sediment s les taken from twenty-two s ling points along Brisbane River over the four different seasons revealed relatively high concentrations of microplastics in river sediments, with abundance ranging from 0.18 to 129.20 mg kg
Water Quality Profile of an Urbanising Catchment
Publisher: American Society of Agricultural and Biological Engineers
Date: 2007
DOI: 10.13031/2013.24016
Inferring structural variant cancer cell fraction
Publisher: Springer Science and Business Media LLC
Date: 05-02-2020
DOI: 10.1038/S41467-020-14351-8
Abstract: We present SVclone, a computational method for inferring the cancer cell fraction of structural variant (SV) breakpoints from whole-genome sequencing data. SVclone accurately determines the variant allele frequencies of both SV breakends, then simultaneously estimates the cancer cell fraction and SV copy number. We assess performance using in silico mixtures of real s les, at known proportions, created from two clonal metastases from the same patient. We find that SVclone’s performance is comparable to single-nucleotide variant-based methods, despite having an order of magnitude fewer data points. As part of the Pan-Cancer Analysis of Whole Genomes (PCAWG) consortium, which aggregated whole-genome sequencing data from 2658 cancers across 38 tumour types, we use SVclone to reveal a subset of liver, ovarian and pancreatic cancers with subclonally enriched copy-number neutral rearrangements that show decreased overall survival. SVclone enables improved characterisation of SV intra-tumour heterogeneity.
Australian Genomics
Publisher: Elsevier BV
Date: 03-2023
Biodegradation of waste refrigerator polyurethane by mealworms
Publisher: Springer Science and Business Media LLC
Date: 20-10-2022
Assessing uncertainty in pollutant wash-off modelling via model validation
Publisher: Elsevier BV
Date: 11-2014
DOI: 10.1016/J.SCITOTENV.2014.08.027
Abstract: Stormwater pollution is linked to stream ecosystem degradation. In predicting stormwater pollution, various types of modelling techniques are adopted. The accuracy of predictions provided by these models depends on the data quality, appropriate estimation of model parameters, and the validation undertaken. It is well understood that available water quality datasets in urban areas span only relatively short time scales unlike water quantity data, which limits the applicability of the developed models in engineering and ecological assessment of urban waterways. This paper presents the application of leave-one-out (LOO) and Monte Carlo cross validation (MCCV) procedures in a Monte Carlo framework for the validation and estimation of uncertainty associated with pollutant wash-off when models are developed using a limited dataset. It was found that the application of MCCV is likely to result in a more realistic measure of model coefficients than LOO. Most importantly, MCCV and LOO were found to be effective in model validation when dealing with a small s le size which hinders detailed model validation and can undermine the effectiveness of stormwater quality management strategies.
Author Correction: Inferring structural variant cancer cell fraction
Publisher: Springer Science and Business Media LLC
Date: 23-08-2021
Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition
Publisher: Springer Science and Business Media LLC
Date: 05-02-2020
DOI: 10.1038/S41588-019-0562-0
Abstract: About half of all cancers have somatic integrations of retrotransposons. Here, to characterize their role in oncogenesis, we analyzed the patterns and mechanisms of somatic retrotransposition in 2,954 cancer genomes from 38 histological cancer subtypes within the framework of the Pan-Cancer Analysis of Whole Genomes (PCAWG) project. We identified 19,166 somatically acquired retrotransposition events, which affected 35% of s les and spanned a range of event types. Long interspersed nuclear element (LINE-1 L1 hereafter) insertions emerged as the first most frequent type of somatic structural variation in esophageal adenocarcinoma, and the second most frequent in head-and-neck and colorectal cancers. Aberrant L1 integrations can delete megabase-scale regions of a chromosome, which sometimes leads to the removal of tumor-suppressor genes, and can induce complex translocations and large-scale duplications. Somatic retrotranspositions can also initiate breakage–fusion–bridge cycles, leading to high-level lification of oncogenes. These observations illuminate a relevant role of 22 L1 retrotransposition in remodeling the cancer genome, with potential implications for the development of human tumors.
Assessment of ecological and human health risks of metals in urban road dust based on geochemical fractionation and potential bioavailability
Publisher: Elsevier BV
Date: 09-2018
DOI: 10.1016/J.SCITOTENV.2018.04.098
Abstract: Metals are one of the primary pollutants in the urban environment that pose adverse ecological and human health impacts. Therefore, the accurate quantification of the risk posed by metals is essential for developing effective risk management strategies to safeguard the urban environment. This study assessed the ecological and human health risks of six metals, commonly present in road dust by improving the original risk indices based on their potential bioavailability characteristics. The bioavailability of metals was determined by considering their distribution between the different geochemical phases of exchangeable, reducible, oxidisable and residual. The results of the modified risk analysis indicated that the road dust poses a low ecological risk in most of the study sites. According to the present situation, the non-cancer risk of in idual metals for both, children and adults followed the decreasing trend of Pb > Cu > Cr > Zn > Ni > Cd. This study also found that depending on the particle size ranges, the potential of multiple metals being able to cause non-cancer health risk was low at most study sites. In terms of cancer health risk, Cr present at most of the study sites was found to be within the cancer threshold limit, even though the Cr content and the bioavailable fractions were relatively low.
Climate change, biodiversity conservation, and the role of protected areas: An australian perspective
Publisher: Informa UK Limited
Date: 11-2008
Whole-genome landscape of pancreatic neuroendocrine tumours
Publisher: Springer Science and Business Media LLC
Date: 15-02-2017
DOI: 10.1038/NATURE21063
Abstract: The diagnosis of pancreatic neuroendocrine tumours (PanNETs) is increasing owing to more sensitive detection methods, and this increase is creating challenges for clinical management. We performed whole-genome sequencing of 102 primary PanNETs and defined the genomic events that characterize their pathogenesis. Here we describe the mutational signatures they harbour, including a deficiency in G:C > T:A base excision repair due to inactivation of MUTYH, which encodes a DNA glycosylase. Clinically sporadic PanNETs contain a larger-than-expected proportion of germline mutations, including previously unreported mutations in the DNA repair genes MUTYH, CHEK2 and BRCA2. Together with mutations in MEN1 and VHL, these mutations occur in 17% of patients. Somatic mutations, including point mutations and gene fusions, were commonly found in genes involved in four main pathways: chromatin remodelling, DNA damage repair, activation of mTOR signalling (including previously undescribed EWSR1 gene fusions), and telomere maintenance. In addition, our gene expression analyses identified a subgroup of tumours associated with hypoxia and HIF signalling.
Author Correction: The evolutionary history of 2,658 cancers
Publisher: Springer Science and Business Media LLC
Date: 25-01-2023
Hydro-conditioning: Advanced approaches for cost-effective water quality management in agricultural watersheds
Publisher: Elsevier BV
Date: 07-2022
DOI: 10.1016/J.WATRES.2022.118647
Abstract: Accurate simulation of landscape hydrological connectivity is pivotal for planning practices required for treating agricultural farm pollution. This study assesses the role of an advanced geospatial approach, namely, 'hydro-conditioning' employed for modifying Digital Elevation Models, termed hDEMs to replicate landscape hydrology by simulating continuous downslope flow through drainage structures such as bridges and culverts. The capabilities of manual and automated hDEMs in delineating optimal locations and water treatment potential of Best Management Practices (BMPs) in a typical agricultural watershed were evaluated. Parallel processing of both hDEMs revealed that 'ground truthing' plays a critical role in the accurate placement of breach lines for allowing water movement through digitally elevated surfaces. Outcomes guide the practitioners in selecting appropriate hDEM (manual or automated) depending on the complexity of modeled hydrological pathways, which is essential for planning BMPs in a cost-effective manner at different spatial scales. Modeling results show that hDEMs greatly influence hydrological connectivity, catchment boundaries, BMP locations, treatment capacities, and related costs. The accuracy of hDEMs was verified using a robust sub-basin scale validation approach. The study recommends a hybrid approach for utilizing the strengths of both, automated and manual hDEMs for efficient agricultural farm pollution in an economical manner.
Pollutant characteristics on roof surfaces for evaluation as a stormwater harvesting catchment
Publisher: Informa UK Limited
Date: 07-2010
Taxonomy of factors which influence heavy metal build-up on urban road surfaces
Publisher: Elsevier BV
Date: 06-2016
DOI: 10.1016/J.JHAZMAT.2016.02.026
Abstract: Heavy metals build-up on urban road surfaces is a complex process and influenced by a erse range of factors. Although numerous research studies have been conducted in the area of heavy metals build-up, limited research has been undertaken to rank these factors in terms of their influence on the build-up process. This results in limitations in the identification of the most critical factor/s for accurately estimating heavy metal loads and for designing effective stormwater treatment measures. The research study undertook an in-depth analysis of the factors which influence heavy metals build-up based on data generated from a number of different geographical locations around the world. Traffic volume was found to be the highest ranked factor in terms of influencing heavy metals build-up while land use was ranked the second. Proximity to arterial roads, antecedent dry days and road surface roughness has a relatively lower ranking. Furthermore, the study outcomes advances the conceptual understanding of heavy metals build-up based on the finding that with increasing traffic volume, total heavy metal build-up load increases while the variability decreases. The outcomes from this research study are expected to contribute to more accurate estimation of heavy metals build-up loads leading to more effective stormwater treatment design.
Author Correction: Disruption of chromatin folding domains by somatic genomic rearrangements in human cancer
Publisher: Springer Science and Business Media LLC
Date: 21-03-2023
Butler enables rapid cloud-based analysis of thousands of human genomes
Publisher: Springer Science and Business Media LLC
Date: 05-02-2020
DOI: 10.1038/S41587-019-0360-3
Abstract: We present Butler, a computational tool that facilitates large-scale genomic analyses on public and academic clouds. Butler includes innovative anomaly detection and self-healing functions that improve the efficiency of data processing and analysis by 43% compared with current approaches. Butler enabled processing of a 725-terabyte cancer genome dataset from the Pan-Cancer Analysis of Whole Genomes (PCAWG) project in a time-efficient and uniform manner.
Conservation: Stop misuse of biodiversity offsets
Publisher: Springer Science and Business Media LLC
Date: 07-2015
DOI: 10.1038/523401A
Catchment based estimation of pollutant event mean concentration (EMC) and implications for first flush assessment
Publisher: Elsevier BV
Date: 02-2021
RAF1 rearrangements are common in pancreatic acinar cell carcinomas.
Publisher: Elsevier BV
Date: 09-2020
Analytical demands to use whole-genome sequencing in precision oncology
Publisher: Elsevier BV
Date: 09-2022
DOI: 10.1016/J.SEMCANCER.2021.06.009
Abstract: Interrogating the tumor genome in its entirety by whole-genome sequencing (WGS) offers an unprecedented insight into the biology and pathogenesis of cancer, with potential impact on diagnostics, prognostication and therapy selection. WGS is able to detect sequence as well as structural variants and thereby combines central domains of cytogenetics and molecular genetics. Given the potential of WGS in directing targeted therapeutics and clinical decision-making, we envision a gradual transition of the method from research to clinical routine. This review is one out of three within this issue aimed at facilitating this effort, by discussing in-depth analytical validation, clinical interpretation and clinical utility of WGS. The review highlights the requirements for implementing, validating and maintaining a clinical WGS pipeline to obtain high-quality patient-specific data in accordance with the local regulatory landscape. Every step of the WGS pipeline, which includes DNA extraction, library preparation, sequencing, bioinformatics analysis, and data storage, is considered with respect to its logistics, necessities, potential pitfalls, and the required quality management. WGS is likely to drive clinical diagnostics and patient care forward, if requirements and challenges of the technique are recognized and met.
Interactions Between Biodiversity Offsets and Protected Area Commitments: Avoiding Perverse Outcomes
Publisher: Wiley
Date: 04-01-2016
DOI: 10.1111/CONL.12222
Analyses of non-coding somatic drivers in 2,658 cancer whole genomes
Publisher: Springer Science and Business Media LLC
Date: 05-02-2020
DOI: 10.1038/S41586-020-1965-X
Abstract: The discovery of drivers of cancer has traditionally focused on protein-coding genes 1–4 . Here we present analyses of driver point mutations and structural variants in non-coding regions across 2,658 genomes from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium 5 of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). For point mutations, we developed a statistically rigorous strategy for combining significance levels from multiple methods of driver discovery that overcomes the limitations of in idual methods. For structural variants, we present two methods of driver discovery, and identify regions that are significantly affected by recurrent breakpoints and recurrent somatic juxtapositions. Our analyses confirm previously reported drivers 6,7 , raise doubts about others and identify novel candidates, including point mutations in the 5′ region of TP53 , in the 3′ untranslated regions of NFKBIZ and TOB1 , focal deletions in BRD4 and rearrangements in the loci of AKR1C genes. We show that although point mutations and structural variants that drive cancer are less frequent in non-coding genes and regulatory sequences than in protein-coding genes, additional ex les of these drivers will be found as more cancer genomes become available.
Role of traffic in atmospheric accumulation of heavy metals and polycyclic aromatic hydrocarbons
Publisher: Elsevier BV
Date: 07-2012
Development of a hybrid pollution index for heavy metals in marine and estuarine sediments
Publisher: Springer Science and Business Media LLC
Date: 30-04-2015
DOI: 10.1007/S10661-015-4563-X
Abstract: Heavy metal pollution of sediments is a growing concern in most parts of the world, and numerous studies focussed on identifying contaminated sediments by using a range of digestion methods and pollution indices to estimate sediment contamination have been described in the literature. The current work provides a critical review of the more commonly used sediment digestion methods and identifies that weak acid digestion is more likely to provide guidance on elements that are likely to be bioavailable than other traditional methods of digestion. This work also reviews common pollution indices and identifies the Nemerow Pollution Index as the most appropriate method for establishing overall sediment quality. Consequently, a modified Pollution Index that can lead to a more reliable understanding of whole sediment quality is proposed. This modified pollution index is then tested against a number of existing studies and demonstrated to give a reliable and rapid estimate of sediment contamination and quality.
Recurrent loss of heterozygosity correlates with clinical outcome in pancreatic neuroendocrine cancer
Publisher: Springer Science and Business Media LLC
Date: 20-07-2018
DOI: 10.1038/S41525-018-0058-3
Abstract: Pancreatic neuroendocrine tumors (pNETs) are uncommon cancers arising from pancreatic islet cells. Here we report the analysis of gene mutation, copy number, and RNA expression of 57 sporadic well-differentiated pNETs. pNET genomes are dominated by aneuploidy, leading to concordant changes in RNA expression at the level of whole chromosomes and chromosome segments. We observed two distinct patterns of somatic pNET aneuploidy that are associated with tumor pathology and patient prognosis. Approximately 26% of the patients in this series had pNETs with genomes characterized by recurrent loss of heterozygosity (LoH) of 10 specific chromosomes, accompanied by bi-allelic MEN1 inactivation and generally poor clinical outcome. Another ~40% of patients had pNETs that lacked this recurrent LoH pattern but had chromosome 11 LoH, bi-allelic MEN1 inactivation, and universally good clinical outcome. The somatic aneuploidy allowed pathogenic germline variants (e.g., ATM ) to be expressed unopposed, with RNA expression patterns showing inactivation of downstream tumor suppressor pathways. No prognostic associations were found with tumor morphology, single gene mutation, or expression of RNAs reflecting the activity of immune, differentiation, proliferative or tumor suppressor pathways. In pNETs, single gene mutations appear to be less important than aneuploidy, with MEN1 the only statistically significant recurrently mutated driver gene. In addition, only one pNET in the series had clearly actionable single nucleotide variants (SNVs) (in PTEN and FLCN ) confirmed by corroborating RNA expression changes. The two clinically relevant patterns of LoH described here define a novel oncogenic mechanism and a plausible route to genomic precision oncology for this tumor type.
Intrinsic and extrinsic factors which influence metal adsorption to road dust
Publisher: Elsevier BV
Date: 03-2018
DOI: 10.1016/J.SCITOTENV.2017.11.047
Abstract: The adsorption behaviour of metals deposited on road surfaces is a complex process and influenced by a range of factors common to the urban environment. However, all factors do not have the same level of importance. It is therefore important to identify the most crucial factors for accurate stormwater quality predictions and to implement effective stormwater pollution mitigation measures. Accordingly, this study investigated the extrinsic and intrinsic factors in terms of their degree of influence on the adsorption of in idual metal cations to particulates. The variability associated with the adsorption of Zn, Cu, Pb, Cd, Cr and Ni to road dust was found to be influenced by changes to the antecedent dry days and land use characteristics. The initial dry days after a storm event exerts a significant influence on adsorption compared to the later dry days in all land uses. In terms of the intrinsic physico-chemical properties of road dust, the parameters that influence the adsorption process differ in terms of the type of metal cation and particle size fractions of solids. Based on the influential parameters identified, the bioavailability characteristics of Zn, Cd, Pb and Ni in <150μm size fraction of road dust and potential stormwater quality impacts can be highlighted.
Understanding nutrient build-up on urban road surfaces
Publisher: Elsevier BV
Date: 06-2010
DOI: 10.1016/S1001-0742(09)60181-9
Abstract: This article discusses the outcomes of a research project on nutrients build-up on urban road surfaces. Nutrient build-up was investigated on road sites belonging to residential, industrial and commercial land use. Collected build-up s les were separated into five particle size ranges and were tested for total nitrogen (TN), total phosphorus (TP) and sub species of nutrients, namely, NO2-, NO3-, TKN and PO4(3-). Multivariate analytical techniques were used to analyse the data and to develop detailed understanding on buildup. Data analysis revealed that the solids loads on urban road surfaces are highly influenced by factors such as land use, antecedent dry period and traffic volume. However, the nutrient build-up process was found to be independent of the type of land use. It was solely dependent on the particle size of solids build-up. Most of the nutrients were associated with the particle size range < 150 microm. Therefore, the removal of particles below 150 microm from road surfaces is of importance for the removal of nitrogen and phosphorus from road surface solids build-up. It is also important to consider the difference in the composition of nitrogen and phosphorus build-up in the context of designing effective stormwater quality mitigation strategies.
Nutrients and metals interactions between water and sediment phases: An urban river case study
Publisher: Elsevier BV
Date: 08-2019
DOI: 10.1016/J.ENVPOL.2019.05.018
Abstract: The provision of water to meet the needs of an ever increasing urban population is a significant challenge. This is because urban receiving waters are constantly at risk from pollutant inputs via stormwater runoff and wastewater discharge. This research study employed multiple approaches including principal component analysis, Bayesian Networks (BNs) modelling and geospatial analysis to identify patterns in the distributions of nutrients and metals in water and sediments in an urban river and the interactions between the two phases. In both, water and sediments, nutrient concentrations/loads varied in the order of total carbon (TC) > total nitrogen (TN) > total phosphorus (TP). The river sediments were found to contain the highest crustal metal loads, while in water, the marine-related metals had the highest concentrations. The BNs modelling of pollutant interactions between water and sediment phases indicated that nitrogen is more likely to be transferred from water to sediment than the opposite, while anthropogenic metals are more likely to be transferred from sediments to water. Further, geospatial analysis showed that TN, crustal metals and anthropogenic metal loads in sediments increased from upstream to downstream, while having a decreasing pattern in water. However, marine-related metals in both, water and sediments had increasing concentrations/loads from upstream to downstream. These spatial patterns are attributed to the interactions between water and sediment phases, sediment transport along the river and seawater intrusion in the estuarine area. The study outcomes are expected to contribute to enhancing the knowledge required for developing mitigation strategies to improve urban receiving water quality.
Stormwater quality, pollutant sources, processes, and treatment options
Publisher: Elsevier
Date: 2018
Gamifying Community Education for Enhanced Disaster Resilience: An Effectiveness Testing Study from Australia
Publisher: MDPI AG
Date: 09-06-2022
DOI: 10.3390/FI14060179
Abstract: Providing convenient and effective online education is important for the public to be better prepared for disaster events. Nonetheless, the effectiveness of such education is questionable due to the limited use of online tools and platforms, which also results in narrow community outreach. Correspondingly, understanding public perceptions of disaster education methods and experiences for the adoption of novel methods is critical, but this is an understudied area of research. The aim of this study is to understand public perceptions towards online disaster education practices for disaster preparedness and evaluate the effectiveness of the gamification method in increasing public awareness. This study utilizes social media analytics and conducts a gamification exercise. The analysis involved Twitter posts (n = 13,683) related to the 2019–2020 Australian bushfires, and surveyed participants (n = 52) before and after experiencing a gamified application—i.e., STOP Disasters! The results revealed that: (a) The public satisfaction level is relatively low for traditional bushfire disaster education methods (b) The study participants’ satisfaction level is relatively high for an online gamified application used for disaster education and (c) The use of virtual and augmented reality was found to be promising for increasing the appeal of gamified applications, along with using a blended traditional and gamified approach.
Pollutant characteristics on roof surfaces for evaluation as a stormwater harvesting catchment
Publisher: Informa UK Limited
Date: 07-2010
EIF1AX and NRAS Mutations Co-occur and Cooperate in Low-Grade Serous Ovarian Carcinomas
Publisher: American Association for Cancer Research (AACR)
Date: 14-08-2017
DOI: 10.1158/0008-5472.CAN-16-2224
Abstract: Low-grade serous ovarian carcinomas (LGSC) are associated with a poor response to chemotherapy and are molecularly characterized by RAS pathway activation. Using exome and whole genome sequencing, we identified recurrent mutations in the protein translational regulator EIF1AX and in NF1, USP9X, KRAS, BRAF, and NRAS. RAS pathway mutations were mutually exclusive however, we found significant co-occurrence of mutations in NRAS and EIF1AX. Missense EIF1AX mutations were clustered at the N-terminus of the protein in a region associated with its role in ensuring translational initiation fidelity. Coexpression of mutant NRAS and EIF1AX proteins promoted proliferation and clonogenic survival in LGSC cells, providing the first ex le of co-occurring, growth-promoting mutational events in ovarian cancer. Cancer Res 77(16) 4268–78. ©2017 AACR.
Water-sediment interactions and mobility of heavy metals in aquatic environments
Publisher: Elsevier BV
Date: 09-2021
Genomic footprints of activated telomere maintenance mechanisms in cancer
Publisher: Springer Science and Business Media LLC
Date: 05-02-2020
DOI: 10.1038/S41467-019-13824-9
Abstract: Cancers require telomere maintenance mechanisms for unlimited replicative potential. They achieve this through TERT activation or alternative telomere lengthening associated with ATRX or DAXX loss. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium , we dissect whole-genome sequencing data of over 2500 matched tumor-control s les from 36 different tumor types aggregated within the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium to characterize the genomic footprints of these mechanisms. While the telomere content of tumors with ATRX or DAXX mutations (ATRX/DAXX trunc ) is increased, tumors with TERT modifications show a moderate decrease of telomere content. One quarter of all tumor s les contain somatic integrations of telomeric sequences into non-telomeric DNA. This fraction is increased to 80% prevalence in ATRX/DAXX trunc tumors, which carry an aberrant telomere variant repeat (TVR) distribution as another genomic marker. The latter feature includes enrichment or depletion of the previously undescribed singleton TVRs TTCGGG and TTTGGG, respectively. Our systematic analysis provides new insight into the recurrent genomic alterations associated with telomere maintenance mechanisms in cancer.
Mathematical modelling of the influence of physico-chemical properties on heavy metal adsorption by biosorbents
Publisher: Elsevier BV
Date: 09-2020
Prediction of the wash-off of traffic related semi- and non-volatile organic compounds from urban roads under climate change influenced rainfall characteristics
Publisher: Elsevier BV
Date: 04-2012
DOI: 10.1016/J.JHAZMAT.2012.01.062
Abstract: Traffic generated semi- and non-volatile organic compounds (SVOCs and NVOCs) pose a serious threat to human and ecosystem health when washed off into receiving water bodies by stormwater. Climate change influenced rainfall characteristics makes the estimation of these pollutants in stormwater quite complex. The research study discussed in the paper developed a prediction framework for such pollutants under the dynamic influence of climate change on rainfall characteristics. It was established through principal component analysis (PCA) that the intensity and durations of low to moderate rain events induced by climate change mainly affect the wash-off of SVOCs and NVOCs from urban roads. The study outcomes were able to overcome the limitations of stringent laboratory preparation of calibration matrices by extracting uncorrelated underlying factors in the data matrices through systematic application of PCA and factor analysis (FA). Based on the initial findings from PCA and FA, the framework incorporated orthogonal rotatable central composite experimental design to set up calibration matrices and partial least square regression to identify significant variables in predicting the target SVOCs and NVOCs in four particulate fractions ranging from >300 to 1 μm and one dissolved fraction of 300-1 μm range, similar distributions of predicted and observed concentrations of the target compounds from minimum to 75th percentile were achieved. The inter-event coefficient of variations for particulate fractions of >300-1 μm was 5-25%. The limited solubility of the target compounds in stormwater restricted the predictive capacity of the proposed method for the dissolved fraction of <1 μm.
Using undisturbed columns to predict long term behaviour of effluent irrigated soils under field conditions
Publisher: CSIRO Publishing
Date: 2006
DOI: 10.1071/SR06030
Abstract: Soils have only a finite capacity for the removal of wastewater pollutants, and with time this capacity could decline. Not all soil types have the capacity to provide adequate treatment and dispersal of sewage effluent. For continued long-term application to be successful, it is essential that infiltration and drainage characteristics of soils do not decline. Also critical is how long-term application of nutrients and cations affects the soils and whether any leaching occurs. The research project described compares the outcomes of detailed field studies with results from an undisturbed soil column study where typical soils in the south-east region of Queensland, Australia, have been subjected to sewage effluent application over a period of 12 months. Multivariate analysis helped to classify the influential soil characteristics and to identify relative changes in each soil after the application of effluent. Identification and correlation of influential soil characteristics in field and accelerated column studies confirmed that undisturbed soil column studies can be useful in predicting long-term behaviour of effluent-irrigated soils.
USE OF UNDISTURBED SOIL COLUMNS TO EVALUATE SOIL CAPABILITY TO RENOVATE ON-SITE SEWAGE TREATMENT SYSTEM EFFLUENT
Publisher: American Society of Agricultural and Biological Engineers
DOI: 10.13031/2013.15777
Characterisation of atmospheric deposited particles during a dust storm in urban areas of Eastern Australia
Publisher: Elsevier BV
Date: 09-2013
DOI: 10.1016/J.SCITOTENV.2013.04.080
Abstract: The characteristics of dust particles deposited during the 2009 dust storm in the Gold Coast and Brisbane regions of Australia are discussed in this paper. The study outcomes provide important knowledge in relation to the potential impacts of dust storm related pollution on ecosystem health in the context that the frequency of dust storms is predicted to increase due to anthropogenic desert surface modifications and climate change impacts. The investigated dust storm contributed a large fraction of fine particles to the environment with an increased amount of total suspended solids, compared to dry deposition under ambient conditions. Although the dust storm passed over forested areas, the organic carbon content in the dust was relatively low. The primary metals present in the dust storm deposition were aluminium, iron and manganese, which are common soil minerals in Australia. The dust storm deposition did not contain significant loads of nickel, cadmium, copper and lead, which are commonly present in the urban environment. Furthermore, the comparison between the ambient and dust storm chromium and zinc loads suggested that these metals were contributed to the dust storm by local anthropogenic sources. The potential ecosystem health impacts of the 2009 dust storm include, increased fine solids deposition on ground surfaces resulting in an enhanced capacity to adsorb toxic pollutants as well as increased aluminium, iron and manganese loads. In contrast, the ecosystem health impacts related to organic carbon and other metals from dust storm atmospheric deposition are not considered to be significant.
The synergistic effect of ultrasound power and magnetite incorporation on the sorption/desorption behavior of Cr(VI) and As(V) oxoanions in an aqueous system
Publisher: Elsevier BV
Date: 06-2020
Role of particle size and composition in metal adsorption by solids deposited on urban road surfaces
Publisher: Elsevier BV
Date: 2014
DOI: 10.1016/J.ENVPOL.2013.08.010
Abstract: Despite common knowledge that the metal content adsorbed by fine particles is relatively higher compared to coarser particles, the reasons for this phenomenon have gained little research attention. The research study discussed in the paper investigated the variations in metal content for different particle sizes of solids associated with pollutant build-up on urban road surfaces. Data analysis confirmed that parameters favourable for metal adsorption to solids such as specific surface area, organic carbon content, effective cation exchange capacity and clay forming minerals content decrease with the increase in particle size. Furthermore, the mineralogical composition of solids was found to be the governing factor influencing the specific surface area and effective cation exchange capacity. There is high quartz content in particles >150 μm compared to particles <150 μm. As particle size reduces below 150 μm, the clay forming minerals content increases, providing favourable physical and chemical properties that influence adsorption.
Sources of hydrocarbons in urban road dust: Identification, quantification and prediction
Publisher: Elsevier BV
Date: 09-2016
DOI: 10.1016/J.ENVPOL.2016.05.042
Abstract: Among urban stormwater pollutants, hydrocarbons are a significant environmental concern due to their toxicity and relatively stable chemical structure. This study focused on the identification of hydrocarbon contributing sources to urban road dust and approaches for the quantification of pollutant loads to enhance the design of source control measures. The study confirmed the validity of the use of mathematical techniques of principal component analysis (PCA) and hierarchical cluster analysis (HCA) for source identification and principal component analysis/absolute principal component scores (PCA/APCS) receptor model for pollutant load quantification. Study outcomes identified non-combusted lubrication oils, non-combusted diesel fuels and tyre and asphalt wear as the three most critical urban hydrocarbon sources. The site specific variabilities of contributions from sources were replicated using three mathematical models. The models employed predictor variables of daily traffic volume (DTV), road surface texture depth (TD), slope of the road section (SLP), effective population (EPOP) and effective impervious fraction (EIF), which can be considered as the five governing parameters of pollutant generation, deposition and redistribution. Models were developed such that they can be applicable in determining hydrocarbon contributions from urban sites enabling effective design of source control measures.
Assessing uncertainty in stormwater quality modelling
Publisher: Elsevier BV
Date: 04-0001
DOI: 10.1016/J.WATRES.2016.07.011
Abstract: Designing effective stormwater pollution mitigation strategies is a challenge in urban stormwater management. This is primarily due to the limited reliability of catchment scale stormwater quality modelling tools. As such, assessing the uncertainty associated with the information generated by stormwater quality models is important for informed decision making. Quantitative assessment of build-up and wash-off process uncertainty, which arises from the variability associated with these processes, is a major concern as typical uncertainty assessment approaches do not adequately account for process uncertainty. The research study undertaken found that the variability of build-up and wash-off processes for different particle size ranges leads to processes uncertainty. After variability and resulting process uncertainties are accurately characterised, they can be incorporated into catchment stormwater quality predictions. Accounting of process uncertainty influences the uncertainty limits associated with predicted stormwater quality. The impact of build-up process uncertainty on stormwater quality predictions is greater than that of wash-off process uncertainty. Accordingly, decision making should facilitate the designing of mitigation strategies which specifically addresses variations in load and composition of pollutants accumulated during dry weather periods. Moreover, the study outcomes found that the influence of process uncertainty is different for stormwater quality predictions corresponding to storm events with different intensity, duration and runoff volume generated. These storm events were also found to be significantly different in terms of the Runoff-Catchment Area ratio. As such, the selection of storm events in the context of designing stormwater pollution mitigation strategies needs to take into consideration not only the storm event characteristics, but also the influence of process uncertainty on stormwater quality predictions.
Assessment of Risk to Human Health from Urban Stormwater Pollution due to Heavy Metals and Polycyclic Aromatic Hydrocarbons
Publisher: Global Science & technology Forum ( GSTF )
Date: 22-02-2016
Compounding effects of urbanization, climate change and sea-level rise on monetary projections of flood damage
Publisher: Elsevier BV
Date: 05-2023
Use of chemometrics methods and multicriteria decision-making for site selection for sustainable on-site sewage effluent disposal
Publisher: Elsevier BV
Date: 03-2004
The landscape of viral associations in human cancers
Publisher: Springer Science and Business Media LLC
Date: 05-02-2020
DOI: 10.1038/S41588-019-0558-9
Abstract: Here, as part of the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, for which whole-genome and—for a subset—whole-transcriptome sequencing data from 2,658 cancers across 38 tumor types was aggregated, we systematically investigated potential viral pathogens using a consensus approach that integrated three independent pipelines. Viruses were detected in 382 genome and 68 transcriptome datasets. We found a high prevalence of known tumor-associated viruses such as Epstein–Barr virus (EBV), hepatitis B virus (HBV) and human papilloma virus (HPV for ex le, HPV16 or HPV18). The study revealed significant exclusivity of HPV and driver mutations in head-and-neck cancer and the association of HPV with APOBEC mutational signatures, which suggests that impaired antiviral defense is a driving force in cervical, bladder and head-and-neck carcinoma. For HBV, HPV16, HPV18 and adeno-associated virus-2 (AAV2), viral integration was associated with local variations in genomic copy numbers. Integrations at the TERT promoter were associated with high telomerase expression evidently activating this tumor-driving process. High levels of endogenous retrovirus (ERV1) expression were linked to a worse survival outcome in patients with kidney cancer.
Impacts of feral horses in the Australian Alps and evidence-based solutions
Publisher: Wiley
Date: 2019
DOI: 10.1111/EMR.12357
High-coverage whole-genome analysis of 1220 cancers reveals hundreds of genes deregulated by rearrangement-mediated cis-regulatory alterations
Publisher: Springer Science and Business Media LLC
Date: 05-02-2020
DOI: 10.1038/S41467-019-13885-W
Abstract: The impact of somatic structural variants (SVs) on gene expression in cancer is largely unknown. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole-genome sequencing data and RNA sequencing from a common set of 1220 cancer cases, we report hundreds of genes for which the presence within 100 kb of an SV breakpoint associates with altered expression. For the majority of these genes, expression increases rather than decreases with corresponding breakpoint events. Up-regulated cancer-associated genes impacted by this phenomenon include TERT , MDM2 , CDK4 , ERBB2 , CD274 , PDCD1LG2 , and IGF2 . TERT -associated breakpoints involve ~3% of cases, most frequently in liver biliary, melanoma, sarcoma, stomach, and kidney cancers. SVs associated with up-regulation of PD1 and PDL1 genes involve ~1% of non- lified cases. For many genes, SVs are significantly associated with increased numbers or greater proximity of enhancer regulatory elements near the gene. DNA methylation near the promoter is often increased with nearby SV breakpoint, which may involve inactivation of repressor elements.
Effect of traffic congestion and vegetation on airborne bacteria in a city of a developing country
Publisher: Springer Science and Business Media LLC
Date: 07-04-2021
Reconstructing evolutionary trajectories of mutation signature activities in cancer using TrackSig
Publisher: Springer Science and Business Media LLC
Date: 05-02-2020
DOI: 10.1038/S41467-020-14352-7
Abstract: The type and genomic context of cancer mutations depend on their causes. These causes have been characterized using signatures that represent mutation types that co-occur in the same tumours. However, it remains unclear how mutation processes change during cancer evolution due to the lack of reliable methods to reconstruct evolutionary trajectories of mutational signature activity. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole-genome sequencing data from 2658 cancers across 38 tumour types, we present TrackSig, a new method that reconstructs these trajectories using optimal, joint segmentation and deconvolution of mutation type and allele frequencies from a single tumour s le. In simulations, we find TrackSig has a 3–5% activity reconstruction error, and 12% false detection rate. It outperforms an aggressive baseline in situations with branching evolution, CNA gain, and neutral mutations. Applied to data from 2658 tumours and 38 cancer types, TrackSig permits pan-cancer insight into evolutionary changes in mutational processes.
Glioma through the looking GLASS: molecular evolution of diffuse gliomas and the Glioma Longitudinal Analysis Consortium
Publisher: Oxford University Press (OUP)
Date: 08-02-2018
Rethinking hydrocarbons build-up on urban roads: A perspective on volatilisation under global warming scenarios
Publisher: Elsevier BV
Date: 09-2019
DOI: 10.1016/J.ENVPOL.2019.06.044
Abstract: Stormwater is viewed as an alternative resource to mitigate water shortages. However, stormwater reuse is constrained due to the presence of many toxic pollutants such as hydrocarbons. Effective mitigation requires robust mathematical models for stormwater quality prediction based on an understanding of pollutant processes. However, the rise in global temperatures will impose changes to pollutant processes. This study has proposed a new perspective on modelling the build-up process of hydrocarbons, with a focus on volatile organic compounds (VOCs). Among organic compounds, VOCs are the most susceptible to changes as a result of global warming due to their volatility. Seven VOCs, namely, benzene, toluene, ethylbenzene, para-xylene, meta-xylene, ortho-xylene and styrene in road dust were investigated. The outcomes are expected to lay the foundation to overcoming the limitations in current modelling approaches such as not considering the influence of temperature and volatility, on the build-up process. A new conceptualisation is proposed for the classical build-up model by mathematically defining the volatility of VOCs in terms of temperature. Uncertainty in the re-conceptualised build-up model was quantified and was used to understand the build-up patterns in the future scenarios of global warming. Results indicated that for the likely scenarios, the variability in VOCs build-up gradually increases at the beginning of the dry period and then rapidly increases after around seven days, while the build-up reaches a near-constant value in a shorter dry period, limiting the variability. These initial research outcomes need to be further investigated given the expected impacts of global warming into the future.
Cancer LncRNA Census reveals evidence for deep functional conservation of long noncoding RNAs in tumorigenesis
Publisher: Springer Science and Business Media LLC
Date: 05-02-2020
DOI: 10.1038/S42003-019-0741-7
Abstract: Long non-coding RNAs (lncRNAs) are a growing focus of cancer genomics studies, creating the need for a resource of lncRNAs with validated cancer roles. Furthermore, it remains debated whether mutated lncRNAs can drive tumorigenesis, and whether such functions could be conserved during evolution. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, we introduce the Cancer LncRNA Census (CLC), a compilation of 122 GENCODE lncRNAs with causal roles in cancer phenotypes. In contrast to existing databases, CLC requires strong functional or genetic evidence. CLC genes are enriched amongst driver genes predicted from somatic mutations, and display characteristic genomic features. Strikingly, CLC genes are enriched for driver mutations from unbiased, genome-wide transposon-mutagenesis screens in mice. We identified 10 tumour-causing mutations in orthologues of 8 lncRNAs, including LINC-PINT and NEAT1 , but not MALAT1 . Thus CLC represents a dataset of high-confidence cancer lncRNAs. Mutagenesis maps are a novel means for identifying deeply-conserved roles of lncRNAs in tumorigenesis.
Prevalence and occurrence of zoonotic bacterial pathogens in surface waters determined by quantitative PCR
Publisher: Elsevier BV
Date: 11-2009
DOI: 10.1016/J.WATRES.2009.03.041
Abstract: The prevalence and concentrations of C ylobacter jejuni, Salmonella spp. and enterohaemorrhagic Escherichia coli (EHEC) were investigated in surface waters in Brisbane, Australia using quantitative PCR (qPCR) based methodologies. Water s les were collected from Brisbane City Botanic Gardens (CBG) Pond, and two urban tidal creeks (i.e., Oxley Creek and Blunder Creek). Of the 32 water s les collected, 8 (25%), 1 (3%), 9 (28%), 14 (44%), and 15 (47%) were positive for C. jejuni mapA, Salmonella invA, EHEC O157 LPS, EHEC VT1, and EHEC VT2 genes, respectively. The presence/absence of the potential pathogens did not correlate with either E. coli or enterococci concentrations as determined by binary logistic regression. In conclusion, the high prevalence, and concentrations of potential zoonotic pathogens along with the concentrations of one or more fecal indicators in surface water s les indicate a poor level of microbial quality of surface water, and could represent a significant health risk to users. The results from the current study would provide valuable information to the water quality managers in terms of minimizing the risk from pathogens in surface waters.
A first-in-class pan-lysyl oxidase inhibitor impairs stromal remodeling and enhances gemcitabine response and survival in pancreatic cancer
Publisher: Springer Science and Business Media LLC
Date: 28-08-2023
DOI: 10.1038/S43018-023-00614-Y
Abstract: The lysyl oxidase family represents a promising target in stromal targeting of solid tumors due to the importance of this family in crosslinking and stabilizing fibrillar collagens and its known role in tumor desmoplasia. Using small-molecule drug-design approaches, we generated and validated PXS-5505, a first-in-class highly selective and potent pan-lysyl oxidase inhibitor. We demonstrate in vitro and in vivo that pan-lysyl oxidase inhibition decreases chemotherapy-induced pancreatic tumor desmoplasia and stiffness, reduces cancer cell invasion and metastasis, improves tumor perfusion and enhances the efficacy of chemotherapy in the autochthonous genetically engineered KPC model, while also demonstrating antifibrotic effects in human patient-derived xenograft models of pancreatic cancer. PXS-5505 is orally bioavailable, safe and effective at inhibiting lysyl oxidase activity in tissues. Our findings present the rationale for progression of a pan-lysyl oxidase inhibitor aimed at eliciting a reduction in stromal matrix to potentiate chemotherapy in pancreatic ductal adenocarcinoma.
Author Correction: The repertoire of mutational signatures in human cancer
Publisher: Springer Science and Business Media LLC
Date: 25-01-2023
The role of connectivity in Australian conservation
Publisher: CSIRO Publishing
Date: 2004
DOI: 10.1071/PC040266
Abstract: The existing system of nature reserves in Australia is inadequate for the long-term conservation and restoration of native biological ersity because it fails to accommodate, among other elements, large scale and long-term ecological processes and change, including physical and biotic transport in the landscape. This paper is an overview of the connectivity elements that inform a scientific framework for significantly improving the prospects for the long-term conservation of Australia's bio ersity. The framework forms the basis for the WildCountry programme. This programme has identified connectivity at landscape, regional and continental scales as a critical component of an effective conservation system. Seven categories of ecological phenomena are reviewed that require landscape permeability and that must be considered when planning for the maintenance of biological ersity and ecological resilience in Australia: (1) trophic relations at regional scales (2) animal migration, dispersal, and other large scale movements of in iduals and propagules (3) fire and other forms of disturbance at regional scales (4) climate variability in space and time and human forced rapid climate change (5) hydroecological relations and flows at all scales (6) coastal zone fluxes of organisms, matter, and energy and, (7) spatially-dependent evolutionary processes at all scales. Finally, we mention eight cross-cutting themes that further illuminate the interactions and implications of the seven connectivity-related phenomena for conservation assessment, planning, research, and management, and we suggest how the results might be applied by analysts, planners, scientists, and community conservationists.
Characterizing molecular transformation of dissolved organic matter during high-solid anaerobic digestion of dewatered sludge using ESI FT-ICR MS
Publisher: Elsevier BV
Date: 04-2023
Characterising nutrients wash-off for effective urban stormwater treatment design
Publisher: Elsevier BV
Date: 05-2013
DOI: 10.1016/J.JENVMAN.2013.02.027
Abstract: This paper characterises nitrogen and phosphorus wash-off processes on urban road surfaces to create fundamental knowledge to strengthen stormwater treatment design. The study outcomes confirmed that the composition of initially available nutrients in terms of their physical association with solids and chemical speciation determines the wash-off characteristics. Nitrogen and phosphorus wash-off processes are independent of land use, but there are notable differences. Nitrogen wash-off is a "source limiting" process while phosphorus wash-off is "transport limiting". Additionally, a clear separation between nitrogen and phosphorus wash-off processes based on dissolved and particulate forms confirmed that the common approach of replicating nutrients wash-off based on solids wash-off could lead to misleading outcomes particularly in the case of nitrogen. Nitrogen is present primarily in dissolved and organic form and readily removed even by low intensity rainfall events, which is an important consideration for nitrogen removal targeted treatment design. In the case of phosphorus, phosphate constitutes the primary species in wash-off for the particle size fraction 75 μm. This means that phosphorus removal targeted treatment design should consider both phosphorus speciation as well as particle size.
Yield performance and adaptation of some Australian-grown rice varieties through multivariate analysis
Publisher: CSIRO Publishing
Date: 2007
DOI: 10.1071/AR06357
Abstract: Rice breeders are involved in developing new varieties for a erse range of production environments to increase average yields. Interpretation of performance of several varieties evaluated in a broad range of environments is usually affected by variety × environment interactions. Application of multivariate analyses, especially multi-criteria decision making (MCDM) methods in variety × environment interaction studies can benefit interpretation of yield performance and adaptation of varieties in response to different environments. The case study discussed in this paper highlights the significant advantages of using MCDM methods to overcome constraints imposed by having to investigate a large number of variables inherent in such analysis. The grain yield of 13 rice varieties with varying characteristics, grown in 4 different regions in southern New South Wales (NSW), Australia, during the 2000–06 growing seasons was analysed using classification techniques and preference ranking organization method for enrichment evaluation (PROMETHEE) analysis. Significant variety × environment interaction was found to influence the yield performance of in idual varieties across a range of environmental conditions. Classification of environments and geometrical analysis for interactive aid (GAIA) plot of PROMETHEE analysis identified the Murrumbidgee Irrigation Area (MIA) and Coleambally Irrigation Area (CIA) as higher yielding regions compared with the Eastern Murray Valley (EMV) and Western Murray Valley (WMV). Turbid water and cold weather conditions are suggested to explain the lower yield obtained in the WMV environment. In terms of varieties, Amaroo and Opus were identified as widely adaptable to most of the environments, while Jarrah was the least adaptable. Illabong can be considered as best adapted to the EMV or WMV regions, while Paragon and Reiziq can be regarded as best adapted to the MIA and CIA regions. Partial and complete ranking showed the interrelationships between the varieties for their yield performance and adaptation across all environments. Amaroo, Illabong, and Opus were ranked as the most preferred varieties, while Koshihikari, Kyeema, and Jarrah were ranked as the least preferred ones. Partial pre-order with 13 classes from PROMETHEE I analysis identified varieties with similar characteristics and aided the selection of suitable alternative varieties. The outcomes from the analyses reported here allow rice varieties or genotypes to be rated for yield stability for a specific or a range of different environments.
Dispersal and transport of microplastics in river sediments
Publisher: Elsevier BV
Date: 06-2021
Significance of QSAR in cancer risk assessment of polycyclic aromatic compounds (PACs)
Publisher: Elsevier
Date: 2023
Connectivity Conservation Management
Publisher: Routledge
Date: 09-02-2010
Assessing social resilience in disaster management
Publisher: Elsevier BV
Date: 2021
Sourcing faecal pollution from onsite wastewater treatment systems in surface waters using antibiotic resistance analysis*
Publisher: Oxford University Press (OUP)
Date: 09-2005
DOI: 10.1111/J.1365-2672.2005.02644.X
Abstract: To identify the sources of faecal contamination in investigated surface waters and to determine the significance of onsite wastewater treatment systems (OWTS) as a major contributor to faecal contamination. Antibiotic resistance patterns (ARP) were established for a library of 717 known Escherichia coli source isolates obtained from human, domesticated animals, livestock and wild sources. Eight commonly used antibiotics, including amoxicillin, cephalothin, erythromycin, gentamicin, ofloxacin, chlortetracycline, tetracycline and moxalactam, at four different concentrations were used to obtain ARPs for E. coli isolates. Discriminant analysis (DA) was used to differentiate between the ARP of sources isolates. The developed ARP library was found to be adequate for discriminating human from nonhuman isolates, and was used to classify 256 enumerated E. coli isolates collected from monitored surface water locations. The resulting ARP DA indicated that a majority of the faecal contamination in more rural areas was nonhuman however, the percentage of human isolates increased significantly in urbanized areas using OWTS for wastewater treatment. This study signifies the feasibility of using ARP for source tracking faecal contamination in surface waters, and linking faecal contamination to OWTS. The information will enable regulatory authorities to implement appropriate management practices to reduce the contamination of water resources caused by high densities and failing OWTS.
Comprehensive genomic and tumour immune profiling reveals potential therapeutic targets in malignant pleural mesothelioma
Publisher: Springer Science and Business Media LLC
Date: 30-05-2022
DOI: 10.1186/S13073-022-01060-8
Abstract: Malignant pleural mesothelioma (MPM) has a poor overall survival with few treatment options. Whole genome sequencing (WGS) combined with the immune features of MPM offers the prospect of identifying changes that could inform future clinical trials. We analysed somatic mutations from 229 MPM s les, including previously published data and 58 s les that had undergone WGS within this study. This was combined with RNA-seq analysis to characterize the tumour immune environment. The comprehensive genome analysis identified 12 driver genes, including new candidate genes. Whole genome doubling was a frequent event that correlated with shorter survival. Mutational signature analysis revealed SBS5/40 were dominant in 93% of s les, and defects in homologous recombination repair were infrequent in our cohort. The tumour immune environment contained high M2 macrophage infiltrate linked with MMP2 , MMP14 , TGFB1 and CCL2 expression, representing an immune suppressive environment. The expression of TGFB1 was associated with overall survival. A small subset of s les (less than 10%) had a higher proportion of CD8 T cells and a high cytolytic score, suggesting a ‘hot’ immune environment independent of the somatic mutations. We propose accounting for genomic and immune microenvironment status may influence therapeutic planning in the future.
A novel approach for delineation of homogeneous rainfall regions for water sensitive urban design - A case study in southeast Queensland
Publisher: MDPI AG
Date: 19-03-2019
DOI: 10.3390/W11030570
Abstract: The delineation of homogeneous regions is primarily based on long-term overall rainfall characteristics and therefore does not necessarily consider the homogeneity of event-based rainfall characteristics. However, event-based rainfall characteristics including antecedent dry days, rainfall intensity, total rainfall and total duration of rainfall events are critical for Water Sensitive Urban Design (WSUD). Accordingly, this study presents a novel approach to objectively identify homogeneous rainfall regions based on event-based rainfall characteristics. This approach uses cluster analysis and Hosking–Wallis heterogeneous tests collectively to test the homogeneity of event-based rainfall characteristics. A case study conducted for southeast Queensland (SEQ), Australia is also presented in this article. This study compares the results of the novel modified approach against results of the conventional approach for the delineation of homogeneous regions. It was evident from the results that the entire SEQ could be treated as a homogeneous rainfall region based on the conventional approach. In contrast, based on the modified approach, the coast and the inland of SEQ were identified as separate homogeneous regions. Further, antecedent dry days and rainfall intensity were recognized as the deciding rainfall characteristics in the delineation of homogeneous rainfall regions.
Influence of urbanisation characteristics on the variability of particle-bound heavy metals build-up: A comparative study between China and Australia
Publisher: Elsevier BV
Date: 11-2018
DOI: 10.1016/J.ENVPOL.2018.07.123
Abstract: Heavy metal pollution of urban stormwater poses potential risks to human and ecosystem health. The design of reliable pollution mitigation strategies requires reliable stormwater modelling approaches. Current modelling practices do not consider the influence of urbanisation characteristics on stormwater quality. This could undermine the accuracy of stormwater quality modelling results. This research study used a database consisting of over 1000 datasets to compare the characteristics of heavy metal build-up (one of the most important stormwater pollutant processes) on urban surfaces under the influence of anthropogenic and natural factors specific to different urban regions from China (Shenzhen) and Australia (Gold Coast), using Bayesian Networks. The outcomes show that the differences in heavy metals build-up loads between the two regions (mean value for Shenzhen - mean value for Gold Coast)/mean value for Shenzhen) were 0.45 (Al), 0.88 (Cr), 0.99 (Mn), 0.68 (Fe), 0.98 (Ni), 0.24 (Cu), 0.47 (Zn) and 0.13 (Pb), respectively. The research outcomes also confirmed that the influence of traffic on the build-up of different sized particles varies between Shenzhen and Gold Coast, and traffic plays distinct roles as a source and as a factor that drives heavy metal re-distribution. The road surface roughness was also found to influence build-up process differently between the two regions. More importantly, the assessment of inherent process uncertainty revealed that heavy metal build-up between different road sites in Shenzhen varies over a wider range than in Gold Coast. The study highlighted a clear distinction in the influence of sources and key anthropogenic factors on the variability of particle-bound heavy metals build-up between geographically different urban regions. The study outcomes provide new knowledge to enhance the accuracy of urban stormwater quality modelling.
Framework for soil suitability evaluation for sewage effluent renovation
Publisher: Springer Science and Business Media LLC
Date: 21-04-2004
Targeting homologous recombination deficiency in uterine leiomyosarcoma.
Publisher: Springer Science and Business Media LLC
Date: 04-05-2023
DOI: 10.1186/S13046-023-02687-0
Abstract: Uterine leiomyosarcoma (uLMS) is a rare and aggressive gynaecological malignancy, with in iduals with advanced uLMS having a five-year survival of 10%. Mutations in the homologous recombination (HR) DNA repair pathway have been observed in ~ 10% of uLMS cases, with reports of some in iduals benefiting from poly (ADP-ribose) polymerase (PARP) inhibitor (PARPi) therapy, which targets this DNA repair defect. In this report, we screened in iduals with uLMS, accrued nationally, for mutations in the HR repair pathway and explored new approaches to therapeutic targeting. A cohort of 58 in iduals with uLMS were screened for HR Deficiency (HRD) using whole genome sequencing (WGS), whole exome sequencing (WES) or NGS panel testing. In iduals identified to have HRD uLMS were offered PARPi therapy and clinical outcome details collected. Patient-derived xenografts (PDX) were generated for therapeutic targeting. All 13 uLMS s les analysed by WGS had a dominant COSMIC mutational signature 3 11 of these had high genome-wide loss of heterozygosity (LOH) ( 0.2) but only two s les had a CHORD score 50%, one of which had a homozygous pathogenic alteration in an HR gene (deletion in BRCA2 ). A further three s les harboured homozygous HRD alterations (all deletions in BRCA2), detected by WES or panel sequencing, with 5/58 (9%) in iduals having HRD uLMS. All five in iduals gained access to PARPi therapy. Two of three in iduals with mature clinical follow up achieved a complete response or durable partial response (PR) with the subsequent addition of platinum to PARPi upon minor progression during initial PR on PARPi. Corresponding PDX responses were most rapid, complete and sustained with the PARP1-specific PARPi, AZD5305, compared with either olaparib alone or olaparib plus cisplatin, even in a paired s le of a BRCA2 -deleted PDX, derived following PARPi therapy in the patient, which had developed PARPi-resistance mutations in PRKDC , encoding DNA-PKcs. Our work demonstrates the value of identifying HRD for therapeutic targeting by PARPi and platinum in in iduals with the aggressive rare malignancy, uLMS and suggests that in iduals with HRD uLMS should be included in trials of PARP1-specific PARPi.
Environmental Risks Posed by Microplastics in Urban Waterways
Publisher: Springer Nature Singapore
Date: 2023
Policy Options for the World's Primary Forests in Multilateral Environmental Agreements
Publisher: Wiley
Date: 14-08-2015
DOI: 10.1111/CONL.12120
Disaster awareness and information seeking behaviour among residents from low socio-economic backgrounds
Publisher: Elsevier BV
Date: 10-2018
Differentiating between pollutants build-up on roads and roofs: Significance of roofs as a stormwater pollutant source
Publisher: Wiley
Date: 12-0002
Faecal pollution source identification in an urbanising catchment using antibiotic resistance profiling, discriminant analysis and partial least squares regression
Publisher: Elsevier BV
Date: 03-2009
DOI: 10.1016/J.WATRES.2008.12.017
Abstract: Increasing urbanisation and changes in land use lead to adverse impacts on the quality of natural water resources. The specific sources of contamination are often difficult to identify using conventional water quality monitoring techniques. This acts as a significant constraint to the development of appropriate management techniques to protect natural water resources. Consequently, alternative means of identifying pollutant sources and their locality are necessary. In this study, Antibiotic Resistance Patterns (ARP) were established for a library of 1005 known Escherichia coli source isolates obtained from human and non-human (domesticated animals, livestock and wild) sources in an urbanizing catchment in Queensland State, Australia. Discriminant Analysis (DA) was used to differentiate between the ARP of source isolates and to identify the sources of faecal contamination. Partial Least Square (PLS) regression was then utilised on identified human source isolates to correlate their locality with specified s ling locations within the catchment. The resulting ARP DA indicated that a majority of the faecal contamination in the rural areas was non-human. However, the percentage of human isolates increased significantly in urbanized areas using on site systems for wastewater treatment. The PLS regression was able to develop predictive models which indicated a high correlation of human source isolates from the urban area. The study results confirm the feasibility of using ARP for source tracking faecal contamination in surface waters, as well as predicting their point of origin.
Assessing uncertainty in pollutant build-up and wash-off processes
Publisher: Elsevier BV
Date: 05-2016
DOI: 10.1016/J.ENVPOL.2016.01.051
Abstract: Assessing build-up and wash-off process uncertainty is important for accurate interpretation of model outcomes to facilitate informed decision making for developing effective stormwater pollution mitigation strategies. Uncertainty inherent to pollutant build-up and wash-off processes influences the variations in pollutant loads entrained in stormwater runoff from urban catchments. However, build-up and wash-off predictions from stormwater quality models do not adequately represent such variations due to poor characterisation of the variability of these processes in mathematical models. The changes to the mathematical form of current models with the incorporation of process variability, facilitates accounting for process uncertainty without significantly affecting the model prediction performance. Moreover, the investigation of uncertainty propagation from build-up to wash-off confirmed that uncertainty in build-up process significantly influences wash-off process uncertainty. Specifically, the behaviour of particles <150 μm during build-up primarily influences uncertainty propagation, resulting in appreciable variations in the pollutant load and composition during a wash-off event.
qmotif: determination of telomere content from whole-genome sequence data
Publisher: Oxford University Press (OUP)
Date: 2022
Abstract: Changes in telomere length have been observed in cancer and can be indicative of mechanisms involved in carcinogenesis. Most methods used to estimate telomere length require laboratory analysis of DNA s les. Here, we present qmotif, a fast and easy tool that determines telomeric repeat sequences content as an estimate of telomere length directly from whole-genome sequencing. qmotif shows similar results to quantitative PCR, the standard method for high-throughput clinical telomere length quantification. qmotif output correlates strongly with the output of other tools for determining telomere sequence content, TelSeq and TelomereHunter, but can run in a fraction of the time—usually under a minute. qmotif is implemented in Java and source code is available at github.com/AdamaJava/adamajava, with instructions on how to build and use the application available from adamajava.readthedocs.io/en/latest/. Supplementary data are available at Bioinformatics Advances online.
Novel RET Fusion
Publisher: American Society of Clinical Oncology (ASCO)
Date: 11-2021
DOI: 10.1200/PO.21.00127
The Role of Geographical Information Systems in Urban Hydrological Modelling
Publisher: Wiley
Date: 06-1999
Engineered hydrochar production methodologies, key factors influencing agriculture wastewater treatment, and life cycle analysis: A critical review
Publisher: Elsevier BV
Date: 12-2023
Combined burden and functional impact tests for cancer driver discovery using DriverPower
Publisher: Springer Science and Business Media LLC
Date: 05-02-2020
DOI: 10.1038/S41467-019-13929-1
Abstract: The discovery of driver mutations is one of the key motivations for cancer genome sequencing. Here , as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium , which aggregated whole genome sequencing data from 2658 cancers across 38 tumour types, we describe DriverPower, a software package that uses mutational burden and functional impact evidence to identify driver mutations in coding and non-coding sites within cancer whole genomes. Using a total of 1373 genomic features derived from public sources, DriverPower’s background mutation model explains up to 93% of the regional variance in the mutation rate across multiple tumour types. By incorporating functional impact scores, we are able to further increase the accuracy of driver discovery. Testing across a collection of 2583 cancer genomes from the PCAWG project, DriverPower identifies 217 coding and 95 non-coding driver candidates. Comparing to six published methods used by the PCAWG Drivers and Functional Interpretation Working Group, DriverPower has the highest F1 score for both coding and non-coding driver discovery. This demonstrates that DriverPower is an effective framework for computational driver discovery.
Analysis of heavy metals in road-deposited sediments
Publisher: Elsevier BV
Date: 07-2006
DOI: 10.1016/J.ACA.2006.04.064
Abstract: Road-deposited sediments were analysed for heavy metal concentrations at three different landuses (residential, industrial, commercial) in Queensland State, Australia. The sediments were collected using a domestic vacuum cleaner which was proven to be highly efficient in collecting sub-micron particles. Five particle sizes were analysed separately for eight heavy metal elements (Zn, Fe, Pb, Cd, Cu, Cr, Al and Mn). At all sites, the maximum concentration of the heavy metals occurred in the 0.45-75 microm particle size range, which conventional street cleaning services do not remove efficiently. Multicriteria decision making methods (MCDM), PROMETHEE and GAIA, were employed in the data analysis. PROMETHEE, a non-parametric ranking analysis procedure, was used to rank the metal contents of the sediments s led at each site. The most polluted site and particle size range were the industrial site and the 0.45-75 microm range, respectively. Although the industrial site displayed the highest metal concentrations, the highest heavy metal loading coincided with the highest sediment load, which occurred at the commercial site. GAIA, a special form of principal component analysis, was applied to determine correlations between the heavy metals and particle size ranges and also to assess possible correlation with total organic carbon (TOC). The GAIA-planes revealed that irrespective of the site, most of the heavy metals are adsorbed to sediments below 150 microm. A weak correlation was found between Zn, Mn and TOC at the commercial site. This could lead to higher bioavailability of these metals through complexation reactions with the organic species in the sediments.
Uncertainty analysis of pollutant build-up modelling based on a Bayesian weighted least squares approach
Publisher: Elsevier BV
Date: 04-2013
DOI: 10.1016/J.SCITOTENV.2013.01.086
Abstract: Reliable pollutant build-up prediction plays a critical role in the accuracy of urban stormwater quality modelling outcomes. However, water quality data collection is resource demanding compared to streamflow data monitoring, where a greater quantity of data is generally available. Consequently, available water quality datasets span only relatively short time scales unlike water quantity data. Therefore, the ability to take due consideration of the variability associated with pollutant processes and natural phenomena is constrained. This in turn gives rise to uncertainty in the modelling outcomes as research has shown that pollutant loadings on catchment surfaces and rainfall within an area can vary considerably over space and time scales. Therefore, the assessment of model uncertainty is an essential element of informed decision making in urban stormwater management. This paper presents the application of a range of regression approaches such as ordinary least squares regression, weighted least squares regression and Bayesian weighted least squares regression for the estimation of uncertainty associated with pollutant build-up prediction using limited datasets. The study outcomes confirmed that the use of ordinary least squares regression with fixed model inputs and limited observational data may not provide realistic estimates. The stochastic nature of the dependent and independent variables need to be taken into consideration in pollutant build-up prediction. It was found that the use of the Bayesian approach along with the Monte Carlo simulation technique provides a powerful tool, which attempts to make the best use of the available knowledge in prediction and thereby presents a practical solution to counteract the limitations which are otherwise imposed on water quality modelling.
Quantifying the influence of surface physico-chemical properties of biosorbents on heavy metal adsorption
Publisher: Elsevier BV
Date: 11-2019
DOI: 10.1016/J.CHEMOSPHERE.2019.06.074
Abstract: Heavy metals present in industrial wastewater contribute to human and ecosystem health risk when discharged without proper treatment. Low-cost biosorbents with high metal-binding capacity are increasingly being utilized for the removal of heavy metals. Inherent physico-chemical properties of biosorbents significantly influence their adsorption capacity. Studies quantifying the influence exerted by these properties on adsorption capacity are scarce. This study quantifies the influence and relative importance of selected physico-chemical properties on the adsorption capacity of three alent heavy metals Cu
Microbial risk from source-separated urine used as liquid fertilizer in sub-tropical Australia
Publisher: Elsevier BV
Date: 04-2016
Widespread shortfalls in protected area resourcing undermine efforts to conserve biodiversity
Publisher: Wiley
Date: 06-05-2019
DOI: 10.1002/FEE.2042
The evolutionary history of 2,658 cancers
Publisher: Springer Science and Business Media LLC
Date: 05-02-2020
DOI: 10.1038/S41586-019-1907-7
Abstract: Cancer develops through a process of somatic evolution 1,2 . Sequencing data from a single biopsy represent a snapshot of this process that can reveal the timing of specific genomic aberrations and the changing influence of mutational processes 3 . Here, by whole-genome sequencing analysis of 2,658 cancers as part of the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA) 4 , we reconstruct the life history and evolution of mutational processes and driver mutation sequences of 38 types of cancer. Early oncogenesis is characterized by mutations in a constrained set of driver genes, and specific copy number gains, such as trisomy 7 in glioblastoma and isochromosome 17q in medulloblastoma. The mutational spectrum changes significantly throughout tumour evolution in 40% of s les. A nearly fourfold ersification of driver genes and increased genomic instability are features of later stages. Copy number alterations often occur in mitotic crises, and lead to simultaneous gains of chromosomal segments. Timing analyses suggest that driver mutations often precede diagnosis by many years, if not decades. Together, these results determine the evolutionary trajectories of cancer, and highlight opportunities for early cancer detection.
Sex differences in oncogenic mutational processes
Publisher: Springer Science and Business Media LLC
Date: 28-08-2020
DOI: 10.1038/S41467-020-17359-2
Abstract: Sex differences have been observed in multiple facets of cancer epidemiology, treatment and biology, and in most cancers outside the sex organs. Efforts to link these clinical differences to specific molecular features have focused on somatic mutations within the coding regions of the genome. Here we report a pan-cancer analysis of sex differences in whole genomes of 1983 tumours of 28 subtypes as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium. We both confirm the results of exome studies, and also uncover previously undescribed sex differences. These include sex-biases in coding and non-coding cancer drivers, mutation prevalence and strikingly, in mutational signatures related to underlying mutational processes. These results underline the pervasiveness of molecular sex differences and strengthen the call for increased consideration of sex in molecular cancer research.
Sustainable urban water environment: Climate, pollution and adaptation
Publisher: Edward Elgar Publishing
Date: 28-03-2014
Modelling Resilience of a Water Supply System under Climate Change and Population Growth Impacts
Publisher: Springer Science and Business Media LLC
Date: 06-04-2017
Fecal indicators and bacterial pathogens in bottled water from Dhaka, Bangladesh
Publisher: FapUNIFESP (SciELO)
Date: 2013
Integrated Genomic Characterization of Pancreatic Ductal Adenocarcinoma
Publisher: Elsevier BV
Date: 08-2017
Assessment of Physical and Chemical Attributes of Sub-Tropical Soil to Predict Long Term Effluent Treatment Potential
Publisher: Informa UK Limited
Date: 05-2005
Influential factors on microplastics occurrence in river sediments
Publisher: Elsevier BV
Date: 10-2020
Understanding road surface pollutant wash-off and underlying physical processes using simulated rainfall
Publisher: IWA Publishing
Date: 04-2008
DOI: 10.2166/WST.2008.260
Abstract: Pollutant wash-off is one of the key pollutant processes that detailed knowledge is required in order to develop successful treatment design strategies for urban stormwater. Unfortunately, current knowledge relating to pollutant wash-off is limited. This paper presents the outcomes of a detailed investigation into pollutant wash-off on residential road surfaces. The investigations consisted of research methodologies formulated to overcome the physical constraints due to the heterogeneity of urban paved surfaces and the dependency on naturally occurring rainfall. This entailed the use of small road surface plots and artificially simulated rainfall. Road surfaces were selected due to its critical importance as an urban stormwater pollutant source. The study results showed that the influence of initially available pollutants on the wash-off process was limited. Furthermore, pollutant wash-off from road surfaces can be replicated using an exponential equation. However, the typical version of the exponential wash-off equation needs to be modified by introducing a non dimensional factor referred to as ‘capacity factor' CF. Three rainfall intensity ranges were identified where the variation of CF can be defined. Furthermore, it was found that particulate density rather than size is the critical parameter that influences the process of pollutant wash-off.
Author Correction: Reconstructing evolutionary trajectories of mutation signature activities in cancer using TrackSig
Publisher: Springer Science and Business Media LLC
Date: 08-12-2021
Temporal trends and bioavailability assessment of heavy metals in the sediments of Deception Bay, Queensland, Australia
Publisher: Elsevier BV
Date: 12-2014
DOI: 10.1016/J.MARPOLBUL.2014.09.030
Abstract: Thirteen sites in Deception Bay, Queensland, Australia were s led three times over a period of 7 months and assessed for contamination by a range of heavy metals, primarily As, Cd, Cr, Cu, Pb and Hg. Fraction analysis, enrichment factors and Principal Components Analysis-Absolute Principal Component Scores (PCA-APCS) analysis were conducted in order to identify the potential bioavailability of these elements of concern and their sources. Hg and Te were identified as the elements of highest enrichment in Deception Bay while marine sediments, shipping and antifouling agents were identified as the sources of the Weak Acid Extractable Metals (WE-M), with antifouling agents showing long residence time for mercury contamination. This has significant implications for the future of monitoring and regulation of heavy metal contamination within Deception Bay.
An inclusive and adaptive framework for measuring social resilience to disasters
Publisher: Elsevier BV
Date: 06-2018
Education in Ecological Engineering—a Need Whose Time Has Come
Publisher: Springer Science and Business Media LLC
Date: 06-2021
DOI: 10.1007/S43615-021-00067-4
Abstract: By providing an integrated, systems-approach to problem-solving that incorporates ecological principles in engineering design, ecological engineering addresses, many of the limitations of Ecology and Engineering needed to work out how people and nature can beneficially coexist on planet Earth. Despite its origins in the 1950s, ecological engineering remains a niche discipline, while at the same time, there has never been a greater need to combine the rigour of engineering and science with the systems-approach of ecology for pro-active management of Earth’s bio ersity and environmental life-support systems. Broad consensus on the scope and defining elements of ecological engineering and development of a globally consistent ecological engineering curriculum are key pillars to mainstream recognition of the discipline and practice of ecological engineering. In this paper, the importance of ecological engineering education is discussed in relation to the perceived need of our society to address global challenges of sustainable development. The perceived needs of industry, practitioners, educators and students for skills in ecological engineering are also discussed. The need for integrative, interdisciplinary education is discussed in relation to the scope of ecology, engineering and the unique role of ecological engineering. The scope for a universally recognised curriculum in ecological engineering is presented. The curriculum recognises a set of overarching principles and concepts that unite multiple application areas of ecological engineering practice. The integrative, systems-based approach of ecological engineering distinguishes it from the trend toward narrow specialisation in education. It is argued that the systems approach to conceptualising problems of design incorporating ecological principles is a central tenant of ecological engineering practice. Challenges and structural barriers to wider adoption of ecological engineering principles, embedded in our society’s reliance on technological solutions to environmental problems, are discussed along with opportunities to increase adoption of ecological engineering practice. It is suggested that unifying the numerous specialist activity areas and applications of ecological engineering under an umbrella encompassing a set of core principles, approaches, tools and way of thinking is required to distinguish ecological engineering from other engineering disciplines and scale up implementation of the discipline. It is concluded that these challenges can only be realised if ecological engineering moves beyond application by a relatively small band of enthusiastic practitioners, learning by doing, to the education of future cohorts of students who will become tomorrow’s engineers, project managers, procurement officers and decision makers, applying principles informed by a growing body of theory and knowledge generated by an active research community, a need whose time has come, if we are to deploy all tools at our disposal toward addressing the grand challenge of creating a sustainable future.
Recurrent loss of heterozygosity correlates with clinical outcome in pancreatic neuroendocrine cancer
Publisher: Cold Spring Harbor Laboratory
Date: 08-11-2017
DOI: 10.1101/214585
Abstract: Pancreatic neuroendocrine tumors (pNETs) are uncommon cancers arising from pancreatic islet cells. Analysis of gene mutation, copy number and RNA expression of 57 sporadic pNETs showed that pNET genomes are dominated by aneuploidy. Remarkably, ~25% of pNETs had genomes characterized by recurrent loss of heterozygosity (LoH) of the same 10 chromosomes, accompanied by bi-allelic MEN1 inactivation, and these cases had generally poor clinical outcome. Another ~25% of all pNETs had chromosome 11 LoH and bi-allelic MEN1 inactivation, lacking the recurrent LoH pattern – these had universally good clinical outcome. Some level of aneuploidy was common, and overall ~80% of pNETs had LoH of ≥1 chromosome. This aneuploidy led to changes in RNA expression at the level of whole chromosomes and allowed pathogenic germline variants (e.g. ATM ) to be expressed unopposed, inactivating downstream tumor suppressor pathways. Some pNETs appear to utilize VHL gene methylation or mutation to activate pseudo-hypoxia. Contrary to expectation neither tumor morphology within well-differentiated pNETs nor single gene mutation had significant associations with clinical outcome, nor did expression of RNAs reflecting the activity of immune, differentiation, proliferative or tumor suppressor pathways. MEN1 was the only statistically significant recurrently mutated driver gene in pNETs. Only one pNET had clearly oncogenic and actionable SNVs (in PTEN and FLCN ) confirmed by corroborating RNA expression changes. The two distinct patterns of aneuploidy described here, associated with markedly poor and good clinical outcome respectively, define a novel oncogenic mechanism and the first route to genomic precision oncology for this tumor type.
Evaluating the relationship between temporal changes in land use and resulting water quality
Publisher: Elsevier BV
Date: 03-2018
DOI: 10.1016/J.ENVPOL.2017.11.096
Abstract: Changes in land use have a direct impact on receiving water quality. Effective mitigation strategies require the accurate prediction of water quality in order to enhance community well-being and ecosystem health. The research study employed Bayesian Network modelling to investigate the validity of using cross-sectional and longitudinal data on water quality and land use for predicting water quality in a mixed use catchment and the role it plays in the generation of blue-green algae in the receiving marine environment. Bayesian Network modelling showed that cross-sectional and longitudinal data analyses generate contrasting information about the influence of different land uses on surface water pollution. The modelling outcomes highlighted the lack of reliability in cross-sectional data analysis, based on the indication of spurious relationships between water quality and land use. On the other hand, the longitudinal data analysis, which accounted for changes in water quality and land use over a ten-year period, informed how catchment water quality varies in response to temporal changes in land use. The longitudinal data analysis further revealed that the types of anthropogenic activities have a more significant influence on pollutant generation than the change in the area extent of different land uses over time. Therefore, the careful interpretation of the findings derived solely from cross-sectional data analysis is important in the design of long-term strategies for pollution mitigation.
Author Correction: Analyses of non-coding somatic drivers in 2,658 cancer whole genomes
Publisher: Springer Science and Business Media LLC
Date: 25-01-2023
Influence of pollutant build-up on variability in wash-off from urban road surfaces
Publisher: Elsevier BV
Date: 09-2015
DOI: 10.1016/J.SCITOTENV.2015.04.093
Abstract: Variability in the pollutant wash-off process is a concept which needs to be understood in-depth in order to better assess the outcomes of stormwater quality models, and thereby strengthen stormwater pollution mitigation strategies. Current knowledge about the wash-off process does not extend to a clear understanding of the influence of the initially available pollutant build-up on the variability of the pollutant wash-off load and composition. Consequently, pollutant wash-off process variability is poorly characterised in stormwater quality models, which can result in inaccurate stormwater quality predictions. Mathematical simulation of particulate wash-off from three urban road surfaces confirmed that the wash-off load of particle size fractions 150 μm after a storm event vary with the build-up of the respective particle size fractions available at the beginning of the storm event. Furthermore, pollutant load and composition associated with the initially available build-up of 150 μm particles on wash-off process variability is significant only for relatively shorter duration storm events.
Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples
Publisher: Springer Science and Business Media LLC
Date: 21-09-2020
DOI: 10.1038/S41467-020-18151-Y
Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA s les, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological ergences between two reproducible somatic variant detection efforts.
A Critical Review of Social Resilience Properties and Pathways in Disaster Management
Publisher: Springer Science and Business Media LLC
Date: 09-11-2021
DOI: 10.1007/S13753-021-00378-Y
Abstract: Resilience as a concept is multi-faceted with complex dimensions. In a disaster context, there is lack of consistency in conceptualizing social resilience. This results in ambiguity of its definition, properties, and pathways for assessment. A number of key research gaps exist for critically reviewing social resilience conceptualization, projecting resilience properties in a disaster-development continuum, and delineating a resilience trajectory in a multiple disaster timeline. This review addressed these research gaps by critically reviewing social resilience definitions, properties, and pathways. The review found four variations in social resilience definitions, which recognize the importance of abilities of social systems and processes in disaster phases at different levels. A review of resilience properties and pathways in the disaster resilience literature suggested new resilience properties—“risk-sensitivity” and “regenerative” in the timeline of two consecutive disasters. This review highlights a causal pathway for social resilience to better understand the resilience status in a multi-shock scenario by depicting inherent and adaptive resilience for consecutive disaster scenarios and a historical case study for a resilience trajectory in a multiple disaster timeline. The review findings will assist disaster management policymakers and practitioners to formulate appropriate resilience enhancement strategies within a holistic framework in a multi-disaster timeline.
Transformation processes of metals associated with urban road dust: A critical review
Publisher: Informa UK Limited
Date: 26-03-2019
Improving sustainability of Indonesian public building: Challenges and policy strategy
Publisher: Springer International Publishing
Date: 12-2019
Determining disaster severity through social media analysis: Testing the methodology with South East Queensland Flood tweets
Publisher: Elsevier BV
Date: 2020
Hydrochar: A Promising Step Towards Achieving a Circular Economy and Sustainable Development Goals
Publisher: Frontiers Media SA
Date: 07-04-2022
DOI: 10.3389/FCENG.2022.867228
Abstract: The United Nations 17 Sustainable Development Goals (SDGs) are a universal call to action to end poverty, protect the environment, and improve the lives and prospects of everyone on this planet. However, progress on SDGs is currently lagging behind its 2030 target. The availability of water of adequate quality and quantity is considered as one of the most significant challenges in reaching that target. The concept of the ‘Circular Economy’ has been termed as a potential solution to fasten the rate of progress in achieving SDGs. One of the promising engineering solutions with applications in water treatment and promoting the concept of the circular economy is hydrochar. Compared to biochar, hydrochar research is still in its infancy in terms of optimization of production processes, custom design for specific applications, and knowledge of its water treatment potential. In this context, this paper critically reviews the role of hydrochar in contributing to achieving the SDGs and promoting a circular economy through water treatment and incorporating a waste-to-value approach. Additionally, key knowledge gaps in the production and utilization of engineered hydrochar are identified, and possible strategies are suggested to further enhance its water remediation potential and circular economy in the context of better natural resource management using hydrochar. Research on converting different waste biomass to valuable hydrochar based products need further development and optimization of parameters to fulfil its potential. Critical knowledge gaps also exist in the area of utilizing hydrochar for large-scale drinking water treatment to address SDG-6.
Targeting DNA Damage Response and Replication Stress in Pancreatic Cancer
Publisher: Elsevier BV
Date: 2021
Weak acid extractable metals in Bramble Bay, Queensland, Australia : temporal behaviour, enrichment and source apportionment
Publisher: Elsevier BV
Date: 02-2015
Using Multivariate Analysis to Predict the Behaviour of Soils Under Effluent Irrigation
Publisher: Springer Science and Business Media LLC
Date: 17-03-2006
Role of residence time on the transformation of Zn, Cu, Pb and Cd attached to road dust in different land uses
Publisher: Elsevier BV
Date: 05-2018
DOI: 10.1016/J.ECOENV.2018.02.007
Abstract: The adsorption behaviour of metals deposited on road surfaces undergo changes during dry weather periods, with the bioavailability varying compared to the original species, prior to incorporation in stormwater runoff. This study investigated the role of antecedent dry days on the transformation characteristics of Zn, Cu, Pb and Cd attached to different geochemical forms of road dust, in order to predict potential stormwater quality impacts. The study outcomes showed that the exchangeable fraction generally decreased with the increase in antecedent dry days, but the reducible, oxidisable and residual fractions increased. This implies that there is a time-dependent transformation of weakly bound metals in road dust to more persistent chemical forms. The transformation rate of metals was found to be in the order of Pb > Cu > Zn > Cd. Significant changes in metal distribution among the geochemical fractions were observed up to seven dry days, suggesting that during the initial antecedent dry days, the transformations can be relatively more significant. Among the analysed metals, Cd present on road surfaces has a higher potential for being bioavailable during the antecedent dry days.
Genomic basis for RNA alterations in cancer
Publisher: Springer Science and Business Media LLC
Date: 05-02-2020
DOI: 10.1038/S41586-020-1970-0
Abstract: Transcript alterations often result from somatic changes in cancer genomes 1 . Various forms of RNA alterations have been described in cancer, including overexpression 2 , altered splicing 3 and gene fusions 4 however, it is difficult to attribute these to underlying genomic changes owing to heterogeneity among patients and tumour types, and the relatively small cohorts of patients for whom s les have been analysed by both transcriptome and whole-genome sequencing. Here we present, to our knowledge, the most comprehensive catalogue of cancer-associated gene alterations to date, obtained by characterizing tumour transcriptomes from 1,188 donors of the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA) 5 . Using matched whole-genome sequencing data, we associated several categories of RNA alterations with germline and somatic DNA alterations, and identified probable genetic mechanisms. Somatic copy-number alterations were the major drivers of variations in total gene and allele-specific expression. We identified 649 associations of somatic single-nucleotide variants with gene expression in cis , of which 68.4% involved associations with flanking non-coding regions of the gene. We found 1,900 splicing alterations associated with somatic mutations, including the formation of exons within introns in proximity to Alu elements. In addition, 82% of gene fusions were associated with structural variants, including 75 of a new class, termed ‘bridged’ fusions, in which a third genomic location bridges two genes. We observed transcriptomic alteration signatures that differ between cancer types and have associations with variations in DNA mutational signatures. This compendium of RNA alterations in the genomic context provides a rich resource for identifying genes and mechanisms that are functionally implicated in cancer.
Engaging residents from different ethnic and language backgrounds in disaster preparedness
Publisher: Elsevier BV
Date: 10-2019
Biochar-supported nanomaterials for environmental applications
Publisher: Elsevier BV
Date: 10-2019
Adsorption of heavy metals by road deposited solids
Publisher: IWA Publishing
Date: 06-2013
DOI: 10.2166/WST.2013.171
Abstract: The research study discussed in the paper investigated the adsorption/desorption behaviour of heavy metals commonly deposited on urban road surfaces, namely, Zn, Cu, Cr and Pb, for different particle size ranges of solids. The study outcomes, based on field studies and batch experiments, confirmed that road deposited solids particles contain a significantly high amount of vacant charge sites with the potential to adsorb additional heavy metals. Kinetic studies and adsorption experiments indicated that Cr is the most preferred metal element to associate with solids due to the relatively high electronegativity and high charge density of trivalent cation (Cr3+). However, the relatively low availability of Cr in the urban road environment could influence this behaviour. Comparing total adsorbed metals present in solids particles, it was found that Zn has the highest capacity for adsorption to solids. Desorption experiments confirmed that a low concentration of Cu, Cr and Pb in solids was present in water-soluble and exchangeable form, whilst a significant fraction of adsorbed Zn has a high likelihood of being released back into solution. Among heavy metals, Zn is considered to be the most commonly available metal among road surface pollutants.
Climate change risk management for public assets in Semarang, Indonesia
Publisher: Springer International Publishing
Date: 12-2019
Time as the critical factor in the investigation of the relationship between pollutant wash-off and rainfall characteristics
Publisher: Elsevier BV
Date: 03-2014
Taxonomy of influential factors for predicting pollutant first flush in urban stormwater runoff
Publisher: Elsevier BV
Date: 12-2019
DOI: 10.1016/J.WATRES.2019.115075
Abstract: Pollutant first flush in urban stormwater runoff is an important phenomenon influenced by a range of rainfall and catchment related variables. Even though numerous studies have been undertaken to mathematically define the first flush and the influential variables of first flush, limited research have been carried out to rank such variables in terms of their level of importance in generating first flush. Identifying the degree of importance of the variables is critical for accurate predictions of first flush occurrence and understanding the main drivers of first flush. This research study undertook a comprehensive analysis of the variables influencing the predictions of first flush occurrence and their relative importance. The study results are expected to contribute to more accurate predictions of first flush by affording greater importance to the highly ranked factors and their impacts. The study outcomes confirmed that total rainfall depth was the most important variable influencing the prediction of first flush events while the maximum intensity was the second. Rain duration, runoff depth, runoff peak and average intensity were the next four most important variables. Antecedent dry period and effective impervious area fraction had relatively low ranking while the time of concentration and the event mean concentration were found to be the least important variables. Furthermore, the study outcomes highlight that the use of a combination of variables and due consideration of their interactions can yield better results than considering their in idual roles.
Characterization and Applications of Biocarbon Materials Produced from Spent Coffee Grounds Using Dry and Wet Methods
Publisher: Elsevier BV
Date: 2023
DOI: 10.2139/SSRN.4333842
Mathematical Interpretation of Pollutant Wash-off from Urban Road Surfaces using Simulated Rainfall
Publisher: Elsevier BV
Date: 07-2007
DOI: 10.1016/J.WATRES.2007.03.037
Abstract: In the context of stormwater quality modelling, an in-depth understanding of underlying physical processes and the availability of reliable and accurate mathematical equations, which can replicate pollutant processes are essential. Stormwater pollutants undergo three primary processes, namely, build-up, wash-off and transport, before accumulating into receiving waters. These processes are expressed mathematically by equations in stormwater quality models. Among the three processes, wash-off is the least investigated. This paper presents the outcomes of an in-depth investigation of pollutant wash-off processes on typical urban road surfaces. The study results showed that a storm event has the capacity to wash-off only a fraction of pollutants available and this fraction varies primarily with rainfall intensity, kinetic energy of rainfall and characteristics of the pollutants. These outcomes suggest that the exponential equation commonly used for mathematically defining pollutant wash-off would need to be modified in order to incorporate the wash-off capacity of rainfall. Consequently, the introduction of an additional term referred to as the 'capacity factor'C(F) is recommended. C(F) primarily varies with rainfall intensity. However, for simplicity three rainfall intensity ranges were identified where the variation of C(F) can be defined. For rainfall intensities less than 40 mm/h, C(F) varies linearly from 0 to 0.5. For rainfall intensities from 40 to around 90 mm/h, C(F) is a constant around 0.5. Beyond 90 mm/h, C(F) varies between 0.5 and 1.
Human and bovine adenoviruses for the detection of source-specific fecal pollution in coastal waters in Australia
Publisher: Elsevier BV
Date: 09-2010
DOI: 10.1016/J.WATRES.2010.05.017
Abstract: In this study, the host-specificity and -sensitivity of human- and bovine-specific adenoviruses (HS-AVs and BS-AVs) were evaluated by testing wastewater/fecal s les from various animal species in Southeast, Queensland, Australia. The overall specificity and sensitivity of the HS-AVs marker were 1.0 and 0.78, respectively. These figures for the BS-AVs were 1.0 and 0.73, respectively. Twenty environmental water s les were collected during wet conditions and 20 s les were colleted during dry conditions from the Maroochy Coastal River and tested for the presence of fecal indicator bacteria (FIB), host-specific viral markers, zoonotic bacterial and protozoan pathogens using PCR/qPCR. The concentrations of FIB in water s les collected after wet conditions were generally higher compared to dry conditions. HS-AVs was detected in 20% water s les collected during wet conditions and whereas BS-AVs was detected in both wet (i.e., 10%) and dry (i.e., 10%) conditions. Both C ylobacter jejuni mapA and Salmonella invA genes detected in 10% s les collected during dry conditions. The concentrations of Salmonella invA ranged between 3.5 × 10(2) and 4.3 × 10(2) genomic copies per 500 ml of water Giardia lamblia β-giardin gene was detected only in one s le (5%) collected during the dry conditions. Weak or significant correlations were observed between FIB with viral markers and zoonotic pathogens. However, during dry conditions, no significant correlations were observed between FIB concentrations with viral markers and zoonotic pathogens. The prevalence of HS-AVs in s les collected from the study river suggests that the quality of water is affected by human fecal pollution and as well as bovine fecal pollution. The results suggest that HS-AVs and BS-AVs detection using PCR could be a useful tool for the identification of human sourced fecal pollution in coastal waters.
Geochemical phase and particle size relationships of metals in urban road dust
Publisher: Elsevier BV
Date: 11-2017
DOI: 10.1016/J.ENVPOL.2017.06.059
Abstract: Detailed knowledge of the processes that metals undergo during dry weather periods whilst deposited on urban surfaces and their environmental significance is essential to predict the potential influence of metals on stormwater quality in order to develop appropriate stormwater pollution mitigation measures. However, very limited research has been undertaken in this area. Accordingly, this study investigated the geochemical phase and particle size relationships of seven metals which are commonly associated with urban road dust, using sequential extraction in order to assess their mobility characteristics. Metals in the sequentially extracted fractions of exchangeable, reducible, oxidisable and residual were found to follow a similar trend for different land uses even though they had variable accumulation loads. The high affinity of Cd and Zn for exchangeable reactions in both, bulk and size-fractionated solid s les confirmed their high mobility, while the significant enrichment of Ni and Cr in the stable residual fraction indicated a low risk of mobility. The study results also confirmed the availability of Cu, Pb and Mn in both, stable and mobile fractions. The fine fraction of solids (<150 μm) and antecedent dry days can be highlighted as important parameters when determining the fate of metals associated with urban road dust. The outcomes from this study are expected to contribute to the development of effective stormwater pollution mitigation strategies by taking into consideration the metal-particulate relationships.
Physico-chemical properties of sediments governing the bioavailability of heavy metals in urban waterways
Publisher: Elsevier BV
Date: 04-2021
Platypus Induced Pluripotent Stem Cells: The Unique Pluripotency Signature of a Monotreme
Publisher: Mary Ann Liebert Inc
Date: 02-2019
Abstract: The platypus (Ornithorhynchus anatinus) is an egg-laying monotreme mammal whose ancestors erged ∼166 million years ago from the evolutionary pathway that eventually gave rise to both marsupial and eutherian mammals. Consequently, its genome is an extraordinary amalgam of both ancestral reptilian and derived mammalian features. To gain insight into the evolution of mammalian pluripotency, we have generated induced pluripotent stem cells from the platypus (piPSCs). Deep sequencing of the piPSC transcriptome revealed that piPSCs robustly express the core eutherian pluripotency factors POU5F1/OCT4, SOX2, and NANOG. Given the more extensive role of SOX3 over SOX2 in avian pluripotency, our data indicate that between 315 and 166 million years ago, primitive mammals replaced the role of SOX3 in the vertebrate pluripotency network with SOX2. DAX1/NR0B1 is not expressed in piPSCs and an analysis of the platypus DAX1 promoter revealed the absence of a proximal SOX2-binding DNA motif known to be critical for DAX1 expression in eutherian pluripotent stem cells, suggesting that the acquisition of SOX2 responsiveness by DAX1 has facilitated its recruitment into the pluripotency network of eutherians. Using the RNAseq data, we were also able to demonstrate that in both fibroblasts and piPSCs, the expression ratio of X chromosomes to autosomes (X
Inherent errors in pollutant build-up estimation in considering urban land use as a lumped parameter
Publisher: Wiley
Date: 09-2012
DOI: 10.2134/JEQ2011.0419
Abstract: Stormwater quality modeling results are subject to uncertainty. The variability of input parameters is an important source of overall model error. An in-depth understanding of the variability associated with input parameters can provide knowledge on the uncertainty associated with these parameters and can assist in uncertainty analysis of stormwater quality models and decision making based on modeling outcomes. This paper discusses the outcomes of a research study undertaken to analyze the variability related to pollutant build-up parameters in stormwater quality modeling. The study was based on the analysis of pollutant build-up s les collected from 12 road surfaces in residential, commercial, and industrial land uses. It was found that build-up characteristics vary appreciably even within the same land use. Therefore, using land use as a lumped parameter would contribute significant uncertainties in stormwater quality modeling. Additionally, it was found that the variability in pollutant build-up can be significant depending on the pollutant type. This underlines the importance of taking into account specific land use characteristics and targeted pollutant species when undertaking uncertainty analysis of stormwater quality models or in interpreting the modeling outcomes.
Transformation and degradation of polycyclic aromatic hydrocarbons (PAHs) in urban road surfaces: Influential factors, implications and recommendations
Publisher: Elsevier BV
Date: 02-2020
DOI: 10.1016/J.ENVPOL.2019.113510
Abstract: Polycyclic aromatic hydrocarbons (PAHs) are prone to post-emission transformation and degradation to yield transformed PAH products (TPPs) that are potentially more hazardous than parent PAHs. This review provides a comprehensive evaluation of the potential environmental processes of PAHs such as sorption, volatilisation, photo- and bio-transformation and degradation on road surfaces, a significant accumulation point of PAHs. The review primarily evaluates key influential factors, toxicity implications, PAHs and TPPs fate and viable options for mitigating environmental and human health impacts. Photolysis was identified as the most significant transformation and degradation process due to the light absorption capacity of most PAHs. Climate conditions, physicochemical properties of road dust (sorbent), PAHs and TPPs and the existence of heavy metals such as Fe (III) are notable underlying factors for photolysis. Available data points to the predominance of carbonyl TPPs than other products such as nitro and hydroxyl TPPs with decreasing concentration trend of 9-fluorenone > 9,10-anthraquinone > benzo[a]fluorenone on road surfaces. The review recommends conducting future investigations targeting the influential factors pertaining to the fate of road deposited PAHs and TPPs. Furthermore, development of cost and time effective modern analytical methods is needed to quantify PAHs and TPPs present in minute quantities of s les. The review also identified that the unavailability of toxicity equivalency factors (TEF) for the most critical TPPs can be addressed using quantitative structure-activity relationship (QSAR) models and bioassays simultaneously. The content of this review is significant to the future work of researchers across various fields including analytical and environmental chemistry, stormwater pollution and toxicology.
Influence of surface hydrophobicity/hydrophilicity of biochar on the removal of emerging contaminants
Publisher: Elsevier BV
Date: 12-2020
Disruption of chromatin folding domains by somatic genomic rearrangements in human cancer
Publisher: Springer Science and Business Media LLC
Date: 05-02-2020
DOI: 10.1038/S41588-019-0564-Y
Abstract: Chromatin is folded into successive layers to organize linear DNA. Genes within the same topologically associating domains (TADs) demonstrate similar expression and histone-modification profiles, and boundaries separating different domains have important roles in reinforcing the stability of these features. Indeed, domain disruptions in human cancers can lead to misregulation of gene expression. However, the frequency of domain disruptions in human cancers remains unclear. Here, as part of the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA), which aggregated whole-genome sequencing data from 2,658 cancers across 38 tumor types, we analyzed 288,457 somatic structural variations (SVs) to understand the distributions and effects of SVs across TADs. Notably, SVs can lead to the fusion of discrete TADs, and complex rearrangements markedly change chromatin folding maps in the cancer genomes. Notably, only 14% of the boundary deletions resulted in a change in expression in nearby genes of more than twofold.
Health risk assessment of heavy metals in atmospheric deposition in a congested city environment in a developing country: Kandy City, Sri Lanka
Publisher: Elsevier BV
Date: 08-2018
DOI: 10.1016/J.JENVMAN.2018.04.036
Abstract: This research study which was undertaken in a congested city environment in a developing country provides a robust approach for the assessment and management of human health risk associated with atmospheric heavy metals. The case study area was Kandy City, which is the second largest city in Sri Lanka and bears the characteristics of a typical city in the developing world such as the urban footprint, high population density and traffic congestion. Atmospheric deposition s les were collected on a weekly basis and analyzed for nine heavy metals common to urban environments, namely, Al, Cr, Mn, Fe, Ni, Cu, Zn, Cd and Pb. Health risk was assessed using hazard quotient (HQ) and hazard index (HI), while the cancer risk was evaluated based on life time daily cancer risk. Al and Fe were found to be in relatively high concentrations due to the influence of both, natural and anthropogenic sources. High Zn loads were attributed to vehicular emissions and the wide use of Zn coated building materials. Contamination factor and geo-accumulation index showed that currently, Al and Fe are at uncontaminated levels and other metals are in the range of uncontaminated to contaminated levels, but with the potential to exacerbate in the long-term. The health risk assessment showed that the influence of the three exposure pathways were in the order of ingestion > dermal contact > inhalation. The HQ and HI values for children for the nine heavy metals were higher than that for adults, indicating that children may be subjected to potentially higher health risk than adults. The study methodology and outcomes provide fundamental knowledge to regulatory authorities to determine appropriate mitigation measures in relation to HM pollution in city environments in the developing world, where to-date only very limited research has been undertaken.
Implementation of Whole-Genome and Transcriptome Sequencing Into Clinical Cancer Care
Publisher: American Society of Clinical Oncology (ASCO)
Date: 12-2022
DOI: 10.1200/PO.22.00245
Abstract: The combination of whole-genome and transcriptome sequencing (WGTS) is expected to transform diagnosis and treatment for patients with cancer. WGTS is a comprehensive precision diagnostic test that is starting to replace the standard of care for oncology molecular testing in health care systems around the world however, the implementation and widescale adoption of this best-in-class testing is lacking. Here, we address the barriers in integrating WGTS for cancer diagnostics and treatment selection and answer questions regarding utility in different cancer types, cost-effectiveness and affordability, and other practical considerations for WGTS implementation. We review the current studies implementing WGTS in health care systems and provide a synopsis of the clinical evidence and insights into practical considerations for WGTS implementation. We reflect on regulatory, costs, reimbursement, and incidental findings aspects of this test. WGTS is an appropriate comprehensive clinical test for many tumor types and can replace multiple, cascade testing approaches currently performed. Decreasing sequencing cost, increasing number of clinically relevant aberrations and discovery of more complex biomarkers of treatment response, should pave the way for health care systems and laboratories in implementing WGTS into clinical practice, to transform diagnosis and treatment for patients with cancer.
Variability and uncertainty of particle build-up on urban road surfaces
Publisher: Elsevier BV
Date: 11-2018
DOI: 10.1016/J.SCITOTENV.2018.05.384
Abstract: Particle build-up is a key stormwater pollutant process that is typically replicated using a power function with increasing antecedent dry days. Though the use of a power function is recommended by a range of researchers, its applicability is demonstrated primarily for residential roads. Particle build-up process is also subjected to significant variability due to catchment heterogeneity and variability associated with source characteristics such as traffic and land use. Variability in the build-up process and use of stereotypical coefficients can lead to significant model uncertainty. This study evaluates particle build-up characteristics on urban road surfaces using an extensive field investigation program, giving specific priority to industrial and commercial roads. Based on the outcomes, particle build-up process characteristics and respective uncertainties were evaluated and compared for road surfaces in residential, industrial and commercial areas. The study primarily found that both, industrial and commercial land uses generally manifested greater particle build-up loads compared to residential land uses. The study provides estimates for build-up coefficients for a range of land uses, including industrial and commercial with their potential uncertainties in build-up predictions. This provides new knowledge to improve stormwater quality modelling. Aside from land use, the proximity of sites to major road networks was also identified as a critical factor influencing the variability and uncertainty in particle build-up. Variability of the fraction of particles in the <75 μm size range with antecedent dry days exerts the most distinct influence on particle build-up variability across all land uses. The outcomes of this research study are expected to enhance stormwater quality monitoring, modelling and remediation, and thereby promoting greater protection of human and aquatic ecosystem health.
New conceptualisation of first flush phenomena in urban catchments
Publisher: Elsevier BV
Date: 03-2021
Shortfalls and Solutions for Meeting National and Global Conservation Area Targets
Publisher: Wiley
Date: 24-02-2015
DOI: 10.1111/CONL.12158
A multivariate approach to the identification of surrogate parameters for heavy metals in stormwater
Publisher: Springer Science and Business Media LLC
Date: 29-11-2013
Understanding the uncertainty associated with particle-bound pollutant build-up and wash-off: A critical review
Publisher: Elsevier BV
Date: 09-2016
DOI: 10.1016/J.WATRES.2016.06.013
Abstract: Accurate prediction of stormwater quality is essential for developing effective pollution mitigation strategies. The use of models incorporating simplified mathematical replications of pollutant processes is the common practice for determining stormwater quality. However, an inherent process uncertainty arises due to the intrinsic variability associated with pollutant processes, which has neither been comprehensively understood, nor well accounted for in uncertainty assessment of stormwater quality modelling. This review provides the context for defining and quantifying the uncertainty associated with pollutant build-up and wash-off on urban impervious surfaces based on the hypothesis that particle size is predominant in influencing process variability. Critical analysis of published research literature brings scientific evidence together in order to establish the fact that particle size changes with time, and different sized particles exhibit distinct behaviour during build-up and wash-off, resulting in process variability. Analysis of the different adsorption behaviour of particles confirmed that the variations in pollutant load and composition are influenced by particle size. Particle behaviour and variations in pollutant load and composition are related due to the strong affinity of pollutants such as heavy metals and hydrocarbons for specific particle size ranges. As such, the temporal variation in particle size is identified as the key to establishing a basis for assessing build-up and wash-off process uncertainty. Therefore, accounting for pollutant build-up and wash-off process variability, which is influenced by particle size, would facilitate the assessment of the uncertainty associated with modelling outcomes. Furthermore, the review identified fundamental knowledge gaps where further research is needed in relation to: (1) the aggregation of particles suspended in the atmosphere during build-up (2) particle re-suspension during wash-off (3) pollutant re-adsorption by different particle size fractions and (4) development of evidence-based techniques for assessing uncertainty and (5) methods for translating the knowledge acquired from the investigation of process mechanisms at small scale into catchment scale for stormwater quality modelling.
Hierarchy of factors which influence polycyclic aromatic hydrocarbons (PAHs) distribution in river sediments
Publisher: Elsevier BV
Date: 04-2017
DOI: 10.1016/J.ENVPOL.2016.12.034
Abstract: The sediment environment provides habitat for fauna and flora. As pollutants can interchange between water and sediments, pollution will exert a significant influence on the water environment. Previous studies on polycyclic aromatic hydrocarbon (PAHs) pollution of sediments have primarily focused on the comparison of concentrations between seasons, land uses and species. Studies on the identification of the hierarchy of factors which influence PAHs distribution and its variability in river sediments are limited. This paper discusses a comprehensive investigation into the inherent variability of PAHs in sediments and the primary factors which influence this variability. The study outcomes confirmed that key factors exerting influence on PAH distribution in sediments can be ranked in the order: land use > population > seasons. Accordingly, intensive urban land use was identified as the most important factor influencing PAHs distribution. Additionally, it was found that with increasing urban development, PAHs concentrations and their variability in sediments increase in terms of the molecular weight of different species. The study outcomes are expected to enhance management strategies to mitigate PAHs pollution of urban water environments including the prioritisation of factors requiring management and the selection of appropriate approaches in the context of cost-effectiveness.
Assessing the significance of climate and community factors on urban water demand
Publisher: Elsevier BV
Date: 12-2015
Impact of roof surface runoff on urban water quality
Publisher: IWA Publishing
Date: 10-2012
DOI: 10.2166/WST.2012.348
Abstract: The pollutant impacts of urban stormwater runoff on receiving waters are well documented in research literature. However, it is road surfaces that are commonly identified as the significant pollutant source. This paper presents the outcomes of an extensive program of research into the role of roof surfaces in urban water quality with particular focus on solids, nutrients and organic carbon. The outcomes confirmed that roof surfaces play an important role in influencing the pollutant characteristics of urban stormwater runoff. Pollutant build-up and wash-off characteristics for roads and roof surfaces were found to be appreciably different. The pollutant wash-off characteristics exhibited by roof surfaces show that it influences the first flush phenomenon more significantly than road surfaces. In most urban catchments, as roof surfaces constitute a higher fraction of impervious area compared with road surfaces, it is important that the pollutant generation role of roof surfaces is specifically taken into consideration in stormwater quality mitigation strategies.
Assessment of high density of onsite wastewater treatment systems on a shallow groundwater coastal aquifer using PCA
Publisher: Wiley
Date: 2005
DOI: 10.1002/ENV.698
Re-thinking classical mechanistic model for pollutant build-up on urban impervious surfaces
Publisher: Elsevier BV
Date: 02-2019
DOI: 10.1016/J.SCITOTENV.2018.09.013
Abstract: Accurate modelling of particulates build-up process is essential for designing effective stormwater management strategies. However, current modelling practice relies on the classical 'power model' which has limitations in accounting for the variability in the build-up process. This research study investigated the relationships between influential factors of the build-up process and coefficients in the power model. The outcomes showed that the coefficient, which determines the build-up rate, is predominantly influenced by land use factors (pervious area, road area, commercial area and residential area), such that land use factors exerted 23 times more influence than the site characteristics (distance to pervious area and road surface texture depth). The coefficient, which determines how quickly build-up reaches equilibrium, was found to be equally influenced by anthropogenic activities (sweeping frequency and traffic volume) and site characteristics. Further, site characteristics were found to play a major role in generating build-up process variability with three times more influence than that of anthropogenic activities. It was found that the power model satisfactorily replicates the build-up of particles 74 μm, a new coefficient, namely, 'coefficient of variability' was introduced in order to improve the prediction performance (up to 17% compared to original power model). The study outcomes provide a deeper understanding into particulates build-up modelling, and can contribute to the formulation of effective stormwater treatment strategies.
TGF-β1 induced S100 family protein expression is associated with epithelial to mesenchymal transition states and poor survival in pancreatic cancer
Publisher: Cold Spring Harbor Laboratory
Date: 26-02-2022
DOI: 10.1101/2022.02.25.481888
Abstract: Epithelial-mesenchymal transition (EMT) is a continuum that includes epithelial, partial EMT (P-EMT) and mesenchymal states, each of which are associated with cancer progression, invasive capabilities and ultimately metastasis. We have employed a lineage traced sporadic model of pancreatic cancer to generate a murine organoid biobank from primary and secondary tumors, including sublines that have undergone P-EMT and complete EMT (C-EMT). Using an unbiased proteomics approach, we found that the morphology of the organoids predicts the EMT state, with solid organoids associated with a P-EMT signature. We also observed that exogenous TGFβ1 induces a solid organoid morphology that is associated with changes in the S100 family, C-EMT and the formation of high-grade tumors. S100A4 may represent a useful biomarker to predict EMT state, disease progression and outcome for pancreatic cancer patients.
Effects of climate change on the wash-off of volatile organic compounds from urban roads
Publisher: Elsevier BV
Date: 09-2011
DOI: 10.1016/J.SCITOTENV.2011.06.032
Abstract: The predicted changes in rainfall characteristics due to climate change could adversely affect stormwater quality in highly urbanised coastal areas throughout the world. This in turn will exert a significant influence on the discharge of pollutants to estuarine and marine waters. Hence, an in-depth analysis of the effects of such changes on the wash-off of volatile organic compounds (VOCs) from urban roads in the Gold Coast region in Australia was undertaken. The rainfall characteristics were simulated using a rainfall simulator. Principal Component Analysis (PCA) and Multicriteria Decision tools such as PROMETHEE and GAIA were employed to understand the VOC wash-off under climate change. It was found that low, low to moderate and high rain events due to climate change will affect the wash-off of toluene, ethylbenzene, meta-xylene, para-xylene and ortho-xylene from urban roads in Gold Coast. Total organic carbon (TOC) was identified as predominant carrier of toluene, meta-xylene and para-xylene in 300 μm fractions under such dominant rain events due to climate change. However, ortho-xylene did not show such affinity towards either TOC or TSS (total suspended solids) under the simulated climatic conditions.
Implications of faecal indicator bacteria for the microbiological assessment of roof-harvested rainwater quality in southeast Queensland, Australia
Publisher: Canadian Science Publishing
Date: 06-2010
DOI: 10.1139/W10-037
Abstract: The study aimed to evaluate the suitability of Escherichia coli , enterococci, and Clostridium perfringens for assessing the microbiological quality of roof-harvested rainwater and assessing whether the concentrations of these faecal indicators can be used to predict the presence or absence of specific zoonotic bacterial or protozoan pathogens. From a total of 100 s les tested, 58%, 83%, and 46% of s les were found to be positive for, respectively, E. coli, enterococci, and Clostridium perfringens spores, as determined by traditional culture-based methods. Additionally, in the s les tested, 7%, 19%, 1%, 8%, 17%, and 15% were PCR positive for Aeromonas hydrophila lip, C ylobacter coli ceuE, C ylobacter jejuni mapA, Legionella pneumophila mip, Salmonella invA, and Giardia lamblia β-giardin genes, respectively. However, none of the s les was positive for E. coli O157 lipopolysaccharide, verocytotoxin 1, and verocytotoxin 2 and Cryptosporidium parvum oocyst wall protein genes. The presence or absence of these potential pathogens did not correlate with any of the faecal indicator bacterial concentrations as determined by a binary logistic regression model. The roof-harvested rainwater s les tested in this study appeared to be of poor microbiological quality, and no significant correlation was found between the concentration of faecal indicators and pathogenic microorganisms. The use of faecal indicator bacteria raises questions regarding their reliability in assessing the microbiological quality of water and particularly their poor correlation with pathogenic microorganisms. The presence of one or more zoonotic pathogens suggests that the microbiological analysis of water should be performed and that appropriate treatment measures should be undertaken, especially in tanks where the water is used for drinking.
Incorporating process variability into stormwater quality modelling
Publisher: Elsevier BV
Date: 11-2015
DOI: 10.1016/J.SCITOTENV.2015.07.008
Abstract: Process variability in pollutant build-up and wash-off generates inherent uncertainty that affects the outcomes of stormwater quality models. Poor characterisation of process variability constrains the accurate accounting of the uncertainty associated with pollutant processes. This acts as a significant limitation to effective decision making in relation to stormwater pollution mitigation. The study undertaken developed three theoretical scenarios based on research findings that variations in particle size fractions 150 μm during pollutant build-up and wash-off primarily determine the variability associated with these processes. These scenarios, which combine pollutant build-up and wash-off processes that takes place on a continuous timeline, are able to explain process variability under different field conditions. Given the variability characteristics of a specific build-up or wash-off event, the theoretical scenarios help to infer the variability characteristics of the associated pollutant process that follows. Mathematical formulation of the theoretical scenarios enables the incorporation of variability characteristics of pollutant build-up and wash-off processes in stormwater quality models. The research study outcomes will contribute to the quantitative assessment of uncertainty as an integral part of the interpretation of stormwater quality modelling outcomes.
Surrogate Measures to Assess Mobility of People as a Resilience Indicator in Disaster Management: An Exploratory Study in Southeastern Sri Lanka
Publisher: Springer Science and Business Media LLC
Date: 02-2020
DOI: 10.1007/S13753-020-00251-4
Abstract: Understanding social resilience can assist in the formulation of disaster management policies to help communities better prepare for, respond to, and recover from disasters. However, direct social resilience measurement methods such as household surveys are not always a practical option as they are a time- and resource-exhaustive process. Existing measures mainly utilize publicly available census data, which often provide a poor and outdated assessment of current social resilience status. Another limitation includes a failure to capture multiple facets of indicators that are process-oriented and dynamic in nature such as mobility of people. These challenges can be addressed by employing a surrogate approach. Surrogates are alternative measures to depict the target indicator. The surrogate approach can capture key facets of a target indicator, which can be used as potential measures for the target indicator. A framework to conceptualize the surrogate approach is presented, and operationalized using a case study approach on the southeastern coast of Sri Lanka to identify surrogates to measure mobility of people as a resilience indicator. Six higher-order themes were identified as potential surrogates to measure mobility of people in a disaster context. The approach proposed to methodically identify potential surrogates and their measurement protocols can help to improve the current knowledge base and understanding of complex interrelationships of social resilience.
S100 family proteins are linked to organoid morphology and EMT in pancreatic cancer
Publisher: Springer Science and Business Media LLC
Date: 24-02-2023
DOI: 10.1038/S41418-023-01126-Z
Abstract: Epithelial-mesenchymal transition (EMT) is a continuum that includes epithelial, partial EMT, and mesenchymal states, each of which is associated with cancer progression, invasive capabilities, and ultimately, metastasis. We used a lineage-traced sporadic model of pancreatic cancer to generate a murine organoid biobank from primary and secondary tumors, including sublines that underwent partial EMT and complete EMT. Using an unbiased proteomics approach, we found that organoid morphology predicts the EMT state, and the solid organoids are associated with a partial EMT signature. We also observed that exogenous TGFβ1 induces solid organoid morphology that is associated with changes in the S100 family, complete EMT, and the formation of high-grade tumors. S100A4 may be a useful biomarker for predicting EMT state, disease progression, and outcome in patients with pancreatic cancer.
Determination of a set of surrogate parameters to assess urban stormwater quality
Publisher: Elsevier BV
Date: 11-2010
DOI: 10.1016/J.SCITOTENV.2010.09.015
Abstract: This paper presents the outcomes of a research project, which focused on developing a set of surrogate parameters to evaluate urban stormwater quality using simulated rainfall. Use of surrogate parameters has the potential to enhance the rapid generation of urban stormwater quality data based on on-site measurements and thereby reduce resource intensive laboratory analysis. The s les collected from rainfall simulations were tested for a range of physico-chemical parameters which are key indicators of nutrients, solids and organic matter. The analysis revealed that [total dissolved solids (TDS) and dissolved organic carbon (DOC)] [total solids (TS) and total organic carbon (TOC)] [turbidity (TTU)] [electrical conductivity (EC)] [TTU and EC] as appropriate surrogate parameters for dissolved total nitrogen (DTN), total phosphorus (TP), total suspended solids (TSS), TDS and TS respectively. Relationships obtained for DTN-TDS, DTN-DOC, and TP-TS demonstrated good portability potential. The portability of the relationship developed for TP and TOC was found to be unsatisfactory. The relationship developed for TDS-EC and TS-EC also demonstrated poor portability.
Adsorption-desorption behavior of heavy metals in aquatic environments
Publisher: Elsevier BV
Date: 2022
Biosorption of heavy metals
Publisher: Elsevier BV
Date: 05-2022
DOI: 10.1016/J.CHEMOSPHERE.2022.133659
Abstract: The design of an industrial water treatment system using sorption is based on laboratory column tests. To verify the applicability of a column sorption system at industrial scale, it is necessary to determine the system's breakthrough time (BT) in a laboratory setting. In a laboratory column set-up, BT is referred to as the time taken by the adsorbate to appear at column outlet for the first time. This is when the mass transfer zone (MTZ), where the equilibrium sorption occurs, reaches the end of the sorbent bed. However, such laboratory set-up requires significant resources including laboratory space, time and multiple trials, which is the opposite to the batch experimental approach that is commonly used to assess efficiency of sorbents. This study identified batch sorption parameters that can be used to determine BT for a column sorption setting for three toxic heavy metals commonly found in industrial wastewater, namely, Pb
Understanding the role of land use for urban stormwater management in coastal waterways
Publisher: Elsevier BV
Date: 10-2023
Influence of traffic characteristics on polycyclic aromatic hydrocarbon build-up on urban road surfaces
Publisher: Springer Science and Business Media LLC
Date: 10-04-2014
Integrated Risk Framework for Onsite Wastewater Treatment Systems
Publisher: Springer Science and Business Media LLC
Date: 15-06-2006
DOI: 10.1007/S00267-005-0280-5
Abstract: Onsite wastewater treatment systems (OWTS) are becoming increasingly important for the treatment and dispersal of effluent in new urbanised developments that are not serviced by centralised wastewater collection and treatment systems. However, the current standards and guidelines adopted by many local authorities for assessing suitable site and soil conditions for OWTS are increasingly coming under scrutiny due to the public health and environmental impacts caused by poorly performing systems, in particular septic tank-soil adsorption systems. In order to achieve sustainable onsite wastewater treatment with minimal impacts on the environment and public health, more appropriate means of assessment are required. This paper highlights an integrated risk based approach for assessing the inherent hazards associated with OWTS in order to manage and mitigate the environmental and public health risks inherent with onsite wastewater treatment. In developing a sound and cohesive integrated risk framework for OWTS, several key issues must be recognised. These include the inclusion of relevant stakeholders throughout framework development, the integration of scientific knowledge, data and analysis with risk assessment and management ideals, and identification of the appropriate performance goals for successful management and mitigation of associated risks. These issues were addressed in the development of the risk framework to provide a generic approach to assessing risk from OWTS. The utilisation of the developed risk framework for achieving more appropriate assessment and management techniques for OWTS is presented in a case study for the Gold Coast region, Queensland State, Australia.
Influence of land use configurations on river sediment pollution
Publisher: Elsevier BV
Date: 10-2017
DOI: 10.1016/J.ENVPOL.2017.06.076
Abstract: Land use is an influential factor in river sediment pollution. However, land use type alone is found to be inadequate to explain pollutant contributions to the aquatic environment since configurations within the same land use type such as land cover and development layout could also exert an important influence. Consequently, this paper discusses a research study, which consisted of an in-depth investigation into the relationship between land use type and river sediment pollution by introducing robust parameters that represent configurations within the primary land use types. Urban water pollutants, namely, nutrients, total carbon, polycyclic aromatic hydrocarbons and metals were investigated in the study. The outcomes show that higher patch density and more erse land use development forms contribute relatively greater pollutant loads to receiving waters and consequently leading to higher sediment pollution. The study outcomes are expected to contribute essential knowledge for creating robust management strategies to minimise waterway pollution and thereby protect the health of aquatic ecosystems.
Methyl‐CpG binding domain 4, DNA glycosylase (MBD4)‐associated neoplasia syndrome associated with a homozygous missense variant in MBD4: Expansion of an emerging phenotype
Publisher: Wiley
Date: 05-04-2022
DOI: 10.1111/BJH.18178
Enrichment, distribution and sources of heavy metals in the sediments of Deception Bay, Queensland, Australia
Publisher: Elsevier BV
Date: 04-2014
DOI: 10.1016/J.MARPOLBUL.2014.01.031
Abstract: Sediment s les from 13 s ling sites in Deception Bay, Australia were analysed for the presence of heavy metals. Enrichment factors, modified contamination indices and Nemerow pollution indices were calculated for each s ling site to determine sediment quality. The results indicate significant pollution of most sites by lead (average enrichment factor (EF) of 13), but there is also enrichment of arsenic (average EF 2.3), zinc (average EF 2.7) and other heavy metals. The modified degree of contamination indices (average 1.0) suggests that there is little contamination. By contrast, the Nemerow pollution index (average 5.8) suggests that Deception Bay is heavily contaminated. Cluster analysis was undertaken to identify groups of elements. Strong correlation between some elements and two distinct clusters of s ling sites based on sediment type was evident. These results have implications for pollution in complex marine environments where there is significant influx of sand and sediment into an estuarine environment.
Behaviour of metals in an urban river and the pollution of estuarine environment
Publisher: Elsevier BV
Date: 11-2019
DOI: 10.1016/J.WATRES.2019.114911
Abstract: The high pollutant loads discharged from cities pose risks to urban waterways, and in turn the estuarine environments, making it challenging to improve urban liveability. Past studies on the behaviour of pollutants in rivers have largely investigated their transport along the waterway, primarily focusing on the movement of water and sediment. However, the current approaches in pollutant transport modelling provide limited insights into how pollutant transfer between water and sediment phases influences their transport from the upstream towards the estuarine environment. This research study firstly identified typical patterns of metal loads along an urban river in a highly populated city in China. The outcomes were then used to conceptualise metal transfer between water and sediment phases. It was noted that physico-chemical characteristics of water and sediments play a key role in metal transfer between the two phases, and the dominant transfer path (sediment to water/water to sediment) is different between different metals, independent of their origin (crustal, anthropogenic or marine-related). Several scenarios were derived from the conceptualisation of metal behaviour. These in turn were then used to develop real-world scenarios of metal transport in rivers based on the field data. The conceptualisation of metal behaviour confirmed that each metal is likely to have a dominant phase of transport (sediment/water), which is influenced by the dominant transfer path of that metal between water and sediments.
Role of organic matter, nitrogen and phosphorous on granulation and settling velocity in wastewater treatment
Publisher: Elsevier BV
Date: 04-2021
Influence of uncertainty inherent to heavy metal build-up and wash-off on stormwater quality
Publisher: Elsevier BV
Date: 03-2016
DOI: 10.1016/J.WATRES.2016.01.028
Abstract: Uncertainty inherent to heavy metal build-up and wash-off stems from process variability. This results in inaccurate interpretation of stormwater quality model predictions. The research study has characterised the variability in heavy metal build-up and wash-off processes based on the temporal variations in particle-bound heavy metals commonly found on urban roads. The study outcomes found that the distribution of Al, Cr, Mn, Fe, Ni, Cu, Zn, Cd and Pb were consistent over particle size fractions 150 μm, with most metals concentrated in the particle size fraction <150 μm. When build-up and wash-off are considered as independent processes, the temporal variations in these processes in relation to the heavy metals load are consistent with variations in the particulate load. However, the temporal variations in the load in build-up and wash-off of heavy metals and particulates are not consistent for consecutive build-up and wash-off events that occur on a continuous timeline. These inconsistencies are attributed to interactions between heavy metals and particulates 150 μm, which are influenced by particle characteristics such as organic matter content. The behavioural variability of particles determines the variations in the heavy metals load entrained in stormwater runoff. Accordingly, the variability in build-up and wash-off of particle-bound pollutants needs to be characterised in the description of pollutant attachment to particulates in stormwater quality modelling. This will ensure the accounting of process uncertainty, and thereby enhancing the interpretation of the outcomes derived from modelling studies.
Gaps and opportunities for the World Heritage Convention to contribute to global wilderness conservation.
Publisher: Wiley
Date: 06-12-2018
DOI: 10.1111/COBI.12976
Abstract: Wilderness areas are ecologically intact landscapes predominantly free of human uses, especially industrial-scale activities that result in substantial biophysical disturbance. This definition does not exclude land and resource use by local communities who depend on such areas for subsistence and bio-cultural connections. Wilderness areas are important for bio ersity conservation and sustain key ecological processes and ecosystem services that underpin planetary life-support systems. Despite these widely recognized benefits and values of wilderness, they are insufficiently protected and are consequently being rapidly eroded. There are increasing calls for multilateral environmental agreements to make a greater and more systematic contribution to wilderness conservation before it is too late. We created a global map of remaining terrestrial wilderness following the established last-of-the-wild method, which identifies the 10% of areas with the lowest human pressure within each of Earth's 62 biogeographic realms and identifies the 10 largest contiguous areas and all contiguous areas >10,000 km
Fecal indicators and bacterial pathogens in bottled water from Dhaka, Bangladesh
Publisher: FapUNIFESP (SciELO)
Date: 2013
Creating a hierarchy of hazard control for urban stormwater management
Publisher: Elsevier BV
Date: 12-2019
DOI: 10.1016/J.ENVPOL.2019.113217
Abstract: Urban stormwater reuse is becoming increasingly prevalent to overcome the serious urban water scarcity being experienced around the world. Therefore, the adoption of reliable approaches to minimise the human health risk posed by pollutants commonly present in urban stormwater such as heavy metals and polycyclic aromatic hydrocarbons (PAHs) is critical for safe stormwater reuse. This study collected a total of 40 pollutant build-up s les and analysed the concentrations of nine heavy metals and 15 PAH species. Based on pollutant build-up data, pollutant concentrations in stormwater were estimated through modelling. Risk assessment was conducted using an existing model developed by previous studies. The study outcomes confirmed that simply evaluating the in idual pollutant concentrations based on guideline threshold values cannot comprehensively estimate the overall human health risk posed by these pollutants. Accordingly, it is recommended that the assessment of the overall human health risk should be based on the pollutant mix present as provided by the models discussed in this paper. The study also demonstrated the practical application of a robust risk assessment model to derive the hierarchy of hazard control to provide a reliable underpinning to urban stormwater risk management. The outcomes suggest that decentralised hazard control methods such as the provision of custom designed Water Sensitive Urban Design (WSUD) measures can be implemented in priority areas with high risk from stormwater pollution based on the risk assessment undertaken. Distributed hazard control methods can be applied to reduce the generation of primary toxic pollutants, especially chromium (Cr) and heavy PAHs, through elimination and substitution measures. The percentage reduction in traffic volume required to mitigate the human health risk can be quantified through the risk models presented. The study outcomes will contribute to the development of efficient, targeted and reliable stormwater management strategies and to identify viable opportunities for stormwater reuse.
Evaluation of pollutant build-up and wash-off from selected land uses at the Port of Brisbane, Australia
Publisher: Elsevier BV
Date: 02-2009
DOI: 10.1016/J.MARPOLBUL.2008.09.025
Abstract: The quality of stormwater runoff from seaports can be an important source of pollution to the marine environment. Currently, little knowledge exists with regards to the pollutant generation capacity specific to seaports as they do not necessarily compare well with conventional urban land use. The research project focussed on the assessment of pollutant build-up and wash-off. The study was undertaken using rainfall simulation and small impervious plots for different port land uses with the results obtained compared to typical urban land uses. The study outcomes confirmed that the Port land uses exhibit comparatively lower pollutant concentrations. However, the pollutant characteristics varied across different land uses. Hence, the provision of stereotypical water quality improvement measures could be of limited value. Particle size < 150microm was predominant in suspended solids. Therefore, if suspended solids are targeted as the surrogate parameter for water quality improvement, this particle size range needs to be removed.
Author Correction: High-coverage whole-genome analysis of 1220 cancers reveals hundreds of genes deregulated by rearrangement-mediated cis-regulatory alterations
Publisher: Springer Science and Business Media LLC
Date: 08-12-2022
Proliferation drives quorum sensing of microbial products in human macrophage populations
Publisher: Cold Spring Harbor Laboratory
Date: 12-05-2022
DOI: 10.1101/2022.05.12.491598
Abstract: Macrophages coordinate the initial host inflammatory response to tissue infection, as well as mediating the reparative phase, by producing growth factors that promote tissue repair. One model of this functional dichotomy is that peripherally recruited monocyte-derived macrophages drive acute inflammatory responses to infection, whereas tissue-resident macrophages are responsible for tissue repair. Alternatively, inflammation and repair may be inter-dependent molecular programs, such that both recruited and resident cells have equivalent capacity to contribute. Repeated exposure to pathogenic challenge results in innate tolerance, which may also alter the contributions of discrete macrophage populations to inflammation or repair. In this study a village model of tissue resident and recruited macrophages was created using induced pluripotent stem cell-derived macrophages and peripheral blood monocyte-derived macrophages, respectively. Population responses to repeated exposure to lipopolysaccharide were assessed with single-cell RNA sequencing and donors demultiplexed with Vireo. A subset of genes escaped classical tolerance programs in the iPSC, but not monocyte-derived macrophages, and this was associated with differences in their proliferative capacity. This suggests that targeting the proliferative resident macrophages would be most effective to limit inflammatory signaling.
Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing
Publisher: Springer Science and Business Media LLC
Date: 05-02-2020
DOI: 10.1038/S41588-019-0576-7
Abstract: Chromothripsis is a mutational phenomenon characterized by massive, clustered genomic rearrangements that occurs in cancer and other diseases. Recent studies in selected cancer types have suggested that chromothripsis may be more common than initially inferred from low-resolution copy-number data. Here, as part of the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA), we analyze patterns of chromothripsis across 2,658 tumors from 38 cancer types using whole-genome sequencing data. We find that chromothripsis events are pervasive across cancers, with a frequency of more than 50% in several cancer types. Whereas canonical chromothripsis profiles display oscillations between two copy-number states, a considerable fraction of events involve multiple chromosomes and additional structural alterations. In addition to non-homologous end joining, we detect signatures of replication-associated processes and templated insertions. Chromothripsis contributes to oncogene lification and to inactivation of genes such as mismatch-repair-related genes. These findings show that chromothripsis is a major process that drives genome evolution in human cancer.
Particulate matter exchange between atmosphere and roads surfaces in urban areas
Publisher: Elsevier BV
Date: 12-2020
Sustainability Evaluation of the Stormwater Drainage System in Six Indian Cities
Publisher: MDPI AG
Date: 16-10-2023
DOI: 10.3390/SU152014906
Quantitative assessment of human health risk posed by polycyclic aromatic hydrocarbons in urban road dust
Publisher: Elsevier BV
Date: 2017
DOI: 10.1016/J.SCITOTENV.2016.09.148
Abstract: Among the numerous pollutants present in urban road dust, polycyclic aromatic hydrocarbons (PAHs) are among the most toxic chemical pollutants and can pose cancer risk to humans. The primary aim of the study was to develop a quantitative model to assess the cancer risk from PAHs in urban road dust based on traffic and land use factors and thereby to characterise the risk posed by PAHs in fine ( 150μm) particles. The risk posed by PAHs was quantified as incremental lifetime cancer risk (ILCR), which was modelled as a function of traffic volume and percentages of different urban land uses. The study outcomes highlighted the fact that cancer risk from PAHs in urban road dust is primarily influenced by PAHs associated with fine solids. Heavy PAHs with 5 to 6 benzene rings, especially dibenzo[a,h]anthracene (D[a]A) and benzo[a]pyrene (B[a]P) in the mixture contribute most to the risk. The quantitative model developed based on traffic and land use factors will contribute to informed decision making in relation to the management of risk posed by PAHs in urban road dust.
Characterising metal build-up on urban road surfaces
Publisher: Elsevier BV
Date: 05-2013
DOI: 10.1016/J.ENVPOL.2013.01.021
Abstract: Reliable approaches for predicting pollutant build-up are essential for accurate urban stormwater quality modelling. Based on the in-depth investigation of metal build-up on residential road surfaces, this paper presents empirical models for predicting metal loads on these surfaces. The study investigated metals commonly present in the urban environment. Analysis undertaken found that the build-up process for metals primarily originating from anthropogenic (copper and zinc) and geogenic (aluminium, calcium, iron and manganese) sources were different. Chromium and nickel were below detection limits. Lead was primarily associated with geogenic sources, but also exhibited a significant relationship with anthropogenic sources. The empirical prediction models developed were validated using an independent data set and found to have relative prediction errors of 12-50%, which is generally acceptable for complex systems such as urban road surfaces. Also, the predicted values were very close to the observed values and well within 95% prediction interval.
The prediction of flood damage in coastal urban areas
Publisher: IOP Publishing
Date: 2020
DOI: 10.1088/1755-1315/419/1/012136
Abstract: The increase of impervious surfaces in the urban area triggers a flood. A flood occurs area with a dense population that will result in a lot of damage. The flood simulation itself is not adequate to calculate the flood damage, as it only shows the flood depth and extent. It needs the capability of mapping software to map the vulnerable area. Accordingly, the research study’s aim is to propose the methodology to predict the flood damage on the coastal urban area by combining the flood simulation model with GIS mapping software. MIKE FLOOD and ArcGIS were used to represent the flood simulation model and mapping software. The flood depth and inundation area were calculated with MIKE FLOOD meanwhile, the residential house was mapped using ArcGIS. Both of MIKE FLOOD and ArcGIS were then combined to obtain the flood depth in each residential house. Moreover, to value the flood damage in monetary terms, the depth-damage curve and average house prices were applied. The result shows that the majority of the inundation caused by riverine flood and coastal area is the place where the largest inundation area occurs. As the flood appears in a residential area, the flood damage of the residential building in terms of annual average damage (AAD) was obtained with the amount of $8,716,227.67 calculated from six AEPs (50%, 20%, 10%, 5%, 2%, and 1%).
Human Health Risk Assessment of Toxic Chemical Pollutants in Stormwater
Publisher: Springer Nature Singapore
Date: 2023
Nitrate-dependent Uranium mobilisation in groundwater
Publisher: Elsevier BV
Date: 11-2019
DOI: 10.1016/J.SCITOTENV.2019.133655
Abstract: Nitrate is a critical substance that determines the prevailing redox conditions in groundwater, and in turn the behaviour of Uranium (U). Therefore, the excessive use of nitrate-fertiliser in agricultural catchments could exert a significant influence on U mobilisation. This is a significant issue in catchments, where groundwater resources are increasingly being exploited for drinking water production. Past studies on U mobility in groundwater have considered in idual hydro-geochemical factors influencing U concentrations, rather than as a single system with multiple factors. This research study investigated nitrate-dependent U mobility within a catchment in Brazil, where a range of intensive agricultural activities are undertaken and the giant Guarani aquifer is located. The study used direct measurements of groundwater redox conditions and other hydro-geochemical parameters. The research outcomes indicated that U could have two hydro-geochemical systems based on positive and negative redox potential of groundwater. The pH, HCO
A Bayesian regression approach to assess uncertainty in pollutant wash-off modelling
Publisher: Elsevier BV
Date: 05-2014
DOI: 10.1016/J.SCITOTENV.2014.02.012
Abstract: Due to knowledge gaps in relation to urban stormwater quality processes, an in-depth understanding of model uncertainty can enhance decision making. Uncertainty in stormwater quality models can originate from a range of sources such as the complexity of urban rainfall-runoff-stormwater pollutant processes and the paucity of observed data. Unfortunately, studies relating to epistemic uncertainty, which arises from the simplification of reality are limited and often deemed mostly unquantifiable. This paper presents a statistical modelling framework for ascertaining epistemic uncertainty associated with pollutant wash-off under a regression modelling paradigm using Ordinary Least Squares Regression (OLSR) and Weighted Least Squares Regression (WLSR) methods with a Bayesian/Gibbs s ling statistical approach. The study results confirmed that WLSR assuming probability distributed data provides more realistic uncertainty estimates of the observed and predicted wash-off values compared to OLSR modelling. It was also noted that the Bayesian/Gibbs s ling approach is superior compared to the most commonly adopted classical statistical and deterministic approaches commonly used in water quality modelling. The study outcomes confirmed that the predication error associated with wash-off replication is relatively higher due to limited data availability. The uncertainty analysis also highlighted the variability of the wash-off modelling coefficient k as a function of complex physical processes, which is primarily influenced by surface characteristics and rainfall intensity.
Enhancing the storm water treatment performance of constructed wetlands and bioretention basins [SpringerBriefs in Water Science and Technology]
Publisher: Springer Singapore
Date: 2016
Atmospheric deposition as a source of heavy metals in urban stormwater
Publisher: Elsevier BV
Date: 04-2013
Determination of refractive and volatile elements in sediment using laser ablation inductively coupled plasma mass spectrometry
Publisher: Elsevier BV
Date: 10-2015
DOI: 10.1016/J.ACA.2015.09.033
Abstract: Wet-milling protocol was employed to produce pressed powder tablets with excellent cohesion and homogeneity suitable for laser ablation (LA) analysis of volatile and refractive elements in sediment. The influence of s le preparation on analytical performance was also investigated, including s le homogeneity, accuracy and limit of detection. Milling in volatile solvent for 40 min ensured s le is well mixed and could reasonably recover both volatile (Hg) and refractive (Zr) elements. With the exception of Cr (-52%) and Nb (+26%) major, minor and trace elements in STSD-1 and MESS-3 could be analysed within ±20% of the certified values. Comparison of the method with total digestion method using HF was tested by analysing 10 different sediment s les. The laser method recovers significantly higher amounts of analytes such as Ag, Cd, Sn and Sn than the total digestion method making it a more robust method for elements across the periodic table. LA-ICP-MS also eliminates the interferences from chemical reagents as well as the health and safety risks associated with digestion processes. Therefore, it can be considered as an enhanced method for the analysis of heterogeneous matrices such as river sediments.
Influence of traffic on build-up of polycyclic aromatic hydrocarbons on urban road surfaces: A Bayesian network modelling approach
Publisher: Elsevier BV
Date: 06-2018
DOI: 10.1016/J.ENVPOL.2017.10.125
Abstract: Due to their carcinogenic effects, Polycyclic Aromatic Hydrocarbons (PAHs) deposited on urban surfaces are a major concern in the context of stormwater pollution. However, the design of effective pollution mitigation strategies is challenging due to the lack of reliability in stormwater quality modelling outcomes. Current modelling approaches do not adequately replicate the interdependencies between pollutant processes and their influential factors. Using Bayesian Network modelling, this research study characterised the influence of vehicular traffic on the build-up of the sixteen US EPA classified priority PAHs. The predictive analysis was conditional on the structure of the proposed BN, which can be further improved by including more variables. This novel modelling approach facilitated the characterisation of the influence of traffic as a source of origin and also as a key factor that influences the re-distribution of PAHs, with positive or negative relationship between traffic volume and PAH build-up. It was evident that the re-distribution of particle-bound PAHs is determined by the particle size rather than the chemical characteristics such as volatility. Moreover, compared to commercial and residential land uses, mostly industrial land use contributes to the PAHs load released to the environment. Carcinogenic PAHs in industrial areas are likely to be associated with finer particles, while PAHs, which are not classified as human carcinogens, are likely to be found in the coarser particle fraction.
Removal of polycyclic aromatic hydrocarbons from wastewater using dual‐mode ultrasound system
Publisher: Wiley
Date: 15-11-2020
DOI: 10.1111/WEJ.12540
Dataset for the quantitative structure-activity relationship (QSAR) modeling of the toxicity equivalency factors (TEFs) of PAHs and transformed PAH products
Publisher: Elsevier BV
Date: 02-2020
Mathematical relationships for metal build-up on urban road surfaces based on traffic and land use characteristics
Publisher: Elsevier BV
Date: 03-2014
DOI: 10.1016/J.CHEMOSPHERE.2013.10.068
Abstract: The study investigated the influence of traffic and land use parameters on metal build-up on urban road surfaces. Mathematical relationships were developed to predict metals originating from fuel combustion and vehicle wear. The analysis undertaken found that nickel and chromium originate from exhaust emissions, lead, copper and zinc from vehicle wear, cadmium from both exhaust and wear and manganese from geogenic sources. Land use does not demonstrate a clear pattern in relation to the metal build-up process, though its inherent characteristics such as traffic activities exert influence. The equation derived for fuel related metal load has high cross-validated coefficient of determination (Q(2)) and low Standard Error of Cross-Validation (SECV) values which indicates that the model is reliable, while the equation derived for wear-related metal load has low Q(2) and high SECV values suggesting its use only in preliminary investigations. Relative Prediction Error values for both equations are considered to be well within the error limits for a complex system such as an urban road surface. These equations will be beneficial for developing reliable stormwater treatment strategies in urban areas which specifically focus on mitigation of metal pollution.
Author Correction: Pathway and network analysis of more than 2500 whole cancer genomes
Publisher: Springer Science and Business Media LLC
Date: 08-12-2022
Pan-cancer analysis of whole genomes
Publisher: Springer Science and Business Media LLC
Date: 05-02-2020
DOI: 10.1038/S41586-020-1969-6
Abstract: Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale 1–3 . Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4–5 driver mutations when combining coding and non-coding genomic elements however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution in acral melanoma, for ex le, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter 4 identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation 5,6 analyses timings and patterns of tumour evolution 7 describes the erse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity 8,9 and evaluates a range of more-specialized features of cancer genomes 8,10–18 .
BRAF mutations in low-grade serous ovarian cancer and response to BRAF inhibition
Publisher: American Society of Clinical Oncology (ASCO)
Date: 11-2018
DOI: 10.1200/PO.17.00221
Abstract: Low-grade serous ovarian carcinoma (LGSC) responds poorly to chemotherapy and is characterized by activating mutations in the Ras sarcoma–mitogen-activated protein kinase (RAS-MAPK) pathway, including oncogenic BRAF. However, response to BRAF inhibitors is tumor-type specific. Significant improvement in survival is seen in patients with BRAF-mutant melanoma, but other cancer types, such as colorectal cancers, are generally less sensitive. We examined the frequency and characteristics of BRAF-mutated LGSC and described the response to treatment with BRAF inhibitors. Mutations were assessed in LGSC (N = 65) by using targeted, exome, and whole-genome sequencing. Patient characteristics, treatment, and clinical outcome were assessed, and the median follow-up time was more than 5 years. BRAF inhibitors were trialed in two patients with a somatic BRAF V600E mutation: one patient received dabrafenib monotherapy and was monitored clinically, biochemically (cancer antigen [CA]-125 levels), and with positron emission tomography (PET) imaging. Expression of the BRAF V600E protein in this patient was assessed by immunohistochemistry. Among patients with LGSC, nine (13.8%) of 65 had a somatic BRAF mutation. Of the nine patients with BRAF mutation–positive LGSC, four experienced progressive disease that did not respond to conventional chemotherapy. Two of the patients experienced progression quickly and died as a result of disease progression, and two received targeted treatment. Two patients with BRAF V600E mutation received BRAF inhibitors at relapse and both achieved durable responses. BRAF mutations are not uncommon in patients with LGSC and should be routinely tested, because BRAF inhibitors can be an effective treatment for these patients. The results highlight the need for targeted treatment in this rare tumor type, and a prospective study is needed to formally assess the response rate and clinical benefit.
Kinetic modelling and performance evaluation of vertical subsurface flow constructed wetlands in tropics
Publisher: Elsevier BV
Date: 12-2020
Solubilization and degradation of polychlorinated biphenyls (PCBs) by naturally occurring facultative anaerobic bacteria
Publisher: Elsevier BV
Date: 02-2019
DOI: 10.1016/J.SCITOTENV.2018.10.127
Abstract: A combination of solubilization and degradation is essential for the bioremediation of environments contaminated with complex polychlorinated biphenyls (PCB) mixtures. However, the application of facultative anaerobic microorganisms that can both solubilize and breakdown hydrophobic PCBs in aqueous media under both anaerobic and aerobic conditions, has not been reported widely. In this comprehensive study, four bacteria discovered from soil and sediments and identified as Achromobacter sp. NP03, Ochrobactrum sp. NP04, Lysinibacillus sp. NP05 and Pseudomonas sp. NP06, were investigated for their PCB degradation efficiencies. Aroclor 1260 (50 mg/L), a commercial and highly chlorinated PCB mixture was exposed to the different bacterial strains under aerobic, anaerobic and two stage anaerobic-aerobic conditions. The results confirmed that all four facultative anaerobic microorganisms were capable of degrading PCBs under both anaerobic and aerobic conditions. The highest chlorine removal (9.16 ± 0.8 mg/L), PCB solubility (14.7 ± 0.93 mg/L) and growth rates as OD
DNA methylation patterns identify subgroups of pancreatic neuroendocrine tumors with clinical association
Publisher: Springer Science and Business Media LLC
Date: 03-02-2021
DOI: 10.1038/S42003-020-01469-0
Abstract: Here we report the DNA methylation profile of 84 sporadic pancreatic neuroendocrine tumors (PanNETs) with associated clinical and genomic information. We identified three subgroups of PanNETs, termed T1, T2 and T3, with distinct patterns of methylation. The T1 subgroup was enriched for functional tumors and ATRX , DAXX and MEN1 wild-type genotypes. The T2 subgroup contained tumors with mutations in ATRX , DAXX and MEN1 and recurrent patterns of chromosomal losses in half of the genome with no association between regions with recurrent loss and methylation levels. T2 tumors were larger and had lower methylation in the MGMT gene body, which showed positive correlation with gene expression. The T3 subgroup harboured mutations in MEN1 with recurrent loss of chromosome 11, was enriched for grade G1 tumors and showed histological parameters associated with better prognosis. Our results suggest a role for methylation in both driving tumorigenesis and potentially stratifying prognosis in PanNETs.
Evaluation of multiple sewage-associated Bacteroides PCR markers for sewage pollution tracking
Publisher: Elsevier BV
Date: 11-2009
DOI: 10.1016/J.WATRES.2009.08.042
Abstract: The host specificity of the five published sewage-associated Bacteroides markers (i.e., HF183, BacHum, HuBac, BacH and Human-Bac) was evaluated in Southeast Queensland, Australia by testing fecal DNA s les (n=186) from 11 animal species including human fecal s les collected via influent to a sewage treatment plant (STP). All human fecal s les (n=50) were positive for all five markers indicating 100% sensitivity of these markers. The overall specificity of the HF183 markers to differentiate between humans and animals was 99%. The specificities of the BacHum and BacH markers were>94%, suggesting that these markers are suitable for the detection of sewage pollution in environmental waters in Australia. The HuBac (i.e., 63%) and Human-Bac (i.e., 79% specificity) markers performed poorly in distinguishing between the sources of human and animal fecal s les. It is recommended that the specificity of the sewage-associated markers must be rigorously tested prior to its application to identify the sources of fecal pollution in environmental waters.
Fees and governance: Towards sustainability in water resources management at schools in post-apartheid South Africa
Publisher: Elsevier BV
Date: 11-2019
Application of Chlorella pyrenoidosa embedded biochar beads for water treatment
Publisher: Elsevier BV
Date: 04-2021
Emerging materials and technologies for landfill leachate treatment: A critical review
Publisher: Elsevier BV
Date: 12-2021
Single-nuclei and bulk-tissue gene-expression analysis of pheochromocytoma and paraganglioma links disease subtypes with tumor microenvironment
Publisher: Springer Science and Business Media LLC
Date: 21-10-2022
DOI: 10.1038/S41467-022-34011-3
Abstract: Pheochromocytomas (PC) and paragangliomas (PG) are rare neuroendocrine tumors associated with autonomic nerves. Here we use single-nuclei RNA-seq and bulk-tissue gene-expression data to characterize the cellular composition of PCPG and normal adrenal tissues, refine tumor gene-expression subtypes and make clinical and genotypic associations. We confirm seven PCPG gene-expression subtypes with significant genotype and clinical associations. Tumors with mutations in VHL , SDH-encoding genes ( SDHx ) or MAML3 -fusions are characterized by hypoxia-inducible factor signaling and neoangiogenesis. PCPG have few infiltrating lymphocytes but abundant macrophages. While neoplastic cells transcriptionally resemble mature chromaffin cells, early chromaffin and neuroblast markers are also features of some PCPG subtypes. The gene-expression profile of metastatic SDHx -related PCPG indicates these tumors have elevated cellular proliferation and a lower number of non-neoplastic Schwann-cell-like cells, while GPR139 is a potential theranostic target. Our findings therefore clarify the erse transcriptional programs and cellular composition of PCPG and identify biomarkers of potential clinical significance.
Understanding the physical processes of pollutant build-up and wash-off on roof surfaces
Publisher: Elsevier BV
Date: 03-2009
DOI: 10.1016/J.SCITOTENV.2008.12.027
Abstract: Pollutants originating with roof runoff can have a significant impact on urban stormwater quality. This signifies the importance of understanding pollutant processes on roof surfaces. Additionally, knowledge of pollutant processes on roof surfaces is important as roofs are used as the primary catchment surface for domestic rainwater harvesting. In recent years, rainwater harvesting has become one of the primary sustainable water management techniques to counteract the growing demand for potable water. This paper presents the outcomes of an in-depth research study into particulate matter build-up and wash-off for roof surfaces. In this research, particulate matter was considered as the indicator pollutant where the processes related to other pollutants can be predicted based on the understanding generated for particulate matter. The study outcomes confirm that the build-up process on roof surfaces is comparatively similar to road surfaces. However, particle loads collected from roofs were significantly less compared to road surfaces and much finer in texture. Wash-off from roofs also showed significant similarities to wash-off from roads. A relatively high concentration of particulate matter was noted during the initial part of storm events. Furthermore, the amount of particulate matter remaining on the roof surfaces was significantly high for less intense rain events.
Wilderness and future conservation priorities in Australia
Publisher: Wiley
Date: 12-10-2009
Influence of photolysis on source characterization and health risk of polycyclic aromatic hydrocarbons (PAHs), and carbonyl-, nitro-, hydroxy- PAHs in urban road dust
Publisher: Elsevier BV
Date: 2021
Embed stormwater use in city planning
Publisher: Springer Science and Business Media LLC
Date: 04-2016
DOI: 10.1038/532037A
Understanding the role of land use in urban stormwater quality management
Publisher: Elsevier BV
Date: 2005
DOI: 10.1016/J.JENVMAN.2004.08.006
Abstract: Urbanisation significantly impacts water environments with increased runoff and the degradation of water quality. The management of quantity impacts are straight forward, but quality impacts are far more complex. Current approaches to safeguard water quality are largely ineffective and guided by entrenched misconceptions with a primary focus on 'end-of-pipe' solutions. The outcomes of a research study presented in the paper, which investigated relationships between water quality and six different land uses offer practical guidance in the planning of future urban developments. In terms of safeguarding water quality, high-density residential development which results in a relatively smaller footprint would be the preferred option. The research study outcomes bring into question a number of fundamental concepts and misconceptions routinely accepted in stormwater quality management. The research findings confirmed the need to move beyond customary structural measures and identified the key role that urban planning can play in safeguarding urban water environments.
Pathway and network analysis of more than 2500 whole cancer genomes
Publisher: Springer Science and Business Media LLC
Date: 05-02-2020
DOI: 10.1038/S41467-020-14367-0
Abstract: The catalog of cancer driver mutations in protein-coding genes has greatly expanded in the past decade. However, non-coding cancer driver mutations are less well-characterized and only a handful of recurrent non-coding mutations, most notably TERT promoter mutations, have been reported. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2658 cancer across 38 tumor types, we perform multi-faceted pathway and network analyses of non-coding mutations across 2583 whole cancer genomes from 27 tumor types compiled by the ICGC/TCGA PCAWG project that was motivated by the success of pathway and network analyses in prioritizing rare mutations in protein-coding genes. While few non-coding genomic elements are recurrently mutated in this cohort, we identify 93 genes harboring non-coding mutations that cluster into several modules of interacting proteins. Among these are promoter mutations associated with reduced mRNA expression in TP53 , TLE4 , and TCF4 . We find that biological processes had variable proportions of coding and non-coding mutations, with chromatin remodeling and proliferation pathways altered primarily by coding mutations, while developmental pathways, including Wnt and Notch, altered by both coding and non-coding mutations. RNA splicing is primarily altered by non-coding mutations in this cohort, and s les containing non-coding mutations in well-known RNA splicing factors exhibit similar gene expression signatures as s les with coding mutations in these genes. These analyses contribute a new repertoire of possible cancer genes and mechanisms that are altered by non-coding mutations and offer insights into additional cancer vulnerabilities that can be investigated for potential therapeutic treatments.
Influence of traffic and land use on urban stormwater quality: Implications for urban stormwater treatment design (SpringerBriefs in Water Science and Technology - BRIEFSWATER)
Publisher: Springer Singapore
Date: 2018
Source quantification and risk assessment as a foundation for risk management of metals in urban road deposited solids
Publisher: Elsevier BV
Date: 04-2021
An Investigation into the role of site and soil characteristics in onsite sewage treatment
Publisher: Springer Science and Business Media LLC
Date: 07-2003
Assessment and management of human health risk from toxic metals and polycyclic aromatic hydrocarbons in urban stormwater arising from anthropogenic activities and traffic congestion
Publisher: Elsevier BV
Date: 02-2017
DOI: 10.1016/J.SCITOTENV.2016.11.015
Abstract: Toxic metals (TMs) and polycyclic aromatic hydrocarbons (PAHs) in urban stormwater pose risk to human health, thereby constraining its reuse potential. Based on the hypothesis that stormwater quality is primarily influenced by anthropogenic activities and traffic congestion, the primary focus of the research study was to analyse the impacts on human health risk from TMs and PAHs in urban stormwater and thereby develop a quantitative risk assessment model. The study found that anthropogenic activities and traffic congestion exert influence on the risk posed by TMs and PAHs in stormwater from commercial and residential areas. Motor vehicle related businesses (FVS) and traffic congestion (TC) were identified as two parameters which need to be included as independent variables to improve the model. Based on the study outcomes, approaches for mitigating the risk associated with TMs and PAHs in urban stormwater are discussed. Additionally, a roadmap is presented for the assessment and management of the risk arising from these pollutants. The study outcomes are expected to contribute to reducing the human health risk associated urban stormwater pollution and thereby enhance its reuse potential.
Understanding heavy metal and suspended solids relationships in urban stormwater using simulated rainfall
Publisher: Elsevier BV
Date: 07-2005
DOI: 10.1016/J.JENVMAN.2005.01.013
Abstract: Urban stormwater from simulated rainfall on three different landuses in Queensland State, Australia (residential, industrial, commercial) was analysed for heavy metals and physico-chemical parameters such as Dissolved Organic Carbon (DOC) and Total Suspended Solids (TSS). Rainfall events were simulated using a specially designed rainfall simulator for paved surfaces. Event mean concentration s les were separated into five different particle sizes and analysed in idually for eight metal elements (Zn, Fe, Cr, Cd, Cu, Al, Mn and Pb). Multivariate data analysis was carried out for the data thus generated. It was found that DOC and TSS influence the distribution of the metals in the different particle size classes. Zn was correlated with DOC at all three sites. Similarly, Pb, Fe and Al were correlated with TSS at all sites. The distribution of Cu was found to vary between the three sites, whilst Cd concentrations were too low to assess any relationships with other parameters. No correlation between Electrical Conductivity (EC), pH and heavy metals was found at the three sites. The identification of physico-chemical parameters influencing the distribution process kinetics of heavy metals in urban stormwater will significantly enhance the efficiency of urban stormwater management systems.
Telomere sequence content can be used to determine ALT activity in tumours
Publisher: Oxford University Press (OUP)
Date: 30-04-2018
DOI: 10.1093/NAR/GKY297
Ranking Three Water Sensitive Urban Design (WSUD) Practices Based on Hydraulic and Water Quality Treatment Performance: Implications for Effective Stormwater Treatment Design
Publisher: MDPI AG
Date: 15-04-2022
DOI: 10.3390/W14081296
Abstract: Bioretention basins, constructed wetlands and roadside swales are among the most common Water-Sensitive Urban Design (WSUD) or stormwater quality treatment systems. Although these systems can reduce stormwater quantity and improve quality, their hydraulic and water quality treatment performances are different. The aim of this study was to investigate the hydraulic and water quality performance of a bioretention basin, a constructed wetland and a roadside swale by analyzing monitored water quantity and quality data from a range of rainfall events using a ranking approach. The study outcomes showed that a bioretention basin performed better in relation to peak flow and runoff volume reduction while the constructed wetland tended to produce better outflow water quality. The roadside swale had a relatively lower capacity for treating stormwater. These results suggest that a bioretention basin could be the preferred option when the primary requirement is water quantity improvement. However, if water quality improvement is the primary consideration, a constructed wetland could be more efficient. Additionally, when designing a treatment train, it appears to be preferable to place a bioretention basin prior to a constructed wetland. Further, a swale appears to be more appropriate for use as a pretreatment device. The research study outcomes will contribute to effective stormwater treatment design.
Author Correction: Cancer LncRNA Census reveals evidence for deep functional conservation of long noncoding RNAs in tumorigenesis
Publisher: Springer Science and Business Media LLC
Date: 08-12-2022
Use of physicochemical signatures to assess the sources of metals in urban road dust
Publisher: Elsevier BV
Date: 2016
DOI: 10.1016/J.SCITOTENV.2015.10.032
Abstract: Road deposited dust is a complex mixture of pollutants derived from a wide range of sources. Accurate identification of these sources is seminal for effective source-oriented control measures. A range of techniques such as enrichment factor analysis (EF), principal component analysis (PCA) and hierarchical cluster analysis (HCA) are available for identifying sources of complex mixtures. However, they have multiple deficiencies when applied in idually. This study presents an approach for the effective utilisation of EF, PCA and HCA for source identification, so that their specific deficiencies on an in idual basis are eliminated. EF analysis confirmed the non-soil origin of metals such as Na, Cu, Cd, Zn, Sn, K, Ca, Sb, Ba, Ti, Ni and Mo providing guidance in the identification of anthropogenic sources. PCA and HCA identified four sources, with soil and asphalt wear in combination being the most prominent sources. Other sources were tyre wear, brake wear and sea salt.
Quantitative PCR assay of sewage-associatedBacteroidesmarkers to assess sewage pollution in an urban lake in Dhaka, Bangladesh
Publisher: Canadian Science Publishing
Date: 10-2010
DOI: 10.1139/W10-070
Abstract: This paper aimed to assess the magnitude of sewage pollution in an urban lake in Dhaka, Bangladesh, by using quantitative PCR of sewage-associated Bacteroides HF183 markers. PCR was also used for the quantitative detection of ruminant wastewater-associated CF128 markers along with the enumeration of traditional fecal indicator bacteria, namely enterococci. The number of enterococci in lake water s les ranged from 1.1 × 10 4 to 1.9 × 10 5 colony-forming units/100 mL water. From the 20 water s les tested, 14 (70%) and 7 (35%) were PCR positive for HF183 and CF128 markers, respectively. The numbers of HF183 and CF128 markers in lake water s les were 3.9 × 10 4 to 6.3 × 10 7 and 9.3 × 10 3 to 6.3 × 10 5 genomic units/100 mL water, respectively. The high numbers of enterococci and HF183 markers are indicative of sewage pollution and potential health risks to those who use the lake water for nonpotable purposes such as bathing and washing clothes. This is the first study that investigated the presence of microbial source tracking markers in Dhaka, Bangladesh, where diarrhoeal disease is one of the major causes of childhood mortality. The molecular assay used in this study can provide valuable information on the extent of sewage pollution, thus facilitating the development of robust strategies to minimize potential health risks.
Process variability of pollutant build-up on urban road surfaces
Publisher: Elsevier BV
Date: 06-2015
DOI: 10.1016/J.SCITOTENV.2015.03.014
Abstract: Knowledge of the pollutant build-up process is a key requirement for developing stormwater pollution mitigation strategies. In this context, process variability is a concept which needs to be understood in-depth. Analysis of particulate build-up on three road surfaces in an urban catchment confirmed that particles 150 μm have characteristically different build-up patterns, and these patterns are consistent over different field conditions. Three theoretical build-up patterns were developed based on the size-fractionated particulate build-up patterns, and these patterns explain the variability in particle behavior and the variation in particle-bound pollutant load and composition over the antecedent dry period. Behavioral variability of particles <150 μm was found to exert the most significant influence on the build-up process variability. As characterization of process variability is particularly important in stormwater quality modeling, it is recommended that the influence of behavioral variability of particles <150 μm on pollutant build-up should be specifically addressed. This would eliminate model deficiencies in the replication of the build-up process and facilitate the accounting of the inherent process uncertainty, and thereby enhance the water quality predictions.
Tailored first-line and second-line CDK4-targeting treatment combinations in mouse models of pancreatic cancer
Publisher: BMJ
Date: 28-10-2017
DOI: 10.1136/GUTJNL-2017-315144
Abstract: Extensive molecular heterogeneity of pancreatic ductal adenocarcinoma (PDA), few effective therapies and high mortality make this disease a prime model for advancing development of tailored therapies. The p16-cyclin D-cyclin-dependent kinase 4/6-retinoblastoma (RB) protein (CDK4) pathway, regulator of cell proliferation, is deregulated in PDA. Our aim was to develop a novel personalised treatment strategy for PDA based on targeting CDK4. Sensitivity to potent CDK4/6 inhibitor PD-0332991 (palbociclib) was correlated to protein and genomic data in 19 primary patient-derived PDA lines to identify biomarkers of response. In vivo efficacy of PD-0332991 and combination therapies was determined in subcutaneous, intrasplenic and orthotopic tumour models derived from genome-sequenced patient specimens and genetically engineered model. Mechanistically, monotherapy and combination therapy were investigated in the context of tumour cell and extracellular matrix (ECM) signalling. Prognostic relevance of companion biomarker, RB protein, was evaluated and validated in independent PDA patient cohorts ( specimens). Subtype-specific in vivo efficacy of PD-0332991-based therapy was for the first time observed at multiple stages of PDA progression: primary tumour growth, recurrence (second-line therapy) and metastatic setting and may potentially be guided by a simple biomarker (RB protein). PD-0332991 significantly disrupted surrounding ECM organisation, leading to increased quiescence, apoptosis, improved chemosensitivity, decreased invasion, metastatic spread and PDA progression in vivo. RB protein is prevalent in primary operable and metastatic PDA and may present a promising predictive biomarker to guide this therapeutic approach. This study demonstrates the promise of CDK4 inhibition in PDA over standard therapy when applied in a molecular subtype-specific context.
Application of multivariate data techniques in photochemical study of polycyclic aromatic hydrocarbons (PAHs) and transformed PAH products in road dust
Publisher: Elsevier BV
Date: 06-2020
Role of Rainfall and Catchment Characteristics on Urban Stormwater Quality
Publisher: Springer Singapore
Date: 2015
Role of adsorption behavior on metal build-up in urban road dust
Publisher: Elsevier BV
Date: 09-2019
DOI: 10.1016/J.JES.2019.03.023
Abstract: Metal pollution of stormwater runoff can cause potential toxic impacts on the receiving water environment and human health. Effective pollution mitigation requires accurate stormwater quality modeling. Even though a significant knowledge base exists on the factors influencing metal build-up on urban roads, very limited studies have investigated how metal-particulate interaction influences metal build-up. This study quantitatively assessed the influence of particulate characteristics, together with vehicular traffic and land use, on the build-up of Zn, Cu, Pb, Cr, Ni and Cd on urban roads. The study outcomes revealed that the variability in metal build-up is highly influenced by the variability associated with metal adsorption to particulates. The percentage contribution from particulate properties influencing metal adsorption in the case of <150 μm size road dust particles was found to be higher (Zn 44%, Cu 52%, Cr 16%, Ni 27% and Cd 45%) when compared to traffic and land use characteristics (Zn 21%, Cu 13%, Cr and Ni 150 μm size road dust particles. Among different particulate properties influencing metal adsorption, effective cation exchange capacity showed a strong positive relationship with the build-up of Cd compared to other metals, highlighting the potential role of Cd in stormwater quality as a readily available metal. The build-up of metals such as Cr and Ni are highly influenced by metal oxides of Al, Fe and Mn and clay forming minerals, indicating that Cr and Ni are relatively stable in nature.
CAF hierarchy driven by pancreatic cancer cell p53-status creates a pro-metastatic and chemoresistant environment via perlecan
Publisher: Springer Science and Business Media LLC
Date: 12-08-2019
DOI: 10.1038/S41467-019-10968-6
Abstract: Heterogeneous subtypes of cancer-associated fibroblasts (CAFs) coexist within pancreatic cancer tissues and can both promote and restrain disease progression. Here, we interrogate how cancer cells harboring distinct alterations in p53 manipulate CAFs. We reveal the existence of a p53-driven hierarchy, where cancer cells with a gain-of-function (GOF) mutant p53 educate a dominant population of CAFs that establish a pro-metastatic environment for GOF and null p53 cancer cells alike. We also demonstrate that CAFs educated by null p53 cancer cells may be reprogrammed by either GOF mutant p53 cells or their CAFs. We identify perlecan as a key component of this pro-metastatic environment. Using intravital imaging, we observe that these dominant CAFs delay cancer cell response to chemotherapy. Lastly, we reveal that depleting perlecan in the stroma combined with chemotherapy prolongs mouse survival, supporting it as a potential target for anti-stromal therapies in pancreatic cancer.
Incorporating ecological and evolutionary processes into continental-scale conservation planning
Publisher: Wiley
Date: 2009
DOI: 10.1890/07-1684.1
Abstract: Systematic conservation planning research has focused on designing systems of conservation areas that efficiently protect a comprehensive and representative set of species and habitats. Recently, there has been an emphasis on improving the adequacy of conservation area design to promote the persistence and future generation of bio ersity. Few studies have explored incorporating ecological and evolutionary processes into conservation planning assessments. Bio ersity in Australia is maintained and generated by numerous ecological and evolutionary processes at various spatial and temporal scales. We accommodated ecological and evolutionary processes in four ways: (1) using sub-catchments as planning units to facilitate the protection of the integrity and function of ecosystem processes occurring on a sub-catchment scale (2) targeting one type of ecological refugia, drought refugia, which are critical for the persistence of many species during widespread drought (3) targeting one type of evolutionary refugia which are important for maintaining and generating unique biota during long-term climatic changes and (4) preferentially grouping priority areas along vegetated waterways to account for the importance of connected waterways and associated riparian areas in maintaining processes. We identified drought refugia, areas of relatively high and regular herbage production in arid and semiarid Australia, from estimates of gross primary productivity derived from satellite data. In this paper, we combined the novel incorporation of these processes with a more traditional framework of efficiently representing a comprehensive s le of bio ersity to identify spatial priorities across Australia. We explored the trade-offs between economic costs, representation targets, and connectivity. Priority areas that considered ecological and evolutionary processes were more connected along vegetated waterways and were identified for a small increase in economic cost. Priority areas for conservation investment are more likely to have long-term benefits to bio ersity if ecological and evolutionary processes are considered in their identification.
Recurrent noncoding regulatory mutations in pancreatic ductal adenocarcinoma
Publisher: Springer Science and Business Media LLC
Date: 08-05-2017
DOI: 10.1038/NG.3861
Sectional analysis of the pollutant wash-off process based on runoff hydrograph
Publisher: Elsevier BV
Date: 02-2014
DOI: 10.1016/J.JENVMAN.2013.12.034
Abstract: The validity of using rainfall characteristics as lumped parameters for investigating the pollutant wash-off process such as first flush occurrence is questionable. This research study introduces an innovative concept of using sector parameters to investigate the relationship between the pollutant wash-off process and different sectors of the runoff hydrograph and rainfall hyetograph. The research outcomes indicated that rainfall depth and rainfall intensity are two key rainfall characteristics which influence the wash-off process compared to the antecedent dry period. Additionally, the rainfall pattern also plays a critical role in the wash-off process and is independent of the catchment characteristics. The knowledge created through this research study provides the ability to select appropriate rainfall events for stormwater quality treatment design based on the required treatment outcomes such as the need to target different sectors of the runoff hydrograph or pollutant species. The study outcomes can also contribute to enhancing stormwater quality modelling and prediction in view of the fact that conventional approaches to stormwater quality estimation is primarily based on rainfall intensity rather than considering other rainfall parameters or solely based on stochastic approaches irrespective of the characteristics of the rainfall event.
Investigating the potential of low-carbon pathways for hydrocarbon-dependent rentier states: Sociotechnical transition in Qatar
Publisher: Elsevier BV
Date: 04-2023
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