ORCID Profile
0000-0003-4743-348X
Current Organisation
University of South Australia
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Publisher: Elsevier BV
Date: 2023
Publisher: Springer Science and Business Media LLC
Date: 30-11-2011
Publisher: Oxford University Press (OUP)
Date: 06-05-2011
DOI: 10.1093/BIOINFORMATICS/BTR291
Abstract: Summary: Bioinformatics research often requires conservative analyses of a group of sequences associated with a specific biological function (e.g. transcription factor binding sites, micro RNA target sites or protein post-translational modification sites). Due to the difficulty in exploring conserved motifs on a large-scale sequence data involved with various signals, a new method, MDDLogo, is developed. MDDLogo applies maximal dependence decomposition (MDD) to cluster a group of aligned signal sequences into subgroups containing statistically significant motifs. In order to extract motifs that contain a conserved biochemical property of amino acids in protein sequences, the set of 20 amino acids is further categorized according to their physicochemical properties, e.g. hydrophobicity, charge or molecular size. MDDLogo has been demonstrated to accurately identify the kinase-specific substrate motifs in 1221 human phosphorylation sites associated with seven well-known kinase families from Phospho.ELM. Moreover, in a set of plant phosphorylation data-lacking kinase information, MDDLogo has been applied to help in the investigation of substrate motifs of potential kinases and in the improvement of the identification of plant phosphorylation sites with various substrate specificities. In this study, MDDLogo is comparable with another well-known motif discover tool, Motif-X. Contact: francis@saturn.yzu.edu.tw Supplementary information: Supplementary data are available at Bioinformatics online.
Publisher: Public Library of Science (PLoS)
Date: 16-11-2011
Publisher: Elsevier BV
Date: 2023
Publisher: Ovid Technologies (Wolters Kluwer Health)
Date: 15-12-2018
Publisher: Wiley
Date: 10-04-2017
DOI: 10.1111/JVH.12701
Abstract: Hepatitis C virus (HCV) transmission is high in prisons. This study investigated trends in HCV incidence and associated factors among a cohort of prisoners with a history of injecting drug use in New South Wales, Australia. Data were available from the Hepatitis C Incidence and Transmission Study-prisons (HITS-p) from 2005 to 2014. Temporal trends in HCV incidence were evaluated. Factors associated with time to HCV seroconversion among people with ongoing injecting was assessed using Cox proportional hazards. Among 320 antibody-negative participants with a history of injecting drug use (mean age 26 72% male), 62% (n=197) reported injecting drug use during follow-up. Overall, 93 infections were observed. HCV incidence was 11.4/100 person-years in the overall population and 6.3/100 person-years among the continually imprisoned population. A stable trend in HCV incidence was observed. Among the overall population with ongoing injecting during follow-up, ≥weekly injecting drug use frequency was independently associated with time to HCV seroconversion. Among continuously imprisoned injectors with ongoing injecting during follow-up, needle/syringe sharing was independently associated with time to HCV seroconversion. This study demonstrates that prison is a high-risk environment for acquisition of HCV infection. Needle and syringe sharing was associated with HCV infection among continually imprisoned participants, irrespective of frequency of injecting or the type of drug injected. These findings highlight the need for the evaluation of improved HCV prevention strategies in prison, including needle/syringe programmes and HCV treatment.
Publisher: Springer Science and Business Media LLC
Date: 10-2011
DOI: 10.1007/S10822-011-9477-2
Abstract: In proteins, glutamate (Glu) residues are transformed into γ-carboxyglutamate (Gla) residues in a process called carboxylation. The process of protein carboxylation catalyzed by γ-glutamyl carboxylase is deemed to be important due to its involvement in biological processes such as blood clotting cascade and bone growth. There is an increasing interest within the scientific community to identify protein carboxylation sites. However, experimental identification of carboxylation sites via mass spectrometry-based methods is observed to be expensive, time-consuming, and labor-intensive. Thus, we were motivated to design a computational method for identifying protein carboxylation sites. This work aims to investigate the protein carboxylation by considering the composition of amino acids that surround modification sites. With the implication of a modified residue prefers to be accessible on the surface of a protein, the solvent-accessible surface area (ASA) around carboxylation sites is also investigated. Radial basis function network is then employed to build a predictive model using various features for identifying carboxylation sites. Based on a five-fold cross-validation evaluation, a predictive model trained using the combined features of amino acid sequence (AA20D), amino acid composition, and ASA, yields the highest accuracy at 0.874. Furthermore, an independent test done involving data not included in the cross-validation process indicates that in silico identification is a feasible means of preliminary analysis. Additionally, the predictive method presented in this work is implemented as Carboxylator ( csb.cse.yzu.edu.tw/Carboxylator/ ), a web-based tool for identifying carboxylated proteins with modification sites in order to help users in investigating γ-glutamyl carboxylation.
Publisher: Elsevier BV
Date: 04-2018
DOI: 10.1016/J.DRUGPO.2017.12.013
Abstract: HCV transmission remains high in prisons globally. Understanding injecting risk behaviours in prisons is crucial to effectively develop and implement HCV prevention programs in this setting including treatment as prevention. HITS-p is a cohort study which enrolled people with a history of injecting drug use in prisons in NSW, Australia from 2005 to 2013. Participants completed an interview at enrolment and follow-up visits to determine injecting behaviours. Generalized estimating equation (GEE) and logistic regression methods were used to assess injecting risk behaviours prior to and following prison entry and to investigate injecting risk behaviours in prison. Overall, 499 participants with a history of injecting drug use were included (median age, 26 years 65% male). Participants were significantly less likely to inject drugs following incarceration. Among injectors, participants were less likely to inject ≥weekly but more likely to share a needle/syringe. At enrolment, the proportion reporting any injecting, ≥weekly injecting, and needle/syringe sharing in prison was highest among younger in iduals. Younger age was associated with both re-initiation and continuation of injecting drug use following prison entry. Among those continuously imprisoned, younger age was associated with increased odds of any injecting, ≥weekly injecting, and sharing a needle/syringe. Upon entry to prison, injecting drug use decreased but syringe sharing increased among injectors. Younger in iduals are most likely to exhibit high-risk injecting behaviours in prison. These data highlight the need for improved HCV prevention strategies (including improved needle/syringe access and scale up of HCV therapy) for those at increased risk of HCV transmission in prison, including younger in iduals.
Publisher: Wiley
Date: 15-07-2021
DOI: 10.1111/ADD.12643
Abstract: To document the relationships between injecting drug use, imprisonment and hepatitis C virus (HCV) infection. Prospective cohort study. Multiple prisons in New South Wales, Australia. HCV seronegative prisoners with a life-time history of injecting drug use (IDU) were enrolled and followed prospectively (n = 210) by interview and HCV antibody and RNA testing 6-12-monthly for up to 4 years when in prison. HCV incidence was calculated using the person-years method. Cox regression was used to identify predictors of incident infection using time-dependent covariates. Almost half the cohort reported IDU during follow-up (103 subjects 49.1%) and 65 (31%) also reported sharing of the injecting apparatus. There were 38 HCV incident cases in 269.94 person-years (py) of follow-up with an estimated incidence of 14.08 per 100 py [confidence interval (CI) = 9.96-19.32]. Incident infection was associated independently with Indigenous background, injecting daily or more and injecting heroin. Three subjects were RNA-positive and antibody-negative at the incident time-point, indicating early infection, which provided a second incidence estimate of 9.4%. Analysis of continuously incarcerated subjects (n = 114) followed over 126.73 py, identified 13 new HCV infections (10.26 per 100 py, CI = 5.46-17.54), one of which was an early infection case. Bleach-cleansing of injecting equipment and opioid substitution treatment were not associated with a significant reduction in incidence. In New South Wales, Australia, imprisonment is associated with high rates of hepatitis C virus transmission. More effective harm reduction interventions are needed to control HCV in prison settings.
Publisher: Springer Science and Business Media LLC
Date: 10-2013
Publisher: Wiley
Date: 12-11-2019
DOI: 10.1111/ADD.14830
Abstract: Australia is currently on track to meet the World Health Organization (WHO) global hepatitis C virus (HCV) elimination goals by 2030, reflecting universal subsidized access to testing and direct‐acting antiviral (DAA) treatment. In New South Wales, DAA treatment in prisons has scaled‐up substantially, with 1000 prisoners treated in 2017. However, HCV prevalence and incidence in this setting is high, which could undermine elimination efforts. This study aimed to test the preventative effects of DAA treatment scale‐up, opiate substitution treatment (OST) and needle and syringe programme (NSP) strategies for prisons. Modelling study using an in idual‐based mathematical model of a typical prison setting. The model was calibrated against Australian epidemiological data sets and executed in‐prison events for each in idual daily, including movements between prisons, changes in risk behaviour and uptake of prevention measures such as OST and NSP, as well as DAA treatment. Scenarios were projected from 2018 to 2030. New South Wales prisons. New South Wales prisoners. Variables including prison populations, prevalence and incidence rate were calculated. Prisoners were described by demographic characteristics, HCV infection history, risk behaviours and accessing treatment and prevention measures in varied security settings. Increasing the number of prisoners treated for HCV to 2000 annually was projected to reduce the HCV incidence rate to 8.69 [95% confidence interval (CI) = 8.17, 9.20] per 100 person‐years (100 p.y.). Combined treatment and prevention strategies were necessary to reduce the projected incidence rate to 5.22 (95% CI = 5.13, 5.52) per 100 p.y. Considering the expected reductions in the prevalence of chronic HCV in the Australian community, incidence rate was predicted to drop to 0.93 (95% CI = 0.92, 0.98) per 100 p.y. by 2030. This model, which simulates prison scenarios to inform Australia's national hepatitis C virus elimination efforts, suggests that continued direct‐acting antiviral (coverage in the community combined with a moderate increase of direct‐acting antiviral treatments in prisons, and introduction of improved harm reduction via opiate substitution treatment and/or needle and syringe programmes, makes hepatitis C virus elimination feasible in Australian prisons.
Publisher: Springer Science and Business Media LLC
Date: 12-2015
Publisher: Public Library of Science (PLoS)
Date: 23-07-2012
Publisher: Springer Science and Business Media LLC
Date: 21-01-2015
Publisher: Public Library of Science (PLoS)
Date: 14-02-2019
Publisher: Cold Spring Harbor Laboratory
Date: 10-05-2023
DOI: 10.1101/2023.05.08.23289690
Abstract: Correctional facilities are high-priority settings for coordinated public health responses to the COVID-19 pandemic. These facilities are at high risk of disease transmission due to close contacts between people in prison and with the wider community. People in prison are also vulnerable to severe disease given their high burden of co-morbidities. We developed a mathematical model to evaluate the effect of various public health interventions, including vaccination, on the mitigation of COVID-19 outbreaks, applying it to prisons in Australia and Canada. We found that, in the absence of any intervention, an outbreak would occur and infect almost 100% of people in prison within 20 days of the index case. However, the rapid rollout of vaccines with other non-pharmaceutical interventions would almost eliminate the risk of an outbreak. Our study highlights that high vaccination coverage is required for variants with high transmission probability to completely mitigate the outbreak risk in prisons. High vaccination coverage is required to eliminate the risk of an outbreak in prisons
Publisher: Springer Science and Business Media LLC
Date: 26-06-2011
Publisher: Centers for Disease Control and Prevention (CDC)
Date: 05-2015
Publisher: Cold Spring Harbor Laboratory
Date: 21-02-2021
DOI: 10.1101/2021.02.18.21252032
Abstract: Correctional facilities are at high risk of COVID-19 outbreaks due to the inevitable close contacts in the environment. Such facilities are a high priority in the public health response to the epidemic. We developed a user-friendly Excel spreadsheet model (building on the previously developed Reci iz model) to analyze COVID-19 outbreaks in correctional facilities and the potential impact of prevention strategies - the COVID-19 Incarceration Model. The model requires limited inputs and can be used by non-modelers. The impact of a COVID-19 outbreak and mitigation strategies is illustrated for an ex le prison setting.
No related grants have been discovered for Neil Arvin Bretana.