ORCID Profile
0000-0002-6605-7478
Current Organisations
Technical University of Denmark
,
University of Sydney
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Applied Statistics | Statistical Theory | Statistics |
Expanding Knowledge in the Agricultural and Veterinary Sciences | Expanding Knowledge in the Mathematical Sciences
Publisher: Springer Science and Business Media LLC
Date: 09-2021
DOI: 10.1007/S00484-021-02180-3
Abstract: This study conducted a retrospective analysis of historical Meat Standard Australia (MSA) carcass data in combination with Bureau of Meteorology (BOM) weather data, to evaluate the relationship between climatic conditions prior to feedlot departure on the incidence of dark cutting grain-fed beef. Data records for 2,795,754 carcasses from 17 commercial feedlots over a 6-year period were evaluated within this study. Carcasses were consigned to 16 abattoirs. Weather data from BOM were recorded at 30-min intervals and were obtained from weather stations with the closest proximity to each feedlot. These data were used to calculate the Temperature Humidity Index (THI). Climatic data were amalgamated into daily observations and a series of predictors including ambient temperature (T
Publisher: Springer Science and Business Media LLC
Date: 15-03-2016
Publisher: Oxford University Press (OUP)
Date: 12-09-2019
DOI: 10.1093/BIOINFORMATICS/BTY783
Abstract: Gene annotation and pathway databases such as Gene Ontology and Kyoto Encyclopaedia of Genes and Genomes are important tools in Gene-Set Test (GST) that describe gene biological functions and associated pathways. GST aims to establish an association relationship between a gene-set of interest and an annotation. Importantly, GST tests for over-representation of genes in an annotation term. One implicit assumption of GST is that the gene expression platform captures the complete or a very large proportion of the genome. However, this assumption is neither satisfied for the increasingly popular boutique array nor the custom designed gene expression profiling platform. Specifically, conventional GST is no longer appropriate due to the gene-set selection bias induced during the construction of these platforms. We propose bcGST, a bias-corrected GST by introducing bias-correction terms in the contingency table needed for calculating the Fisher’s Exact Test. The adjustment method works by estimating the proportion of genes captured on the array with respect to the genome in order to assist filtration of annotation terms that would otherwise be falsely included or excluded. We illustrate the practicality of bcGST and its stability through multiple differential gene expression analyses in melanoma and the Cancer Genome Atlas cancer studies. The bcGST method is made available as a Shiny web application at shiny.maths.usyd.edu.au/bcGST/. Supplementary data are available at Bioinformatics online.
Publisher: MDPI AG
Date: 27-08-2019
DOI: 10.3390/ANI9090612
Abstract: The study evaluated the relationship between pre-slaughter stress, plasma biomarkers and consumer-evaluated eating quality of pasture raised beef cattle (n = 488). The design tested steer only, heifer only and mixed sex cattle with a comparison of direct kill versus a 14 day rest period in abattoir holding paddocks prior to slaughter. Experiment One sourced cattle from four farms and tested shipping and road transport. Experiment Two sourced cattle from four farms and tested a commercial saleyard pathway. The impact on treatment on untrained consumer eating quality scores were tested on five muscle groups, m. psoas major, m. longissimus dorsi lumborum, m. biceps femoris, m. semitendinosis, and m. infraspinatus. Across all muscles, a two-week rest period had the biggest improvement in sensory score. Mixed groups scored lower in the outside muscle than non-mixed groups. However, the mixing response was inconsistent in the eye round muscle and not significant in the other muscles. Plasma glucose and L-lactate indicated a marked acute stress response at slaughter with a small detrimental impact on consumer score. The muscle damage enzyme markers creatine kinase (CK) and aspartate aminotransferase (AST) were strongly associated with a lower meat quality score (MQ4). Neither β-hydroxybutyrate (βHB) nor non-esterified fatty acids (NEFA) were associated with MQ4, suggesting that fat mobilisation does not impact consumer sensory score.
Publisher: Elsevier BV
Date: 2016
Publisher: Foundation for Open Access Statistic
Date: 2018
Publisher: Elsevier BV
Date: 12-2019
Publisher: Elsevier BV
Date: 08-2018
DOI: 10.1016/J.MEATSCI.2018.04.002
Abstract: This experiment examined 3 packaging systems: overwrap packaging using oxygen permeable film (OWP) vacuum skin packaging (VSP) and modified atmosphere packaging (MAP, 80%O
Publisher: MDPI AG
Date: 27-04-2022
DOI: 10.3390/S22093347
Abstract: Automatic identification and sorting of livestock organs in the meat processing industry could reduce costs and improve efficiency. Two hyperspectral sensors encompassing the visible (400–900 nm) and short-wave infrared (900–1700 nm) spectra were used to identify the organs by type. A total of 104 parenchymatous organs of cattle and sheep (heart, kidney, liver, and lung) were scanned in a multi-sensory system that encompassed both sensors along a conveyor belt. Spectral data were obtained and averaged following manual markup of three to eight regions of interest of each organ. Two methods were evaluated to classify organs: partial least squares discriminant analysis (PLS-DA) and random forest (RF). In addition, classification models were obtained with the smoothed reflectance and absorbance and the first and second derivatives of the spectra to assess if one was superior to the rest. The in-s le accuracy for the visible, short-wave infrared, and combination of both sensors was higher for PLS-DA compared to RF. The accuracy of the classification models was not significantly different between data pre-processing methods or between visible and short-wave infrared sensors. Hyperspectral sensors, particularly those in the visible spectrum, seem promising to identify organs from slaughtered animals which could be useful for the automation of quality and process control in the food supply chain, such as in abattoirs.
Publisher: Frontiers Media SA
Date: 06-12-2021
Publisher: Elsevier BV
Date: 04-2020
Publisher: Informa UK Limited
Date: 31-12-2022
Publisher: Informa UK Limited
Date: 10-06-2014
Publisher: Elsevier BV
Date: 11-2020
Publisher: Springer Science and Business Media LLC
Date: 04-07-2022
DOI: 10.1038/S41746-022-00618-5
Abstract: In this modern era of precision medicine, molecular signatures identified from advanced omics technologies hold great promise to better guide clinical decisions. However, current approaches are often location-specific due to the inherent differences between platforms and across multiple centres, thus limiting the transferability of molecular signatures. We present Cross-Platform Omics Prediction (CPOP), a penalised regression model that can use omics data to predict patient outcomes in a platform-independent manner and across time and experiments. CPOP improves on the traditional prediction framework of using gene-based features by selecting ratio-based features with similar estimated effect sizes. These components gave CPOP the ability to have a stable performance across datasets of similar biology, minimising the effect of technical noise often generated by omics platforms. We present a comprehensive evaluation using melanoma transcriptomics data to demonstrate its potential to be used as a critical part of a clinical screening framework for precision medicine. Additional assessment of generalisation was demonstrated with ovarian cancer and inflammatory bowel disease studies.
Publisher: CERN, Geneva
Date: 2016
Publisher: MDPI AG
Date: 10-02-2021
DOI: 10.3390/ANI11020474
Abstract: The aim of this study was to evaluate the effect of carcass traits, lairage time and weather conditions during lairage and abattoir factors that impact the incidence of dark cutting in 142,228 grain-fed carcasses, as defined by Meat Standards Australia (MSA) guidelines. This study was conducted over a 12-month period analysing data from cattle that were supplied from seven feedlots and processed at three abattoirs. Abattoir data indicated that the average incidence of dark cutting within the study was 2.8%. Increased wind speeds (WSs) and rain during lairage at the abattoir was associated with an increased risk of dark cutting, whereas variation in ambient temperature and/or relative humidity did not influence dark cutting. Heavier carcasses with whiter fat, larger hump heights, more rib fat, higher marble scores and lower ossification had lower incidences of dark cutting. The factors abattoir, time in lairage, time to grading and grader within Abattoir had significant effects on the incidence of dark cutting. The results from this study suggest that reducing the time in lairage and increasing the time between slaughter and grading are the two major ways to reduce dark cutting in MSA carcasses.
Publisher: Elsevier BV
Date: 08-2022
Publisher: Elsevier BV
Date: 03-2015
Publisher: Frontiers Media SA
Date: 14-03-2023
Publisher: MDPI AG
Date: 08-08-2019
DOI: 10.3390/FOODS8080332
Abstract: Actinidin is a cysteine protease enzyme which occurs in kiwifruit and has been associated with improved tenderness in red meat. This study evaluated the impact of actinidin, derived from kiwifruit, on consumer sensory outcomes for striploin (M. longissimus lumborum) and outside flat (M. biceps femoris). Striploins and outside flats were collected from 87 grass-fed steers. Carcasses were graded to the Meat Standards Australia (MSA) protocols. Striploins and outside flats were then dissected in half and allocated to one of the following two treatments: (1) not infused (control) and (2) infused with a kiwifruit extract (enhanced), and then prepared as grill and roast s les. Grill and roast s les were then aged for 10 or 28 days. Consumer evaluations for tenderness, juiciness, flavor, and overall liking were conducted using untrained consumer sensory panels consisting of 2080 in idual consumers, in accordance with the MSA protocols. These scores were then used to calculate an overall eating quality (MQ4) score. Consumer sensory scores for tenderness, juiciness, flavor, overall liking, and MQ4 score were analyzed using a linear mixed-effects model. Kiwifruit extract improved consumer scores for tenderness, juiciness, flavor, overall liking, and MQ4 scores for striploins and outside flat (p 0.05). These results suggest that kiwifruit extract provides an opportunity to improve eating experiences for consumers.
Publisher: Emerald Publishing Limited
Date: 25-07-2019
Publisher: MDPI AG
Date: 31-07-2019
DOI: 10.3390/ANI9080503
Abstract: This study considered the relationship between pre-slaughter stressors and plasma biomarkers in 488 pasture-raised cattle across two experiments. The design aimed to test groups consisting of steer only, heifer only, and mixed sex cattle under direct kill versus rested (14 days in abattoir holding paddocks) protocols. In Experiment One, cattle were sourced from four farms, and transported by trucks and ships on the same day. In Experiment Two, cattle were sourced from four farms where a comparison was made between marketing via two commercial saleyards or direct farm gate consignment to abattoir. Blood s les were collected at exsanguination for subsequent analyses and relation to meat quality attributes. Muscle damage, as indicated by creatine kinase, is the biomarker most correlated to ultimate pH and muscle glycogen concentrations. A two-week rest period is effective for lowering this enzyme and improving muscle glycogen concentration. Although the cattle was subjected to a range of stress inducing treatments, we found that plasma biomarkers alone appeared insufficient for use as diagnostic stress indicators.
Publisher: Frontiers Media SA
Date: 30-08-2019
Abstract: Fatty alcohols are widely used in various applications within a erse set of industries, such as the soap and detergent industry, the personal care, and cosmetics industry, as well as the food industry. The total world production of fatty alcohols is over 2 million tons with approximately equal parts derived from fossil oil and from plant oils or animal fats. Due to the environmental impact of these production methods, there is an interest in alternative methods for fatty alcohol production via microbial fermentation using cheap renewable feedstocks. In this study, we aimed to obtain a better understanding of how fatty alcohol biosynthesis impacts the host organism, baker’s yeast Saccharomyces cerevisiae or oleaginous yeast Yarrowia lipolytica . Producing and non-producing strains were compared in growth and nitrogen-depletion cultivation phases. The multi-omics analysis included physiological characterization, transcriptome analysis by RNAseq, 13 Cmetabolic flux analysis, and intracellular metabolomics. Both species accumulated fatty alcohols under nitrogen-depletion conditions but not during growth. The fatty alcohol–producing Y. lipolytica strain had a higher fatty alcohol production rate than an analogous S. cerevisiae strain. Nitrogen-depletion phase was associated with lower glucose uptake rates and a decrease in the intracellular concentration of acetyl–CoA in both yeast species, as well as increased organic acid secretion rates in Y. lipolytica . Expression of the fatty alcohol–producing enzyme fatty acyl–CoA reductase alleviated the growth defect caused by deletion of hexadecenal dehydrogenase encoding genes ( HFD1 and HFD4 ) in Y. lipolytica . RNAseq analysis showed that fatty alcohol production triggered a cell wall stress response in S. cerevisiae . RNAseq analysis also showed that both nitrogen-depletion and fatty alcohol production have substantial effects on the expression of transporter encoding genes in Y. lipolytica . In conclusion, through this multi-omics study, we uncovered some effects of fatty alcohol production on the host metabolism. This knowledge can be used as guidance for further strain improvement towards the production of fatty alcohols.
Publisher: Elsevier BV
Date: 11-2021
Publisher: Informa UK Limited
Date: 03-2012
Publisher: MDPI AG
Date: 05-08-2022
DOI: 10.3390/ANI12151989
Abstract: It has been well-established that dark cutting (DC) is a multifactorial issue that is associated with numerous animal and management factors. However, there is limited understanding of the feedlot-based factors that contribute to the influence of DC. The aim of this study was to evaluate the effect of climate, animal, and feedlot factors on the incidence of pH non-compliance in Australian grain-fed cattle. For this study, feedlot and abattoir records from 142,228 in idual cattle over a 1-year period were investigated. These data incorporated records from seven feedlots that consigned cattle to three abattoirs. The average incidence of DC in these carcasses was 2.8%. The production factors that were associated with increased risk of DC included feedlot, sex, hormone growth promotants (HGP), cattle health, and days on feed (DOF). Additionally, DC also increased by reduced solar radiation (SR, W/m2), lower wind speeds (WS, m/s), increased ambient temperature (TA, °C), higher rainfall, a higher average temperature–humidity index (THI), and increased duration of time above heat-load-index threshold of 86 (HLI ≥ 86) during the 7 days prior to feedlot departure. This study identified the feedlot factors that increase the risk of DC from a feedlot-management perspective.
Publisher: Frontiers Media SA
Date: 25-10-2021
Publisher: Elsevier BV
Date: 2017
DOI: 10.1016/J.MEATSCI.2016.09.005
Abstract: As marbling is a principal input into many grading systems it is important to have an accurate and reliable measurement procedure. This paper compares three approaches to measuring marbling: trained personnel, near infrared spectroscopy (NIR) and image analysis. One 25mm slice of meat was utilised from up to 12 cuts from 48 carcasses processed in Poland and France. Each slice was frozen to enable a consistent post-slaughter period then thawed for image analysis. The images were appraised by experienced beef graders and the s le used to determine fat content by NIR. We find that image analysis based marbling measures are capturing something different to trained personnel and that there is a strong relationship between near infrared spectroscopy and trained personnel. Finally, we demonstrate that marbling measures taken on one muscle can be predictive of marbling in other muscles in the same carcase. This is particularly important for cut based models such as the Meat Standards Australia system.
Publisher: Informa UK Limited
Date: 2012
Publisher: Cambridge University Press (CUP)
Date: 29-04-2015
Publisher: Elsevier BV
Date: 10-2021
Publisher: Wiley
Date: 12-2019
DOI: 10.1111/ANZS.12276
Start Date: 11-2021
End Date: 10-2024
Amount: $390,000.00
Funder: Australian Research Council
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