Influence of caudal epidural analgesia on cortisol concentrations and pain-related behavioral responses in mares during and after ovariectomy via colpotomy.

Objective: To determine the influence of epidural detomidine and morphine on serum corticosteroid concentrations and pain-related behavioral responses in mares during and after ovariectomy via colpotomy.

Study Design: Blinded prospective study.

Animals: Nine university-owned mares.

Low Pathogenic Avian Influenza Exposure Risk Assessment in Australian Commercial Chicken Farms.

This study investigated the pathways of exposure to low pathogenic avian influenza (LPAI) virus among Australian commercial chicken farms and estimated the likelihood of this exposure occurring using scenario trees and a stochastic modeling approach following the World Organization for Animal Health methodology for risk assessment. Input values for the models were sourced from scientific literature and an on-farm survey conducted during 2015 and 2016 among Australian commercial chicken farms located in New South Wales and Queensland. Outputs from the models revealed that the probability of a first LPAI virus exposure to a chicken in an Australian commercial chicken farms from one wild bird at any point in time is extremely low.

Biosecurity practices on Australian commercial layer and meat chicken farms: Performance and perceptions of farmers.

This paper describes the level of adoption of biosecurity practices performed on Australian commercial chicken meat and layer farms and farmer-perceived importance of these practices. On-farm interviews were conducted on 25 free range layer farms, nine cage layer farms, nine barn layer farms, six free range meat chicken farms and 15 barn meat chicken farms in the Sydney basin bioregion and South East Queensland. There was a high level of treatment of drinking water across all farm types; town water was the most common source.

Seven Salmonella Typhimurium Outbreaks in Australia Linked by Trace-Back and Whole Genome Sequencing.

Salmonella Typhimurium is a common cause of foodborne illness in Australia. We report on seven outbreaks of Salmonella Typhimurium multilocus variable-number tandem-repeat analysis (MLVA) 03-26-13-08-523 (European convention 2-24-12-7-0212) in three Australian states and territories investigated between November 2015 and March 2016. We identified a common egg grading facility in five of the outbreaks.

Health Outcomes from Multidrug-Resistant Salmonella Infections in High-Income Countries: A Systematic Review and Meta-Analysis.

Background: Salmonella is a leading cause of foodborne enterocolitis worldwide. Antimicrobial use in food animals is the driving force for antimicrobial resistance among Salmonella particularly in high-income countries. Nontyphoidal Salmonella (NTS) infections that are multidrug resistant (MDR) (nonsusceptible to ≥1 agent in ≥3 antimicrobial categories) may result in more severe health outcomes, although these effects have not been systematically examined.

Modelling low pathogenic avian influenza introduction into the commercial poultry industry.

Outbreaks of highly pathogenic avian influenza (HPAI) in commercial poultry flocks are rare but highly disruptive to the industry. There is evidence that low pathogenic avian influenza (LPAI) can transfer from wild birds to domestic flocks, where it may mutate to HPAI, and the industry is concerned that an increasing demand for free-range produce may affect the risk of LPAI and HPAI outbreaks. In this paper we focus on LPAI introduction and establishment, and formulate a branching process model to compare risk between sectors and their contribution to overall industry-level risk.

Sediment exchange to mitigate pollutant exposure in urban soil.

Urban soil is an ongoing source for lead (Pb) and other pollutant exposure. Sources of clean soil that are locally-available, abundant and inexpensive are needed to place a protective cover layer over degraded urban soil to eliminate direct and indirect pollutant exposures. This study evaluates a novel sediment exchange program recently established in New York City (NYC Clean Soil Bank, CSB) and found that direct exchange of surplus sediment extracted from urban construction projects satisfies these criteria.

Role of the Inducible Adhesin CpAls7 in Binding of Candida parapsilosis to the Extracellular Matrix under Fluid Shear.

The yeast is an increasingly common cause of systemic fungal infections among immunocompromised individuals, including premature infants. Adhesion to host surfaces is an important step in pathogenesis, but this process has not been extensively studied in this organism. A microfluidics assay was developed to test the ability of to adhere to immobilized host extracellular matrix proteins under physiological fluid shear conditions.

Incorporating Whole-Genome Sequencing into Public Health Surveillance: Lessons from Prospective Sequencing of Salmonella Typhimurium in Australia.

In Australia, the incidence of Salmonella Typhimurium has increased dramatically over the past decade. Whole-genome sequencing (WGS) is transforming public health microbiology, but poses challenges for surveillance. To compare WGS-based approaches with conventional typing for Salmonella surveillance, we performed concurrent WGS and multilocus variable-number tandem-repeat analysis (MLVA) of Salmonella Typhimurium isolates from the Australian Capital Territory (ACT) for a period of 5 months.

Ensemble genomic analysis in human lung tissue identifies novel genes for chronic obstructive pulmonary disease.

Background: Genome-wide association studies (GWAS) have identified single nucleotide polymorphisms (SNPs) significantly associated with chronic obstructive pulmonary disease (COPD). However, many genetic variants show suggestive evidence for association but do not meet the strict threshold for genome-wide significance. Integrative analysis of multiple omics datasets has the potential to identify novel genes involved in disease pathogenesis by leveraging these variants in a functional, regulatory context.

Human Lung DNA Methylation Quantitative Trait Loci Colocalize with Chronic Obstructive Pulmonary Disease Genome-Wide Association Loci.

Rationale: As the third leading cause of death in the United States, the impact of chronic obstructive pulmonary disease (COPD) makes identification of its molecular mechanisms of great importance. Genome-wide association studies (GWASs) have identified multiple genomic regions associated with COPD. However, genetic variation only explains a small fraction of the susceptibility to COPD, and sub-genome-wide significant loci may play a role in pathogenesis.

Serotonin receptor 2B signaling with interstitial cell activation and leaflet remodeling in degenerative mitral regurgitation.

Aims: Mitral valve interstitial cells (MVIC) play an important role in the pathogenesis of degenerative mitral regurgitation (MR) due to mitral valve prolapse (MVP). Numerous clinical studies have observed serotonin (5HT) dysregulation in cardiac valvulopathies; however, the impact of 5HT-mediated signaling on MVIC activation and leaflet remodeling in MVP have been investigated to a limited extent. Here we test the hypothesis that 5HT receptors (5HTRs) signaling contributes to MVP pathophysiology.

Clostridium difficile classification overestimates hospital-acquired infections.

Background: Clostridium difficile infections occur frequently among hospitalized patients, with some infections acquired in hospital and others in the community. International guidelines classify cases as hospital-acquired if symptom onset occurs more than two days after admission. This classification informs surveillance and infection control, but has not been verified by empirical or modelling studies.

Estimating drivers of cell state transitions using gene regulatory network models.

Background: Specific cellular states are often associated with distinct gene expression patterns. These states are plastic, changing during development, or in the transition from health to disease. One relatively simple extension of this concept is to recognize that we can classify different cell-types by their active gene regulatory networks and that, consequently, transitions between cellular states can be modeled by changes in these underlying regulatory networks.

A Synthetic Population for Modelling the Dynamics of Infectious Disease Transmission in American Samoa.

Agent-based modelling is a useful approach for capturing heterogeneity in disease transmission. In this study, a synthetic population was developed for American Samoa using an iterative approach based on population census, questionnaire survey and land use data. The population will be used as the basis for a new agent-based model, intended specifically to fill the knowledge gaps about lymphatic filariasis transmission and elimination, but also to be readily adaptable to model other infectious diseases.

Variation in hospital mortality in an Australian neonatal intensive care unit network.

Background: Studying centre-to-centre (CTC) variation in mortality rates is important because inferences about quality of care can be made permitting changes in practice to improve outcomes. However, comparisons between hospitals can be misleading unless there is adjustment for population characteristics and severity of illness.

Objective: We sought to report the risk-adjusted CTC variation in mortality among preterm infants born <32 weeks and admitted to all eight tertiary neonatal intensive care units (NICUs) in the New South Wales and the Australian Capital Territory Neonatal Network (NICUS), Australia.

Understanding Tissue-Specific Gene Regulation.

Although all human tissues carry out common processes, tissues are distinguished by gene expression patterns, implying that distinct regulatory programs control tissue specificity. In this study, we investigate gene expression and regulation across 38 tissues profiled in the Genotype-Tissue Expression project. We find that network edges (transcription factor to target gene connections) have higher tissue specificity than network nodes (genes) and that regulating nodes (transcription factors) are less likely to be expressed in a tissue-specific manner as compared to their targets (genes).

Learning about individuals' health from aggregate data.

There is growing awareness that user-generated social media content contains valuable health-related information and is more convenient to collect than typical health data. For example, Twitter has been employed to predict aggregate-level outcomes, such as regional rates of diabetes and child poverty, and to identify individual cases of depression and food poisoning. Models which make aggregate-level inferences can be induced from aggregate data, and consequently are straightforward to build.

Ensemble transfer learning for Alzheimer's disease diagnosis.

There is considerable interest in developing inexpensive, nonintrusive diagnostic tests for Alzheimer's disease (AD), in the hope these tests will facilitate early diagnosis and support design of effective treatments. While tests based on blood-borne biomarkers such as microRNAs have shown promise, work to date indicates these tests often do not generalize well: diagnostic models derived for one patient group are not accurate when applied to a new cohort. This paper presents a novel ensemble-based transfer learning methodology which induces models that provide accurate diagnoses across distinct patient groups without retraining.

Tissue-aware RNA-Seq processing and normalization for heterogeneous and sparse data.

Background: Although ultrahigh-throughput RNA-Sequencing has become the dominant technology for genome-wide transcriptional profiling, the vast majority of RNA-Seq studies typically profile only tens of samples, and most analytical pipelines are optimized for these smaller studies. However, projects are generating ever-larger data sets comprising RNA-Seq data from hundreds or thousands of samples, often collected at multiple centers and from diverse tissues. These complex data sets present significant analytical challenges due to batch and tissue effects, but provide the opportunity to revisit the assumptions and methods that we use to preprocess, normalize, and filter RNA-Seq data - critical first steps for any subsequent analysis.

Potential impact of a maternal vaccine for RSV: A mathematical modelling study.

Respiratory syncytial virus (RSV) is a major cause of respiratory morbidity and one of the main causes of hospitalisation in young children. While there is currently no licensed vaccine for RSV, a vaccine candidate for pregnant women is undergoing phase 3 trials. We developed a compartmental age-structured model for RSV transmission, validated using linked laboratory-confirmed RSV hospitalisation records for metropolitan Western Australia.