[Experimental] List of manuscripts available for review volunteers
5 manuscripts available for review volunteers
November 29, 2016
Worker honeybees (Apis mellifera) transmit Melissococcus plutonius between colonies. However, the transmission of M. plutonius, which causes European foulbrood (EFB), is poorly understood. To analyze the first EFB outbreak in 40 years in Czechia, we collected 49 hive worker samples from 18 beehives in two diseased apiaries for bacteriome analysis of the V1-V3 portion of the 16S rRNA gene. When we compared control samples obtained outside of the EFB zone, bees from an EFB apiaries containing colonies without clinical symptoms and bees from colonies with EFB clinical symptoms, there was a 100-fold higher occurrence of M. plutonius in colonies with EFB symptoms. The presence of M. plutonius in controls indicated that this pathogen exists in an enzootic state. EFB influenced the core bacteria in the worker bacteriome because the number of Snodgrassella alvi, Lactobacillus mellis, Lactobacillus melliventris, and Fructobacillus fructosus sequences increased, while Bartonella apis, Frischella perrara, and Commensalibacter intestine sequences decreased. Together, the results of this study suggest worker bees from EFB-diseased apiaries serve as vectors of M. plutonius, and eliminating such colonies is an appropriate method to overcome disease outbreaks. Because M. plutonius exists in honeybee colonies in an enzootic state, there may be similar abundances in control colonies outside the EFB zone to those in asymptomatic colonies from EFB apiaries. High-throughput Illumina next-generation sequencing permitted the quantitative interpretation of M. plutonius within the honeybee worker bacteriome. Future studies focusing on honeybee diseases, colony losses, detection of bacterial pathogens and interactions of bacteriome with pathogenic bacteria will benefit of this study.
November 26, 2016
Background. RNA-seq is a useful tool for analysis of gene expression. However its robustness is greatly affected by different artifacts. One of such artifacts is the presence of duplicated reads. Results. To infer the influence of different methods of removal of duplicated reads on estimation of gene expression for cancer genomics we analyzed paired samples of hepatocellular carcinoma (HCC) and non-tumor liver tissue. For each sample, four protocols of data analysis were applied: processing without deduplication, deduplication with method implemented in samtools, and deduplication based on one or two unique molecular indexes (UMI). We also analyzed the influence of sequencing layout (single read or paired end) and read length. We found that deduplication without UMI greatly alters estimated expression values; this effect is the most pronounced for highly expressed genes. Conclusion. The use of unique molecular identifiers greatly improves accuracy of RNA-seq analysis, especially for highly expressed genes. We developed a set of scripts that enable handling of UMI and their incorporation into RNA-seq analysis pipelines. Deduplication without UMI alters results of differential gene expression analysis, creating high fraction of false negative results. The absence of duplicate read removal is biased towards false positives. In cases where the use UMI is not possible, we recommend to use paired-end sequencing layout.
November 15, 2016

Objectives : The use of escorts (chauffeurs and chaperones) while on duty in after-hours-house-call (AHHC) is one key protective option available to doctors in the service and has been linked to low burnout and increased satisfaction in AHHC. This study aims to explore the patterns of engagement of escorts in Australian AHHC.

Method : This is a questionnaire-based, electronic survey of all 300 doctors involved in AHHC through the National Home Doctor Service (NHDS), Australia’s largest providers of the service.

Results :This survey received a total of 168 valid responses, giving a 56.0% response rate.60.8% of the doctors involved in AHHC engaged escorts (chauffeurs and chaperones). Of the doctors that engage chauffeurs, three-quarters do so “all or most times”, while only one-quarter engage chaperones to the same degree of frequency. Hiring escorts is very popular among Brisbane (91.7%) and Sydney-based (88.2%) practitioners, but is unpopular in the City of Gold Coast (26.1%). There were moderate patronages in Adelaide (52.9%) and Melbourne (46.4%). Compared to females, males were more likely to drive themselves (OR 5.34; P=0.001; CI 2.08 to 13.74) and less likely to use chauffeurs (OR 0.19; p<0.001; CI 0.07 to 0.51). Doctors in legally recognized social unions (OR 0.24; p=0.03; CI 0.07 to 0.83) and those that have attained the postgraduate fellowships (OR 0.43; p=0.02; CI 0.21 to 0.87) were both less likely to work without escorts.

Conclusion : More needs to be done to increase the engagement of escorts by doctors involved in the Australian AHHC, particularly given their proven benefits in the service. Future studies may be needed to fully explore the real reasons behind the significant associations identified in this study.

Key Words : General practice; after-hours, safety, protection, home visits, doctors, family physicians.

November 1, 2016
Wildlife collision data are ubiquitous, though challenging for making ecological inference due to typically irreducible uncertainty relating to the sampling process. We illustrate a new approach that is useful for generating inference from predator data arising from wildlife collisions. By simply conditioning on a second prey species sampled via the same collision process, and by using a biologically realistic numerical response functions, we can produce a coherent numerical response relationship between predator and prey. This relationship can then be used to make inference on the population size of the predator species, including the probability of extinction. The statistical conditioning enables us to account for unmeasured variation in factors influencing the runway strike incidence for individual airports and to enable valid comparisons. A practical application of the approach for testing hypotheses about the distribution and abundance of a predator species is illustrated using the hypothesized red fox incursion into Tasmania, Australia. We estimate that conditional on the numerical response between fox and lagomorph runway strikes on mainland Australia, the predictive probability of observing no runway strikes of foxes in Tasmania after observing 15 lagomorph strikes is 0.001. We conclude there is enough evidence to safely reject the null hypothesis that there is a widespread red fox population in Tasmania at a population density consistent with prey availability. The method is novel and has potential wider application.
August 24, 2016
Identifying the separate parts in ultrasound images such as bone and skin plays the crucial role in synovitis detection task. This paper presents a detector of bone and skin regions in the form of a classifier which is trained on a set of annotated images. Selected regions have labels: skin or bone or none. Feature vectors used by the classifier are assigned to image pixels as a result of passing the image through the bank of linear and nonlinear filters. The filters include Gaussian blurring filter, its first and second order derivatives, Laplacian as well as positive and negative threshold operations applied to the filtered images. We compared multiple supervised learning classifiers including Naive Bayes, k-Nearest Neighbour, Decision Trees, Random Forest, AdaBoost and Support Vector Machines (SVM) with various kernels, using four classification performance scores and computation time. The Random Forest classifier was selected for the final use, as it gives the best overall evaluation results.


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