Influenza classification from short reads with VAPOR facilitates robust mapping pipelines and zoonotic strain detection for routine surveillance applications

Motivation: Influenza viruses represent a global public health burden due to annual epidemics and pandemic potential. Due to a rapidly evolving RNA genome, inter-species transmission, intra-host variation, and noise in short-read data, reads can be lost during mapping, and de novo assembly can be time consuming and result in misassembly. We assessed read loss during mapping, and designed a graph-based classifier, VAPOR, for selecting mapping references, assembly validation, and detection of strains of non-human origin. Results: Standard human reference viruses were insufficient for mapping diverse influenza samples in simulation. VAPOR retrieved references for 257 real whole genome sequencing (WGS) samples with a mean of >99.8% identity to assemblies, and increased the proportion of mapped reads by up to 13.3% compared to standard references. VAPOR has the potential to improve the robustness of bioinformatics pipelines for surveillance and could be adapted to other RNA viruses

Medicaid Enrollment among Prison Inmates in a Non-expansion State: Exploring Predisposing, Enabling, and Need Factors Related to Enrollment Pre-incarceration and Post-Release

Prison inmates suffer from a heavy burden of physical and mental health problems and have considerable need for healthcare and coverage after prison release. The Affordable Care Act may have increased Medicaid access for some of those who need coverage in Medicaid expansion states, but inmates in non-expansion states still have high need for Medicaid coverage and face unique barriers to enrollment. We sought to explore barriers and facilitators to Medicaid enrollment among prison inmates in a non-expansion state. We conducted qualitative interviews with 20 recently hospitalized male prison inmates who had been approached by a prison social worker due to probable Medicaid eligibility, as determined by the inmates’ financial status, health, and past Medicaid enrollment. Interviews were transcribed verbatim and analyzed using a codebook with both thematic and interpretive codes. Coded interview text was then analyzed to identify predisposing, enabling, and need factors related to participants’ Medicaid enrollment prior to prison and intentions to enroll after release. Study participants’ median age, years incarcerated at the time of the interview, and projected remaining sentence length were 50, 4, and 2 years, respectively. Participants were categorized into three sub-groups based on their self-reported experience with Medicaid_ (1) those who never applied for Medicaid before prison (n = 6); (2) those who unsuccessfully attempted to enroll in Medicaid before prison (n = 3); and (3) those who enrolled in Medicaid before prison (n = 11). The six participants who had never applied to Medicaid before their incarceration did not hold strong attitudes about Medicaid and mostly had little need for Medicaid due to being generally healthy or having coverage available from other sources such as the Veteran’s Administration. However, one inmate who had never applied for Medicaid struggled considerably to access mental healthcare due to lapses in employer-based health coverage and attributed his incarceration to this unmet need for treatment. Three inmates with high medical need had their Medicaid applications rejected at least once pre-incarceration, resulting in periods without health coverage that led to worsening health and financial hardship for two of them. Eleven inmates with high medical need enrolled in Medicaid without difficulty prior to their incarceration, largely due to enabling factors in the form of assistance with the application by their local Department of Social Services or Social Security Administration, their mothers, medical providers, or prison personnel during a prior incarceration. Nearly all inmates acknowledged that they would need health coverage after release from prison, and more than half reported that they would need to enroll in Medicaid to gain healthcare coverage following their release. Although more population-based assessments are necessary, our findings suggest that greater assistance with Medicaid enrollment may be a key factor so that people in the criminal justice system who qualify for Medicaid—and other social safety net programs—may gain their rightful access to these benefits. Such access may benefit not only the individuals themselves but also the communities to which they return

The Behavioral Roots of Information Systems Security:Exploring Key Factors Related to Unethical IT Use

Unethical information technology (IT) use, related to activities such as hacking, software piracy, phishing, and spoofing, has become a major security concern for individuals, organizations, and society in terms of the threat to information systems (IS) security. While there is a growing body of work on this phenomenon, we notice several gaps, limitations, and inconsistencies in the literature. In order to further understand this complex phenomenon and reconcile past findings, we conduct an exploratory study to uncover the nomological network of key constructs salient to this phenomenon, and the nature of their interrelationships. Using a scenario-based study of young adult participants, and both linear and nonlinear analyses, we uncover key nuances of this phenomenon of unethical IT use. We find that unethical IT use is a complex phenomenon, often characterized by nonlinear and idiosyncratic relationships between the constructs that capture it. Overall, ethical beliefs held by the individuals, along with economic, social, and technological considerations are found to be relevant to this phenomenon. In terms of practical implications, these results suggest that multiple interventions at various levels may be required to combat this growing threat to IS security

Size Doesn't Matter: Towards a More Inclusive Philosophy of Biology

notes: As the primary author, O’Malley drafted the paper, and gathered and analysed data (scientific papers and talks). Conceptual analysis was conducted by both authors.publication-status: Publishedtypes: ArticlePhilosophers of biology, along with everyone else, generally perceive life to fall into two broad categories, the microbes and macrobes, and then pay most of their attention to the latter. ‘Macrobe’ is the word we propose for larger life forms, and we use it as part of an argument for microbial equality. We suggest that taking more notice of microbes – the dominant life form on the planet, both now and throughout evolutionary history – will transform some of the philosophy of biology’s standard ideas on ontology, evolution, taxonomy and biodiversity. We set out a number of recent developments in microbiology – including biofilm formation, chemotaxis, quorum sensing and gene transfer – that highlight microbial capacities for cooperation and communication and break down conventional thinking that microbes are solely or primarily single-celled organisms. These insights also bring new perspectives to the levels of selection debate, as well as to discussions of the evolution and nature of multicellularity, and to neo-Darwinian understandings of evolutionary mechanisms. We show how these revisions lead to further complications for microbial classification and the philosophies of systematics and biodiversity. Incorporating microbial insights into the philosophy of biology will challenge many of its assumptions, but also give greater scope and depth to its investigations

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Testing the robustness of transmission network models to predict ectoparasite loads. One lizard, two ticks and four years

We investigated transmission pathways for two tick species, Bothriocroton hydrosauri and Amblyomma limbatum, among their sleepy lizard (Tiliqua rugosa) hosts in a natural population in South Australia. Our aim was to determine whether a transmission network model continued to predict parasite load patterns effectively under varying ecological conditions. Using GPS loggers we identified the refuge sites used by each lizard on each day. We estimated infectious time windows for ticks that detached from a lizard in a refuge. Time windows were from the time when a detached tick molted and become infective, until the time it died from desiccation while waiting for a new host. Previous research has shown that A. limbatum molts earlier and survives longer than B. hydrosauri. We developed two transmission network models based on these differences in infective time windows for the two tick species. Directed edges were generated in the network if one lizard used a refuge that had previously been used by another lizard within the infectious time window. We used those models to generate values of network node in-strength for each lizard, a measure of how strongly connected an individual is to other lizards in the transmission network, and a prediction of infection risk for each host. The consistent correlations over time between B. hydrosauri infection intensity and network derived infection risk suggest that network models can be robust to environmental variation among years. However, the contrasting lack of consistent correlation in A. limbatum suggests that the utility of the same network models may depend on the specific biology of a parasite species

Behaviour of the western king prawn, Penaeus latisulcatus Kishinouye: effect of food dispersion and crowding

In aquacultural projects, crowding of prawns may adversely influence their growth and survival. In this paper, the behaviour of western king prawns, Penaeus latisulcatus, was investigated in tanks. Six forms of behaviour were identified. Prawns were exclusively nocturnal in their active behaviour. Males and females showed no significant difference in the mean time spent in various behaviours. Feeding efficiency increased as food became more dispersed over the tank floor. Behaviours leading to less efficient feeding increased with increased density, but less severely so if food was evenly dispersed than if food was presented at a point source