Bovine mortality: the utility of two data sources for the provision of population-level surveillance intelligence

Introduction: The use of existing data to provide surveillance intelligence is widely advocated but often presents considerable challenges. Two data sources could be used as proxies for the mortality experienced by the Scottish cattle population: deaths recorded in the mandatory register [Cattle Tracing System (CTS)] and fallen stock collections by the National Fallen Stock Company (NSFCo) with a nationwide voluntary membership.Methods: Data for the period 2011–2016 were described and compared to establish their strengths and limitations. Similarities and differences in their temporal, seasonal and spatial patterns were examined overall, at postcode area level and for different age groups. Temporal aberration detection algorithms (TADA) were fitted.Results: Broadly, similar patterns were observed in the two datasets; however, there were some notable differences. The observed seasonal, annual and spatial patterns match expectations, given knowledge of Scottish cattle production systems. The registry data provide more comprehensive coverage of all areas of Scotland, while collections data provide a more comprehensive measure of the mortality experienced in 0–1-month-old calves.Discussion: Consequently, estimates of early calf mortality and their impact on the livestock sector made using CTS, or successor registers, will be under-estimates. This may apply to other registry-based systems. Fitted TADA detected points of deviations from expected norms some of which coincided in the two datasets; one with a known external event that caused increased mortality. We have demonstrated that both data sources do have the potential to be utilized to provide measures of mortality in the Scottish cattle population that could inform surveillance activities. While neither is perfect, they are complementary. Each has strengths and weaknesses, so ideally, a system where they are analyzed and interpreted in parallel would optimize the information obtained for surveillance purposes for epidemiologists, risk managers, animal health policy-makers and the wider livestock industry sector. This study provides a foundation on which to build an operational system. Further development will require improvements in the timeliness of data availability and further investment of resources

Modular Biological Function Is Most Effectively Captured by Combining Molecular Interaction Data Types

PublishedLarge-scale molecular interaction data sets have the potential to provide a comprehensive, system-wide understanding of biological function. Although individual molecules can be promiscuous in terms of their contribution to function, molecular functions emerge from the specific interactions of molecules giving rise to modular organisation. As functions often derive from a range of mechanisms, we demonstrate that they are best studied using networks derived from different sources. Implementing a graph partitioning algorithm we identify subnetworks in yeast protein-protein interaction (PPI), genetic interaction and gene co-regulation networks. Among these subnetworks we identify cohesive subgraphs that we expect to represent functional modules in the different data types. We demonstrate significant overlap between the subgraphs generated from the different data types and show these overlaps can represent related functions as represented by the Gene Ontology (GO). Next, we investigate the correspondence between our subgraphs and the Gene Ontology. This revealed varying degrees of coverage of the biological process, molecular function and cellular component ontologies, dependent on the data type. For example, subgraphs from the PPI show enrichment for 84%, 58% and 93% of annotated GO terms, respectively. Integrating the interaction data into a combined network increases the coverage of GO. Furthermore, the different annotation types of GO are not predominantly associated with one of the interaction data types. Collectively our results demonstrate that successful capture of functional relationships by network data depends on both the specific biological function being characterised and the type of network data being used. We identify functions that require integrated information to be accurately represented, demonstrating the limitations of individual data types. Combining interaction subnetworks across data types is therefore essential for fully understanding the complex and emergent nature of biological function.JIM was funded by a Biotechnology and Biological Sciences Research Council (BBSRC) CASE studentship with industry partner Pfizer and RMA by a BBSRC studentship. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

Predicting individual-level income from Facebook profiles

Information about a person's income can be useful in several business-related contexts, such as personalized advertising or salary negotiations. However, many people consider this information private and are reluctant to share it. In this paper, we show that income is predictable from the digital footprints people leave on Facebook. Applying an established machine learning method to an income-representative sample of 2,623 U.S. Americans, we found that (i) Facebook Likes and Status Updates alone predicted a person's income with an accuracy of up to r = 0.43, and (ii) Facebook Likes and Status Updates added incremental predictive power above and beyond a range of socio-demographic variables (ΔR2 = 6-16%, with a correlation of up to r = 0.49). Our findings highlight both opportunities for businesses and legitimate privacy concerns that such prediction models pose to individuals and society when applied without individual consent

The first maps of κd - the dust mass absorption coefficient - in nearby galaxies, with DustPedia

The dust mass absorption coefficient, κd is the conversion function used to infer physical dust masses from observations of dust emission. However, it is notoriously poorly constrained, and it is highly uncertain how it varies, either between or within galaxies. Here we present the results of a proof-of-concept study, using the DustPedia data for two nearby face-on spiral galaxies M 74 (NGC 628) and M 83 (NGC 5236), to create the first ever maps of κd in galaxies. We determine κd using an empirical method that exploits the fact that the dust-to-metals ratio of the interstellar medium is constrained by direct measurements of the depletion of gas-phase metals. We apply this method pixel-by-pixel within M 74 and M 83, to create maps of κd. We also demonstrate a novel method of producing metallicity maps for galaxies with irregularly sampled measurements, using the machine learning technique of Gaussian process regression. We find strong evidence for significant variation in κd. We find values of κd at 500 μm spanning the range 0.11-0.25 m^{2 kg^{-1}} in M 74, and 0.15-0.80 m^{2 kg^{-1}} in M 83. Surprisingly, we find that κd shows a distinct inverse correlation with the local density of the interstellar medium. This inverse correlation is the opposite of what is predicted by standard dust models. However, we find this relationship to be robust against a large range of changes to our method - only the adoption of unphysical or highly unusual assumptions would be able to suppress it

A polynomial time biclustering algorithm for finding approximate expression patterns in gene expression time series

<p>Abstract</p> <p>Background</p> <p>The ability to monitor the change in expression patterns over time, and to observe the emergence of coherent temporal responses using gene expression time series, obtained from microarray experiments, is critical to advance our understanding of complex biological processes. In this context, biclustering algorithms have been recognized as an important tool for the discovery of local expression patterns, which are crucial to unravel potential regulatory mechanisms. Although most formulations of the biclustering problem are NP-hard, when working with time series expression data the interesting biclusters can be restricted to those with contiguous columns. This restriction leads to a tractable problem and enables the design of efficient biclustering algorithms able to identify all maximal contiguous column coherent biclusters.</p> <p>Methods</p> <p>In this work, we propose <it>e</it>-CCC-Biclustering, a biclustering algorithm that finds and reports all maximal contiguous column coherent biclusters with approximate expression patterns in time polynomial in the size of the time series gene expression matrix. This polynomial time complexity is achieved by manipulating a discretized version of the original matrix using efficient string processing techniques. We also propose extensions to deal with missing values, discover anticorrelated and scaled expression patterns, and different ways to compute the errors allowed in the expression patterns. We propose a scoring criterion combining the statistical significance of expression patterns with a similarity measure between overlapping biclusters.</p> <p>Results</p> <p>We present results in real data showing the effectiveness of <it>e</it>-CCC-Biclustering and its relevance in the discovery of regulatory modules describing the transcriptomic expression patterns occurring in <it>Saccharomyces cerevisiae </it>in response to heat stress. In particular, the results show the advantage of considering approximate patterns when compared to state of the art methods that require exact matching of gene expression time series.</p> <p>Discussion</p> <p>The identification of co-regulated genes, involved in specific biological processes, remains one of the main avenues open to researchers studying gene regulatory networks. The ability of the proposed methodology to efficiently identify sets of genes with similar expression patterns is shown to be instrumental in the discovery of relevant biological phenomena, leading to more convincing evidence of specific regulatory mechanisms.</p> <p>Availability</p> <p>A prototype implementation of the algorithm coded in Java together with the dataset and examples used in the paper is available in <url>http://kdbio.inesc-id.pt/software/e-ccc-biclustering</url>.</p

Assessing computer skills in Tanzanian medical students: an elective experience

Background: One estimate suggests that by 2010 more than 30% of a physician's time will be spent using information technology tools. The aim of this study is to assess the information and communication technologies (ICT) skills of medical students in Tanzania. We also report a pilot intervention of peer mentoring training in ICT by medical students from the UK tutoring students in Tanzania. Methods: Design: Cross sectional study and pilot intervention study. Participants: Fourth year medical students (n = 92) attending Muhimbili University College of Health Sciences, Dar es Salaam, Tanzania. Main outcome measures: Self-reported assessment of competence on ICT-related topics and ability to perform specific ICT tasks. Further information related to frequency of computer use (hours per week), years of computer use, reasons for use and access to computers. Skills at specific tasks were reassessed for 12 students following 4 to 6 hours of peer mentoring training. Results: The highest levels of competence in generic ICT areas were for email, Internet and file management. For other skills such as word processing most respondents reported low levels of competence. The abilities to perform specific ICT skills were low – less than 60% of the participants were able to perform the core specific skills assessed. A period of approximately 5 hours of peer mentoring training produced an approximate doubling of competence scores for these skills. Conclusion: Our study has found a low level of ability to use ICT facilities among medical students in a leading university in sub-Saharan Africa. A pilot scheme utilising UK elective students to tutor basic skills showed potential. Attention is required to develop interventions that can improve ICT skills, as well as computer access, in order to bridge the digital divide

Molecular and genetic characterization of OSH6 (Oryza sativa Homeobox 6) using dissociation (Ds) insertion mutant rice

Genetic studies of dissociation (Ds) insertion mutant rice plants indicated that ectopic expression of truncated OSH6 (Oryza sativa Homeobox 6) mRNA may be responsible for the mutant phenotype of knotted leaf formation at the peduncle. Additionally, ectopic expression of truncated OSH6 mRNA in the OSH6-Ds mutant plant led to alteration of other homeobox genes including OSH15 in leaf tissues. The OSH6-Ds mutant plant exhibited altered expression of more than 118 genes on a 22K rice microarray in comparison with wild type plants. Of these genes, 20 were up- or down-regulated in both OSH6-Ds and OSH6-overexpressing (OSH6-35S) plants. Especially, OsDof3 was not expressed in floral organs, but was present in the panicles of both OSH6-Ds and OSH6-35S plants. It is assumed that truncated OSH6 transcript might be actively involved in the gene expression during organ development. The genetic relationship between OSH6-Ds and OSH15 suggested that the formation of the extra leaf is independent of OSH6-Ds or OSH15 expression. These results suggest that truncated OSH6 mRNA influences lateral organ growth and development by regulating the expression of specific gene groups.Key words: Oryza sativa Homeobox 6 (OSH6) genes, Ds insertion lines, OSH15 mutant

Effects of brodifacoum and diphacinone exposure on four species of reptiles: tissue residue levels and survivorship

BACKGROUND: Anticoagulant rodenticides are used worldwide to control pest rodent species. However, the risks posed to nontarget reptiles have not been well characterized. In this study, 46 giant ameivas (Ameiva ameiva), 39 boa constrictors (Boa constrictor), 33 wood turtles (Rhinoclemmys pulcherrima), and 47 green iguanas (Iguana iguana) were orally dosed with one of two levels of either diphacinone or brodifacoum anticoagulant in propylene glycol solutions. Dosages were derived using daily food intake (DFI) equations, converting DFI to an equivalent anticoagulant bait amount and gavaging the solution volume needed to deliver the quantity of anticoagulant in that amount of bait. Animals were dosed on days 0 and 7 and monitored for a further 7 days for signs of anticoagulant intoxication and differences in behaviors and postures. At necropsy on day 14, animals were examined for thoracic and abdominal bleeding, and both tissue and organ samples were taken for histology. Liver and wholebody anticoagulant residues were assessed. RESULTS: No turtles or boas died due to anticoagulant exposure. However, anticoagulant intoxication was suspected in one iguana dosed with brodifacoum. A few treated ameivas died but exhibited no hemorrhaging. Liver residue levels were higher than whole-body remainder residue levels for all species. Unlike the other species, turtles had higher diphacinone residue levels than brodifacoum. CONCLUSION: Turtles and boas exhibited a relative insensitivity to diphacinone and brodifacoum, while the lizards appeared to be somewhat more sensitive to these compounds. This study provides data for future assessments of the risks to these species associated with anticoagulant use

Morgagni hernia repair in children over two decades: Institutional experience, systematic review, and meta-analysis of 296 patients

BACKGROUND/PURPOSE: Morgagni diaphragmatic hernia (MH) is rare. We report our experience based on routine patch use in MH repair to curb recurrence. A systematic review and meta-analysis were performed to study the recurrence and complications associated with minimally invasive surgery and the use of patch. METHODS: We retrospectively reviewed all cases of MH who underwent first-time repair in 2012-2017 in our institution to determine recurrence and complication rate. A MEDLINE search related to minimally invasive surgery (MIS) and patch repair of MH was conducted for systematic review. Eligible articles published from 1997-2017 with follow-up data available were included. Primary outcomes measured were recurrence and complication. Meta-analysis to compare open versus MIS and primary versus patch repair in the MIS group were performed in comparative cohorts. Continuous data were presented as median (range), and statistical significance was P<0.05. RESULTS: In our institution, 12 consecutive patients aged 17-month-old (22 days-7 years), underwent laparoscopic patch repair of MH, with one conversion to laparotomy. No recurrence or significant complication occurred over a follow-up period of 8 months (1-48 months). Thirty-six articles were included from literature review and were combined with the current series. All were retrospective case reports or series, of which 6 were comparative cohorts with both MIS and open repairs. A total of 296 patients from 37 series were ultimately used for analysis: 80 had open repair (4 patch) and 216 had MIS repair (32 patch), with a patch rate of 12%. There were 13 recurrences (4%): no difference between open and MIS repairs (4/80 vs 9/216, p=0.75); recurrence rate following primary repair was 13/260 (5%), but no recurrence occurred with 36 patch repairs. Meta-analysis showed no difference in recurrence between open and MIS repair (p=0.83), whereas patch repair was associated with 14% less recurrence compared with primary repair, although it did not reach statistical significance (p=0.12). There were 13 complications (5%): no difference between open and MIS repairs (5/80 vs 8/216, p=0.35). One small bowel obstruction occurred in a patient who had laparoscopic patch repair. CONCLUSION: In MH, recurrence and complication rates are comparable between MIS and open repairs. Use of patch appeared to confer additional benefit in reducing recurrence. TYPE OF STUDY: Systematic review LEVEL OF EVIDENCE: 3A