Ground-truthing airborne EM - Hydrochemical characterization of a coal mine plume

A trial airborne EM (AEM) survey was carried out across a 13 x 9 km area of the northern Nottinghamshire (UK) coalfield. One of the objectives was to examine the influence of collieries situated above the Triassic Sherwood Sandstone aquifer. The conductivity models obtained from the AEM survey revealed extensive zones of enhanced subsurface conductivity in the vicinity of all the collieries in the survey area. The purpose of the present study is to provide information regarding subsequent investigations (ground geophysics and borehole) to confirm the AEM results and to investigate the geochemical nature of the conductive zone identified in the vicinity of one of the collieries

The effects of acute inflammation on cognitive functioning and emotional processing in humans: A systematic review of experimental studies

This is the author accepted manuscript. The final version is available from Elsevier via the DOI in this record Objective The cognitive neuropsychological model of depression proposes that negative biases in the processing of emotionally salient information have a central role in the development and maintenance of depression. We have conducted a systematic review to determine whether acute experimental inflammation is associated with changes to cognitive and emotional processing that are thought to cause and maintain depression. Methods We identified experimental studies in which healthy individuals were administered an acute inflammatory challenge (bacterial endotoxin/vaccination) and standardised tests of cognitive function were performed. Results Fourteen references were identified, reporting findings from 12 independent studies on 345 participants. Methodological quality was rated strong or moderate for 11 studies. Acute experimental inflammation was triggered using a variety of agents (including endotoxin from E. coli, S. typhi, S. abortus Equi and Hepatitis B vaccine) and cognition was assessed over hours to months, using cognitive tests of i) attention/executive functioning, ii) memory and iii) social/emotional processing. Studies found mixed evidence that acute experimental inflammation caused changes to attention/executive functioning (2 of 6 studies showed improvements in attention executive function compared to control), changes in memory (3 of 5 studies; improved reaction time: reduced memory for object proximity: poorer immediate and delayed memory) and changes to social/emotional processing (4 of 5 studies; reduced perception of emotions, increased avoidance of punishment/loss experiences, and increased social disconnectedness). Conclusions Acute experimental inflammation causes negative biases in social and emotional processing that could explain observed associations between inflammation and depression.National Institute for Health Research (NIHR

Which comorbid conditions should we be analyzing as risk factors for healthcare-associated infections?

OBJECTIVETo determine which comorbid conditions are considered causally related to central-line associated bloodstream infection (CLABSI) and surgical-site infection (SSI) based on expert consensus.DESIGNUsing the Delphi method, we administered an iterative, 2-round survey to 9 infectious disease and infection control experts from the United States.METHODSBased on our selection of components from the Charlson and Elixhauser comorbidity indices, 35 different comorbid conditions were rated from 1 (not at all related) to 5 (strongly related) by each expert separately for CLABSI and SSI, based on perceived relatedness to the outcome. To assign expert consensus on causal relatedness for each comorbid condition, all 3 of the following criteria had to be met at the end of the second round: (1) a majority (&gt;50%) of experts rating the condition at 3 (somewhat related) or higher, (2) interquartile range (IQR)≤1, and (3) standard deviation (SD)≤1.RESULTSFrom round 1 to round 2, the IQR and SD, respectively, decreased for ratings of 21 of 35 (60%) and 33 of 35 (94%) comorbid conditions for CLABSI, and for 17 of 35 (49%) and 32 of 35 (91%) comorbid conditions for SSI, suggesting improvement in consensus among this group of experts. At the end of round 2, 13 of 35 (37%) and 17 of 35 (49%) comorbid conditions were perceived as causally related to CLABSI and SSI, respectively.CONCLUSIONSOur results have produced a list of comorbid conditions that should be analyzed as risk factors for and further explored for risk adjustment of CLABSI and SSI.Infect Control Hosp Epidemiol 2017;38:449–454</jats:sec

A transcriptomic time-series reveals differing trajectories during pre-floral development in the apex and leaf in winter and spring varieties of Brassica napus

Oilseed rape (Brassica napus) is an important global oil crop, with spring and winter varieties grown commercially. To understand the transcriptomic differences between these varieties, we collected transcriptomes from apex and leaf tissue from a spring variety, Westar, and a winter variety, Tapidor, before, during, and after vernalisation treatment, until the plants flowered. Large transcriptomic differences were noted in both varieties during the vernalisation treatment because of temperature and day length changes. Transcriptomic alignment revealed that the apex transcriptome reflects developmental state, whereas the leaf transcriptome is more closely aligned to the age of the plant. Similar numbers of copies of genes were expressed in both varieties during the time series, although key flowering time genes exhibited expression pattern differences. BnaFLC copies on A2 and A10 are the best candidates for the increased vernalisation requirement of Tapidor. Other BnaFLC copies show tissue-dependent reactivation of expression post-cold, with these dynamics suggesting some copies have retained or acquired a perennial nature. BnaSOC1 genes, also related to the vernalisation pathway, have expression profiles which suggest tissue subfunctionalisation. This understanding may help to breed varieties with more consistent or robust vernalisation responses, of special importance due to the milder winters resulting from climate change

A 2.75-Approximation Algorithm for the Unconstrained Traveling Tournament Problem

A 2.75-approximation algorithm is proposed for the unconstrained traveling tournament problem, which is a variant of the traveling tournament problem. For the unconstrained traveling tournament problem, this is the first proposal of an approximation algorithm with a constant approximation ratio. In addition, the proposed algorithm yields a solution that meets both the no-repeater and mirrored constraints. Computational experiments show that the algorithm generates solutions of good quality.Comment: 12 pages, 1 figur

The effect of adding comorbidities to current centers for disease control and prevention central-line–associated bloodstream infection risk-adjustment methodology

BACKGROUNDRisk adjustment is needed to fairly compare central-line–associated bloodstream infection (CLABSI) rates between hospitals. Until 2017, the Centers for Disease Control and Prevention (CDC) methodology adjusted CLABSI rates only by type of intensive care unit (ICU). The 2017 CDC models also adjust for hospital size and medical school affiliation. We hypothesized that risk adjustment would be improved by including patient demographics and comorbidities from electronically available hospital discharge codes.METHODSUsing a cohort design across 22 hospitals, we analyzed data from ICU patients admitted between January 2012 and December 2013. Demographics and International Classification of Diseases, Ninth Edition, Clinical Modification (ICD-9-CM) discharge codes were obtained for each patient, and CLABSIs were identified by trained infection preventionists. Models adjusting only for ICU type and for ICU type plus patient case mix were built and compared using discrimination and standardized infection ratio (SIR). Hospitals were ranked by SIR for each model to examine and compare the changes in rank.RESULTSOverall, 85,849 ICU patients were analyzed and 162 (0.2%) developed CLABSI. The significant variables added to the ICU model were coagulopathy, paralysis, renal failure, malnutrition, and age. The C statistics were 0.55 (95% CI, 0.51–0.59) for the ICU-type model and 0.64 (95% CI, 0.60–0.69) for the ICU-type plus patient case-mix model. When the hospitals were ranked by adjusted SIRs, 10 hospitals (45%) changed rank when comorbidity was added to the ICU-type model.CONCLUSIONSOur risk-adjustment model for CLABSI using electronically available comorbidities demonstrated better discrimination than did the CDC model. The CDC should strongly consider comorbidity-based risk adjustment to more accurately compare CLABSI rates across hospitals.Infect Control Hosp Epidemiol 2017;38:1019–1024</jats:sec

Network conduciveness with application to the graph-coloring and independent-set optimization transitions

We introduce the notion of a network's conduciveness, a probabilistically interpretable measure of how the network's structure allows it to be conducive to roaming agents, in certain conditions, from one portion of the network to another. We exemplify its use through an application to the two problems in combinatorial optimization that, given an undirected graph, ask that its so-called chromatic and independence numbers be found. Though NP-hard, when solved on sequences of expanding random graphs there appear marked transitions at which optimal solutions can be obtained substantially more easily than right before them. We demonstrate that these phenomena can be understood by resorting to the network that represents the solution space of the problems for each graph and examining its conduciveness between the non-optimal solutions and the optimal ones. At the said transitions, this network becomes strikingly more conducive in the direction of the optimal solutions than it was just before them, while at the same time becoming less conducive in the opposite direction. We believe that, besides becoming useful also in other areas in which network theory has a role to play, network conduciveness may become instrumental in helping clarify further issues related to NP-hardness that remain poorly understood

A newly-developed community microarray resource for transcriptome profiling in Brassica species enables the confirmation of Brassica-specific expressed sequences

<p>Abstract</p> <p>Background</p> <p>The <it>Brassica </it>species include an important group of crops and provide opportunities for studying the evolutionary consequences of polyploidy. They are related to <it>Arabidopsis thaliana</it>, for which the first complete plant genome sequence was obtained and their genomes show extensive, although imperfect, conserved synteny with that of <it>A. thaliana</it>. A large number of EST sequences, derived from a range of different <it>Brassica </it>species, are available in the public database, but no public microarray resource has so far been developed for these species.</p> <p>Results</p> <p>We assembled unigenes using ~800,000 EST sequences, mainly from three species: <it>B. napus</it>, <it>B. rapa </it>and <it>B. oleracea</it>. The assembly was conducted with the aim of co-assembling ESTs of orthologous genes (including homoeologous pairs of genes in <it>B. napus </it>from each of the A and C genomes), but resolving assemblies of paralogous, or paleo-homoeologous, genes (<it>i.e</it>. the genes related by the ancestral genome triplication observed in diploid <it>Brassica </it>species). 90,864 unique sequence assemblies were developed. These were incorporated into the BAC sequence annotation for the <it>Brassica rapa </it>Genome Sequencing Project, enabling the identification of cognate genomic sequences for a proportion of them. A 60-mer oligo microarray comprising 94,558 probes was developed using the unigene sequences. Gene expression was analysed in reciprocal resynthesised <it>B. napus </it>lines and the <it>B. oleracea </it>and <it>B. rapa </it>lines used to produce them. The analysis showed that significant expression could consistently be detected in leaf tissue for 35,386 unigenes. Expression was detected across all four genotypes for 27,355 unigenes, genome-specific expression patterns were observed for 7,851 unigenes and 180 unigenes displayed other classes of expression pattern. Principal component analysis (PCA) clearly resolved the individual microarray datasets for <it>B. rapa</it>, <it>B. oleracea </it>and resynthesised <it>B. napus</it>. Quantitative differences in expression were observed between the resynthesised <it>B. napus </it>lines for 98 unigenes, most of which could be classified into non-additive expression patterns, including 17 that showed cytoplasm-specific patterns. We further characterized the unigenes for which A genome-specific expression was observed and cognate genomic sequences could be identified. Ten of these unigenes were found to be <it>Brassica</it>-specific sequences, including two that originate from complex loci comprising gene clusters.</p> <p>Conclusion</p> <p>We succeeded in developing a <it>Brassica </it>community microarray resource. Although expression can be measured for the majority of unigenes across species, there were numerous probes that reported in a genome-specific manner. We anticipate that some proportion of these will represent species-specific transcripts and the remainder will be the consequence of variation of sequences within the regions represented by the array probes. Our studies demonstrated that the datasets obtained from the arrays can be used for typical analyses, including PCA and the analysis of differential expression. We have also demonstrated that <it>Brassica</it>-specific transcripts identified <it>in silico </it>in the sequence assembly of public EST database accessions are indeed reported by the array. These would not be detectable using arrays designed using <it>A. thaliana </it>sequences.</p

A carbohydrate-binding protein, B-GRANULE CONTENT 1, influences starch granule size distribution in a dose-dependent manner in polyploid wheat

In Triticeae endosperm (e.g. wheat and barley), starch granules have a bimodal size distribution (with A- and B-type granules) whereas in other grasses the endosperm contains starch granules with a unimodal size distribution. Here, we identify the gene, BGC1 (B-GRANULE CONTENT 1), responsible for B-type starch granule content in Aegilops and wheat. Orthologues of this gene are known to influence starch synthesis in diploids such as rice, Arabidopsis, and barley. However, using polyploid Triticeae species, we uncovered a more complex biological role for BGC1 in starch granule initiation: BGC1 represses the initiation of A-granules in early grain development but promotes the initiation of B-granules in mid grain development. We provide evidence that the influence of BGC1 on starch synthesis is dose dependent and show that three very different starch phenotypes are conditioned by the gene dose of BGC1 in polyploid wheat: normal bimodal starch granule morphology; A-granules with few or no B-granules; or polymorphous starch with few normal A- or B-granules. We conclude from this work that BGC1 participates in controlling B-type starch granule initiation in Triticeae endosperm and that its precise effect on granule size and number varies with gene dose and stage of development