bluuebunny/crossref_metadata_2025_split huggingface dataset:
Minimal-assumption inference from population-genomic data
Authors: Weissman Daniel B. , Hallatschek Oskar 
Published: November 2016

AbstractSamples of multiple complete genome sequences contain vast amounts of information about the evolutionary history of populations, much of it in the associations among polymorphisms at different loci. Current methods that take advantage of this linkage information rely on models of recombination and coalescence, limiting the sample sizes and populations that they can analyze. We introduce a method, Minimal-Assumption Genomic Inference of Coalescence (MAGIC), that reconstructs key features of the evolutionary history, including the distribution of coalescence times, by integrating information across genomic length scales without using an explicit model of recombination, demography or selection. Using simulated data, we show that MAGIC’s performance is comparable to PSMC’ on single diploid samples generated with standard coalescent and recombination models. More importantly, MAGIC can also analyze arbitrarily large samples and is robust to changes in the coalescent and recombination processes. Using MAGIC, we show that the inferred coalescence time histories of samples of multiple human genomes exhibit inconsistencies with a description in terms of an effective population size based on single-genome data.
Ploidy tug-of-war: evolutionary and genetic environments influence the rate of ploidy drive in a human fungal pathogen
Authors: Gerstein Aleeza C. , Lim Heekyung , Berman Judith , Hickman Meleah A. 
Published: November 2016

AbstractVariation in baseline ploidy is seen throughout the tree of life, yet the factors that determine why one ploidy level is selected over another remain poorly understood. Experimental evolution studies using asexual fungal microbes with manipulated ploidy levels intriguingly reveals a propensity to return to the historical baseline ploidy, a phenomenon that we term ‘ploidy drive’. We evolved haploid, diploid, and polyploid strains of the human fungal pathogenCandida albicansunder three different nutrient limitation environments to test whether these conditions, hypothesized to select for low ploidy levels, could counteract ploidy drive. Strains generally maintained or acquired smaller genome sizes in minimal medium and under phosphorus depletion compared to in a complete medium, while mostly maintained or acquired increased genome sizes under nitrogen depletion. Surprisingly, improvements in fitness often ran counter to changes in total nuclear genome size; in a number of scenarios lines that maintained their original genome size often increased in fitness more than lines that converged towards diploidy. Combined, this work demonstrates a role for both the environment and genotype in determination of the rate of ploidy drive, and highlights questions that remain about the force(s) that cause genome size variation.
Phenopolis: an open platform for harmonization and analysis of sequencing and phenotype data
Authors: Pontikos Nikolas , Yu Jing , Blanco-Kelly Fiona , Vulliamy Tom , Wong Tsz Lun , Murphy Cian , Cipriani Valentina , Fiorentino Alessia , Arno Gavin , Greene Daniel , Jacobsen Julius OB , Clark Tristan , Gregory David S , Nemeth Andrea , Halford Stephanie , Downes Susan , Black Graeme C , Webster Andrew R , Hardcastle Alison , Plagnol Vincent 
Published: November 2016

AbstractSummaryPhenopolis is an open-source web server which provides an intuitive interface to genetic and phenotypic databases. It integrates analysis tools which include variant filtering and gene prioritisation based on phenotype. The Phenopolis platform will accelerate clinical diagnosis, gene discovery and encourage wider adoption of the Human Phenotype Ontology in the study of rare disease.Availability and ImplementationA demo of the website is available athttp://phenopolis.github.io(username: demo, password: demo123). If you wish to install a local copy, souce code and installation instruction are available athttps://github.com/pontikos/phenopolis. The software is implemented using Python, MongoDB, HTML/Javascript and various bash shell scripts.Contactn.pontikos@ucl.ac.ukSupplementary informationhttp://phenopolis.github.io
The natural selection of metabolism and mass selects allometric transitions from prokaryotes to mammals
Authors: Witting Lars 
Published: November 2016

AbstractInter-specific body mass allometries can evolve from the natural selection of mass, with ±1/4 and ±3/4 exponents following from the geometry of intra-specific interactions when density dependent foraging occurs in two spatial dimensions (2D, Witting, 1995). The corresponding values for three dimensional interactions (3D) are ±1/6 and ±5/6.But the allometric exponents in mobile organisms are more diverse than the prediction. The exponent for mass specific metabolism tends to cluster around −1/4 and −1/6 in terrestrial and pelagic vertebrates, but it is strongly positive in prokaryotes with an apparent value around 5/6 (DeLong et al., 2010). And a value around zero has been reported in protozoa, and on the macro evolutionary scale from prokaryotes over larger unicells to multicellular vertebrates (Makarieva et al., 2005, 2008).I show that mass specific metabolism can be selected as the pace of the resource handling that generates net energy for self-replication and the selection of mass, and that this selection of metabolism and mass is sufficient to explain metabolic exponents that decline from 5/6 over zero to −1/6 in 3D, and from 3/4 over zero to −1/4 in 2D. The decline follows from a decline in the importance of mass specific metabolism for the selection of mass, and it suggestsi) that the body mass variation in prokaryotes is selected from primary variation in mass specific metabolism,ii) that the variation in multicellular animals are selected from primary variation in the handling and/or densities of the underlying resources,iii) that protozoa are selected as an intermediate lifeform between prokaryotes and multicellular animals, andiv) that macro evolution proceeds along an upper bound on mass specific metabolism.
16S rRNA Gene Sequencing as a Clinical Diagnostic Aid for Gastrointestinal-related Conditions
Authors: Almonacid Daniel E. , Kraal Laurens , Ossandon Francisco J. , Budovskaya Yelena V. , Cardenas Juan Pablo , Richman Jessica , Apte Zachary S. 
Published: November 2016

AbstractAccurate detection of the microorganisms underlying gut dysbiosis in the patient is critical to initiate the appropriate treatment. However, most clinical microbiology techniques used to detect gut bacteria were developed over a century ago and rely on culture-based approaches that are often laborious, unreliable, and subjective. Further, culturing does not scale well for multiple targets and detects only a minority of the microorganisms in the human gastrointestinal tract. Here we present a clinical test for gut microorganisms based on targeted sequencing of the prokaryotic 16S rRNA gene. We tested 46 clinical prokaryotic targets in the human gut, 28 of which can be identified by a bioinformatics pipeline that includes sequence analysis and taxonomic annotation. Using microbiome samples from a cohort of 897 healthy individuals, we established a reference range defining clinically relevant relative levels for each of the 28 targets. Our assay accurately quantified all 28 targets and correctly reflected 38/38 verification samples of real and synthetic stool material containing known pathogens. Thus, we have established a new test to interrogate microbiome composition and diversity, which will improve patient diagnosis, treatment and monitoring. More broadly, our test will facilitate epidemiological studies of the microbiome as it relates to overall human health and disease.
Do latitudinal gradients exist in New Zealand stream invertebrate metacommunities?
Authors: Tonkin Jonathan D. , Death Russell G. , Muotka Timo , Astorga Anna , Lytle David A. 
Published: November 2016

AbstractThat biodiversity declines with latitude is well known, but whether a metacommunity process is behind this gradient has received limited attention. We tested the hypothesis that dispersal limitation is progressively replaced by mass effects with increasing latitude, along with a series of related hypotheses. We explored these hypotheses by examining metacommunity structure in stream invertebrate metacommunities spanning the length of New Zealand’s two largest islands (~1300 km), further disentangling the role of dispersal by deconstructing assemblages into strong and weak dispersers. Given the highly dynamic nature of New Zealand streams, our alternative hypothesis was that these systems are so unpredictable (at different stages of post-flood succession) that metacommunity structure is highly context dependent from region to region. We rejected our primary hypotheses, pinning this lack of fit on the strong unpredictability of New Zealand’s dynamic stream ecosystems and fauna that has evolved to cope with these conditions. While local community structure turned over along this latitudinal gradient, metacommunity structure was highly context dependent and dispersal traits did not elucidate patterns. Moreover, the emergent metacommunity types exhibited no trends, nor did the important environmental variables. These results provide a cautionary tale for examining singular metacommunities. The considerable level of unexplained contingency suggests that any inferences drawn from one-off snapshot sampling may be misleading and further points to the need for more studies on temporal dynamics of metacommunity processes.
Pavian: Interactive analysis of metagenomics data for microbiomics and pathogen identification
Authors: Breitwieser Florian P. , Salzberg Steven L. 
Published: November 2016

AbstractSummaryPavian is a web application for exploring metagenomics classification results, with a special focus on infectious disease diagnosis. Pinpointing pathogens in metagenomics classification results is often complicated by host and laboratory contaminants as well as many non-pathogenic microbiota. With Pavian, researchers can analyze, display and transform results from the Kraken and Centrifuge classifiers using interactive tables, heatmaps and flow diagrams. Pavian also provides an alignment viewer for validation of matches to a particular genome.Availability and implementationPavian is implemented in the R language and based on the Shiny framework. It can be hosted on Windows, Mac OS X and Linux systems, and used with any contemporary web browser. It is freely available under a GPL-3 license fromhttp://github.com/fbreitwieser/pavian. Furthermore a Docker image is provided athttps://hub.docker.com/r/florianbw/pavian.Contactfbreitw1@jhu.eduSupplementary informationSupplementary data is available at Bioinformatics online.
Dyslexia: is it genetic and what does this mean for social inclusion?
Authors: Holttum Sue 
Published: November 2016

Purpose
This paper starts by considering what it means if dyslexia has genetic or environmental causes. The author also explains phrases used by genetic researchers and the kind of things they look for in genetic material. The purpose of this paper is to discuss two recent studies on dyslexia that shed light on either genetic or environmental causes.

Design/methodology/approach
One study was a thorough exploration of possible genetic differences that could be present in children experiencing reading and language difficulties. The other study examined a large sample of the Canadian public to see whether there was a link between dyslexia and having experienced physical abuse as a child or teenager.

Findings
The study on genetic differences found no evidence for some previously suggested genetic causes of dyslexia. Although previous studies have suggested dyslexia runs in families, the genetic contribution may have been overestimated. The study on the Canadian public found that people who reported experiencing physical abuse in their younger years were six to seven times more likely also to have a diagnosis of dyslexia. Childhood trauma is known to affect brain development.

Originality/value
Although this paper only discusses two papers in detail, they are two of the most recent explorations of genetic and environmental links to dyslexia. There could be a case for greater attention to possible traumatic experiences in children identified as dyslexic. Physical abuse is one possibility but should never be assumed. Families can be under strain and may need more support. However, dyslexia and the mental health difficulties that can result from childhood trauma can reduce a child’s current and future social inclusion. Early intervention may avert this outcome.
Characterization of a laccase from a wood‐feeding termite, Coptotermes formosanus
Authors: Geng Alei , Wu Jian , Xie Rong‐Rong , Li Xia , Chang Fu‐Xiang , Sun Jian‐Zhong 
Published: November 2016

AbstractCoptotermes formosanus Shiraki is a wood‐feeding termite which secretes a series of lignolytic and cellulolytic enzymes for woody biomass degradation. However, the lignin modification mechanism in the termite is largely elusive, and the characteristics of most lignolytic enzymes in termites remain unknown. In this study, a laccase gene lac1 from C. formosanus was heterogeneously expressed in insect Sf9 cells. The purified Lac1 showed strong activities toward hydroquinone (305 mU/mg) and 2,6‐dimethoxyphenol (2.9 mU/mg) with low Km values, but not veratryl alcohol or 2,2’‐azino‐bis (3‐ethylbenzothiazoline‐6‐sulfonic acid). Lac1 could function well from pH 4.5 to 7.5, and its activity was significantly inhibited by H2O2 at above 4.85 mmol/L (P < 0.01). In addition, the lac1 gene was found to be mainly expressed in the salivary glands and foregut of C. formosanus, and seldom in the midgut or hindgut. These findings suggested that Lac1 is a phenol‐oxidizing laccase like RflacA and RflacB from termite Reticulitermes flavipes, except that Lac1 was found to be more efficient in phenol oxidation, and it did not require H2O2 for its function. It is suspected that this kind of termite laccase might only be able to directly oxidize low redox‐potential substrates, and the high redox‐potential groups in lignin might be oxidized by other enzymes in the termite or by using the Fenton reaction.
Hippocampal volume and the course of depressive symptoms over eight years of follow‐up
Authors: Buddeke J. , Kooistra M. , Zuithoff N. P. A. , Gerritsen L. , Biessels G. J. , van der Graaf Y. , Geerlings M. I. ,   the SMART Study Group
Published: November 2016

ObjectiveTo estimate the association between hippocampal and total brain volume and the course of depressive symptoms over eight years of follow‐up in patients with a history of vascular disease.MethodWithin the SMART‐Medea study, 636 participants (62 ± 10 years) had a 1.5‐tesla brain MRI obtaining hippocampal and total brain volumes. Depressive symptoms were assessed with the Patient Health Questionnaire‐9 biannually during eight‐year follow‐up. Generalized estimating equation models with robust standard errors were used to assess the associations of hippocampal and total brain volumes with depressive symptoms during follow‐up adjusting for age, sex, education, and intracranial volume. An interaction term between volume and time (6‐month intervals) was included to examine whether the course of depressive symptoms differed according to hippocampal and total brain volume.ResultsThe mean PHQ‐9 score was 2.8 ± 3.5. Smaller hippocampal volumes were associated with an increasing course of depressive symptom levels, while larger volumes were associated with decreasing levels (P‐value interaction = 0.07). Smaller total brain volume was associated with consistently higher levels of depressive symptoms, but not with change in course of depressive symptoms (P‐value interaction = 0.45).ConclusionSmaller hippocampal volume but not total brain volume is associated with poorer course of depressive symptoms over eight years of follow‐up.
Value of temporal artery biopsy length in diagnosing giant cell arteritis
Authors: Oh Lawrence J. , Wong Eugene , Gill Anthony J. , McCluskey Peter , Smith James E. H. 
Published: November 2016

BackgroundGiant cell arteritis (GCA) is considered an ophthalmological emergency with severe sight and life‐threatening sequelae. Temporal artery biopsy (TAB) is the current gold standard for the diagnosis of GCA; however, the required length of biopsy remains an issue of contention in the literature.MethodsRetrospective case–control study of a consecutive cohort of 545 patients who had undergone TABs across five hospitals between 1 January 1992 and 1 January 2016. In patients with either positive or negative TABs, we collected age, sex, biopsy length and erythrocyte sedimentation rate (ESR).ResultsA total of 538 patients were included in the final analysis. Of these, 23.4% of TABs were positive, with the average length being 17.6 mm. There was a significant difference in means for positive (19.9 mm) and negative (16.8 mm) biopsies (P = 0.0009). Each millimetre increase in TAB length increased the odds of a positive TAB by 3.4% (P = 0.024). A cut‐off point of ≥15 mm increased the odds of a positive TAB by 2.25 compared with a TAB <15 mm (P = 0.003). We also found that ESR ≥50 mm/h was a very strong predictor for a positive TAB result (P < 0.0001).ConclusionBiopsy length and ESR were significant predictors of a pathological diagnosis of GCA. We also found that the optimal length threshold predictive for GCA was 15 mm in order to avoid a false‐negative GCA diagnosis. Although TAB remains the gold standard for diagnosis, clinicians should refer to both clinical and pathological data to guide their management.
Computed tomography findings and surgical outcomes of dermoid sinuses: a case series
Authors: Appelgrein C , Hosgood G , Reese SL 
Published: November 2016

ObjectiveThis case series describes the computed tomography (CT) and surgical findings of nine dogs with dermoid sinuses.MethodsMedical records were reviewed and summarised.Results
CT with intravenous contrast showed a superficial, peripherally contrast‐enhancing, fluid‐filled structure with a contrast‐enhancing, soft tissue‐attenuating tract that extended from the skin through the dorsal midline soft tissues, often to the level of the nuchal ligament. The tract often extended in an oblique direction to the nuchal ligament, but the tract ventral to the nuchal ligament, found at surgery, was not always discernible on CT. The dermoid sinuses were excised from all dogs. At surgery, the tract often extended ventral to the nuchal ligament, terminating on the vertebra. The most ventral aspect of the tracts involved a fibrous strand extension of the sinus, which was not discernible on CT.ConclusionPreoperative CT facilitated the diagnosis of a dermoid sinus and directed surgical planning; however, careful dissection beyond the nuchal ligament is imperative for complete excision.
Children's Intrinsic Motivation to Provide Help Themselves After Accidentally Harming Others
Authors: Hepach Robert , Vaish Amrisha , Tomasello Michael 
Published: November 2016

Little is known about the flexibility of children's prosocial motivation. Here, 2‐ and 3‐year‐old children's (n = 128) internal arousal, as measured via changes in pupil dilation, was increased after they accidentally harmed a victim but were unable to repair the harm. If they were able to repair (or if they themselves did not cause the harm and the help was provided by someone else) their arousal subsided. This suggests that children are especially motivated to help those whom they have harmed, perhaps out of a sense of guilt and a desire to reconcile with them. Young children care not only about the well‐being of others but also about the relationship they have with those who depend on their help.
Estimating the Extent of CITES Noncompliance among Traders and End‐Consumers; Lessons from the Global Orchid Trade
Authors: Hinsley Amy , Nuno Ana , Ridout Martin , John Freya A.V. St , Roberts David L. 
Published: November 2016

AbstractThe Convention on the International Trade in Endangered Species of Wild Flora and Fauna (CITES) regulates trade in over 35,000 species, over 70% of which are orchids. To investigate rule‐breaking behavior among traders and buyers in a specific international wildlife trading community, we used direct questions (DQs) and the unmatched count technique (UCT) to survey the orchid growing community about CITES compliance and their knowledge and opinions of the rules. In DQ, 9.9% had smuggled, 4.8% had laundered, and 10.8% had been sent orchids from online purchases without paperwork; UCT estimates did not differ significantly. Growers with greater knowledge of CITES rules were more likely to break them, and there were widespread negative views of CITES among respondents. We recommend targeted enforcement focusing on both online trade and at the point of import, coupled with efforts to encourage traders and end‐consumers to engage with discussions on CITES rule implementation
Relative contributions of environmental and maternal factors to trans‐generational immune priming in T. castaneum
Authors: KENNEDY MEGAN , GRAHAM ANDREA L. , TATE ANN T. 
Published: November 2016

1. Trans‐generational immune priming is a phenomenon in insects in which the offspring of mothers previously challenged with a focal microbe exhibit a survival advantage when challenged with that microbe.2. Maternal egg provisioning with immune factors such as antimicrobial peptides (AMPs) is widely believed to contribute to the primed phenotype. However, other ‘socially mediated’ environmental factors secreted or excreted by the mother and others in the community, such as the gut microbiota or pheromones, may also affect offspring immune phenotype.3. The relative contributions of maternal egg provisioning and socially mediated environmental factors to the primed larval phenotype were assessed by performing a cross‐fostering survival experiment with Tribolium castaneum, in which the eggs of primed or naïve mothers were sterilised, treated with the frass of primed or naïve beetles, and challenged as larvae with the maternal pathogen, Bacillus thuringiensis.4. Larvae from primed mothers showed greater survival than unprimed larvae, regardless of frass treatment; maternal treatment therefore showed a substantially greater contribution to larval priming than frass treatment.5. Planned contrast tests to quantify the contributions of maternal and environmental matching revealed that maternal treatment mattered more for larvae exposed to primed, rather than unprimed, frass. This suggests that the effects of maternal egg provisioning may be exacerbated or mitigated by environmental factors.6. Thus, although maternal egg provisioning plays a predominant role in producing the primed phenotype, environmental matching may matter for priming in some contexts.