bluuebunny/crossref_metadata_2025_split huggingface dataset:
Inference of Cell Type Composition from Human Brain Transcriptomic Datasets Illuminates the Effects of Age, Manner of Death, Dissection, and Psychiatric Diagnosis
Authors: Hagenauer Megan Hastings , Schulmann Anton , Li Jun Z. , Vawter Marquis P. , Walsh David M. , Thompson Robert C. , Turner Cortney A. , Bunney William E. , Myers Richard M. , Barchas Jack D. , Schatzberg Alan F. , Watson Stanley J. , Akil Huda 
Published: November 2016

AbstractPsychiatric illness is unlikely to arise from pathology occurring uniformly across all cell types in affected brain regions. Despite this, transcriptomic analyses of the human brain have typically been conducted using macro-dissected tissue due to the difficulty of performing single-cell type analyses with donated post-mortem brains. To address this issue statistically, we compiled a database of several thousand transcripts that were specifically-enriched in one of 10 primary cortical cell types in previous publications. Using this database, we predicted the relative cell type composition for 833 human cortical samples using microarray or RNA-Seq data from the Pritzker Consortium (GSE92538) or publicly-available databases (GSE53987, GSE21935, GSE21138, CommonMind Consortium). These predictions were generated by averaging normalized expression levels across transcripts specific to each cell type using our R-packageBrainInABlender(validated and publicly-released:https://github.com/hagenaue/BrainInABlender). Using this method, we found that the principal components of variation in the datasets strongly correlated with the neuron to glia ratio of the samples.This variability was not simply due to dissection – the relative balance of brain cell types appeared to be influenced by a variety of demographic, pre- and post-mortem variables. Prolonged hypoxia around the time of death predicted increased astrocytic and endothelial gene expression, illustrating vascular upregulation. Aging was associated with decreased neuronal gene expression. Red blood cell gene expression was reduced in individuals who died following systemic blood loss. Subjects with Major Depressive Disorder had decreased astrocytic gene expression, mirroring previous morphometric observations. Subjects with Schizophrenia had reduced red blood cell gene expression, resembling the hypofrontality detected in fMRI experiments. Finally, in datasets containing samples with especially variable cell content, we found that controlling for predicted sample cell content while evaluating differential expression improved the detection of previously-identified psychiatric effects. We conclude that accounting for cell type can greatly improve the interpretability of transcriptomic data.
Graph regularized, semi-supervised learning improves annotation ofde novotranscriptomes
Authors: Malik Laraib I. , Thatipally Shravya , Junneti Nikhil , Patro Rob 
Published: November 2016

AbstractWe present a new method, GRASS, for improving an initial annotation ofde novotranscriptomes. GRASS makes the shared-sequence relationships between assembled contigs explicit in the form of a graph, and applies an algorithm that performs label propagation to transfer annotations between related contigs and modifies the graph topology iteratively. We demonstrate that GRASS increases the completeness and accuracy of the initial annotation, allows for improved differential analysis, and is very efficient, typically taking 10s of minutes.
Gluten-Free Beer via Hydrodynamic Cavitation Assisted Brewing of Barley Malts
Authors: Albanese Lorenzo , Ciriminna Rosaria , Meneguzzo Francesco , Pagliaro Mario 
Published: November 2016

AbstractWe provide evidence that novel brewing technology based on controlled hydrodynamic cavitation greatly reduces gluten concentration in wort and finished beer. We advance the hypothesis that the degradation of proline, the most recalcitrant among gluten constituents, leads to gluten concentration reduction in the unfermented as well as in the fermenting wort and later during maturation. These findings are significant as the new cavitation-assisted technology could provide coeliac patients and gluten-intolerant people with gluten-free beer of high quality, offering an alternative to existing methods to lower the gluten concentration, which are detrimental to flavor and taste.
Can paid reviews promote scientific quality and offer novel career perspectives for young scientists?
Authors: Wurzbacher Christian , Grossart Hans-Peter , Kristiansson Erik , Nilsson R. Henrik , Unterseher Martin 
Published: November 2016

AbstractWe exemplify how community driven paid reviews could work in conjunction with a feed-back loop to young scientists. This would remove pressure from the conventional peer-review system and promote the integration of reviews into an academic career. This concept may eventually revive the community based journal type.
The Semantics of Adjective Noun Phrases in the Human Brain
Authors: Fyshe Alona , Sudre Gustavo , Wehbe Leila , Rafidi Nicole , Mitchell Tom M. 
Published: November 2016

AbstractAs a person reads, the brain performs complex operations to create higher order semantic representations from individual words. While these steps are effortless for competent readers, we are only beginning to understand how the brain performs these actions. Here, we explore semantic composition using magnetoencephalography (MEG) recordings of people reading adjective-noun phrases presented one word at a time. We track the neural representation of semantic information over time, through different brain regions. Our results reveal two novel findings: 1) a neural representation of the adjective is present during noun presentation, but this neural representation is different from that observed during adjective presentation 2) the neural representation of adjective semantics observed during adjective reading is reactivated after phrase reading, with remarkable consistency. We also note that while the semantic representation of the adjective during the reading of the adjective is very distributed, the later representations are concentrated largely to temporal and frontal areas previously associated with composition. Taken together, these results paint a picture of information flow in the brain as phrases are read and understood.
Inference of candidate germline mutator loci in humans from genome-wide haplotype data
Authors: Seoighe Cathal , Scally Aylwyn 
Published: November 2016

AbstractThe rate of germline mutation varies widely between species but little is known about the extent of variation in the germline mutation rate between individuals of the same species. Here we demonstrate that an allele that increases the rate of germline mutation can result in a distinctive signature in the genomic region linked to the affected locus, characterized by a number of haplotypes with a locally high proportion of derived alleles, against a background of haplotypes carrying a typical proportion of derived alleles. We searched for this signature in human haplotype data from phase 3 of the 1000 Genomes Project and report a number of candidate mutator loci, several of which are located close to or within genes involved in DNA repair or the DNA damage response. To investigate whether mutator alleles remained active at any of these loci, we usedde novomutation counts from human parent-offspring trios in the 1000 Genomes and Genome of the Netherlands cohorts, looking for an elevated number ofde novomutations in the offspring of parents carrying a candidate mutator haplotype at each of these loci. We found some support for two of the candidate loci, including one locus just upstream of theBRSK2gene, which is expressed in the testis and has been reported to be involved in the response to DNA damage.Author SummaryEach time a genome is replicated there is the possibility of error resulting in the incorporation of an incorrect base or bases in the genome sequence. When these errors occur in cells that lead to the production of gametes they can be incorporated into the germline. Such germline mutations are the basis of evolutionary change; however, to date there has been little attempt to quantify the extent of genetic variation in human populations in the rate at which they occur. This is particularly important because new spontaneous mutations are thought to make an important contribution to many human diseases. Here we present a new way to identify genetic loci that may be associated with an elevated rate of germline mutation and report the application of this method to data from a large number of human genomes, generated by the 1000 Genomes Project. Several of the candidate loci we report are in or near genes involved in DNA repair and some were supported by direct measurement of the mutation rate obtained from parent-offspring trios.
Enhancing Knowledge Discovery from Cancer Genomics Data with Galaxy
Authors: Albuquerque Marco A. , Grande Bruno M. , Ritch Elie J. , Jessa Selin , Krzywinski Martin , Grewal Jasleen K. , Shah Sohrab P. , Boutros Paul C. , Morin Ryan D. 
Published: November 2016

AbstractWe present a collection of Galaxy tools representing many popular algorithms for detecting somatic genetic alterations from cancer genome and exome data. We implemented methods for parallelization of these tools within Galaxy to accelerate runtime and have demonstrated their usability on cloud-based infrastructure and commodity hardware. Some tools represents extensions or refinement of existing toolkits to yield visualizations suited to cohort-wide cancer genomic analysis. For example, we present Oncocircos and Oncoprintplus, which generate data-rich summaries of exome-derived somatic mutation. Workflows that integrate several of these to perform some standard data integration and visualization tasks are demonstrated on a cohort of 96 diffuse large B-cell lymphomas, enabling the discovery of multiple candidate lymphoma-related genes that have not been reported previously.
Statistical Quality Scale 6 (SQS-6)
Authors: Fausto de Morais José , Pereira Borges Gecilmar , Fernandes do Prado Gilmar 
Published: November 2016

ABSTRACTContextThe statistical analysis is an important part of the process of assessing the quality of randomized controlled trials, unfortunately it tends to be underestimated or even omitted by editors, in this sense, scales that cover this gap becomes necessary.ObjectiveTo build a definition and a scale for assessing the quality of statistical analysis in randomized controlled trials.MethodsA content analysis on 16 biostatistics texts was considered in the building of the definition and of the scale. The indicators of quality were based on the description and presentation of results of articles.ResultsWe identify 32 quality indicators grouping in six dimensions: randomization and management of lost; sample size computation; use of mean and median; statistical test; use and interpretation of confidence interval and P-values. The scale range from 0 to 6 and score greater than three identify article with appropriate statistical analysis.ConclusionsThe scale presented three dimensions linked to quality of description and three linked to quality of used strategy.
FlyLimbTracker: an active contour based approach for leg segment tracking in unmarked, freely behavingDrosophila
Authors: Uhlmann Virginie , Ramdya Pavan , Delgado-Gonzalo Ricard , Benton Richard , Unser Michael 
Published: November 2016

AbstractUnderstanding the biological underpinnings of movement and action requires the development of tools for precise, quantitative, and high-throughput measurements of animal behavior.Drosophila melanogasterprovides an ideal model for developing such tools: the fly has unparalleled genetic accessibility and depends on a relatively compact nervous system to generate sophisticated limbed behaviors including walking, reaching, grooming, courtship, and boxing. Here we describe a method that uses active contours to semi-automatically track body and leg segments from video image sequences of unmarked, freely behavingDrosophila. We show that this approach is robust to wide variations in video spatial and temporal resolution and that it can be used to measure leg segment motions during a variety of locomotor and grooming behaviors. FlyLimbTracker, the software implementation of this method, is open-source and our approach is generalizable. This opens up the possibility of tracking leg movements in other species by modifications of underlying active contour models.Author SummaryIn terrestrial animals, including humans, fundamental actions like locomotion and grooming emerge from the displacement of multiple limbs through space. Therefore, precise measurements of limb movements are critical for investigating and, ultimately, understanding the neural basis for behavior. The vinegar fly,Drosophila melanogaster, is an attractive animal model for uncovering general principles about limb control since its genome and nervous system are easy to manipulate. However, existing methods for measuring leg movements in freely behavingDrosophilahave significant drawbacks: they require complicated experimental setups and provide limited information about each leg. Here we report a new method - and provide its open-source software implementation, FlyLimbTracker - for tracking the body and leg segments of freely behaving flies using only computational image processing approaches. We illustrate the power of this method by tracking fly limbs during five distinct walking and grooming behaviors and from videos across a wide range of spatial and temporal resolutions. Our approach is generalizable, allowing researchers to use and customize our software for limb tracking inDrosophilaand in other species.
Physical models of spatial genome organization
Authors: Slanina S.V. , Aleshchenko A.V. , Eidelman Y.A. , Andreev S.G. 
Published: November 2016

ABSTRACTRemodeling of nuclear organization occurs during normal cell development, differentiation and cancer. One of the biggest gaps of knowledge remains how to link the information on chromatin and chromosome structural organization with genes activity. In this paper we introduce some physical ideas and a general computational method demonstrating how genome 3D architecture and its remodeling can be quantitatively modeled. We study a hypothetical scenario of alterations of chromosome territories positioning in the course of cell proliferation. On this basis we obtain quantitative information about chromosomal contacts in the nucleus. We predict changes of radial distributions of contacts between chromosomal megabase domains during proliferation. The proposed modeling approach may be helpful in integrating experimental data on nuclear reorganization associated with normal development and with various diseases. This predictive modeling may find applications in genome research of normal and cancer cells, stem cell biology, biology of aging,etc.
Global-scale structure of the eelgrass microbiome
Authors: Fahimipour Ashkaan K , Kardish Melissa R , Eisen Jonathan A , Lang Jenna M , Green Jessica L , Stachowicz John J 
Published: November 2016

AbstractPlant-associated microorganisms are essential for their hosts' survival and performance. Yet, most plant microbiome studies to date have focused on terrestrial plant species sampled across relatively small spatial scales. Here we report results of a global-scale analysis of microbial communities associated with leaf and root surfaces of the marine eelgrassZostera marinathroughout its range in the Northern Hemisphere. By contrasting host microbiomes with those of their surrounding seawater and sediment communities, we uncovered the structure, composition and variability of microbial communities associated withZ. marina. We also investigated hypotheses about the mechanisms driving assembly of the eelgrass microbiome using a whole-genomic metabolic modeling approach. Our results reveal aboveground leaf communities displaying high variability and spatial turnover, that strongly mirror their adjacent coastal seawater microbiomes. In contrast, roots showed relatively low spatial turnover and were compositionally distinct from surrounding sediment communities — a result largely driven by the enrichment of predicted sulfur-oxidizing bacterial taxa on root surfaces. Metabolic modeling of enriched taxa was consistent with an assembly process whereby similarity in resource use drives taxonomic co-occurrence patterns on belowground, but not aboveground, host tissues. Our work provides evidence for a coreZ. marinaroot microbiome with putative functional roles and highlights potentially disparate processes influencing microbiome assembly on different plant compartments.
Locus-specific ChIP combined with NGS analysis reveals genomic regulatory regions that physically interact with thePax5promoter in a chicken B cell line
Authors: Fujita Toshitsugu , Kitaura Fusako , Yuno Miyuki , Suzuki Yutaka , Sugano Sumio , Fujii Hodaka 
Published: November 2016

AbstractChromosomal interactions regulate genome functions, such as transcription, via dynamic chromosomal organization in the nucleus. In this study, we identified genomic regions that physically bind to the promoter region of thePax5gene in the chicken B-cell line DT40, with the goal of obtaining mechanistic insight into transcriptional regulation through chromosomal interaction. Using insertional chromatin immunoprecipitation (iChIP) in combination with next-generation sequencing (NGS) (iChIP-Seq), we found that thePax5promoter bound to multiple genomic regions. The identified chromosomal interactions were independently confirmed byin vitroengineered DNA-binding molecule-mediated ChIP (in vitroenChIP) in combination with NGS (in vitroenChIP-Seq). Comparing chromosomal interactions in wild-type DT40 with those in a macrophage-like counterpart, we found that some of the identified chromosomal interactions were organized in a B cell–specific manner. In addition, deletion of a B cell–specific interacting genomic region in chromosome 11, which was marked by active enhancer histone modifications, resulted in moderate but significant down-regulation ofPax5transcription. Together, these results suggested thatPax5transcription in DT40 cells is regulated by inter-chromosomal interactions. Moreover, these analyses showed that iChIP-Seq andin vitroenChIP-Seq are useful for non-biased identification of functional genomic regions that physically interact with a locus of interest.
fMRI Correlates of Reaction Time Prolongation during intentional False Responding; an inter-individual difference study
Authors: Pishnamazi Morteza , Yeganeh Doost Maral , Ganjgahi Habib , Ekhtiari Hamed , Oghabian Mohammad Ali 
Published: November 2016

ABSTRACTReaction time (RT) is chiefly longer when people lie. However, the baseline speed in answering questions and the amount of RT prolongation during lying show considerable amount of inter-individual variability. In the current study, we exploited this fact to glean insights on the contribution of each lie-related brain region to hampering of response speeds when people try to be deceitful. In an event-related fMRI session, participants were interrogated by yes-no autobiographical questions and were instructed to intentionally provide false responses to a pre-selected subset of questions. Data from twenty healthy volunteers were analyzed.Baseline speed[RTtruth] andrelative appended lie RT[(RTlie− RTtruth) ⁄ RTtruth] measures were calculated for each participant and were included in the group level analysis of [lie > truth] BOLD contrasts. Lying RTs were significantly longer than truth telling RTs. Lie-related increase in activity of right ventrolateral prefrontal cortex (VLPFC) and bilateral paracingulate cortex correlated with the baseline speed of participants, while the increase in activity of Left VLPFC, left lateral occipital cortex and bilateral anterior cingulate areas directly correlated with the amount of lying reaction time cost. Activity within bilateral posterior cingulate cortex and right insular cortex inversely correlated with lying RT-cost. Bilateral supplementary motor areas, internal capsule white matter and left angular gyrus showed lie-related increase in activity but did not correlate with either of behavioral measures. Provisional implications regarding the contribution of these regions to RT prolongation and their cognitive role in deceitful behavior are discussed.
Hyphal aggregation and surface attachment ofStreptomycesis governed by extracellular poly-β-1,6-N-acetylglucosamine
Authors: van Dissel Dino , Willemse Joost , Zacchetti Boris , Claessen Dennis , Pier Gerald B. , van Wezel Gilles P. 
Published: November 2016

ABSTRACTStreptomycetes are multicellular filamentous microorganisms, which are major producers of antibiotics, anticancer drugs and industrial enzymes. When grown in submerged cultures, the preferred enzyme producer,Streptomyces lividans, forms dense mycelial aggregates or pellets, which requires the activity of the proteins encoded by thematABandcslA-glxA. Here we show that matAB encodes the biosynthetic genes for the extracellular polymeric substance (EPS) poly-β-1,6-N-acetylglucosamine or PNAG. Heterologous expression of matAB in actinomycetes that naturally lack these genes was sufficient for PNAG production and induction of mycelial aggregation. Also, overexpression ofmatABin a non-pelletingcslAmutant restored pellet formation, which could effectively be antagonized by the PNAG-specific hydrolase, dispersin B. Extracellular accumulation of PNAG allowedStreptomycesto attach to hydrophilic surfaces, unlike attachment to hydrophobic surfaces, which involves a cellulase-degradable EPS produced by CslA. Altogether, our data support a model in which pellet formation depends on hydrophilic interactions mediated by PNAG and hydrophobic interactions involving the EPS produced by CslA. These new insights may be harnessed to improve growth and industrial exploitation of these highly versatile natural product and enzyme producers.
The Eurozone Crisis and Emerging‐Market Expansion: Capital Switching and the Uneven Geographies of Spanish Urbanization
Authors: Kutz William 
Published: November 2016

AbstractThe theory of capitalist urbanization posits that the built form serves as a crucial sink through which overaccumulated capital is ‘switched' from industrial production into long‐term investment in urban infrastructure. Since Harvey's (1978) deployment of the theory, researchers have attempted to empirically substantiate the switching thesis with limited success. Christophers (2011) revisited the debate with new data and methods to support the claim that significant investment had switched into the built environment at the onset of the 2007/08 financial crisis. However, Christophers' study overlooks how crises are also geographically displaced. This article analyses Spanish trade data for the years 1993 to 2013, the years prior and subsequent to the housing‐induced economic crisis (1997 to 2006). Two studies are undertaken. The first replicates Christophers' methodology to assess how and to what extent a sectoral switch into property investment occurred in Spain between 1997 and 2006. The second modifies the methodology to investigate the extent to which overaccumulated capital in Spain has been geographically displaced through investment in the Moroccan building industry since 2006. These approaches situate uneven development (geographical switching) and turnover time (sectoral switching) as the twin dynamics through which capitalist urbanization is spatio‐temporally fixed.