bluuebunny/crossref_metadata_2025_split huggingface dataset:
Auditory prediction errors and auditory white matter microstructure as predictors of psychotic experiences in healthy individuals
Authors: Randeniya R. , Oestreich L.K.L. , Garrido M.I. 
Published: February 2019

AbstractOur sensory systems actively predict sensory information based on previously learnt patterns. An inability to accurately predict forthcoming information results in prediction errors. Individuals with schizophrenia consistently show reduced auditory prediction errors as well as reduced microstructure in auditory white matter pathways. However, it is not clear if also healthy individuals with psychotic experiences demonstrate such deficits. Participants underwent electroencephalography (EEG) recordings while listening to a simple two-tone duration deviant oddball paradigm (N=103) and a stochastic oddball paradigm (N=89). A subset of participants (N=89) also underwent diffusion-weighted magnetic resonance imaging (MRI), from which fractional anisotropy (FA), a measure of overall white matter microstructure, was obtained for auditory pathways namely the auditory interhemispheric pathway, as well as the left and right arcuate fasciculi. We investigated both structural and functional predictors of positive psychotic experiences in healthy participants as measured by the Community Assessment for Psychic Experiences positive dimension (CAPE+) scores. Prediction errors evoked by the classical oddball paradigm failed to reveal significant effects, whereas the stochastic oddball paradigm revealed significant clusters at typical mismatch negativity periods predictive of CAPE+ scores. Furthermore, we show that white matter microstructure from auditory pathways in addition to mismatches significantly predict CAPE+ scores. We suggest that structural and functional prediction error measures together may have potential in predicting psychotic experiences in the healthy population.
Spatially constrained tumour growth affects the patterns of clonal selection and neutral drift in cancer genomic data
Authors: Chkhaidze Kate , Heide Timon , Werner Benjamin , Williams Marc J. , Huang Weini , Caravagna Giulio , Graham Trevor A. , Sottoriva Andrea 
Published: February 2019

AbstractQuantification of the effect of spatial tumour sampling on the patterns of mutations detected in next-generation sequencing data is largely lacking. Here we use a spatial stochastic cellular automaton model of tumour growth that accounts for somatic mutations, selection, drift and spatial constrains, to simulate multi-region sequencing data derived from spatial sampling of a neoplasm. We show that the spatial structure of a solid cancer has a major impact on the detection of clonal selection and genetic drift from bulk sequencing data and single-cell sequencing data. Our results indicate that spatial constrains can introduce significant sampling biases when performing multi-region bulk sampling and that such bias becomes a major confounding factor for the measurement of the evolutionary dynamics of human tumours. We present a statistical inference framework that takes into account the spatial effects of a growing tumour and allows inferring the evolutionary dynamics from patient genomic data. Our analysis shows that measuring cancer evolution using next-generation sequencing while accounting for the numerous confounding factors requires a mechanistic model-based approach that captures the sources of noise in the data.SummarySequencing the DNA of cancer cells from human tumours has become one of the main tools to study cancer biology. However, sequencing data are complex and often difficult to interpret. In particular, the way in which the tissue is sampled and the data are collected, impact the interpretation of the results significantly. We argue that understanding cancer genomic data requires mathematical models and computer simulations that tell us what we expect the data to look like, with the aim of understanding the impact of confounding factors and biases in the data generation step. In this study, we develop a spatial simulation of tumour growth that also simulates the data generation process, and demonstrate that biases in the sampling step and current technological limitations severely impact the interpretation of the results. We then provide a statistical framework that can be used to overcome these biases and more robustly measure aspects of the biology of tumours from the data.
Intrinsic control of muscle attachment sites matching
Authors: Carayon Alexandre , Bataillé Laetitia , Lebreton Gaëlle , Dubois Laurence , Pelletier Aurore , Carrier Yannick , Wystrach Antoine , Vincent Alain , Frendo Jean-Louis 
Published: February 2019

AbstractHow a stereotypic muscle pattern is established, and adapted to fit locomotion behaviour is a fascinating question. Here we set up the targeted deletion of cis-regulatory modules (CRMs) controlling the transcription ofDrosophilamuscle identity transcription factors (iTF) to generate larval muscle identity mutants. By focusing on one muscle transcription and morphology, we show that selection of muscle attachment sites and the precision of muscle/muscle matching is intrinsic to muscle identity. It involves propagation of the iTF expression code from a founder myoblast to the other syncytial nuclei after fusion. Live imaging indicates that the precise staggered muscle attachment pattern involves attraction to tendon cells and homotypic repulsion. Unbalance leads to the formation of abnormal, branched muscles. Single muscle morphology shifts induce subtle locomotor behaviour. Together this work highlights that CRM deletion is an effective setting for creating muscle-specific defects and branched muscles, as new paradigms to study the development of human myopathies affecting subsets of muscles.Highlights–First muscle-identity mutants, via deletion of specific cis-regulatory modules–Reprogramming of syncytial nuclei is key to muscle morphological identity–Selection of muscle attachment sites; attraction and retraction intrinsic to muscle identity–Genetically controlled formation of branched muscles, a new paradigm for functional studies–Single muscle morphology shift induces subtle locomotor behaviour modification
Genetic, epigenetic and pharmacological influences modulating tissue specific regulation of the cannabinoid receptor-1 gene (CB1); implications for cannabinoid pharmacogenetics
Authors: Hay Elizabeth A. , Cowie Philip , McEwan Andrew , Wilson Dana , Ross Ruth , Barrett Perry , Pertwee Roger G. , MacKenzie Alasdair 
Published: February 2019

AbstractCannabinoid receptor-1 (CB1) represents a potential drug target against conditions that include obesity and substance abuse. However, drug trials targeting CB1(encoded by the CNR1 gene) have been compromised by differences in patient response. Towards addressing the hypothesis that genetic and epigenetic changes within the regulatory regions controlling CNR1 expression contribute to these differences, we isolated the human CNR1 promotor (CNR1prom) and demonstrate its activity in primary cells and transgenic mice. We also provide evidence of CNR1prom in CB1autoregulation and its repression by DNA-methylation. We further characterised a conserved regulatory sequence (ECR1) in CNR1 intron 2 that contained a polymorphism in linkage disequilibrium with disease associated SNPs. Deletion of ECR1 from mice using CRISPR genome editing significantly reduced CNR1 expression in the hippocampus. These mice also displayed reduced ethanol intake and hypothermia response to CB1agonism. Moreover, human specific C-allele variants of ECR1 (ECR1(C)) drove higher levels of CNR1prom activity in hippocampal cells than did the ancestral T-allele. We further demonstrate a role for the AP-1 transcription factor in driving higher ECR1(C) activity. In the context of the known roles of CB1the current study suggests a mechanism through which ECR1(C) may be neuroprotective in the hippocampus against stress. The cell-specific approaches used in our study to determine the functional effects of genetic and epigenetic changes on the activity of tissue-specific regulatory elements at the CNR1 locus represent an important step in gaining a mechanistic understanding of cannabinoid pharmacogenetics.
An Objective Technology-based Assessment of Arm and Hand Sensorimotor Disability in Neurological Disorders
Authors: Kanzler Christoph M. , Rinderknecht Mike D. , Schwarz Anne , Lamers Ilse , Gagnon Cynthia , Held Jeremia , Feys Peter , Luft Andreas R. , Gassert Roger , Lambercy Olivier 
Published: February 2019

AbstractBackgroundDetailed assessments of upper limb disability are essential to understand and monitor sensorimotor recovery. Usually, multiple timeconsuming assessments are required to define a holistic sensorimotor profile of proximal (shoulder-elbow) and distal (wrist-hand) impairments and their impact on the capacity to perform activities. We propose and evaluate a novel physiologically-motivated computational framework for objectively assessing sensorimotor profiles in neurological patients using a single, rapid technology-based assessment involving goal-directed arm and hand movements.MethodsThe Virtual Peg Insertion Test (VPIT) was administered to 121 healthy and 80 neurological subjects. The framework provides 25 kinematic and kinetic metrics expected to describe 12 sensorimotor components representative of ataxia and paresis and their influence on task performance, as well as one overall disability measure. The feasibility (protocol duration), structural validity (factor analysis and correlations ρ between sensorimotor components), concurrent validity (correlation with Action Research Arm Test; ARAT), and discriminant validity (comparing healthy controls and patients, and patients with different disability levels) were evaluated.ResultsThe median VPIT protocol duration was 16.5min in neurological patients. The sensor-based metrics could unambiguously be grouped into 12 mostly independent (median |ρ|=0.14) components. Ten components showed significant differences between healthy and impaired subjects and nine components indicated clear trends across disability levels, without any ceiling effects. The VPIT overall disability measure and ARAT were moderately correlated (ρ=−0.53, p<0.001).ConclusionsThis work demonstrates the possibility to rapidly, holistically, and objectively assess proximal and distal sensorimotor impairments and their influence on the capacity to perform activities with a single assessment.
Marine-freshwater prokaryotic transitions require extensive changes in the proteome
Authors: Cabello-Yeves Pedro J. , Rodriguez-Valera Francisco 
Published: February 2019

AbstractThe comparison of microbial genomes found in either freshwater or marine habitats indicated that in some cases (SynechococcusandCa. Pelagibacter) there were notable differences in the global isoelectric point (pI) of proteins. We have analysed global metagenomic proteomes and have added more prokaryotes to extend the pI comparison. Without exception, in a set that included archaea and multiple bacterial phyla, the proteome pI distribution varied, with more acidic values in marine and neutral/basic in freshwater microbes. Four pairs of highly related prokaryotes of marine and freshwater origin revealed marked differences manifested mostly in the residues located at the protein surface. This study has also shown that the magnitude of the change depended on protein location (secreted > cytoplasmic > transmembrane) and affected proteins encoded at both core and flexible genome. Our results point to a very extensive variation taking place in microbes when they move from marine (salt-rich) to freshwater habitats. These adaptations would require long evolutionary times to produce changes involving many genes in the core genome. They also point to significant differences in the physiology, probably at the level of membrane functioning, bioenergetics, intracellular ion concentration and pH (or all of them).
In planta chromatin immunoprecipitation in Zymoseptoria tritici reveals chromatin-based regulation of putative effector gene expression
Authors: Soyer Jessica L. , Grandaubert Jonathan , Haueisen Janine , Schotanus Klaas , Stukenbrock Eva H. 
Published: February 2019

SummaryDuring infection, pathogens secrete effectors, key elements of pathogenesis. In several phytopathogenic fungi, synchronous waves of effector genes are expressed during plant infection to manipulate and silence plant defenses. In Zymoseptoria tritici, causing septoria leaf blotch of wheat, at least two waves of effector genes are expressed, during the asymptomatic phase and at the switch to necrotrophy. The underlying factors responsible for the fine-tuned regulation of effector gene expression in this pathogen are unknown. Previously, a detailed map of the chromatin structure in vitro of Z. tritici was generated by chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) targeting histone modifications typical for euchromatin (di-methylation of the lysine 4 of the histone H3, H3K4me2) or heterochromatin (tri-methylation of the lysine 9 and 27 of the histone H3, H3K9me3 and H3K27me3). Based on the hypothesis that changes in the histone modifications contribute to the transcriptional control of pathogenicity-related genes, we tested whether different sets of genes are associated with different histone modifications in vitro. We correlated the in vitro histone maps with in planta transcriptome data and show that genes located in heterochromatic domains in vitro are highly up-regulated at the switch toward necrotrophy. We combined our integrated analyses of genomic, transcriptomic and epigenomic data with ChIP-qPCR in planta and thereby provide further evidence for the involvement of histone modifications in the transcriptional dynamic of putative pathogenicity-related genes of Z. tritici.
Patient satisfaction with nursing care in Ethiopia: A systematic review and meta-analysis
Authors: Mulugeta Henok , Wagnew Fasil , Dessie Getenet , Biresaw Henok , Habtewold Tesfa Dejenie 
Published: February 2019

AbstractBackgroundPatient satisfaction with nursing care has been considered as the most important predictor of the overall patient satisfaction with hospital service and quality of health care service at large. However, the national level of patient satisfaction with nursing care remains unknown. Hence, the objective of this systematic review and meta-analysis was to estimate patient satisfaction with nursing care in Ethiopia.MethodsStudies were accessed through an electronic web-based search strategy from PubMed, Cochrane Library, Google Scholar, Embase, PsycINFO and CINAHL by using combination search terms. Qualities of each included article assessed by using a modified version of the Newcastle-Ottawa Scale for cross-sectional studies. All statistical analyses were done using STATA version 14 software. The Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guideline was followed for reporting results.ResultsOf 1,166 records screened, 15 studies with 6091 participants were included. The estimated pooled level of patient satisfaction with nursing care in Ethiopia was 55.15% (95% CI (47.35, 62.95%)). Based on the subgroup analysis, the estimated level of patient satisfaction was 61.84% (95% CI: 44.49, 79.2) in Addis Ababa, 54.24 %(95%CI: 46.84, 61.65) in Amhara region, 44.06% (95%CI: 38.09, 50.03) in SNNP, and 53.02 %(95% CI: 50.03, 56.00) in other regions. Patients who have one nurse in charge [(OR 1.08(0.45, 2.62)], with no history of previous hospitalization [(OR 1.37(0.82, 2.31)], living in the urban area [(OR 1.07(0.70, 1.65)], / and those who have no comorbid disease [(OR 1.08(0.48, 2.62)] were more likely to be satisfied with nursing care than their counterparts even though it was not statistically significant.ConclusionThis meta-analysis revealed that about one in two patients were not satisfied with the nursing care provided in Ethiopia. Therefore, Ministry of Health should give more emphasis to the quality of nursing care in order to increase patient satisfaction which is important to improve the overall quality of healthcare service.
Modelling Subject Variability in the Spatial and Temporal Characteristics of Functional Modes
Authors: Harrison Samuel J. , Bijsterboch Janine D. , Segerdahl Andrew R. , Fitzgibbon Sean P. , Farahibozorg Seyedeh-Rezvan , Duff Eugene P. , Smith Stephen M. , Woolrich Mark W. 
Published: February 2019

AbstractRecent work has highlighted the scale and ubiquity of subject variability in observations from functional MRI data (fMRI). Furthermore, it is highly likely that errors in the estimation of either the spatial presentation of, or the coupling between, functional regions can confound cross-subject analyses, making accurate and unbiased representations of functional data essential for interpreting any downstream analyses.Here, we extend the framework of probabilistic functional modes (PFMs) [Harrison et al. 2015] to capture cross-subject variability not only in the mode spatial maps, but also in the functional coupling between modes and in mode amplitudes. A new implementation of the inference now also allows for the analysis of modern, large-scale data sets, and the combined inference and analysis package, PROFUMO, is available from git.fmrib.ox.ac.uk/samh/profumo. Using simulated data, resting-state data from 1,000 subjects collected as part of the Human Connectome Project [Van Essen et al. 2013], and an analysis of 14 subjects in a variety of continuous task-states [Kieliba et al. 2019], we demonstrate how PFMs are able to capture, within a single model, a rich description of how the spatio-temporal structure of resting-state fMRI activity varies across subjects.We also compare the new PFM model to the well established independent component analysis with dual regression (ICA-DR) pipeline. This reveals that, under PFM assumptions, much more of the (behaviorally relevant) cross-subject variability in fMRI activity should be attributed to the variability in spatial maps, and that, after accounting for this, functional coupling between modes primarily reflects current cognitive state. This has fundamental implications for the interpretation of cross-sectional studies of functional connectivity that do not capture cross-subject variability to the same extent as PFMs.
Long-term mark-recapture and growth data for large-sized migratory brown trout (Salmo trutta) from Lake Mjøsa, Norway
Authors: Moe S. Jannicke , Nater Chloé R. , Rustadbakken Atle , Vøllestad L. Asbjørn , Lund Espen , Qvenild Tore , Hegge Ola , Aass Per 
Published: February 2019

AbstractBackgroundLong-term data from marked animals provide a wealth of opportunities for studies with high relevance to both basic ecological understanding and successful management in a changing world. The key strength of such data is that they allow to quantify individual variation in vital rates (e.g. survival, growth, reproduction) and then link it mechanistically to dynamics at the population level. However, maintaining the collection of individual-based data over long time periods comes with large logistic efforts and costs, and studies spanning over decades are therefore rare. This is the case particularly for migratory aquatic species, many of which are in decline despite their high ecological, cultural, and economical value.New informationThis paper describes two unique publicly available time series of individual-based data originating from a 51-year mark-recapture study of a land-locked population of large-sized migratory brown trout (Salmo trutta) in Norway: the Hunder trout. In the period 1966-2015, nearly 14,000 adult Hunder trout have been captured and individually marked during their spawning migration from Lake Mjøsa to the river Gubrandsdalslågen. Almost a third of those individuals were later recaptured alive during a later spawning run and/or captured by fishermen and reported dead or alive. This has resulted in the first data series: a mark-recapture-recovery dataset spanning half a century and more than 18,000 capture records. The second data series consists of additional data on juvenile and adult growth and life-history schedules from half of the marked individuals, obtained by means of scale sample analysis. The two datasets offer a rare long-term perspective on individuals and population dynamics and provide unique opportunities to gain insights into questions surrounding management, conservation, and restoration of migratory salmonid populations and freshwater ecosystems.
Neural organization of speech production: A lesion-based study of error patterns in connected speech
Authors: Stark Brielle C , Basilakos Alexandra , Hickok Gregory , Rorden Chris , Bonilha Leonardo , Fridriksson Julius 
Published: February 2019

AbstractWhile numerous studies have explored single-word naming, few have evaluated the behavioral and neural correlates of more naturalistic language, like connected speech, which we produce every day. Here, in a retrospective analysis of 120 participants at least six months following left hemisphere stroke, we evaluated the distribution of word errors (paraphasias) and associated brain damage during connected speech (picture description) and object naming. While paraphasias in connected speech and naming shared underlying neural substrates, analysis of the distribution of paraphasias suggested that lexical-semantic load is likely reduced during connected speech. Using voxelwise lesion-symptom mapping (VLSM), we demonstrated that verbal (real word: semantically related and unrelated) and sound (phonemic and neologistic) paraphasias during both connected speech and naming loaded onto the left hemisphere ventral and dorsal streams of language, respectively. Furthermore, for the first time using both connected speech and naming data, we localized semantically related paraphasias to more anterior left hemisphere temporal cortex and unrelated paraphasias to more posterior left temporal and temporoparietal cortex. The connected speech results, in particular, highlight a gradient of specificity as one translates visual recognition from left temporo-occipital cortex to posterior and subsequently anterior temporal cortex. The robustness of VLSM results for sound paraphasias derived during connected speech was notable, in that analyses performed on sound paraphasias from the connected speech task, and not the naming task, demonstrated significant results following removal of lesion volume variance and related apraxia of speech variance. Therefore, connected speech may be a particularly sensitive task on which to evaluate further lexical-phonological processing in the brain. The results presented here demonstrate the related, though different, distribution of paraphasias during connected speech, confirm that paraphasias arising in connected speech and single-word naming likely share neural origins, and endorse the need for continued evaluation of the neural substrates of connected speech processes.