bluuebunny/crossref_metadata_2025_split huggingface dataset:
Disability and Health Consequences of Traumatic Brain Injury
Authors: Jourdan Claire , Azouvi Philippe , Genêt François , Selly Nicolas , Josseran Loic , Schnitzler Alexis 
Published: October 2017

Objective
The aim of the study was to measure the prevalence of traumatic brain injury (TBI)-related disability and health status in the general population.

Design
The French National Survey, conducted in households and institutions, assessed 33,896 adults. Data included sequelae from TBI, impairments, current health conditions, and uses of health services. Analyses, adjusted for age and sex, compared subjects who declared sequelae from TBI (n = 479) with the remaining survey population (n = 33,287). Use of weighting factors ensured that results were representative of the national population.

Results
Prevalence of persistent sequelae from TBI in France was 704/100,000. Median time since injury was 14 yrs. For all Core Set items of the International Classification of Functioning, subjects with TBI reported more impairments than the control population: adjusted odds ratios from 1.7 (behavioral difficulties) to 8.6 (motor difficulties). Rates of cardiovascular, respiratory, musculoskeletal, digestive, urological, neurological, and psychiatric conditions were higher in the TBI population. Use of health services was greater, and women with TBI had higher rates of unmet health needs.

Conclusions
Persistent sequelae from TBI significantly affect health in the general population. Planning of post-TBI care should address the chronic needs of these persons.
Feasibility and Reliability of Functional Muscle Tests in Lung Transplant Recipients
Authors: Kienbacher Thomas , Achim-Gunacker Grace , Pachner Melanie , Kerschan-Schindl Katharina , Gunacker Patrik , Habenicht Richard , Klepetko Walter , Jaksch Peter , Doblhammer Stephan , Ebenbichler Gerold 
Published: October 2017

Objective
This study investigates the feasibility, reliability, and correlations of recommended functional tests in lung transplant recipients shortly after surgery.

Design
This is an observational study.

Methods
Fifty patients (28 females) performed well-standardized maximum isometric back extension in a sitting position, handgrip strength, and Biering-Sørensen endurance tests shortly before discharge from the acute hospital, shortly thereafter, and 2 mos later after subacute rehabilitation.

Results
Back extension testing was well feasible, but only two thirds of the patients could perform the Biering-Sørensen test at baseline and they experienced a greater number of minor but no major adverse events. Absolute reliability measures and the intraclass correlation coefficients were excellent for the strength (0.97–0.98 [0.95–0.99]) and good for the endurance tests (0.69 [0.26–0.87]). Handgrip revealed high correlation with back strength (≥0.75) but not with Biering-Sørensen scores.

Conclusions
Well-controlled maximum back strength testing is feasible and reliable, and the scores are highly correlated with grip strength in lung transplant recipients shortly before hospital discharge. The Biering-Sørensen test should be limited to patients without dominant weakness and/or fear. Future research should investigate whether grip instead of back extension strength can safely be used for proper exercise prescription.
Depressive Symptoms, Antidepressant Medication Use, and Inflammatory Markers in the Diabetes Prevention Program
Authors: de Groot Mary , Marrero David , Mele Lisa , Doyle Todd , Schwartz Frank , Mather Kieren J. , Goldberg Ronald , Price David W. , Ma Yong , Knowler William C. 
Published: October 2017

ABSTRACT

Objective
Antidepressant medication use (ADM) has been shown to predict diabetes. This article assessed the role of inflammatory markers in this relationship within the Diabetes Prevention Program (DPP).

Methods
DPP participants randomized to metformin (MET), life-style intervention (ILS), or placebo (PLB) were assessed for depression (Beck Depression Inventory [BDI]) annually, ADM use semiannually, serum inflammatory markers (C-reactive protein [CRP], interleukin 6 [IL-6]) at baseline and year 1, and diagnosis of type 2 diabetes mellitus (T2DM) semiannually (for 3.2 years).

Results
At baseline (N = 3187), M (SD) body mass index was 34 (6) kg/m2 and the median (interquartile range) BDI score was 3 (1–7). One hundred eighty-one (5.7%) reported ADM use and 328 (10%) had BDI scores of 11 or higher. CRP and IL-6 levels did not differ by treatment group. Baseline ADM, but not BDI score, was associated with higher levels of baseline CRP adjusted for demographic, anthropometric variables, and other medications (20% higher, p = .01). Year 1 CRP decreased for non-ADM users in the MET (−13.2%) and ILS (−34%) groups and ADM users in the ILS group (−29%). No associations were found with IL-6. CRP and continuous use of ADM predicted incident T2DM in the PLB group. In the ILS group, continuous and intermittent ADM, but not CRP, predicted T2DM. In the MET group, CRP predicted incident T2DM. CRP did not mediate the risk of T2DM with ADM use in any group.

Conclusions
ADM was significantly associated with elevated CRP and incident T2DM. In the PLB group, ADM and CRP independently predicted onset of T2DM; however, CRP did not significantly mediate the effect of ADM.
Methods in field chronobiology
Authors: Dominoni Davide M. , Åkesson Susanne , Klaassen Raymond , Spoelstra Kamiel , Bulla Martin 
Published: October 2017

Chronobiological research has seen a continuous development of novel approaches and techniques to measure rhythmicity at different levels of biological organization from locomotor activity (e.g. migratory restlessness) to physiology (e.g. temperature and hormone rhythms, and relatively recently also in genes, proteins and metabolites). However, the methodological advancements in this field have been mostly and sometimes exclusively used only in indoor laboratory settings. In parallel, there has been an unprecedented and rapid improvement in our ability to track animals and their behaviour in the wild. However, while the spatial analysis of tracking data is widespread, its temporal aspect is largely unexplored. Here, we review the tools that are available or have potential to record rhythms in the wild animals with emphasis on currently overlooked approaches and monitoring systems. We then demonstrate, in three question-driven case studies, how the integration of traditional and newer approaches can help answer novel chronobiological questions in free-living animals. Finally, we highlight unresolved issues in field chronobiology that may benefit from technological development in the future. As most of the studies in the field are descriptive, the future challenge lies in applying the diverse technologies to experimental set-ups in the wild.
This article is part of the themed issue ‘Wild clocks: integrating chronobiology and ecology to understand timekeeping in free-living animals’.
Speech tracking in auditory and motor regions reflects distinct linguistic features
Authors: Keitel Anne , Gross Joachim , Kayser Christoph 
Published: October 2017

AbstractDuring online speech processing, our brain tracks the acoustic fluctuations in speech at different time-scales. Previous research has focussed on generic time-scales (for example, delta or theta bands) that are assumed to map onto linguistic features such as prosody or syllables. However, given the high inter-subject variability in speaking patterns, such a generic association between the time-scales of brain activity and speech properties can be ambiguous. Here, we analyse speech tracking in source-localised magnetoencephalographic data by directly focusing on time-scales extracted from statistical regularities in the speech material. This revealed widespread tracking at the time-scales of phrases (0.6 – 1.3 Hz), words (1.8 – 3 Hz), syllables (2.8 – 4.8 Hz), and phonemes (8 – 12.4 Hz). Importantly, when examining the relevance for single-trial comprehension, we found stronger tracking for correctly comprehended trials in the left premotor cortex at the phrasal scale, and in left middle temporal cortex at the word scale. Control analyses using generic bands confirmed that these effects were specific to the stimulus-tailored speech regularities. Furthermore, we found that the phase at the phrasal time-scale coupled to beta-power in motor areas. This cross-frequency coupling likely mediates the comprehension effect in the motor system, and implies top-down temporal prediction in speech perception. Together, our results reveal specific functional and perceptually relevant roles of distinct entrainment processes along the auditory-motor pathway. These processes act concurrently at time-scales within the traditional delta band and highlight the role of neural tracking mechanisms that reflect the temporal characteristics of speech.
Comparing Cell Division- and Cell Reproduction-based Cell Lineage Analysis for Early Embryogenesis ofCaenorhabditis elegans
Authors: Liu Shi V. 
Published: October 2017

ABSTRACTCell lineage analysis holds important stakes for understanding heredity and cell differentiation. Conventional cell lineages are reconstructed according to a cell division doctrine of one mother cell dividing into two daughter cells. An alternative cell lineage reconstruction method followed a cell reproduction discovery of multiple daughter cells reproduced from a same mother cell. To see which reconstruction method reflects reality of early embryogenesis ofCaenorhabditis elegans, a side-by-side comparison was made between two methods. Here I show cell division-based lineage distorted reality and failed in revealing any true genealogy. Cell reproduction – based lineage conformed to reality with exact same number of cells in every developmental stage under examination and showed clear genealogical relationship. A paradigm-shift from cell division-to cell reproduction-based cell lineage analysis is necessary for correct understanding of developmental biology and will lead to a revolution in cell biology and life science.
Working Memory Training Integrates Visual Cortex into Beta-Band Networks in Congenitally Blind Individuals
Authors: Rimmele Johanna M. , Gudi-Mindermann Helene , Nolte Guido , Röder Brigitte , Engel Andreas K. 
Published: October 2017

AbstractCongenitally blind individuals activate the visual cortex during non-visual tasks. Such crossmodal reorganization is likely associated with changes in large-scale functional connectivity, the spectral characteristics of which can be assessed by analysis of neural oscillations. To test visual cortical integration into working memory networks, we recorded magnetoencephalographic data from congenitally blind and sighted individuals during resting state as well as during a voice-based working memory task prior to and following working memory training with voices, or tactile stimuli or a training-control condition. Auditory training strengthened beta-band (17.5-22.5 Hz) connectivity (imaginary coherency) in the blind and theta-band (2.5-5 Hz) connectivity in the sighted during the task, suggesting different neural coupling mechanisms. In the sighted, theta-band connectivity increased between brain areas involved in auditory working memory (inferior frontal, superior temporal, insular cortex). In the blind, beta-band networks largely emerged during the training, and connectivity increased between brain areas involved in auditory working memory and the visual cortex. The prominent involvement of the right fusiform face area in this beta-band network suggests a task-specific integration of visual cortex. Our findings highlight large-scale interactions as a key mechanism of functional reorganization following congenital blindness, and provide new insights into the spectral characteristics of the mechanism.
OPRM1A118G and serum β-endorphin interact with sex and digit ratio (2D:4D) to influence risk and course of alcohol dependence
Authors: Gegenhuber Jordan Bruno , Weinland Christian , Kornhuber Johannes , Mühle Christiane , Lenz Bernd 
Published: October 2017

AbstractActivation of mesolimbic mu-opioid receptor by its endogenous ligand, β-endorphin, mediates part of the rewarding effects of alcohol, yet there is controversial evidence surrounding the relationship between the functional mu-opioid receptor gene (OPRM1) A118G single nucleotide polymorphism and alcohol dependence risk. Some preclinical evidence suggests that sex and sex hormone-dependent prenatal brain organization may interact with the opioid system to influence alcohol drinking behavior. We genotyped 200 alcohol-dependent patients and 240 healthy individuals for the A118G variant and measured serum β-endorphin level at recruitment and during acute withdrawal. We then evaluated the association between these factors and alcohol dependence risk and outcome in the context of both sex and second-to-fourth digit length ratio (2D:4D) – a biomarker of prenatal sex hormone load. For the first time, the AA genotype was found to be associated with elevated alcohol-related hospital readmission risk, more readmissions, and fewer days until first readmission in male but not female patients. Upon accounting for 2D:4D, the G-allele predicted alcohol dependence and more readmissions (1 vs ≥2) in males, suggesting prenatal sex hormones interact withOPRM1to influence addiction pathology. Withdrawal β-endorphin level also correlated negatively with withdrawal severity in females but not in males, indicating β-endorphin might protect against withdrawal-induced stress in a sex-specific manner. Organizational effects of sex hormones may prime individuals for alcohol dependence by inducing permanent changes to the endogenous opioid system.
Microfluidic Transfection for High-Throughput Mammalian Protein Expression
Authors: Woodruff Kristina , Maerkl Sebastian J. 
Published: October 2017

ABSTRACTMammalian synthetic biology and cell biology would greatly benefit from improved methods for highly parallel transfection, culturing and interrogation of mammalian cells. Transfection is routinely performed on high-throughput microarrays, but this setup requires manual cell culturing and precludes precise control over the cell environment. As an alternative, microfluidic transfection devices streamline cell loading and culturing. Up to 280 transfections can be implemented on the chip at high efficiency. The culturing environment is tightly regulated and chambers physically separate the transfection reactions, preventing cross-contamination. Unlike typical biological assays that rely on end-point measurements, the microfluidic chip can be integrated with high-content imaging, enabling the evaluation of cellular behavior and protein expression dynamics over time.
Mapfuser: an integrative toolbox for consensus map construction and Marey maps
Authors: van Muijen Dennis , Basnet Ram K. , Dek Nathalie N.J. , Maliepaard Chris , Gutteling Evert W. 
Published: October 2017

AbstractMotivationWhere standalone tools for genetic map visualisation, consensus map construction, and Marey map analysis offer useful analyses for research and breeding, no single tool combines the three. Manual data curation is part of each of these analyses, which is difficult to standardize and consequently error prone.ResultsMapfuser provides a high-level interface for common analyses in breeding programs and quantitative genetics. Combined with interactive visualisations and automated quality control, mapfuser provides a standardized and flexible toolbox and is available as Shiny app for biologists. Reproducible research in the R package is facilitated by storage of raw data, function parameters, and results in an R object. In the shiny app a rmarkdown report is available.AvailabilityMapfuser is available as R package athttps://github.com/dmuijen/mapfuserunder the GPL-3 License and is available for public use as Shiny application athttps://plantbreeding.shinyapps.io/mapfuser. Documentation for the R package is available as package vignette. Shiny app documentation is integrated in the application.Contactdennis.vanmuijen@wur.nl
Umbilical Cord Blood Diagnostics for Early Onset Sepsis in Premature Infants: Detection of Bacterial DNA and Systemic Inflammatory Response
Authors: Mithal Leena B. , Malczynski Michael , Qi Chao , Green Stefan , Seed Patrick C. , Mestan Karen K. 
Published: October 2017

Statement of financial support:This work has been supported by a Thrasher Research Fund Early Career Award (#12573), National Institutes of Health (K23 HL093302 [KKM], R01GM108494 [PCS])), the Gerber Foundation, the Hartwall Foundation, and the Northwestern Memorial Foundation (Friends of Prentice Grants Initiative).Disclosure statementThe authors of this manuscript have no conflicts of interest to disclose.Category of StudyTranslational
Assessment of batch-correction methods for scRNA-seq data with a new test metric
Authors: Büttner Maren , Miao Zhichao , Wolf F Alexander , Teichmann Sarah A , Theis Fabian J 
Published: October 2017

AbstractSingle-cell transcriptomics is a versatile tool for exploring heterogeneous cell populations. As with all genomics experiments, batch effects can hamper data integration and interpretation. The success of batch effect correction is often evaluated by visual inspection of dimension-reduced representations such as principal component analysis. This is inherently imprecise due to the high number of genes and non-normal distribution of gene expression. Here, we present a k-nearest neighbour batch effect test (kBET,https://github.com/theislab/kBET) to quantitatively measure batch effects. kBET is easier to interpret, more sensitive and more robust than visual evaluation and other measures of batch effects. We use kBET to assess commonly used batch regression and normalisation approaches, and quantify the extent to which they remove batch effects while preserving biological variability. Our results illustrate that batch correction based on log-transformation orscranpooling followed byComBatreduced the batch effect while preserving structure across data sets. Finally we show that kBET can pinpoint successful data integration methods across multiple data sets, in this case from different publications all charting mouse embryonic development. This has important implications for future data integration efforts, which will be central to projects such as the Human Cell Atlas where data for the same tissue may be generated in multiple locations around the world.[Before final publication, we will upload the R package to Bioconductor]
The role of m6A-RNA methylation in stress response regulation
Authors: Engel Mareen , Röh Simone , Eggert Carola , Kaplick Paul M. , Tietze Lisa , Arloth Janine , Weber Peter , Rex-Haffner Monika , Jakovcevski Mira , Uhr Manfred , Eder Matthias , Wotjak Carsten T. , Schmidt Mathias V. , Deussing Jan M. , Binder Elisabeth B. , Chen Alon 
Published: October 2017

SummaryN6-Methyladenosine (m6A) is an abundant internal RNA modification that regulates transcript processing and translation. The regulation of brain m6A by stressful stimuli in vivo and its role in the stress response are currently unknown.Here, we provide a detailed analysis of the stress-epitranscriptome using m6A-Seq, global and gene-specific m6A measurements. We show that stress exposure and glucocorticoids alter m6A and its regulatory network in a region- and time-specific manner. We demonstrate that depletion of the methyltransferase Mettl3 and the demethylase Fto in adult neurons increases fear memory, and alters the transcriptome response to fear as well as synaptic plasticity. Finally, we report that regulation of m6A is impaired in major depressive disorder patients following glucocorticoid receptor activation.Our findings indicate that brain m6A represents a novel layer of complexity in gene expression regulation after stress and that dysregulation of the m6A-response may contribute to the pathophysiology of stress-related psychiatric disorders.Highlightsm6A RNA methylation in adult mouse brain is regulated by stressBrain m6A levels are temporally and spatially regulated by stressMettl3 and Fto-KO alter fear memory, transcriptome response and synaptic plasticityThe m6A-glucocorticoid-response is impaired in major depressive disorder patientseTOC blurbEngel et al. demonstrate a brain-area-specific and time-dependent role for the mRNA modification, m6A, in stress-response regulation. Manipulating m6A-enzymes alters fear-memory, transcriptome-response and synaptic-plasticity. Altered m6A dynamics in depressed patients suggest an involvement of m6A-modifications in stress-related psychiatric disorders.
Identification of Memory Reactivation during Sleep by EEG Classification
Authors: Belal Suliman , Cousins James , El-Deredy Wael , Parkes Laura , Schneider Jules , Tsujimura Hikaru , Zoumpoulaki Alexia , Perapoch Marta , Lewis Penelope 
Published: October 2017

AbstractMemory reactivation during sleep is critical for consolidation, but also extremely difficult to measure as it is subtle, distributed and temporally unpredictable. This article reports a novel method for detecting such reactivation in standard sleep recordings. During learning, participants produced a complex sequence of finger presses, with each finger cued by a distinct audio-visual stimulus. Auditory cues were then re-played during subsequent sleep to trigger neural reactivation through a method known as targeted memory reactivation (TMR). Next, we used electroencephalography data from the learning session to train a machine learning classifier, and then applied this classifier to sleep data to determine how successfully each tone had elicited memory reactivation. Above chance classification was significantly higher in slow wave sleep than in stage 2, suggesting differential efficacy of TMR in these two sleep stages. Interestingly, classification success reduced across numerous repetitions of the tone cue, suggesting either a gradually reducing responsiveness to such cues or a plasticity-related change in the neural signature as a result of cueing. We believe this method will be invaluable for future investigations of memory consolidation.