bluuebunny/crossref_metadata_2025_split huggingface dataset:
Contributions to Executive Dysfunction in Operation Enduring Freedom/Operation Iraqi Freedom Veterans With Posttraumatic Stress Disorder and History of Mild Traumatic Brain Injury
Authors: Jurick Sarah M. , Crocker Laura D. , Sanderson-Cimino Mark , Keller Amber V. , Trenova Liljana S. , Boyd Briana L. , Twamley Elizabeth W. , Rodgers Carie S. , Schiehser Dawn M. , Aupperle Robin L. , Jak Amy J. 
Published: May 2017

Objective:Posttraumatic stress disorder (PTSD), history of mild traumatic brain injury (mTBI), and executive function (EF) difficulties are prevalent in Operation Enduring Freedom/Operation Iraqi Freedom (OEF/OIF) Veterans. We evaluated the contributions of injury variables, lower-order cognitive component processes (processing speed/attention), and psychological symptoms to EF.Participants:OEF/OIF Veterans (N= 65) with PTSD and history of mTBI were administered neuropsychological tests of EF and self-report assessments of PTSD and depression.Results:Those impaired on one or more EF measures had higher PTSD and depression symptoms and lower processing speed/attention performance than those with intact performance on all EF measures. Across participants, poorer attention/processing speed performance and higher psychological symptoms were associated with worse performance on specific aspects of EF (eg, inhibition and switching) even after accounting for injury variables. Although direct relationships between EF and injury variables were equivocal, there was an interaction between measures of injury burden and processing speed/attention such that those with greater injury burden exhibited significant and positive relationships between processing speed/attention and inhibition/switching, whereas those with lower injury burden did not.Conclusion:Psychological symptoms as well as lower-order component processes of EF (attention and processing speed) contribute significantly to executive dysfunction in OEF/OIF Veterans with PTSD and history of mTBI. However, there may be equivocal relationships between injury variables and EF that warrant further study. Results provide groundwork for more fully understanding cognitive symptoms in OEF/OIF Veterans with PTSD and history of mTBI that can inform psychological and cognitive interventions in this population.
Follow-Up Care Adherence After Hospital Discharge in Children With Traumatic Brain Injury
Authors: Spaw Alexandra J. , Lundine Jennifer P. , Johnson Sarah A. , Peng Jin , Wheeler Krista K. , Shi Junxin , Yang Ginger , Haley Kathy J. , Groner Jonathan I. , Xiang Henry 
Published: May 2017

Objective:
To investigate factors associated with follow-up care adherence in children hospitalized because of traumatic brain injury (TBI).

Design:
An urban level 1 children's hospital trauma registry was queried to identify patients (2-18 years) hospitalized with a TBI in 2013 to 2014. Chart reviewers assessed discharge summaries and follow-up instructions in 4 departments.

Main Measures:
Three levels of adherence—nonadherence, partial adherence, and full adherence—and their associations with care delivery, patient, and injury factors.

Results:
In our population, 80% were instructed to follow up within the hospital network. These children were older and had more severe TBIs than those without follow-up instructions and those referred to outside providers. Of the 352 eligible patients, 19.9% were nonadherent, 27.3% were partially adherent, and 52.8% were fully adherent. Those recommended to follow up with more than 1 department had higher odds of partial adherence over nonadherence (adjusted odds ratio [AOR] = 5.8, 95% CI: 1.9-17.9); however, these patients were less likely to be fully adherent (AOR = 0.1; 95% CI: 0.1-0.3). Privately insured patients had a higher AOR of full adherence.

Conclusions:
Nearly 20% of children hospitalized for TBI never returned for outpatient follow-up and 27% missed appointments. Care providers need to educate families, coordinate service provision, and promote long-term monitoring.
Structural Connectivity Related to Persistent Symptoms After Mild TBI in Adolescents and Response to Aerobic Training: Preliminary Investigation
Authors: Yuan Weihong , Wade Shari L. , Quatman-Yates Catherine , Hugentobler Jason A. , Gubanich Paul J. , Kurowski Brad G. 
Published: May 2017

Objective:
To quantify structural connectivity abnormalities in adolescents with mild traumatic brain injury (mTBI) and to investigate connectivity changes following aerobic training using graph theory and diffusion tensor imaging tractography.

Setting:
Outpatient research setting.

Participants:
Twenty-two children (age: 15.83 ± 1.77 years, 10 females) with 4 to 16 weeks of persistent symptoms after mTBI and a matched healthy comparison group.

Design:
Randomized clinical trial of aerobic training and stretching comparison combined with case-control comparison.

Main Measures:
(1) Five global network measures: global efficiency (Eglob), mean local efficiency, modularity, normalized clustering coefficient (γ), normalized characteristic path length (λ), and small-worldness (σ). (2) The self-reported Post-Concussion Symptom Inventory score.

Results:
At initial enrollment, adolescents with mTBI had significantly lower Eglob and higher γ, λ, and σ (all P < .05) than healthy peers. After the intervention, significantly increased Eglob and decreased λ (both P < .05) were found in the aerobic training group. Improvement in Post-Concussion Symptom Inventory scores was significantly correlated with the Eglob increase and λ decrease in the aerobic training and λ decrease in the stretching comparison group (all P < .05).

Conclusion:
This pilot study showed initial evidence that structural connectivity analysis was sensitive to brain network abnormalities and may serve as an imaging biomarker in children with persistent symptoms after mTBI.
The Role of Cognitive Reserve in Recovery From Traumatic Brain Injury
Authors: Steward Kayla A. , Kennedy Richard , Novack Thomas A. , Crowe Michael , Marson Daniel C. , Triebel Kristen L. 
Published: May 2017

Objective:
To examine whether cognitive reserve (CR) attenuates the initial impact of traumatic brain injury (TBI) on cognitive performance (neural reserve) and results in faster cognitive recovery rates in the first year postinjury (neural compensation), and whether the advantage of CR differs on the basis of the severity of TBI.

Setting:
Inpatient/outpatient clinics at an academic medical center.

Participants:
Adults with mild TBI (mTBI; n = 28), complicated mild TBI (cmTBI; n = 24), and moderate to severe TBI (msevTBI; n = 57), and demographically matched controls (n = 66).

Design:
Retrospective, longitudinal cohort assessed at 1, 6, and 12 months postinjury.

Main Measures:
Outcomes were 3 cognitive domains: processing speed/executive function, verbal fluency, and memory. Premorbid IQ, estimated with the Wechsler Test of Adult Reading, served as CR proxy.

Results:
Higher premorbid IQ was associated with better performance on cognitive domains at 1 month postinjury, and the effect of IQ was similarly beneficial for all groups. Cognitive recovery rate was moderated only by TBI severity; those with more severe TBI had faster recovery in the first year.

Conclusion:
Results support only the neural reserve theory of CR within a TBI population and indicate that CR is neuroprotective, regardless of the degree of TBI. Higher premorbid CR does not allow for more rapid adaptation and recovery from injury.
Genetic diseases associated with an increased risk of skin cancer development in childhood
Authors: Fogel Alexander L. , Sarin Kavita Y. , Teng Joyce M.C. 
Published: May 2017

Purpose of review
Childhood skin cancers are relatively rare and may indicate an underlying genetic disorder. The increasing elucidation of genetic pathways is changing the diagnosis and management of genetic skin cancer susceptibility syndromes. In this review, we provide an overview of genetic conditions that predispose to skin cancer development in childhood and signs that providers should assess when evaluating affected individuals.

Recent findings
In basal cell nevus syndrome (BCNS), the patched2 (PTCH2) and suppressor of fused (SUFU) genes have been implicated in disease pathogenesis. The sonic hedgehog (SHH) pathway inhibitor vismodegib was shown in a placebo-controlled phase III randomized trial to reduce the tumor burden in patients with BCNS. Epidermolysis bullosa (EB) has been classified into four major types and more than 30 subtypes based partly on specific mutations, and best clinical practice guidelines for the management of cutaneous squamous cell carcinoma in EB have been developed. Oculocutaneous albinism (OCA) has been associated with new mutations in genes named OCA5, OCA6, and OCA7, bringing to the total number of culprit genes to seven (OCA1–OCA7).

Summary
Advances in our understanding of genetic conditions that predispose to childhood skin cancer include new disease classification systems, management guidelines, and treatment options.
Increased Risk of Myocardial Infarction in HIV-Infected Individuals in North America Compared With the General Population
Authors: Drozd Daniel R. , Kitahata Mari M. , Althoff Keri N. , Zhang Jinbing , Gange Stephen J. , Napravnik Sonia , Burkholder Greer A. , Mathews William C. , Silverberg Michael J. , Sterling Timothy R. , Heckbert Susan R. , Budoff Matthew J. , Van Rompaey Stephen , Delaney Joseph A.C. , Wong Cherise , Tong Weiqun , Palella Frank J. , Elion Richard A. , Martin Jeffrey N. , Brooks John T. , Jacobson Lisa P. , Eron Joseph J. , Justice Amy C. , Freiberg Matthew S. , Klein Daniel B. , Post Wendy S. , Saag Michael S. , Moore Richard D. , Crane Heidi M. 
Published: May 2017

Background:
Previous studies of cardiovascular disease (CVD) among HIV-infected individuals have been limited by the inability to validate and differentiate atherosclerotic type 1 myocardial infarctions (T1MIs) from other events. We sought to define the incidence of T1MIs and risk attributable to traditional and HIV-specific factors among participants in the North American AIDS Cohort Collaboration on Research and Design (NA-ACCORD) and compare adjusted incidence rates (IRs) to the general population Atherosclerosis Risk in Communities (ARIC) cohort.

Methods:
We ascertained and adjudicated incident MIs among individuals enrolled in 7 NA-ACCORD cohorts between 1995 and 2014. We calculated IRs, adjusted incidence rate ratios (aIRRs), and 95% confidence intervals of risk factors for T1MI using Poisson regression. We compared aIRRs of T1MIs in NA-ACCORD with those from ARIC.

Results:
Among 29,169 HIV-infected individuals, the IR for T1MIs was 2.57 (2.30 to 2.86) per 1000 person-years, and the aIRR was significantly higher compared with participants in ARIC [1.30 (1.09 to 1.56)]. In multivariable analysis restricted to HIV-infected individuals and including traditional CVD risk factors, the rate of T1MI increased with decreasing CD4 count [≥500 cells/μL: ref; 350–499 cells/μL: aIRR = 1.32 (0.98 to 1.77); 200–349 cells/μL: aIRR = 1.37 (1.01 to 1.86); 100–199 cells/μL: aIRR = 1.60 (1.09 to 2.34); <100 cells/μL: aIRR = 2.19 (1.44 to 3.33)]. Risk associated with detectable HIV RNA [<400 copies/mL: ref; ≥400 copies/mL: aIRR = 1.36 (1.06 to 1.75)] was significantly increased only when CD4 was excluded.

Conclusions:
The higher incidence of T1MI in HIV-infected individuals and increased risk associated with lower CD4 count and detectable HIV RNA suggest that early suppressive antiretroviral treatment and aggressive management of traditional CVD risk factors are necessary to maximally reduce MI risk.
Hydrogen isotope composition ofThermoanaerobacterium saccharolyticumlipids: comparing wild type to anfn-transhydrogenase mutant
Authors: Leavitt William D. , Murphy Sean Jean-Loup , Lynd Lee R. , Bradley Alexander S. 
Published: May 2017

AbstractThe2H/1H ratio in microbial fatty acids can record information about the energy metabolism of microbes and about the isotopic composition of environmental water. However, the mechanisms involved in the fractionation of hydrogen isotopes between water and lipid are not fully resolved. We provide data aimed at understanding this fractionation in the Gram-positive obligately thermophilic anaerobe,Thermoanaerobacterium saccharolyticum, by comparing a wild-type strain to a deletion mutant in which thenfnABgenes encoding electron-bifurcating transhydrogenase have been removed. The wild-type strain showed faster growth rates and larger overall fractionationthan the mutant strain. The overall trend in growth rate and fractionation, along with the isotopic ordering of individual lipids, is consistent with results reported for the Gram-negative sulfate reducer,Desulfovibrio alaskensisG20.
scNMT-seq enables joint profiling of chromatin accessibility DNA methylation and transcription in single cells
Authors: Clark Stephen J. , Argelaguet Ricard , Kapourani Chantriolnt-Andreas , Stubbs Thomas M. , Lee Heather J. , Alda-Catalinas Celia , Krueger Felix , Sanguinetti Guido , Kelsey Gavin , Marioni John C. , Stegle Oliver , Reik Wolf 
Published: May 2017

AbstractParallel single-cell sequencing protocols represent powerful methods for investigating regulatory relationships, including epigenome-transcriptome interactions. Here, we report a novel single-cell method for parallel chromatin accessibility, DNA methylation and transcriptome profiling. scNMT-seq (single-cell nucleosome, methylation and transcription sequencing) uses a GpC methyltransferase to label open chromatin followed by bisulfite and RNA sequencing. We validate scNMT-seq by applying it to differentiating mouse embryonic stem cells, finding links between all three molecular layers and revealing dynamic coupling between epigenomic layers during differentiation.
An FGF-driven feed-forward circuit patterns the cardiopharyngeal mesoderm in space and time
Authors: Razy-Krajka Florian , Gravez Basile , Kaplan Nicole , Racioppi Claudia , Wang Wei , Christiaen Lionel 
Published: May 2017

AbstractIn embryos, multipotent progenitors divide to produce distinct progeny and express their full potential. In vertebrates, multipotent cardiopharyngeal progenitors produce second-heart-field-derived cardiomyocytes, and branchiomeric skeletal head muscles. However, the mechanisms underlying these early fate choices remain largely elusive. The tunicateCionaemerged as an attractive model to study early cardiopharyngeal development at high resolution: through two asymmetric and oriented divisions, defined cardiopharyngeal progenitors produce distinct first and second heart precursors, and pharyngeal muscle (aka atrial siphon muscle, ASM) precursors. Here, we demonstrate that differential FGF-MAPK signaling distinguishes between heart and ASM precursors. We characterize a feed-forward circuit that promotes the successive activations of essential ASM determinants,Hand-related, Tbx1/10andEbf. Finally, we show that coupling FGF-MAPK restriction and cardiopharyngeal network deployment with cell divisions defines the timing of gene expression and permits the emergence of diverse cell types from multipotent progenitors.
Evaluating the accuracy of DNA stable isotope probing
Authors: Youngblut Nicholas D. , Buckley Daniel H. 
Published: May 2017

Originality-Significance StatementBy combining DNA Stable Isotope Probing (DNA-SIP) with multiplexed high throughput DNA sequencing (HTS-DNA-SIP), it is now possible to identify patterns of isotope incorporation for thousands of microbial taxa. HTS-DNA-SIP has enormous potential to reveal patterns of carbon and nitrogen exchange within microbial food webs. A current limitation is that, due to the expense of these experiments, it has been impossible to evaluate the accuracy of DNA-SIP methods. We have developed a model that simulates DNA-SIP data, and we use the model to systematically evaluate and validate the accuracy of DNA-SIP analyses. This model can determine the analytical accuracy of DNA-SIP experiments in a range of contexts. Furthermore, the ability to predict experimental outcomes, as a function of experimental design and community characteristics, should be of great use in the design and interpretation DNA-SIP experiments.SummaryDNA Stable isotope probing (DNA-SIP) is a powerful method that identifiesin situisotope assimilation by microbial taxa. Combining DNA-SIP with multiplexed high throughput DNA sequencing (HTS-DNA-SIP) creates the potential to mapin situassimilation dynamics for thousands of microbial taxonomic units. However, the accuracy of methods for analyzing DNA-SIP data has never been evaluated. We have developed a toolset (SIPSim) for simulating HTS-DNA-SIP datasets and evaluating the accuracy of methods for analyzing HTS-DNA-SIP data. We evaluated two different approaches to analyzing HTS-DNA-SIP data: “high resolution stable isotope probing” (HR-SIP) and “quantitative stable isotope probing” (q-SIP). HR-SIP was highly specific and moderately sensitive, with very few false positives but potential for false negatives. In contrast, q-SIP had fewer false negatives but many false positives. We also found HR-SIP more robust than q-SIP with respect to experimental variance. Furthermore, we found that the detection sensitivity of HTS-DNA-SIP can be increased without compromising specificity by evaluating evidence of isotope incorporation over multiple windows of buoyant density (MW-HR-SIP). SIPSim provides a platform for determining the accuracy of HTS-DNA-SIP methods across a range of experimental parameters, which will be useful in the design, analysis, and validation of DNA-SIP experiments.
Graph-guided assembly for novel HLA allele discovery
Authors: Lee Heewook , Kingsford Carl 
Published: May 2017

AbstractAccurate typing of human leukocyte antigen (HLA), a histocompatibility test, is important because HLA genes play various roles in immune responses, and have also been shown to be associated with many diseases such as cancer. The current gold standard for HLA typing uses DNA sequencing technology combined with sequence enrichment techniques using specially designed primers or probes, causing it to be slow and labor-intensive. Although there exist enrichment-free computational methods that use various types of sequencing data, hyper-polymorphism found in HLA region of the human genome makes it challenging to type HLA genes with high accuracy from whole genome sequencing data. Furthermore, these methods are database-matching approaches where their output is inherently limited by the completeness of already known types, forcing them to find the best matching known alleles from a database, thereby causing them to be unsuitable for discovery of rare or novel alleles. In order to ensure both high accuracy as well as the ability to type novel alleles, we have developed a graph-guided assembly technique for classical HLA genes, which is capable of assembling phased, full-length haplotype sequences of typing exons given high-coverage (>30-fold) whole genome sequencing data. Our method delivers highly accurate HLA typing, comparable to the current state-of-the-art database-matching methods. We also demonstrate that our method can type novel alleles by experimenting on various data including simulated, Illumina Platinum Genomes, and 1000 Genomes data.
Removal of inhibition uncovers latent movement potential during preparation
Authors: Jagadisan Uday K. , Gandhi Neeraj J. 
Published: May 2017

AbstractThe motor system prepares for movements well in advance of their execution. In the gaze control system, premotor neurons that produce a burst of activity for the movement are also active leading up to the saccade. The dynamics of preparatory neural activity have been well described by stochastic accumulator models, and variability in the accumulation dynamics has been shown to be correlated with reaction times of the eventual saccade, but it is unclear whether this activity is purely preparatory in nature or has features indicative of a hidden movement command. We explicitly tested whether preparatory neural activity in premotor neurons of the primate superior colliculus has “motor potential”. We removed inhibition on the saccadic system using reflex blinks, which turn off downstream gating, and found that saccades can be initiated before underlying activity reaches levels seen under normal conditions. Accumulating low-frequency activity was predictive of eye movement dynamics tens of milliseconds in advance of the actual saccade, indicating the presence of a latent movement command. We also show that reaching threshold is not a necessary condition for movement initiation, contrary to the postulates of accumulation-to-threshold models. The results bring into question extant models of saccade generation and support the possibility of a concurrent representation for movement preparation and generation.Significance StatementHow the brain plans for upcoming actions before deciding to initiate them is a central question in neuroscience. Popular theories suggest that movement planning and execution occur in serial stages, separated by a decision boundary in neural activity space (e.g., “threshold”), which needs to be crossed before the movement is executed. By removing inhibitory gating on the motor system, we show here that the activity required to initiate a saccade can be flexibly modulated. We also show that evolving activity during movement planning is a hidden motor command. The results have important implications for our understanding of how movements are generated, in addition to providing useful information for decoding movement intention based on planning-related activity.Impact StatementNon-invasive disinhibition of the oculomotor system shows that ongoing preparatory activity in the superior colliculus has movement-generating potential and need not rise to threshold in order to produce a saccade.