bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Role of Gastroesophageal Reflux in Provoking High Blood Pressure Episodes in Patients With Hypertension
Authors: Li Zhi-tong , Ji Feng , Han Xin-wei , Wang Li , Yue Yong-qiang , Wang Zhong-gao 
Published: September 2017

Goals:
We assessed the relationship between gastroesophageal reflux disease (GERD) and hypertension and whether antiacid therapy could be used to control blood pressure (BP) on hypertension in patients with GERD.

Background:
Gastroesophageal reflux disease (GERD) may provoke cardiovascular disease. Many factors are involved in the development of essential hypertension, but whether GERD has a role needs further study.

Study:
Patients with essential hypertension (n=86) were studied by 24-hour continuous BP monitoring and esophageal impedance and pH monitoring. Patients fulfilling the GERD criteria received 14-day therapy with omeprazole (20 mg twice a day), and the effect on BP was studied.

Results:
Of the 86 essential hypertension patients, 38 (44.2%) had GERD. Among these 38 patients, 494 episodes of pathologic reflux (PR), and 684 episodes of high BP were recorded. PR was significantly more common at nighttime especially when supine. Of the 684 episodes of hypertension, 102 (14.9%) were synchronous with PR. GERD patients had significantly higher nocturnal BP than non-GERD patients. Antiacid therapy brought about significant reduction in all esophageal monitoring parameters as well as in BP parameters in GERD patients.

Conclusions:
This study demonstrated that there is significant correlation between hypertension and GERD. Antiacid therapy can restore normal esophageal pH and help maintain normal BP.
Health‐related Quality of Life in Adolescent Patients With Hepatitis C Genotype 1 Treated With Sofosbuvir and Ledipasvir
Authors: Younossi Zobair M. , Stepanova Maria , Balistreri William , Schwarz Kathleen , Murray Karen F. , Rosenthal Philip , Bansal Sanjay , Hunt Sharon 
Published: September 2017

ABSTRACTObjective:The aim of the study was to assess the effect of treatment with ledipasvir/sofosbuvir (LDV/SOF) on the health‐related quality of life (HRQL) of pediatric patients with chronic hepatitis C virus (HCV) infection.Methods:Adolescents (12–17 years) with HCV were treated with LDV/SOF (90/400 mg daily) for 12 weeks. HRQL was assessed using the PedsQLv4.0‐SF15 completed by the children and caregivers before, during, and after treatment.Results:We included 100 adolescents with HCV genotype 1 infection (14.7 ± 2.0 years, 1% known cirrhosis, 80% treatment‐naïve, 97% sustained virologic response‐12). At baseline, HRQL the caregiver‐ perceived HRQL scores were lower than adolescents’ self‐reported scores (by 6.7–7.9 points, all P < 0.01). At the end of 12 weeks of treatment, however, the caregiver‐reported HRQL scores showed a significant improvement (+all P < 0.04), whereas the adolescents’ self‐reported scores did not change from the baseline. HRQL scores reported by caregivers remained higher than baseline (by +4.7–+7.5, P < 0.01) through 12 weeks after treatment, as did the adolescents’ self‐reported Emotional Functioning scores (+4.3 from baseline, P = 0.0009); observed improvements were sustained after 24 weeks of follow‐up (all P < 0.04). Multivariate analysis showed that, after adjustment for location, age, and sex, having a history of anxiety and panic disorders were consistent predictors of impaired HRQL in adolescents with HCV infection (P < 0.05).Conclusions:Treatment of HCV in adolescents with LDV/SOF is associated with some improvement in HRQL. Caregivers’ reports of HRQL in adolescents with HCV significantly increased with treatment and were similar to the adolescent self‐reported HRQL after sustained virologic response‐12.
Political Affiliation, Probable PTSD, and Symptoms of Depression in Iraq and Afghanistan Combat Veterans
Authors: Lating Jeffrey M. , Moore Rich A. , Sherman Martin F. , Kirkhart Matthew W. , Everly George S. , Chen Justin K. 
Published: September 2017

Abstract
Ideological commitment of military personnel has been associated with mitigating trauma and protecting mental health. This pilot study assessed whether Democratic and Republican political affiliation differentially predicted probable posttraumatic stress disorder (PTSD) and symptoms of depression in 62 male Iraq and Afghanistan combat veterans. The Liberalism-Conservatism Scale, the PTSD Checklist-Military Version (PCL-M), and the Patient Health Questionnaire–9 (PHQ-9) were assessment measures. Results revealed that Democratic combat veterans had stronger liberal attitudes than Republican combat veterans (r = 0.95). Moreover, of the 50% of the entire sample higher than the cutoff score of 50 on the PCL-M, 84.8% were Democrats compared with 10.3% of Republicans. On the PHQ-9, 46.9% of Democrats compared with 3.7% of Republicans were higher than the cutoff score of 20. These initial results suggest possible mechanisms of action, including differences in shattered world view assumptions, willingness to disclose emotional concerns, and physiological reactions between Democratic and Republican combat veterans.
Case Report: Use of Self-retained Cryopreserved Amniotic Membrane in the Treatment of Acute Chemical Ocular Burn
Authors: Shupe Adam T. , Cheng Anny M. S. 
Published: September 2017

SIGNIFICANCE
Ocular chemical injury is a medical emergency in which immediate treatment is critical to prevent visual morbidity. We report a severe ocular burn case that illustrates in-office management to promote rapid re-epithelialization and reduce inflammation to restore ocular surface integrity.

PURPOSE
To report a case of severe acid burn that was managed successfully with self-retained cryopreserved amniotic membrane (AM).

METHODS
A 43-year-old man presented with complaints of pain, light sensitivity, and blurred vision in both eyes 1 day after ocular exposure to acid. Symptoms and signs were more severe in the left eye. Examination revealed diffuse conjunctival inflammation and extensive corneal, conjunctival, and limbal epithelial defects in the left eye; hence, application of cryopreserved AM was performed.

RESULTS
Placement of three self-retained AMs over a 10-day period resulted in resolution of symptoms, reduction in inflammation, complete re-epithelialization of corneal and limbal defects, and improvement of visual acuity from 20/50 to 20/20. Intriguingly, areas of conjunctival inflammation not covered by the AM remained inflamed.

CONCLUSIONS
In this case of acute chemical burn, application of self-retained AM 24 hours after injury was effective in promoting ocular surface healing, reducing inflammation, and restoring visual acuity.
Impact of advance care planning on end-of-life management
Authors: Lunder Urška , Červ Branka , Kodba-Čeh Hana 
Published: September 2017

Purpose of review
The aim of this review is to critically appraise the recent evidence on different aspects of impact of advance care planning (ACP) in palliative care and to reflect on further implications on practice and research in the future.

Recent findings
Evidence about various ACP impacts is rapidly growing and most common outcome measures are still advance directive completion, change in hospital admission rate and patients’ and families’ views and experiences with ACP. Mainly descriptive studies bring new information of ACP impact for specific groups of patients, their families, settings, countries, contexts, staff and healthcare system as such. It is not yet clear who and when would best conduct ACP, from general practitioners (GPs) to specialists in the hospitals and even lay-navigators for cancer patients; from early ACP conversations to critical ACP in acute events at the end-of-life. The need for ACP impacts high-quality evidence is becoming more urgent because latest future projections are showing higher palliative care needs than previously expected.

Summary
Recent studies on various ACP impacts reveal variety of outcomes for different patient groups and settings, and are contributing to a wider picture of ACP situation around the world. However, high-quality evidence on ACP impact is still urgently expected in times of growing need for system-level changes for effective ACP implementation.
High-resolution genome-wide functional dissection of transcriptional regulatory regions in human
Authors: Wang Xinchen , He Liang , Goggin Sarah , Saadat Alham , Wang Li , Claussnitzer Melina , Kellis Manolis 
Published: September 2017

AbstractGenome-wide epigenomic maps revealed millions of regions showing signatures of enhancers, promoters, and other gene-regulatory elements1. However, high-throughput experimental validation of their function and high-resolution dissection of their driver nucleotides remain limited in their scale and length of regions tested. Here, we present a new method, HiDRA (High-Definition Reporter Assay), that overcomes these limitations by combining components of Sharpr-MPRA2and STARR-Seq3with genome-wide selection of accessible regions from ATAC-Seq4. We used HiDRA to test ~7 million DNA fragments preferentially selected from accessible chromatin in the GM12878 lymphoblastoid cell line. By design, accessibility-selected fragments were highly overlapping (up to 370 per region), enabling us to pinpoint driver regulatory nucleotides by exploiting subtle differences in reporter activity between partially-overlapping fragments, using a new machine learning model SHARPR2. Our resulting maps include ~65,000 regions showing significant enhancer function and enriched for endogenous active histone marks (including H3K9ac, H3K27ac), regulatory sequence motifs, and regions bound by immune regulators. Within them, we discover ~13,000 high-resolution driver elements enriched for regulatory motifs and evolutionarily-conservednucleotides, and help predict causal genetic variants underlying disease from genome-wide association studies. Overall, HiDRA provides a general, scalable, high-throughput, and high-resolution approach for experimental dissection of regulatory regions and driver nucleotides in the context of human biology and disease.
Non-Elastic Remodeling of the 3D Extracellular Matrix by Cell-Generated Forces
Authors: Malandrino Andrea , Mak Michael , Trepat Xavier , Kamm Roger D. 
Published: September 2017

AbstractThe mechanical properties of the extracellular matrix (ECM) – a complex, 3D, fibrillar scaffold of cells in physiological environments – modulate cell behavior and can drive tissue morphogenesis, regeneration, and disease progression. For simplicity, it is often convenient to assume these properties to be time-invariant. In living systems, however, cells dynamically remodel the ECM and create time-dependent local environments. Here, we demonstrate that cell generated contractile forces are capable of producing substantial irreversible changes to the density and architecture of physiologically relevant ECMs – collagen I and fibrin – in a matter of minutes. We measure the 3D mechanical deformation profiles of the ECM surrounding cancer and endothelial cells during stages when force generation is active or inactive. We further correlate these measurements to both discrete fiber simulations that incorporate fiber crosslink unbinding kinetics and continuum-scale modeling. Our findings reveal that plasticity, as a mechanical law in these networks, is fundamentally related to the force-driven unbinding of fiber crosslinks. These results illustrate the dynamic nature of the mechanical environment of physiologically mimicking cell-in-gel systems.
Using Temporal ICA to Selectively Remove Global Noise While Preserving Global Signal in Functional MRI Data
Authors: Glasser Matthew F. , Coalson Timothy S. , Bijsterbosch Janine D. , Harrison Samuel J. , Harms Michael P. , Anticevic Alan , Van Essen David C. , Smith Stephen M. 
Published: September 2017

AbstractTemporal fluctuations in functional Magnetic Resonance Imaging (fMRI) have been profitably used to study brain activity and connectivity for over two decades. Unfortunately, fMRI data also contain structured temporal “noise” from a variety of sources, including subject motion, subject physiology, and the MRI equipment. Recently, methods have been developed to automatically and selectively remove spatially specific structured noise from fMRI data using spatial Independent Components Analysis (ICA) and machine learning classifiers. Spatial ICA is particularly effective at removing spatially specific structured noise from high temporal and spatial resolution fMRI data of the type acquired by the Human Connectome Project and similar studies. However, spatial ICA is mathematically, by design, unable to separate spatially widespread “global” structured noise from fMRI data (e.g., blood flow modulations from subject respiration). No methods currently exist to selectively and completely remove global structured noise while retaining the global signal from neural activity. This has left the field in a quandary—to do or not to do global signal regression—given that both choices have substantial downsides. Here we show that temporal ICA can selectively segregate and remove global structured noise while retaining global neural signal in both task-based and resting state fMRI data. We compare the results before and after temporal ICA cleanup to those from global signal regression and show that temporal ICA cleanup removes the global positive biases caused by global physiological noise without inducing the network-specific negative biases of global signal regression. We believe that temporal ICA cleanup provides a “best of both worlds” solution to the global signal and global noise dilemma and that temporal ICA itself unlocks interesting neurobiological insights from fMRI data.
Histone deacetylase inhibition reduces deleterious cytokine release induced by ingenol stimulation
Authors: Larragoite Erin T. , Nell Racheal A. , Martins Laura J. , Barrows Louis R. , Planelles Vicente , Spivak Adam M. 
Published: September 2017

AbstractIntroductionLatency reversal agents (LRAs), such as protein kinase C (PKC) agonists, constitute a promising strategy for exposing and eliminating the HIV-1 latent reservoir. PKC agonists activate NF-κB and, in turn, induce deleterious pro-inflammatory cytokine production. Adjuvant pharmacological agents, such as ruxolitinib, a JAK inhibitor, and rapamycin, an mTOR inhibitor, have previously been combined with LRAs to reduce deleterious pro-inflammatory cytokine secretion without inhibiting HIV-1 viral reactivation in vitro. Histone deacetylase inhibitors (HDACi) are known to dampen pro-inflammatory cytokine secretion in the context of other diseases and can synergize with other LRAs to bring dormant proviruses out of latency. In this study we investigated whether a broad panel of epigenetic modifiers, including HDACi, could effectively dampen PKC-induced pro-inflammatory cytokine secretion during latency reversal.MethodsWe screened an epigenetic modifier library to identify compounds that reduced intracellular IL-6 production induced by the PKC agonist Ingenol-3,20-dibenzoate. We further tested the most promising epigenetic inhibitor class, HDACi, for their ability to reduce a broad panel of pro-inflammatory cytokines and reactivate latent HIV-1ex vivo.ResultsWe identified nine epigenetic modulators that reduced PKC-induced intracellular IL-6. In cells from aviremic individuals living with HIV-1, the HDAC1-3 inhibitor, suberohydroxamic acid (SBHA), reduced secretion of pro-inflammatory cytokines TNF-α, IL-5, IL-2r, and IL-17 but did not significantly reactivate latent HIV-1 when used in combination with Ingenol-3,20-dibenzoate.ConclusionThe addition of SBHA to Ingenol-3,20-dibenzoate reduces deleterious cytokine production during latency reversal but does not induce significant viral reactivation in aviremic donor PBMCs. The ability of SBHA to reduce PKC-induced pro-inflammatory cytokines when used in combination with Ingenol-3,20-dibenzoate suggests that SBHA can be used to reduced PKC induced pro-inflammatory cytokines but not to achieve latency reversal in the context of HIV-1.
A universal, genome-wide guide finder for CRISPR/Cas9 targeting in microbial genomes
Authors: Spoto Michelle , Fleming Elizabeth , Oh Julia 
Published: September 2017

AbstractBackgroundThe CRISPR/Cas system has significant potential to facilitate gene editing in a variety of bacterial species. CRISPR interference (CRISPRi) and CRISPR activation (CRISPRa) represent modifications of the CRISPR/Cas9 system utilizing a catalytically inactive Cas9 protein for transcription repression or activation, respectively. While CRISPRi and CRISPRa have tremendous potential to systematically investigate gene function in bacteria, no pan-bacterial, genome-wide tools exist for guide discovery. We have created Guide Finder: a customizable, user-friendly program that can design guides for any annotated bacterial genome.ResultsGuide Finder designs guides from NGG PAM sites for any number of genes using an annotated genome and fasta file input by the user. Guides are filtered according to user-defined design parameters and removed if they contain any off-target matches. Iteration with lowered parameter thresholds allows the program to design guides for genes that did not produce guides with the more stringent parameters, a feature unique to Guide Finder. Guide Finder has been tested on a variety of diverse bacterial genomes, on average finding guides for 95% of genes. Moreover, guides designed by the program are functionally useful—focusing on CRISPRi as a potential application—as demonstrated by essential gene knockdown in two staphylococcal species.ConclusionsThrough the large-scale generation of guides, this open-access software will improve accessibility to CRISPR/Cas studies for a variety of bacterial species.
Genome-wide interaction study of a proxy for stress-sensitivity and its prediction of major depressive disorder
Authors: Arnau-Soler Aleix , Adams Mark J. ,   Generation Scotland,   Major Depressive Disorder Working Group of the Psychiatric Genomics Consortium, Hayward Caroline , Thomson Pippa A. 
Published: September 2017

AbstractIndividual response to stress is correlated with neuroticism and is an important predictor of both neuroticism and the onset of major depressive disorder (MDD). Identification of the genetics underpinning individual differences in response to negative events (stress-sensitivity) may improve our understanding of the molecular pathways involved, and its association with stress-related illnesses. We sought to generate a proxy for stress-sensitivity through modelling the interaction between SNP allele and MDD status on neuroticism score in order to identify genetic variants that contribute to the higher neuroticism seen in individuals with a lifetime diagnosis of depression compared to unaffected individuals. Meta-analysis of genome-wide interaction studies (GWIS) in UK Biobank (N = 23,092) and Generation Scotland: Scottish Family Health Study (N = 7,155) identified no genome-wide significance SNP interactions. However, gene-based tests identified a genome-wide significant gene,ZNF366, a negative regulator of glucocorticoid receptor function implicated in alcohol dependence (p= 1.48×10-7; Bonferroni-corrected significance thresholdp< 2.79×10-6). Using summary statistics from the stress-sensitivity term of the GWIS, SNP heritability for stress-sensitivity was estimated at 5.0%. In models fitting polygenic risk scores of both MDD and neuroticism derived from independent GWAS, we show that polygenic risk scores derived from the UK Biobank stress-sensitivity GWIS significantly improved the prediction of MDD in Generation Scotland. This study may improve interpretation of larger genome-wide association studies of MDD and other stress-related illnesses, and the understanding of the etiological mechanisms underpinning stress-sensitivity.
Fennec - Functional Exploration of Natural Networks and Ecological Communities
Authors: Ankenbrand Markus J. , Hohlfeld Sonja , Weber Lorenz , Förster Frank , Keller Alexander 
Published: September 2017

AbstractSpecies composition assessment of ecological communities and networks is an important aspect of biodiversity research. Yet often ecological traits of organisms in a community are more informative than scientific names only. Furthermore, other properties like threat status, invasiveness, or human usage are relevant for many studies, but cannot be evaluated from taxonomy alone. Despite public databases collecting such information, it is still a tedious manual task to enrich community analyses with such, especially for large-scaled data.Thus we aimed to develop a public and free tool that eases bulk trait mapping of community data in a web browser, implemented with current standard web and database technologies.Here we present the Fennec, a workbench that eases the process of mapping publicly available trait data to the user’s communities in an automated process. Usage is either by a local self-hosted or a public instance (https://fennec.molecular.eco) covering exemplary traits. Alongside the software we also provide usage and hosting documentation as well as online tutorials.The Fennecaims to motivate public trait data submission and its reuse in meta-analyses. Further, it is an open-source development project with the code freely available to use and open for community contributions (https://github.com/molbiodiv/fennec).
The Complex Simplicity of the Brittle Star Nervous System
Authors: Zueva Olga , Khoury Maleana , Heinzeller Thomas , Mashanova Daria , Mashanov Vladimir 
Published: September 2017

AbstractBrittle stars (Ophiuroidea, Echinodermata) have been increasingly used in studies of animal behavior, locomotion, regeneration, physiology, and bioluminescence. The success of these studies directly depends on good working knowledge of ophiuroid nervous system. Here, we describe the arm nervous system at different levels of organization: microanatomy of the radial nerve cord and peripheral nerves, neural ultrastructure, and localization of different cell types using specific antibody markers. We standardize the nomenclature of nerves and ganglia and provide an anatomically accurate digital 3D model of the arm nervous system as a reference for future studies. Our results helped identify several general features characteristic to the adult echinoderm nervous system, including the extensive anatomical interconnections between the ectoneural and hyponeural components and neuroepithelial organization of the central nervous system with its supporting scaffold formed by radial glial cells. In addition, we provide further support to the notion that the echinoderm radial glia is a complex and diverse cell population. We also tested the suitability of a range of specific cell-type markers for studies of the brittle star nervous system and established that the radial glial cells are reliably labeled by the ERG1 antibodies, whereas the best neuronal markers are acetylated tubulin, ELAV and synaptotagmin B. The transcription factor Brn1/2/4, a marker of neuronal progenitors, is expressed not only in neurons, but also in a subpopulation of radial glia. For the first time, we describe putative ophiuroid proprioceptors associated with the hyponeural part of the central nervous system.