bluuebunny/crossref_metadata_2025_split huggingface dataset:
Allele specific chromatin signals, 3D interactions, and motif predictions for immune and B cell related diseases
Authors: Cavalli Marco , Baltzer Nicholas , Umer Husen M. , Grau Jan , Lemnian Ioana , Pan Gang , Wallerman Ola , Spalinskas Rapolas , Sahlén Pelin , Grosse Ivo , Komorowski Jan , Wadelius Claes 
Published: February 2019

AbstractSeveral Genome Wide Association Studies (GWAS) have reported variants associated to immune diseases. However, the identified variants are rarely the drivers of the associations and the molecular mechanisms behind the genetic contributions remain poorly understood. ChIP-seq data for TFs and histone modifications provide snapshots of protein-DNA interactions allowing the identification of heterozygous SNPs showing significant allele specific signals (AS-SNPs). AS-SNPs can change a TF binding site resulting in altered gene regulation and are primary candidates to explain associations observed in GWAS and expression studies. We identified 17,293 unique AS-SNPs across 7 lymphoblastoid cell lines. In this set of cell lines we interrogated 85% of common genetic variants in the population for potential regulatory effect and we identified 237 AS-SNPs associated to immune GWAS traits and 714 to gene expression in B cells. To elucidate possible regulatory mechanisms we integrated long-range 3D interactions data to identify putative target genes and motif predictions to identify TFs whose binding may be affected by AS-SNPs yielding a collection of 173 AS-SNPs associated to gene expression and 60 to B cell related traits. We present a systems strategy to find functional gene regulatory variants, the TFs that bind differentially between alleles and novel strategies to detect the regulated genes.
Complex gamma-ray behavior of the radio galaxy M 87
Authors: Ait Benkhali Faical , Chakraborty Nachiketa , Rieger Frank M. 
Published: February 2019

Context. In recent years, non-blazar active galactic nuclei (AGN) such as radio galaxies have emerged as a highly instructive source class providing unique insights into high energy acceleration and radiation mechanisms.
Aims. Here we aim to produce a detailed characterization of the high-energy (HE; >100 MeV) gamma-ray emission from the prominent radio galaxy M 87.
Methods. We analyzed approximately eight years of Fermi-LAT data and derived the spectral energy distribution between 100 MeV and 300 GeV. We extracted lightcurves and investigated the variability behavior for the entire energy range as well as below and above 10 GeV.
Results. Our analysis provides (i) evidence for HE gamma-ray flux variability and (ii) indications for a possible excess over the standard power-law model above Eb ∼ 10 GeV, similar to the earlier indications in the case of Cen A. When viewed in HE–VHE context, this is most naturally explained by an additional component dominating the highest-energy part of the spectrum. Investigation of the γ-ray lightcurves suggests that the lower-energy (<10 GeV) component is variable on timescales of (at least) a few months. The statistics of the high energy component (>10 GeV) does not allow significant constraints on variability. We do, however, find indications for spectral changes with time that support variability of the putative additional component and seem to favor jet-related scenarios for its origin capable of accommodating month-type variability.
Conclusions. The current findings suggest that both the high-energy (>Eb) and the very high energy (VHE; >100 GeV) emission in M 87 are compatible with originating from the same physical component. The variability behavior at VHE then allows further constraints on the location and the nature of the second component. In particular, these considerations suggest that the VHE emission during the quiescent state originates in a similar region as during the flare.
Rare Presentation of a Relapsing Remitting Central Nervous System Vasculitis: A Case Report.
Authors: Brzezicki Maksymilian , Kobetic Matthew , Serena Dillon 
Published: February 2019

ZusammenfassungWir berichten über einen interessanten Fall einer Vaskulitis des zentralen Nervensystems, der eine schubförmig-remittierende Natur und ein bisher nicht berichtetes Profil kognitiver Defizite bei dieser Variante der Erkrankung aufweist.Der Patient stellte sich mit beidseitigem Kopfschmerz, Gesichtsfeldverlust des linken Auges, Dyschromatopsie und vorübergehender Bewusstlosigkeit vor. Er wurde in den letzten acht Jahren auf ähnliche Symptome untersucht. Es gab eine klare schubförmig-remittierende Geschichte, mit Perioden voller Remission von 4-6 Monaten.MRT-Untersuchungen zeigten bilaterale Bereiche von Hyperintensitäten, repräsentativ für kleine „nicht-charakteristische“ Veränderungen, wahrscheinlich vaskulären Ursprungs.In diesem Bericht wird die klinische Konundra während der Evaluation des Patienten diskutiert, mögliche Differentialdiagnosen untersucht und über die hypothetische Rolle der Statinverwendung in ähnlichen Fällen kommentiert.
Duration and Success of Nerve Rehabilitation after Elbow Injuries in Children
Authors: Murtezani Ardiana , Abazi Nerimane , Sllamniku Sabit , Rrecaj-Malaj Shkurta , Kepuska Arbnora B. 
Published: February 2019

AbstractNeurological complications after the supracondylar humerus fractures with a displacement of fragments result from traction, direct trauma, or nerve ischemia. The beginning of early rehabilitation, from when the arm is still immobilized, leads to complete restoration of the elbow joint, and thus any delay in starting the rehabilitation will have consequences, ranging from lighter ones to full disability. This study analyzed the impact of injured nerves, length of immobilization, and interruptions during rehabilitation on the rehabilitation duration (RD). A sample of 140 children of both genders with post-traumatic elbow injuries was considered, from the birth to 15 years. The sample was collected in cooperation with an orthopedist, pediatrician, and physiotherapist. The diagnosis was confirmed by physical and neurological examination and by radiography. The type of injury affects the RD. The supracondylar humerus fracture has a longer RD, with the average 85.45 days. We conducted the linear correlation test, between cases with injured nerves and cases without in relation to RD. The analysis provided significant statistical data (p < 0.01) proving that injured nerves are an important factor in RD. Of cases with radius nerve injury, 62.5% achieved full recovery. The analysis shows that for p < 0.01 (for cases in general) the immobilization duration has a significant impact on RD. Among patients who had no interruptions of rehabilitation, 92 achieved an excellent rehabilitation success, with an average number of 29.7 procedures and an average RD of 56 days. Injured nerves proved to have a great impact on the RD for elbow injuries, while not showing any impact on the rehabilitation success. Interruptions of rehabilitation treatments proved to have a statistical significance, meaning they have a high impact on the RD and success.
Traduction et réécriture dans les textes hétérolingues
Authors: de Sart Amaury 
Published: February 2019

Abstract
This article investigates the role of translation and rewriting in Julián Ríos’s first novel
Larva. Refusing to be read in a linear manner, including thousands of plays-on-words and more than 20
languages besides Spanish, Larva breaks many linguistic, literary and discursive codes. It also displays close
links with translation as it constantly moves from one language to another. The influence of translation and rewriting in the
novel is analyzed from contemporary approaches to Ríos’s views on literature (e.g. Kristeva, Riffaterre) with an aim of
understanding how they shape Larva’s main narrative structures and writing processes. Finally, the case of
Larva leaves the door open for questioning the principles of originality and creation in (heterolingual)
literature.
XB130 deficiency enhances carcinogen-induced skin tumorigenesis
Authors: Cho Hae-Ra , Wang Yingchun , Bai Xiaohui , Xiang Yun-Yan , Lu Christina , Post Alexander , Al Habeeb Ayman , Liu Mingyao 
Published: February 2019

AbstractXB130 is an adaptor protein that functions as a mediator of multiple tyrosine kinases important for regulating cell proliferation, survival, migration and invasion. Formerly predicted as an oncogene, alterations of its expression are documented in various human cancers. However, the exact role of XB130 in tumorigenesis is unknown. To address its function in skin tumorigenesis, a two-stage dimethylbenzanthracene (DMBA)/12-O-tetradecanoylphorbol 13-acetate (TPA) study was performed on XB130 knockout (KO), heterozygous (HZ) and wild-type (WT) littermate mice. DMBA/TPA-treated XB130 KO and HZ males developed a significantly higher number of epidermal tumors that were notably larger in size than did WT mice. Interestingly, DMBA/TPA-treated female mice did not show any difference in tumor multiplicity regardless of the genotypes. The skin tumor lesions of XB130 KO males were more progressed with an increased frequency of keratoacanthoma. Deficiency of XB130 dramatically increased epidermal tumor cell proliferation. The responses to DMBA and TPA stimuli were also individually investigated to elucidate the mechanistic role of XB130 at different stages of tumorigenesis. DMBA-treated male XB130 KO mice showed compensatory p53-mediated stress response. TPA-treated XB130 KO males demonstrated more skin ulceration with more severe edema, enhanced cell proliferation, accumulation of infiltrating neutrophils and increased production of pro-inflammatory cytokine genes compared with WT mice. Enhanced activities of nuclear factor-kappa B pathway, increased protein expression of metalloproteinase-9 and ERK1/2 phosphorylation were found in these KO mice. These findings demonstrate that XB130 acts as a tumor suppressor in carcinogen-induced skin tumorigenesis that may be mediated through inhibiting inflammation.
Association Between Antibiotic Use and Hospital-onset Clostridioides difficile Infection in US Acute Care Hospitals, 2006–2012: An Ecologic Analysis
Authors: Kazakova Sophia V , Baggs James , McDonald L Clifford , Yi Sarah H , Hatfield Kelly M , Guh Alice , Reddy Sujan C , Jernigan John A 
Published: February 2019

Abstract

Background
Unnecessary antibiotic use (AU) contributes to increased rates of Clostridioides difficile infection (CDI). The impact of antibiotic restriction on hospital-onset CDI (HO-CDI) has not been assessed in a large group of US acute care hospitals (ACHs).

Methods
We examined cross-sectional and temporal associations between rates of hospital-level AU and HO-CDI using data from 549 ACHs. HO-CDI was defined as a discharge with a secondary International Classification of Diseases, Ninth Revision, Clinical Modification code for CDI (008.45), and treatment with metronidazole or oral vancomycin &gt; 3 days after admission. Analyses were performed using multivariable generalized estimating equation models adjusting for patient and hospital characteristics.

Results
During 2006–2012, the unadjusted annual rates of HO-CDI and total AU were 7.3 per 10 000 patient-days (PD) (95% confidence interval [CI], 7.1–7.5) and 811 days of therapy (DOT)/1000 PD (95% CI, 803–820), respectively. In the cross-sectional analysis, for every 50 DOT/1000 PD increase in total AU, there was a 4.4% increase in HO-CDI. For every 10 DOT/1000 PD increase in use of third- and fourth-generation cephalosporins or carbapenems, there was a 2.1% and 2.9% increase in HO-CDI, respectively. In the time-series analysis, the 6 ACHs with a ≥30% decrease in total AU had a 33% decrease in HO-CDI (rate ratio, 0.67 [95% CI, .47–.96]); ACHs with a ≥20% decrease in fluoroquinolone or third- and fourth-generation cephalosporin use had a corresponding decrease in HO-CDI of 8% and 13%, respectively.

Conclusions
At an ecologic level, reductions in total AU, use of fluoroquinolones, and use of third- and fourth-generation cephalosporins were each associated with decreased HO-CDI rates.
The multiplex structure of the mental lexicon influences picture naming in people with aphasia
Authors: Castro Nichol , Stella Massimo 
Published: February 2019

Abstract
An emerging area of research in cognitive science is the utilization of networks to model the structure and processes of the mental lexicon in healthy and clinical populations, like aphasia. Previous research has focused on only one type of word similarity at a time (e.g., semantic relationships), even though words are multi-faceted. Here, we investigate lexical retrieval in a picture naming task from people with Broca’s and Wernicke’s aphasia and healthy controls by utilizing a multiplex network structure that accounts for the interplay between multiple semantic and phonological relationships among words in the mental lexicon. Extending upon previous work, we focused on the global network measure of closeness centrality which is known to capture spreading activation, an important process supporting lexical retrieval. We conducted a series of logistic regression models predicting the probability of correct picture naming. We tested whether multiplex closeness centrality was a better predictor of picture naming performance than single-layer closeness centralities, other network measures assessing local and meso-scale structure, psycholinguistic variables and group differences. We also examined production gaps, or the difference between the likelihood of producing a word with the lowest and highest closeness centralities. Our results indicated that multiplex closeness centrality was a significant predictor of picture naming performance, where words with high closeness centrality were more likely to be produced than words with low closeness centrality. Additionally, multiplex closeness centrality outperformed single-layer closeness centralities and other multiplex network measures, and remained a significant predictor after controlling for psycholinguistic variables and group differences. Furthermore, we found that the facilitative effect of closeness centrality was similar for both types of aphasia. Our results underline the importance of integrating multiple measures of word similarities in cognitive language networks for better understanding lexical retrieval in aphasia, with an eye towards future clinical applications.
Long-term survival and frequency of reinterventions after proximal aortic surgery: a retrospective study†
Authors: Vikholm Per , Astudillo Rafael , Thelin Stefan 
Published: February 2019

Abstract

OBJECTIVES:
We sought to analyse perioperative outcome, long-term mortality, frequency and causes of reintervention, and survival benefit in a contemporary cohort of patients undergoing proximal thoracic aortic surgery.

METHODS:
Participants comprised all patients undergoing open surgery for proximal thoracic aortic aneurysm (TAA) (n = 319) and thoracic aortic dissection type A (TAD) (n = 229) during 2005–2014 at the Department of Thoracic Surgery, Uppsala University Hospital. Long-term survival was compared to age- and sex-matched controls. Perioperative mortality and morbidity, event-free survival and causes of reoperation were also analysed.

RESULTS:
Long-term mortality was normalized in patients with TAA, and a survival benefit was seen as early as 20 months when corrected for time lost due to perioperative mortality. Long-term survivors undergoing surgery for TAD, on the other hand, had a 10-year mortality of 130% [95% confidence interval (95% CI) 120–140%] compared to age- and sex-matched controls. Moreover, their event-free survival was half that of patients with TAA (hazard ratio 2.3; 95% CI 1.7–3.2). Reintervention (i.e. reoperation or thoracic endovascular aortic repair) was also twice as common in the TAD patients (odds ratio 2.0; 95% CI 1.1–3.5). The dominant causes for reoperation among TAD patients were aortic insufficiency, aortic arch aneurysm and infection.

CONCLUSIONS:
Surgery for TAA is relatively safe, normalizes long-term mortality and confers an early survival benefit. However, TAD surgery carries a high risk of perioperative mortality and morbidity, as well as increased long-term mortality and risk of reintervention.
Adverse childhood experiences, childhood relationships and associated substance use and mental health in young Europeans
Authors: Hughes Karen , Bellis Mark A , Sethi Dinesh , Andrew Rachel , Yon Yongjie , Wood Sara , Ford Kat , Baban Adriana , Boderscova Larisa , Kachaeva Margarita , Makaruk Katarzyna , Markovic Marija , Povilaitis Robertas , Raleva Marija , Terzic Natasa , Veleminsky Milos , Włodarczyk Joanna , Zakhozha Victoria 
Published: February 2019

Abstract

Background
Adverse childhood experiences (ACEs) can increase risks of health-harming behaviours and poor health throughout life. While increases in risk may be affected by resilience resources such as supportive childhood relationships, to date few studies have explored these effects.

Methods
We combined data from cross-sectional ACE studies among young adults (n = 14 661) in educational institutions in 10 European countries. Nine ACE types, childhood relationships and six health outcomes (early alcohol initiation, problem alcohol use, smoking, drug use, therapy, suicide attempt) were explored. Multivariate modelling estimated relationships between ACE counts, supportive childhood relationships and health outcomes.

Results
Almost half (46.2%) of participants reported ≥1 ACE and 5.6% reported ≥4 ACEs. Risks of all outcomes increased with ACE count. In individuals with ≥4 ACEs (vs. 0 ACEs), adjusted odds ratios ranged from 2.01 (95% CIs: 1.70–2.38) for smoking to 17.68 (95% CIs: 12.93–24.17) for suicide attempt. Supportive childhood relationships were independently associated with moderating risks of smoking, problem alcohol use, therapy and suicide attempt. In those with ≥4 ACEs, adjusted proportions reporting suicide attempt reduced from 23% with low supportive childhood relationships to 13% with higher support. Equivalent reductions were 25% to 20% for therapy, 23% to 17% for problem drinking and 34% to 32% for smoking.

Conclusions
ACEs are strongly associated with substance use and mental illness. Harmful relationships are moderated by resilience factors such as supportive childhood relationships. Whilst ACEs continue to affect many children, better prevention measures and interventions that enhance resilience to the life-long impacts of toxic childhood stress are required.
Practical mixed methods strategies used to integrate qualitative and quantitative methods in community-based primary health care research
Authors: Kaur Navdeep , Vedel Isabelle , El Sherif Reem , Pluye Pierre 
Published: February 2019

Abstract

Background
Mixed methods (MM) are common in community-based primary health care (CBPHC) research studies. Several strategies have been proposed to integrate qualitative and quantitative components in MM, but they are seldom well conceptualized and described. The purpose of the present review was to identify and describe practical MM strategies and combinations of strategies used to integrate qualitative and quantitative methods in CBPHC research.

Methods
A methodological review with qualitative synthesis (grouping) was performed. Records published in English in 2015 were retrieved from the Scopus bibliographic database. Eligibility criteria were: CBPHC empirical study, MM research with detailed description of qualitative and quantitative methods and their integration. Data were extracted from included studies and grouped using a conceptual framework comprised of three theoretical types of MM integration, the seven combinations of these types and nine practical strategies (three per type of integration) and multiple combinations of strategies.

Results
Among the 151 articles reporting CBPHC and MM studies retrieved, 54 (35.7%) met the inclusion criteria for this review. The included studies provided examples of the three theoretical types of MM integration, the seven combinations of these types as well as the nine practical strategies. Overall, 15 combinations of these strategies were observed. No emerging strategy was observed that was not predicted by the conceptual framework.

Conclusions
This review can provide guidance to CBPHC researchers for planning, conducting and reporting practical strategies and combinations of strategies used for integrating qualitative and quantitative methods in MM research.
How emerging data technologies can increase trust and transparency in fisheries
Authors: Probst Wolfgang Nikolaus 
Published: February 2019

Abstract
The ubiquitous spread of digital networks has created techniques which can organize, store, and analyse large data volumes in an automized and self-administered manner in real time. These technologies will have profound impacts on policy, administration, economy, trade, society, and science. This article sketches how three digital data technologies, namely the blockchain, data mining, and artificial intelligence could impact commercial fisheries including producers, wholesalers, retailers, consumers, management authorities, and scientist. Each of these three technologies is currently experiencing an enormous boost in technological development and real-world implementation and is predicted to increasingly affect many aspects of fisheries and seafood trade. As any economic sector acting on global scales, fishing and seafood production are often challenged with a lack of trust along various steps of the production process and supply chain. Consumers are often not well informed on the origin and production methods of their product, management authorities can only partly control fishing and trading activities and producers can be challenged by low market prices and competition with peers. The emerging data technologies can improve the trust among agents within the fisheries sector by increasing transparency and availability of information from net to plate.