bluuebunny/crossref_metadata_2025_split huggingface dataset:
SHEAR: sample heterogeneity estimation and assembly by reference
Authors: Landman Sean R , Hwang Tae Hyun , Silverstein Kevin AT , Li Yingming , Dehm Scott M , Steinbach Michael , Kumar Vipin 
Published: January 2014

Abstract

Background
Personal genome assembly is a critical process when studying tumor genomes and other highly divergent sequences. The accuracy of downstream analyses, such as RNA-seq and ChIP-seq, can be greatly enhanced by using personal genomic sequences rather than standard references. Unfortunately, reads sequenced from these types of samples often have a heterogeneous mix of various subpopulations with different variants, making assembly extremely difficult using existing assembly tools. To address these challenges, we developed SHEAR (Sample Heterogeneity Estimation and Assembly by Reference;http://vk.cs.umn.edu/SHEAR), a tool that predicts SVs, accounts for heterogeneous variants by estimating their representative percentages, and generates personal genomic sequences to be used for downstream analysis.

Results
By making use of structural variant detection algorithms, SHEAR offers improved performance in the form of a stronger ability to handle difficult structural variant types and better computational efficiency. We compare against the lead competing approach using a variety of simulated scenarios as well as real tumor cell line data with known heterogeneous variants. SHEAR is shown to successfully estimate heterogeneity percentages in both cases, and demonstrates an improved efficiency and better ability to handle tandem duplications.

Conclusion
SHEAR allows for accurate and efficient SV detection and personal genomic sequence generation. It is also able to account for heterogeneous sequencing samples, such as from tumor tissue, by estimating the subpopulation percentage for each heterogeneous variant.
A claims data-based comparison of comorbidity in individuals with and without dementia
Authors: Bauer Kathrin , Schwarzkopf Larissa , Graessel Elmar , Holle Rolf 
Published: January 2014

AbstractBackgroundMultimorbidity is common in advanced age, and is usually associated with negative – yet to some extent preventable – health outcomes. Detecting comorbid conditions is especially difficult in individuals with dementia, as they might not always be able to sufficiently express discomfort. This study compares relevant comorbidity complexes in elderly people with and without dementia, with a particular look at gender- and living environment-specific differences. Moreover, associations between selected comorbid conditions and dementia are reviewed more closely.MethodsUsing 2006 claims data from a large German Statutory Health Insurance fund, 9,139 individuals with dementia and 28,614 age- and gender-matched control subjects aged 65 years and older were identified. A total of 30 comorbidity complexes were defined based on ICD-10 codes. Corresponding prevalence rates were calculated, and the association between a distinct condition and dementia was evaluated via logistic regression in the overall sample as well as in analyses stratified by gender and living environment.ResultsIndividuals with dementia were more likely to be diagnosed with 15 comorbidity complexes, including Parkinson’s, stroke, diabetes, atherosclerosis (supposed dementia risk factors) or fluids and electrolyte disorders, insomnia, incontinence, pneumonia, fractures and injuries (supposed sequelae). In contrast, they were less likely to be diagnosed with 11 other conditions, which included vision and hearing problems, diseases of the musculoskeletal system, lipoprotein disorders and hypertension. In a gender-stratified analysis, the patterns remained largely the same, but a bigger comorbidity gap between cases and control subjects emerged in the male population. Restricting the analysis to community-living individuals did not lead to any substantial changes.ConclusionBesides strengthening the evidence on accepted dementia risk factors and sequelae, the analyses point to particular conditions that are likely to remain untreated or even undiagnosed. This issue seems to affect male and female individuals with dementia to varying degrees. Raising awareness of these conditions is important to possibly preventing comorbidity-associated complications and disease progression in dementia patients. To more comprehensively understand the mutual interactions between dementia and comorbidity, further research on diagnostic and treatment attitudes regarding comorbidity in dementia patients and on their gender-specific health-seeking behaviour seems to be required.
Real-time automatic hospital-wide surveillance of nosocomial infections and outbreaks in a large Chinese tertiary hospital
Authors: Du Mingmei , Xing Yubin , Suo Jijiang , Liu Bowei , Jia Na , Huo Rui , Chen Chunping , Liu Yunxi 
Published: January 2014

Abstract

Background
We aimed to develop a real-time nosocomial infection surveillance system (RT-NISS) to monitor all nosocomial infections (NIs) and outbreaks in a Chinese comprehensive hospital to better prevent and control NIs.

Methods
The screening algorithm used in RT-NISS included microbiological reports, antibiotic usage, serological and molecular testing, imaging reports, and fever history. The system could, in real-time, identify new NIs, record data, and produce time-series reports to align NI cases.

Results
Compared with a manual survey of NIs (the gold standard), the sensitivity and specificity of RT-NISS was 98.8% (84/85) and 93.0% (827/889), with time-saving efficiencies of about 200 times. RT-NISS obtained the highest hospital-wide monthly NI rate of 2.62%, while physician and medical record reviews reported rates of 1.52% and 2.35% respectively. It took about two hours for one infection control practitioner (ICP) to deal with 70 new suspicious NI cases; there were 3,500 inpatients each day in the study hospital. The system could also provide various updated data (i.e. the daily NI rate, surgical site infection (SSI) rate) for each ward, or the entire hospital. Within 3 years of implementing RT-NISS, the ICPs monitored and successfully controlled about 30 NI clusters and 4 outbreaks at the study hospital.

Conclusions
Just like the “ICPs’ eyes”, RT-NISS was an essential and efficient tool for the day-to-day monitoring of all NIs and outbreak within the hospital; a task that would not have been accomplished through manual process.
Hydrogen induced redox mechanism in amorphous carbon resistive random access memory
Authors: Chen Yi-Jiun , Chen Hsin-Lu , Young Tai-Fa , Chang Ting-Chang , Tsai Tsung-Ming , Chang Kuan-Chang , Zhang Rui , Chen Kai-Huang , Lou Jen-Chung , Chu Tian-Jian , Chen Jung-Hui , Bao Ding-Hua , Sze Simon M 
Published: January 2014

Abstract
We investigated the bipolar resistive switching characteristics of the resistive random access memory (RRAM) device with amorphous carbon layer. Applying a forming voltage, the amorphous carbon layer was carbonized to form a conjugation double bond conductive filament. We proposed a hydrogen redox model to clarify the resistive switch mechanism of high/low resistance states (HRS/LRS) in carbon RRAM. The electrical conduction mechanism of LRS is attributed to conductive sp2 carbon filament with conjugation double bonds by dehydrogenation, while the electrical conduction of HRS resulted from the formation of insulating sp3-type carbon filament through hydrogenation process.
CD80+ and CD86+B cells as biomarkers and possible therapeutic targets in HTLV-1 associated myelopathy/tropical spastic paraparesis and multiple sclerosis
Authors: Menezes Soraya Maria , Decanine Daniele , Brassat David , Khouri Ricardo , Schnitman Saul V , Kruschewsky Ramon , López Giovanni , Alvarez Carolina , Talledo Michael , Gotuzzo Eduardo , Vandamme Anne-Mieke , Galvão-Castro Bernardo , Liblau Roland , Weyenbergh Johan Van 
Published: January 2014

AbstractBackgroundHuman T-cell lymphotropic virus (HTLV-1) is the causative agent of the incapacitating, neuroinflammatory disease HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP). Currently, there are no disease-modifying therapies with long-term clinical benefits or validated biomarkers for clinical follow-up in HAM/TSP. Although CD80 and CD86 costimulatory molecules play prominent roles in immune regulation and reflect disease status in multiple sclerosis (MS), data in HAM/TSP are lacking.MethodsUsing flow cytometry, we quantifiedex vivoandin vitroexpression of CD80 and CD86 in PBMCs of healthy controls, HTLV-1-infected individuals with and without HAM/TSP, and MS patients. We hypothesizedex vivoCD80 and CD86 expressions and theirin vitroregulation by interferon (IFN)-α/β mirror similarities between HAM/TSP and MS and hence might reveal clinically useful biomarkers in HAM/TSP.ResultsEx vivoexpression of CD80 and CD86 in T and B cells increased in all HTLV-1 infected individuals, but with a selective defect for B cell CD86 upregulation in HAM/TSP. Despite decreased total B cells with increasing disease duration (p = 0.0003,r = −0.72), CD80+B cells positively correlated with disease severity (p = 0.0017,r = 0.69) in HAM/TSP. B cell CD80 expression was higher in women with HAM/TSP, underscoring that immune markers can reflect the female predominance observed in most autoimmune diseases. In contrast to MS patients, CD80+(p = 0.0001) and CD86+(p = 0.0054) lymphocytes expanded uponin vitroculture in HAM/TSP patients. The expansion of CD80+and CD86+T cells but not B cells was associated with increased proliferation in HTLV-1 infection.In vitrotreatment with IFN-β but not IFN-α resulted in a pronounced increase of B cell CD86 expression in healthy controls, as well as in patients with neuroinflammatory disease (HAM/TSP and MS), similar toin vivotreatment in MS.ConclusionsWe propose two novel biomarkers,ex vivoCD80+B cells positively correlating to disease severity and CD86+B cells preferentially induced by IFN-β, which restores defective upregulation in HAM/TSP. This study suggests a role for B cells in HAM/TSP pathogenesis and opens avenues to B cell targeting (with proven clinical benefit in MS) in HAM/TSP but also CD80-directed immunotherapy, unprecedented in both HAM/TSP and MS.
Effects of cyclic equibiaxial mechanical stretch on α-BK and TRPV4 expression in equine chondrocytes
Authors: Hdud Ismail M , Mobasheri Ali , Loughna Paul T 
Published: January 2014

Abstract

Background
Chondrocytes are regularly exposed to load-induced stimuli and have the capability to sense and respond to applied mechanical stress. However, the mechanisms involved in chondrocyte mechanotransduction are not clearly understood. The purpose of this study was to explore the effects of cyclic equibiaxial mechanical stretch on the expression of α-BK and TRPV4 channels.

Findings
Freshly isolated equine articular chondrocytes were subjected to mechanical stress (8% elongation at frequency of 0.5 Hz for 8 h). Western blotting was used to investigate the expression of BKCa and TRPV4 channel proteins. Mechanical stretch increased the expression of BKCa channels by 1.8 fold but TRPV4 expression was not affected.

Conclusions
Upregulation of BKCa channel may be the result of direct membrane stretch or elevated intracellular Ca2+.
Separated representations of 3D elastic solutions in shell geometries
Authors: Bognet Brice , Leygue Adrien , Chinesta Francisco 
Published: January 2014

Abstract

Background
The solution of 3D models in degenerated geometries in which some characteristic dimensions are much lower than the other ones -e.g. beams, plates, shells,...- is a tricky issue when using standard mesh-based discretization techniques.

Methods
Separated representations allow decoupling the meshes used for approximating the solution along each coordinate. Thus, in plate or shell geometries 3D solutions can be obtained from a sequence of 2D and 1D problems allowing fine and accurate representation of the solution evolution along the thickness coordinate while keeping the computational complexity characteristic of 2D simulations. In a former work this technique was considered for addressing the 3D solution of thermoelastic problems defined in plate geometries. In this work, the technique is extended for addressing the solution of 3D elastic problems defined in shell geometries.

Results
The capabilities of the proposed approach are illustrated by considering some numerical examples involving different degrees of complexity, from simple shells to composite laminates involving stiffeners.

Conclusions
The analyzed examples prove the potentiality and efficiency of the proposed strategy, where the computational complexity was found evolving as reported in our former works, proving that 3D solutions can be computed at a 2D cost.
Effect of honey in diabetes mellitus: matters arising
Authors: Erejuwa Omotayo O 
Published: January 2014

AbstractDiabetes mellitus remains an incurable disorder in spite of intense research. As result of limitations and unmet goals associated with the use of anti-diabetic drugs, an increased number of diabetic populations globally now resort to complementary and alternative medicine (CAM) such as herbs and other natural products. There has been a renewed interest in the use of honey in the treatment of diabetes mellitus, partly due to an increase in the availability of evidence-based data demonstrating its benefits in diabetic rodents and patients. This commentary aims to underscore some of the research implications, issues and questions raised from these studies which show the beneficial effects of honey in the treatment of diabetes mellitus. Some of the issues highlighted in this article include: considering honey is sweet and rich in sugars, how could it be beneficial in the management of diabetes mellitus? Are the observed effects of honey or combined with anti-diabetic drugs exclusive to certain honey such as tualang honey? Could these beneficial effects be reproduced with other honey samples? Anti-diabetic drugs in combination with honey improve glycemic control, enhance antioxidant defenses and reduce oxidative damage. These effects are believed to be mediated partly via antioxidant mechanism of honey. This raises another question. Could similar data be obtained if anti-diabetic drugs are co-administered with other potent antioxidants such as vitamin C or E? As the evidence has revealed, the prospect of managing diabetes mellitus with honey or antioxidants (such as vitamin C or E) as an adjunct to conventional diabetes therapy is vast. However, more well-designed, rigorously conducted randomized controlled studies are necessary to further validate these findings.
Nonhypoxic regulation and role of hypoxia-inducible factor 1 in aromatase inhibitor resistant breast cancer
Authors: Kazi Armina A , Gilani Rabia A , Schech Amanda J , Chumsri Saranya , Sabnis Gauri , Shah Preeti , Goloubeva Olga , Kronsberg Shari , Brodie Angela H 
Published: January 2014

Abstract
Introduction
Although aromatase inhibitors (AIs; for example, letrozole) are highly effective in treating estrogen receptor positive (ER+) breast cancer, a significant percentage of patients either do not respond to AIs or become resistant to them. Previous studies suggest that acquired resistance to AIs involves a switch from dependence on ER signaling to dependence on growth factor-mediated pathways, such as human epidermal growth factor receptor-2 (HER2). However, the role of HER2, and the identity of other relevant factors that may be used as biomarkers or therapeutic targets remain unknown. This study investigated the potential role of transcription factor hypoxia inducible factor 1 (HIF-1) in acquired AI resistance, and its regulation by HER2.

Methods
In vitro studies using AI (letrozole or exemestane)-resistant and AI-sensitive cells were conducted to investigate the regulation and role of HIF-1 in AI resistance. Western blot and RT-PCR analyses were conducted to compare protein and mRNA expression, respectively, of ERα, HER2, and HIF-1α (inducible HIF-1 subunit) in AI-resistant versus AI-sensitive cells. Similar expression analyses were also done, along with chromatin immunoprecipitation (ChIP), to identify previously known HIF-1 target genes, such as breast cancer resistance protein (BCRP), that may also play a role in AI resistance. Letrozole-resistant cells were treated with inhibitors to HER2, kinase pathways, and ERα to elucidate the regulation of HIF-1 and BCRP. Lastly, cells were treated with inhibitors or inducers of HIF-1α to determine its importance.

Results
Basal HIF-1α protein and BCRP mRNA and protein are higher in AI-resistant and HER2-transfected cells than in AI-sensitive, HER2- parental cells under nonhypoxic conditions. HIF-1α expression in AI-resistant cells is likely regulated by HER2 activated-phosphatidylinositide-3-kinase/Akt-protein kinase B/mammalian target of rapamycin (PI3K/Akt/mTOR) pathway, as its expression was inhibited by HER2 inhibitors and kinase pathway inhibitors. Inhibition or upregulation of HIF-1α affects breast cancer cell expression of BCRP; AI responsiveness; and expression of cancer stem cell characteristics, partially through BCRP.

Conclusions
One of the mechanisms of AI resistance may be through regulation of nonhypoxic HIF-1 target genes, such as BCRP, implicated in chemoresistance. Thus, HIF-1 should be explored further for its potential as a biomarker of and therapeutic target.
The RNA-binding protein hnRNPLL induces a T cell alternative splicing program delineated by differential intron retention in polyadenylated RNA
Authors: Cho Vicky , Mei Yan , Sanny Arleen , Chan Stephanie , Enders Anselm , Bertram Edward M , Tan Andy , Goodnow Christopher C , Andrews T Daniel 
Published: January 2014

Abstract
Background
Retention of a subset of introns in spliced polyadenylated mRNA is emerging as a frequent, unexplained finding from RNA deep sequencing in mammalian cells.

Results
Here we analyze intron retention in T lymphocytes by deep sequencing polyadenylated RNA. We show a developmentally regulated RNA-binding protein, hnRNPLL, induces retention of specific introns by sequencing RNA from T cells with an inactivating Hnrpll mutation and from B lymphocytes that physiologically downregulate Hnrpll during their differentiation. In Ptprc mRNA encoding the tyrosine phosphatase CD45, hnRNPLL induces selective retention of introns flanking exons 4 to 6; these correspond to the cassette exons containing hnRNPLL binding sites that are skipped in cells with normal, but not mutant or low, hnRNPLL. We identify similar patterns of hnRNPLL-induced differential intron retention flanking alternative exons in 14 other genes, representing novel elements of the hnRNPLL-induced splicing program in T cells. Retroviral expression of a normally spliced cDNA for one of these targets, Senp2, partially corrects the survival defect of Hnrpll-mutant T cells. We find that integrating a number of computational methods to detect genes with differentially retained introns provides a strategy to enrich for alternatively spliced exons in mammalian RNA-seq data, when complemented by RNA-seq analysis of purified cells with experimentally perturbed RNA-binding proteins.

Conclusions
Our findings demonstrate that intron retention in mRNA is induced by specific RNA-binding proteins and suggest a biological significance for this process in marking exons that are poised for alternative splicing.
Progenitor cell therapy for sacral pressure sore: a pilot study with a novel human chronic wound model
Authors: Wettstein Reto , Savic Miodrag , Pierer Gerhard , Scheufler Oliver , Haug Martin , Halter Jörg , Gratwohl Alois , Baumberger Michael , Schaefer Dirk Johannes , Kalbermatten Daniel Felix 
Published: January 2014

Abstract
Introduction
Chronic wounds are a major health-care issue, but research is limited by the complexity and heterogeneity in terms of wound etiology as well as patient-related factors. A suitable animal model that replicates the situation in humans is not available. Therefore, the aim of the present work is to present a standardized human wound model and the data of a pilot study of topically applied progenitor cells in a sacral pressure sore.

Methods
Three patients underwent cell harvest from the iliac crest at the time of the initial debridement. Forty-eight hours after bone marrow harvest and debridement, the CD34+ selected cell suspension was injected into the wound. With the aid of a laser scanner, three-dimensional analyses of wound morphometry were performed until the defect was reconstructed with a local flap 3 weeks after debridement.

Results
Decreases in volume to 60% ± 6% of baseline on the sham side and to 52% ± 3% of baseline on the cell side were measured. Histologic work-up revealed no signs of metaplastic, dysplastic, or neoplastic proliferation/differentiation after progenitor cell treatment. CD34+ cells were detected in the biopsies of day 0.

Conclusions
The pressure sore wound model allows investigation of the initial 3 weeks after cell-based therapy. Objective outcome analysis in terms of wound volume and histology can be performed without, or with, minimal additional morbidity, and the anatomy of the sacral area allows a control and study side in the same patient. Therefore, this model can serve as a standard for wound-healing studies.

Trial registration
ClinicalTrials.gov NCT00535548.
Lausanne-Zagreb via Berlin, or heading for an unforeseen Europeanness
Authors: Lampropoulos Apostolos 
Published: January 2014

Abstract
This article discusses the Eurovision Song Contest and focuses on the two editions of the event immediately before and after the fall of the Berlin Wall, i.e. the 1989 contest that was held in Lausanne and the 1990 contest in Zagreb. It attempts to figure out the different kinds of Europeanness that were outlined on the Eurovision stage before the remapping of Europe during the early 1990s. Reading closely the conformist and narcissistic Eurocentrism of the 1989 contest, as well as the touristic and sometimes patronizing attitude vis-à-vis Europe of the 1990 contest, it spells out some ways in which an emblematic televised show understood its own political dimension and reacted to the emerging realities.
The bibliografting of Montolieu, village du Livre des Arts Graphiques
Authors: Merfeld-Langston Audra 
Published: January 2014

Abstract
In 2010, Montolieu, France celebrated its twentieth anniversary as Montolieu, village du livre et des Arts Graphiques. Within two decades, this town of under 800 residents has witnessed significant economic, cultural, demographic and physical changes that have transformed it from a victim of rural exodus to an increasingly important cultural centre and tourist destination, as well as a desirable location for purchasing second residences. I begin this article by examining the conditions that prompted the rural town’s decision to adopt a new identity based on literary and print culture. I contextualize the development of this village du livre within a growing European book town trend and within a larger French fascination with literature, literary culture and literacy. I next investigate the tensions and challenges that arose in the community as the project began taking shape. Finally, I analyse how the adoption of a new identity has affected the town’s social and physical make-up, especially as evident in three local lieux de mémoire: the Musée Michel Braibant, the Manufacture Royale and the Coopérative, Centre d’Art et de Littérature.
Reviews
Authors: Murphy Michael , O’Callaghan Liam 
Published: January 2014

Abstract
Morrissey: Fandom, Representations and Identities, Eoin Devereux, Aileen Dillane and Martin J. Power (eds) (2011) Bristol: Intellect, 342 pp., ISBN: 9781841504179, h/bk £29.95
Sport, Representation and Evolving Identities in Europe, Philip Dine and Sean Crosson (eds) (2010) Bern: Peter Lang, 369 pp., ISBN: 978-3-03911-977-6, p/bk, €54.40