bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multiple Sclerosis
Authors: Alroughani Raed , Yamout Bassem 
Published: May 2018

AbstractMultiple sclerosis (MS) is a chronic central nervous system inflammatory disease of autoimmune etiology, mediated by activated T cells with evolving evidence of a significant contribution from B cells and cells of the innate immune system. The disease is thought to be due to a complex interaction between different genetic and environmental factors. The prevalence of MS is rising all over the world, due on one hand to earlier diagnosis and prolonged survival, and on the other to a true increase in incidence of the disease. The diagnosis of MS remains clinical despite recent advances in diagnostics and relies on demonstrating dissemination in space and time while excluding alternative diagnoses. The Mc Donald diagnostic criteria, with their recent 2017 revision, are currently widely accepted in the MS community. Although no cure is yet available, many disease-modifying therapies (DMTs) have shown different levels of efficacy in preventing relapses, accumulation of lesions on magnetic resonance imaging (MRI), and disability progression. Current treatment strategies include gradual escalation based on clinical and radiological criteria that determine treatment response, or initial induction with high efficacy DMTs especially in patients with an early aggressive course.
Postoperative Aortic Neck Dilation: Myth or Fact?
Authors: Ribner A.S. , Tassiopoulos A.K. 
Published: May 2018

AbstractThe abdominal aorta is the most common site of an aortic aneurysm. The visceral and most proximal infrarenal segment (aneurysm neck) are usually spared and considered more resistant to aneurysmal degeneration. However, if an abdominal aortic aneurysm (AAA) is left untreated, the natural history of the aortic neck is progressive dilatation and shortening. This may have significant implications for patients undergoing endovascular repair of AAAs (EVAR) as endograft stability and integrity of the repair are dependent on an intact proximal seal zone. Compromised seal zones, caused by progressive diameter enlargement and foreshortening of the aortic neck, may lead to distal endograft migration, type Ia endoleak, aortic sac repressurization, and, ultimately, aortic rupture.
Treatment Outcome of Reconstruction for Isolated Posterior Cruciate Injury: Subjective and Objective Evaluations
Authors: Ochiai Satoshi , Hagino Tetsuo , Senga Shinya , Yamashita Takashi , Haro Hirotaka 
Published: May 2018

AbstractThere is no consensus regarding the treatment method and outcome of posterior cruciate ligament (PCL) injury. We hypothesized that although the outcome of PCL reconstruction was favorable in terms of knee stability, the outcome was unsatisfactory in terms of patient-based assessments. The purpose of this study is to evaluate the treatment outcomes of knees that underwent reconstruction for PCL injury by subjective and objective assessments, and to analyze the correlation between various assessments. Twenty-three patients who underwent PCL reconstruction were studied. All reconstructions were performed arthroscopically by the single-bundle technique using a hamstring tendon autograft. Patients were evaluated clinically before operation and 24 months after operation using the 36-Item Short Form Health Survey (SF-36) which is a patient-based health assessment survey, Lysholm score, tibial translation ratio, Visual Analogue Scale (VAS) for pain, and range of motion (ROM) in the knee. The correlation of these assessment methods was analyzed. For the SF-36 survey, significant improvement was observed after operation in only 3 of 7 subscales compared with before surgery. Furthermore, the scores reached the national standard scores in only 3 subscales. While the Lysholm score and tibial translation ratio were improved significantly, no significant improvement in the VAS pain score was observed. For ROM assessment, approximately 30% of the patients had flexion restriction after operation, and the degree of restriction correlated positively with the VAS score. The present results indicated that although the outcome of PCL reconstruction was favorable in terms of knee stability and motor function, the outcome was unsatisfactory in terms of patient-based assessments. Since pain associated with flexion restriction appears to be a poor prognostic factor and there is a dissociation between subjective and objective assessments, improvement of the surgical method is necessary.
Anterior Cruciate Ligament Reconstruction with LARS Artificial Ligament—Clinical Results after a Long-Term Follow-Up
Authors: Parchi Paolo , Ciapini Gianluca , Paglialunga Carlo , Giuntoli Michele , Picece Carmine , Chiellini Fabio , Lisanti Michele , Scaglione Michelangelo 
Published: May 2018

Purpose The aim of this retrospective study was to evaluate the subjective and functional outcome of anterior cruciate ligament (ACL) reconstruction with the synthetic Ligament Advanced Reinforcement System (LARS) ligament.
Methods Twenty-six patients were reviewed at an average follow-up of 11.6 years. Objective clinical evaluation was performed with stability tests. Patient-reported outcomes (Visual Analogue Scale, Knee Injury and Osteoarthritis Outcome Score, and Cincinnati Knee Rating Scale) were used to assess subjective and functional outcomes.
Results Overall satisfactory results were obtained in 22 cases (84.6%). Four patients (15.4%) showed mechanical failure of the graft. No cases of synovitis or infection were reported.
Conclusion LARS ligament can be considered a safe and suitable option for ACL reconstruction in carefully selected cases, especially elderly patients needing a rapid postoperative recovery.
Level of Evidence Level IV, retrospective case series.
The Modified Iliopubic Tract Repair—A Pain-Free Alternative
Authors: Ali Iqbal , Dikshit Vashisht , Manerikar Kshitij , Dholakia Mirat , Save Maitreyee 
Published: May 2018

Background The open preperitoneal repair offers the benefits of placing the mesh in the preferred position while avoiding the disadvantages of laparoscopic repair.
Methods A total of 60 patients with bilateral inguinal hernias were randomized to undergo either the standard Lichtenstein meshplasty or the modified iliopubic tract repair in a teaching hospital. Outcomes measured were immediate postoperative pain, return to activity, and delayed neurological complications.
Results Patients who underwent the iliopubic tract repair walked out of bed faster than the Lichtenstein group (6.3 hours vs 7.4 hours, p < 0.0001) and experienced significant lower pain as charted by visual analogue scale scores (3.28 vs 2.71 on day 1, 2.16 vs 1.71 on day 2, 1.92 vs 1.08 on day 3; p < 0.05). Delayed complications like chronic inguinal pain and numbness were not seen in the iliopubic tract group. However, this difference was not statistically significant (p > 0.05).
Conclusion The iliopubic tract repair offers an excellent alternative to the Lichtenstein meshplasty, and is associated with lower postoperative pain, earlier return to work, and lower delayed neurological complications.
Concordance of PD-L1 Expression Detection in Non–Small Cell Lung Cancer (NSCLC) Tissue Biopsy Specimens Between OncoTect iO Lung Assay and Immunohistochemistry (IHC)
Authors: Young Stephen , Griego-Fullbright Christen , Wagner Aaron , Chargin Amanda , Patterson Bruce K , Chabot-Richards Devon 
Published: May 2018

AbstractObjectivesWe report on the validity of a fully quantitative technology to determine tumor cells’ PD-L1 expression compared with a standard immunohistochemical (IHC) assay in non–small cell lung cancer.MethodsNineteen fresh tissue specimens were processed into single-cell suspensions using the IncellPREP Kit. Cells were treated with the OncoTect iO Lung Assay, which quantitatively assessed tumor-infiltrating lymphocytes (TILs), DNA content, and PD-L1 expression on diploid and aneuploid tumor populations.ResultsComparison of the OncoTect iO Lung Assay with IHC revealed a concordance of 95% overall (negative percent agreement, 97%; positive percent agreement, 89%). PD-L1 expression varied depending on the DNA content. The number of TILs and antigen-presenting cells (APCs) was significantly decreased in tumor compared with normal lung tissue.ConclusionsThe nonsubjective OncoTect iO Lung Assay has been shown to be at least as accurate and sensitive as IHC for the detection of PD-L1 expression while providing additional information to guide treatment.
The Orphan Receptor GPR35 Contributes to Angiotensin II–Induced Hypertension and Cardiac Dysfunction in Mice
Authors: Divorty Nina , Milligan Graeme , Graham Delyth , Nicklin Stuart A 
Published: May 2018

Abstract

BACKGROUND
The orphan receptor G protein–coupled receptor 35 (GPR35) has been associated with a range of diseases, including cancer, inflammatory bowel disease, diabetes, hypertension, and heart failure. To assess the potential for GPR35 as a therapeutic target in cardiovascular disease, this study investigated the cardiovascular phenotype of a GPR35 knockout mouse under both basal conditions and following pathophysiological stimulation.

METHODS
Blood pressure was monitored in male wild-type and GPR35 knockout mice over 7–14 days using implantable telemetry. Cardiac function and dimensions were assessed using echocardiography, and cardiomyocyte morphology evaluated histologically. Two weeks of angiotensin II (Ang II) infusion was used to investigate the effects of GPR35 deficiency under pathophysiological conditions. Gpr35 messenger RNA expression in cardiovascular tissues was assessed using quantitative polymerase chain reaction.

RESULTS
There were no significant differences in blood pressure, cardiac function, or cardiomyocyte morphology in GPR35 knockout mice compared with wild-type mice. Following Ang II infusion, GPR35 knockout mice were protected from significant increases in systolic, diastolic, and mean arterial blood pressure or impaired left ventricular systolic function, in contrast to wild-type mice. There were no significant differences in Gpr35 messenger RNA expression in heart, kidney, and aorta following Ang II infusion in wild-type mice.

CONCLUSIONS
Although GPR35 does not appear to influence basal cardiovascular regulation, these findings demonstrate that it plays an important pathological role in the development of Ang II–induced hypertension and impaired cardiac function. This suggests that GPR35 is a potential novel drug target for therapeutic intervention in hypertension.
Versatile interactions and bioinformatics analysis of noncoding RNAs
Authors: Chen Qi , Meng Xianwen , Liao Qi , Chen Ming 
Published: May 2018

AbstractAdvances in RNA sequencing technologies and computational methodologies have provided a huge impetus to noncoding RNA (ncRNA) study. Once regarded as inconsequential results of transcriptional promiscuity, ncRNAs were later found to exert great roles in various aspects of biological functions. They are emerging as key players in gene regulatory networks by interacting with other biomolecules (DNA, RNA or protein). Here, we provide an overview of ncRNA repertoire and highlight recent discoveries of their versatile interactions. To better investigate the ncRNA-mediated regulation, it is necessary to make full use of innovative sequencing techniques and computational tools. We further describe a comprehensive workflow for in silico ncRNA analysis, providing up-to-date platforms, databases and tools dedicated to ncRNA identification and functional annotation.
PEA: an integrated R toolkit for plant epitranscriptome analysis
Authors: Zhai Jingjing , Song Jie , Cheng Qian , Tang Yunjia , Ma Chuang 
Published: May 2018

Abstract

Motivation
The epitranscriptome, also known as chemical modifications of RNA (CMRs), is a newly discovered layer of gene regulation, the biological importance of which emerged through analysis of only a small fraction of CMRs detected by high-throughput sequencing technologies. Understanding of the epitranscriptome is hampered by the absence of computational tools for the systematic analysis of epitranscriptome sequencing data. In addition, no tools have yet been designed for accurate prediction of CMRs in plants, or to extend epitranscriptome analysis from a fraction of the transcriptome to its entirety.

Results
Here, we introduce PEA, an integrated R toolkit to facilitate the analysis of plant epitranscriptome data. The PEA toolkit contains a comprehensive collection of functions required for read mapping, CMR calling, motif scanning and discovery and gene functional enrichment analysis. PEA also takes advantage of machine learning (ML) technologies for transcriptome-scale CMR prediction, with high prediction accuracy, using the Positive Samples Only Learning algorithm, which addresses the two-class classification problem by using only positive samples (CMRs), in the absence of negative samples (non-CMRs). Hence PEA is a versatile epitranscriptome analysis pipeline covering CMR calling, prediction and annotation and we describe its application to predict N6-methyladenosine (m6A) modifications in Arabidopsis thaliana. Experimental results demonstrate that the toolkit achieved 71.6% sensitivity and 73.7% specificity, which is superior to existing m6A predictors. PEA is potentially broadly applicable to the in-depth study of epitranscriptomics.

Availability and implementation
PEA Docker image is available at https://hub.docker.com/r/malab/pea, source codes and user manual are available at https://github.com/cma2015/PEA.

Supplementary information
Supplementary data are available at Bioinformatics online.
The size matters? A computational tool to design bivalent ligands
Authors: Pérez-Benito Laura , Henry Andrew , Matsoukas Minos-Timotheos , Lopez Laura , Pulido Daniel , Royo Miriam , Cordomí Arnau , Tresadern Gary , Pardo Leonardo 
Published: May 2018

Abstract

Motivation
Bivalent ligands are increasingly important such as for targeting G protein-coupled receptor (GPCR) dimers or proteolysis targeting chimeras (PROTACs). They contain two pharmacophoric units that simultaneously bind in their corresponding binding sites, connected with a spacer chain. Here, we report a molecular modelling tool that links the pharmacophore units via the shortest pathway along the receptors van der Waals surface and then scores the solutions providing prioritization for the design of new bivalent ligands.

Results
Bivalent ligands of known dimers of GPCRs, PROTACs and a model bivalent antibody/antigen system were analysed. The tool could rapidly assess the preferred linker length for the different systems and recapitulated the best reported results. In the case of GPCR dimers the results suggest that in some cases these ligands might bind to a secondary binding site at the extracellular entrance (vestibule or allosteric site) instead of the orthosteric binding site.

Availability and implementation
Freely accessible from the Molecular Operating Environment svl exchange server (https://svl.chemcomp.com/).

Supplementary information
Supplementary data are available at Bioinformatics online.
LncADeep: anab initiolncRNA identification and functional annotation tool based on deep learning
Authors: Yang Cheng , Yang Longshu , Zhou Man , Xie Haoling , Zhang Chengjiu , Wang May D , Zhu Huaiqiu 
Published: May 2018

AbstractMotivationTo characterize long non-coding RNAs (lncRNAs), both identifying and functionally annotating them are essential to be addressed. Moreover, a comprehensive construction for lncRNA annotation is desired to facilitate the research in the field.ResultsWe present LncADeep, a novel lncRNA identification and functional annotation tool. For lncRNA identification, LncADeep integrates intrinsic and homology features into a deep belief network and constructs models targeting both full- and partial-length transcripts. For functional annotation, LncADeep predicts a lncRNA’s interacting proteins based on deep neural networks, using both sequence and structure information. Furthermore, LncADeep integrates KEGG and Reactome pathway enrichment analysis and functional module detection with the predicted interacting proteins, and provides the enriched pathways and functional modules as functional annotations for lncRNAs. Test results show that LncADeep outperforms state-of-the-art tools, both for lncRNA identification and lncRNA–protein interaction prediction, and then presents a functional interpretation. We expect that LncADeep can contribute to identifying and annotating novel lncRNAs.Availability and implementationLncADeep is freely available for academic use at http://cqb.pku.edu.cn/ZhuLab/lncadeep/ and https://github.com/cyang235/LncADeep/.Supplementary informationSupplementary data are available at Bioinformatics online.
mEBT: multiple-matching evidence-based translator of murine genomic responses for human immunity studies
Authors: Tae Donghyun , Seok Junhee 
Published: May 2018

Abstract

Summary
In this paper, we introduce multiple-matching Evidence-based Translator (mEBT) to discover genomic responses from murine expression data for human immune studies, which are significant in the given condition of mice and likely have similar responses in the corresponding condition of human. mEBT is evaluated over multiple datasets and shows improved inter-species agreement. mEBT is expected to be useful for research groups who use murine models to study human immunity.

Availability and implementation
http://cdal.korea.ac.kr/mebt/

Supplementary information
Supplementary data are available at Bioinformatics online.
A fast, sensitive and cost-effective method for nucleic acid detection using non-radioactive probes
Authors: Viterbo David , Marchal Astrid , Mosbach Valentine , Poggi Lucie , Vaysse-Zinkhöfer Wilhelm , Richard Guy-Franck 
Published: May 2018

Abstract
Nucleic acid detection and quantification using a labeled DNA probe is a very common molecular biology procedure. Here, we describe a new method, based on commonly used laboratory solutions, for nucleic acid hybridization and detection with digoxigenin-labeled DNA probes. The protocol described is faster, more sensitive and much cheaper than a standard protocol using commercial solutions. Comparison with a classical radioactive detection method shows that the latter exhibits less background and shows a greater linear response. Hence, the proposed protocol may be routinely performed for qualitative detection of nucleic acid, but when precise signal quantitation needs to be obtained, radioactive probe hybridization associated to phosphorimaging technology is more reliable.
Duality of graphical models and tensor networks
Authors: Robeva Elina , Seigal Anna 
Published: May 2018

Abstract
In this article we show the duality between tensor networks and undirected graphical models with discrete variables. We study tensor networks on hypergraphs, which we call tensor hypernetworks. We show that the tensor hypernetwork on a hypergraph exactly corresponds to the graphical model given by the dual hypergraph. We translate various notions under duality. For example, marginalization in a graphical model is dual to contraction in the tensor network. Algorithms also translate under duality. We show that belief propagation corresponds to a known algorithm for tensor network contraction. This article is a reminder that the research areas of graphical models and tensor networks can benefit from interaction.
Chromatic Numbers of Stable Kneser Hypergraphs via Topological Tverberg-Type Theorems
Authors: Frick Florian 
Published: May 2018

Abstract
Kneser’s 1955 conjecture—proven by Lovász in 1978—asserts that in any partition of the $k$-subsets of $\{1, 2, \dots , n\}$ into $n-2k+1$ parts, one part contains two disjoint sets. Schrijver showed that one can restrict to significantly fewer $k$-sets and still observe the same intersection pattern. Alon, Frankl, and Lovász proved a different generalization of Kneser’s conjecture for $r$ pairwise disjoint sets. Dolnikov generalized Lovász’ result to arbitrary set systems, while Kříž did the same for the $r$-fold extension of Kneser’s conjecture. Here we prove a common generalization of all of these results. Moreover, we prove additional strengthenings by determining the chromatic number of certain sparse stable Kneser hypergraphs, and further develop a general approach to establishing lower bounds for chromatic numbers of hypergraphs using a combination of methods from equivariant topology and intersection results for convex hulls of points in Euclidean space.
Measurement equivalence of patient safety climate in Chinese hospitals: can we compare across physicians and nurses?
Authors: Zhu Junya 
Published: May 2018

Abstract

Objective
Self-report instruments have been widely used to better understand variations in patient safety climate between physicians and nurses. Research is needed to determine whether differences in patient safety climate reflect true differences in the underlying concepts. This is known as measurement equivalence, which is a prerequisite for meaningful group comparisons. This study aims to examine the degree of measurement equivalence of the responses to a patient safety climate survey of Chinese hospitals and to demonstrate how the measurement equivalence method can be applied to self-report climate surveys for patient safety research.

Methods
Using data from the Chinese Hospital Survey of Patient Safety Climate from six Chinese hospitals in 2011, we constructed two groups: physicians and nurses (346 per group). We used multiple-group confirmatory factor analyses to examine progressively more stringent restrictions for measurement equivalence.

Results
We identified weak factorial equivalence across the two groups. Strong factorial equivalence was found for Organizational Learning, Unit Management Support for Safety, Adequacy of Safety Arrangements, Institutional Commitment to Safety, Error Reporting and Teamwork. Strong factorial equivalence, however, was not found for Safety System, Communication and Peer Support and Staffing. Nevertheless, further analyses suggested that nonequivalence did not meaningfully affect the conclusions regarding physician–nurse differences in patient safety climate.

Conclusions
Our results provide evidence of at least partial equivalence of the survey responses between nurses and physicians, supporting mean comparisons of its constructs between the two groups. The measurement equivalence approach is essential to ensure that conclusions about group differences are valid.
Gravitational wave signals from the first massive black hole seeds
Authors: Hartwig Tilman , Agarwal Bhaskar , Regan John A 
Published: May 2018

ABSTRACT
Recent numerical simulations reveal that the isothermal collapse of pristine gas in atomic cooling haloes may result in stellar binaries of supermassive stars with $M_*\gtrsim 10^4\,\mathrm{M}_{\odot }$. For the first time, we compute the in-situ merger rate for such massive black hole remnants by combining their abundance and multiplicity estimates. For black holes with initial masses in the range $10^{4-6} \,\mathrm{M}_{\odot }$ merging at redshifts z ≳ 15 our optimistic model predicts that Laser Interferometer Space Antenna (LISA) should be able to detect 0.6 mergers yr−1. This rate of detection can be attributed, without confusion, to the in-situ mergers of seeds from the collapse of very massive stars. Equally, in the case where LISA observes no mergers from heavy seeds at z ≳ 15 we can constrain the combined number density, multiplicity, and coalescence times of these high-redshift systems. This letter proposes gravitational wave signatures as a means to constrain theoretical models and processes that govern the abundance of massive black hole seeds in the early Universe.