bluuebunny/crossref_metadata_2025_split huggingface dataset:
Perceived Barriers Among Healthcare Professionals for Access to Physical Therapy Service in Saudi Arabia
Authors: Al Ghamdi Abdulmohsen , Al Shehri Abdullah , Ramirez Oscar , Shamshi Sharick , Khan Shabana 
Published: February 2019

Abstract
Objective To examine physical therapy scope of practice and to describe the barriers and facilitators for access to physical therapy services as reported by healthcare professionals in Saudi Arabia.
Methods Ninety physical therapists from the 6 hospitals in the cities of Riyadh, Jeddah, and Dammam were surveyed by the cross-sectional questionnaire. The questionnaire was distributed through email invitation or in-person. The questionnaire was developed to determine the perceived barriers to direct access to physical therapy service among healthcare professionals.
Results The present study had a response rate of 77.7% (70 out of 90 physical therapists). Majority of the participants were in the age group range of 21–30 years (41.4%) and 68.6% of the respondents’ highest educational qualification is a Baccalaureate degree. The gender distribution showed that the majority of the respondents were female (51.4%). More than a quarter of the participants had a clinical experience that ranges from 6 to 10 years. Majority of the participants were working in the city hospital (88.6%). Most of the participants strongly agreed or -agreed that the factors included in the questionnaire such as geographical accessibility, availability, affordability, and acceptability of services were barriers to provide access to physical therapy services in Saudi Arabia.
Conclusions This study documents many of the perceived barriers for access to providing physical therapy services in Saudi Arabia such as geographical accessibility, availability, affordability, and acceptability of services. Furthermore, the identified barriers could be used as a framework by policymaker and the third party payment system in order to further improve access to physical therapy services in Saudi Arabia.
Suppression of phospholipase D genes improves chalky grain production by high temperature during the grain-filling stage in rice
Authors: Yamaguchi Takeshi , Yamakawa Hiromoto , Nakata Masaru , Kuroda Masaharu , Hakata Makoto 
Published: February 2019

ABSTRACT
High temperature (HT) during the grain developing stage causes deleterious effects on rice quality resulting in mature grains with a chalky appearance. Phospholipase D (PLD) plays an important role in plants, including responses to environmental stresses. OsPLDα1, α3 and β2-knockdown (KD) plants showed decreased production of chalky grains at HT. HT ripening increased H2O2 accumulated in the developing grains. However, the increase was canceled by the knockdown of OsPLDβ2. Expression levels of OsCATA which is one of three rice catalase genes, in developing grains of OsPLDβ2-KD plants at 10 DAF were increased compared with that in vector-controls in HT growth conditions. Overexpression of OsCATA markedly suppressed the production of chalky grains in HT growth conditions. These results suggested that OsPLDβ2 functions as a negative regulator of the induction of OsCATA and is involved in the production of chalky grains in HT growth conditions.
Clustering tennis players’ anthropometric and individual features helps to reveal performance fingerprints
Authors: Cui Yixiong , Gómez Miguel‐Ángel , Gonçalves Bruno , Sampaio Jaime 
Published: February 2019

AbstractThe study was aimed to explore distinct players’ groups according to their anthropometric and individual features, and to identify the key performance indicators that discriminate player groups. Match statistics, anthropometric and personal features of 1188 male players competing during 2015–2017 main draw Grand Slam singles events were collected. Height, weight, experience, handedness and backhand style were used to automatically classify players into different clusters through unsupervised learning model. Afterwards, 29 match variables were analysed through MANOVA and discriminant analysis in order to evaluate the different match performance among player groups and to identify the key performance indicators that best differentiate player clusters in each Grand Slam. The analysis revealed the existence of four clusters, they were classified as Big‐sized Right Two‐handed Players (n = 387), Medium‐sized Right One‐handed Players (n = 265), Small‐sized Right Two‐handed Players (n = 414), and Left Two‐handed Players (n = 122). Serve, winner, net and physical performance‐related indicators (Structure Coefficient ≥ |0.30|) were showed to be the maximum contributors to the group separation. Left‐handed players were the most homogenous group in performance. Taller players outperformed their peers in all Slams except for Roland Garros, where left‐handed players demonstrated certain advantage playing on slow‐pace surface. In Wimbledon and US Open, Medium‐sized Right One‐handed Players showed better net and physical performance. The advantage of left‐handed player is over‐represented at elite level. Current findings promote a better understanding of match‐play from distinct player groups and offer information on evaluating contextual variability for achieving better performances.
Building on Dewaele’s (2018) L1 versus LX Dichotomy: The Language-Usage-Identity State Model
Authors: Thomas Nathan , Osment Christopher 
Published: February 2019

Abstract
In this brief contribution, we will summarize the main arguments in Dewaele’s (2018) ‘Why the Dichotomy “L1 versus LX User” is Better than “Native versus Non-native Speaker”’ and discuss our Language-Usage-Identity State Model, showing how it builds on the core features of Dewaele’s proposal.
PhenoPro: a novel toolkit for assisting in the diagnosis of Mendelian disease
Authors: Li Zixiu , Zhang Feng , Wang Yukai , Qiu Yue , Wu Yang , Lu Yulan , Yang Lin , Qu William J , Wang Huijun , Zhou Wenhao , Tian Weidong 
Published: February 2019

Abstract

Motivation
Whole-exome sequencing (WES) is now being used in clinical practice for the diagnosis of the causal genes of Mendelian diseases. In order to make the diagnosis, however, the clinical phenotypes [e.g. Human Phenotype Ontology (HPO) terms] of a patient are needed for prioritizing the variants called from the WES data of the patient. Computational tools are therefore needed to standardize and accelerate this process.

Results
Here, we introduce a tool named PhenoPro for prioritizing the causal gene of Mendelian disease given both the HPO terms assigned to and the variants called from the WES data of a patient. PhenoPro has been benchmarked using both simulated patients and 287 real diagnosed patients of Chinese ancestry, and shows significant improvements over five previous tools. Moreover, the addition of an internal variant data of Chinese ancestry and the variant data from the patients’ parents can further improve PhenoPro’s performance. To make PhenoPro a fully automated tool, we also include a natural language processing component for automated HPO term assignment from clinical reports, and demonstrate that the natural language processing is as effective as manual HPO assignment using real clinical reports. In conclusion, PhenoPro can be used as a pre-screening tool to assist in the diagnosis of Mendelian disease genes.

Availability and implementation
The web server of PhenoPro is freely available at http://app.tianlab.cn.

Supplementary information
Supplementary data are available at Bioinformatics online.
Driver network as a biomarker: systematic integration and network modeling of multi-omics data to derive driver signaling pathways for drug combination prediction
Authors: Huang Lei , Brunell David , Stephan Clifford , Mancuso James , Yu Xiaohui , He Bin , Thompson Timothy C , Zinner Ralph , Kim Jeri , Davies Peter , Wong Stephen T C 
Published: February 2019

Abstract

Motivation
Drug combinations that simultaneously suppress multiple cancer driver signaling pathways increase therapeutic options and may reduce drug resistance. We have developed a computational systems biology tool, DrugComboExplorer, to identify driver signaling pathways and predict synergistic drug combinations by integrating the knowledge embedded in vast amounts of available pharmacogenomics and omics data.

Results
This tool generates driver signaling networks by processing DNA sequencing, gene copy number, DNA methylation and RNA-seq data from individual cancer patients using an integrated pipeline of algorithms, including bootstrap aggregating-based Markov random field, weighted co-expression network analysis and supervised regulatory network learning. It uses a systems pharmacology approach to infer the combinatorial drug efficacies and synergy mechanisms through drug functional module-induced regulation of target expression analysis. Application of our tool on diffuse large B-cell lymphoma and prostate cancer demonstrated how synergistic drug combinations can be discovered to inhibit multiple driver signaling pathways. Compared with existing computational approaches, DrugComboExplorer had higher prediction accuracy based on in vitro experimental validation and probability concordance index. These results demonstrate that our network-based drug efficacy screening approach can reliably prioritize synergistic drug combinations for cancer and uncover potential mechanisms of drug synergy, warranting further studies in individual cancer patients to derive personalized treatment plans.

Availability and implementation
DrugComboExplorer is available at https://github.com/Roosevelt-PKU/drugcombinationprediction.

Supplementary information
Supplementary data are available at Bioinformatics online.
Choice of species affects phylogenetic stability of deep nodes: an empirical example in Terrabacteria
Authors: Superson Ashley A , Phelan Doug , Dekovich Allyson , Battistuzzi Fabia U 
Published: February 2019

Abstract

Motivation
The promise of higher phylogenetic stability through increased dataset sizes within tree of life (TOL) reconstructions has not been fulfilled. Among the many possible causes are changes in species composition (taxon sampling) that could influence phylogenetic accuracy of the methods by altering the relative weight of the evolutionary histories of each individual species. This effect would be stronger in clades that are represented by few lineages, which is common in many prokaryote phyla. Indeed, phyla with fewer taxa showed the most discordance among recent TOL studies. We implemented an approach to systematically test how the identity of taxa among a larger dataset and the number of taxa included affected the accuracy of phylogenetic reconstruction.

Results
Utilizing an empirical dataset within Terrabacteria we found that even within scenarios consisting of the same number of taxa, the species used strongly affected phylogenetic stability. Furthermore, we found that trees with fewer species were more dissimilar to the tree produced from the full dataset. These results hold even when the tree is composed by many phyla and only one of them is being altered. Thus, the effect of taxon sampling in one group does not seem to be buffered by the presence of many other clades, making this issue relevant even to very large datasets. Our results suggest that a systematic evaluation of phylogenetic stability through taxon resampling is advisable even for very large datasets.

Availability and implementation
https://github.com/BlabOaklandU/PATS.git.

Supplementary information
Supplementary data are available at Bioinformatics online.
G2P: a Genome-Wide-Association-Study simulation tool for genotype simulation, phenotype simulation and power evaluation
Authors: Tang You , Liu Xiaolei 
Published: February 2019

Abstract

Motivation
Plenty of Genome-Wide-Association-Study (GWAS) methods have been developed for mapping genetic markers that associated with human diseases and agricultural economic traits. Computer simulation is a nice tool to test the performances of various GWAS methods under certain scenarios. Existing tools are either inefficient in terms of computation and memory efficiency or inconvenient to use to simulate big, realistic genotype data and phenotype data to evaluate available GWAS methods.

Results
Here, we present a GWAS simulation tool named G2P that can be used to simulate genotype data, phenotype data and perform power evaluation of GWAS methods. G2P is a user-friendly tool with all functions is provided in both graphical user interface and pipeline manners and it is available for Windows, Mac and Linux environments. Furthermore, G2P achieves maximum efficiency in terms of both memory usage and simulation speed; with G2P, the simulation of genotype data that includes 1 000 000 samples and 2 000 000 markers can be accomplished in 5 h.

Availability and implementation
The G2P software, user manual, and example datasets are freely available at GitHub: https://github.com/XiaoleiLiuBio/G2P.

Supplementary information
Supplementary data are available at Bioinformatics online.
Social Work Research with Industry: A Systematic Literature Review of Engagement and Impact
Authors: Zuchowski Ines , Miles Debra , Gair Susan , Tsey Komla 
Published: February 2019

AbstractCurrent research agendas in developed countries focus on academics engaging collaboratively with communities and industry partners to achieve research outcomes that demonstrate reach and significance. Social work academics are in a prime position to undertake collaborative research that has specific project benefits and wider social impacts. This article reports on a systematic literature review of articles in social work journals that reported on academic industry partnerships. The review aimed to analyse publications documenting the engagement of social work academic researchers with industry partners, to examine the nature of the research undertaken through this engagement and to ascertain the reported impact. Findings highlight that collaborative research processes could be described in greater detail, further explicit detail on collaboration and impact is needed, and while project level impacts are described in reviewed publications, most are not presenting broader societal impacts.
High baseline soluble urokinase plasminogen activator receptor (suPAR) serum levels indicate adverse outcome after resection of pancreatic adenocarcinoma
Authors: Loosen Sven H , Tacke Frank , Püthe Niklas , Binneboesel Marcel , Wiltberger Georg , Alizai Patrick H , Kather Jakob N , Paffenholz Pia , Ritz Thomas , Koch Alexander , Bergmann Frank , Trautwein Christian , Longerich Thomas , Roderburg Christoph , Neumann Ulf P , Luedde Tom 
Published: February 2019

AbstractSurgical resection represents the only potentially curative therapy for patients with pancreatic adenocarcinoma (PDAC), an aggressive malignancy with a very limited 5-year survival rate. However, even after complete tumor resection, many patients are still facing an unfavorable prognosis underlining the need for better preoperative stratification algorithms. Here, we explored the role of the secreted glycoprotein soluble urokinase plasminogen activator receptor (suPAR) as a novel circulating biomarker for patients undergoing resection of PDAC. Serum levels of suPAR were measured by enzyme-linked immunosorbent assay (ELISA) in an exploratory as well as a validation cohort comprising a total of 127 PDAC patients and 75 healthy controls. Correlating with a cytoplasmic immunohistochemical expression of uPAR in PDAC tumor cells, serum levels of suPAR were significantly elevated in PDAC patients compared to healthy controls and patient with PDAC precursor lesions. Importantly, patients with high preoperative suPAR levels above a calculated cutoff value of 5.956 ng/ml showed a significantly reduced overall survival after tumor resection. The prognostic role of suPAR was further corroborated by uni- and multivariate Cox-regression analyses including parameters of systemic inflammation, liver and kidney function as well as clinico-pathological patients’ characteristics. Moreover, high baseline suPAR levels identified those patients particularly susceptible to acute kidney injury and surgical complications after surgery. In conclusion, our data suggest that circulating suPAR represents a novel prognostic marker in PDAC patients undergoing tumor resection that might be a useful addition to existing preoperative stratification algorithms for identifying patients that particularly benefit from extended tumor resection.
Changes in Functional Connectivity Predict Outcome of Repetitive Transcranial Magnetic Stimulation Treatment of Major Depressive Disorder
Authors: Corlier Juliana , Wilson Andrew , Hunter Aimee M , Vince-Cruz Nikita , Krantz David , Levitt Jennifer , Minzenberg Michael J , Ginder Nathaniel , Cook Ian A , Leuchter Andrew F 
Published: February 2019

AbstractRepetitive transcranial magnetic stimulation (rTMS) treatment of major depressive disorder (MDD) is associated with changes in brain functional connectivity (FC). These changes may be related to the mechanism of action of rTMS and explain the variability in clinical outcome. We examined changes in electroencephalographic FC during the first rTMS treatment in 109 subjects treated with 10 Hz stimulation to left dorsolateral prefrontal cortex. All subjects subsequently received 30 treatments and clinical response was defined as ≥40% improvement in the inventory of depressive symptomatology-30 SR score at treatment 30. Connectivity change was assessed with coherence, envelope correlation, and a novel measure, alpha spectral correlation (αSC). Machine learning was used to develop predictive models of outcome for each connectivity measure, which were compared with prediction based upon early clinical improvement. Significant connectivity changes were associated with clinical outcome (P &lt; 0.001). Machine learning models based on αSC yielded the most accurate prediction (area under the curve, AUC = 0.83), and performance improved when combined with early clinical improvement measures (AUC = 0.91). The initial rTMS treatment session produced robust changes in FC, which were significant predictors of clinical outcome of a full course of treatment for MDD.
Inherited Interleukin 2–Inducible T-Cell (ITK) Kinase Deficiency in Siblings With Epidermodysplasia Verruciformis and Hodgkin Lymphoma
Authors: Youssefian Leila , Vahidnezhad Hassan , Yousefi Mehdi , Saeidian Amir Hossein , Azizpour Arghavan , Touati Andrew , Nikbakht Neda , Hesari Kambiz Kamyab- , Adib-Sereshki Mohammad Mahdi , Zeinali Sirous , Mansoori Behzad , Jazayeri Ali , Karamzadeh Razieh , Fortina Paolo , Jouanguy Emmanuelle , Casanova Jean-Laurent , Uitto Jouni 
Published: February 2019

Abstract
Biallelic mutations in the ITK gene cause a T-cell primary immunodeficiency with Epstein-Barr virus (EBV)–lymphoproliferative disorders. We describe a novel association of a homozygous ITK mutation with β–human papillomavirus (HPV)–positive epidermodysplasia verruciformis. Thus, loss of function in ITK can result in broad dysregulation of T-cell responses to oncogenic viruses, including β-HPV and EBV.
Dental root development associated with treatments by rapid maxillary expansion/reverse headgear and slow maxillary expansion
Authors: Seker Elif Dilara , Yagci Ahmet , Kurt Demirsoy Kevser 
Published: February 2019

SummaryObjectivesTo assess dental root development in two groups of paediatric patients who received treatments with reverse headgear and rapid maxillary expansion and slow maxillary dental arch expansion.Materials and methodsThe 20 subjects (13 girls, 7 boys; mean age: 8.9 ± 1.3 years) in the first group were treated with a Petit-type reverse headgear attached to a full-coverage bonded rapid maxillary expander via elastics (RME&RHg group). The 20 subjects included in the second group (9 girls, 11 boys; mean age: 9.1 ± 2.2 years) were selected among patients who were treated with Hawley appliances for slow maxillary expansion (SME group). Digitized panoramic radiographs were used. A total of 960 permanent teeth (maxillary–mandibular incisors, canines, premolars, and first molars) were measured quantitatively for pre-treatment and post-treatment.ResultsNo significant increase was found except for the right and left maxillary and mandibular second premolars and left mandibular and first premolar in the RME&RHg group (P < 0.05). Teeth length values increased significantly in all maxillary and mandibular teeth except maxillary first molars and mandibular incisors in the SME group (P < 0.05). Inter-group comparisons showed that statistically significant differences were observed in maxillary and mandibular incisors, left maxillary first premolar, and molar teeth (P > 0.05).LimitationA limitation of this study is the use of two-dimensional radiographic images for root length measurement. However, ethical obligations limit the dental cone beam computed tomography imaging application for protection of paediatric patients from harm.ConclusionsRME&RHg therapy inhibits root development of maxillary and mandibular teeth in the early period. However, further studies should be performed to determine whether this effect on root development is reversible or irreversible.
C-type natriuretic peptide co-ordinates cardiac structure and function
Authors: Moyes Amie J , Chu Sandy M , Aubdool Aisah A , Dukinfield Matthew S , Margulies Kenneth B , Bedi Kenneth C , Hodivala-Dilke Kairbaan , Baliga Reshma S , Hobbs Adrian J 
Published: February 2019

Abstract

Aims
C-type natriuretic peptide (CNP) is an essential endothelium-derived signalling species that governs vascular homoeostasis; CNP is also expressed in the heart but an intrinsic role for the peptide in cardiac function is not established. Herein, we employ unique transgenic strains with cell-specific deletion of CNP to define a central (patho)physiological capacity of CNP in maintaining heart morphology and contractility.

Methods and results
Cardiac structure and function were explored in wild type (WT), cardiomyocyte (cmCNP−/−), endothelium (ecCNP−/−), and fibroblast (fbCNP−/−)—specific CNP knockout mice, and global natriuretic peptide receptor (NPR)-B−/−, and NPR-C−/− animals at baseline and in experimental models of myocardial infarction and heart failure (HF). Endothelium-specific deletion of CNP resulted in impaired coronary responsiveness to endothelium-dependent- and flow-mediated-dilatation; changes mirrored in NPR-C−/− mice. Ex vivo, global ischaemia resulted in larger infarcts and diminished functional recovery in cmCNP−/− and NPR-C−/−, but not ecCNP−/−, vs. WT. The cardiac phenotype of cmCNP−/−, fbCNP−/−, and NPR-C−/− (but not ecCNP−/− or NPR-B−/−) mice was more severe in pressure overload- and sympathetic hyperactivation-induced HF compared with WT; these adverse effects were rescued by pharmacological CNP administration in WT, but not NPR-C−/−, mice. At a molecular level, CNP/NPR-C signalling is impaired in human HF but attenuates activation of well-validated pro-hypertrophic and pro-fibrotic pathways.

Conclusion
C-type natriuretic peptide of cardiomyocyte, endothelial and fibroblast origins co-ordinates and preserves cardiac structure, function, and coronary vasoreactivity via activation of NPR-C. Targeting NPR-C may prove an innovative approach to treating HF and ischaemic cardiovascular disorders.