bluuebunny/crossref_metadata_2025_split huggingface dataset:
Variable Selection from a Feature Representing Protein Sequences: A Case of Classification on Bacterial Type IV Secreted Effectors
Authors: Zhang Jian , Lv Lixin , Lu Donglei , Kong Denan , Al-Alashaari Mohammed Abdoh Ali , Zhao Xudong 
Published: September 2020

Abstract
Background: Classification of certain proteins with specific functions is momentous for biological research. Encoding approaches of protein sequences for feature extraction play an important role in protein classification. Many computational methods (namely classifiers) are used for classification on protein sequences according to various encoding approaches. Commonly, protein sequences keep certain labels corresponding to different categories of biological functions (e.g., bacterial type IV secreted effectors or not), which makes protein prediction a fantasy. As to protein prediction, a kernel set of protein sequences keeping certain labels certified by biological experiments should be existent in advance. However, it has been hardly ever seen in prevailing researches. Therefore, unsupervised learning rather than supervised learning (e.g. classification) should be considered. As to protein classification, various classifiers may help to evaluate the effectiveness of different encoding approaches. Besides, variable selection from an encoded feature representing protein sequences is an important issue that also needs to be considered.Results: Focusing on the latter problem, we propose a new method for variable selection from an encoded feature representing protein sequences. Taking a benchmark dataset as a case, experiments are made to identify bacterial type IV secreted effectors from protein sequences, which indicates the effectiveness of our method. Conclusions: Certain variables other than an encoded feature they belong to do work for discrimination between different types of proteins. In addition, ensemble classifiers with an automatic assignment of different base classifiers do achieve a better classification result.
Heme-deficient metabolism and impaired cellular differentiation as an evolutionary trade-off for human infectivity in Trypanosoma brucei gambiense
Authors: Horáková Eva , Lecordier Laurence , Cunha Paula , Sobotka Roman , Changmai Piya , Langedijk Catharina , Abbeele Jan Van Den , Vanhollebeke Benoit , Lukes Julius 
Published: September 2020

Abstract
Resistance to African trypanosomes in humans relies on targeting of a trypanosome lytic factor 1 (TLF1) to trypanosome haptoglobin-hemoglobin receptor (HpHbR). While
TLF1 avoidance by the inactivation of the HpHbR contributes to Trypanosoma brucei gambiense human infectivity, the evolutionary trade-off of this adaptation is unknown.
Both T. b. gambiense with inactive HpHbR, as well as a genetically engineered T.b.brucei HpHbR knock-out show only trace levels of intracellular heme and lack the downstream hemoprotein activities, thereby providing an extraordinary example of aerobic parasite proliferation in the absence of heme. We further show that HpHbR facilitates the developmental progression by inducing PAD-1 expression that is associated with the formation of cell cycle-arrested stumpy forms in T. b.brucei . Accordingly, T. b. gambiense was found to be poorly competent for slender-to-stumpy differentiation unless a functional HpHbR receptor derived from T. b. brucei was
genetically restored.
Landslide Hazard Assessment Using Probabilistic and Statistical Approaches: A Case Study of Chamba Region, Himachal Pradesh, India
Authors: Pandey Desh Deepak , Banshtu Rajeswar Singh , Singh Kanwarpreet , Versain Laxmi Devi 
Published: September 2020

Abstract
Landslides have adversely affected the southern region of Chamba district during past three decades. To minimize the damage to ecology and environment due to such natural calamities, landslide hazard zonation and mitigation measures are essential component to stabilize the natural slopes and other physiographic features. In order to remodeling lopsidedness in study area analytical hierarchy process and information value methods with applications of remote sensing and geographic information system (GIS) are utilized to delineate the most recumbent landslide hazard zones. Eleven-factor maps like slope gradient, slope aspect, relative relief, land use/ cover etc., were delineated using different sets of data like satellite images and field investigations etc. Depending upon the severity, landslide hazard maps (LHZ) were further divided based upon information value method and analytical hierarchy process models respectively, into five different categories very low (1.2% and 2.95%), low (5.31% and 4.27%), moderate (24.40% and 20.03%), high (29.26% and 31.03%), and very high (40.30% and 44.2%). These hazard maps obtained through both information value and analytical hierarchy process (AHP) were compared for accuracy using success rate curve (SRC) method. Accuracy of the hazard zonation maps was found to be 78.62% for AHP and 85.17% for Inf. Value models.
Added Value of Diaphragm Myofascial Release on Forward Head Posture and Chest Expansion in Patients With Neck Pain: A Randomized Controlled Trial
Authors: Haghighat Farzaneh , Moradi Razieh , Rezaie Mohammadreza , Yarahmadi Nastaran , Ghaffarnejad Farahnaz 
Published: September 2020

Abstract

Background: Despite the increasing use of diaphragm myofascial release technique in clinical practice, there is no study on the effect of this technique on musculoskeletal outcomes of patients with neck pain. The purpose of this study was to evaluate the added value of diaphragm myofascial release on forward head posture, chest expansion, and functional disability in patients with neck pain.Methods: In this randomized controlled trial, 46 women with neck pain between the age of 18 and 45 years old were randomly allocated to two groups; the intervention group received 4 diaphragm myofascial release techniques once a week, for 4 weeks. Both intervention and control groups received the same neck exercise program 3 times a week for 4 weeks. Forward head posture, chest expansion, and neck functional disability were measured using craniovertebral angle, circometry, and Copenhagen neck functional disability index, respectively, before and one day after treatment.Results: The results of the paired t-test showed significant increases in craniovertebral angle (control and intervention: P<0.001) and chest expansion (control: P=0.001, intervention<0.001) and a significant decrease in the functional disability score (control and intervention: P<0.001) of patients with neck pain in both groups. A significant greater craniovertebral angle (P=0.01) and chest expansion (P=0.03) were also seen in the intervention group compared with the controls.Conclusion: Adding diaphragm myofascial release to neck exercises was associated with significantly greater improvements in forward head posture and chest expansion than neck exercises alone. Therefore, the diaphragm myofascial release could be useful in the management of neck pain patients with FHP. Trial registration: IRCT20191116045461N1 (Iranian Registry of Clinical Trials). Registered 23 December 2019, https://en.irct.ir/trial/43741.
Japonica Array NEO with Increased Genome-Wide Coverage and Abundant Disease Risk SNPs
Authors: Sakurai-Yageta Mika , Kumada Kazuki , Gocho Chinatsu , Makino Satoshi , Uruno Akira , Tadaka Shu , Motoike Ikuko N , Kimura Masae , Ito Shin , Otsuki Akihito , Narita Akira , Kudo Hisaaki , Aoki Yuichi , Danjoh Inaho , Yasuda Jun , Kawame Hiroshi , Minegishi Naoko , Koshiba Seizo , Fuse Nobuo , Tamiya Gen , Yamamoto Masayuki , Kinoshita Kengo 
Published: September 2020

Abstract
Background: Increasing the power of genome-wide association studies in diverse populations is important for understanding the genetic determinants of disease risks, and large-scale genotype data are collected by genome cohort and biobank projects all over the world. In particular, ethnic-specific SNP arrays are becoming more important because the use of universal SNP arrays has some limitations in terms of cost-effectiveness and throughput. As part of the Tohoku Medical Megabank Project, which integrates prospective genome cohorts into a biobank, we have been developing a series of Japonica Arrays for genotyping participants based on reference panels constructed from whole-genome sequence data of the Japanese population.Results: We designed a novel version of the SNP Array for the Japanese population, called Japonica Array NEO, comprising a total of 666,883 SNPs, including tag SNPs of autosomes and X chromosome with pseudoautosomal regions, SNPs of Y chromosome and mitochondria, and known disease risk SNPs. Among them, 654,246 tag SNPs were selected from an expanded reference panel of 3,552 Japanese using pairwise r2 of linkage disequilibrium measures. Moreover, 28,298 SNPs were included for the evaluation of previously identified disease risk SNPs from the literature and databases, and those present in the Japanese population were extracted using the reference panel. The imputation performance of Japonica Array NEO was assessed by genotyping 286 Japanese samples. We found that the imputation quality r2 and INFO score in the minor allele frequency bin >2.5%–5% were >0.9 and >0.8, respectively, and >12 million markers were imputed with an INFO score >0.8. After verification, Japonica Arrays were used to efficiently genotype cohort participants from the sample selection to perform a quality assessment of the raw data; approximately 130,000 genotyping data of >150,000 participants has already been obtained. Conclusions: Japonica Array NEO is a promising tool for genotyping the Japanese population with genome-wide coverage, contributing to the development of genetic risk scores for this population and further identifying disease risk alleles among individuals of East Asian ancestry.
Clinical Evaluation of Preoperative Embolization, Vertebroplasty, and Decompression in the Treatment of Aggressive Vertebral Hemangiomas
Authors: Xu Derong , Xi Yongming , Zhou Chuanli , Zhu Kai , Ma Xuexiao 
Published: September 2020

Abstract
Background: Symptomatic aggressive vertebral hemangioma often requires clinical treatment; however, there is great controversy over the treatment plan. We aimed to evaluate the efficacy and safety of different methods including preoperative emobilization, vertebroplasty, decompression and internal fixation in the treatment of aggressive hemangioma.Methods: A retrospective clinical review of patients diagnosed with aggressive vertebral hemangiomas was conducted. All the patients were assigned to 3 groups according to the treatment strategies: patients in Group A underwent embolization before decompression, patients in Group B underwent decompression with vertebroplasty, patients in Group C received all three treatments. Clinical indexes were compared within 3 groups.Results: There were 6 patients received embolization and decompression (Group A), 9 patients underwent decompression with vertebroplasty (Group B) and 6 patients in Group C. The operative duration of patients in group A (198.33±38.43 min) were less than another two groups (P=0.001). The intra-operative blood loss of patients in group C was 713.33±165.13ml, which was significantly less than group A and group B (P=0.045). Patients in group C exhibited the lowest volume of drainage on POD 1 (178.33±66.76ml), which showed significant difference compared with group A (368.33±191.15ml, P=0.01). There was no significant difference of pre-operative and post-operative VAS and JOA score among 3 groups, as well as drainage on POD 2, total volume and hospital duration.Conclusion: The treatment strategy of combined embolization, vertebroplasty and decompression fixation is efficient and safe. For special patients, if such a strategy cannot be adopted, simple embolization plus decompression or vertebroplasty plus decompression is also competent.
Specific serodiagnosis of animal brucellosis based on a recombinant multiepitope protein antigen
Authors: Yin Dehui , Bai Qiongqiong , Li Han , Zhang Jinpeng 
Published: September 2020

Abstract
Background: Brucellosis is a vital zoonotic infectious disease that will cause important public health problems and endanger the development of animal husbandry in endemic areas, causing huge losses of personal property. Early diagnosis of sick animals is a crucial way to reduce the incidence of brucellosis.Results: In this study, we designed a recombinant multiepitope protein (rMEP) as a serum diagnostic antigen for brucellosis. An indirect enzyme-linked immunosorbent assay (ELISA) was used to assess the new rMEP, 159 goat and 153 bovine serum samples were measured, including brucellosis and non-brucellosis. To better observe the effectiveness of rMEP, we performed a receiver operating characteristic (ROC) analysis. The results of 159 goat serum evaluations showed that the area under the ROC curve(AUC) was 0.9976 and compared with SAT and RBPT, the positive and negative diagnostic accuracy of the ELISA was 98.92%(92/93) and 96.97%(64/66), respectively. 153 bovine serum samples evaluations showed the AUC was 0.9974 and compared with SAT and RBPT, the positive and negative diagnostic accuracy of the ELISA was 98.65%(73/74) and 96.20%(76/79), respectively.Conclusions: The results show that rMEP as a protein antigen can be used to diagnose brucellosis with highly accurate both in goat and bovine.
Training Practices and Injuries in Competitive Adolescent Distance Runners: A Retrospective Cross-Sectional Study.
Authors: Mann Robert H , McKay Carly D , Clift Bryan C , Williams Craig A , Barker Alan R 
Published: September 2020

Abstract
Background: Distance running is one of the most popular sports around the world. The epidemiology of running-related injuries (RRI) has been examined in adults, but only a few studies have focused on adolescent distance runners. Therefore, the purpose of this study was 1) to examine the training practices (frequency, volume, and intensity) and descriptive epidemiology of RRI (risks, rates, sites, and severity) in competitive adolescent distance runners (13-18 years) in England, and 2) to explore potential correlates (risk factors) of RRI. Methods: A cross-sectional study design was used. Adolescent distance runners (n = 113) were recruited from England Athletics affiliated athletics clubs. Participants voluntarily completed an online questionnaire between April and December 2018. At the point of completion, responses were based on the participant’s previous 12-months of distance running participation. Injury incidence proportions (IP) and incidence rates (IR) were calculated. Potential correlates of RRI were estimated using an odds ratio (OR) and 95% confidence intervals (CI). Results: The injury IP was 122/100 participants/year (95% CI: 113 to 138). The injury IR was 6.3/1000 participation hours (95% CI: 5.3 to 7.4). The most common injury sites were the knee, foot/toes, and lower leg; primarily caused by overuse. Exploratory univariate analyses showed a larger number of training sessions per week (volume) is associated with a lower risk of RRI (OR = 0.71, 95% CI: 0.53 to 0.94), and that a higher level of specialisation is associated with a lower risk of time loss injury (OR = 0.26, 95% CI: 0.11 to 0.63). Conclusions: Injury is common in adolescent distance runners, aligned with adult-based research. These data provide guidance for the development of appropriate injury prevention interventions.
Copper-oxide impregnated respiratory masks may significantly reduce the risk of SARS-CoV-2 cross-contamination
Authors: Borkow Gadi , Lustiger Danny , Melamed Eyal , Herrera Vicki , Ackerman Daniel , Reid St. Patrick , Santarpia Joshua 
Published: September 2020

Abstract
The use of protective respiratory face masks has been adopted universally as an important measure in the fight against COVID-19. Masks become contaminated by symptomatic and asymptomatic SARS-CoV-2 infected individuals and the virus can remain viable on the surface of the masks for several days. Although the regular respiratory face masks are single use disposable masks, these masks are being largely reused and not often discarded after use by the general population. Mask touching during use, reuse and disposal occurs frequently, and this can lead to increased risk of infection and further transmission. N95s and regular surgical masks were produced in which the external layers were made with nonwoven fabric impregnated with copper-oxide microparticles. The masks reduced the infectious titers of SARS-CoV-2 by more than 99.9% within 1 minute of contact, as determined by TCID50 assay and serial PCR assays. The use of masks capable of rendering the SARS-CoV-2 non-infectious within minutes, may significantly reduce the risk of viral transmission and infection.
HER2 Gene Assessment in Liquid Biopsy of Gastric and Esophagogastric Junction Cancer Patients Qualified for Surgery
Authors: Grenda Anna , Wojas-Krawczyk Kamila , Skoczylas Tomasz , Krawczyk Paweł , Sierocińska-Sawa Jadwiga , Wallner Grzegorz , Milanowski Janusz 
Published: September 2020

Abstract
Background Amplification of HER2 gene (ERBB2) and overexpression of HER2 protein on cancer cells are found in 10-26% of gastric cancer (GC) and esophagogastric junction cancer (EGJC). Gene copy number variation (CNV) could be detected in these patients in liquid biopsy and in cancer cells. Methods We analysed HER2 gene CNV used qPCR method in 87 sera collected from GC and EGJC patients before surgical treatment and in 40 sera obtained from healthy donors. HER2 gene CNV was also assessed in formalin-fixed paraffin-embedded (FFPE) tumor tissue. Furthermore, we assessed the number of HER2 gene copies and HER2 expression in cancer cells using the fluorescent in situ hybridization method (FISH) and immunohistochemistry (IHC). Results We found that the HER2 gene copy number in liquid biopsy was higher in GC and EGJC patients compared to healthy people (p=0.01). Moreover, EGJC patients had higher number of HER2 gene copies than healthy donors (p=0.0016). HER2 CNV examination could distinguish healthy individuals and patients with gastric or esophagogastric junction cancers with sensitivity and specificity of 58% and 98% (AUC=0.707, 95% CI: 0.593-0.821, p=0.004). We found that patients with a high copy number of the HER2 gene in the tumor tissue assessed by qPCR (but not by FISH) have significantly more often a high number of HER2 gene copies in liquid biopsy (p=0.04). Conclusions We suggested that HER2 testing in liquid biopsy could be used as an auxiliary method to analysis of HER2 status in tumor tissue in gastric or esophagogastric junction cancers.
Occupational lifting and risk of hypertension, stratified by use of anti-hypertensives, physical activity and age - a prospective cohort study
Authors: Korshøj Mette , Hannerz Harald , Frikke-Schmidt Ruth , Marott Jacob Louis , Schnohr Peter , Clays Els , Holtermann Andreas 
Published: September 2020

Abstract
Background Prevalence of hypertension varies across occupations, maybe due to differences in exposure to occupational lifting. This study investigated associations between occupational lifting and hypertension, stratified by use of anti-hypertensives, leisure time physical activity (LTPA), occupational physical activity (OPA) and age.Methods Data from the Copenhagen General Population Study were included. The Copenhagen General Population Study was approved by the local ethical committee (H-KF-01-144/01), and all participation were conducted in accordance with the declaration of Helsinki. Multivariable logistic regression models, adjusted for sex, age, BMI, smoking, school education, mental stress and baseline blood pressure (BP), were applied to estimate: the (i) cross-sectional association (n=67,363) between occupational lifting and hypertension (using anti-hypertensives or BP ≥140/≥90 mmHg), (ii) prospective association (n=7,020) between occupational lifting and risk of an above median change in systolic BP (baseline to follow-up) and/or a shift from no use to use of anti-hypertensives, among the included population and stratified by use of anti-hypertensives, LTPA, OPA and age.Results Cross-sectionally, heavy occupational lifting lowered hypertension risk. Mean baseline BP, showed that the higher the level of LTPA the lower mean BP across all levels of OPA were, but only among those not using anti-hypertensives. The prospective analysis showed occupational lifting to increase the risk of hypertension, among workers aged ≥ 50 years, or reporting light to moderate LTPA. Conclusions This study finds positive associations between occupational lifting and risk for hypertension among workers aged ≥ 50 years. Further research on the association between occupational lifting and precursors of cardiovascular disease are needed before recommendations for occupational lifting and cardiovascular health can be established.
Designing Headquarters General Competency Model for The Health Sector
Authors: Fattahi Hamed , Gorji Hasan Abolghasem , Bayat Mahboubeh , Fattahi Arash , Seproo Faezeh Ghasemi 
Published: September 2020

Abstract
Background An effective health headquarters has behaviors, knowledge, skills, and motivations that are behavioral, technical, and motivational prerequisites for successful performance in a job. This study aims to identify the general competencies of health headquarters to meet the needs of the health system.Methods To facilitate a consensus-building process on the development of public competencies, a multi-step approach was used. First, to identify the dimensions and components of general competencies in attracting health headquarters, the systematic review and meta-synthesis were used. Then, using a purposive critical case sampling, twenty-six participants were interviewed and the information was analyzed. In the third stage, the health headquarters were classified into three levels. To present the initial model of competencies, the Mini Delphi method was used. Finally, in the fourth step, to validate and finalize the pattern, the three-step Delphi method was used.Results The six dimensions of competency have been developed, which are (1) leadership and management (12 components), (2) analysis, interpretation, and reporting (6 components), (3) interpersonal relationships (4 components), (4) individual competencies (7 components), (5) cultural and community competencies (5 components), (6), and Administrative competencies (4 components). The leadership and management dimension, in both the first and second stages of this research, had the highest number of codes (42 and 25% of the total codes). Conclusion Since health headquarters play a major role in supervising and directing human resources and promoting the efficiency and effectiveness of the activities of health-related organizations, they should have a high level of management and leadership skills. It is important to pay attention to the competency level of the health headquarters, their classification, and the use of different competencies to attract each group of these headquarters. Also, due to the effective nature of the duties of third-level headquarters who are recruited to work at the highest headquarter level, these headquarters must have a high level of all competencies. Finally, using the competency model of health headquarters can help health organizations in achieving high visions, goals, and self-help strategies.