bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysis of genome-wide mutation profile and establishment of risk signature for prognosis of bladder cancer
Authors: Zhao Yanyun , Ma Rong , Liu Fangxiao , Zhang Liwen , Lv Xuemei , Su Panpan , Fan Yue , Zhang Yifan , Wei Minjie , He Miao 
Published: May 2020

Abstract
Background: Emerging studies have shown that a variety of gene mutations occur in development and progression of cancer and highly mutation genes could play oncogenic or tumor suppressive roles in cancer. Therefore, our aim is to explore mutation genes which affect the prognosis of bladder.Methods: Mutation profile was obtained and analyzed from TCGA data set. A mutation-based signature was established by multivariable Cox regression analysis. Kaplan-Meier was performed to assess the prognostic power of signature. Time-dependent ROC was conducted to evaluate predictive accuracy of signature for bladder cancer patients.Results: There are 20177 genes have alteration in 403 bladder patients and 662 of them were frequently variation (mutation frequency > 5%). In this study, we assessed the prognostic predictive ability of 662 highly mutated genes and identified a mutation signature as an independent indicator for predicting the prognosis of bladder. The time-dependent ROC showed that AUC were 0.893, 0.896, 0.916 and 0.965 at 1, 3, 5 and 10 year, respectively. Stratified analysis and Multivariate Cox analysis showed that this mutation signature was reliable and independent biomarker. Furthermore, the nomogram predictive model can be used to effectively predict clinical prognosis of bladder patients. The decision analysis curve showed patients with risk threshold of 0.03-0.92 potentially yielded clinical net benefit. Finally, we identified several signaling pathways that associated with risk score by GSEA and KEGG analysis including PI3K-Akt signaling pathway and so on.Conclusions: In general, this study provide an optimal mutation signature as potential prognosis biomarker for bladder patients.
Identification and validation of a prognostic 5-protein signature for biochemical recurrence following radical prostatectomy in prostate cancer
Authors: Wu Xiangkun , Li Wenjie , Lv Daojun , Liu Yongda , Gu Di 
Published: May 2020

Abstract
Background : Biochemical recurrence (BCR) is considered as an indicator for prostate cancer (PCa)-specific recurrence and mortality. However, lack of effective prediction model to assess the prognosis of patients for optimization of treatment. The aim of this work was to construct a protein-based nomogram that could predict BCR for PCa.Materials and methods: Univariate Cox regression analysis was conducted to identify candidate proteins from the Cancer Genome Atlas (TCGA) database. LASSO Cox regression was further conducted to pick out the most significant prognostic proteins and formulate the proteins signature for predicting BCR. Additionally, a nomogram was constructed by multivariate Cox proportional hazards regression.Results: We established a 5‐protein-based signature which was well used to identify PCa patients into high‐ and low‐risk groups. Kaplan-Meier analysis demonstrated patients with higher BCR generally had significantly worse survival than those with lower BCR (p<0.0001). Time-dependent receiver operating characteristic curve expounded that ours signature had excellent prognostic efficiency for 1‐, 3‐ and 5‐year BCR (area under curve in training set: 0.691, 0.797, 0.808 and 0.74, 0.739, 0.82 in the test set). Univariable and multivariate Cox regression analysis showed that this 5‐protein signature was an independent of several clinical signatures including age, Gleason score, T stage, N status, PSA and residual tumor. Moreover, a nomogram was constructed and calibration plots confirmed the its predictive value in 3-, 5- and 10-year BCR overall survival.Conclusion: Our study identified a 5-protein-based signature and constructed a prognostic nomogram that reliably predicts BCR in prostate cancer. The findings might be of paramount importance in tumor prognosis and medical decision-making.
Screening and Evaluation of Bioactive Components of Methanol Root Extract of Anthocleista nobilis G. Don. by GCMS Analysis
Authors: Ojatula Adekunle ORIMISAN 
Published: May 2020

Abstract
Background: Medicinal plants have great importance in African medicine and are also used as precursors in drug discovery. The medicinal value of plants lies in their bioactive constituents which usually allow them to fight against several diseases. Plant-based natural constituents can be derived from any part of the plant like roots, bark, leaves, flowers, fruits, seeds. The present study was designed to determine the bioactive/biochemical compounds present in the methanol extract of Anthocleista nobilis root.Materials and Methods: GC -MS analysis of the methanol extract of A. nobilis root was performed using a Perkin Elmer GC Clarus 500 system comprising an Agilent technologies 5975 MSD model detector and a gas chromatograph interfaced to a mass spectrometer with the aid of the Turbo mass 5.0 software.Results: The study results of the GC-MS analysis provided different phytochemical compounds possessing several biological activities such as antimicrobial, antifungal, anticancer, and anti-inflammatory activities. This study therefore, showed that root of Anthocleista nobilis is a source of biologically active metabolites. Furthermore, root extract revealed the presence of diverse chemical constituents.Conclusion: The results of the present study suggest a recommendation of A. nobilis root as a plant of phytopharmaceutical importance.
An initial survey of 150 horses from Thailand for anti-Pythium insidiosum antibodies
Authors: Htun Zin Mar , Laikul Aree , Pathomsakulwong Watcharapol , Yurayart Chompoonek , Lohnoo Tassanee , Yingyong Wanta , Kumsang Yothin , Payattikul Penpan , Sae-Chew Pattarana , Rujirawat Thidarat , Jaturapaktrarak Chalisa , Chongtrakool Piriyaporn , Krajaejun Theerapong 
Published: May 2020

Abstract
Objectives: Pythium insidiosum causes a deadly condition, called pythiosis, in humans and other animals. The organism has been identified in tropical and subtropical environments worldwide. Since 1985, human pythiosis has been increasingly reported from Thailand. Seroprevalence studies estimated that ~32,000 Thai people have been exposed to the pathogen. In 2018, the first animal pythiosis case in Thailand was diagnosed in a horse. In this study, we surveyed anti-P. insidiosum antibodies in a sample of the Thai equine population. Results: Serum samples were available from 150 out of 6,353 registered horses distributed across Thailand. ELISA detected the anti-P. insidiosum antibodies in three horses. Immunochromatography and Western blot confirmed the presence of the antibodies in one of the ELISA-positive horses. Based on one positive out of 150 tested, the Pythium seroprevalence in the Thai equine population was 0.7%, which is 10 times higher than that of the Thai human population. The seroprevalence of the anti-P. insidiosum antibodies in a small sample of horses suggests a higher incidence of pythiosis in horses than in humans. Larger studies will be necessary to obtain the full picture of the epidemiology of animal pythiosis in Thailand.
Comparative genomics and diversity of SARS-CoV-2 suggest potential regional virulence
Authors: Devi Sundru Manjulata , Pamreddy Annapurna , Kasinath Balakuntalam , Sharma Kumar 
Published: May 2020

Abstract
It is widely known fact about the global pandemic caused by Severe Acute Respiratory Syndrome Coronavirus -2 (SARS-CoV-2) to humans, which imposed immediate lockdown of effected territories in the prevailing provinces. However, few provinces were able to control infection severity with lower death rates. Interestingly three types of genomic features were noticed through comparative genomics in the available genome sequences SARS-CoV-2, due to the insertion/deletions of orf3a, orf6, orf7a and orf7b. Whole genome phylogeny (n=75 genomes) revealed a large diversity within the SARS-CoV-2, and distributed in 6 clusters namely China, Diamond princess, Asian, European, USA and Beijing. This study asserts diversity in the genome with high mutation rate and migration of carriers over the world. Here, we describe the polymorphic loci of Spike glycoprotein and its putative mechanism for pathogenicity, which unveiled the presence of GPI anchor amidation, PPI hotspot, O-linked glycosylation, catalytic site, Iron binding site, signal cleavage, disulphide linkage, sulfation, transmembrane region, and C-terminal signal sites. Mutational changes at spike glycoprotein of South Korea, India, Greece, Spain, Australia, Sweden and Yunnan samples possibly suggest the prevalence of mutated strains with either low or high virulence. The regions at the spike glycoprotein also have high binding capacity to angiotensin converting enzyme 2 (ACE2) suggesting a key link for explaining damage to multiple organs including lungs, kidney and heart. Factors influencing the mutations at the spike glycoprotein region will need to be investigated to understand and neutralize the upsurge of the alarming Pandemic and to control the global spread of the disease.
Design, Development And Deployment Of A Web-Based Interoperable Registry For Inherited Retinal Dystrophies In Portugal – The Ird-Pt
Authors: Marques João Pedro , Carvalho Ana Luísa , Henriques José , Murta Joaquim Neto , Saraiva Jorge , Silva Rufino 
Published: May 2020

Abstract
BACKGROUNDThe development of multicenter patient registries promotes the generation of scientific knowledge by using real-world data. A country-wide, web-based registry for inherited retinal dystrophies (IRDs) empowers patients and community organizations, while supporting formal partnerships with investigators and stakeholders in the global aim to develop high-value, high-utility research. We aim to describe the design, development and deployment of a country-wide, web-based, user-friendly and interoperable registry for IRDs – the IRD-PT.RESULTSThe IRD-PT is a clinical/genetic research registry included in the retina.pt platform (http://www.retina.com.pt), which was developed by the Portuguese Retina Study Group. The retina.pt platform collects data on individuals diagnosed with retinal diseases, from several sites across Portugal, with over 1800 participants and over 30,000 consultations to date. The IRD-PT module interacts with the retina.pt core system which provides a range of basic functions for patient data management, while the IRD-PT module allows data capture for the specific purpose of IRDs. All IRDs are coded accordingly to the International Statistical Classification of Diseases and Related Health Problems (ICD) 9, ICD 10, ICD 11, and Orphanet Rare Disease Ontology (ORPHA codes) to make the IRD-PT interoperable with other IRD registries across the world. Furthermore, the genes are coded according to the Ontology of Genes and Genomes and Online Mendelian Inheritance in Man, whereas signs and symptoms are coded according to the Human Phenotype Ontology. The IRD-PT module pre-launched at Centro Hospitalar e Universitário de Coimbra, the largest reference center for IRDs in Portugal. As of April 1st 2020, finalized data from 537 participants were available for this preliminary analysis.CONCLUSIONSIn the specific field of rare diseases, the use of registries increases research accessibility for individuals, while providing clinicians/investigators with a coherent data ecosystem necessary to boost research. Appropriate design and implementation of patient registries enables rapid decision making and ongoing data mining, ultimately leading to improved patient outcomes. We have described here the principles behind the design, development and deployment of a web-based, user-friendly and interoperable software tool aimed to generate important knowledge and collecting high-quality data on the epidemiology, genomic landscape and natural history of IRDs in Portugal.
Cytokine Profile in Aqueous Humor of Patients with Ocular Toxocariasis
Authors: Jiang Zhaoxin , Sun Limei , Wang Weiqing , Ding Xiaohu , Zhang Ting , Li Songshan , Ding Xiaoyan 
Published: May 2020

Abstract
Purpose: Ocular toxocariasis (OT) is a vision-threatening disease with a largely unknown intraocular pathogenesis. Herein, we determined the cytokine expression profile in aqueous humor (AH) of patients with OT.Methods: This is a prospective experimental case-control study of cytokine levels in AH of patients with OT and uveitis and control subjects. Thirty samples from eyes with OT, 23 from eyes with uveitis, and 25 from eyes with age-related cataract were analyzed using a multiplexed magnetic bead immunoassay. Thirty-one cytokines were detected and classified into 5 categories: T-helper type 1 (Th1)-associated cytokines, Th2-associated cytokines, Th17 cytokine, proinflammatory mediators, and growth factors.Results: Higher expression in 19 and decreased expression in 3 cytokines in the OT group were identified, compared with controls. Levels of 17 cytokines were increased in the OT group, compared with the non-OT uveitis and control groups. Levels of 3 cytokines were decreased in the OT group compared with controls; no cytokine level was decreased in the OT and non-OT uveitis groups. Interleukin-10 was the only cytokine showing a significant difference in pairwise comparison among all groups. Th17 levels showed no change, while growth factors and proinflammatory mediators showed some significant changes.Conclusions: We believe this is the first analysis of cytokine expression profile in OT. It revealed that Th2-associated cytokines, especially IL-5, IL-10 and IL-13, present a significantly higher concentration in OT compared with the non-OT uveitis and controls. These cytokines may be important for OT pathogenesis and help identify diagnostic markers and develop treatment strategies in future.
Systemic Inflammatory Response Syndrome and Outcomes in Ischemic Patients Treated with Endovascular Treatment
Authors: xu xiangjun , Yuan Lili , Wang Wenbing , Xu Junfeng , Yang Qian , Zhu Yujuan , Xu Youqing , Yang Ke , Ge Liang , Huang Xianjun , Zhou Zhiming 
Published: May 2020

Abstract
Background The occurrence of systemic inflammatory response syndrome (SIRS) is associated with poor outcomes after ischemic stroke, and the inflammatory response can be significantly attenuated by successful reperfusion, while the SIRS in patients with acute large vessel occlusion stroke (ALVOS) who underwent endovascular treatment (EVT) remain unclear. We aimed to investigate the occurrence rate, predictors, and clinical outcomes of SIRS in patients with ALVOS after EVT. Methods We retrospectively collected EVT data of patients with ALVOS from July 2014 to August 2019 in our center. SIRS in the absence of infection was defined as the presence of ≥2 of the following: (1) heart rate >90 (2) body temperature >38°C or <36°C, (3) white blood cells >12 000/mm or <4000/mm or >10% bands for >24 h or (4) respiratory rate >20. Favorable outcome was defined as obtaining a 90-day modified Rankin Scale (mRS) score ≤2. Results Among the 262 patients who received EVT, 92 (35.1%) developed SIRS, 88 (95.7%) of whom developed SIRS in the first two days after EVT. Patients who developed SIRS had a reduced favorable outcome (OR, 4.112 [95% CI, 1.705–9.920]; P=0.002) and higher mortality (OR, 25.236 [95% CI, 8.578–74.835]; P<0.001) at 90 days. Greater SIRS burden was positively correlated with NIHSS scores at discharge and mRS scores at 90 days (r=0.249, P=0.017; r=0.230, P=0.027). The development of SIRS in patients with ALOVS who underwent EVT was associated with neutrophilic leukocytosis, hyperglycemia, higher admission NIHSS scores, and worse collateral circulation. Conclusions Patients with SIRS had higher odds of poor functional outcomes and higher mortality at 90 days in the EVT-treatment setting. The severity of the inflammatory response was positively correlated with the clinical outcomes of patients. Clinically relevant associations with SIRS were neutrophilic leukocytosis, hyperglycemia and baseline stroke severity, but favorable collateral circulation was a protective factor against SIRS.
The Association Between Dietary Glycemic and Insulin Indices with Incidence of Cardiovascular Disease: Tehran Lipid and Glucose Study
Authors: Teymoori Farshad , Farhadnejad Hossein , Mirmiran Parvin , Azizi Fereidoun , Nazarzadeh Milad 
Published: May 2020

Abstract
Background The aim of this study was to investigate the association of dietary insulin index (II), insulin load (IL), glycemic index (GI), and glycemic load (GL) with risk of cardiovascular disease (CVD) outcomes among adults. Methods This cohort study was conducted within the framework of the Tehran Lipid and Glucose Study on 2198 subjects, aged ≥19 years, who were followed-up for a mean of 4.7 years. Dietary GI, GL, II, IL were calculated using a food frequency questionnaire at baseline. Multivariate Cox proportional hazard regression models, adjusted for potential confounders, were used to estimate risk of CVD across quartiles of dietary insulin and glycemic indices. Results Mean±SD age of the study population (44.9% men) was 38.3±13.4 years. During an average of 2406 ± 417 person-years of follow-up, 76 (3.5%) new cases of CVD were ascertained. The Mean±SD of II, IL, GI, and GL of participants were 51.7±6.5, 235.8±90.2, 61.9±7.8, and 202.2±78.1, respectively. After adjusting for age, sex, smoking, physical activity, daily energy intake, body mass index, diabetes, and hypertension, the hazard ratio (HR) of the highest quartile of dietary GL was 2.77 (95%CI:1.00-7.69, P for trend:0.033) compared with the lowest one. However, there was no significant association between dietary GI, II, IL and risk for CVD incident. Conclusions Our findings suggest that high GL diet can increase the incidence of CVD, whereas high dietary II and IL was not associated with risk of CVD among adults.
Effects of Magnesium Biotinate Supplementation on Serum Insulin, Glucose, and Lipid Parameters Along with Gene Expressions of Intermediary Metabolism in Rats
Authors: Sahin Kazim , ORHAN Cemal , KUCUK Osman , TUZCU Mehmet , SAHIN Nurhan , OJALVO Sara PEREZ , KOMOROWSKI James R 
Published: May 2020

Abstract
Background: The objective of this work was to investigate the effects of a novel form of biotin (magnesium biotinate) at various levels on body weight, serum concentrations of glucose, insulin, cholesterol, and triglycerides, and liver expression of lipid metabolism-related genes such as SREBP-1c, FAS, AMPK-α1, ACC-1, ACC-2, PC, PCC and MCC in rats.Methods: A total of 42 male Sprague-Dawley rats were divided into six treatment groups and fed a standard diet-based egg white powdered diet supplemented with either commercial biotin (d-biotin) at 0.01, 1 or 100 mg/kg body weight or a novel form of biotin (magnesium biotinate) at 0.01, 1, or 100 mg/kg bodyweight for 35 days. The doses used at 0.01, 1 and 100 mg from each source represented a standard dietary dose (control), high dietary dose, and pharmacologic dose, respectively. Results: Bodyweight changes, feed intake, serum concentrations of glucose, insulin, creatine, and urea, and enzyme activities of ALT and AST were similar among treatments (P > 0.05). Serum total cholesterol and triglyceride concentrations of the rats decreased with biotin supplementation from both sources (P < 0.05). Concentrations were significantly lower with magnesium biotinate when comparing the 1 mg/kg dose groups (P < 0.05). Serum, liver, brain biotin concentrations, and liver cGMP contents were greater when rats were treated with magnesium biotinate versus d-biotin, particularly when comparing the 1 mg/kg and 100 mg/kg dose groups (P < 0.05). Both forms of biotin decreased the liver gene expression of SREBP‐1c and FAS and increased liver gene expression of AMPK-α1, ACC-1, ACC-2, PCC and MCC (P < 0.05). The magnitudes of responses were more emphasized with magnesium biotinate. Liver PC gene expression increased with biotin supplementation with no regard to dose or biotin form (P > 0.05).Conclusion: Results of the present work revealed that a new form of biotin, magnesium biotinate, compared with a commercial d-biotin, is more effective in reducing serum lipid concentrations and in regulating gene expressions of intermediary metabolism-related biomarkers.
Assessment of the Effectiveness of Various Adult Mosquito Sampling Methods in a Thickly Populated Urban Slum Settlement - A study from Besant Nagar, Chennai, India
Authors: Ravishankaran Sangamithra , Asokan Aswin , A Johnson Amala Justin N , Thomas Shalu , Joshua Vasna , Mathai Manu Thomas , Eapen Alex 
Published: May 2020

Abstract
BackgroundIn an urban scenario, it is an arduous task to collect adult Anopheles stephensi, unlike the immature forms due to various reasons such as the complex spatial heterogeneity, intricacies in feeding, and resting preferences. Thus it is necessary to have more specific and accurate assessments of adult vector density by performing various collection methods and timeframes to achieve appropriate and sustainable vector control strategies.Methods The study was undertaken in two phases, (i) resting dawn collections in cattle sheds from Jan 2015 to Dec 2016 to assess the possibility of maximum collection of An. stephensi compared to dusk collections done previously and to find out the best appropriate collection strategy for vector control and (ii) light trap collections from Jan 2016 to Apr 2017 to determine the efficiency and reliability of CDC light trap in sampling the anophelines including the urban malaria vector, Anopheles stephensi in human dwellings besides, other mosquito species. The man-hour density of An. stephensi in cattle sheds were calculated and its infection rate was analyzed by circum-sporozoite ELISA (CS-ELISA). Binary logistic regression analysis was done to ascertain the variables associated with the collection of Anopheles stephensi using a light trap.Results The resting collections in cattle sheds indicated that dawn collections yielded more Anopheles stephensi than at dusk. The resting stage female (fully fed, semi-gravid, and gravid) mosquitoes were more in dawn collections than in dusk collections. The CDC-light trap collections revealed that An. stephensi collected indoors were more than outdoor in human dwellings. Further, vector incrimination results observed that 0.56% of the female An. stephensi from cattle sheds were infected in 2014 (dusk), 0.15%, and 0.09% in 2015 and 2016 respectively in dawn collections. Nevertheless, 2.3% of An. stephensi collected by CDC light trap in human dwellings were positive for Plasmodium vivax (Pv210) infection. Binary logistic regression analysis proved that the presence of An. stephensi in human dwellings was significantly influenced by seasons, the number of rooms in the house, number of household members, and also the use of repellents.ConclusionsThe different collection (resting and light trap) approaches were assessed to find out the appropriate collection method and time which could yield the maximum number of An. stephensi with the existing resources. The study revealed that dawn collections during the early hours as the most suitable time to collect wild An. stephensi in an urban setting. The present study thus would help in chalking out an operationally feasible vector control strategy with the most appropriate methodology, timeframe useful for effective control of vectors.