bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effects of Seasonal Freezing-thawing on the Protistan Communities in a Mountain Lake
Authors: Liu Jinxian , Li Xiaoqi , Chai Baofeng 
Published: March 2021

Abstract
Background: Freezing-thawing cycles are common phenomena in temperate regions. Such events may have a significant influence on the composition of the protistan communities in a mountain lake. Protists are single-celled eukaryotic microorganisms that act as links in the aquatic microbial food web, affecting the transfer of substances and energy transformation. Yet little is known about the effects of freezing and thawing on the protistan community in a mountain lake. Results: The protistan communities in the lake were mainly composed of Ochrophyta, Ciliophora, Choanoflagellida, Cryptophyta, Chlorophyta, Stramenopiles_X, Cercozoa, Dinophyta, and Haptophyta. Seasonal freezing and thawing affected the community composition and diversity of protists. The change in the protistan community structure resulted from a significant change in organic carbon from the ice-covered to ice-free period. During the ice-covered and ice-free periods, temperature and nitrate were the main causes, respectively, for the changes in protistan community structure at different depths. Water depth also affected the structure of the protistan community, but it was not the most important factor. Conclusions: This study revealed that duration of lake surface icing might affect the function of subalpine lake ecosystems, including the rate of nutrient cycling and energy flow, owing to changes in the structure and biodiversity of the microbial community.
Can Conventional MRI Features Predict H3K27M Mutation Status of Diffuse Midline Gliomas?
Authors: Chauhan Richa Singh , Kulanthaivelu Karthik , Kathrani Nihar , Kotwal Abhishek , Bhat Maya Dattatraya , Saini Jitender , Prasad Chandrajit , Chakrabarti Dhritiman , Santosh Vani , Uppar Alok Mohan , Srini Dwarakanath 
Published: March 2021

Abstract
Purpose Pre-surgical prediction of H3K27M mutation in diffuse midline gliomas (DMG) on MRI is desirable. The purpose of the study is to elaborate conventional MRI (cMRI) of H3K27M-mutant DMGs and identify features that could discriminate them from WT (wild type)-DMGs.Methods cMRI features of 123 patients with DMG were evaluated conforming to the institutional research protocols. Multimodality MRI was performed on 1.5 or 3.0 Tesla MR Scanners with imaging protocol including T1w, T2w, FLAIR, diffusion-weighted, susceptibility-weighted and post- contrast T1w sequences. Pertinent cMRI features were annotated along the lines of Visually AcceSAble Rembrandt Images (VASARI) features and Intra Tumoral Susceptibility Signal score (ITSS) were evaluated. R software was used for statistical analysis.Results Sixty-one DMGs were H3K27M-mutant (mutant DMGs). The patients in the H3K27M-mutant DMG group were younger compared to the WT-DMG group (WT DMGs) (mean age 24.13+13.13 years vs. 35.79+18.74 years) (P= 0.016). The two groups differed on 5 cMRI features– i) enhancement quality (P=0.032), ii) thickness of enhancing margin (P=0.05), iii) proportion of edema (P=0.002), iv) definition of non-contrast enhancing tumor (NCET) margin (P=0.001) and v) cortical invasion (P=0.037). The mutant DMGs showed greater enhancement and greater thickness of enhancing margin while the WT DMGs exhibited significantly larger edema proportion with poorly defined NCET margins and cortical invasion. ITSS was not significantly different among the groups. Conclusion cMRI features like enhancement quality, thickness of the enhancing margin, proportion of edema, definition of NCET margin and cortical invasion can discriminate between the H3K27M-mutant and WT DMGs.
Evolution of the Illegal Substances Market and Substance Users’ Social Situation and Health During the Covid-19 Pandemic
Authors: Gaume Jacques , Schmutz Elodie , Daeppen Jean-Bernard , Zobel Frank 
Published: March 2021

Abstract

Background: The outbreak of the Covid-19 pandemic and the measures taken for tackling it had the potential to lead to deep modifications in the supply of illegal drugs and to impact substance users’ health and social situation. Methods: To investigate this, we used mixed methods, i.e. quantitative data collected with a brief questionnaire from substance users receiving opioid agonist treatment in a treatment centre in Switzerland (N=49), and qualitative data obtained using semi-structured phone interviews among a sub-group of participants (N=17). We repeated data collection twice over four weeks to investigate trends over time (N=51 and 14 at wave 2). Results: Findings consistently showed limited impact of the Covid-19 outbreak on the illegal substance market. Over the two waves, the supply, price and purity of three main illegal substances did not significantly vary. Substance use was estimated as usual by most, trending toward decrease. The impact of the pandemic on participants’ social situation and health was appraised as low to medium. Nevertheless, a minority of participants reported higher impact related to anxiety, boredom, depression and lack of social contacts. Multivariate analyses also nuanced overall findings and showed a more important impact for those who were female, younger, and not using multiple substances. Conclusions: This process could be implemented quickly and provided an understanding of the short-term impact of the pandemic and related lockdown on drug markets and users. Findings are limited by our sample and further research should address the plight of more vulnerable populations, as well as the long-term effects of this crisis.
Ancestry Specific Associations of a Genetic Risk Score, Dietary Patterns and Metabolic Syndrome: A Longitudinal ARIC Study
Authors: Hardy Dale Sharon , Racette Susan B. , Garvin Jane T. , Gebrekristos Hirut T. , Mersha Tesfaye B. 
Published: March 2021

Abstract
Background: Associations have been observed among genetic variants, dietary patterns, and metabolic syndrome (MetS). A gap in knowledge is whether a genetic risk score (GRS) and dietary patterns interact to increase MetS risk among African Americans. We investigated whether MetS risk was influenced by interaction between a GRS and dietary patterns among Whites and African Americans. A secondary aim examined if molecular genetic clusterings differed by racial ancestry.Methods: We used longitudinal data over 4-visits (1987-1998) that included 10,681 participants aged 45-64y at baseline from the Atherosclerosis Risk in Communities study (8,451 Whites and 2,230 African Americans). We constructed a simple-count GRS as the linear weighted sum of high-risk alleles (0, 1, 2) from cardiovascular disease polymorphisms from the genome-wide association studies catalog associated with MetS risk. Three dietary patterns were determined by factor analysis of food frequency questionnaire data: Western, healthy, and high-fat dairy. MetS was defined according to the 2016 National Cholesterol Education Program Adult Treatment Panel III criteria but used 2017 American Heart Association/American College of Cardiology criteria for elevated blood pressure. Analyses included generalized linear model risk ratios (RR), 95% confidence intervals (CI), and Bonferroni correction for multiple testing.Results: The Western dietary pattern was associated with higher risk for MetS across increasing GRS tertiles among Whites (p<.017). The high-fat dairy pattern was protective against MetS, but its impact was most effective in the lowest GRS tertile in Whites (RR=0.62; CI:0.52-0.74) and African Americans (RR=0.67; CI:0.49-0.91). Among each racial group within GRS tertiles, the Western dietary pattern was associated with development and cycling of MetS status between visits, and the high-fat dairy pattern with being free from MetS (p<.017). The healthy dietary pattern was associated with higher risk of MetS among African Americans which may be explained by higher sucrose intake (p<.0001). Fewer genes, but more metabolic pathways for obesity, body fat distribution, and lipid and carbohydrate metabolism were identified in African Americans than Whites. Some polymorphisms were linked to the Western and high-fat dairy patterns.Conclusion: A dietary pattern characterized by high-fat dairy foods may be protective against MetS among individuals with a genetic predisposition.
Identification of differentially expressed genes, biological pathways and prognostic signature in bladder cancer
Authors: Tang Fucai , Qian Xiayan , Lu Zeguang , Lai Yongchang , Li Zhibiao , He Chengwu , He Zhaohui 
Published: March 2021

Abstract
Background

Bladder cancer (BC) is one of the most common malignant cancer of urinary system in the worldwide. The purpose of the present study was to analysis differentially expressed genes (DEGs), biological pathways and prognostic significance BC by bioinformatics analysis.
Methods

The gene expression dataset GSE7476 and the mRNA Seq sequencing data were downloaded respectively from GEO and TCGA. A total of 220 DEGs were obtained in BC. GO analysis and KEGG pathway analysis were performed for up- and down-regulated DEGs. Then, a protein-protein interaction (PPI) networks and module were constructed by Cytoscape software. Survival analysis of hub genes was performed.
Results

The result of GO analysis revealed that the up-regulated DEGs were enriched mainly in sister chromatid segregation, while the down-regulated DEGs were enriched mainly in muscle contraction. The result of KEGG pathway analysis showed that up-regulated DEGs were enriched mainly in cell cycle, while down-regulated DEGs enriched in IL-17 signaling pathway. 41 hub gene and 3 crucial modules were identified in the PPI network. 15 genes significantly associated with patient prognosis in BC were obtained by Kaplan-Meier analysis.
Conclusions

In summary, the present study identified hub genes, crucial pathways and provide possible the molecular targets and prognostic biomarkers for targeted therapy and prognostic assessment of BC.
The Effectiveness of a Balanced Salt Solution on Dry Eyes in Comatose Patients: A Randomized Trial
Authors: sadeghi-hasanvand Hengameh , Kordestani-Moghadam Parastou , irandoost Farnoosh , ali Seyed hadi , Toulabi Tahereh , Ebrahimzadeh Farzad , heidari Fardin 
Published: March 2021

Abstract
Objective: Dry eye is one of the complications of hospitalization in ICUs. This study was conducted to assess the effectiveness of a Balanced Salt Solution (BSS) on dry eyes in comatose patients. This clinical trial was conducted in 2019 on 34 patients admitted to the ICUs. The control group received sterile eye ointment with artificial tears (2 drops every 6 hours) and a tape over the eye. The trial group also received BSS (2 drops every 6 hours) in the opposite eye over five days. The patients' dry eye was examined on first day and sixth day of the study using Schirmer’s Test (ST) and the Tear Breakup Time Test (TBUT). The data were analyzed in SPSS-21.Results: The results of the paired T-test based on ST and TBUT showed no significant change from first day one to sixth day in the BSS-receiving group (P>0.999 and P=0.187, respectively). Furthermore, no significant difference was observed between the two groups in the mean score of dry eye after eliminating the effect of the demographic and clinical variables (P=0.947). The administration of this solution by nurses seems to be an effective method for preventing the progression of dry eye in ICU patients.
Performance evaluation of the KRYPTOR Compact PLUS analyzer-based B.R.A.M.S CgA II KRYPTOR assay for chromogranin A measurement
Authors: CHOI Yu Jeong , Roh Juhye , Kim Sinyoung , Lee Kyung-A , Park Younhee 
Published: March 2021

Abstract
Background: Numerous immunoassays have been developed to measure the levels of chromogranin A (CgA), a useful biomarker for diagnosing and monitoring generally heterogeneous neuroendocrine tumors (NETs). Here, we evaluated the imprecision and linearity of three such assays: KRYPTOR (ThermoFisher Scientific), NEOLISA (EuroDiagnostica), and CgA-RIA (CisBio) using 123 samples for each assay.Results: The correlation coefficients between the assays were 0.932 (CgA-RIA versus NEOLISA), 0.956 (KRYPTOR versus CgA-RIA), and 0.873 (NEOLISA versus KRYPTOR). KRYPTOR showed good precision, with percent coefficients of variation less than 5% for low and high concentration quality controls. Linearity was maintained over a wide concentration range. Comparison of CgA levels from three disease entities (NETs, non-NET pancreatic tumors, and prostate cancer) and healthy controls showed that patients with NETs had significantly higher CgA levels (n = 57, mean: 1.82 ± 0.43 log ng/mL) than healthy individuals (n = 20, mean: 1.51 ± 0.23 log ng/mL; P = 0.018). No other significant differences between groups were observed.Conclusion: All three immunoassays showed strong correlations in measured CgA levels. Because KRYPTOR operation uses a fully automated random-access system and requires shorter incubation times and smaller sample volumes, the KRYPTOR assay may improve laboratory workflow while maintaining satisfactory analytical performance.
Associations of Gene Expressions in Liver and Blood Cells and Circulating Proteins With Coronary Artery Disease
Authors: Chai Tianci , Wan Zhisheng , Yang Xiaojie , Qiu Zhihuang , Chen Liangwan 
Published: March 2021

Abstract
Background: Circulating low-density lipoprotein cholesterol (LDL-C) plays a causal role in coronary artery disease (CAD). However, genetic risk factors of CAD were not yet fully understood. The aim of the study was to identify additional factors that contributed to CAD.Methods: We conducted integrative analysis on publicly available data from genome-wide association studies and quantitative trait locus studies by employing two-sample Mendelian randomization methods to examine the associations of gene expression and circulating protein levels with LDL-C and CAD.Results: We found that mRNA expression levels of SORT1, PSRC1 and CELSR2 in liver cells were significantly associated with both LDL-C and CAD (P < 5.0 × 10-8). Higher expression levels of SORT1, PSRC1 and CELSR2 in the liver were significantly associated with lower circulating LDL-C level (beta= -0.142, -0.138 and -0.171, respectively) and CAD risk (beta= -0.10, -0.097 and -0.121, respectively). Expression levels of 31 genes in blood cells associated with LDL-C level were found. Expressions of PSRC1, IL6R, GGCX, VAMP8, LIPA, NT5C2, SWAP70, EIF2B2, FURIN, FES and ATP5G1 in blood cells were significantly associated with CAD. Higher circulating granulins and apolipoprotein B levels, which were strongly affected by PSRC1 and APOB variants, were significantly associated with higher LDL-C level (beta = 0.22 and 1.35) and CAD risk, with odds ratios of 1.15 (1.10-1.19) and 1.45 (1.21-1.74), respectively. Conclusions: This study identified gene expressions in liver and blood cells and circulating granulins and apolipoprotein B that were genetically associated with LDL-C and CAD and provided evidence for exploring the potential causal relationship.
Meta-analysis With Zero-event Studies: A Comparative Study With Application to COVID-19 Data
Authors: Wei Jiajin , Lin Enxuan , Shi Jiandong , Yang Ke , Hu Zongliang , Zeng Xian-Tao , Tong Tiejun 
Published: March 2021

Abstract
Background: Meta-analysis is a statistical method to synthesize evidence from a number of independent studies, including those from clinical studies with binary outcomes. In practice, when there are zero events in one or both groups, it may cause statistical problems in the subsequent analysis. Methods: In this paper, by considering the relative risk as the effect size, we conduct a comparative study that consists of four continuity correction methods and another state-of-the-art method without the continuity correction, namely the generalized linear mixed models. To further advance the literature, we also introduce a new method of the continuity correction for estimating the relative risk. Results: From the simulation studies, the new method performs well in terms of mean squared error when there are few studies. In contrast, the generalized linear mixed model performs the best when the number of studies is large. In addition, by reanalyzing a recent COVID-19 data, it is evident that the double-zero-event studies impact on the estimate of the mean effect size.Conclusion: We recommend the new method to handle the zero-event studies when there are only few studies in the meta-analysis, or instead use the GLMM when the number of studies is large. The double-zero-event study may beinformative, and so we suggest not excluding them.
QuantiFERON-TB Gold Plus Testing for the Detection of LTBI in Health Care Workers in the Kyrgyz Republic
Authors: Corbett Caroline Susan , Kalmambetova Gulmira , Umetalieva Nagira , Ahmedov Sevim , Antonenka Uladzimir , Myrzaliev Bakyt , Sahalchyk Evgeni , Vogel Monica , Kadyrov Abdylat , Hoffmann Harald 
Published: March 2021

Abstract
Background: Health care workers (HCW) are at increased risk of TB infection due to their close contact with infected patients with active TB. The objectives of the study were (1) to assess the prevalence of LTBI among HCW in major TB hospitals of the Northern Kyrgyz Republic, and (2) to determine the association of LTBI with certain job positions, hospital units, or hospitals. Methods: HCWs from 4 TB hospitals in the Northern Kyrgyz Republic were tested with the interferon-gamma release assay (IGRA) Quantiferon-TB Gold plus (QFT) for the detection of an immune response to TB as marker of TB infection. Age was controlled for as a confounder. Univariate and multivariable analysis were performed using logistic regression to assess the association of the risk factors (age, job position, and hospital unit) with having a QTF positive result. Firth’s penalized-likelihood estimates were used for determining the odd’s of QFT positivity to account for the small-sample size. Pairwise comparisons using the Bonferroni correction (conservative) and comparisons without adjusting for multiple comparisons (unadjusted) were used to identify the categories where differences occurred.Results: QFT yielded valid results for 404 HCW, with 189 (47%) that had a positive test. In the National Tuberculosis Center, there was an increased odds to have a positive QFT test for the position of physician (OR=8.7, 95%, CI=1.2-60.5, p=0.03) and laboratory staff (OR=19.8, 95% CI=2.9-135.4, p<0.01) when administration staff was used as the baseline and controlling for age. No job position was found to have a significantly higher odds of positivity following a pairwise analysis controlling for multiple comparisons. Fifteen of the 49 HCW with follow-up tests converted from negative to positive at follow-up testing. Conclusions: This is the first report on prevalence and risk factors of LTBI for HCW in the Kyrgyz republic, and results indicate an increased risk for LTBI among physicians and laboratory personnel.
“Prevalence, Predictors and Outcomes of Surgical and Gastrointestinal Bleeding Events in Patients with COVID-19 Infection on Anticoagulation”
Authors: Alkhamis Ahmed , Alshamali Yousef , Alyaqout Khaled , Lari Eisa , Alkhamis Moh A. , Althuwaini Saad , Lari Ali , Alfili Maryam , Alkhayat Ali , Jamal Mohammad H , Alsabah Salman 
Published: March 2021

Abstract
BackgroundThis study aims to examine risk factors and complications associated with bleeding events in patients with coronavirus 19 (COVID-19) who are on anticoagulation. MethodWe conducted retrospective review of a prospectively maintained database of all patients who were admitted with COVID-19 and developed bleeding events. ResultsOf 122 bleeds, there were 67 (28%) non-gastrointestinal (GI) and 55 (28%) GI bleeds. Overall mortality was 59% (n= 72), 34 (28%) and 38 (31%) following non-GI and GI bleeds respectively. The prevalence of therapeutic invasive interventions was 7.5% and 16.3% in non-GI and GI bleeds respectively and all were successful in resolving the bleeding event. We found that having a GI bleeds was associated with higher risk of mortality compared to non-GI bleeds (p= 0.04) and having occult bleeds to be associated with 15 times increased risk of mortality. Furthermore, patients who were on therapeutic dose of anticoagulation were more likely to die compared to patients who were on none (odds ratio (OR) 0.1, 95%CI 0.01-0.86), on prophylactic (OR 0.07,95%CI 0.02-0.28) or intermediate (OR 0.36,95%CI 0.09-1.34) anticoagulation doses.Conclusions Routine prescription of supra-prophylactic dose anticoagulation should be revisited as it appears to be associated with increased of mortality and so more individualized approach to prescription should be the norm. Regardless of the cause of bleeding event it appears that the majority of bleeding events resolve with noninvasive interventions, correction and optimization sepsis therapies. However, when invasive interventions were necessary, they were associated with high success rate despite the delay.
Efficacy and Safety of Remdesivir in COVID-19 Patients: A Retrospective Analysis of Active Surveillance Database
Authors: Gupte Vaishali , Hegde Rashmi , Sawant Sandesh , Kalathingal Kabil , Jadhav Sonali , Malabade Rohit , Gogtay Jaideep 
Published: March 2021

Abstract
Background: Real-world data on safety and efficacy of remdesivir in COVID‑19 management is scant. We present findings of data analysis conducted for assessing the clinical outcomes of remdesivir treatment for COVID-19 in India. Methods: This retrospective analysis used data from an active surveillance programme database of hospitalised patients with COVID-19 who were receiving remdesivir. Results: Of the 2329 patients included, 67.4% were men. Diabetes (29.69%) and hypertension (20.33%) were the most common comorbidities. At remdesivir initiation, 2272 (97.55%) patients were receiving oxygen therapy. Remdesivir was administered for 5 days in 65.38% of patients. Antibiotics (64.9%) and steroids (47.9%) were the most common concomitant medications. Remdesivir was overall well tolerated: 13% of patients reported 119 adverse events; most common were nausea and vomiting in 45.4% and increased liver enzymes in 14.28% patients. 84% of patients were cured/improved, 6.02% died, and 9.16% showed no improvement in their clinical status at data collection. Subgroup analysis showed that the mortality rate was significantly lower in patients < 60 years old than in those > 60 years old. Amongst patients on oxygen therapy, the cure/improvement rate was significantly higher in those receiving standard low-flow oxygen than in those receiving mechanical ventilation, non-invasive ventilation, or high-flow oxygen. Risk factors for higher mortality were age > 60 years, hypertension, cardiac disease, diabetes, and mechanical ventilation. Conclusion: Our analysis showed that remdesivir is well tolerated and has an acceptable safety profile. The cure/improvement rate was 84%, with a higher improvement in patients < 60 years old and on standard low-flow oxygen.