cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Proteomic analysis for the impact of hypercholesterolemia on expressions of hepatic drug transporters and metabolizing enzymes
Creators: name: Liu, Yan
name: Pu, Qiang-Hong
name: Wu, Ming-Jun
name: Yu, Chao
Publisher: name: Taylor & Francis
Year: 2016
Subjects: subject: Biochemistry
subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Physiology
subject: Pharmacology
subject: Chemical Sciences not elsewhere classified
subject: Biological Sciences not elsewhere classified
subject: Cancer
subject: Inorganic Chemistry
subject: FOS: Chemical sciences
subject: Computational Biology

description: 1. Our objective is to investigate the alterations of hepatic drug transporters and metabolizing enzymes in hypercholesterolemia. Male Sprague–Dawley rats were fed high-cholesterol chows for 8 weeks to induce hypercholesterolemia. Protein levels of hepatic drug transporters and metabolizing enzymes were analyzed by iTRAQ labeling coupled with LC TRIPLE-TOF. 2. Total 239 differentially expressed proteins were identified using proteomic analysis. Among those, protein levels of hepatic drug transporters (MRP2, ABCD3, OAT2, SLC25A12, SCL38A3, SLC2A2 and SLC25A5) and metabolizing enzymes (CYP2B3, CYP2C7, CYP2C11, CYP2C13, CYP4A2 and UGT2B) were markedly reduced, but the levels of CYP2C6 and CYP2E1 were increased in hypercholesterolemia group compared to control. Decreased expressions of drug transporters MRP2 and OAT2 were further confirmed by real time quantitative PCR (RT-qPCR) and western blot. 3. Ingenuity pathway analysis revealed that these differentially expressed proteins were regulated by various signaling pathways including nuclear receptors and inflammatory cytokines. One of the nuclear receptor candidates, liver X receptor alpha (LXRα), was further validated by RT-qPCR and western blot. Additionally, LXRα agonist T0901317 rescued the reduced expressions of MRP2 and OAT2 in HepG2 cells in hypercholesterolemic serum treatment. 4. Our present results indicated that hypercholesterolemia affected the expressions of various drug transporters and metabolizing enzymes in liver via nuclear receptors pathway. Especially, decreased function of LXRα contributes to the reduced expressions of MRP2 and OAT2.
Sleep & Affect
Creators: name: Bei, Bei
name: Yap, Yi Yang
name: Wiley, Joshua F.
name: Slavish, Danica
name: Rice-Lacy, Rebecca
name: Shen, Lin
Publisher: name: OSF Registries
Year: 2017

description: Subproject focused on bidirectional relations of daily sleep and affect. Lead: Lin Shen.
Site-specific risk assessment and integrated management decision-making: A case study of a typical heavy metal contaminated site, Middle China
Creators: name: Li, Fei
name: Zhang, Jingdong
name: Yang, Jun
name: Liu, Chaoyang
name: Zeng, Guangming
Publisher: name: Taylor & Francis
Year: 2016
Subjects: subject: Medicine
subject: Biotechnology
subject: Environmental Sciences not elsewhere classified
subject: Chemical Sciences not elsewhere classified
subject: Ecology
subject: FOS: Biological sciences
subject: Biological Sciences not elsewhere classified
subject: Cancer
subject: Science Policy

description: A typical contaminated land was spatially investigated and assessed based on Chinese guidelines to establish remediation strategy for exploring the shortcomings of the current guidelines to suggest improvements. Results showed that Cr, As, Pb, and Cd should be regarded as the priority pollutants under sensitive land use, while Cr and As should be regarded as the priority pollutants under insensitive land use. Ingestion of soil for each studied metal appeared to be the main exposure pathway under both the land uses. The calculated screening values of the priority metals were conservative to certain extent—even some were lower than their background values. Therefore, an integrated risk management strategy was suggested and the hierarchic clean-up values were proposed considering the health risk, local background value, land remediation cases, current remediation technology, and financial cost. Consequently, it was suggested the clean-up values of Cr(VI), Cr, As, Pb, and Cd, under future sensitive land use, should be 7.5, 1000, 30, 250, and 1.4 mg/kg in the first class control layer, respectively. For future insensitive land use, the clean-up values of Cr(VI), Cr, As, Pb, and Cd should be 20.4, 8000, 60, 580, and 4.3 mg/kg in the first class control layer, respectively.
Modeling level-of-safety for bus stops in China
Creators: name: Ye, Zhirui
name: Wang, Chao
name: Yu, Yongbo
name: Shi, Xiaomeng
name: Wang, Wei
Publisher: name: Taylor & Francis
Year: 2016
Subjects: subject: Space Science
subject: Medicine
subject: Sociology
subject: FOS: Sociology
subject: Mathematical Sciences not elsewhere classified
subject: Inorganic Chemistry
subject: FOS: Chemical sciences

description: Objective: Safety performance at bus stops is generally evaluated by using historical traffic crash data or traffic conflict data. However, in China, it is quite difficult to obtain such data mainly due to the lack of traffic data management and organizational issues. In light of this, the primary objective of this study is to develop a quantitative approach to evaluate bus stop safety performance. Methods: The concept of level-of-safety for bus stops is introduced and corresponding models are proposed to quantify safety levels, which consider conflict points, traffic factors, geometric characteristics, traffic signs and markings, pavement conditions, and lighting conditions. Principal component analysis and k-means clustering methods were used to model and quantify safety levels for bus stops. Results: A case study was conducted to show the applicability of the proposed model with data collected from 46 samples for the 7 most common types of bus stops in China, using 32 of the samples for modeling and 14 samples for illustration. Based on the case study, 6 levels of safety for bus stops were defined. Finally, a linear regression analysis between safety levels and the number of traffic conflicts showed that they had a strong relationship (R2 value of 0.908). Conclusions: The results indicated that the method was well validated and could be practically used for the analysis and evaluation of bus stop safety in China. The proposed model was relatively easy to implement without the requirement of traffic crash data and/or traffic conflict data. In addition, with the proposed method, it was feasible to evaluate countermeasures to improve bus stop safety (e.g., exclusive bus lanes).
Additional file 1 of Differences in risk factors for incident and recurrent preterm birth: a population-based linkage of 3.5 million births from the CIDACS birth cohort
Creators: name: Rocha, Aline S.
name: de Cássia Ribeiro-Silva, Rita
name: Fiaccone, Rosemeire L.
name: Paixao, Enny S.
name: Falcão, Ila R.
name: Alves, Flavia Jôse O.
name: Silva, Natanael J.
name: Ortelan, Naiá
name: Rodrigues, Laura C.
name: Ichihara, Maria Yury
name: de Almeida, Marcia F.
name: Barreto, Mauricio L.
Publisher: name: figshare
Year: 2022
Subjects: subject: Medicine
subject: Cell Biology
subject: Biotechnology
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Hematology
subject: 110309 Infectious Diseases
subject: FOS: Health sciences

description: Additional file 1: Table S1. Univariate analyses of factors associated with incident and recurrent preterm birth in the second pregnancy, 2001-2015 (n = 1,764,025). Table S2. Frequency and factors associated with incident and recurrent preterm birth in the second pregnancy, 2012-2015 (n = 189,227). 1Analysis adjusted for all model variables. 2 Pdifference represents the interaction between incident and recurrent preterm birth for the respective characteristic. The equation for this model is as follows: Logit [ Pr (PTB2=1/Risk factors)] = β0 + β1 (PTB1) + β2 (risk factor X2) + β3 (PTB1) × (risk factor X2), where PTB1 and PTB2 are indicators of a preterm birth in the first and second pregnancy, respectively. Table S3. Incident and recurrent preterm birth in the second pregnancy according to change in the number of prenatal visits between the first and the second pregnancies, 2012-2015 (n = 189,482). 1Adjusted analysis by mother’s residence area, family density, mother’s self-declared race/skin color, mother’s level of education, mother’s marital status, maternal age, type of delivery in the second birth. 2Pdifference represents the interaction between incident and recurrent preterm delivery for the respective characteristic. The equation for this model is as follows: Logit [ Pr (PTB2=1/Risk factors)] = β0 + β1 (PTB1) + β2 (risk factor X2) + β3 (PTB1) × (risk factor X2), where PTB1 and PTB2 are indicators of a preterm birth in the first and second pregnancy, respectively. Table S4. Factors associated with incident and recurrent preterm birth in the second pregnancy, using cross-validation technique, 2001-2015. 1Analysis adjusted for all model variables. Figure S1. ROC curve for logistic regression model of incident preterm birth in cross-validation analysis. (A) Empirical ROC curve; (B) Binomial ROC curve. Non-parametric ROC curve not generated due to database size. Figure S2. ROC curve for logistic regression model of recurrent preterm birth in cross-validation analysis. (A) Empirical ROC curve; (B) Binomial ROC curve; (C) Non-parametric ROC curve.
Modeling Level-of-safety for Bus Stops in China
Creators: name: Ye, Zhirui
name: Wang, Chao
name: Yu, Yongbo
name: Shi, Xiaomeng
name: Wang, Wei
Publisher: name: Taylor & Francis
Year: 2016
Subjects: subject: Space Science
subject: Medicine
subject: Sociology
subject: FOS: Sociology
subject: Mathematical Sciences not elsewhere classified
subject: Inorganic Chemistry
subject: FOS: Chemical sciences

description: Objective: Safety performance at bus stops is generally evaluated by using historical traffic crash data or traffic conflict data. However, in China, it is quite difficult to obtain such data mainly due to the lack of traffic data management and organizational issues. In light of this, the primary objective of this study is to develop a quantitative approach to evaluate bus stop safety performance. Methods: The concept of level-of-safety for bus stops is introduced and corresponding models are proposed to quantify safety levels, which consider conflict points, traffic factors, geometric characteristics, traffic signs and markings, pavement conditions, and lighting conditions. Principal component analysis and k-means clustering method were used to model and quantify safety levels for bus stops. Results: A case study was conducted to show the applicability of the proposed model with data collected from 46 samples for the seven most common types of bus stops in China, using 32 of the samples for modeling and 14 samples for illustration. Based on the case study, six levels of safety for bus stops were defined. Finally, a linear regression analysis between safety levels and the number of traffic conflicts showed that they had a strong relationship (R-square value of 0.908). Conclusions: The results indicated the method was well validated and could be practically used for the analysis and evaluation of bus stop safety in China. The proposed model was relatively easy to implement without the requirement of traffic crash data and/or traffic conflict data. In addition, with the proposed method, it was feasible to evaluate countermeasures to improve bus stop safety (e.g., exclusive bus lanes).
Burden of systemic glucocorticoid-related complications in severe asthma
Creators: name: Lefebvre, Patrick
name: Duh, Mei Sheng
name: Marie-Hélène Lafeuille
name: Gozalo, Laurence
name: Desai, Urvi
name: Marie-Noëlle Robitaille
name: Albers, Frank
name: Yancey, Steve
name: Ortega, Hector
name: Forshag, Mark
name: Xiwu Lin
name: Dalal, Anand A.
Publisher: name: Taylor & Francis
Year: 2017
Subjects: subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Immunology
subject: FOS: Clinical medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Cancer
subject: Science Policy

description: Objectives: Although systemic glucocorticoids (SGCs) are efficacious, their chronic use is associated with a range of complications. Yet limited data are available about the risks following chronic use in patients with severe asthma, who are at risk of long-term SGC-related complications. This study was carried out to investigate the risks of developing SGC-related complications, and to quantify the associated healthcare resource utilization and costs for patients with severe asthma in the United States. Methods: This was a longitudinal, open-cohort, observational study. Medicaid claims data (1997–2013) for patients ≥12 years old with ≥2 asthma diagnoses were used. A total of 26,987 SGC non-users were identified for inclusion in the study, alongside 3628 SGC users with ≥6 months’ continuous SGC use. Results: Multivariate generalized estimating equation models were used to estimate the adjusted risk of developing SGC-related complications, and to quantify the associated healthcare resource utilization and costs. This analysis compared SGC users with SGC non-users, and found that SGC users had an increased likelihood of developing complications. A significant dose–response relationship was demonstrated between chronic SGC use and risk of developing any complications (odds ratios for low, medium, and high SGC exposure were 2.03 [p = .0511], 2.85 [p p Conclusions: These findings confirm the risk associated with chronic use of SGCs, irrespective of dose level, and highlight the need for new SGC-sparing treatment strategies for patients with severe asthma.
Occurrence and risk assessment of polycyclic aromatic hydrocarbons in the Hanjiang River Basin and the Danjiangkou Reservoir, China
Creators: name: Qi, Yueling
name: Owino, Anita Awino
name: Anyango Makokha, Victorine
name: Shen, Yun
name: Zhang, Di
name: Wang, Jun
Publisher: name: Taylor & Francis
Year: 2016
Subjects: subject: Biochemistry
subject: Space Science
subject: Microbiology
subject: FOS: Biological sciences
subject: Biotechnology
subject: Environmental Sciences not elsewhere classified
subject: Chemical Sciences not elsewhere classified
subject: Ecology
subject: Biological Sciences not elsewhere classified

description: This study was conducted to investigate the occurrence, distribution, and source of 16 polycyclic aromatic hydrocarbons (PAHs) in the Hanjiang River Basin and the Danjiangkou (DJK) Reservoir. The concentrations of total PAHs in surface water, sediments, and bank soils ranged from 9.42 to 137.94 ng/l, 86.23 to 2514.93 ng/g, and 133.17 to 671.93 ng/g dry weight, respectively. The composition pattern of PAHs showed that 3-ring PAHs were dominated in all of the samples, while the proportion of high molecular weight PAHs (5- to 6-ring PAHs) in sediments and bank soil samples was almost three times higher than water. The source apportionment analysis showed that most of the PAHs in water were derived from sources of petroleum and combustion, while combustion was the predominant source of PAHs in sediments and bank soils. The methods based on toxic equivalency factors, risk quotient, and incremental lifetime cancer risk were used to assess the ecosystem risk and potential health risk of PAHs. The risk assessments showed that PAHs in the DJK Reservoir were out of potential health risk, but the ecological risk for majority of 16 PAHs was in the moderate level.
Dummy data for HR in Matching
Creators: name: Wilde, Henry
Publisher: name: Zenodo
Year: 2020
Subjects: data
matching algorithm
hospital-resident assignment

description: This archive contains the dummy data used in the tutorial, "Allocating university medics to hospital placements," for the Python library Matching's documentation. Each YAML file specifies the preferences and capacities of the players in an instance of the hospital-resident assignment problem (HR).
Additional file 2 of High burden of hypovitaminosis D among the children and adolescents in South Asia: a systematic review and meta-analysis
Creators: name: Siddiqee, Mahbubul H.
name: Bhattacharjee, Badhan
name: Siddiqi, Umme Ruman
name: Rahman, Mohammad Meshbahur
Publisher: name: figshare
Year: 2022
Subjects: subject: Medicine
subject: Biotechnology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Cancer
subject: Science Policy

description: Additional file 2: Figure S2. Funnel plot for weighted mean values of serum vitamin D levels reported by the studies included in this systematic review (where a single dot represents the measurement). High number of observations falling outside the expected range on both sides indicate high heterogenity of reported serum vitamin D levels in South Asia.
Additional file 1 of High burden of hypovitaminosis D among the children and adolescents in South Asia: a systematic review and meta-analysis
Creators: name: Siddiqee, Mahbubul H.
name: Bhattacharjee, Badhan
name: Siddiqi, Umme Ruman
name: Rahman, Mohammad Meshbahur
Publisher: name: figshare
Year: 2022
Subjects: subject: Medicine
subject: Biotechnology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Cancer
subject: Science Policy

description: Additional file 1: Figure S1. Comparative weighted mean of serum D levels among the South Asian countries. The error bars represent weighted standard deviation (except for Afghanistan from where only one study was reported).
Amphetamine-Type-Stimulants (ATS) Use and Homosexuality-Related Enacted Stigma Are Associated With Depression Among Men Who Have Sex With Men (MSM) in Two Major Cities in Vietnam in 2014
Creators: name: Vu, Nga Thi Thu
name: Holt, Martin
name: Phan, Huong Thi Thu
name: La, Lan Thi
name: Gioi Minh Tran
name: Doan, Tung Thanh
name: Nguyen, Trang Nguyen Nhu
name: Wit, John De
Publisher: name: Taylor & Francis
Year: 2017
Subjects: subject: Biotechnology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Sociology
subject: FOS: Sociology
subject: Marine Biology
subject: Cancer
subject: Science Policy
subject: 111714 Mental Health
subject: FOS: Health sciences

description: Background: Men who have sex with men (MSM) are disproportionately affected by mental health concerns, including depression. Amphetamine-type-stimulants (ATS) use and homosexuality-related stigma and discrimination have been found associated with depression among MSM. Objectives: To assess the prevalence of depression and its associations with ATS use and homosexuality-related stigma and discrimination among MSM in Vietnam. Methods: 622 MSM were conveniently recruited in Hanoi and Ho Chi Minh city, Vietnam, from September to December 2014. We collected information on demographic characteristics, ATS, alcohol and other drug use, sexual behaviors, homosexuality-related and discrimination stigma, and sexual sensation-seeking. Depression and suicidal thoughts were assessed by the Patient Health Questionnaire (PHQ-9). We assessed associations of depression with ATS use and homosexuality-related stigma and discrimination using logistic regression. Results: Of 622 sampled MSM, 11.3% were classified as having major depression, 9.8% reported any suicidal thoughts in the last two weeks, 30.4% ever had used any ATS, 88.8% ever ad drank alcohol and 21.5% had ever used any other drugs. In multivariate analysis, depression was significantly associated with ATS use (Adjusted Odds Ratio [AOR: 2.20; (95% Confidence Interval (CI): 1.32–3.67], younger age of sexual debut with another man (AOR: 0.09; 95% CI: 0.02–0.50), and greater enacted homosexuality-related stigma (AOR: 1.97; 95% CI: 1.19–3.26). Conclusions: We found a moderate prevalence of depression among sampled MSM, which was associated with ATS use and enacted homosexuality-related stigma. We recommend integrating assessment and interventions regarding depression and methamphetamine use into gay-friendly, culturally adapted holistic HIV prevention for MSM in Vietnam.
Gestational stress induces depressive-like and anxiety-like phenotypes through epigenetic regulation of BDNF expression in offspring hippocampus
Creators: name: Zheng, Yu
name: Fan, Weidong
name: Zhang, Xianquan
name: Dong, Erbo
Publisher: name: Taylor & Francis
Year: 2016
Subjects: subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Neuroscience
subject: Physiology
subject: Mental Health

description: Exposure to stressful life events during pregnancy exerts profound effects on neurodevelopment and increases the risk for several neurodevelopmental disorders including major depression. The mechanisms underlying the consequences of gestational stress are complex and remain to be elucidated. This study investigated the effects of gestational stress on depressive-like behavior and epigenetic modifications in young adult offspring. Gestational stress was induced by a combination of restraint and 24-hour light disturbance to pregnant dams throughout gestation. Depressive-like and anxiety-like behaviors of young adult offspring were examined. The expression and promoter methylation of brain derived neurotrophic factor (BDNF) were measured using RT-qPCR, Western blot, methylated DNA immunoprecipitation (MeDIP) and chromatin immunoprecipitation (ChIP). In addition, the expressions of histone deacetylases (HDACs) and acetylated histone H3 lysine 14 (AcH3K14) were also analyzed. Our results show that offspring from gestational stress dams exhibited depressive-like and anxiety-like behaviors. Biochemically, stress-offspring showed decreased expression of BDNF, increased expression of DNMT1, HDAC1, and HDAC2, and decreased expression of AcH3K14 in the hippocampus as compared to non-stress offspring. Data from MeDIP and ChIP assays revealed an increased methylation as well as decreased binding of AcH3K14 on specific BDNF promoters. Pearson analyses indicated that epigenetic changes induced by gestational stress were correlated with depressive-like and anxiety-like behaviors. These data suggest that gestational stress may be a suitable model for understanding the behavioral and molecular epigenetic changes observed in patients with depression.
The "Food Studies" Corpus Citation Files
Creators: name: Malin, James Edward
Publisher: name: OSF Registries
Year: 2020
Subjects: Bibliometrics
Food Studies
Multidisciplinary
Scoping Review

description: This dataset of citations was aggregated using a modified scoping review strategy across 5 databases as of Dec 04, 2019. After collection, all citations were screened for relevance.
Gestational Stress Induces Depressive-like and Anxiety-like Phenotypes through Epigenetic Regulation of BDNF Expression in Offspring Hippocampus
Creators: name: Zheng, Yu
name: Fan, Weidong
name: Zhang, Xianquan
name: Dong, Erbo
Publisher: name: Taylor & Francis
Year: 2016
Subjects: subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Neuroscience
subject: Physiology
subject: Mental Health

description: Exposure to stressful life events during pregnancy exerts profound effects on neurodevelopment and increases the risk for several neurodevelopmental disorders including major depression. The mechanisms underlying the consequences of gestational stress are complex and remain to be elucidated. This study investigated the effects of gestational stress on depressive-like behavior and epigenetic modifications in young adult offspring. Gestational stress was induced by a combination of restraint and 24-hour light disturbance to pregnant dams throughout gestation. Depressive-like and anxiety-like behaviors of young adult offspring were examined. The expression and promoter methylation of brain derived neurotrophic factor (BDNF) were measured using RT-qPCR, Western blot, methylated DNA immunoprecipitation (MeDIP) and chromatin immunoprecipitation (ChIP). In addition, the expressions of histone deacetylases (HDACs) and acetylated histone H3 lysine 14 (AcH3K14) were also analyzed. Our results show that offspring from gestational stress dams exhibited depressive-like and anxiety-like behaviors. Biochemically, stress-offspring showed decreased expression of BDNF, increased expression of DNMT1, HDAC1, and HDAC2, and decreased expression of AcH3K14 in the hippocampus as compared to non-stress offspring. Data from MeDIP and ChIP assays revealed an increased methylation as well as decreased binding of AcH3K14 on specific BDNF promoters. Pearson analyses indicated that epigenetic changes induced by gestational stress were correlated with depressive-like and anxiety-like behaviors. These data suggest that gestational stress may be a suitable model for understanding the behavioral and molecular epigenetic changes observed in patients with depression.
Search and Raw Search Result Citation Files
Creators: name: Malin, James Edward
Publisher: name: OSF Registries
Year: 2020

description: This dataset is part of a study that used scoping review methodology to collect and verify the applicability of the phrase "Food Studies" in bibliographic records across five databases. Five large bibliographic databases were identified for size, relevance to food studies, and subject metadata standards. These were ProQuest Central (PQC), EBSCO Discovery Service (EDS), Web Of Science (WOS), PubMed (PM), and PubAg. The phrase “food studies” was then searched within each database, using a scholarly or peer-reviewed filter. The date range for the articles was all-time, through the date of the final search (December 3, 2019.)
Association of CAT–262C/T with the concentration of catalase in seminal plasma and the risk for male infertility in Algeria
Creators: name: Bousnane, Nour El Houda
name: Sadiq May
name: Yahia, Mouloud
name: Alhaija, Abed Alkarem Abu
Publisher: name: Taylor & Francis
Year: 2017
Subjects: subject: Biochemistry
subject: 29999 Physical Sciences not elsewhere classified
subject: FOS: Physical sciences
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Physiology
subject: Biotechnology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Ecology
subject: Developmental Biology
subject: Cancer
subject: Plant Biology

description: Catalase (CAT) plays a central role in the protection of different cell types against the deleterious effects of hydrogen peroxide. In human, CAT is implicated in many physiological and pathological conditions including idiopathic male infertility. In this study we examined the association between CAT levels in seminal plasma with different sperm parameters and with CAT–262 C/T polymorphism and their risk for idiopathic male infertility in Algeria. Semen and blood samples were obtained from 111 infertile males and 104 fertile controls from the region of Eastern Algeria following informed consent. Standard semen parameters, DNA integrity, and CAT concentration in seminal plasma were evaluated. CAT-262C/T genotypes were screened using allele specific PCR. Seminal CAT activity was significantly different (p<0.0001) between infertile males and controls, it was also markedly decreased in oligo-astheno-teratozoospermia (p<0.0001), azoospermia (p<0.0001), and normozoospermia (p=0.045) subgroups compared to controls. Positive correlations between CAT activity and semen parameters (volume, motility, concentration, and morphology) were detected, but not with sperm DNA integrity. There was no direct association between CAT-262C/T polymorphism and general male infertility. However, the results presented in this study showed that CAT activity is remarkably associated with the CAT-262T allele (p=0.001) and the different CAT-262C/T genotypes. This study highlighted the major differences in the seminal plasma CAT content between infertile and fertile males and the differences of CAT concentration between different CAT-262C/T genotypes carriers.
Imputation of missing covariate values in epigenome-wide analysis of DNA methylation data
Creators: name: Wu, Chong
name: W. Demerath, Ellen
name: S. Pankow, James
name: Bressler, Jan
name: Fornage, Myriam
name: L. Grove, Megan
name: Chen, Wei
name: Guan, Weihua
Publisher: name: Taylor & Francis
Year: 2016
Subjects: subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Chemical Sciences not elsewhere classified
subject: Biological Sciences not elsewhere classified
subject: Mathematical Sciences not elsewhere classified
subject: Cancer

description: DNA methylation is a widely studied epigenetic mechanism and alterations in methylation patterns may be involved in the development of common diseases. Unlike inherited changes in genetic sequence, variation in site-specific methylation varies by tissue, developmental stage, and disease status, and may be impacted by aging and exposure to environmental factors, such as diet or smoking. These non-genetic factors are typically included in epigenome-wide association studies (EWAS) because they may be confounding factors to the association between methylation and disease. However, missing values in these variables can lead to reduced sample size and decrease the statistical power of EWAS. We propose a site selection and multiple imputation (MI) method to impute missing covariate values and to perform association tests in EWAS. Then, we compare this method to an alternative projection-based method. Through simulations, we show that the MI-based method is slightly conservative, but provides consistent estimates for effect size. We also illustrate these methods with data from the Atherosclerosis Risk in Communities (ARIC) study to carry out an EWAS between methylation levels and smoking status, in which missing cell type compositions and white blood cell counts are imputed.
Imputation of Missing Covariate Values in Epigenome-Wide Analysis of DNA Methylation Data
Creators: name: Wu, Chong
name: W. Demerath, Ellen
name: S. Pankow, James
name: Bressler, Jan
name: Fornage, Myriam
name: L. Grove, Megan
name: Chen, Wei
name: Guan, Weihua
Publisher: name: Taylor & Francis
Year: 2016
Subjects: subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Chemical Sciences not elsewhere classified
subject: Biological Sciences not elsewhere classified
subject: Mathematical Sciences not elsewhere classified
subject: Cancer

description: DNA methylation is a widely studied epigenetic mechanism and alterations in methylation patterns may be involved in the development of common diseases. Unlike inherited changes in genetic sequence, variation in site-specific methylation varies by tissue, developmental stage, and disease status, and may be impacted by aging and exposure to environmental factors, such as diet or smoking. These non-genetic factors are typically included in epigenome-wide association studies (EWAS) because they may be confounding factors to the association between methylation and disease. However, missing values in these variables can lead to reduced sample size and decrease the statistical power of EWAS. We propose a site selection and multiple imputation (MI) method to impute missing covariate values and to perform association tests in EWAS. Then, we compare this method to an alternative projection-based method. Through simulations, we show that the MI-based method is slightly conservative, but provides consistent estimates for effect size. We also illustrate these methods with data from the Atherosclerosis Risk in Communities (ARIC) study to carry out an EWAS between methylation levels and smoking status, in which missing cell type compositions and white blood cell counts are imputed.
Anacroneuria carchi Stark
Creators: name: Stark, Bill P.
name: Zúñiga, Maria del Carmen
Publisher: name: Zenodo
Year: 2014
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Plecoptera
Perlidae
Anacroneuria
Anacroneuria carchi

description: Anacroneuria carchi Stark (Figs. 6-8) Anacroneuria carchi Stark 2001:11. Holotype ♂ (Carnegie Museum of Natural History), Chical, Carchi Province, Ecuador Anacroneuria carchi: Stark et al., 2012:82. Material examined. Ecuador: Esmeraldas Province, Cantón San Lorenzo, Río Lita, 1830’, 00 ° 51.64’ N, 78 ° 27.16’ W, 2 December 2008, S.M. Clark, R.C. Mower, 2♂, 1♀ (BYUC). Comments. This species was recently recorded by Stark et al. (2012) from two male specimens collected together with the additional males (listed above) and first female specimen recorded here and described below. The adult head and pronotum are also illustrated for the first time (Fig. 6). The Rio Lita collection site is located in the Northwestern Ecuadorian Pacific Zone, which forms part of the Choco Biogeographic Region, an area known for its hot, humid climate. Female. Forewing length 17 mm. Subgenital plate pale, hairy and bilobed, mesal notch relatively narrow and shallow (Fig. 8). Posterior transverse sclerite on sternum 9 pale, mesal field of sternum 9 uniformly covered with moderately long pale setae. Egg. Length ca. 0.32 mm, greatest width ca. 0.19 mm. Spindle shaped with button-like collar (Fig. 7).
description: Published as part of Stark, Bill P. & Zúñiga, Maria del Carmen, 2014, New Species And Records Of Colombian, Ecuadorian And Venezuelan Anacroneuria (Plecoptera: Perlidae), With A Review Of The Anacroneuria Aymara Stark & Sivec Complex, pp. 66-79 in Illiesia 10 (8) on pages 72-73, DOI: 10.5281/zenodo.4752749
description: {"references": ["Stark, B. P. 2001. Records and descriptions of Anacroneuria from Ecuador (Plecoptera: Perlidae). Scopolia, 46: 1 - 42.", "Stark, B. P., B. C. Kondratieff, & B. Gill. 2012. New species and records of Anacroneuria (Plecoptera: Perlidae) from Ecuador and Paraguay. Illiesia, 8: 78 - 93."]}
title: Roland Landman
Creators: name: Leibowitch, Jacques (1942-2020)
Publisher: name: NAKALA - https://nakala.fr (Huma-Num - CNRS)
publisherIdentifier: https://ror.org/04ces3204
publisherIdentifierScheme: ROR
Year: 2020

description: Pièces jointes : corrections à un document (protocole?) sur ICCARRE ; Protocole d'étude clinique ICCARRE. 1 fichier (87 pages)
Convenient and efficient method for synthesis of 2,4,6-triarylpyridines using catalytic amount of PEG1000-based dicationic acidic ionic liquid under solvent-free conditions
Creators: name: Ren, Yi-Ming
name: Zhang, Ze
name: Jin, Shuo
Publisher: name: Taylor & Francis
Year: 2016
Subjects: subject: Biophysics
subject: Biochemistry
subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: Molecular Biology
subject: Biotechnology
subject: Environmental Sciences not elsewhere classified
subject: Chemical Sciences not elsewhere classified

description: A convenient and efficient method for synthesis of substituted 2,4,6-triarylpyridines by the reaction of chalcones and ammonium acetate or via one-pot, three-component condensation of aromatic aldehydes with acetophenones and ammonium acetate has been developed by using the efficient catalyst PEG1000-based dicationic acidic ionic liquid (PEG1000-DAIL) under solvent-free conditions. Recycling studies have shown that the PEG1000-DAIL can be readily recovered and reused several times without significant loss of activity.
Additional file 1 of Acute kidney injury contributes to worse physical and quality of life outcomes in survivors of critical illness
Creators: name: Mayer, Kirby P.
name: Ortiz-Soriano, Victor M.
name: Kalantar, Alborz
name: Lambert, Joshua
name: Morris, Peter E.
name: Neyra, Javier A.
Publisher: name: figshare
Year: 2022
Subjects: subject: Medicine
subject: Immunology
subject: FOS: Clinical medicine
subject: Developmental Biology
subject: Science Policy
subject: 111714 Mental Health
subject: FOS: Health sciences

description: Additional file 1: Supplemental Table 1. Clinical characteristics of critical illness survivors stratified by AKI status with or without RRT during index ICU stay.
Additional file 2 of Acute kidney injury contributes to worse physical and quality of life outcomes in survivors of critical illness
Creators: name: Mayer, Kirby P.
name: Ortiz-Soriano, Victor M.
name: Kalantar, Alborz
name: Lambert, Joshua
name: Morris, Peter E.
name: Neyra, Javier A.
Publisher: name: figshare
Year: 2022
Subjects: subject: Medicine
subject: Immunology
subject: FOS: Clinical medicine
subject: Developmental Biology
subject: Science Policy
subject: 111714 Mental Health
subject: FOS: Health sciences

description: Additional file 2: Supplemental Table 2. Study outcomes of survivors of critical illness at 3 months following hospital discharge according to AKI and RRT status during index ICU admission.
Superbase/saccharide: An ecologically benign catalyst for efficient fixation of CO2 into cyclic carbonates
Creators: name: Cheng, Weiguo
name: Xu, Fei
name: Sun, Jian
name: Dong, Kun
name: Ma, Congkai
name: Zhang, Suojiang
Publisher: name: Taylor & Francis
Year: 2016
Subjects: subject: Biochemistry
subject: Evolutionary Biology
subject: FOS: Biological sciences
subject: Environmental Sciences not elsewhere classified
subject: Chemical Sciences not elsewhere classified
subject: Ecology
subject: Science Policy

description: An ecologically benign catalytic system consisting of superbase and saccharide was developed for CO2 chemical fixation with epoxides under metal-free and halide-free conditions. Because of the synergistic effect played by superbase and saccharide on the activations of CO2 and epoxide, the reaction could be performed with good activity and selectivity. A possible catalytic mechanism of the hydrogen-bonding of saccharide and activation of the carbon atom by 1,8-diazabicyclo[5.4.0]undec-7-ene (DBU) was proposed. The process is a simple, biocompatible, and ecological route for CO2 chemical fixation into high-value chemicals.
Superbase/Saccharide: An Ecological Benign Catalyst for Efficient Fixation of CO2 into Cyclic Carbonates
Creators: name: Cheng, Weiguo
name: Xu, Fei
name: Sun, Jian
name: Dong, Kun
name: Ma, Congkai
name: Zhang, Suojiang
Publisher: name: Taylor & Francis
Year: 2016
Subjects: subject: Biochemistry
subject: Evolutionary Biology
subject: FOS: Biological sciences
subject: Environmental Sciences not elsewhere classified
subject: Chemical Sciences not elsewhere classified

description: An ecological benign catalytic system consisting of superbase and saccharide was developed for CO2 chemical fixation with epoxides under metal-free and halide-free conditions. Due to the synergistic effect played by superbase and saccharide on the activations of CO2 and epoxide, the reaction could be performed with high activity and selectivity. A possible catalytic mechanism of the hydrogen-bonding of saccharide and activation of the carbon atom by DBU was proposed. The process herein represents a simple, biocompatible and ecological route for CO2 chemical fixation into high value chemicals. An ecological benign binary catalytic system consisting of superbase and saccharide was developed for CO2 chemical fixation with epoxides under metal-free and halide-free conditions.
Separation of abietane-type diterpenoids from Clerodendrum kaichianum Hsu by high-speed counter-current chromatography using stepwise elution
Creators: name: Xu, Mingfeng
name: Zhu, Qin
name: Wang, Huizhong
name: Du, Qizhen
name: Xu, Maojun
Publisher: name: Taylor & Francis
Year: 2016
Subjects: subject: Biochemistry
subject: Space Science
subject: Pharmacology
subject: Environmental Sciences not elsewhere classified
subject: Chemical Sciences not elsewhere classified
subject: Sociology
subject: FOS: Sociology
subject: Biological Sciences not elsewhere classified
subject: Science Policy
subject: Plant Biology
subject: FOS: Biological sciences

description: High-speed counter-current chromatography (HSCCC) was successfully used for the separation of abietane-type diterpenoids from the medicinal plant C. kaichianum, which were not separated in our previous study using preparative HPLC. The HSCCC separation employed the lower phases of n-hexane–ethyl acetate–methanol–water (HEMW) 4:5:4:5 and HEMW 4:5:5:4 as the mobile phase for stepwise elution while the upper phase of HEMW 4:5:4:5 was used as the stationary phase. HSCCC separation yielded 90.5 mg of compound 1(kaichianone A), 137.7 mg of compound 2 (kaichianone B), 125.0 mg of compound 3 (teuvincenone E), and 227.6 mg of compound 4 (taxusabietane A) with purities of 95.3%, 97.2%, 97.8%, and 98.6%, respectively, as determined by HPLC. Compounds 1–2 are two new abietane-type diterpenoids while Compounds 3–4 are known abietane-type diterpenoids, analyzed by ESIMS and NMR data. The results demonstrated that HSCCC can be an excellent alternative for other separation methods. The two new compounds showed significant cytotoxicity against ileocecal carcinoma HCT-8 and breast adenocarcinoma MCF-7 cells. High-speed counter-current chromatography (HSCCC) was successfully used for the separation of abietane-type diterpenoids from the medicinal plant C. kaichianum, which were not separated in our previous study using preparative HPLC.
Analysis and exploration of microbial traits in a wet coffee fermentation experiment using MGnify
Creators: name: Peña-González, Angela
name: Muñoz, Alejandro Reyes
Publisher: name: F1000 Research Limited
Year: 2022

description: This CABANA e-Learning tutorial will guide you through the use of the EMBL-EBI web server MGnify to process and analyze multiple shotgun metagenomic datasets derived from a wet coffee fermentation process at different time points.
kerr_data_readme.txt
Creators: name: Kerr, James
name: Hesselmann, Guido
Publisher: name: figshare
Year: 2017
Subjects: subject: 170110 Psychological Methodology, Design and Analysis
subject: FOS: Psychology
subject: 170112 Sensory Processes, Perception and Performance
subject: 170204 Linguistic Processes (incl. Speech Production and Comprehension)

description: Readme file for uploaded breaking continuous flash suppression data.
kerr_data_readme.txt
Creators: name: Kerr, James
Publisher: name: figshare
Year: 2017
Subjects: subject: 170110 Psychological Methodology, Design and Analysis
subject: FOS: Psychology
subject: 170112 Sensory Processes, Perception and Performance
subject: 170204 Linguistic Processes (incl. Speech Production and Comprehension)

description: Readme file for uploaded breaking continuous flash suppression data.
Electronic Supplemental Material from Flightin maintains myofilament lattice organization required for optimal flight power and courtship song quality in Drosophila
Creators: name: Chakravorty, Samya
name: Tanner, Bertrand C. W.
name: Foelber, Veronica Lee
name: Vu, Hien
name: Rosenthal, Matthew
name: Ruiz, Teresa
name: Vigoreaux, Jim O.
Publisher: name: The Royal Society
Year: 2017
Subjects: subject: Biophysics
subject: Evolutionary Biology
subject: FOS: Biological sciences
subject: 60801 Animal Behaviour

description: Supplementary Experimental Procedures, Supplemental Results, Supplemental References, Supplemental Figures
Changes in the components and biotoxicity of dissolved organic matter in a municipal wastewater reclamation reverse osmosis system
Creators: name: Sun, Ying-Xue
name: Hu, Hong-Ying
name: Shi, Chun-Zhen
name: Yang, Zhe
name: Tang, Fang
Publisher: name: Taylor & Francis
Year: 2016
Subjects: subject: Biochemistry
subject: Biotechnology
subject: Environmental Sciences not elsewhere classified
subject: Chemical Sciences not elsewhere classified
subject: Ecology
subject: FOS: Biological sciences
subject: Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Cancer
subject: Computational Biology

description: The characteristics of dissolved organic matter (DOM) and the biotoxicity of these components were investigated in a municipal wastewater reclamation reverse osmosis (mWRRO) system with a microfiltration (MF) pretreatment unit. The MF pretreatment step had little effect on the levels of dissolved organic carbon (DOC) in the secondary effluent, but the addition of chlorine before MF promoted the formation of organics with anti-estrogenic activity. The distribution of excitation emission matrix (EEM) fluorescence constituents exhibited obvious discrepancies between the secondary effluent and the reverse osmosis (RO) concentrate. Using size exclusion chromatography, DOM with low molecular weights of approximately 1.2 and 0.98 kDa was newly formed during the mWRRO. The normalized genotoxicity and anti-estrogenic activity of the RO concentrate were 32.1 ± 10.2 μg4-NQO/mgDOC and 0.36 ± 0.08 mgTAM/mgDOC, respectively, and these values were clearly higher than those of the secondary effluent and MF permeate. The florescence volume of Regions I and II in the EEM spectrum could be suggested as a surrogate for assessing the genotoxicity and anti-estrogenic activity of the RO concentrate.
Supplementary File 1 - Figures and Tables from Oca2 targeting using CRISPR/Cas9 in the Malawi cichlid Astatotilapia calliptera
Creators: name: Clark, Bethan
name: Elkin, Joel
name: Marconi, Aleksandra
name: Turner, George F.
name: Smith, Alan M.
name: Joyce, Domino
name: Miska, Eric A.
name: Juntti, Scott A.
name: Santos, M. Emília
Publisher: name: The Royal Society
Year: 2022
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: Evolutionary Biology
subject: Developmental Biology

description: File containing the supplementary figures and tables supporting the main manuscript.
Baron et al Supplementary Figure, Tables, Analyses, R code from General and species-specific impacts of a neonicotinoid insecticide on the ovary development and feeding of wild bumblebee queens
Creators: name: Baron, Gemma L.
name: Raine, Nigel E.
name: Brown, Mark J. F.
Publisher: name: The Royal Society
Year: 2017
Subjects: subject: Environmental Science
subject: Ecology
subject: FOS: Biological sciences

description: Figures showing relative size of queens who died or survived, table showing life-history traits of the sampled species, table showing collection data, statistical models, and R code used in analyses, with supporting references
Weryfikacja H2
Creators: name: Przybył, Iwona
Publisher: name: OSF Registries
Year: 2020
Subjects: Addiction
EEG
ERP
Emotions
LPP
P3a
Smartphone

description: H2: Amplituda komponenty LPP będzie wyższa w reakcji na sygnały dźwiękowe z aplikacji Facebook Messenger w grupie eksperymentalnej w porównaniu do amplitudy LPP w reakcji na sygnały informujące o przyjściu wiadomości SMS w grupie eksperymentalnej.
Sprachkompetenz(en) im Lateinunterricht - Wie lassen sich sprachliche Erfolge generieren?
Creators: name: Beyer, Andrea
Publisher: name: Zenodo
Year: 2020
Subjects: Sprechsensibler Fachunterricht
Sprachbildung im Lateinunterricht
Sprachsensibler Lateinunterricht
Kompetenzerwerb

description: The talk gives a short overview about language skills and the so-called "Sprachbildung" (language training) in Latin classes in German secondary schools. But during the talk the term "sprachsensibler Lateinunterricht" (language-sensitive Latin teaching) is preferred. In the last part of the talk, two examples of incorrect language use are given to explain the possibilities of practising language skills in Latin classes.
Table S2 Correlation matrix from Tolerance to herbivory and the resource availability hypothesis
Creators: name: Gianoli, Ernesto
name: Salgado-Luarte, Cristian
Publisher: name: The Royal Society
Year: 2017
Subjects: subject: Ecology
subject: FOS: Biological sciences
subject: Plant Biology

description: Table S2. Correlation matrix for the tree species traits included in the multiple regression analysis in the main text. Above the diagonal: correlation coefficients. Below the diagonal: p-values. Traits: RGR (relative growth rate), LSPAN (leaf lifespan), TOUGH (leaf toughness), MLR (minimum light requirement). N = 9 species (see Table S1)