cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.4488194.v1
title: PowerPoint Slides for: Effects of Daprodustat, a Novel Hypoxia-Inducible Factor Prolyl Hydroxylase Inhibitor on Anemia Management in Japanese Hemodialysis Subjects

description: <b><i>Background:</i></b> Daprodustat (GSK1278863) is an oral hypoxia-inducible factor prolyl hydroxylase inhibitor being developed for treatment of anemia associated with chronic kidney disease (CKD). The effect of daprodustat in Japanese CKD patients with anemia has not been previously investigated. <b><i>Methods:</i></b> We evaluated the relationship between daprodustat dose and hemoglobin response in Japanese patients on hemodialysis (HD) with anemia in a 4-week, phase II, double-blind, placebo-controlled study. After interrupting their erythropoiesis-stimulating agent for between 2 and 8 weeks, subjects with hemoglobin 8.5-10.5 g/dL were randomized to placebo or daprodustat 4, 6, 8, or 10 mg orally once daily. Hemoglobin, erythropoietin (EPO), and vascular endothelial growth factor (VEGF) levels during therapy were evaluated. <b><i>Results:</i></b> Eighty-six of 97 randomized subjects completed the study. Mean baseline hemoglobin ranged from 9.68 to 9.92 g/dL across groups. After 4-week administration, mean hemoglobin changes were -0.28, -0.01, 0.54, and 0.97 g/dL in the 4, 6, 8, and 10 mg groups, respectively, as compared to -1.41 g/dL for placebo. Dose-dependent increase in plasma EPO concentration were observed up to 8 mg, with the 10 mg dose responses being similar to 8 mg. Plasma VEGF concentrations were minimally changed, even though 5 subjects treated with 6-10 mg reached EPO &gt;500 mIU/mL. <b><i>Conclusion:</i></b> Daprodustat 4-10 mg once-daily produced dose-dependent increase in hemoglobin relative to placebo in Japanese HD subjects. The doses evaluated in the study have moderately increased endogenous EPO without changes in circulating VEGF levels.
DOI: 10.6084/m9.figshare.4488164
title: Supplementary Material for: The in vivo Inhibition of Oral Biofilm Accumulation and Streptococcus mutans by Ceramic Water

description: Combustion-synthesized titanium carbide ceramics uniformly disperse silver, producing silver ions and hydroxyl radicals in water. This generates antimicrobial activity against various bacteria. One such bacterium is <i>Streptococcus mutans</i>, a gram-positive anaerobic bacterium known as a major pathogen of dental caries. In this study, we analyzed the inhibition of oral biofilms and <i>S. mutans</i> by ceramic water in in vitro and human studies. <i>S. mutans</i> strains showed significantly lower antimicrobial and sucrose-dependent adhesion activity in the presence of ceramic powder compared with untreated culture medium. Confocal microscopy revealed that <i>S. mutans</i> biofilm structures with ceramic powder were thin and coarse. Twenty-seven volunteers (13 males, 14 females; 18-37 years old, mean 25.2 years) were enrolled for subsequent studies. After each meal, one group was asked to rinse with ceramic water while the other rinsed with untreated water for 1 week. After 1 week, the rinsing contents were switched between the groups and the same protocol was followed for an additional week. After rinsing with ceramic water, the average plaque score was 43.0 ± 3.7, which was significantly lower than the baseline value (74.1 ± 5.7, <i>p </i>&lt; 0.001). However, no significant difference was observed when rinsing with untreated water. In addition, the total number of <i>S. mutans</i> in saliva was significantly reduced after rinsing with ceramic water compared with untreated water (<i>p </i>&lt; 0.05). These results suggest that ceramic water possesses antimicrobial activity against <i>S. mutans</i> and inhibits biofilm formation. Rinsing with ceramic water can also inhibit dental plaque formation and <i>S. mutans</i> colonization in humans.
DOI: 10.6084/m9.figshare.4488191.v1
title: Supplementary Material for: Meta-Analysis for Penalized Regression Methods with Multi-Cohort Genome-Wide Association Studies

description: <strong><em>Objective:</em></strong> Penalized regression has been successfully applied in genome-wide association studies. While meta-analysis is often conducted to increase power and protect patients' confidentiality, methods for meta-analyzing results of penalized regression in multi-cohort setting are still under development. <b><i>Methods:</i></b> We propose to use a data-splitting method to obtain valid p values (or equivalently, coefficient estimates and standard errors) for meta-analysis across multiple cohorts. We examine two ways of splitting data in multi-cohort setting and propose three methods to conduct meta-analysis based on p values. We compare the three meta-analysis methods to mega-analysis, which consists of pooling individual level data. We also apply our proposed meta-analysis approaches to the Framingham Heart Study data, where we divide the original dataset into four parts to create a multi-cohort scenario. <b><i>Results:</i></b> The simulations suggest that splitting cohorts has better performance than splitting data within each cohort. The real data application also shows that this method provides results that are similar to the mega-analysis. <b><i>Conclusion:</i></b> After comparing the three methods that we proposed to conduct meta-analysis, we recommend splitting cohorts rather than datasets to obtain valid p values for meta-analysis of results from penalized regression in multi-cohort setting.
DOI: 10.6084/m9.figshare.4488140
title: Supplementary Material for: Associations of Serum Osteocalcin and Polymorphisms of the Osteocalcin Gene with Bone Mineral Density in Postmenopausal and Elderly Chinese Women

description: <b><i>Background:</i></b> The aims of this study were: (1) to evaluate the association of serum osteocalcin with bone mineral density (BMD) and markers of bone metabolism in postmenopausal and elderly Chinese women, and (2) to observe the relationships of single-nucleotide polymorphisms (SNPs) in and around the <i>osteocalcin</i> gene with osteocalcin and BMD. <b><i>Methods:</i></b> A cross-sectional study was conducted with 725 postmenopausal Chinese women. Five SNPs (rs1543294, rs1800247, rs759330, rs2842880, and rs933489) of the <i>osteocalcin</i> gene were genotyped. Serum osteocalcin and intact parathyroid hormone (PTH), 25-hydroxyvitamin D [25(OH)D], and type I collagen containing cross-linked C-telopeptide (β-CTX) were measured. The BMD of the lumbar spine and proximal femur was measured by dual-energy X-ray absorptiometry. <b><i>Results:</i></b> Osteocalcin was positively correlated with serum phosphorus (<i>p</i> = 0.001), alkaline phosphatase (ALP; <i>p</i> &lt; 0.001), PTH (<i>p</i> = 0.002) and β-CTX (<i>p</i> &lt; 0.001), and negatively correlated with BMD at the lumbar spine (<i>p</i> &lt; 0.001) and total hip (<i>p</i> = 0.002). No significant association was obtained between the SNPs, haplotypes of the <i>osteocalcin</i> gene, and BMD or osteocalcin. <b><i>Conclusion:</i></b> Our results suggest that osteocalcin was positively correlated with serum phosphorus, ALP, PTH, and β-CTX, but negatively correlated with BMD at the lumbar spine and total hip. Common genetic variants of the <i>osteocalcin</i> gene may not be a major contributor to variations in serum osteocalcin or BMD in postmenopausal and elderly Chinese women.
DOI: 10.6084/m9.figshare.4488149
title: Code, recordings, validations and Regions of interest

description: Here is the code as well as the the recordings, validations and regions of interest used for the development of the experiment presented in the journal article "Species-specific audio detection: A comparison of three template-based classification algorithms using random forests".
DOI: 10.6084/m9.figshare.4488128
title: Supplementary Material for: Cortical Actin Alteration at the Matrix-Side Cytoplasm in Lung Adenocarcinoma Cells and Its Significance in Invasion

description: <b><i>Objectives:</i></b> Cortical actin is a thin layer of filamentous (F-)actin that lies beneath the plasma membrane, and its role in pathophysiology remains unclear. We investigated the subcellular localization of cortical actin by the histopathological and experimental studies of lung adenocarcinomas. <b><i>Materials and Methods:</i></b> The subcellular localization of cortical actin was studied in surgically resected lung adenocarcinomas tissues and in 3-dimensionally cultured lung adenocarcinoma A549 cells. <b><i>Results:</i></b> In normal type II alveolar cells and the bronchiolar epithelium, cortical actin was localized to the apical-side cytoplasm. In invasive adenocarcinoma cells, cortical actin was frequently localized to the matrix side. The degree of cortical actin localized to the matrix side was associated with the loss of basement membrane and a poor prognosis. In A549 cell spheroids cultured in a type I collagen and basement membrane extract Matrigel™ mixed gel, cortical F-actin was localized to the matrix side with phosphorylated myosin light chain. Super-resolution and electron microscopy results suggest that compact wrinkling of the plasma membrane by myosin-mediated F-actin contraction is an explanation for cortical actin accumulation at the matrix side. The myosin II inhibitor blebbistatin suppressed the 3-dimensional collective migration of A549 cells induced by constitutively active Cdc42 and MT1-MMP. <b><i>Conclusion:</i></b> Cortical actin accumulation at the matrix-side cytoplasm of cancer cells occurs in invasive lung adenocarcinomas and it possibly participates in the migration of cancer cells through myosin-mediated contraction.
DOI: 10.6084/m9.figshare.4488020
title: myData.rar

description: This are medical datasets that are from the UCI machine learning database and some datasets are normalized into the interval [0, 1].
DOI: 10.6084/m9.figshare.4488128.v1
title: Supplementary Material for: Cortical Actin Alteration at the Matrix-Side Cytoplasm in Lung Adenocarcinoma Cells and Its Significance in Invasion

description: <b><i>Objectives:</i></b> Cortical actin is a thin layer of filamentous (F-)actin that lies beneath the plasma membrane, and its role in pathophysiology remains unclear. We investigated the subcellular localization of cortical actin by the histopathological and experimental studies of lung adenocarcinomas. <b><i>Materials and Methods:</i></b> The subcellular localization of cortical actin was studied in surgically resected lung adenocarcinomas tissues and in 3-dimensionally cultured lung adenocarcinoma A549 cells. <b><i>Results:</i></b> In normal type II alveolar cells and the bronchiolar epithelium, cortical actin was localized to the apical-side cytoplasm. In invasive adenocarcinoma cells, cortical actin was frequently localized to the matrix side. The degree of cortical actin localized to the matrix side was associated with the loss of basement membrane and a poor prognosis. In A549 cell spheroids cultured in a type I collagen and basement membrane extract Matrigel™ mixed gel, cortical F-actin was localized to the matrix side with phosphorylated myosin light chain. Super-resolution and electron microscopy results suggest that compact wrinkling of the plasma membrane by myosin-mediated F-actin contraction is an explanation for cortical actin accumulation at the matrix side. The myosin II inhibitor blebbistatin suppressed the 3-dimensional collective migration of A549 cells induced by constitutively active Cdc42 and MT1-MMP. <b><i>Conclusion:</i></b> Cortical actin accumulation at the matrix-side cytoplasm of cancer cells occurs in invasive lung adenocarcinomas and it possibly participates in the migration of cancer cells through myosin-mediated contraction.
DOI: 10.6084/m9.figshare.4487939
title: A3500

description: A replicate dataset based on the A3130 sample set. DNA isolates were re-processed in the same lab as the original samples using a different machine (ABI 3500 Genetic Analyzer).<br>The RData object has two attributes: data - holds the count data of OTU abundances. Rows are samples and columns are OTUs.labels - a corresponding label for each sample in data.
DOI: 10.6084/m9.figshare.4487966
title: M3500

description: A replicate dataset based on the A3130 sample set. The DNA isolates were re-processed in a different lab than the original samples using a different machine (ABI 3500 Genetic Analyzer).<br>The RData object has two attributes: data - holds the count data of OTU abundances. Rows are samples and columns are OTUs.labels - a corresponding label for each sample in data.
DOI: 10.6084/m9.figshare.4487930
title: SIM

description: This is a large synthetic dataset (n=10,000), generated using a Gaussian mixture model based on the A3130 sample set.<br>The RData object has two attributes: data - holds the count data of OTU abundances. Rows are samples and columns are OTUs.labels - a corresponding label for each sample in data.<br>
DOI: 10.6084/m9.figshare.4487939.v1
title: A3500

description: A replicate dataset based on the A3130 sample set. DNA isolates were re-processed in the same lab as the original samples using a different machine (ABI 3500 Genetic Analyzer).<br>The RData object has two attributes: data - holds the count data of OTU abundances. Rows are samples and columns are OTUs.labels - a corresponding label for each sample in data.
DOI: 10.6084/m9.figshare.4487966.v1
title: M3500

description: A replicate dataset based on the A3130 sample set. The DNA isolates were re-processed in a different lab than the original samples using a different machine (ABI 3500 Genetic Analyzer).<br>The RData object has two attributes: data - holds the count data of OTU abundances. Rows are samples and columns are OTUs.labels - a corresponding label for each sample in data.
DOI: 10.6084/m9.figshare.4487924
title: A3130

description: The original dataset. A cohort of 149 individuals (58 healthy children, 91 pediatric IBD patients). This sample set was processed and analyzed in Amsterdam, the Netherlands, using an ABI PRISM 3130 Genetic Analyzer.The RData object has two attributes: data - holds the count data of OTU abundances. Rows are samples and columns are OTUs; labels - holds a corresponding label for each sample in data.
DOI: 10.6084/m9.figshare.4487930.v1
title: SIM

description: This is a large synthetic dataset (n=10,000), generated using a Gaussian mixture model based on the A3130 sample set.<br>The RData object has two attributes: data - holds the count data of OTU abundances. Rows are samples and columns are OTUs.labels - a corresponding label for each sample in data.<br>
DOI: 10.6084/m9.figshare.4487924.v1
title: A3130

description: The original dataset. A cohort of 149 individuals (58 healthy children, 91 pediatric IBD patients). This sample set was processed and analyzed in Amsterdam, the Netherlands, using an ABI PRISM 3130 Genetic Analyzer.The RData object has two attributes: data - holds the count data of OTU abundances. Rows are samples and columns are OTUs; labels - holds a corresponding label for each sample in data.
DOI: 10.6084/m9.figshare.4487834
title: Putative orthologs and conversion lists from Caste-biased gene expression in a facultatively eusocial bee suggests a role for genetic accommodation in the evolution of eusociality

description: BLAST reciprocal best hit results between <i>Megalopta genalis</i> and <i>Apis mellifera</i>, as well as between <i>M. genalis</i> and <i>Bombus terrestris</i>. Conversion lists used to translate between two <i>A. mellifera</i> microarrays, an older (OGSv2.0) and current (OGSv3.2) annotation of the honey bee genome are also provided.
DOI: 10.6084/m9.figshare.4487831
title: Sample information from Caste-biased gene expression in a facultatively eusocial bee suggests a role for genetic accommodation in the evolution of eusociality

description: Information for each sample, including sample ID, caste, tissue, emergence and collection dates, age, head width and ovary information.
DOI: 10.6084/m9.figshare.4487834.v1
title: Putative orthologs and conversion lists from Caste-biased gene expression in a facultatively eusocial bee suggests a role for genetic accommodation in the evolution of eusociality

description: BLAST reciprocal best hit results between <i>Megalopta genalis</i> and <i>Apis mellifera</i>, as well as between <i>M. genalis</i> and <i>Bombus terrestris</i>. Conversion lists used to translate between two <i>A. mellifera</i> microarrays, an older (OGSv2.0) and current (OGSv3.2) annotation of the honey bee genome are also provided.
DOI: 10.6084/m9.figshare.4487828
title: Overlapping gene lists and representation factor results for gene expression studies from Caste-biased gene expression in a facultatively eusocial bee suggests a role for genetic accommodation in the evolution of eusociality

description: For each study comparison, gene lists are provided for the study, the shared universe between studies, as well as direction-specific lists for each comparison. Also provided are the numbers of overlapping genes, the representation factor, and the p-value for each test.
DOI: 10.6084/m9.figshare.4487822
title: Gene expression results from Caste-biased gene expression in a facultatively eusocial bee suggests a role for genetic accommodation in the evolution of eusociality

description: For each tissue, logFC and FDR-corrected p-values are given for each pairwise comparison of groups for all <i>Megalopta genalis</i> contigs expressed in the tissue. Along with contig ID, putative orthologs to <i>Apis mellifera</i> and <i>Bombus terrestris</i> based on BLAST reciprocal best hits and PANTHER annotations are provided.
DOI: 10.6084/m9.figshare.4487831.v1
title: Sample information from Caste-biased gene expression in a facultatively eusocial bee suggests a role for genetic accommodation in the evolution of eusociality

description: Information for each sample, including sample ID, caste, tissue, emergence and collection dates, age, head width and ovary information.
DOI: 10.6084/m9.figshare.4487828.v1
title: Overlapping gene lists and representation factor results for gene expression studies from Caste-biased gene expression in a facultatively eusocial bee suggests a role for genetic accommodation in the evolution of eusociality

description: For each study comparison, gene lists are provided for the study, the shared universe between studies, as well as direction-specific lists for each comparison. Also provided are the numbers of overlapping genes, the representation factor, and the p-value for each test.
DOI: 10.6084/m9.figshare.4487822.v1
title: Gene expression results from Caste-biased gene expression in a facultatively eusocial bee suggests a role for genetic accommodation in the evolution of eusociality

description: For each tissue, logFC and FDR-corrected p-values are given for each pairwise comparison of groups for all <i>Megalopta genalis</i> contigs expressed in the tissue. Along with contig ID, putative orthologs to <i>Apis mellifera</i> and <i>Bombus terrestris</i> based on BLAST reciprocal best hits and PANTHER annotations are provided.
DOI: 10.6084/m9.figshare.4487813
title: Results Tables from Here and there, but not everywhere: repeated loss of <i>uncoupling protein 1</i> in amniotes

description: An excel document with 30 supplmental tables (one per tab). The first tab lists the titles and legends of the tables.
DOI: 10.6084/m9.figshare.4487810
title: Gene Ontology enrichment results from Caste-biased gene expression in a facultatively eusocial bee suggests a role for genetic accommodation in the evolution of eusociality

description: PANTHER pathways and GO-Slim Biological Processes overrepresented in DEGs for each pairwise comparison of groups. Only categories with a Bonferroni-corrected p-value of less than 0.05 are shown. In addition to pairwise lists, results from the comparison between workers and long-term reproductive groups (queens and solitary reproductive females) as shown in Figure 2 are given.
DOI: 10.6084/m9.figshare.4487810.v1
title: Gene Ontology enrichment results from Caste-biased gene expression in a facultatively eusocial bee suggests a role for genetic accommodation in the evolution of eusociality

description: PANTHER pathways and GO-Slim Biological Processes overrepresented in DEGs for each pairwise comparison of groups. Only categories with a Bonferroni-corrected p-value of less than 0.05 are shown. In addition to pairwise lists, results from the comparison between workers and long-term reproductive groups (queens and solitary reproductive females) as shown in Figure 2 are given.
DOI: 10.6084/m9.figshare.4487813.v1
title: Results Tables from Here and there, but not everywhere: repeated loss of <i>uncoupling protein 1</i> in amniotes

description: An excel document with 30 supplmental tables (one per tab). The first tab lists the titles and legends of the tables.
DOI: 10.6084/m9.figshare.4487792
title: Overlapping gene lists and representation factor results for selection studies from Caste-biased gene expression in a facultatively eusocial bee suggests a role for genetic accommodation in the evolution of eusociality

description: For each study comparison, gene lists are provided for the study, the shared universe between studies, and the overlapping gene lists. Also provided are the numbers of overlapping genes, the representation factor, and the p-value for each test.
DOI: 10.6084/m9.figshare.4487774
title: Allelic variation in dopamine D2 receptor gene is associated with attentional impulsiveness on the Barratt Impulsiveness Scale (BIS-11)

description: <b>Objectives:</b> Previous studies have postulated that noradrenergic and/or dopaminergic gene variations are likely to underlie individual differences in impulsiveness, however, few have shown this. The current study examined the relationship between catecholamine gene variants and self-reported impulsivity, as measured by the Barratt Impulsiveness Scale (Version 11; BIS-11) <b>Methods:</b> Six hundred and seventy-seven non-clinical adults completed the Barratt Impulsiveness Scale (BIS-11). DNA was analysed for a set of 142 single-nucleotide polymorphisms (SNPs) across 20 autosomal catecholamine genes. Association was tested using an additive regression model with permutation testing used to control for the influence of multiple comparison. <b>Results:</b> Analysis revealed an influence of rs4245146 of the dopamine D2 receptor (DRD2) gene on the BIS-11 attention first-order factor, such that self-reported attentional impulsiveness increased in an additive fashion with each copy of the T allele. <b>Conclusions:</b> These findings provide preliminary evidence that allelic variation in DRD2 may influence impulsiveness by increasing the propensity for attentional lapses.
DOI: 10.6084/m9.figshare.4487792.v1
title: Overlapping gene lists and representation factor results for selection studies from Caste-biased gene expression in a facultatively eusocial bee suggests a role for genetic accommodation in the evolution of eusociality

description: For each study comparison, gene lists are provided for the study, the shared universe between studies, and the overlapping gene lists. Also provided are the numbers of overlapping genes, the representation factor, and the p-value for each test.