cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7604291.v1
title: Additional file 1: of Association between the insulin-like growth factor 1 gene rs2195239 and rs2162679 polymorphisms and cancer risk: a meta-analysis

description: Table S1. Quality score assessment. Table S2. Sensitivity analyses for rs2195239 and rs2162679 polymorphisms and cancer risk. Table S3. MAFs of rs2195239 (genomic position: chromosome12: 102462924) and rs2162679 (genomic position: Chromosome12: 102477481) and polymorphisms in the populations from the 1000 Genomes Project Phase 3. Table S4. Meta-analysis of the association between rs2195239 polymorphism and cancer risk, omitting the study of Patel or Birmann. Table S5. The OMIM numbers for important genes and pathogenic conditions in this study. Figure S1. Linkage disequilibrium analyses for IGF1 rs2195239 and rs2162679 polymorphisms in populations from the 1000 Genomes Project Phase 3. (ZIP 1155 kb)
DOI: 10.6084/m9.figshare.8128586
title: Additional file 11: of Genome-wide identification of MST, SUT and SWEET family sugar transporters in root parasitic angiosperms and analysis of their expression during host parasitism

description: MEME motifs and their associations with plants studied. These associations were determined by finding the genes that contain a given motif. This was done for (A) MSTs, (B) SUTs, and (C) SWEETs. The plant species with which motifs are most strongly associated was determined by finding the plant with the highest raw number of occurrences of the motif, as well as the representation of that motif as a percentage of instances of that motif in the MST, SUT or SWEEET family. (XLSX 33 kb)
DOI: 10.6084/m9.figshare.8128586.v1
title: Additional file 11: of Genome-wide identification of MST, SUT and SWEET family sugar transporters in root parasitic angiosperms and analysis of their expression during host parasitism

description: MEME motifs and their associations with plants studied. These associations were determined by finding the genes that contain a given motif. This was done for (A) MSTs, (B) SUTs, and (C) SWEETs. The plant species with which motifs are most strongly associated was determined by finding the plant with the highest raw number of occurrences of the motif, as well as the representation of that motif as a percentage of instances of that motif in the MST, SUT or SWEEET family. (XLSX 33 kb)
DOI: 10.34740/kaggle/dsv/7629252
title: OnlineFree
DOI: 10.6084/m9.figshare.8128595
title: Additional file 12: of Genome-wide identification of MST, SUT and SWEET family sugar transporters in root parasitic angiosperms and analysis of their expression during host parasitism

description: MEME motifs and their associations with clades of MSTs, SUTs or SWEETs. These associations were determined by finding which genes to which these motifs belonged, and determined the clade in which these genes belonged. This was done for (A) MSTs, (B) SUTs, and (C) SWEETs. The clade with which motifs are most strongly associated was determined by finding the clade with the highest raw number of occurrences of the motif in that stage, as well as the representation of that motif as a percentage of motifs present in genes that showed strongest expression during that clade. In addition, MEME motifs unique to MST, SUT or SWEET clades were found and counted. (XLSX 43 kb)
DOI: 10.34740/kaggle/dsv/7629250
title: AutoXGB
DOI: 10.6084/m9.figshare.8128595.v1
title: Additional file 12: of Genome-wide identification of MST, SUT and SWEET family sugar transporters in root parasitic angiosperms and analysis of their expression during host parasitism

description: MEME motifs and their associations with clades of MSTs, SUTs or SWEETs. These associations were determined by finding which genes to which these motifs belonged, and determined the clade in which these genes belonged. This was done for (A) MSTs, (B) SUTs, and (C) SWEETs. The clade with which motifs are most strongly associated was determined by finding the clade with the highest raw number of occurrences of the motif in that stage, as well as the representation of that motif as a percentage of motifs present in genes that showed strongest expression during that clade. In addition, MEME motifs unique to MST, SUT or SWEET clades were found and counted. (XLSX 43 kb)
DOI: 10.6084/m9.figshare.8128601
title: Additional file 13: of Genome-wide identification of MST, SUT and SWEET family sugar transporters in root parasitic angiosperms and analysis of their expression during host parasitism

description: MEME motifs in the (A) MST, (B) SUT and (C) SWEET families of sugar transporters. For each motif, the stage in which the genes containing these motifs express most strongly is shown, as well as the plant and clade in which genes containing these motifs are most commonly found, and the consensus sequence for each motif. (XLSX 24 kb)
DOI: 10.6084/m9.figshare.8128601.v1
title: Additional file 13: of Genome-wide identification of MST, SUT and SWEET family sugar transporters in root parasitic angiosperms and analysis of their expression during host parasitism

description: MEME motifs in the (A) MST, (B) SUT and (C) SWEET families of sugar transporters. For each motif, the stage in which the genes containing these motifs express most strongly is shown, as well as the plant and clade in which genes containing these motifs are most commonly found, and the consensus sequence for each motif. (XLSX 24 kb)
DOI: 10.6084/m9.figshare.8128607
title: Additional file 14: of Genome-wide identification of MST, SUT and SWEET family sugar transporters in root parasitic angiosperms and analysis of their expression during host parasitism

description: Orthogroups in each stage of three Orobanchaceae life cycles. The data suggest different orthogroups being expressed in a variety of stages throughout the life cycle, especially in the MST family. (XLSX 21 kb)
DOI: 10.6084/m9.figshare.8128607.v1
title: Additional file 14: of Genome-wide identification of MST, SUT and SWEET family sugar transporters in root parasitic angiosperms and analysis of their expression during host parasitism

description: Orthogroups in each stage of three Orobanchaceae life cycles. The data suggest different orthogroups being expressed in a variety of stages throughout the life cycle, especially in the MST family. (XLSX 21 kb)
DOI: 10.6084/m9.figshare.8128619
title: Additional file 15: of Genome-wide identification of MST, SUT and SWEET family sugar transporters in root parasitic angiosperms and analysis of their expression during host parasitism

description: The species to which orthogroups are most frequently associated. Note the differences between the raw number of members in a certain orthogroup versus the percentage of sequences from a species that are members of that orthogroup. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.8128619.v1
title: Additional file 15: of Genome-wide identification of MST, SUT and SWEET family sugar transporters in root parasitic angiosperms and analysis of their expression during host parasitism

description: The species to which orthogroups are most frequently associated. Note the differences between the raw number of members in a certain orthogroup versus the percentage of sequences from a species that are members of that orthogroup. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.8128628
title: Additional file 16: of Genome-wide identification of MST, SUT and SWEET family sugar transporters in root parasitic angiosperms and analysis of their expression during host parasitism

description: The clades with which each orthogroup is most strongly associated. These orthogroups were identified in the A) MST, B) SUT and C) SWEET families. Note that many sugar transporter clades have at least one orthogroup that is unique to them. In the SUT family, one orthogroup has all SUT1 and SUT4 sequences studied as members. (XLSX 14 kb)
DOI: 10.6084/m9.figshare.8128628.v1
title: Additional file 16: of Genome-wide identification of MST, SUT and SWEET family sugar transporters in root parasitic angiosperms and analysis of their expression during host parasitism

description: The clades with which each orthogroup is most strongly associated. These orthogroups were identified in the A) MST, B) SUT and C) SWEET families. Note that many sugar transporter clades have at least one orthogroup that is unique to them. In the SUT family, one orthogroup has all SUT1 and SUT4 sequences studied as members. (XLSX 14 kb)
DOI: 10.6084/m9.figshare.8128634
title: Additional file 17: of Genome-wide identification of MST, SUT and SWEET family sugar transporters in root parasitic angiosperms and analysis of their expression during host parasitism

description: Every sugar transporter gene, their strongest stage of expression, clade and orthogroup. The clade, stage of strongest expression and orthogroup are listed for genes in the A) MST, B) SUT and C) SWEET families. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.8128634.v1
title: Additional file 17: of Genome-wide identification of MST, SUT and SWEET family sugar transporters in root parasitic angiosperms and analysis of their expression during host parasitism

description: Every sugar transporter gene, their strongest stage of expression, clade and orthogroup. The clade, stage of strongest expression and orthogroup are listed for genes in the A) MST, B) SUT and C) SWEET families. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.8128640
title: Additional file 18: of Genome-wide identification of MST, SUT and SWEET family sugar transporters in root parasitic angiosperms and analysis of their expression during host parasitism

description: The names of the genes on the phylogenetic trees, and their FASTA file aliases. The names as they appear in Figs. 1, 2, 3, 4 and 5 and in Additional files 1, 2, 3, 4, 5 and 7, 8, 9 are shorthand labels that show the species (e.g., Striga hermonthica is shortened to StHe), the clade, and an arbitrarily given number. (XLSX 17 kb)
DOI: 10.6084/m9.figshare.8128640.v1
title: Additional file 18: of Genome-wide identification of MST, SUT and SWEET family sugar transporters in root parasitic angiosperms and analysis of their expression during host parasitism

description: The names of the genes on the phylogenetic trees, and their FASTA file aliases. The names as they appear in Figs. 1, 2, 3, 4 and 5 and in Additional files 1, 2, 3, 4, 5 and 7, 8, 9 are shorthand labels that show the species (e.g., Striga hermonthica is shortened to StHe), the clade, and an arbitrarily given number. (XLSX 17 kb)
DOI: 10.6084/m9.figshare.17041564
title: Multiple Imputation Inference with Integer-Valued Point Estimates

description: We consider settings where an analyst of multiply imputed data desires an integer-valued point estimate and an associated interval estimate, for example, a count of the number of individuals with certain characteristics in a population. Even when the point estimate in each completed dataset is an integer, the multiple imputation point estimator, that is, the average of these completed-data estimators, is not guaranteed to be an integer. One natural approach is to round the standard multiple imputation point estimator to an integer. Another seemingly natural approach is to use the median of the completed-data point estimates (when they are integers). However, these two approaches have not been compared; indeed, methods for obtaining multiple imputation inferences associated with the median of the completed-data point estimates do not even exist. In this article, we evaluate and compare these two approaches. In doing so, we derive an estimator of the variance of the median-based multiple imputation point estimator, as well as a method for obtaining associated multiple imputation confidence intervals. Using simulation studies, we show that both methods can offer well-calibrated coverage rates and have similar repeated sampling properties, and hence are both useful for this analysis task.
DOI: 10.6084/m9.figshare.17041564.v1
title: Multiple Imputation Inference with Integer-Valued Point Estimates

description: We consider settings where an analyst of multiply imputed data desires an integer-valued point estimate and an associated interval estimate, for example, a count of the number of individuals with certain characteristics in a population. Even when the point estimate in each completed dataset is an integer, the multiple imputation point estimator, that is, the average of these completed-data estimators, is not guaranteed to be an integer. One natural approach is to round the standard multiple imputation point estimator to an integer. Another seemingly natural approach is to use the median of the completed-data point estimates (when they are integers). However, these two approaches have not been compared; indeed, methods for obtaining multiple imputation inferences associated with the median of the completed-data point estimates do not even exist. In this article, we evaluate and compare these two approaches. In doing so, we derive an estimator of the variance of the median-based multiple imputation point estimator, as well as a method for obtaining associated multiple imputation confidence intervals. Using simulation studies, we show that both methods can offer well-calibrated coverage rates and have similar repeated sampling properties, and hence are both useful for this analysis task.
DOI: 10.6084/m9.figshare.7604396
title: Additional file 1: of iGUIDE: an improved pipeline for analyzing CRISPR cleavage specificity

description: Table S1. Methods for mapping sites of new DNA cleavage based on incorporation of new DNAs. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.7604396.v1
title: Additional file 1: of iGUIDE: an improved pipeline for analyzing CRISPR cleavage specificity

description: Table S1. Methods for mapping sites of new DNA cleavage based on incorporation of new DNAs. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.7604399
title: Additional file 1: of Low-temperature-induced changes in the transcriptome reveal a major role of CgSVP genes in regulating flowering of Cymbidium goeringii

description: Table S1. The primers used for Realtime RT-PCR. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.7604399.v1
title: Additional file 1: of Low-temperature-induced changes in the transcriptome reveal a major role of CgSVP genes in regulating flowering of Cymbidium goeringii

description: Table S1. The primers used for Realtime RT-PCR. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.8128685
title: Additional file 6: of Genome-wide identification of MST, SUT and SWEET family sugar transporters in root parasitic angiosperms and analysis of their expression during host parasitism

description: Numbers of sugar transporters and their stages of strongest expression in Phelipanche aegyptiaca. The stages of strongest expression are shown for each clade of MSTs, SUTs and SWEETs, as well as for all MSTs, SUTs and SWEETs, in the transcriptomes of P. aegyptiaca, S. hermonthica, T. versicolor. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.8128685.v1
title: Additional file 6: of Genome-wide identification of MST, SUT and SWEET family sugar transporters in root parasitic angiosperms and analysis of their expression during host parasitism

description: Numbers of sugar transporters and their stages of strongest expression in Phelipanche aegyptiaca. The stages of strongest expression are shown for each clade of MSTs, SUTs and SWEETs, as well as for all MSTs, SUTs and SWEETs, in the transcriptomes of P. aegyptiaca, S. hermonthica, T. versicolor. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.7604405
title: Additional file 2: of iGUIDE: an improved pipeline for analyzing CRISPR cleavage specificity

description: Table S2. Oligonucleotides used in this study. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.7604411
title: Additional file 2: of Low-temperature-induced changes in the transcriptome reveal a major role of CgSVP genes in regulating flowering of Cymbidium goeringii

description: Table S2. List of gene ID and transcript fold changes of the all DEGs (differentially expressed genes). (XLSX 47 kb)
DOI: 10.6084/m9.figshare.7604411.v1
title: Additional file 2: of Low-temperature-induced changes in the transcriptome reveal a major role of CgSVP genes in regulating flowering of Cymbidium goeringii

description: Table S2. List of gene ID and transcript fold changes of the all DEGs (differentially expressed genes). (XLSX 47 kb)
DOI: 10.6084/m9.figshare.7604414
title: Additional file 3: of iGUIDE: an improved pipeline for analyzing CRISPR cleavage specificity

description: Table S3. Evidence for mispriming: sequence reads recovered from control reactions containing DNA from T cells that were not treated with the double-stranded oligonucleotide (ODN). We note that additional mispriming events in cells that were transfected with the ODN may have a different character. Inspection of data suggests formation of chimeric PCR products, probably involving DNA chains amplified by priming on the ODN initially, which go on to form complex molecules that under some circumstances map in a fashion paralleling simple mispriming. The iGUIDE method filters out many of these more complex artifacts as well. (XLS 21 kb)
DOI: 10.6084/m9.figshare.7604414.v1
title: Additional file 3: of iGUIDE: an improved pipeline for analyzing CRISPR cleavage specificity

description: Table S3. Evidence for mispriming: sequence reads recovered from control reactions containing DNA from T cells that were not treated with the double-stranded oligonucleotide (ODN). We note that additional mispriming events in cells that were transfected with the ODN may have a different character. Inspection of data suggests formation of chimeric PCR products, probably involving DNA chains amplified by priming on the ODN initially, which go on to form complex molecules that under some circumstances map in a fashion paralleling simple mispriming. The iGUIDE method filters out many of these more complex artifacts as well. (XLS 21 kb)
DOI: 10.6084/m9.figshare.7604417
title: Additional file 3: of Low-temperature-induced changes in the transcriptome reveal a major role of CgSVP genes in regulating flowering of Cymbidium goeringii

description: Table S3. Details of the pathway annotations for the DEGs by KEGG. (XLSX 18 kb)
DOI: 10.6084/m9.figshare.7604417.v1
title: Additional file 3: of Low-temperature-induced changes in the transcriptome reveal a major role of CgSVP genes in regulating flowering of Cymbidium goeringii

description: Table S3. Details of the pathway annotations for the DEGs by KEGG. (XLSX 18 kb)
DOI: 10.6084/m9.figshare.7604423
title: Additional file 4: of Low-temperature-induced changes in the transcriptome reveal a major role of CgSVP genes in regulating flowering of Cymbidium goeringii

description: Table S4. Function annotations of the DEGs after cold treatment. (XLSX 39 kb)
DOI: 10.6084/m9.figshare.7604423.v1
title: Additional file 4: of Low-temperature-induced changes in the transcriptome reveal a major role of CgSVP genes in regulating flowering of Cymbidium goeringii

description: Table S4. Function annotations of the DEGs after cold treatment. (XLSX 39 kb)
DOI: 10.6084/m9.figshare.11274467
title: Melatonin attenuates nicotine-induced autophagy and neurological changes by decreasing the production of reactive oxygen species

description: <b>Purpose:</b> The aim of this study was to explore the mechanism of neurological changes underlying the toxicity of nicotine. <b>Materials and methods:</b> Rat pheochromocytoma 12 (PC12) cells and human neuroglia (HM) cells were used. The ROS levels of the cells were detected by the FACScan. Autophagy flux was monitored by a tandem monomeric RFP-GFP-tagged LC3 lentivirus. The autophagic proteins LC3, SQSTM1/p62 and Beclin1 were detected by western blot assay. In order to evaluate the effects of nicotine and melatonin on the morphological changes of neurons, primary cortical neurons were obtained and immunocytochemistry of TUBB3 tubulin were conducted. <b>Results:</b> Nicotine increased the levels of reactive oxygen species (ROS) in PC12 and HM cells in a concentration-dependent manner. Microscopy showed increased autophagic flux in nicotine-treated PC12 cells. Subsequent western blotting results showed that nicotine induced increase in the levels of LC3B-II and Beclin1, and decreased SQSTM1/p62 in a concentration-dependent manner. Finally, nicotine treatment reduced the length of TUBB3-positive axons and dendrites. Melatonin, a mitochondrially targeted antioxidant, reduced the ROS level, and blocked autophagy activation and the morphologic structural changes induced by nicotine. <b>Conclusions:</b> Our results suggested that the role of nicotine in neuronal toxicity maybe through the induction of ROS and the subsequent activation of autophagy. These effects could be restored by melatonin.
DOI: 10.6084/m9.figshare.11274467.v1
title: Melatonin attenuates nicotine-induced autophagy and neurological changes by decreasing the production of reactive oxygen species

description: <b>Purpose:</b> The aim of this study was to explore the mechanism of neurological changes underlying the toxicity of nicotine. <b>Materials and methods:</b> Rat pheochromocytoma 12 (PC12) cells and human neuroglia (HM) cells were used. The ROS levels of the cells were detected by the FACScan. Autophagy flux was monitored by a tandem monomeric RFP-GFP-tagged LC3 lentivirus. The autophagic proteins LC3, SQSTM1/p62 and Beclin1 were detected by western blot assay. In order to evaluate the effects of nicotine and melatonin on the morphological changes of neurons, primary cortical neurons were obtained and immunocytochemistry of TUBB3 tubulin were conducted. <b>Results:</b> Nicotine increased the levels of reactive oxygen species (ROS) in PC12 and HM cells in a concentration-dependent manner. Microscopy showed increased autophagic flux in nicotine-treated PC12 cells. Subsequent western blotting results showed that nicotine induced increase in the levels of LC3B-II and Beclin1, and decreased SQSTM1/p62 in a concentration-dependent manner. Finally, nicotine treatment reduced the length of TUBB3-positive axons and dendrites. Melatonin, a mitochondrially targeted antioxidant, reduced the ROS level, and blocked autophagy activation and the morphologic structural changes induced by nicotine. <b>Conclusions:</b> Our results suggested that the role of nicotine in neuronal toxicity maybe through the induction of ROS and the subsequent activation of autophagy. These effects could be restored by melatonin.
DOI: 10.6084/m9.figshare.17041641
title: Effects of whole grain intake on glycemic traits: A systematic review and meta-analysis of randomized controlled trials

description: Whole grains (WGs) may have various health benefits, including lowering blood glucose and improving insulin sensitivity. To conduct a meta-analysis of the effects of WGs compared with non-WGs on changes in fasting glucose, fasting insulin, glycated hemoglobin (HbA1c), and homeostasis model assessment of insulin resistance (HOMA-IR). A systematic literature search was performed for all published randomized controlled trials on the effects of WG intake on fasting glucose, fasting insulin, HbA1c and HOMA-IR response up to February 2021. Weighted mean differences (WMD) were calculated. Pre-specified subgroup and univariate meta-regression analyses were explored to identify the sources of heterogeneity. Sensitivity analysis and bias analysis were conducted to appraise study quality. Among 12,435 articles screened for eligibility, data were extracted from 48 articles. Meta-analysis of 4,118 participants showed that WG consumption resulted in a significant reduction in fasting glucose by −0.15 mmol/L, fasting insulin by −2.71 pmol/L, HbA1c by −0.44%, and HOMA-IR by −0.28, respectively. Compared with mixed grains, brown rice, and wheat, oats were significantly lower on marker of glycemic. Besides, multiple interventions per day consolidated effectiveness of WGs. WG consumption decreased the levels of fasting glucose, fasting insulin, HbA1c, and HOMA-IR compared with non-WG consumption.