cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.14684863.v1
title: Additional file 4 of A new KSRP-binding compound suppresses distant metastasis of colorectal cancer by targeting the oncogenic KITENIN complex

description: Additional file 4: Supplementary Figure 4. Differences in cell survival after treatment with 5-FU or oxaliplatin in the presence or absence of DKC1125 in CRC cells overexpressing KITENIN. Various CRC cells (CT-26, Caco2, HCT116, and HT29) were seeded at 5 × 103 cells/well on 96-well plates, and the cytotoxicity of the indicated concentrations of 5-fluorouracil (5-FU, 0.02, 0.1, 0.5 μg/ml, a-c) or oxaliplatin (oxa, 1, 3, 10 μM, d) combined with DKC1125 (#25, 0.5, 1.5, 4.5 μM) was examined by tetrazolium salt (WST-8) assay 72 h after seeding. Data shown in line graphs (mean ± SEM, n = 3) were compared among groups at three time points (24, 48, and 72 h). The optical density (O.D.) values of each time point (24, 48, 72 h) were recalculated using the criterion that the O.D. value of 24 h with no treatment (5-FU and DKC1125) is set to 1.0. The asterisk indicates a significant difference between the indicated groups at each time point (*P
DOI: 10.34944/dspace/6576
title: Opioid Use Disorder and Education and MAT Waiver Rapid Review Search Strategy

description: To identify studies to include or consider for this rapid review, the review team worked with a medical librarian to develop detailed search strategies for each database. The search was developed for PubMed (NLM) and was translated to Embase (Elsevier) and Web of Science (Clarivate Analytics) using a combination of keywords and subject headings. A grey literature search included SAMHSA and the TRIP database. The search included no major limits or date restrictions. The final search was completed on May 7, 2021. The full search details are provided in Appendix(___). PubMed (NLM) from inception to 5/7/2021 (242 Results) Embase (Elsevier) from inception to 5/7/2021 (191 Results) Web of Science (Clarivate Analytics) from inception to 5/7/2021 (78 Results) The search resulted in 651 studies (140 from grey literature sources). 127 duplicate studies were found and omitted using Endnote X.7 for the deduplication of records and 524 references were eligible to screen. Studies were screened by title and abstract by two blinded and independent reviewers. If a tiebreaker was needed, a third reviewer was called in. This process was repeated for full text article screening and article selection.
description: To identify studies to include or consider for this rapid review, the review team worked with a medical librarian to develop detailed search strategies for each database. The search was developed for PubMed (NLM) and was translated to Embase (Elsevier) and Web of Science (Clarivate Analytics) using a combination of keywords and subject headings. A grey literature search included SAMHSA and the TRIP database. The search included no major limits or date restrictions. The final search was completed on May 7, 2021.
DOI: 10.34944/dspace/6577
title: DIEP TRAM Breast Reconstruction Systematic Review Search Strategy

description: Search Methods for Identification of Studies: To identify studies to include or consider for this systematic review, the review team worked with a librarian to develop detailed search strategies for each database. The search was developed for PubMed (NLM) and was translated to Embase (Elsevier), Web of Science (Clarivate Analytics), CINAHL (EBSCOHost) and Cochrane Central (Wiley) using a combination of keywords and subject headings. A grey literature search included ClinicalTrials.gov and the Zetoc research database. The search included no major limits or date restrictions. The final search was completed on May 13, 2021. The full search details are provided in Appendix(___). PubMed (NLM) from inception to 5/13/21 (5,389 Results) Embase (Elsevier) from inception to 5/13/21 (4,577 Results) Web of Science (Clarivate Analytics) from inception to 5/13/21 (3458 Results) CINAHL (EBSCOHost) from inception to 5/13/21 (423 Results) Cochrane Central (Wiley) from inception to 5/13/21 (181 Results) Clinicaltrials.gov from inception to 5/13/21 (74 Results) Zetoc from inception to 5/13/21 (98 Results) The search resulted in 14,200 studies (172 from grey literature sources). 5,945 duplicate studies were found and omitted using Endnote 20 for the deduplication of records and 8,255 references were eligible to screen. Studies were screened by title and abstract by two blinded and independent reviewers. If a tiebreaker was needed, a third reviewer was called in. This process was repeated for full text article screening and article selection.
description: Search Methods for Identification of Studies: To identify studies to include or consider for this systematic review, the review team worked with a librarian to develop detailed search strategies for each database. The search was developed for PubMed (NLM) and was translated to Embase (Elsevier), Web of Science (Clarivate Analytics), CINAHL (EBSCOHost) and Cochrane Central (Wiley) using a combination of keywords and subject headings. A grey literature search included ClinicalTrials.gov and the Zetoc research database. The search included no major limits or date restrictions. The final search was completed on May 13, 2021.
DOI: 10.3886/e141261v1
title: Patient blood type is associated with response to immune checkpoint blockade in metastatic cancer

description: This is the database for the project "Patient blood type is associated with response to immune checkpoint blockade in metastatic cancer".
DOI: 10.6084/m9.figshare.14684995
title: Additional file 2 of Inferring and analyzing gene regulatory networks from multi-factorial expression data: a complete and interactive suite

description: Additional file 2 Network inference report from the M versus MH GRN. Interactive report generated after network inference and edges testing in DIANE. Slight changes might be observed from the textual description of the network because of the stochasticity inherent to the Louvain, Random Forest, and permutations procedures.
DOI: 10.6084/m9.figshare.14684995.v1
title: Additional file 2 of Inferring and analyzing gene regulatory networks from multi-factorial expression data: a complete and interactive suite

description: Additional file 2 Network inference report from the M versus MH GRN. Interactive report generated after network inference and edges testing in DIANE. Slight changes might be observed from the textual description of the network because of the stochasticity inherent to the Louvain, Random Forest, and permutations procedures.
DOI: 10.6084/m9.figshare.14685024
title: Additional file 1 of Histological and ultrastructural degenerative findings in the gluteus medius tendon after hip arthroplasty

description: Additional file 1. Histology original data
DOI: 10.6084/m9.figshare.14685027
title: Additional file 2 of Histological and ultrastructural degenerative findings in the gluteus medius tendon after hip arthroplasty

description: Additional file 2. Electron microscopy original data.
DOI: 10.6084/m9.figshare.14685027.v1
title: Additional file 2 of Histological and ultrastructural degenerative findings in the gluteus medius tendon after hip arthroplasty

description: Additional file 2. Electron microscopy original data.
DOI: 10.6084/m9.figshare.14685024.v1
title: Additional file 1 of Histological and ultrastructural degenerative findings in the gluteus medius tendon after hip arthroplasty

description: Additional file 1. Histology original data
DOI: 10.6084/m9.figshare.14685028
title: Additional file 1 of Lantern: an integrative repository of functional annotations for lncRNAs in the human genome

description: Additional file 1: Table S1. Manual precision calculation for benchmarking extracted ontology annotations.
DOI: 10.6084/m9.figshare.14685028.v1
title: Additional file 1 of Lantern: an integrative repository of functional annotations for lncRNAs in the human genome

description: Additional file 1: Table S1. Manual precision calculation for benchmarking extracted ontology annotations.
DOI: 10.6084/m9.figshare.14685045
title: Additional file 3 of Cataloguing experimentally confirmed 80.7 kb-long ACKR1 haplotypes from the 1000 Genomes Project database

description: Additional file 3 Table S2. Sequence data for the 902 long range ACKR1 haplotypes in the 1000GP.
DOI: 10.6084/m9.figshare.14685045.v1
title: Additional file 3 of Cataloguing experimentally confirmed 80.7 kb-long ACKR1 haplotypes from the 1000 Genomes Project database

description: Additional file 3 Table S2. Sequence data for the 902 long range ACKR1 haplotypes in the 1000GP.
DOI: 10.6084/m9.figshare.14685048
title: Additional file 4 of Cataloguing experimentally confirmed 80.7 kb-long ACKR1 haplotypes from the 1000 Genomes Project database

description: Additional file 4 Table S3. Metadata file for the ACKR1 long range haplotypes in the 1000GP.
DOI: 10.6084/m9.figshare.14685048.v1
title: Additional file 4 of Cataloguing experimentally confirmed 80.7 kb-long ACKR1 haplotypes from the 1000 Genomes Project database

description: Additional file 4 Table S3. Metadata file for the ACKR1 long range haplotypes in the 1000GP.
DOI: 10.6084/m9.figshare.14684280
title: The genome organization of P.trituberculatus mitochondrial DNA

description: The complete mitochondrial DNA sequence for larval <i>Portunus trituberculatus</i> collected from the Yangtze Estuary was determined by Next-generation sequencing. The whole mitochondrial genome of the swimming crab showed routine gene arrangement including 37 genes: 13 protein-coding genes (PCGs), 22 tRNA genes, 2 rRNA genes (<i>rrnL</i>, <i>rrnS</i>) and a control region (D-Loop).
DOI: 10.6084/m9.figshare.14684280.v1
title: The genome organization of P.trituberculatus mitochondrial DNA

description: The complete mitochondrial DNA sequence for larval <i>Portunus trituberculatus</i> collected from the Yangtze Estuary was determined by Next-generation sequencing. The whole mitochondrial genome of the swimming crab showed routine gene arrangement including 37 genes: 13 protein-coding genes (PCGs), 22 tRNA genes, 2 rRNA genes (<i>rrnL</i>, <i>rrnS</i>) and a control region (D-Loop).
DOI: 10.6084/m9.figshare.14681103
title: Development of A Nutrition Education-Based Junior High School Curriculum

description: This project contains the following underlying data:• Dataset of nutrition knowledge, attitude, and practices (Figure 1)• Dataset of core competencies (CC) and basic competencies for junior high school curriculum (Table 2)<br><br>
DOI: 10.6084/m9.figshare.14681103.v1
title: Development of A Nutrition Education-Based Junior High School Curriculum

description: This project contains the following underlying data:• Dataset of nutrition knowledge, attitude, and practices (Figure 1)• Dataset of core competencies (CC) and basic competencies for junior high school curriculum (Table 2)<br><br>
DOI: 10.6084/m9.figshare.14684524.v1
title: Additional file 1 of In silico characterization of putative gene homologues involved in somatic embryogenesis suggests that some conifer species may lack LEC2, one of the key regulators of initiation of the process

description: Additional file 1. Details of conifer homologues involved in somatic embryogenesis – Table S1-Table S10.
DOI: 10.5281/zenodo.4816702
title: The genotypes of variations of VEGFA in Sherpa highlanders and non-Sherpa lowlanders

description: Sherpa highlanders demonstrate extraordinary tolerance to hypoxia at high altitudes, partly by one of the adaptation mechanisms promoting increases of microcirculatory blood flow and capillary density at high altitudes for restoring oxygen supply to tissues. Vascular endothelial growth factors (VEGFs) are important signaling proteins involved in vasculogenesis and angiogenesis stimulated by hypoxia. We hypothesize that the VEGF-A isoform and the gene encoding VEGF-A (<em>VEGFA</em>) are involved with the mechanism of adaptation to high-altitude hypoxia in Sherpa highlanders. <em><strong>Materials & Methods: </strong></em><em> Five-one </em>Sherpa highlanders at a high altitude of 3,440 meters (m) above sea level and 76 non-Sherpa lowlanders at 1,300 m in Nepal were recruited. The plasma VEGF-A concentrations were measured in both groups. Meanwhile, five single-nucleotide polymorphisms (SNPs, rs699947, rs833061, rs1570360, rs2010963, and rs3025039) in the <em>VEGFA</em> were genotyped in the two groups. <em><strong>Results: </strong></em>The average oxygen saturation (SpO<sub>2</sub>) differed significantly between the two groups due to the difference of altitude (93.7 ± 0.2% in Sherpas at 3,440 m vs. 96.7 ± 0.2% in non-Sherpas at 1,330 m, P &lt; 0.05). However, the plasma VEGF-A concentration in Sherpas at high altitude (262.8 ± 17.9 pg/ml) was equivalent to that in non-Sherpas at low altitude (266.8 ± 21.8 pg/ml, P &gt; 0.05), indicating that the plasma VEGF-A concentration did not respond to high-altitude hypoxia to increase its level in Sherpas at high altitude. Moreover, the allele frequencies of the SNPs of rs699947, rs833061, and rs2010963 were significantly diverse between the Sherpa highlanders and non-Sherpa lowlanders (corrected P = 3.30 × 10<sup>−5</sup>, 4.95 × 10<sup>−4</sup>, 1.19 × 10<sup>−7</sup>, respectively). <em><strong>Conclusions:</strong></em> The VEGF-A isoform in Sherpa highlanders exhibited a phenotype of tolerance to high-altitude hypoxia, which was likely based on the distinctive genetic background with significant variations of the <em>VEGFA</em> in Sherpa highlanders.
DOI: 10.5281/zenodo.4686335
title: Robust clustering and interpretation of scRNA-seq data using reference component analysis

description: Datasets and Code accompanying the new release of RCA, RCA2. The R-package for RCA2 is available at GitHub: https://github.com/prabhakarlab/RCAv2/ The datasets included here are: Datasets required for a characterization of batch effects: merged_rna_seurat.rds de_list.rds mergedRCAObj.rds merged_rna_integrated.rds 10X_PBMCs.RDS: Processed 10X PBMC data RCA2 object (10X PBMC example data sets ) NBM_RDS_Files.zip: Several RDS files containing RCA2 object of Normal Bone Marrow (NBM) data, umap coordinates, doublet finder results and metadata information (Normal Bone Marrow use case) Dataset used for the Covid19 example: blish_covid.seu.rds rownames_of_glocal_projection_immune_cells.txt Blish_RCA_no_QC_filtering_project_to_multiple_panels.rds Data sets used to outline the ability of supervised clustering to detect disease states: 809653.seurat.rds blish_covid.seu.rds Performance benchmarking results: Memory_consumption.txt rca_time_list.rds ScanPY input files: input_data.zip The R script provides R code to regenerate the main paper Figures 2 to 7 modulo some visual modifications performed in Inkscape. Provided R scripts are: ComputePairWiseDE_v2.R (Required code for pairwise DE computation) RCA_Figure_Reproduction.R Provided python Code for Scanpy analysis: RA_Scanpy.ipynb CITESeq_Scanpy.ipynb <br>
DOI: 10.5281/zenodo.4816701
title: The genotypes of variations of VEGFA in Sherpa highlanders and non-Sherpa lowlanders

description: Sherpa highlanders demonstrate extraordinary tolerance to hypoxia at high altitudes, partly by one of the adaptation mechanisms promoting increases of microcirculatory blood flow and capillary density at high altitudes for restoring oxygen supply to tissues. Vascular endothelial growth factors (VEGFs) are important signaling proteins involved in vasculogenesis and angiogenesis stimulated by hypoxia. We hypothesize that the VEGF-A isoform and the gene encoding VEGF-A (<em>VEGFA</em>) are involved with the mechanism of adaptation to high-altitude hypoxia in Sherpa highlanders. <em><strong>Materials & Methods: </strong></em><em> Five-one </em>Sherpa highlanders at a high altitude of 3,440 meters (m) above sea level and 76 non-Sherpa lowlanders at 1,300 m in Nepal were recruited. The plasma VEGF-A concentrations were measured in both groups. Meanwhile, five single-nucleotide polymorphisms (SNPs, rs699947, rs833061, rs1570360, rs2010963, and rs3025039) in the <em>VEGFA</em> were genotyped in the two groups. <em><strong>Results: </strong></em>The average oxygen saturation (SpO<sub>2</sub>) differed significantly between the two groups due to the difference of altitude (93.7 ± 0.2% in Sherpas at 3,440 m vs. 96.7 ± 0.2% in non-Sherpas at 1,330 m, P &lt; 0.05). However, the plasma VEGF-A concentration in Sherpas at high altitude (262.8 ± 17.9 pg/ml) was equivalent to that in non-Sherpas at low altitude (266.8 ± 21.8 pg/ml, P &gt; 0.05), indicating that the plasma VEGF-A concentration did not respond to high-altitude hypoxia to increase its level in Sherpas at high altitude. Moreover, the allele frequencies of the SNPs of rs699947, rs833061, and rs2010963 were significantly diverse between the Sherpa highlanders and non-Sherpa lowlanders (corrected P = 3.30 × 10<sup>−5</sup>, 4.95 × 10<sup>−4</sup>, 1.19 × 10<sup>−7</sup>, respectively). <em><strong>Conclusions:</strong></em> The VEGF-A isoform in Sherpa highlanders exhibited a phenotype of tolerance to high-altitude hypoxia, which was likely based on the distinctive genetic background with significant variations of the <em>VEGFA</em> in Sherpa highlanders.
DOI: 10.5281/zenodo.4021966
title: Robust clustering and interpretation of scRNA-seq data using reference component analysis

description: Datasets and Code accompanying the new release of RCA, RCA2. The R-package for RCA2 is available at GitHub: https://github.com/prabhakarlab/RCAv2/ The datasets included here are: Datasets required for a characterization of batch effects: merged_rna_seurat.rds de_list.rds mergedRCAObj.rds merged_rna_integrated.rds 10X_PBMCs.RDS: Processed 10X PBMC data RCA2 object (10X PBMC example data sets ) NBM_RDS_Files.zip: Several RDS files containing RCA2 object of Normal Bone Marrow (NBM) data, umap coordinates, doublet finder results and metadata information (Normal Bone Marrow use case) Dataset used for the Covid19 example: blish_covid.seu.rds rownames_of_glocal_projection_immune_cells.txt Blish_RCA_no_QC_filtering_project_to_multiple_panels.rds Data sets used to outline the ability of supervised clustering to detect disease states: 809653.seurat.rds blish_covid.seu.rds Performance benchmarking results: Memory_consumption.txt rca_time_list.rds ScanPY input files: input_data.zip The R script provides R code to regenerate the main paper Figures 2 to 7 modulo some visual modifications performed in Inkscape. Provided R scripts are: ComputePairWiseDE_v2.R (Required code for pairwise DE computation) RCA_Figure_Reproduction.R Provided python Code for Scanpy analysis: RA_Scanpy.ipynb CITESeq_Scanpy.ipynb <br>
DOI: 10.5281/zenodo.4008213
title: Generational differences in the low tones of Black Lahu

description: We investigate apparent-time tone variation in the Black Lahu language (Loloish/Ngwi, Tibeto-Burman) of Yunnan, China. These are the supplementary materials for the paper "Generational differences in the low tones of Black Lahu," accepted for publication in <em>Linguistics Vanguard</em>. <strong>Appendices: </strong> <strong>Appendix A: </strong>Wordlist (organized by order of appearance in the story) <strong>Appendix B: </strong>Wordless picture book <strong>Appendix C: </strong>Cross-tabulation tables <strong>Appendix D: </strong>F0 trajectory plots by speaker <strong>Appendix E: </strong>LME model results for T45 <strong>Script files contained in the analysis: </strong> <strong>F0_estimation.praat</strong> is the Praat script used for F0 estimation on the wav + Textgrid pairs <strong>Combine_Speaker_Files.R</strong> is used to combine the Praat script output for individual speakers into a single csv file. <strong>Data_processing.R</strong> is the main processing script, works on an Excel csv file that contains the output of the Combine_Speaker_Files.R script <strong>Plotting_Fig1_Lahu_tones.R </strong>plots the F0 trajectories of all the tones of Lahu, averaged across all the speakers, works on an Excel csv file that contains the output of the F0 estimation.praat script. <strong>Plotting_Fig2_age_groups.R</strong> plots the F0 trajectories of T2 and T7, in 15-age groups, works on an Excel csv file that contains the output of the Data_processing.R script. <strong>Plotting_Fig3and6_carryover. R</strong> plots the F0 trajectories of T2, T7 and T4 when they occur after silence or Tones 1-7 in three age groups; works on an Excel csv file that contains the output of the Data_processing.R script. <strong>Plotting_Fig4578_scatterplot.R </strong>plots the scatterplots of F0 onset versus Age, works on an Excel csv file that contains the output of the Data_processing.R script. <strong>Data files contained in this analysis: </strong> <strong>praat_raw_data.csv</strong> is the output of the F0_estimation.praat script. Contains the raw data from all speakers. <strong>Speaker_info.csv</strong> is the demographic data for each speaker <strong>data_forplotting.csv</strong> is the output of the Data_processing.R script. Contains the filtered tokens, normalized for length and converted to speaker-specific semitones. Used to plot Figure 2, Figure 3 and Figure 6 <strong>data_forRbrul.csv</strong> is the output of the Data_processing.R script, the F0 onset and F0 offset for Tones 2, 4, and 7. Used to do linear mixed effects modeling in the Rbrul interface (Johnson 2009).
description: Funding from Scholarly Innovation and Advancement Award, Dartmouth College. Sociolinguistic exploration of a matrilineal/matrilocal society in rural southwest China. 2018-2020. Dr. James N. Stanford (PI), Cathryn Yang (co-investigator).