cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.9258947.v1
title: Table S4

description: Sheet 1: 16S rRNA gene sequences obtained from the SILVA database (version 132) whose taxonomic affiliations in the database do not match our phylogenetic analysis and their respective proposed corrections based on this study. Note: The “Unknown Asgard” sequences are the good quality shorter sequences that did not match to any of the reference sequences in the backbone tree with the given threshold (USEACH: 95% identity). Sheet 2: Accession numbers of all the sequences in the SILVA database that were removed from the analysis in this study due to low quality and chimeric.
DOI: 10.6084/m9.figshare.9258917
title: Supplementary Material for: AGO Recommendations for the Diagnosis and Treatment of Patients with Early Breast Cancer: Update 2019

description: Medicine
DOI: 10.6084/m9.figshare.9258926.v1
title: Table S3

description: List of all Loki- and Thorarchaeota genomes (13 in total) and their related information that has been used for the pan-genomic analyses.
DOI: 10.6084/m9.figshare.9258521
title: Table S2

description: Predicted 62 ribosomal proteins including accession numbers used for the Asgard phylogenetic reconstruction based on their concatenated alignment. <i>Woesearchaeota</i> ribosomal proteins were locally predicted using Prokka (Seemann et al. 2014).
DOI: 10.6084/m9.figshare.9258917.v1
title: Supplementary Material for: AGO Recommendations for the Diagnosis and Treatment of Patients with Early Breast Cancer: Update 2019

description: Medicine
DOI: 10.6084/m9.figshare.9256433
title: Big data to knowledge: common pitfalls in transcriptomics data analysis and representation

description: The omics technologies provide an invaluable opportunity to employ a global view towards human diseases. However, the appropriate translation of big data to knowledge remains a major challenge. In this study, we have performed quality control assessments for 91 transcriptomics datasets deposited in gene expression omnibus database and also have evaluated the publications derived from these datasets. This survey shows that drawbacks in the analyses and reports of transcriptomics studies are more common than one may assume. This report is concluded with some suggestions for researchers and reviewers to enhance the minimal requirements for gene expression data generation, analysis and report.
DOI: 10.6084/m9.figshare.9257885
title: Table S1

description: Taxonomic and genomic accession of the TACK and Bathyarchaeota genomes, from which 16S rRNA gene sequences were extracted for an alignment with the Asgard 16S rRNA gene sequences. In total, 65 sequences were evenly chosen evenly across the TACK and Bathyarchaeota superphyla taxonomic groups.
DOI: 10.6084/m9.figshare.9257885.v1
title: Table S1

description: Taxonomic and genomic accession of the TACK and Bathyarchaeota genomes, from which 16S rRNA gene sequences were extracted for an alignment with the Asgard 16S rRNA gene sequences. In total, 65 sequences were evenly chosen evenly across the TACK and Bathyarchaeota superphyla taxonomic groups.
DOI: 10.6084/m9.figshare.9255797
title: Willingness-to-pay for a hypothetical Ebola vaccine in Indonesia: A cross-sectional study in Aceh

description: The data related to the article "Willingness-to-pay for a hypothetical Ebola vaccine in Indonesia: A cross-sectional study in Aceh" submitted to F1000Research by Mudatsir M, Anwar S, Fajar JK, Yufika A, Ferdian MN, Salwiyadi S, Imanda AS, Azhars R <i>et al.</i><br>
DOI: 10.6084/m9.figshare.9256037
title: Willingness-to-pay for a hypothetical Ebola vaccine in Indonesia: A cross-sectional study in Aceh

description: The data related to the article "Willingness-to-pay for a hypothetical Ebola vaccine in Indonesia: A cross-sectional study in Aceh" submitted to F1000Research by Mudatsir M, Anwar S, Fajar JK, Yufika A, Ferdian MN, Salwiyadi S, Imanda AS, Azhars R <i>et al.</i>
DOI: 10.6084/m9.figshare.9255797.v1
title: Willingness-to-pay for a hypothetical Ebola vaccine in Indonesia: A cross-sectional study in Aceh

description: The data related to the article "Willingness-to-pay for a hypothetical Ebola vaccine in Indonesia: A cross-sectional study in Aceh" submitted to F1000Research by Mudatsir M, Anwar S, Fajar JK, Yufika A, Ferdian MN, Salwiyadi S, Imanda AS, Azhars R <i>et al.</i><br>
DOI: 10.6084/m9.figshare.9256433.v2
title: Big data to knowledge: common pitfalls in transcriptomics data analysis and representation

description: The omics technologies provide an invaluable opportunity to employ a global view towards human diseases. However, the appropriate translation of big data to knowledge remains a major challenge. In this study, we have performed quality control assessments for 91 transcriptomics datasets deposited in gene expression omnibus database and also have evaluated the publications derived from these datasets. This survey shows that drawbacks in the analyses and reports of transcriptomics studies are more common than one may assume. This report is concluded with some suggestions for researchers and reviewers to enhance the minimal requirements for gene expression data generation, analysis and report.
DOI: 10.6084/m9.figshare.9256037.v2
title: Willingness-to-pay for a hypothetical Ebola vaccine in Indonesia: A cross-sectional study in Aceh

description: The data related to the article "Willingness-to-pay for a hypothetical Ebola vaccine in Indonesia: A cross-sectional study in Aceh" submitted to F1000Research by Mudatsir M, Anwar S, Fajar JK, Yufika A, Ferdian MN, Salwiyadi S, Imanda AS, Azhars R <i>et al.</i>
DOI: 10.6084/m9.figshare.9256433.v1
title: Big Data to Knowledge: Common Pitfalls in Transcriptomics Data Analysis and Representation

description: The omics technologies provide an invaluable opportunity to employ a global view toward human diseases. However, the appropriate translation of big data to knowledge remains a major challenge. In this study, we have performed quality control assessments for 91 transcriptomics datasets deposited in gene expression omnibus database and also have evaluated the publications derived from these datasets. This survey shows that drawbacks in the analyses and reports of transcriptomics studies are more common than one may assume. This report is concluded with some suggestions for researchers and reviewers to enhance the minimal requirements for gene expression data generation, analysis and report.
DOI: 10.6084/m9.figshare.9256037.v1
title: Willingness-to-pay for a hypothetical Ebola vaccine in Indonesia: A cross-sectional study in Aceh

description: The data related to the article "Willingness-to-pay for a hypothetical Ebola vaccine in Indonesia: A cross-sectional study in Aceh" submitted to F1000Research by Mudatsir M, Anwar S, Fajar JK, Yufika A, Ferdian MN, Salwiyadi S, Imanda AS, Azhars R <i>et al.</i>
DOI: 10.6084/m9.figshare.9255761
title: luad_tcga_cohorts_isotype_median_values

description: This table contains median values of CD19, IGH, IGG1, IGHA, IGHG4, IGG1/IGH, IGHA/IGH, IGG4/IGH, IGH/MS4A1, IGHG1/MS4A1, IGHA/MS4A1, IGHG4/MS4A1 expression, IGHG1 clonality and IGHA clonality in lung adenocarcinoma TCGA cohorts from our study (KRAS mutated (mut), KRAS wild-type (WT), EGFR mut, STK11 mut, STK11 WT, TP53 mut, TP53 WT, PDL1 high, PDL1 low, proximal proliferative subtype, proximal inflammatory subtype, terminal respiratory unit subtype).
DOI: 10.6084/m9.figshare.9255758
title: PROLIFIC qualitative.zip

description: The interview and focus group transcripts conducted for the qualitative study. COREQ checklist for the qualitative study.Extended data contains the interview guides
DOI: 10.6084/m9.figshare.9255755
title: Willingness-to-pay for a hypothetical Ebola vaccine in Indonesia: A cross-sectional study in Aceh

description: These data related to the article "Willingness-to-pay for a hypothetical Ebola vaccine in Indonesia: A cross-sectional study in Aceh" submitted to F1000Research by Mudatsir M, Anwar S, Fajar JK, Yufika A, Ferdian MN, Salwiyadi S, Imanda AS, Azhars R <i>et al. </i>
DOI: 10.6084/m9.figshare.9255755.v1
title: Willingness-to-pay for a hypothetical Ebola vaccine in Indonesia: A cross-sectional study in Aceh

description: These data related to the article "Willingness-to-pay for a hypothetical Ebola vaccine in Indonesia: A cross-sectional study in Aceh" submitted to F1000Research by Mudatsir M, Anwar S, Fajar JK, Yufika A, Ferdian MN, Salwiyadi S, Imanda AS, Azhars R <i>et al. </i>
DOI: 10.6084/m9.figshare.9255758.v1
title: PROLIFIC qualitative.zip

description: The interview and focus group transcripts conducted for the qualitative study. COREQ checklist for the qualitative study
DOI: 10.6084/m9.figshare.9255761.v1
title: Untitled Item

description: This table contains median values of CD19, IGH, IGG1, IGHA, IGHG4, IGG1/IGH, IGHA/IGH, IGG4/IGH, IGH/MS4A1, IGHG1/MS4A1, IGHA/MS4A1, IGHG4/MS4A1 expression, IGHG1 clonality and IGHA clonality in lung adenocarcinoma TCGA cohorts from our study (KRAS mutated (mut), KRAS wild-type (WT), EGFR mut, STK11 mut, STK11 WT, TP53 mut, TP53 WT, PDL1 high, PDL1 low, proximal proliferative subtype, proximal inflammatory subtype, terminal respiratory unit subtype).
DOI: 10.6084/m9.figshare.9255740
title: Supplementary Material for: An Empirically Based Typology of Alcohol Users in a Community Sample Using Latent Class Analysis

description: <b><i>Background:</i></b> Different classification models have been proposed to explain the heterogeneity of alcohol-related problems in general populations. Such models suggest quantitatively or qualitatively different symptom endorsement characteristics between subgroups of alcohol drinkers. <b><i>Objectives:</i></b> The present study aimed to identify homogenous subgroups of drinkers in a general population sample in addition to examining the relationship between the subgroups and psychopathological symptoms. <b><i>Method:</i></b> Data of past-year alcohol users (<i>n</i> = 1,520) were analyzed from the nationally representative sample of the National Survey on Addiction Problems in Hungary 2015. Latent class analysis (LCA) was conducted to identify subgroups of drinkers based on the dichotomous indicator items of the Alcohol Use Disorders Identification Test questionnaire. Multinomial logistic regression and multiple comparisons were performed to explore the relationship between latent classes and socio-demographical variables and psychopathological symptoms. <b><i>Results:</i></b> LCA suggested a 3-class model: “Light alcohol drinkers” (71.6%), “Alcohol drinkers with low risk of dependence” (19.3%), and “Alcohol drinkers with severe dependence symptoms” (9.1%). More severe subgroups showed significantly higher level of anxiety, depression, hostility, obsessive-compulsivity, interpersonal sensitivity, and psychiatric or alcohol use disorder-related treatment involvement. Male gender, younger age, lower level of educational achievement, and earlier onset of the first alcoholic drink were associated with membership of more severe subgroups. <b><i>Conclusions:</i></b> The present results indicated that severity-based subgroups of drinkers can be discriminated. Approximately 9% of the alcohol users showed severe symptoms of alcohol dependence. The present data also supported the association between more severe forms of alcohol consumption, and internalizing and externalizing characteristics. Although the 2 at-risk classes of alcohol drinkers did not differ in terms of alcohol consumption-related measures, they were distinguished by the level of harmful consequences due to alcohol use, psychopathological symptoms and psychiatric treatment history.
DOI: 10.6084/m9.figshare.9255758.v2
title: PROLIFIC qualitative.zip

description: The interview and focus group transcripts conducted for the qualitative study. COREQ checklist for the qualitative study
DOI: 10.6084/m9.figshare.9255740.v1
title: Supplementary Material for: An Empirically Based Typology of Alcohol Users in a Community Sample Using Latent Class Analysis

description: <b><i>Background:</i></b> Different classification models have been proposed to explain the heterogeneity of alcohol-related problems in general populations. Such models suggest quantitatively or qualitatively different symptom endorsement characteristics between subgroups of alcohol drinkers. <b><i>Objectives:</i></b> The present study aimed to identify homogenous subgroups of drinkers in a general population sample in addition to examining the relationship between the subgroups and psychopathological symptoms. <b><i>Method:</i></b> Data of past-year alcohol users (<i>n</i> = 1,520) were analyzed from the nationally representative sample of the National Survey on Addiction Problems in Hungary 2015. Latent class analysis (LCA) was conducted to identify subgroups of drinkers based on the dichotomous indicator items of the Alcohol Use Disorders Identification Test questionnaire. Multinomial logistic regression and multiple comparisons were performed to explore the relationship between latent classes and socio-demographical variables and psychopathological symptoms. <b><i>Results:</i></b> LCA suggested a 3-class model: “Light alcohol drinkers” (71.6%), “Alcohol drinkers with low risk of dependence” (19.3%), and “Alcohol drinkers with severe dependence symptoms” (9.1%). More severe subgroups showed significantly higher level of anxiety, depression, hostility, obsessive-compulsivity, interpersonal sensitivity, and psychiatric or alcohol use disorder-related treatment involvement. Male gender, younger age, lower level of educational achievement, and earlier onset of the first alcoholic drink were associated with membership of more severe subgroups. <b><i>Conclusions:</i></b> The present results indicated that severity-based subgroups of drinkers can be discriminated. Approximately 9% of the alcohol users showed severe symptoms of alcohol dependence. The present data also supported the association between more severe forms of alcohol consumption, and internalizing and externalizing characteristics. Although the 2 at-risk classes of alcohol drinkers did not differ in terms of alcohol consumption-related measures, they were distinguished by the level of harmful consequences due to alcohol use, psychopathological symptoms and psychiatric treatment history.
DOI: 10.6084/m9.figshare.9255758.v3
title: PROLIFIC qualitative.zip

description: The interview and focus group transcripts conducted for the qualitative study. COREQ checklist for the qualitative study
DOI: 10.6084/m9.figshare.9255710
title: Supplementary Material 4 from Mathematical models incorporating a multi-stage cell cycle replicate normally hidden inherent synchronization in cell proliferation

description: Experimental data for 1205Lu cell line
DOI: 10.6084/m9.figshare.9255713
title: Supplementary Material 3 from Mathematical models incorporating a multi-stage cell cycle replicate normally hidden inherent synchronization in cell proliferation

description: Experimental data for WM983C cell line
DOI: 10.6084/m9.figshare.9255716
title: Supplementary Material 2 from Mathematical models incorporating a multi-stage cell cycle replicate normally hidden inherent synchronization in cell proliferation

description: Experimental data for C8161 cell line
DOI: 10.6084/m9.figshare.9255710.v1
title: Supplementary Material 4 from Mathematical models incorporating a multi-stage cell cycle replicate normally hidden inherent synchronization in cell proliferation

description: Experimental data for 1205Lu cell line
DOI: 10.6084/m9.figshare.9255713.v1
title: Supplementary Material 3 from Mathematical models incorporating a multi-stage cell cycle replicate normally hidden inherent synchronization in cell proliferation

description: Experimental data for WM983C cell line
DOI: 10.6084/m9.figshare.9255716.v1
title: Supplementary Material 2 from Mathematical models incorporating a multi-stage cell cycle replicate normally hidden inherent synchronization in cell proliferation

description: Experimental data for C8161 cell line
DOI: 10.6084/m9.figshare.9255698
title: Mechanical data from Evolution of mantis shrimp telson armour and its role in ritualized fighting

description: Hardness and stiffness of mantis shrimp telsons
DOI: 10.6084/m9.figshare.9255701
title: Impact properties data from Evolution of mantis shrimp telson armour and its role in ritualized fighting

description: Impact parameters for mantis shrimp telsons and adbominal segments
DOI: 10.6084/m9.figshare.9255698.v1
title: Mechanical data from Evolution of mantis shrimp telson armour and its role in ritualized fighting

description: Hardness and stiffness of mantis shrimp telsons
DOI: 10.6084/m9.figshare.9255701.v1
title: Impact properties data from Evolution of mantis shrimp telson armour and its role in ritualized fighting

description: Impact parameters for mantis shrimp telsons and adbominal segments
DOI: 10.6084/m9.figshare.9255674
title: luad_tcga_cohorts_isotype_median_values

description: This table contains median values of CD19, IGH, IGG1, IGHA, IGHG4, IGG1/IGH, IGHA/IGH, IGG4/IGH, IGH/MS4A1, IGHG1/MS4A1, IGHA/MS4A1, IGHG4/MS4A1 expression, IGHG1 clonality and IGHA clonality in lung adenocarcinoma TCGA cohorts from our study (KRAS mutated (mut), KRAS wild-type (WT), EGFR mut, STK11 mut, STK11 WT, TP53 mut, TP53 WT, PDL1 high, PDL1 low, proximal proliferative subtype, proximal inflammatory subtype, terminal respiratory unit subtype).
DOI: 10.6084/m9.figshare.9255671
title: Supplementary Material for: The Prognostic Impact of the Lymphocyte-to-Monocyte Ratio in Resected Pancreatic Head Adenocarcinoma

description: <b><i>Objective:</i></b> Although the prognostic significance of systematic inflammation-based scores, such as the neutrophil-to-lymphocyte ratio (NLR), the platelet-to-lymphocyte ratio (PLR), and the prognostic nutritional index (PNI), has been explored in pancreatic cancers, few reports have investigated the lymphocyte-to-monocyte ratio (LMR). We aimed to retrospectively investigate the prognostic value of the preoperative LMR in patients with resectable pancreatic head cancer (PHC). <b><i>Methods:</i></b> From 2005 to 2016, 165 patients underwent pancreatoduodenectomy for PHC. All samples of peripheral blood were collected within 2 weeks prior to surgery. The best cutoff values of the LMR for predicting survival were determined by using a minimum <i>p</i> value approach (cut-off value: 2.8). The clinicopathological features of LMR &lt;2.8 (<i>n</i> = 25) and ≥2.8 (<i>n</i> = 140) were compared. <b><i>Results:</i></b> Patients with LMR ≥2.8 showed significantly lower NLR and PLR, and significantly higher PNI. Levels of CEA and CA19-9 were similar, and the pathological findings were comparable between the groups. The overall survival of patients with LMR ≥2.8 (66.2% at 1 year) was superior to that of patients with LMR &lt;2.8 (36.1% at 1 year, <i>p</i> = 0.015). Multivariate analysis identified LMR &lt;2.8 (hazard ratio 1.72, 95% CI 1.02–2.89, <i>p</i> = 0.042), lymphatic and venous invasion and positive surgical margin as independent prognostic factors. <b><i>Conclusions:</i></b> LMR may carry important prognostic information for patients with resectable PHC. Preoperative LMR may be considered for use in risk stratification for individual patients with PHC.
DOI: 10.6084/m9.figshare.9255674.v1
title: luad_tcga_cohorts_isotype_median_values

description: This table contains median values of CD19, IGH, IGG1, IGHA, IGHG4, IGG1/IGH, IGHA/IGH, IGG4/IGH, IGH/MS4A1, IGHG1/MS4A1, IGHA/MS4A1, IGHG4/MS4A1 expression, IGHG1 clonality and IGHA clonality in lung adenocarcinoma TCGA cohorts from our study (KRAS mutated (mut), KRAS wild-type (WT), EGFR mut, STK11 mut, STK11 WT, TP53 mut, TP53 WT, PDL1 high, PDL1 low, proximal proliferative subtype, proximal inflammatory subtype, terminal respiratory unit subtype).
DOI: 10.6084/m9.figshare.9255656
title: luad_tcga_cohort_metadata

description: This is a metadata table for a cohort of 442 lung adenocarcinoma patients from TCGA investigated in our study. This table contains information about patients' gender, age, stage, vital status and overall survival (days). It also comprises to which cohorts from our study (KRAS mutated (mut), KRAS wild-type (WT), EGFR mut, STK11 mut, STK11 WT, TP53 mut, TP53 WT, PDL1 high, PDL1 low, proximal proliferative subtype, proximal inflammatory subtype, terminal respiratory unit subtype) do patients belong to. Additionally, the table contains nonsilent mutation burden per Mb values and the values of antibody isotype expressions and clonalities for the patients.
DOI: 10.6084/m9.figshare.9255671.v1
title: Supplementary Material for: The Prognostic Impact of the Lymphocyte-to-Monocyte Ratio in Resected Pancreatic Head Adenocarcinoma

description: <b><i>Objective:</i></b> Although the prognostic significance of systematic inflammation-based scores, such as the neutrophil-to-lymphocyte ratio (NLR), the platelet-to-lymphocyte ratio (PLR), and the prognostic nutritional index (PNI), has been explored in pancreatic cancers, few reports have investigated the lymphocyte-to-monocyte ratio (LMR). We aimed to retrospectively investigate the prognostic value of the preoperative LMR in patients with resectable pancreatic head cancer (PHC). <b><i>Methods:</i></b> From 2005 to 2016, 165 patients underwent pancreatoduodenectomy for PHC. All samples of peripheral blood were collected within 2 weeks prior to surgery. The best cutoff values of the LMR for predicting survival were determined by using a minimum <i>p</i> value approach (cut-off value: 2.8). The clinicopathological features of LMR &lt;2.8 (<i>n</i> = 25) and ≥2.8 (<i>n</i> = 140) were compared. <b><i>Results:</i></b> Patients with LMR ≥2.8 showed significantly lower NLR and PLR, and significantly higher PNI. Levels of CEA and CA19-9 were similar, and the pathological findings were comparable between the groups. The overall survival of patients with LMR ≥2.8 (66.2% at 1 year) was superior to that of patients with LMR &lt;2.8 (36.1% at 1 year, <i>p</i> = 0.015). Multivariate analysis identified LMR &lt;2.8 (hazard ratio 1.72, 95% CI 1.02–2.89, <i>p</i> = 0.042), lymphatic and venous invasion and positive surgical margin as independent prognostic factors. <b><i>Conclusions:</i></b> LMR may carry important prognostic information for patients with resectable PHC. Preoperative LMR may be considered for use in risk stratification for individual patients with PHC.
DOI: 10.6084/m9.figshare.9255662.v1
title: Manuscript dataset

description: Manuscript dataset
DOI: 10.6084/m9.figshare.9255635
title: Study Data.sav

description: Data of all variables pertaining to the study on attachment priming on consolidation of fear conditioning
DOI: 10.6084/m9.figshare.9255635.v1
title: Study Data.sav

description: Data of all variables pertaining to the study on attachment priming on consolidation of fear conditioning
DOI: 10.6084/m9.figshare.9255593
title: cDNA Sequencing

description: ab1 files for cDNA ASS1 mutation sequencing
DOI: 10.6084/m9.figshare.9255596
title: gDNA Sequencing

description: ab1 files gDNA sequencing