cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.9816446.v1
title: Genetic Variant Set-Based Tests Using the Generalized Berk–Jones Statistic With Application to a Genome-Wide Association Study of Breast Cancer

description: Studying the effects of groups of single nucleotide polymorphisms (SNPs), as in a gene, genetic pathway, or network, can provide novel insight into complex diseases such as breast cancer, uncovering new genetic associations and augmenting the information that can be gleaned from studying SNPs individually. Common challenges in set-based genetic association testing include weak effect sizes, correlation between SNPs in a SNP-set, and scarcity of signals, with individual SNP effects often ranging from extremely sparse to moderately sparse in number. Motivated by these challenges, we propose the Generalized Berk–Jones (GBJ) test for the association between a SNP-set and outcome. The GBJ extends the Berk–Jones statistic by accounting for correlation among SNPs, and it provides advantages over the Generalized Higher Criticism test when signals in a SNP-set are moderately sparse. We also provide an analytic <i>p</i>-value calculation for SNP-sets of any finite size, and we develop an omnibus statistic that is robust to the degree of signal sparsity. An additional advantage of our work is the ability to conduct inference using individual SNP summary statistics from a genome-wide association study (GWAS). We evaluate the finite sample performance of the GBJ through simulation and apply the method to identify breast cancer risk genes in a GWAS conducted by the Cancer Genetic Markers of Susceptibility Consortium. Our results suggest evidence of association between FGFR2 and breast cancer and also identify other potential susceptibility genes, complementing conventional SNP-level analysis. Supplementary materials for this article, including a standardized description of the materials available for reproducing the work, are available as an online supplement.
DOI: 10.6084/m9.figshare.9816404.v1
title: C14 Samples - EuroEvol

description: Data set of C14 samples aggregated by the EuroEvol project.
DOI: 10.6084/m9.figshare.9816449.v4
title: Multivariate Bayesian Predictive Synthesis in Macroeconomic Forecasting

description: We present new methodology and a case study in use of a class of Bayesian predictive synthesis (BPS) models for multivariate time series forecasting. This extends the foundational BPS framework to the multivariate setting, with detailed application in the topical and challenging context of multistep macroeconomic forecasting in a monetary policy setting. BPS evaluates—sequentially and adaptively over time—varying forecast biases and facets of miscalibration of individual forecast densities for multiple time series, and—critically—their time-varying inter-dependencies. We define BPS methodology for a new class of dynamic multivariate latent factor models implied by BPS theory. Structured dynamic latent factor BPS is here motivated by the application context—sequential forecasting of multiple U.S. macroeconomic time series with forecasts generated from several traditional econometric time series models. The case study highlights the potential of BPS to improve of forecasts of multiple series at multiple forecast horizons, and its use in learning dynamic relationships among forecasting models or agents. Supplementary materials for this article, including a standardized description of the materials available for reproducing the work, are available as an online supplement.
DOI: 10.6084/m9.figshare.9816452.v2
title: Bayesian Nonparametric Policy Search With Application to Periodontal Recall Intervals

description: Tooth loss from periodontal disease is a major public health burden in the United States. Standard clinical practice is to recommend a dental visit every six months; however, this practice is not evidence-based, and poor dental outcomes and increasing dental insurance premiums indicate room for improvement. We consider a tailored approach that recommends recall time based on patient characteristics and medical history to minimize disease progression without increasing resource expenditures. We formalize this method as a dynamic treatment regime which comprises a sequence of decisions, one per stage of intervention, that follow a decision rule which maps current patient information to a recommendation for their next visit time. The dynamics of periodontal health, visit frequency, and patient compliance are complex, yet the estimated optimal regime must be interpretable to domain experts if it is to be integrated into clinical practice. We combine nonparametric Bayesian dynamics modeling with policy-search algorithms to estimate the optimal dynamic treatment regime within an interpretable class of regimes. Both simulation experiments and application to a rich database of electronic dental records from the HealthPartners HMO shows that our proposed method leads to better dental health without increasing the average recommended recall time relative to competing methods. Supplementary materials for this article, including a standardized description of the materials available for reproducing the work, are available as an online supplement.
DOI: 10.6084/m9.figshare.9816344
title: VTKEL

description: VTKEL dataset for all documents (30k+).
DOI: 10.6084/m9.figshare.9816356
title: Nut1/Hos1 and Sas2/Rpd3 control the H3 acetylation of two different sets of osmotic stress-induced genes

description: Epigenetic information is able to interact with the cellular environment and could be especially useful for reprograming gene expression in response to a physiological perturbation. In fact the genes induced or repressed by osmotic stress undergo significant changes in terms of the levels of various histone modifications, especially in the acetylation levels of histone H3. Exposing yeast to high osmolarity results in the activation of stress-activated protein kinase Hog1, which plays a central role in gene expression control. We evaluated the connection between the presence of Hog1 and changes in histone H3 acetylation in stress-regulated genes. We found a parallel increase in the acetylation of lysines 9 and 14 of H3 in induced genes during stress, which was largely dependent on Hog1 at the genome-wide level. Conversely, we observed that acetylation decreased in repressed genes and was not dependent on Hog1. However, lack of Hog1 sometimes produced different, and even opposite, effects on the induction and acetylation of H3 of each gene. We also found that the acetylation state of lysine 9 of H3 was altered in the strains deficient in Nut1 HAT and Hos1 HDAC in the genes up-regulated during osmotic stress in an Msn2/Msn4-independent manner, while lysine 9 acetylation of H3 varied in the strains deficient in Sas2 HAT and Rpd3 HDAC for the Msn2/Msn4-dependent induced genes. The results presented here show new, unexpected participants in gene regulation processes in response to environmental perturbations.
DOI: 10.6084/m9.figshare.9816356.v1
title: Nut1/Hos1 and Sas2/Rpd3 control the H3 acetylation of two different sets of osmotic stress-induced genes

description: Epigenetic information is able to interact with the cellular environment and could be especially useful for reprograming gene expression in response to a physiological perturbation. In fact the genes induced or repressed by osmotic stress undergo significant changes in terms of the levels of various histone modifications, especially in the acetylation levels of histone H3. Exposing yeast to high osmolarity results in the activation of stress-activated protein kinase Hog1, which plays a central role in gene expression control. We evaluated the connection between the presence of Hog1 and changes in histone H3 acetylation in stress-regulated genes. We found a parallel increase in the acetylation of lysines 9 and 14 of H3 in induced genes during stress, which was largely dependent on Hog1 at the genome-wide level. Conversely, we observed that acetylation decreased in repressed genes and was not dependent on Hog1. However, lack of Hog1 sometimes produced different, and even opposite, effects on the induction and acetylation of H3 of each gene. We also found that the acetylation state of lysine 9 of H3 was altered in the strains deficient in Nut1 HAT and Hos1 HDAC in the genes up-regulated during osmotic stress in an Msn2/Msn4-independent manner, while lysine 9 acetylation of H3 varied in the strains deficient in Sas2 HAT and Rpd3 HDAC for the Msn2/Msn4-dependent induced genes. The results presented here show new, unexpected participants in gene regulation processes in response to environmental perturbations.
DOI: 10.6084/m9.figshare.9816449.v3
title: Multivariate Bayesian Predictive Synthesis in Macroeconomic Forecasting

description: We present new methodology and a case study in use of a class of Bayesian predictive synthesis (BPS) models for multivariate time series forecasting. This extends the foundational BPS framework to the multivariate setting, with detailed application in the topical and challenging context of multistep macroeconomic forecasting in a monetary policy setting. BPS evaluates—sequentially and adaptively over time—varying forecast biases and facets of miscalibration of individual forecast densities for multiple time series, and—critically—their time-varying inter-dependencies. We define BPS methodology for a new class of dynamic multivariate latent factor models implied by BPS theory. Structured dynamic latent factor BPS is here motivated by the application context—sequential forecasting of multiple U.S. macroeconomic time series with forecasts generated from several traditional econometric time series models. The case study highlights the potential of BPS to improve of forecasts of multiple series at multiple forecast horizons, and its use in learning dynamic relationships among forecasting models or agents. Supplementary materials for this article, including a standardized description of the materials available for reproducing the work, are available as an online supplement.
DOI: 10.6084/m9.figshare.9816326
title: Automobiles - Ebay Master Vehicle List - Revised

description: Data set of automobile makes, models and year of production for all car models listed on the Ebay Master Vehicle LIst as of July 2019. This data set has been altered to remove unnecessary fields and include the nation and continent where the car manufacturer is located. The field labeld "diff" indicates the number of years difference between production years of car models.
DOI: 10.6084/m9.figshare.9816344.v1
title: VTKEL

description: VTKEL dataset for all documents (30k+).
DOI: 10.6084/m9.figshare.9816296
title: Data availability--An extended bond-based peridynamic approach for analysis on fracture in brittle materials.zip

description: This is a data about numerical simulation.
DOI: 10.6084/m9.figshare.9816296.v1
title: Data availability--An extended bond-based peridynamic approach for analysis on fracture in brittle materials.zip

description: This is a data about numerical simulation.
DOI: 10.6084/m9.figshare.9816257
title: Supplementary Material for: Association between Deep Gray Matter Changes and Neurocognitive Function in Mild Cognitive Impairment and Alzheimer’s Disease: A Tensor-Based Morphometric MRI Study

description: <b><i>Background:</i></b> Atrophy of the deep gray matter (DGM) has been associated with a risk of conversion from mild cognitive impairment (MCI) to Alzheimer’s disease (AD) and the degree of cognitive impairment. However, specific knowledge of the associations between degenerative DGM changes and neurocognitive functions remains limited. <b><i>Objective:</i></b> To examine degenerative DGM changes and evaluate their association with neurocognitive functions. <b><i>Method:</i></b> We examined DGM volume changes with tensor-based morphometry (TBM) and analyzed the relationships between DGM changes and neurocognitive functions in control (<i>n</i> = 58), MCI (<i>n</i> = 38), and AD (<i>n</i> = 58) groups with multiple linear regression analyses. <b><i>Results:</i></b> In all DGM areas, the AD group had the largest changes in TBM volume. The differences in TBM volume changes were larger between the control group and the AD group than between the other pairs of groups. In the AD group, volume changes of the right thalamus were significantly associated with episodic memory, learning, and semantic processing. Significant or trend-level associations were identified between bilateral caudate nucleus changes and episodic memory as well as semantic processing. In the control and MCI groups, very few significant associations emerged. <b><i>Conclusions:</i></b> Atrophy of the DGM structures, especially the thalamus and caudate nucleus, is related to cognitive impairment in AD. DGM atrophy is associated with tests reflecting both subcortical and cortical cognitive functions.
DOI: 10.6084/m9.figshare.9816224
title: Analysis report.tar.gz

description: BCR CDR3 immunology repertoire:Subjects:Systemic sclerosis (SSc) patients 8: P1-P8.Healthy control 4: H1-H4.The data files:The data file includes Results and Reports, the “Report” part is the sequencing, analysis process and preliminary analysis results.The part of Result includes Clean data.
DOI: 10.6084/m9.figshare.9816242
title: Visual-Textual-Knowledge Entity Linking (VTKEL) dataset

description: VTKEL dataset for 31721 documents.
DOI: 10.6084/m9.figshare.9815753
title: EQiPD systematic review of guidelines for rigor in animal experiments data

description: Dataset generated by the systematic review to identify guidelines for internal validity in the design, conduct and analysis of biomedical experiments involving laboratory animals by the EQiPD (European Quality in Preclinical Data) consortium.<br>
DOI: 10.6084/m9.figshare.9816224.v1
title: report.tar.gz

description: <b> B cell receptor repertoire in systemic sclerosis using high-throughput</b><b> <b>sequencing</b></b>
DOI: 10.6084/m9.figshare.9816242.v1
title: VTKEL dataset

description: VTKEL dataset of all 30k+ documents.
DOI: 10.6084/m9.figshare.9815753.v1
title: SyR_results_guidelines_preclinical_research_quality_EQIPD.csv

description: Semi-Colon delimited CSV file, dataset generated by the systematic review to identify guidelines for internal validity in the design, conduct and analysis of biomedical experiments involving laboratory animals by the EQiPD (European Quality in Preclinical Data) consortium.<br>
DOI: 10.6084/m9.figshare.9816242.v2
title: VTKEL

description: VTKEL dataset of all 30k+ documents.
DOI: 10.6084/m9.figshare.9815753.v2
title: SyR_results_guidelines_preclinical_research_quality_EQIPD.csv

description: Semi-Colon delimited CSV file, dataset generated by the systematic review to identify guidelines for internal validity in the design, conduct and analysis of biomedical experiments involving laboratory animals by the EQiPD (European Quality in Preclinical Data) consortium.<br>
DOI: 10.6084/m9.figshare.9816242.v3
title: Visual-Textual-Knowledge Entity Linking (VTKEL) dataset

description: VTKEL dataset for the 30k+ documents.
DOI: 10.6084/m9.figshare.9816242.v5
title: Visual-Textual-Knowledge Entity Linking (VTKEL) dataset

description: VTKEL dataset for 31721 documents.
DOI: 10.6084/m9.figshare.9816242.v4
title: Visual-Textual-Knowledge Entity Linking (VTKEL) dataset

description: VTKEL dataset for the 30k+ documents.
DOI: 10.6084/m9.figshare.9810830
title: Supplementary Material for: Elder Abuse and Social Capital in Older Adults: The Japan Gerontological Evaluation Study

description: <b><i>Background:</i></b> Elder abuse is a serious public health issue worldwide, but large-scale epidemiologic studies remain sparse. Although social factors in human relations such as social support and social isolation have been proposed as the factors related to elder abuse, cognitive social capital has not been examined. <b><i>Objective:</i></b> This study aims to clarify the prevalence of and the factors associated with elder abuse among independent older adults in Japan. <b><i>Methods:</i></b> The study design is a retrospective observational study. The data were derived from the Japan Gerontological Evaluation Study (JAGES). These self-report data were collected from 26,229 people aged 65 years or older living in 28 municipalities in 2013. The types of elder abuse and factors associated with them were examined using logistic regression analysis. <b><i>Results:</i></b> The prevalence of elder abuse among the sample was 12.3% (11.1% in males and 13.3 in females). In the entire sample, physical, psychological, and financial abuses were reported to be 1.26, 11.12, and 1.45%, respectively. Factors associated with increased odds of experiencing abuse were being a woman, living with family members, having poor self-rated health, and having mild or severe depression. By contrast, age ≥85 years, being widowed, or unmarried, and having a positive view of community trust were associated with a lower risk of experiencing abuse. <b><i>Conclusion:</i></b> While particular demographic factors and health are associated with a greater risk of elder abuse, our findings that trust within the community lessens the risk indicates the importance of social capital. This should be taken into consideration when developing population-based strategies to prevent elder abuse.
DOI: 10.6084/m9.figshare.9810830.v1
title: Supplementary Material for: Elder Abuse and Social Capital in Older Adults: The Japan Gerontological Evaluation Study

description: <b><i>Background:</i></b> Elder abuse is a serious public health issue worldwide, but large-scale epidemiologic studies remain sparse. Although social factors in human relations such as social support and social isolation have been proposed as the factors related to elder abuse, cognitive social capital has not been examined. <b><i>Objective:</i></b> This study aims to clarify the prevalence of and the factors associated with elder abuse among independent older adults in Japan. <b><i>Methods:</i></b> The study design is a retrospective observational study. The data were derived from the Japan Gerontological Evaluation Study (JAGES). These self-report data were collected from 26,229 people aged 65 years or older living in 28 municipalities in 2013. The types of elder abuse and factors associated with them were examined using logistic regression analysis. <b><i>Results:</i></b> The prevalence of elder abuse among the sample was 12.3% (11.1% in males and 13.3 in females). In the entire sample, physical, psychological, and financial abuses were reported to be 1.26, 11.12, and 1.45%, respectively. Factors associated with increased odds of experiencing abuse were being a woman, living with family members, having poor self-rated health, and having mild or severe depression. By contrast, age ≥85 years, being widowed, or unmarried, and having a positive view of community trust were associated with a lower risk of experiencing abuse. <b><i>Conclusion:</i></b> While particular demographic factors and health are associated with a greater risk of elder abuse, our findings that trust within the community lessens the risk indicates the importance of social capital. This should be taken into consideration when developing population-based strategies to prevent elder abuse.
DOI: 10.6084/m9.figshare.9810749
title: Supplemental Table 1 Corticotroph tumors

description: Clinical, demographic, immnohistochemical and molecular characteristics of a series of corticotroph tumors
DOI: 10.6084/m9.figshare.9810749.v1
title: Supplemental Table 1 Corticotroph tumors

description: Clinical, demographic, immnohistochemical and molecular characteristics of a series of corticotroph tumors
DOI: 10.6084/m9.figshare.9810719
title: A high-throughput drug combination screen of targeted small molecule inhibitors in cancer cell lines - supplementary table, code, data

description: Raw and processed data accompanying the Nature Scientific Data article titled "A high-throughput drug combination screen of targeted small molecule inhibitors in cancer cell lines"
DOI: 10.6084/m9.figshare.9810701
title: A high-throughput drug combination screen of targeted small molecule inhibitors in cancer cell lines - data

description: Raw and processed data accompanying the Nature Scientific Data article titled "A high-throughput drug combination screen of targeted small molecule inhibitors in cancer cell lines"
DOI: 10.6084/m9.figshare.9810701.v1
title: A high-throughput drug combination screen of targeted small molecule inhibitors in cancer cell lines - data

description: Raw and processed data accompanying the Nature Scientific Data article titled "A high-throughput drug combination screen of targeted small molecule inhibitors in cancer cell lines"
DOI: 10.6084/m9.figshare.9810677
title: HGF/MET pathway aberrations as diagnostic, prognostic, and predictive biomarkers in human cancers

description: Cancer is a major cause of death worldwide. MET tyrosine kinase receptor [MET, c-MET, hepatocyte growth factor (HGF) receptor] pathway activation is associated with the appearance of several hallmarks of cancer. The HGF/MET pathway has emerged as an important actionable target across many solid tumors; therefore, biomarker discovery becomes essential in order to guide clinical intervention and patient stratification with the aim of moving towards personalized medicine. The focus of this review is on how the aberrant activation of the HGF/MET pathway in tumor tissue or the circulation can provide diagnostic and prognostic biomarkers and predictive biomarkers of drug response. Many meta-analyses have shown that aberrant activation of the MET pathway in tumor tissue, including <i>MET</i> gene overexpression, gene amplification, exon 14 skipping and other activating mutations, is almost invariably associated with shorter survival and poor prognosis. Most meta-analyses have been performed in non-small cell lung cancer (NSCLC), breast, head and neck cancers as well as colorectal, gastric, pancreatic and other gastrointestinal cancers. Furthermore, several studies have shown the predictive value of MET biomarkers in the identification of patients who gain the most benefit from HGF/MET targeted therapies administered as single or combination therapies. The highest predictive values have been observed for response to foretinib and savolitinib in renal cancer, as well as tivantinib in NSCLC and colorectal cancer. However, some studies, especially those based on MET expression, have failed to show much value in these stratifications. This may be rooted in lack of standardization of methodologies, in particular in scoring systems applied in immunohistochemistry determinations or absence of oncogenic addiction of cancer cells to the MET pathway, despite detection of overexpression. Measurements of amplification and mutation aberrations are less likely to suffer from these pitfalls. Increased levels of MET soluble ectodomain (sMET) in circulation have also been associated with poor prognosis; however, the evidence is not as strong as it is with tissue-based biomarkers. As a diagnostic biomarker, sMET has shown its value in distinguishing cancer patients from healthy individuals in prostate and bladder cancers and in melanoma. On the other hand, increased circulating HGF has also been presented as a valuable prognostic and diagnostic biomarker in many cancers; however, there is controversy on the predictive value of HGF as a biomarker. Other biomarkers such as circulating tumor DNA (ctDNA) and tumor HGF levels have also been briefly covered. In conclusion, HGF/MET aberrations can provide valuable diagnostic, prognostic and predictive biomarkers and represent vital assets for personalized cancer therapy.