cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.18585765.v1
title: Additional file 2 of DENA: training an authentic neural network model using Nanopore sequencing data of Arabidopsis transcripts for detection and quantification of N6-methyladenosine on RNA

description: Additional file 2.DENA output containing m6A sites in Col-0, fip37-4 and mtb, and all nonredundant m6A sites identified across all Arabidopsis lines used in this study.
DOI: 10.6084/m9.figshare.14916216
title: The Socioeconomic Gradient in Epigenetic Ageing Clocks: Evidence from the Multi-Ethnic Study of Atherosclerosis and the Health and Retirement Study

description: Epigenetic clocks have been widely used to predict disease risk in multiple tissues or cells. Their success as a measure of biological ageing has prompted research on the connection between epigenetic pathways of ageing and the socioeconomic gradient in health and mortality. However, studies examining social correlates of epigenetic ageing have yielded inconsistent results. We conducted a comprehensive, comparative analysis of associations between various dimensions of socioeconomic status (SES) (education, income, wealth, occupation, neighbourhood environment, and childhood SES) and eight epigenetic clocks in two well-powered US ageing studies: The Multi-Ethnic Study of Atherosclerosis (MESA) (n = 1,211) and the Health and Retirement Study (HRS) (n = 4,018). In both studies, we found robust associations between SES measures in adulthood and the GrimAge and DunedinPoAm clocks (Bonferroni-corrected <i>p</i>-value &lt; 0.01). In the HRS, significant associations with the Levine and Yang clocks were also evident. These associations were only partially mediated by smoking, alcohol consumption, and obesity, which suggests that differences in health behaviours alone cannot explain the SES gradient in epigenetic ageing in older adults. Further analyses revealed concurrent associations between polygenic risk for accelerated intrinsic epigenetic ageing, SES, and the Levine clock, indicating that genetic risk and social disadvantage may contribute additively to faster biological aging.
DOI: 10.6084/m9.figshare.14916216.v1
title: The Socioeconomic Gradient in Epigenetic Ageing Clocks: Evidence from the Multi-Ethnic Study of Atherosclerosis and the Health and Retirement Study

description: Epigenetic clocks have been widely used to predict disease risk in multiple tissues or cells. Their success as a measure of biological ageing has prompted research on the connection between epigenetic pathways of ageing and the socioeconomic gradient in health and mortality. However, studies examining social correlates of epigenetic ageing have yielded inconsistent results. We conducted a comprehensive, comparative analysis of associations between various dimensions of socioeconomic status (SES) (education, income, wealth, occupation, neighbourhood environment, and childhood SES) and eight epigenetic clocks in two well-powered US ageing studies: The Multi-Ethnic Study of Atherosclerosis (MESA) (n = 1,211) and the Health and Retirement Study (HRS) (n = 4,018). In both studies, we found robust associations between SES measures in adulthood and the GrimAge and DunedinPoAm clocks (Bonferroni-corrected <i>p</i>-value &lt; 0.01). In the HRS, significant associations with the Levine and Yang clocks were also evident. These associations were only partially mediated by smoking, alcohol consumption, and obesity, which suggests that differences in health behaviours alone cannot explain the SES gradient in epigenetic ageing in older adults. Further analyses revealed concurrent associations between polygenic risk for accelerated intrinsic epigenetic ageing, SES, and the Levine clock, indicating that genetic risk and social disadvantage may contribute additively to faster biological aging.
DOI: 10.6084/m9.figshare.23819839
title: Additional file 3 of M7G methylated core genes (METTL1 and WDR4) and associated RNA risk signatures are associated with prognosis and immune escape in HCC

description: Additional file 3.
DOI: 10.6084/m9.figshare.23819850
title: Additional file 1 of Clinical plasma cells-related genes to aid therapy in colon cancer

description: Additional file 1.
DOI: 10.6084/m9.figshare.23819850.v1
title: Additional file 1 of Clinical plasma cells-related genes to aid therapy in colon cancer

description: Additional file 1.
DOI: 10.6084/m9.figshare.23819853
title: Additional file 2 of Clinical plasma cells-related genes to aid therapy in colon cancer

description: Additional file 2.
DOI: 10.4121/21207662
title: Data underlying the article: "Ultrahigh Dynamic Range and Low Noise Figure Programmable Integrated Microwave Photonic Filter"

description: Data underlying the article: "Ultrahigh Dynamic Range and Low Noise Figure Programmable Integrated Microwave Photonic Filter".
The data set consists of several different measurement results for the modulation transformer, double injection ring resonator, and microwave photonic filter responses as published in the resource article. 
All data is stored in files using the CSV-format. 
The set is structured to give the data per figure (subfigure), where each subfigure has a folder containing a README-file describing the data in that folder.
DOI: 10.6084/m9.figshare.23819949.v1
title: Additional file 1 of Inhibition of CDC20 potentiates anti-tumor immunity through facilitating GSDME-mediated pyroptosis in prostate cancer

description: Additional file 1: Table S1. List of primers for qRT-PCR. Table S2. The list of human E3 ligases. Table S3. The differential expressing E3 ligase genes between the prostate cancer and normal prostate. Table S4. The analysis of clinical characteristics and the expression of CDC20 by immunohistochemistry. Table S5. The differential expressing genes between the CDC20-low and CDC20-high group. Table S6. List of FACS antibodies. Table S7. Detailed information of datasets used in this study. Table S8. The high confidence results (Core) and CDC20 Expression from TIDE analysis.
DOI: 10.6084/m9.figshare.8113502
title: Additional file 7: of Carbohydrate metabolism and fertility related genes high expression levels promote heterosis in autotetraploid rice harboring double neutral genes

description: Table S5. Correlation analysis between all tissues. (XLSX 96 kb)
DOI: 10.6084/m9.figshare.8113502.v1
title: Additional file 7: of Carbohydrate metabolism and fertility related genes high expression levels promote heterosis in autotetraploid rice harboring double neutral genes

description: Table S5. Correlation analysis between all tissues. (XLSX 96 kb)
DOI: 10.6084/m9.figshare.14889472
title: Additional file 1 of The underlying molecular mechanisms and prognostic factors of RNA binding protein in colorectal cancer: a study based on multiple online databases

description: Additional file 1. The summary of RBPs and their details.
DOI: 10.6084/m9.figshare.14889475
title: Additional file 2 of The underlying molecular mechanisms and prognostic factors of RNA binding protein in colorectal cancer: a study based on multiple online databases

description: Additional file 2. The abnormally expressed RBPs and RBPs related to CRC survival.
DOI: 10.6084/m9.figshare.14889472.v1
title: Additional file 1 of The underlying molecular mechanisms and prognostic factors of RNA binding protein in colorectal cancer: a study based on multiple online databases

description: Additional file 1. The summary of RBPs and their details.
DOI: 10.6084/m9.figshare.23304850.v1
title: Additional file 1 of Steroid responsive idiopathic calcitriol induced hypercalcemia: a case report and review of the literature

description: Supplementary Material 1
DOI: 10.6084/m9.figshare.23304850
title: Additional file 1 of Steroid responsive idiopathic calcitriol induced hypercalcemia: a case report and review of the literature

description: Supplementary Material 1
DOI: 10.6084/m9.figshare.19634698.v1
title: Additional file 1 of Salt-tolerant and thermostable mechanisms of an endoglucanase from marine Aspergillus niger

description: Additional file 1: AnEGL.
DOI: 10.6084/m9.figshare.22269409
title: provin_stat_map.xlsx

description: provincial results by aggregating the biomass resource maps
DOI: 10.6084/m9.figshare.22269451
title: agri_cotton.tif

description: cotton straw map
DOI: 10.6084/m9.figshare.22269454
title: bioenergy_s1_AFE_max.tif

description: agricultural residues, forestry residues, and maximum potential of energy crops
DOI: 10.6084/m9.figshare.22269457
title: agri_soybeans.tif

description: soybeans straw map
DOI: 10.6084/m9.figshare.22269460
title: agri_all.tif

description: agricultural residues map
DOI: 10.6084/m9.figshare.22269463
title: bioenergy_s2_AFE_margin.tif

description: agricultural residues, forestry residues, and energy crops on marginal land
DOI: 10.6084/m9.figshare.22269466
title: bioenergy_s4_AF_max.tif

description: agricultural residues and forestry residues
DOI: 10.6084/m9.figshare.22269466.v1
title: bioenergy_s4_AF_max.tif

description: agricultural residues and forestry residues
DOI: 10.6084/m9.figshare.22269469
title: agri_rice.tif

description: rice straw map
DOI: 10.6084/m9.figshare.22269472
title: agri_maize.tif

description: maize straw map
DOI: 10.6084/m9.figshare.22269475
title: agri_potatoes.tif

description: potatoes straw map
DOI: 10.6084/m9.figshare.22269478
title: agri_peanuts.tif

description: peanuts straw map
DOI: 10.6084/m9.figshare.22269478.v1
title: agri_peanuts.tif

description: peanuts straw map
DOI: 10.6084/m9.figshare.22269481
title: agri_wheat.tif

description: wheat straw map
DOI: 10.6084/m9.figshare.22269484
title: bioenergy_s3_AFE_abandon.tif

description: agricultural residues, forestry residues and energy crops planted on the abandoned cropland
DOI: 10.6084/m9.figshare.17026607
title: Data supporting: Singlet and triplet to doublet energy transfer: improving organic light-emitting diodes with radicals

description: Data supporting: Singlet and triplet to doublet energy transfer: improving organic light-emitting diodes with radicals
DOI: 10.6084/m9.figshare.22269487
title: agri_canola.tif

description: canola straw map
DOI: 10.6084/m9.figshare.22269490
title: agri_other grain.tif

description: the agricultural residues map from other grains
DOI: 10.6084/m9.figshare.22269493
title: bioenergy_s5_AF_min.tif

description: 11% of the agricultural and forestry residues
DOI: 10.6084/m9.figshare.22269496
title: eCrops_best_abandon.tif

description: plant the best energy crops on the abandoned cropland
DOI: 10.6084/m9.figshare.22269499
title: fores_all.tif

description: forestry residues map
DOI: 10.6084/m9.figshare.22269502
title: eCrops_miscanthus_abandon.tif

description: plant miscanthus on the abandoned cropland
DOI: 10.6084/m9.figshare.22269502.v1
title: eCrops_miscanthus_abandon.tif

description: plant miscanthus on the abandoned cropland
DOI: 10.6084/m9.figshare.22269505
title: eCrops_switchgrass_abandon.tif

description: plant switchgrass on the abandoned cropland
DOI: 10.6084/m9.figshare.22269505.v1
title: eCrops_switchgrass_abandon.tif

description: plant switchgrass on the abandoned cropland
DOI: 10.6084/m9.figshare.22269508
title: fores_logging_fuel.tif

description: forestry residues from the logging of the fuel forest
DOI: 10.6084/m9.figshare.22269511
title: eCrops_switchgrass_margin.tif

description: plant switchgrass on the marginal land
DOI: 10.6084/m9.figshare.22269514
title: eCrops_willow_margin.tif

description: plant willow on the marginal land
DOI: 10.6084/m9.figshare.22269517
title: eCrops_poplar_abandon.tif

description: plant poplar on the abandoned cropland
DOI: 10.6084/m9.figshare.22269520
title: fores_logging_protect.tif

description: forestry residues from the logging of the protect forest
DOI: 10.6084/m9.figshare.22269523
title: fores_logging_economic.tif

description: forestry residues from the logging of economic forest.
DOI: 10.6084/m9.figshare.19220905.v1
title: Additional file 2 of Computational identification of clonal cells in single-cell CRISPR screens

description: Additional file 2.
DOI: 10.6084/m9.figshare.22269526
title: eCrops_miscanthus_margin.tif

description: plant miscanthus on the marginal land
DOI: 10.6084/m9.figshare.22269526.v1
title: eCrops_miscanthus_margin.tif

description: plant miscanthus on the marginal land
DOI: 10.6084/m9.figshare.22269529
title: eCrops_eucalypt_margin.tif

description: plant eucalypt on the marginal land
DOI: 10.6084/m9.figshare.22269532
title: eCrops_poplar_margin.tif

description: plant poplar on the marginal land
DOI: 10.6084/m9.figshare.22269532.v1
title: eCrops_poplar_margin.tif

description: plant poplar on the marginal land
DOI: 10.6084/m9.figshare.22269535
title: fores_logging_specialpurpose.tif

description: forestry residues from the logging of the special purpose forest
DOI: 10.6084/m9.figshare.22269538
title: fores_logging_shrub.tif

description: forestry residues from the logging of the shrub forest.
DOI: 10.6084/m9.figshare.22269538.v1
title: fores_logging_shrub.tif

description: forestry residues from the logging of the shrub forest.
DOI: 10.6084/m9.figshare.22269541
title: eCrops_eucalypt_abandon.tif

description: plant eucalypt on the abandoned cropland
DOI: 10.6084/m9.figshare.22269544
title: eCrops_best_margin.tif

description: plant best type of energy crops on marginal land
DOI: 10.6084/m9.figshare.22269544.v1
title: eCrops_best_margin.tif

description: plant best type of energy crops on marginal land
DOI: 10.6084/m9.figshare.22269547
title: eCrops_willow_abandon.tif

description: willow planted on the abandoned cropland
DOI: 10.6084/m9.figshare.22269550
title: fores_logging_sparse.tif

description: forestry residues from the logging of sparse forest
DOI: 10.6084/m9.figshare.22269553
title: fores_woodprocess_bamboo.tif

description: forestry residues from the wood exploitation and process of bamboo
DOI: 10.6084/m9.figshare.22269553.v1
title: fores_woodprocess_bamboo.tif

description: forestry residues from the wood exploitation and process of bamboo
DOI: 10.6084/m9.figshare.22269556
title: fores_woodprocess_log.tif

description: forestry residues from the wood exploitation and process of logs
DOI: 10.6084/m9.figshare.22269559
title: fores_logging_timber.tif

description: forestry residues from the logging of timber forest
DOI: 10.6084/m9.figshare.19634894
title: Additional file 2 of 3-Year outcomes in patients with heavily calcified lesions undergoing percutaneous coronary intervention using cutting balloons

description: Additional file 2: The minimal dataset.
DOI: 10.6084/m9.figshare.22269562
title: fores_woodprocess_fire.tif

description: forestry residues from the wood exploitation and process of fire wood
DOI: 10.6084/m9.figshare.22269565
title: fores_woodprocess_merchant.tif

description: fores_woodprocess_merchant.tif
forestry residues from the wood exploitation and process of commercial wood
DOI: 10.6084/m9.figshare.22269568
title: BioRes_breakdown.nc

description: 36 variables, including 2 variables for marginal land (unit: km2); 10 variables for agricultural residues (tonne); 12 variables for forestry residues (tonne); 6 variables for energy crops on marginal land (tonne); 6 variables for energy crops on abandoned cropland (tonne).
DOI: 10.6084/m9.figshare.19634894.v1
title: Additional file 2 of 3-Year outcomes in patients with heavily calcified lesions undergoing percutaneous coronary intervention using cutting balloons

description: Additional file 2: The minimal dataset.
DOI: 10.6084/m9.figshare.22269571
title: BioEnergy_scenario.nc

description: 5 variables, including s1_AFE_max (GJ), s2_AFE_margin (GJ), s3_AFE_abandon (GJ), s4_AF_max (GJ), s5_AF_min (GJ)
DOI: 10.6084/m9.figshare.24891065
title: Online Statistical Inference for Stochastic Optimization via Kiefer-Wolfowitz Methods

description: This paper investigates the problem of online statistical inference of model parameters in stochastic optimization problems via the Kiefer-Wolfowitz algorithm with random search directions. We first present the asymptotic distribution for the Polyak-Ruppert-averaging type Kiefer-Wolfowitz (AKW) estimators, whose asymptotic covariance matrices depend on the distribution of search directions and the function-value query complexity. The distributional result reflects the trade-off between statistical efficiency and function query complexity. We further analyze the choice of random search directions to minimize certain summary statistics of the asymptotic covariance matrix. Based on the asymptotic distribution, we conduct online statistical inference by providing two construction procedures of valid confidence intervals.
DOI: 10.6084/m9.figshare.24891065.v1
title: Online Statistical Inference for Stochastic Optimization via Kiefer-Wolfowitz Methods

description: This paper investigates the problem of online statistical inference of model parameters in stochastic optimization problems via the Kiefer-Wolfowitz algorithm with random search directions. We first present the asymptotic distribution for the Polyak-Ruppert-averaging type Kiefer-Wolfowitz (AKW) estimators, whose asymptotic covariance matrices depend on the distribution of search directions and the function-value query complexity. The distributional result reflects the trade-off between statistical efficiency and function query complexity. We further analyze the choice of random search directions to minimize certain summary statistics of the asymptotic covariance matrix. Based on the asymptotic distribution, we conduct online statistical inference by providing two construction procedures of valid confidence intervals.
DOI: 10.6084/m9.figshare.24891068
title: Estimating Cell-Type-Specific Gene Co-Expression Networks from Bulk Gene Expression Data with an Application to Alzheimer’s Disease

description: Inferring and characterizing gene co-expression networks has led to important insights on the molecular mechanisms of complex diseases. Most co-expression analyses to date have been performed on gene expression data collected from bulk tissues with different cell type compositions across samples. As a result, the co-expression estimates only offer an aggregated view of the underlying gene regulations and can be confounded by heterogeneity in cell type compositions, failing to reveal gene coordination that may be distinct across different cell types. In this article, we introduce a flexible framework for estimating cell-type-specific gene co-expression networks from bulk sample data, without making specific assumptions on the distributions of gene expression profiles in different cell types. We develop a novel sparse least squares estimator, referred to as CSNet, that is efficient to implement and has good theoretical properties. Using CSNet, we analyzed the bulk gene expression data from a cohort study on Alzheimer’s disease and identified previously unknown cell-type-specific co-expressions among Alzheimer’s disease risk genes, suggesting cell-type-specific disease mechanisms. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.24891068.v2
title: Estimating Cell-Type-Specific Gene Co-Expression Networks from Bulk Gene Expression Data with an Application to Alzheimer’s Disease

description: Inferring and characterizing gene co-expression networks has led to important insights on the molecular mechanisms of complex diseases. Most co-expression analyses to date have been performed on gene expression data collected from bulk tissues with different cell type compositions across samples. As a result, the co-expression estimates only offer an aggregated view of the underlying gene regulations and can be confounded by heterogeneity in cell type compositions, failing to reveal gene coordination that may be distinct across different cell types. In this article, we introduce a flexible framework for estimating cell-type-specific gene co-expression networks from bulk sample data, without making specific assumptions on the distributions of gene expression profiles in different cell types. We develop a novel sparse least squares estimator, referred to as CSNet, that is efficient to implement and has good theoretical properties. Using CSNet, we analyzed the bulk gene expression data from a cohort study on Alzheimer’s disease and identified previously unknown cell-type-specific co-expressions among Alzheimer’s disease risk genes, suggesting cell-type-specific disease mechanisms. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.24891107
title: Dynamic Matrix Recovery

description: Matrix recovery from sparse observations is an extensively studied topic emerging in various applications, such as recommendation system and signal processing, which includes the matrix completion and compressed sensing models as special cases. In this work, we propose a general framework for dynamic matrix recovery of low-rank matrices that evolve smoothly over time. We start from the setting that the observations are independent across time, then extend to the setting that both the design matrix and noise possess certain temporal correlation via modified concentration inequalities. By pooling neighboring observations, we obtain sharp estimation error bounds of both settings, showing the influence of the underlying smoothness, the dependence and effective samples. We propose a dynamic fast iterative shrinkage-thresholding algorithm that is computationally efficient, and characterize the interplay between algorithmic and statistical convergence. Simulated and real data examples are provided to support such findings.
DOI: 10.6084/m9.figshare.24891107.v1
title: Dynamic Matrix Recovery

description: Matrix recovery from sparse observations is an extensively studied topic emerging in various applications, such as recommendation system and signal processing, which includes the matrix completion and compressed sensing models as special cases. In this work, we propose a general framework for dynamic matrix recovery of low-rank matrices that evolve smoothly over time. We start from the setting that the observations are independent across time, then extend to the setting that both the design matrix and noise possess certain temporal correlation via modified concentration inequalities. By pooling neighboring observations, we obtain sharp estimation error bounds of both settings, showing the influence of the underlying smoothness, the dependence and effective samples. We propose a dynamic fast iterative shrinkage-thresholding algorithm that is computationally efficient, and characterize the interplay between algorithmic and statistical convergence. Simulated and real data examples are provided to support such findings.
DOI: 10.6084/m9.figshare.24891116
title: A Kernel Measure of Dissimilarity between <i>M</i> Distributions

description: Given M≥2 distributions defined on a general measurable space, we introduce a nonparametric (kernel) measure of multi-sample dissimilarity (KMD)—a parameter that quantifies the difference between the <i>M</i> distributions. The population KMD, which takes values between 0 and 1, is 0 if and only if all the <i>M</i> distributions are the same, and 1 if and only if all the distributions are mutually singular. Moreover, KMD possesses many properties commonly associated with <i>f</i>-divergences such as the data processing inequality and invariance under bijective transformations. The sample estimate of KMD, based on independent observations from the <i>M</i> distributions, can be computed in near linear time (up to logarithmic factors) using <i>k</i>-nearest neighbor graphs (for k≥1 fixed). We develop an easily implementable test for the equality of <i>M</i> distributions based on the sample KMD that is consistent against all alternatives where at least two distributions are not equal. We prove central limit theorems for the sample KMD, and provide a complete characterization of the asymptotic power of the test, as well as its detection threshold. The usefulness of our measure is demonstrated via real and synthetic data examples; our method is also implemented in an R package. Supplementary materials for this article are available online.