cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.10566959.v1
title: MOESM1 of Identification of key genes and regulators associated with carotenoid metabolism in apricot (Prunus armeniaca) fruit using weighted gene coexpression network analysis

description: Additional file 1. Throughput and quality of RNA-Seq data in apricot fruit.
DOI: 10.6084/m9.figshare.10566965
title: MOESM2 of Identification of key genes and regulators associated with carotenoid metabolism in apricot (Prunus armeniaca) fruit using weighted gene coexpression network analysis

description: Additional file 2. Statistics of assembly quality.
DOI: 10.6084/m9.figshare.22622809.v1
title: Additional file 2 of Sex differences in the intergenerational link between maternal and neonatal whole blood DNA methylation: a genome-wide analysis in 2 birth cohorts

description: Additional file 2. Supplementary Tables.
DOI: 10.6084/m9.figshare.10566965.v1
title: MOESM2 of Identification of key genes and regulators associated with carotenoid metabolism in apricot (Prunus armeniaca) fruit using weighted gene coexpression network analysis

description: Additional file 2. Statistics of assembly quality.
DOI: 10.6084/m9.figshare.22622852
title: Additional file 3 of Differential expression of pyroptosis-related genes in the hippocampus of patients with Alzheimer’s disease

description: Supplementary Material 3
DOI: 10.6084/m9.figshare.22622852.v1
title: Additional file 3 of Differential expression of pyroptosis-related genes in the hippocampus of patients with Alzheimer’s disease

description: Supplementary Material 3
DOI: 10.6084/m9.figshare.22622855
title: Additional file 4 of Differential expression of pyroptosis-related genes in the hippocampus of patients with Alzheimer’s disease

description: Supplementary Material 4
DOI: 10.6084/m9.figshare.12133827
title: Additional file 1 of KIF15 facilitates gastric cancer via enhancing proliferation, inhibiting apoptosis, and predict poor prognosis

description: Additional file 1: Table S1. The green boxes showed seven positive anti-apoptotic proteins which were detected by the Human Apoptosis Antibody Array kit (ab134001).
DOI: 10.6084/m9.figshare.10566977
title: MOESM4 of Identification of key genes and regulators associated with carotenoid metabolism in apricot (Prunus armeniaca) fruit using weighted gene coexpression network analysis

description: Additional file 4. Differentially expressed genes (DEGs) shown in Fig. 3b.
DOI: 10.6084/m9.figshare.10566977.v1
title: MOESM4 of Identification of key genes and regulators associated with carotenoid metabolism in apricot (Prunus armeniaca) fruit using weighted gene coexpression network analysis

description: Additional file 4. Differentially expressed genes (DEGs) shown in Fig. 3b.
DOI: 10.6084/m9.figshare.10566989
title: MOESM6 of Identification of key genes and regulators associated with carotenoid metabolism in apricot (Prunus armeniaca) fruit using weighted gene coexpression network analysis

description: Additional file 6. Significantly enriched differentially expressed genes (DEGs) in Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways during different ripening stages.
DOI: 10.6084/m9.figshare.10566989.v1
title: MOESM6 of Identification of key genes and regulators associated with carotenoid metabolism in apricot (Prunus armeniaca) fruit using weighted gene coexpression network analysis

description: Additional file 6. Significantly enriched differentially expressed genes (DEGs) in Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways during different ripening stages.
DOI: 10.6084/m9.figshare.22619659
title: Additional file 4 of Quantitative proteomics analysis in small cell carcinoma of cervix reveals novel therapeutic targets

description: Additional file 4. Additional Table, supplementary Table 4, the qualitative differences between SCCC and normal tissues.
DOI: 10.6084/m9.figshare.10566995
title: MOESM7 of Identification of key genes and regulators associated with carotenoid metabolism in apricot (Prunus armeniaca) fruit using weighted gene coexpression network analysis

description: Additional file 7. The expression and functional annotation of genes shown in Fig. 5b.
DOI: 10.6084/m9.figshare.10566995.v1
title: MOESM7 of Identification of key genes and regulators associated with carotenoid metabolism in apricot (Prunus armeniaca) fruit using weighted gene coexpression network analysis

description: Additional file 7. The expression and functional annotation of genes shown in Fig. 5b.
DOI: 10.6084/m9.figshare.10567001
title: MOESM8 of Identification of key genes and regulators associated with carotenoid metabolism in apricot (Prunus armeniaca) fruit using weighted gene coexpression network analysis

description: Additional file 8. The expression and functional annotation of genes shown in Fig. 6.
DOI: 10.6084/m9.figshare.10567001.v1
title: MOESM8 of Identification of key genes and regulators associated with carotenoid metabolism in apricot (Prunus armeniaca) fruit using weighted gene coexpression network analysis

description: Additional file 8. The expression and functional annotation of genes shown in Fig. 6.
DOI: 10.6084/m9.figshare.10567007
title: MOESM9 of Identification of key genes and regulators associated with carotenoid metabolism in apricot (Prunus armeniaca) fruit using weighted gene coexpression network analysis

description: Additional file 9. Primer sequences used for real-time quantitative PCR.
DOI: 10.6084/m9.figshare.10567007.v1
title: MOESM9 of Identification of key genes and regulators associated with carotenoid metabolism in apricot (Prunus armeniaca) fruit using weighted gene coexpression network analysis

description: Additional file 9. Primer sequences used for real-time quantitative PCR.
DOI: 10.6084/m9.figshare.10042784
title: Template Independent Component Analysis: Targeted and Reliable Estimation of Subject-level Brain Networks Using Big Data Population Priors

description: Large brain imaging databases contain a wealth of information on brain organization in the populations they target, and on individual variability. While such databases have been used to study group-level features of populations directly, they are currently underutilized as a resource to inform single-subject analysis. Here, we propose leveraging the information contained in large functional magnetic resonance imaging (fMRI) databases by establishing population priors to employ in an empirical Bayesian framework. We focus on estimation of brain networks as source signals in independent component analysis (ICA). We formulate a hierarchical “template” ICA model where source signals—including known population brain networks and subject-specific signals—are represented as latent variables. For estimation, we derive an expectation–maximization (EM) algorithm having an explicit solution. However, as this solution is computationally intractable, we also consider an approximate subspace algorithm and a faster two-stage approach. Through extensive simulation studies, we assess performance of both methods and compare with dual regression, a popular but ad-hoc method. The two proposed algorithms have similar performance, and both dramatically outperform dual regression. We also conduct a reliability study utilizing the Human Connectome Project and find that template ICA achieves substantially better performance than dual regression, achieving 75–250% higher intra-subject reliability. 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.10042784.v2
title: Template Independent Component Analysis: Targeted and Reliable Estimation of Subject-level Brain Networks Using Big Data Population Priors

description: Large brain imaging databases contain a wealth of information on brain organization in the populations they target, and on individual variability. While such databases have been used to study group-level features of populations directly, they are currently underutilized as a resource to inform single-subject analysis. Here, we propose leveraging the information contained in large functional magnetic resonance imaging (fMRI) databases by establishing population priors to employ in an empirical Bayesian framework. We focus on estimation of brain networks as source signals in independent component analysis (ICA). We formulate a hierarchical “template” ICA model where source signals—including known population brain networks and subject-specific signals—are represented as latent variables. For estimation, we derive an expectation–maximization (EM) algorithm having an explicit solution. However, as this solution is computationally intractable, we also consider an approximate subspace algorithm and a faster two-stage approach. Through extensive simulation studies, we assess performance of both methods and compare with dual regression, a popular but ad-hoc method. The two proposed algorithms have similar performance, and both dramatically outperform dual regression. We also conduct a reliability study utilizing the Human Connectome Project and find that template ICA achieves substantially better performance than dual regression, achieving 75–250% higher intra-subject reliability. 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.22619659.v1
title: Additional file 4 of Quantitative proteomics analysis in small cell carcinoma of cervix reveals novel therapeutic targets

description: Additional file 4. Additional Table, supplementary Table 4, the qualitative differences between SCCC and normal tissues.
DOI: 10.6084/m9.figshare.19480083
title: A new high-resolution paleotemperature record during the Middle–Late Ordovician transition derived from conodont δ18O paleo-thermometry

description: Three supplementary tables (S1, S2, and S3) indicating the <i>in-situ</i> oxygen isotopic results of conodont apatite from the Kalpin Shuinichang-Dawangou composite section, Qinghu standard, and Durango standard, respectively.
DOI: 10.6084/m9.figshare.19480083.v1
title: A new high-resolution paleotemperature record during the Middle–Late Ordovician transition derived from conodont δ18O paleo-thermometry

description: Three supplementary tables (S1, S2, and S3) indicating the <i>in-situ</i> oxygen isotopic results of conodont apatite from the Kalpin Shuinichang-Dawangou composite section, Qinghu standard, and Durango standard, respectively.
DOI: 10.6084/m9.figshare.14237212
title: Do combined assays of serum AFP, AFP-L3, DCP, GP73, and DKK-1 efficiently improve the clinical values of biomarkers in decision-making for hepatocellular carcinoma? A meta-analysis

description: <b>Objectives</b>: Serum biomarkers are valuable for clinical decision-making for patients with hepatocellular carcinoma (HCC), among which the most promising are AFP, AFP-L3, DCP, DKK-1, and GP73; however, the efficacy of using combined biomarkers remains controversial. This meta-analysis provides insights regarding this topic. <b>Methods</b>: After systematically surveying the literature available in PubMed, Embase, and Cochrane Library, we identified 28 qualified articles published since January 2015. A random-effects model was used to assess pooled sensitivity, specificity, positive and negative likelihood ratios (PLRs and NLPs), and diagnostic odds ratio (DOR). <b>Results</b>: Values under the summary receiver operating characteristic (SROC) curve varied in different panels of the five biomarkers. Importantly, the sum of sensitivity and specificity of AFP+GP73 was 1.76 (P= 0.0001), which was the best among all the panels. The sum of the triple biomarker panel of AFP, AFP-L3, and DCP was larger (1.64, P= 0.0001) than those of any double biomarker panels of AFP, AFP-L3, and DCP. <b>Conclusions</b>: To the best of our knowledge, this is the first meta-analysis to focus solely on combination assays of multiple biomarkers in HCC. The combined assay of AFP and GP73 conferred the best outcome among all panels. The triple combined panel of AFP, AFP-L3, and DCP showed higher diagnostic potential than individual random double combinations of the three biomarkers. Multiple-biomarker combined assays will be clinically important for decision-making processes for HCC.
DOI: 10.6084/m9.figshare.22619690.v1
title: Additional file 3 of Cell-specific clock-controlled gene expression program regulates rhythmic fiber cell growth in cotton

description: Additional file 3: Table S2. Gene list and expression levels of cell marker genes, the expression levels of DEGs in scRNA-seq, and the highly expressed genes in C3.
DOI: 10.6084/m9.figshare.22619693
title: Additional file 4 of Cell-specific clock-controlled gene expression program regulates rhythmic fiber cell growth in cotton

description: Additional file 4: Table S3. Pseudo-time analysis of scRNA-seq in C1, C2 and C3 cell clusters.
DOI: 10.6084/m9.figshare.22619711.v1
title: Additional file 9 of Cell-specific clock-controlled gene expression program regulates rhythmic fiber cell growth in cotton

description: Additional file 9: Table S8. List of DARs and DAGs for scATAC-seq data.
DOI: 10.6084/m9.figshare.22619714.v1
title: Additional file 10 of Cell-specific clock-controlled gene expression program regulates rhythmic fiber cell growth in cotton

description: Additional file 10: Table S9. List of 8-mer motifs and their target genes.
DOI: 10.6084/m9.figshare.13712996
title: Tagging the main entrances of public buildings based on OpenStreetMap and binary imbalanced learning

description: Determining the location of a building’s entrance is crucial to location-based services, such as wayfinding for pedestrians. Unfortunately, entrance information is often missing from current mainstream map providers such as Google Maps. Frequently, automatic approaches for detecting building entrances are based on street-level images that are not widely available. To address this issue, we propose a more general approach for inferring the main entrances of public buildings based on the association between spatial elements extracted from OpenStreetMap. In particular, we adopt three binary classification approaches, weighted random forest, balanced random forest, and smooth-boost to model the association relationship. There are two types of features considered in the classification: intrinsic features derived from building footprints and extrinsic features derived from spatial contexts, such as roads, green spaces, bicycle parking areas, and neighboring buildings. We conducted extensive experiments on 320 public buildings with an average perimeter of 350 m. The experimental results showed that the locations of building entrances estimated by the weighted random forest and balanced random forest models have a mean linear distance error of 21 m and a mean path distance error of 22 m, ruling out 90% of the incorrect locations of the main entrance of buildings.
DOI: 10.6084/m9.figshare.7945838
title: Lunar Cumulate Mantle Overturn: A Model Constrained by Ilmenite Rheology

description: We investigate the effects of temperature- and ilmenite-dependent mantle rheology on the dynamic process of lunar cumulate mantle overturn and conditions for long wavelength downwellings of an IBC-layer in a 3D spherical geometry. Our results show that the ilmenite-induced rheological weakening is necessary to decouple the IBC layer from the top stagnant lid and facilitate overturn
DOI: 10.6084/m9.figshare.22619650
title: Additional file 1 of Quantitative proteomics analysis in small cell carcinoma of cervix reveals novel therapeutic targets

description: Additional file 1. Additional Table, supplementary Table 1, overview of the proteomics profiles identified by DIA in SCCC and normal cervix tissues.
DOI: 10.6084/m9.figshare.22619653
title: Additional file 2 of Quantitative proteomics analysis in small cell carcinoma of cervix reveals novel therapeutic targets

description: Additional file 2. Additional Table, supplementary Table 2, the differentially expressed proteins (DEPs) associated with SCCC.
DOI: 10.6084/m9.figshare.22619717.v1
title: Additional file 11 of Cell-specific clock-controlled gene expression program regulates rhythmic fiber cell growth in cotton

description: Additional file 11: Table S10. List of G-box containing genes with WT enriched ATAC-seq peak.
DOI: 10.6084/m9.figshare.22623034
title: Additional file 1 of A scoping review on two-stage randomized preference trial in the field of mental health and addiction

description: Additional file 1: Table S1. Number of patients dropout in each arm of the two-stage trials included in the review. Table S2. Outcome mean and standard deviation in each arm of the two-stage trials included in the review.
DOI: 10.6084/m9.figshare.22623034.v1
title: Additional file 1 of A scoping review on two-stage randomized preference trial in the field of mental health and addiction

description: Additional file 1: Table S1. Number of patients dropout in each arm of the two-stage trials included in the review. Table S2. Outcome mean and standard deviation in each arm of the two-stage trials included in the review.
DOI: 10.6084/m9.figshare.22619656
title: Additional file 3 of Quantitative proteomics analysis in small cell carcinoma of cervix reveals novel therapeutic targets

description: Additional file 3. Additional Table, supplementary Table 3, functional enrichment analysis of DEPs associated with SCCC. (a) GO enrichment of DEPs between SCCC and normal cervix tissues. (b) KEGG enrichment of DEPs between SCCC and normal cervix tissues.
DOI: 10.6084/m9.figshare.22619653.v1
title: Additional file 2 of Quantitative proteomics analysis in small cell carcinoma of cervix reveals novel therapeutic targets

description: Additional file 2. Additional Table, supplementary Table 2, the differentially expressed proteins (DEPs) associated with SCCC.
DOI: 10.34740/kaggle/dsv/7588323
title: Global Genomic Neurofibromatosis Neoplasia
DOI: 10.6084/m9.figshare.25187855
title: Teacher Wellbeing Dataset

description: A dataset on the relationships among teachers' subjective wellbeing, religiosity, and trust in science during the Covid-19 pandemic
DOI: 10.6084/m9.figshare.10043090
title: Metadata record for: Global soil, landuse, evapotranspiration, historical and future weather databases for SWAT Applications

description: This dataset contains key characteristics about the data described in the Data Descriptor Global soil, landuse, evapotranspiration, historical and future weather databases for SWAT Applications. <br>
 Contents: <br>
 
 1. human readable metadata summary table in CSV format
 
 
 2. machine readable metadata file in JSON format<br><br>Versioning Note:Version 2 was generated when the metadata format was updated from JSON to JSON-LD. This was an automatic process that changed only the format, not the contents, of the metadata.<br>
DOI: 10.6084/m9.figshare.10043090.v1
title: Metadata record for: Global soil, landuse, evapotranspiration, historical and future weather databases for SWAT Applications

description: This dataset contains key characteristics about the data described in the Data Descriptor Global soil, landuse, evapotranspiration, historical and future weather databases for SWAT Applications. <br>
 Contents: <br>
 
 1. human readable metadata summary table in CSV format
 
 
 2. machine readable metadata file in JSON format
DOI: 10.17632/k8h9mh74vk.2
title: Strata Shaper

description: A numerical modeling assistant software developed for pre-research in applying for National Natural Science Foundation projects.
DOI: 10.17632/k8h9mh74vk.1
title: Strata Shaper

description: Modeling software developed in advance for applying for the Natural Science Foundation of China.
DOI: 10.6084/m9.figshare.22619656.v1
title: Additional file 3 of Quantitative proteomics analysis in small cell carcinoma of cervix reveals novel therapeutic targets

description: Additional file 3. Additional Table, supplementary Table 3, functional enrichment analysis of DEPs associated with SCCC. (a) GO enrichment of DEPs between SCCC and normal cervix tissues. (b) KEGG enrichment of DEPs between SCCC and normal cervix tissues.
DOI: 10.5281/zenodo.10571866
title: Artifacts for "Lightweight Syntactic API Usage Analysis with UCov"

description: The content of this dataset accompanies the paper "Lightweight Syntactic API Usage Analysis with UCov" authored by Gustave Monce, Thomas Couturou, Yasmine Hamdaoui, Thomas Degueule and Jean-Rémy Falleri.

The paper was published at the 46th International Conference on Program Comprehension (ICPC 2024) Research track, in Lisbon, Portugal.

The dataset contains all artefacts used in the UCov paper's exploratory case study, notably:



The code of each library studied (source code, tests, samples)

The code of each client studied (for all libraries)

Reproduction scripts to re-obtain the data used for the paper

Notebooks used to generate graphs used in the paper

UCov binary used for the exploratory case study


Relevant Links



UCov: https://github.com/alien-tools/ucov
DOI: 10.5281/zenodo.10571867
title: Artifacts for "Lightweight Syntactic API Usage Analysis with UCov"

description: The content of this dataset accompanies the paper "Lightweight Syntactic API Usage Analysis with UCov" authored by Gustave Monce, Thomas Couturou, Yasmine Hamdaoui, Thomas Degueule and Jean-Rémy Falleri.

The paper was published at the 46th International Conference on Program Comprehension (ICPC 2024) Research track, in Lisbon, Portugal.

The dataset contains all artefacts used in the UCov paper's exploratory case study, notably:



The code of each library studied (source code, tests, samples)

The code of each client studied (for all libraries)

Reproduction scripts to re-obtain the data used for the paper

Notebooks used to generate graphs used in the paper

UCov binary used for the exploratory case study


Relevant Links



UCov: https://github.com/alien-tools/ucov
DOI: 10.17632/489m7j964j.1
title: JDS appurtenant material

description: This study delves into the effects of Trimethylamine N-oxide (TMAO) on lipid metabolism within bovine liver cells, a pivotal aspect in the onset of fatty liver disease among cattle.
DOI: 10.17632/5wy49h687k.1
title: Quill mites on Birds-of-Paradise

description: Raw data used in the bipartite analysis