cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5937661.v1
title: Additional file 1: of Integrated proteomics and network analysis identifies protein hubs and network alterations in Alzheimerâ s disease

description: Table S1. Demographic and neuropathological data of human AD patient and control cases. For each case, the age, gender, disease status, age at onset, disease duration, Braak stage, CERAD neuritic plaque score, frontal cortex neuritic plaque frequency, ApoE genotype, and postmortem interval (PMI) are provided. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.5937682
title: Additional file 2: of Integrated proteomics and network analysis identifies protein hubs and network alterations in Alzheimer’s disease

description: Table S2. Differential expression analysis of protein abundances in AD and control brains. List of all proteins with complete abundance data in AD and control brains is provided with their fold changes, P values, and q values. Differentially expressed proteins with significantly altered protein abundances (&gt; 1.3-fold change; P &lt; 0.05) in AD versus control are indicated in bold and also provided in separate tabs. (XLSX 660 kb)
DOI: 10.6084/m9.figshare.5937682.v1
title: Additional file 2: of Integrated proteomics and network analysis identifies protein hubs and network alterations in Alzheimer’s disease

description: Table S2. Differential expression analysis of protein abundances in AD and control brains. List of all proteins with complete abundance data in AD and control brains is provided with their fold changes, P values, and q values. Differentially expressed proteins with significantly altered protein abundances (&gt; 1.3-fold change; P &lt; 0.05) in AD versus control are indicated in bold and also provided in separate tabs. (XLSX 660 kb)
DOI: 10.6084/m9.figshare.5937697
title: Additional file 3: of Integrated proteomics and network analysis identifies protein hubs and network alterations in Alzheimerâ s disease

description: Table S3. List of novel proteins with altered abundances in AD identified in the present study. The fold changes of protein abundances in AD versus control are provided with corresponding P values and q values. (XLSX 51 kb)
DOI: 10.6084/m9.figshare.5937697.v1
title: Additional file 3: of Integrated proteomics and network analysis identifies protein hubs and network alterations in Alzheimerâ s disease

description: Table S3. List of novel proteins with altered abundances in AD identified in the present study. The fold changes of protein abundances in AD versus control are provided with corresponding P values and q values. (XLSX 51 kb)
DOI: 10.6084/m9.figshare.5937724
title: Additional file 4: of Integrated proteomics and network analysis identifies protein hubs and network alterations in Alzheimerâ s disease

description: Table S4. Gene ontology (GO) term enrichment for differentially expressed proteins in AD. The enriched GO terms with associated P values (Benjamini-Hochberg FDR corrected) for biological processes, cellular compartments, and molecular functions are provided in separate tabs. (XLSX 35 kb)
DOI: 10.6084/m9.figshare.5937724.v1
title: Additional file 4: of Integrated proteomics and network analysis identifies protein hubs and network alterations in Alzheimerâ s disease

description: Table S4. Gene ontology (GO) term enrichment for differentially expressed proteins in AD. The enriched GO terms with associated P values (Benjamini-Hochberg FDR corrected) for biological processes, cellular compartments, and molecular functions are provided in separate tabs. (XLSX 35 kb)
DOI: 10.6084/m9.figshare.5937742
title: Additional file 5: of Integrated proteomics and network analysis identifies protein hubs and network alterations in Alzheimerâ s disease

description: Table S5. Protein co-expression network analysis by WGCNA. Network analysis of the entire proteomic data set from all AD and control cases identified 24 network modules, M1 to M24, coded by different colors according to the convention of WGCNA. Proteins that were not assigned to any module were coded by the color grey in M0. The complete list of proteins in each module and their module membership values (kME) are provided. (XLSX 724 kb)
DOI: 10.6084/m9.figshare.5937742.v1
title: Additional file 5: of Integrated proteomics and network analysis identifies protein hubs and network alterations in Alzheimerâ s disease

description: Table S5. Protein co-expression network analysis by WGCNA. Network analysis of the entire proteomic data set from all AD and control cases identified 24 network modules, M1 to M24, coded by different colors according to the convention of WGCNA. Proteins that were not assigned to any module were coded by the color grey in M0. The complete list of proteins in each module and their module membership values (kME) are provided. (XLSX 724 kb)
DOI: 10.6084/m9.figshare.5937766
title: Additional file 6: of Integrated proteomics and network analysis identifies protein hubs and network alterations in Alzheimerâ s disease

description: Table S6. Gene ontology (GO) term enrichment for proteins in WGCNA modules. The enriched GO terms with associated P values (Benjamini-Hochberg FDR corrected) for biological processes, cellular components, and molecular functions are provided in separate tabs. (XLSX 147 kb)
DOI: 10.6084/m9.figshare.5937766.v1
title: Additional file 6: of Integrated proteomics and network analysis identifies protein hubs and network alterations in Alzheimerâ s disease

description: Table S6. Gene ontology (GO) term enrichment for proteins in WGCNA modules. The enriched GO terms with associated P values (Benjamini-Hochberg FDR corrected) for biological processes, cellular components, and molecular functions are provided in separate tabs. (XLSX 147 kb)
DOI: 10.6084/m9.figshare.5937805
title: MOESM10 of High-level accumulation of oleyl oleate in plant seed oil by abundant supply of oleic acid substrates to efficient wax ester synthesis enzymes

description: Additional file 10: Table S6. List of DNA constructs used in this study for expressing wax ester synthesis enzymes.
DOI: 10.6084/m9.figshare.5937805.v1
title: MOESM10 of High-level accumulation of oleyl oleate in plant seed oil by abundant supply of oleic acid substrates to efficient wax ester synthesis enzymes

description: Additional file 10: Table S6. List of DNA constructs used in this study for expressing wax ester synthesis enzymes.
DOI: 10.6084/m9.figshare.5937811
title: Additional file 1: of Health care resource use among patients with advanced non-small cell lung cancer: the PIvOTAL retrospective observational study

description: Ethics Committee Names and Locations. (XLSX 13Â kb)
DOI: 10.6084/m9.figshare.5937811.v1
title: Additional file 1: of Health care resource use among patients with advanced non-small cell lung cancer: the PIvOTAL retrospective observational study

description: Ethics Committee Names and Locations. (XLSX 13Â kb)
DOI: 10.6084/m9.figshare.5937835
title: MOESM2 of High-level accumulation of oleyl oleate in plant seed oil by abundant supply of oleic acid substrates to efficient wax ester synthesis enzymes

description: Additional file 2: Table S1. Raw data obtained by GC-FID to quantify the wax ester content in seeds of transgenic Arabidopsis transformed with MaFAR/ScWS, ScWS-MaFAR, ScWS-MaFAR/ScWS-MaFAR, ScWS-MaFAR/MaFAR, MaFAR/AbWSD1, MaFAR/PCOAbWSD1, MaFAR/TMMmAWAT2-AbWSD1 and MaFAR/MaWS2 shown in Figs.Â 1 and 3.
DOI: 10.6084/m9.figshare.5937835.v1
title: MOESM2 of High-level accumulation of oleyl oleate in plant seed oil by abundant supply of oleic acid substrates to efficient wax ester synthesis enzymes

description: Additional file 2: Table S1. Raw data obtained by GC-FID to quantify the wax ester content in seeds of transgenic Arabidopsis transformed with MaFAR/ScWS, ScWS-MaFAR, ScWS-MaFAR/ScWS-MaFAR, ScWS-MaFAR/MaFAR, MaFAR/AbWSD1, MaFAR/PCOAbWSD1, MaFAR/TMMmAWAT2-AbWSD1 and MaFAR/MaWS2 shown in Figs.Â 1 and 3.
DOI: 10.6084/m9.figshare.5937853
title: MOESM3 of High-level accumulation of oleyl oleate in plant seed oil by abundant supply of oleic acid substrates to efficient wax ester synthesis enzymes

description: Additional file 3: Table S2. Raw data obtained by ESI-MS/MS to determine the molecular species of wax esters in seeds of transgenic Arabidopsis transformed with MaFAR/AbWSD1 shown in Fig.Â 4.
DOI: 10.6084/m9.figshare.5937853.v1
title: MOESM3 of High-level accumulation of oleyl oleate in plant seed oil by abundant supply of oleic acid substrates to efficient wax ester synthesis enzymes

description: Additional file 3: Table S2. Raw data obtained by ESI-MS/MS to determine the molecular species of wax esters in seeds of transgenic Arabidopsis transformed with MaFAR/AbWSD1 shown in Fig.Â 4.
DOI: 10.6084/m9.figshare.5937871
title: MOESM4 of High-level accumulation of oleyl oleate in plant seed oil by abundant supply of oleic acid substrates to efficient wax ester synthesis enzymes

description: Additional file 4: Table S3. Raw data obtained by GC-FID to quantify the contents of wax esters in seeds of Camelina MaFAR/ScWS and High Oleic crosses shown in Fig.Â 5.
DOI: 10.6084/m9.figshare.5937871.v1
title: MOESM4 of High-level accumulation of oleyl oleate in plant seed oil by abundant supply of oleic acid substrates to efficient wax ester synthesis enzymes

description: Additional file 4: Table S3. Raw data obtained by GC-FID to quantify the contents of wax esters in seeds of Camelina MaFAR/ScWS and High Oleic crosses shown in Fig.Â 5.
DOI: 10.6084/m9.figshare.5937880
title: MOESM5 of High-level accumulation of oleyl oleate in plant seed oil by abundant supply of oleic acid substrates to efficient wax ester synthesis enzymes

description: Additional file 5: Table S4. Calculation process of ESI-MS/MS data to determine the molecular species of wax esters in seeds of Camelina MaFAR/ScWS and High Oleic crosses shown in Fig.Â 6.
DOI: 10.6084/m9.figshare.5937880.v1
title: MOESM5 of High-level accumulation of oleyl oleate in plant seed oil by abundant supply of oleic acid substrates to efficient wax ester synthesis enzymes

description: Additional file 5: Table S4. Calculation process of ESI-MS/MS data to determine the molecular species of wax esters in seeds of Camelina MaFAR/ScWS and High Oleic crosses shown in Fig.Â 6.
DOI: 10.6084/m9.figshare.5937943
title: MOESM9 of High-level accumulation of oleyl oleate in plant seed oil by abundant supply of oleic acid substrates to efficient wax ester synthesis enzymes

description: Additional file 9: Table S5. List of primers used in this study for amplifying DNA sequences of wax ester synthesis enzymes.
DOI: 10.6084/m9.figshare.5937943.v1
title: MOESM9 of High-level accumulation of oleyl oleate in plant seed oil by abundant supply of oleic acid substrates to efficient wax ester synthesis enzymes

description: Additional file 9: Table S5. List of primers used in this study for amplifying DNA sequences of wax ester synthesis enzymes.
DOI: 10.6084/m9.figshare.5938054
title: Additional file 1: of ATACseqQC: a Bioconductor package for post-alignment quality assessment of ATAC-seq data

description: Commands and scripts used for case studies. (TXT 19 kb)
DOI: 10.6084/m9.figshare.5938054.v1
title: Additional file 1: of ATACseqQC: a Bioconductor package for post-alignment quality assessment of ATAC-seq data

description: Commands and scripts used for case studies. (TXT 19 kb)
DOI: 10.6084/m9.figshare.5938057
title: Additional file 2: of ATACseqQC: a Bioconductor package for post-alignment quality assessment of ATAC-seq data

description: Table S1. Functional comparison between ATACseqQC and existing tools for ATAC-seq data QC analyses. (XLSX 14 kb)
DOI: 10.6084/m9.figshare.5938057.v1
title: Additional file 2: of ATACseqQC: a Bioconductor package for post-alignment quality assessment of ATAC-seq data

description: Table S1. Functional comparison between ATACseqQC and existing tools for ATAC-seq data QC analyses. (XLSX 14 kb)
DOI: 10.6084/m9.figshare.5938060
title: Additional file 3: of ATACseqQC: a Bioconductor package for post-alignment quality assessment of ATAC-seq data

description: Table S2. Summary statistics of base quality of raw reads, mapping and filtering of read alignments. The four datasets chosen for detailed quality control are highlighted in bold. (XLSX 21 kb)
DOI: 10.6084/m9.figshare.5938060.v1
title: Additional file 3: of ATACseqQC: a Bioconductor package for post-alignment quality assessment of ATAC-seq data

description: Table S2. Summary statistics of base quality of raw reads, mapping and filtering of read alignments. The four datasets chosen for detailed quality control are highlighted in bold. (XLSX 21 kb)
DOI: 10.6084/m9.figshare.5943028
title: Additional file 2: of Improving eukaryotic genome annotation using single molecule mRNA sequencing

description: Table of KEGG annotations for AC-Orig and AC-PB. (XLSX 1706Â kb)
DOI: 10.6084/m9.figshare.5943028.v1
title: Additional file 2: of Improving eukaryotic genome annotation using single molecule mRNA sequencing

description: Table of KEGG annotations for AC-Orig and AC-PB. (XLSX 1706Â kb)
DOI: 10.6084/m9.figshare.5943052
title: MOESM7 of Deciphering lignocellulose deconstruction by the white rot fungus Irpex lacteus based on genomic and transcriptomic analyses

description: Additional file 7. Differential expression analysis in comparisons of LC3d versus Glu3d and LC6d versus LC3d.
DOI: 10.6084/m9.figshare.5943052.v1
title: MOESM7 of Deciphering lignocellulose deconstruction by the white rot fungus Irpex lacteus based on genomic and transcriptomic analyses

description: Additional file 7. Differential expression analysis in comparisons of LC3d versus Glu3d and LC6d versus LC3d.
DOI: 10.6084/m9.figshare.5943124
title: Emulation of a process-based estuarine hydrodynamic model

description: Emulation modelling can be an effective alternative to traditional mechanistic approaches for complex environmental systems and, if carefully conceived, can offer significantly reduced run times and user expertise requirements. We present a case study of dynamic emulation for the domain of estuarine water quality modelling, by reporting the development and evaluation of a one-dimensional hydrodynamic model emulator. The proposed “neuroemulator” retains the dynamic nature of the process-based model utilizing a set of artificial neural networks. The underlying hydrodynamic model is routinely used for analysis and management of the northern reach of the San Francisco Bay-Delta estuary, a large complex region of strategic importance for water supply and ecosystem services on the Pacific coast of California, USA. The reduced computational expense of the emulator affords opportunities for direct use, as well as embedded use within other modelling frameworks such as those developed for reservoir operations and socio-hydrology.
DOI: 10.6084/m9.figshare.5943124.v1
title: Emulation of a process-based estuarine hydrodynamic model

description: Emulation modelling can be an effective alternative to traditional mechanistic approaches for complex environmental systems and, if carefully conceived, can offer significantly reduced run times and user expertise requirements. We present a case study of dynamic emulation for the domain of estuarine water quality modelling, by reporting the development and evaluation of a one-dimensional hydrodynamic model emulator. The proposed “neuroemulator” retains the dynamic nature of the process-based model utilizing a set of artificial neural networks. The underlying hydrodynamic model is routinely used for analysis and management of the northern reach of the San Francisco Bay-Delta estuary, a large complex region of strategic importance for water supply and ecosystem services on the Pacific coast of California, USA. The reduced computational expense of the emulator affords opportunities for direct use, as well as embedded use within other modelling frameworks such as those developed for reservoir operations and socio-hydrology.
DOI: 10.6084/m9.figshare.5945551
title: freelancer.zip

description: "expert_skill_project_preprocessed.txt" is the preprocessed file. This file includes 1624 lines. Each line is seperated by a space. The entry starting with 'E_' stands for the experts, starting with 'S_' stands for the skills and starting with 'P_' stands for the projects. For the line starting with 'E_', the second entry stands for the cost when employing this expert. For the line starting with 'P_', the second 
entry stands for the profit after finishing this project.
DOI: 10.6084/m9.figshare.5945551.v1
title: freelancer.zip

description: "expert_skill_project_preprocessed.txt" is the preprocessed file. This file includes 1624 lines. Each line is seperated by a space. The entry starting with 'E_' stands for the experts, starting with 'S_' stands for the skills and starting with 'P_' stands for the projects. For the line starting with 'E_', the second entry stands for the cost when employing this expert. For the line starting with 'P_', the second 
entry stands for the profit after finishing this project.
DOI: 10.6084/m9.figshare.5945557
title: guru.zip

description: "expert_skill_project_1_preprocessed.txt" and "expert_skill_project_2_preprocessed.txt" are two the preprocessed files. The first one includes 5569 lines, and the second one includes 7889 lines. Each line is seperated by a space. The entry 
starting with 'E_' stands for the experts, starting with 'S_' stands 
for the skills and starting with 'P_' stands for the projects. For the 
line starting with 'E_', the second entry stands for the cost when 
employing this expert. For the line starting with 'P_', the second 
entry stands for the profit after finishing this project.
DOI: 10.6084/m9.figshare.5945557.v1
title: guru.zip

description: "expert_skill_project_1_preprocessed.txt" and "expert_skill_project_2_preprocessed.txt" are two the preprocessed files. The first one includes 5569 lines, and the second one includes 7889 lines. Each line is seperated by a space. The entry 
starting with 'E_' stands for the experts, starting with 'S_' stands 
for the skills and starting with 'P_' stands for the projects. For the 
line starting with 'E_', the second entry stands for the cost when 
employing this expert. For the line starting with 'P_', the second 
entry stands for the profit after finishing this project.
DOI: 10.6084/m9.figshare.5945563
title: synthetic.zip

description: In all these files, each line is seperated by a space. The entry 
starting with 'E_' stands for the experts, starting with 'S_' stands 
for the skills and starting with 'P_' stands for the projects. For the 
line starting with 'E_', the second entry stands for the cost when 
employing this expert. For the line starting with 'P_', the second 
entry stands for the profit after finishing this project.
DOI: 10.6084/m9.figshare.5945563.v1
title: synthetic.zip

description: In all these files, each line is seperated by a space. The entry 
starting with 'E_' stands for the experts, starting with 'S_' stands 
for the skills and starting with 'P_' stands for the projects. For the 
line starting with 'E_', the second entry stands for the cost when 
employing this expert. For the line starting with 'P_', the second 
entry stands for the profit after finishing this project.
DOI: 10.6084/m9.figshare.25018313
title: Overview of the included articles and search strings

description: This systematic scoping review examines the available body of research on cooperation in the school community to overcome cyberbullying.
DOI: 10.6084/m9.figshare.5945764
title: Additional file 1: of Expansion of a urethritis-associated Neisseria meningitidis clade in the United States with concurrent acquisition of N. gonorrhoeae alleles

description: List of 353 isolates included in analyses of the U.S. NmNG urethritis clade, including sequence accession information, and provenance, serogroup, molecular typing, and impact of recombination events where available. (XLSX 53 kb)
DOI: 10.6084/m9.figshare.5945800
title: Additional file 3: of Expansion of a urethritis-associated Neisseria meningitidis clade in the United States with concurrent acquisition of N. gonorrhoeae alleles

description: Homologous allele replacements identified by ClonalFrameML, including gene annotations and the results of searching the BLAST RefSeq genomic database. The “Dictionary” worksheet defines the columns used in the “Recombination events” worksheet. (XLSX 230 kb)
DOI: 10.6084/m9.figshare.5945800.v1
title: Additional file 3: of Expansion of a urethritis-associated Neisseria meningitidis clade in the United States with concurrent acquisition of N. gonorrhoeae alleles

description: Homologous allele replacements identified by ClonalFrameML, including gene annotations and the results of searching the BLAST RefSeq genomic database. The “Dictionary” worksheet defines the columns used in the “Recombination events” worksheet. (XLSX 230 kb)
DOI: 10.6084/m9.figshare.5945815
title: Additional file 4: of Expansion of a urethritis-associated Neisseria meningitidis clade in the United States with concurrent acquisition of N. gonorrhoeae alleles

description: Loci affected by homologous allele replacement. The summary worksheet identifies loci where &gt; 50% of the length was involved in a recombination event affecting the ancestor of at least one genome was inferred to have originated with N. gonorrhoeae. The “Dictionary” worksheet defines the columns used in the two “Recombinant loci” worksheets. (XLSX 662 kb)
DOI: 10.6084/m9.figshare.5945815.v1
title: Additional file 4: of Expansion of a urethritis-associated Neisseria meningitidis clade in the United States with concurrent acquisition of N. gonorrhoeae alleles

description: Loci affected by homologous allele replacement. The summary worksheet identifies loci where &gt; 50% of the length was involved in a recombination event affecting the ancestor of at least one genome was inferred to have originated with N. gonorrhoeae. The “Dictionary” worksheet defines the columns used in the two “Recombinant loci” worksheets. (XLSX 662 kb)
DOI: 10.6084/m9.figshare.5945845
title: Additional file 1: of Integrated analyses of multi-omics reveal global patterns of methylation and hydroxymethylation and screen the tumor suppressive roles of HADHB in colorectal cancer

description: Table S1. The basic characteristics of six patients of colorectal cancer. Table S2. Summary of MeDIP-seq and hMeDIP-seq data production. Table S3. Pearson's product-moment correlation for the levels of DNA methylation and DNA hydroxymethylation with the elements in chromosome. Table S4. Differentially methylated regions (DMRs) in promoters. Table S5. Differentially hydroxymethylated regions (DhMRs) in promoters. Table S6. The top 10 pathways enriched in DMRs, DhMRs and DEG. Table S7. Summary of RNA-seq data production. Table S8. Differentially expressed genes (DEGs) in 6 pairs of samples. Table S9. The list of 7 genes of which DEGs contained both DMRs and DhMRs. (XLSX 2853Â kb)
DOI: 10.6084/m9.figshare.5945845.v1
title: Additional file 1: of Integrated analyses of multi-omics reveal global patterns of methylation and hydroxymethylation and screen the tumor suppressive roles of HADHB in colorectal cancer

description: Table S1. The basic characteristics of six patients of colorectal cancer. Table S2. Summary of MeDIP-seq and hMeDIP-seq data production. Table S3. Pearson's product-moment correlation for the levels of DNA methylation and DNA hydroxymethylation with the elements in chromosome. Table S4. Differentially methylated regions (DMRs) in promoters. Table S5. Differentially hydroxymethylated regions (DhMRs) in promoters. Table S6. The top 10 pathways enriched in DMRs, DhMRs and DEG. Table S7. Summary of RNA-seq data production. Table S8. Differentially expressed genes (DEGs) in 6 pairs of samples. Table S9. The list of 7 genes of which DEGs contained both DMRs and DhMRs. (XLSX 2853Â kb)
DOI: 10.6084/m9.figshare.5945935
title: Additional file 1: of Genome-wide identification, phylogeny, evolution, and expression patterns of MtN3/saliva/SWEET genes and functional analysis of BcNS in Brassica rapa

description: Table S1. The MtN3/saliva domain sequences of A. thaliana. (XLSX 27Â kb)