cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.8207150
title: Additional file 8: of Comparative transcriptomic analysis reveals genetic divergence and domestication genes in Diospyros

description: Table S4. Putative orthogroups among the nine Diospyros samples identified based on the OrthoMCL analysis. (XLSX 3354 kb)
DOI: 10.6084/m9.figshare.15020483
title: Additional file 4 of RNA-seq co-expression network analysis reveals anxiolytic behavior of mice with Efnb2 knockout in parvalbumin+ neurons

description: Additional file 4. Gene list of WGCNA.
DOI: 10.6084/m9.figshare.17119991.v1
title: Additional file 1 of An adaptive method of defining negative mutation status for multi-sample comparison using next-generation sequencing

description: Additional file 1. Supplementary tables. Table S1: The list of somatic mutations previously identified from dual-platform single-cell whole-exome sequencing used for the current evaluation. Table S2: The summary of the comparison between the Agilent- and Nextera-runs using different negative-defining methods.
DOI: 10.6084/m9.figshare.15020483.v1
title: Additional file 4 of RNA-seq co-expression network analysis reveals anxiolytic behavior of mice with Efnb2 knockout in parvalbumin+ neurons

description: Additional file 4. Gene list of WGCNA.
DOI: 10.6084/m9.figshare.14498677.v1
title: Characterization of the <i>ERP</i> gene family in <i>Arabidopsis thaliana</i>

description: Plant genomes encode numerous proteins with obscure features (POFs) that lack recognized domains or motifs. However, there is little functional information for POFs even in <i>Arabidopsis</i> because biochemical, physiological, and genetic assay are required for the functional annotations of POFs. Here, we identified a small gene family, the endoplasmic reticulum-localized POF (ERP) family, in <i>Arabidopsis</i>. Phylogenetic analysis revealed that the number of ERP family members was conserved in the plant kingdom, suggesting strong selective pressure was imposed on ERP family during plant evolution. No recognizable domains were identified in the predicted ERP proteins, except for the N-terminal signal peptide. ERPs were found to be widely expressed during <i>Arabidopsis</i> development and showed endoplasmic reticulum localization. It was reported that <i>ERP1</i> is an inositol-1,4,5-trisphosphate 5-phosphatase (5PTase), but <i>ERP1</i> could not substitute for <i>At5PTase12</i> in precocious pollen germination, indicating that <i>ERP1</i> did not have the similar functions as <i>At5PTase12</i> in inositol 1,4,5-trisphosphate [Ins(1,4,5)<i>P3</i>] metabolism. Further studies are needed to dissect the functions of ERP family proteins in <i>Arabidopsis</i> development.
DOI: 10.6084/m9.figshare.19217187
title: Comprehensive bioinformatics analysis reveals the hub genes and pathways associated with multiple myeloma

description: While the prognosis of multiple myeloma (MM) has significantly improved over the last decade because of new treatment options, it remains incurable. Aetiological explanations and biological targets based on genomics may provide additional help for rational disease intervention. Three microarray datasets associated with MM were downloaded from the Gene Expression Omnibus (GEO) database. GSE125364 and GSE39754 were used as the training set, and GSE13591 was used as the verification set. The differentially expressed genes (DEGs) were obtained from the training set, and Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were performed to annotate their functions. The hub genes were derived from the combined results of a protein–protein interaction (PPI) network and weighted gene coexpression network analysis (WGCNA). The receiver operating characteristic (ROC) curves of hub genes were plotted to evaluate their clinical diagnostic value. Biological processes and signaling pathways associated with hub genes were explained by gene set enrichment analysis (GSEA). A total of 1759 DEGs were identified. GO and KEGG pathway analyses suggested that the DEGs were related to the process of protein metabolism. RPN1, SEC61A1, SPCS1, SRPR, SRPRB, SSR1 and TRAM1 were proven to have clinical diagnostic value for MM. The GSEA results suggested that the hub genes were widely involved in the N-glycan biosynthesis pathway. The hub genes identified in this study can partially explain the potential molecular mechanisms of MM and serve as candidate biomarkers for disease diagnosis.
DOI: 10.6084/m9.figshare.19217187.v1
title: Comprehensive bioinformatics analysis reveals the hub genes and pathways associated with multiple myeloma

description: While the prognosis of multiple myeloma (MM) has significantly improved over the last decade because of new treatment options, it remains incurable. Aetiological explanations and biological targets based on genomics may provide additional help for rational disease intervention. Three microarray datasets associated with MM were downloaded from the Gene Expression Omnibus (GEO) database. GSE125364 and GSE39754 were used as the training set, and GSE13591 was used as the verification set. The differentially expressed genes (DEGs) were obtained from the training set, and Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were performed to annotate their functions. The hub genes were derived from the combined results of a protein–protein interaction (PPI) network and weighted gene coexpression network analysis (WGCNA). The receiver operating characteristic (ROC) curves of hub genes were plotted to evaluate their clinical diagnostic value. Biological processes and signaling pathways associated with hub genes were explained by gene set enrichment analysis (GSEA). A total of 1759 DEGs were identified. GO and KEGG pathway analyses suggested that the DEGs were related to the process of protein metabolism. RPN1, SEC61A1, SPCS1, SRPR, SRPRB, SSR1 and TRAM1 were proven to have clinical diagnostic value for MM. The GSEA results suggested that the hub genes were widely involved in the N-glycan biosynthesis pathway. The hub genes identified in this study can partially explain the potential molecular mechanisms of MM and serve as candidate biomarkers for disease diagnosis.
DOI: 10.34740/kaggle/dsv/7656078
title: ⏳ endoflife.date database (duckdb)
DOI: 10.5281/zenodo.10677672
title: Large version of the OmniFold dataset in training and test splits

description: 20M Simulated events based on the dataset of QCD jets used for studying unfolding in OmniFold: A Method to Simultaneously Unfold All Observables split into training and validation.

 

To read, simply open as an hdf5 file. Hard and reconstructed observables are stored into the datasets "hard" and "reco", respectively. These have dimensionality (n_events, 6). The six dimensions are ordered as: "jet mass", "jet width", "jet multiplicity", "jet soft drop mass", "jet groomed momentum fraction z_g", and "jet N-subjettiness ratio tau_21".
DOI: 10.5281/zenodo.10677673
title: Large version of the OmniFold dataset in training and test splits

description: 20M Simulated events based on the dataset of QCD jets used for studying unfolding in OmniFold: A Method to Simultaneously Unfold All Observables split into training and validation.

 

To read, simply open as an hdf5 file. Hard and reconstructed observables are stored into the datasets "hard" and "reco", respectively. These have dimensionality (n_events, 6). The six dimensions are ordered as: "jet mass", "jet width", "jet multiplicity", "jet soft drop mass", "jet groomed momentum fraction z_g", and "jet N-subjettiness ratio tau_21".
DOI: 10.6084/m9.figshare.12923034.v1
title: Additional file 2 of Exploring the protective effect of Modified Xiaochaihu Decoction against hepatic steatosis and inflammation by network pharmacology and validation in ageing rats

description: Additional file 2: Table S2. List of the chemical compounds and putative targets of MXD following screening.
DOI: 10.6084/m9.figshare.12923037.v1
title: Additional file 3 of Exploring the protective effect of Modified Xiaochaihu Decoction against hepatic steatosis and inflammation by network pharmacology and validation in ageing rats

description: Additional file 3: Table S3. List of NAFLD‐related targets
DOI: 10.6084/m9.figshare.12923034
title: Additional file 2 of Exploring the protective effect of Modified Xiaochaihu Decoction against hepatic steatosis and inflammation by network pharmacology and validation in ageing rats

description: Additional file 2: Table S2. List of the chemical compounds and putative targets of MXD following screening.
DOI: 10.6084/m9.figshare.12923046.v1
title: Additional file 6 of Exploring the protective effect of Modified Xiaochaihu Decoction against hepatic steatosis and inflammation by network pharmacology and validation in ageing rats

description: Additional file 6: Table S6. List of 20 potential ingredients related to IL-6, NF-κB, FASN, and ACACA.
DOI: 10.5281/zenodo.8089825
title: NDC-SDG Connections: Data on first NDC submissions (V1)

description: NDC-SDG Connections is a joint initiative of the German Institute of Development and Sustainability (IDOS) and the Stockholm Environment Institute (SEI). The research and visualisation project aims at illuminating synergies between the 2030 Agenda for Sustainable Development and the Paris Agreement, and at identifying entry points for coherent policies that promote just, sustainable and climate-smart development.


The objective of the NDC-SDG Connections is to: foster a dialogue on meaningful interaction between the 2030 Agenda and the Paris Agreement, globally and at the national level; to increase transparency with easy accessibility to all climate activities; and to cultivate learning and catalyse partnerships between countries and other actors to raise the ambition of future NDCs.

With its second version, the NDC-SDG Connections project opened its data for public re-use. The data on first NDC submissions (V1) is provided in the following formats:



	
single .csv files (per data per SDG)
	
zip .csv file (data per SDG for all SDG in one zip)
	
.xlxs file (Excel)



Visit the Online Data Visualisation to interact directly with the data: www.NDC-SDG.info


Additional files:



	
.pdf file documenting the methodological framework including the coding and data validation process of the NDC-SDG Connections project
	
.csv file with all NDCs included into the analysis (V1)




Note: This data set contains  data for first NDC submissions (V1). The terms ‘First’ and ‘Updated’ do not fully follow the UNFCCC nomenclature. For most countries, updated NDCs are called ‘First updated NDC’ or ‘Enhanced NDCs’, while some countries call their updated NDCs for ‘Second NDC’. In order to make it comprehensible, the tool developers have chosen to distinguish between ‘First’ and ‘Updated’. Detailed description of which version is counted as ‘First’ and which as ‘Updated’ has been documented in the data.


 
description: Funded by: 
The Federal Ministry for Economic Cooperation and Development (BMZ),
The Swedish International Development Cooperation Agency (Sida),
Formas: A Swedish Research Council for Sustainable Development.
DOI: 10.5281/zenodo.8089826
title: NDC-SDG Connections: Data on first NDC submissions (V1)

description: NDC-SDG Connections is a joint initiative of the German Institute of Development and Sustainability (IDOS) and the Stockholm Environment Institute (SEI). The research and visualisation project aims at illuminating synergies between the 2030 Agenda for Sustainable Development and the Paris Agreement, and at identifying entry points for coherent policies that promote just, sustainable and climate-smart development.


The objective of the NDC-SDG Connections is to: foster a dialogue on meaningful interaction between the 2030 Agenda and the Paris Agreement, globally and at the national level; to increase transparency with easy accessibility to all climate activities; and to cultivate learning and catalyse partnerships between countries and other actors to raise the ambition of future NDCs.

With its second version, the NDC-SDG Connections project opened its data for public re-use. The data on first NDC submissions (V1) is provided in the following formats:



	
single .csv files (per data per SDG)
	
zip .csv file (data per SDG for all SDG in one zip)
	
.xlxs file (Excel)



Visit the Online Data Visualisation to interact directly with the data: www.NDC-SDG.info


Additional files:



	
.pdf file documenting the methodological framework including the coding and data validation process of the NDC-SDG Connections project
	
.csv file with all NDCs included into the analysis (V1)




Note: This data set contains  data for first NDC submissions (V1). The terms ‘First’ and ‘Updated’ do not fully follow the UNFCCC nomenclature. For most countries, updated NDCs are called ‘First updated NDC’ or ‘Enhanced NDCs’, while some countries call their updated NDCs for ‘Second NDC’. In order to make it comprehensible, the tool developers have chosen to distinguish between ‘First’ and ‘Updated’. Detailed description of which version is counted as ‘First’ and which as ‘Updated’ has been documented in the data.


 
description: Funded by: 
The Federal Ministry for Economic Cooperation and Development (BMZ),
The Swedish International Development Cooperation Agency (Sida),
Formas: A Swedish Research Council for Sustainable Development.
DOI: 10.6084/m9.figshare.12923043
title: Additional file 5 of Exploring the protective effect of Modified Xiaochaihu Decoction against hepatic steatosis and inflammation by network pharmacology and validation in ageing rats

description: Additional file 5: Table S5. Results of KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway enrichment analysis
DOI: 10.6084/m9.figshare.12923046
title: Additional file 6 of Exploring the protective effect of Modified Xiaochaihu Decoction against hepatic steatosis and inflammation by network pharmacology and validation in ageing rats

description: Additional file 6: Table S6. List of 20 potential ingredients related to IL-6, NF-κB, FASN, and ACACA.
DOI: 10.6084/m9.figshare.8207129.v1
title: Additional file 5: of Comparative transcriptomic analysis reveals genetic divergence and domestication genes in Diospyros

description: Table S1. Databases for the de novo sequencing of the transcriptome for the nine Diospyros samples. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.7160348
title: A structural perspective on the PP-loop ATP pyrophosphatase family

description: Derived from an ancient ATP-hydrolyzing Rossmann-like fold protein, members of the PP-loop ATP pyrophosphatase family feature an absolutely conserved P-loop-like “SxGxDS/T” motif used for binding and presenting ATP for substrate adenylylation (AMPylation). Since the first family member was reported more than 20 years ago, numerous representatives catalyzing very diverse reactions have been characterized both functionally and structurally. The availability of more than 100 high quality structures in the protein data bank provides an excellent opportunity to gain structural insights into the generally conserved catalytic mechanism and the uniqueness of the reactions catalyzed by family members. In this work, we conducted a thorough database search for the PP-loop ATP pyrophosphatase family members, resulting in the most comprehensive and up-to-date collection that includes 18 enzyme families. Structure comparison of representative family members allowed us to identify common structure features in the core catalytic domain, as well as four highly variable regions that define the unique chemistry for each enzyme family. The newly identified enzymes, particularly those from pathogens, warrant further research to enlarge the scope of this ever-expanding and highly diverse enzyme superfamily for use in potential bioengineering and biomedical applications.
DOI: 10.6084/m9.figshare.17120174
title: Additional file 5 of Integrated transcriptome and small RNA sequencing analyses reveal a drought stress response network in Sophora tonkinensis

description: Additional file 5: Table S2. Differentially regulated genes in CK vs. MDT and CK vs. SDT.
DOI: 10.6084/m9.figshare.12923031
title: Additional file 1 of Exploring the protective effect of Modified Xiaochaihu Decoction against hepatic steatosis and inflammation by network pharmacology and validation in ageing rats

description: Additional file 1: Table S1. List of active ingredients in Modified Xiaochaihu Decoction (MXD).
DOI: 10.6084/m9.figshare.17120048.v1
title: Additional file 2 of Conditional transcriptional relationships may serve as cancer prognostic markers

description: Additional file 2: Table S1. Prognosis DCLs in five cancer types.
DOI: 10.6084/m9.figshare.17120171
title: Additional file 4 of Integrated transcriptome and small RNA sequencing analyses reveal a drought stress response network in Sophora tonkinensis

description: Additional file 4: Table S1. Primers used for qRT-PCR.
DOI: 10.6084/m9.figshare.17120174.v1
title: Additional file 5 of Integrated transcriptome and small RNA sequencing analyses reveal a drought stress response network in Sophora tonkinensis

description: Additional file 5: Table S2. Differentially regulated genes in CK vs. MDT and CK vs. SDT.
DOI: 10.6084/m9.figshare.14498677
title: Characterization of the <i>ERP</i> gene family in <i>Arabidopsis thaliana</i>

description: Plant genomes encode numerous proteins with obscure features (POFs) that lack recognized domains or motifs. However, there is little functional information for POFs even in <i>Arabidopsis</i> because biochemical, physiological, and genetic assay are required for the functional annotations of POFs. Here, we identified a small gene family, the endoplasmic reticulum-localized POF (ERP) family, in <i>Arabidopsis</i>. Phylogenetic analysis revealed that the number of ERP family members was conserved in the plant kingdom, suggesting strong selective pressure was imposed on ERP family during plant evolution. No recognizable domains were identified in the predicted ERP proteins, except for the N-terminal signal peptide. ERPs were found to be widely expressed during <i>Arabidopsis</i> development and showed endoplasmic reticulum localization. It was reported that <i>ERP1</i> is an inositol-1,4,5-trisphosphate 5-phosphatase (5PTase), but <i>ERP1</i> could not substitute for <i>At5PTase12</i> in precocious pollen germination, indicating that <i>ERP1</i> did not have the similar functions as <i>At5PTase12</i> in inositol 1,4,5-trisphosphate [Ins(1,4,5)<i>P3</i>] metabolism. Further studies are needed to dissect the functions of ERP family proteins in <i>Arabidopsis</i> development.
DOI: 10.6084/m9.figshare.17120171.v1
title: Additional file 4 of Integrated transcriptome and small RNA sequencing analyses reveal a drought stress response network in Sophora tonkinensis

description: Additional file 4: Table S1. Primers used for qRT-PCR.
DOI: 10.6084/m9.figshare.17120183.v1
title: Additional file 6 of Integrated transcriptome and small RNA sequencing analyses reveal a drought stress response network in Sophora tonkinensis

description: Additional file 6: Table S3. Known and novel miRNAs identified in the study.
DOI: 10.6084/m9.figshare.17120105
title: Additional file 1 of Hsa_circ_0008434 regulates USP9X expression by sponging miR-6838-5p to promote gastric cancer growth, migration and invasion

description: Additional file 1.
DOI: 10.15472/doxuuv
title: Fauna y flora del municipio de Tame, Arauca

description: Con el fin de integrar toda la información obtenida a partir de la primera etapa del proyecto Ecopetrol "Planeación ambiental para la conservación de la biodiversidad en las áreas operativas de Ecopetrol", adelantado por el Instituto Humboldt y Ecopetrol, se realizó la integración de los diferentes componentes de investigación durante esta fase, obteniendo información, técnica y científica, que permitirá y apoyara la tomar decisiones pertinentes para la conservación de los Recursos Naturales.  Este proyecto consistió en la  búsqueda, caracterización y descripción en la ventana de Tame (Arauca), a través de la caracterización de grupos de seres vivos (Aves, Peces, Anfibios, Herpetofauna, perifiton, Plantas y macroinvertebrados). Se realizó un reconocimiento del área de estudio y una vez seleccionadas las localidades de muestreo, se llevaron a cabo diferentes metodologías según el grupo biológico. Los resultados obtenidos incluyen un total de 2584 registros biológicos.
DOI: 10.6084/m9.figshare.12923324.v1
title: Additional file 1 of LncRNA PSMB8-AS1 contributes to pancreatic cancer progression via modulating miR-382-3p/STAT1/PD-L1 axis

description: Additional file 1: Table 1. Association of PSMB8-AS1 expression with clinicopathological features of the PC patients.
DOI: 10.6084/m9.figshare.12925928.v1
title: Additional file 11 of The U2AF2 /circRNA ARF1/miR-342–3p/ISL2 feedback loop regulates angiogenesis in glioma stem cells

description: Additional file 11.
DOI: 10.6084/m9.figshare.17120183
title: Additional file 6 of Integrated transcriptome and small RNA sequencing analyses reveal a drought stress response network in Sophora tonkinensis

description: Additional file 6: Table S3. Known and novel miRNAs identified in the study.
DOI: 10.6084/m9.figshare.11353043
title: Additional file 1. Datasets and comparative analyses of Senticaudata mitogenomes. from Disentangling the interplay of positive and negative selection forces that shaped mitochondrial genomes of <i>Gammarus pisinnus</i> and <i>Gammarus lacustris</i>

description: We hypothesized that the mitogenome of <i>Gammarus lacustris</i> (GL), native to the Qinghai-Tibet Plateau, might exhibit genetic adaptations to the extreme environmental conditions associated with high altitudes (greater than 3000 m). To test this, we also sequenced the mitogenome of <i>Gammarus pisinnus</i> (GP), whose native range is close to the Tibetan plateau, but at a much lower altitude (200–1500 m). The two mitogenomes exhibited conserved mitochondrial architecture, but low identity between genes (55% <i>atp8</i> to 76.1% <i>cox1</i>). Standard (homogeneous) phylogenetic models resolved Gammaridae as paraphyletic, but ‘heterogeneous’ CAT-GTR model as monophyletic. In indirect support of our working hypothesis, GL, <i>pisinnus</i> and <i>fossarum</i> exhibit evidence of episodic diversifying selection within the studied Gammaroidea dataset. The mitogenome of GL generally evolves under a strong purifying selection, whereas GP evolves under directional (especially pronounced in <i>atp8</i>) and/or relaxed selection. This is surprising, as GP does not inhabit a unique ecological niche compared to other gammarids. We propose that this rapid evolution of the GP mitogenome may be a reflection of its relatively recent speciation and heightened non-adaptive (putatively metabolic rate-driven) mutational pressures. To test these hypotheses, we urge sequencing mitogenomes of remaining <i>Gammarus</i> species populating the same geographical range as GP.