cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.22260011
title: High risk genetic variants of human insulin receptor substrate 1(IRS1) infer structural instability and functional interference

description: Insulin receptor substrate 1(IRS1) is a signaling adapter protein encoded by the <i>IRS1</i> gene. This protein delivers signals from insulin and insulin-like growth factor-1(IGF-1) receptors to the phosphatidylinositol 3-kinases (P13K)/protein kinase B (Akt) and Extracellular signal-regulated kinases (Erk) - Mitogen-activated protein (MAP) kinase pathways, which regulate particular cellular processes. Mutations in this gene have been linked to type 2 diabetes mellitus, a heightened risk of insulin resistance, and an increased likelihood of developing a number of different malignancies. The structure and function of IRS1 could be severely compromised as a result of single nucleotide polymorphism (SNP) type genetic variants. In this study, we focused on identification of the most harmful non-synonymous SNPs (nsSNPs) of the <i>IRS1</i> gene as well as prediction of their structural and functional consequences. Six different algorithms made the initial prediction that 59 of the 1142 IRS1 nsSNPs would have a negative impact on the protein structure. In-depth evaluations detected 26 nsSNPs located inside the functional domains of IRS1. Following that, 16 nsSNPs were identified as more harmful based on conservation profile, hydrophobic interaction, surface accessibility, homology modelling, and inter-atomic interactions. Following an in-depth analysis of protein stability, M249T (rs373826433), I223T (rs1939785175) and V204G (rs1574667052) were identified as three most deleterious SNPs and were subjected to molecular dynamics simulation for further insights. These findings will help us understand the implications for disease susceptibility, cancer progression, and the efficacy of therapeutic development against <i>IRS1</i> gene mutants. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.22260011.v1
title: High risk genetic variants of human insulin receptor substrate 1(IRS1) infer structural instability and functional interference

description: Insulin receptor substrate 1(IRS1) is a signaling adapter protein encoded by the <i>IRS1</i> gene. This protein delivers signals from insulin and insulin-like growth factor-1(IGF-1) receptors to the phosphatidylinositol 3-kinases (P13K)/protein kinase B (Akt) and Extracellular signal-regulated kinases (Erk) - Mitogen-activated protein (MAP) kinase pathways, which regulate particular cellular processes. Mutations in this gene have been linked to type 2 diabetes mellitus, a heightened risk of insulin resistance, and an increased likelihood of developing a number of different malignancies. The structure and function of IRS1 could be severely compromised as a result of single nucleotide polymorphism (SNP) type genetic variants. In this study, we focused on identification of the most harmful non-synonymous SNPs (nsSNPs) of the <i>IRS1</i> gene as well as prediction of their structural and functional consequences. Six different algorithms made the initial prediction that 59 of the 1142 IRS1 nsSNPs would have a negative impact on the protein structure. In-depth evaluations detected 26 nsSNPs located inside the functional domains of IRS1. Following that, 16 nsSNPs were identified as more harmful based on conservation profile, hydrophobic interaction, surface accessibility, homology modelling, and inter-atomic interactions. Following an in-depth analysis of protein stability, M249T (rs373826433), I223T (rs1939785175) and V204G (rs1574667052) were identified as three most deleterious SNPs and were subjected to molecular dynamics simulation for further insights. These findings will help us understand the implications for disease susceptibility, cancer progression, and the efficacy of therapeutic development against <i>IRS1</i> gene mutants. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.22339744
title: In-silico targeting TMPK from monkey pox virus: Molecular docking analysis, density functional theory studies and molecular dynamic simulation analysis

description: The World Health Organization (WHO) proclaimed the monkeypox epidemic a "public health emergency of worldwide significance" recently. The monkeypox virus is a member of the same Orthopoxvirus genus as the smallpox virus. Although smallpox medications are advised against monkeypox, no monkeypox-specific drugs are currently available. In the event of such an outbreak, in-silico medication identification is a practical and efficient strategy. As a result, we report a computational drug repurposing analysis to discover medicines that may be potential inhibitors of thymidylate kinase, a critical monkeypox viral enzyme. The target protein structure of the monkeypox virus was modeled using the vaccinia virus’s homologous protein structure. Using molecular docking and density functional theory, we found 11 possible inhibitors of the monkeypox virus from an Asinex library of 261120 chemicals. The primary purpose of this in silico work is to find possible inhibitors of monkeypox viral proteins that can then be experimentally tested in order to develop innovative therapeutic medicines for monkeypox infection. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.22339744.v1
title: In-silico targeting TMPK from monkey pox virus: Molecular docking analysis, density functional theory studies and molecular dynamic simulation analysis

description: The World Health Organization (WHO) proclaimed the monkeypox epidemic a "public health emergency of worldwide significance" recently. The monkeypox virus is a member of the same Orthopoxvirus genus as the smallpox virus. Although smallpox medications are advised against monkeypox, no monkeypox-specific drugs are currently available. In the event of such an outbreak, in-silico medication identification is a practical and efficient strategy. As a result, we report a computational drug repurposing analysis to discover medicines that may be potential inhibitors of thymidylate kinase, a critical monkeypox viral enzyme. The target protein structure of the monkeypox virus was modeled using the vaccinia virus’s homologous protein structure. Using molecular docking and density functional theory, we found 11 possible inhibitors of the monkeypox virus from an Asinex library of 261120 chemicals. The primary purpose of this in silico work is to find possible inhibitors of monkeypox viral proteins that can then be experimentally tested in order to develop innovative therapeutic medicines for monkeypox infection. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.22146848.v1
title: Isolation, characterization and <i>in silico</i> study of propenamide alkaloids from <i>Hymenoepmecis bicolor</i> poison against active <i>μ</i>-opioid receptor

description: Some insects produce venoms to defend against predators and directly interact with opioid receptors. In the present study, it was identified two alkaloids in the wasp venom species <i>Hymenoepimecis bicolor</i>. It was demonstrated that these could act as potential inhibitors of opioid receptors through their robust affinity to the receptors. The interaction profile was given to opioid receptors (μOR), with 60% of targets similar to alkaloid 1, with 0.25 probability, and 46.7% of targets similar to alkaloid 2, with a probability 0.17 of affinity as a target, which is considered signaling macromolecules and can mediate the most potent analgesic and addictive properties of opiate alkaloids. Notably, both alkaloids showed −7.6 kcal/mol affinity to the morphine agonies through six residues, Gly124, Asp147, Trp293, Ile296, Ile322, and Tyr326. These observations suggest further research on opioid receptors using <i>in vitro</i> studies of possible therapeutic applications. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.22146848
title: Isolation, characterization and <i>in silico</i> study of propenamide alkaloids from <i>Hymenoepmecis bicolor</i> poison against active <i>μ</i>-opioid receptor

description: Some insects produce venoms to defend against predators and directly interact with opioid receptors. In the present study, it was identified two alkaloids in the wasp venom species <i>Hymenoepimecis bicolor</i>. It was demonstrated that these could act as potential inhibitors of opioid receptors through their robust affinity to the receptors. The interaction profile was given to opioid receptors (μOR), with 60% of targets similar to alkaloid 1, with 0.25 probability, and 46.7% of targets similar to alkaloid 2, with a probability 0.17 of affinity as a target, which is considered signaling macromolecules and can mediate the most potent analgesic and addictive properties of opiate alkaloids. Notably, both alkaloids showed −7.6 kcal/mol affinity to the morphine agonies through six residues, Gly124, Asp147, Trp293, Ile296, Ile322, and Tyr326. These observations suggest further research on opioid receptors using <i>in vitro</i> studies of possible therapeutic applications. Communicated by Ramaswamy H. Sarma
DOI: 10.57745/gvqtrt
title: Read_Me.docx

description: Métadonnées associées aux données transimarsh_biodiversite_carabides_2013_2015.csv
DOI: 10.57745/etpugu
title: transimarsh_biodiversite_carabides_2013_2015.csv

description: Données de piégeage de Coléoptères Carabidés sur 3 années consécutives (2013, 2014 et 2015) dans les bandes enherbées et les surfaces cultivées d'une ferme expérimentale INRAE.
DOI: 10.5517/ccdc.csd.cc20kchg
title: CCDC 1863735: Experimental Crystal Structure Determination

description: Related Article: Xianhui Tang, Chunlong Meng, Nakul Rampal, Aurelia Li, Xu Chen, Wei Gong, Hong Jiang, David Fairen-Jimenez, Yong Cui, Yan Liu|2023|J.Am.Chem.Soc.|145|2561|doi:10.1021/jacs.2c12424
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc20kcjh
title: CCDC 1863736: Experimental Crystal Structure Determination

description: Related Article: Xianhui Tang, Chunlong Meng, Nakul Rampal, Aurelia Li, Xu Chen, Wei Gong, Hong Jiang, David Fairen-Jimenez, Yong Cui, Yan Liu|2023|J.Am.Chem.Soc.|145|2561|doi:10.1021/jacs.2c12424
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc20kckj
title: CCDC 1863737: Experimental Crystal Structure Determination

description: Related Article: Xianhui Tang, Chunlong Meng, Nakul Rampal, Aurelia Li, Xu Chen, Wei Gong, Hong Jiang, David Fairen-Jimenez, Yong Cui, Yan Liu|2023|J.Am.Chem.Soc.|145|2561|doi:10.1021/jacs.2c12424
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc20kclk
title: CCDC 1863738: Experimental Crystal Structure Determination

description: Related Article: Xianhui Tang, Chunlong Meng, Nakul Rampal, Aurelia Li, Xu Chen, Wei Gong, Hong Jiang, David Fairen-Jimenez, Yong Cui, Yan Liu|2023|J.Am.Chem.Soc.|145|2561|doi:10.1021/jacs.2c12424
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc29k759
title: CCDC 2131720: Experimental Crystal Structure Determination

description: Related Article: Xianhui Tang, Chunlong Meng, Nakul Rampal, Aurelia Li, Xu Chen, Wei Gong, Hong Jiang, David Fairen-Jimenez, Yong Cui, Yan Liu|2023|J.Am.Chem.Soc.|145|2561|doi:10.1021/jacs.2c12424
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2c71vj
title: CCDC 2181527: Experimental Crystal Structure Determination

description: Related Article: Wei Gong, Yi Xie, Xingjie Wang, Kent O. Kirlikovali, Karam B. Idrees, Fanrui Sha, Haomiao Xie, Yan Liu, Banglin Chen, Yong Cui, Omar K. Farha|2023|J.Am.Chem.Soc.|145|2679|doi:10.1021/jacs.2c13171
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2c71wk
title: CCDC 2181528: Experimental Crystal Structure Determination

description: Related Article: Wei Gong, Yi Xie, Xingjie Wang, Kent O. Kirlikovali, Karam B. Idrees, Fanrui Sha, Haomiao Xie, Yan Liu, Banglin Chen, Yong Cui, Omar K. Farha|2023|J.Am.Chem.Soc.|145|2679|doi:10.1021/jacs.2c13171
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2c71xl
title: CCDC 2181529: Experimental Crystal Structure Determination

description: Related Article: Wei Gong, Yi Xie, Xingjie Wang, Kent O. Kirlikovali, Karam B. Idrees, Fanrui Sha, Haomiao Xie, Yan Liu, Banglin Chen, Yong Cui, Omar K. Farha|2023|J.Am.Chem.Soc.|145|2679|doi:10.1021/jacs.2c13171
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2c71ym
title: CCDC 2181530: Experimental Crystal Structure Determination

description: Related Article: Wei Gong, Yi Xie, Xingjie Wang, Kent O. Kirlikovali, Karam B. Idrees, Fanrui Sha, Haomiao Xie, Yan Liu, Banglin Chen, Yong Cui, Omar K. Farha|2023|J.Am.Chem.Soc.|145|2679|doi:10.1021/jacs.2c13171
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2c71zn
title: CCDC 2181531: Experimental Crystal Structure Determination

description: Related Article: Wei Gong, Yi Xie, Xingjie Wang, Kent O. Kirlikovali, Karam B. Idrees, Fanrui Sha, Haomiao Xie, Yan Liu, Banglin Chen, Yong Cui, Omar K. Farha|2023|J.Am.Chem.Soc.|145|2679|doi:10.1021/jacs.2c13171
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2g0lkn
title: CCDC 2264691: Experimental Crystal Structure Determination

description: Related Article: Peter M. Waddell, Lei Tian, Anthony R. Scavuzzo, Lalu Venigalla, Gregory D. Scholes, Brad P. Carrow|2023|Chemical Science|14|14217|doi:10.1039/D3SC02588H
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.34740/kaggle/dsv/7229448
title: Global Genomic Neurofibromatosis Neoplasia
DOI: 10.5281/zenodo.10398476
title: Alternative polyadenylation sites in rats

description: A total of 83 WTTS-seq (whole transcriptome termini site sequencing) libraries were constructed individually using total RNA samples derived from several brain tissues of rats. Library sequencing produced a total of 312,092,803 raw reads, but the mapped reads were 240,225,046 (76.97%) on Rnor6.0, while 251,188,567 (80.49%) on mRatBN7.2, respectively. Using 25 reads per clustered site as a cutoff, we identified 173,124 APA sites mapped to the new reference genome, while 167,136 APA sites were assigned to the old reference genome. For Rnor6.0, only 127,460 (76.26%) APA sites were assigned to the genome regions with 18,177 annotated genes. In contrast, 141,399 (81.67%) APA sites were mapped to the 20,102 annotated genes on mRatBN7.2. In brief, our results provide evidence that mRatBN7.2 has improved qualities of both genome assembly and gene annotation in rat. 

Zhou, X., Li, R., Michal, J.J., Wu, X.-L., Liu, Z., Zhao, H., Xia, Y., Du, W., Wildung, M.R., Pouchnik, D.J., et al. (2016). Accurate Profiling of Gene Expression and Alternative Polyadenylation with Whole Transcriptome Termini Site Sequencing (WTTS-Seq). Genetics 203, 683–697.

 

This work was supported by the National Institute of Food and Agriculture, United States Department of Agriculture under Award Numbers 2016-67015-24470/2020-67015-31733/2022-51300-38058/2023-67015-39566/2023-67015-40080 to ZJ.
DOI: 10.5281/zenodo.10398475
title: Alternative polyadenylation sites in rats

description: A total of 83 WTTS-seq (whole transcriptome termini site sequencing) libraries were constructed individually using total RNA samples derived from several brain tissues of rats. Library sequencing produced a total of 312,092,803 raw reads, but the mapped reads were 240,225,046 (76.97%) on Rnor6.0, while 251,188,567 (80.49%) on mRatBN7.2, respectively. Using 25 reads per clustered site as a cutoff, we identified 173,124 APA sites mapped to the new reference genome, while 167,136 APA sites were assigned to the old reference genome. For Rnor6.0, only 127,460 (76.26%) APA sites were assigned to the genome regions with 18,177 annotated genes. In contrast, 141,399 (81.67%) APA sites were mapped to the 20,102 annotated genes on mRatBN7.2. In brief, our results provide evidence that mRatBN7.2 has improved qualities of both genome assembly and gene annotation in rat. 

Zhou, X., Li, R., Michal, J.J., Wu, X.-L., Liu, Z., Zhao, H., Xia, Y., Du, W., Wildung, M.R., Pouchnik, D.J., et al. (2016). Accurate Profiling of Gene Expression and Alternative Polyadenylation with Whole Transcriptome Termini Site Sequencing (WTTS-Seq). Genetics 203, 683–697.

 

This work was supported by the National Institute of Food and Agriculture, United States Department of Agriculture under Award Numbers 2016-67015-24470/2020-67015-31733/2022-51300-38058/2023-67015-39566/2023-67015-40080 to ZJ.
DOI: 10.48544/4010cfcc-7dd3-42bc-b918-366b09854934
title: Moresprudentie en het leren van organisaties over morele vraagstukken
DOI: 10.5281/zenodo.10401250
title: STORMS_Check_list_for_manuscripts

description: STORMS (Strengthening The Organization and Reporting of Microbiome Studies) checklist for submitted manuscript
DOI: 10.5281/zenodo.10401251
title: STORMS_Check_list_for_manuscripts

description: STORMS (Strengthening The Organization and Reporting of Microbiome Studies) checklist for submitted manuscript
DOI: 10.6084/m9.figshare.24849990
title: Data.xlsPhysical activity, weight management, and mental health in healthcare college students during the COVID-19 pandemic

description: 该研究旨在评估校园封锁期间医疗保健学生的身体活动、体重管理行为和心理健康，并分析影响身体活动的因素。这项研究是根据《赫尔辛基宣言》进行的。该研究计划经甘苏省立医院研究委员会批准。
DOI: 10.5281/zenodo.10378144
title: TAU Sound Events and Speech Privacy Preservation

description: The TAU Sound Events and Speech Privacy Preservation Dataset is a collection of audio data used in the work "Adversarial Representation Learning for Robust Privacy Preservation in Audio" by S. Gharib, M. Tran, D. Luong, K. Drossos, and T. Virtanen. The dataset is created by merging subsets of the Freesound 50k Dataset (FSD50K) and the LibriSpeech corpus. Both FSD50K and LibriSpeech are licensed under the Creative Commons license.

The dataset contains of ~5000 one-second sound event samples with or without speech content provided in WAV and NumPy array format (approximately half of the samples contains speech). The creation of the dataset ensures an equal number of samples for male and female speakers across each sound event class. The sound event classes included in this dataset are:



dog barking

glass breaking

gun shot

cough

slam

applause

dished pot pan

toilet flush

cat meowing

doorbell

crying

drill


Please check the README for better understanding of the dataset.
DOI: 10.5281/zenodo.10378145
title: TAU Sound Events and Speech Privacy Preservation

description: The TAU Sound Events and Speech Privacy Preservation Dataset is a collection of audio data used in the work "Adversarial Representation Learning for Robust Privacy Preservation in Audio" by S. Gharib, M. Tran, D. Luong, K. Drossos, and T. Virtanen. The dataset is created by merging subsets of the Freesound 50k Dataset (FSD50K) and the LibriSpeech corpus. Both FSD50K and LibriSpeech are licensed under the Creative Commons license.

The dataset contains of ~5000 one-second sound event samples with or without speech content provided in WAV and NumPy array format (approximately half of the samples contains speech). The creation of the dataset ensures an equal number of samples for male and female speakers across each sound event class. The sound event classes included in this dataset are:



dog barking

glass breaking

gun shot

cough

slam

applause

dished pot pan

toilet flush

cat meowing

doorbell

crying

drill


Please check the README for better understanding of the dataset.
DOI: 10.6084/m9.figshare.22651997
title: Lamin B1 overexpression alters chromatin organization and gene expression

description: Peripheral heterochromatin positioning depends on nuclear envelope associated proteins and repressive histone modifications. Here we show that overexpression (OE) of Lamin B1 (LmnB1) leads to the redistribution of peripheral heterochromatin into heterochromatic foci within the nucleoplasm. These changes represent a perturbation of heterochromatin binding at the nuclear periphery (NP) through a mechanism independent from altering other heterochromatin anchors or histone post-translational modifications. We further show that LmnB1 OE alters gene expression. These changes do not correlate with different levels of H3K9me3, but a significant number of the misregulated genes were likely mislocalized away from the NP upon LmnB1 OE. We also observed an enrichment of developmental processes amongst the upregulated genes. ~74% of these genes were normally repressed in our cell type, suggesting that LmnB1 OE promotes gene de-repression. This demonstrates a broader consequence of LmnB1 OE on cell fate, and highlights the importance of maintaining proper levels of LmnB1.