cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.23619018
title: Post-fire nucleation scenarios after Bourra wildfire (NW Italian Alps)

description: Rasters of Scots pine seedlings probabilities (in folder "probability") and active intervention priorities (in folder "category") according to nucleation scenarios (patchy approach) after Bourra wilfire.
DOI: 10.6084/m9.figshare.23619018.v1
title: Post-fire nucleation scenarios after Bourra wildfire (NW Italian Alps)

description: Rasters of Scots pine seedlings probabilities (in folder "probability") and active intervention priorities (in folder "category") according to nucleation scenarios (patchy approach) after Bourra wilfire.
DOI: 10.18112/openneuro.ds004187.v1.0.1
title: LGN Layers Data
DOI: 10.6084/m9.figshare.22717591
title: Ribosome profiling data from the model diatom <em>Thalassiosira pseudonana Part 1</em>

description: Sequencing data from ribosome profiling run described in the protocol paper 'Ribosome profiling in the model diatom <em>Thalassiosira pseudonana'</em> <br> <em>Undepleted: no rRNA removal step during library prep</em> <em>HL_4: High light exposure (</em>500 μmol photons m<sup>−2</sup>s<sup>−1</sup>) f<em>or 4 hours</em> <em>HL_24: High light exposure</em> (500 μmol photons m<sup>−</sup><sup>2</sup>s<sup>−1</sup>)<em> for 24 hours</em> <br>
DOI: 10.5281/zenodo.7797985
title: Icequake catalogues and velocity model for the publication: Array processing in cryoseismology

description: Icequakes detected using array-based method and network-based method, associated with the publication: Hudson, T. S., Brisbourne, A. M., Kufner, S., Kendall, J., & Smith, M. (2023). Array processing in cryoseismology. Submitted to: <em>The Cryosphere</em>. For the network earthquake catalogue, t0 refers to the origin time of an icequake. For the array earthquake catalogue, t_P and t_S refer to the P and S wave arrival times of an icequake. Also included is a csv file containing the seismic velocity model used in the analysis.
DOI: 10.5281/zenodo.7797986
title: Icequake catalogues for the publication: Array processing in cryoseismology

description: Icequakes detected using array-based method and network-based method, associated with the publication: Hudson, T. S., Brisbourne, A. M., Kufner, S., Kendall, J., & Smith, M. (2023). Array processing in cryoseismology. Submitted to: <em>The Cryosphere</em>. For the network earthquake catalogue, t0 refers to the origin time of an icequake. For the array earthquake catalogue, t_P and t_S refer to the P and S wave arrival times of an icequake.
DOI: 10.5281/zenodo.8120941
title: Icequake catalogues and velocity model for the publication: Array processing in cryoseismology

description: Icequakes detected using array-based method and network-based method, associated with the publication: Hudson, T. S., Brisbourne, A. M., Kufner, S., Kendall, J., & Smith, M. (2023). Array processing in cryoseismology. Submitted to: <em>The Cryosphere</em>. For the network earthquake catalogue, t0 refers to the origin time of an icequake. For the array earthquake catalogue, t_P and t_S refer to the P and S wave arrival times of an icequake. Also included is a csv file containing the seismic velocity model used in the analysis.
DOI: 10.57745/eaimlx
title: clapas.R

description: :unav
DOI: 10.57745/wd7wkz
title: Docuclapas.doc

description: :unav
DOI: 10.57745/xpeihh
title: Tutorial.pdf

description: English version of the tutorial
DOI: 10.57745/oxyvcn
title: training_data.zip

description: training dataset for Clapas tutorial
DOI: 10.57745/rqgyj7
title: Tutoriel.pdf

description: Tutoriel en français
DOI: 10.57745/vtjt1j
title: Docuclapas.pdf

description: Documentation sur les fonctions R de Clapas
DOI: 10.6084/m9.figshare.23509158.v1
title: <strong>Influence of the late Ordovician-early Silurian paleoenvironment and related geological processes on the organic matter accumulation and carbon isotope excursion</strong>

description: Although previous studies have shown that the paleoenvironment and geological processes contributed to the organic matter accumulation (OMA) and carbon isotope excursions (CIEs) during the late Ordovician–early Silurian, the dominated controlling factor for the OMA and the origins of CIEs still remains unclear due to complex interaction between various paleoenvironmental factors and geological processes. Therefore, based on the elemental geochemistry of the Wufeng–Longmaxi Formation shales in the upper Yangtze Platform, we analyzed the late Ordovician–early Silurian paleoenvironment and related geological processes, and further explored the origin of the OMA and CIEs.
DOI: 10.6084/m9.figshare.20721424.v1
title: Solution of Practical Vehicle Routing Problem for Monitoring Water Distribution Networks

description: Public repository that makes available the randomly created instances used to solve the Vehicle Routing Problem for Water Distribution Networks (VRPWDN).
DOI: 10.5517/ccdc.csd.cc29p91c
title: CCDC 2135622: Experimental Crystal Structure Determination

description: Related Article: Zhiyao Zhou, Anne M. LaPointe, Timothy D. Shaffer, Geoffrey W. Coates|2023|CSD Communication|||
description: Related Article: Zhiyao Zhou, Anne M. LaPointe, Timothy D. Shaffer, Geoffrey W. Coates|2023|Nature Chemistry|15|856|doi:10.1038/s41557-023-01187-0
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.cc2fd2rp
title: CCDC 2245942: Experimental Crystal Structure Determination

description: Related Article: Zhipeng Zhou|2023|CSD Communication|||
description: Related Article: Zhipeng Zhou, Lei Zhang, Yonghang Yang, Iñigo J. Vitorica-Yrezabal, Honglei Wang, Fanglin Tan, Li Gong, Yuyao Li, Pohua Chen, Xin Dong, Zihao Liang, Jing Yang, Chao Wang, Yuexian Hong, Yi Qiu, Armin Gölzhäuser, Xudong Chen, Haoyuan Qi, Sihai Yang, Wei Liu, Junliang Sun, Zhikun Zheng|2023|Nature Chemistry|15|841|doi:10.1038/s41557-023-01181-6
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.cc2fkx0y
title: CCDC 2251530: Experimental Crystal Structure Determination

description: Related Article: Rashmirekha Pradhan|2023|CSD Communication|||
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.cc2fkx1z
title: CCDC 2251531: Experimental Crystal Structure Determination

description: Related Article: Rashmirekha Pradhan|2023|CSD Communication|||
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.cc2fl0fh
title: CCDC 2251636: Experimental Crystal Structure Determination

description: Related Article: Huabin Shi|2023|CSD Communication|||
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.cc2fl3gm
title: CCDC 2251730: Experimental Crystal Structure Determination

description: Related Article: Jiyu Cui|2023|CSD Communication|||
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.cc2fl3jp
title: CCDC 2251732: Experimental Crystal Structure Determination

description: Related Article: Jinxu Gao, Kyumin Lee, Kiana Amini, Roy G. Gordon, Michael J. Aziz, Theodore A. Betley|2023|CSD Communication|||
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.cc2fl428
title: CCDC 2251749: Experimental Crystal Structure Determination

description: Related Article: Sheng Jiang|2023|CSD Communication|||
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.cc2fl44b
title: CCDC 2251751: Experimental Crystal Structure Determination

description: Related Article: Zi-Qi Geng|2023|CSD Communication|||
description: Related Article: Zi-Qi Geng, Chunhui Zhao, Hao-Dong Qian, Si-Jia Li, Hao Peng, Hao Xu|2023|Org.Lett.|25|4504|doi:10.1021/acs.orglett.3c01524
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: 10.6084/m9.figshare.20297003
title: A new approach used in docking study for predicting the combination drug efficacy in EML4-ALK target of NSCLC

description: Combination drug treatments are usually used in many diseases, including cancers and AIDS. This treatment strategy is known as one of the cornerstone in therapies, which potentially reduces drug toxicity and drug resistance and also enhances therapeutic efficacy. Before using a drug in treatment, several experimental studies are done in vivo and in vitro to ensure the drug’s efficacy. In such experimental studies, the drug’s efficacy is evaluated with the help of drug dose ratio. In the combination drug experimental studies, the efficacy of the drugs is quantified with the Combination Index (CI) value and then interpreted by various terminologies like synergy, additive, and antagonism. Several computational models have now been invented for the speedy identification of combination drug efficacy. Unfortunately, none of these models have predicted the atomic level interaction of the combination drug with the target protein. This type of intermolecular interaction can be identified with the help of docking software. In the proposed work, we try to identify the intermolecular interaction and efficacy of the combination drug Crzizotinib and Temozolomide in the target of EML4-ALK in NSCLC by in silico study. The result of the study was evaluated with drug properties and Complex Energy (CE) of the docked complex rather than using docking score and binding energy. From this study, we could understand that first, Crizotinib and then after the Temozolomide drug binded on the EML4-ALK protein complex, showed very least CE and also identified that the combination of Crizotinib and Temozolomide drug are more effective in NSCLC. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.20132619
title: Polyketide synthases (PKSs) of secondary metabolism: <i>in silico</i> identification and characterization in orchids

description: Type III polyketide synthases (PKSs) catalyse the formation of an array of polyketides with diverse structures that play an important role in secondary metabolism in plants. This group of enzymes is encoded by a multigene family, the Type III <i>polyketide synthase (PKS)</i> gene family. Vast reserves of secondary metabolites in orchids make these plants suitable candidates for research in the area. In this study, genome-wide searches lead to the identification of five <i>PeqPKS</i>, eight <i>DcaPKS</i> and six <i>AshPKS</i> genes in <i>Phalaenopsis equestris</i>, <i>Dendrobium catenatum</i> and <i>Apostasia shenzhenica,</i> respectively. All the members showed the presence of two characteristic conserved domains (Chal_sti_synt_N and Chal_sti_synt_C) and were generally localised in the cytoplasm. The phylogenetic analysis led to the classification of these proteins into two groups: CHS (chalcone synthase (CHS) and non-CHS. A single protein in <i>P. equestris</i> and two proteins each in <i>D. catenatum</i> and <i>A. shenzhenica</i> clustered within the CHS clade. The majority of the genes exhibited similar structural patterns with a single intron. Expression profiling revealed the tissue-specific expression of these genes with high expression in reproductive tissues for most genes. A number of stress-responsive <i>cis</i>-regulatory elements were predicted, noteworthy amongst these are, ABRE and CGTCA that are chiefly responsible for responding to abscisic acid and methyl jasmonate, respectively. Our study provides a reference framework for future studies involving functional elucidation of <i>PKS</i> genes and biotechnological production of polyketides. Communicated by Ramaswamy H. Sarma Identification of five <i>PeqPKS</i>, eight <i>DcaPKS</i> and six <i>AshPKS</i> genes in <i>Phalaenopsis equestris</i>, <i>Dendrobium catenatum</i> and <i>Apostasia shenzhenica</i> based on genome-wide analysis Presence of characteristic conserved domains (Chal_sti_synt_N, Chal_sti_synt_C) with cytological localisation Phylogenetic clustering into two groups, CHS chalcone synthase (CHS) and non-CHS Expression profiling revealing high expression in reproductive tissues Prediction of stress-responsive cis-regulatory elements like ABRE and CGTCA
DOI: 10.6084/m9.figshare.20297003.v1
title: A new approach used in docking study for predicting the combination drug efficacy in EML4-ALK target of NSCLC

description: Combination drug treatments are usually used in many diseases, including cancers and AIDS. This treatment strategy is known as one of the cornerstone in therapies, which potentially reduces drug toxicity and drug resistance and also enhances therapeutic efficacy. Before using a drug in treatment, several experimental studies are done in vivo and in vitro to ensure the drug’s efficacy. In such experimental studies, the drug’s efficacy is evaluated with the help of drug dose ratio. In the combination drug experimental studies, the efficacy of the drugs is quantified with the Combination Index (CI) value and then interpreted by various terminologies like synergy, additive, and antagonism. Several computational models have now been invented for the speedy identification of combination drug efficacy. Unfortunately, none of these models have predicted the atomic level interaction of the combination drug with the target protein. This type of intermolecular interaction can be identified with the help of docking software. In the proposed work, we try to identify the intermolecular interaction and efficacy of the combination drug Crzizotinib and Temozolomide in the target of EML4-ALK in NSCLC by in silico study. The result of the study was evaluated with drug properties and Complex Energy (CE) of the docked complex rather than using docking score and binding energy. From this study, we could understand that first, Crizotinib and then after the Temozolomide drug binded on the EML4-ALK protein complex, showed very least CE and also identified that the combination of Crizotinib and Temozolomide drug are more effective in NSCLC. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.20132619.v1
title: Polyketide synthases (PKSs) of secondary metabolism: <i>in silico</i> identification and characterization in orchids

description: Type III polyketide synthases (PKSs) catalyse the formation of an array of polyketides with diverse structures that play an important role in secondary metabolism in plants. This group of enzymes is encoded by a multigene family, the Type III <i>polyketide synthase (PKS)</i> gene family. Vast reserves of secondary metabolites in orchids make these plants suitable candidates for research in the area. In this study, genome-wide searches lead to the identification of five <i>PeqPKS</i>, eight <i>DcaPKS</i> and six <i>AshPKS</i> genes in <i>Phalaenopsis equestris</i>, <i>Dendrobium catenatum</i> and <i>Apostasia shenzhenica,</i> respectively. All the members showed the presence of two characteristic conserved domains (Chal_sti_synt_N and Chal_sti_synt_C) and were generally localised in the cytoplasm. The phylogenetic analysis led to the classification of these proteins into two groups: CHS (chalcone synthase (CHS) and non-CHS. A single protein in <i>P. equestris</i> and two proteins each in <i>D. catenatum</i> and <i>A. shenzhenica</i> clustered within the CHS clade. The majority of the genes exhibited similar structural patterns with a single intron. Expression profiling revealed the tissue-specific expression of these genes with high expression in reproductive tissues for most genes. A number of stress-responsive <i>cis</i>-regulatory elements were predicted, noteworthy amongst these are, ABRE and CGTCA that are chiefly responsible for responding to abscisic acid and methyl jasmonate, respectively. Our study provides a reference framework for future studies involving functional elucidation of <i>PKS</i> genes and biotechnological production of polyketides. Communicated by Ramaswamy H. Sarma Identification of five <i>PeqPKS</i>, eight <i>DcaPKS</i> and six <i>AshPKS</i> genes in <i>Phalaenopsis equestris</i>, <i>Dendrobium catenatum</i> and <i>Apostasia shenzhenica</i> based on genome-wide analysis Presence of characteristic conserved domains (Chal_sti_synt_N, Chal_sti_synt_C) with cytological localisation Phylogenetic clustering into two groups, CHS chalcone synthase (CHS) and non-CHS Expression profiling revealing high expression in reproductive tissues Prediction of stress-responsive cis-regulatory elements like ABRE and CGTCA
DOI: 10.6084/m9.figshare.20146940
title: Integrated multi-omic data analysis and validation with yeast model show oxidative phosphorylation modulates protein aggregation in amyotrophic lateral sclerosis

description: Amyotrophic Lateral Sclerosis is a progressive, incurable amyloid aggregating neurodegenerative disease involving the motor neurons. Identifying potential biomarkers and therapeutic targets can assist in the better management of the disease. We used an integrative approach encompassing analysis of transcriptomic datasets of human and mice from the GEO database. Our analysis of ALS patient datasets showed deregulation in Non-alcoholic fatty acid liver disease and oxidative phosphorylation. Transgenic mice datasets of SOD1, FUS and TDP-43 showed deregulation in oxidative phosphorylation and ribosome-associated pathways. Commonality analysis between the human and mice datasets showed oxidative phosphorylation as a major deregulated pathway. Further, protein-protein and protein-drug interaction network analysis of mitochondrial electron transport chain showed enrichment of proteins and inhibitors of mitochondrial Complex III and IV. The results were further validated using the yeast model system. Inhibitor studies using metformin (Complex-I inhibitor) and malonate (Complex-II inhibitor) did not show any effect in mitigating the amyloids, while antimycin (Complex-III inhibitor) and azide (Complex-IV inhibitor) reduced amyloidogenesis. Knock-out of QCR8 (Complex-III) or COX8 (Complex–IV) cleared the amyloids. Taken together, our results show a critical role for mitochondrial oxidative phosphorylation in amyloidogenesis and as a potential therapeutic target in ALS. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.20146940.v1
title: Integrated multi-omic data analysis and validation with yeast model show oxidative phosphorylation modulates protein aggregation in amyotrophic lateral sclerosis

description: Amyotrophic Lateral Sclerosis is a progressive, incurable amyloid aggregating neurodegenerative disease involving the motor neurons. Identifying potential biomarkers and therapeutic targets can assist in the better management of the disease. We used an integrative approach encompassing analysis of transcriptomic datasets of human and mice from the GEO database. Our analysis of ALS patient datasets showed deregulation in Non-alcoholic fatty acid liver disease and oxidative phosphorylation. Transgenic mice datasets of SOD1, FUS and TDP-43 showed deregulation in oxidative phosphorylation and ribosome-associated pathways. Commonality analysis between the human and mice datasets showed oxidative phosphorylation as a major deregulated pathway. Further, protein-protein and protein-drug interaction network analysis of mitochondrial electron transport chain showed enrichment of proteins and inhibitors of mitochondrial Complex III and IV. The results were further validated using the yeast model system. Inhibitor studies using metformin (Complex-I inhibitor) and malonate (Complex-II inhibitor) did not show any effect in mitigating the amyloids, while antimycin (Complex-III inhibitor) and azide (Complex-IV inhibitor) reduced amyloidogenesis. Knock-out of QCR8 (Complex-III) or COX8 (Complex–IV) cleared the amyloids. Taken together, our results show a critical role for mitochondrial oxidative phosphorylation in amyloidogenesis and as a potential therapeutic target in ALS. Communicated by Ramaswamy H. Sarma