cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.8144353
title: RMG-DB-11: Enumerating Reaction Space for Small Molecule Chemistry

description: This repository presents approximately 750 million atom-mapped reaction SMILES. Reactions are generated by applying templates from the Reaction Mechanism Generator (RMG) database to a subset of the species from GDB11. Thus, we refer to this dataset as RMG-DB-11 i.e., the Reaction Mechanism Generator Database whose species contain up to 11 heavy atoms. All SMILES have been canonicalized by RDKit. All reactions are labeled with their corresponding RMG template. This data serves as a crucial starting point for quantitative predictive chemistry. Many methods that search for transition state structures require atom-mapped SMILES, which this repository provides. This data is also well-suited for unsupervised pre-training of various machine learning models. To parse the data with Python, start with <em>import pandas as pd</em>. Reactions with 1-8 heavy atoms can be parsed using the following code snippet: <em>pd.read_csv(&lt;filepath&gt;)</em>. Reactions with 9 heavy atoms can be parsed using <em>pd.read_pickle(&lt;filepath&gt;, compression='zip')</em>. The file names below include the word "zip" as a helpful hint to use the compression argument. Due to the large number of reactions with 10 and 11 heavy atoms, these are split into smaller chunks. First untar the file using <em>tar -xvf &lt;tar_archive&gt;</em> to obtain several zipped pickle files that can each be parsed using the same method as with 9 heavy atoms.
DOI: 10.5281/zenodo.8144352
title: RMG-DB-11: Enumerating Reaction Space for Small Molecule Chemistry

description: This repository presents approximately 750 million atom-mapped reaction SMILES. Reactions are generated by applying templates from the Reaction Mechanism Generator (RMG) database to a subset of the species from GDB11. Thus, we refer to this dataset as RMG-DB-11 i.e., the Reaction Mechanism Generator Database whose species contain up to 11 heavy atoms. All SMILES have been canonicalized by RDKit. All reactions are labeled with their corresponding RMG template. This data serves as a crucial starting point for quantitative predictive chemistry. Many methods that search for transition state structures require atom-mapped SMILES, which this repository provides. This data is also well-suited for unsupervised pre-training of various machine learning models. To parse the data with Python, start with <em>import pandas as pd</em>. Reactions with 1-8 heavy atoms can be parsed using the following code snippet: <em>pd.read_csv(&lt;filepath&gt;)</em>. Reactions with 9 heavy atoms can be parsed using <em>pd.read_pickle(&lt;filepath&gt;, compression='zip')</em>. The file names below include the word "zip" as a helpful hint to use the compression argument. Due to the large number of reactions with 10 and 11 heavy atoms, these are split into smaller chunks. First untar the file using <em>tar -xvf &lt;tar_archive&gt;</em> to obtain several zipped pickle files that can each be parsed using the same method as with 9 heavy atoms.
DOI: 10.6084/m9.figshare.22256035
title: T2Basin.tar.gz

description: Dataset and workflow file for a manuscript "Determining Mid-Ocean Ridge Geography from Upper Mantle Temperature" by Bao, Mittal and Lithgow-Bertelloni<br>
DOI: 10.6084/m9.figshare.22256035.v1
title: T2Basin.tar.gz

description: Dataset and workflow file for a GRL manuscript "Determining Mid-Ocean Ridge Geography from Upper Mantle Temperature" by Bao, Mittal and Lithgow-Bertelloni <br>
DOI: 10.6084/m9.figshare.22256035.v2
title: T2Basin.tar.gz

description: Dataset and workflow file for a manuscript "Determining Mid-Ocean Ridge Geography from Upper Mantle Temperature" by Bao, Mittal and Lithgow-Bertelloni<br>
DOI: 10.22002/e6mz6-r3g90
title: Mayère et al Germ Cell Data meK-Means

description: Male/Female germ cell development dataset from Mayère et al. 2021, saved in a loom file.
DOI: 10.6084/m9.figshare.12999546
title: Transition Readiness Assessment in Adolescents and Young Adults with Neurofibromatosis Type 1 (NF1)

description: Neurofibromatosis type 1 (NF1) conveys significant disease morbidity and lower quality of life compared to the general population. Research has shown that decreased positive health outcomes are directly correlated with inadequate development of health-related self-management skills among similar patient populations, and among these populations a healthcare transition (HCT) intervention improves provision of care and health outcomes. Thus, HCT intervention may improve care and outcomes in NF1. To design a future informed NF1 HCT intervention, baseline transition readiness must be assessed. A survey distributed by Children’s Tumor Foundation (CTF) was developed to assess transition readiness and the impact of NF1 on factors of young adult life. A total of 101 participants aged 14–26 years living in the United States completed the survey with a median [IQR] age of 18 [16, 21]. The majority of participants reported that NF1 had significant or some impact on all factors of young adult life including education, career, relationships, and family planning. The median Transition Readiness Assessment Questionnaire (TRAQ) score in this study (3.50/5.00) was significantly lower than the previously published score of healthy peers (3.93/5.00) (<i>p</i>&lt; .001). Higher TRAQ scores correlated with higher NF1-specific transition knowledge and skills (NF1-TRAQ) (<i>r</i> = 0.632). Participants self-report adequate knowledge of NF1 and comfort in talking to medical providers. They report discomfort with appointment keeping, insurance related tasks, addressing NF1 emergencies, and discussing NF1 with non-medical providers and peers. Further, TRAQ and NF1-TRAQ scores were lower in individuals who reported that their diagnosis of NF1 had some or significant impact on education, career, and relationships. Findings demonstrate that among individuals with NF1 in this study, decreased transition readiness is associated with a negative impact on young adult life. Data from this study supports the need to develop NF1-specific HCT intervention tools, with an effort to improve quality of life and standardize NF1 care.
DOI: 10.6084/m9.figshare.12999546.v1
title: Transition Readiness Assessment in Adolescents and Young Adults with Neurofibromatosis Type 1 (NF1)

description: Neurofibromatosis type 1 (NF1) conveys significant disease morbidity and lower quality of life compared to the general population. Research has shown that decreased positive health outcomes are directly correlated with inadequate development of health-related self-management skills among similar patient populations, and among these populations a healthcare transition (HCT) intervention improves provision of care and health outcomes. Thus, HCT intervention may improve care and outcomes in NF1. To design a future informed NF1 HCT intervention, baseline transition readiness must be assessed. A survey distributed by Children’s Tumor Foundation (CTF) was developed to assess transition readiness and the impact of NF1 on factors of young adult life. A total of 101 participants aged 14–26 years living in the United States completed the survey with a median [IQR] age of 18 [16, 21]. The majority of participants reported that NF1 had significant or some impact on all factors of young adult life including education, career, relationships, and family planning. The median Transition Readiness Assessment Questionnaire (TRAQ) score in this study (3.50/5.00) was significantly lower than the previously published score of healthy peers (3.93/5.00) (<i>p</i>&lt; .001). Higher TRAQ scores correlated with higher NF1-specific transition knowledge and skills (NF1-TRAQ) (<i>r</i> = 0.632). Participants self-report adequate knowledge of NF1 and comfort in talking to medical providers. They report discomfort with appointment keeping, insurance related tasks, addressing NF1 emergencies, and discussing NF1 with non-medical providers and peers. Further, TRAQ and NF1-TRAQ scores were lower in individuals who reported that their diagnosis of NF1 had some or significant impact on education, career, and relationships. Findings demonstrate that among individuals with NF1 in this study, decreased transition readiness is associated with a negative impact on young adult life. Data from this study supports the need to develop NF1-specific HCT intervention tools, with an effort to improve quality of life and standardize NF1 care.
DOI: 10.5517/ccdc.csd.cc2czhzv
title: CCDC 2204068: Experimental Crystal Structure Determination

description: Related Article: Chenfeng Wang, Ming-Der Su, Zijie Fang, Jiahao Zhou, Haoqi Zhang, Xiaodi Li, Darui Zuo, Zheng-Feng Zhang, Yan Li|2023|Chem.Commun.|59|10275|doi:10.1039/D3CC02512H
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.cc2czj1y
title: CCDC 2204070: Experimental Crystal Structure Determination

description: Related Article: Chenfeng Wang, Ming-Der Su, Zijie Fang, Jiahao Zhou, Haoqi Zhang, Xiaodi Li, Darui Zuo, Zheng-Feng Zhang, Yan Li|2023|Chem.Commun.|59|10275|doi:10.1039/D3CC02512H
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.cc2dmnk8
title: CCDC 2223430: Experimental Crystal Structure Determination

description: Related Article: Chenfeng Wang, Ming-Der Su, Zijie Fang, Jiahao Zhou, Haoqi Zhang, Xiaodi Li, Darui Zuo, Zheng-Feng Zhang, Yan Li|2023|Chem.Commun.|59|10275|doi:10.1039/D3CC02512H
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.cc2dmng5
title: CCDC 2223427: Experimental Crystal Structure Determination

description: Related Article: Chenfeng Wang, Ming-Der Su, Zijie Fang, Jiahao Zhou, Haoqi Zhang, Xiaodi Li, Darui Zuo, Zheng-Feng Zhang, Yan Li|2023|Chem.Commun.|59|10275|doi:10.1039/D3CC02512H
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: 10.22002/b8xj7-0t796
title: Mayère et al Germ Cell Metadata meK-Means

description: Metadata (development stage) for cells in male/female germ cell data from Mayère et al. 2021, saved as csv.
DOI: 10.6084/m9.figshare.24045555
title: Data Richness Spreadsheet

description: Data Richness Spreadsheet output
DOI: 10.6084/m9.figshare.24045555.v1
title: Data Richness Spreadsheet

description: Data Richness Spreadsheet output
DOI: 10.6084/m9.figshare.24039192
title: Zhang et al. Nature Comm Biology "<b>Myeloid cell deficiency of the inflammatory transcription factor Stat4 protects long-term synaptic plasticity from the effects of a high-fat, high-cholesterol diet</b>"

description: Raw data in Excel format files for Zhang et al. Nature Communications Biology paper "<b>Myeloid cell deficiency of the inflammatory transcription factor Stat4 protects long-term synaptic plasticity from the effects of a high-fat, high-cholesterol diet</b>"
DOI: 10.6084/m9.figshare.24045564
title: Project Potential Spreadsheet

description: Project Potential Spreadsheet
DOI: 10.6084/m9.figshare.24045564.v1
title: Project Potential Spreadsheet

description: Project Potential Spreadsheet
DOI: 10.6084/m9.figshare.24045573
title: Dataset Log

description: Data Log
DOI: 10.6084/m9.figshare.24045573.v1
title: Dataset Log

description: Data Log
DOI: 10.6084/m9.figshare.21293371
title: A Systematic Review of Clinical Trials in Uveitis: Lessons Learned

description: Clinical trials in uveitis have led to the expansion of therapeutic options for the management of non-infectious uveitis. The purpose of this systematic review is to investigate why some clinical trials have yielded successful results and regulatory approval of new therapies, and some have not. A systematic literature search of the Pubmed/MEDLINE database and clinicaltrials.gov was performed from 2006 to 2021, according to the PRISMA guidelines. Phase III clinical trials of systemic and local therapies in adults with non-infectious intermediate, posterior, and panuveitis were included. A total of 79 clinical trials were collected from ClinicalTrials.gov and PubMed/MEDLINE database search. Based on the inclusion and exclusion criteria, 14 clinical trials were included. This review summarizes the study design, outcome measures, and results of recent phase III trials in non-infectious uveitis, in the interest of understanding limitations and rethinking new methods of defining endpoints in clinical trial design.
DOI: 10.6084/m9.figshare.21293371.v1
title: A Systematic Review of Clinical Trials in Uveitis: Lessons Learned

description: Clinical trials in uveitis have led to the expansion of therapeutic options for the management of non-infectious uveitis. The purpose of this systematic review is to investigate why some clinical trials have yielded successful results and regulatory approval of new therapies, and some have not. A systematic literature search of the Pubmed/MEDLINE database and clinicaltrials.gov was performed from 2006 to 2021, according to the PRISMA guidelines. Phase III clinical trials of systemic and local therapies in adults with non-infectious intermediate, posterior, and panuveitis were included. A total of 79 clinical trials were collected from ClinicalTrials.gov and PubMed/MEDLINE database search. Based on the inclusion and exclusion criteria, 14 clinical trials were included. This review summarizes the study design, outcome measures, and results of recent phase III trials in non-infectious uveitis, in the interest of understanding limitations and rethinking new methods of defining endpoints in clinical trial design.
DOI: 10.5517/ccdc.csd.cc2f1vfs
title: CCDC 2236105: Experimental Crystal Structure Determination

description: Related Article: Tanzilya S. Rizbayeva, Andrey V. Smolobochkin, Almir S. Gazizov, Julia K. Voronina, Victor V. Syakaev, Daria P. Gerasimova, Olga A. Lodochnikova, Sergey V. Efimov, Vladimir V. Klochkov, Alexander R. Burilov, Michail A. Pudovik|2023|J.Org.Chem.|88|11855|doi:10.1021/acs.joc.3c01138
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.cc2f1vgt
title: CCDC 2236106: Experimental Crystal Structure Determination

description: Related Article: Tanzilya S. Rizbayeva, Andrey V. Smolobochkin, Almir S. Gazizov, Julia K. Voronina, Victor V. Syakaev, Daria P. Gerasimova, Olga A. Lodochnikova, Sergey V. Efimov, Vladimir V. Klochkov, Alexander R. Burilov, Michail A. Pudovik|2023|J.Org.Chem.|88|11855|doi:10.1021/acs.joc.3c01138
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.cc2f1vhv
title: CCDC 2236107: Experimental Crystal Structure Determination

description: Related Article: Tanzilya S. Rizbayeva, Andrey V. Smolobochkin, Almir S. Gazizov, Julia K. Voronina, Victor V. Syakaev, Daria P. Gerasimova, Olga A. Lodochnikova, Sergey V. Efimov, Vladimir V. Klochkov, Alexander R. Burilov, Michail A. Pudovik|2023|J.Org.Chem.|88|11855|doi:10.1021/acs.joc.3c01138
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.cc2f1vjw
title: CCDC 2236108: Experimental Crystal Structure Determination

description: Related Article: Tanzilya S. Rizbayeva, Andrey V. Smolobochkin, Almir S. Gazizov, Julia K. Voronina, Victor V. Syakaev, Daria P. Gerasimova, Olga A. Lodochnikova, Sergey V. Efimov, Vladimir V. Klochkov, Alexander R. Burilov, Michail A. Pudovik|2023|J.Org.Chem.|88|11855|doi:10.1021/acs.joc.3c01138
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.cc2f1vkx
title: CCDC 2236109: Experimental Crystal Structure Determination

description: Related Article: Tanzilya S. Rizbayeva, Andrey V. Smolobochkin, Almir S. Gazizov, Julia K. Voronina, Victor V. Syakaev, Daria P. Gerasimova, Olga A. Lodochnikova, Sergey V. Efimov, Vladimir V. Klochkov, Alexander R. Burilov, Michail A. Pudovik|2023|J.Org.Chem.|88|11855|doi:10.1021/acs.joc.3c01138
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.cc2f1vly
title: CCDC 2236110: Experimental Crystal Structure Determination

description: Related Article: Tanzilya S. Rizbayeva, Andrey V. Smolobochkin, Almir S. Gazizov, Julia K. Voronina, Victor V. Syakaev, Daria P. Gerasimova, Olga A. Lodochnikova, Sergey V. Efimov, Vladimir V. Klochkov, Alexander R. Burilov, Michail A. Pudovik|2023|J.Org.Chem.|88|11855|doi:10.1021/acs.joc.3c01138
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.cc2f1vmz
title: CCDC 2236111: Experimental Crystal Structure Determination

description: Related Article: Tanzilya S. Rizbayeva, Andrey V. Smolobochkin, Almir S. Gazizov, Julia K. Voronina, Victor V. Syakaev, Daria P. Gerasimova, Olga A. Lodochnikova, Sergey V. Efimov, Vladimir V. Klochkov, Alexander R. Burilov, Michail A. Pudovik|2023|J.Org.Chem.|88|11855|doi:10.1021/acs.joc.3c01138
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.cc2f3c64
title: CCDC 2237555: Experimental Crystal Structure Determination

description: Related Article: Neha Taneja, Pragya Sharma, Naveen Yadav, Dulal Musib, Chinmoy Kumar Hazra|2023|Org.Lett.|25|6029|doi:10.1021/acs.orglett.3c02181
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.cc2f6btt
title: CCDC 2240426: Experimental Crystal Structure Determination

description: Related Article: Hai-Lei Cui, Xiao-Hui Chen|2023|J.Org.Chem.|88|11935|doi:10.1021/acs.joc.3c01200
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.cc2fb6cc
title: CCDC 2244132: Experimental Crystal Structure Determination

description: Related Article: Thomas Mies, Andrew J. P. White, Henry S. Rzepa, Luciano Barluzzi, Mohit Devgan, Richard A. Layfield, Anthony G. M. Barrett|2023|Inorg.Chem.|62|13253|doi:10.1021/acs.inorgchem.3c01506
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.cc2ch2xw
title: CCDC 2189248: Experimental Crystal Structure Determination

description: Related Article: Yuan-Peng Wang, Ying-Chun Guo, Jing Lu, Yu-Chang Wang, Wen-Fu Yan, Juan Jin, Wei-Tao Zhang, Jia-Jia Zhang, Qing-Feng Yang, Qing-An Qiao|2023|J.Mol.Struct.|1294|136338|doi:10.1016/j.molstruc.2023.136338
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.cc2fft90
title: CCDC 2247602: Experimental Crystal Structure Determination

description: Related Article: Chuhao Lin, Yujie Jin, Jizeng Sun, Zehua Ye, Tao Chen, Jiyong Liu, Simon Duttwyler|2023|Dalton Trans.|52|11042|doi:10.1039/D3DT02275G
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.cc2fftb1
title: CCDC 2247603: Experimental Crystal Structure Determination

description: Related Article: Chuhao Lin, Yujie Jin, Jizeng Sun, Zehua Ye, Tao Chen, Jiyong Liu, Simon Duttwyler|2023|Dalton Trans.|52|11042|doi:10.1039/D3DT02275G
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.