cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.19931582.v1
title: <i>In</i><i>silico</i> models to predict tubular secretion or reabsorption clearance pathway using physicochemical properties and structural characteristics

description: Renal clearance is one of the main pathways for a drug to be cleared from plasma. The aim of this study is to develop <i>in-silico</i> models to find out the relationship between the type of renal clearance, and structural parameters.Literature data were used to categorise the drugs into those that undergo tubular secretion and those that undergo reabsorption. Different structural descriptors (VolSurf descriptors, Abraham solvation parameters, data warrior descriptors, logarithm of distribution coefficient at pH = 7.4 (logD<sub>7.4</sub>)) were applied to develop a mechanistic model for estimating renal clearance class whether its secretion or reabsorption.The results of this study show that logD<sub>7.4</sub> and the number of hydrogen bond donors, as well as available uncharged species (AUS<sub>7.4</sub>), are the most effective descriptors to establish mechanistic models for predicting renal clearance class. The classification models were established with a level of accuracy of more than 75%.Developed models of this study can be helpful to predict renal clearance class for new drug candidates with an acceptable error. Hydrophilicity and hydrogen bond formation ability of drugs are among the main descriptors. Renal clearance is one of the main pathways for a drug to be cleared from plasma. The aim of this study is to develop <i>in-silico</i> models to find out the relationship between the type of renal clearance, and structural parameters. Literature data were used to categorise the drugs into those that undergo tubular secretion and those that undergo reabsorption. Different structural descriptors (VolSurf descriptors, Abraham solvation parameters, data warrior descriptors, logarithm of distribution coefficient at pH = 7.4 (logD<sub>7.4</sub>)) were applied to develop a mechanistic model for estimating renal clearance class whether its secretion or reabsorption. The results of this study show that logD<sub>7.4</sub> and the number of hydrogen bond donors, as well as available uncharged species (AUS<sub>7.4</sub>), are the most effective descriptors to establish mechanistic models for predicting renal clearance class. The classification models were established with a level of accuracy of more than 75%. Developed models of this study can be helpful to predict renal clearance class for new drug candidates with an acceptable error. Hydrophilicity and hydrogen bond formation ability of drugs are among the main descriptors.
DOI: 10.6084/m9.figshare.7834895
title: Variations in circadian genes and individual nocturnal symptoms of insomnia. The HUNT study

description: Insomnia is a condition characterized by three nocturnal symptoms: problems with sleep onset or maintenance and early morning awakenings (terminal insomnia). Affected individuals may present one or more of these symptoms. Several studies have shown that insomnia is moderately heritable and that proxy phenotypes for the three insomnia symptoms show different heritabilities. This suggests that different nocturnal symptoms of insomnia may arise from different genetic and biological backgrounds. Circadian genes are good candidates to account for these differences as they regulate the periodicity of several physiological functions including sleep. Evidence from studies in animals and humans have suggested that circadian genes might be involved in sleep disturbances such as insomnia. In this study, we investigated the association between Single Nucleotide Polymorphisms (SNPs) in circadian genes and individual symptoms of insomnia and their combinations using data from the Nord-Trøndelag Health Study 3 (the HUNT3 study, N = 50807). Participants (N = 6029) provided information about sleep onset insomnia, maintenance insomnia, and terminal insomnia. Participants who responded “several times a week” to at least one question regarding the mentioned symptoms were classified as cases (N = 3577) and categorized in seven subgroups according to possible symptom combinations. Controls (N = 2452) answered “Never/Seldom” to all sleep-related questions. Using multinomial regression, we assessed 73 SNPs in nine circadian genes (<i>PER1, 2, 3, CRY1, 2, TIMELESS, CLOCK, REV-ERBα, ARNTL</i>) for differences among symptoms subgroups. Twenty-five SNPs showed significant p-values and supportive odds-ratios. All significant SNPs in <i>PER3</i> were associated with reporting all three symptoms simultaneously. SNPs in <i>CRY</i> genes were associated with terminal insomnia alone or in combination with other symptoms. Genes <i>PER1</i> and two were mostly associated with sleep maintenance insomnia. However, none of the SNPs remained significant after False Discovery Rate (FDR) correction for multiple statistical testing. In conclusion, even though none of the SNPs remained significant after FDR correction, the clustering of some genes around specific symptoms points to the need for additional research on these relationships.
DOI: 10.6084/m9.figshare.7834895.v1
title: Variations in circadian genes and individual nocturnal symptoms of insomnia. The HUNT study

description: Insomnia is a condition characterized by three nocturnal symptoms: problems with sleep onset or maintenance and early morning awakenings (terminal insomnia). Affected individuals may present one or more of these symptoms. Several studies have shown that insomnia is moderately heritable and that proxy phenotypes for the three insomnia symptoms show different heritabilities. This suggests that different nocturnal symptoms of insomnia may arise from different genetic and biological backgrounds. Circadian genes are good candidates to account for these differences as they regulate the periodicity of several physiological functions including sleep. Evidence from studies in animals and humans have suggested that circadian genes might be involved in sleep disturbances such as insomnia. In this study, we investigated the association between Single Nucleotide Polymorphisms (SNPs) in circadian genes and individual symptoms of insomnia and their combinations using data from the Nord-Trøndelag Health Study 3 (the HUNT3 study, N = 50807). Participants (N = 6029) provided information about sleep onset insomnia, maintenance insomnia, and terminal insomnia. Participants who responded “several times a week” to at least one question regarding the mentioned symptoms were classified as cases (N = 3577) and categorized in seven subgroups according to possible symptom combinations. Controls (N = 2452) answered “Never/Seldom” to all sleep-related questions. Using multinomial regression, we assessed 73 SNPs in nine circadian genes (<i>PER1, 2, 3, CRY1, 2, TIMELESS, CLOCK, REV-ERBα, ARNTL</i>) for differences among symptoms subgroups. Twenty-five SNPs showed significant p-values and supportive odds-ratios. All significant SNPs in <i>PER3</i> were associated with reporting all three symptoms simultaneously. SNPs in <i>CRY</i> genes were associated with terminal insomnia alone or in combination with other symptoms. Genes <i>PER1</i> and two were mostly associated with sleep maintenance insomnia. However, none of the SNPs remained significant after False Discovery Rate (FDR) correction for multiple statistical testing. In conclusion, even though none of the SNPs remained significant after FDR correction, the clustering of some genes around specific symptoms points to the need for additional research on these relationships.
DOI: 10.5281/zenodo.7215110
title: Bio-Optic bio-shortwave model code, initial conditions, river and boundary forcing for "Estimating the seaonal impact of optically significant water constituents on surface heating rates in the Western Baltic Sea" paper.

description: Bio-Optic bio-shortwave model code, initial conditions, river and boundary forcing as well as selected model output used for analysis and producing figures in the paper "Estimating the seaonal impact of optically significant water constituents on surface heating rates in the Western Baltic Sea". Contact Bronwyn Cahill if you have questions at: bronwyn.cahill@io-warnemuende.de
DOI: 10.5281/zenodo.7215109
title: Bio-Optic bio-shortwave model code, initial conditions, river and boundary forcing for "Estimating the seaonal impact of optically significant water constituents on surface heating rates in the Western Baltic Sea" paper.

description: Bio-Optic bio-shortwave model code, initial conditions, river and boundary forcing as well as selected model output used for analysis and producing figures in the paper "Estimating the seaonal impact of optically significant water constituents on surface heating rates in the Western Baltic Sea". Contact Bronwyn Cahill if you have questions at: bronwyn.cahill@io-warnemuende.de
DOI: 10.25934/pr00006053.13
title: Available IPD datapackage for study 'A Phase III, Open-Label, Multicenter, Randomized Study Evaluating the Efficacy and Safety of Atezolizumab (MPDL3280A, Anti-PD-L1 Antibody) in Combination With Carboplatin+Paclitaxel or Atezolizumab in Combination With Carboplatin+Nab-Paclitaxel Versus Carboplatin+Nab-Paclitaxel in Chemotherapy-Naive Patients With Stage IV Squamous Non-Small Cell Lung Cancer'

description: This randomized, open-label study will evaluate the safety and efficacy of atezolizumab (MPDL3280A) in combination with carboplatin + paclitaxel or carboplatin + nab-paclitaxel compared with treatment with carboplatin + nab-paclitaxel in chemotherapy-naive participants with Stage IV squamous NSCLC.
DOI: 10.25934/pr00005796.9
title: Available IPD datapackage for study 'A Phase II, Multicenter, Single-Arm Study OF Atezolizumab In Patients With PD-L1-Positive Locally Advanced Or Metastatic Non-Small Cell Lung Cancer'

description: This multicenter, single-arm study will evaluate the efficacy and safety of Atezolizumab in participants with PD-L1-positive locally advanced or metastatic non-small cell lung cancer (NSCLC). Participants will receive Atezolizumab 1200 milligrams (mg) intravenously every 3 weeks as long as participants are experiencing clinical benefit as assessed by the investigator, that is , in the absence of unacceptable toxicity or symptomatic deterioration attributed to disease progression.
DOI: 10.6084/m9.figshare.22305895
title: Code & data for figures 2, 3 & supplementary figure 1

description: Follow instructions in "Code_for_work_loop_graphs.m"
DOI: 10.6084/m9.figshare.22305895.v1
title: Code & data for figures 2, 3 & supplementary figure 1

description: Follow instructions in "Code_for_work_loop_graphs.m"
DOI: 10.5517/ccdc.csd.cc27lf4f
title: CCDC 2073284: Experimental Crystal Structure Determination

description: Related Article: Zixiao Qin, Jian He, Yin Zhu, Xiaopeng Wei, Jilin Wang, Guoyuan Zheng, Shuyi Mo, Bing Zhou, Fei Long|2023|J.Mol.Struct.|1281|135080|doi:10.1016/j.molstruc.2023.135080
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.cc29306n
title: CCDC 2118050: Experimental Crystal Structure Determination

description: Related Article: Aziza Dellouche Chouiter, Mohamed Oussama Mousser, Henia Bouzidi Mousser, Adel Krid, Lotfi Belkhiri, Solenne Fleutot, Michel François|2023|J.Mol.Struct.|1281|135171|doi:10.1016/j.molstruc.2023.135171
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.cc2c2bjb
title: CCDC 2176991: Experimental Crystal Structure Determination

description: Related Article: Li-Zhen Yang, Ru-Xia Yang, Peng-Yin Zhu, Tian-Cai Yue, Yu-Ming Yu, Duo-Zhi Wang, Lu-Lu Wang|2023|J.Mol.Struct.|1281|135177|doi:10.1016/j.molstruc.2023.135177
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.cc2c2bkc
title: CCDC 2176992: Experimental Crystal Structure Determination

description: Related Article: Li-Zhen Yang, Ru-Xia Yang, Peng-Yin Zhu, Tian-Cai Yue, Yu-Ming Yu, Duo-Zhi Wang, Lu-Lu Wang|2023|J.Mol.Struct.|1281|135177|doi:10.1016/j.molstruc.2023.135177
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.cc2c2bld
title: CCDC 2176993: Experimental Crystal Structure Determination

description: Related Article: Li-Zhen Yang, Ru-Xia Yang, Peng-Yin Zhu, Tian-Cai Yue, Yu-Ming Yu, Duo-Zhi Wang, Lu-Lu Wang|2023|J.Mol.Struct.|1281|135177|doi:10.1016/j.molstruc.2023.135177
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.cc2c2bmf
title: CCDC 2176994: Experimental Crystal Structure Determination

description: Related Article: Li-Zhen Yang, Ru-Xia Yang, Peng-Yin Zhu, Tian-Cai Yue, Yu-Ming Yu, Duo-Zhi Wang, Lu-Lu Wang|2023|J.Mol.Struct.|1281|135177|doi:10.1016/j.molstruc.2023.135177
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.cc2c2bng
title: CCDC 2176995: Experimental Crystal Structure Determination

description: Related Article: Li-Zhen Yang, Ru-Xia Yang, Peng-Yin Zhu, Tian-Cai Yue, Yu-Ming Yu, Duo-Zhi Wang, Lu-Lu Wang|2023|J.Mol.Struct.|1281|135177|doi:10.1016/j.molstruc.2023.135177
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.cc2c2bph
title: CCDC 2176996: Experimental Crystal Structure Determination

description: Related Article: Li-Zhen Yang, Ru-Xia Yang, Peng-Yin Zhu, Tian-Cai Yue, Yu-Ming Yu, Duo-Zhi Wang, Lu-Lu Wang|2023|J.Mol.Struct.|1281|135177|doi:10.1016/j.molstruc.2023.135177
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.cc2c2bqj
title: CCDC 2176997: Experimental Crystal Structure Determination

description: Related Article: Li-Zhen Yang, Ru-Xia Yang, Peng-Yin Zhu, Tian-Cai Yue, Yu-Ming Yu, Duo-Zhi Wang, Lu-Lu Wang|2023|J.Mol.Struct.|1281|135177|doi:10.1016/j.molstruc.2023.135177
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.cc2c2brk
title: CCDC 2176998: Experimental Crystal Structure Determination

description: Related Article: Li-Zhen Yang, Ru-Xia Yang, Peng-Yin Zhu, Tian-Cai Yue, Yu-Ming Yu, Duo-Zhi Wang, Lu-Lu Wang|2023|J.Mol.Struct.|1281|135177|doi:10.1016/j.molstruc.2023.135177
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.22305910
title: PRESCHOOL,covid.sav

description: This data set is of preschoolers including personality traits and mental health scores.
DOI: 10.6084/m9.figshare.22305910.v1
title: PRESCHOOL,covid.sav

description: This data set is of preschoolers including personality traits and mental health scores.
DOI: 10.6084/m9.figshare.22305904
title: ls_repo_VSe2.zip

description: A Quantum Monte Carlo study of the structural, energetic, and magnetic properties of two-dimensional (2D) H and T phase VSe2: Line-search data and analysis <br> Published in Journal of Physical Chemistry Letters (2023) <br> https://arxiv.org/abs/2301.11404 <br> <br> Authors: Daniel Wines, Juha Tiihonen, Kayahan Saritas, Jaron T. Krogel and Can Ataca <br> Author of the data repository: Juha Tiihonen <br> This small data repository contains data and scripts to reproduce geometry relaxation of two-dimensional VSe2 in H and T phases using a line-search tool. The repository has three directories with the following contents: <br> src/ source code for the line-search tool, referred here as the software ls_data/ production data of the line-search iteration and analysis postproc/ postprocessing scripts and figures
DOI: 10.25934/pr00005997.9
title: Available IPD datapackage for study 'A Phase III, Open-Label, Randomized Study of Atezolizumab (Anti-PD-L1 Antibody) in Combination With Bevacizumab Versus Sunitinib in Patients With Untreated Advanced Renal Cell Carcinoma'

description: This multi-center, randomized, open-label study will evaluate the efficacy and safety of atezolizumab plus bevacizumab versus sunitinib in participants with inoperable, locally advanced, or metastatic RCC who have not received prior systemic active or experimental therapy, either in the adjuvant or metastatic setting.
DOI: 10.25378/janelia.20376591
title: Entire C. elegans dauer transmission electron microscopy acquisition (e1370)

description: TEM acquistion of an entire C. elegans in dauer stage (e1370) using 70nm slices. Acquired using the Leginon software, reconstructed with TrakEM2, all nuclei segmented using a custom active contours and machine learning approach.
DOI: 10.25378/janelia.20376591.v1
title: Entire C. elegans dauer transmission electron microscopy acquisition (e1370)

description: TEM acquistion of an entire C. elegans in dauer stage (e1370) using 70nm slices. Acquired using the Leginon software, reconstructed with TrakEM2, all nuclei segmented using a custom active contours and machine learning approach.
DOI: 10.5281/zenodo.7753166
title: Data to run analyses present in the paper: Cell specificity of human regulatory annotations and their genetic effects on gene expression

description: Data for the manuscript: Varshney A., H. VanRenterghem, P. Orchard, A. P. Boyle, M. L. Stitzel, <em>et al.</em>, 2019 Cell Specificity of Human Regulatory Annotations and Their Genetic Effects on Gene Expression. Genetics 211: 549–562. https://doi.org/10.1534/genetics.118.301525 The code to generate these data are at GitHub: https://github.com/ParkerLab/regulatoryAnnotations_comparisons Also see processed data available in this previous Zenodo record: https://zenodo.org/record/1413623
DOI: 10.5281/zenodo.7753165
title: Data to run analyses present in the paper: Cell specificity of human regulatory annotations and their genetic effects on gene expression

description: Data for the manuscript: Varshney A., H. VanRenterghem, P. Orchard, A. P. Boyle, M. L. Stitzel, <em>et al.</em>, 2019 Cell Specificity of Human Regulatory Annotations and Their Genetic Effects on Gene Expression. Genetics 211: 549–562. https://doi.org/10.1534/genetics.118.301525 The code to generate these data are at GitHub: https://github.com/ParkerLab/regulatoryAnnotations_comparisons Also see processed data available in this previous Zenodo record: https://zenodo.org/record/1413623
DOI: 10.25934/pr00005598.11
title: Available IPD datapackage for study 'A Phase III, Open-Label, Multicenter, Randomized Study to Investigate the Efficacy and Safety of Atezolizumab (Anti-PD-L1 Antibody) Compared With Chemotherapy in Patients With Locally Advanced or Metastatic Urothelial Bladder Cancer After Failure With Platinum-Containing Chemotherapy'

description: This is a Phase III, global, multicenter, open-label, two-arm, randomized, controlled study designed to evaluate the efficacy and safety of atezolizumab compared with chemotherapy in participants with locally advanced or metastatic urothelial bladder cancer (UBC) who have progressed during or following a platinum-containing regimen. The anticipated time on study treatment is based on continued clinical benefit, i.e., until disease progression or unacceptable toxicity. The target sample size is 931 participants.
DOI: 10.22002/h88fq-dk449
title: The Materials Experiment Knowledge Graph

description: A Neo4j dump of the Materials Experiment Knowledge Graph (MEKG), a graph database containing metadata and experimental provenance from synthesis to measurement of primarily metal oxide solid state materials resulting from high throughput experimentation. The MEKG is a practical graph restructuring of the Materials Provenance Store, designed for greater querying efficiency through explicit entity relationships which would otherwise require slow table joins in the SQL paradigm. The higher search efficiency of long paths (equivalently multi-table joins) comes at the cost of slower aggregation operations.
DOI: 10.34740/kaggle/dsv/5202650
title: Nigerian Presidential Election 2023 Tweets
DOI: 10.5281/zenodo.7753809
title: Enhancing Mixing During Groundwater Remediation via Engineered Injection-Extraction: The Issue of Connectivity

description: Output data used to elaborate the main figures in section 6: Results and discussion.
DOI: 10.5281/zenodo.7753808
title: Enhancing Mixing During Groundwater Remediation via Engineered Injection-Extraction: The Issue of Connectivity

description: Output data used to elaborate the main figures in section 6: Results and discussion.