cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.8268726
title: Data deposit accompanying Accurate Energy Barriers for Catalytic Reaction Pathways: An Automatic Training Protocol for Machine Learning Force Fields

description: Dataset accompanying the paper: <em>"Accurate Energy Barriers for Catalytic Reaction Pathways: An Automatic Training Protocol for Machine Learning Force Fields"</em>. Contains the training sets curated during active learning as well as .xyz files used for creating the Figures. <br> <br> The paper highlights that the computational efficiency of ML force fields not only results in decreased computational costs for routine catalytic investigations but also facilitates more comprehensive exploration of catalytic pathways. <strong>Published in NPJ Computational Materials</strong>: https://www.nature.com/articles/s41524-023-01124-2<br> Formerly on Arxiv: https://arxiv.org/abs/2301.09931
DOI: 10.5281/zenodo.8268725
title: Data deposit accompanying Accurate Energy Barriers for Catalytic Reaction Pathways: An Automatic Training Protocol for Machine Learning Force Fields

description: Dataset accompanying the paper: <em>"Accurate Energy Barriers for Catalytic Reaction Pathways: An Automatic Training Protocol for Machine Learning Force Fields"</em>. Contains the training sets curated during active learning as well as .xyz files used for creating the Figures. <br> <br> The paper highlights that the computational efficiency of ML force fields not only results in decreased computational costs for routine catalytic investigations but also facilitates more comprehensive exploration of catalytic pathways. <strong>Published in NPJ Computational Materials</strong>: https://www.nature.com/articles/s41524-023-01124-2<br> Formerly on Arxiv: https://arxiv.org/abs/2301.09931
DOI: 10.57967/hf/1183
title: test
DOI: 10.6084/m9.figshare.24241807
title: Data TOF and IT

description: Increased implementation of molecular networking and dereplication in the natural product research in the last years made the expansion of open-access spectra-based databases necessary. The rate of new substance identifications, which lead to a discovery of new natural products with potential pharmacological properties, depends on the quality and extent of used databases.The aim of this master thesis is the establishment of a MS/MS-database in order to increase available data in spectra-based databases. Two natural product classes were selected – sesquiterpenes and triterpenoids. First MS/MS-data for 42 sesquiterpenes and 81 triterpenoids was generated in silico using CFM-ID-Platform. The purity of sesquiterpenes was insufficient for a successful automated mass spectrometry, therefore the MS/MS-spectra were manually produced using direct injection ESI-IT-MS. Nevertheless, the sesquiterpenes were excluded from further work and the focus was placed on triterpenoids.MS/MS-spectra of triterpenoids were obtained using ESI-IT-MS and high-resolution ESI-qTOF-MS. ESI is the most used ionization technique in natural product research and was for this reason applied in this master thesis. IT-MS was performed with and without added buffer in both positive and negative modes. After evaluation of the spectra, it was found that the triterpenoids were better ionizable in the negative mode, which led to qTOF-MS only being performed in the negative mode. For 24 triterpenoids no useful MS/MS spectra were generated by either method, while for 31 triterpenoids fragmentation data were provided by both methods. MGF-Files, containing fragmentation data from the three spectra sources were generated.
DOI: 10.6084/m9.figshare.24241807.v1
title: Data TOF and IT

description: Increased implementation of molecular networking and dereplication in the natural product research in the last years made the expansion of open-access spectra-based databases necessary. The rate of new substance identifications, which lead to a discovery of new natural products with potential pharmacological properties, depends on the quality and extent of used databases.The aim of this master thesis is the establishment of a MS/MS-database in order to increase available data in spectra-based databases. Two natural product classes were selected – sesquiterpenes and triterpenoids. First MS/MS-data for 42 sesquiterpenes and 81 triterpenoids was generated in silico using CFM-ID-Platform. The purity of sesquiterpenes was insufficient for a successful automated mass spectrometry, therefore the MS/MS-spectra were manually produced using direct injection ESI-IT-MS. Nevertheless, the sesquiterpenes were excluded from further work and the focus was placed on triterpenoids.MS/MS-spectra of triterpenoids were obtained using ESI-IT-MS and high-resolution ESI-qTOF-MS. ESI is the most used ionization technique in natural product research and was for this reason applied in this master thesis. IT-MS was performed with and without added buffer in both positive and negative modes. After evaluation of the spectra, it was found that the triterpenoids were better ionizable in the negative mode, which led to qTOF-MS only being performed in the negative mode. For 24 triterpenoids no useful MS/MS spectra were generated by either method, while for 31 triterpenoids fragmentation data were provided by both methods. MGF-Files, containing fragmentation data from the three spectra sources were generated.
DOI: 10.57745/24ezgc
title: hs_2_9_skin.ffn.xz

description: Gene catalogue (nucleotide sequences)
DOI: 10.57745/bwhjsf
title: hs_2_9_skin.faa.xz

description: Gene catalogue (amino acid sequences)
DOI: 10.57745/59ouzt
title: hs_2_9_skin.392_msps.20230629.gtdb_r214_annot_long.tab

description: Taxonomic annotation of the MetaGenomic Species based on GTDB r214
DOI: 10.57745/gwrngg
title: hs_2_9_skin.392_msps.20221012.tsv.xz

description: Gene content of the MetaGenomic Species
DOI: 10.57745/dg62su
title: hs_2_9_skin.392_msps.20221012.no_euk.nwk

description: Phylogenetic tree of the MetaGenomic Species
DOI: 10.57745/bijeod
title: hs_2_9_skin.kegg107.kofam_scan.tsv.xz

description: Functional annotation of the gene catalog with the KEGG 107 database (KO assignments)
DOI: 10.5281/zenodo.8341385
title: Respiration and CO2 evasion dynamics in moving streambeds as a response to flow regimes

description: This dataset contains both raw and processed data utilized in generating the findings outlined in our research paper titled "Respiration and CO2 Evasion Dynamics in Mobile Streambeds in Response to Different Flow Regimes," which has been submitted to the Journal of Hydrology. Additionally, within this dataset, you will find a collection of movies that are part of our Supporting Information. Within this dataset, you will find a sub-dataset for all nine experimental runs. These experimental runs encompass three distinct flow regimes: a constant flow regime (C), a sinusoidal flow regime (S), and a single peak flow event (F). Each of these flow regimes was conducted three times as repeated measurements (RM). The data subsets contain: Raw infrared images captured at the sediment-water interface using an infrared camera. A selection of raw infrared images that correspond to the optode images obtained from our optode camera. Preprocessed optode images captured by the optode camera. The original raw planar optode images. A supplementary text file containing essential data information. Furthermore, the dataset encompasses raw data files related to surface water chemistry data and measurements of CO<sub>2</sub> air concentration and pressure. Also it contains datafiles with all results used in the publication. In the Supporting Information folder, you will find Movies S1 through S18, which visually illustrate the sediment's movement and the dynamic variations in O<sub>2</sub> and CO<sub>2</sub> concentrations within the sediment.
DOI: 10.5281/zenodo.8341384
title: Respiration and CO2 evasion dynamics in moving streambeds as a response to flow regimes

description: This dataset contains both raw and processed data utilized in generating the findings outlined in our research paper titled "Respiration and CO2 Evasion Dynamics in Mobile Streambeds in Response to Different Flow Regimes," which has been submitted to the Journal of Hydrology. Additionally, within this dataset, you will find a collection of movies that are part of our Supporting Information. Within this dataset, you will find a sub-dataset for all nine experimental runs. These experimental runs encompass three distinct flow regimes: a constant flow regime (C), a sinusoidal flow regime (S), and a single peak flow event (F). Each of these flow regimes was conducted three times as repeated measurements (RM). The data subsets contain: Raw infrared images captured at the sediment-water interface using an infrared camera. A selection of raw infrared images that correspond to the optode images obtained from our optode camera. Preprocessed optode images captured by the optode camera. The original raw planar optode images. A supplementary text file containing essential data information. Furthermore, the dataset encompasses raw data files related to surface water chemistry data and measurements of CO<sub>2</sub> air concentration and pressure. Also it contains datafiles with all results used in the publication. In the Supporting Information folder, you will find Movies S1 through S18, which visually illustrate the sediment's movement and the dynamic variations in O<sub>2</sub> and CO<sub>2</sub> concentrations within the sediment.
DOI: 10.5517/ccdc.csd.cc2gsmd9
title: CCDC 2287781: Experimental Crystal Structure Determination

description: Related Article: C. Näther, I. Jess|2023|Acta Crystallogr.,Sect.E:Cryst.Commun.|79|872|doi:10.1107/S2056989023007065
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.cc2gtv27
title: CCDC 2288949: Experimental Crystal Structure Determination

description: Related Article: E.Z. Huseynov, M. Akkurt, I. Brito, A. Bhattarai, R.M. Rzayev, K.A. Asadov, A.M. Maharramov|2023|Acta Crystallogr.,Sect.E:Cryst.Commun.|79|890|doi:10.1107/S2056989023007181
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.cc2bd6fd
title: CCDC 2156683: Experimental Crystal Structure Determination

description: Related Article: M. Lozinšek, T. Pavčnik, J. Bitenc|2023|IUCrData|8|x230716|doi:10.1107/S2414314623007162
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.cc2gwj96
title: CCDC 2290568: Experimental Crystal Structure Determination

description: Related Article: M. Stapf, A. Schwarzer|2023|IUCrData|8|x230743|doi:10.1107/S2414314623007435
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.cc2gwxpz
title: CCDC 2290952: Experimental Crystal Structure Determination

description: Related Article: R. Bansal, R.J. Butcher, S.K. Gupta|2023|Acta Crystallogr.,Sect.E:Cryst.Commun.|79|877|doi:10.1107/S205698902300748X
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.cc2gxlpp
title: CCDC 2291603: Experimental Crystal Structure Determination

description: Related Article: A. El-Mrabet, A. Haoudi, S. Dalbouha, M.K. Skalli, T. Hökelek, F. Capet, Y. Kandri Rodi, A. Mazzah, N.K. Sebbar|2023|Acta Crystallogr.,Sect.E:Cryst.Commun.|79|883|doi:10.1107/S2056989023007557
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.cc2gybvm
title: CCDC 2292321: Experimental Crystal Structure Determination

description: Related Article: S. Yousra, L. El Ghayati, T. Hökelek, F. Ouazzani Chahdi, J.T. Mague, Y. Kandri Rodi, N.K. Sebbar|2023|Acta Crystallogr.,Sect.E:Cryst.Commun.|79|895|doi:10.1107/S2056989023007624
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.cc1m38ff
title: CCDC 1492694: Experimental Crystal Structure Determination

description: Related Article: S.R. Pumford, R.L. LaDuca|2023|IUCrData|8|x230764|doi:10.1107/S2414314623007642
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.cc2gyfwr
title: CCDC 2292415: Experimental Crystal Structure Determination

description: Related Article: Y. Ishimaru, R. Ikeda, T. Fujihara|2023|IUCrData|8|x230766|doi:10.1107/S2414314623007666
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.cc2gzgrp
title: CCDC 2293403: Experimental Crystal Structure Determination

description: Related Article: D.N.K. Pham, N.B. Sackett, A.R. Chadeayne, J.A. Golen, D.R. Manke|2023|IUCrData|8|x230779|doi:10.1107/S2414314623007794
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.22227405
title: The potential of biomarkers for diagnosing insomnia: Consensus statement of the WFSBP Task Force on Sleep Disorders

description: Thus far, the diagnosis of insomnia is based on purely clinical criteria. Although a broad range of altered physiological parameters has been identified in insomniacs, the evidence to establish their diagnostic usefulness is very limited. Purpose of this WFSBP Task Force consensus paper is to systematically evaluate a series of biomarkers as potential diagnostic tools for insomnia. A newly created grading system was used for assessing the validity of various measurements in establishing the diagnosis of insomnia; these measurements originated from relevant studies selected and reviewed by experts. The measurements with the highest diagnostic performance were those derived from psychometric instruments. Biological measurements which emerged as potentially useful diagnostic instruments were polysomnography-derived cyclic alternating pattern, actigraphy, and BDNF levels, followed by heart rate around sleep onset, deficient melatonin rhythm, and certain neuroimaging patterns (mainly for the activity of frontal and pre-frontal cortex, hippocampus and basal ganglia); yet, these findings need replication, as well as establishment of commonly accepted methodology and diagnostic cut-off points. Routine polysomnography, EEG spectral analysis, heart rate variability, skin conductance, thermoregulation, oxygen consumption, HPA axis, and inflammation indices were not shown to be of satisfactory diagnostic value. Apart from psychometric instruments which are confirmed to be the gold standard in diagnosing insomnia, six biomarkers emerge as being potentially useful for this purpose.
DOI: 10.6084/m9.figshare.22227405.v1
title: The potential of biomarkers for diagnosing insomnia: Consensus statement of the WFSBP Task Force on Sleep Disorders

description: Thus far, the diagnosis of insomnia is based on purely clinical criteria. Although a broad range of altered physiological parameters has been identified in insomniacs, the evidence to establish their diagnostic usefulness is very limited. Purpose of this WFSBP Task Force consensus paper is to systematically evaluate a series of biomarkers as potential diagnostic tools for insomnia. A newly created grading system was used for assessing the validity of various measurements in establishing the diagnosis of insomnia; these measurements originated from relevant studies selected and reviewed by experts. The measurements with the highest diagnostic performance were those derived from psychometric instruments. Biological measurements which emerged as potentially useful diagnostic instruments were polysomnography-derived cyclic alternating pattern, actigraphy, and BDNF levels, followed by heart rate around sleep onset, deficient melatonin rhythm, and certain neuroimaging patterns (mainly for the activity of frontal and pre-frontal cortex, hippocampus and basal ganglia); yet, these findings need replication, as well as establishment of commonly accepted methodology and diagnostic cut-off points. Routine polysomnography, EEG spectral analysis, heart rate variability, skin conductance, thermoregulation, oxygen consumption, HPA axis, and inflammation indices were not shown to be of satisfactory diagnostic value. Apart from psychometric instruments which are confirmed to be the gold standard in diagnosing insomnia, six biomarkers emerge as being potentially useful for this purpose.
DOI: 10.25430/researchdata.cab.unipd.it.00001000
title: length of vineyard rows in the basin area of Lierza River from 1960 to 2018

description: These data are collected from aerial photo and orthophoto in the area of the basin of Lierza River. This River is tributary of the Soligo River thet flows in subalpine hills of the Treviso province. The Lierza Basin Area lye into the Valdobbiadene - Conegliano Prosecco DOCG area and it collects the various morphology of the whole DOCG area: Plain, gently hill, steep hill and stepest hill. The vineyard rows were collected as GIS polylines starting from 1960 to 2018 through 8 diachronical steps.
DOI: 10.6084/m9.figshare.24241990
title: Supplementary Material for: Relationship between the ratio of red cell distribution width to albumin and 28-day mortality among Chinese patients over 80 years with atrial fibrillation

description: Introduction: Atrial fibrillation (AF) is a prevalent heart arrhythmia in elderly adults aged 80 years or older. The red cell distribution width to albumin ratio has been acknowledged as a reliable prognostic marker for poor outcomes in a variety of disorders. However, there exists limited scientific evidence on the association of red cell distribution width to albumin (RAR) with mortality in geriatric individuals with AF. Methods: From January 2015 to June 2020, a retrospective study was conducted in a tertiary academic institution that diagnosed 1141 elderly adults with atrial fibrillation (AF). The RAR value was calculated as the ratio of RDW (%) to albumin (g/dL). The potential association between RAR and cardiovascular mortality and the risk of all-cause mortality within 28 days was evaluated by means of multivariable Cox regression analysis. Results: The 28-day all-cause and cardiovascular mortality rates were 8.7% and 3.3%, respectively. Increased RAR tertiles were found to be significantly associated with greater all-cause mortality (T1: 1.6%; T2: 6.2%; T3: 18.1%, P &lt; 0.001) and cardiovascular mortality (T1: 0.8%; T2: 2.9%; T3: 6.3%, P &lt; 0.001) using Kaplan‒Meier analysis. Continuous RAR had a positive association with all-cause mortality (HR=1.42, 95% CI 1.23-1.65) and cardiovascular mortality (HR=1.31, 95% CI 1.05-1.64), even after accounting for numerous confounding variables. In comparison to the T1 group, individuals with the highest RAR levels displayed a greater risk of all-cause mortality (HR=2.73, 95% CI 1.11-6.74) and cardiovascular mortality (HR=2.59, 95% CI 0.69-9.78). Increased RAR levels were related to higher rates of cardiovascular and all-cause mortality across almost all subgroups. Conclusion: RAR is independently correlated with 28-day all-cause mortality and cardiovascular mortality in AF-affected individuals aged ≥ 80. Keywords: cardiovascular disease; mortality; older; red cell distribution width; atrial fibrillation
DOI: 10.6084/m9.figshare.24241990.v1
title: Supplementary Material for: Relationship between the ratio of red cell distribution width to albumin and 28-day mortality among Chinese patients over 80 years with atrial fibrillation

description: Introduction: Atrial fibrillation (AF) is a prevalent heart arrhythmia in elderly adults aged 80 years or older. The red cell distribution width to albumin ratio has been acknowledged as a reliable prognostic marker for poor outcomes in a variety of disorders. However, there exists limited scientific evidence on the association of red cell distribution width to albumin (RAR) with mortality in geriatric individuals with AF. Methods: From January 2015 to June 2020, a retrospective study was conducted in a tertiary academic institution that diagnosed 1141 elderly adults with atrial fibrillation (AF). The RAR value was calculated as the ratio of RDW (%) to albumin (g/dL). The potential association between RAR and cardiovascular mortality and the risk of all-cause mortality within 28 days was evaluated by means of multivariable Cox regression analysis. Results: The 28-day all-cause and cardiovascular mortality rates were 8.7% and 3.3%, respectively. Increased RAR tertiles were found to be significantly associated with greater all-cause mortality (T1: 1.6%; T2: 6.2%; T3: 18.1%, P &lt; 0.001) and cardiovascular mortality (T1: 0.8%; T2: 2.9%; T3: 6.3%, P &lt; 0.001) using Kaplan‒Meier analysis. Continuous RAR had a positive association with all-cause mortality (HR=1.42, 95% CI 1.23-1.65) and cardiovascular mortality (HR=1.31, 95% CI 1.05-1.64), even after accounting for numerous confounding variables. In comparison to the T1 group, individuals with the highest RAR levels displayed a greater risk of all-cause mortality (HR=2.73, 95% CI 1.11-6.74) and cardiovascular mortality (HR=2.59, 95% CI 0.69-9.78). Increased RAR levels were related to higher rates of cardiovascular and all-cause mortality across almost all subgroups. Conclusion: RAR is independently correlated with 28-day all-cause mortality and cardiovascular mortality in AF-affected individuals aged ≥ 80. Keywords: cardiovascular disease; mortality; older; red cell distribution width; atrial fibrillation