cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.10066200
title: Advanced Non-Clear Cell Renal Cell Carcinoma Treatments and Survival: A Real-World Single-Centre Experience

description: Dataset of the paper "Advanced Non-Clear Cell Renal Cell Carcinoma Treatments and Survival: A Real-World Single-Centre Experience"
DOI: 10.5258/soton/d2845
title: Dataset supporting the publication "Boyle's Law ignores dynamic processes in governing barotrauma in fish"

description: This dataset supports the publication by Kerr, J.R., White, P.R., Leighton, T.G., Silva, L.G.M., and Kemp, P.S. "Boyle's Law ignores dynamic processes in governing barotrauma in fish" in JOURNAL: Scientific Reports . The repository includes the three hydropower and one pumping station pressure profiles used in the study: Boyle's Law ignores dynamic processes in governing barotrauma in fish. The data includes 4 csv files: Cougar Dam Ice Harbour Dam Nam Ngum Dam Pumping station This research was funded by 1) an Institutional Links 2017 grant, ID 332396528, under the Newton-Brazil Fund partnership (British Council) (Brazilian funding: FAPEMIG, project ID: CHE-APQ-04822-17, call: CONFAP-British Council) and 2) the Engineering and Physical Sciences Research Council (Reference: EP/N005961/1) through the IDEAS Factory Sandpits programme.
DOI: 10.6084/m9.figshare.24486460
title: Calorimetric_data_Saureus_Sepidermidis.xlsx

description: We conducted research using a substantial set of bacterial isolates sourced from individuals afflicted with prosthetic joint infections, alongside established laboratory strains. Through detailed analysis of their calorimetric profiles and subsequent deconstruction of curve parameters, we detected six calorimetric parameters for precise intra-species identification, particularly in the case of MRSA. Additionally, we observed significant distinctions in the thermograms of ATCC laboratory strains when juxtaposed with the model thermograms generated from our comprehensive set of clinical isolates.
DOI: 10.6084/m9.figshare.24486460.v1
title: Calorimetric_data_Saureus_Sepidermidis.xlsx

description: We conducted research using a substantial set of bacterial isolates sourced from individuals afflicted with prosthetic joint infections, alongside established laboratory strains. Through detailed analysis of their calorimetric profiles and subsequent deconstruction of curve parameters, we detected six calorimetric parameters for precise intra-species identification, particularly in the case of MRSA. Additionally, we observed significant distinctions in the thermograms of ATCC laboratory strains when juxtaposed with the model thermograms generated from our comprehensive set of clinical isolates.
DOI: 10.5281/zenodo.10066295
title: Public transport occupancy capture

description: This repository contains a capture of the occupancy of a campus bus at ESPOL, in Ecuador.
The entry and exit events are recorded in the `measurements` array, `counts` with an `id` of 8 are entry events,
and `counts` with an `id` of 9 are exit events.
The timestamps are incorrect, as the sensor used was not connected to the internet. However, the relative time between events is correct.
The experiment was carried out on July 19, 2023 and lasted 1 hour.
DOI: 10.5281/zenodo.10066294
title: Public transport occupancy capture

description: This repository contains a capture of the occupancy of a campus bus at ESPOL, in Ecuador.
The entry and exit events are recorded in the `measurements` array, `counts` with an `id` of 8 are entry events,
and `counts` with an `id` of 9 are exit events.
The timestamps are incorrect, as the sensor used was not connected to the internet. However, the relative time between events is correct.
The experiment was carried out on July 19, 2023 and lasted 1 hour.
DOI: 10.34740/kaggle/dsv/6863507
title: Global Genomic Neurofibromatosis Neoplasia
DOI: 10.6084/m9.figshare.24482053
title: mRNA sequencing of C4-2 with ACSS2 overexpression

description: mRNA sequecing of C4-2 cell lines, which is a typical HSPC cell line.Group A-wild type; Group B-shACSS2; Group C-ACSS2OE.
DOI: 10.6084/m9.figshare.24482053.v1
title: mRNA sequencing of C4-2 with ACSS2 overexpression

description: mRNA sequecing of C4-2 cell lines, which is a typical HSPC cell line.Group A-wild type; Group B-shACSS2; Group C-ACSS2OE.
DOI: 10.6084/m9.figshare.24486601
title: RefSeq_Gorilla_modified_THRA2.gtf

description: This dataset was used to quantify expression levels of THRA isoform 1 and THRA isoform 2. Given that THRA2 had not been deposited yet, we edited the UCSC Kamilah gorilla genome GGO, version 6 to include THRA2.To localize the genomic coordinates of <i>THRA </i>exon 10 in the gorilla genome, we manually BLAST-aligned the human <i>THRA </i>exon 10 sequence to the gorilla genome (chr5:41,857,943-41,858,305 (-)). Next, we created a custom reference genome by adding an entry for <i>THRA2 </i>(transcript chr5:41,857,944-41,888,473 (-); exons 1 to 9 same as <i>THRA1 </i>entry, exon 10 chr5:41,857,944-41,858,305 (-); 3’UTR chr5:41,857,457-41,857,944 (-); stop codon chr5:41,857,941-41,857,943 (-)).Please refer to linked publication for more details
DOI: 10.6084/m9.figshare.24486601.v2
title: RefSeq_Gorilla_modified_THRA2.gtf

description: This dataset was used to quantify expression levels of THRA isoform 1 and THRA isoform 2. Given that THRA2 had not been deposited yet, we edited the UCSC Kamilah gorilla genome GGO, version 6 to include THRA2.To localize the genomic coordinates of <i>THRA </i>exon 10 in the gorilla genome, we manually BLAST-aligned the human <i>THRA </i>exon 10 sequence to the gorilla genome (chr5:41,857,943-41,858,305 (-)). Next, we created a custom reference genome by adding an entry for <i>THRA2 </i>(transcript chr5:41,857,944-41,888,473 (-); exons 1 to 9 same as <i>THRA1 </i>entry, exon 10 chr5:41,857,944-41,858,305 (-); 3’UTR chr5:41,857,457-41,857,944 (-); stop codon chr5:41,857,941-41,857,943 (-)).Please refer to linked publication for more details
DOI: 10.6084/m9.figshare.24486601.v1
title: RefSeq_Gorilla_modified_THRA2

description: This dataset was used to quantify expression levels of THRA isoform 1 and THRA isoform 2. Given that THRA2 had not been deposited yet, we edited the UCSC Kamilah gorilla genome GGO, version 6 to include THRA2.To localize the genomic coordinates of <i>THRA </i>exon 10 in the gorilla genome, we manually BLAST-aligned the human <i>THRA </i>exon 10 sequence to the gorilla genome (chr5:41,857,943-41,858,305 (-)). Next, we created a custom reference genome by adding an entry for <i>THRA2 </i>(transcript chr5:41,857,944-41,888,473 (-); exons 1 to 9 same as <i>THRA1 </i>entry, exon 10 chr5:41,857,944-41,858,305 (-); 3’UTR chr5:41,857,457-41,857,944 (-); stop codon chr5:41,857,941-41,857,943 (-)).Please refer to linked publication for more details
DOI: 10.34740/kaggle/dsv/6863569
title: 📒Meta Kaggle ported to Parquet Format
DOI: 10.5517/ccdc.csd.cc226hkc
title: CCDC 1912872: Experimental Crystal Structure Determination

description: Related Article: Benita Barton, Mino R. Caira, Muhammad-Ameen Adam, Eric C. Hosten|2023|Cryst.Growth Des.|23|7912|doi:10.1021/acs.cgd.3c00700
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.cc226hmf
title: CCDC 1912874: Experimental Crystal Structure Determination

description: Related Article: Benita Barton, Mino R. Caira, Muhammad-Ameen Adam, Eric C. Hosten|2023|Cryst.Growth Des.|23|7912|doi:10.1021/acs.cgd.3c00700
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.cc226hld
title: CCDC 1912873: Experimental Crystal Structure Determination

description: Related Article: Benita Barton, Mino R. Caira, Muhammad-Ameen Adam, Eric C. Hosten|2023|Cryst.Growth Des.|23|7912|doi:10.1021/acs.cgd.3c00700
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.24466522
title: Genomic variation in 156 quinoa accessions

description: Genomic variation in 156 quinoa accessions inferred from mapping Illumina re-sequencing data against the genome assembly of the Bolivian reference genotype CHEN125.
DOI: 10.5281/zenodo.10066347
title: XYZ coordinates of PtPd structures

description: XYZ coordinates for PtPd structures with N=59,100 and 180 atoms, both for decahedral tetrahedral and fcc shapes, at different compositions.
DOI: 10.5281/zenodo.10066346
title: XYZ coordinates of PtPd structures

description: XYZ coordinates for PtPd structures with N=59,100 and 180 atoms, both for decahedral tetrahedral and fcc shapes, at different compositions.
DOI: 10.5281/zenodo.10066238
title: Hydrogen Transport Between Layers of Transition Metal-Dichalcogenides

description: Abstract
Hydrogen is a crucial source of green energy and has been extensively studied for its potential usage in fuel cells. The advent of two-dimensional crystals (2DCs) has taken hydrogen research to new heights, enabling it to tunnel through layers of 2DCs or be transported within voids between the layers, as demonstrated in recent experiments by Geim's group. In this study, we investigate how the composition and stacking of transition-metal dichalcogenide (TMDC) layers influence the transport and self-diffusion coefficients (D) of hydrogen atoms using well-tempered metadynamics simulations. Our findings show that modifying either the transition metal or the chalcogen atoms significantly affects the free energy barriers (∆F) and, consequently, the self-diffusion of hydrogen atoms between the 2DC layers. In the H^h_h polytype (2H stacking), MoSe2 exhibits the lowest ∆F, while WS2 has the highest, resulting in the largest D for the former system. Additionally, hydrogen atoms inside the R^M_h (or 3R) polytype encounter more than twice lower energy barriers and, thus, much higher diffusivity compared to those within the most stable H^h_h stacking. These findings are particularly significant when investigating twisted layers or homo- or heterostructures, as different stacking areas may dominate over others, potentially leading to directional transport and interesting materials for ion or atom sieving.
https://doi.org/10.48550/arXiv.2308.03418
 
Overview
This repository contains calculation files, optimized structures, plots, and Excel files for studies of H diffusion within vdW crystals. A general guide is written here and also in the README.txt file. The repository classifies based on material type and each material has a specific README.txt file that contains more detailed information. Calculation towards self-diffusion coefficients for each step of each material follows: 

Cell optimization of the pristine material: To optimize lattice constants and structural parameters.
Single H atom site tests. To find a favorable H location within vdW crystals to initialize dynamic calculations.
Molecular dynamics. Pre-optimization of thermal equilibrium before performing metadynamics calculations.
Well-tempered Metadynamics simulations: to get a free-energy surface and ultimately; to get a ∆F to calculate D.
The final FES is plotted, and the calculation of the self-diffusion coefficients is noted down in the Excel file.
 
Acknowledgment
This research was supported by the Deutsche Forschungsgemeinschaft (projects GRK 2721/1 and SFB 1415). The authors acknowledge the high-performance computing center of ZIH Dresden, the Leipzig University Computing Centre, and the Paderborn Center for Parallel Computing (PC2 ) for computational resources. The authors thank  Prof. Thomas Heine for fruitful discussions.
DOI: 10.5281/zenodo.10066237
title: Hydrogen Transport Between Layers of Transition Metal-Dichalcogenides

description: Abstract
Hydrogen is a crucial source of green energy and has been extensively studied for its potential usage in fuel cells. The advent of two-dimensional crystals (2DCs) has taken hydrogen research to new heights, enabling it to tunnel through layers of 2DCs or be transported within voids between the layers, as demonstrated in recent experiments by Geim's group. In this study, we investigate how the composition and stacking of transition-metal dichalcogenide (TMDC) layers influence the transport and self-diffusion coefficients (D) of hydrogen atoms using well-tempered metadynamics simulations. Our findings show that modifying either the transition metal or the chalcogen atoms significantly affects the free energy barriers (∆F) and, consequently, the self-diffusion of hydrogen atoms between the 2DC layers. In the H^h_h polytype (2H stacking), MoSe2 exhibits the lowest ∆F, while WS2 has the highest, resulting in the largest D for the former system. Additionally, hydrogen atoms inside the R^M_h (or 3R) polytype encounter more than twice lower energy barriers and, thus, much higher diffusivity compared to those within the most stable H^h_h stacking. These findings are particularly significant when investigating twisted layers or homo- or heterostructures, as different stacking areas may dominate over others, potentially leading to directional transport and interesting materials for ion or atom sieving.
https://doi.org/10.48550/arXiv.2308.03418
 
Overview
This repository contains calculation files, optimized structures, plots, and Excel files for studies of H diffusion within vdW crystals. A general guide is written here and also in the README.txt file. The repository classifies based on material type and each material has a specific README.txt file that contains more detailed information. Calculation towards self-diffusion coefficients for each step of each material follows: 

Cell optimization of the pristine material: To optimize lattice constants and structural parameters.
Single H atom site tests. To find a favorable H location within vdW crystals to initialize dynamic calculations.
Molecular dynamics. Pre-optimization of thermal equilibrium before performing metadynamics calculations.
Well-tempered Metadynamics simulations: to get a free-energy surface and ultimately; to get a ∆F to calculate D.
The final FES is plotted, and the calculation of the self-diffusion coefficients is noted down in the Excel file.
 
Acknowledgment
This research was supported by the Deutsche Forschungsgemeinschaft (projects GRK 2721/1 and SFB 1415). The authors acknowledge the high-performance computing center of ZIH Dresden, the Leipzig University Computing Centre, and the Paderborn Center for Parallel Computing (PC2 ) for computational resources. The authors thank  Prof. Thomas Heine for fruitful discussions.
DOI: 10.5281/zenodo.10066436
title: Log Density / Location Model

description: Run: python3 Final_Pipeline.py "[cassandra, elasticsearch, flink, hbase, kafka, wicket, zookeeper]" "comb"
The data needs to be in the same folder as the script.
DOI: 10.5281/zenodo.10066435
title: Log Density / Location Model

description: Run: python3 Final_Pipeline.py "[cassandra, elasticsearch, flink, hbase, kafka, wicket, zookeeper]" "comb"
The data needs to be in the same folder as the script.
DOI: 10.5281/zenodo.10065736
title: Activated Carbon Cloth Electrodes for Capacitive Deionization: A Neutron Imaging Study

description: Neutron images of capacitive deionization by activated carbon cloths.
Corresponding readouts from potentiostat.
Nitrogen gas adsorption data of the activated carbon cloths.
DOI: 10.5281/zenodo.10065735
title: Activated Carbon Cloth Electrodes for Capacitive Deionization: A Neutron Imaging Study

description: Neutron images of capacitive deionization by activated carbon cloths.
Corresponding readouts from potentiostat.
Nitrogen gas adsorption data of the activated carbon cloths.
DOI: 10.6084/m9.figshare.24481501
title: Gut Microbial Gene Catalog and MAGs of Pigs

description: The pig gut microbial gene catalog and MAGs are constructed by metagenomic analysis of 112 fecal samples from seven pig breeds.
DOI: 10.6084/m9.figshare.24481501.v2
title: Gut Microbial Gene Catalog and MAGs of Pigs

description: The pig gut microbial gene catalog and MAGs are constructed by metagenomic analysis of 112 fecal samples from seven pig breeds.
DOI: 10.5281/zenodo.10059132
title: PRISMA-P (Preferred Reporting Items for Systematic Review and Meta-Analysis Protocols) of the research entitled "Development of Competences for the Fashion Designer: a Scope Review

description: PRISMA-P (Preferred Reporting Items for Systematic review and Meta-Analysis Protocols) 2015 checklist: recommended items to address in a systematic review protocol and Check list CAPSI - Critical analysis of the articles related to the specific objective: map the current themes that permeate the competencies of fashion design professionals through a scoping review.
DOI: 10.5281/zenodo.10059131
title: PRISMA-P (Preferred Reporting Items for Systematic Review and Meta-Analysis Protocols) of the research entitled "Development of Competences for the Fashion Designer: a Scope Review

description: PRISMA-P (Preferred Reporting Items for Systematic review and Meta-Analysis Protocols) 2015 checklist: recommended items to address in a systematic review protocol and Check list CAPSI - Critical analysis of the articles related to the specific objective: map the current themes that permeate the competencies of fashion design professionals through a scoping review.
DOI: 10.6084/m9.figshare.24486730
title: <b>Data for </b><b>comparison of bacteria isolated from periodontal pockets of participants with or without diabetes mellitus in Uganda: A Case control study.</b>

description: This was data from a case control study to compare bacteria isolated from periodontal pockets of patients with and without diabetes mellitus. A total of 45 samples of gingival crevicular fluid were collected, DNA extracted, and sequencing carried out to determine the alpha and beta diversity. The PDF file is the Output, the rest of the files are R command files and related data to reproduce the output of the PDF file.
DOI: 10.6084/m9.figshare.24486730.v1
title: <b>Data for </b><b>comparison of bacteria isolated from periodontal pockets of participants with or without diabetes mellitus in Uganda: A Case control study.</b>

description: This was data from a case control study to compare bacteria isolated from periodontal pockets of patients with and without diabetes mellitus. A total of 45 samples of gingival crevicular fluid were collected, DNA extracted, and sequencing carried out to determine the alpha and beta diversity. The PDF file is the Output, the rest of the files are R command files and related data to reproduce the output of the PDF file.
DOI: 10.5063/f1vd6wxg
title: The effects of varying temperature on the germination of California natives and invasive plant species

description: 4 different annual plant species found within the California desert were germinated at varying temperatures to determine the overall effect on both successful germination and overall plant mass. 3 species of native plants including Salvia columbarie, Layia platyglossa, and Phacelia tanacetifolia were grown and 1 exotic plant species Bromus rubens. 3 Varying temperature intensities were used including low, medium, and high temperatures. Each species was grown for a total of 6 weeks independently under each treatment. Once the germination trials were completed, individuals were removed from their pots and weighed to determine the overall dry mass.
DOI: 10.6084/m9.figshare.24486847
title: <b>Giant anteaters as bad omens: Determinants and implications of wildlife superstitions</b>

description: 1. Superstitious beliefs threaten wildlife species, yet they have received limited attention in the scientific literature.2. Through a mixed-method approach, including 259 face-to-face interviews, we explored the factors influencing superstitions about giant anteaters in the Brazilian Pantanal and their implications for both people and the species.3. Our results indicated that bad omen superstitions about giant anteaters could be explained by the psychological discomfort felt from the species’ peculiarities, social influence, misconceptions about their biology and behaviour, and the frequency of the species' sightings. Age, gender, and schooling did not influence superstitious adherence.4. Interviewees holding superstitious beliefs of bad luck reported worry, distress, and anxiety in trigger situations. Most engage in superstitious behaviors to ward off bad luck. While some acts were harmless, others threatened people and giant anteaters.5. By explaining misconceptions and demystifying unique species characteristics that evoke psychological discomfort, conservationists might foster better coexistence between people and species historically associated with misfortune. <br>
DOI: 10.6084/m9.figshare.24486847.v1
title: <b>Giant anteaters as bad omens: Determinants and implications of wildlife superstitions</b>

description: 1. Superstitious beliefs threaten wildlife species, yet they have received limited attention in the scientific literature.2. Through a mixed-method approach, including 259 face-to-face interviews, we explored the factors influencing superstitions about giant anteaters in the Brazilian Pantanal and their implications for both people and the species.3. Our results indicated that bad omen superstitions about giant anteaters could be explained by the psychological discomfort felt from the species’ peculiarities, social influence, misconceptions about their biology and behaviour, and the frequency of the species' sightings. Age, gender, and schooling did not influence superstitious adherence.4. Interviewees holding superstitious beliefs of bad luck reported worry, distress, and anxiety in trigger situations. Most engage in superstitious behaviors to ward off bad luck. While some acts were harmless, others threatened people and giant anteaters.5. By explaining misconceptions and demystifying unique species characteristics that evoke psychological discomfort, conservationists might foster better coexistence between people and species historically associated with misfortune. <br>
DOI: 10.5281/zenodo.10066477
title: Hospital Anxiety and Depression Scale (HADS)

description: Data set
DOI: 10.5281/zenodo.10066476
title: Hospital Anxiety and Depression Scale (HADS)

description: Data set