cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5517/ccdc.csd.cc2bdk6j
title: CCDC 2157017: Experimental Crystal Structure Determination

description: Related Article: Daniel Čavlović, Daniel Häussinger, Olivier Blacque, Prince Ravat, Michal Juríček|2022|JACS Au|2|1616|doi:10.1021/jacsau.2c00190
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.20371830
title: S_tragus_fastQ58

description: fastQ files for individuals at site 58, 3 fastQ per individual. Larger two are the paired end reads and the smaller one is reads that could not be assigned to an end.
DOI: 10.6084/m9.figshare.20371830.v1
title: S_tragus_fastQ58

description: fastQ files for individuals at site 58, 3 fastQ per individual. Larger two are the paired end reads and the smaller one is reads that could not be assigned to an end.
DOI: 10.5066/p9bucrf7
title: Database of horizontal component Fourier amplitude spectra of acceleration ground motions from Pacific Northwest earthquakes

description: This dataset includes quadratic mean Fourier amplitude spectra (FAS) of acceleration ground motions from crustal and intraslab earthquakes in the US Pacific Northwest with magnitudes 3.5-6.8 and hypocentral depths 0-62 km. The dataset consists of 8,028 records from 96 different earthquakes between 1999 and 2020. These data were used to study site response and basin amplification in the Pacific Northwest, as well as understand the different ground motions produced by shallow and deep earthquakes.
DOI: 10.5281/zenodo.6903469
title: Myomyrus pharao decontaminated gx

description: .
DOI: 10.5281/zenodo.6903468
title: Myomyrus pharao decontaminated gx

description: .
DOI: 10.6084/m9.figshare.19221678.v6
title: Discrete emotions for Croatian: CROWD-5e dataset.xlsx

description: Normative database for 3,022 Croatian words rated on five discrete emotions: happiness, fear, anger, sadness & disgust. <br>Manuscript: CROWD-5e: A 3,022 Croatian words psycholinguistic database covering affective norms for five discrete emotions<br>
DOI: 10.5281/zenodo.6903483
title: SELF LBNP raw data and analysis

description: Raw data, averaged data, and data analysis code.
DOI: 10.5281/zenodo.6903482
title: SELF LBNP raw data and analysis

description: Raw data, averaged data, and data analysis code.
DOI: 10.5281/zenodo.6903494
title: Parazoanthus atlanticus decontaminated gx

description: .
DOI: 10.5281/zenodo.6903493
title: Parazoanthus atlanticus decontaminated gx

description: .
DOI: 10.5281/zenodo.6903504
title: Plagiodera versicolora decontaminated gx

description: .
DOI: 10.5281/zenodo.6903503
title: Plagiodera versicolora decontaminated gx

description: .
DOI: 10.5281/zenodo.6903489
title: Global offshore wind turbine analysis with Sentinel-1 - supplementary data

description: Gloabl offshore wind turbine analysis with Sentinel-1 - supplementary data The files are supplementary data of the publication: Global dynamics of the offshore wind energy sector monitored with Sentinel-1: Turbine count, installed capacity and site specifications which is currently under review in the International Journal of Applied Earth Observation and Geoinformation supplementary_data_B_OWT_height_capacity.csv holds 50 pairs of offshore wind turbine hub heights and the corresponding installed capacities along with the offshore wind farm project name, the number of turbines of this wind farm, and the source the information originates from. supplementary_data_B_DeepOWT_1_21_2_plus.geojson is the extended version of the DeepOWT data set (https://zenodo.org/record/5933967) with all of the derived attributes in the respective publication e.g. OWT hub height and installed capacity.
DOI: 10.5281/zenodo.6794086
title: Global offshore wind turbine analysis with Sentinel-1 - supplementary data

description: Gloabl offshore wind turbine analysis with Sentinel-1 - supplementary data The files are supplementary data of the publication: Global dynamics of the offshore wind energy sector monitored with Sentinel-1: Turbine count, installed capacity and site specifications which is currently under review in the International Journal of Applied Earth Observation and Geoinformation supplementary_data_B_OWT_height_capacity.csv holds 50 pairs of offshore wind turbine hub heights and the corresponding installed capacities along with the offshore wind farm project name, the number of turbines of this wind farm, and the source the information originates from. supplementary_data_B_DeepOWT_1_21_2_plus.geojson is the extended version of the DeepOWT data set (https://zenodo.org/record/5933967) with all of the derived attributes in the respective publication e.g. OWT hub height and installed capacity.
DOI: 10.6092/unibo/amsacta/6977
title: Raw data – Pipeline Validation of finite element model of a human spine segment

description: The file dataset contains the data used for the validation study on subject-specific finite element model (FEM) of a metastatic spine segment. The model was developed starting from quantitative computed tomography images of a cadaveric lumbar spine segment (L1-L4) obtained by an ethically-approved donation program. Numerical simulations were performed in Ansys Mechanical APDL to simulate the experimental test where the cadaveric specimen was loaded in compression-bending using a uniaxial testing machine. Model predictions in terms of surface displacements on L2 and L3 vertebral bodies were compared to the experimental displacements measured with Digital Image Correlation (DIC). Results obtained from the local comparison between experimental data and simulation results showed good prediction accuracy (R2 &gt; 0.9 and RMSE% &lt; 8%). Specifically, the dataset contains experimental data obtained using the Digital Image Correlation technique and the results of the simulations in term of coordinates and displacement vectors. Two regions of interest (RoIs) were identified in the antero-lateral surfaces of the vertebral bodies: RoI #1 corresponds to the surface of the metastatic vertebra (L2), while RoI #2 is related to the surface of the control vertebra (L3).
DOI: 10.5281/zenodo.6903366
title: Overexpression of VEGF in dermal fibroblast cells accelerates the angiogenesis and wound healing function: in vitro and in vivo studies

description: Human dermal fibroblasts (Hu02) were transfected by pcDNA3.1(-)-VEGF vector. Following selecting fibroblast cells with hygromycin, recombinant cells were investigated in terms of VEGF expression by quantifying method. We used Real-Time PCR assay to quantitate gene expression of vascular endothelial growth factor from manipulated cells and represented VEGF overexpression. Reverse transcription was performed from 1 μg of total RNA transcribed to complementary DNA (cDNA) through 1 μL of random hexamer primer. The reactions were incubated at 70°C for 5 minutes. After that, 5X RT-buffer, dNTP, and RT-enzyme were added, and the mixtures were incubated at 42°C for 60 minutes and 70°C for 10 minutes. Reverse transcription was performed from 500 ng total RNA using the RT2 First Strand Kit (SA Biosciences). Quantitative real-time PCR was performed (Ampliqon, Denmark) with 40 cycles at 95 oC for 15 seconds and 60 oC for 60 seconds. The normalization and all the data analysis were performed according to RESR and Graph pad-Prism 8 software.<br> For the normalization, it uses the housekeeping gene: β-Actin.<br> Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)].<br>
DOI: 10.5281/zenodo.6903365
title: Overexpression of VEGF in dermal fibroblast cells accelerates the angiogenesis and wound healing function: in vitro and in vivo studies

description: Human dermal fibroblasts (Hu02) were transfected by pcDNA3.1(-)-VEGF vector. Following selecting fibroblast cells with hygromycin, recombinant cells were investigated in terms of VEGF expression by quantifying method. We used Real-Time PCR assay to quantitate gene expression of vascular endothelial growth factor from manipulated cells and represented VEGF overexpression. Reverse transcription was performed from 1 μg of total RNA transcribed to complementary DNA (cDNA) through 1 μL of random hexamer primer. The reactions were incubated at 70°C for 5 minutes. After that, 5X RT-buffer, dNTP, and RT-enzyme were added, and the mixtures were incubated at 42°C for 60 minutes and 70°C for 10 minutes. Reverse transcription was performed from 500 ng total RNA using the RT2 First Strand Kit (SA Biosciences). Quantitative real-time PCR was performed (Ampliqon, Denmark) with 40 cycles at 95 oC for 15 seconds and 60 oC for 60 seconds. The normalization and all the data analysis were performed according to RESR and Graph pad-Prism 8 software.<br> For the normalization, it uses the housekeeping gene: β-Actin.<br> Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)].<br>
DOI: 10.6084/m9.figshare.20371854.v1
title: S_tragus_fastQ118

description: fastQ files for individuals at site 118, 3 fastQ per individual. Larger two are the paired end reads and the smaller one is reads that could not be assigned to an end.
DOI: 10.6084/m9.figshare.20371854
title: S_tragus_fastQ118

description: fastQ files for individuals at site 118, 3 fastQ per individual. Larger two are the paired end reads and the smaller one is reads that could not be assigned to an end.
DOI: 10.5281/zenodo.6903545
title: Sintering of alumina nanoparticles: comparison of interatomic potentials, molecular dynamics simulations, and data analysis

description: This is the dataset for the publication in MSMSE 2022 containing all plot scripts and data for reproducing all figures. The dataset is a snapshot of the repository https://gitlab.com/computational-materials-science/public/publication-data-and-code/2022_MSMSE_Roy_et_al_MD-sintering that might contain additional data.
DOI: 10.5281/zenodo.6903575
title: Pollimyrus plagiostoma decontamination gx

description: .
DOI: 10.5281/zenodo.6903574
title: Pollimyrus plagiostoma decontamination gx

description: .
DOI: 10.5281/zenodo.6903597
title: Scorpiodoras heckelii decontaminated gx

description: .
DOI: 10.5281/zenodo.6903596
title: Scorpiodoras heckelii decontaminated gx

description: .
DOI: 10.6084/m9.figshare.20154740
title: Supplementary material

description: This repository contains supplementary data of the manuscript "<em>Acanthamoeba polyphaga</em> <em>de novo</em> transcriptome and its dynamics during Mimivirus infection"
DOI: 10.6084/m9.figshare.20154740.v1
title: Supplementary material

description: This repository contains supplementary data of the manuscript "<em>Acanthamoeba polyphaga</em> <em>de novo</em> transcriptome and its dynamics during Mimivirus infection"
DOI: 10.15139/s3/acil3g
title: Data for Prenatal exposure to metal mixtures and newborn neurobehavior in the Rhode Island Child Health Study (RICHS

description: Background: Prenatal exposure to metals can affect the developing fetus and negatively impact neurobehavior. The associations between individual metals and neurodevelopment have been examined, but little work has explored the potentially detrimental neurodevelopmental outcomes associated with the combined impact of coexisting metals. The objective of this study is to evaluate prenatal metal exposure mixtures in the placenta to elucidate the link between their combined effects on newborn neurobehavior. Method: This study included 192 infants with available placental metal and NICU Network Neurobehavioral Scale data at 24 hours-72 hours age. Eight essential and nonessential metals (cadmium, cobalt, copper, iron, manganese, molybdenum, selenium, zinc) detected in more than 80% of samples were tested for associations with atypical neurobehavior indicated by NICU Network Neurobehavioral Scale using logistic regression and in a quantile g-computation analysis to evaluate the joint association between placental metal mixture and neurobehavioral profiles. Results: Individually, a doubling of placental cadmium concentrations was associated with an increased likelihood of being in the atypical neurobehavioral profile (OR = 2.39; 95% CI = 1.05 to 5.71). In the mixture analysis, joint effects of a quartile increase in exposure to all metals was associated with 3-fold increased odds of newborns being assigned to the atypical profile (OR = 3.23; 95% CI = 0.92 to 11.36), with cadmium having the largest weight in the mixture effect. Conclusions: Prenatal exposure to relatively low levels of a mixture of placental metals was associated with adverse newborn neurobehavior. Examining prenatal metal exposures as a mixture is important for understanding the harmful effects of concomitant exposures in the vulnerable populations.
DOI: 10.5281/zenodo.6903637
title: pLV[Exp]-U6&gt;KAT8_P1_Seq1-hPGK&gt;mApple

description: Plasmid vector encoding a sgRNA sequence which targets the human KAT8 promoter for CRISPRi, under a U6 promoter and a mApple fluorescent reporter. Generated by Vectorbuilder in the pLV[Exp] backbone.
DOI: 10.5281/zenodo.6903636
title: pLV[Exp]-U6&gt;KAT8_P1_Seq1-hPGK&gt;mApple

description: Plasmid vector encoding a sgRNA sequence which targets the human KAT8 promoter for CRISPRi, under a U6 promoter and a mApple fluorescent reporter. Generated by Vectorbuilder in the pLV[Exp] backbone.
DOI: 10.5281/zenodo.6903651
title: pLV[Exp]-U6&gt;PINK1_P1_Seq3-hPGK&gt;mApple

description: Plasmid vector encoding a sgRNA sequence which targets the human PINK1 promoter for CRISPRi, under a U6 promoter and a mApple fluorescent reporter. Generated by Vectorbuilder in the pLV[Exp] backbone.
DOI: 10.5281/zenodo.6903650
title: pLV[Exp]-U6&gt;PINK1_P1_Seq3-hPGK&gt;mApple

description: Plasmid vector encoding a sgRNA sequence which targets the human PINK1 promoter for CRISPRi, under a U6 promoter and a mApple fluorescent reporter. Generated by Vectorbuilder in the pLV[Exp] backbone.
DOI: 10.5281/zenodo.6901866
title: Dataset for an analysis of selected studies on software development and reuse in the field of software documentation

description: The data record contains bibliographical metadata from 2012 to 2023, which have been extracted from the databases ScienceDirect, SpringerLink and IEEE Xplore. It was created in the context of a master thesis which will be published later. The aim was to make a selection of studies on software documentation from the perspective of software development based on the master thesis.
DOI: 10.5281/zenodo.6901865
title: Dataset for an analysis of selected studies on software development and reuse in the field of software documentation

description: The data record contains bibliographical metadata from 2012 to 2023, which have been extracted from the databases ScienceDirect, SpringerLink and IEEE Xplore. It was created in the context of a master thesis which will be published later. The aim was to make a selection of studies on software documentation from the perspective of software development based on the master thesis.
DOI: 10.5281/zenodo.6903659
title: pLV[Exp]-EF1A&gt;V5/hKAT8[NM_032188.3]:IRES:Puro

description: Human KAT8 gene with N-terminal V5 tag cloned into the pLV[Exp] plasmid backbone under a EF1a promoter and including IRES puromycin selection cassette by Vectorbuilder.
DOI: 10.5281/zenodo.6903658
title: pLV[Exp]-EF1A&gt;V5/hKAT8[NM_032188.3]:IRES:Puro

description: Human KAT8 gene with N-terminal V5 tag cloned into the pLV[Exp] plasmid backbone under a EF1a promoter and including IRES puromycin selection cassette by Vectorbuilder.
DOI: 10.5281/zenodo.6903665
title: Sintering of alumina nanoparticles: comparison of interatomic potentials, molecular dynamics simulations, and data analysis

description: This is the dataset for the publication in MSMSE 2022 containing all plot scripts and data for reproducing all figures. The dataset is a snapshot of the repository https://gitlab.com/computational-materials-science/public/publication-data-and-code/2022_MSMSE_Roy_et_al_MD-sintering (SHA 7ad2f421deb055f3384c00ba29f2fb1acd0e78ea) that might contain additional/newer data and scripts.
DOI: 10.5281/zenodo.6903544
title: Sintering of alumina nanoparticles: comparison of interatomic potentials, molecular dynamics simulations, and data analysis

description: This is the dataset for the publication in MSMSE 2022 containing all plot scripts and data for reproducing all figures. The dataset is a snapshot of the repository https://gitlab.com/computational-materials-science/public/publication-data-and-code/2022_MSMSE_Roy_et_al_MD-sintering (SHA 7ad2f421deb055f3384c00ba29f2fb1acd0e78ea) that might contain additional/newer data and scripts.
DOI: 10.5281/zenodo.6903645
title: Raw data for "Interplay of Kinetic and Thermodynamic Reaction Control Explains Incorporation of Dimethylammonium Iodide into CsPbI3"

description: Raw solid-state NMR and XRD data, and input files for DFT and MD calculations shown in https://doi.org/10.1021/acsenergylett.2c00877
DOI: 10.5281/zenodo.6903644
title: Raw data for "Interplay of Kinetic and Thermodynamic Reaction Control Explains Incorporation of Dimethylammonium Iodide into CsPbI3"

description: Raw solid-state NMR and XRD data, and input files for DFT and MD calculations shown in https://doi.org/10.1021/acsenergylett.2c00877
DOI: 10.34992/4xak-8r05
title: AIDJEX STD data
DOI: 10.5281/zenodo.6903671
title: Erythroxylum ulei zanfona 1

description: .
DOI: 10.5281/zenodo.6903670
title: Erythroxylum ulei zanfona 1

description: .
DOI: 10.6084/m9.figshare.20371971.v1
title: S_tragus_fastQ126

description: fastQ files for individuals at site 126, 3 fastQ per individual. Larger two are the paired end reads and the smaller one is reads that could not be assigned to an end.
DOI: 10.6084/m9.figshare.20371971
title: S_tragus_fastQ126

description: fastQ files for individuals at site 126, 3 fastQ per individual. Larger two are the paired end reads and the smaller one is reads that could not be assigned to an end.
DOI: 10.5281/zenodo.6873024
title: Prop3D-20

description: Prop3D-20 is a protein structure dataset that combines 3D atomic coordinates with biophysical and evolutionary properties for every atom in every "cleaned" domain structure from &lt;b&gt;20 CATH [1] Homologous Superfamilies.&lt;/b&gt; Domain structures are 'cleaned' by adding missing residues with MODELLER [2], missing atoms with SCWRL4 [3], and protonating and energy minimizing (simple de-bump) with PDB2PQR [4]. We follow the CATH hierarchy in a hierarchical data format (HDF) file and include atomic level features, residue level features, residue-residue contact, and pre-calculated train (~80%) / test (~10%) / validation (~10%) splits for each superfamily derived from CATH's sequence identity clusters (e.g. S35 for 35% seq ID). This dataset was originally stored in the Highly Scalable Data Service ([HSDS](http://www.github.com/HDFGroup/hsds)), and was exported into this raw .h5 file as backup. We recommend loading this data into HSDS for use in [h5pyd](http://www.github.com/HDFGroup/h5pyd), but the .h5 file can opened using [h5py](http://www.github.com/h5py/h5py) as well. Please see the REAME attached to this dataset to learn how to use this dataset and how it organized. For more information on setting up HSDS and/or recreate this dataset, please see [http://www.github.com/bouralab/Prop3D/README.md](http://www.github.com/bouralab/Prop3D/README.md) References 1. Sillitoe I, Bordin N, Dawson N, Waman VP, Ashford P, Scholes HM, Pang CSM, Woodridge L, Rauer C, Sen N, Abbasian M, Le Cornu S, Lam SD, Berka K, Varekova IH, Svobodova R, Lees J, Orengo CA. CATH: increased structural coverage of functional space. Nucleic Acids Res. 2021 Jan 8;49(D1):D266-D273. doi: 10.1093/nar/gkaa1079. PMID: 33237325; PMCID: PMC7778904. 2. Webb B, Sali A. Comparative Protein Structure Modeling Using MODELLER. Curr Protoc Bioinformatics. 2016 Jun 20;54:5.6.1-5.6.37. doi: 10.1002/cpbi.3. PMID: 27322406; PMCID: PMC5031415. 3. Krivov GG, Shapovalov MV, Dunbrack RL Jr. Improved prediction of protein side-chain conformations with SCWRL4. Proteins. 2009 Dec;77(4):778-95. doi: 10.1002/prot.22488. PMID: 19603484; PMCID: PMC2885146. 4. Jurrus E, Engel D, Star K, Monson K, Brandi J, Felberg LE, Brookes DH, Wilson L, Chen J, Liles K, Chun M, Li P, Gohara DW, Dolinsky T, Konecny R, Koes DR, Nielsen JE, Head-Gordon T, Geng W, Krasny R, Wei GW, Holst MJ, McCammon JA, Baker NA. Improvements to the APBS biomolecular solvation software suite. Protein Sci. 2018 Jan;27(1):112-128. doi: 10.1002/pro.3280. Epub 2017 Oct 24. PMID: 28836357; PMCID: PMC5734301. <br>
DOI: 10.5281/zenodo.6873023
title: Prop3D-20

description: Prop3D-20 is a protein structure dataset that combines 3D atomic coordinates with biophysical and evolutionary properties for every atom in every "cleaned" domain structure from &lt;b&gt;20 CATH [1] Homologous Superfamilies.&lt;/b&gt; Domain structures are 'cleaned' by adding missing residues with MODELLER [2], missing atoms with SCWRL4 [3], and protonating and energy minimizing (simple de-bump) with PDB2PQR [4]. We follow the CATH hierarchy in a hierarchical data format (HDF) file and include atomic level features, residue level features, residue-residue contact, and pre-calculated train (~80%) / test (~10%) / validation (~10%) splits for each superfamily derived from CATH's sequence identity clusters (e.g. S35 for 35% seq ID). This dataset was originally stored in the Highly Scalable Data Service ([HSDS](http://www.github.com/HDFGroup/hsds)), and was exported into this raw .h5 file as backup. We recommend loading this data into HSDS for use in [h5pyd](http://www.github.com/HDFGroup/h5pyd), but the .h5 file can opened using [h5py](http://www.github.com/h5py/h5py) as well. Please see the REAME attached to this dataset to learn how to use this dataset and how it organized. For more information on setting up HSDS and/or recreate this dataset, please see [http://www.github.com/bouralab/Prop3D/README.md](http://www.github.com/bouralab/Prop3D/README.md) References 1. Sillitoe I, Bordin N, Dawson N, Waman VP, Ashford P, Scholes HM, Pang CSM, Woodridge L, Rauer C, Sen N, Abbasian M, Le Cornu S, Lam SD, Berka K, Varekova IH, Svobodova R, Lees J, Orengo CA. CATH: increased structural coverage of functional space. Nucleic Acids Res. 2021 Jan 8;49(D1):D266-D273. doi: 10.1093/nar/gkaa1079. PMID: 33237325; PMCID: PMC7778904. 2. Webb B, Sali A. Comparative Protein Structure Modeling Using MODELLER. Curr Protoc Bioinformatics. 2016 Jun 20;54:5.6.1-5.6.37. doi: 10.1002/cpbi.3. PMID: 27322406; PMCID: PMC5031415. 3. Krivov GG, Shapovalov MV, Dunbrack RL Jr. Improved prediction of protein side-chain conformations with SCWRL4. Proteins. 2009 Dec;77(4):778-95. doi: 10.1002/prot.22488. PMID: 19603484; PMCID: PMC2885146. 4. Jurrus E, Engel D, Star K, Monson K, Brandi J, Felberg LE, Brookes DH, Wilson L, Chen J, Liles K, Chun M, Li P, Gohara DW, Dolinsky T, Konecny R, Koes DR, Nielsen JE, Head-Gordon T, Geng W, Krasny R, Wei GW, Holst MJ, McCammon JA, Baker NA. Improvements to the APBS biomolecular solvation software suite. Protein Sci. 2018 Jan;27(1):112-128. doi: 10.1002/pro.3280. Epub 2017 Oct 24. PMID: 28836357; PMCID: PMC5734301. <br>
DOI: 10.6084/m9.figshare.3761562.v2290
title: Online Labour Index: Measuring the Online Gig Economy for Policy and Research

description: Data repository for the data underlying the Online Labour Index. See http://ilabour.oii.ox.ac.uk online-labour-index/ for details.
DOI: 10.6084/m9.figshare.20372175
title: Dataset for Experiment 1, Experiment 2, and Combined 1&2

description: Experiment 1 Data: 1.0 All Experiment 2 Data: ED2.0 All - Final Experiment 1&2 Combined: 1.0&2.0 <br> Condition: E - Cartoon lesson N - Original slides lesson
DOI: 10.6084/m9.figshare.20163752
title: Proteins list

description: The list of proteins selected after each analysis/cut-off
DOI: 10.5281/zenodo.6903762
title: Colección de datos

description: Conjunto de datos
DOI: 10.5281/zenodo.6903761
title: Colección de datos

description: Conjunto de datos