cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5517/ccdc.csd.cc2df8ch
title: CCDC 2217286: Experimental Crystal Structure Determination

description: Related Article: Ladislav Lóška, Vojtěch Dočekal, Ivana Císařová, Jan Veselý|2023|Org.Lett.|25|174|doi:10.1021/acs.orglett.2c04021
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: 10.5281/zenodo.7549795
title: Improving spectral library search untargeted metabolomics identification by dynamic tolerance peak matching and false discovery estimation

description: <strong>The unprocessed and processed benchmarking data used in the paper of "Improving spectral library search untargeted metabolomics identification by dynamic tolerance peak matching and false discovery estimation"</strong>
DOI: 10.5281/zenodo.7549794
title: Improving spectral library search untargeted metabolomics identification by dynamic tolerance peak matching and false discovery estimation

description: <strong>The unprocessed and processed benchmarking data used in the paper of "Improving spectral library search untargeted metabolomics identification by dynamic tolerance peak matching and false discovery estimation"</strong>
DOI: 10.5519/qd.zgrak83w
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (45 records)
DOI: 10.6084/m9.figshare.21591003
title: MGA grouping sequences

description: Supporting data for Microbiology paper
DOI: 10.6084/m9.figshare.21591003.v1
title: MGA grouping sequences

description: Supporting data for Microbiology paper
DOI: 10.6084/m9.figshare.21602502.v1
title: README.xlsx

description: Population of Labour Force (Population ages 15-64, total), unemployment, total (% of total labor force) (modelled ILO estimate). International Labour Organization, ILOSTAT database, June 2022. World Development Indicators
DOI: 10.5519/qd.3nabh67z
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (2828 records)
DOI: 10.5281/zenodo.7549648
title: temporary_file2

description: temporary file
DOI: 10.5281/zenodo.7549647
title: temporary_file2

description: temporary file
DOI: 10.6084/m9.figshare.21728018
title: Research Main findings on Criss-Crossing, 2022.docx

description: research findings
DOI: 10.6084/m9.figshare.21728018.v1
title: Research Main findings on Criss-Crossing, 2022.docx

description: research findings
DOI: 10.6084/m9.figshare.20284713.v3
title: Data availability for Mirusviricota and the GOEV database

description: Data availability includes supplemental tables, FASTA files corresponding to the GPEV genomic database, genes, proteins, and phylogenetic trees.
DOI: 10.5281/zenodo.7549828
title: Orthrus Dataset

description: Dataset for Orthrus
DOI: 10.5281/zenodo.7549827
title: Orthrus Dataset

description: Dataset for Orthrus
DOI: 10.6084/m9.figshare.21602502
title: README.xlsx

description: Population of Labour Force (Population ages 15-64, total), unemployment, total (% of total labor force) (modelled ILO estimate). International Labour Organization, ILOSTAT database, June 2022. World Development Indicators
DOI: 10.6084/m9.figshare.21602502.v2
title: README.xlsx

description: Population of Labour Force (Population ages 15-64, total), unemployment, total (% of total labor force) (modelled ILO estimate). International Labour Organization, ILOSTAT database, June 2022. World Development Indicators
DOI: 10.6084/m9.figshare.21583287
title: Supplementary Material for: Effectiveness and Safety of Golimumab in the Treatment of Ulcerative Colitis: 52-week Results from Post-marketing Surveillance in Japan

description: Introduction: Real-world evidence for the effectiveness and safety of golimumab (GLM) in patients with ulcerative colitis (UC) is limited. The aim of this study was to investigate the 52-week effectiveness and safety of GLM treatment for UC. Methods: This prospective, multicentre, post-marketing surveillance study is conducted in 393 patients with UC in Japan (UMIN000027542). Clinical remission (partial Mayo score ≤2), adverse drug reactions (ADRs) and their predictors, and treatment persistence were analysed. Results: The safety analysis sets comprised 391 patients. Patients in clinical remission at baseline were excluded, and 336 were used for effectiveness analysis. Clinical remission was 47.9%, 48.5%, 44.6%, and 39.6% at weeks 6, 22, 36, and 52, respectively, in the intent-to-treat analysis. In biologic-naïve patients, clinical remission was slightly higher than that in biologic-experienced patients. At week 52, patients who concomitantly used corticosteroids at baseline showed numerically lower clinical remission rates than non-users of corticosteroids (34.9% vs 44.5%). Multivariate analysis showed that smoking history (P=0.040, odds ratio [OR]=1.911, 95% confidence interval [CI] 1.030–3.546) was an independent factor associated with clinical remission at week 52. ADRs occurred in 71 patients (18.2%) and included 9 cases of rash. Serious ADRs occurred in 40 patients (10.2%), including 8 cases of UC exacerbation. Additionally, the presence of comorbidities was associated with ADR incidence (P=0.010, OR=2.000, 95% CI 1.183–3.380). Conclusion: The real-world effectiveness of GLM treatment was confirmed in biologic-naïve and -experienced populations. The safety profile of GLM treatment was consistent with previous findings.
DOI: 10.5281/zenodo.7492351
title: Dataset for in silico study of Exotoxin A - Elongation Factor 2 interaction

description: BPMD: Binding Pose Metadynamics simulations of ETA with 3 different ligands (NAD+,bTAD, and ADP-ribose). ETA: 200 ns MD simulation trajectories for ETA with 3 different ligands (NAD+,bTAD, and ADP-ribose) in 3 replicas. ETA_EF2_Complexes: 200 ns MD simulation trajectories exploring the interaction between ETA and EF2 with 3 different ligands (NAD+, bTAD, and ADP-ribose non-bonded) in 3 replicas with DTA715 or HIS715 containing eEF2. ETA_EF2_ADP_ribose-Bonded: 200 ns MD simulation trajectories exploring the interaction between ETA and DTA715-containing eEF2 with ADP-ribose covalently bound to DTA715. 3 replicas.
DOI: 10.5281/zenodo.7003643
title: Dataset for in silico study of Exotoxin A - Elongation Factor 2 interaction

description: BPMD: Binding Pose Metadynamics simulations of ETA with 3 different ligands (NAD+,bTAD, and ADP-ribose). ETA: 200 ns MD simulation trajectories for ETA with 3 different ligands (NAD+,bTAD, and ADP-ribose) in 3 replicas. ETA_EF2_Complexes: 200 ns MD simulation trajectories exploring the interaction between ETA and EF2 with 3 different ligands (NAD+, bTAD, and ADP-ribose non-bonded) in 3 replicas with DTA715 or HIS715 containing eEF2. ETA_EF2_ADP_ribose-Bonded: 200 ns MD simulation trajectories exploring the interaction between ETA and DTA715-containing eEF2 with ADP-ribose covalently bound to DTA715. 3 replicas.
DOI: 10.5281/zenodo.7544324
title: Structure of transmembrane and extracellular part of CD95-L trimer

description: Modeled structures of CD95L trimer bound to POPC membrane. One file with waters present, the second without waters. The model was obtained using YASARA (v.19.9.17) with default settings for homology modeling, using CD95L trimer (PDB: 4MSV) and predicted structure form AlphaFold V2.0 (P482023) as templates. HM was performed in order to resolve non-crystallized parts and to generate complete protein model. Obtained structure was prepared using Protein preparation wizard in Schrödinger (2013-3) and POPC membrane model added between amino acids 81-103 of each CD95L monomer.
DOI: 10.5281/zenodo.7544325
title: Structure of transmembrane and extracellular part of CD95-L trimer

description: Modeled structures of CD95L trimer bound to POPC membrane. One file with waters present, the second without waters. The model was obtained using YASARA (v.19.9.17) with default settings for homology modeling, using CD95L trimer (PDB: 4MSV) and predicted structure form AlphaFold V2.0 (P482023) as templates. HM was performed in order to resolve non-crystallized parts and to generate complete protein model. Obtained structure was prepared using Protein preparation wizard in Schrödinger (2013-3) and POPC membrane model added between amino acids 81-103 of each CD95L monomer.
DOI: 10.6084/m9.figshare.21558324
title: Supplementary Material for: Hybrid laparo-endoscopic resection of submucosal cardial tumors assisted by flexible articulated instruments

description: We report a new surgical method in 10 patients that underwent hybrid laparo-endoscopic resection (HLER) of submucosal tumors with the combination of flexible articulated laparoscopic instruments (FALI). We have assessed technical reproducibility, safety and morbidity. Resection was completed in all cases. Mean surgical time was 60 minutes (30-85). Median tumor size was 16 mm (12-30). The more frequent location was gastroesophageal junction. No complications were observed during the procedure. Length of stay was 1 day in all cases. We have found HLER to be a safe procedure allowing margin resection and organ preservation. The addition of FALI added ease of performance in hard-to-reach tumor locations.
DOI: 10.34740/kaggle/dsv/4871342
title: AutoXGB
DOI: 10.6084/m9.figshare.21175042.v1
title: Supplementary Information for: The mitochondrial genome of Isognomon nucleus and mitophylogenomics of Pteriomorphia (Mollusca: Bivalvia: Autobranchia)

description: <strong>Sup.Table 1:</strong> Structural features of the standard mitochondrial genes in the <em>I. nucleus </em>mitogenome <strong>Sup. Table 2:</strong> Summary statistics for ONT reads via NanoStat (within Section 1) <strong>Sup. Table 3:</strong> List of species, accession numbers and mitogenome sizes used in this study (within Section 1) <strong>Sup. Fig. 1. </strong>Length versus base quality plot of ONT reads (within Section 1) <strong>Sup. Fig. 2. </strong>Evidence for a small gap in the <em>I. nucleus </em>mitogenome from ONT-only assembly (within Section 1) <strong>Sup. Fig. 3. </strong>Distribution of observed and theoretical protein sizes from ORFs found in the unannotated portion of the <em>I. nucleus </em>mitogenome (within Section 4) <strong>Section 1: </strong>Expanded Materials and Methods <strong>Section 2: </strong>Lack of a convincing <em>ATP8</em> gene <strong>Section 3: </strong>Sequencing depth analysis <strong>Section 4: </strong>Potential long novel transmembrane domain containing ORFs in <em>I. nucleus </em>and <em>P. fucata martensii</em> <strong>Sup. Data 1. </strong>Sequences of the 4 long <em>Isognomon nucleus </em>proteins with multiple predicted transmembrane domains (these were included in the official annotation of the mitogenome) <strong>Sup. Data 2.</strong> Transmembrane domain identification for the <em>I. nucleus </em>predicted proteins by DeepTMHMM (gff output format) <strong>Sup. Data 3.</strong> Sequences of the 5 long <em>Pinctada fucata martensii</em> proteins with multiple predicted transmembrane domains <strong>Sup. Data 4.</strong> Transmembrane domain identification for the <em>P. fucata martensii</em> predicted proteins by DeepTMHMM (gff output format) <strong>Sup. Data 5.</strong> <em>(Not in this file; available at Figshare)</em> Contains the curated, GBLOCKS-alignment, all files from the IQTREE run and pdf exports of the estimated ML tree from FigTree. [https://figshare.com/projects/Isognomon_mitogenomes_Supplementary_Data_Files_tables/129485] <strong>Sup. Data 6.</strong> Sequences of the 3 additional long <em>Isognomon nucleus </em>proteins with multiple predicted transmembrane domains (these were not included in the official mitogenome annotation)
DOI: 10.34740/kaggle/dsv/4871409
title: Elon Musk Tweets
DOI: 10.6084/m9.figshare.17680328
title: data files , liver in AKI

description: raw data, western blots uncropped images
DOI: 10.6084/m9.figshare.17680328.v1
title: data files , liver in AKI

description: raw data, western blots uncropped images
DOI: 10.6084/m9.figshare.21922032
title: Original dataset from Ants act as olfactory bio-detectors of tumours in patient-derived xenograft mice

description: Early detection of cancer is critical in medical sciences, as the sooner a cancer is diagnosed, the higher are the chances of recovery. Tumour cells are characterized by specific volatile organic compounds (VOCs) that can be used as cancer biomarkers. Through olfactory associative learning, animals can be trained to detect these VOCs. Insects such as ants have a refined sense of smell, and can be easily and rapidly trained with olfactory conditioning. Using urine from patient-derived xenograft mice as stimulus, we demonstrate that individual ants can learn to discriminate the odour of healthy mice from that of tumour-bearing mice and do so after only three conditioning trials. After training, they spend approximately 20% more time in the vicinity of the learned odour than beside the other stimulus. Chemical analyses confirmed that the presence of the tumour changed the urine odour, supporting the behavioural results. Our study demonstrates that ants reliably detect tumour cues in mice urine and have the potential to act as efficient and inexpensive cancer bio-detectors.
DOI: 10.6084/m9.figshare.21922017
title: raw data.zip

description: All the raw data in the manuscript.
DOI: 10.5066/p9v4tiub
title: Satellite tracking data for post-nesting green turtles from Northwest Florida (2002-2020)

description: This dataset includes processed satellite tracking data collected from green turtles between July 2002 and October 2020 in the Gulf of Mexico along the west coast of Florida from the Florida Keys to the Gulf Islands National Seashore. It contains model output including from the state-space model (SSM) described in Lamont et al. (2022) and centroids associated with the 50 percent and 95 percent kernel density estimates for turtles with greater than or equal to 20 days in either foraging or inter-nesting habitat of SSM locations.
DOI: 10.4121/uuid:a07386a5-7be3-4367-9535-70bc9e77dbe6
title: Receipt phase of an environmental permit application process (‘WABO’), CoSeLoG project

description: This data originates from the CoSeLoG project executed under NWO project number 638.001.211. Within the CoSeLoG project the (dis)similarities between several processes of different municipalities in the Netherlands has been investigated. This event log contains the records of the execution of the receiving phase of the building permit application process in an anonymous municipality.
DOI: 10.5281/zenodo.3663616
title: EMG and Video Dataset for sensor fusion based hand gestures recognition

description: This dataset contains data for hand gesture recognition recorded with 3 different sensors. sEMG: recorded via the Myo armband that is composed of 8 equally spaced non-invasive sEMG sensors that can be placed approximately around the middle of the forearm. The sampling frequency of Myo is 200 Hz. The output of the Myo is a.u DVS: Dynamic Video Sensor which is a very low power event-based camera with 128x128 resolution DAVIS: Dynamic Video Sensor which is a very low power event-based camera with 240x180 resolution that also acquires APS frames. The dataset contains recordings of 21 subjects. Each subject performed 3 sessions, where each of the 5 hand gesture was recorded 5 times, each lasting for 2s. Between the gestures a relaxing phase of 1s is present where the muscles could go to the rest position, removing any residual muscular activation. Note: All the information for the DVS sensor has been extracted and can be found in the *.npy files. In case the raw data (.aedat) was needed please contact enea.ceolini@ini.uzh.ch elisa@ini.uzh.ch ==== README ==== DATASET STRUCTURE: EMG, DVS and APS recordings 21 subjects 3 sessions for each subject 5 gestures in each session ('pinky', 'elle', 'yo', 'index', 'thumb') SINGLE DATASETS: - relax21_raw_emg.zip: contains raw sEMG and annotations (ground truth of gestures) in the format `subjectXX_sessionYY_ZZZ` with `XX` subject ID (01 to 21), `YY` session ID (01-03) and `ZZZ` that can be ‘emg’ or ‘ann’. - relax21_raw_dvs.zip: contains the full-frame dvs events in an array with dimensions 0 -&gt; addr_x, 1 -&gt; addr_y, 2 -&gt; timestamp, 3 -&gt; polarity. The timestamps are in seconds and synchronized with the Myo. Each file is in the format `subjectXX_sessionYY_dvs` with `XX` subject ID (01 to 21), `YY` session ID (01-03). - relax21_cropped_aps.zip: contains the 40x40 pixel aps frames for all subjects and trials in the format `subjectXX_sessionYY_Z_W_K` with `XX` subject ID (01 to 21), `YY` session ID (01-03), Z gesture ('pinky', 'elle', 'yo', 'index', 'thumb’), W trial ID (1-5), `K` frame index. - relax21_cropped_dvs_emg_spikes.pkl: spiking dataset that can be used to reproduce the results in the paper. The dataset is a dictionary with the following keys: <strong>- </strong><strong>y</strong>: array of size 1xN with the class (0-&gt;4). <strong>- </strong><strong>sub</strong>: array of size 1xN with the subject id (1-&gt;10). <strong>- </strong><strong>sess</strong>: array of size 1xN with the session id (1-&gt;3). <strong>- </strong><strong>dvs</strong>: list of length N, each object in the list is a 2d array of size 4xT_n where T_n is the number of events in the trial and the 4 dimensions rappresent: 0 -&gt; addr_x, 1 -&gt; addr_y, 2 -&gt; timestamp, 3 -&gt; polarity . <strong>- </strong><strong>emg</strong>: list of length N, each object in the list is a 2d array of size 3xT_n where T_n is the number of events in the trial and the 3 dimensions rappresent: 0 -&gt; addr, 1 -&gt; timestamp, 3 -&gt; polarity.
DOI: 10.5281/zenodo.4308022
title: Monthly values of absolutely measured geomagnetic components (D, I, H, Z, F) of Coimbra observatory in the period1866-2015

description: Monthly values of the absolutely measured geomagnetic components D, I, H, Z, F for the period 1866-2015 of Coimbra observatory. Different combinations of three magnetic elements were used to fully specify the geomagnetic field vector: the HDI components were measured in 1866-1951; HDZ in 1951-2006; and DIF in 2006-2015. It should also be noted that the monthly values of the first period (1866-1951) are based exclusively on the averages of absolute measurements (made on average 3 per month), while from 1951 onwards the monthly averages were calculated from the hourly averages obtained from the magnetograms after baseline calibration.
description: Data used in the manuscript "Homogenization of the historical series from the Coimbra Magnetic Observatory, Portugal", submitted to the data publishing journal Earth System Science Data (ESSD); authors: A. L. Morozova, P. Ribeiro, and M. A. Pais
DOI: 10.5281/zenodo.4308036
title: Homogenized monthly datasets of all geomagnetic components of Coimbra observatory for the time period 1866-2015

description: Homogenized monthly values of all geomagnetic components (D, I, H, X, Y, Z, F) of Coimbra observatory for the period 1866-2015. The homogenization procedures applied to the geomagnetic time series of Coimbra observatory is presented and discussed in Morozova et al. 2020, submitted to Earth System Science Data (ESSD).
DOI: 10.5281/zenodo.7314785
title: Climate network construction and analysis

description: We provide the python codes for paper "Teleconnections among Tipping Elements in the Earth System". The fold named teleconnection_area contains the codes, which are used to calculate the cross-correlation between the nodes in the Amazon and outside. The fold named path contains the codes, which are used to find and plot the shortest path from the Amazon to the TP. The fold named resilience contains the codes, which are used to calculate and plot indicators of Early Warning Signal for the snow cover in the TP.
DOI: 10.3886/e120068v1
title: Data and Code for Democracy and Aid Donorship

description: Democracy and Aid Donorship, Budjan, Angelika J. and Andreas Fuchs, American Economic Journal: Economic Policy. <br>AEA Data and Code Repository project ID: 120068 <br><br>The replication material consists of four Stata do files, four raw input data files contained in the “inputdata” folder and four regression datasets contained in the “outputdata” folder. Analyses have been performed with Stata version 14.0. Running the master do file (“Democracy and Aid Donorship replication file MAIN.do”) will call the configuration do file (“config.do”), the data cleaning do file (“Prepare data.do”), and the data analysis do file (“Analyse data.do”). The configuration do file creates five new folders: the “ado” folder where necessary ado files are stored; the “outputdata” folder where the generated analysis datasets are stored; the “tables” folder where results tables are stored; the “figures” folder where generated figures are stored and the “tempdata” folder where temporary datasets are stored and which are automatically deleted by the end of the script. <br><br>In order to run the master do file (“Democracy and Aid Donorship replication file MAIN.do”), insert the correct folder path in line 19. <br><br>The data analyses do file (“Analyse data.do”) generates four regression datasets in the “outputdata” folder. We have omitted full raw databases of the “input” data from a number of sources due to copyright reasons (Marshall et al. 2016, Coppedge et al. 2016, Banks and Wilson 2016, Bormann et al. 2017, Feenstra et al. 2015, Harborn and Wallensteen 2012, Palmer et al. 2015; Mayer and Zignano 2011, Correlates of War Project 2011, Bailey et al. 2017, OECD Creditor Reporting System 2019, Tierney et al. 2011, Bjornskov and Rode forthcoming, Freedom House 2016). The do file will thus neither run without error nor produce the complete datasets required for the analysis – which we however provide in their entirety in the “outputdata” folder. The four regression datasets are the following: <br> new_donors_MAIN.dta is needed to create Tables 1-3; Figures 2-4 and most tables and figures of the Online Appendix<br> new_donors_limited.dta and new_donors_3yaverages.dta are needed to create robustness test of Table B3 in the Online Appendix <br><br>new_donors_sample_firstaid.dta is needed to create robustness tests of Table C2 in the Online Appendix <br><br><br><br>
DOI: 10.18739/a2wh2df2x
title: Surface sediment samples collected from the Canadian Coast Guard Ship (CCGS) Sir Wilfrid Laurier, Northern Bering Sea to Chukchi Sea, 2014

description: The Pacific sector of the Arctic Ocean is experiencing major reductions in seasonal sea ice extent and increases in sea surface temperatures. One of the key uncertainties in this region is how the marine ecosystem will respond to seasonal shifts in the timing of spring sea ice retreat and/or delays in fall sea ice formation. Variations in upper ocean water hydrography, planktonic production, pelagic-benthic coupling and sediment carbon cycling are all influenced by sea ice and temperature change. To more systematically track the broad biological response to sea ice retreat and associated environmental change, an international consortium of scientists have developed a coordinated Distributed Biological Observatory (DBO) that includes selected biological measurements at multiple trophic levels, along with satellite and mooring measurements. The DBO currently focuses on five regional biological hotspot locations along a latitudinal gradient that allows for consistent sampling and monitoring at five biologically productive locations across a latitudinal gradient: DBO 1 (SLIP)-south of St. Lawrence Island (SLI), DBO2 (Chirikov)-north of SLI, DBO3 (southern Chukchi Sea), DBO4-NE Chukchi Sea, and DBO5-Barrow Canyon. This dataset contains summary measurements of surface sediment collected at each station for the identified cruise, including: sediment grain size (≤0 phi, 1 phi, 2 phi, 3 phi, 4 phi, &gt;=5 phi, 1-4 phi, and modal phi size), total organic carbon (TOC), total organic nitrogen (TON), C/N and surface sediment chlorophyll (chl a). Surface sediment chlorophyll (chl a) content is scaled up to mg Chl a/m2.
DOI: 10.34740/kaggle/ds/1376245
title: Mask R-CNN Pedestrian Tracklets