cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17632/vgjkbk52t2.1
title: Near-Physiological-Temperature Serial Crystallography Reveals Conformations of SARS-CoV-2 Main Protease Active Site for Improved Drug Repurposing. Durdagi et al

description: The COVID-19 pandemic has resulted in 185 million reported infections and more than 4 million deaths as of July 2021 (covid19.who.int). Research to identify effective therapies for COVID-19 includes: i) designing a vaccine as future protection; ii) de novo drug discovery; and iii) identifying existing drugs to repurpose them as effective and immediate treatments. To assist in drug repurposing and design, we determine two apo structures of Severe Acute Respiratory Syndrome CoronaVirus-2 (SARS-CoV-2) main protease at ambient-temperature by Serial Femtosecond X-ray crystallography. We employ detailed molecular simulations of selected known main protease inhibitors with the structures and compare binding modes and energies. The combined structural and molecular modeling studies not only reveal the dynamics of small molecules targeting the main protease but also provide invaluable opportunities for drug repurposing and structure-based drug design strategies against SARS-CoV-2.
DOI: 10.17632/cgrwmy4cb5.1
title: Failure by slow crack growth of SiC-based tows: a Monte Carlo simulation

description: The data are related to a research article entitled “New insight into subcritical rupture of SiC-based bundles at intermediate temperatures (400-900 °C) under air: Simulating the sources of variability”. Supplementary data include the Monte Carlo simulation files for all different fibers, plus the Stress Probability Time diagrams extracted from these simulations. The file named “A evolution with temperature.xlsx” compiles the Arrhenius parameters for SCG of filaments and tows, whereas the file “Fiber type comparison.xls” is a comparison of the 9 fibers discussed in the manuscript: Nicalon NL101, NL207, Hi-Nicalon, Hi-Nialon type S, Tyranno grade S (8.5 and 11 µm mean diameter), Lox-M, ZMI, AM.
DOI: 10.17632/ng8kd9wszx.1
title: Community-level SARS-CoV-2 sequence diversity revealed by wastewater sampling

description: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus responsible for causing the COVID-19 pandemic, can be detected in untreated wastewater. Wastewater surveillance of SARS-CoV-2 complements clinical data by offering earlier community-level detection, removing underlying factors such as access to healthcare, sampling asymptomatic patients, and reaching a greater population. Here, we compare 24-hour composite samples from the influents of two different wastewater treatment plants (WWTPs) in South Carolina, USA: Columbia and Rock Hill. The sampling intervals span the months of July 2020 and January 2021, which cover the first and second waves of elevated SARS-CoV-2 transmission and COVID-19 clinical cases in these regions.
DOI: 10.6084/m9.figshare.14987937
title: Supplementary Material for: A Randomized Clinical Trial of Cognitive-Behavioral Therapy for Insomnia to Augment Posttraumatic Stress Disorder Treatment in Survivors of Interpersonal Violence

description: <b><i>Introduction:</i></b> Individuals exposed to interpersonal violence (IPV) commonly develop posttraumatic stress disorder (PTSD) with co-occurring depression and insomnia. Standard PTSD interventions such as cognitive processing therapy (CPT) do not typically lead to remission or improved insomnia. Cognitive behavioral therapy for insomnia (CBTi) improves insomnia in individuals with PTSD, but PTSD severity remains elevated. <b><i>Objective:</i></b> To determine whether sequential treatment of insomnia and PTSD is superior to treatment of only PTSD. <b><i>Methods:</i></b> In a 20-week trial, 110 participants exposed to IPV who had PTSD, depression and insomnia were randomized to CBTi followed by CPT or to attention control followed by CPT. Primary outcomes following CBTi (or control) were the 6-week change in score on the Insomnia Severity Index (ISI), the Clinician-Administered PTSD Scale (CAPS), and the Hamilton Rating Scale for Depression (HAM-D). Primary outcomes following CPT were the 20-week change in scores. <b><i>Results:</i></b> At 6 weeks, the CBTi condition had greater reductions in ISI, HAM-D, and CAPS scores than the attention control condition. At 20 weeks, participants in the CBTi+CPT condition had greater reductions in ISI, HAM-D, and CAPS scores compared to control+CPT. Effects were larger for insomnia and for depression than for PTSD. Similar patterns were observed with respect to clinical response and remission. A tipping point sensitivity analyses supported the plausibility of the findings. <b><i>Conclusions:</i></b> The sequential delivery of CBTi and CPT had plausible, significant effects on insomnia, depression, and PTSD compared to CPT alone. The effects for PTSD symptoms were moderate and clinically meaningful.
DOI: 10.17632/8pbkt9t64x.1
title: CDI

description: CDI and SARS-CoV-2
DOI: 10.5281/zenodo.5105921
title: CSV-format data for: Increased mortality in community-tested cases of SARS-CoV-2 lineage B.1.1.7

description: This is a supplementary upload to https://zenodo.org/record/4579857. This upload provides the same anonymised individual-level SARS-CoV-2 testing data for England as that earlier upload provided, but provides it in CSV format (comma-separated values) instead of in the previous QS format. The QS format requires specialised software (e.g. the <strong>qs</strong> package for R) to read, so I am providing the data in CSV format to facilitate access to and re-use of the data. Please see the original data upload, https://zenodo.org/record/4579857, the associated journal article, Increased mortality in community-tested cases of SARS-CoV-2 lineage B.1.1.7, and the project's Github repository, https://github.com/nicholasdavies/cfrvoc, for full details.
DOI: 10.5281/zenodo.5105920
title: CSV-format data for: Increased mortality in community-tested cases of SARS-CoV-2 lineage B.1.1.7

description: This is a supplementary upload to https://zenodo.org/record/4579857. This upload provides the same anonymised individual-level SARS-CoV-2 testing data for England as that earlier upload provided, but provides it in CSV format (comma-separated values) instead of in the previous QS format. The QS format requires specialised software (e.g. the <strong>qs</strong> package for R) to read, so I am providing the data in CSV format to facilitate access to and re-use of the data. Please see the original data upload, https://zenodo.org/record/4579857, the associated journal article, Increased mortality in community-tested cases of SARS-CoV-2 lineage B.1.1.7, and the project's Github repository, https://github.com/nicholasdavies/cfrvoc, for full details.
DOI: 10.17632/jy6ww3hmyw.3
title: Multi-Paradigm Modeling for Cyber-Physical Systems literature

description: This dataset includes the set of papers retrieved to perform a systematic mapping review (SMR) on multi-paradigm modelling (MPM) for cyber-physical systems (CPS). Moreover, it includes several tables that map the studies under several perspectives, notably used modelling formalisms and processes, part of the CPS addressed by the research, domain of expertise of paper authors, and relevance of the paper at review date. The set of papers is selected over a period ranging from 2006 to 2017, according to publication dates. The selection of the papers and their mapping has been performed by means of a rigorous process based on precise aspects to be evaluated and peer reviewing. Further, the process has been supported by a web-based survey management application. Both the selection of existing publications and their mappings by means of the included perspectives provide interested readers/researches with interesting data possible re-usable for multiple purposes: analysing the progress of research on modelling of CPS, studying further the papers pertaining to a specific (set of) characteristic(s), performing a follow-up study related to other development technologies, just to mention a few.
DOI: 10.17632/bws2s9t8nx.1
title: Hind paw trajectories from high-speed video of scratching

description: Raw trajectory data from high speed recording of scratching behavior
DOI: 10.5522/04/14976891
title: Functional Data

description: The Functional Data (grouped data) files contains the functional data after grouping: • Cn is a cell of length Numb_patches. Each element of the cell is a d1 x d2 matrix of the correlation image of a different patch in the experiment, where d1 and d2 are the dimensions of the patch. The correlation image is calculated as the correlation of each pixel with its neighbours. • Ain_axons is a cell of length Numb_patches. Each element of the cell is a (d1 * d2) x M matrix corresponding to the spatial filters (masks) of each putative axon after grouping, where M is the number of identified axons in that patch. To visualize, use reshape to convert a column of the matrix Ain_axons{patch_no} into a d1 x d2 matrix corresponding to the patch dimensions, e.g., imagesc(reshape(Ain_axons{patch_number}(:,axon_number),d1,d2)). • dFF_axons is a cell of length Numb_patches. Each element of the cell is an M x T matrix corresponding to the dFF of each putative axon after grouping, where T is the number of timepoints in the experiment. The mth row of dFF_axons{patch_no} and the mth column of Ain_axons{patch_no} corresponds to the same putative axon. • time_axons is a cell corresponding to the times for each axon, same structure as dFF_axons. • dFF_rois, Ain_rois, and time_rois as above, but for individual granule cell varicosities before grouping. • ix_axons_to_rois is a cell of length Numb_patches. Each element of the cell is another cell of length M corresponding the the ROI id numbers for each varicosity associated with that putative axon. The mth element of this cell is a vector containing the ROI id numbers of all varicosities associated with the putative axon corresponding to axon id number m. • axon_ids is a vector whose length is the number of varicosities, which performs the inverse mapping (from ROI id number to axon id number). The ith element of this vector is the axon id number for the varicosity corresponding to ROI id number i.
DOI: 10.5522/04/14976891.v1
title: Functional Data

description: The Functional Data (grouped data) files contains the functional data after grouping: • Cn is a cell of length Numb_patches. Each element of the cell is a d1 x d2 matrix of the correlation image of a different patch in the experiment, where d1 and d2 are the dimensions of the patch. The correlation image is calculated as the correlation of each pixel with its neighbours. • Ain_axons is a cell of length Numb_patches. Each element of the cell is a (d1 * d2) x M matrix corresponding to the spatial filters (masks) of each putative axon after grouping, where M is the number of identified axons in that patch. To visualize, use reshape to convert a column of the matrix Ain_axons{patch_no} into a d1 x d2 matrix corresponding to the patch dimensions, e.g., imagesc(reshape(Ain_axons{patch_number}(:,axon_number),d1,d2)). • dFF_axons is a cell of length Numb_patches. Each element of the cell is an M x T matrix corresponding to the dFF of each putative axon after grouping, where T is the number of timepoints in the experiment. The mth row of dFF_axons{patch_no} and the mth column of Ain_axons{patch_no} corresponds to the same putative axon. • time_axons is a cell corresponding to the times for each axon, same structure as dFF_axons. • dFF_rois, Ain_rois, and time_rois as above, but for individual granule cell varicosities before grouping. • ix_axons_to_rois is a cell of length Numb_patches. Each element of the cell is another cell of length M corresponding the the ROI id numbers for each varicosity associated with that putative axon. The mth element of this cell is a vector containing the ROI id numbers of all varicosities associated with the putative axon corresponding to axon id number m. • axon_ids is a vector whose length is the number of varicosities, which performs the inverse mapping (from ROI id number to axon id number). The ith element of this vector is the axon id number for the varicosity corresponding to ROI id number i.
DOI: 10.17632/9rbd5t9gy5.1
title: JEB TRID treatment 2021

description: To determine the effect on aminoglycosides on keratinocytes from patients with junctional epidermolysis bullosa a hypothesis free gene expression study was performed. A keratinocyte cell line with a specific nonsense mutation in COL17A1 was treated with gentamicin or paromomycin or remained untreated. RNA was extracted in a triplicate experimental setting and submitted to RNA sequencing.
DOI: 10.5522/04/14976837.v1
title: Metadata Files

description: The Metadata files contain metadata and behavioural data. The variables are: • acquisition_rate is a scalar describing the acquisition rate in Hz. • Pixel_size is a scalar describing the size of each pixel in microns. • Numb_patches is a scalar describing the number of patches in the experiment. • Patch_coordinates is a structure containing coordinate information about each patch. Patch_coordinates.data is a matrix in which each row represents a patch, and columns 5, 6, and 7 represent the X, Y, and Z positions (respectively) of that patch. • SpeedDataMatrix and SpeedTimeMatrix are vectors containing the wheel speed time series and times from the wheel encoder. • dlc_whisk_angle and dlc_whisk_time are vectors containing the whisking angle time series and times as determined via DeepLabCut.• wheel_MI is a matrix whose second column contains the wheel motion index time series as determined from the wheel cameras and whose second column contains the corresponding times. Note that this file may also contain variables extracted by now obsolete methods which were not included by the analysis in the paper (e.g., Whiskers_angle_0 for old whisker position detection, Axon_dFF for old grouping procedure). You can ignore these.
DOI: 10.17632/9xwh2hg89x.5
title: Dataset on beach dynamics and beach-casts appearance at the Northern coast of the Sambia Peninsula, the Baltic Sea (Kaliningrad Oblast, Russia)

description: Kaliningrad Oblast, the westernmost region of Russia, suffers from coastal erosion (Łabuz et al., 2018). Sandy beaches are narrow, especially at the Northern shore of the Sambia Peninsula, where the rate of coastal retreat is about 0.5–1.5 m/year (Karmanov et al., 2018), the width of the beach (10–25 m in average) varies in time, the shore is partly protected by old groins (Prushak et al., 2014). The issue of the beach cast is linked to the problems of marine litter and microplastic pollution (Chubarenko I. et al., 2020) and seegrass dumping (Chubarenko B. et al., 2021). To monitor the dynamics of the beach and the release of beach casts on it, the webcam was installed at the northern shore of the Sambia Peninsula (Kaliningrad Oblast, Russia). Primary information (the raw images) is not presented in the database. The secondary data developed after the processing of images are presented in a tabular table, it contains several sheets. Sheet 1 (named "Beach-Cast_data") shows the presence or absence of beach and beach cast; it has 5 columns: Date (shooting date, format YYYY-MM-DD), BeachW (beach present/absent west of groin), BeachE (beach present/absent east of groin), CastW (beach cast present/absent west of groin), CastE (beach cast present/absent east of groin). The absence of the beach or beach cast is designated as "0". The presence of the beach or beach cast is designated as "1", but if the beach cast occupied more the 25% of study area, then it is indicated as "2". Sheet 2 (named "Cast_areas") shows the area occupied by beach cast within the boundaries of the study area; it has 5 columns: Date (shooting date, format YYYY-MM-DD), CastWest means beach cast west of groin and presented by two columns "area" (m2) and percentage ("%"), the CastEast means beach cast east of groin and presented by two columns "area" (m2) and percentage ("%"). Sheet 3 (named "Legend") shows legend described above. References: Chubarenko B., Woelfel J., Hofmann J., Aldag S., Beldowski J., Burlakovs J., Garrels T., Gorbunova J., Guizani S., Kupczyk A., Kotwicki L., Domnin D., Gajewska M., Hogland W., Kołecka K., Nielsen J., Schubert H. Converting beach wrack into a resource as a challenge for the Baltic Sea (an overview). (2021) Ocean & Coastal Management, 200, 105413. Chubarenko I., Esiukova E., Khatmullina L., Lobchuk O., Grave A., Kileso A., Haseler M. (2020) From macro to micro, from patchy to uniform: Analyzing plastic contamination along and across a sandy tide-less coast. Marine Pollution Bulletin, 156, 111198. Łabuz T.A., Grunewald R., Bobykina V., Chubarenko B., Česnulevičius A., Bautrėnas A., Morkūnaitė R., Tõnisson H. (2018) Coastal dunes of the Baltic Sea shores: a review. Quaestiones Geographicae, 37(1), 47-71. Prushak Z., Ostrovsky R., Babakov A.N., Chubarenko B.V. (2014) The main principles of bank stabilization by the groins. Russian Journal of Geomorpholgy, 14(3), 91-105.
DOI: 10.5522/04/14976822
title: Fibre Direction Data

description: These files contain information about the overall fibre orientation as determined from tracing small sections from structural data:<br>• vector_mean is a normalized vector containing the average axon direction over all traced segments in the patch. • angle is a vector listing the deflection of each individual traced axon segment from vector_mean (in radians). • angle_std is the standard deviation of angle (in degrees).<br>
DOI: 10.5522/04/14976822.v1
title: Fibre Direction Data

description: These files contain information about the overall fibre orientation as determined from tracing small sections from structural data:<br>• vector_mean is a normalized vector containing the average axon direction over all traced segments in the patch. • angle is a vector listing the deflection of each individual traced axon segment from vector_mean (in radians). • angle_std is the standard deviation of angle (in degrees).<br>
DOI: 10.5522/04/14976837
title: Metadata Files

description: The Metadata files contain metadata and behavioural data. The variables are: • acquisition_rate is a scalar describing the acquisition rate in Hz. • Pixel_size is a scalar describing the size of each pixel in microns. • Numb_patches is a scalar describing the number of patches in the experiment. • Patch_coordinates is a structure containing coordinate information about each patch. Patch_coordinates.data is a matrix in which each row represents a patch, and columns 5, 6, and 7 represent the X, Y, and Z positions (respectively) of that patch. • SpeedDataMatrix and SpeedTimeMatrix are vectors containing the wheel speed time series and times from the wheel encoder. • dlc_whisk_angle and dlc_whisk_time are vectors containing the whisking angle time series and times as determined via DeepLabCut.• wheel_MI is a matrix whose second column contains the wheel motion index time series as determined from the wheel cameras and whose second column contains the corresponding times. Note that this file may also contain variables extracted by now obsolete methods which were not included by the analysis in the paper (e.g., Whiskers_angle_0 for old whisker position detection, Axon_dFF for old grouping procedure). You can ignore these.
DOI: 10.17632/d6m4xhwtyw.3
title: The efficacy and acceptability of exposure therapy for the treatment of post-traumatic stress disorder in children and adolescents: A systematic review and meta-analysis

description: Efficacy at post-treatment in PTSD symptom severity (continuous variables)，Efficacy of follow-up in PTSD symptom severity (continuous variables)，Depressive symptom (continuous variables)，Quality of life/social functioning (continuous variables)，Acceptability (binary variables)
DOI: 10.17632/nv8dr4fcw9.1
title: Tacuadactylus luciae gen. et sp. nov.

description: 3D scan and rendering of spatula
DOI: 10.25345/c5wv6g
title: MassIVE MSV000087829 - GC/MS an UHPLC/QTOF + and - mass spectra-gut metabolomics after microbiota depletion and selenium supplementation
title: The mass spectra correspond to gut metabolome of conventional mice and microbiota depleted mice after antibiotic treatment feed selenium supplemented diet, regular diet.
DOI: 10.17632/zwxxscny6x.2
title: Impaired emotion perception and categorization in semantic aphasia

description: This data was collected for the manuscript 'Impaired emotion perception and categorization in semantic aphasia'. We studied a sample of left hemisphere stroke patients with 'semantic aphasia', characterised as multimodal impairment in the controlled retrieval of semantic concepts. We tested the constructionist hypothesis of emotion; that emotion perception and categorization is dependent on conceptual representations of discrete emotion states. Based on this hypothesis, impaired semantic processing may also manifest as impaired emotion processing. We assessed the effects of impaired semantic control on the ability to categorize discrete facial emotion portrayals, across two studies. We found evidence for baseline impairments in emotion categorization across two studies. We also found anticipated cueing effects, where facilitating access to relevant conceptual information aided emotion categorization, while distracting miscues had deleterious effects on accuracy. All collected and processed data is uploaded here. The document 'Impaired emotion perception and categorization in semantic aphasia – Data Guide' can be used a guide for interpreting the data with reference to the manuscript.
DOI: 10.17632/628x39mmnm.3
title: Why Do People Sacrifice Themselves For The Country? The Role Of Identity Fusion and Empathic Concern

description: Data and supplementary material from article Why Do People Sacrifice Themselves For The Country? The Role Of Identity Fusion and Empathic Concern
DOI: 10.17632/p4fg6snh3r.1
title: Orion Beam Datasets

description: The datasets provided by this repository comprise experimental data to investigate the nonlinear dynamic behavior of the Orion beam structure, which consists of two duraluminum beams assembled by bolted joints. To retain contact on a small area between both beams, this new lap-joint configuration proposes contact patches at each bolt connection. The Orion beam suggests an assembly configuration that associates bolts dedicated to “static” functions and to those to perform “damping” functions. This ensures a significant increase in the structural damping without degrading the structural stiffness. Experiments have been performed on the laboratory pôle Vibration and Acoustic, located at FEMTO-ST Institute, CNRS/UFC/ENSMM/UTBM, Department of Applied Mechanics, 24 chemin de l’Epitaphe, 25000 Besançon, France. A full description of the data can be seen in the following publications: • R. O. Teloli, P. Butaud, G. Chevallier, S. da Silva, Good practices for designing and experimental testing of dynamically excited jointed structures: The Orion beam, Mechanical Systems and Signal Processing, 163(2022) 108172. https://doi.org/10.1016/j.ymssp.2021.108172. • R. O. Teloli, P. Butaud, G. Chevallier, S. da Silva, Dataset of experimental measurements for the Orion beam structure, Data in Brief Journal, In Press. If you have any questions, please contact us: Rafael Teloli: rafael.teloli@unesp.br Pauline Butaud: pauline.butaud@femto-st.fr Gaël Chevallier: gael.chevallier@univ-fcomte.fr Samuel da Silva: samuel.silva13@unesp.br