cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17632/89y57gwbzk.2
title: Molecular biomarker record of environmental change in the central Mediterranean Sea for the last million years

description: Molecular biomarker data for core LC07 in the Central Mediterranean Sea covering the last million years together with the planktonic foraminifera d18O data (already published in Dinarès-Turell et al. 2003, 3P) but on a slightly refined age scale, and the calculated d18O of seawater. For details please see Martínez-Dios, Ariadna; Pelejero, Carles; Cobacho, Sara; Movilla, Juancho; Dinarès-Turell, Jaume; Calvo, Eva. (2021), “A 1-million-year record of environmental change in the central Mediterranean Sea from organic molecular proxies”, Paleoceanography and Paleoclimatology.
DOI: 10.17632/5yyjv6df2m.1
title: Mass spectrometry based metabolites of cell, medium, and pig heart tissue-05/06/2021

description: This data set includes the abundance of metabolites from cell, medium and pig heart tissue sample using Targeted Liquid Chromatography Tandem Mass Spectrometry. Both the positive and negative ionization mode were used for the metabolites detection.
DOI: 10.17632/97zt9fzky8.3
title: Raw Data, sFlt-1, PLGF

description: Comparison of PLGF and sFlt-1 Level in Placenta Accreta Spectrum Disorder
DOI: 10.17632/stfbjy4vf7.1
title: Similarities in recognition cues lead to the infiltration of non-nestmates in an ant species

description: Abstract
Chemical cues are among the most important information sharing mechanisms in insect societies, in which cuticular hydrocarbons play a central role – e.g. from nestmate recognition to queen signaling. The nestmate recognition mechanism usually prevents intruders from taking advantage of the resources stored in the nest. However, nestmate recognition is not unconditionally effective and foreign individuals can sometimes infiltrate unrelated nests and take advantage of the colony resources. In this study we investigated the role of overall colony odor profiles on the ability of conspecific workers drifting into unrelated colonies. We hypothesized that drifters would have higher chances of success by infiltrating colonies with the odor profiles most similar to their own nest, avoiding being detected as non-nestmates. By performing a drifting bioassay, we found that workers of the ant Formica fusca infiltrated unrelated conspecific colonies at a rate of 2.4 %, significantly infiltrating colonies displaying CHC profiles most similar to their natal nests. Notably, methyl branched hydrocarbons seem to play a role as recognition cues in this species. In addition, we show that environmental rather than genetic factors are responsible for most contributions on the CHC phenotype, presenting ca. of 50 % and 27.5 % of explained variation respectively, and playing a major role on how worker ants detect and prevent the infiltration of non-nestmates in the colony. Hence, relying on cuticular hydrocarbons similarities could be a profitably evolutionary strategy by which workers can identify conspecific colonies, evade detection by guards and avoid competition with genetic relatives.
DOI: 10.17632/cjhprg23g9.1
title: TSA-2018-808

description: Limited dataset for the experimental study investigating the effect of thymoquinone on trauma-induced injury in 4 months old Sprague Dawley albino rats.
Primary outcome: Total histopathologic trauma score
Secondary outcomes: cleavage of caspase-3, glutathione activity, Na,K-ATPase activity, TBARS
DOI: 10.17632/h2fvj7x3vt.1
title: Supplementary material - individual-based network of Noctilio albiventris and streblid bat fly

description: We provide four files, a txt file, an R script, and two csv files containing results. The txt file contains a matrix of interactions between Streblidae species (Noctiliostrebla morena, N. pantaneira and Paradyschiria parvula) and Noctilio albiventris individuals, captured along two sites of riparian forest in the Southern Pantanal, from 25 February to 3 March 2013. The R script contains a series of commands to run network analysis. The "traits_pca.csv" file contains the results from the pca analysis and the modules resulting from the modularity analysis. The "individual_level_indices.csv" file contains the results from the different species/individual-level indices calculated.
DOI: 10.17632/b97d5nrb72.2
title: Mechanistic Insights into COVID-19 by Global Analysis of the SARS-CoV-2 3CLpro Substrate Degradome. Pablos et al.

description: This data comprises all the supplementary tables from the paper published in Cell Reports titled: "Mechanistic Insights into COVID-19 by Global Analysis of the SARS-CoV-2 3CLpro Substrate Degradome",  by Isabel Pablos, I., Machado, Y., Ramos de Jesus, H.C., Mohamud, Y., Kappelhoff, R., Lindskog, C., Vlok, M., Bell, P.A., Butler, G.S., Grin, P.M., Cao, Q.T., Nguyen, J.P., Solis, N., Abbina, S., Rut, W., Vederas, J.C., Szekely, L., Szakos, A., Drag, M., Kizhakkedathu, J.N., Mossman, K., Hirota, J.A., Jan, E., Luo, H., Banerjee, A., Overall, C.M.

Each table contains a legend and a brief experimental explanation of the proteomics and bioinformatics methods used to generate the data published in the Cell Reports paper.

In this paper, Pablos et al delineate the human protein substrate landscape of SARS-CoV-2 main protease, 3CLpro, by TAILS substrate-targeted N-terminomics. We identify >100 substrates in human lung and kidney cells supported by analyses of SARS-CoV-2-infected cells. Enzyme kinetics and molecular docking simulations of 3CLpro engaging substrates reveal how noncanonical cleavage sites, which diverge from SARS-CoV, guide substrate specificity. Cleaving the interactors of essential effector proteins, effectively stranding them from their binding partners, amplifies the consequences of proteolysis. We show that 3CLpro targets the Hippo pathway, including inactivation of MAP4K5, and key effectors of transcription, mRNA processing, and translation. We demonstrate that Spike glycoprotein directly binds galectin-8, with galectin-8 cleavage disengaging CALCOCO2/NDP52 to decouple antiviral autophagy. Indeed, in post-mortem COVID-19 lung samples, NDP52 rarely colocalizes with galectin-8, unlike healthy lung cells. The 3CLpro substrate degradome establishes a foundational substrate atlas to accelerate exploration of SARS-CoV-2 pathology and drug design.

TAILS and MS/MS
To induce interferon-stimulated gene proteins that may be 3CLpro substrates, HEK-293 and BEAS-2B cells were cultured in DMEM/F12 with 10% (v/v) FBS. BEAS-2B cells were treated with 10,000 U/ml carrier-free IFN-α2a or IFN-β1a or medium (control) for 18 h. Cells were harvested, and lysates were prepared under native conditions taking the necessary steps to reduce any cellular proteolytic activity. All steps were performed on ice. Protease inhibitor cocktail and 5 mM N-ethylmaleimide were added to the cell pellet in hypotonic lysis buffer and cells then pushed through a 27-gauge needle for 10 cycles and rested on ice for 1 h with agitations every 10 min. Cell lysates were flash-frozen in liquid N2 and stored at –80°C.

3CLpro or inactive 3CLpro-C145A (control) at 2.5 µM were incubated with 500 µg native cell protein, 37°C for 18 h (see paper: Figure 1A, panel a). The incubated samples were then analyzed by Terminal Amine Isotopic Labeling of Substrates (TAILS) and preTAILS shotgun proteomics (see paper: Figure 1 and Methods) using a modified protocol from (Kleifeld et al., 2011).
DOI: 10.17632/53v5twv757.1
title: Pre-fire climate and snow drought explain most of western U.S. burned area variability

description: Data presented in the manuscript: "Pre-fire climate and snow drought explain most of western U.S. burned area variability" by Abolafia-Rosenzweig, R., He, C., and Chen, F. Details are provided in README.docx. 

Corresponding author: Ronnie Abolafia-Rosenzweig (abolafia@ucar.edu)
DOI: 10.17632/wwyz67nz3h.1
title: Protective potential from Shorea roxburghii against CYP-induced urotoxicity

description: Raw data for the analysis of biochemical parameters for the blood and bladder tissues
DOI: 10.17632/mf5f93t3kn.1
title: Measuring the metabolic evolution of glioblastoma throughout tumor development, regression, and recurrence with hyperpolarized magnetic resonance- Salzillo et al

description: Rapid diagnosis and therapeutic monitoring of aggressive diseases such as glioblastoma can improve patient survival by providing physicians the time to optimally deliver treatment. This research tested whether metabolic imaging with hyperpolarized MRI could detect changes in tumor progression faster than conventional anatomic MRI in patient-derived glioblastoma murine models. To capture the dynamic nature of cancer metabolism, hyperpolarized MRI, NMR spectroscopy, and immunohistochemistry were performed at several time-points during tumor development, regression, and recurrence. Hyperpolarized MRI detected significant changes of metabolism throughout tumor progression whereas conventional MRI was less sensitive. This was accompanied by aberrations in amino acid and phospholipid lipid metabolism and MCT1 expression. Hyperpolarized MRI can help address clinical challenges such as identifying malignant disease prior to aggressive growth, differentiating pseudoprogression from true progression, and predicting relapse. The individual evolution of these metabolic assays as well as their correlations with one another provides context for further academic research.
DOI: 10.17632/4ztpjhtznm.1
title: Raw Experimental Data (Fiber-reinforced Cemented Paste Backfill)

description: In this database, the authors shared the raw experimental data associated with the article: Effect of curing temperature on time-dependent shear behavior and properties of polypropylene fiber-reinforced cemented paste backfill.
DOI: 10.17632/dmw9vfgyng.1
title: Nasal Carriage of Methicillin Resistant Staphylococcus aureus in Children Living with HIV Attending Infectious Diseases Clinics in Kano

description: This dataset contains socio-demographic and clinical characteristics of Children Living With HIV (CLWH), their nasal S. aureus carriage status, antimicrobial susceptibility of S. aureus isolates obtained from the children and presence of the mecA gene in S. aureus isolates.
We estimated the nasal colonization with S. aureus and MRSA in CLWH in Kano State, Nigeria and determined associated factors through a cross-sectional study in the infectious diseases’ clinics of two public hospitals in Kano involving 214 CLWH/caregiver pairs. We selected children from clinic registers by simple random sampling. We used an interviewer-administered questionnaire to elicit factors associated with MRSA carriage from the caregivers. Clinical records were reviewed for patients’ medical history. We used standard antimicrobial techniques to isolate S. aureus from nasal swabs taken from CLWH. MRSA was detected using the cefoxitin disc diffusion method and simple PCR for mecA gene detection. We estimated the prevalence of S. aureus and MRSA carriage in the CLWH and calculated adjusted odds ratios (aOR) for factors associated with MRSA.
Nasal S. aureus carriage in the CLWH was 18.7% (40/214). Cefoxitin disc diffusion revealed 6/214 (2.8%) of CLWH were MRSA carriers, while simple PCR revealed that 9/214 (4.2%) of CLWH were MRSA carriers. Recent hospitalization (aOR: 61.04; 95% CI: 9.01-413.38)) and recent antibiotic therapy (aOR: 7.52; 95% CI: 1.07-52.95) were independent risk factors for MRSA colonization. 
There was MRSA nasal colonization among CLWH in Kano. The hospitals’ Infection Prevention and Control units should institute measures and educate CLWH and their caregivers to reduce MRSA spread.
DOI: 10.17632/6krfj675cs.2
title: Analysis of parasitic motion with the constraint embedded Jacobian for a 3-PRS parallel manipulator

description: This study derives the equation of parasitic motion of 3-DoFs parallel manipulator from the velocity-level analytic-constraint equation and compares it with a well-known position-level geometric method. The velocity-level constraint is formulated based on the extended Jacobian, derived from the instantaneous motion space (IMS) and the instantaneous restriction space (IRS) for free motion and constraint. In contrast, the position-level constraint, adopted in previous studies, is geometrically obtained by analyzing the moving platform and limb motions. The velocity-level analytic-constraint matrix is used to further analyze the task-space motion. In this paper, the procedure of detecting and identifying the parasitic terms from the independent terms is introduced utilizing the property that comes from the virtue of analytic constraint and inverse rate kinematics algorithm. Then, an equation for the constraint-compatible task motion and a coupling relation between the parasitic and independent motions are derived during further analysis. The paper derived the parasitic motion from position constraint, and an algebraic equivalency with the velocity constraint is shown by taking the time derivative of a point-plane position level constraint for comparison. Finally, numerical simulations are provided to validate the proposed approach and demonstrate the effect of the constraints on the given input velocity within the entire rotational workspace.
DOI: 10.17632/3y3m8btcnk.2
title: Effective chimeric antigen receptor T-cells (CAR-Ts) against SARS-CoV-2

description: Raw data related to this paper
DOI: 10.17632/h9n69648d9.1
title: Clean Energy Related Literature Data

description: Files attached here are 2191 clean energy related literature data retrieved from Web of Science Core Database.
DOI: 10.17632/z42m3kkvt4.1
title: Polarized Dishevelled dissolution and reassembly drives embryonic axis specification in sea star oocytes

description: Raw data associated with the publication: 
Polarized Dishevelled dissolution and reassembly drives embryonic axis specification in sea star oocytes
DOI: 10.17632/tcs9wmdht7.4
title: Postmortem investigation of Onnagawa shale by X-ray computed tomography

description: These data were collected by deforming a sample in a high-pressure gas rig and performing a post mortem analysis in a commercially available X-ray CT scanner. An overview of the data is provided in the Repository Overview.pdf file.
DOI: 10.17632/nhv5ztsznf.1
title: Stimulation of the ventral tegmental area induces visual cortical plasticity at the neuronal level

description: fMRI studies have shown that pairing of a task-irrelevant visual feature with electrical micro-stimulation of the ventral tegmentum area (VTA-EM) is sufficient to increase the sensory cortical representation of the paired feature and to improve perceptual performance. However, since fMRI provides an indirect measure of neural activity, the neural response changes underlying the fMRI activations are unknown. Therefore, we paired a task-irrelevant grating orientation with VTA-EM while attention was directed to a difficult orthogonal task. Meanwhile, we examined the changes in neural response properties in macaques by recording spiking activity in the posterior inferior temporal cortex, the locus of fMRI-defined plasticity in previous studies. We observed a relative increase in mean spike rate and preference for the VTA-EM paired orientation compared to unpaired orientation, which was unrelated to attention. These results demonstrate that VTA-EM–stimulus pairing is sufficient to induce sensory cortical plasticity at the spiking level in nonhuman primates.
DOI: 10.5519/qd.215rg97u
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (6320 records)
DOI: 10.18746/bmth.data.00000191
title: Age-related differences in visual encoding and response strategies contribute to spatial memory deficits
DOI: 10.48370/ofd/whsucy/eeuqa3
title: HMW_Poa_trivialis_L._H_5359.jpg

description: :unav
DOI: 10.48370/ofd/whsucy
title: Wiechlina zwyczajna (Poa trivialis L.), 5359

description: Herbarium
DOI: 10.48370/ofd/lta1ny/n2tnvg
title: HMW_Poa_trivialis_L._H_5323.jpg

description: :unav
DOI: 10.48370/ofd/lta1ny
title: Wiechlina zwyczajna (Poa trivialis L.), 5323

description: Herbarium
DOI: 10.48370/ofd/qrbpid/83aire
title: HMW_Poa_trivialis_L._H_2897.jpg

description: :unav
DOI: 10.48370/ofd/qrbpid
title: Wiechlina zwyczajna (Poa trivialis L.), 2897

description: Herbarium
DOI: 10.48370/ofd/5uvogs/yg7fmd
title: HMW_Poa_trivialis_L._H_4439.jpg

description: :unav
DOI: 10.48370/ofd/5uvogs
title: Wiechlina zwyczajna (Poa trivialis L.), 4439

description: Herbarium
DOI: 10.48370/ofd/wqvipd/fhjqjf
title: HMW_Poa_trivialis_L._H_2896.jpg

description: :unav
DOI: 10.48370/ofd/wqvipd
title: Wiechlina zwyczajna (Poa trivialis L.), 2896

description: Herbarium
DOI: 10.48370/ofd/zgxcy1/rdrp5k
title: HMW_Poa_trivialis_L._H_1917.jpg

description: :unav
DOI: 10.48370/ofd/zgxcy1
title: Wiechlina zwyczajna (Poa trivialis L.), 1917

description: Herbarium
DOI: 10.6084/m9.figshare.16772146.v1
title: Effect of urban heat islands and noise on working communities in Cairo, Egypt

description: Worker satisfaction and worker physical and mental well-being when working outside have increased research interest in urban design and the provision of decent work. For decades, urban heat islands (UHI), which are urban areas that are significantly warmer than their surroundings due to human activities, and sound pressure levels have been found to be the most pressing worker challenges. The UN’s Sustainable Development Goals (SDGs), SDG 8, aims to achieve ‘full and productive employment and decent work for all women and men by 2030’. However, the main problem has been that little urban research has paid any attention to this specific goal. Therefore, this study had two main aims. First, a model was developed that could assist urban planners ensure decent work conditions in outside urban spaces. Second, this study investigated safe and convenient working methods that could improve worker productivity in arid regions. Specifically, based on a case study in Cairo, Egypt, the UHI and noise level tolerances were examined to determine the levels needed to ensure outside worker well-being and productivity, and an observation study was conducted that gathered data on worker conditions in situ. It was found that the heat and noise conditions were not suitable to productive work and that the most significant factors affecting outdoor worker productivity and satisfaction were the environmental conditions. This study can inform urban design and town planning policies on the need to consider outdoor worker conditions, especially in arid areas.
DOI: 10.6084/m9.figshare.16772146
title: Effect of urban heat islands and noise on working communities in Cairo, Egypt

description: Worker satisfaction and worker physical and mental well-being when working outside have increased research interest in urban design and the provision of decent work. For decades, urban heat islands (UHI), which are urban areas that are significantly warmer than their surroundings due to human activities, and sound pressure levels have been found to be the most pressing worker challenges. The UN’s Sustainable Development Goals (SDGs), SDG 8, aims to achieve ‘full and productive employment and decent work for all women and men by 2030’. However, the main problem has been that little urban research has paid any attention to this specific goal. Therefore, this study had two main aims. First, a model was developed that could assist urban planners ensure decent work conditions in outside urban spaces. Second, this study investigated safe and convenient working methods that could improve worker productivity in arid regions. Specifically, based on a case study in Cairo, Egypt, the UHI and noise level tolerances were examined to determine the levels needed to ensure outside worker well-being and productivity, and an observation study was conducted that gathered data on worker conditions in situ. It was found that the heat and noise conditions were not suitable to productive work and that the most significant factors affecting outdoor worker productivity and satisfaction were the environmental conditions. This study can inform urban design and town planning policies on the need to consider outdoor worker conditions, especially in arid areas.
DOI: 10.48370/ofd/jwq1ss/pzixf8
title: HMW_Polygala_amara_L._H_1804.jpg

description: :unav
DOI: 10.48370/ofd/jwq1ss
title: Lophodermium arundinaceum (Schrad.) Schevall, 1804

description: Fungarium Mikromycetes
DOI: 10.48370/ofd/xdo7fr/5u48mb
title: HMW_Polygala_amara_L._H_1804.jpg

description: :unav
DOI: 10.48370/ofd/xdo7fr
title: Krzyżownica gorzka (Polygala amara L.), 1804

description: Herbarium
DOI: 10.18746/bmth.data.00000192
title: Age-related changes in visual encoding strategy preferences during a spatial memory task
DOI: 10.48370/ofd/rdtkae/042dis
title: HMW_Polygala_amara_L._H_1537.jpg

description: :unav
DOI: 10.48370/ofd/rdtkae
title: Krzyżownica gorzka (Polygala amara L.), 1537

description: Herbarium
DOI: 10.5281/zenodo.5549964
title: duncanobrien/open-datasets: open-datasets-v1.0

description: First release for published data generated by Duncan O'Brien and collaborators. Uploads date from O'Brien <em>et al.</em> (2020) to O'Brien <em>et al.</em> (2021). The aim is to support data transparency and facilitate accessibility for current and future collaborators.
DOI: 10.5281/zenodo.5549963
title: duncanobrien/open-datasets: open-datasets-v1.0

description: First release for published data generated by Duncan O'Brien and collaborators. Uploads date from O'Brien <em>et al.</em> (2020) to O'Brien <em>et al.</em> (2021). The aim is to support data transparency and facilitate accessibility for current and future collaborators.
DOI: 10.5281/zenodo.5555758
title: Vegetation Stratum Occupancy Prediction from Airborne LiDAR 3D Point Clouds

description: Our proposed dataset comprises 199 cylindrical plots of 10 m radius corresponding to typical pasture land parcels in South-Eastern France. Each plot contains between 3000 and 17000 3D points, and each point is attributed with a total of 10 features: (i) absolute 3D coordinates, (ii) RGB and Near-InfraRed reflectance obtained with aerial cameras, (iii) uncalibrated laser intensity, return number and number of returns provided by the aerial LiDAR. This dataset can be used as training data for our model deep learning model "Vegetation Stratum Occupancy Prediction from Airborne LiDAR 3D Point Clouds" available on https://github.com/ekalinicheva/plot_vegetation_coverage
DOI: 10.5281/zenodo.5555757
title: Vegetation Stratum Occupancy Prediction from Airborne LiDAR 3D Point Clouds

description: Our proposed dataset comprises 199 cylindrical plots of 10 m radius corresponding to typical pasture land parcels in South-Eastern France. Each plot contains between 3000 and 17000 3D points, and each point is attributed with a total of 10 features: (i) absolute 3D coordinates, (ii) RGB and Near-InfraRed reflectance obtained with aerial cameras, (iii) uncalibrated laser intensity, return number and number of returns provided by the aerial LiDAR. This dataset can be used as training data for our model deep learning model "Vegetation Stratum Occupancy Prediction from Airborne LiDAR 3D Point Clouds" available on https://github.com/ekalinicheva/plot_vegetation_coverage
DOI: 10.48370/ofd/lqurvw/eogmky
title: HMW_Polygala_amarella_Crantz_H_06844.jpg

description: :unav
DOI: 10.48370/ofd/lqurvw
title: Krzyżownica gorzkawa (Polygala amarella Crantz), 6844

description: Herbarium
DOI: 10.15468/m59n9y
title: Ditiola haasii (Basidiomycota, Dacrymycetaceae) - taxonomy and ecology of a rare species from Central Europe

description: This dataset contains the digitized treatments in Plazi based on the original journal article Zamora, Juan Carlos, Holec, Jan (2021): Ditiola haasii (Basidiomycota, Dacrymycetaceae) - taxonomy and ecology of a rare species from Central Europe. Phytotaxa 522 (2): 121-130, DOI: 10.11646/phytotaxa.522.2.4