cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.7517966
title: Data and Analysis from "Analysis of context-specific KRAS-effectors (sub)complexes in Caco-2 cells"

description: Data, data processing and data analysis for manuscript "Analysis of context-specific KRAS-effectors (sub)complexes in Caco-2 cells". (Preprint available here) <strong>Analysis of AP-MS data</strong>: analysis.zip Contains the following scripts as well as their outputs: 01_preparation.R R script for filtering and processing our mass spec data. 02_diffbinding.R R script for differential analysis followed by gene set enrichment. 03_funcstats.R R script for statistical analysis over different ontology terms. 04_semantic_analysis.R R script for the GO semantic analysis for the output of 02 and 03. 05_1_random_walks.py Python script for performing random walks for specific functional terms. 05_2_random_walks_analysis.R R script for the analysis and visualization of the output of 05_1. The required input data is deposited in the "data" sub-folder, taken directly from the linked PRoteomics IDEntification database (PRIDE) entry. Interactive visualization of the results of most of this analysis is available on GitHub as a Shiny app. <strong>Analysis of whole cell lysate</strong>: analysis_wholecelllysate.zip Contains the following script, as well as its output: 01_analysis.R R script for loading the data and extracting/visualizing KRAS and effector abundances. The required data is deposited in the "data" sub-folder, taken directly from the linked PRoteomics IDEntification database (PRIDE) entry.
DOI: 10.5281/zenodo.6896563
title: Data and Analysis from "Analysis of context-specific KRAS-effectors (sub)complexes in Caco-2 cells"

description: Data, data processing and data analysis for manuscript "Analysis of context-specific KRAS-effectors (sub)complexes in Caco-2 cells". (Preprint available here) <strong>Analysis of AP-MS data</strong>: analysis.zip Contains the following scripts as well as their outputs: 01_preparation.R R script for filtering and processing our mass spec data. 02_diffbinding.R R script for differential analysis followed by gene set enrichment. 03_funcstats.R R script for statistical analysis over different ontology terms. 04_semantic_analysis.R R script for the GO semantic analysis for the output of 02 and 03. 05_1_random_walks.py Python script for performing random walks for specific functional terms. 05_2_random_walks_analysis.R R script for the analysis and visualization of the output of 05_1. The required input data is deposited in the "data" sub-folder, taken directly from the linked PRoteomics IDEntification database (PRIDE) entry. Interactive visualization of the results of most of this analysis is available on GitHub as a Shiny app. <strong>Analysis of whole cell lysate</strong>: analysis_wholecelllysate.zip Contains the following script, as well as its output: 01_analysis.R R script for loading the data and extracting/visualizing KRAS and effector abundances. The required data is deposited in the "data" sub-folder, taken directly from the linked PRoteomics IDEntification database (PRIDE) entry.
DOI: 10.6084/m9.figshare.21896862
title: Technologies and Best Practices for the Protection of Cyber-Physical Spaces: a Systematic Multivocal Literature Review

description: Replication package of the Systematic Literature Review
DOI: 10.6084/m9.figshare.21896862.v1
title: Technologies and Best Practices for the Protection of Cyber-Physical Spaces: a Systematic Multivocal Literature Review

description: Replication package of the Systematic Literature Review
DOI: 10.6084/m9.figshare.21896895
title: anova

description: Phan tich phuong sai
DOI: 10.6084/m9.figshare.21700955.v1
title: Leaf age-dependent LAI seasonality product (Lad-LAI) over tropical and subtropical evergreen broadleaved forests

description: This dataset provides 0.25 degree spatial resolution leaf age-dependent LAI seasonality product (Lad-LAI) (2001-2018) over tropical and subtropical evergreen broadleaved forests (TEFs). The mapped extent is longitude (-180, 180) and latitude (-30, 30). (1) Methodology and performance The canopy leaves of TEFs were simplified into three age cohorts, i.e., young, mature and old one, with different photosynthesis capacity (maximum carboxylation rate, V<sub>cmax</sub>) to produce a grid dataset of leaf age-dependent LAI product (referred to as Lad-LAI) over the continental scale from satellite observations of TROPOMI sun-induced chlorophyll fluorescence (SIF) as a proxy of leaf photosynthesis. Validations against in situ measurements of seasonal LAI data, satellite based EVI and in situ measurements of seasonal litterfall data demonstrated the products were in high accuracy. (2) Dataset information The dataset is provided in geotif (*.tif) format with pixel values of 0-7 for LAI<sub>young</sub>, LAI<sub>mature</sub> and LAI<sub>old</sub>. Data named "LAI_young_025deg_1.tif" means leaf area index of young leaves mapped in January. <br> Any questions about the dataset can be corresponded to Xiuzhi Chen (chenxzh73@mail.sysu.edu.cn).
DOI: 10.17179/excli2022-5064/supplementary_data
title: Anti-tumor effects of low-dose metronomic vinorelbine in combination with alpelisib in breast cancer cells

description: In metastatic breast cancer (MBC), PIK3CA mutations, activating the phosphatidylinositol 3-kinase (PI3K) signaling pathway seem to be associated with chemotherapy resistance and poor outcome. Inhibition of the PI3K signaling pathway may lead to sensitization and prevention of the development of resistance to cytotoxic drugs. The present study aimed to investigate the anti-tumor activity of low-dose vinorelbine (VRL) combined with alpelisib, an α-selective PI3K inhibitor and degrader, in breast cancer (BC) cells. Human BC cell lines MCF-7, T-47D [both hormone receptor (HR)-positive, human epidermal growth factor receptor 2 (HER2)-negative, PIK3CA-mutated], MDA-MB-231 and BT-549 (both triple-negative, wild-type PIK3CA) were exposed to a combination of low-dose VRL and alpelisib for 3 and 7 days. Cell viability was detected by the Alamar blue assay, and cell proliferation was determined by the BrdU incorporation. The effect of the substances on the p110α protein expression that is encoded by PIK3CA gene was investigated by Western blot. Low-dose VRL plus alpelisib showed synergistic anti-tumor effects and significantly inhibited cell viability and proliferation of MCF-7 and T-47D cells. Even lower alpelisib concentrations (10 ng/ml and 100 ng/ml) combined with low-dose metronomic VRL led to a significant reduction of cell viability of PIK3CA-mutated cells, and the anti-tumor activity was comparable with the effects at 1000 ng/ml alpelisib. Cell viability and proliferation of MDA-MB-231 and BT-549 cells were inhibited by VRL but not by alpelisib alone. This indicates that alpelisib did not significantly affect the cell growth of triple-negative, PIK3CA wild-type BC cells. The p110α expression was downregulated or not affected in PIK3CA-mutated cell lines, and not significantly upregulated in PIK3CA wild-type cell lines. In conclusion, combination of low-dose metronomic VRL and alpelisib showed synergistic anti-tumor effects and significantly inhibited the growth of HR-positive, HER2-negative, PIK3CA-mutated BC cells, providing a rationale for further efforts to evaluate this combination in vivo.
description: EXCLI Journal; 22:Doc114; ISSN 1611-2156
DOI: 10.6084/m9.figshare.21501591.v1
title: Supplementary material for Ancient Egypt, New Technology. The Present and Future of Computer Visualization, Virtual Reality and Other Digital Humanities in Egyptology. Edited by Rita Lucarelli, Joshua Aaron Roberson, and Steve Vinson

description: This volume of collected studies takes stock of most recent developments in Egyptology and the Digital Humanities, considering future directions for the application of new technologies in Egyptology. The book presents the results of an international conference held in 2019 at Indiana University – Bloomington, in which Egyptologists and digital humanists with interest in Egyptology gathered to present current projects in 3D modeling, virtual and augmented reality, game technology, digital pedagogy, database projects, computational and corpus linguistics and E-publications. Those projects, along with a selection of others that were not presented in Bloomington, are now described and discussed in this volume.
DOI: 10.6084/m9.figshare.21501591
title: Supplementary material for Ancient Egypt, New Technology. The Present and Future of Computer Visualization, Virtual Reality and Other Digital Humanities in Egyptology. Edited by Rita Lucarelli, Joshua Aaron Roberson, and Steve Vinson

description: This volume of collected studies takes stock of most recent developments in Egyptology and the Digital Humanities, considering future directions for the application of new technologies in Egyptology. The book presents the results of an international conference held in 2019 at Indiana University – Bloomington, in which Egyptologists and digital humanists with interest in Egyptology gathered to present current projects in 3D modeling, virtual and augmented reality, game technology, digital pedagogy, database projects, computational and corpus linguistics and E-publications. Those projects, along with a selection of others that were not presented in Bloomington, are now described and discussed in this volume.
DOI: 10.25747/gv77-5k64
title: Analysis of the DigitArq archive record entities and their properties in Wikidata and in DBpedia
DOI: 10.26078/zks9-tk94
title: N-back Accuracy and Neural Activation in DLD
DOI: 10.5066/p93teqtu
title: Molecular-scale speciation of germanium and copper within sphalerite from Central Tennessee mining district (TN), Red Dog mining district (AK), and Metaline mining district (WA)

description: Oxidation state and bonding environment of Ge and Cu in ZnS and Zn mineral concentrates from a variety of sources [Central Tennessee mining district (TN), Metaline mining district, (WA), and Red Dog mine (AK)] were determined by linear combination fits from x-ray absorption spectroscopy (XAS) analysis. Sphalerites from the East Tennessee mining district contained Ge in concentrations that were too low to generate a X-ray absorption spectra with an edge step. When applicable, Ge content in quartz was determined using XAS edge steps. Data and methods reported are part of a research study published in the 'Related External Resources' section below.
DOI: 10.5066/p9ahp9bc
title: Database for the isopach map of the Brightseat Formation and Cretaceous?Paleogene boundary in Maryland and Virginia

description: The goal of the Atlantic Subsurface Stratigraphic Initiative (ASSI) is to create isopach and structural contour maps for all Coastal Plain formations within the Salisbury Embayment of Maryland and Virginia. Detailed information regarding thicknesses and extent of formations across state boundaries can then be utilized for more accurate documentation of the subaerial extent of aquifers across states. In support of this goal, lower Paleogene sediment elevation and thickness information from approximately 600+ data points from wells, cores, outcrops, and geologic maps were obtained from published and unpublished resources. Analyses started with production of a structure contour map of the unconformable contact of the Danian Brightseat Formation with underlying Cretaceous sediments, which represents the Cretaceous-Paleogene boundary in the Embayment. In addition, an isopach map of the Brightseat was produced using the Natural Neighbors interpolator in ArcGIS, creating a raster grid file that was symbolized every five feet. Results indicate a central depocenter with a thickness of 95 feet within Maryland with smaller thicknesses of the Brightseat surrounding. Although Danian sediments in southeastern Virginia were removed by the Chesapeake Bay impact event, up to 30 ft of possible Brightseat Formation has been identified from core and well data in southernmost Virginia.
DOI: 10.5281/zenodo.7534829
title: Calcareous sponges under short-term ocean acidification

description: Images and measurements of <em>Paraleucilla magna</em> individuals developed from primmorphs (<em>i</em>.<em>e</em>. sponge cell aggregates) under ocean acidification conditions.
DOI: 10.5281/zenodo.7534828
title: Calcareous sponges under short-term ocean acidification

description: Images and measurements of <em>Paraleucilla magna</em> individuals developed from primmorphs (<em>i</em>.<em>e</em>. sponge cell aggregates) under ocean acidification conditions.
DOI: 10.5281/zenodo.7534851
title: Quantitative Methods in Archaeology - Data

description: Data used in the practical section of Quantitative Methods in Archaeology. These are needed to follow along with the slides: https://doi.org/10.5281/zenodo.7534698 Unfortunately, the data I used in the course are assigned a license that requires me to use the same license when sharing, hence the data are in a separate repository from the slides. The data were originally obtained from the <strong>archdata</strong> R package. The data were 'messified' to teach how to clean the data in R. <strong>House Pits Missouri.csv</strong> requires manual cleaning. <strong>house_pits_cleaned.csv</strong> can be imported directly in R.
DOI: 10.5281/zenodo.7534850
title: Quantitative Methods in Archaeology - Data

description: Data used in the practical section of Quantitative Methods in Archaeology. These are needed to follow along with the slides: https://doi.org/10.5281/zenodo.7534698 Unfortunately, the data I used in the course are assigned a license that requires me to use the same license when sharing, hence the data are in a separate repository from the slides. The data were originally obtained from the <strong>archdata</strong> R package. The data were 'messified' to teach how to clean the data in R. <strong>House Pits Missouri.csv</strong> requires manual cleaning. <strong>house_pits_cleaned.csv</strong> can be imported directly in R.
DOI: 10.6084/m9.figshare.21896982
title: Segundo criterio Mariyama.

description: Frecuencias acumuladas del segundo criterio Moriyama.
DOI: 10.6084/m9.figshare.21896982.v1
title: Segundo criterio Mariyama.

description: Frecuencias acumuladas del segundo criterio Moriyama.
DOI: 10.17638/datacat.liverpool.ac.uk/1992
title: Single-Molecule Conductance Data for a set of organometallic "molecular bundles"

description: As in title. Entry contains both raw data acquired and custom software used for its processing to ASCII tables, which can then be analysed and plotted using any graphing software.
DOI: 10.5281/zenodo.7534902
title: Comparing self-report and performance measurement of wisdom in Turkish sample: Relations with self-transcendence and cognitive flexibility

description: Data set of research named: Comparing self-report and performance measurement of wisdom in Turkish sample: Relations with self-transcendence and cognitive flexibility
DOI: 10.5281/zenodo.7534901
title: Comparing self-report and performance measurement of wisdom in Turkish sample: Relations with self-transcendence and cognitive flexibility

description: Data set of research named: Comparing self-report and performance measurement of wisdom in Turkish sample: Relations with self-transcendence and cognitive flexibility
DOI: 10.5281/zenodo.7534791
title: Supplementary material to: Dengler, J., Jansen., F., … & Gillet, F. (2023) Ecological Indicator Values for Europe (EIVE) 1.0. Vegetation Classification and Survey.

description: The newly developed Ecological Indicator Values for Europe (EIVE) 1.0, together with all source systems in a flexible, harmonised open access database. <br> Supplementary material 2: The analysed 31 EIV systems with original and harmonised plant nomenclature and original and rescaled indicator values for M, N, R, L and T (*.xlsx). Supplementary material 3: Documentation of additions to and modifications of the taxonomic backbone from Euro+Med (2022) in EIVE 1.0 (*.xslx). Supplementary material 8: EIVE 1.0 indicator values for niche position and niche width of M, N, R, L and T (*.xlsx).
description: {"references": ["Dengler, J., Jansen, F., ... J.-P., Gillet, F. 2023. Ecological Indicator Values for Europe (EIVE) 1.0. Vegetation Classification and Survey 4: 7\u201329. DOI: 10.3897/VCS.98324."]}
DOI: 10.6084/m9.figshare.21896961
title: HUVEC and HAEC RNA-seq Gene Expression Values - TPMs

description: Gene expression profiling of human umbilical vein endothelial cells (UEC) and human aortic endotheilal cells (AEC). Poly-A enriched gene expression data is provided as transcripts per million (TPM), processed using the Salmon alignment tool. The experiment was carried out on 4 individual donors of each cell type. Raw data are available on request only due to ethical considerations.
DOI: 10.7303/syn50877110
title: ICI-mono vs ICI-chemo NSCLC
DOI: 10.14284/585
title: Citizen observation of local litter in coastal ecosystems: Animated standard operating procedure (video)

description: This asset concerns the simplified and animated version (*.mp4 files) of the Standard Operating Procedure (SOP) of the Citizen Observation of Local Litter in Coastal ECosysTems (COLLECT) project. COLLECT is a citizen science project from the Partnership for Observation of the Global Ocean (POGO), funded by the Richard Lounsbery Foundation.
description: This asset concerns the simplified and animated version (*.mp4 files) of the Standard Operating Procedure (SOP) of the Citizen Observation of Local Litter in Coastal ECosysTems (COLLECT) project. This SOP is for the use of school students and teachers, and citizens who wish to collect data on plastic distribution and abundance in sandy beaches. The COLLECT project aims to acquire data on the distribution and abundance of coastal debris by citizen scientists (secondary school students). The citizen science activities can be performed by students (15-18 years old) to acquire information and sample macro- (&gt; 25 mm), meso- (5 - 25 mm) and microplastics (&lt; 5 mm, sampled up to 1 mm). This animated SOP is a simplified version of an extended and technical SOP (https://dx.doi.org/10.48470/38), and is accompanied of an illustrated SOP (https://dx.doi.org/10.48470/39). The animated videos are further available on a COLLECT YouTube playlist: youtube.com/playlist?list=PL3Mh9bBxde-Xbv668RRV51xovJlgaKy9e). Videos are available in English, French, and Portuguese and subtitles are available in the referred languages, as well as in Spanish. Videos animated by Science Crunchers (www.sciencecrunchers.com). COLLECT is a citizen science project from the Partnership for Observation of the Global Ocean (POGO), funded by the Richard Lounsbery Foundation.
DOI: 10.5517/ccdc.csd.cc2c87vr
title: CCDC 2182674: Experimental Crystal Structure Determination

description: Related Article: Yüksel Şahin, Esin Poyrazoğlu Çoban, Muhittin Aygün, Resul Sevinçek, Hüseyin Özgener, Hacı Halil Bıyık, Kubilay Metin, Burçin Gürbüz|2023|J.Mol.Struct.|1277|134899|doi:10.1016/j.molstruc.2022.134899
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2c8qgv
title: CCDC 2183127: Experimental Crystal Structure Determination

description: Related Article: Ivy L. Librando, Anup Paul, Abdallah G. Mahmoud, Atash V. Gurbanov, Sónia A. C. Carabineiro, M. Fátima C. Guedes da Silva, Carlos F. G. C. Geraldes, Armando J. L. Pombeiro|2023|RSC Sustainability|1|147|doi:10.1039/D2SU00017B
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.7534934
title: Alignment used for voltage gated ion channels phylogenetic analysis

description: Alignment (performed with MAFFT) of sequences of voltage gated ion channels used to performe the phylogenetic analysis (PhyML SMS option) present in the supplementary figures.
DOI: 10.5281/zenodo.7534933
title: Alignment used for voltage gated ion channels phylogenetic analysis

description: Alignment (performed with MAFFT) of sequences of voltage gated ion channels used to performe the phylogenetic analysis (PhyML SMS option) present in the supplementary figures.
DOI: 10.5522/04/21828975
title: Raw data for eight-probe Neuropixels recordings in the mouse brain

description: This repository contains the raw data from 8-probe Neuropixels recordings in the mouse brain, as described in this paper: <br> C. Stringer, M. Pachitariu, C. Bai Reddy, M. Carandini, K. D. Harris, Spontaneous behaviors drive multidimensional, brainwide activity. Science 364, 255 (2019). https://doi.org/10.1126/science.aav7893 <br> Electrophysiological recordings were performed from each of three mice (named Krebs, Robbins, and Waksman) with eight Neuropixels 1.0 probes simultaneously. <br> This repository contains: raw electrophysiological traces in the high-frequency "AP band" raw electrophysiological traces in the low-pass filtered "LFP band"; movies of the face and of the eye; details of the visual stimuli presented to the mice; synchronization information between these datasets; output of spike sorting (these have not been manually reviewed and should be reviewed before use). For details on the experimental preparation, see the aforementioned paper (Stringer, Pachitariu, et al, <em>Science</em> 2019). <br> The traces in the "AP band" were losslessly compressed using mtscomp algorithm available here: https://github.com/int-brain-lab/mtscomp <br> For details about the behavior videos, or to download these separately, see: https://figshare.com/articles/media/Behavioral_videos_for_8-Neuropixels_recordings_from_Stringer_et_al_2019_Science/8378360 <br> For details about the LFP data, or to download it separately, see: https://figshare.com/articles/dataset/LFP_data_for_8-Neuropixels_recordings_from_Stringer_et_al_2019_Science/8784311 <br> For information about probe locations in CCF coordinates, see: https://figshare.com/articles/dataset/Eight-probe_Neuropixels_recordings_during_spontaneous_behaviors/7739750 <br> For the spiking data used in Stringer, Pachitariu, et al 2019, which are carefully curated spike sorting results from a subset of each recording (containing spontaneous activity but not visual stimulus periods), see: https://figshare.com/articles/dataset/Eight-probe_Neuropixels_recordings_during_spontaneous_behaviors/7739750 <br> <br> <br>
DOI: 10.5281/zenodo.7534942
title: alignment of potassium channels sequences

description: This aligment (MAFFT) was used to perform a phylogenetic analysis (PhyML) to determine the position of the potassium channel sequences of Oopsacas minuta.
DOI: 10.5281/zenodo.7534941
title: alignment of potassium channels sequences

description: This aligment (MAFFT) was used to perform a phylogenetic analysis (PhyML) to determine the position of the potassium channel sequences of Oopsacas minuta.
DOI: 10.25500/edata.bham.00000898
title: OPC-N3 data from EUMETNET Autopollen ADOPT - COST Action Intercomparison Campaign

description: Data collacted from monthly data files for each OPC instrument with Sensor column added; time converted to CET/CEST; particle counts converted to particle number concentrations (m-3); dataset filtered within suitable limits by LaserStat variable and excess columns from the OPC removed. More details are provided in the README file.
description: Data obtained from the SD cards in each of the 3 Alphasense OPC-N3 sensors, functionalised at the University of Birmingham, during the period they participated in the Autopollen intercomparison campaign in Munich. See paper for details.