cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12928757
title: Example Questionnaire Data

description: .csv file of climate change perception data. Note this data is made up as an example for survey analysis so should not be used for any other purposes. <br>For R code for analysis see:<br>For example write-up of this data see:https://figshare.com/account/projects/88601/articles/12928067<br>
DOI: 10.15468/rjhe9j
title: First record of Dosima fascicularis (Ellis & Solander, 1786) (Crustacea, Cirripedia) from Algerian waters (Western Mediterranean)

description: This dataset contains the digitized treatments in Plazi based on the original journal article Mokrane, Z., Belkacem, Y., Soumani, K. (2019): First record of Dosima fascicularis (Ellis & Solander, 1786) (Crustacea, Cirripedia) from Algerian waters (Western Mediterranean). Zootaxa 4559 (3): 577-580, DOI: https://doi.org/10.11646/zootaxa.4559.3.9
DOI: 10.15468/c8mpkt
title: The type specimens of Papilionoidea in the collection of the National Museum of Natural History, Sofia (Lepidoptera)

description: This dataset contains the digitized treatments in Plazi based on the original journal article Abadjiev, Stanislav, Langourov, Mario (2020): The type specimens of Papilionoidea in the collection of the National Museum of Natural History, Sofia (Lepidoptera). Zootaxa 4790 (3): 473-490, DOI: https://doi.org/10.11646/zootaxa.4790.3.3
DOI: 10.6084/m9.figshare.12928892
title: Supplementary Material for: How Does Behavioural Activation Work? A Systematic Review of the Evidence on Potential Mediators

description: <b><i>Introduction:</i></b> Behavioural activation is an effective treatment for depression, but little is known about its working mechanisms. Theoretically, its effect is thought to rely on an interplay between activation and environmental reward. <b><i>Objective:</i></b> The present systematic review examines the mediators of behavioural activation for depression. <b><i>Methods:</i></b> A systematic literature search without time restrictions in Medline, EMBASE, PsycINFO, The Cochrane Library, and CINAHL resulted in 14 relevant controlled and uncontrolled prospective treatment studies that also performed formal mediation analyses to investigate their working mechanisms. After categorising the mediators investigated, we systematically compared the studies’ methodological quality and performed a narrative synthesis of the findings. <b><i>Results:</i></b> Most studies focused on activation or environmental reward, with 21 different mediators being investigated using questionnaires that focused on psychological processes or beliefs. The evidence for both activation and environmental reward as mediators was weak. <b><i>Conclusions:</i></b> Non-significant results, poor methodological quality of some of the studies, and differences in questionnaires employed precluded any firm conclusions as to the significance of any of the mediators. Future research should exploit knowledge from fundamental research, such as reward motivation from neurobiology. Furthermore, the use of experience sampling methods and idiographic analyses in bigger samples is recommended to investigate potential causal pathways in individual patients.
DOI: 10.6084/m9.figshare.12928892.v1
title: Supplementary Material for: How Does Behavioural Activation Work? A Systematic Review of the Evidence on Potential Mediators

description: <b><i>Introduction:</i></b> Behavioural activation is an effective treatment for depression, but little is known about its working mechanisms. Theoretically, its effect is thought to rely on an interplay between activation and environmental reward. <b><i>Objective:</i></b> The present systematic review examines the mediators of behavioural activation for depression. <b><i>Methods:</i></b> A systematic literature search without time restrictions in Medline, EMBASE, PsycINFO, The Cochrane Library, and CINAHL resulted in 14 relevant controlled and uncontrolled prospective treatment studies that also performed formal mediation analyses to investigate their working mechanisms. After categorising the mediators investigated, we systematically compared the studies’ methodological quality and performed a narrative synthesis of the findings. <b><i>Results:</i></b> Most studies focused on activation or environmental reward, with 21 different mediators being investigated using questionnaires that focused on psychological processes or beliefs. The evidence for both activation and environmental reward as mediators was weak. <b><i>Conclusions:</i></b> Non-significant results, poor methodological quality of some of the studies, and differences in questionnaires employed precluded any firm conclusions as to the significance of any of the mediators. Future research should exploit knowledge from fundamental research, such as reward motivation from neurobiology. Furthermore, the use of experience sampling methods and idiographic analyses in bigger samples is recommended to investigate potential causal pathways in individual patients.
DOI: 10.6084/m9.figshare.12925325.v1
title: R0197_20171119a_videos

description: Rat 0197, skilled reaching data collected in Leventhal laboratory by Alexandra Bova
DOI: 10.5281/zenodo.4018856
title: Genomic Evidence for a Case of Reinfection with SARS-CoV-2

description: Tillett, Richard and Sevinsky, Joel and Hartley, Paul and Kerwin, Heather and Crawford, Natalie and Gorzalski, Andrew and Laverdure, Christopher and Verma, Subhash and Rossetto, Cyprian and Jackson, David and Farrell, Megan and Van Hooser, Stephanie and Pandori, Mark, Genomic Evidence for a Case of Reinfection with SARS-CoV-2 (August 25, 2020). Available at SSRN: https://ssrn.com/abstract=3680955 or http://dx.doi.org/10.2139/ssrn.3680955
DOI: 10.5281/zenodo.4019342
title: Inference of the worldwide invasion routes of the pinewood nematode: Datasets, STRUCTURE outputs, ABC configuration files

description: This data archive is associated with the article “Inference of the worldwide invasion routes of the pinewood nematode <em>Bursaphelenchus xylophilus</em> using approximate Bayesian computation analysis”. Authors: Sophie Mallez, Chantal Castagnone, Eric Lombaert, Philippe Castagnone-Sereno & Thomas Guillemaud. The zip files contains the microsatellite dataset, the parameter files and scripts for simulating and summarizing datasets, the ABC reference tables, and the R scripts for analyzing the data. See the Readme file for details.
DOI: 10.6084/m9.figshare.12837797
title: Final data to upload.zip

description: Data that accompany the manuscript titled: Weed-suppressive bacteria effects differ in culture compared to in soils and with or without microbial competition and separation of active ingredient<br>
DOI: 10.6084/m9.figshare.12837797.v1
title: Final data to upload.zip

description: Data that accompany the manuscript titled: Weed-suppressive bacteria effects differ in culture compared to in soils and with or without microbial competition and separation of active ingredient<br>
DOI: 10.34740/kaggle/dsv/1473138
title: YouTube Trending Video Dataset (updated daily)
DOI: 10.21223/nbw7x3/c7ujpi
title: 12136_Data_dictionary.xlsx
DOI: 10.21223/nbw7x3/dlupxb
title: Summary.xlsx

description: :unav
DOI: 10.21223/nbw7x3/egjsay
title: 12136_PTYield072018_UNINAIROBI_exp2.tab
DOI: 10.21223/nbw7x3/lar616
title: 12136_PTYield062018_UNINAIROBI_exp1.tab
DOI: 10.21223/nbw7x3/4gciga
title: 12136_UniqueIdentifier.tab
DOI: 10.21223/nbw7x3/gd0ipu
title: caf1cc988f3c58c6cb1af73bed6ca249.xlsx
DOI: 10.21223/nbw7x3/y0pyzf
title: 12136_PTYield062018_UNINAIROBI_exp1.tab
DOI: 10.21223/nbw7x3/1gydzv
title: 12136_UniqueIdentifier.tab
DOI: 10.21223/nbw7x3
title: Dataset for: Assessment of at least 42 clones sub-Saharan Africa crosses in two locations for high yielding under late blight and virus disease pressure in Kenya

description: Evaluation of yield under late blight and viral disease presence, in Kenya. In the first experiment, 16 clones were evaluated under RCBD with 3 repetitions. In the second experiment, 32 clones were evaluated in RCBD with 3 reps. Both trials were established at University of Nairobi, Kabete Campus, Nairobi-Kenya (1800 m a.s.l.). All late blight evaluations were performed 30, 40, 50, 60, 70, 80 and 90 days after planting. The plots were set with a distance of 0.75 m between rows and 0.20 m plants
DOI: 10.6084/m9.figshare.12928181
title: R0218_20180203a_videos

description: Rat 0218, skilled reaching data collected in Leventhal laboratory by Alexandra Bova
DOI: 10.6084/m9.figshare.12855563
title: IN_mW_Aug2020.csv

description: Dataset for the manuscript "Predicting Heterogeneous Ice Nucleation With a Data-Driven Approach" (DOI: 10.1038/s41467-020-18605-3)
DOI: 10.5281/zenodo.4019087
title: A2aR Oligomeric assemblies identified from MD simulations using in-vivo mimetic biomembranes

description: GPCR oligomerisation is known to play an important role in the receptor signalling. However, due to the technical challenges, the structural information of GPCR oligomerisation is still very limited, which hinders our understanding of GPCR signalling in a fuller picture. In this deposit, we provide the structural coordinates of various oligomeric assemblies of Adenosine A2a receptor that were sampled from unbiased MD simulations. For more information regarding the MD simulations and the findings on A2aR oligomerization, please refer to our paper on BioRxiv: https://www.biorxiv.org/content/10.1101/2020.06.24.168260v1 <em>** Simulation setup **</em><br> 9 copies of A2aR were randomly inserted into an in-vivo mimetic biomembrane to build the initial configuration of the simulations. 10 such systems were setup for A2aR in the inactive state and 10 for the active state. The systems were represented by MARTINI 2 coarse-grained model and simulated for 50 micro-seconds. Protein-protein associations were identified when any atoms from two protomers were getting closer than 0.75 nm. The oligomerisation process was monitored and the sampled oligomeric assemblies were stored. <em>** Coordinate file explained **</em><br> The coarse-grained oligomeric structures were converted back to atomistic model in CHARMM force field. Oligomeric assemblies of the same oligomeric state (OS) were clustered to identify the different arrangements. 100 oligomeric arrangements (or all of the sampled oligomers if the cluster contains less than 100 samples) were randomly taken from each cluster and stored as seperate models in a pdb coordinate file. The pdb coordinate files were named as {Conf. State}_OS{Oligomeric State}_cl{Cluster id}.pdb, and can be viewed by such visualization tools as PyMol, Chimera or JMol etc. A Excel file containing some statistics of the oligomeric assemblies were also provided.
description: {"references": ["Song et al (2020) GPCR Oligomerisation Modulation by Conformational State and Lipid Interactions Revealed by MD Simulations and Markov Models; bioRxiv 2020.06.24.168260; doi: https://doi.org/10.1101/2020.06.24.168260"]}
DOI: 10.21223/qawear
title: The “Stage Selection Gain 1to3” (SSG1to3) - R script

description: The “Stage Selection Gain 1to3” (SSG1to3) in R (SSG1to3_R) or SAS (SSG1to3_SAS) is a simple program to determine the response to selection in standardized units (R) after 1-stage selection with up to three seasons of testing, 2-stage selection with two seasons of testing, and 3-stage selection with three seasons of testing. The required input SSG1to3_R and SSG1to3_SAS is identical and comprising a vector of 17 numbers; note in SSG1to3_R these numbers must be separated by a “,”
DOI: 10.25829/idiv.1841-22-3097
title: A spatially-explicit, 250m resolution composite dataset on primary forests in Europe, their protection gaps and restoration opportunities

description: A set of raster files on the estimated distribution of primary forests in Europe, their likelihood of occurrence, gaps in protections and restoration opportunities across forest types
DOI: 10.5281/zenodo.4019367
title: A2aR Oligomeric assemblies identified from MD simulations using in-vivo mimetic biomembranes

description: GPCR oligomerisation is known to play an important role in the receptor signalling. However, due to the technical challenges, the structural information of GPCR oligomerisation is still very limited, which hinders our understanding of GPCR signalling in a fuller picture. In this deposit, we provide the structural coordinates of various oligomeric assemblies of Adenosine A2a receptor that were sampled from unbiased MD simulations. For more information regarding the MD simulations and the findings on A2aR oligomerization, please refer to our paper on BioRxiv: https://www.biorxiv.org/content/10.1101/2020.06.24.168260v1 <em>** Simulation setup **</em><br> 9 copies of A2aR were randomly inserted into an in-vivo mimetic biomembrane to build the initial configuration of the simulations. 10 such systems were setup for A2aR in the inactive state and 10 for the active state. The systems were represented by MARTINI 2 coarse-grained model and simulated for 50 micro-seconds. Protein-protein associations were identified when any atoms from two protomers were getting closer than 0.75 nm. The oligomerisation process was monitored and the sampled oligomeric assemblies were stored. <em>** Coordinate file explained **</em><br> The coarse-grained oligomeric structures were converted back to atomistic model in CHARMM force field. Oligomeric assemblies of the same oligomeric state (OS) were clustered to identify the different arrangements. 100 oligomeric arrangements (or all of the sampled oligomers if the cluster contains less than 100 samples) were randomly taken from each cluster and stored as seperate models in a pdb coordinate file. The pdb coordinate files were named as {Conf. State}_OS{Oligomeric State}_cl{Cluster id}.pdb, and can be viewed by such visualization tools as PyMol, Chimera or JMol etc. A Excel file containing some statistics of the oligomeric assemblies were also provided.
description: {"references": ["Song et al (2020) GPCR Oligomerisation Modulation by Conformational State and Lipid Interactions Revealed by MD Simulations and Markov Models; bioRxiv 2020.06.24.168260; doi: https://doi.org/10.1101/2020.06.24.168260"]}
DOI: 10.6084/m9.figshare.5286019
title: SQLite database with MGI mouse gene annotations from Mouse Genome Informatics (MGI) at The Jackson Laboratory

description: A SQLite database with two tables: "description" and "genes". The description table includes the URL for the source file. The "genes" table contains the data, with 14 fields including chr (1-19, X, Y, MT), start and stop (in basepairs, GRCm38/mm10 build), source, strand, Name, and type.<br>This is like mouse_genes.sqlite, but just with the records with source=="MGI" and taking just one of each of the duplicate records for a gene.
DOI: 10.21223/5sbctt/fic2g6
title: Genetic_designs.docx
DOI: 10.21223/5sbctt
title: Genetic Designs in HIDAP

description: Database of accurate phenotypic values for main constraints, quality and adaptive traits (viruses, late blight, drought, crop duration) available for promising materials and widely grown varieties. The Automatic reports for the following genetic designs implemented: Line x Tester genetic design and North Carolina I, II and III genetic design. Reports include an analysis of variance and related quantities. The reports are generated in html, word and pdf format. Besides, they can be generated through the HIDAP (Highly Interactive Data Analysis Platform) software available at https://research.cip.cgiar.org/gtdms/hidap/. Source code is available in the GitHub repository https://github.com/reyzaguirre/pepa.
DOI: 10.6084/m9.figshare.12929075
title: Pneumonia_bbl_cmb.xls

description: covid cases
DOI: 10.6084/m9.figshare.5280238
title: SQLite database with mouse gene annotations from Mouse Genome Informatics (MGI) at The Jackson Laboratory

description: A SQLite database with two tables: "description" and "genes". The description table includes the URL for the source file. The "genes" table contains the data, with 15 fields including chr (1-19, X, Y, MT), start and stop (in basepairs, GRCm38/mm10 build), source, strand, Name, and type.
DOI: 10.21223/h3fe8w/fkrxhr
title: VirusDetectWin.zip

description: :unav
DOI: 10.21223/h3fe8w
title: VirusDetect for Windows

description: VirusDetect is a software package that can efficiently and exhaustively analyze large-scale sRNA datasets for virus identification. The program performs reference-guided assembly by aligning sRNA reads to the known virus reference database (GenBank gbvrl) as well as de novo assembly using Velvet with automated parameter optimization. The assembled contigs are compared to the reference virus sequences for virus identification. The contigs were treated as undetermined contigs if they are not hit to any known viruses. The siRNA profile of these undetermined contigs are provided as guidance to discovery novel viruses which do not show sequence similarity with known viruses.
DOI: 10.5517/ccdc.csd.cc14lgfm
title: CCDC 1060430: Experimental Crystal Structure Determination

description: Related Article: You-Zhu Yu, Yue-Qiao Hu, Yu-Hua Guo, Yong-Sheng Niu, Li-Guo Yang, Hai-Xiang Song, Yan-Hong Shen, Xiao-Ming Zheng, Shao-Gang Hou, Guo-Dong Feng|2018|Dalton Trans.|47|10124|doi:10.1039/C8DT01252K
description: Related Article: Youzhu Yu|2017|CSD Communication|||
DOI: 10.5517/ccdc.csd.cc1q1mw8
title: CSD 1580500: Experimental Crystal Structure Determination

description: Related Article: Yangwu Guo, Fei Liang, Molin Zhou, Zheshuai Lin, Jiyong Yao, Yicheng Wu|2018|J.Alloys Compd.|762|143|doi:10.1016/j.jallcom.2018.05.212
DOI: 10.5517/ccdc.csd.cc1q1mx9
title: CSD 1580501: Experimental Crystal Structure Determination

description: Related Article: Yangwu Guo, Fei Liang, Molin Zhou, Zheshuai Lin, Jiyong Yao, Yicheng Wu|2018|J.Alloys Compd.|762|143|doi:10.1016/j.jallcom.2018.05.212
DOI: 10.5517/ccdc.csd.cc1q2x1r
title: CCDC 1581714: Experimental Crystal Structure Determination

description: Related Article: Xiaoyan Zou, Yanping Dong, Fengming Zhang, Guangming Li|2018|Inorg.Chim.Acta|473|37|doi:10.1016/j.ica.2017.12.021
DOI: 10.5517/ccdc.csd.cc1q2wm9
title: CCDC 1581701: Experimental Crystal Structure Determination

description: Related Article: Xiaoyan Zou, Yanping Dong, Fengming Zhang, Guangming Li|2018|Inorg.Chim.Acta|473|37|doi:10.1016/j.ica.2017.12.021
DOI: 10.21223/evszem/5zp6zm
title: R tools using the brapi package.docx

description: :unav
DOI: 10.21223/evszem
title: R tools using the brapi package

description: The Highly Interactive Data Analysis Platform (HiDAP) supports clonal crop breeders at the International Potato Center. BrAPI allows data to be extracted from SweetPotato Base, and into to HiDAP. (https://apps.cipotato.org/hidap_sbase/). A prototype of HiDAP-SweetPotato Base was developed. It not only extracts data from SweetPotatoBase (https://sweetpotatobase.org/) to HiDAP but allows the insertion of data into the database from HiDAP. The R-BrAPI package is available on the following link: https://github.com/CIP-RIU/brapi, it uses the Breeding API (BrAPI) to access plant breeding data. The next steps are to develop BRAPI functionalities for Roots&Tubers Base (BioMart) and specially for CIP’s potato database to connect with other tools and database to take hold of the momentum with the COPs. This implementation plays a crucial role to position CIP informatics tools at the top of CGIAR Centers and partners.
DOI: 10.21223/jb4uku/igvgfn
title: a92aa4965320657affda6da14f89c438.docx
DOI: 10.21223/jb4uku
title: Dataset for: Trait dictionary and ontology include the gender-responsive scoring methods used by the Participatory variety selection (PVS) protocol of potato and is available in the Crop-Ontology platform for use by CIP trial management system

description: The Potato ontology with PVS traits and scoring methods provide a common set of standardized variables for institutions, trainers and facilitators involved in PVS. This ontology is based on the protocol: "Participatory Varietal Selection of Potato (PVS)" developed by the International Potato Center (CIP). In this context, the ontology terms were gathered from farmers and presented: traits, descriptions, methodologies, valid ranges and scales using a standardized template (from the Crop Ontology web page: http://www.cropontology.org/). Finally, this information was curated by breeders and researchers at CIP: The PVS ontology has been integrated with the ontologies available for potato in the CO page. In total, the presented variables for PVS are 45 new variables. It includes: morphological traits (9), agronomic traits (16), biotic stress trait (9), abiotic stress traits (5) and quality traits (6).
DOI: 10.25345/c5fb4h
title: MassIVE MSV000086106 - Receptor-mediated clustering of FIP200 bypasses the role of LC3 lipidation in autophagy
title: Autophagosome formation requires multiple autophagy-related (ATG) factors. However, we find that a subset of autophagy substrates remains robustly targeted to the lysosome in the absence of several core ATGs, including the LC3 lipidation machinery. To address this unexpected result, we performed genome-wide CRISPR screens identifying genes required for NBR1 flux in ATG7KO cells. We find that ATG7-independent autophagy still requires canonical ATG factors including FIP200. However, in the absence of LC3 lipidation, additional factors are required including TAX1BP1 and TBK1. TAX1BP1's ability to cluster FIP200 around NBR1 cargo and induce local autophagosome formation enforces cargo specificity and replaces the requirement for lipidated LC3. In support of this model, we define a ubiquitin-independent mode of TAX1BP1 recruitment to NBR1 puncta, highlighting that TAX1BP1 recruitment and clustering, rather than ubiquitin binding per se, is critical for function. Collectively, our data provide a mechanistic basis for reports of selective autophagy in cells lacking the lipidation machinery, wherein receptor-mediated clustering of upstream autophagy factors drives continued autophagosome formation.
DOI: 10.6084/m9.figshare.12928181.v1
title: R0218_20180203a_videos

description: Rat 0218, skilled reaching data collected in Leventhal laboratory by Alexandra Bova
DOI: 10.7910/dvn/sahdy3/zakcsp
title: 2020PGY_CovidPovertyGenderRaceStudyDescription.pdf

description: :unav
DOI: 10.7910/dvn/sahdy3/gjph71
title: 2020PGY_CovidPovertyGenderRaceIndicatorsDatabase.tab

description: :unav
DOI: 10.7910/dvn/sahdy3/wyrcdv
title: 2020PGY_CovidPovertyGenderRaceStudyDescriptionv2.pdf

description: :unav
DOI: 10.7910/dvn/sahdy3/eamce0
title: 2020PGY_CovidPovertyGenderRaceIndicatorsDatabasev2.1.tab

description: :unav
DOI: 10.7910/dvn/sahdy3/9iliyy
title: 2020PGY_CovidPovertyGenderRaceStudyDescriptionv2.1.pdf

description: :unav
DOI: 10.5519/qd.9sb9ghgb
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (8 records)
DOI: 10.5519/qd.9j3a28a1
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (198 records)
DOI: 10.5519/qd.dehkojka
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (14 records)
DOI: 10.7284/135981
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise AT42-17 using a Hawaii UHDAS instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/135984
title: CTD (Conductivity, Temperature, Depth) data collected during research cruise AT42-17 using a Sea-Bird SBE-911+ instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/135983
title: Expendable Probe data collected during research cruise AT42-17 using a Sippican MK12 instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/135986
title: Fluorometer data collected during research cruise AT42-17 using a WET Labs WETStar instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition