cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.16534932.v1
title: Talon_strain.txt

description: This file provides strain data for the talon finite element analyses.
DOI: 10.6084/m9.figshare.16534935
title: Talon_landmarks.tps

description: This file provides aligned procrustes coordinates for the talon landmarks.
DOI: 10.6084/m9.figshare.16534929.v1
title: Strain_Values_Skull.txt

description: This dataset provides the strain values of for the cranial finite element analyses.
DOI: 10.6084/m9.figshare.16534935.v1
title: Talon_landmarks.tps

description: This file provides aligned procrustes coordinates for the talon landmarks.
DOI: 10.6084/m9.figshare.11720619.v1
title: Family Planning in CDC Plantation Camps: Pre-Intervention Data

description: This data represents the pre-intervention data of a community based house-hold study carried out in the Tiko and Pena Mboko CDC plantation camps. The Tiko camps represents the intervention community while the Pena Mboko camps are used for control. The data was collected using interviewer-administered questionnaire, entered into EpiData version 3.1 and then transformed into Excel format. The data captures participant's locality (Tiko =1, Pena Mboko =2), unique Identification code, socio-demographic information, reproductive history of participants, knowledge, attitude and use of contraception, report on maternal and infant mortality in the camps and unmet needs for family planning.
DOI: 10.6084/m9.figshare.11720619
title: Family Planning in CDC Plantation Camps: Pre and Post-Intervention Data

description: This data represents the pre-intervention data of a community based house-hold study carried out in the Tiko and Pena Mboko CDC plantation camps. The Tiko camps represents the intervention community while the Pena Mboko camps are used for control. The data was collected using interviewer-administered questionnaire, entered into EpiData version 3.1 and then transformed into Excel format. The data captures participant's locality (Tiko =1, Pena Mboko =2), unique Identification code, socio-demographic information, reproductive history of participants, knowledge, attitude and use of contraception, report on maternal and infant mortality in the camps and unmet needs for family planning.
DOI: 10.6084/m9.figshare.11720619.v3
title: Family Planning in CDC Plantation Camps: Pre and Post-Intervention Data

description: This data represents the pre-intervention data of a community based house-hold study carried out in the Tiko and Pena Mboko CDC plantation camps. The Tiko camps represents the intervention community while the Pena Mboko camps are used for control. The data was collected using interviewer-administered questionnaire, entered into EpiData version 3.1 and then transformed into Excel format. The data captures participant's locality (Tiko =1, Pena Mboko =2), unique Identification code, socio-demographic information, reproductive history of participants, knowledge, attitude and use of contraception, report on maternal and infant mortality in the camps and unmet needs for family planning.
DOI: 10.6084/m9.figshare.11720619.v2
title: Family Planning in CDC Plantation Camps: Pre-Intervention Data

description: This data represents the pre-intervention data of a community based house-hold study carried out in the Tiko and Pena Mboko CDC plantation camps. The Tiko camps represents the intervention community while the Pena Mboko camps are used for control. The data was collected using interviewer-administered questionnaire, entered into EpiData version 3.1 and then transformed into Excel format. The data captures participant's locality (Tiko =1, Pena Mboko =2), unique Identification code, socio-demographic information, reproductive history of participants, knowledge, attitude and use of contraception, report on maternal and infant mortality in the camps and unmet needs for family planning.
DOI: 10.6084/m9.figshare.14675454
title: Sitobion avenae functional annotation (primary assembly)

description: Functional annotation using an annotated assembly of the <i>Sitobion avenae</i> (SA3 clone) genome from PacBio HiFi data. Primary assembly generated using hifiasm assembler. Functional annotation of predicted proteins was carried out with InterProScan (v5.51-85.0)
DOI: 10.34740/kaggle/dsv/2873494
title: AutoXGB
DOI: 10.6084/m9.figshare.14675448
title: Sitobion avenae transcripts (alternate)

description: Transcripts predicted from an assembly of the <i>Sitobion avenae</i> (SA3 clone) genome from PacBio HiFi data. Alternate assembly generated using hifiasm assembler.
DOI: 10.6084/m9.figshare.14675448.v1
title: Sitobion avenae transcripts (alternate)

description: Transcripts predicted from an assembly of the <i>Sitobion avenae</i> (SA3 clone) genome from PacBio HiFi data. Alternate assembly generated using hifiasm assembler.
DOI: 10.5281/zenodo.5746626
title: Recognized Fault Locations and Attributes, Getaberget, Åland Islands

description: We mapped faults using their secondary indicators such as damage zones and secondary fracturing at Getaberget shoreline, Åland Islands, Finland. Coordinates are in x and y -columns in<em> EPSG:3067 ETRS-TM35FIN</em> coordinate system. The field mapping and photos were taken as part of a Geological Survey of<br> Finland project, KYT KARIKKO, with funding from Finnish National Nuclear Waste<br> Management Fund (KYT) during the summers of 2020 and 2021.
DOI: 10.5281/zenodo.5746625
title: Recognized Fault Locations and Attributes, Getaberget, Åland Islands

description: We mapped faults using their secondary indicators such as damage zones and secondary fracturing at Getaberget shoreline, Åland Islands, Finland. Coordinates are in x and y -columns in<em> EPSG:3067 ETRS-TM35FIN</em> coordinate system. The field mapping and photos were taken as part of a Geological Survey of<br> Finland project, KYT KARIKKO, with funding from Finnish National Nuclear Waste<br> Management Fund (KYT) during the summers of 2020 and 2021.
DOI: 10.6084/m9.figshare.14675430
title: Sitobion avenae transcripts (primary)

description: Transcripts predicted from an assembly of the <i>Sitobion avenae</i> (SA3 clone) genome from PacBio HiFi data. Primary assembly generated using hifiasm assembler.
DOI: 10.6084/m9.figshare.14675430.v1
title: Sitobion avenae transcripts (primary)

description: Transcripts predicted from an assembly of the <i>Sitobion avenae</i> (SA3 clone) genome from PacBio HiFi data. Primary assembly generated using hifiasm assembler.
DOI: 10.5281/zenodo.5732995
title: Whole-cell modeling in yeast predicts compartment-specific proteome constraints that drive metabolic strategies

description: The pcYeast7.6 model and files, required to reproduce the figures, provided in the publication "Whole-cell modeling in yeast predicts compartment-specific proteome constraints that drive metabolic strategies", accepted in <em>Nat Commun</em>. The Zenodo upload was created by Pranas Grigaitis, p.grigaitis [at] vu.nl. Abstract When conditions change, unicellular organisms rewire their metabolism to sustain cell maintenance and cellular growth. Such rewiring may be understood as resource re-allocation under cellular constraints. Eukaryal cells contain metabolically active organelles such as mitochondria, competing for cytosolic space and resources, and the nature of the relevant cellular constraints remain to be determined for such cells. Here we present a comprehensive metabolic model of the yeast cell, based on its full metabolic reaction network extended with protein synthesis and degradation reactions. The model predicts metabolic fluxes and corresponding protein expression by constraining compartment-specific protein pools and maximising growth rate. Comparing model predictions with quantitative experimental data suggests that under glucose limitation, a mitochondrial constraint limits growth at the onset of ethanol formation - known as the Crabtree effect. Under sugar excess, however, a constraint on total cytosolic volume dictates overflow metabolism. Our comprehensive model thus identifies condition-dependent and compartment-specific constraints that can explain metabolic strategies and protein expression profiles from growth rate optimization, providing a framework to understand metabolic adaptation in eukaryal cells.
description: This work was supported by NWO (NWO ERA-IB-2, project No 053.80.722 to BT and PDL), ERA-IB 4207-00002B DSForsk to JN, and Biotechnology and Biological Sciences Research Council (BB/M025748/1 to SH, BB/M025756/1 to RB). PG and BT also acknowledge support by Marie Skłodowska-Curie Actions ITN "SynCrop" (grant agreement No 764591). We thank SURFsara for the HPC resources through access to the Lisa Compute Cluster.
DOI: 10.6084/m9.figshare.14675421
title: Sitobion avenae proteins (alternate)

description: Proteins predicted from an assembly of the <i>Sitobion avenae</i> (SA3 clone) genome from PacBio HiFi data. Alternate assembly generated using hifiasm assembler.
DOI: 10.6084/m9.figshare.14675421.v1
title: Sitobion avenae proteins (alternate)

description: Proteins predicted from an assembly of the <i>Sitobion avenae</i> (SA3 clone) genome from PacBio HiFi data. Alternate assembly generated using hifiasm assembler.
DOI: 10.5281/zenodo.5732994
title: Whole-cell modeling in yeast predicts compartment-specific proteome constraints that drive metabolic strategies

description: The pcYeast7.6 model and files, required to reproduce the figures, provided in the publication "Whole-cell modeling in yeast predicts compartment-specific proteome constraints that drive metabolic strategies", accepted in <em>Nat Commun</em>. The Zenodo upload was created by Pranas Grigaitis, p.grigaitis [at] vu.nl. Abstract When conditions change, unicellular organisms rewire their metabolism to sustain cell maintenance and cellular growth. Such rewiring may be understood as resource re-allocation under cellular constraints. Eukaryal cells contain metabolically active organelles such as mitochondria, competing for cytosolic space and resources, and the nature of the relevant cellular constraints remain to be determined for such cells. Here we present a comprehensive metabolic model of the yeast cell, based on its full metabolic reaction network extended with protein synthesis and degradation reactions. The model predicts metabolic fluxes and corresponding protein expression by constraining compartment-specific protein pools and maximising growth rate. Comparing model predictions with quantitative experimental data suggests that under glucose limitation, a mitochondrial constraint limits growth at the onset of ethanol formation - known as the Crabtree effect. Under sugar excess, however, a constraint on total cytosolic volume dictates overflow metabolism. Our comprehensive model thus identifies condition-dependent and compartment-specific constraints that can explain metabolic strategies and protein expression profiles from growth rate optimization, providing a framework to understand metabolic adaptation in eukaryal cells.
description: This work was supported by NWO (NWO ERA-IB-2, project No 053.80.722 to BT and PDL), ERA-IB 4207-00002B DSForsk to JN, and Biotechnology and Biological Sciences Research Council (BB/M025748/1 to SH, BB/M025756/1 to RB). PG and BT also acknowledge support by Marie Skłodowska-Curie Actions ITN "SynCrop" (grant agreement No 764591). We thank SURFsara for the HPC resources through access to the Lisa Compute Cluster.
DOI: 10.25345/c5dz99
title: MassIVE MSV000088479 - GNPS_GC_NIE20121023_1-13_2021-12-1
title: detection of mixed small moleculars from soil by GC-MS,NIE20121023
DOI: 10.6084/m9.figshare.14675418.v1
title: Sitobion avenae proteins (primary)

description: Proteins predicted from an assembly of the <i>Sitobion avenae</i> (SA3 clone) genome from PacBio HiFi data. Primary assembly generated using hifiasm assembler.
DOI: 10.6084/m9.figshare.14675418
title: Sitobion avenae proteins (primary)

description: Proteins predicted from an assembly of the <i>Sitobion avenae</i> (SA3 clone) genome from PacBio HiFi data. Primary assembly generated using hifiasm assembler.
DOI: 10.25429/sns.it/lettere/maconda0001
title: MAConDA, Le Mostre d´Arte Moderna nelle Gallerie private in Italia: i due decenni cruciali 1960 - 1980. Gallerie

description: Nell'ambito del Progetto MACoNDA l'interrogazione trasversale di questa banca dati permette di ricostruire l'attività espositiva delle gallerie, con le opere esposte e i testi critici che le hanno accompagnate; confrontare le vicende artistiche delle tre città guida dell'arte moderna in Italia in modi che sono sfuggiti, fino a oggi, negli studi; campionare l'accessibilità visiva delle opere attraverso la diffusione delle loro riproduzioni; avvicinare alla conoscenza, con una documentazione più fondata, delle strategie del mercato dell'arte; confermare o spostare datazioni delle mostre o delle opere; identificare varianti o repliche della stessa opera.
DOI: 10.6084/m9.figshare.17098877.v1
title: Mass-wasting-inferred Variability of 130,000-year Indian Summer Monsoon Intensity from Deposits in the Southeast Tibetan Plateau

description: A large proportion (~80%) of the Indian subcontinent’s precipitation comes from the Indian summer monsoon (ISM), which influences one-fifth of the world’s population. A long-term reliable proxy for ISM is fundamental to understanding previous global climate change. We establish a mass-wasting-inferred proxy to examine the paleohydrogeology (river undercutting history) of the Southeast Tibetan Plateau and reconstruct the variability of ISM intensity (precipitation) in the past 130,000 years. Our data suggest that mass-wasting events, which provides us sufficient samples for paleoclimate research, are prone to dramatic climate changes, especially extreme climate environments. The Southeast Tibetan Plateau was subjected to at least four distinct ISM intensity phases in the past 130,000 years. We conclude that ISM intensity has a cyclicity featured by the Earth’s orbit with obliquity, and that ISM intensity transformation lags the global ice volume (sea level) change by 8–15 kyrs.
DOI: 10.5281/zenodo.5729701
title: Cell type specificity of glucocorticoid signaling in the adult mouse hippocampus

description: The present study is based on the 10X scRNA-seq dataset published by the Allen Institute for Brain Science and publicly available at: https://portal.brain-map.org/atlases-and-data/RNA-seq/mouse-whole-cortex-and-hippocampus-10x. The cells from the hippocampus region were selected from the gene count expression matrix and pre-processed in R v3.6.1 according to the Seurat v3.1.5 standard pre-processing workflow for quality control, normalization, and analysis of scRNA-seq data. Here we make the final seurat object and other datasets further used in the code (https://github.com/eviho/10XHip2021_VihoEMG) available for download.
DOI: 10.5281/zenodo.5729700
title: Cell type specificity of glucocorticoid signaling in the adult mouse hippocampus

description: The present study is based on the 10X scRNA-seq dataset published by the Allen Institute for Brain Science and publicly available at: https://portal.brain-map.org/atlases-and-data/RNA-seq/mouse-whole-cortex-and-hippocampus-10x. The cells from the hippocampus region were selected from the gene count expression matrix and pre-processed in R v3.6.1 according to the Seurat v3.1.5 standard pre-processing workflow for quality control, normalization, and analysis of scRNA-seq data. Here we make the final seurat object and other datasets further used in the code (https://github.com/eviho/10XHip2021_VihoEMG) available for download.
DOI: 10.25429/sns.it/lettere/maconda0002
title: MAConDA. Le Mostre d´Arte Moderna nelle Gallerie private in Italia: i due decenni cruciali 1960 - 1980. Mostre

description: Nell'ambito degli obiettivi primari del progetto MAConDA, la ricerca è partita dalla constatazione della difficile, e in qualche caso proibitiva, accessibilità nelle biblioteche pubbliche (e anche in quelle specialistiche di storia dell'arte) di cataloghi, pieghevoli, inviti e altri materiali di galleria che documentano le mostre in oggetto: mostre che, nel periodo preso in esame, sono state spesso decisive per la storia delle esposizioni perchè hanno iniziato una vera e propria rivoluzione nel rapporto tra l'opera esposta, lo spazio dell'allestimento e il comportamento del visitatore [...] I materiali raccolti hanno permesso anche di ricostruire virtualmente alcune mostre di maggior significato tenute nelle gallerie torinesi Galatea, Il Punto, Notizie, con la puntuale identificazione di opere d'arte esposte.
DOI: 10.5281/zenodo.5746613
title: Estimated height of the OpenStreetMap buildings of 24 French communes using the GeoClimate Software (version 0.0.1)

description: This data contains building geometry footprints of 24 French cities and their corresponding building height as well as averaged building height value aggregated at rectangular grid cell (100 m by 100 m). The footprint geometries comes from the OpenStreetMap project and the building height has been estimated using a RandomForest algorithm using as independent variables indicators describing the building size and shape and the building environment. The data has been produced using the GeoClimate Software (version 0.0.1). A more detailed description of the content can be used in the file "Metadata.csv".
DOI: 10.13012/b2idb-9227641_v1
title: Knowledge, attitudes, and practices of veterinary professionals towards ticks and tick-borne diseases in Illinois

description: An online knowledge, attitudes, and practices survey on ticks and tick-borne diseases was distributed to veterinary professionals in Southern and Central Illinois during summer and fall 2020. These are the raw data associated with that survey and the survey questions used. * NOTE: "age" and "gender" variables were removed from the data to protect participants.
DOI: 10.6084/m9.figshare.14675391
title: Sitobion avenae genome annotation (primary)

description: Annotation of an assembly of the <i>Sitobion avenae</i> (SA3 clone) genome from PacBio HiFi data. Primary assembly generated using hifiasm assembler.
DOI: 10.6084/m9.figshare.14675394
title: Sitobion avenae genome annotation (alternate)

description: Annotation of an assembly of the <i>Sitobion avenae</i> (SA3 clone) genome from PacBio HiFi data. Alternate assembly generated using hifiasm assembler.
DOI: 10.6084/m9.figshare.14675394.v1
title: Sitobion avenae genome annotation (alternate)

description: Annotation of an assembly of the <i>Sitobion avenae</i> (SA3 clone) genome from PacBio HiFi data. Alternate assembly generated using hifiasm assembler.
DOI: 10.6084/m9.figshare.16573454
title: Supplementary Material for: The Screening Test for Aphasia and Dysarthria (STAD) for patients with neurological communicative disorders: a large-scale, multicenter validation study in Japan

description: Medicine
DOI: 10.15151/esrf-es-634064545
title: Structural analysis of protein machineries using single particle cryo-EM

description: Structures of large macromolecular machineries were for long time not studied at atomic level as they were often too large for X-ray crystallography and as electron microscopy was not allowing good enough resolution. In the last decade, however, tremendous progress has been achieved in the field of single particle cryo electron microscopy (cryo-EM), which became the method of choice to structurally characterize such large protein complexes. The goal of this BAG is to determine structures of complex and often dynamic protein machineries including multi-subunit complexes, protein-nucleic acid complexes or membrane protein complexes using cryo-EM. The projects aim at determining structures of macromolecular machineries involved in energy conversion and cellular respiration, in nitrate and ammonium metabolism, in ribosome and ribosome-associated functions and in DNA damage repair and maintenance.
DOI: 10.25442/hku.16634713
title: Supporting data for "Long non-coding RNAs modulate the osteogenic differentiation of healthy and inflamed periodontal ligament cells"

description: Periodontitis is a bacteria‐induced and host‐mediated inflammatory disease that results in the progressive destruction of tooth-supporting tissues and bone. Yet, it is closely associated with various inflammatory comorbidities like cardiovascular disease, diabetes mellitus, and Alzheimer’s disease. Periodontal ligament (PDL), a thin layer of connective tissue between the cementum and alveolar bone, contributes significantly to the development, function, and regeneration of periodontium. The PDL progenitor cells (PDL cells) have multipotent differentiation potential and are considered as an appropriate source of periodontal regeneration for the treatment of periodontitis.The PDL cells have reduced osteogenic potentials in periodontitis patients, with reference to the periodontally healthy individuals. Currently, the primary goal of periodontal therapy is to stop disease progression and achieve a stable periodontal condition. However, it is unknown whether the regenerative potentials of the treated stable periodontium can be fully recovered following periodontal therapy. Therefore, it becomes increasingly important for enhancing the osteogenic potential and ultimately promoting bone formation in periodontally compromised patients.Long non-coding RNAs (LncRNAs) as the critical regulators of diverse biological processes and diseases are involved in the osteogenic differentiation of PDL cells. The current work aimed to elucidate the characteristics and osteogenic potentials of healthy, inflammatory, and treated stable PDL cells, and explore the regulation of lncRNAs in the osteogenic differentiation of these cells.<br>
DOI: 10.25442/hku.16634713.v1
title: Supporting data for "Long non-coding RNAs modulate the osteogenic differentiation of healthy and inflamed periodontal ligament cells"

description: Periodontitis is a bacteria‐induced and host‐mediated inflammatory disease that results in the progressive destruction of tooth-supporting tissues and bone. Yet, it is closely associated with various inflammatory comorbidities like cardiovascular disease, diabetes mellitus, and Alzheimer’s disease. Periodontal ligament (PDL), a thin layer of connective tissue between the cementum and alveolar bone, contributes significantly to the development, function, and regeneration of periodontium. The PDL progenitor cells (PDL cells) have multipotent differentiation potential and are considered as an appropriate source of periodontal regeneration for the treatment of periodontitis.The PDL cells have reduced osteogenic potentials in periodontitis patients, with reference to the periodontally healthy individuals. Currently, the primary goal of periodontal therapy is to stop disease progression and achieve a stable periodontal condition. However, it is unknown whether the regenerative potentials of the treated stable periodontium can be fully recovered following periodontal therapy. Therefore, it becomes increasingly important for enhancing the osteogenic potential and ultimately promoting bone formation in periodontally compromised patients.Long non-coding RNAs (LncRNAs) as the critical regulators of diverse biological processes and diseases are involved in the osteogenic differentiation of PDL cells. The current work aimed to elucidate the characteristics and osteogenic potentials of healthy, inflammatory, and treated stable PDL cells, and explore the regulation of lncRNAs in the osteogenic differentiation of these cells.<br>
DOI: 10.6084/m9.figshare.14675382
title: Sitobion avenae genome sequence (alternate)

description: An assembly of the <i>Sitobion avenae</i> (SA3 clone) genome from PacBio HiFi data. Alternate assembly generated using hifiasm assembler.
DOI: 10.6084/m9.figshare.14675367
title: Sitobion avenae genome sequence (primary)

description: An assembly of the <i>Sitobion avenae</i> (SA3 clone) genome from PacBio HiFi data. Primary assembly generated using hifiasm assembler<sup>1</sup>.<br><sup>1</sup>Cheng, H., Concepcion, G.T., Feng, X., Zhang, H. and Li, H., 2021. Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm. <i>Nature Methods</i>, <i>18</i>(2), pp.170-175.