cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1263925
title: Testing ecological theories with sequence similarity networks: marine ciliates exhibit similar geographic dispersal patterns as multicellular organisms (file : network_output.tab.zip)

description: file : network_output.tab.zip Testing ecological theories with sequence similarity networks: marine ciliates exhibit similar geographic dispersal patterns as multicellular organisms (file : readme_Forster_et_al_BMC) http://dx.doi.org/10.6084/m9.figshare.1264013 Background: High-throughput sequencing technologies are lifting major limitations to molecular-based ecological studies of eukaryotic microbial diversity, but in silico analyses of the resulting millions of short amplicons remain a major bottleneck for these approaches. Here, we introduced the analytical and statistical framework of sequence similarity networks, increasingly used in evolutionary studies and graph theory, into the field of ecology to analyze novel pyrosequenced V4 SSU-rDNA sequence data sets in the context of previous studies, including SSU-rDNA Sanger sequence data from cultured ciliates and from previous environmental diversity inventories.<br>Results: Our broadly applicable protocol quantified progress in the description of genetic diversity of ciliates by environmental rRNA amplicons studies, detected a fundamental historical bias, the tendency to recover already known groups, in these surveys, and revealed substantial amounts of hidden microbial diversity. Moreover, network measures demonstrated that ciliates are not globally dispersed, but present strong local patterns at intermediate geographical scale, as observed for bacteria, plants, and animals.<br>Conclusions: Although currently available ‘universal’ primers used for local in-depth sequencing surveys provide little hope to exhaust the significantly higher ciliate (and most likely microbial) diversity than previously thought, sequence similarity networks, since they identify groups of divergence sequences sharing distinctive similarities, offer a promising way to guide the design of novel primers and to further explore such a vast and structured microbial diversity.
DOI: 10.6084/m9.figshare.1264009
title: Testing ecological theories with sequence similarity networks: marine ciliates exhibit similar geographic dispersal patterns as multicellular organisms (file : details_V4ciliates_Biomarks.tab)

description: file : details_V4ciliates_Biomarks.tab Testing ecological theories with sequence similarity networks: marine ciliates exhibit similar geographic dispersal patterns as multicellular organisms (file : readme_Forster_et_al_BMC) http://dx.doi.org/10.6084/m9.figshare.1264013 Background: High-throughput sequencing technologies are lifting major limitations to molecular-based ecological studies of eukaryotic microbial diversity, but in silico analyses of the resulting millions of short amplicons remain a major bottleneck for these approaches. Here, we introduced the analytical and statistical framework of sequence similarity networks, increasingly used in evolutionary studies and graph theory, into the field of ecology to analyze novel pyrosequenced V4 SSU-rDNA sequence data sets in the context of previous studies, including SSU-rDNA Sanger sequence data from cultured ciliates and from previous environmental diversity inventories.<br>Results: Our broadly applicable protocol quantified progress in the description of genetic diversity of ciliates by environmental rRNA amplicons studies, detected a fundamental historical bias, the tendency to recover already known groups, in these surveys, and revealed substantial amounts of hidden microbial diversity. Moreover, network measures demonstrated that ciliates are not globally dispersed, but present strong local patterns at intermediate geographical scale, as observed for bacteria, plants, and animals.<br>Conclusions: Although currently available ‘universal’ primers used for local in-depth sequencing surveys provide little hope to exhaust the significantly higher ciliate (and most likely microbial) diversity than previously thought, sequence similarity networks, since they identify groups of divergence sequences sharing distinctive similarities, offer a promising way to guide the design of novel primers and to further explore such a vast and structured microbial diversity.
DOI: 10.5281/zenodo.8220240
title: Synchronization of spin-driven limit cycle oscillators optically levitated in vacuum

description: Trajectories of optically levitated particles in vacuum. Trajectories are recorded using quadrant photodiode and ultra-fast CMOS camera. The readme file with more detailed description is added.
DOI: 10.5281/zenodo.8220239
title: Synchronization of spin-driven limit cycle oscillators optically levitated in vacuum

description: Trajectories of optically levitated particles in vacuum. Trajectories are recorded using quadrant photodiode and ultra-fast CMOS camera. The readme file with more detailed description is added.
DOI: 10.5281/zenodo.8220280
title: Salivary chemical barrier proteins in Oral Squamous Cell Carcinoma – Alterations in the defense mechanism of the oral cavity

description: Oral squamous cell carcinoma (OSCC) is one of the most frequent type of head and neck cancers. Despite the genetic and environmental risk factors, OSCC is also associated with microbial infections and/or dysbiosis. The secreted saliva serves as the chemical barrier of the oral cavity and since OSCC can alter the protein composition of saliva, our aim was to analyze the effect of OSCC on the salivary chemical barrier proteins. Publicly available datasets regarding the analysis of salivary proteins from patients with OSCC and controls were collected and examined in order to identify differentially expressed chemical barrier proteins. The network analysis and gene onthology (GO) classification of the differentially expressed chemical barrier proteins were performed, as well. 127 proteins showing different expression pattern between the OSCC and control groups were found. The protein-protein interaction network of up- and down-regulated proteins were constructed and analyzed. The main hub proteins (IL-6, IL-1B, IL-8, TNF, APOA1, APOA2, APOB, APOC3, APOE, and HP) were identified and the enriched GO terms were examined. Our study highlighted the importance of the chemical barrier of saliva in the development of OSCC.
DOI: 10.5281/zenodo.8220279
title: Salivary chemical barrier proteins in Oral Squamous Cell Carcinoma – Alterations in the defense mechanism of the oral cavity

description: Oral squamous cell carcinoma (OSCC) is one of the most frequent type of head and neck cancers. Despite the genetic and environmental risk factors, OSCC is also associated with microbial infections and/or dysbiosis. The secreted saliva serves as the chemical barrier of the oral cavity and since OSCC can alter the protein composition of saliva, our aim was to analyze the effect of OSCC on the salivary chemical barrier proteins. Publicly available datasets regarding the analysis of salivary proteins from patients with OSCC and controls were collected and examined in order to identify differentially expressed chemical barrier proteins. The network analysis and gene onthology (GO) classification of the differentially expressed chemical barrier proteins were performed, as well. 127 proteins showing different expression pattern between the OSCC and control groups were found. The protein-protein interaction network of up- and down-regulated proteins were constructed and analyzed. The main hub proteins (IL-6, IL-1B, IL-8, TNF, APOA1, APOA2, APOB, APOC3, APOE, and HP) were identified and the enriched GO terms were examined. Our study highlighted the importance of the chemical barrier of saliva in the development of OSCC.
DOI: 10.5281/zenodo.7777276
title: Elucidating the conformational change of Dengue envelope protein using Markov State Model

description: This is the dataset of input files, parameter files and run files for the various protein conformations generated in the study "Elucidating the conformational change of Dengue envelope protein using Markov State Model"
DOI: 10.5281/zenodo.7777275
title: Elucidating the conformational change of Dengue envelope protein using Markov State Model

description: This is the dataset of input files, parameter files and run files for the various protein conformations generated in the study "Elucidating the conformational change of Dengue envelope protein using Markov State Model"
DOI: 10.17632/xmnvxzkvx4.1
title: Proteomic analysis of melanoma secretome (SK-MEL-2, G361) after gastrin treatment

description: List of classically secreted isotope labelled proteins with signal peptide sequence showing alteration after gastrin treatment characterised from Skmel-2 (A) and G361 (B) secretome.
DOI: 10.34740/kaggle/dsv/6261531
title: Fixed Wing Drone Detection Dataset
DOI: 10.6084/m9.figshare.23896377
title: Chromosome-level genome assembly of the Stoliczka’s Asian trident bat (Aselliscus stoliczkanus)

description: Stoliczka’s Asian trident bat (<i>Aselliscus stoliczkanus</i>) is a small-bodied species and is sensitive to climate change. Here, we presented a chromosome-level genome assembly of the Stoliczka’s Asian trident bat (<i>Aselliscus stoliczkanus</i>)<i> </i>by combining Illunima sequencing, Nanopore sequencing and high-throughput chromatin conformation capture (Hi-C) sequencing technology. The reference-quality genome of <i>A. stoliczkanus</i><i> </i>provides valuable resource for conservative genomics and landscape genomics in predicting adaptation and vulnerability to climate change.
DOI: 10.6084/m9.figshare.23896377.v1
title: Chromosome-level genome assembly of the Stoliczka’s Asian trident bat (Aselliscus stoliczkanus)

description: Stoliczka’s Asian trident bat (<i>Aselliscus stoliczkanus</i>) is a small-bodied species and is sensitive to climate change. Here, we presented a chromosome-level genome assembly of the Stoliczka’s Asian trident bat (<i>Aselliscus stoliczkanus</i>)<i> </i>by combining Illunima sequencing, Nanopore sequencing and high-throughput chromatin conformation capture (Hi-C) sequencing technology. The reference-quality genome of <i>A. stoliczkanus</i><i> </i>provides valuable resource for conservative genomics and landscape genomics in predicting adaptation and vulnerability to climate change.
DOI: 10.6084/m9.figshare.23866962.v3
title: Untitled Item

description: Regridding Global CMIP6 GCMs dataset(0.5 degree)Historical dataset: 7 CMIP6 GCMs (1850-2014, ACCESS-CM2 to GFDL-ESM4)Future dataset: 7 CMIP6 GCMs and 4 SSP scenarios (2015-2100)Composition of dataset: Average temperature, Maximum temperature, Minimum temperature, Windspeed, Relative humidity, Solar radiationIf you are using our codes and dataset, please use the following references:Song, Y.H., Chung, E.S., Shahid, S., Kim, Y.J., Kim, D.K. 2023. Development of global monthly dataset of CMIP6 climate variables for estimating evapotranspiration. Scientific Data.<br>
DOI: 10.34740/kaggle/ds/3599321
title: New York Cab Rides
DOI: 10.26050/wdcc/ar6.c6spnkk1
title: IPCC DDC: NIMS-KMA KACE1.0-G model output prepared for CMIP6 ScenarioMIP

description: Project: Coupled Model Intercomparison Project Phase 6 (CMIP6) datasets - These data have been generated as part of the internationally-coordinated Coupled Model Intercomparison Project Phase 6 (CMIP6; see also GMD Special Issue: http://www.geosci-model-dev.net/special_issue590.html). The simulation data provides a basis for climate research designed to answer fundamental science questions and serves as resource for authors of the Sixth Assessment Report of the Intergovernmental Panel on Climate Change (IPCC-AR6). CMIP6 is a project coordinated by the Working Group on Coupled Modelling (WGCM) as part of the World Climate Research Programme (WCRP). Phase 6 builds on previous phases executed under the leadership of the Program for Climate Model Diagnosis and Intercomparison (PCMDI) and relies on the Earth System Grid Federation (ESGF) and the Centre for Environmental Data Analysis (CEDA) along with numerous related activities for implementation. The original data is hosted and partially replicated on a federated collection of data nodes, and most of the data relied on by the IPCC is being archived for long-term preservation at the IPCC Data Distribution Centre (IPCC DDC) hosted by the German Climate Computing Center (DKRZ). The project includes simulations from about 120 global climate models and around 45 institutions and organizations worldwide. Summary: These data include the subset used by IPCC AR6 WGI authors of the datasets originally published in ESGF for 'CMIP6.ScenarioMIP.NIMS-KMA.KACE-1-0-G' with the full Data Reference Syntax following the template 'mip_era.activity_id.institution_id.source_id.experiment_id.member_id.table_id.variable_id.grid_label.version'. The KACE1.0-GLOMAP climate model, released in 2018, includes the following components: aerosol: UKCA-GLOMAP-mode, atmos: MetUM-HadGEM3-GA7.1 (N96; 192 x 144 longitude/latitude; 85 levels; top level 85 km), land: JULES-HadGEM3-GL7.1, ocean: MOM4p1 (tripolar primarily 1deg; 360 x 200 longitude/latitude; 50 levels; top grid cell 0-10 m), seaIce: CICE-HadGEM3-GSI8 (tripolar primarily 1deg; 360 x 200 longitude/latitude). The model was run by the National Institute of Meteorological Sciences/Korea Meteorological Administration, Climate Research Division, Seoho-bukro 33, Seogwipo-si, Jejudo 63568, Republic of Korea (NIMS-KMA) in native nominal resolutions: aerosol: 250 km, atmos: 250 km, land: 250 km, ocean: 100 km, seaIce: 100 km.
DOI: 10.26050/wdcc/ar6.c6spnku0
title: IPCC DDC: NIMS-KMA UKESM1.0-LL model output prepared for CMIP6 ScenarioMIP

description: Project: Coupled Model Intercomparison Project Phase 6 (CMIP6) datasets - These data have been generated as part of the internationally-coordinated Coupled Model Intercomparison Project Phase 6 (CMIP6; see also GMD Special Issue: http://www.geosci-model-dev.net/special_issue590.html). The simulation data provides a basis for climate research designed to answer fundamental science questions and serves as resource for authors of the Sixth Assessment Report of the Intergovernmental Panel on Climate Change (IPCC-AR6). CMIP6 is a project coordinated by the Working Group on Coupled Modelling (WGCM) as part of the World Climate Research Programme (WCRP). Phase 6 builds on previous phases executed under the leadership of the Program for Climate Model Diagnosis and Intercomparison (PCMDI) and relies on the Earth System Grid Federation (ESGF) and the Centre for Environmental Data Analysis (CEDA) along with numerous related activities for implementation. The original data is hosted and partially replicated on a federated collection of data nodes, and most of the data relied on by the IPCC is being archived for long-term preservation at the IPCC Data Distribution Centre (IPCC DDC) hosted by the German Climate Computing Center (DKRZ). The project includes simulations from about 120 global climate models and around 45 institutions and organizations worldwide. Summary: These data include the subset used by IPCC AR6 WGI authors of the datasets originally published in ESGF for 'CMIP6.ScenarioMIP.NIMS-KMA.UKESM1-0-LL' with the full Data Reference Syntax following the template 'mip_era.activity_id.institution_id.source_id.experiment_id.member_id.table_id.variable_id.grid_label.version'. The UKESM1.0-N96ORCA1 climate model, released in 2018, includes the following components: aerosol: UKCA-GLOMAP-mode, atmos: MetUM-HadGEM3-GA7.1 (N96; 192 x 144 longitude/latitude; 85 levels; top level 85 km), atmosChem: UKCA-StratTrop, land: JULES-ES-1.0, ocean: NEMO-HadGEM3-GO6.0 (eORCA1 tripolar primarily 1 deg with meridional refinement down to 1/3 degree in the tropics; 360 x 330 longitude/latitude; 75 levels; top grid cell 0-1 m), ocnBgchem: MEDUSA2, seaIce: CICE-HadGEM3-GSI8 (eORCA1 tripolar primarily 1 deg; 360 x 330 longitude/latitude). The model was run by the National Institute of Meteorological Sciences/Korea Meteorological Administration, Climate Research Division, Seoho-bukro 33, Seogwipo-si, Jejudo 63568, Republic of Korea (NIMS-KMA) in native nominal resolutions: aerosol: 250 km, atmos: 250 km, atmosChem: 250 km, land: 250 km, ocean: 100 km, ocnBgchem: 100 km, seaIce: 100 km.
DOI: 10.5281/zenodo.8220302
title: Dataset: vacuum-ultraviolet laser source for spectroscopy of trapped thorium ions

description: This is a data set accompanying the publication "Vacuum-ultraviolet laser source for spectroscopy of trapped thorium ions" in the New Journal of Physics. https://doi.org/10.1088/1367-2630/aced1b
DOI: 10.5281/zenodo.8220301
title: Dataset: vacuum-ultraviolet laser source for spectroscopy of trapped thorium ions

description: This is a data set accompanying the publication "Vacuum-ultraviolet laser source for spectroscopy of trapped thorium ions" in the New Journal of Physics. https://doi.org/10.1088/1367-2630/aced1b
DOI: 10.6084/m9.figshare.23291972.v3
title: Urbanity Colab Data Files

description: Sample subzone files for Urbanity colab demo. Data obtained from GADM database.
DOI: 10.5281/zenodo.8220177
title: Fitness and cold tolerance of Spodoptera frugiperda fed on corn and two winter crops (Original data)

description: 草地贪夜蛾(FAW)草<em>地</em>贪夜蛾是一种主要的迁徙和多噬性害虫。FAW的越冬、迁徙和定植性状与植被和寄主适应性密切相关。在这项研究中,我们调查了春夏作物(玉米)和两种冬季作物(卷心菜,<em>芸苔</em>属和油菜,油菜,油菜)的产卵偏好,喂养<em>偏好,适应性</em>和耐寒性。结果表明,FAW可以通过喂食卷心菜和油菜来完成其生命周期,尽管健康状况不如玉米。以卷心菜为食的FAW存活率、雌蛹质量和宿主适宜性指数高于油菜,幼虫更喜欢以油菜叶为食,雌性更喜欢在油菜植株上产卵。此外,与玉米和油菜相比,以卷心菜为食的FAW幼虫从寒晕中恢复的时间最短,表明以卷心菜为食可提高FAW幼虫的耐寒性。因此,卷心菜可能是FAW的理想宿主,需要在冬季生存和繁殖。研究结果提高了我们对FAW寄主选择和适应的理解,为预测FAW冬季繁殖区奠定了基础。
DOI: 10.5281/zenodo.8220176
title: Fitness and cold tolerance of Spodoptera frugiperda fed on corn and two winter crops (Original data)

description: 草地贪夜蛾(FAW)草<em>地</em>贪夜蛾是一种主要的迁徙和多噬性害虫。FAW的越冬、迁徙和定植性状与植被和寄主适应性密切相关。在这项研究中,我们调查了春夏作物(玉米)和两种冬季作物(卷心菜,<em>芸苔</em>属和油菜,油菜,油菜)的产卵偏好,喂养<em>偏好,适应性</em>和耐寒性。结果表明,FAW可以通过喂食卷心菜和油菜来完成其生命周期,尽管健康状况不如玉米。以卷心菜为食的FAW存活率、雌蛹质量和宿主适宜性指数高于油菜,幼虫更喜欢以油菜叶为食,雌性更喜欢在油菜植株上产卵。此外,与玉米和油菜相比,以卷心菜为食的FAW幼虫从寒晕中恢复的时间最短,表明以卷心菜为食可提高FAW幼虫的耐寒性。因此,卷心菜可能是FAW的理想宿主,需要在冬季生存和繁殖。研究结果提高了我们对FAW寄主选择和适应的理解,为预测FAW冬季繁殖区奠定了基础。
DOI: 10.5281/zenodo.7092419
title: Wolbachia genomes assembled from insect hosts generated by the DToL project

description: This dataset represents the assembly of 110 high-quality complete <em>Wolbachia</em> genomes, from 93 insect species, of which 77 were circular. These genomes are named using the schema Xyz_ToLID_§ where Xyz is the first three letters of the insect order of the host, ToLID is the identifier of the host species, and § indicates the supergroup.
DOI: 10.5281/zenodo.7092420
title: Wolbachia genomes assembled from insect hosts generated by the DToL project

description: This dataset represents the assembly of 110 high-quality complete <em>Wolbachia</em> genomes, from 93 insect species, of which 77 were circular. These genomes are named using the schema Xyz_ToLID_§ where Xyz is the first three letters of the insect order of the host, ToLID is the identifier of the host species, and § indicates the supergroup.
DOI: 10.5281/zenodo.8220344
title: Wolbachia genomes assembled from insect hosts generated by the DToL project

description: This dataset represents the assembly of 110 high-quality complete <em>Wolbachia</em> genomes, from 93 insect species, of which 77 were circular. These genomes are named using the schema Xyz_ToLID_§ where Xyz is the first three letters of the insect order of the host, ToLID is the identifier of the host species, and § indicates the supergroup.
DOI: 10.6084/m9.figshare.23898738
title: anomyzed eco-climatic data

description: Dataset posted on authored by 2023-08-7 authored by Angelo Solimini, Chiara Virgillito, Mattia Manica, Piero Poletti, Giorgio Guzzetta, Giovanni Marini, Roberto Rosà, Federico Filipponi, Paola Scognamiglio, Francesco Vairo, Beniamino Caputo<br>
DOI: 10.6084/m9.figshare.23898738.v1
title: anomyzed eco-climatic data

description: Dataset posted on authored by 2023-08-7 authored by Angelo Solimini, Chiara Virgillito, Mattia Manica, Piero Poletti, Giorgio Guzzetta, Giovanni Marini, Roberto Rosà, Federico Filipponi, Paola Scognamiglio, Francesco Vairo, Beniamino Caputo<br>
DOI: 10.5517/cc102pb3
title: CCDC 926104: Experimental Crystal Structure Determination

description: Related Article: I.Krossing|2013|CSD Communication|||
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.cc21wk4n
title: CCDC 1903311: Experimental Crystal Structure Determination

description: Related Article: Despoina Anastasiadou,  George Psomas,  Stavros Kalogiannis,  George Geromichalos,  Antonios G. Hatzidimitriou,  Paraskevas Aslanidis|2019|J.Inorg.Biochem.|198|110750|doi:10.1016/j.jinorgbio.2019.110750
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.cc22bg0x
title: CCDC 1916668: Experimental Crystal Structure Determination

description: Related Article: Jessica K. Bilyj, Nicole V. Silajew, Graeme R. Hanson, Jeffrey R. Harmer, Paul V. Bernhardt|2019|Dalton Trans.|48|15501|doi:10.1039/C9DT02071C
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.cc22bg2z
title: CCDC 1916670: Experimental Crystal Structure Determination

description: Related Article: Jessica K. Bilyj, Nicole V. Silajew, Graeme R. Hanson, Jeffrey R. Harmer, Paul V. Bernhardt|2019|Dalton Trans.|48|15501|doi:10.1039/C9DT02071C
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: 10.6084/m9.figshare.23898690
title: Data for the paper: Dryland sensitivity to climate change and variability using nonlinear dynamics

description: This file contains the data used in the paper: Dryland sensitivity to climate change and variability using nonlinear dynamics. The first dataset (Data for dryland sensitivity_annual productivity and climates.csv) contains the time-series data of annual productivity and climate variables (annual precipitation, annual mean temperature, summer mean temperature, and annual SPEI). The second dataset (Data for dryland sensitivity_productivity and interannual climate variability.csv) contains the data of mean annual productivity and interannual climate variability (interannual precipitation variability, interannual temperature variability, interannual summer temperature variability, and interannual SPEI variability) in 6y moving windows.