cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.5682654
title: Code and data for "Wild snapdragon plant pedigree sheds light on limited connectivity enhanced by higher migrant reproductive success in a fragmented landscape"

description: Archive file containing all the code and data for producing results and the supplementary result of the MS entitled "Wild snapdragon plant pedigree sheds light on limited connectivity enhanced by higher migrant reproductive success in a fragmented landscape". See README.txt for files descriptions.
DOI: 10.5281/zenodo.5682659
title: Code and data for "Wild snapdragon plant pedigree sheds light on limited connectivity enhanced by higher migrant reproductive success in a fragmented landscape"

description: Archive file containing all the code and data for producing results and the supplementary result of the MS entitled "Wild snapdragon plant pedigree sheds light on limited connectivity enhanced by higher migrant reproductive success in a fragmented landscape". See README.txt for files descriptions.
DOI: 10.5281/zenodo.7438502
title: Code and data for "Wild snapdragon plant pedigree sheds light on limited connectivity enhanced by higher migrant reproductive success in a fragmented landscape"

description: Archive file containing all the code and data for producing results and the supplementary result of the MS entitled "Wild snapdragon plant pedigree sheds light on limited connectivity enhanced by higher migrant reproductive success in a fragmented landscape". See README.txt for files descriptions.
DOI: 10.5281/zenodo.7348563
title: Dataset to manuscript "Trans-cis isomerization kinetics of cyanine dyes reports on the folding states of exogeneous RNA G-quadruplexes in live cells" accepted for publication in Nucleic Acids Research

description: <strong>This folder contains all raw data underlying the results presented in a manuscript, accepted for publication in Nucleic Acids Research, and entitled:</strong> <strong><em>Trans</em></strong><strong>-<em>cis</em> isomerization kinetics of cyanine dyes reports on the folding states of exogeneous RNA G-quadruplexes in live cells </strong> <strong>Authored by:</strong> Akira Kitamura<sup>2,*</sup>, Johan Tornmalm<sup>1,*</sup>, Baris Demirbay<sup>1</sup>, Joachim Piguet<sup>1</sup>, Masataka Kinjo<sup>2</sup>, Jerker Widengren<sup>1+</sup> <sup>1</sup> Experimental Biomolecular Physics, Department of Applied Physics, Royal Institute of Technology (KTH), Stockholm, Sweden <sup>2</sup> Laboratory of Molecular Cell Dynamics, Faculty of Advanced Life Science, Hokkaido University, Sapporo, Japan <sup>* </sup>Contributed equally <sup>+</sup> To whom correspondence should be addressed. Email: jwideng@kth.se. Tel: +46-8-7907813 <strong>The data files are grouped into the different techniques used to generate them, and refer to the figures/tables in the manuscript where the extracted results are presented. </strong> <strong>ABSTRACT</strong> Guanine (G)-rich nucleic acids are prone to assemble into four-stranded structures, so-called G-quadruplexes. Abnormal GGGGCC repeat elongations, and in particular their folding states, are associated with amyotrophic lateral sclerosis and frontotemporal dementia. Due to methodological constraints however, most studies of G quadruplex structures are restricted to <em>in vitro</em> conditions. Evidence of how GGGGCC repeats form into G-quadruplexes <em>in vivo</em> is sparse. We devised a readout strategy, exploiting the sensitivity of <em>trans</em>-<em>cis</em> isomerization of cyanine dyes to local viscosity and sterical constraints. Thereby, folding states of cyanine-labeled RNA, and in particular G-quadruplexes, can be identified in a sensitive manner. The isomerization kinetics, monitored via fluorescence blinking generated upon transitions between a fluorescent <em>trans</em> isomer and a non-fluorescent <em>cis</em> isomer, was first characterized for RNA with GGGGCC repeats in aqueous solution using fluorescence correlation spectroscopy and transient state (TRAST) monitoring. With TRAST, monitoring the isomerization kinetics from how the average fluorescence intensity varies with laser excitation modulation characteristics, we could then detect folding states of fluorescently tagged RNA introduced into live cells.
DOI: 10.5281/zenodo.4633580
title: Dataset to manuscript "Trans-cis isomerization kinetics of cyanine dyes reports on the folding states of exogeneous RNA G-quadruplexes in live cells" accepted for publication in Nucleic Acids Research

description: <strong>This folder contains all raw data underlying the results presented in a manuscript, accepted for publication in Nucleic Acids Research, and entitled:</strong> <strong><em>Trans</em></strong><strong>-<em>cis</em> isomerization kinetics of cyanine dyes reports on the folding states of exogeneous RNA G-quadruplexes in live cells </strong> <strong>Authored by:</strong> Akira Kitamura<sup>2,*</sup>, Johan Tornmalm<sup>1,*</sup>, Baris Demirbay<sup>1</sup>, Joachim Piguet<sup>1</sup>, Masataka Kinjo<sup>2</sup>, Jerker Widengren<sup>1+</sup> <sup>1</sup> Experimental Biomolecular Physics, Department of Applied Physics, Royal Institute of Technology (KTH), Stockholm, Sweden <sup>2</sup> Laboratory of Molecular Cell Dynamics, Faculty of Advanced Life Science, Hokkaido University, Sapporo, Japan <sup>* </sup>Contributed equally <sup>+</sup> To whom correspondence should be addressed. Email: jwideng@kth.se. Tel: +46-8-7907813 <strong>The data files are grouped into the different techniques used to generate them, and refer to the figures/tables in the manuscript where the extracted results are presented. </strong> <strong>ABSTRACT</strong> Guanine (G)-rich nucleic acids are prone to assemble into four-stranded structures, so-called G-quadruplexes. Abnormal GGGGCC repeat elongations, and in particular their folding states, are associated with amyotrophic lateral sclerosis and frontotemporal dementia. Due to methodological constraints however, most studies of G quadruplex structures are restricted to <em>in vitro</em> conditions. Evidence of how GGGGCC repeats form into G-quadruplexes <em>in vivo</em> is sparse. We devised a readout strategy, exploiting the sensitivity of <em>trans</em>-<em>cis</em> isomerization of cyanine dyes to local viscosity and sterical constraints. Thereby, folding states of cyanine-labeled RNA, and in particular G-quadruplexes, can be identified in a sensitive manner. The isomerization kinetics, monitored via fluorescence blinking generated upon transitions between a fluorescent <em>trans</em> isomer and a non-fluorescent <em>cis</em> isomer, was first characterized for RNA with GGGGCC repeats in aqueous solution using fluorescence correlation spectroscopy and transient state (TRAST) monitoring. With TRAST, monitoring the isomerization kinetics from how the average fluorescence intensity varies with laser excitation modulation characteristics, we could then detect folding states of fluorescently tagged RNA introduced into live cells.
DOI: 10.6084/m9.figshare.19435760.v1
title: Macroevolution of protective coloration across caterpillars reflects relationships with host plants

description: data, phylogenetic tree, and other input files used to explore associations between color, pattern, and diet ecology in 1808 species of larval Lepidoptera (caterpillars). Associated scripts are hosted on Github (moria-robinson).
DOI: 10.5281/zenodo.7437856
title: Scanning electron microscope images of spruce needle homogenate and scanning electron microscope images of isolated small cellular particles from spruce needle homogenate

description: Scanning electron microscope images of spruce needle homogenate and of isolated small cellular particles from spruce needle homogenate are presented. Each image is supplemented by description of the preparation of the sample and the data on the imaging technique and equipment. The data are curated by Veronika Kralj-Iglic and University of Ljubljana, Faculty of Health Sciences, Laboratory of Clinical Biophysics, and Anna Romolo, presently at University of Ljubljana, Faculty of Electrical Engineering, Laboratory of Physics, Ljubljana, Slovenia. Present address of Marko Jeran is: Department of Inorganic Chemistry and Technology, “Jožef Stefan” Institute, Ljubljana, Slovenia.
description: {"references": ["Mantile , F.; Kisovec, M.; Adamo , G.; Romancino , D.P.; Ho\u010devar, M.; Bo\u017ei\u010d, D.; Bedina Zavec, A.; Podobnik, M.; Stoppelli , M.P.; Kisslinger , A.; Bongiovanni , A.; Kralj Igli\u010d, V.; Liguori , G.L. A Novel Localization in Human Large Extracellular Vesicles for the EGF CFC Founder Member CRIPTO and Its Biological and Therapeutic Implications . Cancers 2022, 14, 3700. https://doi.org/10.3390/cancers14153700).", "(Bo\u017ei\u010d, D.; Ho\u010devar, M.; Kisovec, M.; Pajni\u010d, M.; Pa\u0111en , L.; Jeran, M.; Zavec Bedina, A.; Podobnik, M.; Kogej, K.; Igli\u010d, A.; Kralj Igli\u010d, V. Stability of erythrocyte derived nanovesicles assessed by light scattering and electron microsco py . Int J Mol Sci . 2021, 22, 12772. doi:10.3390/ijms222312772)."]}
DOI: 10.5281/zenodo.7437855
title: Scanning electron microscope images of spruce needle homogenate and scanning electron microscope images of isolated small cellular particles from spruce needle homogenate

description: Scanning electron microscope images of spruce needle homogenate and of isolated small cellular particles from spruce needle homogenate are presented. Each image is supplemented by description of the preparation of the sample and the data on the imaging technique and equipment. The data are curated by Veronika Kralj-Iglic and University of Ljubljana, Faculty of Health Sciences, Laboratory of Clinical Biophysics, and Anna Romolo, presently at University of Ljubljana, Faculty of Electrical Engineering, Laboratory of Physics, Ljubljana, Slovenia. Present address of Marko Jeran is: Department of Inorganic Chemistry and Technology, “Jožef Stefan” Institute, Ljubljana, Slovenia.
description: {"references": ["Mantile , F.; Kisovec, M.; Adamo , G.; Romancino , D.P.; Ho\u010devar, M.; Bo\u017ei\u010d, D.; Bedina Zavec, A.; Podobnik, M.; Stoppelli , M.P.; Kisslinger , A.; Bongiovanni , A.; Kralj Igli\u010d, V.; Liguori , G.L. A Novel Localization in Human Large Extracellular Vesicles for the EGF CFC Founder Member CRIPTO and Its Biological and Therapeutic Implications . Cancers 2022, 14, 3700. https://doi.org/10.3390/cancers14153700).", "(Bo\u017ei\u010d, D.; Ho\u010devar, M.; Kisovec, M.; Pajni\u010d, M.; Pa\u0111en , L.; Jeran, M.; Zavec Bedina, A.; Podobnik, M.; Kogej, K.; Igli\u010d, A.; Kralj Igli\u010d, V. Stability of erythrocyte derived nanovesicles assessed by light scattering and electron microsco py . Int J Mol Sci . 2021, 22, 12772. doi:10.3390/ijms222312772)."]}
DOI: 10.5281/zenodo.7438567
title: Cowpea GWAS drought stress in early vegetative stage

description: The GWAS outputs for Cowpea (<em>Vigna unguiculata</em>) responses to drought stress at early vegetative stress. The cowpea seedlings (miniCore population) were exposed to drought stress at 17 days after germination using the weight of the pot and AAWEsmo device, developed in Julkowska Lab, Boyce Thompson Institute. The seedlings were kept at 60 and 10% of soil water holding capacity for 2 weeks and the data on cowpea shoot size, evapotranspiration and photosystem II efficiency was collected. The data was assembled and curated (https://rpubs.com/mjulkowska/Cowpea2022alltraits), and subsequently used for GWAS. The GWAS data was analyzed, and the most interesting associations were selected (https://rpubs.com/mjulkowska/Cowpea2022Gwas). The raw data was collected by Hayley Sussman, with help of Olga Khmelnitsky, while GWAS was performed by Magdalena Julkowska, using ASReml script developed by Arthur Korte (https://github.com/arthurkorte/GWAS), adapted for cowpea.
DOI: 10.5281/zenodo.7438566
title: Cowpea GWAS drought stress in early vegetative stage

description: The GWAS outputs for Cowpea (<em>Vigna unguiculata</em>) responses to drought stress at early vegetative stress. The cowpea seedlings (miniCore population) were exposed to drought stress at 17 days after germination using the weight of the pot and AAWEsmo device, developed in Julkowska Lab, Boyce Thompson Institute. The seedlings were kept at 60 and 10% of soil water holding capacity for 2 weeks and the data on cowpea shoot size, evapotranspiration and photosystem II efficiency was collected. The data was assembled and curated (https://rpubs.com/mjulkowska/Cowpea2022alltraits), and subsequently used for GWAS. The GWAS data was analyzed, and the most interesting associations were selected (https://rpubs.com/mjulkowska/Cowpea2022Gwas). The raw data was collected by Hayley Sussman, with help of Olga Khmelnitsky, while GWAS was performed by Magdalena Julkowska, using ASReml script developed by Arthur Korte (https://github.com/arthurkorte/GWAS), adapted for cowpea.
DOI: 10.6084/m9.figshare.19435760
title: Macroevolution of protective coloration across caterpillars reflects relationships with host plants

description: data, phylogenetic tree, and other input files used to explore associations between color, pattern, and diet ecology in 1808 species of larval Lepidoptera (caterpillars). Associated scripts are hosted on Github (moria-robinson).
DOI: 10.6084/m9.figshare.19435760.v2
title: Macroevolution of protective coloration across caterpillars reflects relationships with host plants

description: data, phylogenetic tree, and other input files used to explore associations between color, pattern, and diet ecology in 1808 species of larval Lepidoptera (caterpillars). Associated scripts are hosted on Github (moria-robinson).
DOI: 10.5287/bodleian:zvnyvrw7r
title: Local Field Potential (LFP) data recorded from externalized Essential Tremor DBS Patients during 3 upper-limb movement tasks
DOI: 10.5281/zenodo.7438625
title: AI-SPRINT GPU STochastic Scheduler

description: This repository includes the source code and the datasets used to evaluate the GPU STochastic Scheduler developed in the context of the AI-SPRINT project. The corresponding results are included in the AI-SPRINT project deliverable "D3.3 - Second release and evaluation of the runtime environment".
DOI: 10.5281/zenodo.7438624
title: AI-SPRINT GPU STochastic Scheduler

description: This repository includes the source code and the datasets used to evaluate the GPU STochastic Scheduler developed in the context of the AI-SPRINT project. The corresponding results are included in the AI-SPRINT project deliverable "D3.3 - Second release and evaluation of the runtime environment".
DOI: 10.6084/m9.figshare.21725411
title: Perceived academic stress, hair and saliva cortisol concentrations, and their relationship with anthropometric measures associated with obesity in first year medical students.

description: Cortisol plays an important role between stress, weight gain, and the development of obesity. Therefore, we investigated the association between stress, eating behavior, cortisol, and anthropometric measures related to obesity in a sample of medical students. We determined cortisol concentrations by ELISA and related it to self-reported stress, eating behavior, and anthropometric measurements throughout the academic period. We report an increase in hair cortisol, higher self-reported stress scores, and BMI mainly in females. Finally, we found evidence of positive associations between capillary cortisol and BMI. Also, eating behavior is affected by perceived stress mainly in females. In this database, we provide weight variables, BMI, psychometric tests, and hormonal determinations. You can see two sheets in the Excel file. Sheet 1 includes the raw data and sheet 2 includes a description of each variable, as well as the bibliography (article or book) where each survey or protocol was obtained. In addition, the data specify the units of the hormonal variables, as well as the units of the anthropometric variables. If you have questions about the interpretation of psychometric test scores, you can contact our team for further details.
DOI: 10.6084/m9.figshare.21725411.v1
title: Perceived academic stress, hair and saliva cortisol concentrations, and their relationship with anthropometric measures associated with obesity in first year medical students.

description: Cortisol plays an important role between stress, weight gain, and the development of obesity. Therefore, we investigated the association between stress, eating behavior, cortisol, and anthropometric measures related to obesity in a sample of medical students. We determined cortisol concentrations by ELISA and related it to self-reported stress, eating behavior, and anthropometric measurements throughout the academic period. We report an increase in hair cortisol, higher self-reported stress scores, and BMI mainly in females. Finally, we found evidence of positive associations between capillary cortisol and BMI. Also, eating behavior is affected by perceived stress mainly in females. In this database, we provide weight variables, BMI, psychometric tests, and hormonal determinations. You can see two sheets in the Excel file. Sheet 1 includes the raw data and sheet 2 includes a description of each variable, as well as the bibliography (article or book) where each survey or protocol was obtained. In addition, the data specify the units of the hormonal variables, as well as the units of the anthropometric variables. If you have questions about the interpretation of psychometric test scores, you can contact our team for further details.
DOI: 10.15482/usda.adc/1528345
title: Data from: Modeling the Spread of a Livestock Disease With Semi-Supervised Spatiotemporal Deep Neural Networks

description: This dataset contains the spatiotemporal data used to train the spatiotemporal deep neural networks described in "Modeling the Spread of a Livestock Disease With Semi-Supervised Spatiotemporal Deep Neural Networks". The dataset consists of two sets of NumPy arrays. The first set: X_grid.npy and Y_grid.npy were used to train the convolutional LSTM, while the second set: X_graph.npy, Y_graph.npy, and edge_index.npy were used to train the graph convolutional LSTM. The data consists of spatiotemporally varying environmental and anthropogenic variables along with case reports of vesicular stomatitis.
DOI: 10.5281/zenodo.7438648
title: PLOS Open Science Indicators & Zotero Romania Metadata

description: Matched metadata from PLOS Open Science Indicators and Zotero export
description: {"references": ["Public Library of Science (2022): PLOS Open Science Indicators. Public Library of Science. Dataset. https://doi.org/10.6084/m9.figshare.21687686.v1"]}
DOI: 10.5281/zenodo.7438647
title: PLOS Open Science Indicators & Zotero Romania Metadata

description: Matched metadata from PLOS Open Science Indicators and Zotero export
description: {"references": ["Public Library of Science (2022): PLOS Open Science Indicators. Public Library of Science. Dataset. https://doi.org/10.6084/m9.figshare.21687686.v1"]}
DOI: 10.13012/b2idb-9081595_v1
title: Potential Impacts of Supersonic Aircraft on Stratospheric Ozone and Climate

description: This datasets provide basis of our analysis in the paper - Potential Impacts of Supersonic Aircraft on Stratospheric Ozone and Climate. All datasets here can be categorized into emission data and model output data (WACCM). All the model simulations (background and perturbation) were run to steady-state and only the datasets used in analysis are archived here.
DOI: 10.6084/m9.figshare.21725441.v1
title: Country totals GIR, Nirrig

description: (European) Country data for: - Gross irrigation requirements (km3/yr) - N in irrigation water sources (Gg N/yr) - N in irrigation water sources (kg N/(ha.yr)) <br> <br>
DOI: 10.3886/e170541v2
title: National Getis-Ord Gi* statistics for select populations; 1990-2019

description: Local Getis-Ord Gi* statistics were calculated as a measure of residential racial segregation. Measures were calculated at the census tract level on the proportion of non-Hispanic White, non-Hispanic Black, non-Hispanic Asian [and Pacific Islander for 1990 and 2000 census], and Hispanic persons per census tract. Gi* statistics are Z-scores that compare the proportion of the population in the focal tract and its neighboring tracts, to the average proportion of a larger geographic unit. For the majority of tracts, the larger geographic unit was the Core-Based Statistical Area (CBSA) these tracts belonged to, and for the minority of tracts that fell outside the boundaries of a CBSA, the County was used as the larger unit.<br><br>Data for the measures were obtained from the IPUMS National Historical Geographic Information System (NHGIS) data finder. Data were downloaded for the 1990 and 2000 census, and the 2006-2009, 2010-2014, and 2015-2019 5-year American Community Survey (ACS) estimates. Geographically standardized time series tables were used for 1990 and 2000 census data. All other ACS data were standardized to 2010 census tract boundaries.<br><br>G*statistics were calculated using both Rook and Queen conceptualization of spatial relationships. With Rook contiguity, neighbors are determined by those that share a common edge only, while Queen contiguity neighbors are those that share both an edge or a "corner" (common vertex). See detailed documentation for further details.<br><br><br>
description: Proportion of persons non-Hispanic White, non-Hispanic Black, non-Hispanic Asian and Pacific Islander, and Hispanic in 1990. <br>Proportion of persons non-Hispanic White, non-Hispanic Black, non-Hispanic Asian and Pacific Islander, and Hispanic in 2000. <br>Proportion of persons non-Hispanic White, non-Hispanic Black, non-Hispanic Asian, and Hispanic; 2006-2009 5-year ACS estimates. <br>Proportion of persons non-Hispanic White, non-Hispanic Black, non-Hispanic Asian, and Hispanic; 2010-2014 5-year ACS estimates.<br>Proportion of persons non-Hispanic White, non-Hispanic Black, non-Hispanic Asian, and Hispanic; 2015-2019 5-year ACS estimates. <br>. Smallest Geographic Unit: Census tract