cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25442/hku.17696075.v1
title: Supporting data for 'Targeting CHK2 to Reverse Tamoxifen Resistance by Reducing BQ323636.1 expression in Estrogen Receptor Positive Breast Cancer'

description: This data set is for the thesis entitled 'Targeting CHK2 to Reverse Tamoxifen Resistance by Reducing BQ323636.1 expression in Estrogen Receptor Positive Breast Cancer'. This data set contained cell response data to the drug Tamoxifen and PV1019. Specifically, cell viability data was recorded when both drugs were applied to breast cancer cell lines. In addition, data from assays and experiments were also included.
DOI: 10.25442/hku.17696765
title: Supporting data for “Roles of RNA-binding proteins in thermogenesis”

description: This study is to investigate the dynamics and functional properties of RNA-binding proteins in brown adipose tissue during cold exposure. All wild type mice were purchased from Laboratory Animal Unit at the University of Hong Kong. At 7-week-old of age, mice were placed in rodent incubator at thermoneutrality (30 degree celsius) for 2 weeks. Afterward, mice were exposed to cold (6 degree celsius) for the different period of time. By the end of cold challenge, brown adipose tissue was harvested and multiple RNA-binding proteins were anlaysed by immunoblotting, immunostaining and Real Time PCR.
DOI: 10.25442/hku.17696765.v1
title: Supporting data for “Roles of RNA-binding proteins in thermogenesis”

description: This study is to investigate the dynamics and functional properties of RNA-binding proteins in brown adipose tissue during cold exposure. All wild type mice were purchased from Laboratory Animal Unit at the University of Hong Kong. At 7-week-old of age, mice were placed in rodent incubator at thermoneutrality (30 degree celsius) for 2 weeks. Afterward, mice were exposed to cold (6 degree celsius) for the different period of time. By the end of cold challenge, brown adipose tissue was harvested and multiple RNA-binding proteins were anlaysed by immunoblotting, immunostaining and Real Time PCR.
DOI: 10.25442/hku.17696798
title: Supporting data for "CRISPR-based applications in next-generation diagnostic and pathogenesis in enteroviruses"

description: Clustered regularly interspaced short palindromic repeats (CRISPR) is a versatile gene-editing technology that is widely used in life science research to improve human health. The advancement of CRISPR technologies provided comprehensive information on the pathogenesis of emerging infectious pathogens and their potential applications in rapid detection. In this study, two CRISPR-Cas technologies were being employed in an attempt to improve the diagnosis and elucidate the pathogenesis in enteroviruses. <br><br>In the first part of my study, CRISPR-Cas9-based genome-wide functional screenings were conducted to discover potential host factors for the pathogenesis of enteroviruses.<br><br>In the second part of my study, integration of multiplex RT-LAMP and CRISPR-Cas12a was introduced for the development of a rapid diagnostic tool for EV infection. <br><br>This dataset consists data I generated in my PhD study, particularly for the CRISPR-Cas9 screening project, CRISPR-Cas12a diagnostic project, HCoV-229E project, conferences, and presentations.
DOI: 10.25442/hku.17696798.v1
title: Supporting data for "CRISPR-based applications in next-generation diagnostic and pathogenesis in enteroviruses"

description: Clustered regularly interspaced short palindromic repeats (CRISPR) is a versatile gene-editing technology that is widely used in life science research to improve human health. The advancement of CRISPR technologies provided comprehensive information on the pathogenesis of emerging infectious pathogens and their potential applications in rapid detection. In this study, two CRISPR-Cas technologies were being employed in an attempt to improve the diagnosis and elucidate the pathogenesis in enteroviruses. <br><br>In the first part of my study, CRISPR-Cas9-based genome-wide functional screenings were conducted to discover potential host factors for the pathogenesis of enteroviruses.<br><br>In the second part of my study, integration of multiplex RT-LAMP and CRISPR-Cas12a was introduced for the development of a rapid diagnostic tool for EV infection. <br><br>This dataset consists data I generated in my PhD study, particularly for the CRISPR-Cas9 screening project, CRISPR-Cas12a diagnostic project, HCoV-229E project, conferences, and presentations.
DOI: 10.5281/zenodo.5811810
title: Exploring Mechanistic Routes for Light Alkane Oxidation with an Iron-Triazolate Metal–Organic Framework

description: Dataset to accompany "Exploring Mechanistic Routes for Light Alkane Oxidation with an Iron-Triazolate Metal–Organic Framework" by Andrew S. Rosen, Justin M. Notestein, and Randall Q. Snurr
DOI: 10.5281/zenodo.5811809
title: Exploring Mechanistic Routes for Light Alkane Oxidation with an Iron-Triazolate Metal–Organic Framework

description: Dataset to accompany "Exploring Mechanistic Routes for Light Alkane Oxidation with an Iron-Triazolate Metal–Organic Framework" by Andrew S. Rosen, Justin M. Notestein, and Randall Q. Snurr
DOI: 10.6084/m9.figshare.17871731
title: Quantifying the fractal dimension and morphology of individual atmospheric soot aggregates

description: This is the full dataset shown in the figures and tables in This is the full dataset shown in the figures and tables in <b><i>Quantifying teh fractal dimension and morphology of individual atmospheric soot aggregates</i></b>
DOI: 10.6084/m9.figshare.17871731.v1
title: Quantifying the fractal dimension and morphology of individual atmospheric soot aggregates

description: This is the full dataset shown in the figures and tables in This is the full dataset shown in the figures and tables in <b><i>Quantifying teh fractal dimension and morphology of individual atmospheric soot aggregates</i></b>
DOI: 10.48370/ofd/qpqhct
title: Ragnhildiana ferruginea (Fuckel) U.Braun, C.Nakash., Videira Crous, 1995

description: Fungarium Mikromycetes
DOI: 10.5281/zenodo.5819458
title: assembly

description: assembly
DOI: 10.5281/zenodo.5819457
title: assembly

description: assembly
DOI: 10.17179/excli2021-4347/supplementary_data
title: Feeding to satiation induces mild oxidative/carbonyl stress in the brain of young mice

description: Intermittent fasting as a dietary intervention can prevent overweight and obesity in adult organisms. Nevertheless, information regarding consequences of intermittent fasting for redox status and reactive metabolite-mediated processes that are crucial for the normal functioning of organisms is limited. Since the information on effects of intermittent fasting on parameters of oxidative/carbonyl stress in the brains of young mice was absent, the present study addressed these questions using an every-other-day fasting (EODF) protocol. The levels of carbonyl proteins were ~28 %, 22 % and 18 % lower in the cerebral cortex of EODF males and females and middle parts of the brain of EODF males, respectively, as compared to their ad libitum fed counterparts. Lipid peroxides and α-dicarbonyl compounds were lower only in the cortex and medulla part of EODF male brain. The EODF regimen resulted in higher total non-specific antioxidant capacity in different parts of male brain and a tendency to be higher this parameter in females. At the same time, EODF regimen had no effect on the activities of the defensive antioxidant enzymes, namely superoxide dismutase, catalase, glutathione-S-transferase, glutathione peroxidase, glyoxylase 1 and glucose-6-phosphate dehydrogenase in the cortex of both sexes, but even decreased activities of these enzymes in medulla and middle part of the brain. In general, the results suggest that in the brain of young mice ad libitum feeding induces mild oxidative/carbonyl stress which may be partially alleviated by the EODF regimen. The effect of EODF regimen is more pronounced in the medulla part than in the cortex.
description: EXCLI Journal; 21:Doc77; ISSN 1611-2156
DOI: 10.34740/kaggle/dsv/3006814
title: AutoXGB
DOI: 10.5281/zenodo.5819673
title: version1

description: version1
DOI: 10.5281/zenodo.5819672
title: version1

description: version1
DOI: 10.6084/m9.figshare.17372763
title: Bracken_RScripts_ESM.zip from Flexible group cohesion and coordination, but robust leader–follower roles, in a wild social primate using urban space

description: Zip file of R scripts containing code to reproduce data used in main analyses.
DOI: 10.6084/m9.figshare.17372772
title: Bracken_Dataframes_ESM.zip from Flexible group cohesion and coordination, but robust leader–follower roles, in a wild social primate using urban space

description: Zip file of dataframes used in models. Information about each dataframe is provided in Supplementary Materials.
DOI: 10.6084/m9.figshare.17372763.v1
title: Bracken_RScripts_ESM.zip from Flexible group cohesion and coordination, but robust leader–follower roles, in a wild social primate using urban space

description: Zip file of R scripts containing code to reproduce data used in main analyses.
DOI: 10.6084/m9.figshare.17372772.v2
title: Bracken_Dataframes_ESM.zip from Flexible group cohesion and coordination, but robust leader–follower roles, in a wild social primate using urban space

description: Zip file of dataframes used in models. Information about each dataframe is provided in Supplementary Materials.
DOI: 10.6084/m9.figshare.17372772.v1
title: Bracken_Dataframes_ESM.zip from Flexible group cohesion and coordination, but robust leader–follower roles, in a wild social primate using urban space

description: Zip file of dataframes used in models. Information about each dataframe is provided in Supplementary Materials.
DOI: 10.24378/exe.3763
title: Strong Coupling of Multimolecular Species to Soft Microcavities (dataset)

description: This is the dataset used for the Vasista and Barnes (2022) article "Strong Coupling of Multimolecular Species to Soft Microcavities" published in the Journal of Physical Chemistry Letter.
description: Raw data for figures as text file.
description: The article associated with this dataset is available in ORE at: http://hdl.handle.net/10871/128285
DOI: 10.6084/m9.figshare.17306372
title: Mid-Miocene volcanism SCION model outputs

description: Outputs from SCION biogeochmical cycle modelling as presented in "Assessing volcanic controls on Miocene climate change"by Jack Longman et al., GRL
DOI: 10.6084/m9.figshare.17306372.v1
title: Mid-Miocene volcanism SCION model outputs

description: Outputs from SCION biogeochmical cycle modelling as presented in "Assessing volcanic controls on Miocene climate change"by Jack Longman et al., GRL
DOI: 10.5281/zenodo.5819403
title: Generating Annual 4-m Land Cover Products over 28 Metropolises in China during 2000-2020

description: A 4-m fine-grained land cover products over the 28 provincial capital cities in China (mainly in temperate monsoon climate and subtropical monsoon climate zone, and categorized into 7 classes, i.e., cropland, forest, grass, shrub, water, impervious surface, and bare land) is generated through the proposed model; A 4-m annual land cover products during 2000-2020 in Wuhan, China is generated through the proposed model. To validate the effectiveness of the derived products, three verification approaches are employed. 1) evaluation by the consistency with the contemporary products including 10-m Esri Land Cover, 10-m FROMGLC10, and 30-m GlobeLand30 ; 2) evaluation by the publicly certified 4-m annotation dataset GID; 3) evaluation by the third-party-created annotation samples. The validation results can be viewed in the manuscript, and the reproduction executation details can be viewed at Readme.txt. The products is in .tif format, and validaiton region is in ENVI/hdr format. Users need to install ENVI software or Arcgis to read the product.
DOI: 10.5281/zenodo.5819669
title: Supplementary files for Reconstructing Kinetic Models for Dynamical Studies of Metabolism using Generative Adversarial Networks, additional part 2

description: <strong>Supplementary files containing datasets needed to reproduce the results of the manuscript "Reconstructing Kinetic Models for Dynamical Studies of Metabolism using Generative Adversarial Networks" by S. Choudhury et al.</strong> The code to use with these data and reproduce the manuscript results is available at https://github.com/EPFL-LCSB/rekindle and https://gitlab.com/EPFL-LCSB/rekindle. The execution of parts of this code is dependent on the SkimPy toolbox (https://github.com/EPFL-LCSB/skimpy). Refer to the readme files on the REKINDLE code repositories for more details. <strong>Temporal evolution of perturbations in non-linear ordinary differential equations</strong> <strong>ode_solutions_physiology1_ORACLE.zip</strong> - contains 100 subfolders, each subfolder containing the time-series evolution data of 1000 kinetic models parameterized by ORACLE generated parameter sets for physiology 1, each of the 1000 models having a random perturbation. The detailed instructions and the main body of the dataset is available here: https://zenodo.org/record/5803120
DOI: 10.5281/zenodo.5819668
title: Supplementary files for Reconstructing Kinetic Models for Dynamical Studies of Metabolism using Generative Adversarial Networks, additional part 2

description: <strong>Supplementary files containing datasets needed to reproduce the results of the manuscript "Reconstructing Kinetic Models for Dynamical Studies of Metabolism using Generative Adversarial Networks" by S. Choudhury et al.</strong> The code to use with these data and reproduce the manuscript results is available at https://github.com/EPFL-LCSB/rekindle and https://gitlab.com/EPFL-LCSB/rekindle. The execution of parts of this code is dependent on the SkimPy toolbox (https://github.com/EPFL-LCSB/skimpy). Refer to the readme files on the REKINDLE code repositories for more details. <strong>Temporal evolution of perturbations in non-linear ordinary differential equations</strong> <strong>ode_solutions_physiology1_ORACLE.zip</strong> - contains 100 subfolders, each subfolder containing the time-series evolution data of 1000 kinetic models parameterized by ORACLE generated parameter sets for physiology 1, each of the 1000 models having a random perturbation. The detailed instructions and the main body of the dataset is available here: https://zenodo.org/record/5803120
DOI: 10.25625/hetcyb/ho8ere
title: LCBM_1.0_2021.pdf

description: :unav
DOI: 10.25625/hetcyb
title: List of Coptic Biblical Manuscripts (LCBM) Version 1.0

description: The List of Coptic Biblical Manuscripts (LCBM) is a common list of Coptic biblical manuscripts maintained and regularly updated by the INTF Münster (Siegfried G. Richter and Katharina Schröder) and the Coptic Old Testament project at the Göttingen Academy of Sciences and Humanities. It was the result of an agreement between Siegfried Richter and Frank Feder in 2016 to replace the partly overlapping and competing numbering systems of Karlheinz Schüssler's Biblia Coptica and the SMR (Schmitz-Mink-Richter) list of Coptic New Testament manuscripts. The details are outlined in an article in the Journal of Coptic Studies 22.
DOI: 10.5281/zenodo.5820018
title: msd-errors - Random walk data

description: The data related to the random walk components of the msd-error work, including truly random and temporarily anti-correlated random walks at a series of system and step size. These have either be analysed numerically or analytically (using kinisi).<br><br>Created using showyourwork from this GitHub repo.<br>
DOI: 10.6084/m9.figshare.16676719
title: Germination data

description: Germination rate of the sediment revived Chaetoceros resting spores.
DOI: 10.6084/m9.figshare.16676719.v1
title: Germination data

description: Germination rate of the sediment revived Chaetoceros resting spores.
DOI: 10.34740/kaggle/dsv/3006914
title: Omicron daily cases by country (COVID-19 variant)
DOI: 10.6084/m9.figshare.16616659.v2
title: Processed data and R program

description: a flux calculator of the non-steady-state chamber method, which can be used to estimate fluxes of three major greenhouse gases (CH4、CO2、N2O).
DOI: 10.6084/m9.figshare.16616659.v3
title: Processed data and R program

description: a flux calculator of the non-steady-state chamber method, which can be used to estimate fluxes of three major greenhouse gases (CH4、CO2、N2O).
DOI: 10.6084/m9.figshare.16616659.v4
title: Processed data and R program

description: a flux calculator of the non-steady-state chamber method, which can be used to estimate fluxes of three major greenhouse gases (CH4、CO2、N2O).
DOI: 10.6084/m9.figshare.16616659.v6
title: Processed data and R program

description: a flux calculator of the non-steady-state chamber method, which can be used to estimate fluxes of three major greenhouse gases (CH4、CO2、N2O).
DOI: 10.6084/m9.figshare.16616659.v5
title: Processed data and R program

description: a flux calculator of the non-steady-state chamber method, which can be used to estimate fluxes of three major greenhouse gases (CH4、CO2、N2O).
DOI: 10.48370/ofd/luetia
title: Phyllosticta calabrica Sacc. Trott., 3010

description: Fungarium Micromycetes
DOI: 10.48370/ofd/hbmdio
title: Phyllosticta cruenta (Kunze: Fries) Kickx, 4444

description: Fungarium Micromycetes
DOI: 10.15468/7yxrys
title: Rhamnaceae- Polygalaceae

description: This dataset contains the digitized treatments in Plazi based on the original journal article F. Muñoz garmendia, C. Navarro, A. Quintanar, A. Buira (2015): Rhamnaceae- Polygalaceae. Flora Iberica - Plantas vascularles de la Península Ibérica e Islas Baleares. 9: 1-593, ISBN: 978-84-00-09883-4, DOI: http://doi.org/10.5281/zenodo.5820085
DOI: 10.48370/ofd/o7s0yu
title: Phyllosticta polygonorum Saccardo

description: Fungarium Micromycetes
DOI: 10.48370/ofd/z6rpja
title: Phyllosticta salicina Kabát Bubák, 4508

description: Fungarium Micromycetes
DOI: 10.48370/ofd/pgvyxg
title: Phyllosticta sphaeropsoidea Ellis Everhart, 864

description: Fungarium Micromycetes
DOI: 10.5281/zenodo.5776707
title: NIRSpec IFU simulation of the Orion Bar with F100LP/G140H filter

description: This simulation is a NIRSpec 3D cube (two spatial dimensions and one spectral dimension) of the Orion Bar with F100LP/G140H filter. This simulation is part of the Early Release Sciences program PDRs4all (ID1288, http://pdrs4all.org).
DOI: 10.5281/zenodo.5776706
title: NIRSpec IFU simulation of the Orion Bar with F100LP/G140H filter

description: This simulation is a NIRSpec 3D cube (two spatial dimensions and one spectral dimension) of the Orion Bar with F100LP/G140H filter. This simulation is part of the Early Release Sciences program PDRs4all (ID1288, http://pdrs4all.org).
DOI: 10.5281/zenodo.4954582
title: N application rates from mineral fertiliser and manure

description: Historical N application rates from mineral fertiliser and manure. Prepared for Gridded Global Crop Model Intercomparison (GGCMI) project phase 3. Gridded time series of fertiliser application rates are based on national and sub-national estimates for 141 individual crops for the year 2000 from Mueller et al. (2012) and national time series for five different crop groups from LUH2v2 (Hurtt et al., 2020). Gridded time series of manure application rates on cropland are based on total applied manure per grid cell from Zhang et al. (2017) and cropland extent from LUH2v2 (Hurtt et al., 2020). <strong>Reference</strong> Hurtt, G. C., Chini, L., Sahajpal, R., Frolking, S., Bodirsky, B. L., Calvin, K., Doelman, J. C., Fisk, J., Fujimori, S., Klein Goldewijk, K., Hasegawa, T., Havlik, P., Heinimann, A., Humpenöder, F., Jungclaus, J., Kaplan, J. O., Kennedy, J., Krisztin, T., Lawrence, D., … Zhang, X. (2020). Harmonization of global land use change and management for the period 850–2100 (LUH2) for CMIP6. <em>Geoscientific Model Development</em>, <em>13</em>(11), 5425–5464. https://doi.org/10.5194/gmd-13-5425-2020 Mueller, N. D., Gerber, J. S., Johnston, M., Ray, D. K., Ramankutty, N., & Foley, J. a. (2012). Closing yield gaps through nutrient and water management. <em>Nature</em>, <em>490</em>(7419), 254–257. https://doi.org/10.1038/nature11420 Zhang, B., Tian, H., Lu, C., Dangal, S. R. S., Yang, J., & Pan, S. (2017). Global manure nitrogen production and application in cropland during 1860–2014: a 5 arcmin gridded global dataset for Earth system modeling. <em>Earth System Science Data</em>, <em>9</em>(2), 667–678. https://doi.org/10.5194/essd-9-667-2017
DOI: 10.6084/m9.figshare.16696045
title: Chromatin accessibility and transcriptome reveal that bacteriostatic action of Lactobacillus reuteri in pigs

description: <i>L. reuteri</i> is a probiotic with bacteriostasis, which can effectively inhibit the activity of pathogens, and has the potential to act as a feed additive to regulate intestinal microecological balance. However, the mechanism underlying its inhibition of pathogens remains unclear. In this study, we used ATAC-seq and RNA-seq methods to globally delineate the changes of biological processes and accessible chromatin regions in porcine intestinal epithelial cells stimulated by <i>E. coli</i> and <i>S. enterica</i>, as well as the epigenetic mechanisms by which <i>L. reuteri</i> inhibits pathogens. Totally, we provided 15 ATAC-seq and 15 RNA-seq datasets and demonstrated the good quality of the datasets by quality control and reproducibility analysis, in which we found some interested genes and accessible chromatin regions. In conclusion, our data set give new insights into the expression pattern of functional genes after stimulation of IPEC-J2 cells by pathogenic bacteria leading to diarrhea and the epigenetic mechanism of bacteriostatic effect of <i>L. reuteri</i>, and provide a valuable resource for epigenomic studies of bacterial diseases.
DOI: 10.6084/m9.figshare.16696045.v2
title: Chromatin accessibility and transcriptome reveal that bacteriostatic action of Lactobacillus reuteri in pigs

description: <i>L. reuteri</i> is a probiotic with bacteriostasis, which can effectively inhibit the activity of pathogens, and has the potential to act as a feed additive to regulate intestinal microecological balance. However, the mechanism underlying its inhibition of pathogens remains unclear. In this study, we used ATAC-seq and RNA-seq methods to globally delineate the changes of biological processes and accessible chromatin regions in porcine intestinal epithelial cells stimulated by <i>E. coli</i> and <i>S. enterica</i>, as well as the epigenetic mechanisms by which <i>L. reuteri</i> inhibits pathogens. Totally, we provided 15 ATAC-seq and 15 RNA-seq datasets and demonstrated the good quality of the datasets by quality control and reproducibility analysis, in which we found some interested genes and accessible chromatin regions. In conclusion, our data set give new insights into the expression pattern of functional genes after stimulation of IPEC-J2 cells by pathogenic bacteria leading to diarrhea and the epigenetic mechanism of bacteriostatic effect of <i>L. reuteri</i>, and provide a valuable resource for epigenomic studies of bacterial diseases.