cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.8005563
title: Transposon DNA sequences facilitate the tissue-specific horizontal transfer: te expression supplementary datasets

description: These datasets contain data on analyses of TE expression stability. Raw RNA seq counts were processed using DESeq2 R package. Low count genes and TEs were removed. Counts across samples were normalized for library sizes and log-transformed using 'regularized log' transformation. Batch normalization was performed on log-transformed data with ComBat function from sva R package. Expression variability (EV) of TEs and genes (probes) was estimated using the previously described method [1, 2]. 1. Bashkeel, N., Perkins, T.J., Kærn, M. et al. Human gene expression variability and its dependence on methylation and aging. BMC Genomics 20, 941 (2019). https://doi.org/10.1186/s12864-019-6308-7<br> 2. Alemu EY, Carl JW Jr, Corrada Bravo H, Hannenhalli S. Determinants of expression variability. Nucleic Acids Res. 2014;42(6):3503-3514. doi:10.1093/nar/gkt1364 PC.zip - the results of TE expression and stability in prostate cancer. 0.PC.RlogMAD.pdf - count barplots for TE identified with MAD criteria 0.PC.RlogSD.pdf - count barplots for TE identified with SD criteria 0.PC.TE.rlogcpm.mad.xls -stability measures according MAD (median absolute deviance) criteria 0.PC.TE.rlogcpm.sd.xls - stability measures according SD criteria 0.PC_TE_bootstrap.pdf - TE expression stability PC.deseq.logCPM.csv - TE log transformed expression matrix PC.TE_count_table.csv - TE raw count matrix PC_Deseq2data.Rdata - R data object with deseq objet, raw and normalized counts MM.zip - the results of TE expression and stability in multiple myeloma. 0.MM.RlogMAD.pdf - count barplots for TE identified with MAD criteria 0.MM.RlogSD.pdf - count barplots for TE identified with SD criteria 0.MM_TE_bootstrap.pdf - TE expression stability MM.deseq.logCPM.csv - TE raw count matrix MM.rlog.mad.xlsx- stability measures according MAD (median absolute deviance) criteria MM.rlog.sd.xlsx - stability measures according MAD (median absolute deviance) criteria MM.TE_count_table.csv - TE raw count matrix Myeloma_Deseq2data.Rdata - R data object with deseq objet, raw and normalized counts
DOI: 10.34740/kaggle/dsv/6431031
title: S&P500 - Google Trends
DOI: 10.5281/zenodo.8325377
title: Quality flags for Gaia DR3 effective temperatures

description: Quality flags for Gaia DR3 effective temperatures produced with XGBoost model (threshold-250 version). Models are available at https://github.com/iamaleksandra/Gaia-Teff.
DOI: 10.5281/zenodo.8325376
title: Quality flags for Gaia DR3 effective temperatures

description: Quality flags for Gaia DR3 effective temperatures produced with XGBoost model (threshold-250 version). Models are available at https://github.com/iamaleksandra/Gaia-Teff.
DOI: 10.17632/t4kwnyb7pk.1
title: Initiating adalimumab in conjunction with clindamycin and rifampicin improves clinical response in Hidradenitis Suppurativa

description: Supplemental data to: 'Initiating adalimumab in conjunction with clindamycin and rifampicin improves clinical response in Hidradenitis Suppurativa.'
DOI: 10.6084/m9.figshare.24101013
title: MebiPred predictions for UniProt - Jul 2023

description: The files contain the MeBiPred predictions for all the proteins (&gt;248M) listed in UniProtKB - SwissProt and TrEMBL. MeBiPred could be used to screen proteins that bind to metals (Na, K, Mg, Ca, Mn, Fe, Co, Ni, Cu, Zn). Related links:<b>Publication</b>: https://doi.org/10.1093/bioinformatics/btac358<b>Web App</b>: https://services.bromberglab.org/mebipred/home<b>Python Package</b>: https://pypi.org/project/mymetal/<br><br><br>
DOI: 10.6084/m9.figshare.24101013.v1
title: MebiPred predictions for UniProt - Jul 2023

description: The files contain the MeBiPred predictions for all the proteins (&gt;248M) listed in UniProtKB - SwissProt and TrEMBL. MeBiPred could be used to screen proteins that bind to metals (Na, K, Mg, Ca, Mn, Fe, Co, Ni, Cu, Zn). Related links:<b>Publication</b>: https://doi.org/10.1093/bioinformatics/btac358<b>Web App</b>: https://services.bromberglab.org/mebipred/home<b>Python Package</b>: https://pypi.org/project/mymetal/<br><br><br>
DOI: 10.17632/bxkm2chkxw.3
title: Data Package for “Application of biological early warning systems in wastewater treatment plants: Introducing a promising approach to monitor changing wastewater composition”

description: Data Package provided for the Publication “Application of biological early warning systems in wastewater treatment plants: Introducing a promising approach to monitor changing wastewater composition” of the Journal of Environmental Management
DOI: 10.17632/bxkm2chkxw.4
title: Data Package for “Application of biological early warning systems in wastewater treatment plants: Introducing a promising approach to monitor changing wastewater composition”

description: Data Package provided for the Publication “Application of biological early warning systems in wastewater treatment plants: Introducing a promising approach to monitor changing wastewater composition” of the Journal of Environmental Management
DOI: 10.17632/bxkm2chkxw.5
title: Data Package for “Application of biological early warning systems in wastewater treatment plants: Introducing a promising approach to monitor changing wastewater composition”

description: Data Package provided for the Publication “Application of biological early warning systems in wastewater treatment plants: Introducing a promising approach to monitor changing wastewater composition” of the Journal of Environmental Management
DOI: 10.17632/8vtzbrwy9c.1
title: Manganese oxidation states and availability in forest weathering profiles of contrasting climate

description: The data related to: Manganese oxidation states and availability in forest weathering profiles of contrasting climate
DOI: 10.17632/7vrpfhyvjw.1
title: Original data

description: Original data
DOI: 10.5281/zenodo.8325958
title: SciExpeM - 10.5281/zenodo.8325958

description: Yifan Jin , Xin Li , Xin Wang , Zhihao Ma * , Xianglin Chu
DOI: 10.5281/zenodo.8325957
title: SciExpeM - 10.5281/zenodo.8325958

description: Yifan Jin , Xin Li , Xin Wang , Zhihao Ma * , Xianglin Chu
DOI: 10.17632/6tp23c5dp7.1
title: Performance and Profiling Data of Plane-wave Calculations in Quantum ESPRESSO Simulation on Three Supercomputing Centres  

description: This data was the work of the Thammasat University (Lampang Campus) team from benchmarking the Quantum Espresso simulation to complete a task of the 5th APAC HPC-AI 2022 student competition. The benchmarking and profiling results guided the team to adjust some parameters until achieving the best parameter setting guideline to obtain almost linear scalability of the plane-wave calculation (pw.x) on 48 -  1,536 CPUs.  The findings led the team to win the best HPC performance award of the competition. The dataset comprises three parts i.e., the execution traces collected by the Extrae performance profiling tool, the results of a screening experiment running on three HPC centres, and the multi-node performance results when scaling out the workload on the Gadi supercomputer. The profiling data can be used to gain insights into the parallel and distributed execution behaviour of the pw.x function by using the Paraver visualization tool. The performance data of the screening and scaling out experiments could be used for testing different analysis methods or for finding a way to automate the parameter setting. The results also give guidance on computation resources required to calculate the total energy of the catalysts using the self-consistent field method implemented in the Quantum Espresso simulation.
DOI: 10.17632/6tp23c5dp7.2
title: Performance and Profiling Data of Plane-wave Calculations in Quantum ESPRESSO Simulation on Three Supercomputing Centres  

description: This data was the work of the Thammasat University (Lampang Campus) team from benchmarking the Quantum Espresso simulation to complete a task of the 5th APAC HPC-AI 2022 student competition. The benchmarking and profiling results guided the team to adjust some parameters until achieving the best parameter setting guideline to obtain almost linear scalability of the plane-wave calculation (pw.x) on 48 -  1,536 CPUs.  The findings led the team to win the best HPC performance award of the competition. The dataset comprises three parts i.e., the execution traces collected by the Extrae performance profiling tool, the results of a screening experiment running on three HPC centres, and the multi-node performance results when scaling out the workload on the Gadi supercomputer. The profiling data can be used to gain insights into the parallel and distributed execution behaviour of the pw.x function by using the Paraver visualization tool. The performance data of the screening and scaling out experiments could be used for testing different analysis methods or for finding a way to automate the parameter setting. The results also give guidance on computation resources required to calculate the total energy of the catalysts using the self-consistent field method implemented in the Quantum Espresso simulation.
DOI: 10.17632/kg3dfkyjv5.1
title: Single-cell_transcriptome_analysis_illuminating_the_characteristics_of_species-specific_innate_immune_responses_against_viral_infections_Aso_et_al

description: This is a repository of data used in the preprint ([Aso et al., bioRxiv, 2022](https://doi.org/10.1101/2022.12.06.519403)). The details of analytical pipelines are described elsewhere in the paper. The codes used in this study are deposited on GitHub (https://github.com/TheSatoLab/scRNA-seq_PBMC_Animals_Aso_et_al).

As many of the viruses that have emerged in human societies originate from bat species, it is critical to understand the unique characteristics of bat immunity. To describe the differences in innate immune responses against viral infections among animal species, we analysed single-cell RNA sequencing (scRNA-seq) data of peripheral blood mononuclear cells (PBMCs) obtained from humans (Homo sapiens, Hs), chimpanzees (Pan troglodytes, Pt), rhesus macaques (Macaca mulatta), and Egyptian fruit bats (Rousettus aegyptiacus, Ra) stimulated with pathogenic stimuli, including herpes simplex virus type I (HSV-1), Sendai virus (SeV), and lipopolysaccharide (LPS).
DOI: 10.17632/jffvvr9s9m.1
title: Data for A new digital image correlation method for discontinuous measurement in fracture analysis

description: The dataset encompasses the reference and deformed images utilized in the manuscript.
DOI: 10.17632/jffvvr9s9m.2
title: Data for A new digital image correlation method for discontinuous measurement in fracture analysis

description: The dataset encompasses the reference and deformed images utilized in the manuscript.In this case, the subset radius refers to the radius set for the subset when calculating using the DIC method. Cs refers to the splitting threshold. AD-DIC will recompute subsets with correlation coefficients greater than Cs.
DOI: 10.17632/n8sgj48nvd.1
title: Biofilm.jl: A fast solver for one-dimensional biofilm chemistry and ecology

description: Biofilms are communities of microorganisms that grow on virtually all surfaces with sufficient nutrients including aquatic and industrial water systems and medical devices. Biofilms are complex, structured communities where the interplay of growth, metabolism, and competition between species interact with physical processes of diffusion, convection, attachment, and detachment. This work describes a model of a one-dimensional biofilm in a stirred tank reactor that incorporates these complexities. The model is implemented in the modern Julia programming language providing an efficient tool for studying a large variety of biofilms and the intricate communities the microorganisms create. Details of the new software, known as Biofilm.jl, including the mathematical model and organization and execution of the code, are provided. Examples of biofilms modeled using Biofilm.jl are presented such as a single heterotroph, sulfide-oxidizing bacteria (SOB) and sulfate-reducing bacteria (SRB), and a phototroph. Postprocessing tools are described that allow a Biofilm.jl user to make plots and extract specific values from the solution and explore the simulated biofilm results.
DOI: 10.17632/r6zrzdvdd7.1
title: Optimized mineral structures and reduced partition function ratios for indium isotopes

description: We provide mineral structure parameters and the reduced partition function ratios of indium isotopes for indium-bearing minerals.
DOI: 10.17632/h49vtpjm8f.1
title: Cortical - central amygdala - ventral tegmental area – cortical circuits are differentially engaged in initiation and maintenance of social interaction.

description: The raw data from the manuscript: Cortical - central amygdala - ventral tegmental area – cortical circuits are differentially engaged in initiation and maintenance of social interaction. Authors: K. Rojek-Sito, K. Meyza, K. Ziegart-Sadowska, K. Nazaruk, A. Puścian, A. Hamed, M. Kiełbiński, W. Solecki, E. Knapska
DOI: 10.17632/h49vtpjm8f.2
title: Cortical - central amygdala - ventral tegmental area – cortical circuits are differentially engaged in initiation and maintenance of social interaction.

description: he raw data from the manuscript: Neuronal circuits mediating initiation and maintenance of social interaction: role of the central amygdala – ventral tegmental area – anterior cingulate/orbitofrontal cortex network. Authors: K. Rojek-Sito, K. Meyza, K. Ziegart-Sadowska, K. Nazaruk, A. Puścian, A. Hamed, M. Kiełbiński, W. Solecki, E. Knapska
DOI: 10.17632/h49vtpjm8f.3
title: Optogenetic and chemogenetic approaches reveal differences in neuronal circuits that mediate initiation and maintenance of social interaction

description: he raw data from the manuscript: Neuronal circuits mediating initiation and maintenance of social interaction: role of the central amygdala – ventral tegmental area – anterior cingulate/orbitofrontal cortex network. Authors: K. Rojek-Sito, K. Meyza, K. Ziegart-Sadowska, K. Nazaruk, A. Puścian, A. Hamed, M. Kiełbiński, W. Solecki, E. Knapska
DOI: 10.17632/z77jdscnyc.1
title: GBH diaphragm DOHaD

description: Introduction: Glyphosate is an organophosphate herbicide most used in Latin America, with multisystemic effects, including the respiratory system. In this sense, the objective of this research was to analyze the muscle fibers and neuromuscular junctions (NMJs) of the diaphragm muscle of adult mice exposed to the glyphosate-based herbicide in the peripubertal period. Methods: Twelve male mice were used, divided into a control group (CTL, n=6), which received water and a glyphosate-based herbicide group (GBH, n=6), which received 50 mg/Kg/day of Roundup®, both by gavage from 30 to 60 days. At 150 days, the animals were euthanized and the diaphragm was collected for analysis of the muscle fibers through hematoxylin-eosin, Masson's trichrome and Picrossirius Red and the NMJs through the nonspecific esterases reaction. Results: Rounded fibers, hypereosinophilic sarcoplasm and enlarged nuclei were found predominantly in GBH. A reduction in body weight, an increase in muscle fiber morphometry, an increase in type III collagen, a decrease in the overlapping of type I and III collagen, and an increase in the area and greater diameter of the NMJs in GBH were observed. Conclusion: Peripubertal exposure to glyphosate-based herbicides showed morphological changes characteristic of muscle degeneration and altered the morphometry of muscle fibers and NMJs of the diaphragm of adult mice.
DOI: 10.17632/wp37n92fmg.1
title: Fundamental Guidelines on Enhancing Government Communication Effectiveness in the Information Era: A Systematic Literature Review

description: This is the dataset that my team and I used for research on Fundamental Guidelines on Enhancing Government Communication Effectiveness in the Information Era: A Systematic Literature Review
DOI: 10.17632/3cvckr73y9.1
title: Hepatoprotective activity of Berberis aristata bark extracts against Cyclophosphamide induced hepatic damage in albino rats 

description: These data set contains data of 54 Male Wistar albino have weight between 150-250 gm. These data set reports the hepatoprotective properties through  of In-vivo estimation. Data contains numerical as well as imagery data set in favor of potential hepatoprotective activity of bark of plant of Berberis aristata against Cyclophosphamide (CP) induced hepatotoxicity in albino rat.
DOI: 10.1184/r1/23999709
title: Mobility21_data.zip

description: Dataset generated for Mobility21 analysis report on dynamic parking space reservations (also know as 2023-7-17-10minLimit)
DOI: 10.6073/pasta/964d3375e5bbc81847fa72093bb087ef
title: Wrack classification data based on UAV imagery from Dean Creek on Sapelo Island, GA

description: We used a DJI Matrice 210 UAV with a MicaSense Altum to collect a total of 20 images from January 2020 - December 2021 in a the Dean Creek marsh on Sapelo Island, GA. Wrack was classified using a principal component analysis. Wrack patches under 1 m2 were excluded from analyses. Wrack classifications were converted to polygon and point data where each point represents a 5 cm x 5 cm pixel. Those files were then used to analyze wrack characteristics, their relation to environmental drivers, and landscape based patterns. For both polygon and point data, we used the National Elevation Dataset (https://gdg.sc.egov.usda.gov/Catalog/ProductDescription/NED.html) to determine the elevation of each wrack patch. Creeks and shorelines were digitized and used to determine each wrack patches' distance to water. We calculated the frequency of wrack deposition at each point by adding together the number of images where that pixel was classified as wrack over the course of the study. Polygon data were related to tide height from a NOAA tidal station data product (Ft. Pulaski, Station 8670870; https://tidesandcurrents.noaa.gov) and wind speed and wind direction from the Marsh Landing weather station (downloaded data for the SAPMLMET met station from: https://cdmo.baruch.sc.edu/) to evaluate the relationship of wrack to environmental drivers.
DOI: 10.6073/pasta/40f9ae60d635e5aac0e562ee006d24e2
title: Eight Mile Lake Research Watershed, Thaw Gradient: Peak growing season aboveground biomass 2017

description: In this larger study, we are asking the question: Is old carbon that comprises the bulk of the soil organic matter pool released in response to thawing of permafrost? We are answering this question by using a combination of field and laboratory experiments to measure radiocarbon isotope ratios in soil organic matter, soil respiration, and dissolved organic carbon, in tundra ecosystems. The objective of these proposed measurements is to develop a mechanistic understanding of the SOM sources contributing to C losses following permafrost thawing. We are making these measurements at an established tundra field site near Healy, Alaska in the foothills of the Alaska Range. Field measurements center on a natural experiment where permafrost has been observed to warm and thaw over the past several decades. This area represents a gradient of sites each with a different degree of change due to permafrost thawing. As such, this area is unique for addressing questions at the time and spatial scales relevant for change in arctic ecosystems.
DOI: 10.6073/pasta/f502d8fe1a2e1d6c6b035c198af04f3e
title: Eight Mile Lake Research Watershed, Carbon in Permafrost Experimental Heating Research (CiPEHR): physical and chemical properties of soils, 2009-2013

description: The Carbon in Permafrost Experimental Heating Research (CiPEHR) project addresses the following questions: 1) Does ecosystem warming cause a net release of C from the ecosystem to the atmosphere?, 2) Does the decomposition of old C, that comprises the bulk of the soil C pool, influence ecosystem C loss?, and 3) How do winter and summer warming alone, and in combination, affect ecosystem C exchange? We are answering these questions using a combination of field and laboratory experiments to measure ecosystem carbon balance and radiocarbon isotope ratios at a warming experiment located in an upland tundra field site near Healy, Alaska in the foothills of the Alaska Range. This data set includes measurements of moisture, bulk density, ash, carbon, and nitrogen concentrations, and carbon and nitrogen stable isotope composition (?13C and ?15N) at depth increments in soil cores collected in 2009, 2010, 2011, and 2013 from warming and control treatment plots.
DOI: 10.17894/ucph.f2b0fe46-587d-4084-a24b-c2577cc1680b
title: ackground data for the paper Effect of natural and regulatory conditions on the environmental impacts of pig slurry acidification across different regions in Europe A life cycle assessment
DOI: 10.5281/zenodo.8300016
title: Data for submitted manuscript "Connections between Sub-cloud Coherent Structures and the Life Cycle of Shallow Cumulus Clouds: Evidence from Large Eddy Simulation"

description: This is the dataset for a submitted manuscript "Connections between Sub-cloud Coherent Structures and the Life Cycle of Shallow Cumulus Clouds: Evidence from Large Eddy Simulation" for peer review. The NetCDF file includes masked objects for sub-cloud coherent structures and cloud for tracking.
DOI: 10.5281/zenodo.8300015
title: Data for submitted manuscript "Connections between Sub-cloud Coherent Structures and the Life Cycle of Shallow Cumulus Clouds: Evidence from Large Eddy Simulation"

description: This is the dataset for a submitted manuscript "Connections between Sub-cloud Coherent Structures and the Life Cycle of Shallow Cumulus Clouds: Evidence from Large Eddy Simulation" for peer review. The NetCDF file includes masked objects for sub-cloud coherent structures and cloud for tracking.
DOI: 10.17028/rd.lboro.22303765
title: Research data underlying the manuscript "Classification of Doubly Excited Molecular Electronic States" by M. T. do Casal, J. M. Toldo, M. Barbatti and F. Plasser.

description: Research data underlying the manuscript "Classification of Doubly Excited Molecular Electronic States" by M. T. do Casal, J. M. Toldo, M. Barbatti and F. Plasser. Content: Single point calculations were performed on the systems below. Each molecule folder contains subfolders with inputs and outputs at the electronic structure level indicated below. <br> 1. Formaldehyde Dimer a. ADC(3) 2. Polyenes a. DFT/MRCI b. ADC(3) c. MRCISD d. TDDFT 3. Cycloaddtion of Ethylene a. MRCISD 4. DPP Dimer a. DFT/MRCI 5. Tetracene Dimer a. DFT/MRCI 6. Tetrazine a. DFT/MRCI 7. bis-Thiophene a. DFT/MRCIa singlets <br> DFT/MRCI folders contain the following files: control: TURBOMOLE's input file coord: Input geometry for TURBOMOLE and DFT/MRCI mrci.inp: Input file for DFT/MRCI run_dftci.inp: Input file for the driver interfacing TURBOMOLE and DFT/MRCI mrci.sum: Summary of DFT/MRCI calculations <br> ADC(3) folders contain the following files: qchem-monomer.in: Q-Chem input file qchem.out: Q-Chem output file libwfa_summ.txt: Output file summarising excited state properties <br> MRCISD folders contain: INPUT directory: All necessary input files for COLUMBUS LISTINGS: All output files generated by COLUMBUS <br> TDDFT folders contain: coord.qchem: Input geometry for Q-Chem qchem.in: Q-Chem input file qchem.out: Q-Chem output file libwfa_summ.txt: Output file summarising excited state properties <br> Output files for TheoDORE summarising excited state properties are also provided: tden_summ.txt: Output file from TheoDORE for the transition density matrix analysis sden_summ.txt.: Output file from TheoDORE for the state density matrix analysis. <br> All results used for plotting are compiled in two datasets: cycloaddition.csv and polyenes.csv.