cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25345/c5r20s715
title: MassIVE MSV000094098 - Mannose-6-phosphate isomerase functional status shapes a rearrangement in the proteome and degradome of mannose-treated melanoma cells
title: Metabolic reprogramming is a ubiquitous feature of transformed cells, comprising one of the hallmarks of cancer and enabling neoplastic cells to adapt to new environments. Accumulated evidence reports on the failure of some neoplastic cells to convert mannose-6-phosphate into fructose-6-phosphate, thereby impairing tumor growth in cells displaying low levels of the enzyme mannose-6-phosphate isomerase (MPI). Thus, we performed functional analyses and profiled the proteome landscape and the repertoire of substrates of proteases (degradome) of melanoma cell lines with distinct mutational backgrounds submitted to the treatment with mannose. Our results suggest a significant rearrangement in the proteome and degradome of melanoma cells lines upon mannose treatment, including the activation of catabolic pathways (such as protein turnover) and differences in protein N-terminal acetylation. Such biological implications might reflect the metabolic rewiring caused by the functional status of MPI enzyme and may help target specific molecular players from affected signaling circuits in melanoma.
DOI: 10.25934/pr00006871.1
title: Available IPD datapackage for study 'A Randomized, Double-blind, Multicenter, Active-controlled Study to Evaluate the Efficacy, Safety, and Tolerability of Fixed Doses of Intranasal Esketamine Plus an Oral Antidepressant in Adult Subjects With Treatment-resistant Depression'

description: The purpose of this study is to compare the efficacy and safety of switching treatment-resistant depression (TRD) participants from a prior antidepressant treatment (to which they have not responded) to either intranasal esketamine plus a new oral antidepressant or switching to a new oral antidepressant plus intranasal placebo.
DOI: 10.7294/25222304
title: Behaviors Associated with Behavioral Euthanasia in Pet Dogs Questionnaire Data

description: Provides the survey results of the Behavioral Euthanasia in Pet Dogs Questionnaire for sections pertaining to behavior problems. Collected in QuestionPro. Data from questions 56-84 not included with this data publication.
DOI: 10.7294/25222304.v1
title: Behaviors Associated with Behavioral Euthanasia in Pet Dogs Questionnaire Data

description: Provides the survey results of the Behavioral Euthanasia in Pet Dogs Questionnaire for sections pertaining to behavior problems. Collected in QuestionPro. Data from questions 56-84 not included with this data publication.
DOI: 10.5281/zenodo.10671391
title: Dataset related to article: Coexistence of SCN4A and CLCN1 mutations in a family with atypical myotonic features: a clinical and functional study

description:      Next Generation Sequencing, Functional characterization of K1302R on channel Nav1.4 and of H838P on ClC-1 channel.
DOI: 10.5281/zenodo.10671392
title: Dataset related to article: Coexistence of SCN4A and CLCN1 mutations in a family with atypical myotonic features: a clinical and functional study

description:      Next Generation Sequencing, Functional characterization of K1302R on channel Nav1.4 and of H838P on ClC-1 channel.
DOI: 10.25934/pr00006872.1
title: Available IPD datapackage for study 'A Randomized, Double-blind, Multicenter, Active-controlled Study to Evaluate the Efficacy, Safety, and Tolerability of Flexible Doses of Intranasal Esketamine Plus an Oral Antidepressant in Adult Subjects With Treatment-resistant Depression'

description: The purpose of this study is to compare the efficacy and safety of switching treatment-resistant depression (TRD) subjects from a prior antidepressant treatment (to which they have not responded) to either intranasal esketamine plus a new oral antidepressant or switching to a new oral antidepressant plus intranasal placebo.
DOI: 10.5066/p1qtrneb
title: Hydrodynamic model of the Colorado River, Glen Canyon Dam to Lees Ferry in Glen Canyon National Recreation Area, Arizona: tables of model results and accuracy assessment

description: These data were compiled to provide a resource for other researchers interested in water-surface elevations and flow velocity across a wide range of discharge in the study reach for the project. Objective(s) of our study were to construct a two-dimensional hydrodynamic model for the 15.8 mile tailwater reach of the Colorado River in Glen Canyon between Glen Canyon Dam and Lees Ferry, Arizona. These data represent the results of the two-dimensional modeling effort with each data table (50) including the results of each run of the model. Additionally, other data represent a comparison of modeled water surface elevations to measured water surface elevations for historic Bureau of Reclamation cross sections in the study reach. These data were generated by U.S. Geological Survey personnel on PC-based computers in Flagstaff, Arizona in 2019 using the FaSTMECH solver in the iRIC modeling interface (https://i-ric.org/en/solvers/fastmech/). These data can be a useful resource to researchers interested in water-surface elevations, shoreline extents, water depths, velocities, and other hydraulic characteristics across a range of discharges within the 15.8 mile tailwater reach of the Colorado River in Glen Canyon between Glen Canyon Dam and Lees Ferry, Arizona.
DOI: 10.6073/pasta/2c4c912178519f67e63c78f67fe25530
title: Harvard Forest Schoolyard LTER Data since 2004

description: In the Harvard Forest Schoolyard LTER program, HF ecologists work directly with teachers from public and private schools across New England (and the eastern U.S.) to learn about and initiate ecological research in their classrooms and schoolyards. More than 3500 students each year from grades 4-12 participate in authentic, field-based research projects that address current and important environmental issues. Projects to date have included tree phenology, the hemlock woolly adelgid, vernal pools, intermittent streams, and long-term forest plots. Participating schools submit data to an online database on the Harvard Forest website where the data are reviewed by HF staff and then made freely available for download and for graphing online. The project is supported by the LTER program at the National Science Foundation, the Highstead Foundation, the Salata Institute for Climate and Sustainability at Harvard University, and private donors.
 For current data, please see: https://harvardforest2.fas.harvard.edu/asp/hf/php/k12/k12_project.php.
DOI: 10.4231/r77942vg
title: Ortho-Rectified UAS Air Photo of Staged Crash Scene at INDOT District Office

description: UAS images collected on July 14, 2017, at the Indiana Department of Transportation Crawfordsville District Office. Additional details are provided in the description below.
DOI: 10.4231/r7x63k3m
title: Data for Neural Encoding and Decoding with Deep Learning for Dynamic Natural Vision Tests - Subject 1

description: This is a video-fMRI dataset for subject 1 (out of three) acquired by the Laboratory of Integrated Brain Imaging (LIBI),
DOI: 10.5281/zenodo.10666169
title: Data supporting the research DIV

description: Data are reported in .dat files, organized in columns. Comments describe the content of .dat files.  Figures can be generated running the .p files which are Gnuplot scripts that read the .dat files.

In the Oblate-to-toroidal-MEP directory, the folder "Fields" contains the phase-field of each string image in the r-z plane, together with the r- and z-component of the forces. 

Energies are made dimensionless by dividing by the bending energy of a sphere (8 pi k), while lenghts are scaled with the diffuse interface width parameter 6epsilon = 5 nm.
DOI: 10.5281/zenodo.10666170
title: Data supporting the research DIV

description: Data are reported in .dat files, organized in columns. Comments describe the content of .dat files.  Figures can be generated running the .p files which are Gnuplot scripts that read the .dat files.

In the Oblate-to-toroidal-MEP directory, the folder "Fields" contains the phase-field of each string image in the r-z plane, together with the r- and z-component of the forces. 

Energies are made dimensionless by dividing by the bending energy of a sphere (8 pi k), while lenghts are scaled with the diffuse interface width parameter 6epsilon = 5 nm.
DOI: 10.4231/r7j101bv
title: Data for Neural Encoding and Decoding with Deep Learning for Dynamic Natural Vision Tests - Subject 3

description: This is a video-fMRI dataset for subject 3 (out of three) acquired by the Laboratory of Integrated Brain Imaging (LIBI).
DOI: 10.4231/r7ns0s1f
title: Data for Neural Encoding and Decoding with Deep Learning for Dynamic Natural Vision Tests - Subject 2

description: This is a video-fMRI dataset for subject 2 (out of three) acquired by the Laboratory of Integrated Brain Imaging (LIBI).
DOI: 10.6084/m9.figshare.25233520
title: Bacillus stratosphericus Rastk.gb

description: Genome annotation output of <i>Bacillus stratosphericus </i>AIMST-CREST02 using the RAST toolkit
DOI: 10.14459/2024mp1735029
title: Survey form to evaluate DMP guiding concepts and approaches

description: During the course of study and 
research work participants are provided training and support for managing their research data. At the end of training and support sessions, organisers usually conduct surveys to gather feedback and to evaluate approaches and effectiveness.
This package of data contains survey form for the evaluation of training and support topics/contents, concepts and approaches which were 
developed for in person, digital medium as well as for hybrid environment. The training and support activities were defined for the participants of large Collaborative Research Centres (CRC) e.g. TRR277 AMC (a CRC funded by German Research Council). Research workloads in such centres are usually distributed among various teams and institutions which may geographically be located at distinct locations. The participants come from different domains with varying skills and competencies. Researchers in these centres use and generate heterogeneous, large amount of data. Apart from maintaining data management plan (DMP), maintenance of metadata, compliance with particular research data policy and the use of specific information infrastructure are considered mandatory. In contrast to typical general guidance, training activities and courses which are usually based on theories, general purpose learning and qualification, the guiding and training activities in such projects/ settings are 
more oriented towards formal practices, quick adoption and implementation.
Form in this package contains questions relating to the activities for Data management plans (DMP). For questions specifically relating to the 
overall Research data management (RDM), please refer to the data package “Survey form to evaluate RDM guiding concepts and approaches” available at https://doi.org/10.14459/2024mp1735126 .
Form in this package is provided in two distinct file formats i.e. .pdf, .docx. The PDF file could be used for paper based survey. The MS 
Word i.e. .docx file can be edited and customised further as well as it can be used digitally to fill and save the responses. Please refer to the 
README.txt file for further information. The contents of this form may also be conveniently adopted for Web/digital form applications.
It may be noted that the form contains text specific to AMC settings. That text may be altered by the target groups as per their own preferences.
DOI: 10.6084/m9.figshare.25233610.v1
title: Supplementary Material for: Experimental data on PIRCHE and T-cell reactivity: HLA-DPB1-derived peptides identified by PIRCHE-I show binding to HLA-A*02:01 in vitro and T-cell activation in vivo.

description: INTRODUCTION: Human leukocyte antigen (HLA)-DPB1 mismatches during hematopoietic stem cell transplantation (HSCT) with an unrelated donor result in an increased risk for the development of graft-versus-host disease (GvHD). The number of CD8+ T-cell epitopes available for indirect allorecognition as predicted by the PIRCHE algorithm has been shown to be associated with GvHD development. As a proof of principle, PIRCHE-I predictions for HLA-DPB1 mismatches were validated in vitro and in vivo.
METHODS: PIRCHE-I analysis was performed to identify HLA-DPB1-derived peptides that could theoretically bind to HLA-A*02:01. PIRCHE-I predictions for HLA-DPB1 mismatches were validated in vitro by investigating binding affinities of HLA-DPB1 derived peptides to the HLA-A*02:01 in a competition-based binding assay. To investigate the capacity of HLA-DPB1 derived peptides to elicit a T cell response in vivo, mice were immunized with these peptides. T-cell alloreactivity was subsequently evaluated using an interferon-gamma ELISpot assay.
RESULTS: The PIRCHE-I algorithm identified five HLA-DPB1 derived peptides (RMCRHNYEL, YIYNREEFV, YIYNREELV, YIYNREEYA, and YIYNRQEYA) to be presented by HLA-A*02:01. Binding of these peptides to HLA-A*02:01 was confirmed in a competition-based peptide binding assay, all showing an IC50 value of 21 µM or lower. The peptides elicited an interferon-gamma response in vivo.
CONCLUSION: Our results indicate that the PIRCHE-I algorithm can identify potential immunogenic HLA-DPB1-derived peptides present in recipients of an HLA-DPB1-mismatched donor. These combined in vitro and in vivo observations strengthen the validity of the PIRCHE-I algorithm to identify HLA-DPB1 mismatch-related GvHD development upon HSCT.
DOI: 10.6084/m9.figshare.25233610
title: Supplementary Material for: Experimental data on PIRCHE and T-cell reactivity: HLA-DPB1-derived peptides identified by PIRCHE-I show binding to HLA-A*02:01 in vitro and T-cell activation in vivo.

description: INTRODUCTION: Human leukocyte antigen (HLA)-DPB1 mismatches during hematopoietic stem cell transplantation (HSCT) with an unrelated donor result in an increased risk for the development of graft-versus-host disease (GvHD). The number of CD8+ T-cell epitopes available for indirect allorecognition as predicted by the PIRCHE algorithm has been shown to be associated with GvHD development. As a proof of principle, PIRCHE-I predictions for HLA-DPB1 mismatches were validated in vitro and in vivo.
METHODS: PIRCHE-I analysis was performed to identify HLA-DPB1-derived peptides that could theoretically bind to HLA-A*02:01. PIRCHE-I predictions for HLA-DPB1 mismatches were validated in vitro by investigating binding affinities of HLA-DPB1 derived peptides to the HLA-A*02:01 in a competition-based binding assay. To investigate the capacity of HLA-DPB1 derived peptides to elicit a T cell response in vivo, mice were immunized with these peptides. T-cell alloreactivity was subsequently evaluated using an interferon-gamma ELISpot assay.
RESULTS: The PIRCHE-I algorithm identified five HLA-DPB1 derived peptides (RMCRHNYEL, YIYNREEFV, YIYNREELV, YIYNREEYA, and YIYNRQEYA) to be presented by HLA-A*02:01. Binding of these peptides to HLA-A*02:01 was confirmed in a competition-based peptide binding assay, all showing an IC50 value of 21 µM or lower. The peptides elicited an interferon-gamma response in vivo.
CONCLUSION: Our results indicate that the PIRCHE-I algorithm can identify potential immunogenic HLA-DPB1-derived peptides present in recipients of an HLA-DPB1-mismatched donor. These combined in vitro and in vivo observations strengthen the validity of the PIRCHE-I algorithm to identify HLA-DPB1 mismatch-related GvHD development upon HSCT.
DOI: 10.4231/r71v5c4t
title: Repeated Free-Viewing of a Natural Movie Stimulus Using fMRI

description: Video-fMRI dataset acquired by the Laboratory of Integrated Brain Imaging (LIBI, https://engineering.purdue.edu/libi) at Purdue University.
DOI: 10.6084/m9.figshare.25233637
title: Supplementary Material for: This “<i>mite</i>” Surprise You: Scabies Masquerading as Langerhans Cell Histiocytosis – A Case Report

description: <b><i>Introduction:</i></b> Scabies is a common parasitic infestation caused by the mite <i>Sarcoptes scabiei. </i>Scabies can mimic other entities clinically, resulting in misdiagnosis. The presence of a mite in the stratum corneum on biopsy specimens is diagnostic of scabies. However, there are instances when mites are not visible, and immunohistochemical (IHC) staining may be misleading. An example is when IHC demonstrates Cluster of Differentiation 1a and S100 positivity. The main differential diagnosis for this finding is Langerhans cell histiocytosis, a group of idiopathic disorders of bone marrow-derived Langerhans cells, with manifestations ranging from isolated to life-threatening multisystem disease. <b><i>Case Presentation:</i></b> We present a case of a patient who was diagnosed with Langerhans cell histiocytosis based on histological findings, further review with a repeat reading and deeper sectioning of her biopsy revealed a mite in the stratum corneum, altering the diagnosis, course, and management. She subsequently developed persistent post-scabietic nodules, an underreported entity that may occur following infestation and persist for up to a year. These lesions are self-limiting and do not require repeated courses of treatment. <b><i>Conclusion:</i></b> Langerhans cell hyperplasia may be seen in a multitude of entities, including scabies. Familiarity with this phenomenon is crucial to avoid unnecessary invasive investigations, aggressive management and alleviate patients’ concerns.
DOI: 10.17632/t49cyrgtct.1
title: Dataset for "Coupling Reservoir Operation and Rainfall-Runoff Processes for Streamflow Simulation in Watersheds"

description: This dataset includes all code used to run and evaluate the coupled watershed models described in 'Coupling Reservoir Operation and Rainfall-Runoff Processes for Streamflow Simulation in Watersheds.'

Prior to model calibration and performance evaluation, the codes in Step_A_DataPreprocessing, and Step_B_CreateReservoirModels are to be run for creating set-up files. Outputs from the codes in both folders are already included in the dataset. Separate readme.txt files inside both folders describe each codes' application.

Within the root folder, "Simulating_Coupled_Models_And_Calibrating_ResIgnore.R" is run first to obtain data in the folders "All_Para_Perf" and "Behavioral_Paras_ResIgnore". 
"All_Para_Perf" contains .csv files with metrics quantifying the performance of 10,000 parameter sets generated via Latin Hypercube Sampling (from Step_A_DataPreprocessing). Each row in the .csv file corresponds to a parameter set. One .csv file is generated for each watershed.
"Behavioral_Paras_ResIgnore" contains .csv files with metrics quantifying the performance of models that ignore reservoir operation. One .csv file is generated for each reservoir.

"Analysis.R" generates the main results in the paper. All outputs from "Analysis.R" are in the folder "Results". Comments in the code (Analysis.R) describe each statement.

Apart from Analysis.R and Simulating_Coupled_Models_And_Calibrating_ResIgnore.R, all other codes in the root folder are function files. Each function's description is as follows:

Selecting_Bhv_Paras_NoInflow_2.R    -> To calibrate GDROM/DZTR models using criteria related to watershed outflow.
Selecting_Bhv_Paras_WithInflow_2.R -> To calibrate GDROM/DZTR models using criteria related to watershed outflow and internal flux.
PDSI_Monthly_To_Daily.R                   -> Converts monthly PDSI data to daily values. Constant daily value within each month.
FlowSimulator.R                                   -> The rainfall-runoff model; simulates natural streamflow.
GDROM_Simulator_2.R                      -> Simulates releases using input inflow via GDROM.
DZTR_Simulator.R                               -> Simulates releases using input inflow via DZTR.
Performance_Computer.R                   -> Computes NSE, PBIAS and logNSE for observed and simulated time series.
QuantileSummarizer_2.R                    -> Creates a summary of performance metrics at 0%, 25%, 50%, 75% and 100% quantiles.
PlottingFDCs_5.R                                -> Plots errors in the flow duration curve arising from parametric uncertainties.
PlottingNSEScatter_3.R                       -> Creates a plot with logNSE[Flux] on the x axis and logNSE[Outflow] on the y axis for a particular watershed based on GDROM and DZTR models.
DOI: 10.17632/t49cyrgtct.2
title: Dataset for "Coupling Reservoir Operation and Rainfall-Runoff Processes for Streamflow Simulation in Watersheds"

description: This dataset includes all code used to run and evaluate the coupled watershed models described in 'Coupling Reservoir Operation and Rainfall-Runoff Processes for Streamflow Simulation in Watersheds.'

Prior to model calibration and performance evaluation, the codes in Step_A_DataPreprocessing, and Step_B_CreateReservoirModels are to be run for creating set-up files. Outputs from the codes in both folders are already included in the dataset. Separate readme.txt files inside both folders describe each codes' application.

Within the root folder, "Simulating_Coupled_Models_And_Calibrating_ResIgnore_5.R" is run first to obtain data in the folders "All_Para_Perf" and "Behavioral_Paras_ResIgnore". 
"All_Para_Perf" contains .csv files with metrics quantifying the performance of 10,000 parameter sets generated via Latin Hypercube Sampling (from Step_A_DataPreprocessing). Each row in the .csv file corresponds to a parameter set. One .csv file is generated for each watershed.
"Behavioral_Paras_ResIgnore" contains .csv files with metrics quantifying the performance of models that ignore reservoir operation. One .csv file is generated for each reservoir.

"Analysis.R" generates the main results in the paper. All outputs from "Analysis.R" are in the folder "Results". Comments in the code (Analysis.R) describe each statement.

Apart from Analysis.R and Simulating_Coupled_Models_And_Calibrating_ResIgnore_5.R, all other codes in the root folder are function files. Each function's description is as follows:

Selecting_Bhv_Paras_2.R         -> To calibrate GDROM/DZTR models using criteria related to watershed outflow.
Selecting_Bhv_Paras_3.R         -> To calibrate GDROM/DZTR models using criteria related to watershed outflow with relaxed PBIAS criteria
PDSI_Monthly_To_Daily.R       -> Converts monthly PDSI data to daily values. Constant daily value within each month.
FlowSimulator.R                       -> The rainfall-runoff model; simulates natural streamflow.
GDROM_Simulator_5.R          -> Simulates releases using input inflow via GDROM.
DZTR_Simulator_2.R               -> Simulates releases using input inflow via DZTR.
Hanasaki_Simulator.R              -> Simulates releases using input inflow via Hanasaki et al. (2006) model.
Wisser_Simulator.R                  -> Simulates releases using input inflow via Wisser et al. (2010) model.
Performance_Computer.R       -> Computes NSE, PBIAS and logNSE for observed and simulated time series.
LMoment_Error_Estimator.R  -> Computes errors in the estimates of L-moments from simulated time series
QuantileSummarizer_3.R        -> Creates a summary of performance metrics at 0%, 25%, 50%, 75% and 100% quantiles.
PlottingFDCs_Revision.R         -> Plots errors in the flow duration curve arising from parametric uncertainties.