cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.24556174
title: Supplementary materials

description: By analyzing the content in SGs of BAT at the early phase of cold stress for both sexes, we found more diverse mRNAs docked in the SGs in male mice and these mRNAs representing an extensive cellular reprogramming including apoptosis process and cold-induced thermogenesis. In female mice, the mRNAs in SGs dominantly were comprised of genes regulating ribonucleoprotein complex biogenesis. Conversely, the proteome in SGs was commonly characterized as structure molecules and RNA processing for both sexes. A spectrum of eukaryotic initiation factors (eIFs) was detected in the SGs of both female and male BAT, while those remained unchanged upon cold stress in male mice, various eIF3 and eIF4G isoforms were found reduced in female mice.
DOI: 10.6084/m9.figshare.24599295
title: Multi-omic profiling of clear cell renal cell carcinoma identifies metabolic reprogramming associated with disease progression

description: Clear cell renal cell carcinoma (ccRCC) is a complex disease with remarkable immune and metabolic heterogeneity. Here, we present a TJ-RCC cohort (RCC cohort of Tongji hospital), and we perform genomic, transcriptomic, proteomic, metabonomic and spatial multi-omic profiling on 100 ccRCC cases. Using the scRNA-seq-derived signature, we identify 4 ccRCC subtypes. Multilevel profiling distinguishes a unique ccRCC subtype, De-clear cell differentiated (DCCD) -ccRCC, with distinctive metabolic features. DCCD cancer cells are characterized by fewer lipid droplets, more inhibited metabolic activity, enhanced nutrients uptake capability and a high proliferation rate, leading to poor prognosis. Using single-cell and spatial trajectory analysis, we demonstrate that DCCD is a common mode of ccRCC progression. Even among stage I patients, DCCD is associated with worse outcomes and higher recurrence rate, suggesting it cannot be cured by nephrectomy alone. This study provides a treatment strategy based on immune subtypes, which could guide clinical management of ccRCC.
DOI: 10.5281/zenodo.10182674
title: Dataset of paper "Phosphate recovery from urine-equivalent solutions for fertiliser production for plant growth"

description: Dataset of paper "Phosphate recovery from urine-equivalent solutions for fertiliser production for plant growth"
DOI: 10.5281/zenodo.10182673
title: Dataset of paper "Phosphate recovery from urine-equivalent solutions for fertiliser production for plant growth"

description: Dataset of paper "Phosphate recovery from urine-equivalent solutions for fertiliser production for plant growth"
DOI: 10.25345/c5fx74836
title: MassIVE MSV000093449 - Proteome asymmetry in mouse and human embryos before fate specification
title: Raw files of early-stage mouse and human blastomeres & mouse zygotes
DOI: 10.5281/zenodo.6569449
title: Supplementary data as part of the article "Mechanism of Benzene Hydroxylation on Tri-Iron Oxo-Centered Cluster-Based Metal-Organic Frameworks" (https://doi.org/10.1021/acs.jpcc.3c06423)

description: Cartesian coordinates in the *.XYZ format for all the structures optimized at the M06-L/def2-TZVP in the reactivity study as part of the article "Mechanism of Benzene Hydroxylation on Tri-Iron Oxo-Centered 2 Cluster-Based Metal-Organic Frameworks" (https://doi.org/10.1021/acs.jpcc.3c06423)
DOI: 10.5281/zenodo.6569448
title: Supplementary data as part of the article "Mechanism of Benzene Hydroxylation on Tri-Iron Oxo-Centered Cluster-Based Metal-Organic Frameworks" (https://doi.org/10.1021/acs.jpcc.3c06423)

description: Cartesian coordinates in the *.XYZ format for all the structures optimized at the M06-L/def2-TZVP in the reactivity study as part of the article "Mechanism of Benzene Hydroxylation on Tri-Iron Oxo-Centered 2 Cluster-Based Metal-Organic Frameworks" (https://doi.org/10.1021/acs.jpcc.3c06423)
DOI: 10.22032/dbt.32508
title: Digitale Edition der Briefe Erdmuthe Benignas von Reuß-Ebersdorf (1670-1732)
DOI: 10.25345/c5b853v16
title: MassIVE MSV000093450 - TARGETING NEURONAL FTL1 RESCUES COGNTIVE IMPAIRMENTS IN AGING
title: Raw files of protein abundance from TMT-labeled mouse cortical and hippocampal synaptosomes analyzed on an Orbitrap Fusion Lumos
DOI: 10.5281/zenodo.10182499
title: Bermuda Atlantic Time-Series Study (BATS) Zooplankton Biomass

description: The BATS (Bermuda Atlantic Time-series Study) zooplankton biomass dataset is time-series spanning from 1994 to 2022. The dataset contains zooplankton biomass measurements.
Due to an ambiguity with depth a subset of the dataset been removed as part of the Simons CMAP curation process.  The original dataset is also included here:

Curated by Simons CMAP: BATS_Zooplankton_Biomass_CMAP.xlsx 
Original version as text file: BATS_zooplankton.xlsx
Original version as excel file: BATS_zooplankton.xlsx 
The following dates were impacted by the depth ambiguity: 1994 (4/6 – 12/12); 1995 (1/11 – 4/27, 8/22); 2000 (2/28); 2001 (1/30, 8/7-8/8, 9/12, 10/16); 2004 (2/14, 3/23, 4/7, 7/14-15, 8/16-17); 2005 (1/27); 2006 (5/11, 6/26, 9/4-9/5); 2007 (7/18, 8/9, 10/6); 2008 (6/22); 2009 (2/10, 4/1, 4/15, 5/16, 5/19, 10/10); 2017 (5/9); 2018: (8/13); 2022: (6/29).
This description has been reproduced using https://www.dropbox.com/sh/xo6c72qaeznyv05/AACCiijqHcd2chjbwrqNcxica?dl=0&preview=BATS_zooplankton.txt
DOI: 10.5281/zenodo.10182498
title: Bermuda Atlantic Time-Series Study (BATS) Zooplankton Biomass

description: The BATS (Bermuda Atlantic Time-series Study) zooplankton biomass dataset is time-series spanning from 1994 to 2022. The dataset contains zooplankton biomass measurements.
Due to an ambiguity with depth a subset of the dataset been removed as part of the Simons CMAP curation process.  The original dataset is also included here:

Curated by Simons CMAP: BATS_Zooplankton_Biomass_CMAP.xlsx 
Original version as text file: BATS_zooplankton.xlsx
Original version as excel file: BATS_zooplankton.xlsx 
The following dates were impacted by the depth ambiguity: 1994 (4/6 – 12/12); 1995 (1/11 – 4/27, 8/22); 2000 (2/28); 2001 (1/30, 8/7-8/8, 9/12, 10/16); 2004 (2/14, 3/23, 4/7, 7/14-15, 8/16-17); 2005 (1/27); 2006 (5/11, 6/26, 9/4-9/5); 2007 (7/18, 8/9, 10/6); 2008 (6/22); 2009 (2/10, 4/1, 4/15, 5/16, 5/19, 10/10); 2017 (5/9); 2018: (8/13); 2022: (6/29).
This description has been reproduced using https://www.dropbox.com/sh/xo6c72qaeznyv05/AACCiijqHcd2chjbwrqNcxica?dl=0&preview=BATS_zooplankton.txt
DOI: 10.5281/zenodo.7954656
title: CPT-1 pre-computed whole-proteome variant effect predictions and model source code

description: Cross-protein transfer learning for variant effect prediction
This repository contains the variant effect predictions of CPT-1 for 18,602 human proteins, initially released with the manuscript "Cross-protein transfer learning substantially improves zero-shot prediction of disease variant effects". The proteins are split into three files.
CPT1_score_EVE_set.zip: Proteins in the EVE set (Frazer et al., 2021)
CPT1_score_no_EVE_set_1.zip & CPT1_score_no_EVE_set_2.zip: Proteins not in the EVE set. Predictions for these proteins use imputed values for features depending on the EVE MSA.
The protein names are UniProt gene names.
We also provide source code to train CPT-1 model and reproduce results in the manuscript :
source_code.zip (corresponds to GitHub repository songlab-cal/CPT version as of Jul 12, 2023)
 
Citation
Jagota, M.*, Ye, C.*, Albors, C., Rastogi, R., Koehl, A., Ioannidis, N., and Song, Y.S.†"Cross-protein transfer learning substantially improves zero-shot prediction of disease variant effects", bioRxiv (2022)
*These authors contributed equally to this work.†To whom correspondence should be addressed: yss@berkeley.edu
DOI: https://doi.org/10.1101/2022.11.15.516532
DOI: 10.5281/zenodo.7954657
title: CPT-1 whole-proteome variant effect prediction

description: <strong>Cross-protein transfer learning for variant effect prediction </strong> This repository contains the variant effect preditions of CPT-1 for 18,602 human proteins, initially released with the manuscript "Cross-protein transfer learning substantially improves zero-shot prediction of disease variant effects". The proteins are split into three files. <em>CPT1_score_EVE_set.zip</em>: Proteins in the EVE set (Frazer et al., 2021) <em>CPT1_score_no_EVE_set_1.zip</em> & <em>CPT1_score_no_EVE_set_2.zip</em>: Proteins not in the EVE set. Predictions for these proteins use imputed values for features depending on the EVE MSA. <strong>Citation</strong> Jagota, M.*, Ye, C.*, Rastogi, R., Albors, C., Koehl, A., Ioannidis, N., and Song, Y.S.†<br> "Cross-protein transfer learning substantially improves zero-shot prediction of disease variant effects", bioRxiv (2022) *These authors contributed equally to this work.<br> †To whom correspondence should be addressed: yss@berkeley.edu DOI: https://doi.org/10.1101/2022.11.15.516532
DOI: 10.5281/zenodo.8140323
title: CPT-1 pre-computed whole-proteome variant effect predictions and model source code

description: Cross-protein transfer learning for variant effect prediction
This repository contains the variant effect predictions of CPT-1 for 18,602 human proteins, initially released with the manuscript "Cross-protein transfer learning substantially improves zero-shot prediction of disease variant effects". The proteins are split into three files.
CPT1_score_EVE_set.zip: Proteins in the EVE set (Frazer et al., 2021)
CPT1_score_no_EVE_set_1.zip & CPT1_score_no_EVE_set_2.zip: Proteins not in the EVE set. Predictions for these proteins use imputed values for features depending on the EVE MSA.
The protein names are UniProt gene names.
We also provide source code to train CPT-1 model and reproduce results in the manuscript :
source_code.zip (corresponds to GitHub repository songlab-cal/CPT version as of Jul 12, 2023)
 
Citation
Jagota, M.*, Ye, C.*, Albors, C., Rastogi, R., Koehl, A., Ioannidis, N., and Song, Y.S.†"Cross-protein transfer learning substantially improves zero-shot prediction of disease variant effects", bioRxiv (2022)
*These authors contributed equally to this work.†To whom correspondence should be addressed: yss@berkeley.edu
DOI: https://doi.org/10.1101/2022.11.15.516532
DOI: 10.6073/pasta/86bd3ba5a46393ed987f5eccba341229
title: Marcell Experimental Forest 30-minute air temperature, relative humidity, and barometric pressure, 2015 - ongoing

description: This data publication contains air temperature, relative humidity, and atmospheric pressure data collected at 30-minute resolution from 2015-ongoing at three long term meteorological monitoring stations at the Marcell Experimental Forest (MEF). The MEF is located in Itasca County, Minnesota and is operated and maintained by the USDA Forest Service, Northern Research Station.
DOI: 10.6073/pasta/56432bc2622de6b20ba2897b7ee13e57
title: Marcell Experimental Forest 15-minute precipitation, 2011 - ongoing

description: This data publication contains 15-minute precipitation data collected from 2011-ongoing at the Marcell Experimental Forest (MEF) in Itasca County, Minnesota, which is operated and maintained by the USDA Forest Service, Northern Research Station. The data come from three long-term meteorological monitoring stations.
DOI: 10.6073/pasta/c1f9302b4ccef46cbe003ac41f58ef4a
title: American Residential Macrosystems - Soil chemistry data within parks and residential yards in six major metropolitan areas in the United States, 2017-2018

description: "In six major U.S. metropolitan cities (Boston, Baltimore, Los Angeles, Miami, Minneapolis St. Paul, and Phoenix), 1 meter soil cores were collected to evaluate soil microbial carbon and nitrogen cycle processes that are sensitive to land management. Laboratory methods followed those used by Raciti et al. (2011a,b) to measure microbial biomass carbon and nitrogen content, microbial respiration, potential net nitrogen mineralization, potential net nitrifcation, potential denitrifcation, and pools of extractable ammonium and nitrate. "
DOI: 10.5281/zenodo.7618513
title: Trends in elasmobranchs' feeding ecology studies - Data S1

description: A listed of 418 papers used and fitted the criteria (i.e. feeding studies about elasmobranchs) were reviewed.
DOI: 10.6073/pasta/8b29dc7fd536f4649f8cf6a536421fc9
title: American Residential Macrosystems - Presence/absence of plant species within land use groups in residential yards in six major metropolitan areas in the United States, 2017-2018

description: "This dataset includes presence/absence of plant species recorded in residential yards and nearby natural and interstitial areas (i.e.unmanaged vegetation areas in the residential/wildland interface) in six cities across the U.S. Baltimore, MD, Boston, MA, Los Angeles, CA, Miami, FL, Minneapolis-St. Paul, MN, and Phoenix, AZ. Yards were grouped in 4 categories based on fertilizer input frequency, landscaping style and their impact on hydrology: high-input lawns, low-input lawns, wildlife-certified yards and yards with low impact on hydrology (or rain gardens)."
DOI: 10.25345/c56h4d18b
title: MassIVE MSV000093451 - Development of a point-of-care multiplex immunochromatographic test for the diagnosis of hepatitis B and D
title: Raw files and results from DTH10.1 and DTH10.1-SUMO
DOI: 10.5281/zenodo.10182699
title: Comparison of Biological Potential between Aqueous Extracts of Rumex crispus Leaf and Root as Antibacterial, Synergistic Agents: A TLC-Bioautography and Cytotoxic Study
DOI: 10.5281/zenodo.10182700
title: Comparison of Biological Potential between Aqueous Extracts of Rumex crispus Leaf and Root as Antibacterial, Synergistic Agents: A TLC-Bioautography and Cytotoxic Study
DOI: 10.6073/pasta/37bcca63dea73a0b1386c7a134dedc6b
title: Data and code from "No evidence of sex ratio manipulation by black-throated blue warblers in response to food availability" Kaiser et al. 2023 Behavioral Ecology and Sociobiology

description: This dataset is published in support of "No evidence of sex ratio manipulation by black-throated blue warblers in response to food availability" by Kaiser et al. 2023 in Behavioral Ecology and Sociobiology. Data and code to test the assumptions and key predictions of the Trivers-Willard hypothesis, which proposes that females produce more sons or daughters depending on food availability, in the black-throated blue warbler at the Hubbard Brook Experimental Forest, NH, 2007-2012. Datasets support analyses of sex ratio bias at both the nest and nestling levels. Data tables support the comparison of the ratio of variances in the scaled pre-fledging mass of male and female nestlings using an F test and reproduction of Figures 2a and 2b. Figures are those used in the published manuscript. Code supports the calculation of offspring sex ratio bias at the population level, and considering separately both low- and high-quality habitats, using the Neuhäuser test, statistical models testing the assumptions of the Trivers-Willard hypothesis, effects of food availability and parental provisioning on offspring sex ratio, and effects of food availability on pre-fledging nestling mass of sons and daughters, and a power analysis to determine the power to detect an effect of food supplementation on sex ratio. These data were gathered as part of the Hubbard Brook Ecosystem Study (HBES). The HBES is a collaborative effort at the Hubbard Brook Experimental Forest, which is operated and maintained by the US Forest Service, Northern Research Station.
DOI: 10.17909/jkbe-zn98
title: Data from an systematic method to detect L-variable candidates
DOI: 10.34770/r8b8-k094
title: March Mathness: Effects of basketball on the brain

description: Surprise signals a discrepancy between past and current beliefs. It is theorized to be linked to affective experiences, the creation of particularly resilient memories, and segmentation of the flow of experience into discrete perceived events. However, the ability to precisely measure naturalistic surprise has remained elusive. We used advanced basketball analytics to derive a quantitative measure of surprise and characterized its behavioral, physiological, and neural correlates in human subjects observing basketball games. We found that surprise was associated with segmentation of ongoing experiences, as reflected by subjectively perceived event boundaries and shifts in neocortical patterns underlying belief states. Interestingly, these effects differed by whether surprising moments contradicted or bolstered current predominant beliefs. Surprise also positively correlated with pupil dilation, activation in subcortical regions associated with dopamine, game enjoyment, and long-term memory. These investigations support key predictions from event segmentation theory and extend theoretical conceptualizations of surprise to real-world contexts.
DOI: 10.6084/m9.figshare.24601854
title: oranigbr-BATB-BRTR-P10P.zip

description: Zip files include four scenarios: Scenario 1: Increase of 10 p.p. in the taxation of the sector from 2023;Scenario 2: Increase of 20 p.p. in the taxation of the sector from 2023;Scenario 3: Increase of 30 p.p. in the taxation of the sector from 2023;Scenario 4: Gradual increase from 10 to 30 p.p. in the taxation of the sector between the years 2023 and 2025.
DOI: 10.6084/m9.figshare.24601854.v1
title: oranigbr-BATB-BRTR-P10P.zip

description: Simulation 1 - Increase of 10p.p.
DOI: 10.34740/kaggle/dsv/7021320
title: Balochi Language to English Translation Dataset
DOI: 10.34770/g1rh-nv16
title: Reductions in Retrieval Competition Predict the Benefit of Repeated Testing

description: Repeated testing (as opposed to repeated study) leads to improved long-term memory retention, but the mechanism underlying this improvement remains controversial. In this work, we test the hypothesis that retrieval practice benefits subsequent recall by reducing competition from related memories. This hypothesis implies that the degree of reduction in competition between retrieval practice attempts should predict subsequent memory for the practiced items. To test this prediction, we collected electroencephalography (EEG) data across two sessions. In the first session, participants practiced selectively retrieving exemplars from superordinate semantic categories (high competition), as well as retrieving the names of the superordinate categories from exemplars (low competition). In the second session, participants repeatedly studied and were then tested on Swahili-English vocabulary. One week after session two, participants were again tested on the vocabulary. We trained a within-subject classifier on the data from session one to distinguish high and low competition states. We then used this classifier to measure competition across multiple retrieval practice attempts in the second session. The degree to which competition decreased for a given vocabulary word predicted whether that item was subsequently remembered in the third session. These results are consistent with the hypothesis that repeated testing improves retention by reducing competition. Experiment consisted of 3 sessions: 1 of EEG recording, 1 of EEG and behavior recording in the form of written responses, and 1 of behavior recoding in the form of written responses. 48 subjects participated in the initial EEG recording session, 40 participated in all three sessions. Download the README.txt file for a detailed description of this dataset's content.
DOI: 10.34683/sr1588
title: StoneRounds Case: SR1588
title: AD Stargardt Disease

description: StoneRounds Case SR1588 was diagnosed with AD Stargardt Disease likely caused by mutations in the gene: ELOVL4.
DOI: 10.25422/azu.data.23278289.v1
title: Geomorphological Maps and Depth Maps for Elysium Planitia, Mars

description: The materials uploaded here contain the shapefiles for: 1) the major units; and 2) the flow units used to create the two geomorphological maps in Elysium Planitia on Mars; as well as 3) the depth maps derived from SHARAD of the flow units. The "MajorUnits" and "FlowUnits" files include shapefile format readable in GIS. The major units were digitized at 1:100,000-scale and flow units at 1:80,000, both datasets were mapped based on CTX images (see methods section in Voigt et al. (2023)). The "Depth_maps" file include all SHARAD derived depth maps from Voigt et al. (2023) in a .txt file format.<br><i>For inquiries regarding the contents of this dataset, please contact the Corresponding Author listed in the README.txt file. Administrative inquiries (e.g., removal requests, trouble downloading, etc.) can be directed to data-management@arizona.edu</i>
DOI: 10.5281/zenodo.10011977
title: MD files (psf, pdb, and toppar) for the trajectories of the glycoprotein receptors FSHR and LHCGR.

description: PSF and PDB files for trajectories on FSHR and LHCGR in SDPC lipids. Top and par parameters for charmm36m included.
PDB files and trr files include only backbone atoms. All frames were fitted to the to the transmembrane domains.
DOI: 10.5281/zenodo.10011976
title: MD files (psf, pdb, and toppar) for the trajectories of the glycoprotein receptors FSHR and LHCGR.

description: PSF and PDB files for trajectories on FSHR and LHCGR in SDPC lipids. Top and par parameters for charmm36m included.
PDB files and trr files include only backbone atoms. All frames were fitted to the to the transmembrane domains.
DOI: 10.6084/m9.figshare.24601980
title: current status of WMS data.docx

description: The research reports the status of White mango scale, currently which threatened mango production and utilization in Ethiopia. Since its occurrence in 2010, it causes significant reduction of mango production in Ethiopia. Benishangul Gumuz is one of the major mango growing areas in Ethiopia and production of this crop is indispensable in this region as most of the farming community depend of this for their livelihoods. The study reports he current status and distribution of white mango scale and identify factors contributing for damage level of the pest, in Benishangul Gumuz Region.
DOI: 10.6084/m9.figshare.23535717
title: Data and code for: Hummingbirds use distinct control strategies for forward and hovering flight

description: Data and code for: "Hummingbirds use distinct control strategies for forward and hovering flight" by Baliga VB, Dakin R, Wylie DR, and Altshuler DL; Proceedings of the Royal Society B: Biological SciencesQuestions/concerns/comments: Vikram Baliga (vikram.baliga@ubc.ca)<br>Data:- All data required to re-create analyses and figures are stored within /processed_data_exports. Note that these are not original (Flydra) data; due to file size constraints, Flydra data cannot be included here.- The /lookup_and_metadata directory contains several files that describe the metadata and other important characteristics of the original data and subjectsCode:- All code required to re-create analyses and figures are provided as .R files.- The two "master_script_" files are required to be run prior to recreating figures. Objects that figure creation relies on are generated by the master scripts- Files to support the master scripts are house in /data_import_scripts, but do not need to be called directly by the user. Rather, the master scripts will source these auxiliary files automatically as needed.- Code for each figure is provided within separate .R files. Multi-panel plots are created wherever possible, but might differ slightly in presentation from their final format due to rendering differences across platforms.