cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15156/bio/2938067
title: UNITE general FASTA release for Fungi

description: This release consists of a single FASTA file: the RepS/RefS of all SHs, adopting the dynamically use of clustering thresholds whenever available.
DOI: 10.18728/igb-fred-859.0
title: Eco-phenotypic feedbacks differ in multi-stress environments

description: Density time series and cell size and shape time series of Colpidium and Paramecium in different salinity (0, 0.75, 1.5 and 3 NaCl g/L) in combination with temperature (20, 22, 24 and 26°C).
DOI: 10.21227/9f0p-qx37
title: Mammograms-Breast Cancer Images

description: This is a small dataset as a part of huge dataset of breast cancer images. The images are mammograms.
DOI: 10.22002/d1.20084
title: Caltech Cars 1999

description: Car dataset taken by Markus Weber, Caltech PhD student under Pietro Perona. 126 images of cars from the rear. Approximate scale normalisation. JPEG format. Taken in the Caltech parking lots. 896 x 592 pixels.
DOI: 10.25318/3810024001-eng
title: Irrigation volume by crop type

description: Irrigation volume by month and crop type. The unit of measure is cubic metres.
DOI: 10.25318/3810024101-eng
title: Total area that received irrigation by crop type

description: Total area that received irrigation by crop type, province and drainage region. The unit of measure is hectares.
DOI: 10.5066/p9j0ziof
title: A national harmonized dataset of discrete chlorophyll from lakes and streams (2005-2022)

description: This data release contains a 17-year record (2005-2022) of discrete chlorophyll data from inland waters, collected from across the nation and territories. These data are from discrete samples (collected in the field and analyzed in the laboratory) from plankton (suspended algae) and periphyton (benthic algae) from lakes, streams, rivers, reservoirs, canals, and other sites. These data are gathered to support process and remote sensing modeling and prediction of Harmful Algal Blooms (HABs). The chlorophyll data were compiled from the Water Quality Portal (WQP) and USGS National Water Quality Lab (NWQL). Data for uncorrected chlorophyll a, corrected chlorophyll a, and pheophytin from EPA Methods 445 and 446 are included and reported, following the conventions of EPA section 445: 12.1 uncorrected chlorophyll a ? based on the initial optical measurement of the sample, which includes both chlorophyll a and pheophytin 12.2 corrected chlorophyll a ? based on optical measurement after acidification and calculation to estimate the amount of active chlorophyll in the original sample 12.3 pheophytin ? based on calculations to estimate the amount of pheophytin in the original sample These data were harmonized for reporting units (plankton as �g/L and periphyton as mg/m2), duplicate values, collection depth, site type, negative values, and some extreme values. HABs events are associated with high values of chlorophyll, as algae may be concentrated in dense surface scums. These data may include an indicator for hydrologic event code, which may be helpful in determining HABs events. � Acknowledgements This work was completed as part of two projects in the USGS Water Mission Area (WMA) Water Quality Processes Program: (1) the Improved Understanding and Prediction of Prioritized Constituents Project, an effort to advance datasets and understanding of chlorophyll, nutrient, carbon, and sediment occurrence and transport, and (2) the Proxies Project, an effort to develop estimation methods for PFAS, harmful algal blooms, and metals, at multiple spatial and temporal scales. Arar, E.J. and Collins, G.B. 1997. Method 445.0: In vitro determination of chlorophyll a and pheophytin a in marine and freshwater algae by fluorescence. EPA Office of Research and Development.
DOI: 10.5281/zenodo.10121858
title: Water vapor isotopic data of heavy rainfall events in Nanjing

description: Water vapor isotopic data of heavy rainfall events in Nanjing
DOI: 10.5281/zenodo.11110873
title: Dataset for "Large Language Models as molecular design engines"

description: claude-gpt-paper.zip :This dataset contains data and results associated with the paper "Large Language Models as molecular designengines" The paper investigates the use of large language models, specifically Claude 3 Opus, for generating and analyzing chemical structures based on various prompts from A-H (as mentioned in the manuscript), and guided design related to electron-withdrawing groups (EWG), electron-donating groups (EDG).


The dataset includes:



PM7 MOPAC energy calculations for generated molecules, along with their SMILES representations and molecule IDs.

PM7-calculated charges for the generated molecules.

Output files from the Claude 3 Opus language model for each prompt category along.

Original dataset (subset of ZINC database) used to build common keys and the initial design space.

JSON file containing common keys for featurizing unknown SMILES.

PCA object to convert molecule embeddings to 3-dimensional embeddings.


The data is organized into the following folders:



pm7_charge_results: Contains HOMO-LUMO energy differences for plotting.

pm7_charge_calculation: Contains PM7 MOPAC energy calculations and charges.

out: Contains output files from the Claude 3 Opus language model.

fact-dropbox: Contains the original dataset, common keys, and PCA object file.


The data can be used to reproduce the results presented in the paper and serve as a foundation for further research in this area.

For a detailed description of the folder structure and contents, please refer to the File_descriptions.md file included in the dataset.2. llm-visulizer-dashapp.zipThis is the code for the visualizer app for viewing the molecules generated by the LLM. The README.md file has details about running the app.

3. claude-gpt-paper-codes.zip 

This contains the notebook GPT_modification_just_plots.ipynb for plotting, and other codes. The README.md file has details about running the main notebook for getting the plots.
DOI: 10.5281/zenodo.12760022
title: Genotyping measures and population genetic indices for assesing reproductive modes of polyploid Ludwigia grandiflora subsp. hexapetala in western Europe

description: Raw data used to assess reproductive modes in 53 sampled populations in western Europe (France and northern Spain).

Ludwigia grandiflora subsp. hexapetala (Lgh) is a hermaphrodite, polyploid, partially clonal and heteromorphic plant that recently colonized multiple countries worldwide. Individuals in this species are either self-incompatible caused by a late-acting self-incompatible (LSI) system developing long-styled flowers, or self-compatible (SC) developing short-styled flowers. We used a SNP approach allowing confident allele dosage to genotype 53 LSI and SC populations of Lgh in France and northern Spain. We measured their genetic diversity and assessed their reproductive modes using methods adapted to autopolyploid species.
DOI: 10.5281/zenodo.13733541
title: Neural crest lineage in the proto-vertebrate model Ciona

description: Larva single cell data (SRA accession number: SRR9051005, SRR9051006 and SRR9051007) from Cao and colleagues (GEO accession number: GSE131155; Cao et al, 2019)  were remapped on the Ciona KY21 gene models released in 2022 (Satou et al, 2019; Satou et al, 2022) using CellRanger v7.0.0. The expression matrices were analyzed with the package Seurat v4.3.0 (Butler et al, 2019) in R version 4.2.3 (R, 2022). The different tissue types were first identified (Table1_tissueTypes-wholeLarvae) before the nervous system was subsetted and the neural cell types identified (Table2_cellTypes-nervousSystem). The significantly differentially expressed genes between the Hh2+ ependymal cells (Table3_DEGs) and the rest of the nervous system were identified with Seurat using Wilcoxon rank-sum test with Bonferroni correction (Butler et al, 2019).
DOI: 10.5281/zenodo.13751434
title: Example data and pretrained Translatomer model
DOI: 10.5281/zenodo.13767527
title: Updated Smoke Exposure Estimate for Indonesian Peatland Fires using a Network of Low-cost PM2.5 sensors and a regional air quality model - Purple Air data

description: Daily mean PM2.5 concentrations collected by Purple Air sensors between 2023-08-16 and 2023-12-01. Concentrations have been RH adjusted using the Nilson et al (2022) adjustment.
DOI: 10.5281/zenodo.13767688
title: Updated Smoke Exposure Estimate for Indonesian Peatland Fires using a Network of Low-cost PM2.5 sensors and a regional air quality model - Model Simulation Data

description: WRF-Chem simulated daily mean PM2.5 concentrations for:

1) with fires 

2) without fires

simulations.
DOI: 10.5281/zenodo.13875769
title: Development and validation of a prediction model using sella magnetic resonance imaging-based radiomics and clinical parameters for diagnosis of growth hormone deficiency and idiopathic short stature: A multicenter, cross-sectional study
DOI: 10.5281/zenodo.3618205
title: Selective auditory attention in normal-hearing and hearing-impaired listeners

description: This repository contains the EEG and behavioral data described in: Fuglsang, S A, Märcher-Rørsted, J, Dau, T, Hjortkjær, J (2020). Effects of sensorineural hearing loss on cortical synchronization to competing speech during selective attention. Journal of Neuroscience, 40(12):2562–2572, https://doi.org/10.1523/JNEUROSCI.1936-19.2020 Please cite this paper when using the data The data set consists of response data for 22 hearing-impaired and 22 normal-hearing participants. It includes:<br> - EEG data: responses to two-talker and single-talker speech stimuli<br> - Envelopes of the corresponding speech audio<br> - EEG data: responses to 1 kHz tone beeps for ERPs<br> - EEG data: responses to periodic tone sequences for Envelope-following responses (EFRs)<br> - EEG resting-state data recorded with eyes-open and eyes-closed<br> - inEar EEG data for 19 of the 44 subjects (EEG recorded inside the ear canals)<br> - Behavioral data: speech comprehension scores, task difficulty ratings, speech-in-noise scores (SRTs), tone-in-noise scores, digit span working memory scores, SSQ questionnaire ratings<br> - Pure-tone audiograms For more information, see the README and 'dataset_description.json' file. <br> Format<br> ------<br> The dataset is formatted according to BIDS version 1.3.0 and the BIDS standard extension for EEG (BEP006) that has been merged in the main body of the specification. For more details, see https://bids-specification.readthedocs.io/en/latest/06-extensions.html Behavioural data are stored in the 'participants.tsv' file. Task-difficulty ratings and multiple choice questionnaire data from the selective attention experiment are stored in the events files (see 'task-selectiveattention_events.json'). Code<br> ------<br> Code for analyzing the data is available at: https://gitlab.com/sfugl/snhl Audio<br> ------<br> Envelopes of the audio signals are included in the data set. For inquiries regarding the raw audio data, please send an email to jensh@drcmr.dk with the subject line "ds-eeg-snhl audio". Acknowledgments<br> ----------<br> This work was supported by the EU H2020-ICT grant number 644732 (COCOHA: Cognitive Control of a Hearing Aid) and by the Novo Nordisk Foundation synergy grant NNF17OC0027872 (UHeal). The EarEEG were kindly provided by Eriksholm Research Centre.
description: This work was supported by the EU H2020-ICT grant number 644732 (COCOHA: Cognitive Control of a Hearing Aid) and by the Novo Nordisk Foundation synergy grant NNF17OC0027872 (UHeal).
DOI: 10.7488/ds/7799
title: Intercellular friction and motility drive orientational order in cell monolayers

description: Spatiotemporal patterns in multicellular systems are important to understanding tissue dynamics, for instance, during embryonic development and disease. Here, we use a multiphase field model to study numerically the behavior of a near-confluent monolayer of deformable cells with intercellular friction. Varying friction and cell motility drives a solid-liquid transition, and near the transition boundary, we find the emergence of local nematic order of cell deformation driven by shear-aligning cellular flows. Intercellular friction contributes to the monolayer's viscosity, which significantly increases the spatial correlation in the flow and, concomitantly, the extent of nematic order. We also show that local hexatic and nematic order are tightly coupled and propose a mechanical-geometric model for the colocalization of +1/2 nematic defects and 5-7 disclination pairs, which are the structural defects in the hexatic phase. Such topological defects coincide with regions of high cell-cell overlap, suggesting that they may mediate cellular extrusion from the monolayer, as found experimentally. Our results delineate a mechanical basis for the recent observation of nematic and hexatic order in multicellular collectives in experiments and simulations and pinpoint a generic pathway to couple topological and physical effects in these systems. This dataset contains the simulation code and data underlying the figures of the associated paper.
description: Please see the README file for the file descriptions.
DOI: 10.7799/1909373
title: Long-run Marginal Emission Rates for Electricity - Workbooks for 2022 Cambium Data

description: These workbooks contain modeled estimates of long-run marginal emission rates (LRMER) for the contiguous United States. A LRMER is an estimate of the rate of emissions that would be either induced or avoided by a change in electric demand, taking into account how the change could influence both the operation as well as the structure of the grid (i.e., the building and retiring of capital assets, such as generators and transmission lines). It is therefore distinct from the more-commonly-known short-run marginal, which treat grid assets as fixed. Long-run marginal emissions rates are generally appropriate to use when trying to comprehensively estimate the impact of a long-lived (i.e., more than several years) intervention. There are two workbooks that supply the data at two different geographic resolutions: states and GEA regions (20 regions that are similar to, but not exactly the same as, the US EPA's eGRID regions). For more data underlying these emissions factors, see the Cambium 2022 project at https://scenarioviewer.nrel.gov/. For more details on input assumptions and methodology see the associated report (Cambium 2022 Scenario Descriptions and Documentation, https://www.nrel.gov/docs/fy23osti/84916.pdf). This data is planned to be updated annually. Information on the latest versions can be found at https://www.nrel.gov/analysis/cambium.html.
DOI: 10.17034/478cfcba-381d-4445-ae4b-9c88d4b4d666
title: Primer for the calculation of characteristic loads and performance envelopes

description: PURPOSE The purpose of this dataset is to introduce the concepts of ‘characteristic loads’ and ‘performance envelopes’. BACKGROUND In engineering, it is often necessary to examine during design a large combination of loading scenarios and potential modes of failure to ensure a safe and reliable product. ‘Characteristic loads’ are defined as a set of linearly independent loads acting on a product, identified using Singular Value Decomposition (SVD). Characteristic loads may be used to reconstruct approximations of the loading scenarios of interest. ‘Performance envelopes’ are created within the characteristic load space and define the load bearing capacity of a structure. This dataset considers a simple mechanical engineering problem (a compound bar assembly) to demonstrate the calculation and use of both ‘characteristic loads’ and ‘performance envelopes’. REFERENCE MATERIAL This dataset is referenced in the papers: • Efficient methods to build structural performance envelopes in characteristic load space (in draft) • Load case and constraint down-selection for structural optimisation – applying the concepts of characteristic loads and performance envelopes (in draft) • Calculating critical Reserve Factor sensitivities using performance envelopes (in draft) This dataset is also referenced in the thesis: • Performance envelopes for preliminary sizing of aircraft structures, Doctoral Thesis, Queen's University Belfast, Sriharsha Sheshanarayana, 2020 DATASET CONTENT This dataset contains: • A primer document which explains calculation methods to obtain characteristic loads and performance envelopes. • Three Jupyter Notebooks which contain code and data to enable the reproduction of the results within the primer.
DOI: 10.18434/t4h01c
title: NIST Handprinted Forms and Characters - NIST Special Database 19
DOI: 10.25318/3210042401-eng
title: Cattle inventory on farms, Census of Agriculture, inactive

description: Census of Agriculture, 2011 and 2016. Number of cows, bulls, heifers, steers and calves.
DOI: 10.25318/3210042601-eng
title: Pig inventory on farms, Census of Agriculture, inactive

description: Census of Agriculture, 2011 and 2016. Number of sows, boars, nursing pigs, weaner pigs, and grower and finishing pigs.
DOI: 10.25318/3210042801-eng
title: Poultry inventories on farms, Census of Agriculture, inactive

description: Census of Agriculture, 2011 and 2016. Number of pullets, hens, chickens, turkeys and other poultry.
DOI: 10.25781/kaust-0941j
title: Green turtle tracking leads the discovery of seagrass blue carbon resources

description: Processed green turtle satellite telemetry, polygons generated in ArcMap of 95% and 50% Utilisation Distributions in foraging sites.
DOI: 10.25781/kaust-2988a
title: Green turtle tracking leads the discovery of seagrass blue carbon resources

description: Dry Bulk Density and Organic Carbon content from seagrass meadow sediment in the Red Sea
DOI: 10.5066/f7dn436b
title: Water-quality and streamflow datasets used for estimating long-term mean daily streamflow and annual loads to be considered for use in regional streamflow, nutrient and sediment SPARROW models, United States, 1999-2014

description: The United States Geological Survey's (USGS) SPAtially Referenced Regressions On Watershed attributes (SPARROW) model was developed to aid in the interpretation of monitoring data and simulate water-quality conditions in streams across large spatial scales. SPARROW is a hybrid empirical/process-based mass balance model that can be used to estimate the major sources and environmental factors that affect the long-term supply, transport, and fate of contaminants in streams. The spatially explicit model structure is defined by a river reach network coupled with contributing catchments. The model is calibrated by statistically relating watershed sources and transport-related properties to monitoring-based streamflow and water-quality load estimates. Streamflow and load estimates considered for use in regional SPARROW model applications (2012 base year) are described in Saad and others, 2019 (https://dx.doi.org/10.3133/sir20195069). Load estimation methods described in this report include the Beale Ratio Estimator and Fluxmaster models. This USGS data release contains all of the input and output files necessary to reproduce the load estimates considered for inclusion in the 2012 regional SPARROW models. Data preparation for input to the load estimation models is also fully described in the above-mentioned report.
DOI: 10.5281/zenodo.13836854
title: The Beauty Survey

description: This repository contains the data collected during and the code used to analyze the Beauty Survey. A pre-print of the associated paper including our analysis and findings can be found at this link.

Zip files have been uploaded to this repository to stay within the file limit enforced by Zenodo. To use our code and data simply unzip these folders while mainting the current directory structure. 

While the code here is complete and stands on its own, any new features added can be found in the GitHub repository associated with this project (link).

AG and NO are supported by a nominal grant received at the ELLIS Unit Alicante Foundation from the Regional Government of Valencia in Spain (Convenio Singular signed with Generalitat Valenciana, Conselleria de Innovacion, Industria, Comercio y Turismo, Direccion General de Innovacion), along with grants from the European Union’s Horizon 2020 research and innovation programme - ELISE (grant agreement 951847) and ELIAS (grant agreement  101120237), and by grants from the Banc Sabadell Foundation and Intel corporation. BL is partially supported by the European Union’s Horizon Europe research and innovation program under grant agreement No. 101120237 (ELIAS) and by the PNRR project FAIR - Future AI Research (PE00000013), under the NRRP MUR program funded by the NextGenerationEU.
DOI: 10.5281/zenodo.4030660
title: CSAW-S

description: The CSAW-S is a curated dataset containing mammography images with annotations of breast cancer and breast anatomy from experts and non-experts. It contains mammography screenings from 172 different patients with annotations for semantic segmentation. Additional information about our paper and the source code can be found here. If you use this dataset please cite our work Adding seemingly uninformative labels helps in low data regimes.
DOI: 10.15468/dl.h8zh24
title: Occurrence Download

description: A dataset containing 609 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "TaxonKey is Acer forrestii Diels"
 ]
}

 The dataset includes 609 records from 24 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004099-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fr3pbb
title: Occurrence Download

description: A dataset containing 11364 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Setaria sphacelata (Schumach.) Stapf & C.E.Hubb. ex Moss"
 ]
}

 The dataset includes 11364 records from 264 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004098-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2h3cxy
title: Occurrence Download

description: A dataset listing the 4007711 species recorded in GBIF matching the query:
{ }

 The dataset's 4007711 records were derived from 69267 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004083-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4zzffy
title: Occurrence Download

description: A dataset containing 1054 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is one of (Canada, United States of America)",
 "TaxonKey is Acer ×freemanii A.E.Murray"
 ]
}

 The dataset includes 1054 records from 29 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004100-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bb62fx
title: Occurrence Download

description: A dataset containing 91838 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is one of (Setaria pumila (Poir.) Roem. & Schult., Setaria pumila subsp. pallide-fusca (Schumach.) B.K.Simon)"
 ]
}

 The dataset includes 91838 records from 1212 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004096-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.