cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25452/figshare.plus.24540988
title: Image Data for "Quantum Computing Dataset of Maximum Independent Set Problem on King’s Lattice of over Hundred Rydberg Atoms" including SPAM errors and calibration data

description: This is Image Data for SPAM errors and calibration data described from "Quantum Computing Dataset of Maximum Independent Set Problem on King’s Lattice of over Hundred Rydberg Atoms". Raw image files are in TIF format, constituting a list of image files structured as a three-dimensional array. The first two dimensions denote the image, while the third dimension represents the stack of images across experimental repetitions. The data for the |g⟩ → |r⟩ SPAM error is labeled as ‘SPAM{prg,SPAM#}_X{#}.tif’, where # is assigned in sequential order. Three distinct prg,SPAM# measurements are presented, reflecting variations in cooling laser power conditions leading to different Polarization Gradient Cooling (PGC) rates and, consequently, distinct loss rates. The raw data can be utilized to generate fluorescence data (‘flouAreshape’) and digitized data (‘floudigreshape’), provided in https://doi.org/10.6084/m9.figshare.23828004, using the code (‘Digitze_Data.m’) available on https://doi.org/10.6084/m9.figshare.23911368.<br><br>Finding the maximum independent set (MIS) of a large-size graph is a nondeterministic polynomial-time (NP)-complete problem not efficiently solvable with classical computations but may be suitable for quantum computation. In recent years, there are growing interests in using Rydberg-atom arrays to solve the MIS problem. Here, we report a set of quantum adiabatic computing data of Rydberg-atom experiments performed with up to 141 atoms randomly arranged on the King’s lattice. A total of 582,916 events of Rydberg-atom measurements are collected for experimental MIS solutions of 733,853 different graphs. We provide the raw image data along with the entire binary determinations of the measured many-body ground states and the classified graph data, to offer bench-mark testing and advanced data-driven analyses for validation of the performance of the Rydberg-atom approach as well as system improvements.
DOI: 10.25452/figshare.plus.24540988.v1
title: Image Data for "Quantum Computing Dataset of Maximum Independent Set Problem on King’s Lattice of over Hundred Rydberg Atoms" including SPAM errors and calibration data

description: This is Image Data for SPAM errors and calibration data described from "Quantum Computing Dataset of Maximum Independent Set Problem on King’s Lattice of over Hundred Rydberg Atoms". Raw image files are in TIF format, constituting a list of image files structured as a three-dimensional array. The first two dimensions denote the image, while the third dimension represents the stack of images across experimental repetitions. The data for the |g⟩ → |r⟩ SPAM error is labeled as ‘SPAM{prg,SPAM#}_X{#}.tif’, where # is assigned in sequential order. Three distinct prg,SPAM# measurements are presented, reflecting variations in cooling laser power conditions leading to different Polarization Gradient Cooling (PGC) rates and, consequently, distinct loss rates. The raw data can be utilized to generate fluorescence data (‘flouAreshape’) and digitized data (‘floudigreshape’), provided in https://doi.org/10.6084/m9.figshare.23828004, using the code (‘Digitze_Data.m’) available on https://doi.org/10.6084/m9.figshare.23911368.<br><br>Finding the maximum independent set (MIS) of a large-size graph is a nondeterministic polynomial-time (NP)-complete problem not efficiently solvable with classical computations but may be suitable for quantum computation. In recent years, there are growing interests in using Rydberg-atom arrays to solve the MIS problem. Here, we report a set of quantum adiabatic computing data of Rydberg-atom experiments performed with up to 141 atoms randomly arranged on the King’s lattice. A total of 582,916 events of Rydberg-atom measurements are collected for experimental MIS solutions of 733,853 different graphs. We provide the raw image data along with the entire binary determinations of the measured many-body ground states and the classified graph data, to offer bench-mark testing and advanced data-driven analyses for validation of the performance of the Rydberg-atom approach as well as system improvements.
DOI: 10.25452/figshare.plus.24523198
title: Image Data for "Quantum Computing Dataset of Maximum Independent Set Problem on King’s Lattice of over Hundred Rydberg Atoms" from Exp 31 to 45

description: This is Image Data for Exp 31 to 45 described from "Quantum Computing Dataset of Maximum Independent Set Problem on King’s Lattice of over Hundred Rydberg Atoms". Raw image files are in TIF format, constituting a list of image files structured as a three-dimensional array. The first two dimensions denote the image, while the third dimension represents the stack of images across experimental repetitions. Due to the substantial file size, raw data is segmented into multiple files for the same experiments, named as ‘Exp{Exp#}_X{#}.tif’, where Exp# corresponds to the experiment index, and # is assigned in sequential order. The raw data can be utilized to generate fluorescence data (‘flouAreshape’) and digitized data (‘floudigreshape’), provided in https://doi.org/10.6084/m9.figshare.23828004, using the code (‘Digitze_Data.m’) available on https://doi.org/10.6084/m9.figshare.23911368.Finding the maximum independent set (MIS) of a large-size graph is a nondeterministic polynomial-time (NP)-complete problem not efficiently solvable with classical computations but may be suitable for quantum computation. In recent years, there are growing interests in using Rydberg-atom arrays to solve the MIS problem. Here, we report a set of quantum adiabatic computing data of Rydberg-atom experiments performed with up to 141 atoms randomly arranged on the King’s lattice. A total of 582,916 events of Rydberg-atom measurements are collected for experimental MIS solutions of 733,853 different graphs. We provide the raw image data along with the entire binary determinations of the measured many-body ground states and the classified graph data, to offer bench-mark testing and advanced data-driven analyses for validation of the performance of the Rydberg-atom approach as well as system improvements.
DOI: 10.5281/zenodo.10161839
title: Stage-specific expression patterns and co-targeting relationships among miRNAs in the developing mouse cortex

description: Analysis of expression patterns and co-targeting relationships between miRNAs in the embryonic mouse cortex. The following supplementary data are uploaded:
Supplementary_table_1.xlsx: Differentially expressed miRNAs between E14, E17 and P0 cortical samples as well as in NPCs isolated from the mouse cortex and differentiated into neurons in vitro.
Supplementary_table_2.xlsx: Weighted co-expression gene network analysis of miRNAs in the embryonic mouse cortex.
Supplementary_table_3.xlsx: Gene ontology terms of miRNA targets of the black and green modules from the WCGNA analysis.
Supplementary_table_4.xlsx: Significant co-targeting relationships between miRNAs in the embryonic mouse cortex.
DOI: 10.5281/zenodo.10161840
title: Stage-specific expression patterns and co-targeting relationships among miRNAs in the developing mouse cortex

description: Analysis of expression patterns and co-targeting relationships between miRNAs in the embryonic mouse cortex. The following supplementary data are uploaded:
Supplementary_table_1.xlsx: Differentially expressed miRNAs between E14, E17 and P0 cortical samples as well as in NPCs isolated from the mouse cortex and differentiated into neurons in vitro.
Supplementary_table_2.xlsx: Weighted co-expression gene network analysis of miRNAs in the embryonic mouse cortex.
Supplementary_table_3.xlsx: Gene ontology terms of miRNA targets of the black and green modules from the WCGNA analysis.
Supplementary_table_4.xlsx: Significant co-targeting relationships between miRNAs in the embryonic mouse cortex.
DOI: 10.6084/m9.figshare.24463402
title: Data for acoustic+food experiment with Gryllus lineaticeps

description: Availability of mates and food influence the plasticity in strategies mediating life-history tradeoffs in an insect
DOI: 10.5281/zenodo.10156463
title: Evaluación de la producción científica de la Universidad de Salamanca indexada en SCOPUS (2010-2015)

description: .rda archive machine readable in rstudio with the data collected for the Article  "Evaluación de la producción científica de la Universidad de Salamanca indexada en SCOPUS (2010-2015)" not published yet. 
.xlsx  file with document types per knowledge area
DOI: 10.5281/zenodo.10156464
title: Evaluación de la producción científica de la Universidad de Salamanca indexada en SCOPUS (2010-2015)

description: .rda archive machine readable in rstudio with the data collected for the Article  "Evaluación de la producción científica de la Universidad de Salamanca indexada en SCOPUS (2010-2015)" not published yet. 
.xlsx  file with document types per knowledge area
DOI: 10.5281/zenodo.10161762
title: Data from: experiment using Large Language Models for unit testing generation

description: IMPORTANT: Upon acceptance, all data will be available on Zenodo.org, and the link updated here.
This dataset represents the anonymized information from: background check form, experiment feedback form and test files produced by experiment participants
DOI: 10.5281/zenodo.10161763
title: Data from: experiment using Large Language Models for unit testing generation

description: IMPORTANT: Upon acceptance, all data will be available on Zenodo.org, and the link updated here.
This dataset represents the anonymized information from: background check form, experiment feedback form and test files produced by experiment participants
DOI: 10.5281/zenodo.10162006
title: Analysis of immobilized triflogallate (III) IL catalyst - NCN project OPUS, grant no. 2020/37/B/ST8/00693.

description: Dataset contains results obtained during the NCN project OPUS, grant no. 2020/37/B/ST8/00693. The file presents TGA and SEM-EDX analysis of immobilized triflogallate (III) IL catalyst on silica.
DOI: 10.5281/zenodo.10162005
title: Analysis of immobilized triflogallate (III) IL catalyst - NCN project OPUS, grant no. 2020/37/B/ST8/00693.

description: Dataset contains results obtained during the NCN project OPUS, grant no. 2020/37/B/ST8/00693. The file presents TGA and SEM-EDX analysis of immobilized triflogallate (III) IL catalyst on silica.
DOI: 10.5281/zenodo.10161985
title: Catalytic activity of triflogallate IL catalyst - NCN project OPUS, grant no. 2020/37/B/ST8/00693.

description: Dataset contains results obtained during the NCN project OPUS, grant no. 2020/37/B/ST8/00693. The file presents the catalytic activity of triflogallate (III) IL catalyst in cycloaddition between methyl/ethyl acrylate and cyclopentadiene.
DOI: 10.5281/zenodo.10161986
title: Catalytic activity of triflogallate IL catalyst - NCN project OPUS, grant no. 2020/37/B/ST8/00693.

description: Dataset contains results obtained during the NCN project OPUS, grant no. 2020/37/B/ST8/00693. The file presents the catalytic activity of triflogallate (III) IL catalyst in cycloaddition between methyl/ethyl acrylate and cyclopentadiene.
DOI: 10.5281/zenodo.10161967
title: Catalytic activity of [Mim][OTf]-TiO2 catalyst - NCN project OPUS, grant no. 2020/37/B/ST8/00693.

description: Dataset contains results obtained during the NCN project OPUS, grant no. 2020/37/B/ST8/00693. The file presents the catalytic activity of [Mim][OTf]-TiO2, [Mim][OTf] and TiO2 catalysts in the esterification of oleic acid and 2-ethylhexanol.
DOI: 10.5281/zenodo.10161968
title: Catalytic activity of [Mim][OTf]-TiO2 catalyst - NCN project OPUS, grant no. 2020/37/B/ST8/00693.

description: Dataset contains results obtained during the NCN project OPUS, grant no. 2020/37/B/ST8/00693. The file presents the catalytic activity of [Mim][OTf]-TiO2, [Mim][OTf] and TiO2 catalysts in the esterification of oleic acid and 2-ethylhexanol.
DOI: 10.5281/zenodo.10161955
title: Synthesis of [Mim][OTf]-TiO2 catalyst - NCN project OPUS, grant no. 2020/37/B/ST8/00693.

description: Dataset contains results obtained during the NCN project OPUS, grant no. 2020/37/B/ST8/00693. The file presents the synthetic procedure of [Mim][OTf]-TiO2 catalyst.
DOI: 10.5281/zenodo.10161956
title: Synthesis of [Mim][OTf]-TiO2 catalyst - NCN project OPUS, grant no. 2020/37/B/ST8/00693.

description: Dataset contains results obtained during the NCN project OPUS, grant no. 2020/37/B/ST8/00693. The file presents the synthetic procedure of [Mim][OTf]-TiO2 catalyst.
DOI: 10.5281/zenodo.10161900
title: Analysis of [Mim][OTf]-TiO2 catalyst - NCN project OPUS, grant no. 2020/37/B/ST8/00693.

description: Dataset contains results obtained during the NCN project OPUS, grant no. 2020/37/B/ST8/00693. The file presents NMR, TGA, Raman, IR spectra, TEM-EDX analysis of synthesized [Mim][OTf]-TiO2 catalyst.
DOI: 10.5281/zenodo.10161901
title: Analysis of [Mim][OTf]-TiO2 catalyst - NCN project OPUS, grant no. 2020/37/B/ST8/00693.

description: Dataset contains results obtained during the NCN project OPUS, grant no. 2020/37/B/ST8/00693. The file presents NMR, TGA, Raman, IR spectra, TEM-EDX analysis of synthesized [Mim][OTf]-TiO2 catalyst.
DOI: 10.6084/m9.figshare.24596088
title: Supplementary Data S2: BVBRC genome information, including GenBank accessions, for publicly available Omnitrophota genomes used in this analysis

description: Genome information obtained from BVBRC for genomes labeled "Omnitrophica" added on or before May 18, 2023.
DOI: 10.6084/m9.figshare.24596088.v1
title: Supplementary Data S2: BVBRC genome information, including GenBank accessions, for publicly available Omnitrophota genomes used in this analysis

description: Genome information obtained from BVBRC for genomes labeled "Omnitrophica" added on or before May 18, 2023.
DOI: 10.26093/cds/vizier.36360074
title: HARPS radial velocity database

description: VizieR online Data Catalogue associated with article published in journal Astronomy & Astrophysics with title 'A public HARPS radial velocity database corrected for systematic errors.' (bibcode: 2020A&A...636A..74T)
DOI: 10.5281/zenodo.10161952
title: Dataset of point-clouds generated by UAV LiDAR scanning of barley field-plot trial.

description: Point clouds from eight scanning flights, scanned by UAV LiDAR system VUX-UAV1 (Ricopter GmBh), provided in forms of separated .las files. Dataset represent raw data that were further processed by software ALFA to extract height of canopies in particular field plots. Software serves for monitoring of plant growth dynamics in agricultural or breeding filed-plot trials.
DOI: 10.5281/zenodo.10161951
title: Dataset of point-clouds generated by UAV LiDAR scanning of barley field-plot trial.

description: Point clouds from eight scanning flights, scanned by UAV LiDAR system VUX-UAV1 (Ricopter GmBh), provided in forms of separated .las files. Dataset represent raw data that were further processed by software ALFA to extract height of canopies in particular field plots. Software serves for monitoring of plant growth dynamics in agricultural or breeding filed-plot trials.
DOI: 10.6084/m9.figshare.24596103
title: Supplementary Data S6: Protein Structures

description: Alphafold-predicted and PDB reference structures used in figures throughout this manuscript (designated by directory name and file name).
DOI: 10.6084/m9.figshare.24596103.v1
title: Supplementary Data S6: Protein Structures

description: Alphafold-predicted and PDB reference structures used in figures throughout this manuscript (designated by directory name and file name).
DOI: 10.6084/m9.figshare.24596112
title: Supplementary Data S5: 16RP Phylogeny for Figure 1

description: iQ-TREE estimated treefile as displayed in Figure 1 and Figure 7.
DOI: 10.6084/m9.figshare.24596112.v1
title: Supplementary Data S5: 16RP Phylogeny for Figure 1

description: iQ-TREE estimated treefile as displayed in Figure 1 and Figure 7.
DOI: 10.25345/c5rf5ks1j
title: MassIVE MSV000093439 - Impact of Charge State on Characterization of Large Middle-Down Sized Peptides by Tandem Mass Spectrometry
title: Fragmentation trends of large peptides were characterized by five activation methods, including HCD, ETD, EThcD, 213 nm UVPD and 193 nm UVPD. Sequence coverages and scores were assessed based on charge site, peptide sequence and peptide size. Results from four model peptides, neuromedin, glucagon, galanin and amyloid B, showed a charge state dependence on sequence coverage for collision and electron-based activation methods. The effect of charge state and peptide size on sequence coverage was also explored for a Glu-C digest of E. coli ribosomal proteins, resulting in a maximum sequence coverage between 2-6 kDa depending on the activation method.
DOI: 10.5281/zenodo.10161581
title: The genomic and epidemiological virulence patterns of Salmonella enterica serovars in the United States

description: The serovars of Salmonella enterica display dramatic differences in pathogenesis and host preferences. We developed a process (patent pending) for grouping Salmonella isolates and serovars by their public health risk. We collated a curated set of 12,337 S. enterica isolate genomes from human, beef, and bovine sources in the US. After annotating a virulence gene catalog for each isolate, we used unsupervised random forest methods to estimate the proximity (similarity) between isolates based upon the genomic presentation of putative virulence traits  We then grouped isolates (virulence clusters) using hierarchical clustering (Ward's method), used non-parametric bootstrapping to assess cluster stability, and externally validated the clusters against epidemiological virulence measures from FoodNet, the National Outbreak Reporting System (NORS), and US federal sampling of beef products. We identified five stable virulence clusters of S. enterica serovars. Cluster 1 (higher virulence) serovars yielded an annual incidence rate of domestically acquired sporadic cases roughly one and a half times higher than the other four clusters combined (Clusters 2-5, lower virulence). Compared to other clusters, cluster 1 also had a higher proportion of infections leading to hospitalization and was implicated in more foodborne and beef-associated outbreaks, despite being isolated at a similar frequency from beef products as other clusters. We also identified subpopulations within 11 serovars. Remarkably, we found S. Infantis and S. Typhimurium subpopulations that significantly differed in genome length and clinical case presentation. Further, we found that the presence of the pESI plasmid accounted for the genome length differences between the S. Infantis subpopulations. Our results show that S. enterica strains associated with highest incidence of human infections share a common virulence repertoire. This work could be updated regularly and used in combination with foodborne surveillance information to prioritize serovars of public health concern.  
Files contained in this repository will reproduce elements of figures 3,4,6, and 7 of the accompanying PLOS One manuscript.
DOI: 10.5281/zenodo.10161582
title: The genomic and epidemiological virulence patterns of Salmonella enterica serovars in the United States

description: The serovars of Salmonella enterica display dramatic differences in pathogenesis and host preferences. We developed a process (patent pending) for grouping Salmonella isolates and serovars by their public health risk. We collated a curated set of 12,337 S. enterica isolate genomes from human, beef, and bovine sources in the US. After annotating a virulence gene catalog for each isolate, we used unsupervised random forest methods to estimate the proximity (similarity) between isolates based upon the genomic presentation of putative virulence traits  We then grouped isolates (virulence clusters) using hierarchical clustering (Ward's method), used non-parametric bootstrapping to assess cluster stability, and externally validated the clusters against epidemiological virulence measures from FoodNet, the National Outbreak Reporting System (NORS), and US federal sampling of beef products. We identified five stable virulence clusters of S. enterica serovars. Cluster 1 (higher virulence) serovars yielded an annual incidence rate of domestically acquired sporadic cases roughly one and a half times higher than the other four clusters combined (Clusters 2-5, lower virulence). Compared to other clusters, cluster 1 also had a higher proportion of infections leading to hospitalization and was implicated in more foodborne and beef-associated outbreaks, despite being isolated at a similar frequency from beef products as other clusters. We also identified subpopulations within 11 serovars. Remarkably, we found S. Infantis and S. Typhimurium subpopulations that significantly differed in genome length and clinical case presentation. Further, we found that the presence of the pESI plasmid accounted for the genome length differences between the S. Infantis subpopulations. Our results show that S. enterica strains associated with highest incidence of human infections share a common virulence repertoire. This work could be updated regularly and used in combination with foodborne surveillance information to prioritize serovars of public health concern.  
Files contained in this repository will reproduce elements of figures 3,4,6, and 7 of the accompanying PLOS One manuscript.
DOI: 10.5281/zenodo.10161915
title: ChatGPT Provides Inconsistent Risk-Stratification of Patients With Atraumatic Chest Pain - Dataset

description: Dataset for analysis of the ability of ChatGPT to risk-stratify patients with atraumatic chest pain
DOI: 10.5281/zenodo.10161916
title: ChatGPT Provides Inconsistent Risk-Stratification of Patients With Atraumatic Chest Pain - Dataset

description: Dataset for analysis of the ability of ChatGPT to risk-stratify patients with atraumatic chest pain
DOI: 10.34740/kaggle/dsv/7013762
title: Forex Exchange Rates Since 2004 (Updated Daily)
DOI: 10.5281/zenodo.10096022
title: Seamounts_Oasis_New_Caledonia_BRUVS

description: This dataset contains BRUVS (Baited Remote Underwater Video Station) data for 224 video stations collected in seamounts, continental slopes and coral reefs of New-Caledonia in 2019 and 2020. The data were collected under permits to Laurent Vigliola by the Government of New-Caledonia (permit N° 2019-733/GNC, 2020-503/GNC and 2020-1077/GNC), the Southern Province of New Caledonia (permit N° 898-2019/ARR/DENV, 3066-2019/ARR/DENV, 844-2020/ARR/DDDT and 1955-2020/ARR/DDDT) and the Northern Province of New Caledonia (permit N° 609011/2019/DEPART/JJC , 609011-18/2019/DEPART/JJC and 609011-39/2020/DEPART/JJC). Collection was performed during the SEAMOUNTS and REEF3.0 projects led by Laurent Vigliola. The data contains the outputs of BRUVS video analyses (species id, abundance, size, biomass) as described in Baletaud et al. 2023. The metadata contains information on the stations, sampling locations and associated environmental variables.
DOI: 10.5281/zenodo.10096023
title: Seamounts_Oasis_New_Caledonia_BRUVS

description: This dataset contains BRUVS (Baited Remote Underwater Video Station) data for 224 video stations collected in seamounts, continental slopes and coral reefs of New-Caledonia in 2019 and 2020. The data were collected under permits to Laurent Vigliola by the Government of New-Caledonia (permit N° 2019-733/GNC, 2020-503/GNC and 2020-1077/GNC), the Southern Province of New Caledonia (permit N° 898-2019/ARR/DENV, 3066-2019/ARR/DENV, 844-2020/ARR/DDDT and 1955-2020/ARR/DDDT) and the Northern Province of New Caledonia (permit N° 609011/2019/DEPART/JJC , 609011-18/2019/DEPART/JJC and 609011-39/2020/DEPART/JJC). Collection was performed during the SEAMOUNTS and REEF3.0 projects led by Laurent Vigliola. The data contains the outputs of BRUVS video analyses (species id, abundance, size, biomass) as described in Baletaud et al. 2023. The metadata contains information on the stations, sampling locations and associated environmental variables.