cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.22003/xfel.eu-data-003223-00
title: On the fly crystallization for nucleation studies & higher reliability Serial Femtosecond  Crystallography
DOI: 10.6084/m9.figshare.3761562.v2199
title: Online Labour Index: Measuring the Online Gig Economy for Policy and Research

description: Data repository for the data underlying the Online Labour Index. See http://ilabour.oii.ox.ac.uk online-labour-index/ for details.
DOI: 10.6084/m9.figshare.19651314.v1
title: AbEMap results: Epitope Maps with BM5 Crystal inputs

description: One of AbEMap's applications is to map epitope on a given antigen crystal structure if the antibody structure (bound or unbound) is known. The results in this dataset are pdb files of the 40 antigens in Zhiping Weng's docking benchmark v. 5.0 with their b-factor changed to our protocol's score to reflect the likelihood of each atom being in the epitope.
DOI: 10.6084/m9.figshare.19651404.v1
title: AbEMap results: Confusion Matrix for BM5 Crystal inputs

description: The summary confusion matrix (residue based) for the epitope mapping done by AbEMap on the 40 antibody-antigen complexes with antibody crystal input.
DOI: 10.6084/m9.figshare.19651746.v1
title: AbEMap results: Confusion Matrix for BM5.5 crystal inputs

description: The summary confusion matrix (residue based) for the epitope mapping done by AbEMap on 21 of the new antibody-antigen complexes added to BM5.5 with antibody crystal input. The text file contains the True Positive (TP), False Positive (FP), False Negative (FN) and True Negative (TN) counts for each case at different ranking thresholds (Top1, Top5, Top10, ... Top120)
DOI: 10.6084/m9.figshare.19652442.v1
title: AbEMap results: Confusion Matrix for BM5 sequence inputs

description: The summary confusion matrix (residue based) for the epitope mapping done by AbEMap on the 40 antibody-antigen complexes with antibody sequence input.
DOI: 10.6084/m9.figshare.19652493
title: AbEMap results: Epitope Maps with BM5.5 sequence inputs

description: One of AbEMap's applications is to map epitope on a given antigen crystal structure if teh user only inputs the antibody's sequence. The results in this dataset are pdb files of the 21 antigens in Zhiping Weng's docking benchmark v. 5.5 with their b-factor changed to our protocol's score to reflect the likelihood of each atom being in the epitope when in complex with the respective antibodies.
DOI: 10.6084/m9.figshare.19652493.v1
title: AbEMap results: Epitope Maps with BM5.5 sequence inputs

description: One of AbEMap's applications is to map epitope on a given antigen crystal structure if teh user only inputs the antibody's sequence. The results in this dataset are pdb files of the 21 antigens in Zhiping Weng's docking benchmark v. 5.5 with their b-factor changed to our protocol's score to reflect the likelihood of each atom being in the epitope when in complex with the respective antibodies.
DOI: 10.6084/m9.figshare.19652496.v1
title: AbEMap results: Confusion matrix for BM5.5 sequence inputs

description: The summary confusion matrix (residue based) for the epitope mapping done by AbEMap on 21 of the new antibody-antigen complexes in BM5.5 with antibody sequence input.
DOI: 10.3886/e113641v1-116180
title: Replication data for: Buy the Book? Evidence on the Effect of Textbook Funding on School-Level Achievement

description: This paper considers the effect of textbook funding on school-level test performance by using a quasi-experimental setting in the United States. I consider a lawsuit in California that provided a one-time payment of $96.90 per student for textbooks if schools fell below a threshold of academic performance. Exploiting this variation with a regression discontinuity (RD) design, I find that textbook funding has significant positive effects on school-level achievement in elementary schools and has a high benefit-per-dollar. In contrast to elementary schools, I find no effect in middle and high schools though these estimates are very imprecise.
DOI: 10.6084/m9.figshare.19652508
title: AbEMap results: Epitope Maps with AF2 folded (with NO templates) Ab inputs

description: The third application of AbEmap is to use computationally modelled antibody structures to map epitopes on given antigen structures. This dataset contains epitope mapping results of 40 BM5 antigens when using AlphaFold folded antibody structures (Note - No templates were used in structure prediction). The resulting AbEMap scores are saved as b-factors in the PDB files included in this data set.
DOI: 10.6084/m9.figshare.19652508.v1
title: AbEMap results: Epitope Maps with AF2 folded (with NO templates) Ab inputs

description: The third application of AbEmap is to use computationally modelled antibody structures to map epitopes on given antigen structures. This dataset contains epitope mapping results of 40 BM5 antigens when using AlphaFold folded antibody structures (Note - No templates were used in structure prediction). The resulting AbEMap scores are saved as b-factors in the PDB files included in this data set.
DOI: 10.6084/m9.figshare.19652499
title: AlphaFold Results: Top predicted models for BM5 antibody sequences with NO templates

description: AlphaFold is used to regenerate the antibody structures in BM5 starting only from the sequence and is not allowed to use any templates from the PDB. This dataset contains the top predicted models from these runs for each antibody before any relaxation.
DOI: 10.6084/m9.figshare.19652499.v1
title: AlphaFold Results: Top predicted models for BM5 antibody sequences with NO templates

description: AlphaFold is used to regenerate the antibody structures in BM5 starting only from the sequence and is not allowed to use any templates from the PDB. This dataset contains the top predicted models from these runs for each antibody before any relaxation.
DOI: 10.6084/m9.figshare.19652637
title: AbEMap results: Epitope Maps of AF2 folded (with template) Ab inputs

description: The third application of AbEmap is to use computationally modelled antibody structures to map epitopes on given antigen structures. This dataset contains epitope mapping results of 40 BM5 antigens when using AlphaFold folded antibody structures (Note - Antibody folding was guided by 1 template at a time). The resulting AbEMap scores obtained by using each AF model are averaged and are saved as b-factors in the PDB files included in this data set. eg. Antibodies in PDB IDs 1A6T, 2Z91, 3B9K, 3OPZ, 5KTE, 5KVG and 5TPW were used as templates when folding Antibody Sequence in 1AHW with AF2. The Top model from each run is then run through AbEMap and the final 1AHW's antigen epitope mapping results are the average of all six runs.
DOI: 10.6084/m9.figshare.19652637.v1
title: AbEMap results: Epitope Maps of AF2 folded (with template) Ab inputs

description: The third application of AbEmap is to use computationally modelled antibody structures to map epitopes on given antigen structures. This dataset contains epitope mapping results of 40 BM5 antigens when using AlphaFold folded antibody structures (Note - Antibody folding was guided by 1 template at a time). The resulting AbEMap scores obtained by using each AF model are averaged and are saved as b-factors in the PDB files included in this data set. eg. Antibodies in PDB IDs 1A6T, 2Z91, 3B9K, 3OPZ, 5KTE, 5KVG and 5TPW were used as templates when folding Antibody Sequence in 1AHW with AF2. The Top model from each run is then run through AbEMap and the final 1AHW's antigen epitope mapping results are the average of all six runs.
DOI: 10.5519/qd.hsffmaws
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (338 records)
DOI: 10.5281/zenodo.6330114
title: Diurnal rainfall response to the physiological and radiative effects of CO2 in tropical forests in the Energy Exascale Earth System Model v1

description: Necessary outputs and scripts for recreating the figures for the journal article with the same title.
DOI: 10.5281/zenodo.6330113
title: Diurnal rainfall response to the physiological and radiative effects of CO2 in tropical forests in the Energy Exascale Earth System Model v1

description: Necessary outputs and scripts for recreating the figures for the journal article with the same title.
DOI: 10.5281/zenodo.6373668
title: Fractures on Bennu's boulders

description: This is the data set corresponding to the publication entitled Alignment of fractures on Bennu’s boulders indicative of rapid asteroid surface evolution, by the same authors, which is to be published by Nature Geoscience.
DOI: 10.5281/zenodo.6373667
title: Fractures on Bennu's boulders

description: This is the data set corresponding to the publication entitled Alignment of fractures on Bennu’s boulders indicative of rapid asteroid surface evolution, by the same authors, which is to be published by Nature Geoscience.
DOI: 10.5281/zenodo.6482320
title: CAMI Skin Dataset for the Resmico model

description: This is one of the test datasets used in the Resmico paper. We downloaded the paired-end reads of the Critical Assessment of Metagenome Interpretation (CAMI) human Skin assembly challenges and assembled the reads via metaSPAdes and MEGAHI. For the labels, we identified true misassemblies via MetaQUAST based on the reference genomes.
DOI: 10.5281/zenodo.6482319
title: CAMI Skin Dataset for the Resmico model

description: This is one of the test datasets used in the Resmico paper. We downloaded the paired-end reads of the Critical Assessment of Metagenome Interpretation (CAMI) human Skin assembly challenges and assembled the reads via metaSPAdes and MEGAHI. For the labels, we identified true misassemblies via MetaQUAST based on the reference genomes.
DOI: 10.5281/zenodo.6484868
title: Pharmaceutical advertising and the consumption of over the counter (OTC) medicines in users of the Superfar drugstore in Barrios Altos - Cercado de Lima, 2022.

description: To determine the relationship between pharmaceutical advertising and the consumption of over-the-counter (OTC) medicines in users of the SUPERFAR drugstore in barrios altos -cercado de lima, 2022.
DOI: 10.6084/m9.figshare.19253716
title: Characterization of hydrological features and plankton during neap tides in a subtropical lagoon south of the California Current

description: This study aimed to characterize their Spatio-temporal distribution of hydrological variables and plankton during neap tides in Bahía Magdalena, a subtropical lagoon south of the California Current. We compare data from surface and bottom waters of stations located inside the lagoon with those near the bay's mouth and between surface and bottom. The availability of nutrients and the chlorophyll-a are associated primarily with the intense upwelling activity in spring. Due to direct marine influence, this relationship was more significant at the inlet than inside the lagoon, especially at the bottom. During the intense upwellings marine influence is maintained even during neap tides. The wind probably causes the homogeneous distribution in most variables within the bay's surface; this may also contribute to the re-suspension of nutrients due to vertical water column mixing. Abiotic variables were not linearly related with zooplankton biovolume and the density of diatoms and dinoflagellates. Phytoplankton was composed mainly by the micro fraction and diatoms during spring and nanoplankton in the warmest season of the year; however, the strong upwellings at the spring's end caused a HAB composed for diatoms. Chlorophyll-a concentration and diatoms were more abundant inside the lagoon and could explain the lower nutrient concentration of that zone. Zooplankton biovolume seasonality differed from other years, with higher values during winter and a significant decreasing trend throughout the year, resulting from the phytoplankton variability. Upwelling and wind variability explains the high biological productivity observed over most of the year.
DOI: 10.6084/m9.figshare.19087721
title: Conserve immatures and rebound the potential: stock status and reproduction of whiting (<i>Merlangius merlangus</i> [Linnaeus, 1758]) in the Western Black Sea

description: The stock structure and productivity components (growth, maturity and mortality) of the Black Sea whiting <i>Merlangius merlangus</i> were studied in the western Black Sea for a year. The results aim to improve fisheries management of whiting in the Black Sea. Fresh samples were collected from commercial bottom trawlers between October 2017 and September 2018. Using monthly length-frequency data set for the growth trajectories, a bootstrapped procedure was employed to improve parameter optimization. Duration and timing of the spawning season and size at sexual maturity were modelled using generalized additive models (GAMs). The presence of clear differences in oocyte size groups indicates that oocyte development of Black Sea whiting is a ‘group synchronous’ ovarian developmental process characterized by continuous reproduction. From the gonadosomatic index values, their spawning activity intensifies especially between October and April, captured also in the time component in the GAM modelling. The length at first maturity was 13.9 cm for females and 12.5 cm for males. The mortality rates, yield per recruit analyses, and length-based indicators suggest that whiting is heavily exploited with alarming signs of overexploitation. Undoubtedly, setting catch limits and re-establishing management plans will be the first two steps to ensure reproductive success and prevent overfishing (<i>F</i> &gt; Fmsy).
DOI: 10.6084/m9.figshare.19087721.v1
title: Conserve immatures and rebound the potential: stock status and reproduction of whiting (<i>Merlangius merlangus</i> [Linnaeus, 1758]) in the Western Black Sea

description: The stock structure and productivity components (growth, maturity and mortality) of the Black Sea whiting <i>Merlangius merlangus</i> were studied in the western Black Sea for a year. The results aim to improve fisheries management of whiting in the Black Sea. Fresh samples were collected from commercial bottom trawlers between October 2017 and September 2018. Using monthly length-frequency data set for the growth trajectories, a bootstrapped procedure was employed to improve parameter optimization. Duration and timing of the spawning season and size at sexual maturity were modelled using generalized additive models (GAMs). The presence of clear differences in oocyte size groups indicates that oocyte development of Black Sea whiting is a ‘group synchronous’ ovarian developmental process characterized by continuous reproduction. From the gonadosomatic index values, their spawning activity intensifies especially between October and April, captured also in the time component in the GAM modelling. The length at first maturity was 13.9 cm for females and 12.5 cm for males. The mortality rates, yield per recruit analyses, and length-based indicators suggest that whiting is heavily exploited with alarming signs of overexploitation. Undoubtedly, setting catch limits and re-establishing management plans will be the first two steps to ensure reproductive success and prevent overfishing (<i>F</i> &gt; Fmsy).
DOI: 10.6084/m9.figshare.19253716.v1
title: Characterization of hydrological features and plankton during neap tides in a subtropical lagoon south of the California Current

description: This study aimed to characterize their Spatio-temporal distribution of hydrological variables and plankton during neap tides in Bahía Magdalena, a subtropical lagoon south of the California Current. We compare data from surface and bottom waters of stations located inside the lagoon with those near the bay's mouth and between surface and bottom. The availability of nutrients and the chlorophyll-a are associated primarily with the intense upwelling activity in spring. Due to direct marine influence, this relationship was more significant at the inlet than inside the lagoon, especially at the bottom. During the intense upwellings marine influence is maintained even during neap tides. The wind probably causes the homogeneous distribution in most variables within the bay's surface; this may also contribute to the re-suspension of nutrients due to vertical water column mixing. Abiotic variables were not linearly related with zooplankton biovolume and the density of diatoms and dinoflagellates. Phytoplankton was composed mainly by the micro fraction and diatoms during spring and nanoplankton in the warmest season of the year; however, the strong upwellings at the spring's end caused a HAB composed for diatoms. Chlorophyll-a concentration and diatoms were more abundant inside the lagoon and could explain the lower nutrient concentration of that zone. Zooplankton biovolume seasonality differed from other years, with higher values during winter and a significant decreasing trend throughout the year, resulting from the phytoplankton variability. Upwelling and wind variability explains the high biological productivity observed over most of the year.
DOI: 10.6084/m9.figshare.19450001
title: Hand dredging for the wedge clam (<i>Donax trunculus</i>) in the Algarve coast (southern Portugal): fishing yield, bycatch, discards and damage rates

description: This study aimed to characterize the catches, quantify fishing yield, bycatch and discards, and also estimate damage and mortality rates using hand dredges with two different mesh sizes (20 and 25 mm) for harvesting the wedge clam (<i>Donax trunculus</i>). A total of 160 tows were performed in Lota Beach and Armona Island in the Algarve coast (southern Portugal). Overall, were caught 12,319 individuals (3985 in Lota Beach and 8334 in Armona Island) belonging to 48 <i>taxa</i> distributed among seven phyla (14 <i>taxa</i> in Lota Beach and 44 <i>taxa</i> in Armona Island). Bycatch proportions ranged from 13.1% to 32.0% in abundance and from 10.7% to 32.9% in biomass, with more bycatch using hand dredges with 20 mm mesh size. Commercially undersized <i>D. trunculus</i> (MCRS = 25 mm SL) prevailed within the bycatch, representing over 40% of discards using both mesh sizes. Due to different size selectivity, the target catch (CPUE) and bycatch per unit effort (BCPUE) in abundance and biomass, as well as fishing yield as a function of tow duration and towed area, were lower for hand dredges with 25 mm mesh than with 20 mm mesh. In general, damage and mortality rates were fairly low (1.3–2.6%) independently of mesh size, reinforcing the importance of releasing live bycatch to the sea immediately after sorting the catches. Overall, this study prompted the need to develop a good practice guide for hand dredgers, aiming to mitigate avoidable indirect discards mortality and improve the sustainability of this traditional harvesting activity.
DOI: 10.6084/m9.figshare.19450001.v1
title: Hand dredging for the wedge clam (<i>Donax trunculus</i>) in the Algarve coast (southern Portugal): fishing yield, bycatch, discards and damage rates

description: This study aimed to characterize the catches, quantify fishing yield, bycatch and discards, and also estimate damage and mortality rates using hand dredges with two different mesh sizes (20 and 25 mm) for harvesting the wedge clam (<i>Donax trunculus</i>). A total of 160 tows were performed in Lota Beach and Armona Island in the Algarve coast (southern Portugal). Overall, were caught 12,319 individuals (3985 in Lota Beach and 8334 in Armona Island) belonging to 48 <i>taxa</i> distributed among seven phyla (14 <i>taxa</i> in Lota Beach and 44 <i>taxa</i> in Armona Island). Bycatch proportions ranged from 13.1% to 32.0% in abundance and from 10.7% to 32.9% in biomass, with more bycatch using hand dredges with 20 mm mesh size. Commercially undersized <i>D. trunculus</i> (MCRS = 25 mm SL) prevailed within the bycatch, representing over 40% of discards using both mesh sizes. Due to different size selectivity, the target catch (CPUE) and bycatch per unit effort (BCPUE) in abundance and biomass, as well as fishing yield as a function of tow duration and towed area, were lower for hand dredges with 25 mm mesh than with 20 mm mesh. In general, damage and mortality rates were fairly low (1.3–2.6%) independently of mesh size, reinforcing the importance of releasing live bycatch to the sea immediately after sorting the catches. Overall, this study prompted the need to develop a good practice guide for hand dredgers, aiming to mitigate avoidable indirect discards mortality and improve the sustainability of this traditional harvesting activity.
DOI: 10.25921/m6ew-9219
title: AZFP Water Column Sonar Data Collected During ar049-vac-5144 Deployment
DOI: 10.5517/ccdc.csd.cc26l0vp
title: CCDC 2043112: Experimental Crystal Structure Determination

description: Related Article: Muhammad Nadeem Akhtar, Murad A. AlDamen, Colin D. McMillen, Albert Escuer, Júlia Mayans|2021|Inorg.Chem.|60|9302|doi:10.1021/acs.inorgchem.0c03682
DOI: 10.5517/ccdc.csd.cc26l0wq
title: CCDC 2043113: Experimental Crystal Structure Determination

description: Related Article: Muhammad Nadeem Akhtar, Murad A. AlDamen, Colin D. McMillen, Albert Escuer, Júlia Mayans|2021|Inorg.Chem.|60|9302|doi:10.1021/acs.inorgchem.0c03682
DOI: 10.5517/ccdc.csd.cc26l0tn
title: CCDC 2043111: Experimental Crystal Structure Determination

description: Related Article: Muhammad Nadeem Akhtar, Murad A. AlDamen, Colin D. McMillen, Albert Escuer, Júlia Mayans|2021|Inorg.Chem.|60|9302|doi:10.1021/acs.inorgchem.0c03682
DOI: 10.25497/d7x59z
title: Dangermond Preserve Plant List 2019

description: Voucher status, scientific name, common name, family, provenance, and rarity of the plants found on the Dangermond Preserve
DOI: 10.17909/4nym-qy94
title: Data from XRBs in M81 paper

description: We characterize the optical counterparts to the compact X-ray source population within the nearby spiral galaxy M81 using multi-band Hubble Space Telescope (HST) imaging data. By comparing the optical luminosities and colors measured for candidate donor stars and host clusters to stellar and cluster evolutionary models, respectively, we estimate the likely masses and upper age limits of the field and cluster X-ray binaries. We identify 15 low-mass X-ray binaries (i.e. donor star mass < 3 solar masses) within ancient globular clusters, as well as 42 candidate high-mass X-ray binaries (i.e. donor star mass > 8 solar masses). To estimate the likelihood of misclassifications, we inject 4,000 artificial sources into the HST mosaic image and conclude that our classifications of globular clusters and high-mass X-ray binaries are reliable at the > 90% level. We find that globular clusters that host X-ray binaries are on average more massive and more compact than globular clusters that do not. However, there is no apparent correlation between the X-ray brightness of the clusters and their masses or densities, nor are X-ray binary hosts more X-ray luminous than the general field population of low-mass X-ray binaries. This work represents one of the first in-depth analyses of the population of X-ray binaries within globular clusters in a spiral galaxy.
DOI: 10.7931/hk6f-fy05
title: Hyphodiscaceae in Aotearoa New Zealand
DOI: 10.25497/d7201f
title: Dangermond Preserve Reptile and Amphibian Species List 2019

description: Dangermond Preserve species list cataloging reptiles and amphibians on a 24,000-acre nature preserve.
DOI: 10.25921/nchb-gw46
title: AZFP Water Column Sonar Data Collected During ar040-vac-55144 Deployment