cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.7910/dvn/e9ffzk
title: Replication Data for: Multi-Domain Convolutional Neural Network (MD-CNN) For Radial Reconstruction of Dynamic Cardiac MRI

description: Datasets of radial cine cardiac MRI data collected from 108 subjects (101 patients and 7 healthy subjects). Codes for the Multi-domain network and data reading are also included.
DOI: 10.7910/dvn/e9ffzk/2agxmi
title: Dataset99.dat

description: :unav
DOI: 10.7910/dvn/e9ffzk/4lk97c
title: cmplxBatchNorm.py

description: :unav
DOI: 10.7910/dvn/e9ffzk/dypx7k
title: Dataset03.dat

description: :unav
DOI: 10.7910/dvn/e9ffzk/elevng
title: Dataset95.dat

description: :unav
DOI: 10.7910/dvn/e9ffzk/hbuxbc
title: Dataset21.dat

description: :unav
DOI: 10.17632/87vx6jfnrp.1
title: Dark triad, attractiveness, mate value, and sexual partners

description: It was found positive correlations among the dark triad of personality, self-perceived attractiveness, mate value, and number of sexual partners both in men and women.
DOI: 10.21227/nvce-dz75
title: PROTOKOL TATALAKSANA COVID-19

description: Pada tanggal 31 Desember 2019, Tiongkok melaporkan kasus pneumonia misterius yang tidak diketahui penyebabnya. Dalam 3 hari, pasien dengan kasus tersebut berjumlah 44 pasien dan terus bertambah hingga saat ini berjumlah ribuan kasus. Pada awalnya data epidemiologi menunjukkan 66% pasien berkaitan atau terpajan dengan satu pasar seafood atau live market di Wuhan, Provinsi Hubei Tiongkok. Sampel isolat dari pasien diteliti dengan hasil menunjukkan adanya infeksi coronavirus, jenis betacoronavirus tipe baru, diberi nama 2019 novel Coronavirus (2019-nCoV).2 Pada tanggal 11 Februari 2020, World Health Organization memberi nama virus baru tersebut Severa acute respiratory syndrome coronavirus-2 (SARS-CoV-2) dan nama penyakitnya sebagai Coronavirus disease 2019 (COVID-19). Pada mulanya transmisi virus ini belum dapat ditentukan apakah dapat melalui antara manusia-manusia. Jumlah kasus terus bertambah seiring dengan waktu. Akhirnya dikonfirmasi bahwa transmisi pneumonia ini dapat menular dari manusia ke manusia. Pada tanggal 11 Maret 2020, WHO mengumumkan bahwa COVID-19 menjadi pandemi di dunia.
DOI: 10.25387/g3.12173385.v2
title: Supplemental Material for Lilley et al., 2020

description: Supplementary material for ”Population connectivity predicts vulnerability to white-nose syndrome in the Chilean myotis (Myotis chiloensis) - a genomics approach”
DOI: 10.17632/pd8k46jkj6.1
title: Data for: Evidence of Protective Role of Ultraviolet-B (UVB) Radiation in Reducing COVID-19 deaths

description: Test
DOI: 10.17632/s6ft96dfwr.2
title: Data for: Evidence of Protective Role of Ultraviolet-B (UVB) Radiation in Reducing COVID-19 deaths
DOI: 10.7910/dvn/fpnits/xqrwzl
title: replication2020.zip

description: :unav
DOI: 10.5281/zenodo.3819781
title: The GRISLI-LSCE contribution to ISMIP6-Antarctica

description: The GRISLI-LSCE contribution to ISMIP6-Antarctuca. Experiments IDs as in Nowicki et al.: Nowicki, S., Payne, A. J., Goelzer, H., Seroussi, H., Lipscomb, W. H., Abe-Ouchi, A., Agosta, C., Alexander, P., Asay-Davis, X. S., Barthel, A., Bracegirdle, T. J., Cullather, R., Felikson, D., Fettweis, X., Gregory, J., Hatterman, T., Jourdain, N. C., Kuipers Munneke, P., Larour, E., Little, C. M., Morlinghem, M., Nias, I., Shepherd, A., Simon, E., Slater, D., Smith, R., Straneo, F., Trusel, L. D., van den Broeke, M. R., and van de Wal, R.: Experimental protocol for sealevel projections from ISMIP6 standalone ice sheet models, The Cryosphere Discuss., https://doi.org/10.5194/tc-2019-322, in review, 2020.
DOI: 10.5281/zenodo.3819782
title: The GRISLI-LSCE contribution to ISMIP6-Antarctica

description: The GRISLI-LSCE contribution to ISMIP6-Antarctuca. Experiments IDs as in Nowicki et al.: Nowicki, S., Payne, A. J., Goelzer, H., Seroussi, H., Lipscomb, W. H., Abe-Ouchi, A., Agosta, C., Alexander, P., Asay-Davis, X. S., Barthel, A., Bracegirdle, T. J., Cullather, R., Felikson, D., Fettweis, X., Gregory, J., Hatterman, T., Jourdain, N. C., Kuipers Munneke, P., Larour, E., Little, C. M., Morlinghem, M., Nias, I., Shepherd, A., Simon, E., Slater, D., Smith, R., Straneo, F., Trusel, L. D., van den Broeke, M. R., and van de Wal, R.: Experimental protocol for sealevel projections from ISMIP6 standalone ice sheet models, The Cryosphere Discuss., https://doi.org/10.5194/tc-2019-322, in review, 2020.
DOI: 10.5281/zenodo.3820453
title: Dataset Rodríguez-Ros et al. 2020 / Isoprene in the Southern Ocean - ISOREMS model

description: Dataset of isoprene measurements in the Southern Ocean for the manuscript submitted to the Journal <em>Atmosphere</em>. Rodríguez-Ros et al. 2020 (Submitted): <em>Distribution and drivers of marine isoprene concentration across the Southern Ocean</em> <em>%%%%%%<br> Variables' names contained in "isorems_data.csv"<br> %%%%%%</em> <em>"id" = source of the data ("peg" = PEGASO cruise, "ace" = ACE Expedition, "pml" = ANDREXII, "ooki" = Ooki et al. 2015, "hack" = Hackemberg et al. 2017)</em> <em>"solar_time" = solar time estimated with solaR package on R.</em> <em>"iso_pm" = Isoprene concentration (pM)</em> <em>"chla_fluo" = Chlorophyll-a (fluorometric)</em> <em>"chla_matchup" = Chlorophyll-a (MODIS Aqua)</em> <em>"sst_matchup" = Sea Surface Temperature (MODIS Aqua)</em> <em>"zeu_matchup" = Depth of the Euphotic Layer (MODIS Aqua)</em> <em>"poc_matchup" = Particulate Organic Carbon (MODIS Aqua)</em> <em>"pic_matchup" = Particulate Inorganic Carbon (MODIS Aqua)</em> <em>"mld_matchup" = Mixing Layer Depth (Holte et al. 2017)</em> <em>"par_matchup" = PAR radiation (MODIS Aqua)</em> <em>"lat" = Latitude (decimal degrees)</em> <em>"lon" = Longitude (decimal degrees)</em>
DOI: 10.5281/zenodo.3820454
title: Dataset Rodríguez-Ros et al. 2020 / Isoprene in the Southern Ocean - ISOREMS model

description: Dataset of isoprene measurements in the Southern Ocean for the manuscript submitted to the Journal <em>Atmosphere</em>. Rodríguez-Ros et al. 2020 (Submitted): <em>Distribution and drivers of marine isoprene concentration across the Southern Ocean</em> <em>%%%%%%<br> Variables' names contained in "isorems_data.csv"<br> %%%%%%</em> <em>"id" = source of the data ("peg" = PEGASO cruise, "ace" = ACE Expedition, "pml" = ANDREXII, "ooki" = Ooki et al. 2015, "hack" = Hackemberg et al. 2017)</em> <em>"solar_time" = solar time estimated with solaR package on R.</em> <em>"iso_pm" = Isoprene concentration (pM)</em> <em>"chla_fluo" = Chlorophyll-a (fluorometric)</em> <em>"chla_matchup" = Chlorophyll-a (MODIS Aqua)</em> <em>"sst_matchup" = Sea Surface Temperature (MODIS Aqua)</em> <em>"zeu_matchup" = Depth of the Euphotic Layer (MODIS Aqua)</em> <em>"poc_matchup" = Particulate Organic Carbon (MODIS Aqua)</em> <em>"pic_matchup" = Particulate Inorganic Carbon (MODIS Aqua)</em> <em>"mld_matchup" = Mixing Layer Depth (Holte et al. 2017)</em> <em>"par_matchup" = PAR radiation (MODIS Aqua)</em> <em>"lat" = Latitude (decimal degrees)</em> <em>"lon" = Longitude (decimal degrees)</em>
DOI: 10.5281/zenodo.3820601
title: The delayed and geographically heterogenous diversification of flowering plant families [Data sets]

description: This pre-release includes the data and code that support the findings presented in: Ramírez-Barahona et al. (2020) The delayed and geographically heterogeneous diversification of flowering plant families.
DOI: 10.15468/j42gea
title: Temporary expansion to shelf depths rather than an onshore-offshore trend: the shallow-water rise and demise of the modern deep-sea brittle star family Ophiacanthidae (Echinodermata: Ophiuroidea)

description: This dataset contains the digitized treatments in Plazi based on the original journal article Thuy, Ben (2013): Temporary expansion to shelf depths rather than an onshore-offshore trend: the shallow-water rise and demise of the modern deep-sea brittle star family Ophiacanthidae (Echinodermata: Ophiuroidea). European Journal of Taxonomy 48: 1-242, DOI: http://dx.doi.org/10.5852/ejt.2013.48
DOI: 10.5281/zenodo.3752539
title: Raw diffraction data (CBF) for a structure of SARS-CoV-2 Main Protease bound to 2-Methyl-1-tetralone

description: Data collected at beamline P11/PETRAIII Deutsches Elektronen Synchrotron DESY Info: run type: regular<br> run name: l6p17_09_001<br> start angle: 0.000000deg<br> frames: 1000<br> degrees/frame: 0.200000deg<br> exposure time: 40.000000ms<br> energy: 11.999832keV<br> wavelength: 1.033214A<br> detector distance: 200.000000mm<br> resolution: 1.304257A<br> aperture: 100um<br> filter transmission: 71.798748%<br> filter thickness: 75um<br> ring current: 119.222664mA Crystal-info: Co-crystallization of Sars-CoV-2 MPro with the compound was achieved by equlibrating a 6.25 mg/ml protein solution in 20 mM HEPES buffer (pH 7.8) containing 1 mM DTT, 1mM EDTA, and 150 mM NaCl against a reservoir solution of 100 mM MIB buffer (2:3:3 molar ratio of malonic acid, imidazole, and boric acid), pH 7.5, containing 25% v/v PEG 1500 and 5% v/v DMSO. Prior to crystallization compound solutions in DMSO were dried onto the wells of SwissCI 96-well plates. To achieve reproducible crystal growth seeding was used. Crystals appeared within a few hours and reached their final size after 2 -3 days. Crystals were manually harvested and flash cooled in liquid nitrogen for subsequent X-ray diffraction data collection.
DOI: 10.5281/zenodo.3752540
title: Raw diffraction data (CBF) for a structure of SARS-CoV-2 Main Protease bound to 2-Methyl-1-tetralone

description: Data collected at beamline P11/PETRAIII Deutsches Elektronen Synchrotron DESY Info: run type: regular<br> run name: l6p17_09_001<br> start angle: 0.000000deg<br> frames: 1000<br> degrees/frame: 0.200000deg<br> exposure time: 40.000000ms<br> energy: 11.999832keV<br> wavelength: 1.033214A<br> detector distance: 200.000000mm<br> resolution: 1.304257A<br> aperture: 100um<br> filter transmission: 71.798748%<br> filter thickness: 75um<br> ring current: 119.222664mA Crystal-info: Co-crystallization of Sars-CoV-2 MPro with the compound was achieved by equlibrating a 6.25 mg/ml protein solution in 20 mM HEPES buffer (pH 7.8) containing 1 mM DTT, 1mM EDTA, and 150 mM NaCl against a reservoir solution of 100 mM MIB buffer (2:3:3 molar ratio of malonic acid, imidazole, and boric acid), pH 7.5, containing 25% v/v PEG 1500 and 5% v/v DMSO. Prior to crystallization compound solutions in DMSO were dried onto the wells of SwissCI 96-well plates. To achieve reproducible crystal growth seeding was used. Crystals appeared within a few hours and reached their final size after 2 -3 days. Crystals were manually harvested and flash cooled in liquid nitrogen for subsequent X-ray diffraction data collection.
DOI: 10.5281/zenodo.3820674
title: An information theory-based machine learning approach to detecting functionally conserved and coordinated protein dynamics

description: The application of machine learning classification to the molecular dynamics of the functional states of protein allows for application of an information theoretic framework familiar to traditional bioinformatics. The functional states of proteins involving binding interactions with partners comprised of protein, DNA or small molecules can first be defined in a binary fashion (i.e. bound vs unbound), subsequently simulated in molecular dynamics software, and then employed as a comparative training set for a binary machine learning classifier capable of discerning the complex dynamical consequences of binding interaction. This learner can subsequently be deployed on new simulations of the functionally bound state to validate its ability to recognize the molecular motions that are supporting binding function. Regions of proteins with functionally conserved dynamics will induce significant local correlations in learning performance across independent validation runs. Through case studies of Rbp subunit 4/7 interaction in RNA Pol II and DNA-protein interactions of TATA binding protein, we demonstrate this method of detecting functionally conserved protein dynamics. We also demonstrate how Shannon information, relative entropy and mutual information can be applied to these binary classification states of dynamic simulations in order to compare dynamics and identify concerted motions involved in dynamic interactions across sites.
DOI: 10.5281/zenodo.3820675
title: An information theory-based machine learning approach to detecting functionally conserved and coordinated protein dynamics

description: The application of machine learning classification to the molecular dynamics of the functional states of protein allows for application of an information theoretic framework familiar to traditional bioinformatics. The functional states of proteins involving binding interactions with partners comprised of protein, DNA or small molecules can first be defined in a binary fashion (i.e. bound vs unbound), subsequently simulated in molecular dynamics software, and then employed as a comparative training set for a binary machine learning classifier capable of discerning the complex dynamical consequences of binding interaction. This learner can subsequently be deployed on new simulations of the functionally bound state to validate its ability to recognize the molecular motions that are supporting binding function. Regions of proteins with functionally conserved dynamics will induce significant local correlations in learning performance across independent validation runs. Through case studies of Rbp subunit 4/7 interaction in RNA Pol II and DNA-protein interactions of TATA binding protein, we demonstrate this method of detecting functionally conserved protein dynamics. We also demonstrate how Shannon information, relative entropy and mutual information can be applied to these binary classification states of dynamic simulations in order to compare dynamics and identify concerted motions involved in dynamic interactions across sites.
DOI: 10.25934/00002438.0
title: Available IPD datapackage for study 'Phase II, Dose-Response, Safety and Efficacy Study of Oral TMX-67 in Subjects With Gout.'

description: Vivli is an independent, non-profit organization that has developed a global data-sharing and analytics platform to serve all elements of the international research community. Our mission is to promote, coordinate, and facilitate scientific sharing and reuse of clinical research data through the creation and implementation of a sustainable global data-sharing enterprise. The Vivli platform includes an independent data repository, in-depth search engine and a cloud-based, secure analytics platform.
DOI: 10.5281/zenodo.3820874
title: Prediction of nucleosome dyads for the K562 cell line in the hg19 genome assembly

description: <strong>Predicting dyads from MNase-seq data</strong> I needed the location of nucleosomal dyads in the K562 cell line (ENCODE tier 1 line). Surprisingly, although plenty of MNase-seq data for that cell line is available, no nucleosome and dyad prediction exists. <strong>Running NuMap</strong> I found the NuMap software by Anton Valouev to do exactly what I intended. Since it is in a somewhat obscure page and this seemed to be the only place where this software was, I have uploaded it into a Github repository for the sake of preservation (https://github.com/orphancode/NuMap). Predicting dyads from MNase-seq data with NuMap seemed trivial: I downloaded the K562 MNase-seq data set (11 replicates ~85Gb!!), combined all replicates and ran NuMap on the data(instructions on the Github README). From NuMap output there are dyad positions in bed format and you can also produce several metrics to evaluate how good the prediction was. <strong>Distograms & phasograms</strong> Valouev describes two measurements of the frequencies of distances between MNase-seq reads. The frequency of distances between reads mapping to opposite strands can be used to build a “distogram”, which ilustrates the expected nucleosome length (147 bp) - this is consistent across most eukaryotic cells. The frequency of distances between reads mapping to the same strand gives a measurement of the distance between nucleosomes, as they’re separated by some linker DNA - (Valouev calls this plot a “phasogram”). This measurement, on the other hand tends to be species and cell-type specific. <strong>K562 predictions:</strong> The expected 147 bp nucleosome length in K562 cells. The average distance between dyads in K562 cells seems to be 185 bp. <strong>References:</strong> Valouev, A., Johnson, S. M., Boyd, S. D., Smith, C. L., Fire, A. Z., Sidow, A. (2011). Determinants of nucleosome organization in primary human cells. Nature, 474(7352), 516–520. http://doi.org/10.1038/nature10002
description: Initially posted as a blogpost at https://andre-rendeiro.com/2015/05/12/predicting_dyads_from_mnase
DOI: 10.5281/zenodo.3820875
title: Prediction of nucleosome dyads for the K562 cell line in the hg19 genome assembly

description: <strong>Predicting dyads from MNase-seq data</strong> I needed the location of nucleosomal dyads in the K562 cell line (ENCODE tier 1 line). Surprisingly, although plenty of MNase-seq data for that cell line is available, no nucleosome and dyad prediction exists. <strong>Running NuMap</strong> I found the NuMap software by Anton Valouev to do exactly what I intended. Since it is in a somewhat obscure page and this seemed to be the only place where this software was, I have uploaded it into a Github repository for the sake of preservation (https://github.com/orphancode/NuMap). Predicting dyads from MNase-seq data with NuMap seemed trivial: I downloaded the K562 MNase-seq data set (11 replicates ~85Gb!!), combined all replicates and ran NuMap on the data(instructions on the Github README). From NuMap output there are dyad positions in bed format and you can also produce several metrics to evaluate how good the prediction was. <strong>Distograms & phasograms</strong> Valouev describes two measurements of the frequencies of distances between MNase-seq reads. The frequency of distances between reads mapping to opposite strands can be used to build a “distogram”, which ilustrates the expected nucleosome length (147 bp) - this is consistent across most eukaryotic cells. The frequency of distances between reads mapping to the same strand gives a measurement of the distance between nucleosomes, as they’re separated by some linker DNA - (Valouev calls this plot a “phasogram”). This measurement, on the other hand tends to be species and cell-type specific. <strong>K562 predictions:</strong> The expected 147 bp nucleosome length in K562 cells. The average distance between dyads in K562 cells seems to be 185 bp. <strong>References:</strong> Valouev, A., Johnson, S. M., Boyd, S. D., Smith, C. L., Fire, A. Z., Sidow, A. (2011). Determinants of nucleosome organization in primary human cells. Nature, 474(7352), 516–520. http://doi.org/10.1038/nature10002
description: Initially posted as a blogpost at https://andre-rendeiro.com/2015/05/12/predicting_dyads_from_mnase
DOI: 10.3886/e109704v1
title: Data and Code for: Unemployment Insurance and Means-Tested Program Interactions: Evidence from Administrative Data

description: These files contain the programs and data for the journal article "Unemployment Insurance and Means-Tested Program Interactions: Evidence from Administrative Data," American Economic Journal: Economic Policy.
description: UI claimants in Michigan<br>.
DOI: 10.3886/e109704
title: Data and Code for: Unemployment Insurance and Means-Tested Program Interactions: Evidence from Administrative Data

description: These files contain the programs and data for the journal article "Unemployment Insurance and Means-Tested Program Interactions: Evidence from Administrative Data," American Economic Journal: Economic Policy.
description: UI claimants in Michigan<br>.
DOI: 10.5281/zenodo.3820609
title: alendronate_CRISPRa

description: alendronate CRISPRa screen results
DOI: 10.15468/vf9mrb
title: Taxonomy of the Crematogaster degeeri-species-assemblage in the Malagasy region (Hymenoptera: Formicidae)

description: This dataset contains the digitized treatments in Plazi based on the original journal article Blaimer, Bonnie B., Fisher, Brian L. (2013): Taxonomy of the Crematogaster degeeri-species-assemblage in the Malagasy region (Hymenoptera: Formicidae). European Journal of Taxonomy 51: 1-64, DOI: http://dx.doi.org/10.5852/ejt.2013.51
DOI: 10.15468/4r63bq
title: Two new free-living nematode species (Trefusiina: Trefusiidae) from the Chatham Rise crest, Southwest Pacific Ocean

description: This dataset contains the digitized treatments in Plazi based on the original journal article Leduc, Daniel (2013): Two new free-living nematode species (Trefusiina: Trefusiidae) from the Chatham Rise crest, Southwest Pacific Ocean. European Journal of Taxonomy 55: 1-13, DOI: http://dx.doi.org/10.5852/ejt.2013.55
DOI: 10.15468/c2ybkn
title: Gladiopycnodontidae, a new family of pycnodontiform fishes from the Late Cretaceous of Lebanon, with the description of three genera

description: This dataset contains the digitized treatments in Plazi based on the original journal article Taverne, Louis, Capasso, Luigi (2013): Gladiopycnodontidae, a new family of pycnodontiform fishes from the Late Cretaceous of Lebanon, with the description of three genera. European Journal of Taxonomy 57: 1-30, DOI: http://dx.doi.org/10.5852/ejt.2013.57
DOI: 10.15468/nqer4r
title: Memecylon pseudomegacarpum M. Hughes (Melastomataceae), a new species of tree from Peninsular Malaysia

description: This dataset contains the digitized treatments in Plazi based on the original journal article Hughes, Mark (2013): Memecylon pseudomegacarpum M. Hughes (Melastomataceae), a new species of tree from Peninsular Malaysia. European Journal of Taxonomy 56: 1-9, DOI: http://dx.doi.org/10.5852/ejt.2013.56
DOI: 10.15468/r7msgb
title: Revision of the types of species of Alloxysta described by Cameron and Fergusson (Hymenoptera: Figitidae: Charipinae) and deposited in the Natural History Museum (London), including a key to the fauna of Great Britain

description: This dataset contains the digitized treatments in Plazi based on the original journal article Ferrer-Suay, Mar, Selfa, Jesús, Notton, David G., Pujade-Villar, Juli (2013): Revision of the types of species of Alloxysta described by Cameron and Fergusson (Hymenoptera: Figitidae: Charipinae) and deposited in the Natural History Museum (London), including a key to the fauna of Great Britain. European Journal of Taxonomy 53: 1-27, DOI: http://dx.doi.org/10.5852/ejt.2013.53
DOI: 10.15468/z56z3y
title: Hidden in plain sight, Chaetopterus dewysee sp. nov. (Chaetopteridae, Annelida) - A new species from Southern California

description: This dataset contains the digitized treatments in Plazi based on the original journal article Tilic, Ekin, Rouse, Greg W. (2020): Hidden in plain sight, Chaetopterus dewysee sp. nov. (Chaetopteridae, Annelida) - A new species from Southern California. European Journal of Taxonomy 643: 1-16, DOI: https://doi.org/10.5852/ejt.2020.643
DOI: 10.15468/3dquke
title: Two new charismatic Pristimantis species (Anura: Craugastoridae) from the tepuis of “ The Lost World ” (Pantepui region, South America)

description: This dataset contains the digitized treatments in Plazi based on the original journal article Kok, Philippe J. R. (2013): Two new charismatic Pristimantis species (Anura: Craugastoridae) from the tepuis of “ The Lost World ” (Pantepui region, South America). European Journal of Taxonomy 60: 1-24, DOI: http://dx.doi.org/10.5852/ejt.2013.60
DOI: 10.15468/6z5mk8
title: Oosagitta gen. nov. from tropical Africa, with revision of two species and description of four new species (Coleoptera: Chrysomelidae, Galerucinae)

description: This dataset contains the digitized treatments in Plazi based on the original journal article Kortenhaus, Sabine, Wagner, Thomas (2013): Oosagitta gen. nov. from tropical Africa, with revision of two species and description of four new species (Coleoptera: Chrysomelidae, Galerucinae). European Journal of Taxonomy 58: 1-24, DOI: http://dx.doi.org/10.5852/ejt.2013.58
DOI: 10.18112/openneuro.ds002712.v1.0.1
title: Numbers and Letters
DOI: 10.5519/qd.glxwla3j
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (14 records)