cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.16856206.v1
title: Virtual screening and structure-based 3D pharmacophore approach to identify small-molecule inhibitors of SARS-CoV-2 M<sup>pro</sup>

description: The outbreak caused by a coronavirus 2 has required quick and potential treatment strategies. The main protease enzyme M<sup>pro</sup> plays an important role in the viral replication which renders it an important target for discovering SARS-CoV-2 inhibitors. In this study, 3D pharmacophore structure-based virtual screening and molecular docking were conducted using MOE and Bristol University Docking Engine (BUDE). Around 400,000 molecules of ZINC15 database were docked against the crystal structure of main protease, followed by 3D pharmacophore filtration. Six top-ranked hits (ZINC58717986, ZINC60399606, ZINC58662884, ZINC45988635, ZINC54706757 and ZINC17320595) were identified based on their strong spatial affinity and forming H-bonds with key residues H41, E166, Q189 and T190 of the binding pocket of M<sup>pro</sup> SARS-CoV-2. The 6 hits subjected to molecular dynamics simulations for 100 ns followed by binding free energy calculations using MM-PBSA technique. Interestingly, three hits showed free binding energy (ΔG<sub>binding</sub>) lower than <i>tert</i>-butyl <i>N</i>-[1-[(2<i>S</i>)-1-[[(2<i>S</i>)-4-(benzylamino)-3,4-dioxo-1-[(3<i>S</i>)-2-oxopyrrolidin-3-yl]butan-2-yl]amino]-3-cyclopropyl-1-oxopropan-2-yl]-2-oxopyridin-3-yl]carbamate (α-ketoamide 13 b) (ΔG<sub>binding</sub>) −76.67 ± 0.5 kJ/mol which suggested their potential against SARS-CoV-2. The best binding free energy candidates, ZINC58717986 (ΔG<sub>binding</sub>) −98.41 ± 0.7 kJ/mol. The second-best hit candidate, ZINC54706757 (ΔG<sub>binding</sub>) −83.4 ± 0.6 kJ/mol and the third one ZINC17320595 (ΔG<sub>binding</sub>) −78.85 ± 0.5 kJ/mol. Per residue decomposition free energy indicates H41, S46, H164, E166, D187, Q189 and Q192 are hot spot residues while residues M49, M165, L167 and P168 contribute to the hydrophobic interactions. The pharmacokinetic study suggests that the selected 6 hits possess drug-like properties. The 3D pharmacophore virtual screening, molecular dynamics and MM-PBSA approaches facilitated identification 3 promising hits with low free binding energy as SARS-CoV-2 inhibitors. Communicated by Ramaswamy H. Sarma
DOI: 10.3535/gwp-nyf-ll2
title: †Leptaena Dalman, 1828

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/vk6-4tb-tls
title: †Plectambonitoidea Jones, 1928

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.6084/m9.figshare.26964139.v1
title: ARTICULOS DE REVISIÓN SISTEMATICA FACTORES DESENCADENANTES DE COLOMBIA

description: Las conductas delictivas son una amenaza constante para el bienestar cognitivo y físico de las personas, es así como el propósito del presente metaanálisis es abordar las causas principales de la criminalidad determinando el origen de los comportamientos que hacen que tomen esas decisiones, se ha observado que un factor por el cual inician estas conductas delictivas en las personas es la escasez del empleo que produce su baja estabilidad económica llevando a cometer delitos como el secuestro o la violencia, para lograr su objetivo delictivo obteniendo beneficios económicos propios.
DOI: 10.6084/m9.figshare.3521438.v1
title: Appendix A. Comparisons of model accuracies with literature, species-wise estimates of canopy foliar traits,comparisons of models built with different canopy weighing schemes, comparisons of spatial predictions of foliar traits.

description: Comparisons of model accuracies with literature, species-wise estimates of canopy foliar traits,comparisons of models built with different canopy weighing schemes, comparisons of spatial predictions of foliar traits.
DOI: 10.17632/536557z76f
title: Data for: High consanguinity promotes intergenerational wealth concentration in socioeconomically privileged Krummhörn families of the 18th and 19th centuries

description: # R-Workspace containing two customized functions for plotting, # - grid_arrange_shared_legend taken from: https://github.com/tidyverse/ggplot2/wiki/Share-a-legend-between-two-ggplot2-graphs # - multiplot taken from: http://www.cookbook-r.com/Graphs/Multiple_graphs_on_one_page_%28ggplot2%29/ # # and three data.frames: # - mdat: Raw data of mothers, includimng founder generation (N = 15961, extracted from the Krummhörn pedigree containing 74639 individuals) # - mdat0: Study sample including only mothers with minimum pedigree depth of 4 (N = 6447) # - mdat1: Data set of mothers for which all grandparents of them and their partner(s) are known (N = 2321) # with the variables: # $ momid : num ID of mother # $ incl : num 1 if included in data set of known mothers, otherwise 0 # $ SES : Factor for socioeconomic status (4 levels: "Unknown", "Landless", "small to medium scale farmers", "large scale farmers") # $ minByear : num Birth year of 1st born child # $ maxByear : num Birth year of last born child # $ minDepth : num Pedigree depth as the generation number of known ancestors # $ Fmean : num Inbreeding coefficient F (as calculated by pedigree::calcInbreeding()) # $ cons : num 1 if consanguineous (i.e. F&gt;=0.0156), otherwise 0 # $ cousMarr : num 1 if in 1st cousin marriage (i.e. F~0.0625), otherwise 0 # $ consanguinity : Factor for consanguinity (3 levels: "low (&lt;0.0156)", "medium (&gt;=0.0156)", "high (1st cousins)") # $ docGrasenMean : num Mean number of grasen within a mother's founded families # $ eltnrfGrasenMean : num Number of grasen within the mother's family-of-origin # $ eltnrmGrasenMean : num Mean number of grasen within the mother's partner(s)' family/ies-of-origin # $ mlocal : chr Code of the Kirchspiel, in which the mother was first married # $ decade : Factor fot the decade in which the mother's first marriage occured (28 levels) # $ cross : num 1 if identified as cross-cousin marriage, otherwise 0 # $ paral : num 1 if identified as parallel cousin marriage, otherwise 0
DOI: 10.3535/vxn-ez3-bjs
title: †Diplotrypa petropolitana Nicholson, 1879

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/w7c-nqt-8mc
title: †Archinacella melissa (Billings, 1865)

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.6084/m9.figshare.23869845.v3
title: Greenhouse gas, porewater chemistry, and sediment conditions from experimental TLP plots in a temperate salt marsh

description: Greenhouse gas, sediment parameter data<br>These data and related items of information have not been formally disseminated by NOAA, and do not represent any agency determination, view, or policy
DOI: 10.6084/m9.figshare.4902965.v2
title: Model Parameters

description: Parameters of the fit models of the paper "Is the Public Sector of Your Country a Diffusion Borrower?"<br>
DOI: 10.6084/m9.figshare.8316827.v2
title: Species trees of 571 Rhizobiaceae genomes, with a focus on 41 Pseudorhizobium and Neorhizobium, based on core genome gene concatenates

description: Genomic dataset and gene family classificationWe assembled a complete bacterial genome dataset covering all known representative of the subgroup in the alphaproteobacterial families Rhizobiaceae and (sister group) Aurantimonadaceae. This dataset comprises all 564 genomes available from the NCBI RefSeq Assembly database on the 23 Apr 2018, filtering anomalous genomes and those with a contig N50 &lt; 98kb using query: ‘(txid82115[Organism:exp] OR txid255475[Organism:exp]) AND ("latest refseq"[filter] NOT anomalous[filter]) AND ("98000"[ContigN50] : "20000000"[ContigN50])’. From this dataset we removed assembly GCF_002000045.1 (R. flavum YW14) for which we had a newer, higher quality assembly. To these we added the new genome sequences from the eight strains mentioned above, for a total of 571 genomes (dataset ‘571Rhizob’).<br>Reference species treesFrom the 571Rhizob genome dataset, we define the pseudo-core genome as genes occurring only in a single copy and present in at least 561 out of the 571 genomes (98%). The resulting pseudo-core genome gene set (thereafter referred as pCG<sub>571</sub>) includes 155 loci, which protein alignments were concatenated. This concatenated protein alignment was used to compute a reference species tree (S<sub>ML571</sub>) with RAxML (Stamatakis 2014) under the model PROTCATLGX; branch supports were estimated by generating 200 rapid bootstraps under the same parameters. From the S<sub>ML571</sub> tree, we identified the well-supported clade grouping 41 genomes including all representative of Neorhizobium spp. and Pseudorhizobium spp. and our new isolates (dataset ‘41NeoPseudo’). To gain further phylogenetic resolution in this clade of interest, we restricted the pCG<sub>571</sub> concatenated alignment to the 41 genomes of this smaller genomic dataset, which we used as input to the Phylobayes program for a more accurate (but computationally more expensive) Bayesian phylogenetic inference under the CAT-GTR+G4 model (Lartillot et al. 2007). This provided us with a robust non-ultrametric tree for the 41 genomes (S<sub>BA41</sub>). We finally used this S<sub>BA41</sub> tree as a fixed input topology for Phylobayes to infer an ultrametric tree (unitless ‘time’ tree) under the CIR clock model (Lepage et al. 2007), further referred to as T<sub>BA41</sub>.
DOI: 10.3535/4c8-add-fga
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/x70-nts-slv
title: †Endoceras J. Hall, 1847

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.6084/m9.figshare.1486454.v2
title: Babble Model Parameter Variations Sounds

description: These sounds were produced by a computational spiking neural network model of learning to produce syllabic vocalizations (i.e. canonical babbling) in infancy. The vocalizations produced by each simulation from each parameter combination were sampled at regular intervals. For each simulation, these samples were concatenated into a single sound file that can provide an auditory sense of how the simulation's vocalizations changed over time. The best parameter combination is 200 neurons (200n) and 2 muscle scaling (2n).
DOI: 10.6084/m9.figshare.4212126.v1
title: Eperua falcata : SNPs

description: Population Study site Local habitat<br>pop1 Régina Terra-firme<br>pop2 Régina Bottomland<br>pop3 Laussat Terra-firme<br>pop4 Laussat Bottomland<br><br>
DOI: 10.3535/8hp-mrw-vrv
title: †Anolotichia Ulrich, 1890

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/cnj-1b4-t9g
title: Bioturbation trace fossils

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.6084/m9.figshare.24734454.v1
title: Supplemental Table S2

description: Mean ± standard error (SE), minimum, and maximum values for the parameters a, b, c, d, and f from the Ali Schaffer, Wilmink, and Wood lactation models, milk (MY), fat (FY), protein (PY), and <i>mozzarella</i> (MZY) yields, fat-to-protein ratio (FPR), and somatic cell score (SCS). Features of the marginal posterior distributions of heritability and highest probability density (HPD) of lactation curve parameters from different nonlinear models for each parameter.
DOI: 10.6084/m9.figshare.28548119.v1
title: <i>A. ameliae</i> floral VOC output data

description: These are the <i>Abronia</i><i> </i><i>a</i><i>meliae</i> floral volatile emissions output data from a sand verbena common garden in Okemos, Michigan. Data were collected by Micah Freedman and Eric LoPresti.Supporting file for "Increased reliance on diurnal pollination in a geographically and morphologically atypical sand verbena" by Jaeger, Freedman, Alexander, Hilpman, Weber, and LoPresti. 2025. Journal of Pollination Ecology.
DOI: 10.6084/m9.figshare.28558469.v1
title: S7 Date. Variation of carbonization depth of HCC fillers

description: Variation of carbonization depth of HCC fillers
DOI: 10.17632/3cmknchc2g
title: Combining artificial intelligence and human expertise for more accurate dermoscopic melanoma diagnosis: A two-session retrospective reader study - Supplementary Material

description: In our two-session retrospective reader study, 64 physicians, including 33 dermatologists, 11 dermatology residents, and 20 general practitioners, evaluated a deliberately challenging test set of 100 dermoscopic images comprising 50 melanomas and 50 nevi. In session 1, participants provided diagnoses and management decisions based solely on images. In session 2, conducted 4+ months later, participants evaluated the same images in different sequence, this time with assistance of a CNN-assigned traffic light system.
Supplementary Figure 1 depicts the classification performance (melanoma, benign nevus) of individual physicians in session 1 (without CNN) and session 2 (with CNN). Physicians without CNN denoted by grey dots (n=64) and physicians with CNN denoted by black dots (n=64). Means denoted by squares. Blue line showing CNN’s performance on the test set.
Supplementary Table 1 shows the mean differences in correctly classified lesions (melanoma, benign nevus) between session 1 (without CNN) and session 2 (with CNN) by physician group. Correctly classified lesions include true positives and true negatives.
DOI: 10.17632/b8j9r9vjwk
title: Data for: Parametric Analysis to Quantify Process Input Influence on the Printed Densities of Binder Jetted Alumina Ceramics

description: Measured densities of binder jetted alumina prisms with various process parameter combinations. Parameters were defined by an orthogonal design of experiments detailed in the manuscript.
DOI: 10.17632/zp9p6sr2fk
title: An Inexpensive Modular Gravimetric Robotic Gantry Soil Moisture Screener and Controller

description: Support Files for An Inexpensive Modular Gravimetric Robotic Gantry Soil Moisture Screener and Controller
DOI: 10.3535/bhq-d4x-tq1
title: †Leptaena Dalman, 1828

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.6084/m9.figshare.1050480.v4
title: Temperatures at the rear of Adeilad Alun Roberts

description: This file contains temperature measurements outside the rear of Adeilad Alun Roberts Building on Bangor University campus. The thermistor sensor is located on the external wall of the 8th floor. The large peaks are mainly late afternoon and early evening when the sun can shine directly on that wall, so the data illustrate the wide variations in temperature that occur on a single (NW facing) wall of this building. Times are GMT.
DOI: 10.6084/m9.figshare.22264363.v1
title: Felidae TNFRSF4 Fasta

description: Data Set 1, Fasta file containing genetic sequences used for analysis throughout our project. Coding sequences were obtained through BLAST searches on Ensembl, and alignment of sequences was performed using AliView. Included are 8 sequences comprised of four TNFRSF4 genes from domestic cat, lion, leopard, and canadian lynx, as well as the human TNFRSF4 and domestic cat, lion, and leopard TNFRSF18 genes as outgroups. The resulting Fasta file was used for multiple modes of analyis for our project.
DOI: 10.6084/m9.figshare.28582148.v2
title: Data for rice-associated pentatomoids in Argentina

description: Data for the paper Crop traits influencing abundance and distribution of rice-associated pentatomoids and trophic guilds to unveil potential pests. Agricultural and Forest Entomology
DOI: 10.3535/j3v-8bl-g31
title: Conichnus conicus Männil

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.25549/independent-c69-21450
title: Rick Silverman work product (3 of 4), 1991 Apr. 18 - July

description: Rick Silverman work product (3 of 4), 1991 April 18 - July. PART OF A SERIES: The circumstances surrounding the beating of Rodney King led many to believe that the incident was racially motivated and reflected a spirit of bias and discrimination within the LAPD. Irell & Manella analyzed in depth the LAPD's recruitment, hiring, training, and promotion practices to determine if bias and intolerance were in fact pervasive issues within the Department. The series includes materials related to Irell and Manella's work product, including the firm’s correspondence; summaries of personnel files for potential recruits; records of the Leon Panduro case, in which a citizen was shot by a probationary officer; minutes from the LAPD Professional Advisory Committee maintained between 1983 and 1991; witness files, which consist of written testimony and supplemental materials; and notes, outlines, and drafts maintained over the course of Irell and Manella’s investigation.
DOI: 10.15468/dl.ttei7i
title: Occurrence Download

description: A dataset containing 1005 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cebus albifrons (Humboldt, 1812)"
 ]
}

 The dataset includes 1005 records from 42 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000975-150306150734599/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.e57u4t
title: Occurrence Download

description: A dataset containing 4553 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "PublishingCountry is Colombia",
 {
 "and" : [
 "Country is Colombia",
 {
 "not" : {
 "Issue" : [
 "is Country coordinate mismatch"
 ]
 }
 }
 ]
 }
 ]
 },
 {
 "and" : [
 "StateProvince is one of (valle del cauca)",
 "TaxonKey is one of (Anthurium Schott)"
 ]
 }
 ]
}

 The dataset includes 4553 records from 57 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0024408-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/independent-c69-15104
title: Legal research regarding the history of the Los Angeles charter, 1850-1963 (3b of 3)

description: Municipal and county government section of Town Hall. A study of the Los Angeles City Charter: a report. Los Angeles, California: Town Hall, Biltmore Hotel, 1963 December. PART OF A SERIES: A critical component of the Commission's investigation centered on the idea that governance of the LAPD was shared between the Office of the Chief of Police, an administrative body, and the Board of Police Commissioners, a citizen body. To better understand the dynamic between these two entities, the staff of Heller, Ehrman, White, & McAuliffe researched the history of the Los Angeles City Charter, focusing primarily on its provisions regarding the distribution of power and the structure and organization of the LAPD. Included in the series are reproductions of reports, dissertations, article clippings, excerpts from city documents, and charter amendments related to the charter's conception and development over time. The series also includes several summaries of expert witness interviews regarding the effectiveness of this structure.
DOI: 10.15468/dl.9q3yy9
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Afrosoricida",
 "HasCoordinate is true",
 "Country is Japan",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006913-231120084113126/datasets/export for details.
DOI: 10.25549/independent-c69-20962
title: Correspondence, vol. 1 (1 of 2), 1991 Apr. 3-30

description: Correspondence, vol. 1 (1 of 2), 1991 April 3-30. PART OF A SERIES: Jones, Day, Reavis & Pogue investigated how LAPD administrators respond to personnel complaints and allegations of misconduct. Materials in the series were collected and analyzed by the firm for this purpose, and include summaries of witness interviews; article clippings discussing instances of alleged police misconduct; source materials related to the LAPD’s use-of-force policies; a transcript of a court case involving officer misconduct; summaries of personnel complaint statistics; and excerpts taken from the personnel files of officers with multiple complaints and misconduct charges. Also included is correspondence sent and received by the firm over the course of its investigation.
DOI: 10.15468/dl.qerhur
title: Occurrence Download

description: A dataset containing 26509 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Asplenium adiantum-nigrum L.",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 26509 records from 156 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000975-150330110031120/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.f37u7u
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Didelphimorphia",
 "HasCoordinate is true",
 "Country is Japan",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006914-231120084113126/datasets/export for details.
DOI: 10.25549/independent-c69-15120
title: Legal research regarding the history of the Los Angeles charter, 1850-1963 (3b of 3)

description: Municipal and county government section of Town Hall. A study of the Los Angeles City Charter: a report. Los Angeles, California: Town Hall, Biltmore Hotel, 1963 December. PART OF A SERIES: A critical component of the Commission's investigation centered on the idea that governance of the LAPD was shared between the Office of the Chief of Police, an administrative body, and the Board of Police Commissioners, a citizen body. To better understand the dynamic between these two entities, the staff of Heller, Ehrman, White, & McAuliffe researched the history of the Los Angeles City Charter, focusing primarily on its provisions regarding the distribution of power and the structure and organization of the LAPD. Included in the series are reproductions of reports, dissertations, article clippings, excerpts from city documents, and charter amendments related to the charter's conception and development over time. The series also includes several summaries of expert witness interviews regarding the effectiveness of this structure.
DOI: 10.25549/independent-c69-20776
title: Rick Silverman work product (1 of 4), 1984 - 1991 June 27

description: Rick Silverman work product (1 of 4), 1984 - 1991 June 27. PART OF A SERIES: The circumstances surrounding the beating of Rodney King led many to believe that the incident was racially motivated and reflected a spirit of bias and discrimination within the LAPD. Irell & Manella analyzed in depth the LAPD's recruitment, hiring, training, and promotion practices to determine if bias and intolerance were in fact pervasive issues within the Department. The series includes materials related to Irell and Manella's work product, including the firm’s correspondence; summaries of personnel files for potential recruits; records of the Leon Panduro case, in which a citizen was shot by a probationary officer; minutes from the LAPD Professional Advisory Committee maintained between 1983 and 1991; witness files, which consist of written testimony and supplemental materials; and notes, outlines, and drafts maintained over the course of Irell and Manella’s investigation.