cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.16577823.v1
title: Host-pathogen interactions of clinical <i>S. aureus</i> isolates to induce infective endocarditis

description: To evaluate potential pathomechanisms in the induction of infective endocarditis (IE), 34 <i>Staphylococcus aureus</i> (<i>S. aureus</i>) isolates, collected from patients with <i>S. aureus</i> endocarditis and from healthy individuals were investigated both <i>in vitro</i> and <i>in vivo. S. aureus</i> isolates were tested <i>in vitro</i> for their cytotoxicity, invasion and the association with platelets. Virulence factor expression profiles and cellular response were additionally investigated and tested for correlation with the ability of <i>S. aureus</i> to induce vegetations on the aortic valves <i>in vivo</i>. In an animal model of IE valvular conspicuity was assessed by <i>in vivo</i> magnetic resonance imaging at 9.4 T, histology and enrichment gene expression analysis. All <i>S. aureus</i> isolates tested <i>in vivo</i> caused a reliable infection and inflammation of the aortic valves, but could not be differentiated and categorized according to the measured <i>in vitro</i> virulence profiles and cytotoxicity. Results from <i>in vitro</i> assays did not correlate with the severity of IE. However, the isolates differed substantially in the activation and inhibition of pathways connected to the extracellular matrix and inflammatory response. Thus, comprehensive approaches of host-pathogen interactions and corresponding immune pathways are needed for the evaluation of the pathogenic capacity of bacteria. An improved understanding of the interaction between virulence factors and immune response in <i>S. aureus</i> infective endocarditis would offer novel possibilities for the development of therapeutic strategies and specific diagnostic imaging markers.
DOI: 10.5281/zenodo.5669133
title: IODP Expedition 351, Hole U1438D - Well Logging Data

description: Logging data are measurements of physical properties of the formation surrounding a borehole, acquired in situ after completion of coring (wireline logging) or during drilling (Logging-While-Drilling, LWD). The range of data (resistivity, gamma radiation, velocity, density, borehole images,…) in any hole depends on the scientific objectives and operational constraints.
description: IODP Expedition 351: Izu-Bonin-Mariana Arc Origins
DOI: 10.5281/zenodo.5669132
title: IODP Expedition 351, Hole U1438D - Well Logging Data

description: Logging data are measurements of physical properties of the formation surrounding a borehole, acquired in situ after completion of coring (wireline logging) or during drilling (Logging-While-Drilling, LWD). The range of data (resistivity, gamma radiation, velocity, density, borehole images,…) in any hole depends on the scientific objectives and operational constraints.
description: IODP Expedition 351: Izu-Bonin-Mariana Arc Origins
DOI: 10.5281/zenodo.5669148
title: IODP Expedition 351, Hole U1438E - Well Logging Data

description: Logging data are measurements of physical properties of the formation surrounding a borehole, acquired in situ after completion of coring (wireline logging) or during drilling (Logging-While-Drilling, LWD). The range of data (resistivity, gamma radiation, velocity, density, borehole images,…) in any hole depends on the scientific objectives and operational constraints.
description: IODP Expedition 351: Izu-Bonin-Mariana Arc Origins
DOI: 10.5281/zenodo.5669147
title: IODP Expedition 351, Hole U1438E - Well Logging Data

description: Logging data are measurements of physical properties of the formation surrounding a borehole, acquired in situ after completion of coring (wireline logging) or during drilling (Logging-While-Drilling, LWD). The range of data (resistivity, gamma radiation, velocity, density, borehole images,…) in any hole depends on the scientific objectives and operational constraints.
description: IODP Expedition 351: Izu-Bonin-Mariana Arc Origins
DOI: 10.5281/zenodo.5669176
title: IODP Expedition 351, Hole U1438F - Well Logging Data

description: Logging data are measurements of physical properties of the formation surrounding a borehole, acquired in situ after completion of coring (wireline logging) or during drilling (Logging-While-Drilling, LWD). The range of data (resistivity, gamma radiation, velocity, density, borehole images,…) in any hole depends on the scientific objectives and operational constraints.
description: IODP Expedition 351: Izu-Bonin-Mariana Arc Origins
DOI: 10.5281/zenodo.5669175
title: IODP Expedition 351, Hole U1438F - Well Logging Data

description: Logging data are measurements of physical properties of the formation surrounding a borehole, acquired in situ after completion of coring (wireline logging) or during drilling (Logging-While-Drilling, LWD). The range of data (resistivity, gamma radiation, velocity, density, borehole images,…) in any hole depends on the scientific objectives and operational constraints.
description: IODP Expedition 351: Izu-Bonin-Mariana Arc Origins
DOI: 10.6084/m9.figshare.16983499
title: Post-Processed DNA Methylation Data

description: Processed data for well-covered CpG triplets WGBS data from 121 experimental replicates representing 77 unique biological samples, publicly available from ENCODE. These replicates include clinical tissue samples, cell lines, and primary cells. We selected replicates using single-end reads which were not flagged by ENCODE as having low coverage or insufficient read length. The list of the sample identifiers is found in ENCODE_IDs.xlsx. Each replicate is associated with a BAM file generated by mapping reads to GRCh38 using Bismark. We used the MethPipe methylation software suite to convert BAM files into MethPipe format and generate epiread files, an efficient format reporting the genomic index and methylation status of each CpG contained in a read. Within each biological replicate, we used the epireads file generated to extract data from ``well-covered'' triplets. After discarding reads which reported a CpG with ambiguous methylation status, we considered a triplet well-covered within a replicate if all three CpGs are jointly covered by at least $100$ reads from that sequencing run. Across all 121 replicates, we found $650,152$ well-covered triplets, representing $75,212$ unique loci total. For each autosome in each sample we estimated the exchangeable weight of each well-covered triplet and corrected for estimator bias using a sample mean of N=1000 full bootstrap resamples. Although each estimate of a triplet's exchangeable weight $\hat\lambda$ lies in $[0,1]$, the bias-adjusted estimate $(\hat\lambda-\bar{\hat\lambda^*})$ may be larger than $1$ or smaller than $0$. Therefore we truncate these estimates to $[0,1]$. The tsv files here contain processed triplets corresponding to each BAM file ID. Each row corresponds to a well-covered triplet, with columns corresponding to 1) chromosome number, 2) index of the first CpG in the triplet on the chromosome, 3) position of the first CpG in the triplet on the chromosome, 4) position of the nearest transcription start site, 5) distance between the triplet centroid and nearest transcription start site, 6) an estimate of the total variation distance to the class of exchangeable distributions, 7) an estimate of the exchangeable weight of the triplet (bias-corrected), 8) a bootstrap estimate of the standard deviation of $\hat\lambda$, 9-16) the counts of each of the $8$ possible triplet configurations (ordered lexicographically, i.e. `000', `001', etc.), and 17-24) an estimate of the largest exchangeable component<br>
DOI: 10.6084/m9.figshare.16983478
title: Supplementary Data of Zhang et al.xlsx

description: This file contains the original data of dose rates, De values and ages of samples from Luochuan section in the Chinese Loess Plateau.
DOI: 10.6084/m9.figshare.16983478.v1
title: Supplementary Data of Zhang et al.xlsx

description: This file contains the original data of dose rates, De values and ages of samples from Luochuan section in the Chinese Loess Plateau.
DOI: 10.18120/t3g1-ej86
title: An integrated single-neuronal, population-, local network- and stimulation-based prefrontal investigation of human social cognition
DOI: 10.15468/dempyd
title: Contribution to the knowledge of Chinese Gryllacrididae (Orthoptera) I: New additions of Homogryllacris Liu, 2007 from Guangxi and Yunnan

description: This dataset contains the digitized treatments in Plazi based on the original journal article Liu, Jing, Yang, Dongdong, Bian, Xun (2021): Contribution to the knowledge of Chinese Gryllacrididae (Orthoptera) I: New additions of Homogryllacris Liu, 2007 from Guangxi and Yunnan. Zootaxa 5067 (2): 285-295, DOI: https://doi.org/10.11646/zootaxa.5067.2.11
DOI: 10.18120/tdg3-v813
title: Defining Targets for Tic Detection and Suppression in Tourette Syndrome Deep Brain Stimulation
DOI: 10.5281/zenodo.5669199
title: IODP Expedition 349, Hole U1431E - Well Logging Data

description: Logging data are measurements of physical properties of the formation surrounding a borehole, acquired in situ after completion of coring (wireline logging) or during drilling (Logging-While-Drilling, LWD). The range of data (resistivity, gamma radiation, velocity, density, borehole images,…) in any hole depends on the scientific objectives and operational constraints.
description: IODP Expedition 349: South China Sea Tectonics
DOI: 10.5281/zenodo.5669198
title: IODP Expedition 349, Hole U1431E - Well Logging Data

description: Logging data are measurements of physical properties of the formation surrounding a borehole, acquired in situ after completion of coring (wireline logging) or during drilling (Logging-While-Drilling, LWD). The range of data (resistivity, gamma radiation, velocity, density, borehole images,…) in any hole depends on the scientific objectives and operational constraints.
description: IODP Expedition 349: South China Sea Tectonics
DOI: 10.25345/c5ns0b
title: MassIVE MSV000088341 - GNPS - Tiny Earth Fall 2021 TECH11 and TE3760
title: TECH11 and TECH3760 culture extracts grown and extracted as part of Tiny Earth Fall 2021 course at Point Loma Nazarene University then run on Qtof
DOI: 10.25345/c5hz97
title: MassIVE MSV000088342 - Mechanistic Studies and In Vivo Efficacy of the Oxadiazole-Containing Antibiotic, HSGN-94, which Inhibits Lipoteichoic Acid Biosynthesis in Staphylococcus aureus
title: Methicillin-resistant Staphylococcus aureus (MRSA) is considered a serious threat that requires development of new therapeutics. MRSA affects around 330,000 patients every year, resulting in almost 11,000 deaths. Despite the availability of FDA-approved therapeutics to combat this pathogen, there is a need for new chemical entities. The oxadiazole-containing compound, HSGN-94, has been shown to reduce lipoteichoic acid (LTA) in S. aureus, but the mechanism that accounts for LTA biosynthesis inhibition remains uncharacterized. Here, we report the elucidation of the mechanism by which HSGN-94 inhibits LTA biosynthesis via utilization of global proteomics, activity-based protein profiling, and lipid analysis via multiple reaction monitoring (MRM). Our data suggest that HSGN-94 inhibits LTA biosynthesis via direct binding to PgcA and downregulation of PgsA. We further show that HSGN-94 reduces MRSA load in a murine model of skin infection and reduced the pro-inflammatory cytokines in MRSA infected wounds. Collectively, these results indicate that HSGN-94 merits further consideration as a new therapeutic option for treatment of staphylococcal infections.
DOI: 10.7302/3xwv-7n71
title: Batch-Mask: An automated Mask R-CNN workflow to isolate non-standard biological specimens for color pattern analysis (Data set)
DOI: 10.6084/m9.figshare.16983577
title: LS-14685_E1-50_AAGAGGCA-AAGGAGTA.Aligned.out.bam

description: bam file of scrnaseqdata
DOI: 10.6084/m9.figshare.16983577.v1
title: LS-14685_E1-50_AAGAGGCA-AAGGAGTA.Aligned.out.bam

description: bam file of scrnaseqdata
DOI: 10.25345/c5d868
title: MassIVE MSV000088343 - Comparative Studies to Uncover Further Mechanisms of Action of N-(1,3,4-oxadiazol-2-yl)benzamide Containing Antibacterial Agents
title: Drug-resistant bacterial pathogens still cause high levels mortality annually despite the availability of many antibiotics. Staphylococcus aureus (MRSA) is especially problematic and the rise in resistance to front line treatments like vancomycin and linezolid calls for new chemical modalities to treat chronic and relapsing S, aureus infections. Halogenated N-(1,3,4-oxadiazol-2-yl)benzamides are interesting class of antimicrobial agents, which have been described by multiple groups to be effective against different bacterial pathogens. The modes of action of a few N-(1,3,4-oxadiazol-2-yl)benzamides have been elucidated. For example, oxadiazoles KKL-35 and MBX-4132, have been described as inhibitors of trans-translation (a ribosome rescue pathway) while HSGN-94 was shown to inhibit lipoteichoic acid. However other similarly halogenated N-(1,3,4-oxadiazol-2-yl)benzamides neither inhibit trans-translation nor LTA but are potent antimicrobial agents. For example, HSGN-220, -218, and -144 are N-(1,3,4-oxadiazol-2-yl)benzamides that are modified with OCF3, SCF3 or SF5, and have remarkable minimum inhibitory concentrations (MICs) ranging from 1 to 0.06 microgram per mL against MRSA clinical isolates and show a low propensity to resistance to MRSA over 30 days. The mechanism of action (MOA) of these highly potent oxadiazoles is however unknown. To provide insights into how these halogenated N-(1,3,4-oxadiazol-2-yl)benzamides inhibit bacterial growth, we performed global proteomics and RNA expression analysis of some essential genes of S. aureus treated with HSGN-220, -218, and -144. These studies revealed that the oxadiazoles HSGN-220, -218, and -144 are multi-action antibiotics that regulate menaquinone biosynthesis and other essential proteins like DnaX, Pol IIIC, BirA, LexA, and DnaC. In addition, these halogenated N-(1,3,4-oxadiazol-2-yl)benzamides were able to depolarize bacterial membranes and regulate siderophore biosynthesis and heme regulation. Iron starvation appears to be part of the MOA that led to bacterial killing. This study demonstrates that N-(1,3,4-oxadiazol-2-yl)benzamides are indeed privileged scaffolds for the development of antibacterial agents and that subtle modifications lead to changes to MOA.
DOI: 10.5281/zenodo.5645415
title: Chen et al (2021) Mesoscale and Submesoscale Shelf-Ocean Exchanges Initialize an Advective Marine Heatwave

description: data and software for Chen et al (2021) "Mesoscale and Submesoscale Shelf-Ocean Exchanges Initialize an Advective Marine Heatwave" in Journal of Geophysical Research: Oceans
DOI: 10.5281/zenodo.5645414
title: Chen et al (2021) Mesoscale and Submesoscale Shelf-Ocean Exchanges Initialize an Advective Marine Heatwave

description: data and software for Chen et al (2021) "Mesoscale and Submesoscale Shelf-Ocean Exchanges Initialize an Advective Marine Heatwave" in Journal of Geophysical Research: Oceans
DOI: 10.15468/vwc2uk
title: Mikrischyrum musicum, a new katydid species from montane rainforest in southern Ecuador with complex pure-tone calling song (Orthoptera: Tettigoniidae: Pseudophyllinae: Platyphyllini)

description: This dataset contains the digitized treatments in Plazi based on the original journal article Braun, Holger (2021): Mikrischyrum musicum, a new katydid species from montane rainforest in southern Ecuador with complex pure-tone calling song (Orthoptera: Tettigoniidae: Pseudophyllinae: Platyphyllini). Zootaxa 5067 (2): 267-272, DOI: https://doi.org/10.11646/zootaxa.5067.2.8
DOI: 10.25345/c58k30
title: MassIVE MSV000088344 - RyR2/IRBIT regulates insulin gene transcription, insulin content, and secretion in the insulinoma cell line INS-1
title: The role of ER Ca2+ release via ryanodine receptors (RyR) in pancreatic B-cell function is not well defined. Deletion of RyR2 from the rat insulinoma INS-1 enhanced the Ca2+ integral (AUC) stimulated by glucose, and reduced levels of the protein IRBIT (AHCYL1). Deletion of IRBIT increased the Ca2+ AUC in response to glucose via enhanced IP3 receptor activity. Insulin content, basal and glucose-stimulated insulin secretion (GSIS), and INS2 mRNA levels were reduced in both RyR2KO and IRBITKO cells. Nuclear localization of S-adenosylhomocysteinase (AHCY) was increased in RyR2KO and IRBITKO cells, and exon 2 of the INS1 and INS2 genes was more extensively methylated in RyR2KO and IRBITKO cells. Deletion of RyR2 or IRBIT resulted in differential regulation of 314 and 137 proteins, respectively, with 41 in common. We conclude that RyR2 regulates IRBIT levels in INS-1 cells, and together regulate insulin content, GSIS, and the proteome, perhaps via DNA methylation.
DOI: 10.5281/zenodo.3690070
title: Data for resonator behavior in the paper "Self-sensing, tunable monolayer MoS2 nanoelectromechanical resonators"

description: Data for resonator behavior in the paper "Self-sensing, tunable monolayer MoS2<br> nanoelectromechanical resonators", <em>Nat. Commun.</em> 10, 4831 (2019); DOI:10.1038/s41467-019-12795-1.
description: {"references": ["Nat. Commun. 10, 4831 (2019)"]}
DOI: 10.5281/zenodo.3690069
title: Data for resonator behavior in the paper "Self-sensing, tunable monolayer MoS2 nanoelectromechanical resonators"

description: Data for resonator behavior in the paper "Self-sensing, tunable monolayer MoS2<br> nanoelectromechanical resonators", <em>Nat. Commun.</em> 10, 4831 (2019); DOI:10.1038/s41467-019-12795-1.
description: {"references": ["Nat. Commun. 10, 4831 (2019)"]}
DOI: 10.15151/esrf-es-616858037
title: iNEXT discovery: Structural biology for translational research and discovery
DOI: 10.5281/zenodo.5668527
title: SIRIUS Project - comparative dataset on socio-cultural, political and legal indicators

description: This is an ad hoc dataset on socio-economic, cultural, political and legal indicators on migration covering all SIRIUS countries (Czech Republic, Denmark, Finland, Greece, Italy, Switzerland, United Kingdom), created by retrieving and systematizing a number of indicators available in the most relevant databases. The dataset has been created as part of the work package 2 of the SIRIUS Project "Skills and Integration of Migrants, Refugees and Asylum Applicants in European Labour markets". The work package, titled “Legal barriers and enablers”, examined the legal and institutional framework of migration and asylum, integrated with critical insights on the cultural and socio-economic environment of the SIRIUS countries. <strong>Acknowledgments and disclaimers</strong><br> This research was conducted under the Horizon 2020 project ‘SIRIUS’ (770515).<br> The sole responsibility of this publication lies with the author. The European Union is not responsible for any use that may be made of the information contained therein.
DOI: 10.5281/zenodo.5668526
title: SIRIUS Project - comparative dataset on socio-cultural, political and legal indicators

description: This is an ad hoc dataset on socio-economic, cultural, political and legal indicators on migration covering all SIRIUS countries (Czech Republic, Denmark, Finland, Greece, Italy, Switzerland, United Kingdom), created by retrieving and systematizing a number of indicators available in the most relevant databases. The dataset has been created as part of the work package 2 of the SIRIUS Project "Skills and Integration of Migrants, Refugees and Asylum Applicants in European Labour markets". The work package, titled “Legal barriers and enablers”, examined the legal and institutional framework of migration and asylum, integrated with critical insights on the cultural and socio-economic environment of the SIRIUS countries. <strong>Acknowledgments and disclaimers</strong><br> This research was conducted under the Horizon 2020 project ‘SIRIUS’ (770515).<br> The sole responsibility of this publication lies with the author. The European Union is not responsible for any use that may be made of the information contained therein.
DOI: 10.6084/m9.figshare.16984648
title: sorted.test1.bam

description: SCbam file
DOI: 10.6084/m9.figshare.16984648.v1
title: sorted.test1.bam

description: SCbam file
DOI: 10.6084/m9.figshare.16984651
title: sorted.test1.bam.bai

description: scbam ind
DOI: 10.6084/m9.figshare.16984651.v1
title: sorted.test1.bam.bai

description: scbam ind
DOI: 10.5281/zenodo.5669236
title: Pulotu: Database of Austronesian Religions

description: Cite the source of the dataset as: Watts J., Sheehan O., Greenhill S.J., Gomes-Ng S., Atkinson Q.D., Bulbulia J., Gray R.D. (2015). Pulotu: Database of Austronesian Supernatural Beliefs and Practices. PLoS ONE 10(9). DOI: https://doi.org/10.1371/journal.pone.0136783
DOI: 10.15468/bkfvg6
title: Kryptochroma: a new genus of bark-dwelling crab spiders (Araneae, Thomisidae)

description: This dataset contains the digitized treatments in Plazi based on the original journal article Machado, Miguel, Viecelli, Rafaela, Guzati, Catherine, Grismado, Cristian J., Teixeira, Renato A. (2021): Kryptochroma: a new genus of bark-dwelling crab spiders (Araneae, Thomisidae). European Journal of Taxonomy 778: 26-70, DOI: https://doi.org/10.5852/ejt.2021.778.1565
DOI: 10.5281/zenodo.5669064
title: Ariopsis seemanni decontaminated FSCR

description: .
DOI: 10.5281/zenodo.5669063
title: Ariopsis seemanni decontaminated FSCR

description: .
DOI: 10.5519/qd.ko13p0xf
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (84 records)
DOI: 10.17632/h2krvxjtzv.1
title: Rising Up: Interim 24-week analysis

description: A phase 3 randomized, multi-center, double-blind study to evaluate the safety of upadacitinib in combination with topical corticosteroids in adolescent and adult patients in Japan with moderate-to-severe atopic dermatitis (Rising Up): Interim 24-week analysis
DOI: 10.17632/hzfwzzsk8f.3
title: Electric current consumption and meteorological data of Alto Paraná, Paraguay

description: The data set provides information of electric current consumption and meteorological data of the region of Alto Paraná, Paraguay. Electric current consumption set includes datetime (ISO 8601 without timezone), substation, feeder and consumption (amperage) with an hourly frequency. Meteorological data includes datetime (ISO 8601 without timezone), temperature (Celsius) , relative humidity (percentage), wind speed (km/h, kilometers per hour) and atmospheric pressure (hPa, hectopascal) at the station level with a frequency of every three hours. 

Both dataset spans from January 2017 to December 2020, the meteorological set contains  22.445 records of one weather station and electricity consumption set contains data from 55 feeders distributed in 14 substations, includes a total of 1.848.947 records.

This set can be used to train and validate the performance of machine learning algorithms used in regression and classification as well as modelling, simulation and optimization problems related to energy consumption and climate.
DOI: 10.17632/fdm8924tkp.1
title: Diploid male production sheds light on the distinct colony phenotypes in the buff-tailed bumblebee Bombus terrestris

description: Datasets and R script used for the study.
DOI: 10.17632/snzrkfrg7x.2
title: Active Pharmaceutical Ingredients from Brazilian Pharmacopeia in 2Dsdf, 3Dsdf and Mol2 format

description: Active Pharmaceutical Ingredients (APIs) are molecules that can be used for the manufacturing of Drugs. The Brazilian Health Regulatory Agency (Agência Nacional de Vigilância Sanitária) is responsible for the oversight and approval of production and distribution of all drugs in Brazilian territory. The dataset containing 2Dsdf, 3Dsdf and Mol2 format files may be useful in a vast range of in silico techniques.

“APIs Anvisa sdf” is composed of 2D sdf format files, obtained from PubChem or DrugBank databases, where the download of the molecules were made manually and individually;
“APIs Anvisa MOL2” is composed of mol2 format files;
“APIs Anvisa 3Dsdf” having three-dimensional structures in sdf format.

The data conversion was made by using the OpenBabel and Marvin software.