cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5066/p9pbacxv
title: The ontogeny of eDNA shedding during early development in Chinook Salmon

description: We conducted a lab study to explore eDNA shedding during early life history (from fertilized eggs until near yolk sac absorption) in Chinook Salmon at three biomasses: 10 eggs, 100 eggs, and 1,000 eggs, and each egg biomass was replicated (indicated as replicates 1 and 2). Water samples were collected at several time points before, during, and after hatch for detection of Chinook Salmon DNA. On days when water samples were collected, we counted the number of dead eggs and the number of viable eggs hatched (identified as larvae emerged from eggs) until hatching was completed. The dataset represents the results from testing water samples for Chinook Salmon DNA using a quantitative polymerase chain reaction (qPCR) assay and the number of dead eggs and the number of viable eggs hatched.
DOI: 10.6084/m9.figshare.16900057
title: Subcutaneous remdesivir administration prevents interstitial pneumonia in rhesus macaques inoculated with SARS-CoV-2

description: The efficacy of remdesivir treatment in COVID-19 patients is likely limited at least in part by the necessity to administer this antiviral intravenously, that has limited its’ use to hospitalized patients. Here, we tested a novel, subcutaneous formulation of remdesivir in the rhesus macaque model of SARS-CoV-2 infection that was previously used to establish the efficacy of remdesivir against this virus in vivo. Compared to vehicle treated animals, macaques treated with remdesivir subcutaneously showed reduced signs of respiratory disease, a reduction of virus replication in the lower respiratory tract, and a complete absence of interstitial pneumonia.
DOI: 10.6084/m9.figshare.16900057.v1
title: Subcutaneous remdesivir administration prevents interstitial pneumonia in rhesus macaques inoculated with SARS-CoV-2

description: The efficacy of remdesivir treatment in COVID-19 patients is likely limited at least in part by the necessity to administer this antiviral intravenously, that has limited its’ use to hospitalized patients. Here, we tested a novel, subcutaneous formulation of remdesivir in the rhesus macaque model of SARS-CoV-2 infection that was previously used to establish the efficacy of remdesivir against this virus in vivo. Compared to vehicle treated animals, macaques treated with remdesivir subcutaneously showed reduced signs of respiratory disease, a reduction of virus replication in the lower respiratory tract, and a complete absence of interstitial pneumonia.
DOI: 10.5066/p9zs5iwf
title: Disruption of Francisella noatunensis orientalis pdpA gene results in virulence attenuation and protection in zebrafish

description: Several Francisella spp. including F. noatunensis are regarded as important emerging pathogens of wild and farmed fish. However, very few studies have investigated the virulence factors that allow these bacterial species to be pathogenic in fish. The Francisella Pathogenicity Island (FPI) is a well-described, gene-dense region encoding major virulence factors for the genus Francisella. PdpA is a member of the pathogenicity determining protein genes encoded by the FPI that are implicated in the ability of the mammalian pathogen, F. tularensis, to escape and replicate in infected host cells. Using a sacB suicide approach, we generated pdpA knockouts to address the role of PdpA as a virulence factor for F. noatunensis. Since polarity can be an issue in gene-dense regions, we generated two different marker-based mutants in opposing polarity (FnoDpdpA1 and DpdpA2). Both mutants were attenuated (p&lt;0.05), all of which could be restored to wild-type (WT) levels by complementation. Importantly, differences were found for bacterial burden and induction of acute phase and pro-inflammatory genes for Fno-pdpA1 and pdpA2 compared to WT during acute infection. In addition, neither mutant resulted in significant histopathological changes. Finally, immunization with Fno pdpA1 led to protection (p&lt;0.012) against an acute lethal-dose 40 challenge with WT Fno in the zebrafish model of infection. The results from this study further demonstrate physiological similarities within the genus Francisella relative to their physiological relationships and the utility of zebrafish for addressing virulence factors for the genus.
DOI: 10.17632/3f564s62gy.1
title: Indium Tin Oxide thermoelectric dataset

description: Data on electrical conductivity, Seebeck coefficient and thermal conductivity of the Indium Tin Oxide obtained by 'a robust system for thermoelectric device characterization system' presented in the paper: doi 10.1109/TIM.2021.3115213.
DOI: 10.17632/k2jtwn2jbn.1
title: Zooplankton of the Lower Irtysh floodplain 

description: The data on the current species composition, abundance and bioproductivity of zooplankton in rivers of different types in the lower Irtysh floodplain (Western Siberia) are presented.
DOI: 10.17632/s3sb6v7y5b.1
title: Collective self-doubt

description: Data and analysis scripts for "Collective Self-Doubt: Does Subjective SES Predict Behavioral Self-Handicapping Tendency in College Students?"
DOI: 10.17632/vz7wktbvkd.1
title: Associations between TON-17, PA and FCV-19S in university students

description: The data include demographic variables, orthorexia (TON-17), physical activity (PA), and Fear of COVID-19 Scale (FCV-19S) in 473 university students from Poland, during the COVID-19 pandemic.
DOI: 10.17632/tfg4byhch8.1
title: I(V) data sets on Thermoelectric Generators

description: Current voltage data of Thermoelectric Generators (TEGs), model SP-184827145.
DOI: 10.17632/vd6mt5r5jm.1
title: Data to Accompany: Cannabinoid- and Substance- Relationships of European Congenital Anomaly Patterns: A Space-Time Panel Regression and Causal Inferential Study

description: Data accompanies paper of the same name.
DOI: 10.17632/6gvs94p6r2.2
title: R modeling code, high-speed video, sound files and other data from: Long- and short-range bimodal signals mediate mate location and recognition in yellow fever mosquitoes 

description: This data set is supplementary to the manuscript "Long- and short-range bimodal signals mediate mate location and recognition in yellow fever mosquitoes". This publication used high-speed video to demonstrate the wing flash phenomena in both laboratory populations of the yellow fever mosquito, Aedes aegypti, and field populations of dipterans. We also tested the attractiveness of flashing LED arrays as stand-ins for mosquito swarms. Additionally, we used LED arrays coupled with earbud speakers as swarm stand-ins. Using the LED arrays, we exposed Ae. aegypti and males of the northern house mosquito, Culex pipiens, to various frequencies and combinations of flashing lights and acoustic signals. The methods used to produce the data and other files are fully described in the main pulbication. The abstract for the publication is reproduced below.


"Mate location and mate selection behavior in diurnally-active yellow fever mosquitoes, Aedes aegypti, take place in mating swarms but the mechanisms underlying swarm formation and long-range detection of females by males remain largely unexplored. In high-speed video recordings we show that incident light reflects off the wings of swarming males, and in behavioral experiments we demonstrate that swarm formation and mate recognition are mediated, in part, by these wingbeat light flashes and by wingbeat sound signals that operate at long and short range, respectively. To test for range-dependent effects of these signals, we presented ‘mating swarms’ in form of two paired 8-LED assemblies that were fitted with micro-speakers and placed either well separated in a large space or side-by-side in a small space. In the large but not the small space, the LED assembly flashing light at the wingbeat frequency of females (665 Hz), and emitting their wingbeat sound (665 Hz), attracted and prompted 5.8-times more alightings by males than the LED assembly emitting constant light and wingbeat sound. In the small space, the LED assembly flashing light and emitting wingbeat sound induced 5.0-times more alightings by males than the LED assembly flashing light without wingbeat sound. The attractiveness of light flash signals to males increased with increasing numbers of signals but did not vary according to their wavelengths (UV or blue). Females responded to light flash signals of males. As predicted by the sensory drive theory, light flashes had no signal function for crepuscular house mosquitoes, Culex pipiens."


This dataset contains (1) sound files utilized in experiments, (2) spectra of LEDs and illumination sources used in bioassays, (3) files associated with measurements of mosquito wing spectra, (4) Raw data from each experiment, alongside R code used in statistical analysis, and (5) high-speed video and analysis. Further details can be found in the description or "read me.txt" files associated with each subfolder.
DOI: 10.17632/fxbmcb8czp.1
title: Lamotrigine and Levetiracetam Serum/Plasma Levels and Toxicity

description: Supplementary file 1: Data for 5,046 measurements of lamotrigine serum/plasma drug levels on 1,930 unique patients (1,068 female, 862 male).  The retrospective timeframe is August 1, 1996 through November 15, 2018.

Supplementary file 2: Data for 597 measurements on 293 unique patients (163 female, 130 male) for which the lamotrigine serum/plasma drug level was greater than 14.0 mg/L.  Data includes information from detailed chart review.    The retrospective timeframe is August 1, 1996 through November 15, 2018.

 Supplementary file 3: Data for 4,359 measurements of levetiracetam serum/plasma drug levels on 2,451 unique patients (1,225 female, 1,226 male).  The retrospective timeframe is January 1, 2005 and November 15, 2018.

Supplementary file 4: Data for 134 measurements on 106 unique patients (33 female, 73 male) for which the levetiracetam serum/plasma drug level was 80 mg/L or higher.  Data includes information from detailed chart review.   The retrospective timeframe is January 1, 2005 and November 15, 2018.
DOI: 10.17632/3z2dh6f739.1
title: Professor of Oral Medicine and Periodontology  

description: Professor of Oral Medicine and Periodontology
DOI: 10.17632/36wbbhkc3v.1
title: Facies stacking and distribution in the Gabbs Formation (Late Triassic, west-Central Nevada, USA): An environmental baseline to the end-Triassic carbonate crisis

description: Additional file formats for maps and cross section
DOI: 10.6084/m9.figshare.12853766
title: Phosphorus and nitrogen forms in liquid fraction of digestates from agricultural biogas plants

description: The novelty of the presented research is the determination of the nitrogen and phosphorus fraction in the liquid fraction of digestate from agricultural biogas plants. This information is important because it can help in proposing possible further liquid fraction management or developing of new technologies for their purification. The research covered digestates from agricultural biogas plants, obtained from the fermentation of three different groups of waste, i.e. agricultural lignocellulosic waste (where corn silage was a monosubstrate or a dominant co-substrate), food waste (where fruit and vegetable waste or distillery residue were monosubstrate or dominant co-substrate) and livestock manure (where cow manure was a monosubstrate or a dominant co-substrate). Concentrations of nutrients in the liquid fraction of digestates varied within a wide range (230.9–649.1 mg PO<sub>4</sub><sup>3−</sup>/L and 1363–3211 mg N/L), and their content was determined by the feedstock characteristic. The highest concentrations of organic phosphorus were found in the liquid fraction of digestates from the fermentation of distillery brew and livestock manure, and the lowest in the fermentation of fruit and vegetable waste. In the liquid fraction of digestates from agricultural biogas plants, regardless of the composition of the feedstock, the dominant nitrogen form was ammonium nitrogen (from 60% to 90% TN). Organic nitrogen was dominated by CON fraction, which was from 35% to 54% of ON. It was 1.3–1.6 times higher than the DON fraction.
DOI: 10.6084/m9.figshare.12853766.v1
title: Phosphorus and nitrogen forms in liquid fraction of digestates from agricultural biogas plants

description: The novelty of the presented research is the determination of the nitrogen and phosphorus fraction in the liquid fraction of digestate from agricultural biogas plants. This information is important because it can help in proposing possible further liquid fraction management or developing of new technologies for their purification. The research covered digestates from agricultural biogas plants, obtained from the fermentation of three different groups of waste, i.e. agricultural lignocellulosic waste (where corn silage was a monosubstrate or a dominant co-substrate), food waste (where fruit and vegetable waste or distillery residue were monosubstrate or dominant co-substrate) and livestock manure (where cow manure was a monosubstrate or a dominant co-substrate). Concentrations of nutrients in the liquid fraction of digestates varied within a wide range (230.9–649.1 mg PO<sub>4</sub><sup>3−</sup>/L and 1363–3211 mg N/L), and their content was determined by the feedstock characteristic. The highest concentrations of organic phosphorus were found in the liquid fraction of digestates from the fermentation of distillery brew and livestock manure, and the lowest in the fermentation of fruit and vegetable waste. In the liquid fraction of digestates from agricultural biogas plants, regardless of the composition of the feedstock, the dominant nitrogen form was ammonium nitrogen (from 60% to 90% TN). Organic nitrogen was dominated by CON fraction, which was from 35% to 54% of ON. It was 1.3–1.6 times higher than the DON fraction.
DOI: 10.5281/zenodo.5608575
title: Impact on energy and air quality of connected and autonomous vehicles in an urban context

description: Despite numerous studies related to autonomous vehicles and connected vehicles (CAVs) and their impact on the economy or on traffic performance (eg, flow management, accidents), there are not many studies that relate these benefits to the environmental component. In this context, the objective of this work consisted in the integrated assessment of the impacts of CAVs on traffic performance, atmospheric emissions CO<sub>2</sub> and NO<sub>x, </sub>and air quality. To this end, a roundabout in the city of Aveiro was selected as a case study, and different scenarios were created: base scenario, considering the current typology of vehicles (conventional); scenario 2, considering defensive behavior CAVs; scenario 3, considering assertive behavior CAVs; and scenario 1, considering all types of vehicles mentioned above. To ensure a comprehensive analysis, all scenarios were evaluated for a period of 24 hours, corresponding to the period of the experimental campaign carried out, and a cascade of models was applied. First, the PTV VISSIM model was applied which allowed, configuring, calibrating and validating the network under study for an evaluation of the traffic performance. Second, the VSP model was applied to estimate atmospheric emissions, Finally, the CFD VADIS model was applied to air quality assessment. The results obtained allowed us to conclude that the introduction of CAVs, promotes longer travel times, especially during times of higher traffic, and an increase in emissions, mainly by the CAVs with defensive behavior. In terms of air quality, there were large differences in terms of NO<sub>2</sub> concentrations, with the CAVs promoting a degradation of air quality, especially during peak traffic hours.
DOI: 10.5281/zenodo.5608574
title: Impact on energy and air quality of connected and autonomous vehicles in an urban context

description: Despite numerous studies related to autonomous vehicles and connected vehicles (CAVs) and their impact on the economy or on traffic performance (eg, flow management, accidents), there are not many studies that relate these benefits to the environmental component. In this context, the objective of this work consisted in the integrated assessment of the impacts of CAVs on traffic performance, atmospheric emissions CO<sub>2</sub> and NO<sub>x, </sub>and air quality. To this end, a roundabout in the city of Aveiro was selected as a case study, and different scenarios were created: base scenario, considering the current typology of vehicles (conventional); scenario 2, considering defensive behavior CAVs; scenario 3, considering assertive behavior CAVs; and scenario 1, considering all types of vehicles mentioned above. To ensure a comprehensive analysis, all scenarios were evaluated for a period of 24 hours, corresponding to the period of the experimental campaign carried out, and a cascade of models was applied. First, the PTV VISSIM model was applied which allowed, configuring, calibrating and validating the network under study for an evaluation of the traffic performance. Second, the VSP model was applied to estimate atmospheric emissions, Finally, the CFD VADIS model was applied to air quality assessment. The results obtained allowed us to conclude that the introduction of CAVs, promotes longer travel times, especially during times of higher traffic, and an increase in emissions, mainly by the CAVs with defensive behavior. In terms of air quality, there were large differences in terms of NO<sub>2</sub> concentrations, with the CAVs promoting a degradation of air quality, especially during peak traffic hours.
DOI: 10.6078/m74j0c7t
title: Osteometric Database of South American Camelids
DOI: 10.25345/c52c32
title: MassIVE MSV000088278 - Trapping and visualization of outer membrane 1 protein folding intermediates
title: Native MS data on BamA showing preference for metal ion containing moiety binding to inhibitor
DOI: 10.17632/g64mnvkgyk.1
title: Structural basis of polyamine transport by human ATP13A2 (PARK9). Sim et al.

description: Fig. S1A_Size-exclusion_profile_coomasie
DOI: 10.17632/jzsx489pmk.1
title: Broadly neutralizing antibodies target a hemagglutinin anchor epitope, Guthmiller et al. 2021

description: This study was designed to analyze the B cell repertoire of cH5/1 binding B cells following vaccination with the cHA platform. Human B cells (CD19+IgM-CD27+cH5/1+) were sorted at day 113 and were used for downstream sequencing. This dataset is comprised of a collection of BCR sequences of 1952 antibodies with paired heavy chain and light chain, a collection of BCR sequences of 119 anchor antibodies, and a collection of BCR sequences of 365 VH1-69&kappa. 

PROTOCOLS: 
cH5/1+ memory B cells (CD19+CD27+HA+) were bulk sorted and partitioned into nanoliter-scale Gel Bead-In-Emulsions (GEMs) to achieve single cell resolution using the 10x Genomics Chromium Controller and according to the manufacturer’s instruction (10x Genomics). The sorted single cells were processed according to 5’ gene expression and B cell Immunoglobulin (Ig) enrichment instruction to prepare the libraries for sequencing. Libraries were sequenced using an Illumina HiSeq 4000 at Northwestern University or an Illumina NextSeq 500 at the University of Chicago. 

Cellranger Single-Cell Software Suite (version 3.0) was used to perform sample de-multiplexing, barcode processing, and single-cell 5’ and V(D)J counting, and Cellranger mkfastq was used to de-multiplex raw base call (BCL) files into sample-specific fastq files. Subsequently, GRCh38-1.2.0 and cellranger-vdj-GRCh38-alta-ensembl-2.0.0 were used as references for the transcriptome and V(D)J assembly, respectively. Cellranger counts and Cellranger vdj package were used to identify gene expression and assemble V(D)J pairs of antibodies. BCR sequences were then processed by IgBlast and our in-house software VGenes. 

Please see readme.xlsx file for more details.
DOI: 10.17632/8465mbnxt7.1
title: Markovina_CommunBiol_rawdata

description: Raw data files for Wang et al, submitted to Communications Biology on 2/10/2021.
DOI: 10.17632/8ph6zcd6p3.1
title: Does postural feedback reduce musculoskeletal risk?: An experimental study

description: A multi-component intervention was designed and applied, the results showed that this program could significantly reduce musculoskeletal risk. Here are the sociodemographic data of the participants and the scores of the two assessments. Since some variables involve the personal information of patients and participants, the public data has been anonymized.
DOI: 10.17632/cdt269pw7m.1
title: Cell-Fit-HD4D Matlab Codes

description: The provided Matlab codes were used to extract data from microscopy time series and LevelSetTracker for single cell tracking.
All files marked with "MC" describe Monte Carlo simulations for error estimation.
detClon: determination of cellular clonality from LevelSetTracker-derived analyses matrices
detPot: determination of proliferative potential of single cells from LevelSetTracker-derived analyses matrices
division: Uses LevelSetTracker-generated files for determination of cell clonogenicity and basic cell division trees
IntranuclearHits_MC: Error estimation of hit determination for single cells via Mone Carlo Simulation
IntranuclearHits_and_Dose_MC: Error estimation of hit and dose determination for single cells via Mone Carlo Simulation
RIF_in_individual_cells: Save and extraction of RIF number of single cells at single time points
RIFinCell: Class representing a single cell with RIF number  at a single time point
RIFinCelloverT: Class representing a single cell containing its RIF kinetics over time
searchDiv: Searches and connects mother cells to daughter cells within a matrix
searchPot: Searches for second generation daughter cells and by that calculates division potential of a given cell
DOI: 10.17632/tr8y8tgcyv.2
title: codon usage of mycovirus

description: This data contains the detailed nucleotide composition and the relative abundance of 16 dinucleotides of 98 RNA mycoviruses. This data also contains the analyses of effective number of codons (ENc) and relative synonymous codon usage (RSCU) in 98 RNA mycoviruses. This data lists the hosts genes that have similar codon usage to mycoviruses in R. solani, F. graminearum, B. cinerea, and S. sclerotiorum, and GO enrichment results of these genes are listed in this data. The GO enrichment results of up-regulated and down-regulated genes of S. sclerotiorum in SsMYRV4 and F. graminearum in FgV1 FgV2, FgV3, FgV4, and FgHV1 infections are also listed in this data.  
Supplementary Data 1. The detailed information for all selected mycoviruses. 
Supplementary Data 2. The detailed nucleotide composition of selected mycovirus. 
Supplementary Data 3. The effective number of codons (ENc) of selected mycovirus and the genes of R. solani, F. graminearum, B. cinerea, and S. sclerotiorum. 
Supplementary Data 4. The relative abundance of dinucleotide among selected mycovirus. 
Supplementary Data 5. The relative synonymous codon usage (RSCU) values for mycoviruses and the genes of R. solani, F. graminearum, B. cinerea, and S. sclerotiorum. 
Supplementary Data 6. The list of mycoviruses with codon usage similar to fungal genes.  
Supplementary Data 7. The list of hosts genes with codon usage similar to mycoviruses and the GO enrichment results of those genes, and the GO enrichment results of up-regulated/down-regulated S. sclerotiorum and F. graminearum genes in the case of SsMYRV4, FgV1, FgV2, FgV3, FgV4, and FgHV1.