cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7586033.v1
title: Morphometric data and locomotor and social behavior data of male Japanese quail during in a Social Interaction test, in birds reared in an enriched or a standard environment.

description: <b>Environmental enrichment (EE) protocol</b>During the EE in the brood boxes (8-28 days old), 3 different sets of enrichments were rotated between boxes every 7 days. After reallocation in home cages at 28 days of age, EE was applied in 3 periods with different enrichment sets. Within each period, EE home cages received weekly one of the three enrichment sets in a random order in such a manner that all EE animals were exposed to the 3 enrichment sets. The replacement of the enrichment items was done on a fixed day and time every week, and during this procedure all the animals were removed from the box and placed in a basket. Control animals underwent the same manipulation procedure.<br><b>Social Interaction Test</b> was performed between 118 and 130 days of age. This test is described in detail in Caliva et al (2017, Pout. Sci) including a figure with the schematic representation of the test procedure. Briefly, the SI test consists in encounters between an unfamiliar test adult male and a PC stimulus adult male, in the presence of the test bird’s female cagemate (audience). First, the test male and it’s female cagemate were placed in a central compartment separated by an opaque partition from a PC stimulus male. After 2 min, the test male and the PC stimulus male, remained in the same compartment, while the female cagemate was placed in a nearby compartment at one side of the apparatus, and used as a social audience. Immediately after, the central opaque partition was removed and the test and PC stimulus birds were allowed to interact. Direct interaction lasted a maximum of 10 min. However, if during the interaction a quail received more than 5 consecutive aggressive pecks, showed a clear and continued escaping (retrieval) behavior, and/or showed any sign of physical damage, the interaction was immediately interrupted. A video-camera was positioned 1 m above the apparatus and connected to a computer that allowed constant monitoring and recording during the test while out of the sight of the birds. Using ANY-maze the following aggressive behaviors were recorded: pecks, grabs, mounts, cloacal contacts, threats, chase, and attack with claws. Herein, when grabs, mounts or cloacal contacts were performed by one male towards another male, they were considered as aggressive behaviors. Males that performed more than 5 aggressiveness behaviors were considered aggressive (Ag), and males that did not perform any aggressive behavior towards PC opponent were considered non-aggressive (nonAg).Males exposed to the experimental apparatus without the presence of an opponent (testCON) and non-manipulated males that always remained in the home cage (Naive) with their cagemate were used as control groups.<br>
DOI: 10.6084/m9.figshare.7585277
title: Variational Bayes Estimation of Discrete-Margined Copula Models With Application to Time Series

description: We propose a new variational Bayes (VB) estimator for high-dimensional copulas with discrete, or a combination of discrete and continuous, margins. The method is based on a variational approximation to a tractable augmented posterior and is faster than previous likelihood-based approaches. We use it to estimate drawable vine copulas for univariate and multivariate Markov ordinal and mixed time series. These have dimension <i>rT</i>, where <i>T</i> is the number of observations and <i>r</i> is the number of series, and are difficult to estimate using previous methods. The vine pair-copulas are carefully selected to allow for heteroscedasticity, which is a feature of most ordinal time series data. When combined with flexible margins, the resulting time series models also allow for other common features of ordinal data, such as zero inflation, multiple modes, and under or overdispersion. Using six example series, we illustrate both the flexibility of the time series copula models and the efficacy of the VB estimator for copulas of up to 792 dimensions and 60 parameters. This far exceeds the size and complexity of copula models for discrete data that can be estimated using previous methods. An online appendix and MATLAB code implementing the method are available as supplementary materials.
DOI: 10.7284/120990
title: Multibeam Echosounder data collected during research cruise FK151221 using a Kongsberg EM302 instrument system onboard the platform RV Falkor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/120991
title: Multibeam Echosounder data collected during research cruise FK151221 using a Kongsberg EM710 instrument system onboard the platform RV Falkor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7585277.v1
title: Variational Bayes Estimation of Discrete-Margined Copula Models with Application to Time Series

description: We propose a new variational Bayes estimator for high-dimensional copulas with discrete, or a combination of discrete and continuous, margins. The method is based on a variational approximation to a tractable augmented posterior, and is faster than previous likelihood-based approaches. We use it to estimate drawable vine copulas for univariate and multivariate Markov ordinal and mixed time series. These have dimension <i>rT</i>, where <i>T</i> is the number of observations and <i>r</i> is the number of series, and are difficult to estimate using previous methods. The vine pair-copulas are carefully selected to allow for heteroskedasticity, which is a feature of most ordinal time series data. When combined with flexible margins, the resulting time series models also allow for other common features of ordinal data, such as zero inflation, multiple modes and under- or over-dispersion. Using six example series, we illustrate both the flexibility of the time series copula models, and the efficacy of the variational Bayes estimator for copulas of up to 792 dimensions and 60 parameters. This far exceeds the size and complexity of copula models for discrete data that can be estimated using previous methods. An Online Appendix and MATLAB code implementing the method are available as Supplementary Materials.
DOI: 10.6084/m9.figshare.7584449
title: Antimicrobial resistance surveillance among gram negative bacterial isolates from patients in hospitals in Khartoum State, Sudan .xlsx

description: Antimicrobial resistance surveillance is key for determining the prevalence patterns of Antimicrobial resistance, which is fundamental for the development of national and international treatment strategies. This surveillance study was undertaken in order to find out the different types of the AMR patterns of bacterial pathogens isolated from patients in Khartoum State, Sudan.
DOI: 10.7284/120993
title: SSV (Sound Speed Velocimeter) data collected during research cruise FK151221 using a Valeport MiniSVS instrument system onboard the platform RV Falkor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7584446
title: Site-level biodiversity estimates for sites in different land uses, for Mediterranean and dryland environments

description: Site-level estimates of biodiversity (total abundance, species richness, Simpson diversity index, Berger-Parker dominance index and average species range size) that underlie the publication 'Assessing the effects of land use on biodiversity in the world's drylands and Mediterranean environments' by Diego Garcia-Vega and Tim Newbold.
DOI: 10.6084/m9.figshare.7584446.v1
title: Site-level biodiversity estimates for sites in different land uses, for Mediterranean and dryland environments

description: Site-level estimates of biodiversity (total abundance, species richness, Simpson diversity index, Berger-Parker dominance index and average species range size) that underlie the publication 'Assessing the effects of land use on biodiversity in the world's drylands and Mediterranean environments' by Diego Garcia-Vega and Tim Newbold.
DOI: 10.6084/m9.figshare.7584449.v1
title: Antimicrobial resistance surveillance among gram negative bacterial isolates from patients in hospitals in Khartoum State, Sudan .xlsx

description: Antimicrobial resistance surveillance is key for determining the prevalence patterns of Antimicrobial resistance, which is fundamental for the development of national and international treatment strategies. This surveillance study was undertaken in order to find out the different types of the AMR patterns of bacterial pathogens isolated from patients in Khartoum State, Sudan.
DOI: 10.7284/121441
title: TSG (Thermosalinograph) data collected during research cruise FK151221 using a Sea-Bird SBE-45 instrument system onboard the platform RV Falkor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7584431
title: Biodiversity data in different land uses, for Mediterranean and dryland environments

description: Abundance and occurrence data for species that underlie the publication 'Assessing the effects of land use on biodiversity in the world's drylands and Mediterranean environments' by Diego Garcia-Vega and Tim Newbold.<br>
DOI: 10.7284/121562
title: CTD (Conductivity, Temperature, Depth) data collected during research cruise FK160115 using a Sea-Bird SBE-911+ instrument system onboard the platform RV Falkor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7584431.v1
title: Biodiversity data in different land uses, for Mediterranean and dryland environments

description: Abundance and occurrence data for species that underlie the publication 'Assessing the effects of land use on biodiversity in the world's drylands and Mediterranean environments' by Diego Garcia-Vega and Tim Newbold.<br>
DOI: 10.7284/121563
title: Expendable Probe data collected during research cruise FK160115 using a Turo Quoll instrument system onboard the platform RV Falkor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/121565
title: Fluorometer data collected during research cruise FK160115 using a WET Labs ECO-FLNTU instrument system onboard the platform RV Falkor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/121561
title: GNSS (Global Navigation Satellite System) data collected during research cruise FK160115 using a C&C C-Nav 3050 instrument system onboard the platform RV Falkor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/121560
title: Gyrocompass data collected during research cruise FK160115 using a Raytheon STD 22 instrument system onboard the platform RV Falkor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7584230
title: HEK293 nicastrin heterozygous deletion amplicon-seq - target coverage

description: This is the coverage of a nicastrin amplicon in a HEK293 line with heterozygous deletion of nicastrin.<br>
DOI: 10.6084/m9.figshare.7584239
title: HEK293 nicastrin heterozygous deletion amplicon-seq - samtools flagstat

description: These data are the samtools flagstat of an amplicon-seq from a HEK293 cell line with heterozygous deletion of nicastrin.<br>
DOI: 10.7284/121570
title: INS (Inertial Navigation System) data collected during research cruise FK160115 using a Kongsberg Seapath 320 instrument system onboard the platform RV Falkor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7584221
title: Wildtype HEK293 nicastrin amplicon-seq - samtools flagstat

description: These are the samtools flagstat output for an amplicon-seq of HEK293 wildtype cells for a nicatrin amplicon.<br>
DOI: 10.6084/m9.figshare.7584230.v1
title: HEK293 nicastrin heterozygous deletion amplicon-seq - target coverage

description: This is the coverage of a nicastrin amplicon in a HEK293 line with heterozygous deletion of nicastrin.<br>
DOI: 10.6084/m9.figshare.7584215
title: Wildtype HEK293 nicastrin amplicon-seq - target coverage

description: This is an amplicon-seq of a wildtype HEK293 cell line targeting nicastrin. The coverage over the target was calculated with bedtools.<br>
DOI: 10.7284/121568
title: Meteorological Station data collected during research cruise FK160115 using a Gill MetPak Pro instrument system onboard the platform RV Falkor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7584167
title: Shared data from Is neurogenesis in two songbird species related to their song sequence variability?

description: shared data
DOI: 10.7284/121566
title: Multibeam Echosounder data collected during research cruise FK160115 using a Kongsberg EM302 instrument system onboard the platform RV Falkor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7584167.v1
title: Shared data from Is neurogenesis in two songbird species related to their song sequence variability?

description: shared data
DOI: 10.7284/121567
title: Multibeam Echosounder data collected during research cruise FK160115 using a Kongsberg EM710 instrument system onboard the platform RV Falkor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/121564
title: Splitbeam Echosounder data collected during research cruise FK160115 using a Kongsberg EK60 instrument system onboard the platform RV Falkor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/121569
title: SSV (Sound Speed Velocimeter) data collected during research cruise FK160115 using a Valeport MiniSVS instrument system onboard the platform RV Falkor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7584038
title: Fungal files

description: Fungal microbiota files.
DOI: 10.7284/121571
title: TSG (Thermosalinograph) data collected during research cruise FK160115 using a Sea-Bird SBE-45 instrument system onboard the platform RV Falkor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7583999
title: Influence of storage environment on maize grain: CO<sub>2</sub> production, dry matter losses and aflatoxins contamination

description: Poor storage of cereals, such as maize can lead to both nutritional losses and mycotoxin contamination. The aim of this study was to examine the respiration of maize either naturally contaminated or inoculated with <i>Aspergillus flavus</i> to examine whether this might be an early and sensitive indicator of aflatoxin (AF) contamination and relative storability risk. We thus examined the relationship between different interacting storage environmental conditions (0.80–0.99 water activity (<i>a<sub>w</sub></i>) and 15–35°C) in naturally contaminated and irradiated maize grain + <i>A. flavus</i> on relative respiration rates (<i>R</i>), dry matter losses (DMLs) and aflatoxin B1 and B2 (AFB1-B2) contamination. Temporal respiration and total CO<sub>2</sub> production were analysed by GC-TCD, and results used to calculate the DMLs due to colonisation. AFs contamination was quantified at the end of the storage period by HPLC MS/MS. The highest respiration rates occurred at 0.95 <i>a<sub>w</sub></i> and 30–35°C representing between 0.5% and 18% DMLs. Optimum AFs contamination was at the same <i>a<sub>w</sub></i> at 30°C. Highest AFs contamination occurred in maize colonised only by <i>A. flavus</i>. A significant positive correlation between % DMLs and AFB1 contamination was obtained (<i>r</i> = 0.866, <i>p</i> A. flavus. In naturally contaminated maize + <i>A. flavus</i> inoculum loss of only 0.56% DML resulted in AFB1 contamination levels exceeding the EU legislative limits for food. This suggests that there is a very low threshold tolerance during storage of maize to minimise AFB1 contamination. This data can be used to develop models that can be effectively used in enhancing management for storage of maize to minimise risks of mycotoxin contamination.
DOI: 10.6084/m9.figshare.7584038.v2
title: Fungal files

description: Fungal microbiota files.
DOI: 10.6084/m9.figshare.7583999.v1
title: Influence of storage environment on maize grain: CO<sub>2</sub> production, dry matter losses and aflatoxins contamination

description: Poor storage of cereals, such as maize can lead to both nutritional losses and mycotoxin contamination. The aim of this study was to examine the respiration of maize either naturally contaminated or inoculated with <i>Aspergillus flavus</i> to examine whether this might be an early and sensitive indicator of aflatoxin (AF) contamination and relative storability risk. We thus examined the relationship between different interacting storage environmental conditions (0.80–0.99 water activity (<i>a<sub>w</sub></i>) and 15–35°C) in naturally contaminated and irradiated maize grain + <i>A. flavus</i> on relative respiration rates (<i>R</i>), dry matter losses (DMLs) and aflatoxin B1 and B2 (AFB1-B2) contamination. Temporal respiration and total CO<sub>2</sub> production were analysed by GC-TCD, and results used to calculate the DMLs due to colonisation. AFs contamination was quantified at the end of the storage period by HPLC MS/MS. The highest respiration rates occurred at 0.95 <i>a<sub>w</sub></i> and 30–35°C representing between 0.5% and 18% DMLs. Optimum AFs contamination was at the same <i>a<sub>w</sub></i> at 30°C. Highest AFs contamination occurred in maize colonised only by <i>A. flavus</i>. A significant positive correlation between % DMLs and AFB1 contamination was obtained (<i>r</i> = 0.866, <i>p</i> A. flavus. In naturally contaminated maize + <i>A. flavus</i> inoculum loss of only 0.56% DML resulted in AFB1 contamination levels exceeding the EU legislative limits for food. This suggests that there is a very low threshold tolerance during storage of maize to minimise AFB1 contamination. This data can be used to develop models that can be effectively used in enhancing management for storage of maize to minimise risks of mycotoxin contamination.
DOI: 10.7284/121574
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise FK160305 using a Hawaii UHDAS instrument system onboard the platform RV Falkor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/121575
title: Fluorometer data collected during research cruise FK160305 using a WET Labs ECO-FLNTU instrument system onboard the platform RV Falkor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7583963
title: Supplemental Data.pdf

description: Supplemental data: Legends, Figures,Table and Video
DOI: 10.6084/m9.figshare.7583960
title: Photoconversion of Hoechst

description: The data set provided is a time series of image stacks showing the 405 nm laser-induced emission change of the DNA intercalating dye Hoechst from blue to green in living U2OS cells.<br> <br>It is part of the following research note:<br>Hurst V and Gasser SM. The study of protein recruitment to laser-induced DNA lesions can be distorted byphotoconversion of the DNA binding dye Hoechst. F1000Research , :104. <br>Experimental details:<br>U2OS cells (a gift from Prof. Primo Leo Schaer, Department of Biomedicine, University of Basel) were incubated with 1.5 µg/ml Hoechst 33342 (Thermo Fisher Scientific, H1399) for at least 30 minutes prior to photoconversion. Photoconversion was induced with a VisiFRAP module (Visitron) mounted on the backport of the microscope and equipped with a 405 nm laser (Toptica, illumination power at the objective 12.8 mW). Confocal images were acquired with an Olympus IX81 microscope equipped with a PlanApo 100x/1.45 TIRFM oil objective, a CSU-X1 scan-head (Yokogawa), an Evolve 512 EMCCD camera (Photometrics), a 491nm laser (Cobolt Calypso 100), a 488/568 dichroic (Semrock Di01-T488/568-13x15x0.5), a band-pass 525/40 emission filter (Semrock FF01-525/40-25) and controlled with the Visiview Software (Visitron).<br>
DOI: 10.6084/m9.figshare.7583963.v1
title: Supplemental Data.pdf

description: Supplemental data: Legends, Figures,Table and Video
DOI: 10.7284/121573
title: GNSS (Global Navigation Satellite System) data collected during research cruise FK160305 using a C&C C-Nav 3050 instrument system onboard the platform RV Falkor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7583909
title: Supplementary material for article "Analyzing Groups of Replications in Software Engineering: a Procedure and Guidelines"

description: -Code.R: file containing the R code to analyze SE groups of replications<br>-Raw Data.xlsx: file containing the raw data <br>-Characteristics.xlsx: file containing the experiment-level characteristics of the replications<br>-Rnotebook.Rmd: R notebook that applies Code.R to analyze the raw data in Raw Data.xlsx<br>-R tutorial: tutorial with embedded R code, mathematical formulae, and datasets descriptions, to ease the understanding of the analysis procedure
DOI: 10.7284/121572
title: Gyrocompass data collected during research cruise FK160305 using a Raytheon STD 22 instrument system onboard the platform RV Falkor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7583909.v1
title: R code and rawdata to reproduce analyses

description: R code and rawdata to reproduce analyses from paper "Analyzing Groups of Replications in Software Engineering: a Procedure and Guidelines", submitted to Transactions in Software Engineering
DOI: 10.7284/121579
title: INS (Inertial Navigation System) data collected during research cruise FK160305 using a Kongsberg Seapath 320 instrument system onboard the platform RV Falkor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7583909.v2
title: R code and raw data to reproduce analyses

description: R code and raw data to reproduce analyses from paper "Analyzing Groups of Replications in Software Engineering: a Procedure and Guidelines", submitted to Transactions in Software Engineering
DOI: 10.6084/m9.figshare.7583909.v3
title: R code and raw data for article "Analyzing Groups of Replications in Software Engineering: a Procedure and Guidelines"

description: R code and raw data to reproduce analyses from paper "Analyzing Groups of Replications in Software Engineering: a Procedure and Guidelines", Transactions in Software Engineering
DOI: 10.7284/121577
title: Meteorological Station data collected during research cruise FK160305 using a Gill MetPak Pro instrument system onboard the platform RV Falkor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7583909.v4
title: R code, R notebook, and raw data for article "Analyzing Groups of Replications in Software Engineering: a Procedure and Guidelines"

description: R code, R notebook, and raw data to reproduce analyses from paper "Analyzing Groups of Replications in Software Engineering: a Procedure and Guidelines", Transactions in Software Engineering
DOI: 10.7284/121576
title: Multibeam Echosounder data collected during research cruise FK160305 using a Kongsberg EM302 instrument system onboard the platform RV Falkor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7583909.v5
title: R code, R notebook, and raw data for article "Analyzing Groups of Replications in Software Engineering: a Procedure and Guidelines"

description: R code, R notebook, and raw data to reproduce analyses from paper "Analyzing Groups of Replications in Software Engineering: a Procedure and Guidelines", Transactions in Software Engineering
DOI: 10.7284/121578
title: SSV (Sound Speed Velocimeter) data collected during research cruise FK160305 using a Valeport MiniSVS instrument system onboard the platform RV Falkor

description: Original (unprocessed) data collected during a Field_expedition