cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7693082.v1
title: Additional file 2: of Transcriptome, proteome and draft genome of Euglena gracilis

description: Table S1. Raw data for proteomics and transcriptomics of E. gracilis under adaptive conditions. Cells were grown under dark or light conditions as described in methods and subjected to protein or RNA extraction and analysed by mass spectrometry or RNAseq. Each condition was analysed in triplicate (n = 3) and data for individual samples together with the merged data are provided (Transcripts, Proteome), together with BLAST annotation of altered transcripts (additional tabs). (XLSX 19876 kb)
DOI: 10.7284/122174
title: Radiometer data collected during research cruise AT34 using a Eppley PIR instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/122175
title: Radiometer data collected during research cruise AT34 using a Eppley PSP instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/122138
title: Singlebeam Echosounder data collected during research cruise AT34 using a Knudsen 320B/R instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7693043
title: Additional file 4: of In silico characterization of multiple genes encoding the GP63 virulence protein from Leishmania braziliensis: identification of sources of variation and putative roles in immune evasion

description: Table S4. Table showing the recombination events found for the L. braziliensis GP63 genes, followed by the programs that detected it and their p-value. Detailed description of the recombination events throughout the L. braziliensis GP63 genes. (XLSX 16 kb)
DOI: 10.6084/m9.figshare.7693043.v1
title: Additional file 4: of In silico characterization of multiple genes encoding the GP63 virulence protein from Leishmania braziliensis: identification of sources of variation and putative roles in immune evasion

description: Table S4. Table showing the recombination events found for the L. braziliensis GP63 genes, followed by the programs that detected it and their p-value. Detailed description of the recombination events throughout the L. braziliensis GP63 genes. (XLSX 16 kb)
DOI: 10.7284/122139
title: Singlebeam Echosounder data collected during research cruise AT34 using a Knudsen 3260 instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/123661
title: Multiplexed data collected during research cruise AT36 using a WHOI Calliope instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/123656
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise AT36 using a Hawaii UHDAS instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/123657
title: CTD (Conductivity, Temperature, Depth) data collected during research cruise AT36 using a Sea-Bird SBE-911+ instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/123655
title: Expendable Probe data collected during research cruise AT36 using a Sippican MK12 instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/123654
title: Fluorometer data collected during research cruise AT36 using a WET Labs WETStar instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/123653
title: GNSS (Global Navigation Satellite System) data collected during research cruise AT36 using a C&C C-Nav 2050G instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/123727
title: Gravimeter data collected during research cruise AT36 using a Bell BGM-3 instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/123659
title: Meteorological Station data collected during research cruise AT36 using a Vaisala WXT520 instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/123660
title: Meteorological Station data collected during research cruise AT36 using a Vaisala WXT520 instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/123658
title: Multibeam Echosounder data collected during research cruise AT36 using a Kongsberg EM122 instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/123728
title: Radiometer data collected during research cruise AT36 using a Eppley RAD instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/123730
title: Water Temperature data collected during research cruise AT36 using a Sea-Bird SBE-48 instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/123729
title: TSG (Thermosalinograph) data collected during research cruise AT36 using a Sea-Bird SBE-45 instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/123669
title: Multiplexed data collected during research cruise AT37-01 using a WHOI Calliope instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7692398
title: Comparison of murine steatohepatitis models identifies a dietary intervention with robust fibrosis, ductular reaction and rapid progression to cirrhosis, cancer

description: supplementary figures and tables
DOI: 10.7284/123664
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise AT37-01 using a Hawaii UHDAS instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7692365
title: Molecular evidence supports a genic capture resolution of the lek paradox

description: Allele frequency data for populations of Drosophila melanogaster (columns 6:27). Populations were artificially selected for success (S) or failure (F) in male mating success for 14 generations. There were also three control (C) populations maintained with random males. Data are presented as the counts of the rare (q) and common (p) allele for each population.<br>DiffStat scores were calculated as the minimum allele frequency difference between any combination of success- versus failure-selected line, and is zero unless all four lines of one selection regimen have higher or lower allele frequencies than all four lines of the other selection regimen.<br><br>DiffStat loci are considered significant if the DiffStat (i.e. the minimum difference between regimens) is larger than variation caused by drift (calculated as the maximum allele frequency difference within any regimen).<br>q values were obtained by running quasibinomial GLMs for each locus (success- versus failure-selected), and correcting for multiple testing.<br>The type of polymorphism and gene names for each locus are also presented.
DOI: 10.7284/123665
title: CTD (Conductivity, Temperature, Depth) data collected during research cruise AT37-01 using a Sea-Bird SBE-911+ instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7692350
title: Data set of the quantity, quality and genetic components of pollination effectiveness of the pollinator assemblage of "Erysimum mediohispanicum".

description: - QLC_Valverde_2019_NewPhytol.txt:<br>Dataset containing information about the fruit set and seed set produced after single visits of pollinators to virgin flowers of Erysimum mediohispanicum.<br><br>- plant_visitation_Valverde_2019_NewPhytol.txt:<br>Dataset containing visitation rates of pollinators per plant and day.<br><br>- contacted_flowers_Valverde_2019_NewPhytol.txt<br>Dataset containing information about the number of flowers contacted per visited plant.<br><br>-mother_and_pollen_donors_genotypes_Valverde_2019_NewPhytol.txt:<br>Dataset containing genotypes (SSR) of mother plants and pollen donors. For pollen donors information about the spatial location is provided.<br><br>- offspring_genotypes_Valverde_2019_NewPhytol.txt:<br>Dataset with information genotypes (SSR) of the offspring produced after single visits to virgin flowers. Spatial location of the mother plant at the moment of the pollination event is also provided.<br>
DOI: 10.6084/m9.figshare.7692350.v1
title: Data set of the quantity, quality and genetic components of pollination effectiveness of the pollinator assemblage of "Erysimum mediohispanicum".

description: - QLC_Valverde_2019_NewPhytol.txt:<br>Dataset containing information about the fruit set and seed set produced after single visits of pollinators to virgin flowers of Erysimum mediohispanicum.<br><br>- plant_visitation_Valverde_2019_NewPhytol.txt:<br>Dataset containing visitation rates of pollinators per plant and day.<br><br>- contacted_flowers_Valverde_2019_NewPhytol.txt<br>Dataset containing information about the number of flowers contacted per visited plant.<br><br>-mother_and_pollen_donors_genotypes_Valverde_2019_NewPhytol.txt:<br>Dataset containing genotypes (SSR) of mother plants and pollen donors. For pollen donors information about the spatial location is provided.<br><br>- offspring_genotypes_Valverde_2019_NewPhytol.txt:<br>Dataset with information genotypes (SSR) of the offspring produced after single visits to virgin flowers. Spatial location of the mother plant at the moment of the pollination event is also provided.<br>
DOI: 10.7284/123663
title: Fluorometer data collected during research cruise AT37-01 using a WET Labs WETStar instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/123662
title: GNSS (Global Navigation Satellite System) data collected during research cruise AT37-01 using a C&C C-Nav 2050G instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7692230
title: Worknet graph

description: cooperation network
DOI: 10.7284/123723
title: Gravimeter data collected during research cruise AT37-01 using a Bell BGM-3 instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7692125
title: Quantitative trends in 8 properties of inorganic compounds via machine learning

description: For the 114'872 distinct inorganic compounds we predicted 8 thermodynamic, mechanical, and electronic properties, using the only crystalline structures as an input.
DOI: 10.6084/m9.figshare.7692269.v1
title: High-Load Reovirus Infections Do Not Imply Physiological Impairment in Salmon - Collected and Generated Data

description: Data collected and generated as part of:<br>Zhang Y, Polinski MP, Morrison PR, Brauner CJ, Farrell APand Garver KA (2019) High-Load Reovirus Infections Do Not Imply Physiological Impairment in Salmon. Front. Physiol. 10:114. doi: 10.3389/fphys.2019.00114
DOI: 10.7284/123667
title: Meteorological Station data collected during research cruise AT37-01 using a Vaisala WXT520 instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/123668
title: Meteorological Station data collected during research cruise AT37-01 using a Vaisala WXT520 instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/123666
title: Multibeam Echosounder data collected during research cruise AT37-01 using a Kongsberg EM122 instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/123724
title: Radiometer data collected during research cruise AT37-01 using a Eppley RAD instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/123670
title: Singlebeam Echosounder data collected during research cruise AT37-01 using a Knudsen 320B/R instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7689161
title: Evolution of hybridogenetic lineages in Cataglyphis ants -Variant file in VCF format.

description: Several species of Cataglyphis desert ants have evolved a peculiar breeding system called social hybridogenesis. Under this system, two divergent genetic lineages coexist within a species. Workers develop from hybrid crosses between lineages, whereas queens and males are produced by parthenogenesis and carry only the maternal genome. To gain a better understanding of the evolutionary history of social hybridogenesis in Cataglyphis, we studied its phylogeographic distribution in the Iberian Peninsula using both SNP nuclear markers.
DOI: 10.7284/123671
title: Singlebeam Echosounder data collected during research cruise AT37-01 using a Knudsen 3260 instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7689110
title: Effect of folic acid supplementation on nerve conduction velocity in diabetic polyneuropathy patients

description: <b>Objectives</b>: In diabetic polyneuropathy (DPN) patients, the effect of folic acid and homocysteine has been related to components of nerve conduction velocity (NCV). The objective of this study was to determine the effect of folic acid supplementation on NCV in DPN patients. <b>Methods</b>: Patients were randomized to receive either 1 mg of folic acid (n = 40) or placebo (n = 40) for 16 weeks. Blood samples were collected to assess serum folic acid and homocysteine concentrations, and NCV was performed for assessment of diabetic neuropathy. <b>Results</b>: At 16 weeks, in the supplemented group, serum levels of folic acid (p <b>Conclusion</b>: Our data suggest that supplementation with 1 mg of folic acid for 16 weeks may be useful for enhancing NCV in DPN patients.
DOI: 10.7284/123726
title: Water Temperature data collected during research cruise AT37-01 using a Sea-Bird SBE-48 instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7689110.v1
title: Effect of folic acid supplementation on nerve conduction velocity in diabetic polyneuropathy patients

description: <b>Objectives</b>: In diabetic polyneuropathy (DPN) patients, the effect of folic acid and homocysteine has been related to components of nerve conduction velocity (NCV). The objective of this study was to determine the effect of folic acid supplementation on NCV in DPN patients. <b>Methods</b>: Patients were randomized to receive either 1 mg of folic acid (n = 40) or placebo (n = 40) for 16 weeks. Blood samples were collected to assess serum folic acid and homocysteine concentrations, and NCV was performed for assessment of diabetic neuropathy. <b>Results</b>: At 16 weeks, in the supplemented group, serum levels of folic acid (p <b>Conclusion</b>: Our data suggest that supplementation with 1 mg of folic acid for 16 weeks may be useful for enhancing NCV in DPN patients.
DOI: 10.7284/123725
title: TSG (Thermosalinograph) data collected during research cruise AT37-01 using a Sea-Bird SBE-45 instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7688966
title: Bias in Small-Sample Inference With Count-Data Models

description: Both Poisson and negative binomial regression can provide quasi-likelihood estimates for coefficients in exponential-mean models that are consistent in the presence of distributional misspecification. It has generally been recommended, however, that inference be carried out using asymptotically robust estimators for the parameter covariance matrix. As with linear models, such robust inference tends to lead to over-rejection of null hypotheses in small samples. Alternative methods for estimating coefficient estimator variances are considered. No one approach seems to remove all test bias, but the results do suggest that the use of the jackknife with Poisson regression tends to be least biased for inference.
DOI: 10.6084/m9.figshare.7688963
title: Plotting Likelihood-Ratio-Based Confidence Regions for Two-Parameter Univariate Probability Models

description: Plotting two-parameter confidence regions is nontrivial. Numerical methods often rely on a computationally expensive grid-like exploration of the parameter space. A recent advance reduces the two-dimensional problem to many one-dimensional problems employing a trigonometric transformation that assigns an angle ϕ from the maximum likelihood estimator, and an unknown radial distance to its confidence region boundary. This paradigm shift can improve computational runtime by orders of magnitude, but it is not robust. Specifically, parameters differing greatly in magnitude and/or challenging nonconvex confidence region shapes make the plot susceptible to inefficiencies and/or inaccuracies. This article improves the technique by (i) keeping confidence region boundary searches in the parameter space, (ii) selectively targeting confidence region boundary points in lieu of uniformly spaced ϕ angles from the maximum likelihood estimator and (iii) enabling access to regions otherwise unreachable due to multiple roots for select ϕ angles. Two heuristics are given for ϕ selection: an elliptic-inspired angle selection heuristic and an intelligent smoothing search heuristic. Finally, a jump-center heuristic permits plotting otherwise inaccessible multiroot regions. This article develops these heuristics for two-parameter likelihood-ratio-based confidence regions associated with univariate probability distributions, and introduces the R conf package, which automates the process and is publicly available via CRAN.
DOI: 10.7284/123680
title: Multiplexed data collected during research cruise AT37-02 using a WHOI Calliope instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7688957
title: Samples: Correlations between a heterogeneous mantle and multiple stages of crustal growth: a review of the Dun Mountain ophiolite, New Zealand

description: Whole-rock geochemistry samples used in this paper from other works.
DOI: 10.6084/m9.figshare.7688966.v1
title: Bias in Small-Sample Inference with Count-Data Models

description: Both Poisson and negative binomial regression can provide quasi-likelihood estimates for coefficients in exponential-mean models that are consistent in the presence of distributional misspecification. It has generally been recommended, however, that inference be carried out using asymptotically robust estimators for the parameter covariance matrix. As with linear models, such robust inference tends to lead to over-rejection of null hypotheses in small samples. Alternative methods for estimating coefficient estimator variances are considered. No one approach seems to remove all test bias, but the results do suggest that the use of the jackknife with Poisson regression tends to be least biased for inference.
DOI: 10.6084/m9.figshare.7688966.v2
title: Bias in Small-Sample Inference With Count-Data Models

description: Both Poisson and negative binomial regression can provide quasi-likelihood estimates for coefficients in exponential-mean models that are consistent in the presence of distributional misspecification. It has generally been recommended, however, that inference be carried out using asymptotically robust estimators for the parameter covariance matrix. As with linear models, such robust inference tends to lead to over-rejection of null hypotheses in small samples. Alternative methods for estimating coefficient estimator variances are considered. No one approach seems to remove all test bias, but the results do suggest that the use of the jackknife with Poisson regression tends to be least biased for inference.
DOI: 10.6084/m9.figshare.7688957.v1
title: Samples: Correlations between a heterogeneous mantle and multiple stages of crustal growth: a review of the Dun Mountain ophiolite, New Zealand

description: Whole-rock geochemistry samples used in this paper from other works.
DOI: 10.6084/m9.figshare.7688963.v2
title: Plotting Likelihood-Ratio-Based Confidence Regions for Two-Parameter Univariate Probability Models

description: Plotting two-parameter confidence regions is nontrivial. Numerical methods often rely on a computationally expensive grid-like exploration of the parameter space. A recent advance reduces the two-dimensional problem to many one-dimensional problems employing a trigonometric transformation that assigns an angle ϕ from the maximum likelihood estimator, and an unknown radial distance to its confidence region boundary. This paradigm shift can improve computational runtime by orders of magnitude, but it is not robust. Specifically, parameters differing greatly in magnitude and/or challenging nonconvex confidence region shapes make the plot susceptible to inefficiencies and/or inaccuracies. This article improves the technique by (i) keeping confidence region boundary searches in the parameter space, (ii) selectively targeting confidence region boundary points in lieu of uniformly spaced ϕ angles from the maximum likelihood estimator and (iii) enabling access to regions otherwise unreachable due to multiple roots for select ϕ angles. Two heuristics are given for ϕ selection: an elliptic-inspired angle selection heuristic and an intelligent smoothing search heuristic. Finally, a jump-center heuristic permits plotting otherwise inaccessible multiroot regions. This article develops these heuristics for two-parameter likelihood-ratio-based confidence regions associated with univariate probability distributions, and introduces the R conf package, which automates the process and is publicly available via CRAN.