cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12072021.v1
title: Degradation & microplastics Dec2018 data to upload.xlsx

description: Dataset for: McCormick MI, Chivers DP, Ferrari MCO, Blandford MI, Nanninga GB, Richardson C, Fakan EP, and Allan BJM. Submitted. Microplastic exposure interacts with habitat degradation to affect behaviour and survival of juvenile fish in the field.I single Excel datafile<br>Abstract: Here we explore how the dual threat of habitat degradation and microplastic exposure may affect the behaviour and survival of coral reef fish in the field. Fish were caught prior to settlement and pulse fed polystyrene microplastic six times over four days, then placed in the field on live or dead-degraded coral patches. Exposure to microplastics or dead coral led fish to be bolder, more active and stray further from shelter compared to control fish. Effect sizes indicated that plastic exposure had a greater effect on behavior than degraded habitat and we found no evidence of synergistic effects. This pattern was also displayed in their survival in the field. Our results highlight that the reduction of microplastic in the environment will be a useful management strategy, since minimising microplastic intake by fishes will work concurrently with reef restoration strategies to enhance the resilience of coral reef communities<br><br><br>
DOI: 10.6084/m9.figshare.12071961
title: Dataset describing Titan's Flux Ropes

description: Tables of data describing the flux ropes found in Titan's ionosphere. Supporting 1 shows the time, date, Cassini revolution, Titan flyby, and other fitting parameters of each flux rope found. Supporting 2 shows the environment Titan was found in during each Titan flyby, along with how many flux ropes are found along each trajectory. More information can be found in the associated papers.
DOI: 10.6084/m9.figshare.12071961.v1
title: Dataset describing Titan's Flux Ropes

description: Tables of data describing the flux ropes found in Titan's ionosphere. Supporting 1 shows the time, date, Cassini revolution, Titan flyby, and other fitting parameters of each flux rope found. Supporting 2 shows the environment Titan was found in during each Titan flyby, along with how many flux ropes are found along each trajectory. More information can be found in the associated papers.
DOI: 10.6084/m9.figshare.12071580
title: Semi-Automated Ground Truth Labels Image Dataset

description: This dataset contains the 16 bit of the semi-automatically generated ground truth labels for the nuclei that were used both in training (Labelled as "Original") or inference (Labelled as "Biological" or "Technical) for the MRCNN and FPN2-WS networks
DOI: 10.6084/m9.figshare.12071520
title: Input GrayScale Image Dataset

description: This dataset contains the 16 bit images of DAPI stained nuclei used both in training (Labelled as "Original") or inference (Labelled as "Biological" or "Technical) for the MRCNN and FPN2-WS networks
DOI: 10.6084/m9.figshare.12071517
title: Mojave micronet

description: At four sites within the Mojave National Preserve, California, USA, micro-climate was monitored under desert shrub and cactus canopies and in the open. Hobo environmental loggers were used with Hobo pendants. The scale sampled was 1 m in each instance. There are a total of 196780 hourly observations. Sensors were deployed under the foundation plant canopy (sheltered from direct sunlight) or at adjacent, open paired-microsites within 1.5m of a focal shrub. Data were collected from 2013 and 2015 - 2019. Key ecological variables included microsite, location and foundation plant species. For sites with multiple species, 'rep' is within species. Temperatures listed are in degrees Celsius, relative humidity is in percent from 0 to 100 and light intensity is in lux.
DOI: 10.6084/m9.figshare.12071580.v2
title: Semi-Automated Ground Truth Labels Image Dataset

description: This dataset contains the 16 bit of the semi-automatically generated ground truth labels for the nuclei that were used both in training (Labelled as "Original") or inference (Labelled as "Biological" or "Technical) for the MRCNN and FPN2-WS networks
DOI: 10.6084/m9.figshare.12071580.v1
title: Ground Truth Labels Image Dataset

description: This dataset contains the 16 bit of the ground truth labels for the nuclei that were used both in training (Labelled as "Original") or inference (Labelled as "Biological" or "Technical) for the MRCNN and FPN2-WS networks
DOI: 10.6084/m9.figshare.12071505
title: A Simplified Formulation of Likelihood Ratio Confidence Intervals Using a Novel Property

description: <b>This article describes a novel property of likelihood ratio (LR) confidence intervals which is subsequently used to formulate an alternative approach for their calculation. It is shown that LR confidence limits can be defined as the minimum and maximum values of a parameter (or a function of parameters) that satisfy a set value of the log-likelihood. The proposed formulation allows straightforward implementation in end-user computing settings and it is particularly useful for the computation of intervals on noninvertible functions of model parameters. The main goal of the article is to expose this little-known property of LR confidence limits to the practitioner and research communities. Two case studies based on applications in product quality and reliability improvement are used for illustration. The first case study deals with interval estimation of the difference between the means of two lognormal populations. The second application concerns interval estimation for misclassification probabilities attributable to measurement error. Supplementary materials for this article are available online.</b>
DOI: 10.6084/m9.figshare.12071517.v2
title: Mojave micronet

description: At four sites within the Mojave National Preserve, California, USA, micro-climate was monitored under desert shrub and cactus canopies and in the open. Hobo environmental loggers were used with Hobo pendants. The scale sampled was 1 m in each instance. There are a total of 196780 hourly observations. Sensors were deployed under the foundation plant canopy (sheltered from direct sunlight) or at adjacent, open paired-microsites within 1.5m of a focal shrub. Data were collected from 2013 and 2015 - 2019. Key ecological variables included microsite, location and foundation plant species. For sites with multiple species, 'rep' is within species. Temperatures listed are in degrees Celsius, relative humidity is in percent from 0 to 100 and light intensity is in lux.
DOI: 10.6084/m9.figshare.12071505.v1
title: A Simplified Formulation of Likelihood Ratio Confidence Intervals Using a Novel Property

description: <b>This article describes a novel property of likelihood ratio (LR) confidence intervals which is subsequently used to formulate an alternative approach for their calculation. It is shown that LR confidence limits can be defined as the minimum and maximum values of a parameter (or a function of parameters) that satisfy a set value of the log-likelihood. The proposed formulation allows straightforward implementation in end-user computing settings and it is particularly useful for the computation of intervals on noninvertible functions of model parameters. The main goal of the article is to expose this little-known property of LR confidence limits to the practitioner and research communities. Two case studies based on applications in product quality and reliability improvement are used for illustration. The first case study deals with interval estimation of the difference between the means of two lognormal populations. The second application concerns interval estimation for misclassification probabilities attributable to measurement error. Supplementary materials for this article are available online.</b>
DOI: 10.6084/m9.figshare.12071517.v1
title: Mojave micronet

description: At four sites within the Mojave National Preserve, California, USA, micro-climate was monitored under desert shrub and cactus canopies and in the open. Hobo environmental loggers were used with Hobo pendants. The scale sampled was 1 m in each instance. There are a total of 196780 hourly observations. Sensors were deployed under the foundation plant canopy (sheltered from direct sunlight) or at adjacent, open paired-microsites within 1.5m of a focal shrub. Data were collected from 2013 and 2015 - 2019. Key ecological variables included microsite, location and foundation plant species. For sites with multiple species, 'rep' is within species. Temperatures listed are in degrees Celsius, relative humidity is in percent from 0 to 100 and light intensity is in lux.
DOI: 10.6084/m9.figshare.12071427
title: Nitric oxide mediates metabolic functions in the bivalve Arctica islandica under hypoxia

description: Short description of experiments and analyses: The formation of nitric oxide (NO) was examined in live hemocyte cells and gill filaments of the bivalve <i>Arctica islandica</i> at different partial pressures of oxygen (pO<sub>2</sub>; measurements conducted with ISO-NOP electrode & confocal microscopy). To establish whether cellular NO formation of <i>A. islandica</i> is catalyzed enzymatically, NO production was measured in the presence and absence of the nitric oxide synthase inhibitor (L-NAME). In a second set of experiments, the effect of chemically (by spremineNONOate) produced NO on gill respiration and cytochrome-c-oxidase activity was examined during phased reduction of pO<sub>2</sub> (16 kPa-2 kPa; measurements conducted with oxygen meter & spectrophotometer). Further, nitrite and nitrate contents were determined in the hemolymph of bivalves after 3.5 days of exposure to normoxic, hypoxic, and anoxic conditions (measurements conducted with microplate reader).<br><br>
DOI: 10.6084/m9.figshare.12071427.v1
title: Nitric oxide mediates metabolic functions in the bivalve Arctica islandica under hypoxia

description: Short description of experiments and analyses: The formation of nitric oxide (NO) was examined in live hemocyte cells and gill filaments of the bivalve <i>Arctica islandica</i> at different partial pressures of oxygen (pO<sub>2</sub>; measurements conducted with ISO-NOP electrode & confocal microscopy). To establish whether cellular NO formation of <i>A. islandica</i> is catalyzed enzymatically, NO production was measured in the presence and absence of the nitric oxide synthase inhibitor (L-NAME). In a second set of experiments, the effect of chemically (by spremineNONOate) produced NO on gill respiration and cytochrome-c-oxidase activity was examined during phased reduction of pO<sub>2</sub> (16 kPa-2 kPa; measurements conducted with oxygen meter & spectrophotometer). Further, nitrite and nitrate contents were determined in the hemolymph of bivalves after 3.5 days of exposure to normoxic, hypoxic, and anoxic conditions (measurements conducted with microplate reader).<br><br>
DOI: 10.6084/m9.figshare.12071358
title: Half of resources in threatened species conservation plans are allocated to research and monitoring

description: Data examining the resources allocated to research and monitoring versus action in threatened species budgets in New Zealand, the United States, and New South Wales, Australia.<br>Some columns have been deleted identifying species codes, in compliance with USFWS and others request.<br>RPN taxonomy, success, and benefit are also excluded.<br>
DOI: 10.6084/m9.figshare.12071226
title: Zhao_et_al_2020_SourceData.zip

description: Datasets used in Zhao et al. 2020 Nature Neuroscience paper
DOI: 10.6084/m9.figshare.12071223
title: Supplementary Data for Kogay et al (2020)

description: This dataset contains supplementary data for the bioinformatic analyses presented in:<br>Roman Kogay, Yuri I. Wolf, Eugene V. Koonin, and Olga Zhaxybayeva: Selection for energy savings during protein production drives the GC content and amino acid composition bias in gene transfer agents (under review.)<br><b>Dataset Contents:</b><br><b>MovieS1.mpg. </b>Visualization of the inferred positively selected sites in Sphingomonadales on a 3D structural model of the T5 bacteriophage major capsid protein. The hexamer structure is shown in green as a cartoon of secondary structure elements. Atoms of the amino acids that are inferred to be under the positive selection in Sphingomonadales are highlighted as pink spheres. The structure is rotated to facilitate visualization of the position of the positively selected amino acids.<br><br><b>212_alphaproteobacterial_genomes_list.xlsx:</b> Taxonomic names and RefSeq assembly accession numbers for 212 alphaproteobacterial genomes with GTA regions.<br><br><b>Detected_GTA_homologs.zip:</b> Amino acid sequences of GTA genes detected in alphaproteobacteria and viruses. The filename prefices (g1, …, g15) refer to the GTA gene name, while the filename suffices (_gta, _virus) designate to the gene origin. The sequences are in the FASTA format.<br><br><b>PAML_Branch_siteA_test_alns_trees.zip:</b> Codon alignments and phylogenetic trees that were used as an input for the branch site A model test in PAML. The alignments are in FASTA format and phylogenetic trees are in Newick format. The same phylogenetic trees were also used in the analyses of carbon utilization change in selected viruses. The filename prefices (g2, …, g15) refer to the GTA gene name.<br><br><b>reference_aln_tree.zip:</b> Concatenated alignment of 31 phylogenetic marker genes in 212 alphaproteobacterial genomes in FASTA format (reference_alignment.fasta), information about partitions and substitution models used in phylogenetic reconstruction (reference_partitions.txt), and the reference phylogenetic tree in Newick format (reference_tree.treefile).<br><br><b>ancestral_reconstructions.zip: </b>Alignments and phylogenetic trees that were used in the ancestral sequence reconstruction via FastML. The alignments are in FASTA format and phylogenetic trees are in Newick format. The filename prefices (g6, …, g15) refer to the GTA gene name.<br><br><b>net_carbon_change_bootstrapping.zip:</b> Alignments of selected viruses and their inferred GTA ancestors. These alignments were used to generate 1000 bootstrap replicates to assess significance of the net change in the carbon utilization in selected viral homologs. The alignments are in FASTA format. The filename prefices (g6, …, g15) refer to the RcGTA gene name. The calculated net changes in the carbon utilization across bootstrap replicates are in net_carbon_change_bootstrapping.xlsx file.<b><br><br><br></b><b><br></b>
DOI: 10.6084/m9.figshare.12071166
title: Data

description: <b>Variation</b><b> and </b><b>reactivity</b><b> of organic matter </b><b></b>
DOI: 10.6084/m9.figshare.12071166.v1
title: Data for Variation and reactivity of organic matter in the surface sediments of the Changjiang Estuary and its adjacent East China Sea.xls

description: <b>Variation</b><b> and </b><b>reactivity</b><b> of organic matter in </b><b>the surface </b><b>sediments of </b><b>the Changjiang Estuary and its adjacent East China Sea</b><b></b>
DOI: 10.6084/m9.figshare.12071223.v2
title: Supplementary Data for Kogay et al (2020)

description: This dataset contains supplementary data for the bioinformatic analyses presented in:<br>Roman Kogay, Yuri I. Wolf, Eugene V. Koonin, and Olga Zhaxybayeva: Selection for energy savings during protein production drives the GC content and amino acid composition bias in gene transfer agents (under review.)<br><b>Dataset Contents:</b><br><b>MovieS1.mpg. </b>Visualization of the inferred positively selected sites in Sphingomonadales on a 3D structural model of the T5 bacteriophage major capsid protein. The hexamer structure is shown in green as a cartoon of secondary structure elements. Atoms of the amino acids that are inferred to be under the positive selection in Sphingomonadales are highlighted as pink spheres. The structure is rotated to facilitate visualization of the position of the positively selected amino acids.<br><br><b>212_alphaproteobacterial_genomes_list.xlsx:</b> Taxonomic names and RefSeq assembly accession numbers for 212 alphaproteobacterial genomes with GTA regions.<br><br><b>Detected_GTA_homologs.zip:</b> Amino acid sequences of GTA genes detected in alphaproteobacteria and viruses. The filename prefices (g1, …, g15) refer to the GTA gene name, while the filename suffices (_gta, _virus) designate to the gene origin. The sequences are in the FASTA format.<br><br><b>PAML_Branch_siteA_test_alns_trees.zip:</b> Codon alignments and phylogenetic trees that were used as an input for the branch site A model test in PAML. The alignments are in FASTA format and phylogenetic trees are in Newick format. The same phylogenetic trees were also used in the analyses of carbon utilization change in selected viruses. The filename prefices (g2, …, g15) refer to the GTA gene name.<br><br><b>reference_aln_tree.zip:</b> Concatenated alignment of 31 phylogenetic marker genes in 212 alphaproteobacterial genomes in FASTA format (reference_alignment.fasta), information about partitions and substitution models used in phylogenetic reconstruction (reference_partitions.txt), and the reference phylogenetic tree in Newick format (reference_tree.treefile).<br><br><b>ancestral_reconstructions.zip: </b>Alignments and phylogenetic trees that were used in the ancestral sequence reconstruction via FastML. The alignments are in FASTA format and phylogenetic trees are in Newick format. The filename prefices (g6, …, g15) refer to the GTA gene name.<br><br><b>net_carbon_change_bootstrapping.zip:</b> Alignments of selected viruses and their inferred GTA ancestors. These alignments were used to generate 1000 bootstrap replicates to assess significance of the net change in the carbon utilization in selected viral homologs. The alignments are in FASTA format. The filename prefices (g6, …, g15) refer to the RcGTA gene name. The calculated net changes in the carbon utilization across bootstrap replicates are in net_carbon_change_bootstrapping.xlsx file.<b><br><br><br></b><b><br></b>
DOI: 10.6084/m9.figshare.12068379
title: Trust in the smart home-dataset

description: Dataset from a nationally representative sample of 2,101 participants in the United Kingdom.<br> Participants were recruited through the online market research sample aggregator Qualtrics . The quotas for the sample were based on 2016 European statistical datasets for population by age and gender, and educational attainment level. Age values: &lt;17, 18-24, 25-34, 35-49, 50-64, 65+ Gender values: Male, Female Education values: ISCED 0-2 includes Pre-primary education, Primary Education and GCSE/Vocational GCSE or equivalent (incl. O-levels). ISCED 3-4 includes A-level/Vocational A-level or equivalent (incl. AS-level), Higher Diplomas below degree level/as gateways to degree. ISCED 5-6 includes Undergraduate degree and Postgraduate degree (Master and PhD). Our questionnaire contained a total of 18 items relating to acceptability of Internet of Things, including eight questions which related to trust. Questions E5, E6, E7, S16 apply to IoT experienced users only, n=1422 The rest of the questions apply to the whole sample, include both experienced and inexperienced IoT users, n=2101 <b></b><i></i><sub></sub><sup></sup><br>
DOI: 10.6084/m9.figshare.12068379.v1
title: Trust in the smart home: findings from a nationally representative survey in the UK (dataset)

description: Dataset from a nationally representative sample of 2,101 participants in the United Kingdom.<br> Participants were recruited through the online market research sample aggregator Qualtrics . The quotas for the sample were based on 2016 European statistical datasets for population by age and gender, and educational attainment level. Age values: &lt;17, 18-24, 25-34, 35-49, 50-64, 65+ Gender values: Male, Female Education values: ISCED 0-2 includes Pre-primary education, Primary Education and GCSE/Vocational GCSE or equivalent (incl. O-levels). ISCED 3-4 includes A-level/Vocational A-level or equivalent (incl. AS-level), Higher Diplomas below degree level/as gateways to degree. ISCED 5-6 includes Undergraduate degree and Postgraduate degree (Master and PhD). Our questionnaire contained a total of 18 items relating to acceptability of Internet of Things, including eight questions which related to trust. Questions E5, E6, E7, S16 apply to IoT experienced users only, n=1422 The rest of the questions apply to the whole sample, include both experienced and inexperienced IoT users, n=2101 <b></b><i></i><sub></sub><sup></sup><br>
DOI: 10.6084/m9.figshare.12067350
title: exampleDataP3J10000.Rdata

description: example data file<br>
DOI: 10.6084/m9.figshare.12067350.v1
title: exampleDataP3J10000.Rdata

description: example data file<br>
DOI: 10.6084/m9.figshare.12067401
title: Code and summary results for: Analysis of electronic health records reveals medication-related interference on point-of-care urine drug screening assays

description: Zip file contains parameter and metadata files, sql and R scripts, and results in the form of figures and csv files.
DOI: 10.6084/m9.figshare.12067233
title: Code and summary results for: A computational approach to identify interfering medications on urine drug screening assays without data from confirmatory testing

description: Zip file contains parameter and metadata files, data from spiking experiments, sql and R scripts, and results in the form of figures and csv files.
DOI: 10.6084/m9.figshare.12067233.v2
title: Code and summary results for: A computational approach to identify interfering medications on urine drug screening assays without data from confirmatory testing

description: Zip file contains parameter and metadata files, data from spiking experiments, sql and R scripts, and results in the form of figures and csv files.
DOI: 10.6084/m9.figshare.12067332.v1
title: Data.zip

description: This dataset contains all the inference results for 83 runs of training experiments on the FPN2-WS and MRCNN nuclear segmentation models
DOI: 10.6084/m9.figshare.12067233.v1
title: Code and summary results for: A computational approach to identify interfering medications on urine drug screening assays without data from confirmatory testing

description: Zip file contains parameter and metadata files, data from spiking experiments, sql and R scripts, and results in the form of figures and csv files.
DOI: 10.6084/m9.figshare.12066882
title: Table S5 from Behavioural traits modulate the use of heterospecific social information for nest site selection: experimental evidence from a wild bird population

description: Dataset used for analyses
DOI: 10.6084/m9.figshare.12066882.v1
title: Table S5 from Behavioural traits modulate the use of heterospecific social information for nest site selection: experimental evidence from a wild bird population

description: Dataset used for analyses
DOI: 10.6084/m9.figshare.12066879
title: ESM 2 from Behavioural traits modulate the use of heterospecific social information for nest site selection: experimental evidence from a wild bird population

description: R code used for the statistical analyses
DOI: 10.6084/m9.figshare.12067332.v2
title: DL_Models_Inference_Results

description: This dataset contains all the inference results for 83 runs of training experiments on the FPN2-WS and MRCNN nuclear segmentation models
DOI: 10.6084/m9.figshare.12066873
title: Table S1 from Behavioural traits modulate the use of heterospecific social information for nest site selection: experimental evidence from a wild bird population

description: Description of the 24 studies reporting a link between personality and social information use
DOI: 10.6084/m9.figshare.12066879.v1
title: ESM 2 from Behavioural traits modulate the use of heterospecific social information for nest site selection: experimental evidence from a wild bird population

description: R code used for the statistical analyses
DOI: 10.6084/m9.figshare.12066873.v1
title: Table S1 from Behavioural traits modulate the use of heterospecific social information for nest site selection: experimental evidence from a wild bird population

description: Description of the 24 studies reporting a link between personality and social information use