cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.23931632
title: Molecular characterization of the <i>HMTp210</i> gene of <i>Avibacterium paragallinarum</i> and the proposition of a new genotyping method as alternative for classical serotyping

description: <i>Avibacterium paragallinarum (A. paragallinarum)</i> is the aetiological agent of infectious coryza (IC) in chickens and characterized by acute respiratory distress and severe drop in egg production. Vaccination is important in the control of IC outbreaks and the efficacy of vaccination is dependent on <i>A. paragallinarum</i> serovars included in the vaccine. Classical serotyping of <i>A. paragallinarum</i> is laborious and hampered by poor availability of antigens and antisera. The haemagglutinin, important in classical serotyping, is encoded by the <i>HMTp210</i> gene. <i>HMTp210</i> gene analysis has been shown to have potential as alternative to classical serotyping. The aim of the present study was to further investigate the potential of sequence analyses of partial region 1 of the <i>HMTp210</i> gene, the <i>HMTp210</i> hypervariable region and the concatenated sequences of both fragments. For this analysis, 123 <i>HMTp210</i> gene sequences (field isolates, <i>A. paragallinarum</i> serovar reference strains and vaccine strains) were included. Evaluation of serovar references and vaccine strains revealed a need for critical evaluation, especially within Page serovar B and C. Phylogenetic analysis of <i>HMTp210</i> region 1 resulted in a separation of Page serovar A, B and C strains. Analysis of the <i>HMTp210</i> HVR alone was not sufficient to discriminate all nine different Kume serovar references. The concatenated sequences of <i>HMTp210</i> region 1 and <i>HMTp210</i> HVR resulted in 14 clusters with a high correlation with Page serovar and with the nine currently known Kume serovars and is therefore proposed as a novel genotyping method that could be used as an alternative for classical serotyping of <i>A. paragallinarum</i>.
DOI: 10.6084/m9.figshare.23931632.v1
title: Molecular characterization of the <i>HMTp210</i> gene of <i>Avibacterium paragallinarum</i> and the proposition of a new genotyping method as alternative for classical serotyping

description: <i>Avibacterium paragallinarum (A. paragallinarum)</i> is the aetiological agent of infectious coryza (IC) in chickens and characterized by acute respiratory distress and severe drop in egg production. Vaccination is important in the control of IC outbreaks and the efficacy of vaccination is dependent on <i>A. paragallinarum</i> serovars included in the vaccine. Classical serotyping of <i>A. paragallinarum</i> is laborious and hampered by poor availability of antigens and antisera. The haemagglutinin, important in classical serotyping, is encoded by the <i>HMTp210</i> gene. <i>HMTp210</i> gene analysis has been shown to have potential as alternative to classical serotyping. The aim of the present study was to further investigate the potential of sequence analyses of partial region 1 of the <i>HMTp210</i> gene, the <i>HMTp210</i> hypervariable region and the concatenated sequences of both fragments. For this analysis, 123 <i>HMTp210</i> gene sequences (field isolates, <i>A. paragallinarum</i> serovar reference strains and vaccine strains) were included. Evaluation of serovar references and vaccine strains revealed a need for critical evaluation, especially within Page serovar B and C. Phylogenetic analysis of <i>HMTp210</i> region 1 resulted in a separation of Page serovar A, B and C strains. Analysis of the <i>HMTp210</i> HVR alone was not sufficient to discriminate all nine different Kume serovar references. The concatenated sequences of <i>HMTp210</i> region 1 and <i>HMTp210</i> HVR resulted in 14 clusters with a high correlation with Page serovar and with the nine currently known Kume serovars and is therefore proposed as a novel genotyping method that could be used as an alternative for classical serotyping of <i>A. paragallinarum</i>.
DOI: 10.6084/m9.figshare.24018594
title: Coefficients for KYNEBBRR model

description: The tables attached contain coefficients A', B', C', D' for polynomial approximations of polarization degree versus energy computed for X-ray single-temperature blackbody radiation passing through a passive constant-density slab. The models were originally computed with TITAN (Dumont et al., 2003) and STOKES (Goosmann and Gaskell, 2007) codes. The details of the modelling with full description of these tables are given in the doctoral thesis Podgorný (2023) and in less detail in Ratheesh et al. (2023). The method and origins date back to Taverna et al. (2021). Once computed in high energy resolution in the limit of high ionization, the polarization degree versus energy was smoothed at 1-9 keV range and at 9-20 keV range, using y = A'x^3 + B'x^2 + C'x + D'.Usage:First unzip the main file. Then each table in the main directory contains in the 1st column a value of cosine of the emission angle measured from the disc normal. In the 2nd to 5th column values of the coefficients A', B', C', D' obtained by the Python numpy.polyfit routine in the 1-9 keV range. The same for 9-20 keV range is in the 6th to 9th columns. Each table is called "n18", according to the n<sub>H</sub> = 10<sup>18</sup> cm<sup>-3</sup> density used and then with "xiBB", suggesting the blackbody normalization of the illumination in photoionization equlibrium. Then the number after "T" in the name of each file sets the single-temperature value of the blackbody in keV, i.e. 0.50 keV, 0.80 keV, 1.15 keV, or 1.40 keV. Last number in the file name after "tau" is the total Thomson optical depth, given by the slab height in STOKES, i.e. 0.2, 0.4, 0.67, 1, 1.3, 1.5, 2, 3, 5, 7, or 10 values. As such, the tables are ready to use inside the KYNEBBRR routine, which integrates them accross the accretion disc, taking into account all relativistic effects. This routine is part of the KY codes (Dovčiak et al. 2004, 2011, Taverna et al. 2020, Mikušincová et al. 2023), which are suitable for fitting with XSPEC (Arnaud, 1996).
DOI: 10.5281/zenodo.7761447
title: DFT, potential optimization and LAMMPS MD data for BaZrO3

description: Data generated as part of the Automated Potential Development (APD) workflow applied to BaZrO3. Includes: CASTEP DFT data, including the original molecular dynamics (MD) and also query-by-committee single-shot calculations; potential optimization jobs using MEAMfit; and LAMMPS MD simulations.
DOI: 10.5281/zenodo.7761446
title: DFT, potential optimization and LAMMPS MD data for BaZrO3

description: Data generated as part of the Automated Potential Development (APD) workflow applied to BaZrO3. Includes: CASTEP DFT data, including the original molecular dynamics (MD) and also query-by-committee single-shot calculations; potential optimization jobs using MEAMfit; and LAMMPS MD simulations.
DOI: 10.35077/age-hub
title: NC82_brain: Confocal z-stack of whole fly brain, stained using NC82 antibody

description: Confocal z-stacks (.tiff stacks) transgenic driver lines that express in mechanosensory neurons innervating specific bristle populations on the Drosophila melanogaster head. The bristle mechanosensory neurons (BMNs) were labeled by expressing mCD8::GFP under control of the UAS or LexAop promotors, and then stained using anti-GFP (green channel) and NC82 antibodies (red channel). The processed images of the BMNs are published in Figure 3 and Figure 3 – figure supplement 1 of the manuscript “Somatotopic organization among parallel sensory pathways that promote a grooming sequence in Drosophila (https://doi.org/10.1101/2023.02.11.528119)”. The confocal stacks used to produce these images are organized based on the driver line used in each figure panel.
description: A full protocol describing this work is available in the associated manuscript at manuscript “Somatotopic organization among parallel sensory pathways that promote a grooming sequence in Drosophila (https://doi.org/10.1101/2023.02.11.528119)”.
description: DATASET METADATA: title:'NC82_brain: Confocal z-stack of whole fly brain, stained using NC82 antibody', GeneralModality:'other', Technique:'other', Other:'GAL4 and LexA expression' SPECIMEN METADATA: LocalID:'NC82_brain', Species:'Fruit fly', NCBITaxonomy:'NCBI:txid7227', Age:'5 to 8', Ageunit:'Days', Sex:'Male', Genotype:'w; 28D07_AD (attP40)/+; VT050279_DBD (attP2)/20XUAS-IVS- mCD8::GFP (attP2)', OrganName:'Brain', SampleLocalID:'C1-20201007_VT050279_DBD_28D07_AD_20x_GFP_brain_3_template', Locations:'Subesophageal zone (SEZ)' INSTRUMENT METADATA: MicroscopeType:'Confocal', MicroscopeManufacturerAndModel:'Zeiss LSM 800 Axio Imager.Z2', ObjectiveName:'Zeiss 20x objective (Plan-Apochromat 20x/0.8)', ObjectiveNA:'0.8', ObjectiveMagnification:'20x' IMAGE METADATA: xAxis:'left-to-right', yAxis:'left-to-right', zAxis:'left-to-right', Number:'1,2,red,green', displayColor:'(1.0, 0.0, 0.0),(0.0, 1.0, 0.0)', stepSizeX:'0.6239', stepSizeY:'0.6239'
DOI: 10.6084/m9.figshare.24018735
title: DATA - Marco Polo Study.xlsx

description: This file includes survey data used to examine differences in perceptions of instructor social presence and classroom community between graduate students in online counseling programs who communicated with course instructors and peers via asynchronous video messages and a comparison group whose members communicated with instructors and peers via email. Data were collected via an electronic survey that investigators emailed to students through Qualtrics. The survey included three sections. Section 1 comprised 12 items that were used to collect students’ demographic information and information about their technology habits. Arbaugh et al.’s (2008) Community of Inquiry Survey and Pollard et al.’s (2014) Instructor Social Presence Survey provided the 10 items in Section 2 that addressed the construct, <i>instructor social presence</i>, and Rovai’s (2002) Classroom Community Scale provided the nine items in Section 3 that addressed the construct, <i>classroom community.</i> Students rated each item in Sections 2 and 3 using a Likert scale to indicate their degree of agreement.
DOI: 10.35077/age-hug
title: R52A06_GAL4_brain: Whole-brain confocal imaging of fly driver line R52A06_GAL4 expressing mCD8::GFP, stained using GFP (green channel) and NC82 (red channel) antibodies

description: Confocal z-stacks (.tiff stacks) transgenic driver lines that express in mechanosensory neurons innervating specific bristle populations on the Drosophila melanogaster head. The bristle mechanosensory neurons (BMNs) were labeled by expressing mCD8::GFP under control of the UAS or LexAop promotors, and then stained using anti-GFP (green channel) and NC82 antibodies (red channel). The processed images of the BMNs are published in Figure 3 and Figure 3 – figure supplement 1 of the manuscript “Somatotopic organization among parallel sensory pathways that promote a grooming sequence in Drosophila (https://doi.org/10.1101/2023.02.11.528119)”. The confocal stacks used to produce these images are organized based on the driver line used in each figure panel.
description: A full protocol describing this work is available in the associated manuscript at manuscript “Somatotopic organization among parallel sensory pathways that promote a grooming sequence in Drosophila (https://doi.org/10.1101/2023.02.11.528119)”.
description: DATASET METADATA: title:'R52A06_GAL4_brain: Whole-brain confocal imaging of fly driver line R52A06_GAL4 expressing mCD8::GFP, stained using GFP (green channel) and NC82 (red channel) antibodies', GeneralModality:'other', Technique:'other', Other:'GAL4 and LexA expression' SPECIMEN METADATA: LocalID:'R52A06_GAL4_brain', Species:'Fruit fly', NCBITaxonomy:'NCBI:txid7227', Age:'5 to 8', Ageunit:'Days', Sex:'Male', Genotype:'w;; R52A06_GAL4 (attP2)/20XUAS-IVS- mCD8::GFP (attP2)', OrganName:'Brain', SampleLocalID:'20210919_52A06_GAL4_20x_GFP_40x_brain_3', Locations:'Subesophageal zone (SEZ)' INSTRUMENT METADATA: MicroscopeType:'Confocal', MicroscopeManufacturerAndModel:'Zeiss LSM 800 Axio Imager.Z2', ObjectiveName:'Zeiss 20x objective (Plan-Apochromat 20x/0.8)', ObjectiveNA:'0.8', ObjectiveMagnification:'20x' IMAGE METADATA: xAxis:'left-to-right', yAxis:'left-to-right', zAxis:'left-to-right', Number:'1,2,red,green', displayColor:'(1.0, 0.0, 0.0),(0.0, 1.0, 0.0)', stepSizeX:'0.6239', stepSizeY:'0.6239'
DOI: 10.6084/m9.figshare.24018564
title: Genes and genetic loci involved in regulation of plant architecture

description: A list of genes / alleles described in the literature to regulate plant architecture. The genes have been classified into playing a role in Root System Architecture (Tab 1), Shoot System Architecture (Tab 2) or Leaf System Architecture (Tab 3). The individual genes are highlighted with red or blue for their role in promoting or repressing of specific aspect of plant architecture. The source literature used for specific gene description is listed in the "Reference" column. We do recognize that the presented list is not exhaustive, but propose that this forms a starting point for further expansions of genes and their functions in regulating plant architecture under non-stress as well as environmental stress conditions.
DOI: 10.6084/m9.figshare.24018564.v1
title: Genes and genetic loci involved in regulation of plant architecture

description: A list of genes / alleles described in the literature to regulate plant architecture. The genes have been classified into playing a role in Root System Architecture (Tab 1), Shoot System Architecture (Tab 2) or Leaf System Architecture (Tab 3). The individual genes are highlighted with red or blue for their role in promoting or repressing of specific aspect of plant architecture. The source literature used for specific gene description is listed in the "Reference" column. We do recognize that the presented list is not exhaustive, but propose that this forms a starting point for further expansions of genes and their functions in regulating plant architecture under non-stress as well as environmental stress conditions.
DOI: 10.5281/zenodo.6617149
title: TrainRuns.jl: an Open-Source Tool for Running Time Estimation - Supplement Data

description: This additional data contains the initial data and the calculated results for comparing FBS and TrainRuns.jl. <strong>File description</strong> freight.yaml: input parameters for the train running_path.yaml: input parameters for the path FBS.csv: export of calculation from FBS TrainRuns.csv: export of calculation from TrainRun.jl converted in FBS units diff.csv: the calculated difference between FBS.csv and TrainRuns.csv running_path.csv: converted running_path.yaml for displaying comparison.tex: LaTeX code for the graph in comparison.pdf <strong>Sources</strong> The calculations in FBS were done with the file 'Ostsachsen_V220.railml'. FBS needs a commercial license, which can be purchased. License for 'Ostsachsen_V220.railml' is Attribution-NonCommercial-NoDerivs 3.0 Unported (CC BY-NC-ND 3.0).<br> The file 'Ostsachsen_V220.railml' can be found at:<br> https://www.railml.org/en/user/exampledata.html (last accessed 2022-06-06 with login) -&gt; "Real world railway examples from professional tools" -&gt; "East Saxony railway network by FBS" -&gt; "Ostsachsen_V220.railml" Other sources are mentioned in the files.
DOI: 10.5281/zenodo.6617148
title: TrainRuns.jl: an Open-Source Tool for Running Time Estimation - Supplement Data

description: This additional data contains the initial data and the calculated results for comparing FBS and TrainRuns.jl. <strong>File description</strong> <em>local.yaml</em>: input parameters for the local train <em>freight.yaml</em>: input parameters for the freight train <em>running_path.yaml</em>: input parameters for the path <em>freight_FBS.csv</em>: export of calculation from FBS for the freight train <em>freight_TrainRuns.csv</em>: export of calculation from TrainRun.jl converted in FBS units for the freight train <em>freight_diff.csv</em>: the calculated difference between FBS.csv and TrainRuns.csv for the freight train <em>local_FBS.csv</em>: export of calculation from FBS for the local train <em>local_TrainRuns.csv</em>: export of calculation from TrainRun.jl converted in FBS units for the local train <em>local_diff.csv</em>: the calculated difference between FBS.csv and TrainRuns.csv for the local train <em>running_path.csv</em>: converted running_path.yaml for displaying <em>comparison.tex</em>: LaTeX code for the graph in comparison.pdf <strong>Sources</strong> The calculations in FBS were done with the file 'Ostsachsen_V220.railml'. FBS needs a commercial license, which can be purchased. License for 'Ostsachsen_V220.railml' is Attribution-NonCommercial-NoDerivs 3.0 Unported (CC BY-NC-ND 3.0).<br> The file 'Ostsachsen_V220.railml' can be found at:<br> https://www.railml.org/en/user/exampledata.html (last accessed 2022-06-06 with login) -&gt; "Real world railway examples from professional tools" -&gt; "East Saxony railway network by FBS" -&gt; "Ostsachsen_V220.railml" Other sources are mentioned in the files.
DOI: 10.5281/zenodo.6842604
title: TrainRuns.jl: an Open-Source Tool for Running Time Estimation - Supplement Data

description: This additional data contains the initial data and the calculated results for comparing FBS and TrainRuns.jl. <strong>File description</strong> <em>local.yaml</em>: input parameters for the local train <em>freight.yaml</em>: input parameters for the freight train <em>running_path.yaml</em>: input parameters for the path <em>freight_FBS.csv</em>: export of calculation from FBS for the freight train <em>freight_TrainRuns.csv</em>: export of calculation from TrainRun.jl converted in FBS units for the freight train <em>freight_diff.csv</em>: the calculated difference between FBS.csv and TrainRuns.csv for the freight train <em>local_FBS.csv</em>: export of calculation from FBS for the local train <em>local_TrainRuns.csv</em>: export of calculation from TrainRun.jl converted in FBS units for the local train <em>local_diff.csv</em>: the calculated difference between FBS.csv and TrainRuns.csv for the local train <em>running_path.csv</em>: converted running_path.yaml for displaying <em>comparison.tex</em>: LaTeX code for the graph in comparison.pdf <strong>Sources</strong> The calculations in FBS were done with the file 'Ostsachsen_V220.railml'. FBS needs a commercial license, which can be purchased. License for 'Ostsachsen_V220.railml' is Attribution-NonCommercial-NoDerivs 3.0 Unported (CC BY-NC-ND 3.0).<br> The file 'Ostsachsen_V220.railml' can be found at:<br> https://www.railml.org/en/user/exampledata.html (last accessed 2022-06-06 with login) -&gt; "Real world railway examples from professional tools" -&gt; "East Saxony railway network by FBS" -&gt; "Ostsachsen_V220.railml" Other sources are mentioned in the files.
DOI: 10.5281/zenodo.6836598
title: Global trends in migratory fish studies using biogeochemical tags

description: Migratory fishes are widespread and critical for the functioning of distantly interconnected ecosystems, and they are gravely imperilled by global river fragmentation. However, the lack of a comprehensive review of migratory fish studies using the most accessible natural biogeochemical tags has hampered the improvement of research representativeness and gap identification and thus fish conservation and associated ecosystem management. Here, we conducted a global synthesis on this topic. A total of 904 studies were included after screening 19,642 documents, and 10,824 extracted sampling points successfully revealed distribution imbalances in multiple dimensions, such as ecosystems (inland 48% vs. marine 52%), major fishing areas (primarily in the Northern Hemisphere), migration categories, taxonomic groups, biogeochemical tags, and tissues. Less than one fifth of migratory fishes have been studied, usually using otoliths and point/line scanning. Bulk element: Ca ratios were examined more frequently than isotopic ratios (64% vs. 36%), led by Sr/Ca, Mg/Ca, Ba/Ca and 87Sr/86Sr, δ13C, δ18O, respectively. The mean values for these elements detected in fish otolith cores were significantly different across migratory categories, but all showed considerable variation. The findings indicate that migratory fishes are likely to have more diverse and complex life histories than commonly thought. The identified knowledge gaps should therefore be filled to promote the application of biogeochemical tags and the conservation and management of migratory fishes.
description: The datasets and R scripts that support the findings of this study are openly available at https://github.com/Otoliths/FishBT. Additionally, we have developed an online database (named FishBT, Fish Biogeochemical Tags; https://fish-ecology.shinyapps.io/fishbt) providing detailed, integrated biogeochemical data on migratory fish species all around the world. The database is an open, updatable and free platform for data query and visualization tools on migratory fish studies using biogeochemical tags.
DOI: 10.5281/zenodo.7277802
title: MFishBT: A global database of biogeochemical tags in migratory fish

description: Humans have long been fascinated by the mysteries surrounding fish migrations, and addressing these puzzling migrations requires large datasets. Biogeochemical tags, including bulk elements and isotopic ratios, are the most accessible biomarkers for powerfully tracking fish migrations. However, standardized datasets on biogeochemical tags for migratory fish research are rarely available, which limits our understanding of the evolutionary origins, driving mechanisms, distribution, migration timing and routes of migratory fishes, as well as to develop conservation strategies and inform management actions. Here, we present MFishBT, a living, open and global database of Migratory Fish’sBiogeochemical Tags. Currently (November 2022), it contains biogeochemical records from 903 studies. Among them, 60% of the studies used element-to-calcium (E/Ca) ratios, 27% used isotopic ratios, and 13% used both tags. The database covers 10,665 field sampling sites (inland 49% vs. marine 51%) around the global major fishing areas and 346 migratory fishes belonging to 31 orders/suborders and 99 families. Seventy-five trace elements and 10 isotopes were detected across various biomineral archives of fish (e.g., otolith, scale, eye lenses and vertebra). E/Ca ratios were examined more frequently than isotopic ratios (64% vs. 36%), led by Sr/Ca, Mg/Ca, Ba/Ca and <sup>87</sup>Sr/<sup>86</sup>Sr, δ<sup>13</sup>C, δ<sup>18</sup>O, respectively. The MFishBT comprises 5,494 geo-referenced records with biogeochemical element data detected in the edges of archived tissues. This is the most comprehensive open global database on biogeochemical tags in migratory fish to date, which can serve a variety of needs in scientific research, conservation and management of migratory fish. We encourage researchers to add more datasets to this database in the future. This database is released for non-commercial use only. There are no copyright restrictions, and please cite this paper when using these data, or a subset of these data, for publication.
description: MFishBT(https://fish-ecology.shinyapps.io/mfishbt)