cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5264086
title: dual-registered trial data 26/07/17

description: trials dual-registered on clinicaltrials.gov and EUCTR as of 26/07/17
DOI: 10.6084/m9.figshare.5264119.v2
title: Counteracting structural errors in ensemble forecast of influenza outbreaks (data sets)

description: This dataset contains the GFT ILI+ data, absolute humidity data and matlab codes that support the study in S. Pei, J. Shaman, Counteracting structural errors in ensemble forecast of influenza outbreaks. Nature Communications (2017).
DOI: 10.6084/m9.figshare.5264086.v1
title: dual-registered trial data 26/07/17

description: trials dual-registered on clinicaltrials.gov and EUCTR as of 26/07/17
DOI: 10.6084/m9.figshare.5264119.v1
title: Counteracting structural errors in ensemble forecast of influenza outbreaks

description: This dataset contains the GFT ILI+ data, absolute humidity data and matlab codes that support the study in S. Pei, J. Shaman, Counteracting structural errors in ensemble forecast of influenza outbreaks. Nature Communications (2017).
DOI: 10.6084/m9.figshare.5263900
title: Human salivary microbiome diversity in India

description: This dataset comprise of various DNA fasta files and tables for studying human salivary microbiome diversity in India
DOI: 10.6084/m9.figshare.5263885
title: Simulation Materials for ASPEN

description: This supplement contains the phylogenies and the simulated family sequences as a test set for phylogenetic reconstruction.
DOI: 10.6084/m9.figshare.5263900.v1
title: Human salivary microbiome diversity in India

description: This dataset comprise of various DNA fasta files and tables for studying human salivary microbiome diversity in India
DOI: 10.6084/m9.figshare.5263777
title: Detailed fluvial-geomorphologic mapping of wadeable streams: a proposal of universal map symbology

description: Detailed maps are important components of fluvial-geomorphological research, connecting several tools, namely field mapping of presented channel and floodplain forms and the assessment of fluvial processes and hydromorphological conditions of current river management. In this paper, we propose a universal map legend for the complex mapping of small stream channels in a detailed scale, which means including both the channel and adjacent floodplain segments. With the help of the symbology we are able to demonstrate both fluvial forms (i.e. individual features, grain size of bed sediments and fluvial deposits) and fluvial processes (i.e. contemporary trends in channels, character of lateral sediment inputs and flow characteristics) in a single map. In total, nearly 150 symbols were proposed and created as a combination of TrueType font and ArcGIS Style files. However, the principle can be used in various software. The work is accompanied by three map examples from the Nízký Jeseník Mts (the Stará Voda Stream) and the Moravskoslezské Beskydy Mts (the Lubina and Bystrý Streams).
DOI: 10.6084/m9.figshare.5263777.v1
title: Detailed fluvial-geomorphologic mapping of wadeable streams: a proposal of universal map symbology

description: Detailed maps are important components of fluvial-geomorphological research, connecting several tools, namely field mapping of presented channel and floodplain forms and the assessment of fluvial processes and hydromorphological conditions of current river management. In this paper, we propose a universal map legend for the complex mapping of small stream channels in a detailed scale, which means including both the channel and adjacent floodplain segments. With the help of the symbology we are able to demonstrate both fluvial forms (i.e. individual features, grain size of bed sediments and fluvial deposits) and fluvial processes (i.e. contemporary trends in channels, character of lateral sediment inputs and flow characteristics) in a single map. In total, nearly 150 symbols were proposed and created as a combination of TrueType font and ArcGIS Style files. However, the principle can be used in various software. The work is accompanied by three map examples from the Nízký Jeseník Mts (the Stará Voda Stream) and the Moravskoslezské Beskydy Mts (the Lubina and Bystrý Streams).
DOI: 10.6084/m9.figshare.5263585
title: Generate Panoramic Volumes

description: The visual reconstructions and program files and code for generating panoramic image volumes.
DOI: 10.6084/m9.figshare.5263594
title: Generate catchment volume

description: Code files for calculating catchment volumes using either hill climbs (with a threshold) or gradients descents. Requires transIDF volume data file.
DOI: 10.6084/m9.figshare.5263597
title: Processed Data transIDF & catchment volumes

description: The transIDF volume for three site, with up to three treatments and for reference images of difference heights.
DOI: 10.6084/m9.figshare.5263591
title: TransIDF calculation visualisation

description: The matlab code for calculating tranIDFs for a volume of panoramic images given either a comparison image or a reference image height (takes the centre-most reference image).
DOI: 10.6084/m9.figshare.5263594.v1
title: Generate catchment volume

description: Code files for calculating catchment volumes using either hill climbs (with a threshold) or gradients descents. Requires transIDF volume data file.
DOI: 10.6084/m9.figshare.5263597.v1
title: Processed Data transIDF & catchment volumes

description: The transIDF volume for three site, with up to three treatments and for reference images of difference heights.
DOI: 10.6084/m9.figshare.5263585.v1
title: Generate Panoramic Volumes

description: The visual reconstructions and program files and code for generating panoramic image volumes.
DOI: 10.6084/m9.figshare.5263591.v1
title: TransIDF calculation visualisation

description: The matlab code for calculating tranIDFs for a volume of panoramic images given either a comparison image or a reference image height (takes the centre-most reference image).
DOI: 10.6084/m9.figshare.5263576
title: A checklist of the genus <i>Tomosvaryella</i> Aczél (Diptera: Pipunculidae) from the Middle East with the description of a new species

description: A checklist of 39 species of the genus <i>Tomosvaryella</i> Aczél (Diptera, Pipunculidae) known from the Middle East is provided. A new species, <i>T. hamata</i> Majnon Jahromi & Kehlmaier sp. n. is described from southern Iran and diagnostic characters of male and female terminalia are illustrated. <i>Tomosvaryella dentiterebra</i> (Collin, 1949) is redescribed and male and female terminalia are illustrated for the first time. A phylogenetic maximum-likelihood analysis and uncorrected pairwise genetic distances of 18 out of 22 Iranian species of <i>Tomosvaryella</i> based on DNA barcodes of the mitochondrial COI gene are presented and also discussed. http://www.zoobank.org/urn:lsid:zoobank.org:pub:FF8C116D-0C92-431A-B52C-11F3711B6A62
DOI: 10.6084/m9.figshare.5263579
title: Spherical projection

description: The program and code for remapping a cubemap of 6 panoramic images that are 128x128 pixels with a fov of 95 degrees. Uses visual studio 2013, c++ code and requires openCV
DOI: 10.6084/m9.figshare.5263576.v1
title: A checklist of the genus <i>Tomosvaryella</i> Aczél (Diptera: Pipunculidae) from the Middle East with the description of a new species

description: A checklist of 39 species of the genus <i>Tomosvaryella</i> Aczél (Diptera, Pipunculidae) known from the Middle East is provided. A new species, <i>T. hamata</i> Majnon Jahromi & Kehlmaier sp. n. is described from southern Iran and diagnostic characters of male and female terminalia are illustrated. <i>Tomosvaryella dentiterebra</i> (Collin, 1949) is redescribed and male and female terminalia are illustrated for the first time. A phylogenetic maximum-likelihood analysis and uncorrected pairwise genetic distances of 18 out of 22 Iranian species of <i>Tomosvaryella</i> based on DNA barcodes of the mitochondrial COI gene are presented and also discussed. http://www.zoobank.org/urn:lsid:zoobank.org:pub:FF8C116D-0C92-431A-B52C-11F3711B6A62
DOI: 10.6084/m9.figshare.5263567
title: Is there a link between aging and microbiome diversity in exceptional mammalian longevity?

description: Microbiome reads from 52 samples<br>
DOI: 10.6084/m9.figshare.5263552
title: Bni.genewise.final.cds.fa

description: The coding sequences of 42,463 genes predicted from the ramie genome
DOI: 10.6084/m9.figshare.5263552.v1
title: Bni.genewise.final.cds.fa

description: The coding sequences of 42,463 genes predicted from the ramie genome
DOI: 10.6084/m9.figshare.5263555.v1
title: Structural insights into Rab21 GTPase activation mechanism by molecular dynamics simulations

description: Rab proteins belong to the family of monomeric GTPases which are involved in the cellular membrane trafficking. Rab21 protein exists in interchangeable GTP- and GDP-bound states. Rabs switch between two active and inactive conformations like other GTPases. The inactive form of Rab is bound to GDP while its active form is bounded with the GTP. Interexchange between active and inactive form is mediated by the GDP/GTP exchange factor (GEF) which catalyses the conversion from GDP-bound to GTP-bound form, thereby activating the Rab. While the GTP hydrolysis of Rabs is regulated by a GTPase-activating protein (GAP) which causes Rab inactivation. Here, we report the structural flexibility of the Rab21-GTP and Rab21-GDP complexes by docking and molecular dynamics (MD) simulations. Structural analysis of exchange mechanisms of the co-factors complexed with Rab21 reveals that Cys29, Thr33, His48, Gln78 and Lys133 are essentially important in the activation of proteins. Furthermore, a significant change in the orientation of the interacting co-factors, with slight variation in the free energy of binding was observed. Complexation of GEF with Rab21-GTP and Rab21-GDP reveal a flipping of the switchable residues. Finally, 50 ns MD simulations confirm that the GTP-bound Rab21 complex is thermodynamically more favoured than the corresponding GDP-bound complex. This study provides a detailed understanding of the structural elements involved in the conformational changes of Rab21.
DOI: 10.6084/m9.figshare.5263489
title: Mixed-nitrogen nutrition-mediated enhancement of drought tolerance of rice seedlings associated with photosynthesis, hormone balance and carbohydrate partitioning

description: Fig. 1 Leaf photosynthetic rate (<i>P<sub>n</sub></i>), stomatal conductance (g<sub>s</sub>), intercellular CO<sub>2</sub> concentration (<i>C<sub>i</sub></i>), and transpiration rate (<i>T<sub>r</sub></i>) of rice plants subjected to different N forms and water regimens. N, NP, A, AP, NA and NAP represent the nitrate (NO<sub>3</sub><sup>-</sup>), NO<sub>3</sub><sup>-</sup>+PEG 6000, ammonium (NH<sub>4</sub><sup>+</sup>), NH<sub>4</sub><sup>+</sup>+PEG 6000, mixture of NO<sub>3</sub><sup>-</sup> and NH<sub>4</sub><sup>+</sup> (NO<sub>3</sub><sup>-</sup>+NH<sub>4</sub><sup>+</sup>) and NO<sub>3</sub><sup>-</sup>+NH<sub>4</sub><sup>+</sup>+PEG 6000 treatments, respectively. The same occurs below. Fig. 2 Rice leaf Chl, total N, and Rubisco contents under the different N form and water conditions Fig. 3 Concentrations of ABA, IAA, and CTKs, and the IAA/CTK in the leaves and roots of rice seedlings subjected to different N forms and water regimens Fig. 4 Concentrations of soluble sugar and starch in the leaves and roots of rice seedlings subjected to different N forms and water regimens Fig. 5 Activities of sucrose-phosphate synthase (SPS) and sucrose synthase in the synthetic direction (SSs) in the leaves of rice seedlings subjected to different N forms and water regimens Fig. 6 Activities of acid invertase (InvA), neutral/alkaline invertase (InvN), and sucrose synthase in the cleavage direction (SSc) in the leaves of rice seedlings subjected to different N forms and water regimens Fig. 7 Activities of acid invertase (InvA), neutral/alkaline invertase (InvN), and sucrose synthase in the cleavage direction (SSc) in the roots of rice seedlings subjected to different N forms and water regimens.
DOI: 10.6084/m9.figshare.5263489.v1
title: Mixed-nitrogen nutrition-mediated enhancement of drought tolerance of rice seedlings associated with photosynthesis, hormone balance and carbohydrate partitioning

description: Fig. 1 Leaf photosynthetic rate (<i>P<sub>n</sub></i>), stomatal conductance (g<sub>s</sub>), intercellular CO<sub>2</sub> concentration (<i>C<sub>i</sub></i>), and transpiration rate (<i>T<sub>r</sub></i>) of rice plants subjected to different N forms and water regimens. N, NP, A, AP, NA and NAP represent the nitrate (NO<sub>3</sub><sup>-</sup>), NO<sub>3</sub><sup>-</sup>+PEG 6000, ammonium (NH<sub>4</sub><sup>+</sup>), NH<sub>4</sub><sup>+</sup>+PEG 6000, mixture of NO<sub>3</sub><sup>-</sup> and NH<sub>4</sub><sup>+</sup> (NO<sub>3</sub><sup>-</sup>+NH<sub>4</sub><sup>+</sup>) and NO<sub>3</sub><sup>-</sup>+NH<sub>4</sub><sup>+</sup>+PEG 6000 treatments, respectively. The same occurs below. Fig. 2 Rice leaf Chl, total N, and Rubisco contents under the different N form and water conditions Fig. 3 Concentrations of ABA, IAA, and CTKs, and the IAA/CTK in the leaves and roots of rice seedlings subjected to different N forms and water regimens Fig. 4 Concentrations of soluble sugar and starch in the leaves and roots of rice seedlings subjected to different N forms and water regimens Fig. 5 Activities of sucrose-phosphate synthase (SPS) and sucrose synthase in the synthetic direction (SSs) in the leaves of rice seedlings subjected to different N forms and water regimens Fig. 6 Activities of acid invertase (InvA), neutral/alkaline invertase (InvN), and sucrose synthase in the cleavage direction (SSc) in the leaves of rice seedlings subjected to different N forms and water regimens Fig. 7 Activities of acid invertase (InvA), neutral/alkaline invertase (InvN), and sucrose synthase in the cleavage direction (SSc) in the roots of rice seedlings subjected to different N forms and water regimens.
DOI: 10.6084/m9.figshare.5263462
title: Broad spectrum pesticide application alters natural enemy communities and may facilitate secondary pest outbreaks

description: Paper accepted at PeerJ. Datasets and code for analysis.<br>
DOI: 10.6084/m9.figshare.5263462.v1
title: Broad spectrum pesticide application alters natural enemy communities and may facilitate secondary pest outbreaks

description: Dataset for paper currently under review. Description to follow.<br>
DOI: 10.6084/m9.figshare.5263462.v3
title: Broad spectrum pesticide application alters natural enemy communities and may facilitate secondary pest outbreaks

description: Dataset for paper currently under review. Description to follow.<br>
DOI: 10.6084/m9.figshare.5263462.v2
title: Broad spectrum pesticide application alters natural enemy communities and may facilitate secondary pest outbreaks

description: Dataset for paper currently under review. Description to follow.<br>
DOI: 10.6084/m9.figshare.5263399
title: The Bedside/Clinical Evaluation of Swallowing Disorders» Review & Contemporary management of dysphagia – Seminar in Greek Language. [Abstract]

description: E.G.D.G. (European Study Group for Dysphagia and Globus Annual Meeting), Thessaloniki 2010. <br>
DOI: 10.6084/m9.figshare.5263396
title: Single therapy rehabilitation program for oral stage muscles, a Parkinson case report. [Abstract]

description: E.G.D.G. European Study Group for Dysphagia and Globus Annual Meeting, Thessaloniki 24 – 26 September 2010<br>
DOI: 10.6084/m9.figshare.5263399.v1
title: The Bedside/Clinical Evaluation of Swallowing Disorders» Review & Contemporary management of dysphagia – Seminar in Greek Language. [Abstract]

description: E.G.D.G. (European Study Group for Dysphagia and Globus Annual Meeting), Thessaloniki 2010. <br>
DOI: 10.6084/m9.figshare.5263396.v2
title: Single therapy rehabilitation program for oral stage muscles, a Parkinson case report. [Abstract]

description: E.G.D.G. European Study Group for Dysphagia and Globus Annual Meeting, Thessaloniki 24 – 26 September 2010<br>
DOI: 10.6084/m9.figshare.5263381
title: Monitoring physiological and psychological parameters at the end of the soccer season in elite female athletes

description: Spss files to analyze relationship between HRV and fatige in female soccer. and yo-yo test and cooper test
DOI: 10.6084/m9.figshare.5263381.v1
title: Monitoring physiological and psychological parameters at the end of the soccer season in elite female athletes

description: Spss files to analyze relationship between HRV and fatige in female soccer. and yo-yo test and cooper test
DOI: 10.6084/m9.figshare.5263252
title: Skeletal muscle regeneration involves macrophage-myoblast bonding

description: Regeneration in adult skeletal muscle relies on the activation, proliferation, and fusion of myogenic precursor cells (MPC), mostly resident satellite cells (SC). However, the regulatory mechanism during this process is still under evaluation, with the final aim to manipulate regeneration when the intrinsic mechanism is corrupted. Furthermore, intercellular connections during skeletal muscle regeneration have not been previously thoroughly documented. Our hypothesis was that a direct and close cellular interaction between SC/MPC and invading myeloid cells is a key step to control regeneration. We tested this hypothesis during different steps of skeletal muscle regeneration: (a) the recruitment of activated SC; (b) the differentiation of MPC; (c) myotubes growth, in a mouse model of crush injury. Samples harvested (3 and 5 days) post-injury were screened by light and confocal microscopy. Ultrastructural analysis was performed by conventional transmission electron microscopy (TEM) and scanning transmission electron microscopy (STEM) followed by 3D modeling of electron tomography (ET) data. This revealed a new type of interaction between macrophages and myogenic cells by direct heterocellular surface apposition over large areas and long linear distances. In the analyzed volume, regions spaced below 20 nm, within molecular range, represented 31% of the macrophage membrane surface and more than 27% of the myotube membrane. The constant interaction throughout all stages of myogenesis suggests a potential new type of regulatory mechanism for the myogenic process. Thus, deciphering structural and molecular mechanisms of SC-macrophage interaction following injury might open promising perspectives for improving muscle healing.
DOI: 10.6084/m9.figshare.5263243
title: Spatially Dependent Responses of a Large-River Fish Assemblage to Bank Stabilization and Side Channels

description: The alteration of rivers by anthropogenic bank stabilization to prevent the erosion of economically valuable lands and structures has become commonplace. However, such alteration has ambiguous consequences for fish assemblages, especially in large rivers. Because most large, temperate rivers have impoundments, it can be difficult to separate the influences of bank stabilization structures from those of main-stem impoundments, especially because both stabilization structures and impoundments can cause side-channel loss. Few large rivers are free flowing and retain extensive side channels, but the Yellowstone River (our study area) is one such river. We hypothesized that in this river (1) bank stabilization has changed fish assemblage structure by altering habitats, (2) side-channel availability has influenced fish assemblage structure by providing habitat heterogeneity, and (3) the influences of bank stabilization and side channels on fish assemblages were spatially scale dependent. We developed a spatially explicit framework to test these hypotheses. Fish assemblage structure varied with the extent of bank stabilization and the availability of side channels; however, not all assemblage subsets were influenced. Nevertheless, bank stabilization and side channels had different and sometimes opposite influences on the fish assemblage. The effects of side channels on fish were more consistent and widespread than those of bank stabilization; the catches of more fishes were positively correlated with side-channel availability than with the extent of bank stabilization. The influences of bank stabilization and side channels on the relative abundances of fish also varied, depending on species and river bend geomorphology. The variation in river morphology probably contributed to the assemblage differences between stabilized and reference river bends; stabilized alluvial pools were deeper than reference alluvial pools, but the depths of stabilized and reference bluff pools did not differ. The strengths of the relationships among fish assemblages, bank stabilization, and side channels were spatially scale dependent; optimum spatial scales ranged from less than 200 m to 3,200 m up- and downstream, suggesting that bank stabilization and side channels influenced fish assemblages across multiple spatial scales. Received October 7, 2016; accepted January 23, 2017 Published online July 31, 2017
DOI: 10.6084/m9.figshare.5263252.v1
title: Skeletal muscle regeneration involves macrophage-myoblast bonding

description: Regeneration in adult skeletal muscle relies on the activation, proliferation, and fusion of myogenic precursor cells (MPC), mostly resident satellite cells (SC). However, the regulatory mechanism during this process is still under evaluation, with the final aim to manipulate regeneration when the intrinsic mechanism is corrupted. Furthermore, intercellular connections during skeletal muscle regeneration have not been previously thoroughly documented. Our hypothesis was that a direct and close cellular interaction between SC/MPC and invading myeloid cells is a key step to control regeneration. We tested this hypothesis during different steps of skeletal muscle regeneration: (a) the recruitment of activated SC; (b) the differentiation of MPC; (c) myotubes growth, in a mouse model of crush injury. Samples harvested (3 and 5 days) post-injury were screened by light and confocal microscopy. Ultrastructural analysis was performed by conventional transmission electron microscopy (TEM) and scanning transmission electron microscopy (STEM) followed by 3D modeling of electron tomography (ET) data. This revealed a new type of interaction between macrophages and myogenic cells by direct heterocellular surface apposition over large areas and long linear distances. In the analyzed volume, regions spaced below 20 nm, within molecular range, represented 31% of the macrophage membrane surface and more than 27% of the myotube membrane. The constant interaction throughout all stages of myogenesis suggests a potential new type of regulatory mechanism for the myogenic process. Thus, deciphering structural and molecular mechanisms of SC-macrophage interaction following injury might open promising perspectives for improving muscle healing.