cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5379280
title: I-TASSER Gateway for Protein Structure Prediction and Structure-based Function Annotation

description: I-TASSER (Iterative Threading ASSembly Refinement) is a composite pipeline for protein structure prediction and structure-based protein function annotation. Starting from sequence of a target protein, structure templates are identified by threading from the PDB. Full-length target structure is then constructed by fragment re-assembly simulation. The final structure model is further compared to entries in BioLiP structure-function database for biological function interference. Recently, I-TASSER is implemented as an XSEDE science gateway, which helped &gt;14,000 users to decipher structure and function of &gt;38,000 proteins in the last 12 months. The I-TASSER gateway is available at http://zhanglab.ccmb.med.umich.edu/I-TASSER/.
DOI: 10.6084/m9.figshare.24085707
title: Raw seismic reflection data from Three Sisters Rifting zone, Bransfield Strait, Antarctica (2019)

description: Raw seismic data from submarine Three Sisters rifting, Bransfield Strait, acquired onboard the Spanish vessel Sarmiento de Gamboa in the framework of the BRAVOSEIS PROJECT (2019).
DOI: 10.6084/m9.figshare.24085707.v1
title: Raw seismic reflection data from Three Sisters Rifting zone, Bransfield Strait, Antarctica (2019)

description: Raw seismic data from submarine Three Sisters rifting, Bransfield Strait, acquired onboard the Spanish vessel Sarmiento de Gamboa in the framework of the BRAVOSEIS PROJECT (2019).
DOI: 10.6084/m9.figshare.5383672
title: A tile-based method for geodesic buffer generation in a virtual globe

description: Geometric buffers are important for spatial analysis in many applications of geographic information systems (GISs), such as environmental measurement and management, human health, urban planning, etc. Geometric buffer generation algorithms are well studied in the Euclidean space where the buffer distance is measured by Euclidean metrics; however, very few algorithms are available for generating geometric buffers on the terrain surface in a virtual globe where the buffer distance is measured by geodesic metrics. This paper proposes a tile-based method for geodesic buffer generation according to the characteristics of a virtual globe. It extends the vector tile model (VTM) to organize terrain and vector data, and the XYH algorithm is improved to build geodesic distance fields for terrain meshes. Based on the data organization and the improved XYH algorithm, a geodesic buffer is generated via three main steps: selecting and assembling tiles, updating geodesic distance fields and tracing the boundaries of buffer zones. This method is implemented with multi-scale terrain and vector data, and the experimental results show that it is valid and exact and can be applied in practical applications.
DOI: 10.6084/m9.figshare.5383672.v1
title: A tile-based method for geodesic buffer generation in a virtual globe

description: Geometric buffers are important for spatial analysis in many applications of geographic information systems (GISs), such as environmental measurement and management, human health, urban planning, etc. Geometric buffer generation algorithms are well studied in the Euclidean space where the buffer distance is measured by Euclidean metrics; however, very few algorithms are available for generating geometric buffers on the terrain surface in a virtual globe where the buffer distance is measured by geodesic metrics. This paper proposes a tile-based method for geodesic buffer generation according to the characteristics of a virtual globe. It extends the vector tile model (VTM) to organize terrain and vector data, and the XYH algorithm is improved to build geodesic distance fields for terrain meshes. Based on the data organization and the improved XYH algorithm, a geodesic buffer is generated via three main steps: selecting and assembling tiles, updating geodesic distance fields and tracing the boundaries of buffer zones. This method is implemented with multi-scale terrain and vector data, and the experimental results show that it is valid and exact and can be applied in practical applications.
DOI: 10.6084/m9.figshare.5383699
title: HFMD-orignal.xlsx

description: Economic burden and health related quality of life for Hand, Foot and Mouth Disease in China
DOI: 10.17633/rd.brunel.5383951
title: Analysis of the Effect of the Bore/Stroke (B/S) Ratio and Scavenge Port Angles on the Scavenging Process in a 2-Stroke Boosted Uniflow Scavenged Direct Injection Gasoline (BUSDIG) Engine

description: The data used in the following paper is archived here:<br>Wang, X., Ma, J., and Zhao, H., "Analysis of the Effect of the Bore/Stroke (B/S) Ratio and Scavenge Port Angles on the Scavenging Process in a 2-Stroke Boosted Uniflow Scavenged Direct Injection Gasoline (BUSDIG) Engine". Proc. IMechE, Part D: Journal of Automobile Engineering.2017 Accepted.<br>The descriptions for each data are listed in "captions.docx".
DOI: 10.17633/rd.brunel.5383951.v1
title: Analysis of the Effect of the Bore/Stroke (B/S) Ratio and Scavenge Port Angles on the Scavenging Process in a 2-Stroke Boosted Uniflow Scavenged Direct Injection Gasoline (BUSDIG) Engine

description: The data used in the following paper is archived here:<br>Wang, X., Ma, J., and Zhao, H., "Analysis of the Effect of the Bore/Stroke (B/S) Ratio and Scavenge Port Angles on the Scavenging Process in a 2-Stroke Boosted Uniflow Scavenged Direct Injection Gasoline (BUSDIG) Engine". Proc. IMechE, Part D: Journal of Automobile Engineering.2017 Accepted.<br>The descriptions for each data are listed in "captions.docx".
DOI: 10.6084/m9.figshare.5384167
title: Data and code from: Asynchrony among local communities stabilizes ecosystem function of metacommunities

description: R code, derived metrics, and limited metadata associated with Wilcox et al. (2017). Asynchrony among local communities stabilizes ecosystem function of metacommunities. Ecology Letters.<br>When using this data or code, please cite the original publication:<br>Wilcox, K.R., A.T. Tredennick, S. Koerner, E. Grman, L. Hallett, M. Avolio, K. La Pierre, G. Houseman, F. Isbell, D. Johnson, J. Alatalo, A. Baldwin, E. Bork, E. Boughton, W. Bowman, A. Britton, J. Cahill, S. Collins, G-Z. Du, A. Eskelinen, L. Gough, A. Jentsch, C. Kern, K. Klanderud, A. Knapp, J. Kreyling, Y. Luo, J. McLaren, P. Megonigal, V. Onipchenko, J. Prevéy, J. Price, C. Robinson, O. Sala, M. Smith, N. Soudzilovskaia, L. Souza, D. Tilman, S. White, Z. Xu, L. Yahdjian, Q. Yu, P. Zhang, Y, Zhang. (2017). Asynchrony among local communities stabilizes ecosystem function of metacommunities. <i>Ecology Letters</i> 20(12):1534–1545.<br>Additionally, please cite the Figshare file set:<br>Wilcox, K.R., A.T. Tredennick, S. Koerner, E. Grman, L. Hallett, M. Avolio, K. La Pierre. (2017). Data and code from: Asynchrony among local communities stabilizes ecosystem function of metacommunities. Figshare. https://dx.doi.org/10.6084/m9.figshare.5384167.<br><b>R Code</b>The analysis proceeds in several steps, which can be viewed most easily by examining the ~/Wilcox_etal_DerivedData_and_Code/analysis_scripts/main_text_scripts/patches_source_all_scripts.R file. Questions about the code or analysis should be directed to Kevin Wilcox (wilcoxkr@gmail.com) or Andrew Tredennick (atredenn@gmail.com).<br><b>Derived Data</b>We provide the full set of metrics (e.g., alpha, beta, and gamma stability and diversity) for each of our study sites. The main analysis and all figures in the paper can be reproduced using these metrics. Metrics were calculated from time series of abundance data from 62 grassland sites around the globe, although primarily from North America and Europe. The data is part of the CoRRE Data Base (http://corredata.weebly.com/), and those interested in using proprietary data not included in this fileset are encouraged to contact the CoRRE data base maintainers (http://corredata.weebly.com/contact.html).<br>
DOI: 10.6084/m9.figshare.5386744
title: Evaluation and Impact Factors of the Mechanical Properties of Phloem Bundle Fibers Obtained from Kenaf Germplasm

description: The mechanical properties of kenaf phloem bundle fibers are valuable for reinforced composites or boards, more so than similar materials also used in textile or papermaking applications. 55 kenaf germplasm studied here showed an average phloem bundle fiber tensile strength of 643.6 MPa and an average elastic modulus of 23.3 GPa after chemical retting treatment. 19 of these kenaf germplasm had fiber tensile strengths &gt;700 MPa, which can be attributed to intensive breeding programs. The fiber tensile strength and elastic modulus of kenaf germplasm had a significant positive correlation, but there was no such correlation between a fiber’s mechanical properties and its diameter or agronomic characteristics. Among 56 hybridized combination F<sub>1</sub> generations, the highest tensile strength was 928.3 MPa from a combination of No.30 of Xinan Wuchi × Guatemala 4. Therefore, breeding and screening are both useful for improving the mechanical properties of kenaf phloem bundle fibers. However, the effects of the used bundle fiber preparation method or cultivation year on the fiber’s mechanical properties were more pronounced than those of the type of kenaf germplasm or breeding operation used. The mechanical properties of kenaf phloem bundle fibers treated by chemical retting were superior to those treated using natural retting.
DOI: 10.6084/m9.figshare.5386744.v1
title: Evaluation and Impact Factors of the Mechanical Properties of Phloem Bundle Fibers Obtained from Kenaf Germplasm

description: The mechanical properties of kenaf phloem bundle fibers are valuable for reinforced composites or boards, more so than similar materials also used in textile or papermaking applications. 55 kenaf germplasm studied here showed an average phloem bundle fiber tensile strength of 643.6 MPa and an average elastic modulus of 23.3 GPa after chemical retting treatment. 19 of these kenaf germplasm had fiber tensile strengths &gt;700 MPa, which can be attributed to intensive breeding programs. The fiber tensile strength and elastic modulus of kenaf germplasm had a significant positive correlation, but there was no such correlation between a fiber’s mechanical properties and its diameter or agronomic characteristics. Among 56 hybridized combination F<sub>1</sub> generations, the highest tensile strength was 928.3 MPa from a combination of No.30 of Xinan Wuchi × Guatemala 4. Therefore, breeding and screening are both useful for improving the mechanical properties of kenaf phloem bundle fibers. However, the effects of the used bundle fiber preparation method or cultivation year on the fiber’s mechanical properties were more pronounced than those of the type of kenaf germplasm or breeding operation used. The mechanical properties of kenaf phloem bundle fibers treated by chemical retting were superior to those treated using natural retting.
DOI: 10.6084/m9.figshare.24085509
title: Raw seismic reflection data from Humpback Volcano, Bransfield Strait, Antarctica (2019)

description: Raw seismic data from submarine Humpback Volcano, Bransfield Strait, acquired onboard the Spanish vessel Sarmiento de Gamboa in the framework of the BRAVOSEIS PROJECT.
DOI: 10.6084/m9.figshare.24085509.v1
title: Raw seismic reflection data from Humpback Volcano, Bransfield Strait, Antarctica (2019)

description: Raw seismic data from submarine Humpback Volcano, Bransfield Strait, acquired onboard the Spanish vessel Sarmiento de Gamboa in the framework of the BRAVOSEIS PROJECT.
DOI: 10.6084/m9.figshare.5393314
title: Systems approach to the pharmacological actions of HDAC inhibitors reveals EP300 activities and convergent mechanisms of regulation in diabetes

description: Given the skyrocketing costs to develop new drugs, repositioning of approved drugs, such as histone deacetylase (HDAC) inhibitors, may be a promising strategy to develop novel therapies. However, a gap exists in the understanding and advancement of these agents to meaningful translation for which new indications may emerge. To address this, we performed systems-level analyses of 33 independent HDAC inhibitor microarray studies. Based on network analysis, we identified enrichment for pathways implicated in metabolic syndrome and diabetes (insulin receptor signaling, lipid metabolism, immunity and trafficking). Integration with ENCODE ChIP-seq datasets identified suppression of EP300 target genes implicated in diabetes. Experimental validation indicates reversal of diabetes-associated EP300 target genes in primary vascular endothelial cells derived from a diabetic individual following inhibition of HDACs (by SAHA), EP300, or <i>EP300</i> knockdown. Our computational systems biology approach provides an adaptable framework for the prediction of novel therapeutics for existing disease.
DOI: 10.6084/m9.figshare.5393314.v2
title: Systems approach to the pharmacological actions of HDAC inhibitors reveals EP300 activities and convergent mechanisms of regulation in diabetes

description: Given the skyrocketing costs to develop new drugs, repositioning of approved drugs, such as histone deacetylase (HDAC) inhibitors, may be a promising strategy to develop novel therapies. However, a gap exists in the understanding and advancement of these agents to meaningful translation for which new indications may emerge. To address this, we performed systems-level analyses of 33 independent HDAC inhibitor microarray studies. Based on network analysis, we identified enrichment for pathways implicated in metabolic syndrome and diabetes (insulin receptor signaling, lipid metabolism, immunity and trafficking). Integration with ENCODE ChIP-seq datasets identified suppression of EP300 target genes implicated in diabetes. Experimental validation indicates reversal of diabetes-associated EP300 target genes in primary vascular endothelial cells derived from a diabetic individual following inhibition of HDACs (by SAHA), EP300, or <i>EP300</i> knockdown. Our computational systems biology approach provides an adaptable framework for the prediction of novel therapeutics for existing disease.
DOI: 10.6084/m9.figshare.24084945
title: Processed seismic data from Humpback volcano during the BRAVOSEIS expedition (2019)

description: Processed profiles at Humpback Volcano, Bransfield Strait, in the framework of BRAVOSEIS expedition onboard the Spanish vessel Sarmiento de Gamboa (2019)
DOI: 10.6084/m9.figshare.24084945.v1
title: Processed seismic data from Humpback volcano during the BRAVOSEIS expedition (2019)

description: Processed profiles at Humpback Volcano, Bransfield Strait, in the framework of BRAVOSEIS expedition onboard the Spanish vessel Sarmiento de Gamboa (2019)
DOI: 10.6084/m9.figshare.24631410.v3
title: <b>Flight behaviour diverge more between seasonal forms than between species in </b><b><i>Pieris</i></b><b> </b><b>butterflies</b>

description: Data accompanying the following publication:Kleckova I., Linke D., De Moraes Rezende F., Rauscher L., Le Roy C., Matos-Maraví P. (submitted) Flight behaviour diverge more between seasonal forms than between species in Pieris butterflies
DOI: 10.6084/m9.figshare.24085080
title: Three Sisters Rift processed seismic data, Bransfield Strait. BRAVOSEIS Project

description: Processed seismic data from Three Sisters rifting at Brnasfield Strait. BRAVOSEIS PROJECT. Data acquired onboard the Sarmiento de Gamboa vessel (2019)
DOI: 10.6084/m9.figshare.24085080.v1
title: Three Sisters Rift processed seismic data, Bransfield Strait. BRAVOSEIS Project

description: Processed seismic data from Three Sisters rifting at Brnasfield Strait. BRAVOSEIS PROJECT. Data acquired onboard the Sarmiento de Gamboa vessel (2019)
DOI: 10.6084/m9.figshare.5400511.v1
title: Adaptive Response Criteria in Road Hazard Detection Among Older Drivers

description: <b>OBJECTIVES</b>: The majority of existing investigations on attention, aging, and driving have focused on the negative impacts of age-related declines in attention on hazard detection and driver performance. However, driving skills and behavioral compensation may accommodate the negative effects that age-related attentional decline places on driving performance. In this study, we examined an important question that had been largely neglected in the literature linking attention, aging, and driving: can top-down factors such as behavioral compensation, specifically adaptive response criteria, accommodate the negative impacts from age-related attention declines on hazard detection during driving? <b>METHODS</b>: In the experiment, we used the Drive Aware Task, a task combining the driving context with well-controlled laboratory procedures measuring attention. We compared younger (n = 16, age 21 – 30) and older (n = 21, age 65 – 79) drivers on their attentional processing of hazards in driving scenes, indexed by percentage of correct response and reaction time of hazard detection, as well as sensitivity and response criterion using the signal detection analysis. <b>RESULTS</b>: Older drivers, in general, were less accurate and slower on the task than younger drivers. However, results from this experiment revealed that older, but not younger, drivers adapted their response criteria when the traffic condition changed in the driving scenes. When there was more traffic in the driving scene, older drivers became more liberal in their responses, meaning that they were more likely to report that a driving hazard was detected. <b>CONCLUSIONS</b>: Older drivers adopt compensatory strategies on hazard detection during driving. Our findings showed that, in the driving context, even at an old age our attentional functions are still adaptive according to environmental conditions. This leads to considerations on potential training methods to promote adaptive strategies which may help older drivers maintain performance in road hazard detection.
DOI: 10.6084/m9.figshare.24084810
title: Processed Multichannel seismic data at Orca Volcano, Bransfield Strait, Antarctica (2019)

description: Processed Multichannel seismic data at Orca Volcano, Bransfield Strait, Antarctica (2019)
DOI: 10.6084/m9.figshare.24084810.v1
title: Processed Multichannel seismic data at Orca Volcano, Bransfield Strait, Antarctica (2019)

description: Processed Multichannel seismic data at Orca Volcano, Bransfield Strait, Antarctica (2019)
DOI: 10.6084/m9.figshare.5402143
title: A plant origin of Chinese propolis: <i>Populus canadensis</i> Moench

description: Honey bees make propolis from resins depending on resinous plants available in a particular environment. The aim of this work was to identify the plant origin of Chinese propolis. Through a combination of phytochemical analysis and behavior observation of worker bees, we find that worker bees collected resin on the bud surface of <i>Populus canadensis</i> Moench, and bud resin of <i>P. canadensis</i> presented high similarities between resin in worker bees’ corbiculae and propolis. The results reveal that <i>P. canadensis</i>, a hybrid variety of <i>Populus nigra</i> L. × <i>Populus deltoides</i>, is a plant origin of Chinese propolis. Characteristic components of Chinese propolis included benzyl caffeate, phenethyl caffeate, cinnamyl caffeate, cinnamyl <i>p</i>-cinnamate, pinobanksin-3-acetate, chrysin, pinocembrin, galangin, 5-methoxy pinobanksin, and pinobanksin. These compounds represented more than 80% of the total phenolic contents. This finding will help evaluate the quality and authenticity of poplar type propolis.
DOI: 10.6084/m9.figshare.5405275
title: Data from: Scenarios reveal pathways to sustain future ecosystem services in an agricultural landscape.

description: Projected changes of nine ecosystem services at 220-m×220-m from 2010 to 2070 under four contrasting scenarios in the 1345-km<sup>2
</sup>Yahara Watershed (Wisconsin, USA) using Agro-IBIS, a dynamic model of
terrestrial ecosystem processes, biogeochemistry, water and energy balance. Please refer to the meta-data page of this data for additional details.
DOI: 10.6084/m9.figshare.5405275.v1
title: Data from: Scenarios reveal pathways to sustain future ecosystem services in an agricultural landscape.

description: Projected changes of nine ecosystem services at 220-m×220-m from 2010 to 2070 under four contrasting scenarios in the 1345-km<sup>2
</sup>Yahara Watershed (Wisconsin, USA) using Agro-IBIS, a dynamic model of
terrestrial ecosystem processes, biogeochemistry, water and energy balance. Please refer to the meta-data page of this data for additional details.
DOI: 10.6084/m9.figshare.5405620
title: The evolutionary history of vertebrate RNA viruses

description: Virus genomesSequence alignmentRooted and unrooted phylogenies
DOI: 10.6084/m9.figshare.5406124
title: Reconstructed 3D hummingbird wing grid data from Quantifying the dynamic wing morphing of hovering hummingbird

description: Time series of the reconstructed three-dimensional hummingbird wing model during hovering.
DOI: 10.6084/m9.figshare.5406124.v1
title: Reconstructed 3D hummingbird wing grid data from Quantifying the dynamic wing morphing of hovering hummingbird

description: Time series of the reconstructed three-dimensional hummingbird wing model during hovering.
DOI: 10.17633/rd.brunel.5414059
title: Analysis of Mixture Formation Process in a 2-Stroke Boosted Uniflow Scavenged Direct Injection Gasoline (BUSDIG) engine

description: The data used in the following paper is archived here:<br>Wang, X., Ma, J., and Zhao, H., "Analysis of Mixture Formation Process in a 2-Stroke Boosted Uniflow Scavenged Direct Injection Gasoline (BUSDIG) engine". International Journal of Engine Research. 2017 Accepted.<br>The descriptions for each data are listed in "captions.docx".
DOI: 10.17633/rd.brunel.5414059.v1
title: Analysis of Mixture Formation Process in a 2-Stroke Boosted Uniflow Scavenged Direct Injection Gasoline (BUSDIG) engine

description: The data used in the following paper is archived here:<br>Wang, X., Ma, J., and Zhao, H., "Analysis of Mixture Formation Process in a 2-Stroke Boosted Uniflow Scavenged Direct Injection Gasoline (BUSDIG) engine". International Journal of Engine Research. 2017 Accepted.<br>The descriptions for each data are listed in "captions.docx".
DOI: 10.6084/m9.figshare.5414605
title: Deep multiple instance learning for automatic detection of diabetic retinopathy in retinal images

description: This code is about the deep multiple instance learning for automatic detection of diabetic retinopathy (DR) in retinal images. We hope more people can get involved in the research field of weakly supervised learning for DR detection.
DOI: 10.6084/m9.figshare.5414605.v1
title: Deep multiple instance learning for automatic detection of diabetic retinopathy in retinal images

description: This code is about the deep multiple instance learning for automatic detection of diabetic retinopathy (DR) in retinal images. We hope more people can get involved in the research field of weakly supervised learning for DR detection.
DOI: 10.6084/m9.figshare.5418655
title: Plant endophytes and arbuscular mycorrhizal fungi alter plant competition.xlsx

description: Effects of endophyte infection, mycorrhizal colonization, plant mixture type on plant biomass, phosphorus
(P) content, mycorrhizal colonization rate and mycorrhizal growth response
(MGR) of <i>Achnatherum sibiricum</i> and <i>Stipa grandis</i>, and the effects of endophyte infection and mycorrhizal colonization on the aggressivity index (AGR) for <i>A. sibiricum</i> and the relative interaction intensity
indices (RII) for <i>A</i>. <i>sibiricum</i> and <i>S. grandis</i>.