cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.11370225.v1
title: Fig1_code from Vector-borne parasite invasion in communities across space and time

description: While vector-borne parasite transmission often operates via generalist-feeding vectors facilitating cross-species transmission in host communities, theory describing the relationship between host species diversity and parasite invasion in these systems is underdeveloped. Host community composition and abundance vary across space and time, generating opportunities for parasite invasion. To explore how host community variation can modify parasite invasion potential, we develop a model for vector-borne parasite transmission dynamics that includes a host community of arbitrary richness and species' abundance. To compare invasion potential across communities, we calculate the community basic reproductive ratio of the parasite. We compare communities comprising a set of host species to their subsets, which allows for flexible scenario building including the introduction of novel host species and species loss. We allow vector abundance to scale with, or be independent of, community size, capturing regulation by feeding opportunities and non-host effects such as limited oviposition sites. Motivated by equivocal data relating host species competency to abundance, we characterize plausible host communities via phenomenological relationships between host species abundance and competency. We identify an underappreciated mechanism whereby changes to communities simultaneously alter average competency and the vector to host ratio and demonstrate that the interaction can profoundly influence invasion potential.
DOI: 10.6084/m9.figshare.11370231.v1
title: Fig3_code from Vector-borne parasite invasion in communities across space and time

description: While vector-borne parasite transmission often operates via generalist-feeding vectors facilitating cross-species transmission in host communities, theory describing the relationship between host species diversity and parasite invasion in these systems is underdeveloped. Host community composition and abundance vary across space and time, generating opportunities for parasite invasion. To explore how host community variation can modify parasite invasion potential, we develop a model for vector-borne parasite transmission dynamics that includes a host community of arbitrary richness and species' abundance. To compare invasion potential across communities, we calculate the community basic reproductive ratio of the parasite. We compare communities comprising a set of host species to their subsets, which allows for flexible scenario building including the introduction of novel host species and species loss. We allow vector abundance to scale with, or be independent of, community size, capturing regulation by feeding opportunities and non-host effects such as limited oviposition sites. Motivated by equivocal data relating host species competency to abundance, we characterize plausible host communities via phenomenological relationships between host species abundance and competency. We identify an underappreciated mechanism whereby changes to communities simultaneously alter average competency and the vector to host ratio and demonstrate that the interaction can profoundly influence invasion potential.
DOI: 10.6084/m9.figshare.11370213
title: Wu-SI-Tables-1912.docx

description: Geochronology analysis data
DOI: 10.6084/m9.figshare.11370222.v1
title: Invasive Prosopis juliflora reduces density and species composition of co-occurring woody plants in the Lower Moshi rangelands, Tanzania

description: In this study, we assessed effects of <i>Prosopis juliflora</i> by comparing species composition attributes of native<i> </i>woody plants between <i>Prosopis</i>-invaded, and the adjacent uninvaded sites in Lower Moshi rangelands, Northern Tanzania. We used a plot technique to sample woody plants in the two sites. Within each plot, we recorded the abundance of woody species and calculated the diversity index, richness, evenness, and density of each woody species. This study provides habitat-specific information for planning appropriate management and control strategies at the local scale to avoid further spread of <i>Prosopis juliflora</i> to neighboring areas.
DOI: 10.6084/m9.figshare.11370228.v1
title: Fig2_code from Vector-borne parasite invasion in communities across space and time

description: While vector-borne parasite transmission often operates via generalist-feeding vectors facilitating cross-species transmission in host communities, theory describing the relationship between host species diversity and parasite invasion in these systems is underdeveloped. Host community composition and abundance vary across space and time, generating opportunities for parasite invasion. To explore how host community variation can modify parasite invasion potential, we develop a model for vector-borne parasite transmission dynamics that includes a host community of arbitrary richness and species' abundance. To compare invasion potential across communities, we calculate the community basic reproductive ratio of the parasite. We compare communities comprising a set of host species to their subsets, which allows for flexible scenario building including the introduction of novel host species and species loss. We allow vector abundance to scale with, or be independent of, community size, capturing regulation by feeding opportunities and non-host effects such as limited oviposition sites. Motivated by equivocal data relating host species competency to abundance, we characterize plausible host communities via phenomenological relationships between host species abundance and competency. We identify an underappreciated mechanism whereby changes to communities simultaneously alter average competency and the vector to host ratio and demonstrate that the interaction can profoundly influence invasion potential.
DOI: 10.6084/m9.figshare.11370213.v1
title: Wu-SI-Tables-1912.docx

description: Geochronology analysis data
DOI: 10.6084/m9.figshare.11370087
title: Characterization of ripplocation mobility in graphite

description: Recent work suggests that layered solids deform through buckling of basal planes. When isolated locally, as in graphite, these buckles, termed ripplocations, behave superficially similar to dislocations, but have no Burgers vectors. Through atomistic simulations, we demonstrate the easy transitions of ripplocations in graphite between many closely-spaced energy states, even at low temperatures. Between 60 and 350 K, their migration barrier is estimated at 32 meV, independent of segment length. Ripplocations spontaneously migrate towards vacancies and away from compressive stresses. These results shed more light on this new micromechanism and potentially explain experimental observations that evade sufficient description through dislocation-based models. These results shed more light on this new micromechanism and the high mobility and vacancy interactions of ripplocations potentially explain experimental observations that evade sufficient description through dislocation-based model.
DOI: 10.6084/m9.figshare.11370087.v1
title: Characterization of ripplocation mobility in graphite

description: Recent work suggests that layered solids deform through buckling of basal planes. When isolated locally, as in graphite, these buckles, termed ripplocations, behave superficially similar to dislocations, but have no Burgers vectors. Through atomistic simulations, we demonstrate the easy transitions of ripplocations in graphite between many closely-spaced energy states, even at low temperatures. Between 60 and 350 K, their migration barrier is estimated at 32 meV, independent of segment length. Ripplocations spontaneously migrate towards vacancies and away from compressive stresses. These results shed more light on this new micromechanism and potentially explain experimental observations that evade sufficient description through dislocation-based models. These results shed more light on this new micromechanism and the high mobility and vacancy interactions of ripplocations potentially explain experimental observations that evade sufficient description through dislocation-based model.
DOI: 10.6084/m9.figshare.11369985
title: RNA-seq transcriptome of Pseudomonas putida KT2440 subsisting on succinate as sole carbon source

description: Succinate is an intermediate in the tricarboxylic acid cycle. A dicarboxylic acid, succinate is seldom used as a carbon source for cultivating microorganisms. Thus, this work presents a unique opportunity to analyse the RNA-seq transcriptome of <i>Pseudomonas putida</i> KT2440 (ArrayExpress accession number: E-GEOD-46491) fed with succinate as sole carbon source. Through profiling 0.7 million reads, the transcriptome image gathered suggests a predominance of non-ribosomal peptide synthesis genes and outer membrane proteins. Expression of non-ribosomal peptide synthetase is particularly interesting given that RNA was extracted from cells in the mid-exponential phase. In total, highly expressed genes were: non-ribosomal peptide synthetase <i>pvdL</i>, flagellin <i>fliC</i>, TonB-dependent outer membrane ferripyoverdine <i>fpvA</i>, putative surface adhesion protein, non-ribosomal peptide synthetase <i>pvdD</i>, non-ribosomal peptide synthetase <i>pvdJ</i>, L-ornithine 5-monooxygenase <i>pvdA</i>, chaperonin GroEL, <i>groL</i>, non-ribosomal peptide synthetase <i>pvdI</i>, bifunctional succinyl-CoA synthetase subunit <i>sucC</i>, class 2 fumarate hydratase <i>fumC-1</i>, and succinyl-CoA synthetase subunit alpha <i>sucD</i>. High expression levels of <i>sucC </i>and <i>sucD </i>illustrated that part of the genome of <i>P. putida</i> KT2440 was sensitive to succinate and responded to its presence; thereby, implying the existence of a succinate regulon that remains to be deciphered. Hopefully, deeper analysis of the presented RNA-seq transcriptome with those of <i>P. putida</i> KT2440 subsisting on other carbon substrates would illuminate a more comprehensive picture of the differential gene expression pattern associated with succinate catabolism.<br><br>
DOI: 10.6084/m9.figshare.11369985.v1
title: RNA-seq transcriptome of Pseudomonas putida KT2440 subsisting on succinate as sole carbon source

description: Succinate is an intermediate in the tricarboxylic acid cycle. A dicarboxylic acid, succinate is seldom used as a carbon source for cultivating microorganisms. Thus, this work presents a unique opportunity to analyse the RNA-seq transcriptome of <i>Pseudomonas putida</i> KT2440 (ArrayExpress accession number: E-GEOD-46491) fed with succinate as sole carbon source. Through profiling 0.7 million reads, the transcriptome image gathered suggests a predominance of non-ribosomal peptide synthesis genes and outer membrane proteins. Expression of non-ribosomal peptide synthetase is particularly interesting given that RNA was extracted from cells in the mid-exponential phase. In total, highly expressed genes were: non-ribosomal peptide synthetase <i>pvdL</i>, flagellin <i>fliC</i>, TonB-dependent outer membrane ferripyoverdine <i>fpvA</i>, putative surface adhesion protein, non-ribosomal peptide synthetase <i>pvdD</i>, non-ribosomal peptide synthetase <i>pvdJ</i>, L-ornithine 5-monooxygenase <i>pvdA</i>, chaperonin GroEL, <i>groL</i>, non-ribosomal peptide synthetase <i>pvdI</i>, bifunctional succinyl-CoA synthetase subunit <i>sucC</i>, class 2 fumarate hydratase <i>fumC-1</i>, and succinyl-CoA synthetase subunit alpha <i>sucD</i>. High expression levels of <i>sucC </i>and <i>sucD </i>illustrated that part of the genome of <i>P. putida</i> KT2440 was sensitive to succinate and responded to its presence; thereby, implying the existence of a succinate regulon that remains to be deciphered. Hopefully, deeper analysis of the presented RNA-seq transcriptome with those of <i>P. putida</i> KT2440 subsisting on other carbon substrates would illuminate a more comprehensive picture of the differential gene expression pattern associated with succinate catabolism.<br><br>
DOI: 10.6084/m9.figshare.11369979
title: RNA-seq transcriptome of Pseudomonas putida KT2440 subsisting on fructose as sole carbon source

description: Fructose is a metabolizable sugar that is able to tap on central carbon metabolism for its catabolism. But, fructose is not commonly used as a substrate for cultivating cells in biotechnology applications. In this contribution, the RNA-seq of <i>Pseudomonas putida</i> KT2440 (ArrayExpress accession number: E-GEOD-46491) subsisting on fructose as sole carbon source was analysed by an in-house MATLAB transcriptome analysis software. A total of 0.7 million reads were analysed, and the resulting transcriptome paints a picture of a cell devoting significant metabolic resources in expressing cell surface proteins. Specifically, the highly expressed genes were: putative surface adhesion protein, surface adhesion protein, ribosome modulation factor, quinoprotein ethanol dehydrogenase, flagellin, porin F, major outer membrane lipoprotein, non-ribosomal peptide synthetase, and basic amino acid specific porin OprD. High expression level of a fructose transporter, PTS fructose transporter subunit EI/HPr/IIA, fruB, indicated that <i>P. putida</i> KT2440 could sense presence of fructose, and activate a differential gene expression programme centred around the fructose regulon. Overall, the RNA-seq transcriptome presented in this work should find use in fundamental biology studies seeking to understand bacterial fructose metabolism in general, and how <i>P. putida</i> KT2440 uses this non-conventional sugar in particular.<br><br>
DOI: 10.6084/m9.figshare.11369973
title: Evaluation of antioxidant , antibacterial and wound healing activities of Vitex pinnata

description: The data sets generated from studies involving the extract of the plant Vitex pinnata in antibacterial, antioxidant (DPPH analysis) and excision wound healing studies
DOI: 10.6084/m9.figshare.11369973.v1
title: Evaluation of antioxidant , antibacterial and wound healing activities of Vitex pinnata

description: The data sets generated from studies involving the extract of the plant Vitex pinnata in antibacterial, antioxidant (DPPH analysis) and excision wound healing studies
DOI: 10.6084/m9.figshare.11369940
title: Integrating reservoir dynamics, crustal stress, and geophysical observations of the Laguna del Maule magmatic system by FEM models and data assimilation

description: Data for the paper:<br>Integrating reservoir dynamics, crustal stress, and geophysical observations of the Laguna del Maule magmatic system by FEM models and data assimilation<br>Y. Zhan<sup>1</sup>, P. M. Gregg<sup>1</sup>, H. Le Mével<sup>2</sup>, C. A. Miller<sup>3</sup>, and C. Cardona<sup>4</sup><br><sup>1</sup>Department of Geology, University of Illinois - Urbana-Champaign, Urbana, Illinois, USA<sup>2</sup>Department of Terrestrial Magnetism, Carnegie Institution for Science, Washington, District of Columbia, USA<sup>3</sup>GNS Science, Wairakei Research Center, Private Bag 2000, Taupo 3352, New Zealand<sup>4</sup>Observatorio Volcanológico de los Andes del Sur, Servicio Nacional de Geologia y Minería, Avenida Rudecindo Ortega 03850, Temuco, ChileCorresponding author: Yan Zhan (yanzhan3@illinois.edu) <br><br>Instruction:COMSOL_model -&gt; folder for COMSOL modelsStress_Gravity_Results -&gt; folder for Stress, Strain, and Gravity results, including the scripts for plotting Figure 6 ~ 9.<br>
DOI: 10.17633/rd.brunel.11369928
title: Effect of piston shape design on the scavenging performance and mixture preparation 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. and Zhao, H., "Effect of piston shape design on the scavenging performance and mixture preparation in a 2-stroke boosted uniflow scavenged direct injection gasoline (BUSDIG) engine". International Journal of Engine Research.2019. Accepted.<br>The descriptions for each data are listed in "captions.docx".
DOI: 10.26180/5df6ed2dc5ed5
title: Poças et al: When does diet matter?

description: This is the data set for a manuscript entitled: When does diet matter? The roles of larval and adult nutrition in regulating adult size traits <br>Here we include body weight, wing size, and femur size data for male and female <i>Drosophila melanogaster.</i> We have manipulated larval and adult diets in one of two ways: by changing the macronutrient content of the diet, or by changing the caloric content of the diet.<br><br>
DOI: 10.17633/rd.brunel.11369928.v1
title: Effect of piston shape design on the scavenging performance and mixture preparation 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. and Zhao, H., "Effect of piston shape design on the scavenging performance and mixture preparation in a 2-stroke boosted uniflow scavenged direct injection gasoline (BUSDIG) engine". International Journal of Engine Research.2019. Accepted.<br>The descriptions for each data are listed in "captions.docx".
DOI: 10.6084/m9.figshare.11369922
title: US Federal Affiliations and RORs

description: Tab separated values of Department,Organization Name, and ROR for Federal research organizations extracted from ROR data dump: Community, ROR (2019): ROR Data. figshare. Collection. https://doi.org/10.6084/m9.figshare.c.4596503.v3.
DOI: 10.6084/m9.figshare.11369922.v1
title: US Federal Affiliations and RORs

description: Tab separated values of Department,Organization Name, and ROR for Federal research organizations extracted from ROR data dump: Community, ROR (2019): ROR Data. figshare. Collection. https://doi.org/10.6084/m9.figshare.c.4596503.v3.
DOI: 10.6084/m9.figshare.11369832
title: KonsTestingOnly

description: Lorem ipsum dolor sit amet.
DOI: 10.6084/m9.figshare.11369751
title: Degasparro et al. Hydrobiologia Data

description: Please read dataset description in the metadata file.
DOI: 10.6084/m9.figshare.11369832.v1
title: KonsTestingOnly

description: Lorem ipsum dolor sit amet.
DOI: 10.6084/m9.figshare.11369832.v3
title: KonsTestingOnly

description: Lorem ipsum dolor sit amet.
DOI: 10.6084/m9.figshare.11369751.v1
title: Degasparro et al. Hydrobiologia Data

description: Please read dataset description in the metadata file.
DOI: 10.6084/m9.figshare.11369832.v2
title: KonsTestingOnly

description: Lorem ipsum dolor sit amet.
DOI: 10.6084/m9.figshare.11369661
title: Data Set

description: Data sets, statistics, figures and blots from :Elucidating the mechanism of action of alpha-1-antitrypsin using retinal pigment epithelium cells exposed to high glucose. Potential use in diabetic retinopathy<b></b>
DOI: 10.6084/m9.figshare.11369649
title: A multicriteria optimization framework for the definition of the spatial granularity of urban social media analytics

description: Data and codes used to support the research article entitled "A multicriteria optimization framework for the definition of the spatial granularity of urban social media analytics", which was published in the International Journal of Geographical Information Science.<br>
DOI: 10.6084/m9.figshare.11369661.v1
title: Data Set

description: Data sets, statistics, figures and blots from :Elucidating the mechanism of action of alpha-1-antitrypsin using retinal pigment epithelium cells exposed to high glucose. Potential use in diabetic retinopathy<b></b>
DOI: 10.6084/m9.figshare.11369469
title: MOESM7 of Nested plant LTR retrotransposons target specific regions of other elements, while all LTR retrotransposons often target palindromes and nucleosome-occupied regions: in silico study

description: Additional file 7. GFF3 files of fully annotated nested-original pairs and non-nested LTR retrotransposons used in this study.
DOI: 10.6084/m9.figshare.11369466
title: MOESM6 of Nested plant LTR retrotransposons target specific regions of other elements, while all LTR retrotransposons often target palindromes and nucleosome-occupied regions: in silico study

description: Additional file 6. Python scripts used for recalculation of genomic coordinates of protein domains in analyzed LTR retrotransposons annotated using DANTE tool, RepeatExplorer.
DOI: 10.6084/m9.figshare.11369469.v1
title: MOESM7 of Nested plant LTR retrotransposons target specific regions of other elements, while all LTR retrotransposons often target palindromes and nucleosome-occupied regions: in silico study

description: Additional file 7. GFF3 files of fully annotated nested-original pairs and non-nested LTR retrotransposons used in this study.
DOI: 10.6084/m9.figshare.11369466.v1
title: MOESM6 of Nested plant LTR retrotransposons target specific regions of other elements, while all LTR retrotransposons often target palindromes and nucleosome-occupied regions: in silico study

description: Additional file 6. Python scripts used for recalculation of genomic coordinates of protein domains in analyzed LTR retrotransposons annotated using DANTE tool, RepeatExplorer.
DOI: 10.6084/m9.figshare.11369436
title: Cholera Outbreak 2005 data

description: The Data that have been used in PhD thesis of Dr Frank Osei and also the analysis and comparison done of the model data and the real data
DOI: 10.6084/m9.figshare.11369436.v1
title: Cholera Outbreak 2005 data

description: The Data that have been used in PhD thesis of Dr Frank Osei and also the analysis and comparison done of the model data and the real data
DOI: 10.6084/m9.figshare.11369403
title: RNA-seq transcriptome of Pseudomonas putida KT2440 subsisting on glycerol as sole carbon source

description: Glycerol is a potential carbon source for the cultivation of various bacterial species given the presence of metabolic pathways for its catabolism. But, its use lags behind the preferred carbon source, glucose. However, glycerol is increasingly being produced as a byproduct in biodiesel production, and thus, efforts have been expended in exploring the use of glycerol as carbon source in support of microbial fermentation. This work hopes to make a contribution in this direction by analysing the RNA-seq transcriptome of <i>Pseudomonas putida</i> KT2440 (ArrayExpress accession number: E-GEOD-46491) cultivated with glycerol as sole carbon source. Although <i>P. putida</i> KT2440 is commonly used in environmental remediation as opposed to biotechnology, it nevertheless might inform the metabolism of glycerol given the versatile metabolism encoded by a relatively large genome. Buttressed by a dataset comprising 0.7 million reads, the RNA-seq transcriptome of <i>P. putida</i> KT2440 showed a preponderance of non-ribosomal peptide synthesis enzymes being highly expressed together with cell surface proteins. High expression of non-ribosomal peptide synthetase is unusual given that RNA was extracted from cells in the mid-exponential phase. In total, the most highly expressed genes were: non-ribosomal peptide synthetase <i>pvdL</i>, surface adhesion protein, putative surface adhesion protein, quinoprotein ethanol dehydrogenase <i>qedH-I</i>, non-ribosomal peptide synthetase <i>pvdD</i>, aldehyde dehydrogenase <i>aldB-II</i>, diaminobutyrate-2-oxoglutarate transaminase <i>pvdH</i>, ribosome modulation factor <i>rmf</i>, non-ribosomal peptide synthetase <i>pvdJ</i>, and L-ornithine 5-monooxygenase <i>pvdA</i>. Overall, much remains to be deciphered from the RNA-seq transcriptome of <i>P. putida</i> KT2440 utilising glycerol as sole carbon source. Even though <i>P. putida</i> KT2440 is not a microbial cell factory, its gene expression pattern while utilising glycerol may still offer clues to the activation of specific branches of central carbon metabolism that have not been observed to date. <br><br>