cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.4595800
title: HIV viral kinetics and T cell dynamics in antiretroviral naïve persons starting an integrase strand transfer inhibitor and protease inhibitor regimen

description: <b>Background</b>: Nucleos(t)ide reverse transcriptase inhibitor (NRTI)-sparing regimens may potentially minimize antiretroviral (ART) toxicities, but demonstrate mixed efficacy and toxicity results. The impact of an integrase strand transfer inhibitor (INSTI) and protease inhibitor (PI) regimen on HIV viral dynamics and T cell kinetics remains underdescribed. <b>Objective</b>: To compare the effect of raltegravir + ritonavir boosted lopinavir (RAL + LPV/r) to efavirenz/tenofovir disoproxil fumarate/emtricitabine (EFV/TDF/FTC) on HIV kinetics and T cell dynamics. <b>Methods</b>: Fifty participants naïve to ART underwent HIV viral kinetic sampling evaluated using biexponential mixed effects modeling. A subset of 28 subjects (with complete viral suppression) underwent flow cytometry and evaluation of soluble markers of inflammation at weeks 0, 4, and 48 of ART. <b>Results</b>: RAL + LPV/r compared to EFV/TDF/FTC resulted in a prolonged first phase viral decay rate (18 vs. 13 days <i>p</i> + T cells (−3.81 vs. −1.18 <i>p</i> = 0.09) and less decreases in activated effector memory CD4<sup>+</sup> T cells (−0.63 vs. −2.69 <i>p</i>-0.07). These trends did not persist to week 48. No differences were noted at any time point for soluble markers of immune activation. <b>Conclusions</b>: The prolonged first phase viral decay observed with RAL + LPV/r in persons starting ART did not result in differences in viral suppression at week 48. We also observed trends in declines in certain cellular markers of immune activation but it remains unclear if this could translate to long-term immunologic benefits in persons on an INSTI + PI.
DOI: 10.17028/rd.lboro.4595770
title: Passive System Energy Assessment Tool (PSEAT)

description: This is an excel file submitted as "Appendix P" for the thesis: "Passive system integration for office buildings in hot climates".
DOI: 10.6084/m9.figshare.4595800.v1
title: HIV viral kinetics and T cell dynamics in antiretroviral naïve persons starting an integrase strand transfer inhibitor and protease inhibitor regimen

description: <b>Background</b>: Nucleos(t)ide reverse transcriptase inhibitor (NRTI)-sparing regimens may potentially minimize antiretroviral (ART) toxicities, but demonstrate mixed efficacy and toxicity results. The impact of an integrase strand transfer inhibitor (INSTI) and protease inhibitor (PI) regimen on HIV viral dynamics and T cell kinetics remains underdescribed. <b>Objective</b>: To compare the effect of raltegravir + ritonavir boosted lopinavir (RAL + LPV/r) to efavirenz/tenofovir disoproxil fumarate/emtricitabine (EFV/TDF/FTC) on HIV kinetics and T cell dynamics. <b>Methods</b>: Fifty participants naïve to ART underwent HIV viral kinetic sampling evaluated using biexponential mixed effects modeling. A subset of 28 subjects (with complete viral suppression) underwent flow cytometry and evaluation of soluble markers of inflammation at weeks 0, 4, and 48 of ART. <b>Results</b>: RAL + LPV/r compared to EFV/TDF/FTC resulted in a prolonged first phase viral decay rate (18 vs. 13 days <i>p</i> + T cells (−3.81 vs. −1.18 <i>p</i> = 0.09) and less decreases in activated effector memory CD4<sup>+</sup> T cells (−0.63 vs. −2.69 <i>p</i>-0.07). These trends did not persist to week 48. No differences were noted at any time point for soluble markers of immune activation. <b>Conclusions</b>: The prolonged first phase viral decay observed with RAL + LPV/r in persons starting ART did not result in differences in viral suppression at week 48. We also observed trends in declines in certain cellular markers of immune activation but it remains unclear if this could translate to long-term immunologic benefits in persons on an INSTI + PI.
DOI: 10.17028/rd.lboro.4595770.v1
title: Passive System Energy Assessment Tool (PSEAT)

description: This is an excel file submitted as "Appendix P" for the thesis: "Passive system integration for office buildings in hot climates".
DOI: 10.6084/m9.figshare.4595719
title: Supplementary Data Set. Gene expression (qPCR) and protein abundance data. from Immune system stimulation by the native gut microbiota of honeybees

description: Gut microbial communities can greatly affect host health by modulating the host's immune system. For many important insects, however, the relationship between the gut microbiota and immune function remains poorly understood. Here, we test whether the gut microbial symbionts of the honeybee can induce expression of antimicrobial peptides (AMPs), a crucial component of insect innate immunity. We find that bees up-regulate gene expression of the AMPs apidaecin and hymenoptaecin in gut tissue when the microbiota is present. Using targeted proteomics, we detected apidaecin in both the gut lumen and the haemolymph; higher apidaecin concentrations were found in bees harbouring the normal gut microbiota than in bees lacking gut microbiota. In <i>in vitro</i> assays, cultured strains of the microbiota showed variable susceptibility to honeybee AMPs, although many seem to possess elevated resistance compared to <i>Escherichia coli</i>. In some trials, colonization by normal gut symbionts resulted in improved survivorship following injection with <i>E. coli</i>. Our results show that the native, non-pathogenic gut flora induces immune responses in the bee host. Such responses might be a host mechanism to regulate the microbiota, and could potentially benefit host health by priming the immune system against future pathogenic infections.
DOI: 10.6084/m9.figshare.4595719.v1
title: Supplementary Data Set. Gene expression (qPCR) and protein abundance data. from Immune system stimulation by the native gut microbiota of honeybees

description: Gut microbial communities can greatly affect host health by modulating the host's immune system. For many important insects, however, the relationship between the gut microbiota and immune function remains poorly understood. Here, we test whether the gut microbial symbionts of the honeybee can induce expression of antimicrobial peptides (AMPs), a crucial component of insect innate immunity. We find that bees up-regulate gene expression of the AMPs apidaecin and hymenoptaecin in gut tissue when the microbiota is present. Using targeted proteomics, we detected apidaecin in both the gut lumen and the haemolymph; higher apidaecin concentrations were found in bees harbouring the normal gut microbiota than in bees lacking gut microbiota. In <i>in vitro</i> assays, cultured strains of the microbiota showed variable susceptibility to honeybee AMPs, although many seem to possess elevated resistance compared to <i>Escherichia coli</i>. In some trials, colonization by normal gut symbionts resulted in improved survivorship following injection with <i>E. coli</i>. Our results show that the native, non-pathogenic gut flora induces immune responses in the bee host. Such responses might be a host mechanism to regulate the microbiota, and could potentially benefit host health by priming the immune system against future pathogenic infections.
DOI: 10.6084/m9.figshare.4595683
title: Table S_2. a) Original spreadsheets used to evaluate RAFI in the ecosystems considered in the manuscript; b) User spreadsheets to be filled with own data for computing the Relative Abundance of Trophic Resources (RAFI) in other ecosystems. Please fill only the white cells: other cells must not be modified. Do not consider empty stations: they all result equal to "1.0" due to lack of data from Relating trophic resources to community structure: a predictive index of food availability

description: The abundance and the distribution of trophic resources available for consumers influence the productivity and the diversity of natural communities. Nevertheless, assessment of the actual abundance of food items available for individual trophic groups has been constrained by differences in methods and metrics used by various authors. Here we develop an index of food abundance, the framework of which can be adapted for different ecosystems. The relative available food index (RAFI) is computed by considering standard resource conditions of a habitat and the influence of various generalized anthropogenic and natural factors. RAFI was developed using published literature on food abundance and validated by comparison of predictions versus observed trophic resources across various marine sites. RAFI tables here proposed can be applied to a range of marine ecosystems for predictions of the potential abundance of food available for each trophic group, hence permitting exploration of ecological theories by focusing on the deviation from the observed to the expected.
DOI: 10.6084/m9.figshare.4595683.v1
title: Table S_2. a) Original spreadsheets used to evaluate RAFI in the ecosystems considered in the manuscript; b) User spreadsheets to be filled with own data for computing the Relative Abundance of Trophic Resources (RAFI) in other ecosystems. Please fill only the white cells: other cells must not be modified. Do not consider empty stations: they all result equal to "1.0" due to lack of data from Relating trophic resources to community structure: a predictive index of food availability

description: The abundance and the distribution of trophic resources available for consumers influence the productivity and the diversity of natural communities. Nevertheless, assessment of the actual abundance of food items available for individual trophic groups has been constrained by differences in methods and metrics used by various authors. Here we develop an index of food abundance, the framework of which can be adapted for different ecosystems. The relative available food index (RAFI) is computed by considering standard resource conditions of a habitat and the influence of various generalized anthropogenic and natural factors. RAFI was developed using published literature on food abundance and validated by comparison of predictions versus observed trophic resources across various marine sites. RAFI tables here proposed can be applied to a range of marine ecosystems for predictions of the potential abundance of food available for each trophic group, hence permitting exploration of ecological theories by focusing on the deviation from the observed to the expected.
DOI: 10.6084/m9.figshare.4595635.v1
title: A juvenile specimen of <i>Anteosaurus magnificus</i> Watson, 1921 (Therapsida: Dinocephalia) from the South African Karoo, and its implications for understanding dinocephalian ontogeny

description: Anteosaurid dinocephalians were the apex terrestrial predators of the latter part of the Guadalupian (middle Permian) and became extinct at the end of that epoch. The group was relatively diverse in Russia, but represented by only two genera, <i>Australosyodon</i> and <i>Anteosaurus</i>, in the Karoo rocks of South Africa. A newly discovered skull of <i>Anteosaurus magnificus</i> from the Abrahamskraal Formation is unique among specimens of this taxon in having most of the individual cranial bones disarticulated, permitting accurate delimitation of cranial sutures for the first time. The relatively large orbits and unfused nature of the cranial sutures suggest juvenile status for the specimen. A computer-aided 3D reconstruction of the skull, and comparison with 11 additional individuals, enabled an allometric study of cranial growth in the species. Positive allometry for four of the measurements suggests rapid growth in the temporal region, and a significant difference in the development of the postorbital bar and suborbital bar between juveniles and adults. Pachyostosis was an important process in the cranial ontogeny of <i>Anteosaurus</i>, significantly modifying the skull roof of adults. This condition is more obvious in large individuals of the species, but it is recognized that variation may also be independent of growth and could be related to sexual dimorphism. Growth of the skull in <i>Anteosaurus</i> shows similar morphological trends to that of the Russian <i>Titanophoneus</i> and the Chinese <i>Sinophoneus</i>. The overall morphology of the juvenile <i>Anteosaurus</i> is clearly reminiscent of the adult skull of the Russian medium-sized <i>Syodon</i>, a condition that is more likely a result of similar skull sizes and the lack of strong pachyostosis in adult <i>Syodon</i>.
DOI: 10.6084/m9.figshare.4595572
title: The effect of main urine inhibitors on the activity of different DNA polymerases in loop-mediated isothermal amplification

description: <b>Background</b>: The use of rapid amplification methods to detect pathogens in biological samples is mainly limited by the amount of pathogens present in the sample and the presence of inhibiting substances. Inhibitors can affect the amplification efficiency by either binding to the polymerase, interacting with the DNA, or interacting with the polymerase during primer extension. Amplification is performed using DNA polymerase enzymes and even small changes in their activity can influence the sensitivity and robustness of molecular assays <b>Methods</b>: The main purpose of this research was to examine which compounds present in urine inhibit polymerases with strand displacement activity. To quantify the inhibition, we employed quantitative loop-mediated isothermal amplification <b>Results</b>: The authors found that the presence of BSA, Mg 2+, and urea at physiologically relevant concentrations, as well as acidic or alkaline conditions did not affect the activity of any of the tested polymerases. However, addition of salt significantly affected the activity of the tested polymerases. <b>Conclusion</b>: These findings may aid in the development of more sensitive, robust, cost effective isothermal amplification based molecular assays suitable for both point-of-care testing and on-site screening of pathogens directly from unprocessed urine which avoid the need for long and tedious DNA purification steps prior to amplification
DOI: 10.6084/m9.figshare.4595572.v1
title: The effect of main urine inhibitors on the activity of different DNA polymerases in loop-mediated isothermal amplification

description: <b>Background</b>: The use of rapid amplification methods to detect pathogens in biological samples is mainly limited by the amount of pathogens present in the sample and the presence of inhibiting substances. Inhibitors can affect the amplification efficiency by either binding to the polymerase, interacting with the DNA, or interacting with the polymerase during primer extension. Amplification is performed using DNA polymerase enzymes and even small changes in their activity can influence the sensitivity and robustness of molecular assays <b>Methods</b>: The main purpose of this research was to examine which compounds present in urine inhibit polymerases with strand displacement activity. To quantify the inhibition, we employed quantitative loop-mediated isothermal amplification <b>Results</b>: The authors found that the presence of BSA, Mg 2+, and urea at physiologically relevant concentrations, as well as acidic or alkaline conditions did not affect the activity of any of the tested polymerases. However, addition of salt significantly affected the activity of the tested polymerases. <b>Conclusion</b>: These findings may aid in the development of more sensitive, robust, cost effective isothermal amplification based molecular assays suitable for both point-of-care testing and on-site screening of pathogens directly from unprocessed urine which avoid the need for long and tedious DNA purification steps prior to amplification
DOI: 10.6084/m9.figshare.4595488
title: Response Data And Analytic Script For Categorical TI Experiment

description: Raw data for two monkeys performing a categorical transitive inference task, as well as the R script used to analyze the data.
DOI: 10.6084/m9.figshare.4595473
title: MD Simulations of Lipid A Phosphoethanol Transferase from Neisseria meningitidis (NmEptA) in pure DPPE and mixed PE/PG bilayer

description: MD simulations of a full-length Lipid A phosphoethanolamine transferase from <i>Neisseria meningitidis </i>(<i>Nm</i>EptA, PDB code: 5FGN). NmEptA decorates lipid A with phosphoethanolamine (PEA) by transferring the moiety from phosphoethanolamine (PE) lipids found in the bacterial membrane, resulting with the reduced negative charge of the bacterial surface and increased colistin resistance. The full publication can be found here: <br>doi: 10.1073/pnas.1612927114The uploaded files contain total of 9 independent simulations of <i>Nm</i>EptA embedded in two membrane models - pure DPPE bilayer and mixed PE/PG bilayer. A set of three simulations were carried out in DPPE bilayer ar 298 K and three at 310 K, while another set of triplicates was run in a bilayer containing 80% PE and 20% PG lipids at 298 K. A detailed description of MD setup is uploaded in a separate file and the input files used to run the simulations are also provided (.<i>mdp</i>). All the simulations were carried out using GROMACS 3.3.3 engine in conjunction with GROMOS 54a7 force field. Links to the lipid parameters used in these simulations are given below.<br>The uploaded files contain:* The starting structure of <i>Nm</i>EptA embedded in the DPPE bilayer (NmEptA_DPPE_Zn.gro) and the mixed PE/PG bilayer (NmEptA_PEPG_Zn.gro).* Set of trajectories in DPPE bilayer and the corresponding input <i>mdp</i> files at 298 K (NmEptA_DPPE_run1-3-298K.xtc/mdp) and at 310 K (NmEptA_DPPE_run1-3-310K.xtc/mdp).* Set of trajectories in PE/PG bilayer and the corresponding mdp files run at 298 K (NmEptA_PEPG_run1-3-298K.xtc/mdp).* PPoPE lipid paramteres (<i>PPoPE.itp</i>) and the equilibrated mixed PE/PG bilayer snapshot (80_PPoPE-20_DMPG.pdb).* MD simulation protocol (MD_Setup.pdf)<br><br>
DOI: 10.6084/m9.figshare.4595455
title: The Future of Science: A Study on Interests Across the World

description: This study was conducted to identify correlations between Altmetric data and its set of scientific topics. The scholarly articles published online were organized by distribution source, totaling the popularity of each article and its topic. In this case, topic refers to any scientific field of study and the data sets used were retrieved from Altmetric and Twitter sources. The purpose of this study is to help gain insight into where the future of science lies in subject matter as well as professional and public practice. as well as distinguish between what research the public favours to focus on in relation to privatized interests. Publishing dates, Scopus subjects, and Altmetric scores were extracted from the Altmetric data. This data was compared with Twitter posters, helping differentiate the professional and public demographics that were interested in this field. Through the results, it was identified that the data showed that different cohorts – types of demographics – have different interests. Therefore, the future of science cannot be limited to single fields, rather an amalgamation of those popular among scholarly and public interests.
DOI: 10.6084/m9.figshare.4595455.v1
title: The Future of Science: A Study on Interests Across the World

description: This study was conducted to identify correlations between Altmetric data and its set of scientific topics. The scholarly articles published online were organized by distribution source, totaling the popularity of each article and its topic. In this case, topic refers to any scientific field of study and the data sets used were retrieved from Altmetric and Twitter sources. The purpose of this study is to help gain insight into where the future of science lies in subject matter as well as professional and public practice. as well as distinguish between what research the public favours to focus on in relation to privatized interests. Publishing dates, Scopus subjects, and Altmetric scores were extracted from the Altmetric data. This data was compared with Twitter posters, helping differentiate the professional and public demographics that were interested in this field. Through the results, it was identified that the data showed that different cohorts – types of demographics – have different interests. Therefore, the future of science cannot be limited to single fields, rather an amalgamation of those popular among scholarly and public interests.
DOI: 10.6084/m9.figshare.4595473.v1
title: MD Simulations of Lipid A Phosphoethanol Transferase from Neisseria meningitidis (NmEptA) in pure DPPE and mixed PE/PG bilayer

description: MD simulations of a full-length Lipid A phosphoethanolamine transferase from <i>Neisseria meningitidis </i>(<i>Nm</i>EptA, PDB code: 5FGN). NmEptA decorates lipid A with phosphoethanolamine (PEA) by transferring the moiety from phosphoethanolamine (PE) lipids found in the bacterial membrane, resulting with the reduced negative charge of the bacterial surface and increased colistin resistance. The full publication can be found here: <br>doi: 10.1073/pnas.1612927114The uploaded files contain total of 9 independent simulations of <i>Nm</i>EptA embedded in two membrane models - pure DPPE bilayer and mixed PE/PG bilayer. A set of three simulations were carried out in DPPE bilayer ar 298 K and three at 310 K, while another set of triplicates was run in a bilayer containing 80% PE and 20% PG lipids at 298 K. A detailed description of MD setup is uploaded in a separate file and the input files used to run the simulations are also provided (.<i>mdp</i>). All the simulations were carried out using GROMACS 3.3.3 engine in conjunction with GROMOS 54a7 force field. Links to the lipid parameters used in these simulations are given below.<br>The uploaded files contain:* The starting structure of <i>Nm</i>EptA embedded in the DPPE bilayer (NmEptA_DPPE_Zn.gro) and the mixed PE/PG bilayer (NmEptA_PEPG_Zn.gro).* Set of trajectories in DPPE bilayer and the corresponding input <i>mdp</i> files at 298 K (NmEptA_DPPE_run1-3-298K.xtc/mdp) and at 310 K (NmEptA_DPPE_run1-3-310K.xtc/mdp).* Set of trajectories in PE/PG bilayer and the corresponding mdp files run at 298 K (NmEptA_PEPG_run1-3-298K.xtc/mdp).* PPoPE lipid paramteres (<i>PPoPE.itp</i>) and the equilibrated mixed PE/PG bilayer snapshot (80_PPoPE-20_DMPG.pdb).* MD simulation protocol (MD_Setup.pdf)<br><br>