cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6827201.v2
title: De novo assemblies, annotations, and gene expression profiling of gill epithelium from 16 species of Fundulus killifish in response to salinity change.

description: P51<br>Ion and Acid-Base Regulation in Fish Symposium#<strong>ICBF2018</strong><br>13th International Congress on the Biology of FishCalgary, Alberta, July 15-19, 2018<br>Estuaries are characterized by periodic fluxes in salinity. Many species of North American killifish (Fundulus) are estuarine specialists and harbor euryhaline phenotypes. Three clades within Fundulus independently radiated into freshwater environments and have lost their abilities to tolerate high salinity. We use Fundulus as a comparative model system for studying the physiological and genetic mechanisms that diverge between euryhaline and freshwater species. We examined 16 estuarine and freshwater species with representation from each of three clades. Fish from all species were acclimated to either brackish or fresh water then exposed to an acute brackish water challenge. Gill transcriptome data were collected. To enable multi-species comparisons, reference transcriptome assemblies were generated de novo for each species then used to analyze transcriptional responses to salinity change by clade and physiology. We find differences in the gene expression between euryhaline and freshwater species, some of which are shared across clades, implicating molecular mechanisms that contribute to divergent osmoregulatory physiologies.<br><br>Fundulus Multispecies Osmotic Transcriptome Sequencing Project (FMOTSP)<br>https://doi.org/10.17605/OSF.IO/M4XEG<br>Analysis scripts:https://github.com/ljcohen/RNAseq_15killifish<br>Raw data:https://www.ncbi.nlm.nih.gov/bioproject/473009<br>
DOI: 10.6084/m9.figshare.6827144
title: Sample metadata from Ruiz Gonzalez et al. FEMS Microbiology Ecology article

description: Sample metadata for bacterial communities sampled at the Montreal IDENT experiment in Ste-Anne de Bellevue.<br>These sample metadata accompany the 16S data:<br>https://doi.org/10.6084/m9.figshare.6654287.v1<br>Data collection procedures are described in the paper "Soils associated to different tree communities do not elicit predictable responses in lake bacterial community structure and function" by Clara Ruiz Gonzalez et al., in press at FEMS Microbiology Ecology.<br>Data are in comma-separated text file format.<br>
DOI: 10.6084/m9.figshare.6827144.v1
title: Sample metadata from Ruiz Gonzalez et al. FEMS Microbiology Ecology article

description: Sample metadata for bacterial communities sampled at the Montreal IDENT experiment in Ste-Anne de Bellevue.<br>These sample metadata accompany the 16S data:<br>https://doi.org/10.6084/m9.figshare.6654287.v1<br>Data collection procedures are described in the paper "Soils associated to different tree communities do not elicit predictable responses in lake bacterial community structure and function" by Clara Ruiz Gonzalez et al., in press at FEMS Microbiology Ecology.<br>Data are in comma-separated text file format.<br>
DOI: 10.15468/t34drx
title: New species of the superfamily Euphthiracaroidea (Acari: Oribatida) from Madagascar and Tanzania

description: This dataset contains the digitized treatments in Plazi based on the original journal article Niedbała, Wojciech, Starý, Josef (2014): New species of the superfamily Euphthiracaroidea (Acari: Oribatida) from Madagascar and Tanzania. Journal of Natural History 49 (27): 1689-1702, DOI: 10.1080/00222933.2014.976670
DOI: 10.6084/m9.figshare.6826970
title: Metabolic engineering of <i>Escherichia coli</i> W3110 strain by incorporating genome-level modifications and synthetic plasmid modules to enhance L-Dopa production from glycerol

description: L-Tyrosine which is one of the terminal metabolites of highly regulated aromatic amino-acid biosynthesis pathway in <i>Escherichia coli</i> is a precursor for synthesis of L-Dopa. In this study, we report over production of L-Dopa by enhancing expression of rate limiting isoenzyme of shikimate kinase (aroL), chorismate synthase (aroC), aromatic-amino-acid aminotransferase (tyrB) and 3-phosphoshikimate 1-carboxyvinyltransferase (aroA) form a plasmid module harboring five enzymes under two inducible promoters converting shikimate to tyrosine. 4-hydroxyphenylacetate-3-hydrolase (hpaBC) which converts L-Tyrosine to L-Dopa was expressed constitutively from a separate plasmid module. Feedback deregulated expression of 3-Deoxy-D-arabinoheptulosonate-7-phosphate (DAHP) synthase (aroG*) replacing wild type aroG under its natural promoter led to enhancement of L-Dopa production. Deletion of transcriptional repressor tyrR and links to other competing pathways improved titers of L-Dopa. We focused on having a balanced flux by constitutive expression of pathway enzymes from plasmid constructs rather than achieving higher amounts of catalytic protein by induction. We observed glycerol when used as a carbon source for the final strain led to low acid production. The best performing strain led to decoupling of acid production and product formation in bioreactor. Fed batch analysis of the final strain led to 12.5 g/L of L-Dopa produced in bioreactor.
DOI: 10.6084/m9.figshare.6826970.v1
title: Metabolic engineering of <i>Escherichia coli</i> W3110 strain by incorporating genome-level modifications and synthetic plasmid modules to enhance L-Dopa production from glycerol

description: L-Tyrosine which is one of the terminal metabolites of highly regulated aromatic amino-acid biosynthesis pathway in <i>Escherichia coli</i> is a precursor for synthesis of L-Dopa. In this study, we report over production of L-Dopa by enhancing expression of rate limiting isoenzyme of shikimate kinase (aroL), chorismate synthase (aroC), aromatic-amino-acid aminotransferase (tyrB) and 3-phosphoshikimate 1-carboxyvinyltransferase (aroA) form a plasmid module harboring five enzymes under two inducible promoters converting shikimate to tyrosine. 4-hydroxyphenylacetate-3-hydrolase (hpaBC) which converts L-Tyrosine to L-Dopa was expressed constitutively from a separate plasmid module. Feedback deregulated expression of 3-Deoxy-D-arabinoheptulosonate-7-phosphate (DAHP) synthase (aroG*) replacing wild type aroG under its natural promoter led to enhancement of L-Dopa production. Deletion of transcriptional repressor tyrR and links to other competing pathways improved titers of L-Dopa. We focused on having a balanced flux by constitutive expression of pathway enzymes from plasmid constructs rather than achieving higher amounts of catalytic protein by induction. We observed glycerol when used as a carbon source for the final strain led to low acid production. The best performing strain led to decoupling of acid production and product formation in bioreactor. Fed batch analysis of the final strain led to 12.5 g/L of L-Dopa produced in bioreactor.
DOI: 10.6084/m9.figshare.6826958
title: Experimental and modeling assessment of a novel automotive cabin PM<sub>2.5</sub> removal system

description: Poor air quality inside vehicles and its impact on human health is an issue requiring attention, with drivers and passengers facing levels of air pollution potentially greater than street-side outdoor air. This paper assesses the potential effectiveness of a car cabin filtration system to remove fine particulate matter PM<sub>2</sub><i><sub>.</sub></i><sub>5</sub> and improve air quality for car passengers. The study was conducted as a practical evaluation coupled to a model implementation. First, the effectiveness of PM<sub>2</sub><i><sub>.</sub></i><sub>5</sub> filter material was investigated in a chamber experiment under a range of environmental and loading conditions using a realistic automotive auxiliary scrubber. Second, implementation of such a system was evaluated in a full air flow 3D computational fluid dynamical model configured for a realistic cabin and ventilation system, and related to the chamber results through a simple decay model. Additionally, performance of low-cost dust sensors was evaluated as potential cabin monitoring devices. The experiment and modeling support the feasibility of a robust system which could be integrated into automotive designs in a straightforward manner. Results suggest that an auxiliary scrubber in the rear of the cabin alone would provide suboptimal performance, but that by incorporating a PM<sub>2</sub><i><sub>.</sub></i><sub>5</sub> filter into the main air handling system, cabin PM<sub>2</sub><i><sub>.</sub></i><sub>5</sub> concentrations could be reduced from 100 <i>µ</i>g m<i><sup>−</sup></i><sup>3</sup> to less than 25 <i>µ</i>g m<i><sup>−</sup></i><sup>3</sup> in 100 s and to 5 <i>µ</i>g m<i><sup>−</sup></i><sup>3</sup> in 250 s. A health impact assessment for hypothetical occupational driver populations using such technology long term showed considerable reductions in indicative PM<sub>2</sub><i><sub>.</sub></i><sub>5</sub> attributable mortality. Copyright © 2018 The Authors. Published with license by Taylor & Francis Group, LLC
DOI: 10.6084/m9.figshare.6826958.v2
title: Experimental and modeling assessment of a novel automotive cabin PM<sub>2.5</sub> removal system

description: Poor air quality inside vehicles and its impact on human health is an issue requiring attention, with drivers and passengers facing levels of air pollution potentially greater than street-side outdoor air. This paper assesses the potential effectiveness of a car cabin filtration system to remove fine particulate matter PM<sub>2</sub><i><sub>.</sub></i><sub>5</sub> and improve air quality for car passengers. The study was conducted as a practical evaluation coupled to a model implementation. First, the effectiveness of PM<sub>2</sub><i><sub>.</sub></i><sub>5</sub> filter material was investigated in a chamber experiment under a range of environmental and loading conditions using a realistic automotive auxiliary scrubber. Second, implementation of such a system was evaluated in a full air flow 3D computational fluid dynamical model configured for a realistic cabin and ventilation system, and related to the chamber results through a simple decay model. Additionally, performance of low-cost dust sensors was evaluated as potential cabin monitoring devices. The experiment and modeling support the feasibility of a robust system which could be integrated into automotive designs in a straightforward manner. Results suggest that an auxiliary scrubber in the rear of the cabin alone would provide suboptimal performance, but that by incorporating a PM<sub>2</sub><i><sub>.</sub></i><sub>5</sub> filter into the main air handling system, cabin PM<sub>2</sub><i><sub>.</sub></i><sub>5</sub> concentrations could be reduced from 100 <i>µ</i>g m<i><sup>−</sup></i><sup>3</sup> to less than 25 <i>µ</i>g m<i><sup>−</sup></i><sup>3</sup> in 100 s and to 5 <i>µ</i>g m<i><sup>−</sup></i><sup>3</sup> in 250 s. A health impact assessment for hypothetical occupational driver populations using such technology long term showed considerable reductions in indicative PM<sub>2</sub><i><sub>.</sub></i><sub>5</sub> attributable mortality. Copyright © 2018 The Authors. Published with license by Taylor & Francis Group, LLC
DOI: 10.6084/m9.figshare.6826958.v1
title: Experimental and modelling assessment of a novel automotive cabin PM<sub>2.5</sub> removal system

description: Poor air quality inside vehicles and its impact on human health is an issue requiring attention, with drivers and passengers facing levels of air pollution potentially greater than street-side outdoor air. This paper assesses the potential effectiveness of a car cabin filtration system to remove fine particulate matter PM<sub>2.5</sub> and improve air quality for car passengers. The study was conducted as a practical evaluation coupled to a model implementation. First, the effectiveness of PM<sub>2.5</sub> filter material was investigated in a chamber experiment under a range of environmental and loading conditions using a realistic automotive auxiliary scrubber. Second, implementation of such a system was evaluated in a full air flow 3D computational fluid dynamical (CFD) model configured for a realistic cabin and ventilation system, and related to the chamber results through a simple decay model. Additionally, performance of low-cost dust sensors were evalu- ated as potential cabin monitoring devices. The experiment and modelling support the feasibility of a robust system which could be integrated into automotive designs in a straightforward manner. Results suggest that an auxiliary scrubber in the rear of the cabin alone would provide sub-optimal performance, but that by incorporating a PM<sub>2.5</sub> filter into the main air handling system, cabin PM<sub>2.5</sub> concentrations could be reduced from 100 <i>µ</i>g m<i><sup>−</sup></i><sup>3</sup> to less than 25 <i>µ</i>g m<i><sup>−</sup></i><sup>3</sup> in 100 seconds and to 5 <i>µ</i>g m<i><sup>−</sup></i><sup>3</sup> in 250 seconds. A health impact assessment for hypothetical occupational driver populations using such technology long term showed considerable reductions in indicative PM<sub>2.5</sub> attributable mortality.
DOI: 10.6084/m9.figshare.6826949.v1
title: Functional Data Analysis of Dynamic PET Data

description: One application of positron emission tomography (PET), a nuclear imaging technique, in neuroscience involves in vivo estimation of the density of various proteins (often, neuroreceptors) in the brain. PET scanning begins with the injection of a radiolabeled tracer that binds preferentially to the target protein; tracer molecules are then continuously delivered to the brain via the bloodstream. By detecting the radioactive decay of the tracer over time, dynamic PET data are constructed to reflect the concentration of the target protein in the brain at each time. The fundamental problem in the analysis of dynamic PET data involves estimating the impulse response function (IRF), which is necessary for describing the binding behavior of the injected radiotracer. Virtually all existing methods have three common aspects: summarizing the entire IRF with a single scalar measure; modeling each subject separately; and the imposition of parametric restrictions on the IRF. In contrast, we propose a functional data analytic approach that regards each subject’s IRF as the basic analysis unit, models multiple subjects simultaneously, and estimates the IRF nonparametrically. We pose our model as a linear mixed effect model in which population level fixed effects and subject-specific random effects are expanded using a <i>B</i>-spline basis. Shrinkage and roughness penalties are incorporated in the model to enforce identifiability and smoothness of the estimated curves, respectively, while monotonicity and non-negativity constraints impose biological information on estimates. We illustrate this approach by applying it to clinical PET data with subjects belonging to three diagnosic groups. We explore differences among groups by means of pointwise confidence intervals of the estimated mean curves based on bootstrap samples.
DOI: 10.6084/m9.figshare.6826937.v1
title: Bayesian Uncertainty Directed Trial Designs

description: Most Bayesian response-adaptive designs unbalance randomization rates towards the most promising arms with the goal of increasing the number of positive treatment outcomes during the study, even though the primary aim of the trial is different. We discuss Bayesian uncertainty directed designs (BUD), a class of Bayesian designs in which the investigator specifies an information measure tailored to the experiment. All decisions during the trial are selected to optimize the available information at the end of the study. The approach can be applied to several designs, ranging from early stage multi-arm trials to biomarker-driven and multi-endpoint studies. We discuss the asymptotic limit of the patient allocation proportion to treatments, and illustrate the finite-sample operating characteristics of BUD designs through examples, including multi-arm trials, biomarker-stratified trials, and trials with multiple co-primary endpoints.
DOI: 10.6084/m9.figshare.6826937.v2
title: Bayesian Uncertainty Directed Trial Designs

description: Most Bayesian response-adaptive designs unbalance randomization rates toward the most promising arms with the goal of increasing the number of positive treatment outcomes during the study, even though the primary aim of the trial is different. We discuss Bayesian uncertainty directed designs (BUD), a class of Bayesian designs in which the investigator specifies an information measure tailored to the experiment. All decisions during the trial are selected to optimize the available information at the end of the study. The approach can be applied to several designs, ranging from early stage multi-arm trials to biomarker-driven and multi-endpoint studies. We discuss the asymptotic limit of the patient allocation proportion to treatments, and illustrate the finite-sample operating characteristics of BUD designs through examples, including multi-arm trials, biomarker-stratified trials, and trials with multiple co-primary endpoints. Supplementary materials for this article, including a standardized description of the materials available for reproducing the work, are available as an online supplement.
DOI: 10.6084/m9.figshare.6826910
title: Numerical investigation of flame splitting phenomenon in upward flame spread over solids with a two-stage pyrolysis model

description: Upward flame spread over thin solids is numerically studied using an in-house three-dimensional transient numerical model with a two-stage solid pyrolysis. The simulation results reveal fundamentally different flame behaviors in different pressure conditions. At low pressures, conventional continuous flame spread is observed. Upon ignition, the flame grows and spreads upward until it reaches the end of the sample. At high pressures, the flame splits into two flames shortly after ignition. The two flames spread upward separately at different spread rates. In a transitional pressure region, cyclic flame splitting was observed. The flame splits periodically during the upward spreading process. In each splitting cycle, the bottom flame extinguishes shortly after splitting while the top flame continuously spreads upward and starts a new splitting cycle. This flame splitting phenomenon was previously observed experimentally, but to the authors’ knowledge is numerically captured for the first time in this study. The splitting process is presented in detail and compared with the continuous flame spread process. The numerical results indicate that the multi-stage pyrolysis is responsible for the flame splitting.
DOI: 10.6084/m9.figshare.6826910.v1
title: Numerical investigation of flame splitting phenomenon in upward flame spread over solids with a two-stage pyrolysis model

description: Upward flame spread over thin solids is numerically studied using an in-house three-dimensional transient numerical model with a two-stage solid pyrolysis. The simulation results reveal fundamentally different flame behaviors in different pressure conditions. At low pressures, conventional continuous flame spread is observed. Upon ignition, the flame grows and spreads upward until it reaches the end of the sample. At high pressures, the flame splits into two flames shortly after ignition. The two flames spread upward separately at different spread rates. In a transitional pressure region, cyclic flame splitting was observed. The flame splits periodically during the upward spreading process. In each splitting cycle, the bottom flame extinguishes shortly after splitting while the top flame continuously spreads upward and starts a new splitting cycle. This flame splitting phenomenon was previously observed experimentally, but to the authors’ knowledge is numerically captured for the first time in this study. The splitting process is presented in detail and compared with the continuous flame spread process. The numerical results indicate that the multi-stage pyrolysis is responsible for the flame splitting.
DOI: 10.6073/pasta/ed18869514947f930c1feb9dc668cb4b
title: Algal Nutrient Limitation Bioassays in Sycamore Creek, Arizona, USA (2010-2020)

description: The primary objective of this project is to understand how long-term climate variability and change influence the structure and function of desert streams via effects on hydrologic disturbance regimes. Climate and hydrology are intimately linked in arid landscapes; for this reason, desert streams are particularly well suited for both observing and understanding the consequences of climate variability and directional change. Researchers try to (1) determine how climate variability and change over multiple years influence stream biogeomorphic structure (i.e., prevalence and persistence of wetland and gravel-bed ecosystem states) via their influence on factors that control vegetation biomass, and (2) compare interannual variability in within-year successional patterns in ecosystem processes and community structure of primary producers and consumers of two contrasting reach types (wetland and gravel-bed stream reaches). This dataset addresses patterns of nutrient limitation by primary producers as indicated by *in situ* growth on artificial substrates.
DOI: 10.6084/m9.figshare.6826850
title: Supplementary File 1

description: Supplementary File 1. A complete list of all examined Ceraphronoidea specimens from the Muséum National d'Histoire Naturelle, Paris (MNHN). In the "Collecting Event/Verbatim Label" column, the symbol "||" is used to indicate separate lines on the same label and the symbol "++" is used to indicate a separate label.<br>This work is supported by U. S. National Science Foundation grants DBI-1356381 and DEB-1353252.
DOI: 10.6084/m9.figshare.6826862
title: Supplementary File 2_ Darwincore

description: Supplementary File 2. A Darwincore file of all examined Ceraphronoidea specimens from the Muséum National d'Histoire Naturelle, Paris (MNHN).<br>This work is supported by U. S. National Science Foundation grants DBI-1356381 and DEB-1353252.
DOI: 10.6084/m9.figshare.6826862.v1
title: Supplementary File 2_ Darwincore

description: Supplementary File 2. A Darwincore file of all examined Ceraphronoidea specimens from the Muséum National d'Histoire Naturelle, Paris (MNHN).<br>This work is supported by U. S. National Science Foundation grants DBI-1356381 and DEB-1353252.
DOI: 10.6084/m9.figshare.6826844
title: Table 3

description: This table is a list of all Kieffer specimens stored in ethanol at the Muséum National d'Histoire Naturelle, Paris (MNHN) and their associated type numbers assigned by Kieffer. <br><br>This work is supported by U. S. National Science Foundation grants DBI-1356381 and DEB-1353252.
DOI: 10.6084/m9.figshare.6826829
title: Table 2

description: This table is a list of all specimens stored in alcohol and their associated identifiers. <br><br>This work is supported by U. S. National Science Foundation grants DBI-1356381 and DEB-1353252.
DOI: 10.6084/m9.figshare.6826844.v1
title: Table 3

description: This table is a list of all Kieffer specimens stored in ethanol at the Muséum National d'Histoire Naturelle, Paris (MNHN) and their associated type numbers assigned by Kieffer. <br><br>This work is supported by U. S. National Science Foundation grants DBI-1356381 and DEB-1353252.
DOI: 10.6084/m9.figshare.6826829.v1
title: Table 2

description: This table is a list of all specimens stored in alcohol and their associated identifiers. <br><br>This work is supported by U. S. National Science Foundation grants DBI-1356381 and DEB-1353252.