cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.95x69p8fx
title: Performance evaluation of a laboratory developed PCR test for quantitation of HIV-2 viral RNA

description: Management of Human Immunodeficiency Virus Type 2 (HIV-2) infections
 present unique challenges due to low viral titers, slow disease
 progression, and poor response to standard antiviral therapies. 
 The need for a nucleic acid assay to detect and quantify HIV-2 virus has
 led to the development of a number of molecular-based assays for detection
 and/or quantification of HIV-2 viral RNA in plasma in order to provide
 laboratory evidence of HIV-2 infection and viral loads for use in
 treatment decisions.  As HIV-2 is less pathogenic and
 transmissible than HIV-1 and has resistance to several of the
 antiretroviral drugs, delay of treatment is common. Cross sero-reactivity
 between HIV-1 and HIV-2 makes it difficult to distinguish between the two
 viruses based upon serological tests.  As such we developed a
 quantitative reverse transcription PCR (qRT-PCR) assay targeting the 5’
 long terminal repeat of HIV-2 for detection and quantification of HIV-2
 viral RNA in plasma to identify HIV-2 infection and for use in viral load
 monitoring.  Serial dilutions of cultured HIV-2 virus
 demonstrated a wide dynamic range (10 to 100,000 copies/ml) with excellent
 reproducibility (standard deviation from 0.12 - 0.19), linearity (R2 =
 0.9994), and a lower limit of detection at 79 copies/ml (NIH-Z). 
 The assay is highly specific for HIV-2 Groups A and B and exhibits no
 cross reactivity to HIV-1, HBV or HCV.  Precision of the
 assay was demonstrated for the High (Mean = 6.41; SD = 0.12) and Medium
 (Mean = 4.46; SD = 0.13) HIV-2 positive controls.  Replicate
 testing of clinical specimens showed good reproducibility above 1,000
 copies/ml, with higher variability under 1,000 copies/ml. 
 Analysis of 220 plasma samples from HIV-2 infected West African
 individuals demonstrated significantly lower viral loads than those
 observed in HIV-1 infections,  consistent with results of
 previous studies.  Slightly more than seven percent of clinical
 samples (7.3%) demonstrated viral loads above 100,000 copies/ml, while
 37.3%  of samples were undetectable.  The high
 sensitivity, specificity, precision, and linearity of the WRAIR qRT-PCR
 assay makes it well suited for detection and monitoring of HIV-2 RNA
 levels in plasma of infected individuals.
description: Real-time quantiative RT-PCR results from 7500 Fast DX. Data
 converted to copies/ml or log10-transformed for analysis. Data analysis
 completed and included in PLOS ONE publication as Figures 1 - 6.
description: One data point is missing in Figure 1 data.
 Otherwise data is complete for Figures in PLOS ONE
 publication.
DOI: 10.5061/dryad.4j0zpc87k
title: Predicting the strength of urban-rural clines in a Mendelian polymorphism along a latitudinal gradient

description: Cities are emerging as models for addressing the fundamental question of
 whether populations evolve in parallel to similar environments. Here, we
 examine the environmental factors that drive the evolution of parallel
 urban-rural clines in a Mendelian trait—the cyanogenic antiherbivore
 defense of white clover (Trifolium repens). Previous work suggested
 urban-rural gradients in frost and snow depth could drive the evolution of
 reduced hydrogen cyanide (HCN) frequencies in urban populations. Here, we
 sampled over 700 urban and rural clover populations across 16 cities along
 a latitudinal transect in eastern North America. In each population, we
 quantified changes in the frequency of genotypes that produce HCN, and in
 a subset of the cities we estimated the frequency of the alleles at the
 two genes (CYP79D15 and Li) that epistatically interact to produce HCN. We
 then tested the hypothesis that cold climatic conditions are necessary for
 the evolution of cyanogenesis clines by comparing the strength of clines
 among cities located along a gradient of winter temperatures and frost
 exposure. Overall, half of the cities exhibited urban-rural clines in the
 frequency of HCN, whereby urban populations evolved lower HCN frequencies.
 Clines did not evolve in cities with the lowest temperatures and greatest
 snowfall, supporting the hypothesis that snow buffers plants against
 winter frost and constrains the formation of clines. By contrast, the
 strongest clines occurred in the warmest cities where snow and frost are
 rare, suggesting that alternative selective agents are maintaining clines
 in warmer cities. Some clines were driven by evolution at only CYP79D15,
 consistent with stronger and more consistent selection on this locus than
 on Li. Together, our results demonstrate that urban environments often
 select for similar phenotypes, but different selective agents and targets
 underlie the evolutionary response in different cities.
description: Plants were collected in the field and brought back to the lab
 for phenotyping.  Environmental data was collected from
 publically available datasets.  Phenotype and
 environmental data were processed in R v3.6.1. All scripts used for data
 processing and analyses are contained in the ZIP file associated with this
 repository.  Code and data are similarly available in
 this Github
 repository
description: See README files in atached ZIP folder.
DOI: 10.7280/d1m38z
title: Stochastic hydro-financial watershed modeling for environmental impact bonds

description: Stream erosion, poor water quality, and degraded ecosystems impose major
 cost burdens and challenges for stormwater managers. We present a
 stochastic hydro-financial watershed modeling framework for designing an
 Environmental Impact Bond (EIB) - a new form of financing for
 comprehensive, watershed scale interventions. EIB's provide capital
 for interventions that is repaid over time with interest by stakeholders
 who experience reduced costs (savings). The framework not only estimates
 cost savings from interventions, but aleatory and epistemic uncertainty in
 costs - precisely the information needed by investors for interest rates
 and payment periods. This work links the probability distributions of
 watershed states and fluxes with financial paramters and thus overcomes a
 barrier to the widespread adoptation of EIBs. The framework is applied to
 a trans-national pollution and sedimentation problem on the U.S. - Mexico
 border, and has broad applicability for a wide range of environmental
 problems.
description: The dataset for raingague data was collected in Los Laureles
 Canyon in Mexico using a tipping bucket raingauge and is found in
 San_Diego_Rainfall_Data_v2.xlsx. The dataset for the Lindbergh airfield
 rainfall is collected from the NOAA National Centers for Environmental
 Information (Station #USW00023188) and is again found in
 San_Diego_Rainfall_Data_v2.xlsx.  The MCMC generator
 for turning the San Diego Rainfield data (dat.mat) into future potential
 values of rainfall for LLC is located in the MATLAB script
 &lt;MCMC_Generator_v3_04022020_parmsmooth.mat&gt;. This MCMC data
 of future rainfall was then run through the AnnAGNPS model (http://go.usa.gov/KFO)
 to develop future watershed sediment yeilds. These yields were then fit to
 a statisical model and and used to generate 500,000 MC realizations of
 future sediment loads over a 10-year period for LLC under the different
 sediment management scenarios using the MATLAB script
 &lt;MCMC_PVsed_01102020&gt;. Finally, these generated sediment
 load data (J_CC.mat, J_BMP.mat, J_PV.mat, and J_BMP_PV.mat) were used in
 the financial model in the MATLAB script
 &lt;financial_modelv12_shtrll_gul_removed_04302020.mat&gt; to
 generate Figure 9 and Table 2.
DOI: 10.6078/d1311x
title: Stepping into the past to conserve the future: archived skin swabs from extant and extirpated populations inform genetic management of an endangered amphibian

description: Moving animals on a landscape through translocations and reintroductions
 is an important management tool used in the recovery of endangered
 species, particularly for the maintenance of population genetic diversity
 and structure. Management of imperiled amphibian species rely heavily on
 translocations and reintroductions, especially for species that have been
 brought to the brink of extinction by the fungal pathogen,
 Batrachochytrium dendrobatidis. One striking example of disease-related
 declines and associated management efforts is in California’s Sequoia and
 Kings Canyon National Parks with the mountain yellow-legged frog complex
 (Rana sierrae/muscosa). Limited knowledge of the population genetics of
 mountain yellow-legged frogs has made long-term conservation planning
 difficult. To address this, we used 598 archived skin swabs from both
 extant and extirpated populations across 48 lake basins to generate a
 robust Illumina-based nuclear amplicon dataset. We found that samples
 grouped into three main genetic clusters, concordant with watershed
 boundaries. We also found evidence for historical gene flow across
 watershed boundaries with a north-to-south axis of migration. Finally, our
 results indicate that genetic diversity is not significantly different
 between populations with different disease statuses. Our study provides a
 population genetic framework for leveraging minimally-invasive samples to
 be used in conservation management of threatened species.
DOI: 10.5061/dryad.tb2rbnzwx
title: Mouse substantia nigra responses to optogenetic stimulation of projections from striatum and globus pallidus

description: As a rodent basal ganglia (BG) output nucleus, the substantia nigra pars
 reticulata (SNr) is well positioned to impact behavior.  SNr
 neurons receive GABAergic inputs from the striatum (direct pathway) and
 globus pallidus (GPe, indirect pathway). Dominant theories of action
 selection rely on these pathways' inhibitory actions.  Yet,
 experimental results on SNr responses to these inputs are limited and
 include excitatory effects. Our study combines experimental and
 computational work to characterize, explain, and make predictions about
 these pathways.  We observe diverse SNr responses to stimulation
 of SNr-projecting striatal and GPe neurons, including biphasic and
 excitatory effects, which our modeling shows can be explained by
 intracellular chloride processing.  Our work predicts that
 ongoing GPe activity could tune the SNr operating mode, including its
 responses in decision-making scenarios, and GPe output may modulate
 synchrony and low-frequency oscillations of SNr neurons, which we confirm
 using optogenetic stimulation of GPe terminals within the SNr.
description: This data was collected in the lab of Aryn Gittis at Carnegie
 Mellon University.  There is data from slice recordings and data from in
 vivo recordings, both in mice.  The slice data were collected with a
 MultiClamp 700B amplifier (Molecular Devices) and ITC-18 analog-to-digital
 board (HEKA) using Igor Pro software (Wavemetrics, RRID:SCR\_000325) and
 custom acquisition routines (Recording Artist; Richard C. Gerkin,
 Phoenix). Data were collected at 10 kHz and digitized at 40
 kHz. 
description: This data set includes many text files listing spike times from
 substantia nigra pars reticulata neurons in the slice, recorded
 under striatal and GPe stimulation.  It also includes an Excel spreadsheet
 with spike times and various other data from substantia nigra pars
 reticulata neurons recorded in vivo under dopamine depletion.
 Addtional information available in attached readme.txt
DOI: 10.15468/dl.z9jn2h
title: Occurrence Download

description: A dataset containing 148 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Phosichthys argenteus",
 "HasCoordinate is true",
 "DecimalLatitude is greater than -90",
 "DecimalLatitude is less than 90",
 "DecimalLongitude is greater than -180",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 2015"
 ]
}

 The dataset includes 148 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002213-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.k0p2ngf4w
title: Interactive effects of previous and current thermal conditions on gene expression in Manduca sexta

description: High temperatures can negatively impact performance and survival of
 organisms, particularly ectotherms. While an organism’s response to high
 temperature stress clearly depends on current thermal conditions, its
 response may also be affected by the temporal pattern and duration of past
 temperature exposures. We used RNA sequencing of Manduca sexta larvae fat
 body tissue to evaluate how diurnal temperature fluctuations during
 development affected gene expression both independently and in conjunction
 with subsequent heat stress. Additionally, we compared gene expression
 between two M. sexta populations, a lab colony and a genetically related
 field population that have been separated for more than 300 generations
 and differ in their thermal sensitivities. Lab-adapted larvae were
 predicted to show increased expression responses to both single and
 repeated thermal stress, whereas recurrent exposure could decrease later
 stress responses for field individuals. We found large differences in
 overall gene expression patterns between the two populations (across all
 temperature treatments), as well as population-specific transcriptomic
 responses to temperature; most differentially expressed genes were
 upregulated in the field compared with lab larvae. Developmental
 temperature fluctuations alone had minimal effects on long-term gene
 expression patterns, with the exception of a somewhat elevated stress
 response in the lab population. Fluctuating rearing conditions did alter
 gene expression during exposure to later heat stress, but this effect
 depended on both the population and the particular temperature conditions.
 This study contributes to increased knowledge of molecular mechanisms
 underlying physiological responses of organisms to temperature
 fluctuations, which is needed for the development of more accurate thermal
 performance models. 
description: 1. <strong>RNAseq_counts.zip</strong> contains count
 files (number of reads that mapped to each gene) for all samples of the
 RNA sequencing dataset used in this study. Count files were generated
 using HTSeq. 2. <strong>RNAseq_DE_Analysis.Rmd</strong> is the R Markdown file containing code used to run differential expression analysis.  3. <strong>MS_sample_table.txt</strong> contains metadata for samples in RNAseq_counts.zip (required to run differential expression analysis using RNAseq_DE_Analysis.Rmd). 4. <strong>HSP_list.txt</strong> contains a list of <em>Manduca sexta</em> genes annotated as heat shock proteins (required to run RNAseq_DE_Analysis.Rmd). 5. <strong>Supplemental_figures_and_tables.pdf</strong> contains additional figures and tables that are not included in journal online supplement.
DOI: 10.5061/dryad.h9w0vt4f9
title: A lack of genetically compatible mates constrains the spread of an invasive weed

description: Introduced populations often experience lag-times prior to invasion, but
 the mechanisms constraining rapid expansions of introduced populations are
 unclear. Solidago altissima is a North American native plant with highly
 invasive Japanese populations, and introduced Australian populations that
 are not invasive despite the climatic and ecological suitability of the
 region. By contrasting Australian with Japanese populations, we tested the
 hypothesis that Australian population growth is limited by a lack of
 long-distance dispersal via seeds due to limited number of compatible
 mates.  In the field, Australian populations rarely produced
 viable seeds. A cross-pollination experiment found that Australian plants
 are fertile, yet lack compatible mates within Australia. Genetic analysis
 revealed that Australian individuals descend from a small set of
 self-incompatible genetic clones, which explains the negligible seed set
 within Australia. Our results show that low genetic diversity, leading to
 mate incompatibility, inhibits invasiveness of Australian S. altissima,
 and provides compelling evidence for genetic, rather than ecological,
 factors constraining invasion in Australia.
DOI: 10.15468/dl.r9e8rb
title: Occurrence Download

description: A dataset containing 71 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Adenolobus pechuelii",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 71 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002214-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.c59zw3r40
title: Population genomic analyses of the sea urchin Echinometra sp. EZ across an extreme environmental gradient

description: Extreme environmental gradients represent excellent study systems to
 better understand the variables that mediate patterns of genomic variation
 between populations. They also allow for more accurate predictions of how
 future environmental change might affect marine species. The
 Persian/Arabian Gulf is extreme in both temperature and salinity, whereas
 the adjacent Gulf of Oman has conditions more typical of tropical oceans.
 The sea
 urchin Echinometra sp. EZ inhabits
 both of these seas and plays a critical role in coral reef health as a
 grazer and bioeroder, but, to date, there have been no population genomic
 studies on this or any urchin species in this unique region. E.
 sp. EZ’s life history traits (e.g., large population sizes, large
 reproductive clutches, and long life spans), in theory, should homogenize
 populations unless nonneutral processes are occurring. Here, we generated
 a draft genome and a restriction site-associated DNA sequencing data set
 from seven populations along an environmental gradient across the
 Persian/Arabian Gulf and the Gulf of Oman. The estimated genome size
 of E. sp. EZ was 609 Mb and the heterozygosity
 was among the highest recorded for an echinoderm at 4.5%. We recovered 918
 high-quality SNPs from 85 individuals which we then used in downstream
 analyses. Population structure analyses revealed a high degree of
 admixture between all sites, although there was population differentiation
 and significant pairwise FST values between the two
 seas. Preliminary results suggest migration is bidirec- tional between the
 seas and nine candidate loci were identified as being under putative
 natural selection, including one collagen gene. This study is the first to
 investigate the population genomics of a sea urchin from this extreme
 environmental gradient and is an important contribution to our
 understanding of the complex spatial patterns that drive genomic
 divergence.
description: <strong>FILES</strong> (please see manuscript for
 more details): ESPEZ_final_v2.fa : Final assembled
 draft genome for <em>Echinometra</em> sp.
 <em>EZ</em>. barcodes.txt: RAD barcode
 file raw.vcf : The raw vcf file generated by aligning
 RADtags to the draft genome (for this alignment, we removed the reads
 which were &lt;200bp from the draft genome), and running Freebayes to
 call SNPs.  SNP_FINAL_HARDFILT_918.vcf : Final filtered
 VCF file used for all downstream analyses, contains 918 high quality
 SNPs.
DOI: 10.15468/dl.m2zcte
title: Occurrence Download

description: A dataset containing 12049235 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Ecuador",
 "Year 2006-2026"
 ]
}

 The dataset includes 12049235 records from 934 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002185-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.0gb5mkkxn
title: Data from: Presence of same-sex kin promotes explorative behavior in subadult cichlid fish

description: While the importance of kin discrimination, i.e. kin recognition and
 subsequent differential treatment of kin and non-kin, is well established
 for kin-directed cooperation or altruism, the role of kin discrimination
 in the context of kin competition and kin avoidance is largely unexplored.
 Theory predicts that individuals avoiding competition with kin should be
 favored by natural selection due to indirect fitness benefits. Using an
 experimental approach, we investigated whether the presence of same-sex
 kin affects avoidance and explorative behavior in subadult Pelvicachromis
 taeniatus, a West African cichlid fish with strong intra-sexual
 competition in both sexes. P. taeniatus is capable of recognizing kin
 using phenotype matching and shows kin discrimination in diverse contexts.
 When exposed to a same-sex conspecific, both males and females tended to
 interact less with the related opponent. Moreover, individuals explored a
 novel environment faster after exposure to kin than to nonkin. This effect
 was more pronounced in females. Individuals avoiding the proximity of
 same-sex relatives may reduce kin competition over resources such as
 mating partners or food.
DOI: 10.5061/dryad.z612jm68c
title: Three-dimensional wing structure attenuates aerodynamic efficiency in flapping fly wings

description: The aerial performance of flying insects ultimately depends on how
 flapping wings interact with the surrounding air. It has previously been
 suggested that the wing’s three-dimensional camber and corrugation help to
 stiffen the wing against aerodynamic and inertial loading during flapping
 motion. Their contribution to aerodynamic force production, however, is
 under debate. Here we investigated the potential benefit of
 three-dimensional wing shape in three different-sized species of flies
 using models of mCT-scanned natural wings and models in which we removed
 either the wing's camber, corrugation, or both properties. Forces and
 aerodynamic power requirements during root flapping were derived from
 three-dimensional computational fluid dynamics modelling. Our data show
 that three-dimensional camber has no benefit for lift production and
 attenuates Rankine-Froude flight efficiency by up to ~12% compared to a
 flat wing. Moreover, we did not find evidence for lift-enhancing trapped
 vortices in corrugation valleys at Reynolds numbers between 137 and 1623.
 We found, however, that in all tested insect species, aerodynamic pressure
 distribution during flapping is closely aligned to the wing’s venation
 pattern. Altogether, our study strongly supports the assumption that the
 wing’s three-dimensional structure provides mechanical support against
 external forces rather than improving lift or saving energetic costs
 associated to active wing flapping.
description: The supplementary data
 contain: STL
 files of all 12 wings used in the present study (four models for each of
 the three species). INI
 files required to run the simulations. The main parameters are
 species-dependent and can be found in PARAMS_corrugation_singlewing_*.ini
 when running the code, this file goes in the command-line call: $mpi
 ./flusi PARAMS_corrugation_singlewing_calliphora.ini.
 The kinematics are encoded as Fourier
 coefficients in
 corrugation_kinematics_JEB2011.ini. For each wing
 model, a separate ini file is used, e.g.,
 Calliphora_C01leftuCTiso5k_profilo170512c_color_original.ini is the
 natural wing of the Calliphora model. This file needs to be set in the
 main ini file ( PARAMS_corrugation_singlewing_*.ini) in the line
 WingShape=*;. DATA files of the shown
 figures.