cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.18931zcw1
title: Shards, sequences, and shorelines: two new species of Bembidion from North America (Coleoptera: Carabidae)

description: Two new species of Bembidion are described from river
 shores in North America.  One, Bembidion
 mimbres sp. nov., from the Gila River watershed in the lands of
 the Mimbres culture in New Mexico and Arizona, is closely related to the
 widespread Bembidion levigatum. DNA sequences from several
 linkage groups provide evidence of the distinctiveness of B.
 mimbres. The second, Bembidion corgenoma sp. nov., has
 been the subject of recent genomic and transcriptomic
 studies.  It belongs in the Bembidion
 transversale subgroup, and occurs from California north to
 British Columbia, east to Montana and Nevada. The B.
 transversale subgroup as a whole is reviewed, and characters that
 distinguish B. corgenoma from the similar and
 sympatric B. transversale and B.
 erosum are described and illustrated.  DNA
 sequences of these three species show no consistent differences in 28S,
 COI, CAD, and Topoisomerase, and a coalescent species delimitation
 analysis reveals no notable structure within the complex. This is the
 first known trio of species within Bembidion for which
 those genes provide no clear signal of species boundaries. A neotype is
 designated for the one name in the group that lacks a primary
 type, Bembidium haplogonum Chaudoir. Chromosomes of the
 new species and their relatives are as is typical for Bembidion,
 with 11 pairs of autosomes and an XY/XX sex chromosome system.
description: Extracted DNA was subjected to PCR, and the products Sanger
 sequenced.  Maximum likelihood analysis was conducted using IQ-TREE
 .
DOI: 10.5061/dryad.mkkwh70xz
title: Pot-1::mCherry transgene images from: Gametes deficient for Pot1 telomere binding proteins alter levels of telomeric foci for multiple generations

description: These images are raw data associated with the figures for the
 Communications Biolgoy manuscript "Gametes deficient for Pot1
 telomere binding proteins alter levels of telomeric foci for multiple
 generations" (Lister-Shimauchi et. al., 2020). Subjects are C.
 elegans containing a pot-1::mCherry transgene. Some also contain a
 mNeonGreen::pot-2 transgene. Most subjects are early stage embryos.
description: Images are of live whole worms or embryos. Embryos were mounted
 on 2% agarose pads and imaged live using a DeltaVision Elite microscope
 (Applied Precision) with a 60x Silicon oil objective lens. Whole worms
 were similarly mounted with the addition of levamisole for
 immobilization. Fluorescent stacks of images were
 captured to visualize pot-1::mCherry and mNeonGreen::pot-2 transgenes. A
 single DIC image was also captured for each stack, focusing at the level
 of the central slice. Most files were aquired in semi-automated fashion,
 with the microscope capturing a rectangular grid of images whose
 boundaries were set by the user; for this reason many fields of view are
 empty.
description: Data are grouped into folders based on which figure panel it
 relates to. Data are further grouped based on genotype or generation. All
 images are of red fluorescence from a pot-1::mCherry transgene. Some also
 include green fluorescence from a mNeonGreen::pot-2 transgene. Each stack
 also includes a DIC image at the central focal plane.
 See attached readme.rtf for additional information.
DOI: 10.5061/dryad.70rxwdbwb
title: Disentangling interactions among mercury, immunity, and infection in a Neotropical bat community

description: Contaminants such as mercury are pervasive and can have immunosuppressive
 effects on wildlife. Impaired immunity could be important for forecasting
 pathogen spillover risks, as many land-use changes that generate mercury
 contamination also bring wildlife into close contact with humans and
 domestic animals. However, the interactions among contaminants, immunity,
 and infection are difficult to study in natural systems, and empirical
 tests of possible directional relationships remain rare. We capitalized on
 extreme mercury variation in a diverse bat community in Belize to test
 association among contaminants, immunity, and infection. By comparing a
 previous dataset of bats sampled in 2014 with new data from 2017,
 representing a period of rapid agricultural land conversion, we first
 confirmed bat species more reliant on aquatic prey had higher fur mercury.
 Bats in the agricultural habitat also had higher mercury in recent years.
 We then tested covariation between mercury and cellular immunity and
 determined if such relationships mediated associations between mercury and
 common bacterial pathogens . As bat ecology can dictate exposure to
 mercury and pathogens, we also assessed species-specific patterns in
 mercury–infection relationships. Across the bat community, individuals
 with higher mercury had fewer neutrophils but not lymphocytes, suggesting
 stronger associations with innate immunity. However, the odds of infection
 for hemoplasmas and Bartonella spp. were generally lowest in bats with
 high mercury, and relationships between mercury and immunity did not
 mediate infection patterns. Mercury also showed species- and
 clade-specific relationships with infection, being associated with
 especially low odds for hemoplasmas in Pteronotus mesoamericanus and
 Dermanura phaeotis. For Bartonella spp., mercury was associated with
 particularly low odds in the genus Pteronotus but high odds in the
 Stenodermatinae. Synthesis and application: Lower general infection risk
 in bats with high mercury despite weaker innate defense suggests
 contaminant-driven loss of pathogen habitat (i.e., anemia) or vector
 mortality as possible causes. Greater attention to these potential
 pathways could help disentangle relationships among contaminants,
 immunity, and infection in anthropogenic habitats and help forecast
 disease risks. Our results also suggest contaminants may increase
 infection risk in some taxa but not others, emphasizing the importance of
 considering surveillance and management at different phylogenetic scales.
DOI: 10.5061/dryad.d2547d824
title: Town of Ennis traffic calming project August - October 2020

description: The Western Transporation Institute in partnership with the Town of Ennis
 and the Montana Department of Transportation conducted a temporary traffic
 calming project on Main Street in Ennis, MT.  The
 project was installed on August 3rd and was removed on October
 19th. The traffic calming included the use of curb extensions,
 road diets, crosswalks, and restriping to simulate a reconstruction
 project.  The goal of the project was to improve safety for
 pedestrians along and crossing Main St.  Pre-installation data
 collection was conducted between July 24th and July 30th and
 post-installation data collection was conducted between September 3rd and
 September 8th.  Speed & volume data, pedestrian counts,
 and driver yielding rates data were all collected before and
 after the installation of the traffic calming to determine any impact on
 these indicators.  In addition, a community survey was created in
 partnership with the Town of Ennis to get feedback from community members
 and visitors about the project, it's perception, and perceived
 impact.  
description: The Town of Ennis Community Survey was collected via a QR code
 that was placed at the installation site as well as through a weblink that
 was shared with the Town of Ennis Commission for distribution.  The
 weblink was: https://www.surveymonkey.com/r/TownOfEnnis.  Data was
 analyzed using Survey Monkey Analyze Tool. Speed and
 volume data was collected utilizing two Metrocount 500 Counters including
 tubes for roadway installation.  The data was analyzed using Metrocount
 Traffic Executive Version 5.7 data analysis in partnership with Metrocount
 Staff. Pedestrian Counts and Driver Yielding rate data
 was collected utilizing CountCam2 video collection technology.  Video data
 was analyzed by MSU ITE students as well as WTI staff utilizing American
 Planning Association procedures for pedestrian counts and driver yielding
 rates were analyzed using procedures designed by the City of
 Milwaukee.
DOI: 10.6071/m3xq12
title: Electronic properties of oligothiophenes

description: Despite the remarkable progress of machine learning (ML) techniques in
 chemistry, modeling the optoelectronic properties of long conjugated
 oligomers and polymers with ML remains challenging due to the difficulty
 in obtaining sufficient training data. Here we use transfer learning to
 address the data scarcity issue by pre-training graph neural networks
 using data from short oligomers. With only a few hundred training data, we
 are able to achieve an average error of about 0.1 eV for excited state
 energy of oligothiophenes against TDDFT calculations. We show that the
 success of our transfer learning approach relies on the relative locality
 of low-lying electronic excitations in long conjugated oligomers. Finally,
 we demonstrate the transferability of our approach by modeling the
 lowest-lying excited-state energies of poly(3-hexylthiopnene) (P3HT) in
 its single-crystal and solution phases using the transfer learning models
 trained with data of gas-phase oligothiophenes. The transfer learning
 predicted excited-state energy distributions agree quantitatively with
 TDDFT calculations and capture some important qualitative features
 observed in experimental absorption spectra.
description: The data were obtained from quantum chemical calculations on
 oligothiophenes (2T to 16T). More information about data generation can be
 found in the preprint (https://doi.org/10.26434/chemrxiv.13238414). The
 output and the xyz coordinates of the molecules are stored in the json and
 xyz files respectively, and the data for oligothiophenes of different
 lengths are saved in different subfolders with self-explanatory
 folder names. 
description: After the tar.gz file is downloaded, one can use the Linux
 command "tar -xzvf  data_for_repository.tar.gz" to extract the
 contents. In the extractetd "data_for_repository" folder, there
 are subfolders titled tddft_traj_tX, where X=2,...,16. For example,
 "tddft_traj_t15" contains all the quantum chemical data for 15T,
 and the json file names are the indices for the 15T configurations
 harvested from molecular dynamics simulations, whose xyz coordinates are
 all saved in the xyz file in the same folder (e.g., t15_traj.xyz). The
 json file is a structured plain text file, and was generated using
 Python's json module. The xyz file is a common plain text file for
 chemical structure, and was generated using the VMD program.
DOI: 10.5061/dryad.1c59zw3tc
title: A meta-analysis of effects of physiological integration in clonal plants under homogeneous vs. heterogeneous environments

description: Summary 1. Clonal plants play key roles in maintaining community
 productivity and stability in many ecosystems. Connected individuals
 (ramets) of clonal plants can translocate and share e.g. photosynthates,
 water and nutrients, and such physiological integration may affect
 performance of clonal plants both in heterogeneous and homogeneous
 environments. However, we still lack a general understanding of whether or
 how physiological integration in clonal plants differs across homogeneous
 vs. heterogeneous environments. 2. We compiled data from 198 peer reviewed
 scientific studies conducted in 19 countries with 108 clonal plant species
 from 35 families, and carried out a meta-analysis of effects of
 physiological integration on 16 traits related to plant growth,
 morphology, physiology or allocation. Our analyses evaluated these
 relationships in A) heterogeneous environments where at least one resource
 essential for plant growth (e.g. light, soil water and mineral nutrients)
 or non-resource factor (e.g. grazing, trampling and burial) is spatially
 non-uniformly distributed, and B) homogeneous environments where all these
 factors are spatially uniformly distributed. 3. Physiological integration
 increased growth of whole clones in both homogeneous and heterogeneous
 environments due to its highly significant contribution to growth of
 recipient ramets. Integration did not affect growth of donor ramets in
 heterogeneous environments, but decreased it in homogeneous environments.
 4. Integration affected physiological traits of donor ramets in neither
 homogeneous nor heterogeneous environments. It did not affect any
 physiological traits of recipient ramets in homogeneous environments, but
 increased most of them in heterogeneous environments. For donor ramets,
 integration increased height by 53% and internode length by 37% in
 heterogeneous environments, but had no effect in homogeneous environments.
 For recipient ramets, integration increased height by 73% in homogeneous
 environments and by 115% in heterogeneous environments, and increased
 internode length by 35% only under heterogeneous environments. In
 heterogeneous environments, integration increased biomass allocation to
 roots of donor ramets under high water/nutrient conditions and decreased
 it under high light. 5. Physiological integration plays a strong role in
 clonal plant physiology, morphology, and growth, especially for recipient
 ramets in heterogeneous environments. Therefore, physiological integration
 may have contributed to the widespread of clonal plants in nature and
 their dominance in many ecosystems. It may also play important roles in
 invasion success of alien clonal plants and in maintaining functions and
 stability of ecosystems where clonal plants are abundant.
DOI: 10.5061/dryad.s7h44j15s
title: Clinical data for individuals from families with SLC32A1 variants

description: Objective: To identify the causative gene in a large unsolved family with
 genetic epilepsy with febrile seizures plus (GEFS+), we sequenced the
 genomes of family members, and then determined the contribution of the
 identified gene to the pathogenicity of epilepsies by examining sequencing
 data from 2772 additional patients. Methods: We performed whole genome
 sequencing of three members of a GEFS+ family. Subsequently, whole exome
 sequencing (ES) data from 1165 epilepsy patients from the Epi4K dataset
 and 1329 Australian epilepsy patients from the Epi25 dataset was
 interrogated. Targeted resequencing was performed on 278 patients with FS
 or GEFS+ phenotypes. Variants were validated and familial segregation
 examined by Sanger sequencing. Results: Eight previously
 unreported missense variants were identified in SLC32A1, coding for the
 vesicular inhibitory amino acid co-transporter VGAT. Two variants co-
 segregated with the phenotype in two large GEFS+ families containing eight
 and ten affected individuals, respectively. Six further variants were
 identified in smaller families with GEFS+ or idiopathic generalized
 epilepsy (IGE). Conclusions: Missense variants in SLC32A1 cause GEFS+ and
 IGE. These variants are predicted to alter GABA transport into synaptic
 vesicles, leading to altered neuronal inhibition. Examination of further
 epilepsy cohorts will determine the full genotype-phenotype spectrum
 associated with SLC32A1 variants.
DOI: 10.5061/dryad.zgmsbcc97
title: Genetic insights into the globally invasive and taxonomically problematic tree genus Prosopis

description: Accurate taxonomic identification of alien species is crucial to detect
 new incursions, prevent or reduce the arrival of new invaders and
 implement management options such as biological control. Globally, the
 taxonomy of non-native Prosopis species is
 problematic due to misidentification and extensive hybridization. We
 performed a genetic analysis on
 several Prosopis species, and their putative hybrids,
 including both native and non-native populations, with a special
 focus on Prosopis invasions in Eastern Africa (Ethiopia,
 Kenya and Tanzania). We aimed to clarify the taxonomic placement
 of non-native populations and to infer the introduction histories
 of Prosopis in Eastern Africa. DNA sequencing data
 from nuclear and chloroplast markers
 showed high homology (almost 100%) between most species
 analysed. Analyses based on seven nuclear microsatellites confirmed weak
 population genetic structure among Prosopis species.
 Hybrids and polyploid individuals were recorded in both native and
 non-native populations. Invasive genotypes of P.
 juliflora in Kenya and Ethiopia could have a similar native
 Mexican origin, while Tanzanian genotypes likely are from a different
 source. Native Peruvian Prosopis pallida genotypes
 showed high similarity with non-invasive genotypes from Kenya. Levels of
 introduced genetic diversity, relative to native populations, suggest that
 multiple introductions of P. juliflora and P.
 pallida occurred to Eastern Africa. Polyploidy may explain the
 successful invasion of P. juliflora in Eastern Africa.
 The polyploid Prosopis juliflora was highly
 differentiated from the rest of the (diploid) species within the genus.
 The lack of genetic differentiation between most diploid species in their
 native ranges supports the notion that hybridization between allopatric
 species may occur frequently when they are co-introduced into non-native
 areas. For regulatory purposes, we propose to treat
 diploid Prosopis taxa from the Americas as a single
 taxonomic unit in non-native ranges.
description: Eleven previously-published nuclear microsatellite loci were amplified in a variety of <em>Prosopis</em> species. Amplified fragments were submitted for gel capillary electrophoresis at Stellenbosch University’s Central Analytical Facility. Automated allele scoring was done using the GeneMarker version 2.6.4 software (SoftGenetics LLC, Pennsylvania, United States) and all alleles were manually checked. The data is provided in GenAlex format (Peakall and Smouse 2012). Reference: Peakall, R. and Smouse P.E. (2012) GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research-an update. Bioinformatics 28, 2537-2539.
description: Missing data (alleles) are indicated as 0's. A separate tab
 in the spreadsheet provide metadat on location and species
 identities.
DOI: 10.5061/dryad.c59zw3r67
title: Raw nucleotide counts for clinal Misty Lake and stream stickleback samples

description: How ecological divergence causes strong reproductive isolation between
 populations in close geographic contact remains poorly understood at the
 genomic level. We here study this question in a stickleback fish
 population pair adapted to contiguous, ecologically different lake and
 stream habitats. Clinal whole-genome sequence data reveal numerous genome
 regions (nearly) fixed for alternative alleles over a distance of just a
 few hundred meters. This strong polygenic adaptive divergence must
 constitute a genome-wide barrier to gene flow because a steep cline in
 allele frequencies is observed across the entire genome, and because the
 cline center co-localizes with the habitat transition. Simulations confirm
 that such strong divergence can be maintained by polygenic selection
 despite high dispersal and small per-locus selection coefficients.
 Finally, comparing samples from near the habitat transition before and
 after an unusual ecological perturbation demonstrates the fragility of the
 balance between gene flow and selection. Overall, our study highlights the
 efficacy of divergent selection in maintaining reproductive isolation
 without physical isolation, and the analytical power of studying
 speciation at a fine eco-geographic and genomic scale.  
description: This data set contains raw nucleotide counts across all
 genome-wide base positions for 13 total clinal stickleback field samples
 from the Misty Lake watershed on Vancouver Island, Canada (11 different
 clinal locations; one location is represented by 3 temporal replicates).
 Each sample represents a DNA pool obtained by combining equimolar DNA from
 dozens of individuals. The samples were Illumina-sequenced and aligned to
 the stickleback reference genome. Finally, the nucleotide counts were
 generated with the <em>pileup</em> R function applied to each
 of the 13 alignments.
description: For each sample, the nucleotide count data ('freqSum')
 are provided separately for each of the 21 chromosomes, plus for a
 scaffold lacking in the stickleback genome assembly (pitx1), for the
 artificial chromosome combining all unanchored scaffolds (chrUn), and for
 the mitochondrial chromosome (chrM). Hence, there are 24 total nucleotide
 count data files per sample site. The sample site identifiers are
 incorporated in all file names and correspond to the sample site names
 used in the paper. For the marsh site M1, 'M1' denotes the main
 sample used for the standard genomic analyses, while 'M1_F' and
 'M1_17' represent the same site sampled during the flood and one
 year later (2017 as oppopsed to 2016). In each nucleotide count file, the
 first column specifies the chromosome, the second column gives the genomic
 position, and the remaining columns indicate how often each of the four
 nucleotides was observed across the alignment. The data are ordinary text
 files (.txt) provided as a gzip-compressed tar archive. The compressed
 archive uses 25.4 Gb, the uncompressed archive 139.1 Gb of disk
 space.
DOI: 10.15468/dl.m7sygr
title: Occurrence Download

description: A dataset containing 36 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-95.37146 18.82759,-95.30501 18.28763,-94.69859 18.31255,-94.75674 18.70298,-95.01426 18.77775,-95.37146 18.82759))",
 "OccurrenceStatus is Present",
 "TaxonKey is Macrobrachium carcinus"
 ]
}

 The dataset includes 36 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002686-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.