cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.zkh1893fs
title: The LakePulse Metagenome-Assembled Genome catalogue

description: Lakes are heterogenous ecosystems inhabited by a rich microbiome whose
 genomic diversity is poorly defined. We present a continental-scale study
 of metagenomes representing 6.5-million km2 of the most lake-rich
 landscape on Earth. Analysis of 308 Canadian lakes resulted in a
 metagenome-assembled genome (MAG) catalogue of 1,008 mostly novel
 bacterial genomospecies. Lake trophic state was a leading driver of
 taxonomic and functional diversity among MAG assemblages, reflecting the
 responses of communities profiled by 16S rRNA amplicons and gene-centric
 metagenomics. Coupling the MAG catalogue with watershed geomatics revealed
 terrestrial influences of soils and land use on assemblages. Agriculture
 and human population density were drivers of turnover, indicating
 detectable anthropogenic imprints on lake bacteria at the continental
 scale. The sensitivity of bacterial assemblages to human impact reinforces
 lakes as sentinels of environmental change. Overall, the LakePulse MAG
 catalogue greatly expands the freshwater genomic landscape, advancing an
 integrative view of diversity across Earth's microbiomes.
description: Please see our publication for detailed methods. Scripts
 associated with this study are available at https://github.com/rebeccagarner/lakepulse_mags.
description: Metagenome-assembled genome (MAG) contig nucleotide
 sequences are provided in FASTA format (.fa file extension).
 MAG amino acid sequences are provided in FASTA format
 (.faa). MAG genomic features are provided in General
 Feature Format v. 3 (.gff). Metagenome co-assembly
 contig nucleotide sequences are provided in compressed FASTA format
 (.fa.gz).
DOI: 10.5061/dryad.msbcc2g41
title: Data for: The pathogenic T42A mutation in SHP2 rewires interaction specificity and enhances signaling

description: Mutations in the tyrosine phosphatase SHP2 are associated with various
 human diseases. Most of these mutations increase the basal catalytic
 activity of SHP2 by disrupting auto-inhibitory interactions between its
 phosphatase domain and N-terminal SH2 (phosphotyrosine recognition)
 domain. By contrast, several other disease-associated mutations located in
 the ligand-binding pockets of the N- or C-terminal SH2 domains do not
 increase basal activity and likely exert their pathogenicity through
 alternative mechanisms. We lack a molecular understanding of how these SH2
 mutations impact SHP2 structure, activity, and signaling. Here, we
 characterize five SHP2 SH2 domain ligand-binding pocket mutants through a
 combination of high-throughput biochemical screens, biophysical and
 biochemical measurements, molecular dynamics simulations, and cellular
 assays. We show that, while several of these mutants alter binding
 affinity to phosphorylation sites, the T42A mutation in the N-SH2 domain
 is unique in that it also alters ligand-binding specificity. The
 functional consequence of this altered specificity is that the T42A mutant
 has biased sensitivity toward a subset of activating ligands. Our study
 highlights an example of a nuanced mechanism of action for a
 disease-associated mutation, characterized by a change in protein-protein
 interaction specificity that alters enzyme activation.
description: The molecular dynamics data were generated using the Amber
 Molecular Dynamics Package, as described in the associated manuscript.
 Data were processed using the CPPTRAJ program within AmberTools. Deep
 sequencing data are the result of high-throughput peptide display screens,
 conducted as described in the manuscript. Data were generated using an
 Illumina MiSeq or NextSeq instrument. Data were processed in three steps:
 (1) FLASh (https://ccb.jhu.edu/software/FLASH/) was used for paired-end read merging, (2) CutAdapt (https://cutadapt.readthedocs.io/en/stable/) was used to trim flanking sequences, and (3) trimmed sequences were translated and counted using in-house Python scripts (https://github.com/nshahlab/2022_Li-et-al_peptide-display) as described in PMID: 36927728.
description: Molecular dynamics trajectories can be opened/analyzed using
 AmberTools, VMD, or other common molecular dynamics visualization and
 analysis software. The *.pse files can be viewed using the PyMOL molecular
 graphics software. FASTQ sequencing files can be read using any plain text
 editor and analyzed/processed using any common tool for analyzing FASTQ
 sequence files.
DOI: 10.5061/dryad.xd2547dnv
title: Data from: Genomic diversity and geographical structure of the Pyrenean desman

description: The Pyrenean desman (Galemys pyrenaicus) is a small semi-aquatic mammal
 endemic to the Iberian Peninsula. The species has recently experienced a
 strong decline and some of its populations are severely threatened with
 extinction. To help in the preservation of this species, it is critical to
 understand its genetic structure and main evolutionary units, as these may
 have specific local adaptations and could be of great conservation value.
 Sequencing reduced representation libraries (ddRAD) from 26 specimens
 selected from across its entire range, we obtained around 45,000 loci per
 specimen and 1185 single nucleotide polymorphisms. Heterozygosity varied
 substantially among individuals from different areas. Interestingly,
 specimens from the southeastern Pyrenees had some of the lowest
 proportions of heterozygous positions inferred from genome-wide data in
 mammals so far. In addition, we estimated a tree reflecting genomic
 divergence, performed a principal component analysis, and carried out a
 Bayesian analysis of the population structure. Combined evidence supported
 the existence of five distinct genomic clusters largely coincident with
 the main mountain ranges where the species occurs, with few specimens
 presenting relevant admixture levels. There was good correspondence
 between these populations and the mitochondrial lineages detected in a
 previous study, yet substantial differences in some areas demonstrate the
 importance of performing genomic analysis to reveal the whole population
 history. Although the analysis of further specimens is necessary to better
 characterize the distribution of the different evolutionary units, the
 distinctive geographical structure of this species revealed by the genomic
 data should be considered in future conservation plans.
DOI: 10.5061/dryad.pg4f4qrvz
title: Site-directed placement of three-dimensional DNA origami

description: The combination of lithographic methods with 2D DNA origami self-assembly
 has led, among others, to the development of photonic crystal cavity
 arrays and the exploration of sensing nanoarrays where molecular devices
 are patterned on the sub-micron scale. Here we extend this concept to the
 third dimension by mounting 3D DNA origami onto nano-patterned substrates,
 followed by silicification to provide mechanical and chemical stability.
 We created fully addressable, three-dimensional nanopatterns of hybrid
 DNA-silica structures with heights up to 50 nm and feature size in the
 sub-10-nm regime. Our versatile and scalable method relying on
 self-assembly at ambient temperatures offers the potential to 3D-position
 any inorganic and organic components compatible with DNA origami
 nanoarchitecture, demonstrated with gold nanoparticles. This way of
 nanotexturing could provide a route for the low-cost production of complex
 and 3D-patterned surfaces and integrated devices designed on the molecular
 level while reaching macroscopic dimensions.
DOI: 10.5061/dryad.n5tb2rc1m
title: Timing of invasive species removal influences nonnative biotic resistance and trajectories of community reassembly

description: As biological invasions increasingly threaten biodiversity, the removal of
 invasive nonnative species emerges as a possibility to recover the
 structure and function of native communities. Yet, we have limited
 knowledge of how communities assemble after nonnative removals. Since most
 ecosystems are invaded by multiple nonnative species, the impact of their
 removal likely depends on the interactions among nonnative species which,
 in turn, are contingent on the environmental context in which they
 occur.  We evaluated the community assembly after the targeted
 removal of two highly invasive shrubs, Sweetbriar rose (Rosa rubiginosa)
 and Scotch broom (Cytisus scoparius). The removal was performed at two
 different times in the growing season (early or late removal) in field and
 mesocosm communities. In search of general patterns across species, we
 modeled species responses as a function of their origin (i.e., native /
 nonnative) and functional traits. We found evidence for negative and
 asymmetric interactions between dominant invasive species that translated
 into changes in the abundances of the rest of the species in the
 community. Depending on the identity of the removed species, the removal
 of invasive species affected community assembly by promoting other
 nonnative species or hindering the performance of native species. These
 effects were modulated by the timing of removal and did not depend on leaf
 or seed traits. Synthesis: Accounting for nonnative interactions and their
 temporal dependency should improve our inferences about assembly
 processes and the effectiveness of nonnative removal aimed at
 reducing the accumulation of nonnatives.
DOI: 10.5061/dryad.p2ngf1vws
title: Species delimitation with limited sampling: an example from rare trapdoor spider genus Cyclocosmia (Mygalomorphae, Halonoproctidae)

description: The outcome of species delimitation depends on many factors, including
 conceptual framework, study design, data availability, methodology
 employed, and subjective decision-making. Obtaining sufficient taxon
 sampling in endangered or rare taxa might be difficult, particularly when
 non-lethal tissue collection cannot be utilized. The need to avoid
 overexploitation of the natural populations may thus limit the
 methodological framework available for downstream data analyses and bias
 the results. We test species boundaries in rare North American trapdoor
 spider genus Cyclocosmia Ausserer (1871) inhabiting the Southern Coastal
 Plain biodiversity hotspot with the use genomic data and two multispecies
 coalescent model methods. We evaluate the performance of each methodology
 within a limited sampling framework. To mitigate the risk of species
 over-splitting, common in taxa with highly structured populations, we
 subsequently implement a species validation step via genealogical
 diversification index (gdi), which accounts for both genetic isolation and
 gene flow. We delimited eight geographically restricted lineages within
 North American Cyclocosmia, suggesting that major river drainages in the
 region are likely barriers to dispersal. Our results suggest that
 utilizing BPP in the species discovery step might be a good option for
 datasets comprising hundreds of loci, but fewer individuals, which may be
 a common scenario for rare taxa. However, we also show that such results
 should be validated via gdi, in order to avoid over-splitting.
description: Genomic data were obtained via Anchored Hybrid Enrichment (AHE)
 sequencing.
description: Any type of text editor; Geneious
DOI: 10.5061/dryad.cfxpnvxbn
title: Potato super pangenome v1.0

description: Potato (Solanum sp., family Solanaceae) is the most important noncereal
 food crop globally. It has over 100 wild relatives in the Solanum section
 Petota, which features species with both sexual and asexual reproduction
 and varying ploidy levels. A pangenome of Solanum section Petota composed
 of 296 accessions was constructed including diploids and polyploids
 compared via presence/absence variation (PAV). The Petota core (genes
 shared by at least 97% of the accessions) and shell genomes (shared by 3
 to 97%) are enriched in basic molecular and cellular functions, while the
 cloud genome (genes present in less than 3% of the member accessions)
 showed enrichment in transposable elements (TEs). Comparison of PAV in
 domesticated vs. wild accessions was made, and a phylogenetic tree was
 constructed based on PAVs, grouping accessions into different clades,
 similar to previous phylogenies produced using DNA markers. A cladewise
 pangenome approach identified abiotic stress response among the core genes
 in clade 1+2 and clade 3, and flowering/tuberization among the core genes
 in clade 4. The TE content differed between the clades, with clade 1+2,
 which is composed of species from North and Central America with
 reproductive isolation from species in other clades, having much lower TE
 content compared to other clades. In contrast, accessions with in vitro
 propagation history were identified and found to have high levels of TEs.
 Results indicate a role for TEs in adaptation to new environments, both
 natural and artificial, for Solanum section Petota.
DOI: 10.15468/dl.nunh2j
title: Occurrence Download

description: A dataset containing 1124867 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Calluna vulgaris"
 ]
}

 The dataset includes 1124867 records from 1912 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003511-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.tfdd5w
title: Occurrence Download

description: A dataset containing 579 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Brazil",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Polybia ignobilis"
 ]
}

 The dataset includes 579 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0025414-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.d97y4q
title: Occurrence Download

description: A dataset containing 1282348 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Lauraceae"
 ]
}

 The dataset includes 1282348 records from 2832 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005636-260129131611470/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.prxaa8
title: Occurrence Download

description: A dataset containing 3376 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Uganda",
 "DatasetKey is one of (EOD – eBird Observation Dataset, NMNH Extant Specimen Records (USNM, US))",
 "Geometry POLYGON((32.31862 0.24639,32.8718 0.24639,32.8718 0.75357,32.31862 0.75357,32.31862 0.24639))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Month is April"
 ]
}

 The dataset includes 3376 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016492-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gbjmad
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "BasisOfRecord is one of (Human Observation, Machine Observation, Occurrence evidence, Observation)",
 "TaxonKey is one of (Glyphorynchus spirurus (Vieillot, 1819))",
 "Country is one of (Afghanistan, Armenia, Azerbaijan, Bahrain, Bangladesh, Bhutan, Brunei Darussalam, Cambodia, China, Cyprus, Georgia, Hong Kong, India, Indonesia, Iran (Islamic Republic of), Iraq, Israel, Japan, Jordan, Kazakhstan, Korea (Democratic People’s Republic of), Korea, Republic of, Kuwait, Kyrgyzstan, Lao People’s Democratic Republic, Lebanon, Macao, Malaysia, Maldives, Mongolia, Myanmar, Nepal, Oman, Pakistan, Palestine, State of, Philippines, Qatar, Saudi Arabia, Singapore, Sri Lanka, Syrian Arab Republic, Tajikistan, Thailand, Timor-Leste, Türkiye, Turkmenistan, United Arab Emirates, Uzbekistan, Viet Nam, Yemen)"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016490-250525065834625/datasets/export for details.
DOI: 10.15468/dl.kmtw32
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "ScientificName" : [
 "is Mephitis macroura"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001739-250424135625364/datasets/export for details.
DOI: 10.15468/dl.mrjbu7
title: Occurrence Download

description: A dataset containing 81807 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Orectolobiformes"
 ]
}

 The dataset includes 81807 records from 411 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001725-250424135625364/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xsn4gr
title: Occurrence Download

description: A dataset containing 6 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Euphilotes pallescens confusa Pratt & J.Emmel, 1998"
 ]
}

 The dataset includes 6 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001740-250424135625364/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.z3buhv
title: Occurrence Download

description: A dataset containing 6 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Euphilotes pallescens confusa Pratt & J.Emmel, 1998"
 ]
}

 The dataset includes 6 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001741-250424135625364/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.7944/d0ap-f077
title: Dataset: GPS locations of Bobcats on and around Laguna Atascosa National Wildlife Refuge.

description: U.S. Fish and Wildlife Service (USFWS) studied bobcats around Laguna Atascosa National Wildlife Refuge in Texas. Bobcats were captured in box-traps, sedated, anesthetized, fit with a GPS collar, and released on the Refuge.  GPS collars were used to assess movements of bobcats on and around the Refuge for various projects relating to the recovery of the endangered ocelot. This dataset includes around over 4,400 locations from 5 bobcats from 2011-2021. These locations are stored using latitude and longitude with a WGS84 reference system.
DOI: 10.6084/m9.figshare.29218688
title: Original gene gun without the FGB (No Barrel) CFD and particle physics simulation.

description: Simulation of original gene gun without FGB (No Barrel).
DOI: 10.6084/m9.figshare.29218688.v1
title: Original gene gun without the FGB (No Barrel) CFD and particle physics simulation.

description: Simulation of original gene gun without FGB (No Barrel).
DOI: 10.18739/a27940w32
title: Thaw depth measurements from the Circumpolar Active Layer Monitoring (CALM) project for site 'Barrow, CRREL Plots' (U2), Alaska North Slope, United States, Alaska (1962-2023)

description: This site is registered with the Circumpolar Active Layer Monitoring (CALM) program. It is one among a network of sites that represent a coordinated effort to standardize the collection and access to thaw measurements in representative undisturbed permafrost landscapes. This dataset contains long-term spatial thaw depth observations using mechanical probing. To ensure relative consistency within the record, end-of-season measurement dates are within the same Julian calendar week during the height of the thaw season (mid-August to mid-September). It is important to note that the date of maximum annual thaw, interpreted as the active layer thickness, can vary from year to year and between sites.
DOI: 10.15468/dl.23urd9
title: Occurrence Download

description: A dataset containing 47 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Vachellia farnesiana",
 "Country is India",
 "HasCoordinate is true"
 ]
}

 The dataset includes 47 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0024923-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.r9f2j5
title: Occurrence Download

description: A dataset containing 33 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Vachellia farnesiana",
 "Country is Guatemala",
 "HasCoordinate is true"
 ]
}

 The dataset includes 33 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0024921-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.73a22g
title: Occurrence Download

description: A dataset containing 616 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Liriodendron chinense"
 ]
}

 The dataset includes 616 records from 68 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0049693-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3xw7q4
title: Occurrence Download

description: A dataset containing 8234 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Neochonetes Muir-Wood, 1962"
 ]
}

 The dataset includes 8234 records from 31 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010216-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17632/5hzbvn5fr2
title: EVAL3Di supplementary

description: Supplementary tables and figures for the article entitled “Remote Evaluation of General Skin Diseases using 3D Total Body Photography: An Observer Agreement Study”
DOI: 10.17632/5hzbvn5fr2.1
title: EVAL3Di supplementary

description: Supplementary tables and figures for the article entitled “Remote Evaluation of General Skin Diseases using 3D Total Body Photography: An Observer Agreement Study”
DOI: 10.17632/cn5x7gmhv4.1
title: LINF_180019900

description: calcium-binding domain-containing protein; Leishmania infantum (strain JPCM5)
DOI: 10.15468/dl.qa4vk4
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Winteria telescopa Brauer, 1901",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((35.9648 -7.1504,26.9648 -7.1504,26.9648 -16.1504,35.9648 -16.1504,35.9648 -7.1504))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010034-250525065834625/datasets/export for details.
DOI: 10.17632/cn5x7gmhv4
title: LINF_180019900

description: Calcium-binding domain-containing protein | FAZ34; Leishmania infantum (strain JPCM5)
DOI: 10.17632/cn5x7gmhv4.2
title: LINF_180019900

description: Calcium-binding domain-containing protein | FAZ34; Leishmania infantum (strain JPCM5)