cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.c866t1g8r
title: Data for: Self-cleaving 2A peptides allow for expression of multiple genes in Dictyostelium discoideum

description: The social amoeba Dictyostelium discoideum is a model for a wide range of
 biological processes including chemotaxis, cell-cell communication,
 phagocytosis, and development.  Interrogating these processes
 with modern genetic tools often requires the expression of multiple
 transgenes. While it is possible to transfect multiple transcriptional
 units, the use of separate promoters and terminators for each gene leads
 to large plasmid sizes and possible interference between units. In many
 eukaryotic systems this challenge has been addressed through polycistronic
 expression mediated by 2A viral peptides, permitting efficient,
 co-regulated gene expression. Here, we screen the most commonly used 2A
 peptides, porcine teschovirus-1 2A (P2A), Thosea asigna virus 2A (T2A),
 equine rhinitis A virus 2A (E2A), and foot-and-mouth disease virus 2A
 (F2A), for activity in D. discoideum and find that all the screened 2A
 sequences are effective. However, combining the coding sequences of two
 proteins into a single transcript leads to notable strain-dependent
 decreases in expression level, suggesting additional factors regulate gene
 expression in D. discoideum that merit further investigation. Our results
 show that P2A is the optimal sequence for polycistronic expression in D.
 discoideum, opening up new possibilities for genetic engineering in this
 model system.
DOI: 10.5061/dryad.g79cnp5rj
title: Evolutionary causes and consequences of ungulate migration

description: Ungulate migrations are crucial for maintaining abundant populations and
 functional ecosystems. However, little is known about how or why migratory
 behavior evolved in ungulates. To investigate the evolutionary origins of
 ungulate migration, we employed phylogenetic path analysis using a
 comprehensive species-level phylogeny of mammals. We found that 95 of 207
 extant ungulate species are at least partially migratory, with migratory
 behavior originating independently in 17 lineages. The evolution of
 migratory behavior is associated with reliance on grass forage and living
 at higher latitudes wherein seasonal resource waves are most prevalent.
 Indeed, originations coincide with mid-Miocene cooling and the subsequent
 rise of C4 grasslands. Also, evolving migratory behavior supported the
 evolution of larger bodies, allowing ungulates to exploit novel ecological
 space. Reconstructions of migratory behavior further reveal that seven of
 ten recently extinct species were probably migratory, suggesting that
 contemporary migrations are important models for understanding the ecology
 of the past.
description: Data were collected via targeted literature search and/or were
 generated from IUCN species range maps and the Global Inventory Modelling
 and Mapping Studies database (GIMMS) Normalized Difference Vegetation
 Index (NDVI) remote sensing product.
description: Please consult the correpsonding README file for information on
 data sources and variable meanings.
DOI: 10.5061/dryad.qfttdz0k2
title: Data for: Wild microbiomes of striped plateau lizards vary with sex, body size, and reproductive season

description: Long-term natural studies are valuable for examining the effects of host
 demographics and environmental factors on animal microbiomes, and how
 those effects interact and shift over time. We examined how the cloacal
 microbiome of Sceloporus virgatus (the striped plateau lizard) varies
 under natural conditions in southeastern Arizona, USA, in a multi-year
 study. Cloacal swabs were collected from wild-caught lizards across their
 entire active season over three years. Analyses of 16S rRNA data generated
 on the Illumina platform revealed cloacal microbiomes of S. virgatus vary
 as a function of sex, season, size, and reproductive state, and do so
 independently of one another. Briefly, microbial diversity was higher in
 females than in males, increased with body size, was lowest in both sexes
 during the reproductive season, and was lowest in females when they were
 vitellogenic. It was not significantly affected by hibernation. This study
 highlights the importance of long term, wide scale microbiome studies for
 capturing accurate perspectives on microbiome diversity and composition in
 a given species. It also serves as a warning for comparisons of
 microbiomes across species, as each may be under a different suite of
 selective pressures from external or innate factors, which may differ in a
 species-specific manner.
description: Sequences of the 16s V4 regions were generated at IBest Genomics
 Core (University of Idaho) on the Illumina MiSeq platform. Detailed
 methodology can be found in Bunker et al., 2022, Wild microbiomes of
 striped plateau lizards vary with sex, body size, and reproductive season
 (2022), or in the attached README file.
DOI: 10.5061/dryad.b2rbnzshm
title: Phylogeography of the tepui brush finch, Atlapetes personatus (Passeriformes: Passerellidae): Extensive differentiation on the sky islands of the Venezuelan Pantepui

description: The biogeography and genetic structure of species endemic to the high
 elevation sky islands (tepuis) of the Guiana Shield in eastern and
 southern Venezuela and adjacent areas of Brazil and Guyana are poorly
 known. We investigated the phylogeography and population structure of the
 tepui brush finch (Atlapetes personatus) as an exemplar of that biota.
 Mitochondrial DNA sequences revealed three monophyletic clades that
 correspond to major morphological subspecies groups occurring in eastern,
 southern, and northwestern regions of the Pantepui. Differentiation among
 the clades accounted for 95% of the total genetic variance. DNA sequences
 from three nuclear loci also showed marked divergence among those three
 regions. Estimates of gene flow between regions and sampled populations
 were all less than one individual per generation. Consequently, these
 subspecies groups ought to be recognized as species-level taxa. The
 results suggest there is more large-scale biogeographic structure within
 the Pantepui region than generally recognized. Additionally, within two of
 the three regions, genetic variance among tepuis was substantial at both
 mitochondrial and nuclear loci. Many of the sampled populations appear to
 be genetically independent units that are nearly cryptic morphologically.
 The sampled tepuis may be islands of habitat for this taxon and for
 conservation purposes.
DOI: 10.5061/dryad.w3r2280sq
title: Combining GWAS and population genomic analyses to characterize coevolution in a legume-rhizobia symbiosis

description: The mutualism between legumes and rhizobia is clearly the product of past
 coevolution. However, the nature of ongoing evolution between these
 partners is less clear. To characterize the nature of recent coevolution
 between legumes and rhizobia, we used population genomic analysis to
 characterize selection on functionally annotated symbiosis genes as well
 as on symbiosis gene candidates identified through a two-species
 association analysis. For the association analysis, we inoculated each of
 202 accessions of the legume host Medicago truncatula with a community of
 88 Ensifer meliloti strains. Multi-strain inoculation, which better
 reflects the ecological reality of rhizobial selection in nature than
 single-strain inoculation, allows strains to compete for nodulation
 opportunities and host resources and for hosts to preferentially form
 nodules and provide resources to some strains. We found extensive host by
 symbiont, i.e., genotype-by-genotype, effects on rhizobia fitness and some
 annotated rhizobia genes bear signatures of recent positive selection.
 However, neither genes responsible for this variation nor annotated host
 symbiosis genes are enriched for signatures of either positive or
 balancing selection. This result suggests that stabilizing selection
 dominates selection acting on symbiotic traits and that variation in these
 traits is under mutation-selection balance. Consistent with the lack of
 positive selection acting on host genes, we found that among-host
 variation in growth was similar whether plants were grown with rhizobia or
 N-fertilizer, suggesting that the symbiosis may not be a major driver of
 variation in plant growth in multi-strain contexts.
description: These data were collected from an experiment with 202 accessions
 of <em>Medicago truncatula</em> inoculated with a mixture of
 88 strains of <em>Ensifer</em> (Sinorhizobium)
 <em>meliloti</em>. The frequency of each strain was estimated
 before inoculation and in the nodules at the end of the experiment using
 pooled genome sequencing. The data include association analyses (GWAS) on
 the differences in strain composition among host genotypes and the
 differences in fitness among rhizobial strains.
description: Please see the README file for details on the data archived here.
 All files are some variety of plain text format, which can opened with
 text editors, spreadsheet programs, and standard bioinformatic
 tools.
DOI: 10.5061/dryad.sn02v6x65
title: Data from: Shifts in growth light optima among diatom species support their succession during the spring bloom in the Arctic

description: Diatoms of the Arctic Ocean annually experience extreme changes of light
 environment linked to photoperiodic cycles and seasonal variations of the
 snow and sea-ice cover extent and thickness which attenuate light
 penetration in the water column. Arctic diatom communities exploit this
 complex seasonal dynamic through a well-documented species succession
 during spring, beginning in sea-ice and culminating in massive
 phytoplankton blooms underneath sea-ice and in the marginal ice zone. The
 pattern of diatom taxa sequentially dominating this succession is
 relatively well conserved interannually, and taxonomic shifts seem to
 align with habitat transitions. To understand whether differential
 photoadaptation strategies among diatom taxa explain these recurring
 succession sequences, we coupled lab experiments with field work in Baffin
 Bay at 67.5°N. Based on field data, we selected five diatom species
 typical of different ecological niches and measured their growth rates
 under light intensity ranges representative of their natural habitats. To
 characterize their photoacclimative responses, we sampled pigments and
 total particulate carbon, and conducted 14C-uptake photosynthesis response
 curves and variable fluorescence measurements. We documented a gradient in
 species respective light intensity for maximal growth suggesting divergent
 light response plasticity, which for the most part align with species
 sequential dominance. Other photophysiological parameters supported this
 ecophysiological framing, although contrasts were always clear only
 between succession endmembers, Nitzschia frigida and Chaetoceros
 neogracilis. To validate that these photoacclimative responses are
 representative of in situ dynamics, we compared them to the chlorophyll
 a-specific light-limited slope (α*) and saturated rate of photosynthesis
 (P*M), monitored in Baffin Bay on sea-ice and planktonic communities. This
 complementary approach confirmed that unusual responses in α* and P*M as a
 function of light history intensity are similar between sentinel sympagic
 species N. frigida and natural ice-core communities. While no
 light-history-dependent trends were observed in planktonic communities,
 their α* and P*M values were in the range of measurements from our
 monospecific cultures.  Synthesis. Our results suggest that
 Arctic diatoms species photoadaptation strategy is tuned to the light
 environment of the habitats in which they dominate and indeed drives the
 seasonal taxonomic succession.
DOI: 10.57903/uj/zgfgic
title: Many-body localization crossover is sharper in a quasiperiodic potential - replication data

description: This dataset contains the data (average gap ratio, entanglement entropy, and Schmidt gap) used in the study of MBL crossover in disordered spin chains. It contains a Jupyter notebook named "Many-body localization crossover is sharper in a quasiperiodic potential.ipynb", which will help with the readability of the dataset and generate the figures. Additionally, you can also get a detailed description in the readme.txt files. The generation of the cost function plot (Fig.8 of the manuscript) is described in "CostFunction_KIM_QP.ipynb
DOI: 10.15468/dl.jzk3tf
title: Occurrence Download

description: A dataset containing 649 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is 2021_kbif_joint_survey_insect_specimen_information_nsmk_649"
 ]
}

 The dataset includes 649 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003075-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.dncjsxm21
title: Dataset for: Intercontinental analysis of temperate steppe stream food webs reveals consistent autochthonous support of fishes

description: Quantifying the trophic basis of production for freshwater metazoa at
 broad spatial scales is key to understanding ecosystem function and has
 been a research priority for decades. However, previous lotic food web
 studies have been limited by geographic coverage or methodological
 constraints. We used compound-specific stable carbon isotope analysis of
 amino acids to estimate basal resource contributions to fish consumers in
 streams spanning grassland, montane, and semi-arid ecoregions of the
 temperate steppe biome on two continents. Across a range of stream sizes
 and light regimes, we found consistent trophic importance of aquatic
 resources. Essential amino acids of heterotrophic microbial origin
 generally provided secondary support for fishes, while terrestrial carbon
 did not seem to provide any significant, direct support. These findings
 provide strong evidence for the dominant contribution of carbon to
 higher-order consumers by aquatic autochthonous resources (primarily) and
 heterotrophic microbial communities (secondarily) in temperate steppe
 streams.
DOI: 10.6078/d18m5v
title: Ultrafast two-photon fluorescence imaging of cerebral blood circulation in the mouse brain in vivo

description: Characterizing blood flow dynamics in vivo is critical to understand the
 function of vascular network under physiological and pathological
 conditions. Existing methods for hemodynamic imaging have insufficient
 spatial and temporal resolution to monitor blood flow at cellular level in
 large blood vessels. By employing an ultrafast line-scanning module based
 on free-space angular chirped enhanced delay (FACED), we achieved
 two-photon fluorescence imaging of cortical blood flow at 1,000 2D frames
 and 1,000,000 1D line scans per second in the awake mouse. This
 orders-of-magnitude increase in temporal resolution allowed us to measure
 cerebral blood flow up to 49 mm/s and observe pulsatile blood flow at
 harmonics of heart rate. Directly visualizing red blood cell (RBC) flow
 through vessels down to &gt;800 µm in depth, we characterized
 cortical-layer-dependent flow velocity distributions of capillaries,
 obtained radial velocity profiles and kilohertz 2D velocity mapping of
 multi-file blood flow, and carried out RBC flux measurements from
 penetrating blood vessels.
DOI: 10.5061/dryad.x3ffbg7mp
title: Data for: Screening of stapled peptides for inhibition of calcium-triggered exocytosis

description: The so-called primary interface between the SNARE complex and
 synaptotagmin-1 (Syt1) is essential for Ca2+-triggered neurotransmitter
 release in neuronal synapses. The interacting residues of the primary
 interface are conserved across different species for synaptotagmins (Syt1,
 Syt2, Syt9), SNAP-25, and syntaxin-1A homologs involved in fast
 synchronous release. This Ca2+-independent interface forms prior to
 Ca2+-triggering and plays a role in synaptic vesicle priming. This primary
 interface is also conserved in the fusion machinery, that is, responsible
 for mucin granule membrane fusion. Ca2+ stimulated mucin secretion is
 mediated by the SNAREs syntaxin-3, SNAP-23, VAMP8, synaptotagmin-2, and
 other proteins. Here, we designed and screened a series of
 hydrocarbon-stapled peptides consisting of SNAP-25 fragments that included
 some of the key residues involved in the primary interface as observed in
 high-resolution crystal structures. We selected a subset of four stapled
 peptides that were highly α-helical as assessed by circular dichroism and
 that inhibited both Ca2+-independent and Ca2+-triggered ensemble
 lipid-mixing with neuronal SNAREs and Syt1. In a single-vesicle
 content-mixing assay with reconstituted neuronal SNAREs and
 synaptotagmin-1 or with reconstituted airway SNAREs and synaptotagmin-2,
 the selected peptides also suppressed Ca2+-triggered fusion. Taken
 together, hydrocarbon-stapled peptides that interfere with the primary
 interface consequently inhibit Ca2+-triggered exocytosis. Our inhibitor
 screen suggests that these compounds may be useful to combat mucus
 hypersecretion, that is, a major cause of airway obstruction in the
 pathophysiology of asthma and cystic fibrosis.
description: See Methods in Lai, Y., et al. (2022). Inhibition of
 Ca2+-triggered secretion by hydrocarbon-stapled peptides. Nature, 1–65.
 doi:10.1038/s41586-022-04543-1 and in Lai, Y., et al., Frontiers in
 Pharmacology, https://doi.org/10.3389/fphar.2022.891041 (2022).
description: See README files for instructions. For a quick look, you can use
 ImageJ to inspect the .tif files, and any text editor or spreadsheet
 program to inspect the .txt files.
DOI: 10.5061/dryad.g79cnp5rk
title: Capturing functional relations in ﬂuid-structure interaction via machine learning

description: While fluid-structure interaction (FSI) problems are ubiquitous in various
 applications from cell-biology to aerodynamics, they involve huge
 computational overhead. In this paper, we adopt a machine learning
 (ML)-based strategy to bypass the detailed FSI analysis that requires
 cumbersome simulations in solving the Navier-Stokes (N-S) equations. To
 mimic the effect of fluid on an immersed beam, we have introduced
 dissipation into the beam model with time-varying forces acting on it. The
 forces in a discretized setup have been decoupled via an appropriate
 linear algebraic operation, which generates the ground truth force/moment
 data for the ML analysis. The adopted ML technique, symbolic regression,
 generates computationally tractable functional forms to represent the
 force/moment with respect to space and time. These estimates are fed into
 the dissipative beam model to generate the immersed beam's
 deflections over time, which are in conformity with the detailed FSI
 solutions. Numerical results demonstrate that the ML-estimated continuous
 force and moment functions are able to accurately predict the beam
 deflections under different discretizations.
description: Note: For further understanding of the above flow, please refer
 to Figure 2 of the manuscript: "Capturing functional relations in
 fluid-structure interactionvia machine learning".
 Note: We have uploaded the IB2D code for completeness. However,
 IB2D is an opensource code which is avilable via the following link
 :"https://github.com/nickabattista/IB2d".
DOI: 10.5061/dryad.zw3r2289c
title: Population genetic and environmental data for Chamaecrista fasciculata

description: Chamaecrista fasciculata is a widely distributed, phenotypically variable
 species in the eastern U.S. Whereas studies have demonstrated genetic
 structure and local adaptation in northern areas of its distribution,
 there has been no comparison of genetic variability among populations at
 the southern extent where phenotypic variation is more complex. We
 characterized genetic variation at 14 microsatellite loci for populations
 in Mississippi and Alabama and compared this to variation in a phenotypic
 trait, leaf pubescence. Geographic distance, climatic variables, and
 elevation were evaluated as factors to explain the observed patterns of
 genetic diversity. A significant amount of variation (19%) resided among
 populations, but most variation (68%) was among individuals. Assignment of
 individuals into genetic groups suggests two primary clusters, but these
 groups are not concordant with known geographical or ecological breaks,
 nor phenotypic variants. Genetic structure at a regional scale can be
 characterized as isolation by distance, while environmental factors may
 play a secondary role in limiting gene flow at local scales. Mean
 population FST is strongly associated with allelic diversity and
 heterozygosity, suggesting that genetic drift influences population
 variation. Despite the presence of genetic and phenotypic variation in
 southern populations of C. fasciculata, the lack of concordant patterns
 between these types of variation indicate that they are not driven by the
 same factors. This study demonstrates how local factors differentially
 influence the maintenance of intraspecific variation and suggest the
 southern distributional range is an active area of evolution for C.
 fasciculata
description: The genetic data consist of allelic variation at 14
 microsatellite markers specifically designed from the transcriptome of
 Chamaecrista fasciculata. Alleles were amplified by PCR and assessed using
 fluorescent genotyping methods. The genetic data are provided in GenAlEx
 format.  The environmental data were downloaded from
 the Worldclim dataset based on the GPS coordinate of each sample location
 (taken in the field at the time of collection). 
description: Missing values are coded as 0 in the genetic data set.
DOI: 10.13140/rg.2.2.24657.80482
title: WhatsApp Image 2026-01-28 at 2.29.19 PM
DOI: 10.5281/zenodo.18399904
title: Dataset for paper "First principles study of photocatalytic activity in ZnO-Janus van der Waals heterostructures" (https://doi.org/10.1039/D4CP03691C)
DOI: 10.5281/zenodo.18399903
title: Dataset for paper "First principles study of photocatalytic activity in ZnO-Janus van der Waals heterostructures" (https://doi.org/10.1039/D4CP03691C)
DOI: 10.57707/fmi-b2share.f5d99-3a994
title: Data for manuscript "Emulator-based calibration of a dynamic grassland model using recurrent neural networks and Hamiltonian Monte Carlo" by Aakula et al.

description: Data and python code for the manuscript "Emulator-based calibration of a dynamic grassland model using recurrent neural networks and Hamiltonian Monte Carlo", for performing emulator hyperparameter optimization and training. Python file optimize_LSTM_emulator.py can be used either for training an LSTM emulator with predefined hyperparameters or to optimize hyperparameters from a given hyperparameter space. The training data for each fold is included in the files of shape training_data_fold_{}.parquet. The data is obtained from model simulations, including model inputs (meteorological forcings obtained from ERA5 data), model parameters (sampled from distributions defined in the manuscript) and model (BASGRA) outputs. Text file examples.txt gives instructions and examples on running the script.