cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.7280/d1269d
title: Data from: Consecutive treatments of methamphetamine promote the development of cardiac pathological symptoms in zebrafish

description: Chronic methamphetamine use, a widespread drug epidemic, has been
 associated with cardiac morphological and electrical remodeling, leading
 to the development of numerous cardiovascular diseases. While
 methamphetamine has been documented to induce arrhythmia, most results
 originate from clinical trials from users who experienced different
 durations of methamphetamine abuse, providing no documentation on the use
 of methamphetamine in standardized settings. Additionally, the underlying
 molecular mechanism on how methamphetamine affects the cardiovascular
 system remains elusive. A relationship was sought between cardiotoxicity
 and arrhythmia with associated methamphetamine abuse in zebrafish to
 identify and to understand the adverse cardiac symptoms associated with
 methamphetamine. Zebrafish were first treated with methamphetamine 3 times
 a week over a 2-week duration. Immediately after treatment, zebrafish
 underwent electrocardiogram (ECG) measurement using an in-house developed
 acquisition system for electrophysiological analysis. Subsequent analyses
 of cAMP expression and Ca2+ regulation in zebrafish cardiomyocytes were
 conducted. cAMP is vital to development of myocardial fibrosis and
 arrhythmia, prominent symptoms in the development of cardiovascular
 diseases. Ca2+ dysregulation is also a factor in inducing arrhythmias.
 During the first week of treatment, zebrafish that were administered with
 methamphetamine displayed a decrease in heart rate, which persisted
 throughout the second week and remained significantly lower than the heart
 rate of untreated fish. Results also indicate an increased heart rate
 variability during the early stage of treatment followed by a decrease in
 the late stage for methamphetamine-treated fish over the duration of the
 experiment, suggesting a biphasic response to methamphetamine exposure.
 Methamphetamine-treated fish also exhibited reduced QTc intervals
 throughout the experiment. Results from the cAMP and Ca2+ assays
 demonstrate that cAMP was upregulated and Ca2+ was dysregulated in
 response to methamphetamine treatment. Collagenic assays indicated
 significant fibrotic response to methamphetamine treatment. These results
 provide potential insight into the role of methamphetamine in the
 development of fibrosis and arrhythmia due to downstream effectors of
 cAMP.
DOI: 10.15468/dl.fc7kz2
title: Occurrence Download

description: A dataset containing 51 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Country is Spain",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Polycarpaea filifolia"
 ]
}

 The dataset includes 51 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003554-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.cfxpnvxbj
title: Data and reproducible code for Honor et al: Direct and indirect fitness effects of competition limit evolution of allelopathy in an invading plant

description: Upon introduction to new continents, invading species encounter novel
 communities of consumers, pathogens, and competitors. Both phenotypic
 plasticity and rapid evolution can facilitate adaptation across these
 heterogenous communities, facilitating further invasion. However, the rate
 and extent of adaptive evolution on contemporary timescales can be
 constrained by phenotypic plasticity and limits imposed by genetic
 co-variation for traits under selection. We measured phenotypic plasticity
 and quantified genetic co-variation for growth, competition, and fitness
 among 23 naturally inbred seed families of Alliaria petiolata
 (garlic mustard) collected across its invasive range in eastern North
 America. After growing a self-pollinated generation in a uniform common
 garden to reduce maternal effects, we reared second-generation plants in a
 two-year greenhouse and field experiment with naïve soil from an uninvaded
 habitat. We measured selection gradients and lifetime fitness when reared
 alone, with an intraspecific competitor, and under interspecific
 competition with naïve Acer saccharum (sugar maple) saplings. Total
 glucosinolate production was strongly correlated with the production of
 chlorophyll a (Chl a) (R2 = 0.45) such that first principal
 component (PC1) accounted for 84% of variation in these two traits.
 Furthermore, PC1 exhibited high plasticity across growing environments (p
 &lt; 0.001) with limited broad-sense heritability (H2 = 2.91; p =
 0.08). In contrast, investment in glucosinolate production relative to Chl
 a (PC2) was significantly heritable (H2 =16.91, p &lt; 0.001) with
 minimal plasticity across treatments. Causal analysis revealed that
 plastic variation for higher Chl a + glucosinolate production (PC1) had an
 indirect positive effect on A. petiolata fitness via a direct, negative
 effect on A. saccharum performance. In contrast, heritable variation for
 higher glucosinolate investment (PC2) had a direct, positive effect on A.
 saccharum performance and an indirect negative effect on A. petiolata
 fitness.  Applying causal inference, we find that evolution of
 allelopathy in A. petiolata has been constrained by (i) a lack of genetic
 variation, (ii) selection against glucosinolate investment under
 interspecific competition, and (iii) phenotypic plasticity. These factors
 limit adaptive evolution but maintain fitness during population growth as
 plants switch from interspecific to intraspecific competition during
 invasion.
description: As described in our bioRxiv manuscript and outlined in the
 README.md file.
description: Python (python.org)<br>R (r-cran.org)
DOI: 10.15468/dl.y9upwf
title: Occurrence Download

description: A dataset containing 143 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Country is Spain",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Polycarpaea latifolia"
 ]
}

 The dataset includes 143 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003556-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.cnp5hqc9j
title: Data from: Hemin treatment drives viral reactivation and plasma cell differentiation of EBV latently infected B cells

description: Epstein-Barr virus (EBV) and Plasmodium falciparum have a well described
 role in the development of endemic Burkitt lymphoma (BL), yet the
 mechanisms involved remain unknown. A major hallmark of malarial disease
 is hemolysis and bystander eryptosis of red blood cells, which causes
 release of free heme in large quantities into peripheral blood. We
 hypothesized that heme released during malaria infection drives
 differentiation of latently infected EBV-positive B cells, resulting in
 viral reactivation and release of infectious virus. To test this
 hypothesis, we used the EBV-positive Mutu I B-cell line and treated with
 hemin (the oxidized form of heme) and evaluated for evidence of EBV
 reactivation­. Hemin treatment resulted in the expression of EBV immediate
 early, early and late lytic gene transcripts. In addition, expression of
 CD138, a marker of plasma cells was co-expressed with the late lytic
 protein gp350 on hemin treated Mutu I cells. Finally, DNase-resistant EBV
 DNA indicative of virion production was detected in supernatant. To assess
 the transcriptional changes induced by hemin treatment, RNA sequencing was
 performed on mock- and hemin-treated Mutu I cells, and a shift from mature
 B cell transcripts to plasma cell transcripts was identified. To identify
 the mechanism of hemin-induced B cell differentiation, we measured levels
 of the plasma cell transcriptional repressor, BACH2, that contains
 specific heme binding sites. Hemin treatment caused significant
 degradation of BACH2 by 24 hours post-treatment in four BL cell lines (two
 EBV positive, two EBV negative). Knockdown of BACH2 in Mutu I cells using
 siRNAs significantly increased CD138+gp350+ cells to levels similar to
 treatment with hemin. This suggested that hemin induced BACH2 degradation
 was responsible for plasma cell differentiation and viral reactivation.
 Together, these data support a model where EBV reactivation can occur
 during malaria infection via heme modulation, providing a mechanistic link
 between malaria and EBV. 
description: This data was collected using the following methods: western
 blot, flow cytometry, total RNA sequencing, RT-qPCR, and DNA
 sequencing. 
description: Applications that are needed to access the data files: Flow Jo,
 PowerPoint and GraphPad Prism.
DOI: 10.5061/dryad.7d7wm3817
title: Data from: Quantum computation of frequency-domain molecular response properties using a three-qubit iToffoli gate

description: The quantum computation of molecular response properties on near-term
 quantum hardware is a topic of substantial interest. Computing these
 properties directly in the frequency domain is desirable, but the circuits
 require large depth if the typical hardware gate set consisting of single-
 and two-qubit gates is used. Here, we report the application of a
 high-fidelity multipartite gate, the iToffoli gate, to the computation of
 frequency-domain response properties of diatomic molecules. The iToffoli
 gate enables a ~50% reduction in circuit depth and ~40% reduction in
 circuit execution time compared to the traditional gate set. We show that
 the molecular properties obtained with the iToffoli gate exhibit
 comparable or better agreement with theory than those obtained with the
 native CZ gates. Our work is among the first demonstrations of the
 practical usage of a native multi-qubit gate in quantum simulation, with
 diverse potential applications to near-term quantum computation.
description: The simulated data are obtained from running simulations with the
 Cirq package. The experimental data are collected from a superconducting
 quantum processor located at University of California at Berkeley and
 postprocessed according to the methodologies described in the
 paper.
DOI: 10.15468/dl.j9pmta
title: Occurrence Download

description: A dataset containing 1931 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Hedysarum boreale",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 1931 records from 111 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003553-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.ns1rn8q00
title: Raman spectra and SEM EDX analyses of artifacts resembling Ediacaran / Cambrian fossils

description: This data is related to the paper: "Artifacts resembling Ediacaran /
 Cambrian fossils: how to identify them and avoid their generation"
 submitted for publication in the "Journal of Micropaleontology"
 on March 24, 2023. The reaction between hydrogen peroxide and pyrite can
 lead to the generation of objects very similar to Ediacaran and Cambrian
 fossils, such as Cloudina. This dataset and related paper provides
 criteria to distinguish artifacts from fossils based on their composition
 and structure. This dataset cotains all the Raman spectra and SEM/EDX
 analyses of artifacts that characterize them and are used for discussion
 in the related paper.
description: Raman spectrometry:
 used for identifying the mineralogical / molecular composition of
 artifacts. These analyses were carried out at the Brazilian
 Research Unit of Astrobiology (NAP/Astrobio) using a Renishaw inVia
 micro-Raman, with laser
 excitation wavelength of 785 nm, 1% power, acquisition time of 1 s and 30
 accumulations. Scanning Electron Microscopy with Energy
 Dispersive X-Ray Analyzer (SEM/EDX): The artifacts were covered with
 carbon and analyzed in order to characterize their ultrastructure and
 elemental composition. These analyses were carried out in the Laboratory
 of Scanning Electron Microscopy, at the Institute of Geosciences of USP using a LEO 440
 scanning electron microscope coupled with an Oxford energy
 dispersive X-ray spectrometer.
description: Raman spectra are saved in .txt and .wdf SEM
 images are saved in .tif EDX analyses are saved in
 .docx
DOI: 10.5061/dryad.wdbrv15tp
title: Great Plains grassland methane dynamics

description: The grassland biome is an important sink for CH4, a major greenhouse gas.
 There is considerable uncertainty in the grassland CH4 sink capacity due
 to diverse environmental gradients in which grasslands occur, and many
 environmental conditions can affect abiotic (e.g., CH4 diffusivity into
 soils) and biotic (e.g., methanotrophy) factors that determine spatial and
 temporal CH4 dynamics. We investigated the relative importance of a soil’s
 gas diffusivity vs. net methanotroph activity in 22 field plots in seven
 sites distributed across the US Great Plains by making ca. bi-weekly
 measures during the growing seasons over three years. We quantified net
 methanotroph activity and diffusivity by using an approach combining a gas
 tracer, chamber headspace measurements, and a mathematical model. At each
 plot, we also measured environmental characteristics, including
 water-filled pore space (WFPS), soil temperature and inorganic nitrogen
 contents, and examined the relative importance of these for controlling
 diffusivity and net methanotroph activity. At most of the plots across the
 seven sites, CH4 uptake rates were consistently greatest when WFPS was
 intermediate at the plot level. Our results show that variation in net
 methanotroph activity was more important than diffusivity in explaining
 temporal variations in net CH4 uptake, but the two factors were equally
 important for driving spatial variation across the seven sites. 
 Water-filled pore space was a significant predictor for diffusivity only
 in plots with sandy soils. Water-filled pore space was the most important
 control on net methanotroph activity, with net methanotroph activity
 showing a parabolic response to WFPS (concave down), and the shape of this
 response differed significantly among sites. Moreover, we found that the
 WFPS level at peak net methanotroph activity was strongly correlated with
 mean annual precipitation of the site. These results suggest that local
 precipitation regime determines unique sensitivity of CH4 uptake rates to
 soil moisture. Our findings indicate that grassland CH4 uptake may be
 predicted using local soil water conditions. More variable soil moisture,
 potentially induced through predicted future extremes of rainfall and
 drought, could reduce grassland CH4 sink capacity in the future.
DOI: 10.5061/dryad.79cnp5j1k
title: Thermal refuge use and parasitism: spatiotemporal variation in anchor worm and lamprey wounds on Klamath redband trout

description: Climate warming is increasing maximum temperatures during summer, such
 that they more frequently exceed the thermal tolerances of ectotherms,
 particularly cold-water fishes. One way that species can avoid thermal
 stress is by moving to thermal refuge habitats. Thermal refuges remain
 suitably cool during summer and are often complementary to foraging,
 spawning, and rearing habitats. Although the benefits associated with the
 thermal aspects of refuges are well studied, much less is known about
 potential costs associated with non-thermal aspects. For example, crowding
 of cold-water fishes into seasonal refuge habitats could increase parasite
 loads and cause declines in fitness. We assessed lamprey and anchor worm
 parasitism in Upper Klamath Lake where adfluvial redband trout
 (Oncorhynchus mykiss newberii) move to thermal refuge habitats during
 summer. We sampled trout in Upper Klamath Lake during spring and in
 adjacent thermal refuge habitats during summer. We also evaluated survival
 as a function of lamprey wounding using motion-sensing radio tags. There
 was a 4-fold decline in the number of lamprey wounds on trout upon the
 onset of thermal refuge use. In contrast, cases of severe anchor worm (≥20
 sores) increased 3-fold during thermal refuge use. Survival in thermal
 refuge was not different for lamprey-wounded trout compared to trout that
 migrated to thermal refuge without lamprey wounds. We found that both
 parasites were absent in a lotic population of redband trout downstream
 that lacked access to thermal refuge. Thus, the effects of seasonal refuge
 use on parasite load varied depending on the parasite taxon considered and
 local habitat conditions implying that managers will likely require
 empirical data for focal habitats and taxa to understand how parasitism
 affects thermal refuge use.
description: Wound count for lamprey or anchorworm was collected by hook and
 line sampling. Each trout was visually assessed for a wound count from
 either lamprey or anchorworm.
description: RStudio was used to analyze data.
DOI: 10.5061/dryad.vdncjsz11
title: Genotypes for yardstick population from the Nakai Plateau, Lao PDR at 25 loci

description: Conservation biologists often deal with species that have small,
 fragmented populations throughout their range, making it necessary to
 prioritize populations for management. Genetics provides tools to assist
 with prioritization according to the levels and distribution of genetic
 diversity and evolutionary distinctiveness. Many studies have used nuclear
 microsatellite loci to measure genetic diversity in disparate populations
 and mitochondrial DNA to assess genetic distinctiveness. However,
 comparing metrics based on microsatellite genotypes ascertained in
 different laboratories is complicated by the selection of different loci
 with distinct nucleotide repeat motifs. This issue may be resolved by
 comparing metrics to a well-characterized reference population with shared
 microsatellite markers. The Asian elephant, Elephas maximus, is an
 endangered species with 50–60% of populations in India and Sri Lanka, and
 small, fragmented populations throughout southeast and insular Asia. We
 assessed range-wide genetic diversity of the Asian elephant by directly
 comparing allelic diversity and heterozygosity estimates from 35
 populations, overcoming marker selection bias by calibrating metrics to a
 large population on the Nakai Plateau, Lao PDR, genotyped at 25 loci. We
 coupled these results with mtDNA analysis to evaluate genetic
 distinctiveness and identify potential conservation management units. We
 found the greatest diversity in the populations of southeast Asia and the
 greatest genetic distinctiveness among the subspecies designations,
 particularly Borneo and Sumatra, and other southeast Asian populations.
 The populations of southeast Asia, albeit small, fragmented, and at high
 risk of extirpation, contain valuable diversity and distinctiveness and
 are thus of high priority for the preservation of the Asian elephant.
description: Yardstick population was genotyped from dung samples collected at
 the Nakai Plateau, Lao PDR – 91 unique individuals at 25 microsatellite
 loci mtDNA control region haplotypes were compiled from
 published articles, reports and GenBank accessions.
description: The data file is a text file in GenePop format - 91 samples at 25
 microsatellite loci for a single population.
DOI: 10.25338/b8693k
title: Bulk RNAseq of K7M2 osteosarcoma cells in engineered bone marrow treated with Doxorubicin

description: Osteosarcoma (OS) is the most common primary malignant bone cancer in
 children and adolescents. While numerous other cancers now have promising
 therapeutic advances with immunotherapies, targeted therapies, and stem
 cells, treatment options for patients with OS have remained unchanged for
 more than four decades since the advent of standard chemotherapeutics and
 offer less than a 25% 5-year survival rate for those with metastatic
 disease. This dearth of clinical progress underscores a lack of
 understanding of OS progression and metastagenesis and necessitates the
 study of this disease in a novel system. Here, we adapt a previously
 described engineered bone marrow (eBM) construct for use as a 3D platform
 to study how microenvironmental and immune factors affect OS tumor
 progression. We form eBM by implanting acellular bone-forming materials in
 mice and explanting the cellularized constructs for study after eight
 weeks. We interrogate the influence of the anatomical implantation site on
 the quality of generated tissue, test ex vivo stability under normoxic (5%
 O2) and standard (21% O2) culture conditions, and culture OS cells within
 these eBM constructs. We show that eBM accurately and stably recapitulates
 the composition of native bone marrow. OS cells exhibit differential
 behavior dependent on metastatic potential when cultured in eBM, thus
 closely mimicking in vivo conditions. Furthermore, we highlight the
 clinical applicability of eBM as a drug-screening platform through
 doxorubicin treatment of OS cultured in monolayer, Matrigel, or eBM, and
 we show that eBM confers a protective effect on OS cells that parallel
 clinical responses. Combined, this work presents eBM as a cellular
 construct that mimics the complex bone marrow environment that may be
 useful for mechanistic bone cancer research and drug screening.
description: eBM was minced into &lt;= 0.5mm cubes and collected in 500
 micro liter of TRIzol Reagent (Invitrogen). Samples were then homogenized
 with a Tissue-tearor (BioSpec, Bartlesville, OK) at highest speed for 10 s
 intervals totaling 30 s, followed by sonication for another 10 s.
 Following RNA isolation, sequencing libraries were prepared using Illumina
 Stranded mRNA Prep kit using manufacturer's recommendations and then
 sequenced on an Illumina NextSeq 500 sequencer. Conversion of Illumina
 base calls to sequences and sample demultiplexing was performed using
 bcl2fastq.