cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.0zpc866x0
title: Data from: Genetic or toxicant-induced disruption of vesicular monoamine storage and global metabolic profiling in Caenorhabditis elegans

description: The proper storage and release of monoamines contributes to a wide range
 of neuronal activity. Here, we examine the effects of altered vesicular
 monoamine transport in the nematode C. elegans. The gene cat-1 is
 responsible for the encoding of the vesicular monoamine transporter (VMAT)
 in C. elegans and is analogous to the mammalian vesicular monoamine
 transporter 2 (VMAT2). Our laboratory has previously shown that reduced
 VMAT2 activity confers vulnerability on catecholamine neurons in mice. The
 purpose of this paper was to determine whether this function is conserved
 and to determine the impact of reduced VMAT activity in C.
 elegans.  Here we show that deletion of cat-1/VMAT increases
 sensitivity to the neurotoxicant 1-methyl-4-phenylpyridinium (MPP+) as
 measured by enhanced degeneration of dopamine neurons.  Reduced
 cat-1/VMAT also induces changes in dopamine-mediated behaviors.
 High-resolution mass spectrometry-based metabolomics in the whole organism
 reveals changes in amino acid metabolism, including tyrosine metabolism in
 the cat-1/VMAT mutants. Treatment with MPP+ disrupted tryptophan
 metabolism. Both conditions altered glycerophospholipid metabolism,
 suggesting a convergent pathway of neuronal dysfunction.  Our
 results demonstrate the evolutionarily conserved nature of monoamine
 function in C. elegans and further suggest that HRMS-based metabolomics
 can be used in this model to study environmental and genetic contributors
 to complex human disease.
description: High-resolution metabolomics data was generated using samples
 collected per the methods described in the manuscript. Files generated
 from the Thermo orbitrap instrument were extracted using the apLCMS and
 xMSanalyzer R packages.
description: The raw data in sheet 1 should be treated as follows:
 Retain a feature in the feature table if its intensity is 1.5
 times that of the average intensity of the feature in the M9 blank sample.
 Null (intensity = 0) values should be replaced with half the value of the
 minimum intensity of that feature.  The biological
 relevance of the features significantly associated with the genetic or
 toxicant perturbation can be determined using pathway analysis hosted on
 MetaboAnalyst.
DOI: 10.5061/dryad.5mkkwh74x
title: Structure determination of oleanolic and ursolic acids: a combined DFT/vibrational spectroscopy methodology

description: Raw samples of oleanolic and ursolic acids, a class of terpenoid acids
 mainly found in the leaf and fruit cuticles of some plant species, can be
 defined as a blend of clusters of different conformers aggregated in
 dimers and tetramers by means of hydrogen bonds and stabilized by
 non-electrostatic interactions.
description: This file contains the raw dataset for Figure 2, Figure 3, Figure
 8, Figure S3, Figure S5, Figure S7, Figure S9 and Figure S10 of the
 associated article and its electronic supplementary material.
DOI: 10.5281/zenodo.18393588
title: Energy Efficiency in RFID Systems: A Systematic Mapping Study of Trends, Trade-offs, and Validation Methodologies
DOI: 10.5281/zenodo.18396569
title: Energy Efficiency in RFID Systems: A Systematic Mapping Study of Trends, Trade-offs, and Validation Methodologies
DOI: 10.5061/dryad.pk0p2ngmv
title: Bisulfite sequencing (RRBS-seq): CpG methylation reports for Australian invasive cane toads

description: In response to novel environments, invasive populations often evolve
 rapidly. Standing genetic variation is an important predictor of
 evolutionary response but epigenetic variation may also play a role. Here
 we use an iconic invader, the cane toad (Rhinella marina), to investigate
 how manipulating epigenetic status affects phenotypic traits. We collected
 wild toads from across Australia, bred them, and experimentally
 manipulated DNA methylation of the subsequent two generations (G1, G2)
 through exposure to the DNA methylation inhibitor zebularine and/or
 conspecific tadpole alarm cues. Direct exposure to alarm cues (an
 indicator of predation risk) increased the potency of G2 tadpole chemical
 cues, but this was accompanied by reductions in survival. Exposure to
 alarm cues during G1 also increased the potency of G2 tadpole cues,
 indicating intergenerational plasticity in this inducible defence. In
 addition, the negative effects of alarm cues on tadpole viability (i.e.,
 the costs of producing the inducible defence) were minimised in the second
 generation. Exposure to zebularine during G1 induced similar
 intergenerational effects, suggesting a role for alteration in DNA
 methylation. Accordingly, we identified intergenerational shifts in DNA
 methylation at some loci in response to alarm cue exposure. Substantial
 demethylation occurred within the Sodium Channel Epithelial 1 Subunit
 Gamma gene (SCNN1G) in alarm cue-exposed individuals and their offspring.
 This gene is a key to regulation of sodium in epithelial cells and may
 help to maintain the protective epidermal barrier. These data suggest that
 early-life experiences of tadpoles induce intergenerational effects
 through epigenetic mechanism, which enhance larval fitness.
description: See README.
DOI: 10.5061/dryad.sf7m0cg5d
title: Data from: Estimating encounter location distributions from animal tracking data

description: 1. Ecologists have long been interested in linking individual
 behavior with higher-level processes. For motile species, this
 'upscaling' is governed by how well any given movement strategy
 maximizes encounters with positive factors, and minimizes encounters with
 negative factors. Despite the importance of encounter events for a broad
 range of ecological processes, encounter theory has not kept pace with
 developments in animal tracking or movement modeling. Furthermore,
 existing work has focused primarily on the relationship between animal
 movement and encounter rates while the relationship between
 individual movement and the spatial locations of encounter events
 in the environment has remained conspicuously understudied. 2. Here, we
 bridge this gap by introducing a method for describing the long-term
 encounter location probabilities for movement within home ranges, termed
 the conditional distribution of encounters (CDE). We then derive this
 distribution, as well as confidence intervals, implement its statistical
 estimator into open source software, and demonstrate the broad ecological
 relevance of this distribution. 3. We first use simulated data to show how
 our estimator provides asymptotically consistent estimates. We then
 demonstrate the general utility of this method for three simulation-based
 scenarios that occur routinely in biological systems: i) a population of
 individuals with home ranges that overlap with neighbors; ii) a pair of
 individuals with a hard territorial border between their home ranges; and
 iii) a predator with a large home range that encompassed the home ranges
 of multiple prey individuals. Using GPS data from white-faced capuchins
 (Cebus capucinus) tracked on Barro Colorado Island, Panama, and sleepy
 lizards (Tiliqua rugosa) tracked in Bundey, South Australia, we then show
 how the CDE can be used to estimate the locations of territorial borders,
 identify key resources, quantify the potential for competitive or
 predatory interactions, and/or identify any changes in behaviour that
 directly result from location-specific encounter probability. 4. The CDE
 enables researchers to better understand the dynamics of populations of
 interacting individuals. Notably, the general estimation framework
 developed in this work builds straightforwardly off of home range
 estimation and requires no specialised data collection protocols. This
 method is now openly available via the ctmm R package.
DOI: 10.5061/dryad.44j0zpcd3
title: Data from: Hymenophyllum subg. Hymenophyllum (Hymenophyllaceae) in the Brazilian Atlantic forest

description: A revision of the species of Hymenophyllum subg. Hymenophyllum in the
 Brazilian Atlantic forest domain is presented. Morphological and molecular
 analyses were performed, based on herbarium material and samples collected
 during fieldwork. For the molecular analyses, data of the plastidial
 markers rbcL, rbcL-accD, rps4-trnS and trnG-trnR were used. The analyses
 demonstrated the existence of three distinct and independent lineages of
 subgenus Hymenophyllum in Atlantic forest domain. Three taxa were
 recognized: H. fucoides, H. megachilum, and an additional new species, H.
 bradeanum, a narrow endemic to the Itatiaia Massif, southeastern Brazil.
 Distribution maps, identification keys, descriptions and illustrations are
 present, together with an update of the conservation status of the
 species.
DOI: 10.5061/dryad.k6djh9w5m
title: Conspecific leaf litter induces negative feedbacks in Asteraceae seedlings

description: The plant soil feedback (PSF) framework has been instrumental in
 quantifying soil microbial impacts on plant fitness and mechanisms for
 species coexistence. The recent extension of the PSF framework to microbes
 associated with aboveground tissues of plants, termed here as plant
 phyllosphere feedbacks (PPFs), can also help determine the role of
 aboveground microbes as drivers of plant-plant interactions. However,
 experimental tests of PPFs in wild hosts is nascent and their prevalence
 across diverse hosts remains largely unknown. Additionally, the
 relationship between plant host characteristics, such as functional traits
 and evolutionary history, with PPFs is unclear, in contrast to a
 substantial body of PSF literature. To test for the prevalence and
 mechanisms driving PPFs across diverse hosts, plant litter from ten
 Asteraceae species spanning slow to fast life history strategies was used
 to inoculate con- and heterospecific seedlings in a full factorial
 experimental design. We found that four species experienced significant
 negative PPFs and three experienced marginally significant negative
 feedbacks, while the feedback estimates for all ten species were negative.
 However, neither plant functional traits, nor phylogenetic distance were
 predictive of PPFs among species pairs, suggesting that other mechanisms
 or traits not measured may be driving these negative PPFs. Our results
 indicate that negative PPFs are common among native Asteraceae species and
 that they may have substantial impacts on plant growth and plant-plant
 interactions, particularly during early plant development.
DOI: 10.5061/dryad.w3r2280q0
title: Insights into the aggregation mechanism of RRM domains in TDP-43: A theoretical exploration

description: The transactive response DNA-binding protein 43 (TDP-43) is associated
 with several diseases such as Amyotrophic lateral sclerosis (ALS) and
 Frontotemporal lobar degeneration (FTLD) due to pathogenic aggregations.
 In this work, we examined the dimer, tetramer and hexamer models built
 from the RRM domains of TDP-43 using molecular dynamics simulations in
 combination with the protein-protein docking. Our results showed that the
 formations of the dimer models are mainly achieved by the interactions of
 the RRM1 domains. The parallel β-sheet layers between the RRM1 domains in
 these oligomer models, which provide the potential binding sites in the
 aggregation process, are formed energetically favorable. The approaching
 of the parallel β-sheet layers from small oligomer models gradually expand
 to large ones through the allosteric communication between the α1/α2
 helices of the RRM1 domains, which maintains the binding affinities and
 interactions in the larger oligomer models. Using the
 repeatable-superimposing method based on the tetramer models, we proposed
 a new aggregation mechanism of RRM domains in TDP-43, which could well
 characterize the formation of the large aggregation models with the
 repeated, helical and rope-like structures. These new insights help to
 understand the amyloid-like aggregation phenomena of TDP-43 protein in ALS
 and FTLD diseases.
DOI: 10.15468/dl.rhrqhp
title: Occurrence Download

description: A dataset listing the 4 species recorded in GBIF matching the query:
{
 "and" : [
 "Country is Lao People’s Democratic Republic",
 "TaxonKey is Ichthyophis"
 ]
}

 The dataset's 4 records were derived from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002763-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gsvaec
title: Occurrence Download

description: A dataset containing 249280 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "Country is one of (Brunei Darussalam, Cambodia, Indonesia, Lao People’s Democratic Republic, Malaysia, Myanmar, Philippines, Singapore, Thailand, Viet Nam, Timor-Leste)",
 {
 "not" : {
 "Issue" : [
 "is Country coordinate mismatch"
 ]
 }
 }
 ]
 },
 "TaxonKey is one of (Amphibia [GBIF Backbone Taxonomy])"
 ]
}

 The dataset includes 249280 records from 234 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002742-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.c2fqz6178
title: Data from: SNF1-related protein kinase 1: the many-faced signaling hub regulating developmental plasticity in plants

description: The Snf1-Related Protein Kinase 1 (SnRK1) is the plant homolog of the
 heterotrimeric AMP-activated Protein Kinase/ Sucrose Non-Fermenting 1
 (AMPK/Snf1), which works as a major regulator of growth under
 nutrient-limiting conditions in eukaryotes. Along with its conserved role
 as a master regulator of sugar starvation responses, SnRK1 is involved in
 controlling the developmental plasticity and resilience under diverse
 environmental conditions in plants. In this review, through mining and
 analyzing the interactome and phosphoproteome data of SnRK1, we are
 highlighting its role in fundamental cellular processes such as gene
 regulation, protein synthesis, primary metabolism, protein trafficking,
 nutrient homeostasis, autophagy, etc. Along with the well-characterized
 molecular interaction in SnRK1 signaling, our analysis highlights several
 unchartered regions of SnRK1 signaling in plants such as its possible
 communication with chromatin remodelers, histone modifiers, inositol
 phosphate signaling, etc. We also discuss potential reciprocal
 interactions of SnRK1 signaling with other signaling pathways and cellular
 processes, which could be involved in maintaining flexibility and
 homeostasis under different environmental conditions. Overall, this review
 provides a comprehensive overview of the SnRK1 signaling network in plants
 and suggests many novel directions for future research.
DOI: 10.5061/dryad.pc866t1nd
title: Determination of volatile substances in olives and their effect on reproduction of the olive fruit fly

description: Females of the olive fruit fly Bactrocera oleae lay their eggs on olives
 mainly using fruit volatile stimuli. Using GC-MS analysis, we determined
 the chemical composition of the volatile blend emitted from
 field-collected olive fruit of cv. Megaritiki, at different stages of
 growth. The identified chemicals were tested in the laboratory with regard
 to their effect on mating and egg production of the fly. GC-MS analysis
 demonstrated qualitative and quantitative differences in the headspace
 blend emitted by the olive fruits. Certain chemicals such as toluene,
 n-octane, α-pinene, limonene, ethyl hexanol, nonanal n-dodecane, decanal
 and n-tetradecane were detected in the greatest amounts, irrespective of
 the growing stage of the fruits. Exposure of the flies to some of these
 chemicals as noctane and α-pinene, as well as to a mixture consisting of
 n-octane, α-pinene, limonene, ethyl hexanol, nonanal, n-dodecane, decanal,
 n –tetradecane favoured mating success and egg production. The results may
 contribute to the improvement of mass rearing of the fly, through the
 knowledge of the positive effect that certain fruit volatile chemicals
 have on fly’s reproduction and a better understanding of the
 relation between the fly and the host fruit.
DOI: 10.5061/dryad.vhhmgqns9
title: Aggregated filter-feeders govern the flux and stoichiometry of locally available energy and nutrients in rivers

description: Biogeochemical cycling has often been characterized by physical and
 microbial processes, yet animals can be essential mediators of energy and
 nutrients in ecosystems. Excretion by aggregated animals can be an
 important local source of inorganic nutrients in green food webs, however,
 whether animals are a source of dissolved energy that can support brown
 food webs is understudied. We tested whether animal aggregations are a
 substantial flux of bioavailable dissolved organic matter (DOM) by
 studying spatially stable, biogeochemical hotspots formed by
 filter-feeding freshwater mussels. We used parallel-factor analysis to
 quantify DOM fluorescent components composition of mussel excretion and
 expected digestive breakdown of particulate food sources would lead to
 excretion of labile DOM. Next, we combined measured excretion rates of
 DOM, ammonium (NH4+, N), and phosphorous (SRP; P) for 22 species with
 biomass estimates for 14 aggregations to quantify contributions of DOM, N,
 and P to local availability. Because mussels occupy distinct
 stoichiometric niches, we anticipated that differences in species biomass
 and assemblage structure would elicit different flux and stoichiometries
 of aggregate excretion. Aggregate dissolved organic carbon (DOC) excretion
 was minor (1-11%) compared to N (12-2860%) and P (1-97%), yet generalities
 across assemblages emerged regarding organic matter transformation by
 mussels towards labile protein-like compounds compared to abundant
 aromatic, humic compounds in ambient water. Aggregate excretion of labile
 DOM was a substantial pool of bioavailable energy, contributing 2 – 114%
 of local labile DOM. Spatial differences in assemblage structure led to
 strong differences in aggregate flux and stoichiometry driven by biomass
 and stoichiometric trait expression of species with contrasting dominance
 patterns. Under the nutrient conditions of our study (high C:nutrient),
 biogeochemical hotspots associated with low-trophic position animal
 biomass may indirectly control energy flow to the brown food web by
 shifting C:nutrient stoichiometry available to microbes or directly by
 increasing the flux of microbially available DOM. Collectively, our
 results highlight a potentially substantial flux of labile energy and
 nutrients to microbial communities through the transformation of ingested
 organic matter by aggregations of animals and emphasize that shared
 functional trait classification may not translate into shared ecological
 function.
description: Data covers figures 2, 3, and 4. Excel files contain read me,
 detailed key to all column headers/variables, and species list to decipher
 short hand species codes.
DOI: 10.5061/dryad.66t1g1k1k
title: Application of next-generation sequencing for the determination of the bacterial community in the gut contents of brackish copepod species (Acartia hudsonica, Sinocalanus tenellus, and Pseudodiaptomus inopinus)

description: The gut bacterial communities of copepods can affect metabolic processes,
 and consequently, their activity can be related to the release of organic
 substances to the environment. Hence, they are important for organic
 matter cycling in marine coast food webs. However, information regarding
 the variation in gut bacterial communities based on copepod species and
 environmental variations is limited. We analysed the differences in gut
 bacterial communities from dominant copepod species, i.e., Acartia
 hudsonica, Sinocalanus tenellus, and Pseudodiaptomus inopinus, in a
 brackish reservoir. The core bacteria among the copepod species and
 locations consisted of the following main operational taxonomic units
 (OTUs): Novosphingobium capsulatum and the family Rhodobacteraceae
 belonging to Alphaproteobacteria which is abundant in seawater and
 freshwater aquatic ecosystems as a zooplankton-associated bacterial
 community. The bacterial community composition of each copepod (except the
 core species) showed high variability. The bacterial community diversity
 differed depending on the copepod species and the sites’ environmental
 conditions, especially salinity, e.g. compositional variations in the
 bacterial community of P.inopinus were high at sites with low salinity.
 Therefore, the gut bacterial community of each copepod species responds
 differently to the environment.
DOI: 10.5061/dryad.ttdz08kx9
title: Average neural activity patterns for safe and risky offers

description: Our ability to effectively choose between dissimilar options implies that
 information regarding the options’ values must be available, either
 explicitly or implicitly, in the brain. Explicit realizations of value
 involve single neurons whose responses depend on value and not on the
 specific features that determine it. Implicit realizations, by contrast,
 come from the coordinated action of neurons that encode specific features.
 One signature of implicit value coding is that population responses to
 offers with the same value but different features should occupy semi- or
 fully orthogonal neural subspaces that are nonetheless linked. Here, we
 examined responses of neurons in six core value-coding areas in a choice
 task with risky and safe options. Using stricter criteria than some past
 studies have used, we find, surprisingly, no evidence for abstract (i.e.
 cross offer-type) value neurons in any of these regions. Moreover,
 population codes for value resided in orthogonal subspaces; these
 subspaces were linked through a linear transform of each of their
 constituent subspaces. These results suggest that in all six regions,
 populations of neurons embed value implicitly in a distributed population.