cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.qz612jmmq
title: Data from: Developmental exposure to the Parkinson’s disease-associated organochlorine pesticide dieldrin alters dopamine neurotransmission in α-synuclein pre-formed fibril (PFF)-injected mice

description: Parkinson’s disease (PD) is the fastest-growing neurological diseases
 worldwide, with increases outpacing aging and most rapid in recently
 industrialized areas, suggesting the role of environmental factors.
 Together, epidemiological studies, post-mortem analysis and mechanistic
 studies suggest that exposure to persistent organic pollutants, including
 the organochlorine pesticide dieldrin, increases PD risk. In mouse models,
 developmental dieldrin exposure causes male-specific exacerbation of
 neuronal susceptibility to MPTP and synucleinopathy. Specifically,
 developmental dieldrin exposure induces male-specific exacerbation of
 toxicity in the α-synuclein (α-syn) pre-formed fibril (PFF) model with
 increased deficits in striatal dopamine (DA) turnover and motor deficits
 on the challenging beam. Here, we hypothesized that alterations in DA
 handling contribute to the observed changes and assessed vesicular
 monoamine transporter 2 (VMAT2) function and DA release in this
 dieldrin/PFF two-hit model. Female C57BL/6 mice were exposed to 0.3 mg/kg
 dieldrin or vehicle every 3 days by feeding, starting at 8 weeks of age by
 ingestion and continuing throughout breeding, gestation, and lactation.
 Male offspring from independent litters underwent unilateral,
 intrastriatal injections of α-syn PFFs at 12 weeks of age and vesicular
 3H-DA uptake assays and fast-scan cyclic voltammetry (FSCV) were performed
 at 4 months post-PFF injection. We observed a dieldrin-induced increase in
 DA release in striatal slices in PFF-injected animals, but no change in
 VMAT2 activity. These results suggest that developmental dieldrin exposure
 increases a compensatory response to synucleinopathy-triggered striatal DA
 loss and supports our hypothesis that alterations in DA handling may
 underly the observed exacerbation of PFF-induced deficits in motor
 behavior and DA turnover.
description: GraphPad Prism files (pzfx) can be opened in GraphPad Prism or
 viewed in the free Viewer mode, or data can be extracted by viewing files
 in a text editor.  R and RStudio are freely available
 for running Rmd files.  AxioScan czi files can be
 opened in Zeiss Zen software (proprietary) or ImageJ (open
 source) Raw data from FSCV experiments (tdms and txt
 files) requires Python (open source) and Demon Voltammetry and Analysis
 Software (free license from Wake Forest Innovations).
 csv files can be opened in a spreadsheet software or text
 editor
DOI: 10.15468/tgapyk
title: Lebiasina yepezi, a new Lebiasininae (Characiformes: Lebiasinidae) from the Serra Parima-Tapirapecó mountains

description: This dataset contains the digitized treatments in Plazi based on the original journal article Netto-Ferreira, André L., Oyakawa, Osvaldo T., Zuanon, Jansen, Nolasco, José C. (2011): Lebiasina yepezi, a new Lebiasininae (Characiformes: Lebiasinidae) from the Serra Parima-Tapirapecó mountains. Neotropical Ichthyology 9 (4): 767-775, DOI: 10.1590/S1679-62252011000400008, URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1679-62252011000400008&lng=en&tlng=enLebiasina yepezi, a new Lebiasininae with a conspicuous color pattern, is described. The new species is endemic of the headwaters of the rio Negro, rio Branco, and rio Orinoco in the Serra Parima-Tapirapecó Mountains, at the border of Brazil and Venezuela. The new species is readily distinguished from all other Lebiasininae by the presence of four black longitudinal stripes on the trunk, and the triangular shaped dorsal surface of the mesethmoid, lacking lateral projections. The unusual color pattern is contrasted with those of other lebiasinin, as well as members of the pyrrhulinin genus Nannostomus. A close relationship between Lebiasina yepezi and the Gran Sabana (Venezuela) species is suggested based in color pattern features. The present contribution corresponds to a further refutation of the type locality of L. intermedia, as suggested on its description, since Lebiasinins, except L. bimaculata, L. boruca, and L. festae, do not occur in low land waters.Lebiasina yepezi, um novo Lebiasininae com um conspícuo padrão de colorido, é descrito. A nova espécie é endêmica das cabeceiras do rio Negro, rio Branco e rio Orinoco, na Serra Parima-Tapirapecó, ao longo da fronteira entre Brasil e Venezuela. A nova espécie é prontamente diferenciada das demais espécies pela presença de quatro faixas longitudinais escuras ao longo do corpo, e a superfície dorsal do mesetmoide com o formato triangular, não apresentando projeções laterais. O padrão de colorido incomum é comparado com o dos demais Lebiasininae e também com o dos Pyrrhulininae do gênero Nannostomus. Uma próxima relação é proposta entre Lebiasina yepezi e as espécies da Gran Sabana (Venezuela) com base em caracteres de colorido. A presente contribuição corresponde a mais uma refutação da localidade-tipo de L. intermedia conforme sugerida na descrição daquela espécie, uma vez que os lebiasiníneos, com exceção de L. bimaculata, L. boruca e L. festae, não ocorrem em rios de terras baixas.
DOI: 10.5061/dryad.3ffbg79px
title: Data from: To eat, or not to eat: A phantom decoy affects information-gathering behavior by a free-ranging mammalian herbivore

description: When foraging, making appropriate food choices is crucial to an
 animal's fitness. Classic foraging ecology theories assume animals
 choose food of greatest benefit based on their absolute value across
 multiple dimensions. Consequently, poorer options are considered
 irrelevant alternatives that should not influence decision-making among
 better options. But heuristic studies demonstrate that irrelevant
 alternatives (termed decoys) can influence decisions of some animals,
 indicating they use a relative rather than absolute evaluation system. Our
 aim was to test whether a decoy influenced the decision-making process –
 i.e. information-gathering and food choice – of a free-ranging mammalian
 herbivore. We tested swamp wallabies, Wallabia bicolor, comparing
 their behavior towards, and choice of, two available food options over
 time in the absence or presence of the decoy. We used a phantom
 decoy—unavailable option—and ran two trials in different locations and
 seasons. Binary preferences (decoy absent) for the two available food
 options differed between trials. Irrespective of this difference, across
 both trials the presence of the decoy resulted in animals more likely to
 overtly investigate available food options. But the decoy only shifted
 food choice, weakly, in one trial. Our results indicate that the decoy
 influenced the information-gathering behavior during decision-making,
 providing first evidence that decoys can affect decision-making process of
 free-ranging mammalian herbivores in an ecologically realistic context. It
 is premature to say these findings confirm the use of relative evaluation
 systems. Whether the foraging outcome is more strongly affected by other
 decoys, food dimensions, or ecological contexts, is yet to be determined.
DOI: 10.14749/31170454
title: National Research and Experimental Development Survey (R&D) 2022-23: All provinces in South Africa - Aggregated

description: &lt;p&gt; This data set contains aggregated data on the R&amp;D expenditure by province, type of R&amp;D, research fields, socioeconomic objectives, sources of funds and province. R&amp;D personnel data is also included. The data is recorded for each of the following economic sectors of the South African economy: Business, Government, Higher Education, Not-for-Profit Organisations and Science Councils.&lt;/p&gt;&lt;p&gt; Response rate = 100 x [Responses/(Responses + Non-responses - Out-of-scopes)], where non-responses include refusals and out-of-scopes. Out-of-scopes include categories: closed down, non-R&amp;D performer. (Note: return to sender, untraceable is not OOS).&lt;/p&gt;&lt;ul&gt; &lt;li&gt;  Business sector response rate = 100 x [233/ (233 + 270 - 50] = 51.3%&lt;/li&gt; &lt;li&gt;  Not-for-profit sector response rate = 100 x [34/(34 + 24 - 6)] = 65.4%&lt;/li&gt; &lt;li&gt;  Government sector response rate = 100 x [41/(41 + 27 - 7)] = 67.2%&lt;/li&gt; &lt;li&gt;  Science Councils sector response rate = 100 x [11/(11 + 0 - 0)] = 100.0%&lt;/li&gt; &lt;li&gt;  Higher Education sector (Public) response rate = 100 x [19/(19 + 6 - 0)] = 76.0%&lt;/li&gt; &lt;li&gt;  Higher Education sector (Private) response rate = 100 x [3/(3+ 3 - 0)] =50.0%&lt;/li&gt;&lt;/ul&gt;&lt;p&gt; Overall survey response rate = 100 x [341/(341 + 331 - 63] = 56.0%&lt;/p&gt;
DOI: 10.5061/dryad.2ngf1vhv4
title: Data from: Sex-specific effects of inbreeding in juvenile brown trout

description: Inbreeding depression, i.e., the reduction of health and vigour in
 individuals with high inbreeding coefficients, is expected to increase
 with environmental, social, or physiological stress. It has therefore been
 predicted that sexual selection and the associated stress usually lead to
 higher inbreeding depression in males than in females. However,
 sex-specific differences in life history may reverse that pattern during
 certain developmental stages. In some salmonids, for example, female
 juveniles start developing their gonads earlier than males who instead
 grow faster. We tested whether the sexes are differently affected by
 inbreeding during that time. To study the effects of inbreeding
 coefficients that may be typical for natural populations of brown trout
 (Salmo trutta), and also to control for potentially confounding maternal
 or paternal effects, we sampled males and females from the wild, used
 their gametes in a block-wise full-factorial breeding design to produce 60
 full-sib families, released the offspring as yolk-sac larvae into the
 wild, sampled them 6 months later, identified their genetic sex, and used
 microsatellites to assign them to their parents. We used whole-genome
 resequencing to calculate the kinship coefficients for each breeding pair
 and hence the expected average inbreeding coefficient per family. Juvenile
 growth could be predicted from these expected inbreeding coefficients and
 the genetic sex: Females reached lower body sizes with increasing
 inbreeding coefficient, while no such link could be found in males. This
 sex-specific inbreeding depression led to the overall pattern that females
 were on average smaller than males by the end of their first summer.
description: See methods in: Bylemans, J., Marques da Cunha, L., Sarmiento
 Cabello, S., Nusbaumer, D., Uppal, A. and Wedekind, C. (2024) Sex-specific
 effects of inbreeding in juvenile brown trout. (Molecular
 Ecology).
description: # Data from: Sex-specific effects of inbreeding in juvenile brown trout
 CSV files for dams, sires,
 sib groups, and juveniles are provided along with corresponding README
 files. For all but two breeders (one dam and one sire) high quality DNA
 extracts or tissue samples could be used for whole genome resequencing to
 calculate the kinship coefficients for each breeding pair; the
 corresponding VCF file contains the relevant data.
DOI: 10.5061/dryad.95x69p8qc
title: Beyond trait distances: Functional distinctiveness captures the outcome of plant competition

description: Functional trait distances between coexisting organisms reflect not only
 complementarity in the way they use resources, but also differences in
 their competitive abilities. Accordingly, absolute and relative trait
 distances have been widely used to capture the effects of niche
 dissimilarity and competitive hierarchies, respectively, on the
 performance of plants in competition. However, multiple dimensions of the
 plant phenotype are involved in these plant-plant interactions (PPI),
 challenging the use of relative trait distances to predict their outcomes.
 Furthermore, estimating the effects of competitive hierarchy on the
 performance of a group of coexisting plants remains particularly difficult
 since relative trait distances relate to the effects of a focal plant on
 another. We argue that trait distinctiveness, an emerging facet of
 functional diversity that characterizes the eccentric position of a
 species (or genotype) in a phenotypic space, can reveal the unique role
 played by a given individual plant in a group of competing plants . We
 used the model crop species Oryza sativa spp. japonica to evaluate the
 ability of trait distances and trait distinctiveness to predict the
 outcome of intraspecific PPI on the performance of single genotype and
 genotype mixtures. We performed a screening experiment to characterize the
 phenotypic space of 49 rice genotypes based on 11 aboveground and root
 traits. We selected nine genotypes with contrasting positions in the
 phenotypic space and grew them in pots following a complete pairwise
 interaction design. Relative distances and distinctiveness based on traits
 associated with light competition were by far the best predictors of the
 performance of single genotypes - taller genotypes that acquired resource
 faster being the best competitors - while absolute trait distances had no
 effect. These results indicate that competitive hierarchy for light
 dominates PPI in this experiment. Consistently, trait distinctiveness in
 plant height and age at flowering had the strongest, positive effects on
 mixture performance, confirming that functional distinctiveness captures
 the effects of trait hierarchies and asymmetric PPI at this scale. Our
 findings shed new light on the role of trait diversity in regulating PPI
 and ecosystem processes and call for a greater consideration of functional
 distinctiveness in studies of coexistence mechanisms.
description: We provided the raw data and the R script used to process and
 analyze the data. The raw data come from an experiment conducted by the
 co-authors as indicated in the paper's materials and
 methods.
description: R is needed to process and analyze the data. All the necessary
 library are listed in the script.
DOI: 10.5061/dryad.mw6m9062d
title: Thiol catalyzed NO-ferro-heme signaling

description: Nitric oxide (NO) is an endogenously produced signaling molecule that
 regulates blood flow and platelet activation. However, intracellular and
 intravascular diffusion of NO are severely limited by scavenging reactions
 with hemoglobin, myoglobin, and other hemoproteins, raising unanswered
 questions as to how free NO can signal in hemoprotein-rich environments.
 We explored the hypothesis that NO could be stabilized as a ferrous
 heme-nitrosyl complex (Fe2+-NO, NO-ferroheme. Unexpectedly, we observed a
 rapid reaction of NO with labile ferric heme (Fe3+) and a reduced thiol to
 yield NO-ferroheme and a thiyl radical. This thiol-catalyzed reductive
 nitrosylation reaction occurs readily when hemin is solubilized in
 lipophilic environments, such as red blood cell membranes or bound to
 serum albumin. The resulting NO-ferroheme is stable, even in the presence
 of oxyhemoglobin, and potently inhibits platelet activation. NO-ferroheme
 albumin administered intravenously to mice results in dose-dependent
 vasodilation at low- to mid-nanomolar concentrations. In conclusion, we
 report the fastest rate of reductive nitrosylation observed to date to
 generate a NO-ferroheme molecule that resists oxidative inactivation, is
 soluble in cell membranes, and is transported intravascularly by albumin
 to promote potent vasodilation.  
description: Methods are described in the paper and preprint.
description: Almost all data is in Excel and can also be opened with Google
 Sheets. There are a few JPEG image files.
DOI: 10.5061/dryad.v41ns1s2c
title: Ehretia pranomiana sp. nov. (Boraginales: Ehretiaceae), a new scrambler from Thailand

description: Ehretia pranomiana sp. nov. is illustrated and described from northern and
 south-western Thailand. The new species is similar to E. macrophylla and
 E. acuminata by having elliptic leaves with a serrate margin, but can be
 distinguished by its scrambling shrubs, leaf blades with densely hispid,
 corymbose inflorescence with 4–10 flowers, the corolla with erect lobes
 and the calyx longer than fruit at maturity. An updated species
 identification key is provided.
description: Specimens from AAU, ABD, BK, BKF, BM, CMU, E, K, KKU, L, QBG and
 SING were consulted (abbreviations following Thiers, 2022). Species
 delimitation was examined by consulting relevant literature: Clarke 1885,
 Gagnepain and Courchet 1914, Johnston 1951, Zhu et al. 1995, Riedl 1997,
 Mill 1999, Kress et al. 2003. All morphological characters were described
 using the terminology presented by Weberling (1992). Qualitative
 observations and measurements were made from the specimens, and
 descriptions and illustrations were prepared using these data.
 Distribution, ecology, and phenology were recorded from specimen labels
 and fieldwork. The collection sites were imported into SimpleMappr
 (Shorthouse 2010) to create a distribution map. GeoCAT (Bachman et al.
 2011) was used to calculate the area of occupancy (AOO) and extent of
 occurrence (EOO). Preliminary conservation assessments were prepared using
 the Categories and Criteria of IUCN Standards and Petition Committee
 (2019).
DOI: 10.5061/dryad.qz612jmms
title: Computational IHC-H&E mapping in mouse models of colitis (H&E WSIs from paired H&E-IHC WSIs)

description: Inflammatory Bowel Disease (IBD) is characterized by chronic, dysregulated
 inflammation in the gastrointestinal tract. The heterogeneity of IBD is
 reflected through two major subtypes, Crohn’s Disease (CD) and Ulcerative
 Colitis (UC). CD and UC differ across symptomatic presentation, histology,
 immune responses, and treatment. While colitis mouse models have been
 influential in deciphering IBD pathogenesis, no single model captures the
 full heterogeneity of clinical disease. The translational capacity of
 mouse models may be augmented by shifting to multi-mouse model studies
 that aggregate analysis across various well-controlled phenotypes. Here,
 we evaluate the value of histology in multi-mouse model characterizations
 by building upon a previous pipeline that detects histological disease
 classes in hematoxylin and eosin (H&E)-stained murine colons.
 Specifically, we map immune marker positivity across serially-sectioned
 slides to H&E histological classes across the dextran sodium
 sulfate (DSS) chemical induction model and the intestinal
 epithelium-specific, inducible Villin-CreERT2;Klf5fl/fl
 (Klf5ΔIND) genetic model. In this study, we construct the beginning
 frameworks to define H&E-patch-based immunophenotypes based on
 IHC-H&E mappings.
description: The slides are multi-resolution and openable utilizing WSI
 viewing software, such as QuPath. Data can also be accessed using standard
 Python libraries like Openslide.
DOI: 10.5061/dryad.37pvmcvr2
title: Data for: Reproductive strategies of native plant populations altered by a plant invasion

description: Invasive plant transformers substantially change the abiotic environment
 of invaded ecosystems and thus habitat suitability to resident species.
 Post-invasion environmental alteration can also modify the selective
 pressure acting on native plants. Here, I explored whether the decrease in
 light availability due to an invasion of Heracleum mantegazzianum drives
 evolution of reproductive strategies of Veronica chamaedrys, a perennial
 plant combining sexual and clonal reproduction. Using a common garden
 experiment with plant material of V. chamaedrys from 23 sites with
 distinct invasion history and light conditions, I searched for changes in
 reproductive allocation. I also asked whether evolution of the two modes
 can be constrained by the genetic trade-off between them. Furthermore, the
 phenotypic trade-off between the two modes was explored in a field
 experiment. I found that invaded populations increased investments in
 clonal reproduction, a shift that was driven by decreased light
 availability, particularly in the early invasion phases. However, as light
 availability rebounded in the more advanced phases of invasion, so
 decreased allocation to clonal structures. In terms of relative
 allocation, increased investment in ramets was paralleled by reduced seed
 production, and the changes were underpinned by genetic trade-off.
 Finally, the phenotypic trade-off was demonstrated in the field experiment
 by showing that plants producing more ramets were also less likely to
 flower. These results suggest that an exotic plant invasion can drive
 evolution of reproductive allocation, here observed on a timescale of tens
 of years. This knowledge is important not only to predict long-term
 invasion impacts but also, more generally, to provide novel insights into
 the process of adaptation of plants to changing abiotic
 conditions.
DOI: 10.5061/dryad.931zcrjrm
title: Data for: Genome material costs and functional tradeoffs in the autopolyploid Solidago gigantea (Giant Goldenrod) series

description: Premise of study: Increased genomic “material costs” of nitrogen (N) and
 phosphorus (P) atoms inherent to organisms with larger genome sizes (GS)
 has been proposed to limit growth under nutrient scarcities and promote
 growth under nutrient enrichments. Such responsiveness may reflect a
 nutrient-dependent diploid versus polyploid advantage that could have vast
 ecological and evolutionary implications, but direct evidence that
 material costs increase with ploidy-level and/or influence
 cytotype-dependent growth, metabolic, and/or resource-use tradeoffs is
 limited. Methods: We grew diploid, auto-tetraploid, and
 auto-hexaploid Solidago gigantea plants under one of four ambient
 and enriched N:P treatments and measured traits related to material costs,
 primary and secondary metabolism, and resource-use. Key results: Relative
 to diploids, polyploids invested more N and P into cells and tetraploids
 grew more following N-enrichments, suggesting that material costs increase
 with ploidy-level. Polyploids also generally exhibited strategies that
 could minimize material-cost-constraints over both long (reduced monoploid
 GS) and short (more extreme transcriptome downsizing, reduced
 photosynthesis rates and terpene concentrations, enhanced N-use
 efficiencies) evolutionary time periods. Furthermore, polyploids had lower
 transpiration rates but higher water-use-efficiencies than diploids, both
 of which were more pronounced under nutrient-limiting conditions.
 Conclusions: Collectively we found that NP material costs increase with
 ploidy-level but that material-cost-constraints might be lessened by
 organismal resource allocation/investment mechanisms that can also alter
 ecological dynamics and selection. Our results enhance mechanistic
 understanding of how global increases in nutrients might provide a release
 from material-cost-constraints in polyploids that could impact ploidy (or
 GS)-specific performances, cytogeographic patterning, and multispecies
 community structuring.
description: JMP Pro Version 16.0 was used to analyze the data, and all files
 are accessible using Microsoft Excel.