cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.sk2155m
title: Data from: DNA metabarcoding unveils multi‐scale trophic variation in a widespread coastal opportunist

description: A thorough understanding of ecological networks relies on comprehensive
 information on trophic relationships among species. Since unpicking the
 diet of many organisms is unattainable using traditional morphology‐based
 approaches, the application of high‐throughput sequencing methods
 represents a rapid and powerful way forward. Here, we assessed the
 application of DNA‐metabarcoding with nearly universal primers for the
 mitochondrial marker cytochrome c oxidase I (COI) in defining the trophic
 ecology of adult brown shrimp, Crangon crangon, in six European estuaries.
 The exact trophic role of this abundant and widespread coastal benthic
 species is somewhat controversial, while information on geographical
 variation remains scant. Results revealed a highly opportunistic
 behaviour. Shrimp stomach contents contained hundreds of taxa
 (&gt;1000 molecular operational taxonomic units), of which 291 were
 identified as distinct species, belonging to 35 phyla. Only twenty
 ascertained species had a mean relative abundance of more than 0.5%.
 Predominant species included other abundant coastal and estuarine taxa,
 including the shore crab Carcinus maenas and the amphipod Corophium
 volutator. Jacobs’ selectivity index estimates based on DNA extracted from
 both shrimp stomachs and sediment samples were used to assess the
 shrimp's trophic niche indicating a generalist diet, dominated by
 crustaceans, polychaetes and fish. Spatial variation in diet composition,
 at regional and local scales, confirmed the highly flexible nature of this
 trophic opportunist. Furthermore, the detection of a prevalent, possibly
 endoparasitic fungus (Purpureocillium lilacinum) in the shrimp's
 stomach demonstrates the wide range of questions that can be addressed
 using metabarcoding, towards a more robust reconstruction of ecological
 networks.
description: MOTU table Brown shrimp
 diet metabarcodingTable including the
 taxonomic assignment (using ecotag), the abundances per sample and the
 sequence of 8,352 COI-MOTUs found in sediment and pooled Crangon crangon
 stomach samples collected from 24 sites in the Netherlands, Portugal and
 United Kingdom. Ordered in the following columns: (A) id, (B) rank, (C)
 scientific_name, (D) best_identity, (E) superkingdom, (F) kingdom, (H)
 phylum, (H) class, (I) order, (J) family, (K) genus, (L) species, (M to
 AI) abundances in the different sediment samples, (AJ to CI) abundances in
 the different full stomach samples, (CJ-CL) abundances in the different
 empty stomach samples, (CM) sequence_length, (CN)
 sequence.Abiotic variables Brown
 shrimp diet metabarcodingTable including the
 environmental variables of 23 sites in the Netherlands, Portugal and
 United Kingdom measured in May-July 2016. Ordered in the following
 columns: (A) SiteID, (B) Country, (C) Estuary, (D) Temperature [°C], (E)
 Salinity, (F) pH, (H) Turbidity [NTU], (H) Oxygen [%], (I) Grain_Size
 [µM], (J) TOM [%]
DOI: 10.15468/dl.779t7j
title: Occurrence Download

description: A dataset containing 1787 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Phyllodoce empetriformis",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 1787 records from 102 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001550-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.6467hv5
title: Data from: Convergent evolution of the ladder-like ventral nerve cord in Annelida

description: Background: A median, segmented, annelid nerve cord has repeatedly been
 compared to the arthropod and vertebrate nerve cords and became the most
 used textbook representation of the annelid nervous system. Recent
 phylogenomic analyses, however, challenge the hypothesis that a
 subepidermal rope-ladder-like ventral nerve cord (VNC) composed of a
 paired serial chain of ganglia and somata-free connectives represents
 either a plesiomorphic or a typical condition in annelids. Results: Using
 a comparative approach by combining phylogenomic analyses with
 morphological methods (immunohistochemistry and CLSM, histology and TEM),
 we compiled a comprehensive dataset to reconstruct the evolution of the
 annelid VNC. Our phylogenomic analyses generally support previous
 topologies. However, the so far hard-to-place Apistobranchidae and
 Psammodrilidae are now incorporated among the basally branching annelids
 with high support. Based on this topology we reconstruct an intraepidermal
 VNC as the ancestral state in Annelida. Thus, a subepidermal ladder-like
 nerve cord clearly represents a derived condition. Conclusions: Based on
 the presented data, a ladder-like appearance of the ventral nerve cord
 evolved repeatedly, and independently of the transition from an
 intraepidermal to a subepidermal cord during annelid evolution. Our
 investigations thereby propose an alternative set of neuroanatomical
 characteristics for the last common ancestor of Annelida or perhaps even
 Spiralia.
description: Assembled
 dataset_MARE_1.5 analysisAssembled molecular
 dataset underlying the MARE 1.5 analysis.Neurophyl_Matrix_MARE_15.fasAssembled dataset_MARE_2 analysisAssembled datatset underlying the MARE 2 analysis.Neurophyl_Matrix_MARE_2.fas
DOI: 10.5061/dryad.c1p6t1f
title: Data from: Apparent inbreeding preference despite inbreeding depression in the American crow

description: Although matings between relatives can have negative effects on offspring
 fitness, apparent inbreeding preference has been reported in a growing
 number of systems, including those with documented inbreeding depression.
 Here, we examined evidence for inbreeding depression and inbreeding
 preference in two populations (Clinton, New York and Davis, California,
 USA) of the cooperatively breeding American crow (Corvus brachyrhynchos).
 We then compared observed inbreeding strategies with theoretical
 expectations for optimal, adaptive levels of inbreeding, given the
 inclusive fitness benefits and population-specific magnitude of inbreeding
 depression. We found that low heterozygosity at a panel of 33
 microsatellite markers was associated with low survival probability
 (fledging success) and low white blood cell counts among offspring in both
 populations. Despite these costs, our data were more consistent with
 inbreeding preference than avoidance: the observed heterozygosity among
 396 sampled crow offspring was significantly lower than expected if local
 adults were mating by random chance. This pattern was consistent across a
 range of spatial scales in both populations. Theoretically adaptive levels
 of inbreeding, given the magnitude of inbreeding depression, were
 predicted to be very low in the California population, whereas complete
 disassociative mating was predicted in the New York population. Sexual
 conflict might have contributed to the apparent absence of inbreeding
 avoidance in crows. These data add to an increasing number of examples of
 an “inbreeding paradox,” where inbreeding appears to be preferred despite
 inbreeding depression.
description: 1_IR_observed vs.
 expected#### 1. Observed vs.
 expected IR ### Data sheet includes obsetved and simulated (expected)
 values from both populations (NY and CA), given in 4 ways. #### (1) Adults
 in sample = known breeders (according to CERVUS) at Scale = Broad local
 scale #### (2-4) Adults in sample = All local adults at three different
 scales: Scale = Broad local scale, Intermediate local scale, and
 neighborhood scale. ### Analyses in the manuscript are run (1) with known
 breeders (according to CERVUS) at Scale = Broad local scale, and (2-4) at
 each of the three scales, using all local adults. #### All analyses are
 subsetted by population (CA or NY) and use the following model:
 model1&lt;-lm(IR~Treatment) summary(model1)1_DRYAD_IR_observed vs.
 expected.txt2_fledge with
 IRFledging success with
 IR.3_WBC and
 IRWhite blood cell counts
 with IRCode_MolEcol_Townsend et
 al 2018Description of data
 files and associated code
DOI: 10.5061/dryad.770nj18
title: Data from: Bisphenol A promotes the invasive and metastatic potential of ductal carcinoma in situ and pro-tumorigenic polarization of macrophages

description: Increased cancer risk and immune disorders linked with exposure to
 environmental endocrine disruptors like bisphenol A (BPA) have been
 steadily reported. Nevertheless, the impacts of BPA on the breast ductal
 carcinoma in situ (DCIS) progression and macrophage polarization remain to
 be elucidated. Here, we analyzed the differentially expressed genes in
 BPA-exposed DCIS cells and explored BPA effects on DCIS progression and
 macrophage polarization in vitro and in vivo. 291 genes were
 differentially expressed in 10-8 M BPA-exposed DCIS cells, in which the
 gene ontology terms of biological processes associated with negative
 regulation of cell death, cell adhesion and immune response was enriched.
 10-8 M BPA promoted the proliferation and migration of DCIS cells and the
 migration of macrophages, and upregulated the expression of M1 (NOS2) or
 M2 markers (Arg-1 and CD206) in macrophages. In co-culture system, the
 migratory capacity of both cells and the expression levels of NOS2, Arg-1
 and CD206 in macrophages were significantly enhanced upon 10-8 M BPA. In a
 DCIS xenograft model, oral exposure to an environmentally human-relevant
 low dose of 2.5 µg/L BPA for 70 days via drinking water led to an ~2-fold
 promotion in the primary tumor growth rate and a significant enhancement
 of lymph node metastasis along with increased pro-tumorigenic CD206+ M2
 polarization of macrophages. These results demonstrate that BPA acts as an
 accelerator to promote DCIS progression to invasive breast cancer by
 affecting DCIS cell proliferation and migration as well macrophage
 polarization toward a pro-tumorigenic phenotype.
description: Table S1. Analysis of
 axillary LN metastasis by immunohistochemistry for CK5 in DCIS
 tumor-bearing miceToxicol Sciences_Kim H et
 al_Supplementary Table.docxToxicol Sciences_Kim H
 et al_Supple Fig1Figure S1. Low dose BPA
 promotes the proliferation and migration capacities of DCIS.com, MCF-7 and
 MDA-MB-231 cells.Toxicol Sciences_Kim H
 et al_Supple Fig2Figure S2. Low dose BPA
 promotes the migration capacities of RAW264.7 cells, also increases M1 and
 M2 polarization markers in a dose- and time-dependent
 manner.Toxicol Sciences_Kim H
 et al_Supple Fig3Figure S3. Low dose BPA
 promotes the migration capacities of J774A.1 cells and upregulates NOS2,
 Arg-1 and CD206.Toxicol Sciences_Kim H
 et al_Supple Fig4Figure S4. High dose BPA
 does not significantly promote the tumor growth in DCIS xenograft
 models.Fig1_RAW DATA_READ
 COUNTFigure 1. Differentially
 expressed genes (DEGs) clusters and Gene Ontology (GO) categorization
 between BPA-exposed DCIS.com cells and control. RAW data in RNA-seq
 analysis.
DOI: 10.5061/dryad.7b3c73k
title: Data from: UV bullseye contrast of Hemerocallis flowers attracts hawkmoths but not swallowtail butterflies

description: The colour and patterns of animal-pollinated flowers are known to have
 effects on pollinator attraction. In this study, the relative importance
 of flower colour and colour contrast patterns on pollinator attraction was
 examined in two pollinator groups, swallowtail butterflies and hawkmoths
 using two Hemerocallis species; butterfly-pollinated H. fulva and
 hawkmoth-pollinated H. citrina, having reddish and yellowish flowers in
 human vision, respectively. Flowers of both species have UV bullseye
 patterns, composed of UV-absorbing centres and UV-reflecting peripheries,
 known to function as a typical nectar guide, but UV reflectance was
 significantly more intense in the peripheries of H. citrina flowers than
 in those of H. fulva flowers. Comparison based on the visual systems of
 butterflies and hawkmoths showed that the colour contrast of the bullseye
 pattern in H. citrina was more intense than that in H. fulva. To evaluate
 the relative importance of flower colour and the colour contrast of
 bullseye pattern on pollinator attraction, we performed a series of
 observations using experimental arrays consisting of Hemerocallis species
 and their hybrids. As a result, swallowtail butterflies and
 crepuscular/nocturnal hawkmoths showed contrasting preferences for flower
 colour and patterns: butterflies preferred H. fulva-like coloured flower
 whereas the preference of hawkmoths was affected by the colour contrast of
 the bullseye pattern rather than flower colour. Both crepuscular and
 nocturnal hawkmoths consistently preferred flowers with stronger contrast
 of the UV bullseye pattern, whereas the preference of hawkmoths for flower
 colour was incoherent. Our finding suggests that hawkmoths can use
 UV-absorbing/reflecting bullseye patterns for foraging under light-limited
 environments and that the intensified bullseye contrast of H. citrina
 evolved as an adaptation to hawkmoths. Our results also showed the
 difference of visual systems between pollinators, which may have promoted
 floral divergence.
description: Floral spectral
 reflectance of H. fulva, H. citrina and hybridsThis file contains
 reflectance spectra in the central part and the peripheral part of tepals
 of H. fulva, H. citrina, and their F2 hybrids.RelativeReflectance.csvFloral traits and pollinator visitations in experiment 1Experiment1.csvFloral traits and pollinator visitations in Experiment 2Experiment2.csvFloral traits and pollinator visitations in Experiment 3Experiment3.csv
DOI: 10.5061/dryad.jn44bq4
title: Data from: Ecology and macroevolution – evolutionary niche monopolisation as a mechanisms of niche conservatism

description: Explaining macroevolution from microevolution is a key issue in
 contemporary evolutionary theory. A recurrent macroevolutionary pattern is
 that some niche‐related traits consistently evolve slower than others, so
 called niche conservatism. Despite a growing amount of data, the
 underlying evolutionary processes are not fully understood. I here analyse
 adaptive radiations in an individual‐based eco‐evolutionary model. I find
 a coevolutionary mechanism – evolutionary niche monopolisation – as a
 possibly important generator of niche conservatism. A single lineage of a
 radiating clade can monopolise, and later diversify within, a substantial
 part of the available niche space – much larger than what can be explained
 by limiting similarity. This leads to niche conservatism, since no species
 evolves into or out of the monopolised region. The region can in this
 sense also be described as an adaptive zone. The model indicates that
 evolutionary niche monopolisation is operative in a large part of
 parameter space, underlining its possible importance. The mechanism is
 driven by competitive interactions and differences in niche widths in
 alternative niche dimensions. I discuss plausible examples of evolutionary
 niche monopolisation in well‐studied natural systems.
description: Code package for
 simulation (C++) and analysis (Matlab)Please read the Readme
 fileCode.zip
DOI: 10.6084/m9.figshare.29162245
title: Personality traits in people with multiple sclerosis: A systematic review and meta-analysis

description: <b>Objective:</b> Although numerous studies have investigated personality traits in people with multiple sclerosis (PwMS), a thorough systematic review and meta-analysis of this evidence has not been conducted. This review aimed to elucidate the personality profile of PwMS relative to healthy controls (HCs) and to assess the overall correlations between personality traits and mood, cognitive performances, fatigue, and physical function in PwMS. <b>Methods:</b> PubMed/MEDLINE, Scopus, Embase, and Web of Sciences were systematically searched up to 18 August 2024, to identify studies (1) comparing personality traits, including Agreeableness, Conscientiousness, Extraversion, Neuroticism, and Openness, between PwMS and HCs or (2) assessing the correlation between personality traits, anxiety, depression, cognition, fatigue, and physical function in PwMS. The pooled standardized mean differences (SMDs) or correlations were estimated. <b>Results:</b> Sixty-three studies on 8068 PwMS and 1588 HCs were included. PwMS exhibited different personality traits, notably higher Neuroticism, compared to HCs. Furthermore, Neuroticism showed the most significant pooled correlations with mood and fatigue, while Conscientiousness demonstrated the greatest pooled correlations with disability and cognitive performance in PwMS. The meta-analysis confirmed these findings, revealing that PwMS have higher Neuroticism (SMD = 0.35) than HCs. Additionally, higher Neuroticism was significantly linked to increased anxiety (<i>r</i> = 0.78), depression (<i>r</i> = 0.53), and fatigue (<i>r</i> = 0.35), and Conscientiousness was significantly correlated with decreased Expanded Disability Status Scale (EDSS) (<i>r</i> = −0.21) and Symbol Digit Modalities Test (SDMT) (<i>r</i> = 0.13). <b>Conclusions:</b> PwMS exhibited distinct personality traits compared to healthy individuals. Additionally, personality traits, particularly Neuroticism and Conscientiousness, had relationships with mood, cognitive performance, fatigue, and physical function of PwMS.
DOI: 10.6084/m9.figshare.29162245.v1
title: Personality traits in people with multiple sclerosis: A systematic review and meta-analysis

description: <b>Objective:</b> Although numerous studies have investigated personality traits in people with multiple sclerosis (PwMS), a thorough systematic review and meta-analysis of this evidence has not been conducted. This review aimed to elucidate the personality profile of PwMS relative to healthy controls (HCs) and to assess the overall correlations between personality traits and mood, cognitive performances, fatigue, and physical function in PwMS. <b>Methods:</b> PubMed/MEDLINE, Scopus, Embase, and Web of Sciences were systematically searched up to 18 August 2024, to identify studies (1) comparing personality traits, including Agreeableness, Conscientiousness, Extraversion, Neuroticism, and Openness, between PwMS and HCs or (2) assessing the correlation between personality traits, anxiety, depression, cognition, fatigue, and physical function in PwMS. The pooled standardized mean differences (SMDs) or correlations were estimated. <b>Results:</b> Sixty-three studies on 8068 PwMS and 1588 HCs were included. PwMS exhibited different personality traits, notably higher Neuroticism, compared to HCs. Furthermore, Neuroticism showed the most significant pooled correlations with mood and fatigue, while Conscientiousness demonstrated the greatest pooled correlations with disability and cognitive performance in PwMS. The meta-analysis confirmed these findings, revealing that PwMS have higher Neuroticism (SMD = 0.35) than HCs. Additionally, higher Neuroticism was significantly linked to increased anxiety (<i>r</i> = 0.78), depression (<i>r</i> = 0.53), and fatigue (<i>r</i> = 0.35), and Conscientiousness was significantly correlated with decreased Expanded Disability Status Scale (EDSS) (<i>r</i> = −0.21) and Symbol Digit Modalities Test (SDMT) (<i>r</i> = 0.13). <b>Conclusions:</b> PwMS exhibited distinct personality traits compared to healthy individuals. Additionally, personality traits, particularly Neuroticism and Conscientiousness, had relationships with mood, cognitive performance, fatigue, and physical function of PwMS.
DOI: 10.6084/m9.figshare.29039856
title: Validation of the Spanish version of the cerebellar cognitive-affective syndrome scale

description: <b>Objective:</b> To validate the Spanish version of the Cerebellar Cognitive-Affective Syndrome scale (CCAS-S), originally published in 2018, in patients with cerebellar ataxia and healthy subjects, as an adapted Spanish version based on normative data has not yet been published or validated. <b>Methods:</b> Spanish CCAS-S was ­administered prospectively to 158 patients with cerebellar ataxia and 164 matched healthy subjects from ­different regions of Spain. Discriminant validity and reliability were evaluated. A subgroup of 30 patients underwent detailed neuropsychological examinations to confirm the construct validity. The Scale for the Assessment and Rating of Ataxia (SARA) and the Brief Ataxia Rating Scale (BARS) were used to assess motor performance. <b>Results:</b> This Spanish instrument demonstrates reliability and exhibits statistically significant differences in performance between patients and healthy subjects. Our analysis revealed lower values for specificity in detecting possible, probable, or definite CCAS compared to those reported in the US validation study when utilizing the original cutoff values. Upon application of the appropriate ­correction factor for education, the specificity values approximated those reported for probable and definite CCAS diagnostics in the original investigation. <b>Conclusions:</b> The adapted Spanish CCAS-S has demonstrated validity and good reliability in this cohort. Discriminant validity was satisfactory for probable and definite CCAS when the correction for education was applied, and modified template and instructions have been developed. Further research is necessary to investigate the significance of the possible CCAS category, as diagnosed using the Spanish version, as well as to assess the performance of the corrected scale in other Spanish-speaking countries.
DOI: 10.6084/m9.figshare.29039856.v1
title: Validation of the Spanish version of the cerebellar cognitive-affective syndrome scale

description: <b>Objective:</b> To validate the Spanish version of the Cerebellar Cognitive-Affective Syndrome scale (CCAS-S), originally published in 2018, in patients with cerebellar ataxia and healthy subjects, as an adapted Spanish version based on normative data has not yet been published or validated. <b>Methods:</b> Spanish CCAS-S was ­administered prospectively to 158 patients with cerebellar ataxia and 164 matched healthy subjects from ­different regions of Spain. Discriminant validity and reliability were evaluated. A subgroup of 30 patients underwent detailed neuropsychological examinations to confirm the construct validity. The Scale for the Assessment and Rating of Ataxia (SARA) and the Brief Ataxia Rating Scale (BARS) were used to assess motor performance. <b>Results:</b> This Spanish instrument demonstrates reliability and exhibits statistically significant differences in performance between patients and healthy subjects. Our analysis revealed lower values for specificity in detecting possible, probable, or definite CCAS compared to those reported in the US validation study when utilizing the original cutoff values. Upon application of the appropriate ­correction factor for education, the specificity values approximated those reported for probable and definite CCAS diagnostics in the original investigation. <b>Conclusions:</b> The adapted Spanish CCAS-S has demonstrated validity and good reliability in this cohort. Discriminant validity was satisfactory for probable and definite CCAS when the correction for education was applied, and modified template and instructions have been developed. Further research is necessary to investigate the significance of the possible CCAS category, as diagnosed using the Spanish version, as well as to assess the performance of the corrected scale in other Spanish-speaking countries.