cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.p2ngf1vng
title: Data from: Transoceanic dispersal of terrestrial species by debris rafting

description: Rare, long-distance dispersal events are a key process in generating and
 maintaining patterns in biological diversity and species distributions
 across space and time. The 9.0 magnitude earthquake that struck the
 eastern coast of Japan in 2011, and the subsequent 38 m high tsunami
 washed large amounts of shoreline debris into the Pacific Ocean that led
 to a large-scale biological rafting event carrying nearly 300 marine
 species to the western shores of North America. Whether oceanic,
 trans-Pacific dispersal via rafting generates long distance dispersal
 events for small, flightless, terrestrial species is unknown. By sampling
 beach debris associated with known hot-spots of tsunami debris along the
 north and east shores of Graham Island, Haida Gwaii, Canada, I document
 significantly dissimilar invertebrate communities associated with
 tide-line beach debris and the occurrence of several putative Japanese
 species of soil-dwelling mites (Acari: Oribatida). Previous explanations
 of Haida Gwaii’s unique flora and fauna have been attributed to a
 proximity to the Beringian land bridge and the accumulated evidence of
 near-offshore glacial refugia during the last glacial period. However, my
 research also suggests that stochastic, trans-Pacific rafting events
 contribute to the biodiversity and biogeography of soil communities on the
 west coast of North America.
description: Species abundance data were generated at locations with
 previously documented Japan Tsunami Marine Debris (JTMD) along the north
 and east shorelines (North Beach and East Beach) of Graham Island, Haida
 Gwaii, British Columbia, Canada. Samples were collected from beach, tidal
 edge, and forest locations in Summer 2017 over a one-week period following
 the morning high tide.  Beach samples consisted of approx. 20 cm2 of
 debris from multiple items collected along the shoreline representing the
 daily tide line.  Shoreline vegetation and leaf litter at the tidal edge
 zone were sampled to represent the first possible, but likely non-optimal
 habitat that would allow for colonization of new terrestrial migrants. 
 Forest floor samples were also collected for comparison with long-term
 resident species.  Where possible beach, edge and forest samples were
 collected at the same location.  All samples were extracted on portable
 Berlese faunal extractors over 72 hrs into 75% ethanol, and specimens
 observed were subsequently identified to species-level using keys from the
 primary literature, and compared against &gt;3000 curated specimens in
 the author’s taxonomic collection.
DOI: 10.5061/dryad.qfttdz0dr
title: Association of APOE gene polymorphisms with primary open angle glaucoma in Brazilian patients

description: Background: Primary open-angle glaucoma (POAG) is a
 multifactorial disease that affects 65.5 million people
 worldwide.  In addition to the genetic variants already
 established as indicators of greater risk for POAG, the apolipoprotein
 (APOE) gene has been studied in some populations, with controversial
 results. The aim of this study is to investigate the frequency of the
 genetic variants of APOE in the Brazilian population, and to evaluate the
 association between these polymorphisms and the risk of POAG.
 Methods: APOE variants (rs429358; rs7412) were genotyped in 402
 POAG patients and 401 controls. We evaluated the association
 between APOE genetic variants and the risk for POAG, as well as
 the correlation between the requirement of glaucoma surgery and
 the APOE polymorphisms.  Results: Among the
 three APOE gene isoforms, we found a low frequency of APOE alleles ε2
 (7.34%) and ε4 (11.76%), but a high frequency of ε3 (80.88%) in our
 population. When compared to ε3ε3 reference genotype, ε2 allele-carriers
 (OR=1.516; p-value=0.04) and ε2ε3 genotype (OR=1.655;
 p-value=0.02) were associated with a greater risk for POAG. An
 additive genetic model confirmed the influence of the ε2 allele in the
 risk of POAG in this sample of the Brazilian population
 (OR=1.502; p-value=0.04). There was no significant association
 between the analyzed genotypes and the requirement or number of glaucoma
 surgeries (p&gt;0.05).  Conclusion: Brazilian
 individuals carrying the APOEε2 allele may be at an increased risk for
 the development of POAG.
description: All this data was collected from Hospital de Clinicas -
 University of Campinas - Brazil. <i>APOE</i> variants (rs429358; rs7412) were genotyped in 402 POAG patients and 401 controls. We evaluated the association between <i>APOE</i> genetic variants and the risk for POAG, as well as the correlation between the requirement of glaucoma surgery and the <i>APOE</i> polymorphisms.
description: We also investigated the correlation between the requirement of
 glaucoma surgery, or the number of antiglaucomatous surgeries performed by
 each patient,  and the <i>APOE</i> polymorphisms. Among the
 402 POAG patients, 383 (95.27%) were analyzed with respect to surgical
 treatment, since 19 patients had insufficient
 information/follow-up.
DOI: 10.5061/dryad.44j0zpcbh
title: Fruit orchards and woody semi-natural habitat provide complementary resources for pollinators in agricultural landscapes

description: To safeguard insect pollinators and their pollination services, we need to
 understand how landscape structure regulates the distribution of resources
 that sustain pollinator populations. However, evidence of how pollinator
 communities benefit from the variety of resources distributed across
 different habitat types is scarce. To explore complementary resource
 provision, we conducted a field study to examine the resources available
 to pollinators in fruit orchards and woody semi-natural
 habitat. We studied 13 landscapes containing both habitat types
 in Flanders, Belgium. In every habitat element, we surveyed nesting
 resources, floral resources and wild pollinators (i.e. wild bees and hover
 flies) during three consecutive time periods in the season (once before-
 and twice after mass-flowering of the fruit orchards). We
 concluded that the composition of nesting resources for wild bees was
 clearly different between both habitat types. Woody semi-natural habitat
 also provided more diverse- and a higher cover of floral resources
 compared to fruit orchards. In addition, the composition of these floral
 resources became more and more distinct between the two habitat types as
 the season progressed. Based on the plant−pollinator network we identified
 key plant species for inclusion in management schemes to support
 pollinators. Our study highlights that fruit orchards and woody
 semi-natural habitat provide a set of different, complementary resources
 during the flight season, for pollinating insects. Due to the higher
 diversity and abundance of resources in woody semi-natural habitat,
 conservation of woody semi-natural habitat is essential for the support of
 pollinators in agricultural landscapes.
description: See Eeraerts et al. (2021)
description: See Eeraerts et al. (2021) and Eeraerts_ReadMe.word
DOI: 10.5061/dryad.np5hqbzqg
title: Adaptation and latitudinal gradients in species interactions: nest predation in birds

description: Are rates of biotic interactions are stronger in the tropics? Here we
 investigate nest predation rates in birds, a canonical example of a strong
 tropical biotic interaction. Counter to expectations, daily rates of nest
 predation vary minimally with latitude. However, life history traits that
 influence nest predation have diverged between latitudes. For example,
 tropical species have evolved a longer average nesting period, which is
 associated with reduced rates of nest attendance by parents. Daily nest
 mortality declines with nesting period duration within regions, but
 tropical species have a higher intercept. Consequently, for the same
 nesting period length, tropical species experience higher daily nest
 predation rates than temperate species. The implication of this analysis
 is that the evolved difference between latitudes in nesting period length
 produces a flatter latitudinal gradient in daily nest predation than would
 otherwise be predicted. We propose that adaptation may frequently dampen
 geographic patterns in interaction rates.
DOI: 10.5061/dryad.931zcrjh8
title: Spatial predictors of genomic and phenotypic variation differ in a lowland Middle American bird (Icterus gularis)

description: Spatial patterns of intraspecific variation are shaped by factors such as
 geographic distance among populations, historical changes in gene flow and
 interactions with local environments. Although these factors are not
 mutually exclusive and operate on both genomic and phenotypic variation,
 it is unclear how they affect these two axes of variation. We address this
 question by exploring the predictors of genomic and phenotypic divergence
 in Icterus gularis, a broadly distributed Middle American bird that
 exhibits marked geographic variation in body size across its range. We
 combined a comprehensive SNP and phenotypic dataset to test whether
 genome-wide genetic and phenotypic differentiation are best explained by
 (a) isolation by distance, (b) isolation by history, or (c) isolation by
 environment. We find that the pronounced genetic and phenotypic variation
 in I. gularis are only partially correlated and differ regarding spatial
 predictors. Whereas genomic variation is largely explained by historical
 barriers to gene flow, phenotypic diversity can be best predicted by
 contemporary environmental heterogeneity. Our genomic analyses reveal
 strong phylogeographic structure coinciding with the Chivela Pass at the
 Isthmus of Tehuantepec and was formed in the Pleistocene, when populations
 were isolated in north-south refugia. In contrast, we found a strong
 association between body size and environmental variables, such as
 temperature and precipitation. The relationship between body size and
 local climate is consistent with a pattern produced by either natural
 selection or environmental plasticity. Overall, these results provide
 empirical evidence for why phenotypic and genomic data are often in
 conflict in taxonomic and phylogeographic studies.
description: <strong>icterus_ingroup_6xcov_090diff_min5.vcf</strong> SNP dataset assembled using iPyRAD (90% sequence identity, min coverage 6x, max missing data 50%) <strong>Icterus_gularis_ND2.fasta</strong> Alignment of ND2 sequences <strong>Measurements-TOTAL_DATASET.csv</strong> Phenotypic measurements of museum-vouchered specimens <strong>Maxent_model_LQHP_05_full_data.asc</strong> Ecological niche model (ENM) for the current climate <strong>MidHolocene_average.asc</strong> Ecological niche model (ENM) for the Mid-Holocene averaged across climate models <strong>LGM_average.asc</strong> Ecological niche model (ENM) for the Last Glacial Maximum averaged across climate models
DOI: 10.5061/dryad.sxksn030r
title: Gestational Cd exposure in the CD-1 mouse induces sex-specific hepatic insulin insensitivity, obesity and metabolic syndrome in adult female offspring

description: There is compelling evidence that developmental exposure to some toxic
 metals increases risk for obesity and obesity-related morbidity including
 cardiovascular disease and type 2 diabetes in adults. To explore the
 hypothesis that developmental Cd exposure increased risk of obesity later
 in life, male and female CD-1 mice were maternally exposed to 500 ppb
 CdCl2 in drinking water during a human gestational equivalent period (GD0
 - PND10). Hallmark indicators of metabolic disruption, hepatic steatosis,
 and metabolic syndrome were evaluated prior to birth through adulthood.
 Blood Cd levels in dams were similar to those observed in human pregnancy
 cohorts. There were no observed impacts of exposure on dams or
 pregnancy-related outcomes. Results of glucose and insulin tolerance
 testing revealed that Cd-exposure impaired glucose homeostasis in young
 adult offspring. Exposure-related increases in circulating triglycerides
 and hepatic steatosis were apparent only in females. By PND120, Cd-exposed
 females had become 30% heavier with 700% more perigonadal fat than
 unexposed control females. There was no evidence of dyslipidemia,
 steatosis, increased weight gain, nor increased adiposity in Cd-exposed
 male offspring. Hepatic transcriptome analysis at PND1, PND21, and PND42
 revealed evidence for female-specific increases in oxidative stress and
 mitochondrial dysfunction with significant early disruption of retinoic
 acid signaling and altered insulin receptor signaling consistent with
 hepatic insulin sensitivity in adult females. The observed steatosis and
 metabolic syndrome-like phenotypes resulting from exposure to 500 ppb
 CdCl2 during the pre- and perinatal period of development equivalent to
 human gestation indicate that Cd acts developmentally as a sex-specific
 delayed obesogen.
DOI: 10.15468/dl.sg5d5r
title: Occurrence Download

description: A dataset containing 475 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Austrosteenisia blackii",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 475 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002401-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.kh1893239
title: Additional information and tables for: Association of circulating metabolites in plasma or serum and risk of stroke: Meta-analysis from seven prospective cohorts

description: Objective: To conduct a comprehensive analysis of circulating metabolites
 and incident stroke in large prospective population-based settings.
 Methods: We investigated the association of metabolites with risk of
 stroke in seven prospective cohort studies including 1,791 incident stroke
 events among 38,797 participants in whom circulating metabolites were
 measured by Nuclear Magnetic Resonance (1H-NMR) technology. The
 relationship between metabolites and stroke was assessed using Cox
 proportional hazards regression models. The analyses were performed
 considering all incident stroke events and ischemic and hemorrhagic events
 separately. Results: The analyses revealed ten significant metabolite
 associations. Amino acid histidine (hazard ratio (HR) per standard
 deviation (SD) = 0.90, 95% confidence interval (CI): 0.85, 0.94; P =
 4.45×10-5), glycolysis-related metabolite pyruvate (HR per SD = 1.09, 95%
 CI: 1.04, 1.14; P = 7.45×10-4), acute phase reaction marker glycoprotein
 acetyls (HR per SD = 1.09, 95% CI: 1.03, 1.15; P = 1.27×10-3), cholesterol
 in high-density lipoprotein (HDL) 2 and several other lipoprotein
 particles were associated with risk of stroke. When focusing on incident
 ischemic stroke, a significant association was observed with phenylalanine
 (HR per SD = 1.12, 95% CI: 1.05, 1.19; P = 4.13×10-4) and total and free
 cholesterol in large HDL particles. Conclusions: We found association of
 amino acids, glycolysis-related metabolites, acute phase reaction markers,
 and several lipoprotein subfractions with the risk of stroke. These
 findings support the potential of metabolomics to provide new insights
 into the metabolic changes preceding stroke.
DOI: 10.5061/dryad.31zcrjdhk
title: Nano MOFs as targeted drug delivery agents to combat antibiotic resistant bacterial infections

description: The drug resistance of bacteria is a significant threat to human
 civilization while the action of antibiotics against drug-resistant
 bacteria is severely limited due to the hydrophobic nature of drug
 molecules, which unquestionably inhibit its permanency for clinical
 applications. The antibacterial action of nanomaterials offers major
 modalities to combat drug resistance of bacteria. The current work
 reports, the use of nano MOFs encapsulating drug molecules to enhance its
 antibacterial activity against model drug-resistant free living bacteria
 and biofilm of the bacteria. We have attached rifampicin (RF), a
 well-documented antituberculosis drug with tremendous pharmacological
 significance, into the pore surface of zeolitic imidazolate framework 8
 (ZIF8) by a simple synthetic procedure. The synthesized ZIF8 has been
 characterized using X-ray diffraction (XRD) method before and after drug
 encapsulation. The electron microscopic strategies such as scanning
 electron microscope (SEM) and transmission electron microscope (TEM)
 methods was performed to characterize the binding between ZIF8 and RF. We
 have also performed picosecond resolved fluorescence spectroscopy to
 validate the formation of the ZIF8-RF nanohybrids (NHs). The drug release
 profile experiment demonstrates that ZIF8-RF depicts pH-responsive drug
 delivery and ideal for targeting bacterial disease corresponding to its
 inherent acidic nature. Most remarkably, ZIF8-RF gives enhanced
 antibacterial activity against methicillin-resistant S. aureus (MRSA)
 bacteria and also prompts entire damage of structurally robust bacterial
 biofilms. Overall, the present study depicts a detailed physical insight
 for manufactured antibiotic-encapsulated NHs presenting tremendous
 antimicrobial activity that can be beneficial for manifold practical
 applications.
description: This file includes raw data used for making figures (Figure 1b,
 Figure 1c, Figure 4a, Figure 4b, Figure 4c, Figure 4d, Figure 5a, Figure
 5b, and Figure 6a).
DOI: 10.5061/dryad.s1rn8pk53
title: Def6 regulates endogenous type-I interferon responses in osteoblasts and suppresses osteogenesis

description: Normal bone remodeling involves a balance between osteoclast-mediated bone
 resorption and osteoblast/osteocyte-mediated bone formation and is
 critical for maintaining healthy bone mass. This balance is often
 disrupted in disease conditions, such as osteoporosis and rheumatoid
 arthritis (RA). The mechanisms underlying bone remodeling especially in
 disease settings are far from well understood. DEF6 is recently identified
 as a novel loci associated with bone mineral density. However, it is
 unclear how Def6 impacts bone remodeling. We previously reported that the
 immunoregulator Def6 is a key inhibitor of osteoclast differentiation and
 bone resorption in both physiological and TNFα-mediated inflammatory
 conditions. In this study, we identify Def6 as a novel osteoblastic
 regulator that suppresses osteoblast differentiation and bone formation.
 Def6 deficiency enhances both osteoclastic bone resorption and
 osteoblastic osteogenesis. The enhanced bone resorption in Def6-/- mice
 dominates, leading to osteoporosis. Mechanistically, Def6 inhibits the
 differentiation of both osteoclasts and osteoblasts via a common mechanism
 through endogenous type I IFN-mediated feedback inhibition, highlighting
 an immunoregulatory function of Def6 in bone cells. The presence of IFN
 stimulated gene (ISG) expression in osteoblast differentiation is a recent
 topic of interest. Our genome-wide RNAseq analysis shows expression of a
 group of ISGs during osteoblast differentiation and demonstrates that Def6
 is a key upstream regulator of ISG expression in osteoblasts.
 Collectively, our results identify novel immunoregulatory function of Def6
 in both osteoclastic bone resorption and osteoblastic bone formation in
 bone remodeling, and shed insights into the interaction between immune
 system and bone turn over. In TNFα-mediated inflammatory bone loss, TNFα
 decreases Def6 expression in osteoclasts but does not impact Def6
 expression in osteoblasts. This differential regulation of Def6 expression
 by TNFα leads to enhanced osteoclast differentiation and reduced
 osteoblast differentiation, leading to drastically enhanced bone
 resorption with limited new bone formation in response to TNFα. These
 results revealed an important mechanism by which TNFα disrupts normal bone
 remodeling, and suggest that differential modulation of Def6 expression in
 different bone cells may represent novel therapeutic strategies to treat
 inflammatory bone loss.
DOI: 10.6084/m9.figshare.27890484.v2
title: Supplementary Data of Wahlenbergia ceracea genome assembly from Notarnicola et al 2024

description: Supplementary Data providing genome assembly and predicted annotations (produced by BRAKER2 supplemented with mRNA-sequencing), including nucleotide and protein sequences, for Wahlenbergia ceracea.Description of files:<i>wceracea_genome.fa</i>: Genome assembly in FASTA format.<i>braker_wceracea.sorted.gtf</i>: BRAKER identified genes sorted by genomic coordinates in GTF format.<i>braker_wceracea.codingseq</i>: Coding sequences of BRAKER identified genes in FASTA format.<i>braker_wceracea.aa</i>: Protein sequences for BRAKER identified genes.<i>import_kallisto_tximport.r</i>: R script for importing transcript and gene IDs defined by BRAKER.<i>braker_wceracea.sorted.kallisto.idx</i>: Kallisto-generated index used for transcript abundance estimation based on BRAKER annotation.<br>
DOI: 10.5061/dryad.3ffbg79fw
title: Understanding degraded speech leads to perceptual gating of a brainstem reflex in human listeners

description: The ability to navigate “cocktail-party” situations by focussing on sounds
 of interest over irrelevant, background sounds is often considered in
 terms of cortical mechanisms. However, subcortical circuits such as the
 pathway underlying the medial olivocochlear (MOC) reflex modulate the
 activity of the inner ear itself, supporting the extraction of salient
 features from auditory scene prior to any cortical processing. To
 understand the contribution of auditory subcortical nuclei and the cochlea
 in complex listening tasks, we made physiological recordings along the
 auditory pathway while listeners engaged in detecting non(sense)-words in
 lists of words. Both naturally spoken and intrinsically noisy, vocoded
 speech—filtering that mimics processing by a cochlear
 implant—significantly activated the MOC reflex, but this was not the case
 for speech in background noise, which more engaged midbrain and cortical
 resources. A model of the initial stages of auditory processing reproduced
 specific effects of each form of speech degradation, providing a rationale
 for goal-directed gating of the MOC reflex based on enhancing the
 representation of the energy envelope of the acoustic waveform. Our data
 reveals the co-existence of two strategies in the auditory system that may
 facilitate speech understanding in situations where the signal is either
 intrinsically degraded or masked by extrinsic acoustic energy. Whereas
 intrinsically degraded streams recruit the MOC reflex to improve
 representation of speech cues peripherally, extrinsically masked streams
 rely more on higher auditory centres to de-noise signals.
description: Dataset includes all sound and sentence wav-files used to
 generate auditory nerve spikes.  Model of the auditory periphery and
 auditory brainstem (MAP_BS) is the work of Meddis group and is available
 here but can also be originally found (alongside more information about
 previous versions of the model) at http://essexpsychology.webmate.me/HearingLab/modelling.html.  Please refer to https://www.researchgate.net/publication/307583615_MAP-BSa_Matlab_Auditory_Processing_software_platform_for_studying_Auditory_BrainStem_activity for further information about MAP_BS and its origins. Two analysis files are included to perform Shuffled Auto-/Cross- Correlograms of either Individual Words (list of words used in the article are found in 'Balanced_NS_and_S_lists.mat') or Mava Corpus sentences (https://app.alveo.edu.au/catalog/mava).
description: Please read README.docx for an overview of source data in this
 dataset. There is also reading material to understand workings of MAP_BS
 Auditory nerve model (included in MAP_BSpublic_forDryad.zip). Please unzip
 Additional_PlosBio_files_for_MAP_BS.zip for custom mfiles and instructions
 on how to run simulations/analysis for individual words.