cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.0sf2hm8
title: Data from: Hierarchical Hybrid Enrichment: multi-tiered genomic data collection across evolutionary scales, with application to chorus frogs (Pseudacris)

description: Determining the optimal targets of genomic sub-sampling for phylogenomics,
 phylogeography, and population genomics remains a challenge for
 evolutionary biologists. Of the available methods for sub-sampling the
 genome, hybrid enrichment (sequence capture) has become one of the primary
 means of data collection for systematics, due to the flexibility and cost
 efficiency of this approach. Despite the utility of this method,
 information is lacking as to what genomic targets are most appropriate for
 addressing questions at different evolutionary scales. In this study,
 first we compare the benefits of target loci developed for deep- and
 shallow-scales by comparing these loci at each of three taxonomic levels:
 within a genus (phylogenetics), within a species (phylogeography) and
 within a hybrid zone (population genomics). Specifically, we target
 evolutionary conserved loci that are appropriate for deep phylogenetic
 scales and more rapidly evolving loci that are informative for
 phylogeographic and population genomic scales. Second, we assess the
 efficacy of targeting multiple locus sets for different taxonomic levels
 in the same hybrid enrichment reaction, an approach we term hierarchical
 hybrid enrichment. Third, we apply this approach to the North American
 chorus frog genus Pseudacris to answer longstanding evolutionary questions
 across taxonomic and temporal scales. We demonstrate that in this system
 the type of genomic target that produces the most resolved gene trees
 differs depending on the taxonomic level, although the potential for error
 is substantially lower for the deep-scale loci at all levels. We
 successfully recover data for the two different locus sets with high
 efficiency. Using hierarchical data targeting deep and shallow levels, we
 (a) resolve the phylogeny of the genus Pseudacris and introduce a novel
 visual and hypothesis-testing method that uses nodal heat maps to examine
 the robustness of branch support values to the removal of sites and loci;
 (b) estimate the phylogeographic history of P. feriarum, which reveals
 five independent invasions of sympatry by this species to form replicated
 reinforcement contact zones with P. nigrita with ongoing gene flow into
 sympatry; and (c) quantify with high confidence the frequency of
 hybridization in one of these zones between P. feriarum and P. nigrita,
 which is much lower than previously found by microsatellite-based studies.
 We find that the hierarchical hybrid enrichment approach offers an
 efficient, multi-tiered data collection method for simultaneously
 addressing questions spanning multiple evolutionary scales.
description: SupplementalFiguresAndCaptionsSupplementalTablesSupplementalTableCaptionsSupplementalMaterialsProbeDesignsBanker-etal_ProbeDesigns.zipSequencesBanker-etal_Sequences.zipAlignmentsBanker-etal_Alignments.zipTreesBanker-etal_Trees.zip
DOI: 10.5281/zenodo.18317421
title: Pre-injury warning signals in drivers with traumatic spinal cord injury: a case-control study utilizing electronic health records

description: An anonymized SPSS data file and analysis outputs have been uploaded before manuscript submission to journal. Aim of this study was to determine whether pre-injury healthcare utilization patterns in national EHRs can serve as warning signals for subsequent driver/rider-related TSCI.
DOI: 10.5061/dryad.v6r0758
title: Data from: Parental genetic similarity and offspring performance in blue tits in relation to brood size manipulation

description: In birds, as in many other taxa, the level of genetic similarity between
 parents is an important source of variation in offspring fitness. The
 majority of avian studies which explore the influence of mates’ genetic
 similarity on offspring viability have focused on hatching success as a
 viability measure. Yet, viability benefits may extend into later life
 stages, including the nestling period and beyond. Here, we analysed data
 from free-living blue tits (Cyanistes caeruleus) across three breeding
 seasons. We investigate whether parental genetic similarity influences
 offspring viability in terms of body mass, tarsus length and
 immunocompetence. Additionally, using brood size manipulation we tested
 whether environmental conditions influence the magnitude and direction of
 the relationship between parental genetic similarity and offspring
 performance. Sixteen microsatellite markers were used to measure genetic
 similarity between biological parents. We found that a higher genetic
 similarity of parents negatively affects offspring immune response to a
 novel antigen - phytohaemagglutinin, and this effect was independent from
 the experimental brood size manipulation.
description: gs_arct_ecolevol2019
DOI: 10.5281/zenodo.18393013
title: WAYS OF ORGANIZING INTERDISCIPLINARY INTEGRATION IN PRIMARY CLASSES

description: This article highlights the theoretical foundations, pedagogical significance, and practical opportunities for organizing interdisciplinary integration in the primary education system. The essence of interdisciplinary integration is substantiated by its role in helping students perceive the environment holistically and acquire knowledge in a systematic and logically connected manner. This article is of practical importance for primary school teachers, students of pedagogical faculties, and researchers interested in applying innovative approaches in the educational process.
DOI: 10.5281/zenodo.18393014
title: WAYS OF ORGANIZING INTERDISCIPLINARY INTEGRATION IN PRIMARY CLASSES

description: This article highlights the theoretical foundations, pedagogical significance, and practical opportunities for organizing interdisciplinary integration in the primary education system. The essence of interdisciplinary integration is substantiated by its role in helping students perceive the environment holistically and acquire knowledge in a systematic and logically connected manner. This article is of practical importance for primary school teachers, students of pedagogical faculties, and researchers interested in applying innovative approaches in the educational process.
DOI: 10.5061/dryad.05c6v93
title: Data from: Spectroscopic and molecular docking studies reveal binding characteristics of nazartinib (EGF816) to human serum albumin

description: The interactions of novel anti-cancer therapeutic agents with the
 different plasma and tissue components,
 specifically serum albumins, have lately gained
 considerable attention due to the significant influence of such
 interactions on the pharmacokinetics and/or -dynamics of this important
 class of therapeutics. Nazartinib (EGF 816; NAZ) is a
 new anti-cancer candidate proposed as a third-generation epidermal growth
 factor receptor (EGFR) tyrosine kinase inhibitor that is being developed
 and clinically tested for the management of non-small cell lung cancer
 (NSCLC). The current study aimed to characterize the interaction between
 NAZ and human serum albumin (HSA)
 using experimental and theoretical approaches. Experimental results of
 fluorescence quenching of HSA induced by NAZ revealed the development of a
 statically formed complex between NAZ and HSA. Interpretation of the
 observed fluorescence data using Stern–Volmer, Lineweaver-Burk, and
 double-log formulae resulted in binding constants for
 HSA-NAZ complex in the range of (2.34 to 2.81)× 104M-1 over the studied
 temperatures. These computed values were further used to elucidate
 thermodynamic attributes of the interaction, which showed that NAZ
 spontaneously binds to HSA with a postulated electrostatic force-driven
 interaction. This was further verified by theoretical examination of the
 NAZ docking on the HSA surface that revealed an HSA-NAZ
 complex where NAZ is bound to HSA Sudlow site I driven by hydrogen bonding
 in addition to electrostatic forces in the form of pi-H bond. The
 HSA binding pocket for NAZ was shown to encompass ARG
 257, ARG 222, LYS 199, and GLU 292 with a
 total binding energy of -25.59 kJ mol-1
description: EGF_QuenchingEGF_stern volmerEGF_Lineweaver-BurkEGF_binding curveEGF_UV.opjEGF_Synchronous
DOI: 10.15468/dl.a4xsra
title: Occurrence Download

description: A dataset containing 15015 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Observation, Human Observation)",
 "CoordinateUncertaintyInMeters 0.0-1000.0",
 "EstablishmentMeans is one of (introducedAssistedColonisation, introduced, nativeReintroduced, native, nativeEndemic)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Thymus vulgaris"
 ]
}

 The dataset includes 15015 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001859-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xdyh5w
title: Occurrence Download

description: A dataset containing 1671 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Melanosuchus niger"
 ]
}

 The dataset includes 1671 records from 71 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001860-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.q1857f6
title: Data from: Colonization history and population differentiation of the Honey Bees (Apis mellifera L.) in Puerto Rico

description: Honey bees (Apis mellifera L.) are the primary commercial pollinators
 across the world. The subspecies A. m. scutellata originated in Africa and
 was introduced to the Americas in 1956. For the last 60 years it
 hybridized successfully with European subspecies, previous residents in
 the area. The result of this hybridization was called Africanized Honey
 Bee (AHB). AHB has spread since then, arriving to Puerto Rico (PR) in
 1994. The honey bee population on the island acquired a mosaic of features
 from AHB or the European Honey Bee (EHB). AHB in Puerto Rico shows a major
 distinctive characteristic, docile behavior, and are called gentle
 Africanized Honey Bees (gAHB). We used 917 SNPs to examine the population
 structure, genetic differentiation, origin and history of range expansion
 and colonization of gAHB in PR. We compared gAHB to populations that span
 the current distribution of A. mellifera worldwide. The gAHB population is
 shown to be a single population that differs genetically from the examined
 populations of AHB. Texas and PR groups are the closest genetically. Our
 results support the hypothesis that the Texas AHB population is the source
 of gAHB in Puerto Rico.
description: SM1-R
 ScriptClustersSpecific R scripts and
 detailed package references, bioogeographic origin of samples and SNPs
 data matrix are available as supplemental material.
DOI: 10.5061/dryad.b74d971
title: Data from: City sicker? a meta-analysis of wildlife health and urbanization

description: Urban development can alter resource availability, land use, and community
 composition, in turn influencing wildlife health. Generalizable
 relationships between wildlife health and urbanization have yet to be
 quantified, and could vary across health metrics and animal taxonomy. We
 present a phylogenetic meta-analysis of 516 records spanning 81 wildlife
 species from 106 studies comparing the toxicant loads, parasitism, body
 condition, or stress of urban and non-urban wildlife populations in 30
 countries. We find a significantly negative relationship between
 urbanization and wildlife health, driven by higher toxicant loads and
 greater parasitism by parasites transmitted through close contact.
 Invertebrates and amphibians were particularly affected, with higher
 toxicant loads and physiological stress in urban populations as compared
 to their non-urban counterparts. We also found strong geographic and
 taxonomic bias in research effort, highlighting future research needs. Our
 results suggest urban wildlife experience several health risks with
 potential threats to conservation.
description: Data from: City sicker?
 A meta-analysis of wildlife health and urbanizationData recorded from 106
 studies that compared the health of urban and non-urban populations of the
 same species. Columns contain information on statistical comparisons,
 study locations, host species, and level of urbanization. Column headings
 are defined in the readme file.Murray Sanchez et al_urban
 wildlife May 20 2019.csvMurray Sanchez et al_R
 codeR
 code used to perform the phylogenetic meta-analysis in the manuscript
 "City sicker? a meta-analysis of wildlife health and
 urbanization". We used a hierarchical random-effects model (REM)
 accounting for phylogenetic dependence of individual species relatedness
 and multiple records within each study to estimate the size and strength
 of the overall relationship between urbanization and wildlife health and
 fit a set of mixed-effect models (MEMs) considering taxonomic group,
 health metric, species life history. We then fit sets of MEMs separately
 to each health metric dataset to assess if urbanization-wildlife health
 relationships vary by wildlife species traits (taxonomic group, life
 history), parasite traits (parasite type, transmission route), health
 metric methodology, and study country metrics (mean country GHF, log GDP)
 and level of urbanization when study location was provided. Please see the
 README file for variable name definitions.
DOI: 10.5061/dryad.8fb87c9
title: Data from: Endogenetic structure of filter bubble in social networks

description: The filter bubble is an intermediate structure to provoke polarization and
 echo chamber in social network, and it has become one of the most urgent
 issues for social media of the time. Previous studies usually equated
 filter bubbles with community structures and emphasized this exogenous
 isolation effect, but there is a lack of full discussion of the internal
 organization of filter bubbles. Here, we design an experiment for
 analyzing filter bubbles taking advantage of social bots. We deployed 128
 bots to Weibo (the largest microblogging network in China), and each bot
 consumed a specific topic (entertainment or sci-tech) and ran for at least
 two months. In total, we recorded about 1.3 million messages exposed to
 these bots and their social networks. By analyzing the text received by
 the bots and motifs in their social networks, we found that a filter
 bubble is not only a dense community of users with the same preferences
 but also presents an endogenetic unidirectional star-like structure. The
 structure could spontaneously exclude non-preferred information and cause
 polarization. Moreover, our work proved that the felicitous use of
 artificial intelligence technology could provide an useful experimental
 approach that combines privacy protection and controllability in studying
 social media.
description: Data generated by the
 social botsCollected Weibo
 data.zipsource code of social
 bots (Java)Experimental codes in
 Java.zip
DOI: 10.5061/dryad.g0r454r
title: Data from: Reinstatement and revision of the genus Adelmeria (Zingiberaceae) endemic in the Philippines

description: In 1909, Ridley published Adelmeria characterized by its congested
 terminal inflorescence with large persistent floral bracts. All five
 species at some point placed in Adelmeria were synonymized in Alpinia by
 Loesener and subsequent authors. Several phylogenetic studies revealed
 that Alpinia is highly polyphyletic, suggesting that it should be split
 into several genera. In the present study, we sampled all five species
 initially placed in Adelmeria plus additional ones with a similar
 morphology. The combined analysis of the ITS and trnK/matK region showed
 that these species formed a strongly supported monophyletic group inside
 the Alpinia eubractea clade of the tribe Alpinieae. Although not
 completely diagnostic, the following morphological characters separate
 Adelmeria from most of the species currently inside the Alpinia eubractea
 clade: bilobed ligules; congested inflorescences; utricular bracteoles;
 sessile flowers; crestless anthers; obovoid fruits. Considering this
 molecular and morphological evidence, the recognition of Adelmeria is
 highly justified. In this present paper, we reinstate the genus which is
 endemic to the Philippines and provide a comprehensive taxonomic revision
 including a discussion of the application of the name Elmeria. A key to
 nine species of Adelmeria, four of which (A. dicranochila, A. isarogensis,
 A. leonardii, A. undulata) are new to science, is provided as well as full
 descriptions and preliminary conservation assessments. Interestingly,
 monoecy was observed in A. oblonga and reported for the first time for
 Adelmeria. Four lectotypes and one epitype are designated in this study.
description: Adelmeria_Combined_Data_MatrixAdelmeria_Combined_Bayesian_TreeAdelmeria_Combined_ML_Tree
DOI: 10.5061/dryad.2v7m744
title: Data from: Longitudinal optic neuritis-unrelated visual evoked potential changes in NMO spectrum disorders

description: Objective: To investigate, if neuromyelitis optica spectrum disorder
 (NMOSD) patients develop subclinical visual pathway impairment independent
 of acute attacks. Methods: 548 longitudinally assessed full-field visual
 evoked potentials (VEP) of 167 NMOSD patients from 16 centers were
 retrospectively evaluated for changes of P100-latencies and
 P100-N140-amplitudes. Rates of change in latencies (RCL) and amplitudes
 (RCA) over time were analyzed for each individual eye using linear
 regression and compared using generalized estimating equation models.
 Results: The rates of change in the absence of optic neuritis (ON) for
 minimal VEP intervals of ≥3 months between baseline and last follow-up
 were +1.951ms/year (N=101 eyes; SD=6.274; p=0.012) for the P100-latencies
 and -2.149µV/year (N=64 eyes; SD=5.013; p=0.005) for the
 P100-N140-amplitudes. For minimal VEP intervals of ≥12 months the RCL was
 +1.768ms/year (N=59 eyes; SD=4.558; p=0.024) and the RCA was -0.527µV/year
 (N=44 eyes; SD=2.123; p=0.111). The history of a previous ON &gt;6
 months before baseline VEP had no influence on RCL and RCA. ONs during the
 observational period led to mean RCL and RCA of +11.689ms/year (N=16 eyes;
 SD=17.593; p=0.003) and -1.238µV/year (N=11 eyes; SD=3.708; p=0.308),
 respectively. Conclusions: This first longitudinal VEP study of NMOSD
 patients provides evidence of progressive VEP latency delay occurring
 independently of acute ON. Prospective longitudinal studies are needed to
 corroborate these findings and help to interpret the clinical relevance.
description: Supplemental
 Figure1Figure e-1: Longitudinal
 P100-latency and P100-N140-amplitude changes in AQP4-Ab seropositive
 patients.Figure1-suppl-named.pdfSupplemental Figure2Figure e-2: Rate of change comparison of HON-eyes vs. NO-HON-eyes in AQP4-Ab seropositive patients.Figure2-suppl-named.pdfSupplemental Figure3Figure e-3: Possible influence of contralateral optic neuritis in AQP4-Ab seropositive patients.Figure3-suppl-named.pdf
DOI: 10.15468/dl.6ws8zn
title: Occurrence Download

description: A dataset containing 130728 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Asia",
 "Country is Iran (Islamic Republic of)",
 "Issue is one of (Zero coordinate, Coordinate out of range, Coordinate invalid, Coordinate rounded, Geodetic datum invalid, Geodetic datum assumed WGS84, Continent coordinate mismatch, Footprint WKT invalid, Footprint WKT mismatch, Country coordinate mismatch, Footprint SRS invalid)",
 "Month is one of (December, November, October, September, August, July, June, May, April, March, February, January)",
 "OccurrenceStatus is Present",
 "Year 2000-2026"
 ]
}

 The dataset includes 130728 records from 506 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001826-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.31t3425
title: Stochastic cell-cycle entry and cell-state-dependent fate outputs of injury-reactivated tectal radial glia in zebrafish

description: Gliosis defined as reactive changes of resident glia is the primary
 response of the central nervous system (CNS) to trauma. The proliferation
 and fate controls of injury-reactivated glia are essential but remain
 largely unexplored. In zebrafish optic tectum, we found that stab injury
 drove a subset of radial glia (RG) into the cell cycle, and surprisingly,
 proliferative RG responding to sequential injuries of the same site were
 distinct but overlapping, which was in agreement with stochastic
 cell-cycle entry. Single-cell RNA sequencing analysis and functional
 assays further revealed the involvement of Notch/Delta lateral inhibition
 in this stochastic cell-cycle entry. Furthermore, the long-term clonal
 analysis showed that proliferative RG were largely gliogenic. Notch
 inhibition of reactive RG, not dormant and proliferative RG, resulted in
 an increased production of neurons, which were short-lived. Our findings
 gain new insights into the proliferation and fate controls of
 injury-reactivated CNS glia in zebrafish.
description: RData file and cell
 ranger matrices
DOI: 10.5061/dryad.7kj764d
title: Data from: The evolution of the modern avian digestive system – insights from paravian fossils from the Yanliao and Jehol biotas

description: The avian digestive system, like other aspects of avian biology, is highly
 modified relative to other reptiles. Together these modifications have
 imparted the great success of Neornithes, the most diverse clade of
 amniotes alive today. It is important to understand when and how aspects
 of the modern avian digestive system evolved among neornithine ancestors
 in order to elucidate the evolutionary success of this important clade and
 to understand the biology of stem birds and their closest dinosaurian
 relatives – Mesozoic Paraves. Although direct preservation of the soft
 tissue of the digestive system has not yet been reported, ingested remains
 and their anatomical location preserved in articulated fossils hint at the
 structure of the digestive system and its abilities. Almost all data
 concerning direct evidence of diet in Paraves comes from either the Upper
 Jurassic Yanliao Biota or the Lower Cretaceous Jehol Biota, both which are
 known from deposits in north-eastern China. Here, the sum of the data
 gleaned from the thousands of exceptionally well-preserved fossils of
 paravians is interpreted with regards to the structure and evolution of
 the highly modified avian digestive system and feeding apparatus. This
 information suggests intrinsic differences between closely related stem
 lineages implying strong homoplasy and that the modern digestive system is
 limited to the crownward lineage.
description: Appendix
 S1Table 1, list of all
 non-avian paravian specimens preserving ingested remains; table 2, list of
 all stem-birds preserving ingested remains.