cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.qt528n0
title: Data from: Fin whale (Balaenoptera physalus) mitogenomics: a cautionary tale of defining sub-species from mitochondrial sequence monophyly

description: The advent of massive parallel sequencing technologies has resulted in an
 increase of studies based upon complete mitochondrial genome DNA sequences
 that revisit the taxonomic status within and among species. Spatially
 distinct monophyly in such mitogenomic genealogies, i.e., the sharing of a
 recent common ancestor among con-specific samples collected in the same
 region has been viewed as evidence for subspecies. Several recent studies
 in cetaceans have employed this criterion to suggest subsequent
 intraspecific taxonomic revisions. We reason that employing
 intra-specific, spatially distinct monophyly at non-recombining, clonally
 inherited genomes is an unsatisfactory criterion for defining subspecies
 based upon theoretical (genetic drift) and practical (sampling effort)
 arguments. This point was illustrated by a re-analysis of a global
 mitogenomic assessment of fin whales, Balaenoptera physalus spp.,
 published by Archer et al. (2013), which proposed to further subdivide the
 Northern Hemisphere fin whale subspecies, B. p. physalus. The proposed
 revision was based upon the detection of spatially distinct monophyly
 among North Atlantic and North Pacific fin whales in a genealogy based
 upon complete mitochondrial genome DNA sequences. The extended analysis
 conducted in this study (1,676 mitochondrial control region, 162 complete
 mitochondrial genome DNA sequences and 20 microsatellite loci genotyped in
 358 samples) revealed that the apparent monophyly among North Atlantic fin
 whales reported by Archer et al. (2013) to be due to low sample sizes. In
 conclusion, defining sub-species from monophyly (i.e., the absence of
 para- or polyphyly) can lead to erroneous conclusions due to relatively
 “trivial” aspects, such as sampling. Basic population genetic processes
 (i.e., genetic drift and migration) also affect the time to the most
 recent common ancestor and hence the probability that individuals in a
 sample are monophyletic.
description: Cabrera_etal_2019_FinWhaleInput files for the analyses in this study. Mitochondrial DNA sequence data and microsatellite genotypes.
DOI: 10.5061/dryad.2dr683g
title: Data from: Conformity in the collective: differences in hunger affect individual and group behaviour in fish

description: Animal groups are often composed of individuals that vary according to
 behavioural, morphological and internal state parameters. Understanding
 the importance of such individual-level heterogeneity to the establishment
 and maintenance of coherent group responses is of fundamental interest in
 collective behaviour. We examined the influence of hunger on the
 individual and collective behaviour of groups of shoaling fish, x-ray
 tetras (Pristella maxillaris). Fish were assigned to one of two
 nutritional states, satiated or hungry, and then allocated to 5 treatments
 that represented different ratios of satiated to hungry individuals (8
 hungry, 8 satiated, 4:4 hungry: satiated, 2:6 hungry: satiated, 6:2
 hungry: satiated). Our data show that groups with a greater proportion of
 hungry fish swam faster and exhibited greater nearest-neighbour distances.
 Within groups, however, there was no difference in the swimming speeds of
 hungry versus well-fed fish, suggesting that group members conform and
 adapt their swimming speed according to the overall composition of the
 group. We also found significant differences in mean group transfer
 entropy, suggesting stronger patterns of information flow in groups
 comprising all, or a majority of, hungry individuals. In contrast, we did
 not observe differences in polarization, a measure of group coherence,
 within groups across treatments. Taken together these results demonstrate
 that the nutritional state of animals within social groups impacts both
 individual and group behaviour, and that members of heterogenous groups
 can adapt their behaviour to facilitate coherent collective motion.
description: MI_TE
 tetrasmutual
 information/transfer entropy tetra dataTetra individual level
 dataTetra individual level
 dataTetraIndividualLevelData.csvTetraGroupLevelDataTetra group level data
DOI: 10.5061/dryad.tg8nn49
title: Data from: Context-dependent strategies of food allocation among offspring in a facultative cooperative breeder

description: Natural selection should favor adoption of parental strategies that
 maximize fitness when allocating investment among offspring. In birds,
 begging displays often convey information of nestling need and quality,
 allowing parents to make adaptive food allocation decisions. We
 investigated how adults utilized cues likely to represent nestling
 competitive ability (begging position) and need (begging intensity), and a
 cue independent of nestling control (nestling sex) to distribute food
 among nestlings in a facultative cooperative breeder, the black-throated
 tit (Aegithalos concinnus). We found that parents reduced their efforts
 when helped, suggesting that parents of helped broods would have the
 potential to satisfy nestling needs more than unhelped parents. This
 suggestion was supported by the fact that nestling mass increased faster
 in helped than in unhelped nests. We found no effect of nestling sex on
 food allocation, but, as predicted, we found that adults responded
 differently to begging signals in relation to the presence of helpers and
 brood size. First, helped parents were more responsive to nestling begging
 intensity than parents without helpers. Second, female parents and helpers
 had a stronger preference for nestling begging position in large than in
 small broods. Third, the preference for nestling begging position was
 greater for unhelped than for helped female parents. These results provide
 evidence that carers adjust their preference for different offspring
 begging signals based on availability of food resources.
description: Data_for_Li_et_al._Context-dependent_strategies_of_food_allocation_among_offspring_in_a_facultative_cooperative_breederThe file contains all data for nestling provisioning rates, nestling mass and adult food allocation among nestlings during each feeding event.
DOI: 10.5061/dryad.63p3r08
title: Data from: Tungsten blocks murine B lymphocyte differentiation and proliferation through downregulation of IL-7 receptor/Pax5 signaling

description: Tungsten is an emerging environmental toxicant associated with several
 pediatric leukemia clusters, although a causal association has not been
 established. Our previous work demonstrated that tungsten exposure
 resulted in an accumulation of pre-B cells in the bone marrow, the same
 cell type that accumulates in pediatric acute lymphoblastic leukemia
 (ALL). To better understand the relevant molecular mechanisms, we
 performed RNA sequencing on flow sorted pre-B cells from control and
 tungsten-exposed mice. Tungsten decreased the expression of multiple genes
 critical for B cell development, including members of the IL-7R and
 pre-BCR signaling pathways, such as Jak1, Stat5a, Erb1, Pax5, Syk, and
 Ikzf3. These results were confirmed in an in vitro model of B cell
 differentiation, where tungsten arrested differentiation at the pro-B cell
 stage and inhibited proliferation. These changes were associated with
 decreased expression of multiple genes in the IL-7R signaling pathway and
 decreased percentage of IL-7R, phosphorylated STAT5 (pSTAT5)
 double-positive cells. Supplementation with IL-7 or overexpression of
 Pax5, the transcription factor downstream of IL-7R, rescued the
 tungsten-induced differentiation block. Together, these data support the
 hypothesis that IL-7R/Pax5 signaling axis is critical to tungsten-mediated
 effects on pre-B cell development. Importantly, many of these molecules
 are modulated in ALL.
description: C (Control) raw RNA-Seq
 BAM fileC/C’ pre-B cells sorted
 from control mice. This is the BAM file containing the unprocessed, raw
 reads for the control sample. The data is provided in BAM format for
 convenience. MD5: 1db0c4591f24b1e9d4b21b75d33df614C.bamW (Tungsten) raw RNA-Seq BAM fileC/C’ pre-B cells sorted from 15 ppm tungsten-exposed mice. This is the BAM file containing the unprocessed, raw reads for the sample that was exposed to Tungsten. The data is provided in BAM format for convenience. MD5: aa45a303ffea757c2649592df91015acW.bam
DOI: 10.5061/dryad.m6f721d
title: Data from: Expected total thyroxine (TT4) concentrations and outlier values in 531,765 cats in the United States (2014-2015)

description: Background: Levels exceeding the standard reference interval (RI) for
 total thyroxine (TT4) concentrations are diagnostic for hyperthyroidism,
 however some hyperthyroid cats have TT4 values within the RI. Determining
 outlier TT4 concentrations should aid practitioners in identification of
 hyperthyroidism. The objective of this study was to determine the expected
 distribution of TT4 concentration using a large population of cats
 (531,765) of unknown health status to identify unexpected TT4
 concentrations (outlier), and determine whether this concentration changes
 with age. Methodology/Principle Findings: This study is a
 population-based, retrospective study evaluating an electronic database of
 laboratory results to identify unique TT4 measurement between January 2014
 and July 2015. An expected distribution of TT4 concentrations was
 determined using a large population of cats (531,765) of unknown health
 status, and this in turn was used to identify unexpected TT4
 concentrations (outlier) and determine whether this concentration changes
 with age. All cats between the age of 1 and 9 years (n=141,294) had the
 same expected distribution of TT4 concentration (0.5-3.5ug/dL), and cats
 with a TT4 value &gt;3.5ug/dL were determined to be unexpected
 outliers. There was a steep and progressive rise in both the total number
 and percentage of statistical outliers in the feline population as a
 function of age. The greatest acceleration in the percentage of outliers
 occurred between the age of 7 and 14 years, which was up to 4.6 times the
 rate seen between the age of 3 and 7 years. Conclusions: TT4
 concentrations &gt;3.5ug/dL represent outliers from the expected
 distribution of TT4 concentration. Furthermore, age has a strong influence
 on the proportion of cats. These findings suggest that patients with TT4
 concentrations &gt;3.5ug/dL should be more closely evaluated for
 hyperthyroidism, particularly between the ages of 7 and 14 years. This
 finding may aid clinicians in earlier identification of hyperthyroidism in
 at-risk patients.
description: Feline T4 2014 till July
 2015 by RegionFeline Total T4 by Breed
 Excel
DOI: 10.5281/zenodo.18390399
title: Daten der Notaufnahmesurveillance

description: Der Datensatz "Daten der Notaufnahmesurveillance" wird durch das Robert Koch-Institut und das AKTIN-Notaufnahmeregister bei Krankenhausaufnahmen bereitgestellt. Der Datensatz beinhaltet aggregierte Routinedaten aus deutschen Notaufnahmen zur syndromischen Überwachung von akuten Erkrankungen. Dazu zählen grippeähnliche Erkrankungen (ILI), Coronavirus-Erkrankungen (COVID-19), akute respiratorische Erkrankungen (ARE), gastrointestinale Infektionen (GI) und schwere akute respiratorische Infektionen (SARI). Dabei wird der relative Anteil dieser Erkrankungen an der Gesamtzahl der Notaufnahmevorstellungen sowie die berechneten Erwartungswerte und Prädiktionsintervalle ausgewiesen. Die Daten sind nach Notaufnahmetypen und Altersgruppen aggregiert. Damit bietet der Datensatz eine wertvolle Ressource für die Forschung im Bereich der Notfallmedizin und der Überwachung akuter Gesundheitsereignisse in Deutschland.
DOI: 10.5061/dryad.d53g10q
title: Data from: The role of recombination, niche-specific gene pools and flexible genomes in the ecological speciation of bacteria

description: Bacteria diversify into genetic clusters analogous to those observed in
 sexual eukaryotes, but the definition of bacterial species is an ongoing
 problem. Recent work has focused on adaptation to distinct ecological
 niches as the main driver of clustering, but there remains debate about
 the role of recombination in that process. One view is that homologous
 recombination occurs too rarely for gene flow to constrain divergent
 selection. Another view is that homologous recombination is frequent
 enough in many bacterial populations that barriers to gene flow are needed
 to permit divergence. Niche‐specific gene pools have been proposed as a
 general mechanism to limit gene flow. We use theoretical models to
 evaluate additional hypotheses that evolving genetic architecture,
 specifically the effect sizes of genes and gene gain and loss, can limit
 gene flow between diverging populations. Our model predicts that (a) in
 the presence of gene flow and recombination, ecological divergence is
 concentrated in few loci of large effect and (b) high rates of gene flow
 plus recombination promote gene loss and favor the evolution of
 niche‐specific genes. The results show that changing genetic architecture
 and gene loss can facilitate ecological divergence, even without
 niche‐specific gene pools. We discuss these results in the context of
 recent studies of sympatric divergence in microbes.
description: Simulation code and
 outputsZipped file with
 simulation code in R for two versions of the model - fixed effect sizes
 and evolving effect sizes - and code for analysing outputs from those in
 R.Schmutzer.DryadCode.zip
DOI: 10.5281/zenodo.18279506
title: Visible-Light–Triggered BMP-2 Release from Enzymatically Crosslinked Marine Collagen–Alginate Hydrogels

description: This repository contains raw and processed datasets supporting the article “Visible-Light–Triggered BMP-2 Release from Enzymatically Crosslinked Marine Collagen–Alginate Hydrogel Blends Enhances Osteogenesis in Dental Pulp Stem Cells.”

The dataset includes BMP-2 release kinetics (ELISA), hydrogel rheology, oxygen microprofiling, light-calibration logs, cell viability assays, osteogenic differentiation data (ALP, qPCR, mineralization), and imaging (confocal, SEM) analysis.

All experiments were performed using marine-derived thiolated gelatin crosslinked with microbial transglutaminase and a 405 nm-cleavable coumarin photocage. The dataset enables independent verification of light-triggered BMP-2 release, cytocompatibility, and osteogenic outcomes.
DOI: 10.5281/zenodo.18279505
title: Visible-Light–Triggered BMP-2 Release from Enzymatically Crosslinked Marine Collagen–Alginate Hydrogels

description: This repository contains raw and processed datasets supporting the article “Visible-Light–Triggered BMP-2 Release from Enzymatically Crosslinked Marine Collagen–Alginate Hydrogel Blends Enhances Osteogenesis in Dental Pulp Stem Cells.”

The dataset includes BMP-2 release kinetics (ELISA), hydrogel rheology, oxygen microprofiling, light-calibration logs, cell viability assays, osteogenic differentiation data (ALP, qPCR, mineralization), and imaging (confocal, SEM) analysis.

All experiments were performed using marine-derived thiolated gelatin crosslinked with microbial transglutaminase and a 405 nm-cleavable coumarin photocage. The dataset enables independent verification of light-triggered BMP-2 release, cytocompatibility, and osteogenic outcomes.
DOI: 10.5061/dryad.tm28hb6
title: Data from: Use and categorization of Light Detection and Ranging vegetation metrics in avian diversity and species distribution research

description: Aim: Vegetation structure is a key determinant of animal diversity and
 species distributions. The introduction of Light Detection and Ranging
 (LiDAR) has enabled the collection of massive amounts of point cloud data
 for quantifying habitat structure at fine resolution. Here, we review the
 current use of LiDAR-derived vegetation metrics in diversity and
 distribution research of birds, a key group for understanding
 animal-habitat relationships. Location: Global. Methods: We review 50
 relevant papers and quantify where, in which habitats, at which spatial
 scales and with what kind of LiDAR data current studies make use of LiDAR
 metrics. We also harmonize and categorize LiDAR metrics and quantify their
 current use and effectiveness. Results: Most studies have been conducted
 at local extents in temperate forests of North America and Europe.
 Rasterization is currently the main method to derive LiDAR metrics,
 usually from airborne laser scanning data with low point densities
 (&lt;10 points/m2) and small footprints (&lt;1 m diameter). Our
 metric harmonization suggests that 40% of the currently used metric names
 are redundant. A categorisation scheme allowed to group all metric names
 into 18 out of 24 theoretically possible classes, defined by vegetation
 part (total vegetation, single trees, canopy, understory, and other single
 layers as well as multi-layer) and structural type (cover, height,
 horizontal variability, vertical variability). Metrics related to canopy
 cover, canopy height and canopy vertical variability are currently most
 often used, but not always effective. Main conclusions: LiDAR metrics play
 an important role in understanding animal space use. Our review and the
 developed categorization scheme may facilitate future studies in the
 selection, prioritization and ecological interpretation of LiDAR metrics.
 The increasing availability of airborne and spaceborne LiDAR data and the
 development of voxel-based and object-based approaches will further allow
 novel ecological applications, also for open habitats and other vertebrate
 and invertebrate taxa.
description: LiDAR_articles_dataExtracted data from articles studying bird species distributions and diversity in relation to Light Detection and Ranging (LiDAR)
DOI: 10.5061/dryad.jp76nv2
title: Data from: Sporadic late-onset nemaline myopathy: clinical spectrum, survival and treatment outcomes

description: OBJECTIVES: To describe the clinical phenotype, long-term treatment
 outcome and overall survival of sporadic late onset nemaline myopathy
 (SLONM) with or without a monoclonal protein (MP). METHODS: we conducted a
 retrospective chart review of patients seen between September 2000 and
 June 2017 and collected clinical, laboratory and survival data. Treatment
 response was classified as mild, moderate, or marked as adjudged by
 predefined criteria. RESULTS: We identified 28 patients with SLONM, 17
 (61%) had an associated MP. Median age at symptom onset was 62 years.
 Diagnosis was often delayed by a median of 35 months from symptom onset.
 There was no difference in clinical or laboratory features between
 patients with or without MP. Although the majority of patients had
 proximal or axial weakness at onset, about 18% of patients had atypical
 presentations. 7/9 (78%) patients receiving intravenous immunoglobulin
 (IVIG), 6/8 (75%) receiving hematologic therapy as either autologous stem
 cell transplant (ASCT), or chemotherapy and 1/8 (13%) receiving
 immunosuppressive therapies responded to treatment (p=0.001). All 3
 patients with marked response were treated with IVIG, 2 of them had a MP.
 The 5-year and 10-year overall survivals from symptom onset were 92% and
 68% respectively, with no difference between patients with or without MP.
 CONCLUSIONS: SLONM has a wide spectrum of clinical presentations. In this
 contemporary case series, overall survival of patients did not seem to be
 affected by the presence of a MP. Initial treatment with IVIG is
 reasonable in all patients, followed by ASCT or chemotherapy as
 second-line therapy in patients with an associated MP.
description: Supplemental table e1_
 laboratory resultsLaboratory
 resultsSupplemental table
 e2_treatment detailsTreatment
 details
DOI: 10.5061/dryad.md0rs60
title: Data from: Bachelors level soil science training at land grant institutions in the USA and its territories

description: Concern over the status of soil science education in the USA has led to a
 number of publications in recent years that track trends in student
 enrollment and offer suggestions for attracting more students to soil
 science. However, there is little information about changes in the number
 of degree programs that prepare students for careers as soil scientists,
 and such changes are obviously an important measure of the status of our
 field. This study established criteria to identify bachelor’s degree
 programs that prepare students for soil science careers and used websites
 at land grant colleges to review the degree offerings of these schools in
 USA states and territories to determine if they met the established
 criteria. Fifty-nine land grant colleges were identified that offer
 bachelor’s degree programs that prepare students for soil science careers,
 with a total of 61 degree programs since two of the schools had two
 separate bachelor’s degrees that met the established criteria. This study
 provides guidelines for conducting similar future studies and a baseline
 against which they can be compared to allow us to determine whether we are
 gaining or losing soil science programs at the land grant colleges over
 time.
description: Undergraduate Soils
 Programs at USA Land Grant Colleges 2018A complete list of the
 land grant colleges and universities in the USA that offered training that
 met the Federal Government 0470 soil science series criteria as of
 December 2018. Includes notes on why some schools were found not to meet
 the criteria and the degrees offered that met the
 criteria.Land Grant Undergrad
 Soils.xlsx
DOI: 10.5061/dryad.8s0s050
title: Data from: The role of variation and plasticity in parental care during the adaptive radiation of threespine sticklebacks

description: Phenotypic plasticity might influence evolutionary processes such as
 adaptive radiations. Plasticity in parental care might be especially
 effective in facilitating adaptive radiations if it allows populations to
 persist in novel environments. Here, we test the hypothesis that
 behavioral plasticity by parents in response to predation risk facilitated
 the adaptive radiation of threespined sticklebacks (Gasterosteus
 aculeatus). We compared the behavior of fathers across multiple ancestral
 (marine) and derived (freshwater) stickleback populations that differ in
 time since establishment. We measured behavioral plasticity in fathers in
 response to a predator found only in freshwater environments, simulating
 conditions marine males experience when colonizing freshwater. The
 anti-predator behavior of males from newly-established freshwater
 populations was intermediate between marine populations and
 well-established freshwater populations. In contrast to our predictions,
 on average, there was greater behavioral plasticity in derived freshwater
 populations than in ancestral marine populations. However, we found
 greater individual variation in behavioral reaction norms in marine
 populations compared to well-established freshwater populations, with
 newly-established freshwater populations intermediate. This suggests that
 standing variation in behavioral reaction norms within ancestral
 populations might provide different evolutionary trajectories, and
 illustrates how plasticity can contribute to adaptive radiations.
description: Stickleback parental
 dataAll parental care data
 obtained during this study, including from individuals that did not
 experience the Odonate predator (Trt = “C”). Includes behaviors not
 analyzed in this paper, such as time at nest, activity, and gluing. TT
 indicates “Total Time” and is presented in seconds.Stein_Bell_SticklebackParentalData.csvStickleback predator dataData collected in relation to exposure to the Odonate predator.Stein_Bell_SticklebackPredatorData.csvCode for Stein and Bell 2019, EvolutionA knitted R file displaying code used for analysis of data.Stein_Bell_VariationPlasticitySticklebackEvolution_Code.html