cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.24378/exe.31161238.v1
title: Anonymised qualitative interview excerpts underpinning Phase 2 of the RecoverED programme theory development process

description: This dataset is associated with the publication <i>Developing a programme theory of a complex, home-based rehabilitation intervention for recovery after an episode of delirium</i> (PLOS ONE, accepted).The publication reports the process of developing and refining a programme theory underpinning RecoverED, a novel, home-based, multicomponent rehabilitation intervention designed to support recovery following an episode of delirium in older adults. The paper focuses on the methodological process and synthesis of evidence and does not report primary qualitative findings in detail.The dataset shared here comprises anonymised qualitative interview excerpts from Phase 2 of the programme theory development process. Phase 2 involved semi-structured qualitative interviews with key stakeholders, including older adults with lived experience of delirium, family carers, and healthcare professionals. These interviews were conducted to explore experiences of delirium and recovery, perceived support needs, and views on intervention components, mechanisms, and delivery.The interview data were used to inform, refine, and substantiate the developing programme theory, contributing to the identification of key intervention components, hypothesised mechanisms of action, and contextual factors. The excerpts provided represent the minimal qualitative dataset underpinning the analytic interpretations presented in the paper and are shared to support transparency, reproducibility, and reuse.All data have been fully anonymised in accordance with ethical approvals and participant consent. The dataset contains coded interview excerpts linked to analytic themes and does not include full interview transcripts.
DOI: 10.5061/dryad.tht76hf3v
title: Lead exposure is correlated with reduced nesting success of an urban songbird

description: Lead exposure is a concern in urban ecosystems, with physiological and
 behavioral effects well documented in humans. Wildlife inhabiting urban
 ecosystems are also exposed to lead, yet little work has documented the
 sublethal effects of lead exposure in urban wildlife. We studied northern
 mockingbirds (Mimus polyglottos) in three neighborhoods of New Orleans,
 Louisiana, two with high soil lead and one with low soil lead, to better
 understand how lead exposure may influence mockingbirds' reproductive
 biology. We monitored nesting attempts, measured lead concentrations in
 the blood and feathers of nestling mockingbirds, documented egg hatching
 and nesting success, and assessed rates of sexual promiscuity in relation
 to neighborhood soil lead levels. We found that nestling mockingbirds’
 blood and feather lead levels reflected the lead levels of their
 neighborhood soil lead level and nestling blood lead levels were similar
 to adult mockingbirds in the same neighborhoods. Nest success, as
 evaluated by daily survival rates, was higher in the lower lead
 neighborhood. Clutch sizes varied substantially across neighborhoods, but
 rates of unhatched eggs did not covary with neighborhood lead levels,
 suggesting that other drivers are influencing variation in clutch sizes
 and hatching success in urban habitats. At least one-third of nestling
 mockingbirds were sired by an extra-pair male, and there was no
 relationship between extra-pair paternity rates and neighborhood lead
 levels. This study provides insight into how lead contamination may
 influence reproduction in urban-dwelling wildlife and suggests that
 nestling birds could serve as useful bioindicators of lead levels in urban
 neighborhoods.
description: These datasets correspond to data presented in the named
 manuscript. Datasets include mockingbird nesting and egg data, nestling
 blood and feather lead concentration data, and nestling
 relatedness/sibship data. Please see README file for more
 information.
description: These datasets are all stored as .csv files and may be opened
 with any supporting program, including Microsoft Excel and
 RStudio.
DOI: 10.25349/d9802s
title: Predicting the distribution of serotonergic axons: A supercomputing simulation of reflected fractional Brownian motion in a 3D-mouse brain model

description: The self-organization of the brain matrix of serotonergic axons (fibers)
 remains an unsolved problem in neuroscience. The regional densities of
 this matrix have major implications for neuroplasticity, tissue
 regeneration, and the understanding of mental disorders, but the
 trajectories of its fibers are strongly stochastic and require novel
 conceptual and analytical approaches. In a major extension to our previous
 studies, we used a supercomputing simulation to model around one thousand
 serotonergic fibers as paths of superdiffusive fractional Brownian motion
 (FBM), a continuous-time stochastic process. The fibers produced long
 walks in a complex, three-dimensional shape based on the mouse brain and
 reflected at the outer (pial) and inner (ventricular) boundaries. The
 resultant regional densities were compared to the actual fiber densities
 in the corresponding neuroanatomically-defined regions. The relative
 densities showed strong qualitative similarities in the forebrain and
 midbrain, demonstrating the predictive potential of stochastic modeling in
 this system. The current simulation does not respect tissue
 heterogeneities but can be further improved with novel models of
 multifractional FBM. The study demonstrates that serotonergic fiber
 densities can be strongly influenced by the geometry of the brain, with
 implications for brain development, plasticity, and evolution.
description: See the Methods section of the published article (Janusonis S.,
 Haiman J.H., Metzler R., Vojta T. (2023) Predicting the distribution of
 serotonergic axons: A supercomputing simulation of reflected fractional
 Brownian motion in a 3D-mouse brain model. <em>Frontiers in
 Computational Neuroscience</em> 17: 1189853).
description: The density files can be opened with any text editor. They can be
 converted to heatmaps with the included reader written in Wolfram
 Mathematica 13.2.
DOI: 10.5061/dryad.j6q573njs
title: Age-specific survival of territorial and nonterritorial male chamois

description: How alternative reproductive tactics (ARTs) are maintained in wildlife
 populations is one of the major questions in evolutionary biology. As a
 dominant status, territoriality is typically linked to increased mating
 opportunities, and one explanation for why this behaviour coexists with
 other tactics is that dominance implies survival costs. Such a trade-off
 may occur in the Northern chamois Rupicapra rupicapra, as
 reproductive advantages of territorial males over nonterritorial males
 could be counterbalanced by a reduction in survival mediated through
 energy expenditure, stress and parasitic infections, ultimately favouring
 ART coexistence. Here, we analysed age-dependent survival probabilities of
 territorial (n=15) and nonterritorial (n=16) adult chamois using
 information collected over 12 years between 2010 and 2021 in the Gran
 Paradiso National Park (Western Italian Alps). Survival rates were
 estimated with a CMR approach using Burnham’s joint modelling of live
 encounter and dead recovery data. The model selection procedure, based on
 AICc value minimisation, supported a linear decrease of survival with age
 but did not match our predictions, as territorial chamois did not have
 lower survival rates than nonterritorial chamois. In contrast, territorial
 males appeared to enjoy reproductive success at lower survival costs.
 This, in turn, supports the role of other factors, such as snow-dependent
 environmental stochasticity, in the maintenance of ARTs in chamois
 populations. The limited sample size, however, calls for caution in
 interpretation, and long-term studies of lifetime reproductive success and
 survival are necessary to clarify the mechanisms underlying the expression
 and coexistence of different reproductive behaviours in this species.
DOI: 10.5061/dryad.crjdfn38s
title: Data for: Host-specific plasmid evolution explains the variable spread of clinical antibiotic-resistance plasmids

description: Antibiotic resistance encoded on plasmids is a pressing global health
 problem. Predicting which plasmids spread in the long term remains very
 challenging, even though some key parameters influencing plasmid stability
 have been identified, such as plasmid growth costs and horizontal transfer
 rates. Here, we show these parameters evolve in a strain-specific way
 among clinical plasmids and bacteria, and this occurs rapidly enough to
 alter the relative likelihoods of different bacterium-plasmid combinations
 spreading. We used experiments with Escherichia coli and
 antibiotic-resistance plasmids isolated from patients, paired with a
 mathematical model, to track long-term plasmid stability (beyond
 antibiotic exposure). Explaining variable stability across six
 bacterium-plasmid combinations required accounting for evolutionary
 changes in plasmid-stability traits, whereas initial variation of these
 parameters was a relatively poor predictor of long-term outcomes.
 Evolutionary trajectories were specific to particular bacterium-plasmid
 combinations, as evidenced by genome sequencing and genetic manipulation.
 This revealed epistatic (here, strain-dependent) effects of key genetic
 changes affecting horizontal plasmid transfer. Several genetic changes
 involved mobile elements and pathogenicity islands. Rapid strain-specific
 evolution can thus outweigh ancestral phenotypes as a predictor of plasmid
 stability. Accounting for strain-specific plasmid evolution in natural
 populations could improve our ability to anticipate and manage successful
 bacterium-plasmid combinations.
DOI: 10.5061/dryad.fj6q57406
title: Country uptake of WHO recommendations on differentiated HIV testing services approaches: A global policy review

description: Objectives In 2015 and 2016, the World Health Organization (WHO) issued
 guidelines on HIV testing services (HTS) highlighting recommendations for
 a strategic mix of differentiated HTS approaches. The Policy review
 examines the uptake of differentiated HIV Testing service (HTS) approaches
 recommendations. Methods Data were extracted from all available national
 policies published between January 2015 and June 2019 and stored in WHO’s
 national policy repository. WHO recommended as HTS approaches
 facility-based testing, community-based testing, HIV self-testing and
 provider-assisted referral (or assisted partner notification); in terms of
 testing components: pre-test information, lay provider testing and rapid
 testing. Descriptive analyses were conducted to examine availability of
 policies and adherence to WHO-differentiated HTS recommendations. Results
 Of 194 countries worldwide, 65 published policies were identified in the
 review period. 24 were from the African region (51% of African countries,
 24/47), six from the Eastern Mediterranean region (29%, 6/21), 21 from the
 European region (40%, 21/53), five from the American region (14%, 5/35),
 four from the South East Asia region (36%, 4/11) and five from the Western
 Pacific Region (19%, 5/27). Only five countries were compliant with
 recommendations and 63 included at least one. 85% (n=55) included
 facility-based testing for pregnant women, 75% (n=49) facility-based
 testing for key populations, 74% (n=48) community-based testing for key
 populations, 38% (n=25) HIV self-testing, 25% (n=16) provider-assisted
 referral, 69% (n=45) rapid testing, 57% (n=37) post-test counselling, 45%
 (n=29) lay provider testing and 29% (n=19) pre-test information. The
 highest uptake of WHO recommendations was seen in countries from the
 African and Eastern Mediterranean region. Conclusions There was
 substantial variability in the uptake of WHO HTS recommendations, ranging
 from 25% to 85%. Uptake was above 50% for facility-based testing for
 pregnant women and key populations, community-based testing, rapid
 diagnostic testing and post-test counselling; uptake was between 25% and
 45% for all the other recommendations.
DOI: 10.5061/dryad.1g1jwsv1w
title: Urban flask measurements of CO2ff and CO to identify emission sources at different site types in Auckland, New Zealand

description: As part of the CarbonWatch-NZ research programme, air samples were
 collected at 28 sites around Auckland, New Zealand to determine the
 atmospheric ratio (RCO) of excess (local enhancement over background)
 carbon monoxide to fossil CO2 (CO2ff). Sites were categorised into seven
 types (background, forest, industrial, suburban, urban, downwind, and
 motorway) to observe RCO around Auckland. Flasks from motorway sites
 observed RCO of 14 ± 1 ppb/ppm and were used to evaluate traffic RCO. The
 similarity between suburban (14 ± 1 ppb/ppm) and traffic RCO suggests that
 traffic dominates suburban CO2ff emissions during daytime hours, the
 period of flask collection. The lower urban RCO (11 ± 1 ppb/ppm) suggests
 that urban CO2ff emissions are comprised of more than just traffic, with
 contributions from residential, commercial, and industrial sources, all
 with a lower RCO than traffic. Finally, the downwind sites were believed
 to best represent RCO for Auckland City overall (11 ± 1 ppb/ppm). We
 demonstrate that the initial discrepancy between the downwind RCO and
 Auckland’s estimated daytime inventory RCO (15 ppb/ppm) can be attributed
 to an overestimation in inventory traffic CO emissions. After revision
 based on our observed motorway RCO, the revised inventory RCO (12 ppb/ppm)
 is consistent with our observations.
DOI: 10.5061/dryad.8w9ghx3rp
title: Data for: Nanotopography modulates intracellular excitable systems through cytoskeleton actuation

description: Cellular sensing of most environmental cues involves receptors that affect
 a signal-transduction excitable network (STEN), which is coupled to a
 cytoskeletal excitable network (CEN).  In this work, we monitored
 the dynamics of intracellular cytoskeleton and signaling transduction
 molecules in Dictyostelium discoideum plated on various
 nano-topographies. We show that the mechanism of sensing of
 nanoridges is fundamentally different. CEN activity occurs preferentially
 on nanoridges, whereas STEN activity is constrained between nanoridges. In
 the absence of STEN, waves disappear, but long-lasting F-actin puncta
 persist along the ridges. When CEN is suppressed, wave propagation is no
 longer constrained by nanoridges. A computational model reproduces these
 experimental observations. Our findings indicate that nanotopography is
 sensed directly by CEN, whereas STEN is only indirectly affected due to a
 CEN-STEN feedback loop. These results explain why texture sensing is
 robust, and acts cooperatively with multiple other guidance cues in
 complex microenvironments.
description: Microscopic data related to chemically induced dimerization (CID)
 experiments were collected by the Zeiss LSM780 and Zeiss LSM800 GaAsP
 single-point laser-scanning microscope at room temperature. Other data in
 this dataset were collected using PerkinElmer spinning disk microscope
 (Yokogawa CSU-X1 spinning disk scan head (5000 rpm)) with Hamamatsu EMCCD
 camera and Velocity analysis software.
description: Image-J can open all the .tif and .lsm data formats in this data
 set.
DOI: 10.5061/dryad.z08kprrj3
title: Strong habitat-specific phenotypic plasticity but no genome-wide differentiation across a rainforest gradient in an African butterfly

description: Habitat-specific thermal responses are well documented in various
 organisms and likely determine the vulnerability of populations to climate
 change. However, the underlying roles of genetics and plasticity that
 shape such habitat-specific patterns are rarely investigated together.
 Here we examined the thermal plasticity of the butterfly Bicyclus dorothea
 originating from rainforest and ecotone habitats in Cameroon under common
 garden conditions. We also sampled wild-caught butterflies from forest and
 ecotone sites and used RADseq to explore genome-wide population
 differentiation. We found differences in the level of phenotypic
 plasticity across habitats. Specifically, ecotone populations exhibited
 greater sensitivity in wing eyespot features with variable development
 temperatures relative to rainforest populations. Known adaptive roles of
 wing eyespots in Bicyclus species suggest that this morphological
 plasticity is likely under divergent selection across environmental
 gradients. However, we found no distinct population structure of
 genome-wide variation between habitats, suggesting high levels of ongoing
 gene flow between habitats is homogenizing most parts of the genome.
description: RADseq data was collected and processed using methods described
 in the paper. Files include: 1. fasta sequences of de
 novo assembled RAD loci 2. genotype information of the
 156 good quality samples, with posterior cutoff of 0.99 and minimum sample
 cutoff of 0.8 3. morphological data: each row
 represents a single individual butterfly belonging to a given site and
 habitat. For each individual, we collected the following morphological
 characteristics on the fore and hindwing (values are in mm). Temperatures
 are in the Celsius scale (°C). LFW = Length of the
 forewing; LHW = length of the hindwing; WHW = width of the hindwing; WFW =
 width of the forewing; E1FW = diameter of the first eyespot forewing; E2FW
 = diameter of the second eyespot forewing; E1HW = diameter of the first
 eyespot hindwing; E2HW = diameter of the second eyespot hindwing; E3HW =
 diameter of the third eyespot hindwing; E4HW = diameter of the fourth
 eyespot hindwing; E5HW = diameter of the fifth eyespot hindwing; E6HW =
 diameter of the sixth eyespot hindwing; E7HW = diameter of the seventh
 eyespot hindwing.
DOI: 10.5061/dryad.83bk3j9wh
title: Complete organelle genomes of Korean fir, Abies koreana and phylogenomics of the gymnosperm genus Abies using nuclear and cytoplasmic DNA sequence data

description: Background Abies koreana E. H. Wilson is an endangered evergreen
 coniferous tree that is native to high altitudes in South Korea and
 susceptible to the effects of climate change. Hybridization and reticulate
 evolution have been reported in the genus; therefore, multigene datasets
 from nuclear and cytoplasmic genomes are needed to better understand its
 evolutionary history. Results Using Illumina NovaSeq6000 and Oxford
 Nanopore Technologies (ONT) PromethION platforms, we generated complete
 mitochondrial (1,174,803 bp) and plastid (121,341 bp) genomes from A.
 koreana. The mitochondrial genome is highly dynamic, transitioning from
 cis- to trans-splicing and breaking the conserved gene clusters. In the
 case of the plastome, the ONT reads revealed two structural conformations
 of A. koreana. The short inverted repeats (1,186 bp) of the A. koreana
 plastome are associated with the different structural types.
 Transcriptomic sequencing revealed 1,356 sites of C-to-U RNA editing in
 the 41 mitochondrial genes. Using A. koreana as a reference, we
 additionally produced nuclear ribosomal DNA and organelle genomic
 sequences from eight Abies species and generated multiple datasets for
 maximum likelihood and network analyses. Three sections (Balsamea, Momi,
 and Pseudopicea) were well grouped in the nuclear phylogeny, but the
 phylogenomic relationships showed conflicting signals in the mitochondrial
 and plastid genomes, indicating a complicated evolutionary history that
 may have included introgressive hybridization. Conclusions These results
 illustrate that phylogenomic analyses based on the sequences from
 differently inherited organelle genomes resulted in conflicting trees.
 Organellar capture, organellar genome recombination, and incomplete
 lineage sorting in an ancestral heteroplasmic individual can contribute to
 phylogenomic discordance. We provide strong support for the relationships
 within Abies and new insights into the phylogenomic complexity of this
 genus.
DOI: 10.5061/dryad.sxksn037k
title: Data for: Nestling mouth colors mediate parental favoritism but minimally influence detectability

description: Young animals often solicit care from their parents using behaviors and
 morphologies collectively termed begging. Many nestling altricial birds
 add to their familiar postures and vocalizations by displaying colorful
 mouthparts, hypothesized to enhance their visual conspicuousness and/or
 signal information about individual quality. We evaluated these hypotheses
 with three experimental manipulations of the flange tissue of house
 sparrow (Passer domesticus) nestlings. We allowed parents to interact with
 nestlings that appeared to have either carotenoid-rich or carotenoid-poor
 flanges, and then with nestlings that appeared similar in
 carotenoid-richness but differed in either brightness (total light
 reflected) or ultraviolet richness. These three features of flange color
 comprise much of the variation observed both within and among species.
 Neither our manipulation of apparent carotenoid- nor UV-richness shaped
 parents’ ability to transfer prey efficiently to nestlings, a proxy for
 how visually detectable nestlings were. We found some evidence that
 brightness shaped parents’ ability to transfer large prey items. Parents
 preferentially allocated prey to nestlings that appeared carotenoid-rich,
 but did not bias allocation when we manipulated brightness or UV
 reflectance. These patterns suggest that nestlings displaying
 carotenoid-rich flanges benefit from parental favoritism, and that any
 role of brightness in offspring-parent interactions comes via
 detectability benefits. UV reflectance does not seem to shape parental
 care. Efforts to understand mouth color in the context of offspring-parent
 communication and visual signal evolution may benefit from considering the
 component parts of color, as they may function, be constrained, and evolve
 independently.
description: Data are summaries of video recordings, scored by hand, of house
 sparrow parents interacting with nestlings. In three experiments, two
 nestlings were manipulated to appear i) yellow/pale
 (carotenoid-rich/carotenoid-poor), ii) bright or dull, and iii) control or
 UV reduced. The two files reflect different analyses conduced with these
 observations: We counted prey items allocated to each
 nestlings overall and when both nestlings were begging (i.e., parents were
 presented with a binary choice). We measured the time it took parents to
 transfer each prey item, as well as the number of transfer attempts. Data
 in both files are organized by experiment. 
description: Data can be accessed using Excel or other csv reader.