cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.g4f4qrfmm
title: Data from: A stochastic model for predicting age and mass at maturity of insects

description: Variation in age and mass at maturity is commonly observed in populations,
 even among individuals with the same genetic and environmental
 backgrounds. Accounting for such individual variation with a stochastic
 model is important for estimating optimal evolutionary strategies and for
 understanding potential trade-offs among life history traits. However,
 most studies employ stochastic models that are either phenomenological or
 account for variation in only one life history trait. We propose a model
 based on the developmental biology of the moth Manduca sexta that accounts
 for stochasticity in two key life history traits, age and mass at
 maturity. The model is mechanistic, describing feeding behavior and common
 insect developmental processes including the degradation of juvenile
 hormone prior to molting. We derive a joint probability density function
 for the model and explore how the distribution of age and mass at maturity
 is affected by different parameter values. We find that the joint
 distribution is generally non-normal and highly sensitive to parameter
 values. In addition, our model predicts previously observed effects of
 temperature change and nutritional quality on the expected values of
 insect age and mass. Our results highlight the importance of integrating
 multiple sources of stochasticity into life history models.
description: This ZIP archive contains R files for simulating the stochastic
 maturation and growth model, and for evaluating the joint probability
 density function.
DOI: 10.5061/dryad.5dv41ns38
title: Clinical significance of post-liver transplant hepatitis E seropositivity in high prevalence area of hepatitis E genotype 3: a prospective study

description: High hepatitis E (HEV) seroprevalence has been reported in the general
 population and in post-liver transplant (LT) cases in several regions,
 including Thailand, with genotype 3 being a predominant genotype. We
 hypothesized that HEV might persist at a subclinical level and might pose
 clinical risks in the post-LT period. We performed a cross-sectional study
 with 108 post-LT patients and found an IgG seroprevalence of 55.6%.
 Subsequently, 91 cases without clinical evidence of HEV-related hepatitis
 were enrolled in 1 year of prospective follow-up to determine clinical
 status, serologies and serum/feces HEV RNA every 4 months. HEV RNA was
 detected, indicating subclinical infections in patients with or without
 seropositivity, with an annual incidence of 7.7%. Our results suggest that
 subclinical HEV infection exists among LT patients in this high-prevalence
 area. Thus, clinicians should be aware of the possibility of disease
 reemergence and HEV viral transmission in LT patients.
description: Post-LT patients receiving care at the
 King Chulalongkorn Memorial Hospital were approached for study enrollment
 between October 2015 and June 2016. The study protocol is shown
 in Figure 1. A total of 108 patients provided a 10-mL blood sample (for
 serum testing for HEV IgG and IgM antibodies, and HEV RNA detection) and a
 fresh feces sample (for HEV RNA detection). Each patient’s demographic and
 clinical data, including the patient’s medical history; current
 medication(s), especially immunosuppressive agents; and laboratory results
 were retrieved from the medical records. Patients who had a previous
 relevant history, active acute or chronic hepatitis E, or active
 malignancy and those who were unable to attend regular follow-up visits
 were excluded from the study. After recruitment, the patients attended
 follow-up visits every 4 months for 12 months for a clinical assessment,
 basic laboratory tests, and blood/feces sample collection. All samples
 were stored at -70°C and simultaneously tested at the end of the
 study.
DOI: 10.5061/dryad.fqz612jpx
title: Hovering flight in hummingbird hawkmoths: Kinematics, wake dynamics and aerodynamic power

description: Hovering insects are divided into two categories: ‘normal’ hoverers that
 move the wing symmetrically in a horizontal stroke plane, and those with
 an inclined stroke plane. Normal hoverers have been suggested to support
 their weight during both downstroke and upstroke, shedding vortex rings
 each half-stroke. Insects with an inclined stroke plane should, according
 to theory, produce flight forces only during downstroke, and only generate
 one set of vortices. The type of hovering is thus linked to the power
 required to hover. Previous efforts to characterize the wake of hovering
 insects have used low-resolution experimental techniques or simulated the
 flow using computational fluid dynamics, and so it remains to be
 determined whether insect wakes can be represented by any of the suggested
 models. Here, we used tomographic particle image velocimetry, with a
 horizontal measurement volume placed below the animals, to show that the
 wake shed by hovering hawkmoths is best described as a series of
 bilateral, stacked vortex ‘rings’. While the upstroke is aerodynamically
 active, despite an inclined stroke plane, it produces weaker vortices than
 the downstroke. In addition, compared with the near wake, the far wake
 lacks structure and is less concentrated. Both near and far wakes are
 clearly affected by vortex interactions, suggesting caution is required
 when interpreting wake topologies. We also estimated induced power (Pind)
 from downwash velocities in the wake. Standard models predicted a Pind
 more than double that from our wake measurements. Our results thus
 question some model assumptions and we propose a reevaluation of the model
 parameters.
description: The data was collected using a tomoPIV setup in a horizontally
 aligned thin volume in the Lund University wind tunnel. The setup captures
 the wake of moths hovering at a feeder above the laser light sheet
 illuminating the tomo volume.
description: The data is structured as a matrix with x, y, z coordinates in
 the first columns, followed by the velocity vectors u,v,w. The time
 between each file in a sequence is 1/640 s.
DOI: 10.5061/dryad.r7sqv9s83
title: Forest microclimate dynamics drive plant responses to warming

description: Climate warming is causing a shift in biological communities in favor of
 warm-affinity species (i.e., thermophilisation). However, species
 responses often lag behind climate warming and local microclimates
 modulated by vegetation and topography are usually ignored. Here we
 analyze multidecadal understorey microclimate dynamics in European forests
 and show that thermophilisation and the climatic lag in forest plant
 communities are primarily controlled by microclimate. Increasing tree
 canopy cover reduces warming rates inside forests, but loss of
 canopy cover leads to increased microclimatic heat that exacerbates the
 disequilibrium between community responses and climate change. Reciprocal
 effects between plants and microclimates are key to understanding the
 response of forest biodiversity and functioning to climate and land-use
 changes.
description: Please refer to the published paper.
DOI: 10.5061/dryad.pvmcvdnhb
title: Extreme genomic volatility characterises the evolution of the immunoglobulin heavy chain locus in cyprinodontiform fishes

description: The evolution of the adaptive immune system has provided vertebrates with
 a uniquely sophisticated immune toolkit, enabling them to mount precise
 immune responses against a staggeringly diverse range of antigens. Like
 other vertebrates, teleost fishes possess a complex and functional
 adaptive immune system; however, our knowledge of the complex
 antigen-receptor genes underlying its functionality has been restricted to
 a small number of experimental and agricultural species, preventing a
 systematic investigation of how these crucial gene loci evolve. Here, we
 analyse the genomic structure of the immunoglobulin heavy chain (IGH) gene
 loci in the cyprinodontiforms, a diverse and important group of teleosts
 present in many different habitats across the world. We reconstruct the
 complete IGH loci of the turquoise killifish (Nothobranchius furzeri) and
 the southern platyfish (Xiphophorus maculatus) and analyse their in vivo
 gene expression, revealing the presence of species-specific splice
 isoforms of transmembrane IGHM. We further characterise the IGH constant
 regions of ten additional cyprinodontiform species, including guppy,
 amazon molly, mummichog and mangrove killifish. Phylogenetic analysis of
 these constant regions suggests multiple independent rounds of duplication
 and deletion of the teleost-specific antibody class IGHZ in the
 cyprinodontiform lineage, demonstrating the extreme volatility of IGH
 evolution. Focusing on the cyprinodontiforms as a model taxon for
 comparative evolutionary immunology, this work provides novel genomic
 resources for studying adaptive immunity and sheds light on the
 evolutionary history of the adaptive immune system.
DOI: 10.5061/dryad.bcc2fqz8d
title: Plant evolution can mediate negative effects from honey bees on wild pollinators

description: 1. Pollinators are introduced to agroecosystems to provide pollination
 services. Introductions of managed pollinators often promote ecosystem
 services, but it remains largely unknown whether they also affect
 evolutionary mutualisms between wild pollinators and plants. 2. Here we
 developed a model to assess effects of managed honey bees on mutualisms
 between plants and wild pollinators. Our model tracked how interactions
 among wild pollinators and honey bees affected pollinator and plant
 populations. 3. We show that when managed honey bees have a competitive
 advantage over wild pollinators, or a greater carrying capacity, the honey
 bees displace the wild pollinator. This leads to reduced plant density
 because plants benefit less by visits from honey bees than wild
 pollinators that co-evolved with the plants. 4. As wild pollinators are
 displaced, plants evolve by increasing investment in traits that are
 attractive for honey bees but not wild pollinators. This evolutionary
 switch promotes wild pollinator displacement. However, higher mutualism
 investment costs by the plant to the honey bee can promote pollinator
 co-existence. 5. Our results show plant evolution can promote displacement
 of wild pollinators by managed honey bees, while limited plant evolution
 may lead to pollinator co-existence. More broadly, effects of honey bees
 on wild pollinators in agroecosystems, and effects on ecosystem services,
 may depend on the capacity of plant populations to evolve.
description: This is an R script for a model considering evolution of two
 pollinators and a plant.
DOI: 10.15468/dl.ggj9bu
title: Occurrence Download

description: A dataset containing 3531 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Asterias forbesi"
 ]
}

 The dataset includes 3531 records from 61 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002252-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.qnk98sfcg
title: Data from: Genome-wide association analysis of type 2 diabetes in the EPIC-InterAct study

description: Type 2 diabetes (T2D) is a global public health challenge. Whilst the
 advent of genome-wide association studies has identified &gt;400
 genetic variants associated with T2D, our understanding of its biological
 mechanisms and translational insights is still limited. The EPIC-InterAct
 project, centred in 8 countries in the European Prospective Investigations
 into Cancer and Nutrition study, is one of the largest prospective studies
 of T2D. Established as a nested case-cohort study to investigate the
 interplay between genetic and lifestyle behavioural factors on the risk of
 T2D, a total of 12,403 individuals were identified as incident T2D cases
 and a representative sub-cohort of 16,154 individuals was selected from a
 larger cohort of 340,234 participants with a follow-up time of 3.99
 million person-years. We describe the results from a genome-wide
 association analysis between more than 8.9 million SNPs and T2D risk among
 22,326 individuals (9,978 cases and 12,348 non-cases) from the
 EPIC-InterAct study. The summary statistics to be shared provide a
 valuable resource to facilitate further investigations into the genetics
 of T2D.
description: The steps for generating these datasets have been described in
 the corresponding journal article (in Scientific Data).
 EPIC-InterAct T2D GWAS summary statistics (logistic regression) :
 meta_result_EPICInterAct_T2D_GWAS_summary_stats_logit_n22326_08Jul2020_LCAI.txt.gz; Cox Regression results for 370 Top T2D SNPs  (from Mahajan <em>et al</em>, 2018) in EPIC-InterAct: CoxReg_on_T2D_Mahajan370SNPs_available_in_InterAct_Jul2020_LCAI.txt A README file is available accompanying the result files. By downloading this data, you agree to not attempt to identify individuals in the study.
DOI: 10.5061/dryad.pzgmsbcgr
title: Sick leave and return to work after surgery for type II SLAP lesions of the shoulder. A secondary analysis of a randomised sham - controlled study

description: Objectives: To compare days on sick leave and assess predictors of return
 to work following shoulder surgery. Design: A secondary analysis of a
 randomised controlled trial. Setting: Orthopaedic Department.
 Participants: 114 patients with type II superior labral tear from anterior
 to posterior (SLAP) lesions of the shoulder. Interventions: Labral repair,
 biceps tenodesis or sham surgery. Outcome measures: Sick leave was
 obtained from national registers for the last year before and two years
 following surgery. Total and shoulder related number of days on sick leave
 were obtained, using international diagnostic codes. We applied the
 difference-in-difference (DID) approach to compare the differences in the
 change in mean work days on sick leave between groups over time, backwards
 logistic regression and lasso regression to evaluate predictors. Results:
 Mean total number of work days on sick leave during the 2 years after
 surgery was 148 (range 0 to 460) days. More than 80% of the sick leave
 days were taken by 25% of the patients. Days on sick leave classified as
 shoulder-related constituted 80% of the total. In all three treatment
 groups, the mean total number of days on sick leave doubled the year after
 surgery. Sick leave for the 2-year postoperative period was not
 significantly different between groups when adjusted for days of sick
 leave the year before surgery. Predictors of return to work at 2 years
 analysed by logistic regression were no sick leave (OR 8.0, 95% CI 2.4 to
 26.0) and moderate symptoms of anxiety or depression (OR 0.16, 95% CI 0.05
 to 0.5) at inclusion. Similar results were obtained by lasso regression
 but manual work was an additional predictor. Conclusions: In this study,
 sham surgery and labral repair were significantly different from biceps
 tenodesis in terms of post-operative days on sickness absence.
  Sick leave, symptoms of anxiety and depression and manual work
 at inclusion predicted work status 2 years after surgery.
DOI: 10.5061/dryad.44j0zpc9q
title: Data from: Tough fishing and severe seasonal food insecurity in Amazonian flooded forests

description: Billions of people rely on harvesting wildlife for food, and must contend
 with catch rates that vary in space (e.g. overharvesting near communities)
 and time (e.g. seasonal migrations). Yet, research has overlooked
 potential linkages between reduced wildlife catch rates
 (catch-per-unit-effort) and food security. Moreover, assumptions that
 people living in biologically rich environments are food secure lack
 empirical testing. This is problematic given that food security rests on
 having stable access to sufficient food, rather than there being
 sufficient food. We examine spatiotemporal variation in fish catch rates
 and perceived food security among rural communities in Amazonian flooded
 forests. We also assess social inequities in food insecurity. We used
 structured interviews to collect data on fishing, hunting, chicken and
 beef consumption, and perceptions of food security. We did so during 556
 household visits along a spatial gradient (1267km) of commercial fishing
 pressure, during high and low-water seasons. We provide the first
 empirical evidence of simultaneous seasonal crashes in wildlife catch
 rates and food insecurity. During the high-water season fish catch rates
 were 73% lower, and the probability of not eating for a whole day was four
 times higher. With a third of households skipping meals and a sixth not
 eating for a whole day during this season, food security can be classed as
 severe. However, less-deprived households tended to avoid severe food
 insecurity. Fish catch rates and perceived food security did not vary
 along a spatial gradient of commercial overfishing. River-dwelling
 Amazonians increased fishing and hunting efforts during the high-water
 season, without eating more chicken and beef, emphasising the importance
 of stable access to wild fish and bushmeat. This study shows how wildlife
 catch rates and food security can crash seasonally and simultaneously,
 demonstrating the fallacies of environmental and social policies which
 assume stability of food availability in resource-rich areas. Our results
 have implications for degraded habitats where falls in catch rates also
 occur. This suggests that overharvesting, as with other causes of reduced
 catch rates, could cause food insecurity in wildlife-reliant populations.
description: Please see data key in first tab of the spreadsheet.
DOI: 10.5061/dryad.m63xsj3z8
title: Honey bee virus causes context-dependent changes in host social behavior

description: Anthropogenic changes create evolutionarily novel environments that
 present opportunities for emerging diseases, potentially changing the
 balance between host and pathogen. Honey bees provide essential
 pollination services, but intensification and globalization of honey bee
 management has coincided with increased pathogen pressure, primarily due
 to a parasitic mite/virus complex. Here, we investigated how honey bee
 individual and social phenotypes are altered by a virus of concern,
 Israeli acute paralysis virus (IAPV). Using automated and manual
 behavioral monitoring of IAPV-inoculated individuals, we find evidence for
 pathogen manipulation of worker behavior by IAPV, and reveal that this
 effect depends on social context; i.e., within vs between colony
 interactions. Experimental inoculation reduced social contacts between
 honey bee colony members, suggesting an adaptive host social immune
 response to diminish transmission. Parallel analyses with
 dsRNA-immunostimulated bees revealed these behaviors are part of a
 generalized social immune defensive response. Conversely, inoculated bees
 presented to groups of bees from other colonies experienced reduced
 aggression compared dsRNA-immunostimulated bees, facilitating entry into
 susceptible colonies. This reduction was associated with a shift in
 cuticular hydrocarbons, the chemical signatures used by bees to
 discriminate colony members from intruders. These responses were specific
 to IAPV infection, suggestive of pathogen manipulation of the host.
 Emerging bee pathogens may thus shape host phenotypes to increase
 transmission, a strategy especially well-suited to the unnaturally high
 colony densities of modern apiculture. These findings demonstrate how
 anthropogenic changes could affect arms races between human-managed hosts
 and their pathogens to potentially impact global food security.
DOI: 10.5061/dryad.wstqjq2h8
title: Brevity is not a universal in animal communication: evidence for compression depends on the unit of analysis in small ape vocalizations

description: Evidence for compression, or minimization of code length, has been found
 across biological systems from genomes to human language and music. Two
 linguistic laws—Menzerath’s law (which states that longer sequences
 consist of shorter constituents) and Zipf’s law of abbreviation (a
 negative relationship between signal length and frequency of use) are
 predictions of compression. It has been proposed that compression is a
 universal in animal communication, but there have been mixed results,
 particularly in reference to Zipf’s law of abbreviation. Like songbirds,
 male gibbons (Hylobates muelleri) engage in long solo bouts with unique
 combinations of notes which combine into phrases. We found strong support
 for Menzerath’s law as the longer a phrase, the shorter the notes. To
 identify phrase types, we used state-of-the-art affinity propagation
 clustering, and were able to predict phrase types using support vector
 machines with a mean accuracy of 74%. Based on unsupervised phrase type
 classification, we did not find support for Zipf’s law of abbreviation.
 Our results indicate that adherence to linguistic laws in male gibbon
 solos depends on the unit of analysis. We conclude that principles of
 compression are applicable outside of human language, but may act
 differently across levels of organization in biological systems.
description: We include Raven selection tables and R code necessary to
 recreate all analyses.
description: Sound files can be accessed via the permant repository
 here: https://cornell.box.com/s/0pqxw6gxvg69nb1ipcy25j4zs5r0q2ua. Please contact corresponding author with any comments or questions.
DOI: 10.5061/dryad.xwdbrv19t
title: Data from: Network structure and the optimisation of proximity-based association criteria

description: Animal social network analysis (SNA) often uses proximity data obtained
 from automated tracking of individuals. Identifying associations based on
 proximity requires deciding on quantitative criteria such as the maximum
 distance or the longest time interval between visits of different
 individuals to still consider them associated. These quantitative criteria
 are not easily chosen based on a priori biological arguments alone. Here
 we propose a procedure for optimising proximity-based association criteria
 in SNA, whereby different spatial and temporal criteria are screened to
 determine which combination detects more network structure. If we assume
 that biologically-relevant associations among individuals are non-random,
 and that proximity data are mostly influenced by those associations, then
 it is logical to select criteria that minimise random associations and
 show the underlying network structure more clearly. We first used
 simulations to evaluate which of four simple descriptors of network
 structure remain unbiased (i.e., do not change directionally) when
 reducing the number of observations, since unbiased descriptors are
 necessary for comparing the structure of networks using different
 association criteria. Then, using two of those descriptors (coefficient of
 variation of the strength of associations, and network entropy), and
 empirical proximity data from automated tracking of common waxbills
 (Estrilda astrild) in a mesocosm environment, we found that the
 structure-based optimisation procedure selected the most
 biologically-relevant combination of spatial and temporal proximity
 criteria, in the sense that those criteria were also the best at
 distinguishing between previously known social sub-groups of individuals.
 These results indicate that, provided that the assumptions for
 structure-based optimisation are met, this procedure can find the most
 biologically-relevant association criteria. Thus, under the condition that
 proximity data are shaped by non-random social associations, and if using
 adequate descriptors of network structure, structure-based optimisation
 may be a useful tool for SNA, particularly when a priori biological
 arguments are insufficient to inform the choice of proximity-based
 association criteria.