cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.q573n5th3
title: Foraging behaviour alters with social environment in a juvenile songbird

description: Early independence from parents is a critical period where social
 information acquired vertically may become outdated, or conflict with new
 information. However, across natural populations it is unclear if
 newly-independent young persist in using information from parents, or if
 group-level effects of conformity override previous behaviours. Here we
 test if wild juvenile hihi (Notiomystis cincta, a New Zealand passerine)
 retain a foraging behaviour from parents, or if they change in response to
 the behaviour of peers. We provided feeding stations to parents during
 chick-rearing to seed alternative access routes, and then tracked their
 offspring’s behaviour. Once independent, juveniles formed mixed-treatment
 social groups, where they did not retain preferences that we detected when
 with parents. Instead, juvenile groups converged over time to use one
 access route per group, and juveniles that moved between groups switched
 to copy the locally-favoured option. Juvenile hihi did not copy specific
 individuals, even if they were more familiar with the preceding bird. Our
 study shows that early social experiences with parents affect initial
 foraging decisions, but social environments encountered later on can
 update transmission of arbitrary behaviours. This suggests that conformity
 may be widespread in animal groups, with potential cultural, ecological,
 and evolutionary consequences.
description: Data on visits to feeders were collected using Radio Frequency
 Identification (RFID) Passive Integrated Transponder (PIT) tags fitted to
 each individual bird in our study population. Individual-level data (i.e.
 metal ring number, age) on the birds associated with each transponder ID
 were collected as part of the ongoing yearly monitoring of the study
 population during the breeding season. Social network metrics (i.e.
 degree) were obtained prior to main experiment data collection. Full
 information can be found in the Methods sections of the article.
description: There are four files associated with this dataset:
 group_side choice_data.csv: datasheet including all records of
 visits to group-site feeders, with associated variables included in main
 article;  group_first visit times_data.csv:
 datasheet including the subset of first visits for feeder nest juveniles
 at group-site feeders, with relevant treatment variables given in the main
 article; README.txt: details of all variables in the
 datasheets; Franks et al. parents vs peers R code_final
 241020.R: R code file for all analyses in the main article. Terms for the
 variables correspond to the column names in the datasheets.
DOI: 10.5061/dryad.s4mw6m958
title: Treelists, constraints and logfiles for: Relative time constraints improve molecular dating

description: Dating the tree of life is central to understanding the evolution of life
 on Earth. Molecular clocks calibrated with fossils represent the state of
 the art for inferring the ages of major groups. Yet, other information on
 the timing of species diversification can be used to date the tree of
 life. This is the case for instance for horizontal gene transfer events
 and ancient coevolutionary relationships such as (endo)symbioses, which
 can imply temporal relationships between two nodes in a phylogeny (Davin
 et al. 2018). This can be particularly helpful when the geological record
 is sparse, e.g. for microorganisms, which represent the vast majority of
 extant and extinct biodiversity. Here, we demonstrate that relative age
 constraints, when combined with fossil calibrations, can significantly
 improve both the accuracy and resolution of molecular clock estimates. We
 provide an implementation of relative age constraints in RevBayes (Hoehna
 et al. 2016) that can be combined in a modular manner with the wide range
 of molecular dating methods available in the software. To validate our
 method in a realistic data setting we apply it to two data sets of 40
 Cyanobacteria and 62 Archaea respectively, and provide cross-validations
 of fossil calibrations and relative age constraints.
description: The data set contains, for both Archaea and Bacteria:
 1. concatenated CAT GTR
 treelists used in approximating the phylogenetic likelihood, obtained
 using PhyloBayes<br> 2. constraints used for the dating;<br>
 3. log files used in producing the plots in the paper
DOI: 10.5061/dryad.7d7wm37sz
title: Neurologic complications of COVID-19

description: Objective: The SARS-Cov2 virus is protean in its manifestations, affecting
 nearly every organ system.  However, nervous system involvement
 and its impact on disease outcome are poorly characterized. The objective
 of the study is to determine if neurological syndromes are associated with
 increased risk of inpatient mortality. Methods: 581 hospitalized patients
 with confirmed SARS-Cov2 infection, neurological involvement and
 brain-imaging were compared to hospitalized non-neurological COVID-19
 patients.  Four patterns of neurological manifestations were
 identified –acute stroke, new or recrudescent seizures, altered mentation
 with normal imaging, and neuro-COVID-19 complex. Factors present on
 admission were analyzed as potential predictors of in-hospital mortality,
 including sociodemographic variables, pre-existing comorbidities,
 vital-signs, laboratory values, and pattern of neurological
 manifestations. Significant predictors were incorporated into a
 disease-severity score.  Patients with neurological
 manifestations were matched with patients of the same age and disease
 severity to assess the risk of mortality. Results:  4711 patients
 with confirmed SARS-Cov2 infection were admitted to one medical system in
 New York City during a 6-week period.  Of these, 581 (12%) had
 neurological issues of sufficient concern to warrant
 neuro-imaging.  These patients were compared to 1743
 non-neurological COVID-19 patients matched for age and disease-severity
 admitted during the same period. Patients with altered mentation (n=258, p
 =0.04, OR 1.39, CI 1.04 – 1.86) or radiologically confirmed stroke (n=55,
 p = 0.001, OR 3.1, CI 1.65-5.92) had a higher risk of mortality than age
 and severity-matched controls.  Conclusions:  The
 incidence of altered mentation or stroke on admission predicts a modest
 but significantly higher risk of in-hospital mortality independent of
 disease severity. While other biomarker factors also predict mortality,
 measures to identify and treat such patients may be important in reducing
 overall mortality of COVID-19.
description: Retrospective observational cohort study.
DOI: 10.5061/dryad.547d7wm6n
title: Male and female genotype and a genotype-by-genotype interaction mediate the effects of mating on cellular but not humoral immunity in female decorated crickets

description: Sexually antagonistic coevolution is predicted to lead to the divergence
 of male and female genotypes related to the effects of substances
 transferred by males at mating on female physiology. The outcome of mating
 should thus depend on the specific combination of mating genotypes.
 Although mating has been shown to influence female immunity in diverse
 insect taxa, a male-female genotype-by-genotype effect on female immunity
 post-mating remains largely unexplored. Here, we investigate the effects
 of mating on female decorated cricket baseline immunity and the potential
 for a male-by-female genotype interaction affecting this response. Females
 from three distinct genotypic backgrounds were left unmated or singly
 mated in a fully reciprocal design to males from the same three genotypic
 backgrounds. Hemocytes and hemocyte microaggregations were quantified for
 female cellular immunity, and phenoloxidase, involved in melanization, and
 antibacterial activity for humoral immunity. In this system, female
 cellular immunity was more reactive to mating, and mating effects were
 genotype dependent. Specifically, for hemocytes, a genotype-mating status
 interaction mediated the effect of mating per se, and a significant
 male-female genotype-by-genotype interaction determined hemocyte depletion
 post-mating. Microaggregations were influenced by the female’s genotype or
 that of her mate. Female humoral immune measures were unaffected,
 indicating the propensity for post-mating effects on female is dependent
 on the component of baseline immunity. The genotype-by-genotype effect on
 hemocytes supports a role of sexual conflict in post-mating immune
 suppression, suggesting divergence of male genotypes with respect to
 modification of female post-mating immunity, and divergence of female
 genotypes in resistance to these effects.
description: See the uploaded readme file (Hampton_GxG_data_readme.txt).
DOI: 10.5061/dryad.sbcc2fr4x
title: Empirical and methodological challenges to the model-based inference of diversification rates in extinct clades

description: Changes in speciation and extinction rates are key to the dynamics of
 clade diversification, but attempts to infer them from phylogenies of
 extant species face challenges. Methods capable of synthesizing
 information from extant and fossil species have yielded novel insights
 into diversification rate variation through time, but little is known
 about their behavior when analyzing entirely extinct clades. Here, we use
 empirical and simulated data to assess how two popular methods, PyRate and
 Fossil BAMM, perform in this setting. We inferred the first tip-dated
 trees for ornithischian dinosaurs, and combined them with fossil
 occurrence data to test whether the clade underwent an end-Cretaceous
 decline. We then simulated phylogenies and fossil records under empirical
 constraints to determine whether macroevolutionary and preservation rates
 can be teased apart under paleobiologically realistic conditions. We
 obtained discordant inferences about ornithischian macroevolution
 including a long-term speciation rate decline (BAMM), mostly flat rates
 with (PyRate) or without (BAMM) a steep diversification drop, and episodes
 of implausibly accelerated speciation and extinction (PyRate). Simulations
 revealed little to no conflation between speciation and preservation, but
 yielded spuriously correlated speciation and extinction estimates while
 time-smearing tree-wide shifts (BAMM) or overestimating their number
 (PyRate). Our results indicate that the small phylogenetic
 datasets available to vertebrate paleontologists and the assumptions
 made by current model-based methods combine to hinder inferences
 about the diversification of extinct clades. We provide
 guidelines for interpreting the results of the existing approaches
 in light of their limitations, and suggest how the latter may be
 mitigated.
DOI: 10.5061/dryad.pg4f4qrn3
title: Coagulation profile of COVID-19 patients admitted to the ICU: an exploratory study

description: Background Coagulation abnormalities in COVID-19 patients have not been
 addressed in depth. Objective: To perform a longitudinal evaluation of
 coagulation profile of patients admitted to the ICU with COVID-19. Methods
 Conventional coagulation tests, rotational thromboelastometry (ROTEM),
 platelet function, fibrinolysis, antithrombin, protein C and S were
 measured at days 0, 1, 3, 7 and 14. Based on median total maximum SOFA
 score, patients were divided in two groups: SOFA ≤ 10 and SOFA &gt;
 10. Results Thirty patients were studied. Conventional coagulation tests
 remained unchanged during the study period, while the majority of patients
 exhibited a hypercoagulability state based on ROTEM. Fibrinogen levels
 were increased in both groups. ROTEM maximum clot firmness increased in
 both groups. ROTEM – FIBTEM maximum clot firmness was high in both groups,
 with a slight decrease from day 0 to day 14 in group SOFA ≤ 10 and a
 slight increase during the same period in group SOFA &gt; 10.
 Fibrinolysis was low and decreased over time in all groups, with the most
 pronounced decrease observed in INTEM maximum lysis in group SOFA &gt;
 10. Protein C plasma levels increased over time in both groups, although
 patients in group SOFA &gt; 10 exhibited lower values in comparison to
 patients in group SOFA ≤ 10. Conclusion COVID-19 patients have a
 pronounced hypercoagulability state, characterized by impaired endogenous
 anticoagulation and decreased fibrinolysis. The magnitude of coagulation
 abnormalities seems to correlate with the severity of organ dysfunction.
 The hypercoagulability state of COVID-19 patients was only detected by
 ROTEM.
description: We performed a single center prospective longitudinal study in an
 ICU of a private tertiary care hospital in São Paulo, Brazil. Thirty
 patients aged ≥18 years old admitted to the ICU with confirmed diagnosis
 of COVID-19 were included in this study. Laboratory confirmation of
 SARS-CoV-2 infection was based on positive
 reverse-transcriptase-polymerasechain-reaction (RT-PCR) assay.
 Laboratory tests were performed at the time of study inclusion
 (baseline), and at days 1, 3, 7 and 14 after enrollment unless the patient
 had died or was discharged from the hospital.
 Conventional coagulation tests included: platelet count, plasma
 fibrinogen concentration, aPTT, PT and INR and ionic calcium. Rotational
 thromboelastometry analyses were performed with EXTEM, INTEM and FIBTEM.
 D-dimer, serum plasminogen, alpha-2 antiplasmin, antithrombin.
DOI: 10.5061/dryad.2bvq83bp1
title: Tuning cell behavior with nanoparticle shape

description: We investigated how the shape of polymeric vesicles, made by the exact
 same material, impacts the replication activity and metabolic state of
 both cancer and non-cancer cell types. First, we isolated discrete
 geometrical structures (spheres and tubes) from a heterogeneous sample
 using density-gradient centrifugation. Then, we characterized the cellular
 internalization and the kinetics of uptake of both types of polymersomes
 in different cell types (either cancer or non-cancer cells). We also
 investigated the cellular metabolic response as a function of the shape of
 the structures internalized and discovered that tubular vesicles induce a
 significant decrease in the replication activity of cancer cells compared
 to spherical vesicles. We related this effect to the significant
 up-regulation of the tumor suppressor genes p21 and p53 with a concomitant
 activation of caspase 3/7. Finally, we demonstrated that combining the
 intrinsic shape-dependent effects of tubes with the delivery of
 doxorubicin significantly increases the cytotoxicity of the system. Our
 results illustrate how the geometrical conformation of nanoparticles could
 impact cell behavior and how this could be tuned to create novel drug
 delivery systems tailored to specific biomedical application.
DOI: 10.5061/dryad.w0vt4b8pm
title: Jaskuła et al. Morphological variability in Lophyra flexuosa (Fabricius, 1787) (Coleoptera: Cicindelidae) in desert countries: sexual dimorphism and geographic aspect

description: The file with raw data which includes morphometric measuremens for all
 specimens of Lophyra flexuosa from Morocco and Tunisia studied in the
 manuscript entitled "Morphological variability in Lophyra flexuosa
 (Fabricius, 1787) (Coleoptera: Cicindelidae) in desert countries: sexual
 dimorphism and geographic aspect". Details about all sampling sites
 for this species (altitude, habitat type, and climatic zone) are also
 included in the file.
DOI: 10.5061/dryad.gmsbcc2kr
title: Data from: Light environment drives evolution of color vision genes in butterflies and moths

description: Opsins, combined with a chromophore, are the primary light-sensing
 molecules in animals and are crucial for color vision. Throughout animal
 evolution duplications and losses of opsin proteins are common, but it is
 unclear what is driving these gains and losses. Light availability is
 implicated, and dim environments are often associated with low opsin
 diversity and loss. Correlations between high opsin diversity and bright
 environments, however, are tenuous. To test if increased light
 availability is associated with opsin diversification, we examined diel
 niche and identified opsins using transcriptomes and genomes of 175
 butterflies and moths (Lepidoptera). We found 14 independent opsin
 duplications associated with bright environments. Estimating their rates
 of evolution revealed that opsins from diurnal taxa evolve faster — at
 least 13 amino acids were identified with higher dN/dS rates, with a
 subset close enough to the chromophore to tune the opsin. These results
 demonstrate that high light availability increases opsin diversity and
 evolution rate in Lepidoptera
description: Please refer to Readme file for details on dataset.
DOI: 10.5061/dryad.mpg4f4qxc
title: Raw data for sexually selected traits and life history traits of major and minor males in the horned flour beetle Gnatocerus cornutus

description: 1. Expression of weapons and weapon sizes are remarkably affected by
 environmental factors in armed insects, resulting in remarkable
 morphological difference in larger and smaller males i.e., male dimorphism
 2. The phenotypic plasticity is one example of alternative mating
 phenotypes. Selection on the alternative phenotype generates different
 suites of multiple traits between larger and smaller males such as
 morphology, behaviors and life history. The different subsets of traits
 can contribute to reproductive success of larger and smaller males,
 respectively. 3. In order to understand how alternative phenotypes evolve,
 studies that couple differences in life history and reproductive traits
 between larger and smaller males are required. Here we investigated
 differences in morphology, behaviors, and life history in Gnatocerus
 cornutus. 4. Larger males have relatively larger mandibles and the
 advantage in male fighting to access females. Also, the developmental
 period was significantly shorter in the larger males than in the smaller
 males. 5. Smaller males with rudimentary weapons have higher locomotion
 ability. This suggests higher performance in the dispersal to new
 territories. Larger and smaller males showed different suites of multiple
 traits, and the combinations of multiple traits are probably related to
 expression of weapons.
DOI: 10.5061/dryad.15dv41nw4
title: Data for: Spontaneous choices for insect-pollinated flower shapes by wild non-eusocial halictid bees

description: The majority of angiosperms require animal pollination for reproduction
 and insects are the dominant group of animal pollinators. Bees are
 considered one of the most important and abundant insect pollinators.
 Research into bee behaviour and foraging decisions has typically centred
 on managed eusocial bee species, Apis mellifera and Bombus terrestris.
 Non-eusocial bees are understudied with respect to foraging strategies and
 decision-making, such as flower preferences. Understanding whether there
 are fundamental foraging strategies and preferences which are features of
 insect groups can provide key insights into the evolution of
 flower-pollinator co-evolution. In the current study, Lasioglossum
 (Chilalictus) lanarium and L. (Parasphecodes) sp., two native Australian
 generalist halictid bees, were tested for flower shape preferences between
 native insect-pollinated and bird-pollinated flowers. Each bee was
 presented with achromatic images of either insect-pollinated or
 bird-pollinated flowers in a circular arena. Both native bee species
 demonstrated a significant preference for images of insect-pollinated
 flowers. These preferences are similar to those found in A. mellifera,
 suggesting that flower shape preference may be a deep-rooted evolutionary
 occurrence within bees. With growing interest in the sensory capabilities
 of non-eusocial bees as alternative pollinators, the current study also
 provides a valuable framework for further behavioural testing of such
 species.
description: See the ReadMe file.
DOI: 10.5061/dryad.ns1rn8pr0
title: Data from: Large-scale meta-analysis on rheumatoid arthritis across East Asian and European populations

description: Objective: Nearly 110 susceptibility loci for rheumatoid arthritis (RA)
 with modest effect sizes have been identified by population-based genetic
 association studies, suggesting a large number of undiscovered variants
 behind a highly polygenic genetic architecture of RA. Here, we performed
 the largest-ever trans-ancestral meta-analysis with the aim to identify
 new RA loci and to better understand RA biology underlying genetic
 associations. Methods: Genome-wide RA association summary statistics in
 three large case-control collections consisting of 311,292 individuals of
 Korean, Japanese, and European populations were used in an
 inverse-variance-weighted fixed-effects meta-analysis. Several
 computational analyses using public omics resources were conducted to
 prioritize causal variants and genes, RA variant-implicating features
 (tissues, pathways, and transcription factors), and potentially
 repurposable drugs for RA treatment. Results: We identified 11 new RA
 susceptibility loci that explained 6.9% and 1.8% of the SNP-based
 heritability in East Asians and Europeans, respectively, and confirmed 71
 known non-HLA susceptibility loci, identifying 90 independent association
 signals. The RA variants were preferentially located in binding sites of
 various transcription factors and in cell type-specific
 transcription-activation histone marks that simultaneously highlighted the
 importance of CD4+ T-cell activation and the potential role of non-immune
 organs in RA pathogenesis. A total of 615 plausible effector genes, based
 on gene-based associations, expression-associated variants, and chromatin
 interaction, included targets of drugs approved for RA treatments and
 potentially repurposable drugs approved for other indications. Conclusion:
 Our findings provide useful insights regarding RA genetic etiology and
 variant-driven RA pathogenesis.
description: The association summary statistics were generated from a
 genome-wide association study in rheumatoid arthritis using large
 cohorts of Korean, Japanese, and European populations (311,292
 individuals). Please find detailed information from our
 research article: Eunji Ha, Sang-Cheol Bae, and
 Kwangwoo Kim; "Large-scale meta-analysis across East Asian and
 European populations updated genetic architecture and variant-driven
 biology of rheumatoid arthritis, identifying 11 novel susceptibility
 loci."; <em>Annals of the Rheumatic Disease</em>; in
 press<em>.</em>