cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.63qp0
title: Data from: Dose-dependent effects of an immune challenge at both ultimate and proximate levels in Drosophila melanogaster

description: Immune responses are highly dynamic. The magnitude and efficiency of an
 immune response to a pathogen can change markedly across individuals, and
 such changes may be influenced by variance in a range of intrinsic (e.g.
 age, genotype, sex) and external (e.g. abiotic stress, pathogen identity,
 strain) factors. Life history theory predicts that up-regulation of the
 immune system will come at a physiological cost, and studies have
 confirmed that increased investment in immunity can reduce reproductive
 output and survival. Furthermore, males and females often have divergent
 reproductive strategies, and this might drive the evolution of
 sex-specific life history trade-offs involving immunity, and sexual
 dimorphism in immune responses per se. Here, we employ an experiment
 design to elucidate dose-dependent and sex-specific responses to exposure
 to a nonpathogenic immune elicitor at two scales – the ‘ultimate’ life
 history and the underlying ‘proximate’ immune level in Drosophila
 melanogaster. We found dose-dependent effects of immune challenges on both
 male and female components of reproductive success, but not on survival,
 as well as a response in antimicrobial activity. These results indicate
 that even in the absence of the direct pathogenic effects that are
 associated with actual disease, individual life histories respond to a
 perceived immune challenge – but with the magnitude of this response being
 contingent on the initial dose of exposure. Furthermore, the results
 indicate that immune responses at the ultimate life history level may
 indeed reflect underlying processes that occur at the proximate level.
description: Antimicrobial
 responseData from lytic zone
 assay, where inhibition zones created by heamolymph was measured in (mm).
 PlateNumber describes the individual agar plate.Early Surival both
 sexesData describing 72 h
 survival in males and femalesEarly survival both sexes
 1.xlsxBinary egg
 successData describing whether
 females laid and egg or notEggtoAdult viability
 dataNumber of eggs that
 hatch out to adults.Female fecundity
 dataTotal number of eggs for
 each female, including individuals laying no eggs.Sperm
 competitionIncluding data on sperm
 competition and on sperm competition success as binary data (yes or
 no).SurvivalFemalesLong-term survival females (used in proportional hazard model).Survival MalesLong-term survival males (used in proportional hazard model).SurvivalMales 1.csvCorrelations Fitness ImmunityOverall means (n=5) of fitness and immune data used for supporting material.
DOI: 10.5061/dryad.k183ft7
title: Data from: Rapid buildup of sympatric species diversity in Alpine whitefish

description: Adaptive radiations in postglacial fish offer excellent settings to study
 the evolutionary mechanisms involved in the rapid buildup of sympatric
 species diversity from a single lineage. Here, we address this by
 exploring the genetic and ecological structure of the largest Alpine
 whitefish radiation known, that of Lakes Brienz and Thun, using
 microsatellite data of more than 2000 whitefish caught during extensive
 species‐targeted and habitat‐randomized fishing campaigns. We find six
 strongly genetically and ecologically differentiated species, four of
 which occur in both lakes, and one of which was previously unknown. These
 four exhibit clines of genetic differentiation that are paralleled in
 clines of eco‐morphological and reproductive niche differentiation,
 consistent with models of sympatric ecological speciation along
 environmental gradients. In Lake Thun, we find two additional species, a
 profundal specialist and a species introduced in the 1930s from another
 Alpine whitefish radiation. Strong genetic differentiation between this
 introduced species and all native species of Lake Thun suggests that
 reproductive isolation can evolve among allopatric whitefish species
 within 15,000 years and persist in secondary sympatry. Consistent with
 speciation theory, we find stronger correlations between genetic and
 ecological differentiation for sympatrically than for allopatrically
 evolved species.
description: Doenz_etal_Alpinewhitefish_genetic_morphological_ecological_data2Individual genetic, morphological and ecological data for whitefish caught in Lake Thun and Brienz. Individuals were genotyped at 10 microsatellite loci (missing data=999). Sampling type is either species_targeted (species-targeted fishing on known spawning grounds) or habitat_randomized (quantitative and taxonomically unbiased sampling across the entire lake). Sampling location is not indicated for species targeted fishing to protect spawning grounds. Capture habitat is given for habitat randomized fishing; all fish caught &gt;5 m above ground were considered pelagic. Structure assignment is based on the assignment analysis using reference populations as described in the paper; here, individuals were assigned to species by considering their maximum assignment proportion. The second sheet contains genotypic data for whitefish caught in Lake Constance before/during its eutrophication period.
DOI: 10.5061/dryad.mj18p
title: Data from: Steep clines within a highly permeable genome across a hybrid zone between two subspecies of the European rabbit

description: Maintenance of genetic distinction in the face of gene flow is an
 important aspect of the speciation process. Here, we provide a detailed
 spatial and genetic characterization of a hybrid zone between two
 subspecies of the European rabbit. We examined patterns of allele
 frequency change for 22 markers located on the autosomes, X-chromosome,
 Y-chromosome, and mtDNA in 1078 individuals sampled across the hybrid
 zone. While some loci revealed extremely wide clines (w&gt;=300 km)
 relative to an estimated dispersal of 1.95-4.22 km/generation, others
 showed abrupt transitions (w = 10 km), indicating localized genomic
 regions of strong selection against introgression. The subset of loci
 showing steep clines had largely coincident centers and stepped changes in
 allele frequency that did not co-localize with any physical barrier or
 ecotone, suggesting that the rabbit hybrid zone is a tension zone. The
 steepest clines were for X and Y chromosome markers. Our results are
 consistent with previous inference based on DNA sequence variation of
 individuals sampled in allopatry in suggesting that a large proportion of
 each genome has escaped the overall barrier to gene flow in the middle of
 the hybrid zone. These results imply an old history of hybridization and
 high effective gene flow, and anticipate that isolation factors should
 often localize to small genomic regions.
description: Genotypes_Carneiro_et_alGenotypic data used in the study. The coordinates for the different populations and information on the different markers can be found in the Supplementary Material associated with the manuscript and main manucsript, respectively.
DOI: 10.5061/dryad.vn806pd
title: Data from: Systemic inflammation during midlife and cognitive change over 20 years: the ARIC study

description: Objective: To examine the association between systemic inflammation
 measured during midlife and 20-year cognitive decline. Methods: Within the
 Atherosclerosis Risk in Communities cohort study, inflammatory biomarkers
 were measured during middle adulthood. We created an inflammation
 composite score using four blood biomarkers measured at Visit 1
 (fibrinogen, white blood cell count, von Willebrand factor, and Factor
 VIII); we measured C-reactive protein (CRP) at Visit 2. Cognition was
 assessed over three visits spanning 20 years using measures of memory,
 executive function, and language. Results: 12,336 participants (baseline
 age 56.8 [5.7], 21% black, 56% women) were included. After adjusting for
 demographic variables, vascular risk factors and comorbidities, each
 standard deviation (SD) increase in midlife inflammation composite score
 was associated with an additional 20-year decline of -0.035 SD (95% CI:
 -0.062, -0.007) on the cognitive composite score. We found a similar
 association between each SD increase in midlife CRP level and additional
 20-year cognitive decline (-0.038 SD, 95% CI: -0.057, -0.019).
 Participants with a midlife inflammation composite score in the top
 quartile had a 7.8% steeper cognitive decline, compared to participants in
 the lowest quartile; CRP in the top quartile was associated with an 11.6%
 steeper cognitive decline. In cognitive domain-specific analyses, elevated
 midlife inflammatory markers were most consistently associated with
 declines in memory. Results were similar after adjusting for attrition
 using inverse probability weighting. Conclusions: Our findings highlight
 what may be an early pathogenic role for systemic inflammation as a driver
 of cognitive decline in the decades leading up to older adulthood.
description: Supplementary Material -
 Inflammation, Cog Decline (Neurology)Supplementary material
 for article titled "Systemic inflammation during midlife and
 cognitive change over 20 years: The ARIC study."
DOI: 10.5061/dryad.f34p5
title: Data from: Fire frequency drives habitat selection by a diverse herbivore guild impacting top–down control of plant communities in an African savanna

description: In areas with diverse herbivore communities such as African savannas, the
 frequency of disturbance by fire may alter the top–down role of different
 herbivore species on plant community dynamics. In a seven year experiment
 in the Kruger National Park, South Africa, we examined the habitat use of
 nine common herbivore species across annually burned, triennially burned
 and unburned areas. We also used two types of exclosures (plus open access
 controls) to examine the impacts of different herbivores on plant
 community dynamics across fire disturbance regimes. Full exclosures
 excluded all herbivores &gt; 0.5 kg (e.g. elephant, zebra, impala)
 while partial exclosures allowed access only to animals with shoulder
 heights ≤ 0.85 m (e.g. impala, steenbok). Annual burns attracted a diverse
 suite of herbivores, and exclusion of larger herbivores (e.g. elephant,
 zebra, wildebeest) increased plant abundance. When smaller species, mainly
 impala, were also excluded there were declines in plant diversity, likely
 mediated by a decline in open space available for colonization of uncommon
 plant species. Unburned areas attracted the least diverse suite of
 herbivores, dominated by impala. Here, herbivore exclusion, especially of
 impala, led to strong declines in plant richness and diversity. With no
 fire disturbance, herbivore exclusion led to competitive exclusion via
 increases in plant dominance and light limitation. In contrast, on
 triennial burns, herbivore exclusion had no effect on plant richness or
 diversity, potentially due to relatively little open space for
 colonization across exclosure treatments but also little competitive
 exclusion due to the intermediate fire disturbance. Further, the diverse
 suite of grazers and browsers on triennial burns may have had a
 compensating effect of on the diversity of grasses and forbs. Ultimately,
 our work shows that differential disturbance regimes can result in
 differential consumer pressure across a landscape and result in
 heterogeneous patterns in top–down control of community dynamics.
description: KNP_EBP_Partial_Species_CompThis data come from Kruger National Park (Kruger), Mpumalanga, South Africa near the Satara rest camp. This set from Kruger is of the partial exclosures, full exclosures, and paired plots that were established in 2007. Species composition was collect at the beginning (January) and end (March) of each growing season. Each plant species’ cover in 4 permanent 1x1m subplots inside and outside the exclosure was recorded to the nearest one percent twice a year. The maximum value of the two samplings was used, and data presented here are the mean of the 4 subplots.
DOI: 10.5061/dryad.1355
title: Data from: Elevated substitution rate estimates from ancient DNA: model violation and bias of Bayesian methods

description: The increasing ability to extract and sequence DNA from
 non-contemporaneous tissue offers biologists the opportunity to analyze
 ancient DNA (aDNA) together with modern DNA (mDNA) to address the taxonomy
 of extinct species, evolutionary origins, historical phylogeography and
 biogeography. Perhaps more exciting are recent developments in
 coalescence-based Bayesian inference that offer the potential to use
 temporal information from aDNA and mDNA for the estimation of substitution
 rates and divergence dates as an alternative to fossil and geological
 calibration. This comes at a time of growing interest in the possibility
 of time dependency for molecular rate estimates. Here we provide a
 critical assessment of Bayesian MCMC analysis for the estimation of
 substitution rate using simulated samples of aDNA and mDNA. We conclude
 that the current models and priors employed in Bayesian MCMC analysis of
 heterochronous mtDNA are susceptible to an upward bias in the estimation
 of substitution rates due to model misspecification when the data comes
 from populations with less than simple demographic histories, including
 sudden short-lived population bottlenecks or pronounced population
 structure. However when model misspecification is only mild, then the 95%
 HPD intervals provide adequate frequentist coverage of the true rates.
description: input
 files.zipEach folder contains 10
 original input files for each of the 11 models in Table
 1
DOI: 10.5281/zenodo.18381687
title: Natural history specimens collected and/or identified and deposited.

description: Natural history specimen data collected and/or identified by Sabine von Mering, https://orcid.org/0000-0003-2982-7792. Claims or attributions were made on Bionomia, https://bionomia.net using specimen data from the Global Biodiversity Information Facility, https://gbif.org.
DOI: 10.5061/dryad.1kh77
title: Data from: Does multiple paternity affect seed mass in angiosperms? An experimental test in Dalechampia scandens

description: Flowers fertilized by multiple fathers may be expected to produce heavier
 seeds than those fertilized by a single father. However, the adaptive
 mechanisms leading to such differences remain unclear, and the evidence
 inconsistent. Here, we first review the different hypotheses predicting an
 increase in seed mass when multiple paternity occurs. We show that
 distinguishing between these hypotheses requires information about average
 seed mass, but also about within-fruit variance in seed mass, bias in
 siring success among pollen donors, and whether siring success and seed
 mass are correlated. We then report the results of an experiment on
 Dalechampia scandens (Euphorbiaceae), assessing these critical variables
 in conjunction with a comparison of seed mass resulting from crosses with
 single vs. multiple pollen donors. Siring success differed among males
 when competing for fertilization, but average seed mass was not affected
 by the number of fathers. Furthermore, paternal identity explained only
 3.8% of the variance in seed mass, and siring success was not correlated
 with the mass of the seeds produced. Finally, within-infructescence
 variance in seed mass was not affected by the number of fathers. These
 results suggest that neither differential allocation nor sibling rivalry
 has any effect on the average mass of seeds in multiply sired fruits in D.
 scandens. Overall, the limited paternal effects observed in most studies
 and the possibility of diversification bet hedging among flowers (but not
 within flowers), suggest that multiple paternity within fruits or
 infructescence is unlikely to affect seed mass in a large number of
 angiosperm species.
description: Multiple paternity in
 Dalechampia scandensMultipaternity_pelabon et
 al_2015_JEB.txt
DOI: 10.5061/dryad.v2k7s
title: Data from: Reliability-based weighting of visual and vestibular cues in displacement estimation

description: When navigating through the environment, our brain needs to infer how far
 we move and in which direction we are heading. In this estimation process,
 the brain may rely on multiple sensory modalities, including the visual
 and vestibular systems. Previous research has mainly focused on heading
 estimation, showing that sensory cues are combined by weighting them in
 proportion to their reliability, consistent with statistically optimal
 integration. But while heading estimation could improve with the ongoing
 motion, due to the constant flow of information, the estimate of how far
 we move requires the integration of sensory information across the whole
 displacement. In this study, we investigate whether the brain optimally
 combines visual and vestibular information during a displacement
 estimation task, even if their reliability varies from trial to trial.
 Participants were seated on a linear sled, immersed in a stereoscopic
 virtual reality environment. They were subjected to a passive linear
 motion involving visual and vestibular cues with different levels of
 visual coherence to change relative cue reliability and with cue
 discrepancies to test relative cue weighting. Participants performed a
 two-interval two-alternative forced-choice task, indicating which of two
 sequentially perceived displacements was larger. Our results show that
 humans adapt their weighting of visual and vestibular information from
 trial to trial in proportion to their reliability. These results provide
 evidence that humans optimally integrate visual and vestibular information
 in order to estimate their body displacement.
description: RAW subject
 data
DOI: 10.5281/zenodo.3549016
title: Natural history specimens collected and/or identified and deposited.

description: Natural history specimen data collected and/or identified by Sabine von Mering, https://orcid.org/0000-0003-2982-7792. Claims or attributions were made on Bionomia, https://bionomia.net using specimen data from the Global Biodiversity Information Facility, https://gbif.org.
DOI: 10.5061/dryad.8r351
title: Data from: Release of 50 new, drug-like compounds and their computational target predictions for open source anti-tubercular drug discovery

description: As a follow up to the antimycobacterial screening exercise and the release
 of GSK´s first Tres Cantos Antimycobacterial Set (TCAMS-TB), this paper
 presents the results of a second antitubercular screening effort of two
 hundred and fifty thousand compounds recently added to the GSK collection.
 The compounds were further prioritized based on not only antitubercular
 potency but also on physicochemical characteristics. The 50 most
 attractive compounds were then progressed for evaluation in three
 different predictive computational biology algorithms based on structural
 similarity or GSK historical biological assay data in order to determine
 their possible mechanisms of action. This effort has resulted in the
 identification of novel compounds and their hypothesized targets that will
 hopefully fuel future TB drug discovery and target validation programs
 alike.
description: TBset all data - article
 Rebollo et al - Plos One - 2015all data generated for
 the 50 compounds released in the article
DOI: 10.5061/dryad.71hp4
title: Data from: Cataract surgery visual outcomes and associated risk factors in secondary level eye care centers of L V Prasad Eye Institute, India

description: Purpose: To evaluate cataract surgery visual outcomes and associated risk
 factors in rural secondary level eye care centers of L V Prasad Eye
 Institute (LVPEI), India. Methods: The Eye Health pyramid of LVPEI has a
 network of rural secondary care centres (SCs) and attached vision centres
 (VCs) that provide high quality comprehensive eye care with permanent
 infrastructure to the most disadvantaged sections of society. The most
 common procedure performed at SCs is cataract surgery. We audited the
 outcome of a random sample of 2,049 cataract surgeries done from October
 2009-March 2010 at eight rural SCs. All patients received a comprehensive
 ophthalmic examination, both before and after surgery. The World Health
 Organization recommended cataract surgical record was used for data entry.
 Visual outcomes were measured at discharge, 1–3 weeks and 4–11 weeks
 follow up visits. Poor outcome was defined as best corrected visual acuity
 &lt;6/18. Results: Mean age was 61.8 years (SD: 8.9 years) and 1,133
 (55.3%) surgeries were performed on female patients. Pre-existing ocular
 co-morbidity was present in 165 patients (8.1%). The most common procedure
 was small incision cataract surgery (SICS) with intraocular lens (IOL)
 implantation (91.8%). Intraoperative complications were seen in 29 eyes
 (1.4%). At the 4–11 weeks follow-up visit, based on presenting visual
 acuity (PVA), 61.8% had a good outcome and based on best-corrected visual
 acuity (BCVA), 91.7% had a good outcome. Based on PVA and BCVA, those with
 less than 6/60 were only 2.9% and 1.6% respectively. Using multivariable
 analysis, poor visual outcomes were significantly higher in patients aged
 ≥70 (OR 4.63; 95% CI 1.61, 13.30), in females (OR 1.58; 95% CI 1.04,
 2.41), those with preoperative comorbidities (odds ratio 4.68; 95% CI
 2.90, 7.57), with intraoperative complications (OR 8.01; 95% CI 2.91,
 22.04), eyes that underwent no IOL or anterior chamber-IOL (OR 12.63; 95%
 CI 2.65, 60.25) and those undergoing extracapsular cataract extraction (OR
 9.39; 95% CI 1.18, 74.78). Conclusions: This study demonstrates that
 quality cataract surgeries can be achieved at rural SCs. The concept of
 the LVPEI SCs can be applied to other developing countries, allowing rural
 patients to attain better vision through cataract surgery. Despite
 improvements in quality of cataract surgery, gender discrimination in
 terms of outcome continues to be an issue and needs further investigation.
description: OutcomeThis contains data on visual outcomes in eight secondary level eye care centers of L V Prasad Eye Institute, India
DOI: 10.5061/dryad.56q7c2k
title: Data from: Hawkmoth flight in the unsteady wakes of flowers

description: Flying animals maneuver and hover through environments where wind gusts
 and flower wakes produce unsteady flow. Although both flight maneuvers and
 aerodynamic mechanisms have been studied independently, little is known
 about how these interact in an environment where flow is already unsteady.
 Moths forage from flowers by hovering in the flower’s wake.We investigated
 hawkmoths tracking a 3D-printed robotic flower in a wind tunnel.We
 visualized the flow in the wake and around the wings and compared tracking
 performance with previous experiments in a still-air flight chamber. As in
 still air, moths flying in the flower wake exhibit near-perfect tracking
 at low frequencies where natural flowers move. However, tracking in the
 flower wake results in a larger overshoot between 2 and 5 Hz. System
 identification of flower tracking reveals that moths also display
 reduced-order dynamics in wind compared with still air. Smoke
 visualization of the flower wake shows that the dominant vortex shedding
 corresponds to the same frequency band as the increased overshoot. Despite
 these large effects on tracking dynamics in wind, the leading edge vortex
 (LEV) remains bound to the wing throughout the wingstroke and does not
 burst. The LEV also maintains the same qualitative structure seen in
 steady air. Persistence of a stable LEV during decreased flower tracking
 demonstrates the interplay between hovering and maneuvering.
description: Tracking data for
 hawkmoths in windThe zip file contains 5
 data files (described in detail in the README text file). These include
 the raw tracked points (in the x- and y-directions) for hawkmoth and
 flower motion during the wind tunnel experiments. A conversion factor from
 pixel values to real units is included. There is also a file for the
 frequency response found for hawkmoths tracking flowers in
 wind.Matthews_HawkmothUnsteadyWake_data.zip