cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.zs7h44j51
title: Data from: Benefits of an anti-parasite treatment are influenced by within-brood size variation in Tree Swallows (Tachycineta bicolor)

description: In all animals, susceptibility to parasites can differ among individuals.
 Young, nest-bound birds are exposed to a diversity
 of nest-dwelling ectoparasites that typically feed on their
 blood. Within broods, hatching asynchrony creates size
 hierarchies that result in morphological and physiological
 variation among nest mates, and susceptibility to parasites also may
 vary predictably with this size hierarchy. Our objective was to
 use a broad-spectrum, anti-parasite drug, ivermectin (IVM),
 to treat individual nestling Tree Swallows (Tachycineta bicolor)
 and assess how nestling susceptibility to parasites varied
 both within and among broods. Broods were either assigned to an
 IVM group, where half of the nestlings in a brood received IVM
 injections and half received control injections of pure sesame oil, or to
 a control group, where all nestlings received oil injections. We
 found that the IVM treatment reduced parasite loads for broods as a whole,
 thereby benefiting all nestlings in IVM broods and suggesting our
 treatment resulted in herd immunity. Specifically, nestlings from IVM
 broods had higher hemoglobin concentrations, regardless of
 whether they received injections with IVM or oil, and greater fledging
 success, than nestlings from control broods. On the contrary, IVM
 treatment did not strongly affect nestling morphology, with
 only marginal effects on the growth rate of ninth primary
 feathers, and the effects of the treatment on 2 other morphological
 traits depending on temporal factors. Variation in size within
 broods, however, influenced the chance of an individual
 fledging, which increased with relative size within a brood, but
 only under lower parasite loads (i.e. IVM broods). By
 experimentally manipulating nestling susceptibility to parasites,
 we have demonstrated variation in nestling response to an
 anti-parasite treatment both within and among broods, and future
 studies should investigate the underlying mechanism for why
 certain nestlings along the brood size hierarchy are more
 susceptible to parasites.
DOI: 10.5061/dryad.zgmsbcc6v
title: Transient intracellular acidification regulates the core transcriptional heat shock response

description: Heat shock induces a conserved transcriptional program regulated by heat
 shock factor 1 (Hsf1) in eukaryotic cells. Activation of this heat-shock
 response is triggered by heat-induced misfolding of newly synthesized
 polypeptides, and so has been thought to depend on ongoing protein
 synthesis. Here, using the budding yeast Saccharomyces
 cerevisiae, we report the discovery that Hsf1 can be robustly
 activated when protein synthesis is inhibited, so long as cells undergo
 cytosolic acidification. Heat shock has long been known to cause transient
 intracellular acidification which, for reasons which have remained
 unclear, is associated with increased stress resistance in eukaryotes. We
 demonstrate that acidification is required for heat shock response
 induction in translationally inhibited cells, and specifically affects
 Hsf1 activation. Physiological heat-triggered acidification also increases
 population fitness and promotes cell cycle reentry following heat shock.
 Our results uncover a previously unknown adaptive dimension of the
 well-studied eukaryotic heat shock response. 
description: Raw data: Flow cytometry .fcs files (contained in zipped
 directories starting with 'Triandafillou') are raw flow
 cytometry data; the experiment names contain the metadata. The script
 'process-raw-data.R' processes raw flow cytometry
 data (internally normalizes fluorescent readings and performs calibration
 curve analysis to calculate intracellular pH where appropriate) and
 combines experiments into tidy datasets. Processed
 data: Processed data are .tsv and .csv files and include processed flow
 datasets (generated by 'process-raw-data.R'). Raw qPCR data, and
 raw protein translation data (generated by liquid scintillation counting
 (LSC) of samples from radiolabeled amino acid incorporation
 experiments) are also included. Zipped
 directory 2017-11-18_pH-TSP-bio1.zip contains SDS-PAGE gel and Western
 Blot data; protocol, raw images, quantification, and processed images and
 summaries are all included.
description: analysis-scripts.zip contains R markdown notebooks that generate
 figures from the raw LSC and qPCR data.
DOI: 10.5061/dryad.3xsj3txbr
title: Microhabitat partitioning correlates with opsin gene expression in coral reef cardinalfishes (Apogonidae)

description: Fish are the most diverse vertebrate group, and they have evolved equally
 diverse visual systems, varying in terms of eye morphology, number and
 distribution of spectrally distinct photoreceptor types, visual opsin
 genes and opsin gene expression levels. This variation is mainly due to
 adaptations driven by two factors: differences in the light environments
 and behavioural tasks. However, while the effects of large-scale habitat
 differences are well described, it is less clear whether visual systems
 also adapt to differences in environmental light at the microhabitat
 level. To address this, we assessed the relationship between microhabitat
 use and visual system features in fishes inhabiting coral reefs, where
 habitat partitioning is particularly common. We suggest that differences
 in microhabitat use by cardinalfishes (Apogonidae) drive morphological and
 molecular adaptations in their visual systems. To test this, we
 investigated diurnal microhabitat use in 17 cardinalfish species and
 assessed whether this correlated with differences in visual opsin gene
 expression and eye morphology. We found that cardinalfishes display six
 types of microhabitat partitioning behaviours during the day, ranging from
 specialists found exclusively in the water column to species that are
 always hidden inside the reef matrix. Species predominantly found in
 exposed microhabitats had higher expression of the short-wavelength
 sensitive violet opsin (SWS2B) and lower expression of the dim-light
 active rod opsin (RH1). Species of intermediate exposure, on the other
 hand, expressed opsins that are mostly sensitive to the blue-green central
 part of the light spectrum (SWS2As and RH2s), while fishes entirely hidden
 in the reef substrate had a higher expression of the long-wavelength
 sensitive red opsin (LWS). We also found that eye size relative to body
 size differed between cardinalfish species, and relative eye size
 decreased with an increase in habitat exposure. Retinal topography did not
 show co-adaptation with microhabitat use, but data suggested co-adaptation
 with feeding mode. We suggest that, although most cardinalfishes are
 nocturnal foragers, their visual systems – and possibly those of other
 (reef) fishes – have also adapted to the light intensity and the light
 spectrum of their preferred diurnal microhabitats.
DOI: 10.5061/dryad.1vhhmgqpp
title: The hidden army: coralivorous Crown of Thorns seastars can spend years as herbivorous juveniles

description: Crown of Thorns seastar (COTS) outbreaks are a major threat to coral
 reefs. Although the herbivorous juveniles and their switch to corallivory
 are key to seeding outbreaks, they remain a black box in our understanding
 of COTS. We investigated the impact of a delay in diet transition due to
 coral scarcity in cohorts reared on coralline algae for 10 months and 6.5
 yrs before being offered coral. Both cohorts achieved an asymptotic size
 (16–18 mm diameter) on algae and had similar exponential growth on coral.
 After 6.5 yrs of herbivory, COTS were competent coral predators. This
 trophic and growth plasticity results in a marked age-size disconnect
 adding unappreciated complexity to COTS boom-bust dynamics. The potential
 that herbivorous juveniles accumulate in the reef infrastructure to seed
 outbreaks when favourable conditions arise has implications for management
 of COTS populations.
DOI: 10.5061/dryad.bnzs7h46r
title: Data from: Sex, synchrony and skin contact: integrating multiple behaviors to assess pathogen transmission risk

description: Direct pathogen and parasite transmission is fundamentally driven by a
 population’s contact network structure, its demographic composition, and
 is further modulated by pathogen life history traits. Importantly,
 populations are most often concurrently exposed to a suite of pathogens,
 which is rarely investigated, because contact networks are typically
 inferred from spatial proximity only. Here, we use five years of detailed
 observations of Indo-Pacific bottlenose dolphins (Tursiops aduncus) that
 distinguish between four different types of social contact. We investigate
 how demography (sex, age) affects these different social behaviors. Three
 of the four social behaviors can be used as a proxy for understanding key
 routes of direct pathogen transmission (sexual contact, skin contact, and
 aerosol contact of respiratory vapor above the water surface). We quantify
 the demography-dependent network connectedness, representing the risk of
 exposure associated with the three pathogen transmission routes, quantify
 co-exposure risks and relate them to individual sociability. Our results
 suggest demography-driven disease risk in bottlenose dolphins, with males
 at greater risk than females, and transmission route-dependent
 implications for different age classes. We hypothesize that male
 alliance-formation and the divergent reproductive strategies in males and
 females drive the demography-dependent connectedness and hence exposure
 risk to pathogens. Our study provides evidence for the risk of co-exposure
 to pathogens transmitted along different transmission routes and that they
 relate to individual sociability. Hence, our results highlight the
 importance of a multi-behavioral approach for a more complete
 understanding of the overall pathogen transmission risk in animal
 populations, as well as the cumulative costs of sociality.
description: Please see the ReadMe.txt file for details on the data
 files.
DOI: 10.5061/dryad.bk3j9kd70
title: Fitness consequences of divorce in the azure-winged magpie depends on the breeding experience of a new mate

description: Sexual conflict in producing and raising offspring is a critical issue in
 evolutionary ecology research. Individual experience affects their
 breeding performance, as measured by such traits of provisioning of
 offspring and engagement in extra-pair copulations, and may cause an
 imbalance in sexual conflict. Thus, divorce is hypothesized to occur
 within aged social pairs, irrespective of current reproductive success.
 This concept was explored in the azure-winged magpie (Cyanopica cyanus) by
 investigating the divorce of a social pair and its relationship to their
 changes in breeding performance with prior experience. Females engaging in
 extra-pair copulation may intensify sexual conflicts and may be the main
 reason for divorce. Once divorced, females re-pairing with an
 inexperienced male realized higher reproductive success than that
 re-pairing with an experienced male; males re-pairing with an experienced
 female realized higher reproductive success than that re-pairing with an
 inexperienced female. This finding indicates that the fitness consequence
 of divorce depends on the breeding experience of new mates. Divorced
 females can obtain more extra-pair copulations, whereas divorced males
 cannot, when they re-pair with inexperienced breeders. Divorced females
 provisioned a brood at lower rates than inexperienced females whereas
 divorced males had no such difference. It appears that divorced females
 can obtain an advantage in sexual conflicts with inexperienced mates in
 future reproduction. Consequently, females are probably more active than
 males in divorcing their aged mates so as to select an inexperienced male
 as a new mate. Azure-winged magpies thus provide novel insights into
 implications of sexual conflict in birds.
description: These datasets were collected in a field study. Data of the
 breeding biology has not been processed, and the data about divorce and
 cuckoldry have been processed. 
description: No, all data needed have been supplied here.
DOI: 10.5061/dryad.w6m905qkq
title: The community-level scaling relationship between leaf nitrogen and phosphorus changes with plant growth, climate and nutrient limitation

description: This dataset contains community-level leaf nitrogen (N) and phosphorus (P)
 concentration data from an intensive field investigation across China,
 including 1080 shrub-community sites from shrublands and 2087
 tree-community sites from forests. Mean annual temperature and
 Thornthwaite moisture index,  net primary productivity, and soil
 total N and P concentrations of each site are also included in this
 dataset.
DOI: 10.5061/dryad.kh189322c
title: The evolutionary advantage of fitness-dependent recombination in diploids: a deterministic mutation–selection–balance model

description: Recombination’s omnipresence in nature is one of the most intriguing
 problems in evolutionary biology. The question of why recombination
 exhibits certain general features is no less interesting than that of why
 it exists at all. One such feature is recombination’s fitness dependence
 (FD). The so far developed population-genetics models have focused on the
 evolution of FD recombination mainly in haploids, although the empirical
 evidence for this phenomenon comes mostly from diploids. Using numerical
 analysis of modifier models for infinite panmictic populations, we show
 here that FD recombination can be evolutionarily advantageous in diploids
 subjected to purifying selection. We ascribe this advantage to the
 differential rate of disruption of lower- vs higher-fitness genotypes,
 which can be manifested in selected systems with at least three loci. We
 also show that if the modifier is linked to such selected system, it can
 additionally benefit from modifying this linkage in a fitness-dependent
 manner. The revealed evolutionary advantage of FD recombination appeared
 robust to crossover interference within the selected system, either
 positive or negative. Remarkably, FD recombination was often favored in
 situations where any constant non-zero recombination was evolutionarily
 disfavored, implying a relaxation of the rather strict constraints on
 major parameters (e.g., selection intensity and epistasis) required for
 the evolutionary advantage of non-zero recombination formulated by
 classical models.
description: The archive contains the codes used for the simulations, as well
 as the corresponding input and output files.
description: The codes are written using PascalABC.NET.
DOI: 10.5061/dryad.mpg4f4qvh
title: Data from: Ecosystem size predicts the probability of speciation in migratory freshwater fish

description: Predicting speciation is a fundamental goal of research in evolutionary
 ecology. The probability of speciation is often positively correlated with
 ecosystem size. Although the mechanisms driving this correlation are
 generally difficult to identify, a shared geographic and ecological
 context provides a suitable condition to study the mechanisms that promote
 speciation in large ecosystems by reducing the number of factors to be
 considered. Here, we determined the correlation between speciation and
 ecosystem size, and discussed the underlying mechanisms of this
 relationship, using a probable parallel ecotype formation for freshwater
 fish. Our population genetic analysis revealed that speciation of the
 landlocked goby, Rhinogobius sp. YB, of the Ryukyu Archipelago, Japan,
 from its migratory ancestor, R. brunneus, occurred in parallel across five
 islands. Logistic regression analysis showed that speciation probability
 could be predicted using island size. The results suggest that ecosystem
 size predicts the occurrence of adaptation and reproductive isolation,
 likely through its association with three possible factors: divergent
 selection strength, population persistence, and occurrence probability of
 habitat separation.
DOI: 10.5061/dryad.37pvmcvft
title: Two new species of Kaempferia subgenus Protanthium (Zingiberaceae) from Northern Thailand

description: Kaempferia aurora Noppornch. & Jenjitt., from Tak province near
 the Thailand-Myanmar border, and K. caespitosa Noppornch. &
 Jenjitt., from Lampang province, Northern Thailand, are described as new
 species of subgenus Protanthium (Horan.) Baker. The diagnostic characters
 are clearly compared with the similar species. Detailed illustrations,
 photographs of floral dissection, information of phenology, distribution
 and ecology, and preliminary conservation status are provided for each new
 taxon. An identification key to the species of Kaempferia subgen.
 Protanthium in Thailand are also revised and presented.
description: Field studies have been conducted throughout Northern Thailand
 and living materials of each new taxon were collected. The morphological
 and phenological characters were mainly obtained through the study of
 living specimens in their natural habitat and in cultivation, especially
 the Ginger and rare plant nurseries at QSBG in Chiang Mai, Thailand.
 Protologues and herbarium specimens of <i>Kaempferia
 </i>subgen. <i>Protanthium</i> held in BK, BKF, QBG,
 SING, Suan Luang RAMA IX herbarium, and several online herbarium specimen
 databases, especially Kew Herbarium Catalogue and Chinese Virtual
 Herbarium (CVH) were also intensively examined. Taxonomic descriptions,
 flower dissection, distribution and ecology information, detailed
 photographs and line illustration, and preliminary conservation status
 were carried out and provided for each new species. Diagnostic
 morphological and flowering phenological characteristics of new taxa were
 compered with the close morphologically similar species. A key to
 identification of the species of <i>Kaempferia</i> subgen.
 <i>Protanthium</i> was reconstructed, modified from
 Nopporncharoenkul & Jenjittikul (2017). Type specimens with
 duplicates were prepared and deposited at BK, BKF, QBG, and
 SING.
DOI: 10.6075/j0ft8n0n
title: Maui Nui 2023-07 (Expedition) - Maui (Island) - Raw Images. In Long-term Coral Reef Monitoring Across Leeward Maui

description: In July of 2023 the Smith Lab visited Maui to collect large-area imagery as part of the Maui Nui 2023-07 expedition. The imagery collected here are resurveys of permanent sites established during the Maui 2014-07 expedition as part of the Smith Lab Maui large-area imagery timeseries. For each site, a preview image and the raw digital images used to create composite large-area image products of the underwater sites have been made available. A general description of the methods used to acquire the images can be found in a README.txt file for each site. Site specific metadata can be found within a METADATA.txt file for each site.
DOI: 10.6075/j0b27w87
title: Maui 2014-07 (Expedition) - Maui (Island) - Raw Images. In Long-term Coral Reef Monitoring Across Leeward Maui

description: In July of 2014 the Smith Lab visited Maui to collect large-area imagery as part of the Maui 2014-07 expedition. The imagery collected here marks the beginning of the Smith Lab Maui large-area imagery timeseries, with 20 sites established. For each site, a preview image and the raw digital images used to create composite large-area image products of the underwater sites have been made available. A general description of the methods used to acquire the images can be found in a README.txt file for each site. Site specific metadata can be found within a METADATA.txt file for each site.
DOI: 10.5061/dryad.gqnk98shr
title: Joining a group diverts regret and responsibility away from the individual

description: It has recently been proposed that a key motivation for joining groups is
 the protection from negative consequences of undesirable outcomes. To test
 this claim we investigated how experienced outcomes triggering loss and
 regret impacted people’s tendency to decide alone or join a group, and how
 decisions differed when voluntarily made alone vs in group. Replicated
 across two experiments, participants (N=125 and N=496) selected whether to
 play alone or contribute their vote to a group decision. Next, they chose
 between two lotteries with different probabilities of winning and losing.
 The higher the negative outcome, the more participants switched from
 deciding alone to with others.  When joining a group to choose
 the lottery, choices were less driven by outcome and regret anticipation.
 Moreover, negative outcomes experienced alone, not part of a group vote,
 led to worse subsequent choices than positive outcomes. These results
 suggest that the protective shield of the collective reduces the influence
 of negative emotions that may help individuals re-evaluate past choices.
description: The data was collected online on Amazon Mechanical Turk and
 Prolific. It was processed and analyzed using Matlab and R. 
description: Experiments 1 and 2 are included in the main text. Experiment 2b
 is an older version of Experiment 2: in this version, because of a an
 error in the experiment code, only half of the total of 48 lottery choices
 were shown to participants. <b>Description of the
 variables in the open data sheets:</b> Sub:
 subject number. Age: subject’s age.
 Gender: subject’s gender. Proportion play
 alone: proportion of trials the subject chose to play alone.
 Gamble resp: Choice of Lottery 1 (1) or Lottery 2 (0).
 EV: Difference in expected value between Lottery 1 and Lottery
 2. AR: Difference in anticipated regret between Lottery
 1 and Lottery 2. Group resp/current condition: Choice
 to play alone (0) or as a group (1). Experienced
 outcome: Obtained – Unobtained outcome from the previous round.
 Previous condition: Previous round played alone (1) or in group
 (2). Group status: Previous round in group majority (1)
 or minority (2). 0 corresponds to previous rounds played alone.
DOI: 10.5061/dryad.crjdfn31d
title: Effect of ocrelizumab on vaccine responses in patients with multiple sclerosis: The VELOCE study

description: Objective The phase IIIb VELOCE study (NCT02545868) assessed responses to
 selected vaccines in ocrelizumab (OCR)-treated patients with relapsing
 multiple sclerosis. Methods Patients were randomized 2:1 into Group OCR
 (n=68; OCR 600mg); or Control (n=34; interferon-β or no disease-modifying
 therapy). All received tetanus toxoid (TT)-containing vaccine, Pneumovax®
 (23-PPV) and keyhole limpet hemocyanin (KLH). Group OCR was subdivided
 into OCR1 (n=33) and OCR2 (n=35) at randomization. OCR1 received Prevnar®
 (13-PCV) 4 weeks after 23-PPV; OCR2 and Control received influenza
 vaccine. Vaccinations started 12 weeks after OCR initiation (Group OCR) or
 on Day 1 (Control). Results Positive response rate to TT vaccine at 8
 weeks was 23.9% in OCR vs 54.5% in Control. Positive response rate to ≥5
 serotypes in 23-PPV at 4 weeks was 71.6% in OCR and 100% in Control.
 Prevnar® did not enhance response to pneumococcal serotypes in common with
 Pneumovax®. Humoral response to KLH was decreased in OCR vs Control.
 Seroprotection rates at 4 weeks against five influenza strains ranged from
 55.6–80.0% in OCR2 and 75.0–97.0% in Control. Conclusion Peripherally
 B-cell depleted OCR recipients mounted attenuated humoral responses to
 clinically relevant vaccines and the neoantigen, KLH, suggesting use of
 standard non-live vaccines while on OCR treatment remains a consideration.
 For seasonal influenza vaccines, it is recommended to vaccinate patients
 on OCR, as a potentially protective humoral response, even if attenuated,
 can be expected.
description: Dataset Contents Overview <b>Figure e-1
 </b>Patient disposition.  <b>Figure e-2
 </b>Positive response to <i>S. pneumoniae
 </i>serotypes.  <b>Figure e-3
 </b>Response against (A) mumps, (B) rubella, and (C) varicella
 zoster in patients with RMS.  <b>Table e-1
 </b>Post-vaccination influenza seroconversion rates 
 <b>Table e-2 </b>Geometric mean titers for individual
 23-PPV serotypes prior to and 4- and 8-week post- vaccination 
 <b>Table e-3 </b>Quantitative immunoglobulin
 levels