cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.qbzkh18hm
title: Data from: The effects of phylogeny, habitat, and host characteristics on the thermal sensitivity of helminth development

description: Helminth parasites are part of almost every ecosystem, with more than
 300 000 species worldwide. Helminth infection dynamics are expected to be
 altered by climate change, but predicting future changes is difficult due
 to lacking thermal sensitivity data for greater than 99.9% of helminth
 species. Here, we compiled the largest dataset to date on helminth
 temperature sensitivities and used the Metabolic Theory of Ecology to
 estimate activation energies (AEs) for parasite developmental rates. The
 median AE for 129 thermal performance curves was 0.67, similar to
 non-parasitic animals. Although exceptions existed, related species tended
 to have similar thermal sensitivities, suggesting some helminth taxa
 are inherently more affected by rising temperatures than others.
 Developmental rates were more temperature-sensitive for species from
 colder habitats than those from warmer habitats, and more temperature
 sensitive for species in terrestrial than aquatic habitats. AEs did not
 depend on whether helminth life stages were free-living or within hosts,
 whether the species infected plants or animals, or whether the species had
 an endotherm host in its life cycle. The phylogenetic
 conservatism of AE may facilitate predicting how temperature change
 affects the development of helminth species for which empirical data are
 lacking or difficult to obtain.Helminth parasites are part of almost every
 ecosystem, with more than 300 000 species worldwide. Helminth infection
 dynamics are expected to be altered by climate change, but predicting
 future changes is difficult due to lacking thermal sensitivity data for
 greater than 99.9% of helminth species. Here, we compiled the largest
 dataset to date on helminth temperature sensitivities and used the
 Metabolic Theory of Ecology to estimate activation energies (AEs) for
 parasite developmental rates. The median AE for 129 thermal performance
 curves was 0.67, similar to non-parasitic animals. Although exceptions
 existed, related species tended to have similar thermal sensitivities,
 suggesting some helminth taxa are inherently more affected by
 rising temperatures than others. Developmental rates were more
 temperature-sensitive for species from colder habitats than those from
 warmer habitats, and more temperature sensitive for species in terrestrial
 than aquatic habitats. AEs did not depend on whether helminth life stages
 were free-living or within hosts, whether the species infected plants or
 animals, or whether the species had an endotherm host in its life
 cycle. The phylogenetic conservatism of AE may facilitate predicting how
 temperature change affects the development of helminth species for which
 empirical data are lacking or difficult to obtain.
DOI: 10.5061/dryad.hmgqnk9hj
title: Systematic prediction of EMS-induced mutations in a sorghum mutant population

description: Sorghum is a next-generation crop species with tremendous potential for
 discovering highly desirable agronomical traits. We described an improved
 method for the systematic detection of EMS-induced mutations in the
 previous sequencing of the M3 generation of 600 sorghum BTx623 mutants. We
 used both SAMtools and GATK-based variant-calling algorithms to
 demonstrate the general utility of the method. The approach also includes
 a clustering algorithm for detecting likely false-negative EMS-induced
 mutations. We detected 3,497,654 EMS-induced single nucleotide
 polymorphisms (SNPs) in 30,285 distinct sorghum genes, and cataloged
 10,263 high impact and 136,639 moderate impact SNPs. We also implemented a
 light-weight web portal for searching the mutation database for the 600
 sorghum mutants.
description: NGS Sequencing data: Illumina Sequencing of
 mutant individuals at 6X coverage. Sequencing data is available at the NCB
 SRA (SRA Accession Number SRP065118). SNP Calling:
 SAMtools and GATK SNP Annotations: snpEff and
 SIFT4G Gene Annotation: Phytozome gene annotation for
 sorghum BTx623
DOI: 10.5061/dryad.sj3tx965j
title: Oxygen sensing with individual ZnO:Sb Micro-wires: Effects of temperature and light exposure on the sensitivity and stability

description: Nanostructured ZnO has been widely investigated as a gas sensing
 material. Antimony is an important dopant for ZnO that catalyzes
 its surface reactivity and thus strengthens its gas sensing
 capability. However, there are little to no studies on the gas
 sensing of antimony-doped ZnO single wires. We fabricated and
 characterized ZnO/ZnO:Sb core/shell micro-wires and demonstrated that
 individual wires are sensitive to oxygen gas flow. Temperature and light
 illumination strongly affect the oxygen gas sensitivity and stability of
 these individual wires. It was found that these micro- and nano-wire
 oxygen sensors at 200˚C give the highest response to oxygen, yet a
 vanishingly small effect of light and temperature variations. The
 underlying physics and the interplay between these effects are discussed
 in terms of surface-adsorbed oxygen, oxygen vacancies and hydrogen doping.
description: All four file names correspond directly with the figure
 numbers. All data was collected using Labview Software,
 which saved the raw data as Excel (.xlxs) files.<br> Columns are
 labeled properly, where the first column is usually time.<br> Other
 columns are either the resistance of the ZnO:Sb individual wire (in
 Mega-Ohms) or its temperature. The column is labeled properly in each
 case.<br> Figure insets are meant to focus the attention on some
 specific parts of the data, but do not have any 'new' datasets
 other than those used to produce the actual figures.
DOI: 10.5061/dryad.bcc2fqzcv
title: The conventional genetic basis for obesity is impacted by adverse childhood experiences: a multi-ethnic study of gene-environment effects

description: Adverse Childhood Experiences are stressful and traumatic events occurring
 before the age of eighteen known to cause mental and physical health
 problems, including increased risk of obesity. Obesity remains an ongoing
 national challenge with no predicted solution.  We examine a
 subset of the Healthy Nevada Project, focusing on a multi-ethnic cohort of
 15,886 sequenced participants with recalled adverse childhood events to
 study how ACEs and their genotype-environment interactions affect BMI.
 Specifically, the Healthy Nevada Project participants sequenced by the
 Helix Exome+ platform were cross-referenced to their electronic medical
 records and social health determinants questionnaire to identify: (1) the
 effect of ACEs on BMI in the absence of genetics; (2) the effect of
 genotype-environment interactions on BMI; (3) how these gene-environment
 interactions differ from canonical genetic associations of BMI. 
 The study found very strong significant associations between the number of
 adverse childhood experiences and adult obesity. Additionally, we
 identified fifty-five common and rare variants that exhibited
 gene-interaction effects including three variants in the CAMK1D gene and
 four variants in LHPP; both genes are linked to schizophrenia.
 Surprisingly, none of the variants identified with interactive effects
 were in canonical obesity-related genes. Here we show the delicate balance
 between genes and environment, and how the two strongly influence each
 other.
DOI: 10.5061/dryad.1g1jwstwx
title: Divorce in Northern Flickers

description: Divorce is widespread among species of birds and may either be an adaptive
 strategy to secure a better mate or territory or be a non-adaptive result
 of a failure to maintain the pairbond. I examined the causes and
 consequences for divorce in the Norther Flicker (Colaptes auratus), a
 migratory woodpecker with a high annual mortality rate. In a long-term
 population study of 1793 breeding pairs over 17 years, the within-season
 divorce rate was 4.6% and the between-season divorce rate was 15.5%.
 Retained pairs within a season initiated their renest 5 days faster than
 divorced birds which had no greater fledgling production, suggesting that
 within-season divorce was making the best of a bad job with severe time
 constraints. Poor performance in the year prior to divorce was not
 strongly associated with divorce and analysis of multiple breeding stages
 revealed that divorcing individuals in the subsequent year had later
 laying dates, smaller clutches and fewer fledglings than retained pairs
 but no better performance than widowed individuals. Analyzing the data
 separately by sex showed that neither males nor females benefitted from
 divorce. Thus, there is a reproductive cost linked to finding a new
 partner per se, but no reproductive advantage associated with divorce. New
 mates after divorce were usually not older (not higher quality) than
 previous mates, so intrasexual competition was probably not driving
 partnership splits. The most plausible explanation seems to be a
 "bet-hedging" hypothesis in which birds re-pair rapidly in
 spring if their previous mate does not quickly arrive during spring
 migration. Divorce in Northern Flickers does not appear to be adaptive and
 future studies on arrival and interactions of individuals in spring will
 elucidate proximate constraints on relocating the previous partner.
DOI: 10.5061/dryad.mpg4f4r0v
title: Brief structured respiration practices enhance mood and reduce physiological arousal

description: Controlled Breathwork practices have emerged as potential tools for stress
 management and well-being. Here we report a remote, randomized, controlled
 study (NCT05304000) of three different daily five-minute Breathwork
 exercises in comparison to an equivalent period of Mindfulness Meditation,
 over one month. The breathing conditions are 1) Cyclic Sighing, which
 emphasizes prolonged exhalations, 2) Box Breathing, which is equal
 duration of inhalations, breath retentions and exhalations, and 3) Cyclic
 Hyperventilation with Retention, with longer inhalations and shorter
 exhalations. The primary endpoints are improvement in mood and anxiety as
 well as reduced physiological arousal (respiratory rate, heart rate, and
 heart rate variability). Using a mixed-effects model, we show that
 Breathwork, especially the exhale-focused Cyclic Sighing produces greater
 improvement in mood (p &lt; 0.05) and reduction in respiratory rate (p
 &lt; 0.05) compared to Mindfulness Meditation. Daily 5-minute Cyclic
 Sighing has promise as an effective stress management exercise. 
description: This data was collected remotely with a wearable WHOOP tracker
 and daily surveys and contains physiological and subjective measures of
 mood and wellbeing.
DOI: 10.6078/d13d9r
title: Single-nucleus RNA-sequencing in pre-cellularization Drosophila melanogaster embryos

description: Using 10x Genomics Single-Cell Gene Expression (v3 chemistry) and the
 Illumina NovaSeq SP we sequenced RNA in nuclei isolated from control and
 maternal null CTCF pre-cellularization Drosophila melanogaster embryos, or
 nuclear cycle 14 and 9-13 OreR embryos. 
description: Nuclei were isolated from control and dCTCF maternal null early
 to mid-nuclear cycle 14 Drosophila melanogaster embryos. Full protocol in
 associated publication.  Note (11/01/2023 upload): NC14
 and NC9-13 data were not used in the linked manuscript; however, these are
 uploaded for use by the community. 
description: See README.txt for additional information.
DOI: 10.5061/dryad.hhmgqnkh9
title: Data from: High spatiotemporal overlap in the non-breeding season despite geographically dispersed breeding locations in the eastern whip-poor-will (Antrostomus vociferus)

description: The eastern whip-poor-will (Antrostomus vociferus) is a Neotropical
 migrant that has declined by 70% in recent decades, yet when and where
 populations are limited throughout the annual cycle is poorly understood.
 We deployed 115 archival GPS tags across a 9.5-degree latitudinal span
 (~1000 km; midwestern US) on whip-poor-wills in the summers of 2017 and
 2019, and extracted data from 52 tags. The associated .csv file exhibits
 the raw movement data extracted from the archival GPS tags, where each row
 represents a GPS fix location for a given bird. The columns present are
 largely those generated by Lotek, although researchers created a few
 columns to aid in identification of birds and downstream data analysis. Of
 particular note is the “season” column, where we quantified the likely
 behavior (e.g., fall migration) of the individual at the given time and
 location. These points essentially represent the migratory tracks from
 both fall and spring (when available), including both the breeding and
 wintering grounds location. We found that whip-poor-wills circumvented the
 Gulf of Mexico, and populations across a large latitudinal gradient came
 together in eastern Texas in early October, resulting in decreased
 connectivity throughout migration. Breeding-winter migratory connectivity
 was low (MC = 0.22 ± 0.12), with extensive overlap of core wintering areas
 in southern Mexico and Guatemala. See methods in manuscript for more info.
description: See ReadMe file and associated manuscript (including the
 supporting information).
description: See ReadMe file and associated manuscript (including the
 supporting information).
DOI: 10.5061/dryad.pc866t1pf
title: Safe traveling in public transport amid COVID-19

description: Several intense policies, such as mandatorily wearing masks and practicing
 social distancing, have been implemented in South Korea to prevent the
 spread of the novel coronavirus disease (COVID-19). In this study, we
 analyzed and measured the impact of the aforementioned policies by
 calculating the degree of infection exposure in public transportation.
 Specifically, we simulated how passengers encounter and infect each other
 during their journeys in public transportation by tracking movements of
 passengers. The probabilities of exposure to infections in public
 transportation were compared via a combination of the aforementioned
 policies by using the SEIR model, a respiratory infectious disease
 diffusion model. We determined that the mandatorily wearing of masks
 exhibits similar effects to maintaining social distancing 2 m in
 preventing COVID-19. During peak hours, in the cases of mandatorily
 wearing and practicing social distancing with masks, the reduction in
 infection rates corresponded to 93.5% and 98.1%, respectively.
DOI: 10.25338/b8gs7d
title: Phylogeny and secondary sexual trait evolution in Schizocosa wolf spiders (Araneae, Lycosidae) shows evidence for multiple gains and losses of ornamentation and species delimitation uncertainty

description: Members of the Nearctic spider genus Schizocosa Chamberlin, 1904 have
 garnered much attention in behavioral studies and over many decades, a
 number of species have developed as model systems for investigating
 patterns of sexual selection and multimodal communication. Many of these
 studies have employed a comparative approach using putative, but not
 rigorously tested, sister species pairs that have distinctive
 morphological traits and attendant behaviors. Despite past emphasis on the
 efficacy of these presumably comparative-based studies of closely related
 species, generating a robust phylogenetic hypothesis for Schizocosa has
 been an ongoing challenge. Here, we apply a phylogenomic approach using
 anchored hybrid enrichment to generate a data set comprising over 400 loci
 representing a comprehensive taxonomic sample of 23 Nearctic Schizocosa.
 Our sampling also includes numerous outgroup lycosid genera that allow for
 a robust evaluation of genus monophyly. Based on analyses using
 concatenation and coalescent-based methods, we recover a well-supported
 phylogeny that infers the following: 1) The New World Schizocosa do not
 form a monophyletic group; 2) Previous hypotheses of North American
 species require reconsideration along with the composition of species
 groups; 3) Multiple longstanding model species are not genealogically
 exclusive and thus are not “good” species; 4) This updated phylogenetic
 framework establishes a new working paradigm for studying the evolution of
 characters associated with reproductive communication and mating.
 Ancestral character state reconstructions show a complex pattern of
 homoplasy that has likely obfuscated previous attempts to reconstruct
 relationships and delimit species. Important characters presumably related
 to sexual selection, such as foreleg pigmentation and dense bristle
 formation, have undergone repeated gain and loss events, many of which
 have led to increased morphological divergence between sister-species.
 Evaluation of these traits in a comparative framework illuminates how
 sexual selection and natural selection influence character evolution and
 provides a model for future studies of multimodal communication evolution
 and function.
description: Anchored Hybrid Enrichment sequence data.
DOI: 10.5061/dryad.g1jwstqrh
title: Within-year and among-year variation in impacts of targeted conservation management on juvenile survival in a threatened population

description: 1. Overall impacts of targeted conservation interventions on population
 growth rate (λ) will depend on within-year and among-year variation in
 exposure of target individuals to interventions, and in intervention
 efficacy in increasing vital rates of exposed individuals. Juvenile
 survival is one key vital rate that commonly varies substantially within
 and among years, and consequently drives variation in λ. However,
 within-year, among-year and overall impacts of targeted interventions on
 population-wide survival probabilities of potentially mobile juveniles are
 rarely quantified, precluding full evaluation and evidence-based
 refinement of interventions. 2. We applied multi-state mark-recapture
 models to eight years of ring-resighting data from a threatened red-billed
 chough (Pyrrhocorax pyrrhocorax) population to quantify within-year and
 among-year variation in juvenile exposure to a targeted intervention of
 supplementary feeding and parasite treatment, and to estimate efficacy in
 increasing juvenile survival probability. We then combined and up-scaled
 these estimated effects to evaluate the impact of the eight-year
 intervention on overall population-wide survival probability and resulting
 population size. 3. High proportions of surviving juveniles (&gt;70%)
 were exposed to the intervention across the annual biological cycle in all
 years. Exposure was associated with higher short-term survival
 probabilities through the full annual cycle. Consequently, management
 increased estimated population-wide annual juvenile survival by
 approximately 0.14. However, such effects were only evident in cohorts
 with low overall annual survival. 4. Population models projected that
 these impacts on annual juvenile survival substantially reduced population
 decline, such that population size at the end of the eight-year
 intervention was approximately double that without management. 5.
 Synthesis and applications. Our results show how complex patterns of
 within-year and among-year variation in exposure and efficacy of targeted
 conservation interventions can arise and scale up to affect
 population-level outcomes. We demonstrate positive effects of a major
 intervention, but also highlight potential routes to improve efficacy, for
 example through more precise targeting of agricultural management actions
 in the context of among-year variation in environmental conditions.
DOI: 10.5061/dryad.jm63xsjbn
title: Phylogenetic diversity rankings in the face of extinctions: The robustness of the fair proportion index

description: Planning for the protection of species often involves difficult choices
 about which species to prioritize, given constrained resources. One way of
 prioritizing species is to consider their  "evolutionary
 distinctiveness'', i.e. their relative evolutionary isolation on
 a phylogenetic tree. Several evolutionary isolation metrics or
 phylogenetic diversity indices have been introduced in the literature,
 among them the so-called Fair Proportion index (also known as
 the  "evolutionary distinctiveness" score).
 This index apportions the total diversity of a tree among all leaves,
 thereby providing a simple prioritization criterion for
 conservation.  Here, we focus on the prioritization order
 obtained from the Fair Proportion index and analyze the effects of species
 extinction on this ranking. More precisely, we analyze the extent to which
 the ranking order may change when some species go extinct and the Fair
 Proportion index is re-computed for the remaining taxa. We show that for
 each phylogenetic tree, there are edge lengths such that the extinction of
 one leaf per cherry completely reverses the ranking. Moreover, we show
 that even if only the lowest ranked species goes extinct, the ranking
 order may drastically change.  We end by analyzing the effects of
 these two extinction scenarios (extinction of the lowest ranked species
 and extinction of one leaf per cherry) for a collection of empirical and
 simulated trees. In both cases, we can observe significant changes in the
 prioritization orders, highlighting the empirical relevance of our
 theoretical findings.
description: Identifiers retrieved from public database TreeBase; simulations
 run on computer algebra system Mathematica
DOI: 10.5061/dryad.6m905qg0s
title: The correlation between education levels and COVID-19 vaccination in Turkey

description: In this work, we investigated the correlation between education levels and
 COVID-19 vaccination in 36 cities in Turkey. We demonstrated if
 the percentage of people less educated than high school level
 increases, the percentage of unvaccinated people increases too. The
 correlation value between the percentage of people less educated
 than high school level and the percentage of unvaccinated people
 is 0.9198. The methods used are correlation
 matrix and linear regression.
description: Education levels data are collected from Turkish Statistical
 Institute, and vaccination percentage of the cities data are collected
 from the national public broadcaster of Turkey, Turkish Radio and
 Television Corporation.
description: Description of variables in the file: Cities
 contains 36 cities of Turkey. College_graduate contains
 the percentage of people who have at least a college degree
 or equivalent. High_school_graduate contains the
 percentage of people who have at least a high school diploma or
 equivalent. Less_than_high_school contains the
 percentage of people who are less educated than high school
 level. COVID-19_Vaccination contains the vaccination
 percentage of cities. Unvaccinated contains the
 percentage of unvaccinated people.