cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.8b5v2r6
title: Data from: How much does it cost to save a species from extinction? Costs and rewards of conserving the Lear’s macaw

description: Although the limited resources available to save species from extinction
 necessitate the optimization of conservation actions, little is known
 about their costs and effectiveness. We developed a costs-rewards
 framework that integrates information on which sectors of society
 contribute to funding conservation, how much is contributed, how funds are
 distributed among conservation targets, and how these investments drive
 not only conservation rewards but also the economic and ecosystem services
 that benefit society. We applied this framework to the Lear’s macaw
 (Anodorhynchus leari), a species discovered in the wild in 1978 with only
 60 individuals. Funds invested over the last 25 years reached US$ 3.66
 million. The contribution of governments, NGOs and private funders varied
 over time, as did the funding targets. Funds were proportionally invested
 to mitigate the main causes of mortality, while no funds were devoted to
 protecting foraging habitats. Conservation rewards were satisfactory, with
 the cost and time needed to downlist the species from Critically
 Endangered to Endangered similar to those invested in other bird species.
 However, economic rewards (through ecotourism and handicrafts linked to
 the conservation of the species) were low and require promotion, while
 ecosystem services provided by Lear’s macaws have yet to be quantified.
description: Birds
 DateSpreadsheet with birds
 number removed of nature by each threat.birds.csvEstimates Cost DatasSpreadsheet with conservation cost of Lear's Macaw.Data.xlsx
DOI: 10.5061/dryad.8hd6764
title: Data from: Beyond preference and performance: host plant selection by monarch butterflies, Danaus plexippus

description: The connection between adult preferences and offspring performance is
 long-standing issue in understanding the evolutionary and ecological
 forces that dictate host associations and specialization in herbivorous
 insects. Indeed, decisions made by females about where to lay their eggs
 have direct consequences for fitness and are influenced by interacting
 factors including offspring performance, defence, and competition.
 Nonetheless, in addition to these attributes of the offspring, a female’s
 choices may be affected by her own prior experience. Here we examined
 oviposition preference, larval performance, and the role of learning in
 the monarch butterfly, Danaus plexippus, which encounters diverse milkweed
 host species across its broad range and over the course of migration.
 Monarch females consistently preferred to oviposit on Asclepias incarnata
 subspecies pulchra. This plant, however, was associated with poor
 caterpillar growth, low sequestration of toxins, and the highest plant
 defences (latex and trichomes). We examined flexibility in this apparently
 maladaptive preference by testing the impact of previous experience and
 competition on preference. Experience laying on an alternative plant
 species enhanced preference for that species in contrast to A. i. pulchra.
 In addition, presence of a (competing) conspecific caterpillar on A. i.
 pulchra had a strongly deterrent effect and reversed host plant
 preferences. Thus, monarch butterflies exhibit preferences contrary to
 what would be expected based on offspring development and sequestered
 defences, but their preferences are altered by learning and competition,
 which may allow butterflies to shift preferences as they encounter diverse
 milkweeds across the landscape. Learning and perception of threats (i.e.,
 competition or predation) may be critical for most herbivorous insects,
 which universally experience heterogeneity among their potential host
 plants.
description: caterpillar_performancecompetition_ovipositionHPLC datalatex dataoviposition_experiencetrichome data
DOI: 10.5061/dryad.fk52454
title: Data from: Slower senescence in a wild insect population in years with a more female-biased sex ratio

description: Life-history theories of senescence are based on the existence of a
 trade-off in resource allocation between body maintenance and
 reproduction. This putative trade-off means that environmental and
 demographic factors affecting the costs of reproduction should be
 associated with changes in patterns of senescence. In many species,
 competition among males is a major component of male reproductive
 investment, and hence variation in the sex ratio is expected to affect
 rates of senescence. We test this prediction using nine years of
 demographic and behavioural data from a wild population of the annual
 field cricket Gryllus campestris. Over these generations the sex ratio at
 adulthood varied substantially, from years with an equal number of each
 sex to years with twice as many females as males. Consistent with the
 predictions of theory, we found that in years with a greater proportion of
 females, both sexes experienced a slower increase in mortality rate with
 age. Additionally, phenotypic senescence in males was slower in years when
 there were more females. Sex ratio did not affect the baseline mortality
 rate in males, but females suffered higher age-independent mortality rates
 when males were in short supply.
description: Capture-recapture
 datasetData on date of birth,
 data of death, and lifetime recaptures in a wild population of the field
 cricket Gryllus campestris with sex and population sex ratio as
 covariatesActuarialSenescence.csvPhenotypicSenescenceData on male calling activity with age for a wild population of Gryllus campestris with sex ratio as a covariate
DOI: 10.5061/dryad.pc3f9d8
title: Wildfires and climate change push low-elevation forests across a critical climate threshold for tree regeneration

description: Climate change is increasing fire activity in the western United States,
 which has the potential to accelerate climate-induced shifts in vegetation
 communities. Wildfire can catalyze vegetation change by killing adult
 trees that could otherwise persist in climate conditions no longer
 suitable for seedling establishment and survival. Recently documented
 declines in postfire conifer recruitment in the western United States may
 be an example of this phenomenon. However, the role of annual climate
 variation and its interaction with long-term climate trends in driving
 these changes is poorly resolved. Here we examine the relationship between
 annual climate and postfire tree regeneration of two dominant,
 low-elevation conifers (ponderosa pine and Douglas-fir) using annually
 resolved establishment dates from 2,935 destructively sampled trees from
 33 wildfires across four regions in the western United States. We show
 that regeneration had a nonlinear response to annual climate conditions,
 with distinct thresholds for recruitment based on vapor pressure deficit,
 soil moisture, and maximum surface temperature. At dry sites across our
 study region, seasonal to annual climate conditions over the past 20 years
 have crossed these thresholds, such that conditions have become
 increasingly unsuitable for regeneration. High fire severity and low seed
 availability further reduced the probability of postfire regeneration.
 Together, our results demonstrate that climate change combined with high
 severity fire is leading to increasingly fewer opportunities for seedlings
 to establish after wildfires and may lead to ecosystem transitions in
 low-elevation ponderosa pine and Douglas-fir forests across the western
 United States.
description: Plot data from:
 Wildfires and climate change push low-elevation forests across a critical
 climate threshold for tree regeneration This file contains
 annual recruitment rates for post-fire sites in Montana, Idaho, Colorado,
 New Mexico, Arizona, and California. The rates were determined by
 destructively sampling trees to age precisely at the root-shoot boundary
 (see manuscript for more details). Also included in this file is relevant
 site information. Davis_et_al_recruitment_plot_data.csv   Davis_et_al_climate_timeseries This file contains annual climate timeseries for each site for the climate variables used in the boosted regression tree models. See manuscript for detailed information about how climate data was obtained and/or modeled.     Davis_et_al_code This file contains the R code used in the analysis.   Davis_et_al_figure_code This file contains the R code used to make the figures in the manuscript.
DOI: 10.5061/dryad.q8kh0p9
title: Data from: The use and utility of surrogates in biodiversity monitoring programmes

description: Monitoring programmes are intended to inform effective biodiversity
 conservation and management (Legge et al. 2018). Well‐designed programmes
 can establish baseline conditions, determine trends in threatened species
 populations, quantify the effects of management, and provide warning of
 ecosystem changes (Magurran et al. 2010). For these reasons, biodiversity
 monitoring underpins the activities of land management agencies worldwide.
 However, it is not always possible to directly monitor key variables at
 ideal spatio‐temporal resolutions, due to resourcing or logistic
 constraints. For example, direct monitoring of koalas (Phascolarctos
 cinereus) can be cost‐ and time‐intensive as koalas are cryptic, occur at
 low densities, and are difficult to reliably observe in dense forest
 canopies (McAlpine et al. 2006).
description: Sato et
 al_JApplEcol_surrogate-workshop-dataThis data file includes
 two xls spreadsheets with the workshop data for Figure 1 and Table S1 of
 Sato,CF et al. The use and utility of surrogates in biodiversity
 monitoring programmes.Sato et
 al_2019_JApplEcol_surrogate-workshop-data.xls
DOI: 10.5061/dryad.8k1c2p1
title: Data from: A novel resistance gene for bacterial blight in rice, Xa43(t) identified by GWAS and confirmed by QTL mapping using a bi-parental population

description: Bacterial blight (BB) caused by the Xanthomonas oryzae pv. oryzae (Xoo)
 pathogen is a significant disease in most rice cultivation areas. The
 disease is estimated to cause annual rice production losses of 20–30
 percent throughout rice-growing countries in Asia. The discovery and
 deployment of durable resistance genes for BB is an effective and
 sustainable means of mitigating production losses. In this study QTL
 analysis and fine mapping were performed using an F2 and a BC2F2
 population derived from a cross with a new R-donor having broad spectrum
 resistance to Korean BB races. The QTL qBB11 was identified by composite
 interval mapping and explained 31.25% of the phenotypic variation (R2)
 with LOD values of 43.44 harboring two SNP markers. The single major
 R-gene was designated Xa43 (t). Through dissection of the target region we
 were able to narrow the region to within 27.83–27.95 Mbp, a physical
 interval of about 119-kb designated by the two flanking markers
 IBb27os11_14 and S_BB11.ssr_9. Of nine ORFs in the target region two ORFs
 revealed significantly different expression levels of the candidate genes.
 From these results we developed a marker specific to this R-gene, which
 will have utility for future BB resistance breeding and/or R-gene
 pyramiding using marker assisted selection. Further characterization of
 the R-gene would be helpful to enhance understanding of mechanisms of BB
 resistance in rice.
description: Genotypic data used for
 GAPIT analysisThis file contains the
 genotypic data used for the GAPIT genome wide association
 analysis.GAPIT_mdp_genotype_test.hmp.txtGAPIT trait score for the core 120 Japonica MAGIC linesFor each or the Japonica MAGIC lines in the core set of 120 lines, these are the reactions to BB inoculationGAPIT_trait core 120.xlsxGenotypic data for the F2 mapping populationThese are the genotypic data for the F2 mapping populationICIM genotype data RiceF2P8.xlsxPhenotypic data for the F2 populationThis file contains the phenotypic data (lesion length after inoculation) of the F2 populations used for Composite Interval Mapping analysisICIM phenotype data RiceF2P8IP.xlsx
DOI: 10.6084/m9.figshare.31158115
title: Supplementary Materials

description: This item contains supplementary figures and tables supporting the findings of the associated manuscript.
DOI: 10.6084/m9.figshare.31158115.v1
title: Supplementary Materials

description: This item contains supplementary figures and tables supporting the findings of the associated manuscript.
DOI: 10.5061/dryad.p7410jm
title: Data from: Habitat use of the ocelot (Leopardus pardalis) in Brazilian Amazon

description: Amazonia forest plays a major role in providing ecosystem services for
 human and sanctuaries for wildlife. However, ongoing deforestation and
 habitat fragmentation in the Brazilian Amazon has threatened both. The
 ocelot is an ecologically important mesopredator and a potential
 conservation ambassador species, yet there are no previous studies on its
 habitat preference and spatial patterns in this biome. From 2010 to 2017,
 twelve sites were surveyed, totaling 899 camera trap stations, the largest
 known dataset for this species. Using occupancy modeling incorporating
 spatial autocorrelation, we assessed habitat use for ocelot populations
 across the Brazilian Amazon. Our results revealed a positive sigmoidal
 correlation between remote‐sensing derived metrics of forest cover,
 disjunct core area density, elevation, distance to roads, distance to
 settlements and habitat use, and that habitat use by ocelots was
 negatively associated with slope and distance to river/lake. These
 findings shed light on the regional scale habitat use of ocelots and
 indicate important species–habitat relationships, thus providing valuable
 information for conservation management and land‐use planning.
description: Data folder for habitat
 use of the ocelotCovariates for all
 camera trap stations of ocelots; detection history matrics; camera
 trapping effortsdata.zip
DOI: 10.5061/dryad.k59bc2m
title: Data from: Human plague system associated with rodent diversity and other environmental factors

description: Plague remains a threat to public health and is considered as a
 re-emerging infectious disease today. Rodents play an important role as
 major hosts in plague persistence and driving plague outbreaks in natural
 foci; however, few studies have tested the association between host
 diversity in ecosystems and human plague risk. Here we use Zero-Inflated
 Generalized Additive Models to examine the association of species richness
 with human plague presence (where plague outbreaks could occur) and
 intensity (the average number of annual human cases when they occurred) in
 China during the Third Pandemic. We also account for transportation
 network density, annual precipitation levels, and human population size.
 We found rodent species richness, particularly of rodent plague hosts, is
 positively associated with the presence of human plague. Further
 investigation shows that species richness of both wild and commensal
 rodent plague hosts are positively correlated with the presence, but only
 the latter correlated with the intensity. Our results indicated a positive
 relationship between rodent diversity and human plague, which may provide
 suggestions for the plague surveillance system.
description: Data for GAM
 analysisData.csvCodes for GAM analysisModel.Code.R
DOI: 10.5061/dryad.6vq2mp0
title: Data from: Defining host–pathogen interactions employing an artificial intelligence workflow

description: For image-based infection biology, accurate unbiased quantification of
 host–pathogen interactions is essential, yet often performed manually or
 using limited enumeration employing simple image analysis algorithms based
 on image segmentation. Host protein recruitment to pathogens is often
 refractory to accurate automated assessment due to its heterogeneous
 nature. An intuitive intelligent image analysis program to assess host
 protein recruitment within general cellular pathogen defense is lacking.
 We present HRMAn (Host Response to Microbe Analysis), an open-source image
 analysis platform based on machine learning algorithms and deep learning.
 We show that HRMAn has the capacity to learn phenotypes from the data,
 without relying on researcher-based assumptions. Using Toxoplasma gondii
 and Salmonella enterica Typhimurium we demonstrate HRMAn’s capacity to
 recognize, classify and quantify pathogen killing, replication and
 cellular defense responses. HRMAn thus presents the only intelligent
 solution operating at human capacity suitable for both single image and
 high content image analysis.
description: GBP
 recruitmentThis dataset can be used
 to study recruitment of murine Gbps to Toxoplasma vacuoles using HRMAn. A
 description of the dataset and an instruction on how to use it can be
 found in the README file contained in the archive.GBP_recruitment.zipInterferon titration A549 cellsThis dataset can be used to study the effect of IFNg treatment on Toxoplasma replication in human A549 cells using HRMAn. A description of the dataset and an instruction on how to use it can be found in the README file contained in the archive.Interferon_titration_A549_cells.zipProtein translocationThis dataset can be used to study translocation of Toxoplasma effector proteins to the nucleus of the infected host cell using HRMAn. A description of the dataset and an instruction on how to use it can be found in the README file contained in the archive.Protein_translocation.zipSalmonella ubiquitinationThis dataset can be used to study ubiquitination of Salmonella enterica Typhimurium in HeLa cells using HRMAn. A description of the dataset and an instruction on how to use it can be found in the README file contained in the archive.Salmonella_ubiquitination.zip
DOI: 10.5281/zenodo.18350586
title: KEYS_BRAND7_450F_8_23C_0k_EDLC_single
DOI: 10.5281/zenodo.18350585
title: KEYS_BRAND7_450F_8_23C_0k_EDLC_single
DOI: 10.5061/dryad.sv2j191
title: Data from: Nonlinearity of root trait relationships and the root economics spectrum

description: The root economics spectrum (RES), a common hypothesis postulating a
 tradeoff between resource acquisition and conservation traits, is being
 challenged by conflicting relationships between root diameter, tissue
 density (RTD) and root nitrogen concentration (RN). Here, we analyze a
 global trait dataset of absorptive roots for over 800 plant species. For
 woody species (but not for non-woody species), we find nonlinear
 relationships between root diameter and RTD and RN, which stem from the
 allometric relationship between stele and cortical tissues. These
 nonlinear relationships explain how sampling bias from different ends of
 the nonlinear curves can result in conflicting trait relationships.
 Further, the shape of the relationships varies depending on evolutionary
 context and mycorrhizal affiliation. Importantly, the observed nonlinear
 trait relationships do not support the RES predictions. Allometry-based
 nonlinearity of root trait relationships improves our understanding of the
 ecology, physiology and evolution of absorptive roots.
description: Average mass for the
 first order rootsThis dataset includes
 average dry mass for the first order roots of 96 woody species. These
 species are the same as those in our previous published paper, i.e., Kong
 et al. (2014) Leading dimensions in absorptive root trait variation across
 96 subtropical forest species. New Phytologist 203:
 863-872.Source
 Data.xlsx
DOI: 10.5061/dryad.m29k410
title: Data from: Seasonal climate effects on the survival of a hibernating mammal

description: Global climate change and associated regional climate variability is
 impacting the phenology of many species, ultimately altering individual
 fitness and population dynamics. Yet, few studies have considered the
 effects of pertinent seasonal climate variability on phenology and
 fitness. Hibernators may be particularly susceptible to changes in
 seasonal climate since they have a relatively short active season in which
 to reproduce and gain enough mass to survive the following winter. To
 understand whether and how seasonal climate variability may be affecting
 hibernator fitness, we estimated survival from historical (1964-1968) and
 contemporary (2014-2017) mark-recapture data collected from the same
 population of Uinta ground squirrels (UGS, Urocitellus armatus), a
 hibernator endemic to the western United States. Despite a locally warming
 climate, the phenology of UGS did not change over time, yet
 season-specific climatic variables were important in regulating survival
 rates. Specifically, older age classes experienced lower survival when
 winters or the following spring were warm, while juveniles benefited from
 warmer winter temperatures. Although metabolic costs decrease with
 decreasing temperature in the hibernacula, arousal costs increase with
 decreasing temperature. Our results suggest that this trade-off is
 experienced differently by immature and mature individuals. We also
 observed an increase in population density during that time period,
 suggesting resources are less limited today than they used to be.
 Cheatgrass is now dominating the study site and may provide a better food
 source to UGS than native plants did historically.
description: E&E_CMR_Code_CleanedCMR code
DOI: 10.5061/dryad.6gt88dv
title: Data from: Early predictors of outcomes of hospitalization for cirrhosis and assessment of the impact of race and ethnicity at safety-net hospitals

description: Background. Safety-net hospitals provide care for racially/ethnically
 diverse and disadvantaged urban populations. Their hospitalized patients
 with cirrhosis are relatively understudied and may be vulnerable to poor
 outcomes and racial/ethnic disparities. Aims. To examine the outcomes of
 patients with cirrhosis hospitalized at regionally diverse safety-net
 hospitals and the impact of race/ethnicity. Methods. A study of patients
 with cirrhosis hospitalized at 4 safety-net hospitals in 2012 was
 conducted. Demographic, clinical factors, and outcomes were compared
 between centers and racial/ethnic groups. Study endpoints included
 mortality and 30-day readmission. Results. In 2012, 733 of 1,212 patients
 with cirrhosis were hospitalized for liver-related indications (median age
 55 years, 65% male). The cohort was racially diverse (43% White, 25%
 black, 22% Hispanic, 3% Asian) with cirrhosis related to alcohol and viral
 hepatitis in 635 (87%) patients. Patients were hospitalized mainly for
 ascites (35%), hepatic encephalopathy (20%) and gastrointestinal bleeding
 (GIB) (17%). Fifty-four (7%) patients died during hospitalization and 145
 (21%) survivors were readmitted within 30 days. Mortality rates ranged
 from 4 to 15% by center (p=.007 ) and from 3 to 10% by race/ethnicity
 (p=.03), but 30-day readmission rates were similar. Mortality was
 associated with Model for End-stage Liver Disease (MELD), acute-on-chronic
 liver failure, hepatocellular carcinoma, sodium and white blood cell
 count. Thirty-day readmission was associated with MELD and Charlson
 Comorbidity Index &gt;4, with lower risk for GIB. We did not observe
 geographic or racial/ethnic differences in hospital outcomes in the
 risk-adjusted analysis. Conclusions. Hospital mortality and 30-day
 readmission in patients with cirrhosis at safety-net hospitals are
 associated with disease severity and comorbidities, with lower
 readmissions in patients admitted for GIB. Despite geographic and
 racial/ethnic differences in hospital mortality, these factors were not
 independently associated with mortality.
description: Hospitalized cirrhosis
 databasePlease see README.xlsx
 file for variable definitions.PONE-D-18-29048R1_data_file.csvREADME