cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.pnvx0k6hg
title: The Relationship between Obesity-Related Factors and Graves' Orbitopathy

description: Background/Objectives: The aim of this study was to investigate whether
 there are relationships between obesity-related factors including body
 mass index (BMI), diabetes or prediabetes, hyperlipidemia, fasting plasma
 glucose, fasting plasma insulin, homeostasis model assessment-estimated
 insulin resistance (HOMA-IR), and high sensitive C-reactive protein
 (hs-CRP) and Graves’ orbitopathy (GO). Subjects/Methods: Eighty-four
 patients with Graves’ disease (GD) (42 without GO and 42 with GO) were
 enrolled in this Cross-sectional cohort study. Sex, age, GD treatment
 history, height, body weight, waist circumference, smoking status,
 co-morbidities, and levels of free thyroxin, thyroid-stimulating hormone,
 thyroid-stimulating hormone receptor (TSHR) antibodies, fasting plasma
 glucose and insulin, and hs-CRP were recorded. Eye condition was evaluated
 using the NOSPECS classification and clinical activity score. Results:
 BMI, fasting plasma insulin, and HOMA-IR were associated with the presence
 of GO after adjusting for age, sex, smoking, TSHR antibodies, and steroid
 usage (adjusted odd’s ratio〔OR〕1.182, 95% confidence interval (95% CI),
 1.003-1.393, p=0.046; adjusted OR 1.165, 95% CI, 1.001-1.355, p=0.048; and
 adjusted OR 1.985, 95% CI, 1.046-3.764, p=0.036, respectively). In
 addition, BMI, fasting plasma glucose, fasting plasma insulin, HOMA-IR,
 and hs-CRP levels were positively correlated with the severity of GO
 (Spearman’s rho=0.285, p=0.009; Spearman’s rho=0.298, p=0.006; Spearman’s
 rho=0.243, p=0.026; Spearman’s rho=0.270, p=0.013; and Spearman’s
 rho=0.299, p=0.006, respectively). Conclusion: The findings of this study
 suggest that obesity and obesity-related factors, and especially fasting
 plasma insulin and HOMA-IR are related to GO.
description: Eighty-four patients with Graves’ disease (GD) (42 without GO and
 42 with GO) were enrolled in this Cross-sectional cohort study. Sex, age,
 GD treatment history, height, body weight, waist circumference, smoking
 status, co-morbidities, and levels of free thyroxin, thyroid-stimulating
 hormone, thyroid-stimulating hormone receptor (TSHR) antibodies, fasting
 plasma glucose and insulin, and hs-CRP were recorded. Eye condition was
 evaluated using the NOSPECS classification and clinical activity
 score.
description: BMI: body mass index central obesity: 0= no,
 1=yes treatment period of GD(Graves' disease):
 years DM(diabetes mellitus)+preDM: 0= no,
 1=yes H/T(hypertension): 0= no, 1=yes
 
 hyperlipidemia smoking(broad speaking) steroid usage anti-thyroid drug(1=yes) thyroidectomy(1=yes) I131 thyroid dysfuction(1=yes) TSH R Ab(thyroid-stimulating hormone receptor antibodies):% thyroid-stimulating hormone receptor: mg/dL insulin:uIU/mL HOMA-IR(homeostasis model assessment-estimated insulin resistance) hs-CRP(high sensitive C-reactive protein) CAS(clinical activity score) GO(Graves' ophthalmopathy)
DOI: 10.5061/dryad.9ghx3ffd4
title: Back to the brink: phylogeography and demographic history of the endangered Torreya jackii

description: Both natural and anthropogenic factors can negatively affect species
 demography and even lead to species extinction, but their relative
 importance in driving species rarity remains poorly understood. To this
 end, we investigated the phylogeography and demographic history of the
 endemic endangered conifer species Torreya jackii. We collected samples
 from all the 13 extant wild populations, and analyzed the genetic
 variation using 8 nuclear microsatellites and 4 chloroplast and 1
 mitochondrial DNA fragments. Low genetic and nucleotide diversity was
 revealed, which could explain the absence of spatial and phylogeographic
 structure. Using a hierarchical approximate Bayesian computation
 technique, we identified the demographic scenario that best fit with the
 genetic data, where the effective population size of the plant was low at
 least 200,000 years ago but expanded after the last glacial maximum (LGM).
 The scenarios accounting for population decline during the LGM had
 significantly smaller posterior probabilities, suggesting in situ survival
 of this species during the LGM. The palaeoclimatic niche model revealing a
 profound impact of precipitation on the distribution of T. jackii also
 predicted that the current distribution areas were suitable during the
 LGM. Although the post-LGM expansion pulled T. jackii from the brink of
 long-term rarity, the best-supported scenario nevertheless indicated
 population collapse during recent centuries with a population size
 reduction by more than 80%, bringing the plant back to the brink. Our
 study thus sheds light on how historical factors and human impacts jointly
 threaten the persistence of species and should be considered in
 biodiversity conservation.
DOI: 10.5061/dryad.8pk0p2nhz
title: Data from: Altitude shapes the environmental drivers of large-scale variation in abundance of a widespread mammal species

description: Habitat quality and heterogeneity directly influence the distribution and
 abundance of organisms at different spatial scales. Determining the main
 environmental factors driving the variation in species abundance is
 crucial to understand the underlying ecological processes and this is
 especially important for widely distributed species living in contrasting
 environments. However, the responses to environmental variation are
 usually described at relatively small spatial scales. Here, we studied the
 variation in abundance of a widely distributed mustelid, the European
 badger (Meles meles), across France. We used (1) direct detections of
 9,439 dead and living badgers, from 2006 to 2009, to estimate badger
 relative abundance in 703 small agricultural regions of metropolitan
 France and (2) a Bayesian modelling approach to identify the main
 environmental determinants influencing badger abundance. Despite a
 continuous distribution of badger in France, we found large variation in
 badger abundance between regions, explained by environmental factors.
 Among a set of 13 environmental variables, we demonstrated that badger
 abundance in lowlands (&lt; 400 m a.s.l.) was mostly driven by biotic
 factors such as potential food resources (earthworm abundance and fruits
 crops) and forest fragmentation. Conversely, in mountainous areas, abiotic
 factors (i.e. soil texture and climate) drove the variation in badger
 relative abundance. These results underline the importance of mapping the
 abundance of wildlife species based on environmental suitability, and
 highlight the complexity of drivers influencing species abundance at such
 large spatial scales. Altitude shaped the environmental drivers (biotic
 vs. abiotic) that most influenced relative abundance of a widespread
 species. In the case of badger, such abundance maps are crucial to
 identify critical areas for species management as this mustelid is a main
 wild vector of bovine tuberculosis in several countries.
description: <strong>Jacquier_etal_ECE_Detections.txt</strong> Column 1 : identification number of the French department, Column 2 : year of the observation, Column 3 : species latin name, Column 4 : status dead (D) or alive (L), Column 5 : identification number of the small agricultural region, Column 6 : identification number of the car <strong>Jacquier_etal_ECE_Cars.txt</strong> Column 1 : identification number of the car, Column 2 : year, Column 3 : identification number of the French department, Column 4 : kilometers travelled with the car
DOI: 10.5061/dryad.v41ns1rrp
title: Data from: The Chord-Normalized Expected Species Shared (CNESS)-distance represents a superior measure of species turnover patterns

description: 1.    Measures of β-diversity characterizing
 the difference in species composition between samples are commonly used in
 ecological studies. Nonetheless, commonly used dissimilarity measures
 require high sample completeness, or at least similar sample sizes between
 samples. In contrast, the Chord-Normalized Expected Species Shared (CNESS)
 dissimilarity measure calculates the probability of collecting the same
 set of species in random samples of a standardized size, and hence is not
 sensitive to completeness or size of compared samples. To date, this index
 has enjoyed limited use due to difficulties in its calculation and
 scarcity of studies systematically comparing it with other measures.
 2.    Here, we developed a novel R function
 that enables users to calculate ESS (Expected Species Shared)-associated
 measures. We evaluate the performance of the CNESS index based on
 simulated datasets of known species distribution structure, and compared
 CNESS with more widespread dissimilarity measures (Bray-Curtis index,
 Chao-Sørensen index, and proportionality based Euclidean distances) for
 varying sample completeness and sample sizes. 3.  
  Simulation results indicated that for small sample size (m)
 values, CNESS chiefly reflects similarities in dominant species, while
 selecting large m values emphasizes differences in the overall species
 assemblages. Permutation tests revealed that CNESS has a consistently low
 CV (coefficient of variation) even where sample completeness varies, while
 the Chao-Sørensen index has a high CV particularly for low sampling
 completeness. CNESS distances are also more robust than other indices with
 regards to undersampling, particularly when chiefly rare species are
 shared between two assemblages. 4.    Our
 results emphasize the superiority of CNESS for comparisons of samples
 diverging in sample completeness and size, which is particularly important
 in studies of highly mobile and species-rich taxa where sample
 completeness is often low. Via changes in the sample size parameter m,
 CNESS furthermore cannot only provide insights into the similarity of the
 overall distribution structure of shared species, but also into the
 differences in dominant and rare species, hence allowing additional,
 valuable insights beyond the capability of more widespread measures.
  
description: <strong>ESS.R</strong> R scripts
 to calculate the Expected Species Shared (ESS)-associated dissimilarity
 measures
 <strong>Simulation.R</strong>
 Simulation R scripts
DOI: 10.3886/e244688v1
title: Kurt ve 7 Küçük Keçi

description: Kurt ve 7 Küçük Keçi
DOI: 10.5061/dryad.nzs7h44ms
title: The amount of RNA editing sites in liverwort organellar genes is correlated with GC content and nuclear PPR protein diversity

description: RNA editing occurs in the organellar mRNAs of all land plants but the
 marchantioid liverworts, making liverworts a perfect group for studying
 the evolution of RNA editing. Here we profiled the RNA editing of 42
 exemplars spanning the ordinal phylogenetic diversity of liverworts, and
 screened for the nuclear-encoded PPR proteins in the transcriptome
 assemblies of these taxa. We identified 7,428 RNA editing sites in 128
 organellar genes from 31 non-marchantioid liverwort species, and
 characterized 25,059 PPR protein sequences. The abundance of organellar
 RNA editing sites varies greatly among liverwort lineages, genes, and
 codon positions, and shows strong positive correlations with the GC
 content of protein-coding genes, and the diversity of the PLS class of
 nuclear PPR proteins.
DOI: 10.5061/dryad.xwdbrv193
title: Links between prey assemblages and poison frog toxins: a landscape ecology approach to assess how biotic interactions affect species phenotypes

description: Ecological studies of species pairs showed that biotic interactions
 promote phenotypic change and eco-evolutionary feedbacks. However, it is
 unclear how phenotypes respond to synergistic interactions with multiple
 taxa. We investigate whether interactions with multiple prey species
 explain spatially structured variation in the skin toxins of the
 Neotropical poison frog Oophaga pumilio. Specifically, we assess how
 dissimilarity (i.e., beta diversity) of alkaloid-bearing arthropod prey
 assemblages (68 ant species) and evolutionary divergence between frog
 populations (from a neutral genetic marker) contribute to frog poison
 dissimilarity (toxin profiles composed of 230 different lipophilic
 alkaloids sampled from 934 frogs at 46 sites). We find that models that
 incorporate spatial turnover in the composition of ant assemblages explain
 part of the frog alkaloid variation, and we infer unique alkaloid
 combinations across the range of O. pumilio. Moreover, we find that
 alkaloid variation increases weakly with the evolutionary divergence
 between frog populations. The analytical framework proposed here can be
 extended to other multi-trophic systems, coevolutionary mosaics, microbial
 assemblages, and ecosystem services.
DOI: 10.5061/dryad.vmcvdncp8
title: Healthy lifestyle and the risk of Alzheimer's dementia: Findings from two longitudinal studies

description: Objective To quantify the impact of a healthy lifestyle on the risk of
 Alzheimer's dementia. Methods Using data from the Chicago Health and
 Aging Project (CHAP n=1,845) and the Rush Memory and Aging Project (MAP
 n=920), we defined a healthy lifestyle score on the basis of non-smoking,
 &gt;=150 min/week moderate/vigorous intensity physical activity,
 light-to-moderate alcohol consumption, high-quality MIND diet (upper 40%),
 and engagement in late-life cognitive activities (upper 40%), giving an
 overall score ranging from 0 to 5. Cox proportional hazard models were
 used for each cohort to estimate the hazard ratio (HR) and 95% confidence
 interval (95%CI) of the lifestyle score with Alzheimer’s dementia and a
 random effect meta-analysis was used to pool the results. Results During a
 median follow-up of 5.8 years in CHAP and 6.0 years in MAP, 379 and 229
 participants, respectively had incident Alzheimer's dementia. In
 multivariable-adjusted models, the pooled HR (95%CI) of Alzheimer’s
 dementia across two cohorts was 0.73 (95%CI, 0.66-0.80) per each
 additional healthy lifestyle factor. Compared to participants with 0-1
 healthy lifestyle factor, the risk of Alzheimer’s dementia was 37% lower
 (pooled HR 0.63; 95%CI, 0.47-0.84) in those with 2-3 healthy lifestyle
 factors, and 60% lower (pooled HR 0.40; 95%CI, 0.28-0.56) in those with
 4-5 healthy lifestyle factors.  Conclusion A healthy lifestyle as
 a composite score is associated with a substantially lower risk of
 Alzheimer’s dementia.
description: Data File Contents <strong>Table 1</strong>: Contribution of healthy lifestyle factors to the score (<em>Update 5/5/23: Corrected the labeling for the MAP study</em>). <strong>Table 2:</strong> Hazard ratios of Alzheimer’s dementia according to the adherence to healthy lifestyle factors in adjusted model for cardiovascular risk factors. <strong>Table 3:</strong> Hazard ratios of Alzheimer’s dementia according to the adherence to healthy lifestyle factors in adjusted model for depressive symptoms (CESD score). <strong>Table 4:</strong> Hazard ratios of Alzheimer’s dementia according to the adherence to healthy lifestyle factors in excluding events during 2.5 years of follow-up. <strong>Table 5:</strong> Hazard ratios of Alzheimer’s dementia according to the adherence to healthy lifestyle factors in excluding events after 10 years of follow-up. <strong>Table 6:</strong> Hazard ratios of Alzheimer’s dementia according to the adherence to healthy lifestyle factors in the score without light-to-moderate alcohol intake. <strong>Table 7:</strong> Hazard ratios of Alzheimer’s dementia according to the adherence to healthy lifestyle factors in the score with never smokers are in a healthy category. <strong>Table 8:</strong> Hazard ratios of Alzheimer’s dementia according to the adherence to healthy lifestyle factors by race among APOE e4 allele carriers in CHAP. <strong>Table 9:</strong> Characteristics of the CHAP study populations at the baseline. Data are weighted for the stratified random sampling
DOI: 10.5061/dryad.k6djh9w36
title: Data from: Understory diversity and composition after planting of teak and mahogany in Yogyakarta, Indonesia

description: Forest rehabilitation is when a desired tree species is planted in
 degraded forests or lands. Rehabilitation by planting a single tree
 species is a common way to restore exploited forests to maintain
 ecological processes. We compared woody and herbaceous understory
 vegetation between forests rehabilitated by mahogany (N = 12) or teak (N =
 12) planted from 1941 until 2003 in Yogyakarta, Indonesia. Understory
 vegetation of these areas were compared with that of three native forests.
 Species richness, species diversity, density of plants and proportion of
 native plants did not differ between the rehabilitated areas and the
 native forest. Recently rehabilitated areas were different from the native
 forests while 41-74 years after rehabilitation, characteristics of
 understory vegetation approached those of native forest. We described
 species composition using ordination, and found it to differ between areas
 rehabilitated with teak and with mahogany and, particularly, between the
 rehabilitated areas and the native forests. Time since rehabilitation and
 tree species planted were important for the species composition of
 understory vegetation. We conclude that the selection of species for
 rehabilitation and letting rehabilitated areas mature are important for
 understory development and species diversity.
DOI: 10.5061/dryad.pk0p2nghr
title: Data from: Molecular responses to freshwater limitation in the mangrove tree Avicennia germinans (Acanthaceae)

description: Environmental variation along the geographical space can shape populations
 by natural selection. In the context of global warming and changing
 precipitation regimes, it is crucial to understand the role of
 environmental heterogeneity in tropical trees adaptation, given their
 disproportional contribution to water and carbon biogeochemical cycles.
 Here, we investigated how heterogeneity in freshwater availability along
 tropical wetlands has influenced molecular variations of the Black
 Mangrove (Avicennia germinans). Fifty-seven trees were sampled in seven
 sites differing markedly in precipitation regime and riverine freshwater
 inputs. Using 2,297 genome-wide single nucleotide polymorphic markers, we
 found signatures of natural selection by the association between
 variations in allele frequencies and environmental variables, including
 the precipitation of the warmest quarter and annual precipitation.
 Additionally, we found candidate loci for selection based on statistical
 deviations from neutral expectations of interpopulation genetic
 differentiation. Most candidate loci within transcribed sequences were
 functionally associated with central aspects of drought-tolerance or plant
 response to drought. Moreover, our results suggest the occurrence of rapid
 evolution of a population, likely in response to sudden and persistent
 limitation in plant access to soil water, following a road construction in
 1974. Observations supporting rapid evolution included the reduction in
 tree size and changes in allele frequencies and in transcripts expression
 levels associated with increased drought-tolerance, through accumulation
 of osmoprotectants and antioxidants, biosynthesis of plant cuticle,
 protection against stress-induced proteins degradation, stomatal closure,
 photorespiration and photosynthesis. We describe a major role of spatial
 heterogeneity in freshwater availability in the specialization of this
 typically tropical tree. 
description: Here, we provide the SNP genotype dataset used for all population
 genetics analyses performed in our study. Our genotype dataset is
 available in *.raw format, along with its complementary text file,
 containing all samples identification. Additionally, we provide an R
 script describing all the criteria we used to assemble this *.raw genotype
 dataset from the original *.vcf file received from the SNPsaurus
 sequencing facility, which has performed the next-RAD sequencing of
 <em>Avicennia germinans</em> samples from the North-Northeast
 Brazilian coastline. Moreover, this R script contains the command
 lines used to perform genetic structure analyses and to export the SNP
 genotype dataset to different formats required to run all the analyses
 described in our study.
DOI: 10.5061/dryad.rbnzs7h76
title: Sociality and tattoo skin disease among bottlenose dolphins in Shark Bay, Australia

description: Social behavior is an important driver of infection dynamics, though
 identifying the social interactions that foster infectious disease
 transmission is challenging. Here we examine how social behavior impacts
 disease transmission in Indo-Pacific bottlenose dolphins (Tursiops
 aduncus) using an easily identifiable skin disease and social network
 data. We analyzed tattoo skin disease (TSD) lesions based on photographs
 collected as part of a 34-year longitudinal study in relation to the
 sociality of T. aduncus using three metrics (degree, time spent
 socializing, and time in groups) and network structure, using the k-test.
 We show that calves with TSD in the second year of life associated more
 with TSD-positive individuals in the first year of life compared with
 calves that did not have TSD. Additionally, the network k-test showed that
 the social network links are epidemiologically relevant for transmission.
 However, degree, time spent in groups, and time spent socializing were not
 significantly different between infected and uninfected groups. Our
 findings indicate that association with infected individuals is predictive
 of an individual’s risk for TSD and that the social association network
 can serve as a proxy for studying the epidemiology of skin diseases in
 bottlenose dolphins.
description: Data was collected in Monkey Mia, Western Australia from boat
 based observations. Data presented here as been limited in accordance with
 the linked publication and identifiers have been removed.
DOI: 10.5281/zenodo.18393965
title: Data Repository: Stabilizing Pd catalysts for liquid-phase hydrogenation of N-heterocyclic hydrogen carriers through zeolite encapsulation
title: Data Repository
DOI: 10.5281/zenodo.18393964
title: Data Repository: Stabilizing Pd catalysts for liquid-phase hydrogenation of N-heterocyclic hydrogen carriers through zeolite encapsulation
title: Data Repository
DOI: 10.5061/dryad.2jm63xsjv
title: Data from: Spatial and temporal patterns of environmental DNA detection to inform sampling protocols in lentic and lotic systems

description: The development of efficient sampling protocols for the capture of
 environmental DNA (eDNA) could greatly help improve accuracy of occupancy
 monitoring for species that are difficult to detect. However, the process
 of developing a protocol in situ is complicated for rare species by the
 fact that animal locations are often unknown. We tested sampling designs
 in lake and stream systems to determine the most effective eDNA sampling
 protocols for two rare species: the Sierra Nevada yellow-legged frog (Rana
 sierrae) and the foothill yellow-legged frog (R. boylii). We varied water
 volume, spatial sampling, and seasonal timing in lakes and streams; in
 lakes we also tested multiple filter types. We found that filtering 2 L
 versus 1 L increased the odds of detection in streams 5.42X (95% CI:
 3.2-9.19X) in our protocol, from a probability of 0.51 to 0.85 per
 technical replicate. Lake sample volumes were limited by filter clogging
 and we found no effect of volume or filter type. Sampling later in the
 season increased the odds of detection in streams by 1.96X for every 30
 days (95% CI: 1.3 - 2.97X) but there was no effect for lakes. Spatial
 autocorrelation of the quantity of yellow-legged frog eDNA captured in
 streams between 100 and 200 m, indicating that sampling at close intervals
 is important.