cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.4f4qrfj7w
title: Arsenic (+3 oxidation state) methyltransferase gene polymorphisms and expression on bladder cancer

description: Inorganic arsenic (iAs) is a recognized environment-related factor for
 bladder cancer (BCa). Arsenic (+3 oxidation state) methyltransferase
 (AS3MT) gene might influence BCa by regulating iAs
 metabolism. The objectives of the present study were to systematically
 review eligible case-control studies about
 AS3MT polymorphisms and BCa and to
 further compare the genotype distribution and allele distribution
 between BCa patients and controls by meta-analysis for humans. Besides, to
 clarify the effects of AS3MT expression on BCa clinical outcomes and
 survival time, we also conducted a series of analyses based on The Cancer
 Genome Atlas (TCGA) dataset. Databases were systematically retrieved and
 we applied Stata software to perform meta-analysis. The registration of
 this study protocol is at PROSPERO and ID is CRD42019133947. Five
 articles were recruited and pooled results demonstrated
 that rs3740393 and rs11191438 polymorphisms were related to BCa
 risk in overall population (P&lt;0.05) in the overall
 population. In addition, GG and GC genotypes in rs3740393 and GG
 genotype in rs11191438 might be the susceptibility genotypes for BCa.
 Results based on 168 BCa samples from TGCA indicated that
 patients with higher expression of AS3MT had poor overall
 survival time and AS3MT expression is an
 independent indicator for BCa survival. This study
 identified that AS3MT polymorphisms could affect BCa
 risk and AS3MT expression was pivotal in prognosis of BCa.
DOI: 10.5061/dryad.73n5tb2t3
title: Data from: Social determinants of food group consumption based on Mediterranean diet pyramid: a cross-sectional study of university students

description: Considering food habits as a modifiable risk factor, an early intervention
 on youth people could avoid future health and social costs. We aim to
 determine the level of compliance with the recommendations of the
 Mediterranean diet pyramid according to social determinants in university
 students and to analyse the association of these social determinants (and
 their interaction with gender) with different food group consumption. We
 used the records of an electronic cross-sectional survey on university
 students (n=593) from inland Spain. The results show, generally, that
 university students do not fully comply with the recommendations and that
 gender is the social determinant with the greatest effect on differences
 in food group consumption. Women have a lower consumption of dairy
 products, olives, nuts and seeds, red meat, and processed meat, sweets,
 eggs, alcoholic drinks and fast food; and a higher consumption of fruit,
 compared with men. Socioeconomic status, geographic area, and whether
 students cook for themselves have a limited influence on differences in
 food group consumption, which is inconsistent with the literature. Policy
 makers should consider this gender gap if they wish to implement a policy
 based on healthy diet, considering that other social determinants are also
 important, and could interact with gender.
description: This study was conducted in the Autonomous Community of
 Castilla-La Mancha, located in central Spain. Students from the University
 of Castilla-La Mancha in the cities of Albacete, Ciudad Real, Cuenca,
 Talavera de la Reina and Toledo participated in the study. We conducted an
 electronic cross-sectional survey with university students.
description: There are two sheets containing values of the survey. The first
 one includes all participants without missing values. The second one
 includes all participants with and without missing values.
DOI: 10.5061/dryad.t1g1jwsz8
title: The role of spines in anthropogenic seed dispersal on the Galápagos islands

description: Dispersal has important ecological and evolutionary consequences for
 populations, but understanding the role of specific traits in dispersal
 can be difficult and requires careful experimentation. Moreover,
 understanding how humans alter dispersal is an important question,
 especially on oceanic islands where anthropogenic disturbance through
 species introductions can dramatically alter native ecosystems. 
 In this study, we investigated the functional role of spines in seed
 dispersal of the plant caltrop (Tribulus cistoides L.,
 Zygophyllaceae) by anthropogenic agents. We also tested whether
 anthropogenic or wildlife are more important seed dispersers
 of T. cistoides on the Galápagos.  Tribulus
 cistoides is found on tropical mainland and oceanic island
 habitats. The dispersal structure of T. cistoides is
 called a mericarp, and they are typically protected by one pair of upper
 spines and a second pair of lower spines, but the presence and size of
 spines varies within and between populations. On the Galápagos, the upper
 and lower spines protect mericarps from seed predation by Darwin’s
 finches. We tested whether spines play a dual role in dispersal by
 factorially manipulating the presence/absence of the upper and lower
 spines to simulate the natural variation in mericarp morphology. The upper
 spines greatly facilitated seed dispersal, whereas the lower spines had no
 discernible effect on dispersal. The presence of upper spines increased
 dispersal rate on shoes by pedestrians 23-fold, on fabrics (e.g. towels)
 and cars by nearly 2-fold, and the presence of upper spines increased
 dispersal distance by cars 6-fold. When comparing dispersal rates in
 habitats with high (roads and foot paths) versus low (arid forest)
 anthropogenic activity, dispersal rates were demonstrably higher in the
 habitats with more human activity.  These results have important
 implications for understanding the ecology and evolution of plant
 dispersal in the Anthropocene. Spines on the fruits of T.
 cistoides play important functional roles in anthropogenic
 dispersal, whereas native and introduced wildlife play a minor role in
 dispersal on inhabited islands of the Galápagos. Our results imply that
 seed predators and humans are jointly shaping the ecology and evolution of
 contemporary populations of T. cistoides on the
 Galápagos.
DOI: 10.7280/d1667w
title: Greenland Marine-Terminating Glacier Retreat Data

description: The thinning, acceleration, and retreat of Greenland glaciers since the
 mid-1990s has been attributed to the enhanced intrusion of warm Atlantic
 Waters (AW) into fjords, but this assertion has not been quantitatively
 tested on a Greenland-wide basis or included in numerical models. Here, we
 investigate how AW influenced the retreat of 226 marine-terminating
 glaciers by combining ocean modeling, remote sensing, and in-situ
 observations. We identify 74 glaciers standing in deep fjords with warm AW
 that retreated when ocean warming induced a 48% increase in glacier
 undercutting that controlled 62% of the glacier mass loss in 1992-2017.
 Conversely, 27 glaciers calving on protective, shallow ridges and 24
 glaciers standing in cold, shallow waters did not retreat; and 10 glaciers
 retreated when their floating sections collapsed. The mechanisms of ice
 front evolution remain undiagnosed at 87 glaciers with no ocean and
 bathymetry data, but these glaciers only account for 16% of the retreat.
 Projections of glacier evolution that exclude ocean-induced glacier
 undercutting may underestimate future mass losses by at least a factor
 two.   In this dataset, we present data for 226 glaciers over the
 time period 1985-2017. In particular, we provide estimates of glacier
 geometry, ocean thermal forcing on the continental shelf and at the
 glacier terminus, ice velocity, ocean-induced melt, and thinning-induced
 retreat. Most of the data is compiled in a netCDF file for each of the 226
 glaciers investigated durign the study period, with the exception of ice
 front boundaries for the years 1985-2019 digitized from Landsat 5, 7, and
 8 imagery, which we provide in a single shapefile. In addition, we include
 a PDF which displays the data enclosed for each glacier.
DOI: 10.5061/dryad.xksn02vbn
title: Data from: Widespread dysregulation of long non-coding genes associated with fatty acid metabolism, cell division, and immune response gene networks in xenobiotic-exposed rat liver

description: Xenobiotic exposure dysregulates hundreds of protein-coding genes in
 mammalian liver, impacting many physiological processes and inducing
 diverse toxicological responses. Little is known about xenobiotic effects
 on long noncoding RNAs (lncRNAs), many of which have important regulatory
 functions. Here, we present a computational framework to discover
 liver-expressed, xenobiotic-responsive lncRNAs (xeno-lncs) with strong
 functional, gene regulatory potential and elucidate the impact of
 xenobiotic exposure on their gene regulatory networks. We assembled the
 long non-coding transcriptome of xenobiotic-exposed rat liver using
 RNA-seq datasets from male rats treated with 27 individual chemicals,
 representing seven mechanisms of action (MOAs). Ortholog analysis was
 combined with co-expression data and causal inference methods to infer
 lncRNA function and deduce gene regulatory networks, including causal
 effects of lncRNAs on protein-coding gene expression and biological
 pathways. We discovered &gt;1,400 liver-expressed xeno-lncs, many with
 human and/or mouse orthologs. Xenobiotics representing different MOAs
 often regulated common xeno-lnc targets: 123 xeno-lncs were dysregulated
 by &gt; 10 chemicals, and 5 xeno-lncs responded to &gt; 20 of the
 27 chemicals investigated; 81 other xeno-lncs served as MOA-selective
 markers of xenobiotic exposure. Xeno-lnc−protein-coding gene co-expression
 regulatory network analysis identified xeno-lncs closely associated with
 exposure-induced perturbations of hepatic fatty acid metabolism, cell
 division, or immune response pathways, and with apoptosis or cirrhosis. We
 also identified hub and bottleneck lncRNAs, which are expected to be key
 regulators of gene expression. This work elucidates extensive networks of
 xeno-lnc−protein-coding gene interactions and provides a framework for
 understanding the widespread transcriptome-altering actions of foreign
 chemicals in a key responsive mammalian tissue.
description: These files contain supplementary datasets for K Karri and DJ
 Waxman (2020) Toxicological Sciences,
 https://doi.org/10.1093/toxsci/kfaa001, PMID:31926019.
 Supplemental Figures S1 to S12 are included in a single pdf
 file. Individual CSV files are provided for each of the
 Excel Worksheets. Full gene and isoform structure
 information is provided for the set of 5,795 liver-expressed lncRNA genes
 in the GTF file: Rat_lncRNA_GTF_Karri_Waxman_ToxSci_2020.gtf. Also, see
 the accompanying GTF_README file. Gene Networks
 associated with this dataset are found here:
 http://www.ndexbio.org/#/networkset/74ed1c25-2fab-11e9-9f06-0ac135e8bacf?accesskey=838f4dc32739041a462f9ca9a80f628b8194c78d71eaf0ac8d8fef716743c5ab
DOI: 10.5061/dryad.tdz08kpw7
title: Data from: Patterns of annual and seasonal immune investment in a temporal reproductive opportunist

description: Historically, investigations of how organismal investments in immunity
 fluctuate in response to environmental and physiological changes have
 focused on seasonally breeding organisms that confine reproduction to
 seasons with mild environmental conditions and abundant resources. The red
 crossbill, Loxia curvirostra, is a songbird that can breed
 opportunistically if conifer seeds are abundant, on both short, cold, and
 long, warm days, providing an ideal system to investigate interactions
 between immunity, reproduction, and environmental fluctuations. In this
 study, we measured inter- and intra-annual variation in complement,
 natural antibodies, PIT54, and leukocytes in crossbills across four
 summers (2010-2013) and multiple seasons within one year (summer
 2011-spring 2012). Overall, we observed substantial changes in crossbill
 immune investment among summers, with interannual variation driven largely
 by food resources, while seasonal variation was less pronounced and lacked
 a dominant predictor of immune investment. However, we found weak evidence
 that physiological processes (e.g., reproductive condition, moult) or
 abiotic factors (e.g., temperature, precipitation) affect immune
 investment. Collectively, this study suggests that a reproductively
 flexible organism may simultaneously invest in both reproduction and
 survival-related processes, potentially by exploiting rich patches with
 abundant resources. More broadly, these results emphasize the need for
 more longitudinal studies of trade-offs associated with immune investment.
DOI: 10.5061/dryad.6q573n5vs
title: From pup to predator; generalized hidden Markov models reveal rapid development of movement strategies in a naïve long‐lived vertebrate

description: Rapid development of a successful foraging strategy is critical for
 juvenile survival, especially for naïve animals that receive no parental
 guidance. However, this process is poorly understood for many species.
 Although observation of early-life movements is increasingly possible with
 miniaturisation of animalborne telemetry devices, analytical limitations
 remain. Here, we tracked 29 recently-weaned, grey seal Halichoerus grypus
 pups from colonies in two geographically distinct regions of the United
 Kingdom. We analysed at-sea movements of pups throughout their initial
 months of nutritional independence to investigate the ontogeny of
 behaviour-specific (foraging and travelling) movement patterns. Using
 generalized hidden Markov models (HMMs), we extended the conventional HMM
 framework to account for temporal changes in putative foraging and
 travelling movement characteristics, and investigate the effects of
 intrinsic (sex) and extrinsic (environment) factors on this process.
 Putative foraging behaviour became more tortuous with time, and travelling
 became faster and more directed, suggesting a reduction in search scale
 and an increase in travel efficiency as pups shifted from exploration to
 an adult-like repeatable foraging strategy. Sex differences in movement
 characteristics were evident from colony departure, but sex-specific
 activity budgets were only detected in one region. We show that
 sex-specific behavioural strategies emerge before sexual size dimorphism
 in grey seals, and suggest that this phenomenon may occur in other
 long-lived species. Our results also indicate that environmental variation
 may affect the emergence of sex-specific foraging behaviour, highlighting
 the need to consider interacting intrinsic and extrinsic factors in
 shaping movement strategies of long-lived vertebrates. Moreover, comparing
 the behavioural state estimations to those of a conventional HMM (no
 variation in statespecific movement parameters) revealed differences in
 the amount and location of foraging activity, with implications for
 spatial conservation management. Overlooking intrinsic and extrinsic
 variation in movement processes could distort our understanding of
 foraging ecology, population dynamics, and conservation requirements.
description: GPS-GSM tracking data from recently-weaned grey seal pups tagged
 on UK colonies
description: See README file for further instructions
DOI: 10.5061/dryad.k3j9kd53x
title: Early life learning ability predicts adult social structure, with potential implications for fitness outcomes in the wild

description: 1. Social environments influence important ecological processes and can
 determine how selection acts on traits. Cognitive abilities can shape
 these social environments and in turn, affect individuals' fitness.
 2. To understand how cognitive abilities evolve, we need to understand the
 complex interplay between an individual's cognitive abilities, the
 social environment that they inhabit and the fitness consequences of these
 relationships. 3. We measured the associative learning ability of pheasant
 chicks, Phasianus colchicus, then released them into the wild where we
 quantified their social position by observing their associations at
 feeding stations and monitored the number of days survived. 4. We observed
 disassortative mixing by learning performance at the population level, and
 poor learners had more associates than good learners. Learning was
 beneficial for survival when focal individuals had fewer than four
 associates, but survival probability across learning abilities equalized
 for individuals with more than four associates. 5. While the mechanisms
 underlying these relationships remain to be determined, the patterns of
 association exhibited by pheasants at feeders can be predicted by
 individual variation in cognitive performances and we suspect these
 patterns are related to differences in information use. Critically, these
 resulting patterns of association have fitness consequences for
 individuals that cannot be explained directly by their cognitive ability,
 but which could mediate selection on cognition.
DOI: 10.5061/dryad.msbcc2ftw
title: Close relatives in population samples: Evaluation of the consequences for genetic stock identification

description: Determining the origin of individuals in mixed population samples is key
 in many ecological, conservation and management contexts. Genetic data can
 be analyzed using Genetic Stock Identification (GSI), where the origin of
 single individuals is determined using Individual Assignment (IA) and
 population proportions are estimated with Mixed Stock Analysis (MSA). In
 such analyses, allele frequencies in a reference baseline are required.
 Unknown individuals or mixture proportions are assigned to source
 populations based on the likelihood that their multilocus genotypes occur
 in a particular baseline sample. Representative sampling of populations
 included in a baseline is important when designing and performing GSI.
 Here we investigate the effects of family sampling on GSI, using both
 simulated and empirical genotypes for Atlantic salmon (Salmo salar). We
 show that non-representative sampling leading to inclusion of close
 relatives in a reference baseline may introduce bias in estimated
 proportions of contributing populations in a mixed sample, and increases
 the amount of incorrectly assigned individual fish. Simulated data further
 show that the induced bias increases with increasing family structure, but
 that it can be partly mitigated by increased baseline population sample
 sizes. Results from standard accuracy tests of GSI (using only a reference
 baseline and/or self-assignment) gave a false and elevated indication of
 the baseline power and accuracy to identify stock proportions and
 individuals. These findings suggest that family structure in baseline
 population samples should be quantified and its consequences evaluated,
 before carrying out GSI.
description: Tissue samples collected from Atlantic salmon. Tissue samples
 consisted of fin clips from hatcheries stored individually in labeled
 tubes with ethanol (95%). DNA was extracted followed by PCR and genotyping
 of 17 polymorphic microsatellite markers (on average c. 10
 alleles/locus).
description: Among the 1870 individuals in the original empirical baseline
 population samples, 96.5 % had complete genotypes at all 17
 microsatellites; one individual had missing data at three loci, five at
 two loci and 60 at one locus, resulting in overall 0.23 % missing
 genotypes. Repeat genotyping of a sub-set of individuals resulted in a
 repeatability of 100 %, and hence an estimated error rate of
 zero.
DOI: 10.5061/dryad.xd2547dd2
title: Methane emission and sulfide levels increase in tropical seagrass sediments during temperature stress: a mesocosm experiment

description: Climate change-induced ocean warming is expected to greatly affect carbon
 dynamics and sequestration in vegetated shallow waters, especially in the
 upper subtidal where water temperatures may fluctuate considerably and can
 reach high levels at low tides. This might alter the greenhouse gas
 balance and significantly reduce the carbon sink potential of tropical
 seagrass meadows. In order to assess such consequences, we simulated
 temperature stress during low tide exposures by subjecting seagrass plants
 (Thalassia hemprichii) and associated sediments to elevated midday
 temperature spikes (31, 35, 37, 40 and 45ºC) for seven consecutive days in
 an outdoor mesocosm setup. During the experiment, methane release from the
 sediment surface was estimated using gas chromatography. Sulfide
 concentration in the sediment pore water was determined
 spectrophotometrically, and the plant’s photosynthetic capacity as
 Electron Transport Rate (ETR) and maximum quantum yield (Fv/Fm) was
 assessed using pulse-amplitude modulated (PAM) fluorometry. The highest
 temperature treatments (40 and 45ºC) had a clear positive effect on
 methane emission and the level of sulfide in the sediment and, at the same
 time, clear negative effects on the photosynthetic performance of seagrass
 plants. The effects observed by temperature stress were immediate (within
 hours) and seen in all response variables, including ETR, Fv/Fm, methane
 emission and sulfide levels. In addition, both the methane emission and
 the size of the sulfide pool were already negatively correlated to changes
 in the photosynthetic rate (ETR) during the first day, and with time, the
 correlations became stronger. These findings show that increased
 temperature will reduce primary productivity and increase methane and
 sulfide levels. Future increases in the frequency and severity of extreme
 temperature events could hence reduce the climate mitigation capacity of
 tropical seagrass meadows by reducing CO2 sequestration, increase damage
 from sulfide toxicity, and induce the release of larger amounts of
 methane.