cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.fn2z34tws
title: Metabolite profiling of the social spider Stegodyphus dumicola along a climate gradient

description: Animals experience climatic variation in their natural habitats, which may
 lead to variation in phenotypic responses among populations through local
 adaptation or phenotypic plasticity. In ectotherm arthropods, the
 expression of thermoprotective metabolites such as free amino acids,
 sugars, and polyols, in response to temperature stress, may facilitate
 temperature tolerance by regulating cellular homeostasis. If populations
 experience differences in temperatures, individuals may exhibit
 population-specific metabolite profiles through differential accumulation
 of metabolites that facilitate thermal tolerance. Such thermoprotective
 metabolites may originate from the animals themselves or from their
 associated microbiome, and hence microbial symbionts may contribute to
 shape the thermal niche of their host. The social spider Stegodyphus
 dumicola has extremely low genetic diversity, yet it occupies a relatively
 broad temperature range occurring across multiple climate zones in
 Southern Africa. We investigated whether the metabolome, including
 thermoprotective metabolites, differs between populations, and whether
 population genetic structure or the spider microbiome may explain
 potential differences. To address these questions, we assessed metabolite
 profiles, phylogenetic relationships, and microbiomes in three natural
 populations along a temperature gradient. The spider microbiomes in three
 genetically distinct populations of S. dumicola showed no significant
 population-specific pattern, and none of its dominating genera (Borrelia,
 Diplorickettsia, and Mycoplasma) are known to facilitate thermal tolerance
 in hosts. These results do not support a role of the microbiome in shaping
 the thermal niche of S. dumicola. Metabolite profiles of the three spider
 populations were significantly different. The variation was driven by
 multiple metabolites that can be linked to temperature stress (e.g.
 lactate, succinate or xanthine) and thermal tolerance (e.g. polyols,
 trehalose, or glycerol): these metabolites had higher relative abundance
 in spiders from the hottest geographic region. These distinct metabolite
 profiles are consistent with a potential role of the metabolome in
 temperature response.
DOI: 10.5061/dryad.7d7wm37x8
title: Meta-analysis of phenotypic plasticity in response to thermal treatments in invertebrates

description: Populations must adapt to environmental changes to remain viable. Both
 evolution and phenotypic plasticity contribute to adaptation, with
 plasticity possibly being more important for coping with rapid change.
 Adaptation is complex in species with separate sexes, as the sexes can
 differ in the strength or direction of natural selection, the genetic
 basis of trait variation, and phenotypic plasticity. Many species show sex
 differences in plasticity, yet how these differences influence extinction
 susceptibility remains unclear. We first extend theoretical models of
 population persistence in changing environments and show that persistence
 is affected by sexual dimorphism for phenotypic plasticity, trait genetic
 architecture, and sex-specific selection. Our models predict that
 female-biased adaptive plasticity—particularly in traits with
 modest-to-low cross-sex genetic correlations— typically promotes
 persistence, though we also identify conditions where sexually monomorphic
 or male-biased plasticity promotes persistence. We then perform a
 meta-analysis of sex-specific plasticity under manipulated thermal
 conditions. Although examples of sexually dimorphic plasticity are widely
 observed, systematic sex differences are rare. An exception—cold
 resistance—is systematically female-biased and represents a trait wherein
 sexually dimorphic plasticity might elevate population viability in
 changing environments. We discuss our results in light of debates about
 the roles of evolution and plasticity in extinction susceptibility.
DOI: 10.6086/d1wt25
title: US and Japanese adolescents’ emotions across time: variation by valence and arousal

description: Experiencing emotions is a complex process that varies across social
 contexts (e.g., culture) and over time. The current research examined the
 levels and trajectories of self-reported emotions among US (n = 321) and
 Japanese (n = 388) adolescents (age range: 11–14 at Time 1). Emotions were
 conceptualized as high arousal positive (HAP), low arousal positive (LAP),
 high arousal negative (HAN), and low arousal negative (LAN). At each time
 point, US adolescents (vs. Japanese) showed greater positive and lower
 negative emotions (both arousal levels). Positive and negative emotions
 were negatively associated in the US, but the associations were not
 present or were positive in Japan. While US adolescents’ HAP and LAN
 emotions remained stable, Japanese adolescents showed increases in HAP and
 LAN emotions over time. However, both groups showed increases at similar
 rates for HAN and no change in LAP emotions. Collectively, findings
 suggest that emotions are both pancultural and culture-specific and
 highlight the value of considering valence and arousal in cross-cultural
 examinations of emotions.
description: Adolescents in the US were recruited from four middle schools in
 one school district and one summer program from another school
 district. Adolescents in Japan were recruited from two middle
 schools.
description: # US and Japanese adolescents’ emotions across time: variation by valence
 and arousal File name:
 Emotion_Deidenfitied_rev.csv Authors: Yena Kyeong, Sarah E. Knapp, Yusuke
 Takahashi, Elizabeth L. Davis, & Cecilia Cheung Methodology:
 Adolescents in the US (n = 321) were recruited from four middle schools in
 one school district and one summer program from another school
 district. Adolescents in Japan (n = 388) were recruited from two middle
 schools. They self-reported their emotions at three time points over the
 course of 18 months. Participants indicated the extent to which they had
 experienced certain discrete emotions during the past week, using a
 5-point Likert Scale (1 = never, 5 = very often). Dataset structure: This
 dataset contains row variables. Country and gender are binary variables,
 and emotions at each time point (a = Time1; b = Time2; c = Time3) appear
 from Columns C to AN. * Variables: * Country: 1 = US; 2 = Japan * Gender:
 1 = Male; 2 = Female * Emotion items: * Columns C through O: Emotions
 meausured at Time 1 * Columns P through AB: Emotions measured at Time 2 *
 Columns AC through AN: Emotions measured at Time 3 * Scoring of the
 emotion dimensions: Mean of items for each dimension at each time point
 can be taken. * High Arousal Positive: Happy, Excited * Low Arousal
 Positive: Calm, Relaxed, Peaceful * High Arousal Negative: Ashamed,
 Worried, Afraid, Guilty, Angry * Low Arousal Negative: Depressed, Sad,
 Tired *Missing values are coded as 999.
DOI: 10.5061/dryad.hhmgqnkjc
title: Corneal endothelial morphology of healthy myopic Malaysian children of Chinese ethnicity aged 8-9 years and its association with axial length

description: Clinical Relevance: This study is to further understand the effects of
 axial length elongation on the corneal endothelial cell's morphology
 in myopic children. Abnormal changes in the morphology of cornea
 endothelium are indicators of corneal stress or instability which could be
 linked to myopia.  Background: To examine the morphology of
 corneal endothelium cells in healthy Chinese Malaysian school children
 with emmetropia and mild to moderate myopia and its association with axial
 length.  Methodology: A total of 111 school children comprising
 of 37 emmetropes, 37 mild myopes and 37 moderate myopes aged 8-9 years old
 were recruited. Visual Acuity was measured using the LogMar chart,
 cycloplegic refraction was determined using an open-field autorefractor
 (Grand Seiko WAM-5100, Hiroshima, Japan) and refined using subjective
 refraction. Morphology of cornea endothelial cells [ECD- endothelial cells
 density, COV- coefficient of variation, HEX- Hexagonility and CCT-central
 corneal thickness] was evaluated using a non-contact specular miscroscope
 (Topcon SP-2000P). Axial length was measured with A-Scan ultrasound
 biometry (PacScan Plus, Sonomed Escalon, NY). The correlation between
 morphology of cornea endothelial cells and axial length were assessed
 using Pearson Correlation and Linear Regression Analysis. 
 Results: There was no significant difference in cornea endothelial cells
 and axial length between gender (p&gt;0.05). Significant reduction in
 ECD and HEX and increased COV was found in eyes of higher myopic power
 which had longer AL when compared to emmetropes (p&lt;0.001). Except
 for CCT, all corneal endothelial cells parameters correlated significantly
 with axial length (p&lt;0.05). For every 1mm increase in axial length,
 endothelial cells density decreased by 73.27 cells/mm2, hexagonality
 decreased by 2.32% and coefficient of variation increased by
 1.75%.  Conclusion: There were significant changes in morphology
 of cornea endothelial cells in young moderate myopic children of Chinese
 ethnicity at 8-9 years of age. This result provides normative data for
 Malaysian children of Chinese ethnicity that can be used for comparison
 and reference for clinical procedures, thereby facilitating decision
 making with respect to interventions for myopia control, especially in
 prescribing contact lens for children. 
description: Corneal endothelial cells were manually selected on the specular
 miscroscope (SP-3000P; Topcon, Tokyo, Japan) of a 0.5x0.25mm section of
 endothelial surface. The specular miscrcrosope provided histogram
 determining the ECD, HEX, COV, CCT, population size and specified the
 minimum, maximum, and the average cell size of the selected area. The
 procedure was repeated three times and average values noted. 
 The data obtained in this study were then analysed using SPSS
 version 21.0. 
description: There is no missing values in the dataset.
DOI: 10.5061/dryad.mw6m905zk
title: GO and KEGG terms analysis files between TLR2-4 and WT cells

description: Staphylococcus aureus infections pose a potential threat to livestock
 production and public health. A novel strategy is needed to control S.
 aureus infection due to its adaptive evolution to antibiotics. Autophagy
 plays a key role in degrading bacteria for innate immune cells. In order
 to promote S. aureus clearance via TLR induced autophagy pathway, the
 domain fusion TLR2-4 with the extracellular domain of TLR2, specific
 recognizing S. aureus, and transmembrane and intracellular domains of TLR4
 is assembled, then the goats expressing TLR2-4 is generated. TLR2-4
 substantially augments the removal of S. aureus within macrophages by
 elevating autophagy level. Phosphorylated JNK/ERK1/2 promote LC3-puncta in
 TLR2-4 macrophages during S. aureus-induced autophagy via MyD88-mediated
 the TAK1 signaling cascade. Meantime, the TRIF-dependent TBK1-TFEB-OPTN
 signaling is involved in TLR2-4-triggered autophagy after S. aureus
 challenge. Moreover, the transcript of ATG5 and ATG12 is significantly
 increased via cAMP-PKA-NF-kB signaling, which facilitates S.
 aureus-induced autophagy in TLR2-4 macrophages. Overall, the novel
 receptor TLR2-4 enhances the autophagy-dependent clearance of S. aureus in
 macrophages via TAK1/TBK1-JNK/ERK, TBK1-TFEB-OPTN and cAMP-PKA-NF-kB-ATGs
 signaling pathways, which provide an alternative approach to resistant
 against S. aureus infection.
description: For the RNA-seq alignment,
 purified sequence data was aligned to reference goat genome downloaded
 from Ensembl website (https://asia.ensembl.org/index.html) by HISAT2. Read
 count matrices were obtained using Feature Counts. Differentially
 expressed genes were accessed using R package DESeq2, with a false
 discovery rate less than 0.05 and ∣log2foldchange∣&gt; 2 or 3. Principal component analysis
 was also performed by DESeq2. Both GO and KEGG functional enrichment
 analysis or visualization were finished by R package ClusterProfiler or
 ClueGO, a plug-in of Cytoscape. Additionally, autophagy related gene sets
 were obtained from Molecular Signatures Database (MSigDB)
 (http://www.broadinstitute.org).
DOI: 10.5061/dryad.vq83bk3v9
title: Clearance rates of Mytilus edulis exposed to parasites and microplastic

description: Fear is an integral part of predator-prey interactions with cascading
 effects on the structure and function of ecosystems. Fear of parasitism
 holds a similar ecological potential but our understanding of the
 underlying mechanisms in host-parasite interactions is limited by lack of
 empirical examples. Here, we experimentally test if blue mussels Mytilus
 edulis respond behaviourally to the mere presence of infective
 transmission stages of the trematode Himasthla elongata by ceasing
 filtration activity, thereby avoiding infection. Our results show that
 blue mussels reduced clearance rates by more than 30% in presence of
 parasites. The reduced filtration activity resulted in lower infection
 rates in experimental mussels. The identified parasite-specific avoidance
 behaviour can be expected to play a significant role in regulating the
 ecosystem engineering function of blue mussels in coastal habitats.
DOI: 10.5061/dryad.rxwdbrvbg
title: Genomic shifts, phenotypic clines and fitness costs associated with cold-tolerance in the Asian tiger mosquito

description: Climatic variation is a key driver of genetic differentiation and
 phenotypic traits evolution, and local adaptation to temperature is
 expected in widespread species. We investigated phenotypic and genomic
 changes in the native range of the Asian tiger mosquito, Aedes albopictus.
 We first refine the phylogeographic structure based on genome-wide regions
 (1,901 double-digest restriction-site associated DNA single nucleotide
 polymophisms [ddRAD SNPs]) from 41 populations. We then explore the
 patterns of cold adaptation using phenotypic traits measured in common
 garden (wing size and cold tolerance) and genotype–temperature
 associations at targeted candidate regions (51,706 exon-capture SNPs) from
 nine populations. We confirm the existence of three evolutionary lineages
 including clades A (Malaysia, Thailand, Cambodia, and Laos), B (China and
 Okinawa), and C (South Korea and Japan). We identified
 temperature-associated differentiation in 15 out of 221 candidate regions
 but none in ddRAD regions, supporting the role of directional selection in
 detected genes. These include genes involved in lipid metabolism and a
 circadian clock gene. Most outlier SNPs are differently fixed between
 clades A and C, whereas clade B has an intermediate pattern. Females are
 larger at higher latitudes yet produce no more eggs, which might favor the
 storage of energetic reserves in colder climates. Nondiapausing eggs from
 temperate populations survive better to cold exposure than those from
 tropical populations, suggesting they are protected from freezing damages
 but this cold tolerance has a fitness cost in terms of egg viability.
 Altogether, our results provide strong evidence for the thermal adaptation
 of A. albopictus across its wide temperature range.
DOI: 10.5061/dryad.prr4xgxp3
title: Missing data in sea turtle population monitoring: a Bayesian statistical framework accounting for incomplete sampling

description: Monitoring how populations respond to sustained conservation measures is
 essential to detect changes in their population status and
 determine the effectiveness of any interventions. In the case of sea
 turtles, their populations are difficult to assess because of their
 complicated life histories. Ground-derived clutch counts are most often
 used as an index of population size for sea turtles; however, data are
 often incomplete with varying sampling intensity within and among sites
 and seasons. To address these issues, we: (1) develop a Bayesian
 statistical modelling framework that can be used to account for sampling
 uncertainties in a robust probabilistic manner within a given site and
 season; and (2) apply this to a previously unpublished long-term sea
 turtle dataset (n = 17 years) collated for the Republic of the Congo,
 which hosts two sympatrically nesting species of sea turtle (leatherback
 turtle [Dermochelys coriacea] and olive ridley turtle [Lepidochelys
 olivacea]). The results of this analysis suggest that leatherback turtle
 nesting levels dropped initially and then settled into quasi-cyclical
 levels of interannual variability, with an average of 573 (mean, 95%
 prediction interval: 554–626) clutches laid annually between 2012
 and 2017. In contrast, nesting abundance for olive ridley turtles has
 increased more recently, with an average of 1,087 (mean, 95% prediction
 interval: 1,057–1,153) clutches laid annually between 2012 and 2017. These
 findings highlight the regional and global importance of this rookery with
 the Republic of the Congo, hosting the second largest documented
 populations of olive ridley and the third largest for leatherback turtles
 in Central Africa; and the fourth largest non-arribada olive ridley
 rookery globally. Furthermore, whilst the results show that Congo’s single
 marine and coastal national park provides protection for over half of sea
 turtle clutches laid in the country, there is scope for further protection
 along the coast. Although large parts of the African coastline remain to
 be adequately monitored, the modelling approach used here will be
 invaluable to inform future status assessments for sea turtles given that
 most datasets are temporally and spatially fragmented. 
description: Sea turtle nest count data at 6 sites inside Conkouati-Douli
 National Park in the Republic of the Congo. Data obtained following beach
 patrols conducted at dawn to record the previous night's nesting
 activity, with field assistants surveying the entire nesting beach. At
 least two people were engaged in each patrol to ensure that the total
 width of beach available for nesting was surveyed for signs of visible
 activity - with one field assistant walking along the vegetation line and
 the other along the high tide line.
DOI: 10.5061/dryad.gmsbcc2qf
title: Historical connections between Atlantic Forest and Amazonia drove genetic and ecological diversity in Lithobates palmipes (Anura, Ranidae)

description: The Atlantic and Amazon rainforests have a shared but unclear past, with
 intermittent connections resulting from historical climate change. We
 investigate these connections by studying the phylogeography and climatic
 niche of the disjunct distributed frog Lithobates palmipes. We sequenced
 two fragments of mitochondrial DNA from Atlantic Forest (AtF) and Amazonia
 (AmF) individuals and evaluated how genetic diversity is distributed in
 space and whether past demographic changes occurred. Also, we evaluated
 the existence of past suitable connections between biomes for L. palmipes
 through ecological niche models (ENM) and tested for niche divergence. The
 AtF group is nested within the AmF group and closely related to
 individuals from eastern Amazonia, a pattern recovered in many species
 that used northeast connection routes. We found evidence of recurrent use
 of connections in different directions and time during the Pleistocene,
 resulting in genetic structure between biomes, with no signal of
 demographic change and evidence of niche divergence across both genetic
 groups. ENMs indicated suitable areas connecting forests throughout
 northeastern Brazil during the Pleistocene. Mitochondrial lineages do not
 match biomes exactly. One lineage is composed of AtF populations and
 eastern Amazonia individuals. The other is composed of western Amazonia
 individuals, suggesting an effect of past climatic heterogeneity within
 the Amazonia forest. This is the first evidence that this route drove
 genetic and ecological diversity for amphibians recently, a group with
 habits and ecological requirements different from other vertebrates that
 have been shown to use this putative corridor.
DOI: 10.5281/zenodo.18391426
title: Datalog dataset
DOI: 10.5281/zenodo.18399683
title: Datalog dataset
DOI: 10.15468/dl.j4m7gc
title: Occurrence Download

description: A dataset containing 324 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Apoplymus pectoralis"
 ]
}

 The dataset includes 324 records from 33 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003078-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.8cz8w9gsm
title: Application of sulfur and nitrogen doped carbon quantum dots as sensitive fluorescent nanosensors for the determination of saxagliptin and gliclazide

description: In this study, highly fluorescent sulfur and nitrogen doped carbon quantum
 dots (S,N-CQDs) were used as fluorescent nanosensors for direct
 spectrofluorimetric estimation of each of gliclazide and saxagliptin
 without any pre-derivatization steps for the first time. S,N-CQDs were
 synthesized employing a simple hydrothermal technique using citric acid
 and thiosemicarbazide. The produced S,N-CQDs were characterized using
 different techniques including fluorescence emission spectroscopy, UV
 spectrophotometry, high resolution transmission electron microscopy, and
 FT-IR spectroscopy. Following excitation at 360 nm, S,N-CQDs exhibited a
 strong emission peak at 430 nm. The native fluorescence of S,N-CQDs was
 quantitatively enhanced by addition of increased concentrations of the
 studied drugs. The fluorescence enhancement of S,N-CQDs and the
 concentrations of the studied drugs revealed a wide linear relationship in
 the range of 30.0-500.0 μM and 75.0-600.0 µM with limits of
 detection of 5.0 μM and 10.15 µM for gliclazide and saxagliptin,
 respectively. The proposed method was efficiently utilized for
 determination of cited drugs in their commercial tablets with % recoveries
 ranging from 98.6 to 101.2% and low % RSD values (less than 2%). The
 mechanism of interaction between S,N-CQDs and the two drugs was studied.
 Validation of the proposed method was carried out in accordance with ICH
 guidelines.
DOI: 10.5061/dryad.7wm37pvw2
title: Using single-worm data to quantify heterogeneity in Caenorhabditis elegans-bacterial interactions

description: The nematode Caenorhabditis elegans is a model system for host-microbe and
 host-microbiome interactions. Many studies to date use batch digests
 rather than individual worm samples to quantify bacterial load in this
 organism. Here it is argued that the large inter-individual variability
 seen in bacterial colonization of the C. elegans intestine is informative,
 and that batch digest methods discard information that is important for
 accurate comparison across conditions. As describing the variation
 inherent to these samples requires large numbers of individuals, a
 convenient 96-well plate protocol for disruption and colony plating of
 individual worms is established.
description: Data are CFU/worm measurements for individual <em>C.
 elegans</em>. Raw data were CFU counts from spotting or spreading
 ten-fold serial dilutions on agar plates after mechanical disruption of
 worms in 200 uL buffer/worm to release bacteria. Data here were converted
 from raw counts as (counts)*(correction factor to 200 uL)*10^(dilution
 factor).