cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.3ffbg79fp
title: S. neglecta parasitism in O. nigricornis: 2018 collection

description: In July 2018, we collected O. nigricornis crickets in
 southern Ontario (Canada) and New York State (United States of America):
 from the Koffler Scientific Reserve (coded as K or site 2) (King City
 Ontario, 44.03°N, 79.53°W), rare Charitable Research Reserve (coded as R
 or site 4) (Cambridge Ontario, 43.38°N, 80.39°W), the University
 of Toronto at Mississauga (coded as M or site 3) (43.55°N,
 79.66°W), and the Edmund Niles Huyck Preserve and Biological Research
 Station (coded as H or site 1) (Rensselaerville, New York, 42.10°N,
 74.10°W).  Crickets were dissected and photographed using an
 AmScope 5MP digital microscope camera attached to a Wild M5A dissecting
 microscope. Following dissection, abdomens were examined for the presence
 of S. neglecta eggs and/or larvae. Crickets containing fly eggs
 and/or larvae were given a fitness score of 0, while those that did not
 contain either were given a fitness score of 1. Crickets were photographed
 under the microscope and digital photos measured using ImageJ software.
 Measurements of pronotum length, femur length and head width were
 taken. 
description: Sex of crickets collected at Edmund Niles Huyck Preserve and
 Biological Research Station was not collected.
DOI: 10.5061/dryad.1vhhmgqq5
title: Data from: Unraveling B-lymphocytes in CNS inflammatory diseases: Distinct mechanisms and treatment targets

description: Specific therapies targeting B lymphocytes in multiple sclerosis (MS) have
 demonstrated reductions in disease activity and disability progression.
 Several observational studies have also shown the effects of targeting B
 lymphocytes in other rare CNS inflammatory diseases, such as neuromyelitis
 optica spectrum disorder (NMOSD) and autoimmune encephalitis (AE).
 However, some drugs targeting cytokine receptors involved in B-lymphocyte
 maturation and proliferation resulted in negative outcomes in MS. These
 apparently conflicting findings have stimulated research on the
 pathophysiologic mechanisms of B lymphocytes in CNS inflammatory diseases.
 It has been demonstrated that B-lymphocytes participate in the
 pathogenesis of these conditions as antigen-presenting cells, producing
 proinflammatory cytokines that induce Th1 and Th17 responses and producing
 antibodies. However, they are also able to produce anti-inflammatory
 cytokines, such as interleukin (IL)-10, functioning as regulators of
 autoimmunity. Understanding these diverse effects is essential for the
 development of focused treatments. In this review, we discuss the possible
 mechanisms that underlie B lymphocyte involvement in MS, NMOSD, and AE,
 and the outcomes obtained by treatments targeting B lymphocytes.
DOI: 10.5061/dryad.xsj3tx9bw
title: Rest-task modulation of fMRI-derived global signal topography is mediated by transient co-activation patterns

description: Recent resting-state fMRI studies have revealed that the global signal
 (GS) exhibits a non-uniform spatial distribution across the gray matter.
 Whether this topography is informative remains largely unknown. We
 therefore tested rest-task modulation of global signal topography by
 analyzing static global signal correlation and dynamic co-activation
 patterns in a large sample of fMRI dataset (n=837) from the Human
 Connectome Project. The GS topography in the resting-state and in seven
 different tasks was first measured by correlating the global signal with
 the local timeseries (GSCORR). In the resting state, high GSCORR was
 observed mainly in the primary sensory and motor regions, while low GSCORR
 was seen in the association brain areas. This pattern changed during the
 seven tasks, with mainly decreased GSCORR in sensorimotor cortex.
 Importantly, this rest-task modulation of GSCORR could be traced to
 transient co-activation patterns at the peak period of global signal
 (GS-peak). By comparing the topography of GSCORR and respiration effects,
 we observed that the topography of respiration mimicked the topography of
 global signal in the resting-state whereas both differed during the task
 states; due to such partial dissociation, we assume that GSCORR could not
 be equated with a respiration effect. Finally, rest-task modulation of GS
 topography could not be exclusively explained by other sources of
 physiological noise. Together, we here demonstrate the informative nature
 of global signal topography by showing its rest-task modulation, the
 underlying dynamic co-activation patterns, and its partial dissociation
 from respiration effects during task states.
description: The data set was from the Human Connectome Project (HCP). The 3
 Tesla dataset was served for main analyses, and 7 Tesla served for
 replication. All subjects from the HCP 1200-subject data release (Mar 01,
 2017) having completed fMRI sessions were included (837 subjects in 3
 Tesla and 145 subjects in7 Tesla, respectively).
  
description: The filename describes to which figure the data is used for, for
 example, 'fig_4B_s2.mat' means this data is used for Fig 4B and
 S2 Fig. <br> All datasets are saved in .mat. For gifti strcuture in
 '.mat', the vaule can be found in '.cdata' field, and
 this brain map can be visualized by Connectome Workbench.<br> For
 more detials about visualization, please visit
 https://www.humanconnectome.org/software/connectome-workbench<br>
  <br> If you have any other questions, feel free to contact me
 (Jianfeng Zhang): jianfeng_zhang@zju.edu.cn
DOI: 10.5061/dryad.r7sqv9s8g
title: Data from: Chromosome-level genome assembly of a cyprinid fish Onychostoma macrolepis by integration of Nanopore Sequencing, Bionano and Hi-C technology

description: Onychostoma macrolepis is an emerging commercial cyprinid fish species. It
 is a model system for studies of sexual dimorphism and genome evolution.
 Here, we report the chromosome-level assembly of the O.macrolepis genome
 obtained from the integration of Nanopore long-read sequencing with
 physical maps produced using Bionano and Hi-C technology. A total of 87.9
 Gb of Nanopore sequence provided approximately 100-fold coverage of the
 genome. The preliminary genome assembly was 883.2 Mb in size with a contig
 N50 size of 11.2 Mb. The 969 corrected contigs obtained from Bionano
 optical mapping were assembled into 853 scaffolds and produced an assembly
 of 886.5 Mb with a scaffold N50 of 16.5 Mb. Finally, using the Hi-C data,
 881.3 Mb (99.4% of genome) in 526 scaffolds were anchored and oriented in
 25 chromosomes ranging in size from 25.27 to 56.49 Mb. In total, 24,770
 protein-coding genes were predicted in the genome, and ~96.85% of the
 genes were functionally annotated. The annotated assembly contains 93.3%
 complete genes from the BUSCO reference set. In addition, we identified
 409 Mb (46.23% of the genome) of repetitive sequence, and 11,213
 non-coding RNAs, in the genome. Evolutionary analysis revealed that
 O.macrolepis diverged from common carp approximately 24.25 million years
 ago. The chromosomes of O.macrolepis showed an unambiguous correspondence
 to the chromosomes of zebrafish. The high-quality genome assembled in this
 work provides a valuable genomic resource for further biological and
 evolutionary studies of O. macrolepis.
description: The prediction of protein-coding genes was performed using a
 combination of the homology-based, de novo based and RNA sequences-based
 gene methods. The annotation of repetitive sequences was constructed by
 RepeatModeler, Repbase and RepeatMasker.Non-coding RNAs, including rRNAs,
 snRNAs, and miRNAs were identified by aligning <i>Onychostoma
 macrolepis</i> genome to the Rfam database. The tRNAs were predicted
 using tRNAscan-SE. The rRNAs and their subunits were predicted using
 RNAmmer.
DOI: 10.5061/dryad.c2fqz615b
title: Data from: Effects of inbreeding on behavioural plasticity of parent-offspring interactions in a burying beetle

description: Inbreeding depression is defined as a fitness decline in progeny resulting
 from mating between related individuals, the severity of which may vary
 across environmental conditions. Such inbreeding-by-environment
 interactions might reflect that inbred individuals have a lower capacity
 for adjusting their phenotype to match different environmental conditions
 better, as shown in prior studies on developmental plasticity. Behavioural
 plasticity is more flexible than developmental plasticity because it is
 reversible and relatively quick, but little is known about its sensitivity
 to inbreeding. Here we investigate effects of inbreeding on behavioural
 plasticity in the context of parent-offspring interactions in the burying
 beetle Nicrophorus vespilloides. Larvae increase begging with the level of
 hunger, and parents increase their level of care when brood sizes
 increase. Here we find that inbreeding increased behavioural plasticity in
 larvae, reducing their time spent associating with a parent in response to
 the length of food-deprivation more than outbred larvae. However,
 inbreeding had no effect on the behavioural plasticity of offspring
 begging or any parental behaviour. Overall, our results show that
 inbreeding can increase behavioural plasticity. We suggest that
 inbreeding-by-environment interactions might arise when inbreeding is
 associated with too little or too much plasticity in response to changing
 environmental conditions.
description: This spreadsheet provides data of two separate experiments
 investigating the effects of inbreeding status on larval and parental
 behaviour in the burying beetle <em>Nicrophorus
 vespilloides</em>. Each line represents an observation. In the first
 expeirment each brood was observed three times and in the second
 experiment each parent was observed twice. Missing data are recorded as
 NA.
DOI: 10.5061/dryad.zw3r2285w
title: Geometric structure and electronic properties of boron-substituted silicene

description: The essential properties of monolayer silicene greatly enriched by boron
 substitutions are thoroughly explored through first -principles
 calculations. Delicate analyses are conducted on the highly non-uniform
 Moire superlattices, atom-dominated band structures, charge density
 distributions and atom- & orbital-decomposed van Hove
 singularities. The hybridized 2pz-3pz and [2s, 2px, 2py]-[3s, 3px, 3py]
 bondings, with orthogonal relations, are obtained from the developed
 theoretical framework. The red-shifted Fermi level and the modified Dirac
 cones/π bands/σ bands are clearly identified under various concentrations
 and configurations of guest atoms. Our results demonstrate that the charge
 transfer leads to the non-uniform chemical environment that creates
 diverse electronic properties.  
description: This dataset was collected by by density functional theory (DFT)
 implemented in Vienna ab initio simulation package (VASP). We used the
 Perdew-Burke-Ernzerhof (PBE) functional under the generalized gradient
 approximation for the exchange and correlation energies. Beside, the
 projector augmented wave (PAW) pseudopotentials can characterize the
 electron-ion interactions. The first Brillouin zones are sampled by 9 × 9
 × 1 and 100 × 100 × 1 k-points, respectively for optimal geometric
 structures and calculations of the electronic properties.
description: We can use p4vasp software to read these files to know the
 geometric structures. Besides, the readers who want to reproduce this
 study can rebuild the sample using the VESTA software. This two software
 is free.   http://www.p4vasp.at/<br>
 http://jp-minerals.org/vesta/en/ However, to collect
 the electronic properties, we need to use the Vienna Ab initio Simulation
 Package (VASP), a commercial software.
 https://www.vasp.at
DOI: 10.5061/dryad.qz612jmbk
title: Data from: Seasonality determines patterns of growth and age structure over a geographic gradient in an ectothermic vertebrate

description: Environmental variation connected with sea- sonality is likely to affect
 the evolution of life-history strategies in ectotherms, but there is no
 consensus as to how important life-history traits like body size are
 influ- enced by environmental variation along seasonal gradients. We
 compared adult body size, skeletal growth, mean age, age at first
 reproduction and longevity among 11 common frog (Rana temporaria)
 populations sampled along a 1,600-km-long latitudinal gradient across
 Scandinavia. Mean age, age at first reproduction and longevity increased
 linearly with decreasing growth season length. Lifetime activity (i.e. the
 estimated number of active days during life-time) was highest at
 mid-latitudes and females had on average more active days throughout their
 lives than males. Variation in body size was due to differences in
 lifetime activity among populations—individuals (especially females) were
 largest where they had the longest cumula- tive activity period—as well as
 to differences between populations in skeletal growth rate as determined
 by skel- etochronological analyses. Especially, males grew faster
 at intermediate latitudes. While life-history trait variation was
 strongly associated with latitude, the direction and shape of these
 relationships were sex- and trait-specific. These context-dependent
 relationships may be the result of life- history trade-offs enforced by
 differences in future reproductive opportunities and time constraints
 among the populations. Thus, seasonality appears to be an important
 environmental factor shaping life-history trait variation in common frogs.
description: Field collected data on adult common frogs from 11 locations
 along a 1600 km latitudinal gradient from southern Sweden to northern
 Finland. Ages of collected individuals were estimated with
 skeletochronological methods in laboratory. Available are also e.g. body
 sizes (snout-vent lenghts) and weighs of the individuals.
description: For methods of age estimation, consult the published paper.
DOI: 10.5061/dryad.ghx3ffbkc
title: Data from: Artificial selection on sexual aggression: correlated traits and possible trade‐offs

description: Forced copulation is an extreme form of sexual aggression that can affect
 the evolution of sex-specific anatomy, morphology and behavior. To
 characterize mechanistic and evolutionary aspects of forced copulation, we
 artificially selected male fruit flies based on their ability to succeed
 in the naturally prevalent behavior of forced matings with newly eclosed
 (teneral) females. The low and high forced copulation lineages showed
 rapid divergence, with the high lineages ultimately showing twice the
 rates of forced copulation as the low lineages. While males from the high
 lineages spent more time aggressively pursuing and mounting teneral
 females, their behavior towards non-teneral and heterospecific females was
 similar to that of males from the low lineages. Males from the low and
 high lineages also showed similar levels of male-male aggression. This
 suggests little or no genetic correlations between sexual aggression and
 non-aggressive pursuit of females, and between male aggression towards
 females and males. Surprisingly however, males from the high lineages had
 twice as high mating success than males from the low lineages when allowed
 to compete for consensual mating with mature females. In further
 experiments, we found no evidence for trade-offs associated with high
 forced mating rates: males from the high lineages did not have lower
 longevity than males from the low lineages when housed with females, and
 four generations of relaxed selection did not lead to convergence in
 forced mating rates. Our data indicate complex interactions among forced
 copulation success and consensual mating behaviour, which we hope to
 clarify in future genomic work.
DOI: 10.5061/dryad.3bk3j9kg9
title: Longitudinal change in dopamine transporter availability in idiopathic REM sleep behavior disorder

description: Objective: To elucidate longitudinal changes in the dopamine transporter
 (DAT) availability in association with the prodromal markers in idiopathic
 rapid-eye-movement sleep behavior disorder (iRBD), we analyzed a
 longitudinal prospective iRBD cohort data. Method: The study cohort
 consisted of iRBD, Parkinson’s disease (PD) patients and healthy controls.
 All participants were evaluated for olfaction, neuropsychological tests,
 the Movement disorders society-Unified Parkinson’s disease Rating Scale
 and underwent 18F-FP-CIT PET scans every 2 years. We calculated the DAT
 pattern by performing the principal component analysis of tracer uptakes
 in 6 striatal regions. Results: DAT patterns in iRBD patients with
 baseline hyposmia, constipation and mild parkinsonian signs distributed
 toward PD-pattern and clearly distinguished from the healthy control
 pattern. The DAT pattern moved toward PD-pattern over time in some iRBD
 patients during the follow-up and baseline hyposmia was the only biomarker
 significantly associated with this change. Baseline PD-pattern of DAT
 predicted 58% of disease converters (Hazard Ratio=4.95 [1.16~21.08]). The
 combination of hyposmia and baseline PD pattern of DAT predicted 67% of
 the conversion (Hazard Ratio=7.89 [1.85~33.69]). The estimated sample size
 required for a simulated neuroprotective clinical trial was 63 per group
 when the annual change of DAT pattern was used as an outcome in the
 subgroup with baseline DAT PD-pattern and hyposmia, which is the smallest
 number reported so far. Conclusion: Baseline and longitudinal monitoring
 of the DAT pattern can be a useful biomarker in identifying individuals
 with a high risk of disease conversion and in selecting the potential
 population for clinical trials in iRBD.
DOI: 10.5061/dryad.4f4qrfj8h
title: Endocrine disruptors cause multigenerational and transgenerational epigenetic changes in fish exposed during early life

description: The inland silverside, Menidia beryllina, is a euryhaline fish and a model
 organism in ecotoxicology. We previously showed that exposure to picomolar
 (ng/L) levels of endocrine disrupting chemicals (EDCs) can cause a variety
 of effects in M. beryllina, from changes in gene expression to phenotypic
 alterations. Here we explore the potential for early life exposure to EDCs
 to modify the epigenome in silversides, with a focus on multi- and
 transgenerational effects. EDCs included contaminants of emerging concern
 (the pyrethroid insecticide bifenthrin and the synthetic progestin
 levonorgestrel), as well as a commonly detected synthetic estrogen
 (ethinylestradiol), and a synthetic androgen (trenbolone) at exposure
 levels ranging from 3 to 10 ng/L. In a multigenerational experiment, we
 exposed parental silversides to EDCs from fertilization until 21 days post
 hatch (dph). Then we assessed DNA methylation patterns for three
 generations (F0, F1, and F2) in whole body larval fish using reduced
 representation bisulfite sequencing (RRBS). We found significant ( =
 0.05) differences in promoter and/or gene body methylation in treatment
 fish relative to controls for all EDCs and all generations indicating that
 both multigenerational (F1) and transgenerational (F2) effects that were
 caused by strict inheritance of DNA methylation alterations and the
 dysregulation of epigenetic control mechanisms. Using gene ontology and
 pathway analyses, we found enrichment in biological processes and pathways
 representative of growth and development, immune function, reproduction,
 pigmentation, epigenetic regulation, stress response and repair (including
 pathways important in carcinogenesis). Further, we found that a subset of
 potentially EDC responsive genes (EDCRGs) were differentially methylated
 across all treatments and generations and included hormone receptors,
 genes involved in steroidogenesis, prostaglandin synthesis, sexual
 development, DNA methylation, protein metabolism and synthesis, cell
 signaling, and neurodevelopment. The analysis of EDCRGs provided
 additional evidence that differential methylation is inherited by the
 offspring of EDC-treated animals, sometimes in the F2 generation that was
 never exposed. These findings show that low, environmentally relevant
 levels of EDCs can cause altered methylation in genes that are
 functionally relevant to impaired phenotypes documented in EDC-exposed
 animals and EDC exposure has the potential to affect epigenetic regulation
 in fish that have not been directly exposed.
description: Genome, Transcriptome, and RRBS Menidia beryllina raw data
DOI: 10.5061/dryad.41ns1rnb6
title: Adaptive zones shape the magnitude of premating reproductive isolation in Timema stick insects

description: Simpson's fossil-record inspired model of ‘adaptive zones’ proposes
 that evolution is dominated by small fluctuations within adaptive zones,
 occasionally punctuated by larger shifts between zones. This model can
 help explain why the process of population divergence often results in
 weak or moderate reproductive isolation (RI), rather than strong RI and
 distinct species. Applied to the speciation process, the adaptive zones
 hypothesis makes two inter-related predictions: (i) large shifts between
 zones are relatively rare, (ii) when large shifts do occur they generate
 stronger RI than shifts within zones. Here we use ecological,
 phylogenetic, and behavioural data to test these predictions in Timema
 stick insects. We show that host use in Timema is dominated by moderate
 shifts within the systematic divisions of flowering plants and conifers,
 with only a few extreme shifts between these divisions. However, when
 extreme shifts occur they generate greater RI than do more moderate
 shifts. Our results support the adaptive zones model, and suggest that the
 net contribution of ecological shifts to diversification is dependent on
 both their magnitude and frequency. We discuss the generality of our
 findings in light of emerging evidence from diverse taxa that the
 evolution of RI is not always the only factor determining the origin of
 species diversity
DOI: 10.7272/q6xg9pcw
title: Data from: Similarities and differences in interoceptive bodily awareness between US-American and Japanese cultures: A focus-group study in bicultural Japanese-Americans

description: Interoceptive awareness is the conscious perception of sensations that
 create the sense for the physiological condition of the body. A validation
 study for the Japanese translation of the Multidimensional Assessment of
 Interoceptive Awareness (MAIA) surprised with a factor structure different
 from the original English-language version by eliminating two of eight
 scales. This prompted an exploration of the similarities and differences
 in interoceptive bodily awareness between Japanese and European-Americans.
 Bicultural Japanese-Americans discussed concepts and experiences in the
 two cultures. We conducted focus groups and standard qualitative
 content-based analyses of transcribed recordings.
 Sixteen participants illustrated cross-cultural differences in
 interoceptive bodily awareness: switching between languages changes
 embodied experience; external versus internal attention focus; social
 expectations and body sensations; emphasis on form versus self-awareness;
 personal space; and mind-body relationship; context dependency of bodily
 awareness and self-construal. The participants explained key concepts that
 present challenges for a Japanese cultural adaptation of the MAIA,
 specifically the concept of self-regulation lost in the factor analysis.
 In Japanese culture, self-regulation serves the purpose of conforming to
 social expectations, rather than achieving an individual self-comforting
 sense of homeostasis. Our findings will inform the next phase of improving
 the MAIA’s cross-cultural adaptation.
description: Focus group transcriptes and coding process