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Datasets for feature-specific class prediction, from readings in several cell-types.
<p>The cell-types featured here are A549, H1ESC, HeLa, IMR90, K562, and MCF7. These happen to be the 6 cell-types out of 8 existing in our integrative database, GREG (https://doi.org/10.1093/database/baz162). The normalized read-coverages from features (variables) like DNA-Protein bindings, histone modifications; ChIP-Seq data, are mapped through genomic intervals of 2 Kbs, genome-wide. These genomic intervals (technically <em>bins</em>), are classified as <em><strong>Hubs</strong></em> or <strong><em>Non-Hubs</em></strong>. Hubs are those bins that are engaged in genomic crosstalk at a distance of 1Mb or Inf., and are Non-Hubs otherwise.</p> <p>Note that features are inconsistent across different cell-types, due to the availability of data. The BAM files have been sourced from ENCODE and NCBI repositories. Also, the users might want to use <em>unique() in R</em> or something similar to refine the datasets for non-redundant instances (if existing).<em> </em></p> <p>The analysis following this data can be tracked at https://github.com/mora-lab/GREG-Hubs.</p>
Depot-specific analysis of human adipose cells and their responses to Bisphenol S
<p class="CxSpFirst">Exposure to endocrine disrupting chemicals (EDCs) is associated with adverse health outcomes including obesity and diabetes. Obesity, and more specifically visceral obesity, is correlated with metabolic disease. The adipose tissue is an endocrine organ and a potential target for many environmental pollutants including bisphenols. The subcutaneous and the omental (visceral) depots are comprised of mature adipocytes and residing progenitors, which may be different between the depots and may be EDCs targets. Bisphenol A (BPA) is a suspected metabolic disruptor, and is being replaced with structurally similar compounds such as bisphenol S (BPS). Like BPA, BPS induces adipogenesis in murine and primary human subcutaneous preadipocytes. However, the effect of BPS on omental preadipocytes is not known. In this study, we show that human primary progenitors from omental depots have a distinct transcriptomic signature as compared to progenitors derived from donor-matched subcutaneous depots. Furthermore, we show that BPS increases adipogenesis of both omental and subcutaneous preadipocytes and can mimic the action of glucocorticoids or peroxisome proliferator-activated receptor g (PPARg) agonists. We also show that BPS treatment, at 0.1 µM and 25 µM, modifies the adipokine profiles of both omental and subcutaneous derived adipocytes, in a depot specific manner. Taken together our data show distinct gene expression profiles in the omental versus subcutaneous progenitors and similar responses to the BPA analogue, BPS.</p>
Data Repository: Single-cell mapper (scMappR): using scRNA-seq to infer cell-type specificities of differentially expressed genes
<p>Data repository for the scMappR manuscript:</p> <p>Abstract from biorXiv (https://www.biorxiv.org/content/10.1101/2020.08.24.265298v1.full).</p> <p>RNA sequencing (RNA-seq) is widely used to identify differentially expressed genes (DEGs) and reveal biological mechanisms underlying complex biological processes. RNA-seq is often performed on heterogeneous samples and the resulting DEGs do not necessarily indicate the cell types where the differential expression occurred. While single-cell RNA-seq (scRNA-seq) methods solve this problem, technical and cost constraints currently limit its widespread use. Here we present single cell Mapper (scMappR), a method that assigns cell-type specificity scores to DEGs obtained from bulk RNA-seq by integrating cell-type expression data generated by scRNA-seq and existing deconvolution methods. After benchmarking scMappR using RNA-seq data obtained from sorted blood cells, we asked if scMappR could reveal known cell-type specific changes that occur during kidney regeneration. We found that scMappR appropriately assigned DEGs to cell-types involved in kidney regeneration, including a relatively small proportion of immune cells. While scMappR can work with any user supplied scRNA-seq data, we curated scRNA-seq expression matrices for ∼100 human and mouse tissues to facilitate its use with bulk RNA-seq data alone. Overall, scMappR is a user-friendly R package that complements traditional differential expression analysis available at CRAN.</p>
Cellular (0.5deg), crop-specific land use intensity (tau) for 1995 and 2000
<p>tau_data_1995-2000.mz contains the cellular and crop-specific numbers as they are reported in the paper (Dietrich J.P., Schmitz C., Müller C., Fader M., Lotze-Campen H., Popp A., "Measuring agricultural land-use intensity – A global analysis using a model-assisted approach", Ecological Modelling, Volume 232, 10 May 2012, Pages 109-118, ISSN 0304-3800, 10.1016/j.ecolmodel.2012.03.002.), using query.csv one can aggregate this data to ISO countries.</p>
Species-specific but not phylosymbiotic gut microbiomes of New Guinean Passerines are shaped by diet and flight-associated gut modifications
<p>The folder includes the r script and main data files used to conduct main analyses</p>
The evolution of age-specific choosiness when mating
<p>Mate choice is a crucial element of many processes in evolutionary biology. Empirical research has shown that mating preference and choosiness often change with age. Understanding the evolutionary causes of patterns of age-specific choosiness is challenging because different mechanisms can give rise to the same pattern. Instead of focusing on the optimal age-specific choosiness strategy given fitness trade-offs, we approach this question from a more general standpoint and ask how the strength of selection on choosiness changes with the age at which it is expressed. We show that the strength of selection on a modifier of choosiness at a given age depends on the relative contribution of this age class to the pool of offspring but does not depend directly on the strength of selection on fitness components at the age affected by the modifier. We illustrate our results by contrasting two life histories from the literature. We further show how mutation-selection balance at the choosiness locus can shape age-specific choosiness. Our results provide new insights for understanding the evolution of choosiness throughout life, with implications for understanding the evolution of mate choice and reproductive isolation.</p>
Personality-specific carry-over effects on breeding
Carry-over effects describe the phenomenon whereby an animal's previous conditions influence its subsequent performance. Carry-over effects are unlikely to affect individuals uniformly, but the factors modulating their strength are poorly known. Variation in the strength of carry-over effects may reflect individual differences in pace-of-life: slow-paced, shyly behaved individuals are thought to favour allocation to self-maintenance over current reproduction, compared to their fast-paced, boldly behaved conspecifics (the pace-of-life syndrome hypothesis). Therefore, detectable carry-over effects on breeding should be weaker in bolder individuals, as they should maintain allocation to reproduction irrespective of previous conditions, while shy individuals should experience stronger carry-over effects. We tested this prediction in black-legged kittiwakes breeding in Svalbard. Using miniature biologging devices, we measured non-breeding activity of kittiwakes, and monitored their subsequent breeding performance. We report a number of negative carry-over effects of non-breeding activity on breeding, which were generally stronger in shyer individuals: more active winters were followed by later breeding phenology and poorer breeding performance in shy birds, but these effects were weaker or undetected in bolder individuals. Our study quantifies individual variability in the strength of carry-over effects on breeding, and provides a mechanism explaining widespread differences in individual reproductive success.
Public-private partnerships in nutrition specific interventions in Eastern Mediterranean Region countries
<p class="MDPI17abstract"><b>Introduction:</b> Public Private Partnerships (PPPs) in public health have been widely promoted as an effective tool for accelerating progress toward achieving the United Nation's Sustainable Development Goals (SDGs), including SDG 2 "to eliminate hunger." At the global level, partnership with the private sector was found to be very instrumental in <span>improving the nutritional status of poor and food-insecure people,</span> promoting healthy lifestyle, and developing initiatives to prevent childhood obesity. In countries of the Eastern Mediterranean Region (EMR), PPPs in nutrition actions has been mainly driven by UN and International development agencies to support low and middle -income countries in achieving better health outcomes. Despite the increased prominence of engaging the private sector in public health actions in countries of the EMR, the evidence on the role of the private sector in the design/implementation of these actions is still not documented.</p> <p class="MDPI21heading1"><b>Objectives</b>: The objective of this study is to assess the role and contribution of the private sector in the design/ implementation of nutrition- specific interventions addressing the double burden of malnutrition in countries from the EMR and identifying the key factors for successful PPP implementation.</p> <p><span><b>Methods</b>: <span>The study design was descriptive using secondary data obtained from digital internet sources, including WHO databases, grey literature, and websites of UN and International development agencies. </span></span></p> <p><span><b><span>Results</span></b><span>: The desk review revealed that the private sector has played a sizable role in the implementation of food fortification initiatives and in the implementation of nutritional policies promoting healthy diets. The experience of the Region shows the significant impact of government commitment, and the availability of national policies and systems for monitoring and enforcement on the sustainability and effectiveness of PPPs specific nutrition interventions.</span></span></p> <p><span><b><span>Conclusion</span></b><span>: The study emphasizes the key actions recommended for the governments to enhance the application of PPPs as a tool to accelerate the EMR countries' progress toward achieving the nutrition targets under SDG 2 by 2030. </span></span></p>
PLATE 3 in Revealing the specific status of Mellicta distans Higgins, 1955, stat. n. (Lepidoptera Nymphalidae) with morphological and molecular characters
PLATE 3. Wing pattern of M. distans stat. n. (1) and M. aurelia (2).
Isoform specific activities of androgen receptor and its splice variants in prostate cancer cells
<p>Androgen receptor (AR) signaling continues to drive castration resistant prostate cancer (CRPC) in spite of androgen deprivation therapy (ADT). Constitutively active shorter variants of AR, lacking the ligand binding domain, are frequently expressed in CRPC and have emerged as a potential mechanism for prostate cancer to escape ADT. ARv7 and AR<sup>v567es </sup>are two of the most commonly detected variants of AR in clinical samples of advanced, metastatic prostate cancer. It is not clear if variants of AR merely act as weaker substitutes for AR or can mediate unique isoform specific activities different from AR. In this study, we employed LNCaP prostate cancer cell lines with inducible expression of ARv7 or AR<sup>v567es </sup>to delineate similarities and differences in transcriptomics, metabolomics and lipidomics resulting from the activation of AR, ARv7 or AR<sup>v567es</sup>. While the majority of target genes were similarly regulated by the action of all three isoforms, we found a clear difference in transcriptomic activities of AR versus the variants, and a few differences between ARv7 and AR<sup>v567es</sup>. Some of the target gene regulation by AR isoforms was similar in the VCaP background as well. Differences in downstream activities of AR isoforms were also evident from comparison of the metabolome and lipidome in an LNCaP model. Overall our study implies that shorter variants of AR are capable of mediating unique downstream activities different from AR and some of these are isoform specific.</p>
Data from: Sex-specific associations between life history traits and a novel reproductive polymorphism in the Pacific field cricket
<p>Associations between heritable polymorphisms and life-history traits, such as development time or reproductive investment, may play an underappreciated role in maintaining polymorphic systems. This is because selection acting on a particular morph could be bolstered or disrupted by correlated changes in life-history or vice versa. In a Hawaiian population of the Pacific field cricket (<em>Teleogryllus oceanicus</em>), a novel mutation (flatwing) on the X-chromosome is responsible for a heritable polymorphism in male wing structure. We used laboratory cricket colonies fixed for male wing morph to investigate whether males and females bearing the flatwing or normal-wing (wild-type) allele differed in their life-history traits. We found that flatwing males developed faster and had heavier testes than normal-wings, whereas flatwing homozygous females developed slower and had lighter reproductive tissues than normal-wing homozygous females. Our results advance our understanding of the evolution of polymorphisms by demonstrating that the genetic change responsible for a reproductive polymorphism can also have consequences for fundamental life-history traits in both males and females.</p>
Raw - EBV-specific CD8 T lymphocytes and B cells during glatiramer acetate therapy in patients with MS
<p>Intracellular staining overnight</p>
Habitat-specific survival of golden-winged warblers (Vermivora chrysoptera) during the non-breeding season in an agricultural landscape
<p>Nearctic-Neotropical migratory birds are considered priority species for conservation because they are subject to threats at distinct breeding, migratory and stopover locations throughout their annual cycle, and many species have undergone severe population declines. Research during the non-breeding season has focused on identifying the locations and habitats that migrants use, but wintering migrants are known to occupy habitats of both high and low quality, especially when the best sites are saturated by conspecifics. Thus, the presence or abundance of a species may not be a reliable indicator of winter habitat quality. The habitat associations of the golden-winged warbler <i>Vermivora chrysoptera</i>, a Nearctic-Neotropical migrant bird species of elevated conservation concern, are relatively well studied, yet conservation efforts are hindered by lack of information about basic demographic rates. In particular, no published estimates exist for non-breeding season survival, which can be a key vital rate affecting population viability, nor how survival rates vary among habitats, which is important to designing conservation programs to support populations during the winter period. We studied a color-banded population of golden-winged warblers in Costa Rica over a 3-year period and estimated overall survival rates, and the effects of habitat characteristics on survival. We found that monthly survival of juveniles (0.881) was lower than adult birds (0.978). Monthly survival during the non-breeding season (0.967) was higher than monthly survival during the rest of the annual cycle (0.930). Survival was negatively related to canopy height, and we observed a significant quadratic effect where survival peaked at intermediate levels of vine tangles and dead hanging leaves, which corresponds to habitat features associated with abundance in prior studies at this same site. Our findings contribute to our existing knowledge about the potential impacts of winter-season events on Nearctic-Neotropical migratory bird populations, and also informs potential conservation strategies for wintering golden-winged warblers.</p>
Data from: Exogenous restoration of TUSC2 expression induces responsiveness to erlotinib in wildtype epidermal growth factor receptor (EGFR) lung cancer cells through context specific pathways resulting in enhanced therapeutic efficacy
Expression of the tumor suppressor gene TUSC2 is reduced or absent in most lung cancers and is associated with worse overall survival. In this study, we restored TUSC2 gene expression in several wild type EGFR non-small cell lung cancer (NSCLC) cell lines resistant to the epidermal growth factor receptor (EGFR) tyrosine kinase inhibitor erlotinib and analyzed their sensitivity to erlotinib in vitro and in vivo. A significant inhibition of cell growth and colony formation was observed with TUSC2 transient and stable expression. TUSC2-erlotinib cooperativity in vitro could be reproduced in vivo in subcutaneous tumor growth and lung metastasis formation lung cancer xenograft mouse models. Combination treatment with intravenous TUSC2 nanovesicles and erlotinib synergistically inhibited tumor growth and metastasis, and increased apoptotic activity. High-throughput qRT-PCR array analysis enabling multi-parallel expression profile analysis of eighty six receptor and non-receptor tyrosine kinase genes revealed a significant decrease of FGFR2 expression level, suggesting a potential role of FGFR2 in TUSC2-enhanced sensitivity to erlotinib. Western blots showed inhibition of FGFR2 by TUSC2 transient transfection, and marked increase of PARP, an apoptotic marker, cleavage level after TUSC2-erlotinb combined treatment. Suppression of FGFR2 by AZD4547 or gene knockdown enhanced sensitivity to erlotinib in some but not all tested cell lines. TUSC2 inhibits mTOR activation and the latter cell lines were responsive to the mTOR inhibitor rapamycin combined with erlotinib. These results suggest that TUSC2 restoration in wild type EGFR NSCLC may overcome erlotinib resistance, and identify FGFR2 and mTOR as critical regulators of this activity in varying cellular contexts. The therapeutic activity of TUSC2 could extend the use of erlotinib to lung cancer patients with wildtype EGFR.
Data from: General and species-specific impacts of a neonicotinoid insecticide on the ovary development and feeding of wild bumblebee queens
Bumblebees are essential pollinators of crops and wild plants, but are in decline across the globe. Neonicotinoid pesticides have been implicated as a potential driver of these declines, but most of our evidence base comes from studies of a single species. There is an urgent need to understand whether such results can be generalized across a range of species. Here, we present results of a laboratory experiment testing the impacts of field-relevant doses (1.87–5.32 ppb) of the neonicotinoid thiamethoxam on spring-caught wild queens of four bumblebee species: Bombus terrestris, B. lucorum, B. pratorum and B. pascuorum. Two weeks of exposure to the higher concentration of thiamethoxam caused a reduction in feeding in two out of four species, suggesting species-specific anti-feedant, repellency or toxicity effects. The higher level of thiamethoxam exposure resulted in a reduction in the average length of terminal oocytes in queens of all four species. In addition to providing the first evidence for general effects of neonicotinoids on ovary development in multiple species of wild bumblebee queens, the discovery of species-specific effects on feeding has significant implications for current practices and policy for pesticide risk assessment and use.
Data from: Sex-specific heterogeneity in fixed morphological traits influences individual fitness in a monogamous bird population
Theoretical work has emphasized the important role of individual traits on population dynamics, but empirical models are often based on average or stage-dependent demographic rates. In this study on a monogamous bird, the Eurasian hoopoe (Upupa epops), we show how the interactions between male and female fixed and dynamic heterogeneity influence demographic rates and population dynamics. We built an integral projection model including individual sex, age, condition (reflecting dynamic heterogeneity) and fixed morphology (reflecting fixed heterogeneity). Fixed morphology was derived from a principal component analysis of six morphological traits. Our results revealed that reproductive success and survival were linked to fixed heterogeneity whereas dynamic heterogeneity influenced mainly the timing of reproduction. Fixed heterogeneity had major consequences for the population growth rate, but interestingly, its effect on population dynamics differed between the sexes. Female fixed morphology was directly linked to annual reproductive success whereas male fixed morphology influenced also annual survival, being twice higher in large than in small males. Even in a monogamous bird with shared parental care, large males can reach 10\% higher fitness than females. Including the dynamics of male and female individual traits in population models refines our understanding of the individual mechanisms that influence demographic rates and population dynamics and can help identifying differences in sex-specific strategies.
Data from: Lineage-specific sequence evolution and exon edge conservation partially explain the relationship of evolutionary rate and expression level in A. thaliana
Rapidly evolving proteins can aid the identification of genes underlying phenotypic adaptation across taxa, but functional and structural elements of genes can also affect evolutionary rates. In plants, the 'edges' of exons, flanking intron junctions, are known to contain splice enhancers and to have a higher degree of conservation compared to the remainder of the coding region. However, the extent to which these regions may be masking indicators of positive selection or account for the relationship between dN/dS and other genomic parameters is unclear. We investigate the effects of exon edge conservation on the relationship of dN/dS to various sequence characteristics and gene expression parameters in the model plant Arabidopsis thaliana. We also obtain lineage-specific dN/dS estimates, making use of the recently sequenced genome of Thellungiella parvula, the second closest sequenced relative after the sister species Arabidopsis lyrata. Overall, we find that the effect of exon edge conservation, as well as the use of lineage-specific substitution estimates, upon dN/dS ratios partly explains the relationship between the rates of protein evolution and expression level. Furthermore, the removal of exon edges shifts dN/dS estimates upwards, increasing the proportion of genes potentially under adaptive selection. We conclude that lineage-specific substitutions and exon edge conservation have an important effect on dN/dS ratios and should be considered when assessing their relationship with other genomic parameters..
Data from: Time-dependent decline of body-specific attention to the paretic limb in chronic stroke patients
Objective: To examine whether reduced body-specific attention to paretic limb is found in chronic stroke patients in the time-dependent manner. Methods: Twenty-one patients with chronic hemiparesis (10 left and 11 right hemiparesis) after subcortical stroke and 18 age-matched healthy controls were recruited in this study. Standard neuropsychological examinations showed no clear evidence of spatial neglect in all patients. In order to quantitatively measure the spatial attention to paretic hand, a visual detection task for detecting a target appearing on the surface of either a paretic or dummy hand was used. This task can measure the body facilitation effect, which makes faster detection of a target on the body compared with one far from the body. Results: In stroke patients, there was no difference in the reaction time for visual target between on the paretic and the dummy hands, while the healthy participants showed faster detection for the visual target on the real hand than that on dummy one. The Index of the body facilitation effect, subtracting the reaction time for the target-on-paretic hand from that for the target-on-dummy one, was correlated with the duration since onset and with finger function test on the Stroke Impairment Assessment Set. Conclusions: The reduction of the body facilitation effect in paretic limb suggests the decline of body-specific attention to the paretic one in patients with chronic hemiparesis. This decline of the body-specific attention, leading to neglect for paretic limb, will be one of the most serious problems for rehabilitation based on use-dependent plasticity.
Data from: Insulin signaling's role in mediating tissue-specific nutritional plasticity and robustness in the horn-polyphenic beetle Onthophagus taurus
Organisms cope with nutritional variation via developmental plasticity, adjusting trait size to nutrient availability for some traits while enabling others to develop in a nutritionally robust manner. Yet, the developmental mechanisms that regulate organ-specific growth across nutritional gradients remain poorly understood. We assessed the functions of members of the insulin/insulin-like signaling pathway (IIS) in the regulation of nutrition sensitivity and robustness in males of the horn-polyphenic beetle Onthophagus taurus, as well as potential regulatory interactions between IIS and two other growth-regulating pathways: Doublesex and Hedgehog signaling. Using RNA interference (RNAi) we experimentally knocked down both insulin receptors (InR1, InR2) and Foxo, a growth inhibitor. We then performed morphometric measurements on horns, a highly nutrition-sensitive trait, and genitalia, a largely nutrition-insensitive trait. Finally, we used qRT-PCR to assess expression levels of Doublesex and the Hedgehog-signaling gene smoothened following IIS-RNAi. Our results suggest that nutrition responsiveness of both traits is regulated by different IIS components, which transduce nutritional conditions to both Doublesex and Hedgehog pathways, albeit via different IIS pathway members. Combined with previous studies our findings suggest that separate origins of trait exaggeration among insect lineages were enabled through the independent cooption of IIS, yet via reliance on different components therein.
Data from: Do males pay for sex? Sex-specific selection coefficients suggest not
Selection acting on males can reduce mutation load of sexual relative to asexual populations, thus mitigating the two-fold cost of sex, provided that it seeks and destroys the same mutations as selection acting on females, but with higher efficiency. This could happen due to sexual selection – a potent evolutionary force that in most systems predominantly affects males. We used replicate populations of red flour beetles (Tribolium castaneum) to study sex-specific selection against deleterious mutations introduced with ionizing radiation. We found no evidence for selection being stronger in males than in females; in fact, we observed a non-significant trend in the opposite direction. This suggests that selection on males does not reduce mutation load below the level expected under the (hypothetical) scenario of asexual reproduction. Additionally, we employed a novel approach, based on a simple model, to quantify the relative contributions of sexual and offspring viability selection to the overall selection observed in males. We found them to be similar in magnitude; however, only the offspring viability component was statistically significant. In summary, we found no support for the hypothesis that selection on males in general, and sexual selection in particular, contributes to the evolutionary maintenance of sex.
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.