Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
54,099
datasets available to search
ShareScore release 0.9.0
Dataset results
54,099 results for “Expression”
Data from: Genomic identification, characterization and differential expression analysis of SBP-box gene family in Brassica napus
Background: SBP-box genes belong to one of the largest families of transcription factors. Though members of this family have been characterized to be important regulators of diverse biological processes, information of SBP-box genes in the third most important oilseed crop Brassica napus is largely undefined. Results: In the present study, by whole genome bioinformatics analysis and transcriptional profiling, 58 putative members of SBP-box gene family in oilseed rape (Brassica napus L.) were identified and their expression pattern in different tissues as well as possible interaction with miRNAs were analyzed. In addition, B. napus lines with contrasting branch angle were used for investigating the involvement of SBP-box genes in plant architecture regulation. Detailed gene information, including genomic organization, structural feature, conserved domain and phylogenetic relationship of the genes were systematically characterized. By phylogenetic analysis, BnaSBP proteins were classified into eight distinct groups representing the clear orthologous relationships to their family members in Arabidopsis and rice. Expression analysis in twelve tissues including vegetative and reproductive organs showed different expression patterns among the SBP-box genes and a number of the genes exhibit tissue specific expression, indicating their diverse functions involved in the developmental process. Forty-four SBP-box genes were ascertained to contain the putative miR156 binding site, with 30 and 14 of the genes targeted by miR156 at the coding and 3′UTR region, respectively. Relative expression level of miR156 is varied across tissues. Different expression pattern of some BnaSBP genes and the negative correlation of transcription levels between miR156 and its target BnaSBP gene were observed in lines with different branch angle. Conclusions: Taken together, this study represents the first systematic analysis of the SBP-box gene family in Brassica napus. The data presented here provides base foundation for understanding the crucial roles of BnaSBP genes in plant development and other biological processes.
Data from: Determinants and co-expression of anti-predator responses in amphibian tadpoles: a meta-analysis
A wide range of taxa respond to perceived predation risk (PPR) through inducible defenses, and many prey are capable of responding both behaviorally and morphologically to the same risk event. In cases where multiple defenses confer protection by independent means (i.e., they are mechanistically independent) responses will either be co-expressed, or the expression of one defense will limit the capacity (or need) to respond along another axis. Our ability to generate a broad understanding of these patters has been limited, in part, by difficulties in comparing results across studies that employ distinct experimental protocols. Using the extensive literature on tadpole responses to PPR, we conducted a meta-analysis to identify the ecological and experimental determinants of inducible defence expression. We then assessed whether the magnitude of response to PPR along behavioural versus morphological response axes was positively, or negatively, correlated. The most commonly quantified responses to perceived risk in tadpoles included reductions in movement and swimming behaviour, and altered tail morphology. Our analyses reveal that tadpole behavioural responses are strongly influenced by prey family, predator taxon, evolutionary history with the predator (native vs. non-native), amount of prey consumed by the predator, and how perceived risk was manipulated (e.g., presence vs. absence of alarm cues). Tail morphology was similarly influenced by these factors, but also whether the target prey was palatable to predators. Thus, our results identify ecological and experimental features that critically influence the observed effect size in tadpole responses to PPR. A positive correlation between behavioural and morphological responses in studies where both were measured indicates that trait co-specialization is the predominant pattern of defense deployment in larval amphibians. This positive relationship suggests that survival tends to be maximized in tadpoles through equivalent coactivation of multiple independent axes of protection, opposed to maximal expression along any single axis.
Data from: There's no place like home: the contribution of direct and extended phenotypes on the expression of spider aggressiveness
Architectural constructions allow animals to modify their environment in order to improve their reproductive success. Constructions also modulate the expression of individual behavior, ultimately affecting the presence and importance of animal personality within populations. The exact impact of constructions on personality is seldom investigated. We quantified experimentally the impact of web characteristics on individual foraging behavior in the Western black widow spider (Latrodectus hesperus). We assayed aggressiveness toward a prey cue, and boldness while individuals resided on their own web versus after being translocated onto webs built by con-specifics. We quantified the importance of individual differences in aggressiveness and boldness while accounting for differences in web characteristics. We tested for relationships between web building, aggressiveness, and boldness. Web characteristics affected spider aggressiveness and interacted with individual web-building behavior to explain up to a fifth of the variation in foraging aggression, but did not affect spider boldness. Even after accounting for web characteristics, individuals still exhibited important differences in aggressiveness. We detected no relationship between an individual's aggressiveness behavioral type and the characteristics of the web it built. Surprisingly, web characteristics impacted aggressiveness differently from one individual to the next. Hence the effect of web characteristics on foraging behavior might depend on condition or past experience. Webs contributed mostly to the variation in aggressiveness within-individuals. Variation in web building behavior might affect the amount of consistent differences in foraging, mating, and anti-predator behavior among individuals and needs to be accounted for when quantifying individual variation in behavior in spiders.
Data from: "NGS based generation of expressed sequence tags for Lymantria dispar and Lymantria monacha, two closely related lepidopteran species with different responses to parasitism by Glyptapanteles liparidis" in Genomic Resources Notes accepted 1 December 2013 to 31 January 2014
Introduction: The gypsy moth, Lymantria dispar, and the nun moth, Lymantria monacha, are closely related species (Lepidoptera, Lymantriidae), co-seasonal and economically important forest pests on broadleaf and coniferous trees. In Central Europe, gypsy moth larvae are frequently parasitized by the gregarious, endoparasitic wasp Glyptapanteles liparidis (Hymenoptera, Braconidae). At oviposition, the female wasp injects between 10 and up to 100 eggs into the hemocoel of a single host larva, together with venom and calyx fluid containing polydnavirus (PDV) particles that subsequently play a critical role in suppressing the host immune response so that successful development of the parasitoid can proceed (Schopf 2007). These viruses, which are integrated in the genomic DNA of the wasp and undergo replication only in the female's ovary, rapidly enter host hemocytes, fat body, and nervous system following parasitization, and viral genes are expressed. In L. dispar larvae parasitized by G. liparidis, the host's hemocytes alter their behavior, fail to spread properly (thereby inhibiting the encapsulation response) and partly undergo programmed cell death (apoptosis), resulting in a dramatic drop in the host's total hemocyte number (Schafellner and Schläger 2009).
Data from: Characterization of the genome and transcriptome of the blue tit Cyanistes caeruleus: polymorphisms, sex-biased expression and selection signals
Decoding genomic sequences and determining their variation within populations has potential to reveal adaptive processes and unravel the genetic basis of ecologically relevant trait variation within a species. The blue tit Cyanistes caeruleus – a long-time ecological model species – has been used to investigate fitness consequences of variation in mating and reproductive behaviour. However, very little is known about the underlying genetic changes due to natural and sexual selection in the genome of this songbird. As a step to bridge this gap, we assembled the first draft genome of a single blue tit, mapped the transcriptome of five females and five males to this reference, identified genomewide variants and performed sex-differential expression analysis in the gonads, brain and other tissues. In the gonads, we found a high number of sex-biased genes, and of those, a similar proportion were sex-limited (genes only expressed in one sex) in males and females. However, in the brain, the proportion of female-limited genes within the female-biased gene category (82%) was substantially higher than the proportion of male-limited genes within the male-biased category (6%). This suggests a predominant on-off switching mechanism for the female-limited genes. In addition, most male-biased genes were located on the Z-chromosome, indicating incomplete dosage compensation for the male-biased genes. We called more than 500 000 SNPs from the RNA-seq data. Heterozygote detection in the single reference individual was highly congruent between DNA-seq and RNA-seq calling. Using information from these polymorphisms, we identified potential selection signals in the genome. We list candidate genes which can be used for further sequencing and detailed selection studies, including genes potentially related to meiotic drive evolution. A public genome browser of the blue tit with the described information is available at http://public-genomes-ngs.molgen.mpg.de.
Data from: HDAC1/2-dependent P0 expression maintains paranodal and nodal integrity independently of myelin stability through interactions with neurofascins
The pathogenesis of peripheral neuropathies in adults is linked to maintenance mechanisms that are not well understood. Here, we elucidate a novel critical maintenance mechanism for Schwann cell (SC)–axon interaction. Using mouse genetics, ablation of the transcriptional regulators histone deacetylases 1 and 2 (HDAC1/2) in adult SCs severely affected paranodal and nodal integrity and led to demyelination/remyelination. Expression levels of the HDAC1/2 target gene myelin protein zero (P0) were reduced by half, accompanied by altered localization and stability of neurofascin (NFasc)155, NFasc186, and loss of Caspr and septate-like junctions. We identify P0 as a novel binding partner of NFasc155 and NFasc186, both in vivo and by in vitro adhesion assay. Furthermore, we demonstrate that HDAC1/2-dependent P0 expression is crucial for the maintenance of paranodal/nodal integrity and axonal function through interaction of P0 with neurofascins. In addition, we show that the latter mechanism is impaired by some P0 mutations that lead to late onset Charcot-Marie-Tooth disease.
Data from: Genetic variation underlying the expression of a polyphenism
Polyphenic traits are widespread, and represent a conditional strategy sensitive to environmental cues. The environmentally cued threshold (ET) model considers the switchpoint between alternative phenotypes as a polygenic quantitative trait with normally distributed variation. However, the genetic variation for switchpoints has rarely been explored empirically. Here we used inbred lines to investigate the genetic variation for the switchpoint in the mite Rhizoglyphus echinopus, in which males are either fighters or scramblers. The conditionality of male dimorphism varied among inbred lines, indicating that there was genetic variation for switchpoints in the base population, as predicted by the ET model. Our results also suggest a mixture between canalised and conditional strategists in R. echinopus. We propose that major genes that canalise morph expression and affect the extent to which a trait can be conditionally expressed could be a feature of the genetic architecture of threshold traits in other taxa.
Data from: Notch and Nodal control expression of a forkhead factor in the specification network of a multipotent progenitor population in sea urchin
Indirect development, where embryogenesis gives rise to a larval form, requires that some cells retain developmental potency until they contribute to the different tissues in the adult, including the germ line, in a later, post-embryonic phase. In sea urchins, the coelomic pouches are the major contributor to the adult but how coelomic pouch cells (CPCs) are specified during embryogenesis is unknown. We here identify the key signaling inputs into the CPC specification network and show the forkhead factor foxY is the first transcription factor specifically expressed in CPC progenitors. Through dissection of its cis-regulatory apparatus we determine that the foxY expression pattern is the result of two signaling inputs: First, Delta/Notch signaling activates foxY in CPC progenitors and, second, Nodal signaling restricts its expression to the left side, where the adult rudiment will form, through direct repression by the Nodal target pitx2. A third signal, Hedgehog, is required for coelomic pouch morphogenesis and institution of laterality but does not directly affect foxY transcription. Knockdown of foxY results in failure to form coelomic pouches and disrupts expression of virtually all transcription factors known to be expressed in this cell type. Our experiments place foxY at the top of the regulatory hierarchy underlying specification of a cell type maintaining developmental potency.
Microhabitat partitioning correlates with opsin gene expression in coral reef cardinalfishes (Apogonidae)
<ol> <li>Fish are the most diverse vertebrate group, and they have evolved equally diverse visual systems, varying in terms of eye morphology, number and distribution of spectrally distinct photoreceptor types, visual opsin genes and opsin gene expression levels.</li> <li>This variation is mainly due to adaptations driven by two factors: differences in the light environments and behavioural tasks. However, while the effects of large-scale habitat differences are well described, it is less clear whether visual systems also adapt to differences in environmental light at the microhabitat level.</li> <li>To address this, we assessed the relationship between microhabitat use and visual system features in fishes inhabiting coral reefs, where habitat partitioning is particularly common.</li> <li>We suggest that differences in microhabitat use by cardinalfishes (Apogonidae) drive morphological and molecular adaptations in their visual systems. To test this, we investigated diurnal microhabitat use in 17 cardinalfish species and assessed whether this correlated with differences in visual opsin gene expression and eye morphology.</li> <li>We found that cardinalfishes display six types of microhabitat partitioning behaviours during the day, ranging from specialists found exclusively in the water column to species that are always hidden inside the reef matrix.</li> <li>Species predominantly found in exposed microhabitats had higher expression of the short-wavelength sensitive violet opsin (<i>SWS2B</i>) and lower expression of the dim-light active rod opsin (<i>RH1</i>). Species of intermediate exposure, on the other hand, expressed opsins that are mostly sensitive to the blue-green central part of the light spectrum (<i>SWS2As</i> and <i>RH2s</i>), while fishes entirely hidden in the reef substrate had a higher expression of the long-wavelength sensitive red opsin (<i>LWS</i>).</li> <li>We also found that eye size relative to body size differed between cardinalfish species, and relative eye size decreased with an increase in habitat exposure.</li> <li>Retinal topography did not show co-adaptation with microhabitat use, but data suggested co-adaptation with feeding mode.</li> <li>We suggest that, although most cardinalfishes are nocturnal foragers, their visual systems – and possibly those of other (reef) fishes – have also adapted to the light intensity and the light spectrum of their preferred diurnal microhabitats.</li> </ol>
Data from: Condition-dependent expression of pre- and postcopulatory sexual traits in guppies
Female choice can impose persistent directional selection on male sexually selected traits, yet such traits often exhibit high levels of phenotypic variation. One explanation for this paradox is that if sexually selected traits are costly, only the fittest males are able to acquire and allocate the resources required for their expression. Furthermore, because male condition is dependent on resource allocation, condition dependence in sexual traits is expected to underlie trade-offs between reproduction and other life-history functions. In this study we test these ideas by experimentally manipulating diet quality (carotenoid levels) and quantity in the guppy (Poecilia reticulata), a livebearing freshwater fish that is an important model for understanding relationships between pre- and post-copulatory sexually selected traits. Specifically, we test for condition dependence in the expression of pre- and postcopulatory sexual traits (behavior, ornamentation, sperm traits) and determine whether diet manipulation mediates relationships among these traits. Consistent with prior work we found a significant effect of diet quantity on the expression of both pre- and postcopulatory male traits; diet-restricted males performed fewer sexual behaviors and exhibited significant reductions in color ornamentation, sperm quality, sperm number, and sperm length than those fed ad libitum. However, contrary to our expectations, we found no significant effect of carotenoid manipulation on the expression of any of these traits, and no evidence for a trade-off in resource allocation between pre- and postcopulatory episodes of sexual selection. Our results further underscore the sensitivity of behavioral, ornamental, and ejaculate traits to dietary stress, and highlight the important role of condition dependence in maintaining the high variability in male sexual traits.
Gene expression for 26 species of Aselloidea isopods
<p>Gene expression used in "<strong>No evidence that nitrogen limitation influences the elemental composition of isopod transcriptomes and proteomes"</strong></p> <p>The archive contains 26 tables of TPM expression with Trinity as well as ACNUC accession numbers.</p> <p> </p>
Large scale expression and purification of full length huntingtin Q23 from baculovirus expression system (2016/08/29)
<p>Open lab notebook huntingtin structure function project.<br> </p>
Expression and purification of huntingtin domain constructs spanning aa. P80-G428 (2016/11/29)
<p>Open lab notebook huntingtin structure function project.<br> </p>
GAN Generated Images for Facial Expression Recognition systems
<p>Most facial expression recognition (FER) systems rely on machine learning approaches that require large databases (DBs) for effective training. As these are not easily available, a good solution is to augment the DBs with appropriate techniques, which are typically based on either geometric transformation or deep learning based technologies (e.g., Generative Adversarial Networks (GANs)). Whereas the first category of techniques has been fairly adopted in the past, studies that use GAN-based techniques are limited for FER systems. To advance in this respect, we evaluate the impact of the GAN techniques by creating a new DB containing the generated synthetic images. </p> <p>The face images contained in the KDEF DB serve as the basis for creating novel synthetic images by combining the facial features of two images (i.e., Candie Kung and Cristina Saralegui) selected from the YouTube-Faces DB. The novel images differ from each other, in particular concerning the eyes, the nose, and the mouth, whose characteristics are taken from the Candie and Cristina images.</p> <p>The total number of novel synthetic images generated with the GAN is 980 (70 individuals from KDEF DB x 7 emotions x 2 subjects from YouTube-Faces DB).</p> <p>The zip file "GAN_KDEF_Candie" contains the 490 images generated by combining the KDEF images with the Candie Kung image. The zip file "GAN_KDEF_Cristina" contains the 490 images generated by combining the KDEF images with the Cristina Saralegui image. The used image IDs are the same used for the KDEF DB. The synthetic generated images have a resolution of 562x762 pixels.</p> <p> </p> <p><strong>If you make use of this dataset, please consider citing the following publication:</strong></p> <p>Porcu, S., Floris, A., & Atzori, L. (2020). Evaluation of Data Augmentation Techniques for Facial Expression Recognition Systems. Electronics, 9, 1892, doi: 10.3390/electronics9111892, url: https://www.mdpi.com/2079-9292/9/11/1892.</p> <p>BibTex format:</p> <p>@article{porcu2020evaluation, title={Evaluation of Data Augmentation Techniques for Facial Expression Recognition Systems}, author={Porcu, Simone and Floris, Alessandro and Atzori, Luigi}, journal={Electronics}, volume={9}, pages={108781}, year={2020}, number = {11}, article-number = {1892}, publisher={MDPI}, doi={10.3390/electronics9111892} }</p> <p> </p>
PRAGMATIC FEATURES OF THE EXPRESSION OF PHRASEOLOGICAL UNITS IN HUMOROUS DISCOURSE
Open the record for dataset details and reuse information.
SPEECH CLICHES AS A COMPONENT OF EXPRESSIVE ORAL SPEECH
Open the record for dataset details and reuse information.
THE NOMINATIVE FIELD OF MEANS EXPRESSING THE CONCEPT OF "MOUTH" IN ENGLISH AND UZBEK
Open the record for dataset details and reuse information.
LINGUISTIC AND CULTURAL EXPRESSION IN TRANSLATION STUDIES
Open the record for dataset details and reuse information.
ELLIPTIC SENTENCES AND THEIR EXPRESSION IN DIFFERENT STYLES
Open the record for dataset details and reuse information.
SOME CONSIDERATIONS ON THE FORMATION OF MEANS OF EXPRESSING THE CONCEPT OF KINSHIP
Open the record for dataset details and reuse information.
ScienceDex guides
Understand access before you commit
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.