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13,587 results for “specification”
Figure 1 in Karyotype stasis but species-specific repetitive DNA patterns in Anguis lizards (Squamata: Anguidae), in the evolutionary framework of Anguiformes
Figure 1. Karyograms of Anguis and Pseudopus. Male karyograms are shown, the karyograms of A. veronensis and P. apodus are from a juvenile of unknown sex. All tested individuals including females share the karyotype of 2n = 44 consisting of 20 macrochromosomes and 24 microchromosomes. Where available, karyograms of both sexes are shown in Supporting Information Figure S1. Scale bar = 10 µm. Photos on the right, not to scale.
Figure 6 in Karyotype stasis but species-specific repetitive DNA patterns in Anguis lizards (Squamata: Anguidae), in the evolutionary framework of Anguiformes
Figure 6. Schematic illustration of the homeology of the Varanus and Anguis + Pseudopus macrochromosomes with respect to the putative toxicoferan ancestor. The simplified arrangement of the macrochromosomes of the toxicoferan ancestor follows the hypothesis of Deakin and Ezaz (2019). Based on the fission(s) leading to Varanus and Anguis, we can assume that both lizards exhibit a derived stage of macrochromosome organization rather than variants of the putative ancestral arrangement of their common anguiform ancestor. The homeology of VKO 5 and AFR 6 (red and white hatched) is tentative and requires further evidence. The colour code depicts the chromosome homeology.
Cell-type-specific cis-eQTLs data in SMR format from https://doi.org/10.1038/s41593-022-01128-z
<p>Cell-type-specific cis-eQTLs data in SMR format from https://doi.org/10.1038/s41593-022-01128-z</p> <p>The hg38 version of the coordinates is used</p>
Supplementary Material, Towards the LLM-Based Generation of Formal Specifications from Natural-Language Contracts: Early Experiments with Symboleo
<p>This repository contains all the files used in the experiments described in the paper "Towards the LLM-Based Generation of Formal Specifications from Natural-Language Contracts: Early Experiments with Symboleo", which appeared in "RAISE 2025: Requirements engineering for AI-powered SoftwarE", an ICSE 2025 workshop, Ottawa, May 3, 2025.</p>
Formal-Specification-to-Code Trace Links Recovery
<p>The experiment data and the code used in our experiments to evaluate the performance of the proposed formal-specification-to-code trace links establishment method, and the other exsiting text-based trace links recovery methods, including Latent Semantic Indexing, Vector Space Model, Word2Vec embeddings, and LLM-based embeddings, are here. It originate from three projects. The first one is an open source VDM-SL specification of an AccountSys and its Java implementation. It comes from the book “Formal Software Development: From VDM to Java” written by Quentin Charatan and Aaron Kans. Both the VDM-SL formal specification and the Java implementation of the AccountSys were developed and provided by Prof. Aaron Kans from University of East London. It illustrates how to model bank accounts and transactions made on these as a series of deposits and withdrawals. Bank.java file implementing the GUI of the system in the source code is not used since it contains syntactical error and cannot build AST. The second project involves the SOFL specification and the Java implementation of an ATM system. The operations on current accounts of an ATM, such as deposit, withdraw, show balance, print out transaction records are specified by using SOFL formal language and implemented by using Java langauge. The third project involves an open source VDM-SL specification of a hotel system along with its C implementation. The specification describes a hotel management system where guests can check in, enter rooms, and manage cards associated with rooms and keys. The VDM-SL specification, created by Daniel Jackson and presented in his book “Software Abstractions: Logic, Language, and Analysis”. </p>
Supplemental tables of Growth, puberty and testicular function in boys born small for gestational age with non-specific disorder of sex development
<p>Being born small for gestational age (SGA) is frequently associated with unexplained disorder of sex development (non-specific DSD) in boys. Little is known about their future growth, puberty and testicular function. Our objective is to determine the long-term endocrine outcome of boys born SGA who have a non-specific DSD. Cases and controls were retrieved through the international DSD registry and retrospective data collected, based on a spreadsheet containing 102 items. 46,XY boys with a non-specific DSD (n = 179) were included. Males born SGA (n=115) were compared to males born appropriate for gestational age (AGA) (n=64). Their growth and pubertal development were compared. Serum LH, FSH, testosterone, AMH and inhibin B levels in infancy and puberty were analyzed to assess testicular function. At two years of age, 30% of boys born SGA had incomplete or absent catch-up growth. Boys born SGA also had higher LH during minipuberty and lower testosterone in stimulation tests (p=.037 and .040 respectively), as compared to boys with non-specific DSD born AGA. No differences were observed in timing or course of puberty or end-pubertal hormone levels. Almost one out of three SGA boys with a non-specific DSD experiences insufficient catch-up growth. In addition, our data suggest dysfunction of infantile Leydig cells or altered regulation of the hypothalamic-pituitary-gonadal axis in SGA boys during childhood. Sex steroid production during puberty seems unaffected. </p>
Data from: Temporal turnover of the soil microbiome composition is guild-specific
<p>Although spatial and temporal variation are both important components structuring microbial communities, the exact quantification of temporal turnover rates of fungi and bacteria has not been performed to date. In this study, we utilized repeated resampling of bacterial and fungal communities at specific locations across multiple years to describe their patterns and rates of temporal turnover. Our results show that microbial communities undergo temporal change at a rate of 0.010-0.025 per year (in units of Sorensen similarity), and the change in soil is slightly faster in fungi than in bacteria, with bacterial communities changing more rapidly in litter than soil. Importantly, temporal development differs across fungal guilds and bacterial phyla with different ecologies. While some microbial guilds show consistent responses across regional locations, others show site-specific development with weak general patterns. These results indicate that guild-level resolution is important for understanding microbial community assembly, dynamics and responses to environmental factors.</p>
Data in support of: Species-specific interactions in an avian-bryophyte dispersal network
<p>Animal dispersal of plant propagules fundamentally alters the success of dispersal events, and thus shapes plant community composition through time. While this is well-documented in seed plants, spore-bearing plants have received little attention with regard to this phenomenon. Birds are particularly attractive as a potential bryophyte dispersal vector given their highly motile nature as well as their association with bryophytes when foraging and building nests. Despite this, species-specific dispersal relationships between birds and bryophytes have never been examined. We captured birds in Gifford Pinchot National Forest in the Pacific Northwest of the United States to sample their legs and tails for bryophyte spores. We found 24 bryophyte species across 34 species of bird. We examined the level of specialization 1) within the overall interaction network to assess community-level patterns and 2) at the plant species level to determine the effect of bird behavioral type on the plant-animal interaction. Our results suggest that associations within the network are more constrained (specialized) than expected by chance. Additionally, we found that avian foraging guild impacted the variety of bryophytes found on an individual bird. Foliage gleaners and ground foragers had particularly specialized associations within the overall disperser-bryophyte network. Our findings suggest that diffuse bird-bryophyte dispersal networks are likely to be common in habitats where birds readily encounter bryophytes and that further work aimed at understanding individual bird-bryophyte species relationships may prove valuable in determining nuance within this newly described dispersal mechanism.</p>
29 Atrial Models created with a Patient-specific Augmented Atrial model Generation Tool (AugmentA)
<p>This dataset is part of the publication "AugmentA: Patient-specific Augmented Atrial model Generation Tool" (L. Azzolin et al., Preprint: <a href="https://doi.org/10.1101/2022.02.13.22270835">doi:10.1101/2022.02.13.22270835</a>). It consists of 29 statistical shape model instances derived using a non-rigid fitting algorithm to 29 magnetic resonance imaging segmentations from the University Heart Center Freiburg-Bad Krozingen. Our Patient-specific Augmented Atrial model Generation Tool (AugmentA) provided bilayer atrial models resampled with an average edge length of 0.4 mm and augmented with anatomical labels and fiber orientation so that they are ready to use for electrophysiological simulations.</p> <p> </p>
Transcriptional analysis of peripheral memory T cells reveals Parkinson's disease-specific gene signatures--Fluorospot SFC
<p>Fluorospot SFC (combined IFNg, IL-5, and IL-10) data and corresponding HC-PD group IDs described in "Transcriptional analysis of peripheral memory T cells reveals Parkinson’s disease-specific gene signatures"</p>
Imaris files showing specific T cells and malaria parasites in the liver
<p>Imaris files showing specific T cells and malaria parasites in the liver; the T cells kill the parasites, we attempt to ascertain if the T cells hunt the parasites or move randomly. One file shows a scenario where no/few T cells find the parasite (unclustered) and the other shows a scenario where several T cells have already found the parasite..</p>
Single-molecule analysis of specificity and multivalency in binding of short linear substrate motifs to the APC/C
<p>Robust regulatory signals in the cell often depend on interactions between short linear motifs (SLiMs) and globular proteins. Many of these interactions are poorly characterized because the binding proteins cannot be produced in the amounts needed for traditional methods. To address this problem, we developed a single-molecule off-rate (SMOR) assay based on microscopy of fluorescent ligand binding to immobilized protein partners. We used it to characterize substrate binding to the Anaphase-Promoting Complex/Cyclosome (APC/C), a ubiquitin ligase that triggers chromosome segregation. We find that SLiMs in APC/C substrates (the D box and KEN box) display distinct affinities and specificities for the substrate-binding subunits of the APC/C, and we show that multiple SLiMs in a substrate generate a high-affinity multivalent interaction. The remarkably adaptable substrate-binding mechanisms of the APC/C have the potential to govern the order of substrate destruction in mitosis.</p>
Data from: Species-specific responses to warming alter community composition
<p>1. Species are responding to global climate change in varied and nuanced ways. However, how species-specific responses to climate change affect interactions among species remains poorly understood. It is important to understand species interactions under potential climate change scenarios because those interactions can in turn alter community dynamics.</p> <p>2. In this study, we conducted two complementary experiments to examine how simulated warming might alter larval intraguild predation (IGP) rates and resulting adult assemblage composition in three species of North American dragonflies: <i>Pachydiplax longipennis</i>, <i>Plathemis lydia</i>, and <i>Libellula luctuosa</i>.</p> <p>3. First, using both <i>P. longipennis</i> and <i>L. luctuosa</i>, we isolated inter- and intraspecific pairs of larval dragonflies of different size differentials to determine how size and species identity might influence IGP rates.</p> <p>4. In tandem, we conducted a year-long mesocosm experiment with all three species to assess how simulated warming and heat waves influenced the resulting adult dragonfly assemblages.</p> <p>5. IGP trials revealed that <i>P. longipennis</i> individuals were much more likely to engage in IGP than <i>L. luctuosa</i>, regardless of size differential. In the mesocosm experiment, emerging adult assemblages were dominated by <i>P. longipennis</i> individuals, a pattern that was most pronounced in the control treatment.</p> <p>6. Our results indicate that while <i>P. longipennis</i> may be the competitively dominant species under current ambient conditions, warming may alter this dynamic and lessen the dominance of this species on resulting assemblage composition.</p>
Language Specific Event Recommendation Ground Truth
<p>This is a multilingual ground truth dataset for training, evaluating and testing the LaSER (Language-Specific Event Recommendation) model. It contains language-specific relevance scores for event-centric click-through pairs according to the publicly available Clickstream dataset in German, French and Russian as well as the user study annotations conducted for evaluating the language-specific recommendations by LaSER. For more details, refer to <a href="https://github.com/saraabdollahi/EventKG-Click">EventKG+Click</a> and <a href="https://github.com/saraabdollahi/LaSER">LaSER</a>.<br> <br> This dataset consists of two sets of files as follows:<br> 1. The ground truth dataset that is used for training the learning to rank (LTR) model in LaSER in three languages. The following files contain the language-specific relevance scores between a source and target entity based on EventKG+Click dataset:</p> <ul> <li>german_ground_truth.txt</li> <li>french_ground_truth.txt</li> <li>russian_ground_truth.txt</li> </ul> <p>In these files source and target represent the label of entities and events in the respective language. </p> <p>2. The second set contains the user study participants' annotations regarding different relevance criteria of recommended events by LaSER. The following three files contain the annotations of at least three participants per event:</p> <ul> <li>german_user_study_annotations.csv</li> <li>french_user_study_annotations.csv</li> <li>russian_user_study_annotations.csv</li> </ul> <p>In these files, "r1", "r2" and "r3" denote relevance to the topic, language community and general audience respectively. And topic and event represent the wikidata-id of entities and events. </p>
Raw data of manuscript "Downregulated dual-specificity protein phosphatase 1 in ovarian carcinoma: a comprehensive study with multiple methods" submitted to PeerJ
<p>Some raw data and original calculating results of this manuscript.</p>
Sex-specific maternal programming of corticosteroid binding globulin by predator odour
<p>Predation is a key organizing force in ecosystems. The threat of predation may act to program the endocrine hypothalamic-pituitary-adrenal axis during development to prepare offspring for the environment they are likely to encounter. Such effects are typically investigated through measurement of corticosteroids (Cort). Corticosteroid-binding globulin (CBG) plays a key role in regulating the bioavailability of Cort, with only free unbound Cort being biologically active. We investigated the effects of prenatal predator odour exposure (POE) in mice on offspring CBG and its impact on Cort dynamics before, during, and after restraint stress in adulthood. POE males, but not females, had significantly higher serum CBG at baseline and during restraint and lower circulating levels of Free Cort. Restraint stress was associated with reduced liver transcript abundance of <i>SerpinA6 </i>(CBG-encoding gene) only in control males. POE did not affect <i>SerpinA6</i> promoter DNA methylation. Our results indicate that prenatal exposure to a natural stressor led to increased CBG levels, decreased percent of Free Cort relative to total, and inhibited restraint stress-induced downregulation of CBG transcription.<i> </i>These changes suggest an adaptive response to a high predator risk environment in males but not females, that could buffer male offspring from chronic Cort exposure.</p>
Identification of a 41-bp Embryonic Cell-Specific Region within the Pineapple SERK1 Promoter
<p>Plant regeneration via somatic embryogenesis (SE) is a key step during genetic engineering. <em>AcSERK1</em> is a gene specifically expressed in the early stage of SE in pineapple (<em>Ananas comosus</em>), suggesting that the promoter of <em>SERK1</em> might contain specific cis-acting element to regulate SE.</p>
Population specific annual cycles and migration strategies in a leap-frog migrant
<p>A common migratory pattern in birds is that northerly breeding populations migrate to more southerly non-breeding sites compared to southerly: a pattern called <i>leap-frog </i>migration. Not only do populations experience differences in migration distances, but also different environmental conditions, which may vary spatiotemporally within their annual cycles, crating distinctive selective pressures and migratory behaviors. Information on how populations schedule their annual cycles according to environmental conditions and by extension, adapt their migratory behaviors is important to understand drivers of migration and evolution of migration patterns at large. Here we use light level geolocators and citizen science data on regional spring arrivals to compare two populations of common ringed plover <i>Charadrius hiaticula </i>– a textbook example of a leap-frog migrant – breeding at different latitudes. We 1) describe and characterize the spatiotemporal patterns of the annual cycles, and 2) test predictions regarding speed and timing of migration derived from the population specific characterizations of the annual cycles. Winter distributions followed a leap-frog migration pattern, i.e. northern breeding population (NBP) wintered in W Africa and the southern (SBP) mainly in W Europe. The annual cycles were shifted temporally so that the NBP was always later in all stages compared to the SBP. The SBP spent more than twice as long time in the breeding area, but there was no difference in winter residency. There was no difference in migration duration, nor migration speed, between the two seasons within population, but the NBP spent more time on migration in both seasons and migrated faster in spring compared to the SBP. We also found a larger variation in spring arrival times across years in the SBP. This suggests that a complex interaction of population specific timing and variation of breeding onset, length of breeding season and proximity to the breeding area shape the annual cycle and migratory behaviors.</p>
Characterization of Site-Specific Vegetation Activity in Alaskan Wet and Dry Tundra as Related to Climate and Soil State DATA
<p>We present discrete (2-hour resolution) multi-year (2008 – 2017) <em>in situ </em>measurements of seasonal vegetation growth and soil biophysical properties from two sites on Alaska’s North Slope, USA, representing dry and wet sedge tundra. We examine measurements of vertical active soil layer temperature and soil moisture profiles (freeze/thaw status), woody shrub vegetation physiological activity, and meteorological site data to assess interrelationships within (and between) these two study sites.</p> <p>Vegetation phenophases (cold de-hardening start, physiological function start, stem growth start, stem growth end, physiological function end, cold hardening completion) were found to have greater inter-annual Day-Of-Year (DOY) occurrence variability at the dry site compared to the wet site. At the dry site, vegetation activity begins on average ~ 7 days earlier and ends ~ 11 days earlier. The mean active stem growth window lasts ~ 54 days for the dry site and ~51 days for the wet site. Vegetation, in both tundra environments, began cold de-hardening functions (warm season prep) prior to atmospheric temperatures warming above 0°C. Similar results were found related to the critical soil freeze/thaw/transition dates; the dry site had a DOY phenophase occurrence range that was 8 days larger than that of the wet site. A longer continuous summer thaw period was captured at the wet site by ~ 26 days throughout the active layer. In addition, the dry site was measured to have longer spring and fall soil isothermal conditions than the wet site by ~ 9 and 5 days throughout the active layer. These results show that the dry site’s willow shrub vegetation physiology and soil condition phenology is more variable than the wet site.</p> <p>Alongside the <em>in situ</em> data, a remote sensing product from NASA’s MEaSUREs program was utilized; our research indicates that the AMSR derived satellite product is more precise over the wet tundra site with critical date alignment between remote sensing observations and <em>in situ</em> measurements ranging from ~ 4 to 11 days. Furthermore, the AMSR product was shown to preemptively estimate land surface condition change during the spring transition for both tundra types while lagging during the fall transition and freeze-up periods.</p>
How well does molecular simulation reproduce environment-specific conformations of the intrinsically disordered peptides PLP, TP2 and ONEG?
<p>Simulation trajectory dataset to accompany publication:</p> <p>Reid, L.M., Guzzetti, I., Svensson, T., Carlsson, A-C., Su, W., Leek, T., von Sydow, L., Czechtizky, W., Miljak, M., Verma, C., De Maria, L., Essex, J.W., Chem. Sci., 2022, DOI: 10.1039/d1sc03496k</p> <p> </p>
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.