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13,587 results for “specification”
Species and sex specific chemical composition in a concealed gland from an internal gland-like tissue of an African frog family
<p><span>Intraspecific chemical communication in frogs is understudied and the few published cases are limited to externally visible and male-specific breeding glands. Frogs of the family Odontobatrachidae, a West African endemic complex of five morphologically cryptic species, have large, fatty gland-like strands along their lower mandible. We investigated the general anatomy of this strand and analyzed its chemical composition. We found the strand to be present in males and females of all species. The strand varies in markedness, with well-developed strands usually found in reproductively active individuals. Although the strands are situated under the skin, they are connected to particular skin sections, the vocal sac in male frogs and a respective area in females. Gas-chromatography/mass spectrometry and multivariate analysis revealed, that the strands contain sex- and species-specific chemical profiles, which are consistent across geographically distant populations. The profiles varied between reproductive and non-reproductive individuals. Our results indicate that the gland-like strand in the Odontobatrachidae comprise a so far overlooked type of breeding related organ, potentially a gland, that most likely plays a role in the mating and/or breeding behavior of the five Odontobatrachus species. Our results highlight the relevance of multimodal signaling in anurans, and indicate that chemical signaling may not be restricted to sexually dimorphic, apparent skin glands.</span></p>
FIGURE 4 in Specific damage recognised on land snail shells as a tool for studying predation intensity: differences related to habitat and predator types
FIGURE 4 Variation in the minimal rate of predation recorded in six samples collected in each of five habitat types. Different letters refer to significant differences (p <0.05) among habitat types, based on a generalised linear model. The central line of each box refers to the median value, box height to the interquartile range, whiskers to the non-outlier range (i.e., 1.5 times the interquartile range at each side), and small circles to outliers.
FIGURE 5 in Specific damage recognised on land snail shells as a tool for studying predation intensity: differences related to habitat and predator types
FIGURE 5 Relative representation of individual predation types recognised in six samples collected at each of five habitat types. The height of the column represents the average value, while the lines indicate the standard deviation.
FIGURE 2 in Specific damage recognised on land snail shells as a tool for studying predation intensity: differences related to habitat and predator types
FIGURE 2 Examples of the recorded evidence of predation caused by various predators. a) shell of Cochlicopa lubrica predated on by a snail; b) characteristic damage caused by a carabid beetle, here on a shell of Discus rotundatus; c) puparium of the parasitoid dipteran fly Pherbellia limbata within a Granaria frumentum shell (the shell was crushed manually); d) external damage to a Xerolenta obvia shell caused by bird predation; e) Drilus beetle larval exuviae within an Alinda biplicata shell (the shell was crushed manually).
Species‑specific influence of powdery mildew mycelium on the efficiency of PM accumulation by urban greenery - Data
<p>Dataset of article: Przybysz, A., Nawrocki, A., Mirzwa-Mróz, E. <em>et al.</em> Species-specific influence of powdery mildew mycelium on the efficiency of PM accumulation by urban greenery. <em>Environ Sci Pollut Res</em> (2023). https://doi.org/10.1007/s11356-023-28371-6</p>
Elucidating molecular mechanisms of protoxin-2 state-specific binding to the human NaV1.7 channel
<p>Human voltage-gated sodium (hNaV) channels are responsible for initiating and propagating action potentials in excitable cells and mutations have been associated with numerous cardiac and neurological disorders. hNaV1.7 channels are expressed in peripheral neurons and are promising targets for pain therapy. The tarantula venom peptide protoxin-2 (PTx2) has high selectivity for hNaV1.7 and is a valuable scaffold for designing novel therapeutics to treat pain. Here, we used computational modeling to study the molecular mechanisms of the state-dependent binding of PTx2 to hNaV1.7 voltage-sensing domains (VSDs). Using Rosetta structural modeling methods, we constructed atomistic models of the hNaV1.7 VSD II and IV in the activated and deactivated states with docked PTx2. We then performed microsecond-long all-atom molecular dynamics (MD) simulations of the systems in hydrated lipid bilayers. Our simulations revealed that PTx2 binds most favorably to the deactivated VSD II and activated VSD IV. These state-specific interactions are mediated primarily by PTx2's residues R22, K26, K27, K28, and W30 with VSD and the surrounding membrane lipids. Our work revealed important protein-protein and protein-lipid contacts that contribute to high-affinity state-dependent toxin interaction with the channel. The workflow presented will prove useful for designing novel peptides with improved selectivity and potency for more effective and safe treatment of pain.</p>
Data set for "Distributed and specific encoding of sensory, motor and decision information in the mouse neocortex during goal-directed behavior"
<p>Data set for: Oryshchuk A, Sourmpis C, Weverbergh J, Asri R, Esmaeili V, Modirshanechi A, Gerstner W, Petersen CCH, Crochet S (2024) Distributed and specific encoding of sensory, motor and decision information in the mouse neocortex during goal-directed behavior. Cell Reports 43: 113618. https://doi.org/10.1016/j.celrep.2023.113618</p> <p> </p> <p>There are 2 files in this upload:</p> <p> </p> <p>1. The file named "2024_Oryshchuk_CellReports.pdf" is the Open Access pdf of the online publication in Cell Reports.</p> <p> </p> <p>2. The file named " Oryshchuk _data_code.zip" (~1.8 GB) is a zipped version of a folder "Oryshchuk _data_code" (~2.3 GB), which contains the preprocessed data analyzed in the study along with the Matlab and Python codes used to generate the published figures. To access the data and codes, first unzip the file.</p> <p>· The subfolder “Atlas” contains templates from the Allen Mouse Brain Reference Altas of anatomical brain sections used to map the location of the silicon probes (Supplementary Figure S1).</p> <p>· The subfolder “Clustering-master” contains the Matlab codes used for the clustering on neuronal activity (Figure 1). The output is the data structure ‘Data_Clustering.mat’ file already provided in the folder ‘Data’.</p> <p>· The subfolder “Code” contains the main Matlab codes used to analyze the data and plot the figures. The ouput from the clustering and decoding analyses are provided in the ‘Data’ folder, thus the Matlab codes can be run independently, without running the ‘clustering’ or ‘decoding’ codes first.</p> <p>· The subfolder “Data” contains the Matlab data structures containing the electrophysiological and behavioral data from whisker rewarded (‘DataWR.mat’) and non-rewarded (‘DataWnonR.mat’) mice, the behavioral data for optogenetic inactivation in rewarded mice, the clustering results (‘Data_Clustering.mat’) and a subfolder containing the results from the decoding analyses (“Decoding”).</p> <p>· The subfolder “decoding” contains the Python codes used for the decoding analyses. The required configuration can be found in the file ‘requirements.txt’. To run the codes, follow instructions from the ‘README.md’ file.</p> <p>· The subfolder “Figures” will be populated with figures saved in .png and .eps formats as well as a ‘Methods.txt’ files when running the main Matlab codes.</p> <p>· The subfolder “Functions” contains subfunctions used by the main Matlab codes to analyze the data and plot the figures.</p> <p>· The subfolder “Results” will be populated with Matlab data structures as well as a ‘.xlsx’ files when running the main Matlab codes.</p> <p>When running the code, you need to set the Matlab file path to be "Oryshchuk _data_code". In addition, you should add the folder "Oryshchuk_data_code" with subfolders to the Matlab path. Some parts of the code rely upon previous results, and need to be executed sequentially in the order of the figure panels in the journal publication. Please note that some of the code can take several hours to execute.</p>
Water depth influences survival and predator-specific patterns of nest loss in three secretive marsh bird species
<p>Wetlands have become increasingly rare in the United States, negatively influencing wetland-dependent birds, and many remaining wetlands are intensively managed through seasonal dewatering mimicking historic flood pulses during spring and summer. However, water around nests may provide protection from terrestrial predators, and lowering water levels during the breeding season of wetland birds may increase predation risk and exacerbate marsh bird population declines. Understanding interactions between water depth, nesting marsh birds, and nest predators is critical to aid managers in developing a multi-species management approach in emergent wetlands. During the 2020 and 2021 breeding seasons, we examined nest survival of 148 marsh bird nests (American Coot, <em>Fulica americana</em>, <em>n</em> = 1; Common Gallinule, <em>Gallinula galeata</em>, <em>n</em> = 64; and Least Bittern; <em>Ixobrychus exilis</em>, <em>n</em> = 83) and installed cameras at 78 nests to identify predators at a large, restored floodplain wetland in Illinois where the primary management technique is seasonal water removal to stimulate germination of moist soil plants. We found nest predation of, and abandonment by, Least Bittern and Common Gallinule were related to shallower water, and early season, high volume dewatering. Least Bitterns nested more commonly along wetland edges and nests farther from the shore were more likely to survive. Similarly, we found mammalian depredation of nests and nest abandonment decreased when deeper water was present around nests. Alternatively, snake predation was observed earlier in the year prior to water removal from inundated emergent vegetation. Our results demonstrate water depth may be an important deterrent of nest predators, especially mammals, during the breeding season. Further, we recommend managers delay dewatering until after the nesting season at sites where management for conservation-priority marsh birds is a focus.</p>
Raw differential gene expression data, data S1, from: Molecular cascades and cell type-specific signatures in ASD revealed by single cell genomics
<p>Genomic profiling in post-mortem brain from autistic individuals has consistently revealed convergent molecular changes. What drives these changes and how they relate to genetic susceptibility in this complex condition is not understood. We performed deep single nuclear RNA sequencing (snRNAseq) to examine cell composition and transcriptomics, identifying dysregulation of cell type-specific gene regulatory networks (GRNs) in autism, which we corroborated using snATAC-seq and spatial transcriptomics. Transcriptomic changes were primarily cell type-specific, involving multiple cell types, most prominently interhemispheric and callosal-projecting neurons, interneurons within superficial laminae, and distinct glial reactive states involving oligodendrocytes, microglia, and astrocytes. Autism-associated GRN drivers and their targets were enriched in rare and common genetic risk variants, connecting autism genetic susceptibility and cellular and circuit alterations in the human brain. This data is the raw differential gene expression comparing ASD versus CTL subjects for each cell cluster. </p>
Data from: Sex-specific effects of inbreeding in juvenile brown trout
<p>Inbreeding depression, i.e., the reduction of health and vigour in individuals with high inbreeding coefficients, is expected to increase with environmental, social, or physiological stress. It has therefore been predicted that sexual selection and the associated stress usually lead to higher inbreeding depression in males than in females. However, sex-specific differences in life history may reverse that pattern during certain developmental stages. In some salmonids, for example, female juveniles start developing their gonads earlier than males who instead grow faster. We tested whether the sexes are differently affected by inbreeding during that time. To study the effects of inbreeding coefficients that may be typical for natural populations of brown trout (<em>Salmo trutta</em>), and also to control for potentially confounding maternal or paternal effects, we sampled males and females from the wild, used their gametes in a block-wise full-factorial breeding design to produce 60 full-sib families, released the offspring as yolk-sac larvae into the wild, sampled them 6 months later, identified their genetic sex, and used microsatellites to assign them to their parents. We used whole-genome resequencing to calculate the kinship coefficients for each breeding pair and hence the expected average inbreeding coefficient per family. Juvenile growth could be predicted from these expected inbreeding coefficients and the genetic sex: Females reached lower body sizes with increasing inbreeding coefficient, while no such link could be found in males. This sex-specific inbreeding depression led to the overall pattern that females were on average smaller than males by the end of their first summer.</p>
Subject-specific knee models, data, and results for specimen S192803
<p>This dataset is part of an ongoing manuscript to validate that sources of data from currently available in vivo methods are sufficient to create computational models of the knee compared with existing in vitro techniques. The data included in this repository is for the S192803 specimen of that dataset and includes experimental data, working models, code, and results obtained for that model and used in that manuscript.</p>
Pneumatic elastostatics of multi-functional inflatable lattices: Realization of extreme specific stiffness with active modulation and deployability
<p>Supplementary codes and data: Elastostatics of multi-functional inflatable lattices: Realization of extreme specific stiffness with active modulation and deployability</p>
Different components of cognitive-behavioural therapy affect specific cognitive mechanisms: supporting data
<p>This repository holds data associated with the manuscript "Different components of cognitive-behavioural therapy affect specific cognitive mechanisms" (<a href="https://osf.io/preprints/psyarxiv/ydct5">https://osf.io/preprints/psyarxiv/ydct5</a>).</p><ul><li>rew-eff-planningX .csv files represent data from experiments testing effects of a planning/goal-setting intervention on reward-effort decision-making (X=1, initial discovery sample, X=2, replication sample)</li><li>causal-attr-X .csv files represent data from experiments testing the effects of a cognitive restructuring intervention on causal attribution tendencies (X=1, initial discovery sample, X=2, replication sample)</li><li>crossover-study-X .csv files represent data from the crossover-design study (data saved separately for participants randomly allocated to complete the reward-effort vs causal attribution tasks).</li></ul><p>Data-generating task code and full analysis code can be found at <a href="https://github.com/agnesnorbury/cognitive-mechanisms-psychotherapy">https://github.com/agnesnorbury/cognitive-mechanisms-psychotherapy</a>.</p>
Energy input, habitat heterogeneity, and host specificity on avian haemosporidian diversity at continental scales
<p>The correct identification of biotic and abiotic drivers affecting parasite diversity and assemblage composition at different spatial scales is crucial for understanding how pathogen distribution responds to anthropogenic disturbance and climate change. Here, we used a database of avian haemosporidian parasites to identify such drivers and their effect on the taxonomic and phylogenetic diversity of genera Plasmodium, Haemoproteus, and Leucocytozoon from three zoogeographic regions. We explored how parasite diversity is related to energy input (i.e., temperature, precipitation, and potential evapotranspiration [PET]), to habitat heterogeneity (i.e., climatic seasonality, vegetation density, ecosystem heterogeneity, human disturbance, and host richness), and to a novel assemblage-level metric related to parasite niche overlap (degree of generalism). We found that the relative importance of the predictors differed between the three studied parasite genera and across diversity metrics. Among the most consistent predictors, host richness was positively related to the taxonomic diversity of the three genera. Energy input and human footprint explained the phylogenetic diversity of Haemoproteus. Finally, the degree of generalism explained the diversity of Plasmodium and Leucocytozoon. Our results suggest that different dimensions of haemosporidian diversity are shaped by energy input, host heterogeneity, and assembly processes related to parasite resource use within local parasite assemblages.</p>
Data for: The CD4 transmembrane GGXXG and juxtamembrane (C/F)CV+C motifs mediate pMHCII-specific signaling independently of CD4-Lck interactions
<p>We previously reported that the transmembrane GGXXG motif co-arose with the cytoplasmic juxtamembrane (C/F)CV+C motif in eutherian (placental mammal) CD4 and that constituent residues therein evolve under purifying selection (Lee, et al., 2022). These data led us to discover that mutating these motifs together increased CD4-Lck association but reduced CD3z, Zap70, and Plcg1 phosphorylation levels as well as IL-2 production. Because these mutants preferentially localized CD4-Lck pairs to non-membrane raft fractions, one potential explanation for our results was that they impaired proximal signaling by sequestering Lck away from TCR-CD3. An alternative hypothesis is that the mutations directly impacted TCR-CD3 signaling because the wild type motifs play a Lck-independent role in signaling. Here we used a reductionist approach to discriminate between these possibilities (Lee, et al., 2023). Our current data lead us to conclude that: intracellular CD4-Lck interactions are not necessary for pMHCII-specific signal initiation; the GGXXG and (C/F)CV+C motifs are key determinants of CD4-mediated pMHCII-specific signal amplification; the GGXXG and (C/F)CV+C motifs exert their functions independently of direct CD4-Lck association. These data provide a mechanistic explanation for why residues within these motifs are under purifying selection. The results are also important to consider for biomimetic engineering of synthetic receptors.</p>
Data from: Seed preference is only weakly linked to seed-type-specific feeding performance in a songbird
<p>The dehusking of seeds by granivorous songbirds is a complex process that requires fast, coordinated and sensory-feedback-controlled movements of beak and tongue. Hence, efficient seed handling requires a high degree of sensorimotoric skill and behavioural flexibility, since seeds vary considerably in size, shape and husk structure. To deal with this variability, individuals might specialise on specific seed types, which could result in greater seed handling efficiency of the preferred seed type, but lower efficiency for other seed types. To test this, we assessed seed preferences of canaries (Serinus canaria) through food choice experiments and related these to data of feeding performance, seed handling skills and beak kinematics during feeding on small, spindle-shaped canary seeds and larger, spheroid-shaped hemp seeds. We found great variety in seed preferences among individuals: some had no clear preference, while others almost exclusively fed on hemp seeds, or even prioritized novel seed types (millet seed). Surprisingly, we only observed few and weak effects of seed preference on feeding efficiency. This suggests that either the ability to handle seeds efficiently can be readily applied across various seed types, or alternatively, it may indicate that achieving high levels of seed-specific handling skills does not require extensive practice.</p>
Figure 9 in A new icriodontid conodont cluster with specific mesowear supports an alternative apparatus motion model for Icriodontidae
Figure 9. Model of masticatory motion of icriodontid I elements. A, oblique lateral view; B, 'anterior' view.
Figure 8 in A new icriodontid conodont cluster with specific mesowear supports an alternative apparatus motion model for Icriodontidae
Figure 8. Motion of P1 elements of ozarkodinid apparatuses summarized from the literature. A, Idiognathodus (Pennsylvanian); B, Novispathodus (Early Triassic); C, Wurmiella excavata (Silurian); D, Pseudofurnishius murcianus (Middle–Late Triassic); E, Polygnathus xylus xylus (Middle Devonian). Grey dots mark the pivot point; black arrows indicate the direction of occlusion and interlocking of P1 elements, grey arrows its reversal.
Figure 7. Hypothetical apparatus reconstruction deduced from the element arrangement within the Caudicriodus woschmidti conodont cluster. A, Model 1 in A new icriodontid conodont cluster with specific mesowear supports an alternative apparatus motion model for Icriodontidae
Figure 7. Hypothetical apparatus reconstruction deduced from the element arrangement within the Caudicriodus woschmidti conodont cluster. A, Model 1 with tips of coniform elements pointing dorsally and 'posterior' part of icriodontan elements oriented ventrally. B, Model 2 with tips of coniform elements and 'posterior' part of icriodontan elements oriented ventrally. C, Model 3 with tips of coniform elements pointing ventrally and 'posterior' part of icriodontan elements oriented dorsally. D, Model 4 with tips of coniform elements and 'posterior' part of icriodontan elements oriented ventrally. Coniform elements are arranged in multiple rows.
Figure 5 in A new icriodontid conodont cluster with specific mesowear supports an alternative apparatus motion model for Icriodontidae
Figure 5. Denticle tip wear of icriodontid I elements. A–C, Icriodus aff. michiganus, dextral I element, lateral and oral view; Middle Devonian, Eifel, Germany; sample BL-12-29c-9. D–F, Icriodus sp., dextral I element, lateral and oral view; Middle Devonian, Eifel, Germany; sample BL-12-29c-3. Extent and orientation of tip wear are indicated by dotted lines and arrowheads.
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.