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124 results for “Signal pattern”
Рис. 2. Варианты преΑсказанной Αоменной структуры патогенраспознающих моΛекуΛ гемоцитов моΛΛюсков Planorbarius corneus. a — фибриногенпоΑобные беΛки, b — гаΛектины, c — F-Λектины. УсΛовные обозначения и сокращения, зΑесь и ΑаΛее: горизонтаΛьные красные поΛоски — сигнаΛьный пептиΑ, горизонтаΛьные розовые — обΛасть низкой сΛожности, вертикаΛьные синие поΛоски — трансмембранная обΛасть, FBG — фибриногеновый Αомен, FTP — Αомен фукоΛектина, EGF — Αомен эпиΑермаΛьного фактора роста, EGF_CA — каΛьцийсвязывающий EGF-поΑобный Αомен, PAN_AP — APPLE-поΑобный Αомен, SCAN — обΛасть, богатая Λейцином, GLECT — гаΛактозосвязывающий Λектин, CLECT — Λектин C-типа, Gal-bind — гаΛактозиΑ–связывающий Λектин, ML — MD-2- поΑробный Αомен распознавания ΛипиΑов Fig. 2. Variants of the predicted domain structure of pattern recognition molecules from hemocytes of Planorbarius corneus molluscs. a — fibrinogen-related proteins, b — galectins, c — F-lectins. Symbols and abbreviations (here and further): horizontal red stripes — signal peptide, horizontal pink stripes — a low complexity region, vertical blue stripes — transmembrane region, FBG — fibrinogen-related domain, FTP — fucolectin domain, EGF — epidermal growth factor-like domain, EGF_CA — calcium-binding EGF-like domain, PAN_AP — APPLE-like domain, SCAN — leucine rich region, Apple — APPLE domain, GLECT — galactose-binding lectin, CLECT — C-type lectin, Gal-bind — galactoside-binding lectin, ML — MD-2-related lipid-recognition domain in Pathogen recognition molecules from hemocytes of Planorbarius corneus molluscs (Planorbidae, Pulmonata)
Рис. 2. Варианты преΑсказанной Αоменной структуры патогенраспознающих моΛекуΛ гемоцитов моΛΛюсков Planorbarius corneus. a — фибриногенпоΑобные беΛки, b — гаΛектины, c — F-Λектины. УсΛовные обозначения и сокращения, зΑесь и ΑаΛее: горизонтаΛьные красные поΛоски — сигнаΛьный пептиΑ, горизонтаΛьные розовые — обΛасть низкой сΛожности, вертикаΛьные синие поΛоски — трансмембранная обΛасть, FBG — фибриногеновый Αомен, FTP — Αомен фукоΛектина, EGF — Αомен эпиΑермаΛьного фактора роста, EGF_CA — каΛьцийсвязывающий EGF-поΑобный Αомен, PAN_AP — APPLE-поΑобный Αомен, SCAN — обΛасть, богатая Λейцином, GLECT — гаΛактозосвязывающий Λектин, CLECT — Λектин C-типа, Gal-bind — гаΛактозиΑ–связывающий Λектин, ML — MD-2- поΑробный Αомен распознавания ΛипиΑов Fig. 2. Variants of the predicted domain structure of pattern recognition molecules from hemocytes of Planorbarius corneus molluscs. a — fibrinogen-related proteins, b — galectins, c — F-lectins. Symbols and abbreviations (here and further): horizontal red stripes — signal peptide, horizontal pink stripes — a low complexity region, vertical blue stripes — transmembrane region, FBG — fibrinogen-related domain, FTP — fucolectin domain, EGF — epidermal growth factor-like domain, EGF_CA — calcium-binding EGF-like domain, PAN_AP — APPLE-like domain, SCAN — leucine rich region, Apple — APPLE domain, GLECT — galactose-binding lectin, CLECT — C-type lectin, Gal-bind — galactoside-binding lectin, ML — MD-2-related lipid-recognition domain
Figure2. Generation of negative feedbacks gets tuned once a TCR completes stimulation beyond the threshold l. A TCell generates activation signal to BCell once it gets stimulation of its k-TCRs.-AIDEN: A Density Conscious Artificial Immune System for Automatic Discovery of Arbitrary Shape Clusters in Spatial Patterns
<p>A TCR at position p is stimulated if rp (x) - rn(x) > l. Figure 1 depicts this process. When a T<br> Cell receives stimulations on more than k receptors, it generates activation signal to a B Cell, as<br> represented in Figure2.</p>
Figure1. Static stimulation of a single TCR- The kinetic proofreading by the receptor on input x Є X forwards the receptor position p toward l. The receptor will generate negative feedback if p > β. The receptor will generate success signal when p== l.-AIDEN: A Density Conscious Artificial Immune System for Automatic Discovery of Arbitrary Shape Clusters in Spatial Patterns
<p>A TCR at position p is stimulated if rp (x) - rn(x) > l. Figure 1 depicts this process. When a T<br> Cell receives stimulations on more than k receptors, it generates activation signal to a B Cell, as<br> represented in Figure2.</p>
BRAIN Journal-A Repeated Signal Difference for Recognising Patterns-Figure 3. Binary input stimulus dataset
<p>If the input value is 1, then the neuron is likely to be part of the cohesive set and would update the weight and also the global and local counts each event. If the input value is 0, then the neuron is not likely to be part of the cohesive set. For this case, it would not update the weight value as it is 0. It does update the global count as that uses unit increments, but only updates the local count when an earlier trigger switch tells it to. Each update event is also counted, so that averaged totals can be produced. </p>
BRAIN Journal-A Repeated Signal Difference for Recognising Patterns-Figure 2. Schematic of the same neuron N1, shared between 2 different patterns P1 and P2.
<p>It can be assumed that only one pattern fires during each time unit, where Rule 1 of the Introduction states that if a neuron fires a stronger signal for a pattern, it sends feedback to ask it to fire again, the next time unit. If it fires a weaker signal, the request is not to fire next time. Stronger and weaker relates to a more variable type of on or off. As the mechanism is not final yet, there could be some flexibility with it. Rule 1 also states that if the neuron does not fire for the current pattern, it receives the switch command from the last pattern it did fire for. Note that the actual firing event can produce either zero or some input and so an earlier event can also force a weak feedback signal. Rule 2 states that this particular feedback is only the on/off switch command and does not affect the size of the output value. A schematic of the idea is illustrated in Figure 2, which relates to the same neuron shared between 2 pattern events, at times t1 and t2. The schematic is described further in section 0. </p>
Repository for: Combinatorial Wnt signaling landscape during brachiopod anteroposterior patterning
<p>This repository contains the data and analyses for the manuscript:</p> <p>Vellutini, B. C., Martín-Durán, J. M., Børve, A. & Hejnol, A. <strong>Combinatorial Wnt signaling landscape during brachiopod anteroposterior patterning.</strong> BMC Biol. 22, 1–23 (2024). <a href="https://doi.org/10.1186/s12915-024-01988-w" rel="nofollow">https://doi.org/10.1186/s12915-024-01988-w</a></p> <p>The source is maintained at <a href="https://github.com/bruvellu/terebratalia-wnts">https://github.com/bruvellu/terebratalia-wnts</a>.</p>
Simulation Data for "How GPCR phosphorylation patterns orchestrate arrestin-mediated signaling"
<p>Simulation data and analysis code for Latorraca, Masureel et al., How GPCR Phosphorylation Patterns Orchestrate Arrestin-Mediated Signaling, Cell (2020), https://doi.org/10.1016/j.cell.2020.11.014. Please see included readme files for more information. </p>
A tale of four bears: Environmental signal on the phylogeographical patterns within the extant Ursus species
<p>Aim: Assessing the relevance of niche evolution in the diversification patterns and geographical distribution of species driven by climate remains a challenge. We apply an integrative approach to evaluate the role of the environment on the phylogeography of bear species, incorporating fossil data to characterize the changes in the ecological niche through time. We evaluate our approach with the four extant species of bears within Ursus, the best represented taxon in the fossil record of the family Ursidae.</p> <p>Location: Eurasia and North America.</p> <p>Taxa: Asian black bear, Ursus thibetanus; American black bear, U. americanus; Brown bear, U. arctos; and Polar bear, U. maritimus.</p> <p>Methods: We built a genetic and a geographical database from all published mitochondrial DNA sequences and of species occurrence records. We defined the most significant climatic variables based on each species ecological realm using correlation matrices, and characterized the ecological niches and existing environmental conditions with ellipsoid models. We inferred their current and Last Glacial Maximum (LGM) ecological niche modellings (ENMs) and compared the results with the fossil record. We estimated the times of divergence (d‐loop sequences) of lineages and applied a phyloclimatespace approach to discern the phylogeographical patterns along each species' ecological space.</p> <p>Results: Ecological niche modelling showed wider niches for U. thibetanus and U. americanus encompassing higher temperature and precipitation, while U. arctos and<br> U. maritimus showed an opposite pattern. LGM models were consistent with the fossil record, predicting 55%–89% of the fossil occurrences (within their suitability<br> areas). The phyloclimatespace revealed different degrees of environmental signal in the lineages' phylogeographical patterns and ecological trajectories associated with<br> LGM climatic conditions. Results indicated habitat tracking and ecological expansion since the LGM towards more extreme precipitation and temperature conditions for<br> three species, except U. maritimus that showed ecological niche reduction.</p> <p>Main Conclusions: Incorporating fossil information from the LGM improved our characterization and interpretation of ecological models, by enabling definition of the limits of the climatic conditions explored by the species in the past. Our approach also provided insights about the existing set of environmental conditions shaping the ecological niche divergence of Ursus bears. We were able to depict key features of the lineages' evolutionary history, ecology and distribution, revealing the dynamics of niche occupation and the environmental signal on the phylogeographical patterns of Ursus.</p>
Unexpected colour pattern variation in mimetic frogs: implication for the diversification of warning signals in the genus Ranitomeya
<p>Predation is expected to promote uniformity in the warning colouration of defended prey, but also mimicry convergence between aposematic species. Despite selection constraining both colour-pattern and population divergence, many aposematic animals display numerous geographically structured populations with distinct warning signals. Here, we explore the extent of phenotypic variation of sympatric species of <em>Ranitomeya</em> poison frogs and test for theoretical expectations on variation and convergence in mimetic signals. We demonstrate that both warning signal and mimetic convergence are highly variable and are negatively correlated: some localities display high variability and no mimicry while in others the phenotype is fixed and mimicry is perfect. Moreover, variation in warning signals is always present within localities, and in many cases, this variation overlaps between populations, such that variation is continuous. Finally, we show that coloration is consistently the least variable element and is likely of greater importance for predator avoidance compared to patterning. We discuss the implications of our results in the context of warning signal diversification and suggest that, like many other locally adapted traits, a combination of standing genetic variation and founding effect might be sufficient to enable divergence in colour pattern.</p>
Genetic drift does not sufficiently explain patterns of electric signal variation among populations of the mormyrid electric fish Paramormyrops kingsleyae
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Data from: Progressively shifting patterns of co-modulation among premotor cortex neurons carry dynamically similar signals during action execution and observation
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A tale of four bears: Environmental signal on the phylogeographical patterns within the extant Ursus species
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Unexpected colour pattern variation in mimetic frogs: implication for the diversification of warning signals in the genus Ranitomeya
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Confirming an antiphasic bicyclic pattern of forward entrainment in signal detection: a reanalysis of Sun et al. (2021)
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Data from: Patterns of genomic divergence and signals of selection in sympatric and allopatric northeastern Pacific and Sea of Cortez populations of the sargo (Anisotremus davidsonii) and longjaw mudsucker (Gillichthys mirabilis)
<p><span><span>Studying how isolation can impact population divergence and adaptation in co-distributed species can bring us closer to understanding how landscapes affect biodiversity. The Sargo, </span><i><span>Anisotremus davidsonii </span></i><span>(Haemulidae), and the Longjaw mudsucker, </span><i><span>Gillichthys mirabilis </span></i><span>(Gobiidae), offer a notable framework to study such mechanisms as their Pacific populations cross phylogeographic breaks at Point Conception, California, USA, and Punta Eugenia, Mexico, and are separated to those in the Sea of Cortez by the Baja California peninsula. Here, thousands of loci are genotyped from 48 Sargos and 73 mudsuckers using RADseq to characterize overall genomic divergence, and search for common patterns of putatively neutral and non-neutral structure based on outlier loci among populations with hypothesized different levels of isolation.</span></span><span> </span><span><span>We further search for parallels between population divergence and the total proportion of outliers, outlier </span></span><span><span>F</span><sub><span>ST</span></sub></span><span><span> distribution, and </span></span><span><span>the proportion of outliers matching coding regions in GenBank. This dataset consists of demultiplexed sequence data from Sbf1 single digest RADseq analysis of poulations of both fish species throughout their distributions. </span></span></p>
Data from: Conflicting phylogenomic signals reveal a pattern of reticulate evolution in a recent high-Andean diversification (Asteraceae: Astereae: Diplostephium)
High-throughput sequencing is helping biologists to overcome the difficulties of inferring the phylogenies of recently diverged taxa. The present study analyzes the phylogenetic signal of genomic regions with different inheritance patterns using genome skimming and ddRAD-seq in a species-rich Andean genus (Diplostephium) and its allies. We analyzed the complete nuclear ribosomal cistron, the complete chloroplast genome, a partial mitochondrial genome, and a nuclear-ddRAD matrix separately with phylogenetic methods. We applied several approaches to understand the causes of incongruence among datasets, including simulations and the detection of introgression using the D-statistic (ABBA-BABA test). We found significant incongruence among the nuclear, chloroplast, and mitochondrial phylogenies. The strong signal of hybridization found by simulations and the D-statistic among genera and inside the main clades of Diplostephium indicate reticulate evolution as a main cause of phylogenetic incongruence. Our results add evidence for a major role of reticulate evolution in events of rapid diversification. Hybridization and introgression confound chloroplast and mitochondrial phylogenies in relation to the species tree as a result of the uniparental inheritance of these genomic regions. Practical implications regarding the prevalence of hybridization are discussed in relation to the phylogenetic method.
Data from: Congruent signals of population history but radically different patterns of genetic diversity between mitochondrial and nuclear markers in a mountain lizard
Historical factors, current population size, population connectivity and selective processes at linked loci contribute to shaping contemporary patterns of neutral genetic diversity. It is now widely acknowledged that nuclear and mitochondrial markers react differently to current demography as well as to past history, so the use of both types of markers is often advocated to gain insight on both historical and contemporary processes. We used 12 microsatellite loci genotyped in 13 populations of a mountain lizard (Iberolacerta bonnali) to test if the historical scenario favoured by a previous mitochondrial study was also supported by nuclear markers and thereby evaluated the consequences of post-glacial range movements on nuclear diversity. Congruent signals of recent history were revealed by nuclear and mitochondrial markers using an Approximate Bayesian Computation approach but contemporary patterns of mtDNA and nuclear DNA diversity were radically different. Although dispersal in this species is probably highly restricted at all spatial scales, colonisation abilities have been historically good, suggesting capability for reestablishment of locally extinct populations except in fully disconnected habitats.
Data from: Anthropogenic ecosystem fragmentation drives shared and unique patterns of sexual signal divergence among three species of Bahamian mosquitofish
When confronted with similar environmental challenges, different organisms can exhibit dissimilar phenotypic responses. Therefore, understanding patterns of phenotypic divergence for closely related species requires considering distinct evolutionary histories. Here, we investigated how a common form of human-induced environmental alteration, habitat fragmentation, may drive phenotypic divergence among three closely related species of Bahamian mosquitofish (Gambusia spp.). Focusing on one phenotypic trait (male coloration), having a priori predictions of divergence, we tested whether populations persisting in fragmented habitats differed from those inhabiting unfragmented habitats and examined the consistency of the pattern across species. Species exhibited both shared and unique patterns of phenotypic divergence between the two types of habitats, with shared patterns representing the stronger effect. For all species, populations in fragmented habitats had fewer dorsal-fin spots. In contrast, the magnitude and trajectory of divergence in dorsal-fin color, a sexually selected trait, differed among species. We identified fragmentation-mediated increased turbidity as a possible driver of these trait shifts. These results suggest that even closely related species can exhibit diverse phenotypic responses when encountering similar human-mediated selection regimes. This element of unpredictability complicates forecasting the phenotypic responses of wild organisms faced with anthropogenic change – an important component of biological conservation and ecosystem management.
Figs 110–122 in Comparison of interspecific differences in coloration, morphology, and male calling signal patterns in two genera of Idiocerini (Homoptera: Cicadellidae: Eurymelinae)
Figs 110–122. Oscillograms of male calling signals of species of Idiocerus. 110–113 — I. lituratus; 114–118 — I. herrichii; 119– 122 — I. stigmaticalis. Faster oscillograms of the parts of signals indicated as "112–113", "116–118", and "121–122" are given under the same numbers. Рис. 110–122. Осциллограммы приЗывных сигналов самцов Idiocerus. 110–113 — I. lituratus; 114–118 — I. herrichii; 119– 122 — I. stigmaticalis. Фрагменты сигналов, обоЗначенные цифрами "112–113", "116–118" и "121–122", представлены на осциллограммах под такими же номерами.
Figs 65–82 in Comparison of interspecific differences in coloration, morphology, and male calling signal patterns in two genera of Idiocerini (Homoptera: Cicadellidae: Eurymelinae)
Figs 65–82. Male abdominal apodemes and genitalia of species of Idiocerus. 65–67, 74–76 — I. lituratus; 68–70, 77–79 — I. herrichii; 71–73, 80–82 — I. stigmaticalis; 65, 68, 71 — apodemes of the 3rd tergum; 66, 69, 72 — same, 1st sternum; 67, 70, 73 — same, 2nd sternum; 74, 77, 80 — penis, back view; 75, 78, 81 — same, side view; 76, 79, 82 — style. Рис. 65–82. Аподемы брюШных сегментов и гениталии самцов Idiocerus. 65–67, 74–76 — I. lituratus; 68–70, 77–79 — I. herrichii; 71–73, 80–82 — I. stigmaticalis; 65, 68, 71 — аподемы III тергита; 66, 69, 72 — аподемы I стернита; 67, 70, 73 — аподемы II стернита; 74, 77, 80 — пенис, сЗади; 75, 78, 81 — то же, сбоку; 76, 79, 82 — стилус.
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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.