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773 results for “bounds”
Bound within boundaries: How well do protected areas match movement corridors of their most mobile protected species?
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Outer bounds: forest edges emulate vertical strata as a habitat filter for butterfly assemblages.
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Data from: Apolipoprotein M-bound sphingosine-1-phosphate regulates blood-brain barrier paracellular permeability and transcytosis
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Data from: Flight reconstruction of two European enantiornithines (Aves, Pygostylia) and the achievement of bounding flight in Early Cretaceous birds
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3D model of the human ACE2 receptor bound to the SARS-CoV-2 Spike RBD
<p>3D structure model of the receptor-binding domain of SARS-CoV-2 (top) bound to the human ACE2 receptor (bottom). The two highlighted aminoacids - ACE2 D30 (red) and RBD K417 (blue) - are part of a set of interactions that is conserved in animal species susceptible to infection by the virus but are absent from immune species.</p>
Dataset from the EMNLP 2020 article "Modeling the Music Genre Perception across Language-Bound Cultures"
<p>We release the data required to reproduce the experiments from the article <em>Modeling the Music Genre Perception across Language-Bound Cultures</em> presented at the <a href="https://2020.emnlp.org">EMNLP 2020</a> conference.</p> <p>More information about this data and how it should be used in the experiments can be found in the GitHub repository <a href="https://github.com/deezer/CrossCulturalMusicGenrePerception">deezer/CrossCulturalMusicGenrePerception</a>.</p> <p>Please cite our paper if you use the code or data in your work.</p>
Data from: Using branch-and-bound algorithms to optimize selection of a fixed-size breeding population under a relatedness constraint
Tree breeders often face the challenge of conserving genetic diversity, while at the same time maximizing response to selection. When selecting advanced-generation breeding populations, the best-performing candidates will quite often be closely related and selecting them without consideration of their relatedness will very quickly erode genetic diversity. Optimal selection will not completely avoid kinship, but rather maximize gain while imposing a constraint on average relatedness. Genetic contributions are most easily optimized if breeders can manage a real, continuous distribution of contributions from parents. While generally possible when establishing seed orchards, unequal contributions to a breeding population may present difficult and time-consuming operational constraints. In these situations, a specified number of parents contributing equally may be a preferred configuration for the breeding population. Here we formulate the selection of a fixed-size breeding population while imposing a constraint on relatedness of the population members. The problem is expressed as a Mixed Integer Quadratically Constrained Optimization (MIQCO) and solved using branch-and-bound techniques (BB). An open-source solver, dsOpt, was developed and embedded into a user-friendly tool, OPSEL, designed to simplify the process of optimizing selection of breeding populations. Case studies optimizing selection of breeding populations for Scots pine and loblolly pine illustrate the superiority of the BB solution compared with selection from ranked lists with restrictions on numbers of genotypes contributed by each full-sib family, and with solutions from GENCONT, a publically available optimum selection program using an algorithm with Lagrangian multipliers. The case studies also illustrate the extreme differences that can occur with respect to time required to confirm the optimality of solutions found by BB.
Data from: A novel, bounding gait in swimming turtles: implications for aquatic locomotor diversity
Turtles are an iconic lineage in studies of animal locomotion, typifying the use of slow, alternating footfalls during walking. Alternating movements of contralateral limbs are also typical during swimming gaits for most freshwater turtles. Here, we report a novel gait in turtles, in which the pleurodire Emydura subglobosa swims using a bounding gait that coordinates bilateral protraction of both forelimbs with bilateral retraction of both hindlimbs. Use of this bounding gait is correlated with increased limb excursion and decreased stride frequency, but not increased velocity when compared to standard swimming strokes. Bounding by E. subglobosa provides a second example of a non-mammalian lineage that can use bounding gaits, and may give insight into the evolution of aquatic flapping. Parallels in limb muscle fascicle properties between bounding turtles and crocodylids suggest a possible musculoskeletal mechanism underlying the use of bounding gaits in particular lineages.
Data from: Inferring bounded evolution in phenotypic characters from phylogenetic comparative data
Our understanding of phenotypic evolution over macroevolutionary timescales largely relies on the use of stochastic models for the evolution of continuous traits over phylogenies. The two most widely used models, Brownian motion and the Ornstein–Uhlenbeck (OU) process, differ in that the latter includes constraints on the variance that a trait can attain in a clade. The OU model explicitly models adaptive evolution toward a trait optimum and has thus been widely used to demonstrate the existence of stabilizing selection on a trait. Here we introduce a new model for the evolution of continuous characters on phylogenies: Brownian motion between two reflective bounds, or Bounded Brownian Motion (BBM). This process also models evolutionary constraints, but of a very different kind. We provide analytical expressions for the likelihood of BBM and present a method to calculate the likelihood numerically, as well as the associated R code. Numerical simulations show that BBM achieves good performance: parameter estimation is generally accurate but more importantly BBM can be very easily discriminated from both BM and OU. We then analyze climatic niche evolution in diprotodonts and find that BBM best fits this empirical data set, suggesting that the climatic niches of diprotodonts are bounded by the climate available in Australia and the neighboring islands but probably evolved with little additional constraints. We conclude that BBM is a valuable addition to the macroevolutionary toolbox, which should enable researchers to elucidate whether the phenotypic traits they study are evolving under hard constraints between bounds.
Data from: An upper bound for accuracy of prediction using GBLUP
This study aims at characterizing the asymptotic behavior of genomic prediction R2 as the size of the reference population increases for common or rare QTL alleles through simulations. Haplotypes derived from whole-genome sequence of 85 Caucasian individuals from the 1,000 Genomes Project were used to simulate random mating in a population of 10,000 individuals for at least 100 generations to create the LD structure in humans for a large number of individuals. To reduce computational demands, only SNPs within a 0.1M region of each of the first 5 chromosomes were used in simulations, and therefore, the total genome length simulated was 0.5M. When the genome length is 30M, to get the same genomic prediction R2 as with a 0.5M genome would require a reference population 60 fold larger. Three scenarios were considered varying in minor allele frequency distributions of markers and QTL, for h2 = 0.8 resembling height in humans. Total number of markers was 4,200 and QTL were 70 for each scenario. In this study, we considered the prediction accuracy in terms of an estimability problem, and thereby provided an upper bound for reliability of prediction, and thus, for prediction R2. Genomic prediction methods GBLUP, BayesB and BayesC were compared. Our results imply that for human height variable selection methods BayesB and BayesC applied to a 30M genome have no advantage over GBLUP when the size of reference population was small (<6,000 individuals), but are superior as more individuals are included in the reference population. All methods become asymptotically equivalent in terms of prediction R2, which approaches genomic heritability when the size of the reference population reaches 480,000 individuals.
Data from: Bounds to parapatric speciation: A dobzhansky-muller incompatibility model involving autosomes, X chromosomes and mitochondria
We investigate the conditions for the origin and maintenance of postzygotic isolation barriers, so called (Bateson-)Dobzhansky-Muller incompatibilities or DMIs, among populations that are connected by gene flow. Specifically, we compare the relative stability of pairwise DMIs among autosomes, X chromosomes, and mitochondrial genes. In an analytical approach based on a continent-island framework, we determine how the maximum permissible migration rates depend on the genomic architecture of the DMI, on sex bias in migration rates, and on sex-dependence of allelic and epistatic effects, such as dosage compensation. Our results show that X-linkage of DMIs can enlarge the migration bounds relative to autosomal DMIs or autosome-mitochondrial DMIs, in particular in the presence of dosage compensation. The effect is further strengthened with male-biased migration. This mechanism might contribute to a higher density of DMIs on the X chromosome (large X-effect) that has been observed in several species clades. Furthermore, our results agree with empirical findings of higher introgression rates of autosomal compared to X-linked loci.
A Petri net tool for software performance estimation based on upper throughput bounds
<p>Functional and non-functional properties analysis (i.e., dependability, security, or performance) ensures that requirements are fulfilled during the design phase of software systems. However, the Unified Modelling Language (UML), standard <em>de facto</em> in industry for software systems modelling, is unsuitable for any kind of analysis but can be tailored for specific analysis purposes through profiling. For instance, the MARTE profile enables to annotate performance data within UML models that can be later transformed to formal models (e.g., Petri nets or timed automatas) for performance evaluation. A performance (or throughput) estimation in such models normally relies on a whole exploration of the state space, which becomes unfeasible for large systems. To overcome this issue upper throughput bounds are computed, which provide an approximation to the real system throughput with a good complexity-accuracy trade-off. This paper introduces a tool, namedPeabraiN, that estimates the performance of software systems via their UML models. To do so, UML models are transformed to Petri nets where performance is estimated based on upper throughput bounds computation. PeabraiN also allows to compute other features on Petri nets, such as the computation of upper and lower marking place bounds, and to simulate using an approximate (continuous) method. We show the applicability of PeabraiN by evaluating the performance of a building closed circuit TV system.</p>
Multiresolution molecular dynamics simulations reveal the interplay between conformational variability and functional interactions in membrane-bound cytochrome 2B4
<p>This dataset contains coordinate files, scripts and input parameters to run and analyse molecular dynamics simulations of membrane bound CYP 2B4.</p> <p> </p> <p>The associated study is described in: </p> <p>data - containes input data & last simulation frames for all of the described MD simulations and analyses described in the manuscript</p> <p>Structures_used_for_figures - contains .pdb and .pse files of all protein structures depicted in the manuscript</p>
3D localization AFM (3D-LAFM) density map of Annexin-V, membrane-bound in a p6 lattice
<p>3D localization AFM (3D-LAFM) density map of Annexin-V, membrane-bound in a p6 lattice, in <code>.afm</code> format and in <code>.mrc</code> format.</p> <p>Note: The <code>.afm</code> file encodes details for constructing 3D-LAFM density maps and includes experimental conditions in its header. Using <code>.afm</code> files requires the additional installation of the AFM file encoder (available from <a href="https://github.com/rafaeljiang23/3D-LAFM/tree/main/ChimeraX-AfmFormat_v2">GitHub</a>). Once the relevant installation is complete, <code>.afm</code> files can be opened in ChimeraX via drag-and-drop. In contrast, <code>.mrc</code> files, which encode only the density values equivalent to <code>.afm</code> files, can be directly opened in ChimeraX without requiring additional software installation.</p> <p>The deposited <code>.afm</code> file follows the 'AFM1' (metacode) format standard.</p>
Twin-Width Benchmark Results for Branch & Bound and SAT Encodings
<p>Benchmark results on TWLIB and PACE 2023 benchmarks for different twin-width algorithms.</p>
Dataset for Prolonged storage of bound organic carbon in wetland but not upland soils: A 13C and 14C perspective
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Nitrogen enrichment buffers phosphorus limitation by mobilizing mineral-bound soil phosphorus in grasslands
<p>Phosphorus (P) limitation is expected to increase due to nitrogen (N)-induced terrestrial eutrophication, although most soils contain large P pools immobilized in minerals (P<sub>i</sub>) and organic matter (P<sub>o</sub>). Here we assessed whether transformations of these P pools can increase plant available pools alleviating P limitation under enhanced N availability. The mechanisms underlying these possible transformations were explored by combining results from a 10-year field N-addition experiment and a 3700-km transect covering wide ranges in soil pH, soil N, aridity, leaching, and weathering that can affect soil P status in grasslands. Nitrogen addition promoted dissolution of immobile P<sub>i</sub> (mainly Ca-bound recalcitrant P) to more available forms of P<sub>i</sub> (including Al- and Fe-bound P fractions and Olsen P) by decreasing soil pH from 7.6 to 4.7, but did not affect P<sub>o</sub>. Soil total P declined by 10% from 385±6.8 to 346±9.5 mg kg<sup>-1</sup>, while available-P increased by 546% from 3.5±0.3 to 22.6±2.4 mg kg<sup>-1</sup> after 10-year N addition, associated with an increase in P<sub>i</sub> mobilization, plant uptake, and leaching. Similar to the N-addition experiment, the drop in soil pH from 7.5 to 5.6 and increase in soil N concentration along the grassland transect were associated with an increased ratio between relatively mobile P<sub>i</sub> and immobile P<sub>i</sub>. Our results provide a new mechanistic understanding of the important role of soil P<sub>i</sub> mobilization in maintaining plant P supply and accelerating biogeochemical P cycles under anthropogenic N enrichment. This mobilization process temporarily buffers ecosystem P-limitation or even causes P eutrophication but will extensively deplete soil P pools in the long run.</p>
TCR repertoire sequencing related to "Unique roles of coreceptor-bound LCK in helper and cytotoxic T cells"
<p>This archive contains datasets needed for recapitulating the analysis of TCR repertoires for the manuscript <em>“Unique roles of coreceptor-bound LCK in helper and cytotoxic T cells”</em> by Horkova et al., 2022. The code for the analysis can be found on GitHub: https://github.com/Lab-of-Adaptive-Immunity/lck-tcrseq. Raw data are deposited in the SRA (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA872031).</p> <p>The Zenodo archive contains the following files, which are needed to run the analysis script:</p> <ul> <li>merged outputs from MiXCR <code>merged_TCR_repertoires.csv</code></li> <li>metadata file <code>metadata_Lck.csv</code></li> <li>TRA and TRB repertoires prepared for processing with the Immunarch package <code>immdata_tra.rds</code>, <code>immdata_trb.rds</code></li> </ul>
In vitro and in vivo characterization and protein-bound structural elucidation of three microbial choline TMA lyase inhibitors
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Fig. 21 in Review of the East African species of the phaneropterine genus Parapyrrhicia Brunner von Wattenwyl, 1891 (Insecta: Orthoptera): secret communication of a forest-bound taxon
Fig. 21 Oszillograms of the male calling songs of Parapyrrhicia species at different time scales
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.