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625 results for “Rules”
Evaluation Artifacts of RESTRuler, a Static Analysis Tool to Detect Design Rule Violations in OpenAPI Definitions
<p>All artifacts related to the empirical evaluation of the RESTRuler CLI, a Java-based tool to identify design rule violations in OpenAPI descriptions</p> <p>You can find the latest version here: <a href="https://github.com/restful-ma/rest-ruler-evaluation">https://github.com/restful-ma/rest-ruler-evaluation</a></p>
Rules for dissipationless topotronics
<p>Topological systems hosting gapless boundary states have attracted significant attention as promising components for next-generation information processing, attributed to their capacity for dissipationless electronics. Nevertheless, recent theoretical and experimental inquiries have revealed the emergence of energy dissipation in precisely quantized electrical transport. Here, we present a criterion for the realization of truly no-dissipation design, characterized as N_in=N_tunl+N_bs, where N_in, N_tunl, and N_bs represent the number of modes participating in injection, tunneling, and backscattering processes, respectively. The key lies in matching the number of injecting, tunneling, and backscattering modes, ensuring the equilibrium among all engaged modes inside the device. Among all the topological materials, we advocate for the indispensability of Chern insulators exhibiting higher Chern numbers to achieve functional devices and uphold the no-dissipation rule simultaneously. Furthermore, we design the topological current divider and collector, evading dissipation upon fulfilling the established criterion. Our work paves the path for developing the prospective topotronics.</p>
Testing the simple and complex versions of Gloger's rule in the Variable Antshrike (Thamnophilus caerulescens, Thamnophilidae)
<p>Gloger's rule is a classic ecogeographical principle that, in its simplest version, predicts animals should be darker in warmer and wetter climates. In a rarely-tested more complex version, it also predicts animals should be more rufous in warmer and drier climates. The Variable Antshrike is a widely-distributed South American passerine that presents an impressive amount of plumage color variation and occupies a wide variety of climatic conditions. Moreover, genetic and vocal evidence indicate ongoing hybridization in south-central Bolivia among three populations with very distinct plumages. We collected color data from 232 specimens from throughout this species' distribution to test the predictions of Gloger's rule. We found a negative correlation between brightness and precipitation, consistent with the simple version of Gloger's rule. In contrast, we found that birds were darker in cooler climates, contrary to the simple version of Gloger's rule, but consistent with recent findings in other taxa. We found support for both predictions of complex Gloger's rule and suggest it might be driven by background matching. We conclude by concurring with a recent suggestion that the simple version of Gloger's rule should be reformulated exclusively in terms of humidity.</p>
Deriving population scaling rules from individual-level metabolism and life history traits - Code and Data
<p>Individual metabolism generally scales with body mass with an exponent around 3/4. From dimensional arguments it follows that maximum population growth rate (rmax) scales with a -1/4 exponent. However, the dimensional argument implicitly assumes that offspring size is proportional to adult size. Here we calculate rmax from metabolic scaling at the level of individuals within size-structured populations while explicitly accounting for offspring size. We identify four general patterns of how rmax scales with adult mass based on four empirical life-history patterns employed by groups of species. These life-history patterns are determined by how traits of somatic growth rate and/or offspring mass relate to adult mass. One life-history pattern -- constant adult:offspring mass ratio and somatic growth rate independent of adult mass -- leads to the classic -1/4 scaling of rmax. The other three life-history patterns lead either to non-metabolic population growth scaling with adult mass or do not follow a power-law relationship at all. Using life-history data of five marine taxa and terrestrial mammals, we identify species groups that belong to one of each case. We predict that elasmobranchs, copepods, and mammals follow standard -1/4 power-law scaling, whereas teleost fish and bivalves do not have a pure power-law scaling. Our work highlights how taxa may deviate from the classic -1/4 metabolic scaling pattern of maximum population growth. The approach is generic and can be applied to any taxa.</p>
Pre-parsed reaction rule files from RetroRules (rr02-rp3-hs)
<p>RetroRules (https://retrorules.org/) is a database of reaction rules for metabolic pathway discovery and metabolic engineering. Reaction rules are generic descriptions of reactions to be used in retrosynthesis workflows in order to enumerate possible biosynthetic routes connecting target molecules to precursors. The use of such rules is becoming more and more important in the context of synthetic biology applied to de novo pathway discovery and in systems biology to discover underground metabolism due to enzyme promiscuity.</p> <p>Pre-parsed reaction rule files are ready-to-use files that provide all the non-stereo reaction rules for diameter 2 to 16. The present dataset have the following specifications:</p> <ul> <li>release: rr02</li> <li>diameters: 2 to 16</li> <li>Hs handling: explicit</li> <li>Compatibility: RetroPath RL ready</li> </ul> <p>How to cite: Duigou T, du Lac M, Carbonell P, Faulon JL. RetroRules: a database of reaction rules for engineering biology. <em>Nucleic Acids Research</em>, 2019. | doi: <a href="https://doi.org/10.1093/nar/gky940">10.1093/nar/gky940</a> | PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/30321422">30321422</a></p> <p> </p>
Dataset for "selection rules in symmetry-broken systems by symmetries in synthetic dimensions"
<p>Data for the article "Selection rules in symmetry-broken systems by symmetries in synthetic dimensions" by Matan Even Tzur, Ofer Neufeld, Eliyahu Bordo, Avner Fleischer, and Oren Cohen.</p>
Unique and shared effects of local and catchment predictors over distribution of hyporheic organisms: does the valley rule the stream?
<p>This dataset describe the distribution of two hyporheic crustacean taxa (Bogidiellidae, Amphipoda and Anthuridae, Isopoda) in streams of New Caledonia. We sampled the two taxa at 228 sites. At each site, we quantified nine local predictors related to habitat area and stability, sediment metabolism and water origin, and eight catchment predictors related to geology, area, primary productivity, land use and specific discharge.</p>
Exploring Hierarchy and Dependency of Rules for Consistency Checking Between Code and Model (Evaluation Data)
<p>This repository contains the data related to the protocol and results of the evaluation conducted on the HiDeoCR approach. </p>
Data from: Thermal adaptation best explains Bergmann's and Allen's rule across ecologically diverse shorebirds
<p>Bergmann's and Allen's rules state that endotherms should be larger and have shorter appendages in cooler climates. However, the drivers of these rules are not clear. Both rules could be explained by adaptation for improved thermoregulation, including plastic responses to temperature in early life. Non-thermal explanations are also plausible as climate impacts other factors that influence size and shape, including starvation risk, predation risk, and foraging ecology. We assess the potential drivers of Bergmann's and Allen's rules in 30 shorebird species using extensive field data (>200,000 observations). We show birds in hot, tropical northern Australia have longer bills and smaller bodies than conspecifics in temperate, southern Australia, conforming with both ecogeographical rules. This pattern is consistent across ecologically diverse species, including migratory birds that spend early life in the Arctic. Our findings best support the hypothesis that thermoregulatory adaptation to warm climates drives latitudinal patterns in shorebird size and shape. </p>
A test of Bergmann's rule in the Early Triassic: Latitude, body size, and sampling in Lystrosaurus
<p>The ecogeographical rule known as Bergmann's rule suggests that there is a positive relationship between body size and latitude when comparing closely related taxa. The underlying mechanism, or mechanisms, to explain this pattern vary as widely as the taxa that seem to follow it, which has led to skepticism over whether Bergmann's rule should be considered a rule at all. Despite this, Bergmann's rule is widespread among modern birds, mammals, beetles, and some amphibians, but far fewer extinct taxa have been subjected to tests of Bergmann's rule. To test whether Bergmann's rule is detected in extinct taxa, we compared body size proxies in <em>Lystrosaurus</em> recovered from Early Triassic-aged strata in Antarctica, South Africa, India, and China. Our results reveal that average body size is largest at mid-northern paleolatitudes (~45°N) instead of the highest southern paleolatitudes (~70°S). Additionally, maximum body size is consistent across northern and southern hemispheres, indicating that Bergmann's rule did not apply for <em>Lystrosaurus</em> during the Early Triassic. To test potential sample size biases in our results, we used rarefaction and subsampling to show that only the Karoo Basin is well sampled, and that large individuals are exceedingly rare except in the Turpan-Junggar Basin of Xinjiang, China. Taken together, our results suggest that <em>Lystrosaurus</em> had the potential to reach large body sizes in each of the latitudinally widespread tectonic basins studied here, but that local conditions may have allowed individuals at mid-northern paleolatitudes a greater chance of reaching large size compared to southern congeners that suffered increased mortality at young/small sizes.</p>
Conformity to Bergmann's rule in birds depends on nest design and migration
<p>Ecogeographical rules attempt to explain large-scale spatial patterns in biological traits. One of the most enduring examples is Bergmann's rule, which states that species should be larger in colder climates due to the thermoregulatory advantages of larger body size. Support for Bergmann's rule, however, is not consistent across taxonomic groups, raising questions about what factors may moderate its effect. Behaviour may play a crucial, yet so far underexplored, role in mediating the extent to which species are subject to environmental selection pressures in colder climates. Here, we tested the hypothesis that nest design and migration influence conformity to Bergmann's rule in a phylogenetic comparative analysis of the birds of the Western Palearctic, a group encompassing dramatic variation in both climate and body mass. We predicted that migratory species and those with more protected nest designs would conform less to the rule than sedentary species and those with more exposed nests. We find that sedentary, but not short- or long-distance migrating species, are larger in colder climates. Among sedentary species, conformity to Bergmann's rule depends, further, on nest design: species with open nests, in which parents and offspring are most exposed to adverse climatic conditions during breeding, conform most strongly to the rule. Our findings suggest that enclosed nests and migration enable small birds to breed in colder environments than their body size would otherwise allow. Therefore, we conclude that behaviour can substantially modify species' responses to environmental selection pressures.</p>
Raw NGS Data for "Deep mutational scanning and machine learning reveal structural and molecular rules governing allosteric hotspots in homologous proteins"
<p>This directory contains relevant fastq files used for deep sequencing analysis in the publication “Deep mutational scanning and machine learning reveal structural and molecular rules governing allosteric hotspots in homologous proteins”. </p> <p>Fastq files are provided for presorted, uninduced and induced populations from DMS experiments of four homologs (TtgR, TetR, RolR, and MphR). Three replicates were performed for each sample.</p> <p>Data analysis of this deep sequencing data was performed using custom scripts, which are described in the methods section of the publication.</p>
Book of Pirate Rules - Week 5
[](https://sketchfab.com/blogs/community/sketchfab-weekly/?ref=sfb) Rule Number 1: *Always sail to new horizons* Source: Objaverse 1.0 / Sketchfab
Figure 6. Forward walking image sequence-Design and Implementation of an Autonomous Humanoid Robot Based on Fuzzy Rule-Based Motion Controller
<p>The image sequences of sideward walking and turning are shown in Figure 6 respectively.</p>
Data from: Rapoport's rule explains the range size distribution of butterflies along the Eastern Himalayan elevation gradient
<p>Understanding elevational range size distribution of organisms can provide valuable insights on biogeographic pattern of species and their conservation. Rapoport's rule posits that the elevational range size of species increases with increasing elevation. However, the validity of this rule is often questioned due to variations in methodologies across studies and inconsistencies among different groups of organisms. In this study we examined the elevational range size distribution of butterflies in the Eastern Himalaya, and assessed the applicability of Rapoport's rule using different approaches, which perhaps is the first of its kind in the Himalaya. We sampled butterflies along the elevational gradient of 16 elevational bands (300 – 3,300 m) using point count method along the transect. The sampled butterflies were grouped into various sub-groups based on family, biogeographic affinity, and larval feeding pattern. We found that the majority of the butterfly species (total as well as sub-groups) had small range sizes, and their elevational range distribution showed support for the Rapoport's rule. Increase in variation in temperature as measured by temperature seasonality and mean annual temperature range were the most important predictors of range size distribution pattern of the overall butterfly community. However, the relationship between range size and climatic variability differed among various sub-groups implying that the perceived pattern may vary even within the species of the same taxon.</p>
Fig. 17.5 in Chapter 17: Gigantism, Dwarfism, and Cope's Rule: "Nothing in Evolution Makes Sense without a Phylogeny"
Fig. 17.5. Three examples of bodysize evo
Training data composition determines machine learning generalization and biological rule discovery
<p>Github: https://github.com/csi-greifflab/negative-class-optimization</p> <p>Preprint: https://www.biorxiv.org/content/10.1101/2024.06.17.599333v1</p>
Molecular structure discovery for untargeted metabolomics using biotransformation rules and global molecular networking
<p>Comparative analysis of SIRIUS to evaluate our method, Biotransformation-based Annotation Method (BAM). This dataset includes all scripts, data, and results relevant to this analysis. BAM can be found on GitHub (https://github.com/HassounLab/BAM). </p> <p> </p> <p> </p>
Data from: Contingency rules for pathogen competition and antagonism in a genetically based, plant defense hierarchy
1. Plant defense against pathogens includes a range of mechanisms, including, but not limited to, genetic resistance, pathogen-antagonizing endophytes, and pathogen competitors. The relative importance of each mechanism can be expressed in a hierarchical view of defense. Several recent studies have shown that pathogen antagonism is inconsistently expressed within the plant defense hierarchy. Our hypothesis is that the hierarchy is governed by contingency rules that determine when and where antagonists reduce plant disease severity. 2. Here, we investigated whether pathogen competition influences pathogen antagonism using Populus as a model system. In three independent field experiments, we asked whether competition for leaf mesophyll cells between a Melampsora rust pathogen and a microscopic, eriophyid mite affects rust pathogen antagonism by fungal leaf endophytes. The rust pathogen has an annual, phenological disadvantage in competition with the mite because the rust pathogen must infect its secondary host in spring before infecting Populus. We varied mite-rust competition by utilizing Populus genotypes characterized by differential genetic resistance to the two organisms. We inoculated plants with endophtyes and allowed mites and rust to infect plants naturally. 3. Two contingency rules emerged from the three field experiments: 1) pathogen antagonism by endophytes can be preempted by host genes for resistance that suppress pathogen development, and 2) pathogen antagonism by endophtyes can secondarily be preempted by competitive exclusion of the rust by the mite. 4. Synthesis: Our results point to a Populus defense hierarchy with resistance genes on top, followed by pathogen competition, and finally pathogen antagonism by endophytes. We expect these rules will help to explain the variation in pathogen antagonism that is currently attributed to context dependency.
Figure 6. Majority–rule consensus tree from 8 in A new species of the genus Lightiella: the first record of Cephalocarida (Crustacea) in Europe
Figure 6. Majority–rule consensus tree from 8 primary trees.
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.