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625 results for “Rules”
Exceptions to the rule: Relative roles of time, diversification rates and regional energy in shaping the inverse latitudinal diversity gradient
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SpaCy affixes: SpaCy support for affixes splitting for Freeling-like affixes rules and dictionaries.
<p>This library was born to split clitics from verbs so POS tagging works out-of-the-box with spaCy models.</p>
Data corresponding to the publication "The limited predictive power of the Pauling Rules"
<p>This is the data set corrresponding to the publication "The limited predictive power of the Pauling rules" (see https://onlinelibrary.wiley.com/doi/full/10.1002/anie.202000829). This data can be reproduced with the following code: https://doi.org/10.5281/zenodo.3654428.</p>
Data, plotting scripts, and figures for "Applying the swept rule for explicit partial differential equation solutions on heterogeneous computing systems"
<p>This dataset contains the figures, as well as the necessary plotting scripts and data to reproduce them, for the article "Applying the swept rule for explicit partial differential equation solutions on heterogeneous computing systems" by Daniel J. Magee, Anthony S. Walker, and Kyle E. Niemeyer (2020).</p> <p>The plotting scripts were all run using Python 3.7.6, and should be compatible with >3.6, but this has not been tested.</p> <p>The code included in this dataset is released under the BSD 3-Clause License. The figures are shared under the Creative Commons Attribution 4.0 International License (CC BY 4.0, https://creativecommons.org/licenses/by/4.0/).</p>
Data from: One panel to rule them all: DArTcap genotyping for population structure, historical demography, and kinship analyses, and its application to a threatened shark
With recent advances in sequencing technology, genomic data are changing how important conservation management decisions are made. Applications such as Close-Kin Mark-Recapture demand large amounts of data to estimate population size and structure, and their full potential can only be realised through ongoing improvements in genotyping strategies. Here we introduce DArTcap, a cost-efficient method that combines DArTseq and sequence capture, and illustrate its use in a high resolution population analysis of Glyphis garricki, a rare, poorly known and threatened euryhaline shark. Clustering analyses and spatial distribution of kin pairs from four different regions across northern Australia and one in Papua New Guinea, representing its entire known range, revealed that each region hosts at least one distinct population. Further structuring is likely within Van Diemen Gulf, the region that included the most rivers sampled, suggesting additional population structuring would be found if other rivers were sampled. Coalescent analyses and spatially explicit modelling suggest that G. garricki experienced a recent range expansion during the opening of the Gulf of Carpentaria following the conclusion of the Last Glacial Maximum. The low migration rates between neighbouring populations of a species that is found only in restricted coastal and riverine habitats show the importance of managing each population separately, including careful monitoring of local and remote anthropogenic activities that may affect their environments. Overall we demonstrated how a carefully chosen SNP panel combined with DArTcap can provide highly accurate kinship inference and also support population structure and historical demography analyses, therefore maximising cost-effectiveness.
Datasets - Evolutionary history, not ecogeographic rules, explains size variation of tropical insects along elevational gradients
<p>One of the best-known biogeographic rules for ectotherms is the temperature-size rule, which asserts that ectotherms produce smaller adults at warmer temperatures. Although this is often true, it has become clear that there is no single process behind the pattern and many exceptions to the rule. To disentangle such complex temperature-size relationships, individual clades must be examined at ecological and evolutionary scales.</p> <p>We examined temperature-size relationships for 2106 individuals from 64 populations and 40 species of <i>Cephaloleia</i> rolled-leaf beetles (Chrysomelidae; Cassidinae)<b> </b>occurring along two tropical elevational gradientss: Barva and the Talamanca Cordillera in Costa Rica, Central America. We tested whether the temperature-size rule applied to interspecific elevational assemblages, intraspecific elevational populations, or different rearing temperatures for individual populations.</p> <p>At the interspecific scale, evolutionary history, rather than elevation, explains body size. At the intraspecific scale, only one of seven species followed the temperature-size rule across elevations. When larvae were reared at different temperatures, only one of five populations followed the temperature-size rule. Most populations grew to a fixed size regardless of temperature.</p> <p>Size in <i>Cephaloleia</i> beetles is constrained by their evolutionary history and responds to factors that rarely correlate with temperature. As temperature increases, ectotherms will not universally shrink, but determining if and why their size will change will require further investigation.</p> <p>Here we provide the following datasets used to determine effects of temperature on insect body size at population and community levels: <i>Supplement S1.</i> Body length for 2106 individuals representing 64 populations from 40 species of <i>Cephaloleia </i>rolled-leaf beetle along the Barva and Talamanca elevational gradients, Costa Rica<i>. Supplement S2.</i> Intraspecific differences in length for 798 individuals from seven <i>Cephaloleia </i>species present at multiple life zone<i>.</i><i> Supplement S3.</i> Effects of developmental temperatures on <i>Cephaloleia </i>adult size in 968 individuals from four species and five populations reared in the laboratory at temperatures between 10 and 35 °C.</p>
The relationship between a combinatorial processing rule and a continuous mate preference function in an insect
<p>Mate choice involves processing signals that can reach high levels of complexity and feature multiple components, even in small animals with tiny brains. This raises the question of whether and how such organisms deal with this complexity. One solution involves combinatorial processing, whereby different signal elements are processed as single units. Combinatorial processing has been described in several mammals and birds, and recently in a vibrationally signalling insect, Enchenopa treehoppers. Here, we ask about the relationship between combinatorial rules and mate preferences for continuously varying signal features. Enchenopa male advertisement signals are composed of two elements: a 'whine' followed by a set of pulses. The dominant frequency of the whine and element combination both matter to females. We presented synthetic signals varying in element order (natural [whine-pulses], reverse [pulses-whine]) and in frequency to Enchenopa females and recorded their responses. The reverse combination resulted in a decrease in attractiveness of the signals, and also slightly changed the shape of the preference for frequency. We found that females could be classified into three 'types': females with both a strong preference and a strong combinatorial rule, females with both a weak preference and weak rule and females with a strong preference but a weak rule. Our results suggest that in Enchenopa signal processing, the mate preference for a continuous signal feature 'takes precedence' over, but also interacts with, the combinatorial rule. The relationship between the preference and the rule could evolve to take different forms according to selection on mate choice decisions. We suggest that exploring the relationship between such preferences and rules in species with more complex signals will bring insight into the evolution of the multi-component communication systems.</p>
Lineage-specific patterns of chromosome evolution are the rule not the exception in Polyneoptera insects
The structure of a genome can be described at its simplest by the number of chromosomes and the sex chromosome system it contains. Despite over a century of study, the evolution of genome structure on this scale remains recalcitrant to broad generalisations that can be applied across clades. To address this issue, we have assembled a dataset of 823 karyotypes from the insect group Polyneoptera. This group contains orders with a range of variations in chromosome number, and offer the opportunity to explore the possible causes of these differences. We have analysed this data using both phylogenetic and taxonomic approaches. Our analysis allows us to assess the importance of rates of evolution, phylogenetic history, sex chromosome systems, parthenogenesis, and genome size on variation in chromosome number within clades. We find that fusions play a key role in the origin of new sex chromosomes and that orders exhibit striking differences in rates of fusions, fissions, and polyploidy. Our results suggest that the difficulty in finding consistent rules that govern evolution at this scale may be due to the presence of many interacting forces that can lead to variation among groups.
Rethinking Gloger's Rule: climate, light environments and color in a large family of tropical birds (Furnariidae)
Ecogeographic rules provide a framework within which to test evolutionary hypotheses of adaptation. Gloger's rule predicts endothermic animals should have darker colors in warm and rainy climates. This rule also predicts animals should be redder in warm and dry climates, the so-called "complex Gloger's rule." Empirical studies frequently demonstrate that animals are darker in cool and wet rather than warm and wet climates. Further, sensory ecology predicts that, to enhance crypsis, animals should be darker in darker light environments. We aimed to disentangle the effects of climate and light environments on plumage brightness and redness in the large Neotropical passerine family Furnariidae. Birds in cooler and rainier climates had darker plumage, even after controlling for habitat type. Birds in darker habitats had darker plumage, even after controlling for climate. The effects of temperature and brightness interact so that the negative effect of precipitation on brightness is strongest in cool temperatures. Finally, birds tended to be redder in warm and dry habitats but also, surprisingly, in cool and wet locales. We suggest Gloger's rule results from complementary selective pressures arising from myriad ecological factors, including crypsis, thermoregulation, parasite deterrence and resistance to feather abrasion.
Phylogenetic diversity and environment form assembly rules for Arctic diatom genera – a study on recent and ancient sedimentary DNA
<p><span><b>Aim</b></span></p> <p><span>This study investigates taxonomic and phylogenetic diversity in diatom genera to evaluate assembly rules for eukaryotic microbes across the Siberian treeline. We first analysed how phylogenetic distance relates to taxonomic richness and turnover. Second, we used relatedness indices to evaluate if environmental filtering or competition influences the assemblies in space and through time. Third, we used distance-based ordination to test which environmental variables shape diatom turnover.</span></p> <p><span><b>Location</b></span></p> <p><span>Yakutia and Taymyria, Russia: we sampled 78 surface sediments and a sediment core, extending to 7000 years before present, to capture the forest–tundra transition in space and time, respectively. </span></p> <p><span><b>Taxon</b></span></p> <p><span>Arctic freshwater diatoms.</span></p> <p><span><b>Methods</b></span></p> <p><span>We applied metabarcoding to retrieve diatom diversity from surface and core sedimentary DNA. The taxonomic assignment binned sequence types (lineages) into genera and created taxonomic (abundance of lineages within different genera) and phylogenetic datasets (phylogenetic distances of lineages within different genera).</span></p> <p><span><b>Results</b></span></p> <p><span>Contrary to our expectations, we find a unimodal relationship between phylogenetic distance and richness in diatom genera. We discern a positive relationship between phylogenetic distance and taxonomic turnover in spatially and temporally distributed diatom genera. Further, we reveal positive relatedness indices in diatom genera across the spatial environmental gradient and predominantly in time-slices at a single location, with very few exceptions assuming effects of competition. Distance-based ordination of taxonomic and phylogenetic turnover indicates that lake environment variables, like HCO<sub>3</sub><sup>–</sup> and water depth, largely explain diatom turnover. </span></p> <p><span><b>Main conclusion</b></span></p> <p>Phylogenetic and abiotic assembly rules are important in understanding the regional assembly of diatom genera across lakes in the Siberian treeline ecotone. Using a space–time approach we are able to exclude the influence of geography and elucidate that lake environmental variables primarily shape the assemblies. We conclude that some diatom genera have greater capabilities to adapt to environmental changes, whereas others will be putatively replaced or lost due to the displacement of the Arctic tundra biome under recent global warming.</p>
Interspecific allometry for sexual shape dimorphism: macroevolution of multivariate sexual phenotypes with application to Rensch's rule
<p>Allometric trends in the degree of sexual dimorphism with body size have long fascinated evolutionary biologists. Many male-biased clades display more prominent sexual dimorphism in larger taxa (Rensch's rule), with most examples documenting this pattern for body size dimorphism. While sexual dimorphism in traits other than body size is equally functionally relevant, characterizing allometric patterns of sexual dimorphism in such traits is hampered by lack of an analytical framework that can accommodate multivariate phenotypes. In this paper we derive a multivariate equivalency for investigating trends in sexual dimorphism – relative to overall body size – across taxa and provide a generalized test to determine whether such allometric patterns correspond with Rensch's rule. For univariate linear traits like body size, our approach yields equivalent results to those from standard procedures, but our test is also capable of detecting trends in multivariate datasets like shape. Computer simulations reveal the method displays appropriate statistical properties, and an empirical example in Mediterranean lizards provides the first demonstration of Rensch's rule in a multivariate phenotype (head shape). Our generalized procedure substantially extends the analytical toolkit for investigating macroevolutionary patterns of sexual dimorphism and seeking a better understanding of the processes that underlie them.</p>
Data from: A test of a corollary of Allen's rule suggests a role for population density
A body of research by Russell Greenberg, Glenn Tattersall, and their colleagues has proposed a corollary of Allen's Rule: that in freshwater‐limited environments, bill surface area increases with temperature. Increases in both population density and sexual dimorphism, however, could also explain increases in bill surface area. After controlling for the effects of a hybrid zone, we tested whether temperature or population density in the Saltmarsh Sparrow (Ammospiza caudacuta), a sexually monomorphic estuarine specialist, explained greater variance in bill surface area. This allowed us to examine multiple potential selective mechanisms underlying the Greenberg‐Tattersall Corollary. We found that Saltmarsh Sparrows follow the general pattern of the Corollary (larger bills in warmer summer climates) but only after controlling for population density. The relationship between bill surface area and temperature varied inversely with population density. We discuss the relative abilities of sexual selection and ecological competition to explain these results.
Data from: A test of community assembly rules using foliar endophytes from a tropical forest canopy
<p>Community assembly theory assumes that ecological communities are spatially delimited into patches. Within these patches, coexistence results from environmental filtering, competition, and immigration. Truly delineated communities exist in laboratory studies of microbial cultures in Petri dishes, yet empirical tests conducted in continuous environments often use patches defined by convention as opposed to realised boundaries. Here we perform a test of ecological community assembly rules using foliar endophyte communities from a tropical rainforest, where leaves are considered as patches for both fungal and bacterial communities. We determined the diversity of fungal and bacterial endophytes using environmental DNA sequencing of 365 top-canopy leaves, collected from 38 host trees belonging to 22 different species across a 4-hectare research plot. Three leaves were collected from three or more branches within each tree crown. We tested the effect of host tree species and their level of phylogenetic relatedness on community composition as well as the contribution of geographic distance between leaves to endophyte community diversity. Endophyte diversity significantly differed across host tree species, as did community composition. Within certain endophytic orders (Xylariales, Rhizobiales) species assemblages significantly differed across host tree species, but this trend was weaker or non-existent in other orders known to contain pathogens and saprotrophs (Polyporales, Solirubrobacterales). Phylogenetically related host tree species displayed more similar endophyte communities than expected by chance, but geographically close trees did not. Consistent with the finding of host-specificity, nearby leaves tended to host more similar communities than distantly positioned ones. These findings demonstrate that foliar endophytes are structured by dispersal across small spatial scales, but at the scale of the canopy they display patterns of neutral filtering, with only a small part of variation described by host tree differences. Endophyte communities thus act as a model system in evoking the rules predicted by theoretical community ecology.</p>
Wall memorial St Rule's Tower, St Andrews
This memorial situated on a wall within the remains of St Rule's Church, St Andrews. The church dates from around 1133. Today only the tower and a small section at the rear remains today, inside is a small selection of wall mounted memorials. This particular one I find interesting due to the skeleton which lies in a hammock. The top of the memorial is around 12 feet off the ground and the photographs were taken from ground level so the upper portion isn't as detailed as I would like. Source: Objaverse 1.0 / Sketchfab
Figure 2. - Bayesian (GTR+Γ+I and HKY+Γ models) and maximum likelihood 50% majority-rule consensus tree. Numbers in the nodes represent posterior probabilities (GTR+Γ+I and HKY+Γ, respectively), and bootstrap value for maximum likelihood and parsimony analyses, respectively. c1–Bragança, Pará; c2–Santa Maria do Pará, Pará; c3–National Forest of Amapá, Amapá; c4–Belém, Pará; i1–Solimões River, near Manaus, Amazonas; i2–Xingu River, Altamira, Pará; i3 and i4–Itacoatiara, Amazonas. MYBP–million years before present.
Figure 2. - Bayesian (GTR+Γ+I and HKY+Γ models) and maximum likelihood 50% majority-rule consensus tree. Numbers in the nodes represent posterior probabilities (GTR+Γ+I and HKY+Γ, respectively), and bootstrap value for maximum likelihood and parsimony analyses, respectively. c1–Bragança, Pará; c2–Santa Maria do Pará, Pará; c3–National Forest of Amapá, Amapá; c4–Belém, Pará; i1–Solimões River, near Manaus, Amazonas; i2–Xingu River, Altamira, Pará; i3 and i4–Itacoatiara, Amazonas. MYBP–million years before present.
Efficient spherical quadrature rules with positive weights
<p>The function "SphQuadrat.m" returns efficient quadrature rules on the sphere in a 3-dimensional space. The quadrature rules consist of the coordinates of the samling points and the (positive) weights of each point. Cartesian and spherical coordinate systems are available; please note that the notation of elevation angles <em>θ</em> in the spherical coordinate systems differs from that in MATLAB. That is, the function returns vertical angles <em>θ</em> measured from the z-axis.</p> <p>Available exactitude degrees of the quadratures are 0,2,4,...,100.</p> <p>MAT files containing the points and the weights of the quadratures are named as "xxx-yyyyy.mat", where "xxx" denotes the degree of exactitude and "yyyyy" denotes the number of points.</p> <p>By default, the weights are normalized as sum(weight)=1, while the function also provides 4pi-normalization sum(weight)=4*pi and the-number-of-points-normalization sum(weight)=numel(weight).</p> <p>Reference: Manuel Gräf, <a href="https://www-user.tu-chemnitz.de/~potts/workgroup/graef/quadrature/papers/Gr13Diss.pdf">Efficient Algorithms for the Computation of Optimal Quadrature Points on Riemannian Manifolds</a>, Ph.D. thesis, Technische Universität Chemnitz, (2013)</p>
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.
USPTO Dataset for: Fast Chemical Reaction Condition Suggestion via Rule-Based Classification and Similarity Search
<p>USPTO database that is analyzed with Rxn-INSIGHT (<a href="https://github.com/mrodobbe/Rxn-INSIGHT">https://github.com/mrodobbe/Rxn-INSIGHT</a>).</p><p>This gzip file contains a very large Pandas DataFrame that can be loaded via pd.read_parquet('uspto_rxn_insight.gzip'). Because of the large size of the data, PyArrow version 13.0 must be used. </p><p>To use parquet in Pandas, install PyArrow and fastparquet using pip:</p><p>pip install pyarrow==13.0<br>pip install fastparquet</p>
scRNA-seq revealed the rules for CDR3 length pairing in TCR beta and alpha chains and BCR heavy and light chains
<p>The scRNAseq datasets of CDR3 length pairing in TCR beta and alpha chains which come from human cental and peripheral samples and mouse peripheral samples.</p> <p>The scRNAseq datasets of CDR3 length pairing in BCR heavy and light chainsCDR3 length pairing in TCR beta and alpha chains and BCR heavy and light chains human cental and peripheral samples and mouse cental and peripheral samples.</p> <p> </p>
Bygrave slide rule
Hohenrechenschieber HR 1 is the German version of a slider used for navigation, mainly in air and sea. Dennert & Pape – manufactory 1938–1944, Hamburg Jagiellonian University Museum Collegium Maius Inventory number: 4860; 865/V https://muzea.malopolska.pl/en/objects-list/2789 Source: Objaverse 1.0 / Sketchfab
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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)
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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.