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10,812 results for “novels”
Novel plant-microbe interactions: rapid evolution of a legume-rhizobium mutualism in restored prairies
1. When plants colonize new habitats, the novel interactions they form with new mutualists or enemies can immediately affect plant performance. These novel interactions also may provoke rapid evolutionary responses and can be ideal scenarios for investigating how species interactions influence plant evolution. 2. To explore how mutualists influence the evolution of colonizing plant populations, we capitalized on an experiment in which two former agricultural fields were seeded with identical prairie seed mixes in 2010. Six years later, we compared how populations of the legume Chamaecrista fasciculata from these sites and their original (shared) source population responded to nitrogen-fixing rhizobia from the restoration sites in a greenhouse reciprocal cross-inoculation experiment. 3. We found that the two populations differed both from their original source population and from each other in the benefits they derive from rhizobia, that one population has evolved reduced allocation to rhizobia (i.e., forms fewer rhizobium-housing nodules). 4. Synthesis. Our results suggest that these plant populations have evolved different ways of interacting with rhizobia, potentially in response to differences in rhizobium quality between sites. Our study illustrates how microbial mutualists may shape plant evolution in new environments and highlights how variation in microbial mutualists potentially may select for different evolutionary strategies in plant hosts.
Data from: Phenotypic plasticity facilitates initial colonization of a novel environment
Phenotypic plasticity can allow organisms to respond to environmental changes by producing better matching phenotypes without any genetic change. Because of this, plasticity is predicted to be a major mechanism by which a population can survive the initial stage of colonizing a novel environment. We tested this prediction by challenging wild Drosophila melanogaster with increasingly extreme larval environments and then examining expression of alcohol dehydrogenase (ADH) and its relationship to larval survival in the first generation of encountering a novel environment. We found that most families responded in the adaptive direction of increased ADH activity in higher alcohol environments and families with higher plasticity were also more likely to survive in the highest alcohol environment. Thus, plasticity of ADH activity was positively selected in the most extreme environment and was a key trait influencing fitness. Furthermore, there was significant heritability of ADH plasticity which can allow plasticity to evolve in subsequent generations after initial colonization. The adaptive value of plasticity, however, was only evident in the most extreme environment and had little impact on fitness in less extreme environments. The results provide one of the first direct test of the adaptive role of phenotypic plasticity in colonizing a novel environment.
Data from: A novel, porcinated human Butyrylcholinesterase catalytically degrades the chemical warfare nerve agent, sarin
<p>Chemical warfare nerve agents (CWNAs) present a global threat to both military and civilian populations. The acute toxicity of CWNAs stems from their ability to effectively inhibit acetylcholinesterase (AChE). This inhibition can lead to uncontrolled cholinergic cellular signaling, resulting in cholinergic crisis and, ultimately, death. While the current FDA-approved standard of care is moderately effective when administered early, development of novel treatment strategies is necessary. Butyrylcholinesterase (BChE) is an enzyme which displays a high degree of structural homology to AChE. Unlike AChE, the roles of BChE are uncertain and possibilities are still being explored. However, BChE appears to primarily serve as a bioscavenger of toxic esters due to its ability to accommodate a wide variety of substrates within its active site. Like AChE, BChE is also readily inhibited by CWNAs. Due to its high affinity for binding CWNAs, and that null-BChE yields no apparent health effects, exogenous BChE has been explored as a candidate therapeutic for CWNA intoxication. Despite years of research, minimal strides have been made to develop a catalytic bioscavenger. Further, BChE is only in early clinical trials as a stoichiometric bioscavenger of CWNAs, and large quantities must be administered to treat CWNA toxicity. Here we describe previously unidentified mutations to residues within and adjacent to the acyl binding pocket (positions 282-285 were mutagenized from YGTP to NHML) of BChE that confer catalytic degradation of the CWNA, sarin. These mutations, along with corresponding future efforts, may finally lead to a novel therapeutic to combat CWNA intoxication.</p>
Data from: Time of emergence of novel climates for North American migratory bird populations
To better understand the ecological implications of global climate change for species that display geographically and seasonally dynamic life-history strategies, we need to determine where and when novel climates are projected to first emerge. Here, we use a multivariate approach to estimate time of emergence (ToE) of novel climates based on three climate variables (precipitation, minimum and maximum temperature) at a weekly temporal resolution within the Western Hemisphere over a 280-year period (2021-2300) under a high emissions scenario (RCP8.5). We intersect ToE estimates with weekly estimates of relative abundance for 77 passerine bird species that migrate between temperate breeding grounds in North America and southern tropical and subtropical wintering grounds using observations from the eBird citizen-science database. During the non-breeding season, migrants that winter within the tropics are projected to encounter novel climates during the second half of this century. Migrants that winter in the subtropics are projected to encounter novel climates during the first half of the next century. During the beginning of the breeding season, migrants on their temperate breeding grounds are projected to encounter novel climates during the first half of the next century. During the end of the breeding season, migrants are projected to encounter novel climates during the second half of this century. Thus, novel climates will first emerge ca. 40-50 years earlier during the second half of the breeding season. These results emphasize the large seasonal and spatial variation in the formation of novel climates, and the pronounced challenges migratory birds are likely to encounter during this century, especially on their tropical wintering grounds and during the transition from breeding to migration. When assessing the ecological implications of climate change, our findings emphasize the value of applying a full annual cycle perspective using standardized metrics that promote comparisons across space and time.
Data from: Vertical differentiation in tropical forest butterflies: a novel mechanism generating insect diversity?
Many tropical fruit-feeding nymphalid butterflies are associated with either the forest canopy or the understory, however, the exceptions offer insights into the origins of tropical diversity. As it occurs in both habitats of tropical forests in Ecuador and Peru, Archaeoprepona demophon is one such exception. We compared patterns of occurrence of A. demophon in the canopy and understory and population genomic variation for evidence of ecological and genetic differentiation between habitats. We found that butterfly occurrences in the canopy were largely uncorrelated with occurrences in the understory at both localities, indicating independent demographic patterns in the two habitats. We also documented modest, significant genome-level differentiation at both localities. Genetic differentiation between habitat types (approximately 20m in elevation) were comparable to levels of differentiation between sampling locations (approximately 1500km). We conclude that canopy and understory populations of A. demophon represent incipient independent evolutionary units. These findings support the hypothesis that divergence between canopy and understory-associated populations might be a mechanism generating insect diversity in the tropics.
Data from: A ketocarotenoid-based color polymorphism in the Sira poison frog Ranitomeya sirensis indicates novel gene interactions underlying aposematic signal variation
<p>The accumulation of red ketocarotenoids is an important component of coloration in many organisms, but the underlying mechanisms are poorly understood. In some organisms, ketocarotenoids are sequestered from the diet and can accumulate when enzymes responsible for carotenoid breakdown are disrupted. In other organisms, ketocarotenoids are formed endogenously from dietary precursors via oxidation reactions carried out by carotenoid ketolase enzymes. Here, we study the genetic basis of carotenoid coloration in an amphibian. We demonstrate that a red/yellow polymorphism in the dendrobatid poison frog <em>Ranitomeya sirensis</em> is due to the presence/absence of ketocarotenoids. Using whole-transcriptome sequencing of skins and livers, we found that a transcript encoding a cytochrome P450 enzyme (CYP3A80) is expressed 3.4-fold higher in livers of red frogs versus yellow. As CYP3A enzymes are known carotenoid ketolases in other organisms, our results point to CYP3A80 as a strong candidate for a carotenoid ketolase in amphibians. Furthermore, in red frogs, the transcript encoding the carotenoid cleavage enzyme BCO2 is expressed at a low level or as a splice variant lacking key catalytic amino acids. This suggests that BCO2 function may be disrupted in red frogs, providing a mechanism whereby the accumulation of ketocarotenoids and their dietary precursors may be enhanced.</p>
Supplementary Material for Frontiers Plant Genetics and Genomics 'Novel R tools for analysis of genome-wide population genetic data with emphasis on clonality'
<p>Authors</p> <p>Zhian N. Kamvar, Jonah C. Brooks, and Niklaus J. Grünwald</p>
Twelve Novels by Arthur Conan Doyle (TXM corpus)
<p>This is a sample dataset of twelve novels written by Arthur Conan Doyle (all in the public domain). The novels have been prepared for use with the TXM text analysis software, including lemmatisation and part-of-speech tagging using TreeTagger. The collection contains twelve novels belonging to different subgenres: detective fiction (Sherlock Holmes novels), adventure novels, historical novels, horror novels and other novels. See the metadata file (metadata.csv) for details. The corpus file (doyle.txm) is a binary format that can be directly loaded into TXM (see http://textometrie.ens-lyon.fr/).</p>
A sharper view of Pal 5's tails: Discovery of stream perturbations with a novel non-parametric technique
<p>Here we release some data on the Pal 5 stellar stream from the arXiv:1609.01282 paper.</p> <p> The file pal5_measurements.fits stores the Pal 5 stream measurements , as shown on Figure 5 of the paper, with the following columns</p> <ul> <li>phi1 Angle along the stream in degrees ( the coordinate system is defined in the paper)</li> <li>phi2 Angle across the stream in degrees</li> <li>sbstream Central surface brightness of the stream in stars per square arcmin</li> <li>ldens Linear density of the stream in stars/arcmin</li> <li>cumdens Cumulative density of the (leading/trailing) tail from the progenitor</li> <li>width Gaussian sigma of the stream in degrees</li> <li>bgdens density of background stars</li> </ul> <p>The columns with _16, _50, _84 appended to their name refer to the 16%, 50% 84% percentiles inferred from the posterior samples.</p> <p>We also provide the MCMC chains that could be used to measure the covariance matrices of different parameters:</p> <p>The chains are stored in the fits file with the columns</p> <p>phi2_i, logI_j, logSig_j, logB0_j, logB1_j referring to the stream track values at the nodes, log of stream surface brightness, log of stream width, log of the background density and log of background density slope (see paper for more details).</p> <p> </p> <p> </p>
DeepAnnotation: A novel interpretable deep learning-based genomic selection model that integrates comprehensive functional annotations
<p>1. Update package, example dataset, and demo code of DeepAnnotation</p> <p>2. Update the transformed genotype data, the phenotype data, the comprehensive functional annotation data for Duroc prepared by RNAfold, DeepSEA, easyMF models, and the four types of input data for training DeepAnnotation model</p> <p>3. Add the conserved functional annotation</p> <p> </p>
Data from: How far can I extrapolate my species distribution model? Exploring Shape, a novel method
<p>Species distribution and ecological niche models (hereafter SDMs) are popular tools with broad applications in ecology, biodiversity conservation, and environmental science. Many SDM applications require projecting models in environmental conditions non-analog to those used for model training (extrapolation), giving predictions that may be statistically unsupported and biologically meaningless. We introduce a novel method, Shape, a model-agnostic approach that calculates the extrapolation degree for a given projection data point by its multivariate distance to the nearest training data point. Such distances are relativized by a factor that reflects the dispersion of the training data in environmental space. Distinct from other approaches, Shape incorporates an adjustable threshold to control the binary discrimination between acceptable and unacceptable extrapolation degrees. We compared Shape's performance to five extrapolation metrics based on their ability to detect analog environmental conditions in environmental space and improve SDMs suitability predictions. To do so, we used 760 virtual species to define different modeling conditions determined by species niche tolerance, distribution equilibrium condition, sample size, and algorithm. All algorithms had trouble predicting species niches. However, we found a substantial improvement in model predictions when model projections were truncated independently of extrapolation metrics. Shape's performance was dependent on extrapolation threshold used to truncate models. Because of this versatility, our approach showed similar or better performance than the previous approaches and could better deal with all modeling conditions and algorithms. Our extrapolation metric is simple to interpret, captures the complex shapes of the data in environmental space, and can use any extrapolation threshold to define whether model predictions are retained based on the extrapolation degrees. These properties make this approach more broadly applicable than existing methods for creating and applying SDMs. We hope this method and accompanying tools support modelers to explore, detect, and reduce extrapolation errors to achieve more reliable models.</p>
Dataset for paper 'McAN: a novel computational algorithm and platform for constructing and visualizing haplotype networks'
<p>The .zip file includes four datasets for testing the performance of McAN (doi: https://doi.org/10.1093/bib/bbad174).</p>
Data from: A pioneering experimental investigation of a novel in-situ dynamic characterization of the tensile/compression stress-strain mechanism on human plantar soft tissue
<p><span>We have conducted the first in-situ and in-vivo dynamic mechanical test on human plantar soft tissue. A dynamic mechanical analysis (DMA)-like device has been invented to perform the in-situ and in-vivo stress-strain tests on living plantar in order to characterize the material mechanism of biological soft tissue, whereas it is nearly impossible to prepare a sample from a living body for classical tests. A series of pioneering tests of tensile/compression on the heel of ten volunteers are reported, with the reference of tests on mimic foot model made by silicon rubber, standard silicon rubber brick sample, and finite elementary analysis. In addition to demonstrating the effectiveness of the device and approach, interesting correlations between the results and clinic data were found, suggesting considerable potential for the invention in future research.</span></p>
Twelve Novels by Arthur Conan Doyle (Doyle-Novels)
<p>This dataset contains twelve novels by Arthur Conan Doyle in various formats: as plain text files, as one-text-per-line plain text corpus, as a linguistically-annotated corpus for analysis with TXM, as a term-document matrix. There is also a metadata file that provides titles, years of first publication, subgenres and narrative perspective for each novel. </p><p>This dataset is suitable for a range of use cases in Digital Humanities teaching, among them corpus analysis using TXM, corpus querying using Python and even Topic Modeling, although it is a bit small for this purpose. </p>
Average sentence length in novels dataset (Avg-Sent-Len)
<p>This dataset includes values on average sentence length per novel, as well as very basic metadata (author name and year of firstpublication), for several sets of 100 novels in multiple languages (English, French, German and Hungarian, for the period 1840-1920) derived from the European Literary Text Collection (ELTeC) as well as for one larger set of 1150 English-language novels from Project Gutenberg (for the period 1800-1960). </p><p>This dataset is suitable for learning data visualization (scatterplots and regression plots) as well as data analytics (linear / polynomial regression). </p><p>Source of the data: <a href="https://github.com/christofs/sentlens">https://github.com/christofs/sentlens</a>. </p><p>Use of the data: <a href="https://dragonfly.hypotheses.org/1152">https://dragonfly.hypotheses.org/1152</a>. </p>
Window[1]resorcin[3]arenes: A novel macrocycle able to self-assemble to a catalytically active hexameric cage
<p>open data for paper Window[1]resorcin[3]arenes: A novel macrocycle able to self-assemble to a catalytically active hexameric cage</p>
Data from: Mouse gingival single cell transcriptomic atlas identified a novel fibroblast subpopulation activated to guide oral barrier immunity in periodontitis
<p>Periodontitis, one of the most common non-communicable diseases, is characterized by chronic oral inflammation and uncontrolled tooth supporting alveolar bone resorption. Its underlying mechanism to initiate aberrant oral barrier immunity has yet to be delineated. Here, we report a unique fibroblast subpopulation activated to guide oral inflammation (AG fibroblasts) identified in a single-cell RNA sequencing gingival cell atlas constructed from the mouse periodontitis models. AG fibroblasts localized beneath the gingival epithelium and in the cervical periodontal ligament responded to the ligature placement and to the discrete topical application of Toll-like receptor stimulants to mouse maxillary tissue. The upregulated chemokines and ligands of AG fibroblasts linked to the putative receptors of neutrophils in the early stages of periodontitis. In the established chronic inflammation, neutrophils together with AG fibroblasts appeared to induce type 3 innate lymphoid cells (ILC3s) that were the primary source of interleukin-17 cytokines. The comparative analysis of <em>Rag2-/-</em> and <em>Rag2gc-/-</em> mice suggested that ILC3 contributed to the cervical alveolar bone resorption interfacing the gingival inflammation. We propose that the AG fibroblast–neutrophil–ILC3 axis as a previously unrecognized mechanism which could be involved in the complex interplay between oral barrier immune cells contributing to pathological inflammation in periodontitis.</p>
Dataset for "Mo-Si alloys studied by atomistic computer simulations using a novel machine-learning interatomic potential: Thermodynamics and interface phenomena"
<p>This dataset was used to fit a general purpose machine-learning interatomic potential for Mo-Si alloys based on the Atomic Cluster Expansion (ACE) formalism. It supports the paper "Mo-Si alloys studied by atomistic computer simulations using a novel machine-learning interatomic potential: Thermodynamics and interface phenomena".</p>
Data associated with: Recording animal-view videos of the natural world using a novel camera system and software package
<p>Data associated with Vasas V, Lowell MC*, Villa J*, Jamison QD*, Siegle AG*, Katta PVR*, Bhagavathula P*, Kevan PG, Fulton D, Losin N, Kepplinger D, Salehian S, Forkner RE, Hanley D (2023) Recording animal-view videos of the natural world using a novel camera system and software package. PLoS Biology. DOI: 10.1371/journal.pbio.3002444</p>
the supplementary of Novel plastid genome characteristics in Fugacium kawagutii and accelerated evolution of plastid proteins in dinoflagellates
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Allen Brain Atlas
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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.