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2,960 results for “elements”
Comparing ultraconserved elements and exons for phylogenomic analyses of Middle American cichlids: When data agree to disagree
<p>Choosing among types of genomic markers to be used in a phylogenomic study can have a major influence on the cost, design, and results of a study. Yet few attempts have been made to compare categories of next-generation sequence markers limiting our ability to compare the suitability of these different genomic fragment types. Here we explore properties of different genomic markers to find if they vary in the accuracy of component phylogenetic trees and to clarify the causes of conflict obtained from different datasets or inference methods. As a test case, we explore the causes of discordance between phylogenetic hypotheses obtained using a novel dataset of ultraconserved elements (UCEs) and a recently published exon dataset of the cichlid tribe Heroini. Resolving relationships among heroine cichlids has historically been difficult, and the processes of diversification and colonization of Middle America and the Greater Antilles are not yet well understood. Despite differences in informativeness and levels of gene tree discordance between UCEs and exons, the resulting phylogenomic hypotheses generally agree on most relationships. The independent datasets disagreed in areas with low phylogenetic signal that were overwhelmed by noise and non-phylogenetic signals. For UCEs, high levels of incomplete lineage sorting (ILS) seem to be a major cause of noise, whereas, for exons, non-phylogenetic signal may be caused by a reduced number of highly informative loci. This paucity of informative loci in exons might be due to heterogeneous substitution rates that are problematic to model (i.e., computationally restrictive) resulting in systematic errors that UCEs (being less informative individually but more uniform) are less prone to. These results generally demonstrate the robustness of phylogenomic methods to accommodate genomic markers with different biological and phylogenetic properties. However, we identify common and unique pitfalls of different categories of genomic fragments when inferring enigmatic phylogenetic relationships.</p>
A phylogenomic perspective on the evolutionary history of the stonefly genus Suwallia (Plecoptera: Chloroperlidae) revealed by ultraconserved genomic elements
<p>Evolutionary biologists have long sought to disentangle phylogenetic relationships among taxa spanning the tree of life, an increasingly important task as anthropogenic influences have caused, and are expected to continue to cause, population declines and species extinctions, particularly in insects. Advances in DNA sequencing techniques have increasingly facilitated the ability of researchers to apply genomic methods to phylogenetic analyses, even for non-model organisms which have historically lacked the genomic resources to do so. Phylogenetic relationships within the stonefly genus <i>Suwallia</i> (Insecta: Plecoptera: Chloroperlidae) are poorly understood, and have never been assessed using molecular data. We used DNA sequence data from genome-wide ultraconserved element loci to generate the first molecular phylogeny for the group and assess its monophyly. Our results reveal that the monospecific chloroperlid <i>Neaviperla forcipata</i> renders <i>Suwallia</i> paraphyletic, and we recommend a taxonomic revision for its inclusion in <i>Suwallia</i>. We also found that Palearctic and Nearctic <i>Suwallia</i> do not form reciprocally monophyletic clades, and that a biogeographic history including dispersal, vicariance, and founder event speciation via jump dispersal best explains the geographic distribution of this group. Moreover, some <i>Suwallia</i> species (e.g., <i>S. amoenacolens</i>, <i>S. kerzhneri</i>, <i>S. marginata, S. pallidula, </i>and<i> S. starki</i>) exhibit pronounced cryptic diversity that is worthy of further investigation. These findings provide a first glimpse into the evolutionary history of <i>Suwallia</i>, improve our understanding of stonefly diversity, and highlight areas where additional research is needed.</p>
Dcp2 C-terminal cis-binding elements control selective targeting of the decapping enzyme by forming distinct decapping complexes
<p>A single Dcp1-Dcp2 decapping enzyme targets diverse classes of yeast mRNAs for decapping-dependent 5' to 3' decay, but the molecular mechanisms controlling selective mRNA targeting by the enzyme remain elusive. Through extensive genetic analyses we uncover <i>cis</i>-regulatory elements in the Dcp2 C-terminal domain that control selective targeting of the decapping enzyme by forming distinct decapping complexes. Two Upf1-binding motifs target the decapping enzyme to NMD substrates, and a single Edc3-binding motif targets both Edc3 and Dhh1 substrates. Pat1-binding leucine-rich motifs target Edc3 and Dhh1 substrates under selective conditions. Although it functions as a unique targeting component of specific complexes, Edc3 is a common component of multiple complexes. Xrn1 also has a specific Dcp2 binding site, allowing it to be directly recruited to decapping complexes. Collectively, our results demonstrate that Upf1, Edc3, and Pat1 function as regulatory subunits of the holo-decapping enzyme, controlling both its targeting specificity and enzymatic activation</p>
A phylogeny of white-eyes based on ultraconserved elements
<p><span><span><span><span><span><span><span><span><span><span><span>White-eyes are an iconic radiation of passerine birds that have been the subject of studies in evolutionary biology, biogeography, and speciation theory. <i>Zosterops </i>white-eyes in particular are thought to have radiated rapidly across continental and insular regions of the Afro- and Indo-Pacific tropics, yet, their phylogenetic history remains equivocal. Here, we sampled 77% of the genera and 47% of known white-eye species and sequenced thousands of ultraconserved elements to infer the phylogeny of the avian family Zosteropidae. We used concatenated maximum likelihood and species tree methods and found strong support for seven clades of white-eyes and three clades within the species-rich <i>Zosterops </i>radiation.</span></span></span></span></span></span></span></span></span></span></span></p>
Figure 12. Borealestes serendipitus skull elements. A1–6 in New species of mammaliaform and the cranium of Borealestes (Mammaliformes: Docodonta) from the Middle Jurassic of the British Isles
Figure 12. Borealestes serendipitus skull elements. A1–6, premaxillae with incisors and anterior nasal part (NMS G.1992.47.121.4), with diagrammatic illustrations: A1, left lateral view; A2, right lateral view; A3, anterior view; A4, dorsal view; A5, ventral view; A6, semitransparent digital rendering of reconstructed premaxillae and incisors, showing path of premaxillary canal. B1–4, nasal anterior part: B1 ventral view; B2, medial view; B3, dorsal view; B4, left lateral view. Arrows indicate anterior direction. Dark grey areas on diagrammatic illustrations indicate broken surfaces. Scale bar equals 1 mm, scale same throughout.
Evolutionary relationships of anglerfishes (Lophiiformes) reconstructed using ultraconserved elements
<p>The macroevolutionary consequences of evolving in the deep-sea remain poorly understood and are compounded by the fact that convergent adaptations for living in this environment makes elucidating phylogenetic relationships difficult. Lophiiform anglerfishes exhibit extreme habitat and predatory specializations, including the use of a fin-spine system as a luring device and unique reproductive strategies where parasitic males attach and fuse to females. Despite their notoriety for these odd characteristics, evolutionary relationships among these fishes remain unclear. We sought to clarify the evolutionary history of Lophiiformes using data from 1,000 ultraconserved elements and phylogenomic inference methods with particular interest paid to the Ceratioidei (deep-sea anglerfishes) and Antennarioidei (frogfishes and handfishes). At the suborder level, we recovered similar topologies in separate phylogenomic analyses: The Lophioidei (monkfishes) are the sister group to the rest of the Lophiiformes, Ogcocephaloidei (batfishes) and Antennarioidei (frogfishes) form a sister group, and Chaunacioidei (coffinfishes) and Ceratioidei (deep-sea anglerfishes) form a clade. The relationships we recover within the ceratioids disagree with most previous phylogenetic investigations, which used legacy phylogenetic markers or morphology. We recovered non-monophyletic relationships in the Antennarioidei and proposed three new families based on molecular and morphological evidence: Histiophrynidae, Rhycheridae, and Tathicarpidae. Antennariidae was re-evaluated to include what was known as Antennariinae, but not Histiophryninae. Non-bifurcating signal in splits network analysis indicated reticulations among and within suborders, supporting the complicated history of the Lophiiformes previously found with morphological data. Although we resolve relationships within Antennarioidei, Ceratioidei relationships remain somewhat unclear without better taxonomic sampling.</p>
RegEl corpus: Identifying DNA regulatory elements in the scientific literature
<pre>@article{garda2022regel, title={RegEl corpus: identifying DNA regulatory elements in the scientific literature}, author={Garda, Samuele and Lenihan-Geels, Freyda and Proft, Sebastian and Hochmuth, Stefanie and Sch{\"u}lke, Markus and Seelow, Dominik and Leser, Ulf}, journal={Database}, volume={2022}, year={2022}, publisher={Oxford Academic} } </pre>
RegEl Database: text-mined regulatory elements from the literature and their associations to genes and disease
<pre>@article{garda2022regel, title={RegEl corpus: identifying DNA regulatory elements in the scientific literature}, author={Garda, Samuele and Lenihan-Geels, Freyda and Proft, Sebastian and Hochmuth, Stefanie and Sch{\"u}lke, Markus and Seelow, Dominik and Leser, Ulf}, journal={Database}, volume={2022}, year={2022}, publisher={Oxford Academic} } </pre> <p># RegEl PubMed Database</p> <p>This database contains the annotations generated by running [HunFlair](https://github.com/flairNLP/flair/blob/master/resources/docs/HUNFLAIR.md) models trained on the [RegEl corpus](https://zenodo.org/record/5776679) over >20M PubMed abstracts.</p> <p>By pairing these annotations with the one provided by PubTator this generates a large text mining database of regulatory elements associated with genes (normalized to NCBI Gene ids) and disease (normalized to either MeSH or OMIM).</p> <p>The tables composing the database are:</p> <p>* abstracts.db:<br> - pmid = PubMed ID of the given abstracts<br> - sid = sentence ID of the given abstracts (from 0 to # of sentences)<br> - text = text of the given sentence</p> <p>* gene.db and disease.db:<br> - pmid = PubMed ID of the given abstracts<br> - sid = sentence ID of the given abstracts (from 0 to # of sentences)<br> - etype = entity type (enhancer, promoter, TFBS)<br> - ann_text = mention of the regulatory element as found in the abstract<br> - start = position (# character) in which the mention begins<br> - end = position (# characters) in which the mention ends<br> - score = model's confidence<br> - cui = gene or disease identifier<br> - cui_symbol = official symbol of cui (if available)</p>
Modeling Sequences of Earthquakes and Aseismic Slip (SEAS) in Elasto-Plastic Fault Zones With a Hybrid Finite Element Spectral Boundary Integral Scheme
<p>This repository contains the results of 2D simulations of the earthquake cycles accounting for off-fault plasticity.</p> <p>Folder Case1 contains the slip rate and time history for all simulations with cohesion c = 47 MPa</p> <p>Folder Case2 contains the slip rate and time history for all simulations with cohesion c = 25 MPa</p> <p>the mat files contain equivalent plastic strain of each element stored at the start and end of each event with element connectivity and node coordinates.</p>
the data of "High-pressure behavior of synthetic quenchable hydroxylbastnasite-(Sm): Implications for rare earth elements, carbon, and water transmission into the deep earth"
<p>This is the package of the Raman data of synthesized Sm(CO<sub>3</sub>)OH at high-pressure and ambient temperature and synchrotron radiation X-Ray data of synthesized Sm(CO<sub>3</sub>)OH at high-pressure and ambient temperature, they are in *.asc and *.chi respectively.</p>
Elemental and S isotopic composition data for "Sulfur isotopic fractionation of the youngest Chang'e-5 basalts: Constraints on the magma degassing and geochemical features of the mantle source"
<p>Data for "Sulfur isotopic fractionation of the youngest Chang'e-5 basalts: Constraints on the magma degassing and geochemical features of the mantle source".</p>
Data from: Using ultraconserved elements to reconstruct the termite tree of life
<p><span>The phylogenetic history of termites has been investigated using mitochondrial genomes and transcriptomes. However, both sets of markers have specific limitations. Mitochondrial genomes represent a single genetic marker likely to yield phylogenetic trees presenting incongruences with species trees, and transcriptomes can only be obtained from well-preserved samples. In contrast, ultraconserved elements (UCEs) include a great many independent markers that can be retrieved from poorly preserved samples. Here, we designed termite-specific baits targeting </span><span>50,616 UCE loci. We tested our UCE bait set on 42 samples of termites and three samples of <em>Cryptocercus</em>, for which we generated low-coverage highly-fragmented genome assemblies and successfully extracted <em>in silico</em> between 3,426 to 42,860 non-duplicated UCEs per sample. Our maximum likelihood phylogenetic tree, reconstructed using the 5,934 UCE loci retrieved from upward of 75% of samples, was congruent with transcriptome-based phylogenies, demonstrating that our UCE bait set is reliable and phylogenetically informative. Combined with non-destructive DNA extraction protocols, our UCE bait set provides the tool needed to carry out a global taxonomic revision of termites based on poorly preserved specimens such as old museum samples. The Termite UCE database is maintained at: </span><span><a href="https://github.com/oist/TER-UCE-DB/"><span>https://github.com/oist/TER-UCE-DB/</span></a></span><span>.</span></p>
Data From - TE Density: a tool to investigate the biology of transposable elements
<p><strong>Background</strong>: Transposable elements (TEs) are powerful creators of genotypic and phenotypic diversity due to theirinherent mutagenic capabilities and in this way they serve as a deep reservoir of sequences for genomic variation. As agents of genetic disruption, a TE's potential to impact phenotype is partially a factor of its location in the genome. Previous research has shown TEs' ability to impact the expression of neighboring genes, however our understanding of this trend is hampered by the exceptional amount of diversity in the TE world, and a lack of publicly availablecomputational methods that quantify the presence of TEs relative to genes.</p> <p><strong>Results: </strong>Here, we have developed a tool to more easily quantify TE presence relative to genes through the useof only a gene and TE annotation, yielding a new metric we call TE density. Briefly defined as the proportion of TE-occupied base-pairs relative to a window-size of the genome. This new pipeline reports TE density for each gene in the genome, for each type descriptor of TE (order and superfamily), and for multiple positions and distances relative to the gene (upstream, intragenic, and downstream) over sliding, user-defined windows. In this way, we overcome previous limitations to the study of TE-gene relationships by focusing on all TE types present in the genome, utilizing flexible genomic distances for measurement, and reporting a TE presence metric for every gene in the genome.</p> <p><strong>Conclusions: </strong>Together, this new tool opens up new avenues for studying TE-gene relationships, genome architecture,comparative genomics, along with the tremendous diversity present in the TE world.</p> <p><strong>Data Availability: </strong>TE Density is open-source and freely available at: https://github.com/sjteresi/TE_Density.</p>
Dataset presented in the recently submitted AGU manuscript "A multi-resolution finite-element approach for global electromagnetic induction modeling with application to southeast China coastal geomagnetic observatory studies"
<p>Dataset presented in the recently submitted AGU paper "A multi-resolution finite-element approach for global electromagnetic induction modeling with application to southeast China coastal geomagnetic observatory studies"</p>
NOMAD element annotation bowtie2 indices
<p>Default list of bowtie2 annotations used in NOMAD manuscript</p>
Element annotations indices for NOMAD
<p>Default set of bowtie2 annotations, used in the element annotation step of the NOMAD pipeline</p>
Data from: The effect of the intensity of the element that distinguishes flavor on the memory and perception of Peruvian millennials and centennials
<p>Globalization has facilitated a lot the access to all kinds of products and brands from different parts of the world, which has increased consumer choice and also competition among packaged products. For this reason, the package design of a brand to attract<br> consumers must be able to stand out among so much supply, especially if it is a new product or a new flavor. The packaging of the product has a strong direct influence on consumers and therefore it becomes necessary to explore dimensions of packaging design that allow a high degree of differentiation or at least enough to differentiate from the competition and the same product line. In this line, there are very efficient strategies and approaches used in the literature to perform this exploration in packaging, such as evaluations of perception measured with attributes and the use of eye-tracking technology that records direct information about visual attention on the most distinctive elements. Thus, this study aims to determine the impact of the presentation of a new flavor on the packaging by varying the intensity of the stimulus that represents it according to the Weber-Fechner law, using the three main elements of the packaging: text, color and image. The experiment exposed three groups of participants (n=30) to 3 stimuli, which were based on the addition of an element as the intensity of the flavor description of three products from three different food categories was intended to increase. This study used the eye-tracking platform via RealEye webcam to measure attention, and a self-administered questionnaire was used to examine perception and recall.</p>
Stowaways Supplement Table S2. Ma'agan Mikhael B Rattus rattus Skeletal Element Identification (NISP) Datasheet
<p>Number of identified specimens of black rat (Rattus rattus) skeletal elements recovered from the early Islamic period shipwreck Ma'agan Mikhael B (Israel). Dataset includes catalogue number, skeletal element, side, part, epiphyseal fusion status, and tooth wear stage (TWS; following Armitage in Morales & Rodríguez [1997]).</p> <p>***Version 2 added two new specimens from the September 2022 excavation season.</p>
Sacrobosco Visual Element Dataset (S-VED)
<p>The Sacrobosco Visual Elements Dataset (S-VED) is derived from 359 Sphaera editions, centered on the Tractatus de sphaera by Johannes de Sacrobosco (—1256) and printed between 1472 and 1650. The Sphaera editions were primarily used to teach geocentric astronomy to university students across Europe. Their visual elements, therefore, played an essential role in visualizing the ideas, messages, and concepts that the texts transmitted. As a precondition for studying the relation between text and visual elements, a time-consuming image labelling process was conducted as part of “The Sphere” project (<a href="https://sphaera.mpiwg-berlin.mpg.de/">https://sphaera.mpiwg-berlin.mpg.de</a>) in order to extract and label the visual elements from the 76,000 pages of the corpus. This process resulted in the creation of the Extended Sacrobosco Visual Elements Dataset (S-VED𝑋) of which S-VED is a subset of. Due to copyright reasons only S-VED is made publicly available. S-VED consists of 4000 pages of which 2040 contain a total of 2927 visual elements. The visual elements are defined by bounding boxes and labels within a CSV file. For more information on the Sphaera corpus, feel free to check the project’s database at <a href="http://db.sphaera.mpiwg-berlin.mpg.de/">http://db.sphaera.mpiwg-berlin.mpg.de/</a>.</p>
Fig. 3 in Understanding UCEs: A Comprehensive Primer on Using Ultraconserved Elements for Arthropod Phylogenomics
Fig. 3. Breakdown of the phylogenetic programs used by arthropod UCE-based publications (as of July 2019).
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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.