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1,199 results for “Alignement”
Mitogenome alignment of 159 unique haplotypes representing 455 individual killer whales
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Suboptimal is good enough: Aligning thermal sensitivity to habitat temperature across season
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Progressive Cactus alignment of 298 drosophilid species
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Phylogenetic and recombination analysis of adenovirus isolates reveals discordance between serotype and phylogeny: Multiple sequence alignments
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Alignments used for the phylogenetic analysis of sweet cucumber (Solanum muricatum, Solanaceae)
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Data: Large old trees increase growth under shifting climatic constraints: Aligning tree longevity and individual growth dynamics in primary mountain spruce forests
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Dataset from: In-situ bidirectional human-robot value alignment
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Data for: Rapid alignment updating with Extensiphy
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Alignment between CARE Principles and Data Repository Activities
This dataset is designed to accompany the paper submitted to Data Science Journal: O'Brien et al, "Earth Science Data Repositories: Implementing the CARE Principles". This dataset holds a list of activites typically carried out by repositories that are related to the CARE Principles for Indigenous Data Governance. Activities are divided into four categories to reflect broad skill sets usually found in repository personnel: Situational Awareness, Outreach, Repository Protocols, Technology. Each activity was mapped to one or more of the CARE sub-principles, with booleans in individual columns.
Community gardening in disadvantaged neighborhoods in Phoenix, Arizona, March 2010: Aligning programs with perceptions
This study examined a struggling community gardening program in a low-income minority community in Phoenix, Arizona. The gardening program exists within a larger local food initiative organized by a nonprofit community development organization. The nonprofit's goals for the community gardening program are to provide residents with opportunities for education, extra income and socializing. In partnership with the nonprofit and local residents, we undertook a study to determine the potential for increasing the recruitment and retention of local gardeners in order to sustain a successful community gardening program. We used interviews and participant observation to create an exploratory survey that measured residents' perceptions of benefits and burdens associated with gardening. Results revealed that while respondents had a level of gardening interest and experience in the community, they also lacked awareness about the gardening program. Perceptions of the benefits and burdens of gardening varied among current gardeners, ex-gardeners, and people who had never gardened. The benefits of gardening suggested by many residents differed from the local food initiative goals. If community gardens and local food initiatives are to succeed, organizers should align their programs with the desires of neighborhood residents and educate them about a wide range of potential benefits of gardening to both individuals and neighborhoods.
Video for: The role of hydrodynamic forces in synchronisation and alignment of mammalian motile cilia
<p>Here you can find all the videos of the PhD thesis: </p> <p>The role of hydrodynamic forces in synchronisation and alignment of mammalian motile cilia.</p> <p>by Nicola Pellicciotta</p> <p>Video1: This example shows a movie of a single cell, being subjected to an external oscillatory flow. Images were acquired at 500\,fps using a 60X objective, then analysed using background subtraction and spatial median filter of 3x3 pixels. Chapter 3</p> <p>Video 2: we show the entrainment of a group of cells with very strong oscillatory external flow $v_\mathrm{EX}= 2$\,mm/s at $f_\mathrm{EX}=12$\,Hz. This s flow induced entrainment and also alignment of beating direction of some cells that were beating misaligned to the external flow. The original direction of beating was recovered after the flow stopped. Chapter 3</p> <p>Video3 and Video4: we depolymerised cell actin by adding 2uM Cytochalasin-D in the cell culture medium for 48hr. After imaging, cells (control and dug treated) were stained in 4\% PFA for 10 minutes, permeabilised with Triton x-100 0.1\% in PBS, and incubated for 1 hour with Nucblue R37605 (1 drop for mL of PBS) and with phalloidin for actin (Sir-Actin, 0.2 uM) following proprietary protocols. Z-stack were taken with confocal microscope (slices of distance of 0.15um each) and can be found at the following links: DMSO treated cells (control) Video 3, and Cytochalasin-D treated, Video 4. Chapter 3</p> <p>Video5: The maximal beating amplitude for a cilium within each cell was measured by inspecting the recordings from top view and marking two extreme points at the power and recovery stroke. Chapter 3</p> <p>Video6: Experimental procedure and the image analysis methods for Chapter 4. Continuous fluid flow is applied for three days on cells cultured in Transwell-chips. The chips are then removed from the flow and cilia motility is imaged with the microscope. From high speed Bright Field movies we identify ciliary beating frequency and cell position, while from tracer particles we measure ciliary beating direction. </p> <p>Video7: Video of Propelled particles in a culture at 29 DIV and treated with shear stress τ ≈0.8 dyne/cm2. Chapter 4</p> <p> </p>
Signing up to Open Science: Open Peer Review and Aligning Core Values
<p><strong>Episode Summary:</strong></p> <p>In this episode we are talking to Dr Guillaume Filion from the Center for Genomic Regulation (CRG), Barcelona about his decision to put his name on all his peer reviews, why he feels this makes him more accountable, and what choices researchers need to make about whether their values align with those who they will work with. </p> <p><strong>Resources and Links:</strong></p> <ul> <li><a href="https://www.orion-openscience.eu/node/201">Factsheets</a></li> <li><a href="https://www.crg.eu/en/programmes-groups/filion-lab">Dr Guillaume Filion</a> <ul> <li><a href="https://twitter.com/thegrandlocus">Twitter Page</a></li> </ul> </li> <li><a href="http://blog.thegrandlocus.com/2018/09/on-open-peer-review">Original Blog Post by Dr Guillaume Filion</a></li> <li><a href="https://www.fosteropenscience.eu/learning/open-peer-review/#/id/5a17e150c2af651d1e3b1bce">FOSTER+ Information on Open Peer Review </a></li> </ul> <p><strong>Episode Quotes:</strong></p> <p>“I had the feeling I would do a better job as a reviewer, if I put my name on it, if I put my name on the line then it would force me not to do a bad job”</p>
Aggregated frequencies of transcription initiations observed in FANTOM5 CAGE data on GRCm38, including alignments with low mapping qualities
<p><strong>Overview</strong></p> <p>Aligned reads of the FANTOM5 CAGE data have been used after filtering (ones with mapping quality less than 20 or percent identity less than 85% were discarded) for general purpose, resulting in the data set consisting of only the reads aligned with confidence. The filtering process made possible to interpret the data without ambiguity, however it also limited interpretation of paralogous or duplicated regions within the genome. Here all of the 5'-ends of the CAGE read alignments, including the ones with low mapping quality, were counted. The counts in the individual profiles were aggregated and summed up. </p> <p>This data set is produced for mouse, in the same way to the one for human data set http://doi.org/10.5281/zenodo.1410835</p> <p> </p> <p><strong>Data files</strong></p> <p>The resulting data files are formatted as bigWig (https://genome.ucsc.edu/FAQ/FAQformat.html#format6.1). '*.fwd.bw' and '*.rev.bw' represent forward and reverse strand on the genome, respectively. </p> <p> </p> <p><strong>Methods</strong></p> <p>The BAM files under https://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v7/basic/ were subjected to 5'-end counting by bedtools v2.27.1 (https://github.com/arq5x/bedtools2), followed by conversion into bigWig with jksrc v366 (http://hgdownload.cse.ucsc.edu/admin/).</p>
Supplementary tables S5, S7, S9, S10, original protein models fasta files used for alignments, aligned and manually curated protein modes files used for phylogenies (PHYLIP format), and phylogenetic trees of plant cell wall decomposition gene families from 44 basidiomycete genomes (.tre files)
<p><span><span><span><span><span><span><span><span><span><span><span>Litter-decomposing Agaricales play key role in terrestrial carbon cycling, but little is known about their decomposition mechanisms. We assembled datasets of 42 gene families involved in plant-cell-wall decomposition from seven newly sequenced litter decomposers and 35 other Agaricomycotina members, mostly white-rot and brown-rot species. Using sequence similarity and phylogenetics, we split the families into phylogroups and compared their gene composition across nutritional strategies. Subsequently, we used Raman spectroscopy to examine the ability of litter decomposers, white-rot fungi, and brown-rot fungi to decompose crystalline cellulose. Both litter decomposers and white-rot fungi share the enzymatic cellulose decomposition, whereas brown-rot fungi possess a distinct mechanism that disrupts cellulose crystallinity. However, litter decomposers and white-rot fungi differ with respect to hemicellulose and lignin degradation phylogroups, suggesting adaptation of the former group to the litter environment. Litter decomposers show high phylogroup diversity, which is indicative of high functional versatility within the group, whereas a set of white-rot species shows adaptation to bulk-wood decomposition. In both groups, we detected species that have unique characteristics associated with hitherto unknown adaptations to diverse wood and litter substrates. Our results suggest that the terms white-rot fungi and litter decomposers mask a much larger functional diversity.</span></span></span></span></span></span></span></span></span></span></span></p>
Aligned DNA sequence matrix for phylogenetic analyses in the article "Fifty years after: a taxonomic revision of the amphibian species from the Ecuadorian biodiversity hotspot Abra de Zamora, with description of two new Pristimantis species"
<p>The aligned matrices are in fasta format. Genes are arranged as follows:</p> <p>Subgenus Huicundomantis (Huicundomantis.fas):</p> <p>12S = 1–905</p> <p>16S = 906–1820</p> <p>RAG-1 = 1821–2463</p> <p> </p> <p>Genus Lynchius (Lynchius.fas):</p> <p>12S = 1–1028</p> <p>16S = 1029–2313</p> <p>RAG-1 = 2314–2925</p> <p> </p> <p>Pristimantis orestes group (Pristimantis_orestes.fas):</p> <p>12S = 1–964</p> <p>16S = 965–2041</p> <p>RAG-1 = 2042–2683</p>
Nucleotide alignments of eight meiosis genes under extreme selection following whole genome duplication in Arabidopsis lyrata/A.arenosa.
<p>In this study we performed a genotype-phenotype association analysis of meiotic stability in 10 autotetraploid <em>Arabidopsis lyrata</em> and <em>A</em>. <em>lyrata/A</em>. <em>arenosa</em> hybrid populations collected from the Wachau region and East Austrian Forealps. The aim was to determine the effect of eight meiosis genes under extreme selection upon adaptation to whole genome duplication. Individual plants were genotyped by high-throughput sequencing of the eight meiosis genes (<em>ASY1</em>, <em>ASY3</em>, <em>PDS5b</em>, <em>PRD3</em>, <em>REC8</em>, <em>SMC3</em>, <em>ZYP1a/b</em>) implicated in synaptonemal complex formation and phenotyped by assessing meiotic metaphase I chromosome configurations. Our results reveal that meiotic stability varied greatly (20–100%) between individual tetraploid plants and associated with segregation of a novel <em>ASYNAPSIS3</em> (<em>ASY3</em>) allele derived from <em>A</em>. <em>lyrata</em>. The <em>ASY3</em> allele that associates with meiotic stability possesses a putative in-frame tandem duplication (TD) of a serine-rich region upstream of the coiled-coil domain that appears to have arisen at sites of DNA microhomology. The frequency of multivalents observed in plants homozygous for the <em>ASY3 TD</em> haplotype was significantly lower than in plants heterozygous for <em>ASY3 TD/ND</em> (non-duplicated) haplotypes. The chiasma distribution was significantly altered in the stable plants compared to the unstable plants with a shift from proximal and interstitial to predominantly distal locations. The number of HEI10 foci at pachytene that mark class I crossovers was significantly reduced in a plant homozygous for <em>ASY3 TD</em> compared to a plant heterozygous for <em>ASY3 ND/TD</em>. Fifty-eight alleles of the 8 meiosis genes were identified from the 10 populations analysed, demonstrating dynamic population variability at these loci. Widespread chimerism between alleles originating from <em>A</em>. <em>lyrata/A</em>. <em>arenosa</em> and diploid/tetraploids indicates that this group of rapidly evolving genes may provide precise adaptive control over meiotic recombination in the tetraploids, the very process that gave rise to them.</p>
Multiple alignment of DNA-B sequences from EACMV, EACMKV, EACMMV, EACMZV, SACMV (5 "species")
<p>All sequences available in GenBank as of 2019-06-03 were downloaded via the Taxonomy Browser interface. Sequence names were normalized/simplified and orientations of these circular sequences were standardized to begin at the replication origin nick site. Sequences were aligned with MUSCLE and alignments were adjusted with SeAl (A. Rambaut) and AliView (A. Larsson).</p> <p>These results are described in a paper by Crespo-Bellido et al. (2021) https://doi.org/10.1128/JVI.00541-21</p>
Multiple alignment of ICMV and SLCMV DNA-B sequences
<p>All sequences available in GenBank as of 2019-06-03 were downloaded via the Taxonomy Browser interface. Sequence names were normalized/simplified and orientations of these circular sequences were standardized to begin at the replication origin nick site. Sequences were aligned with MUSCLE and alignments were adjusted with SeAl and AliView.</p> <p>Note added 2020-09-07: AJ575821 is listed in the file as ICMV based on its assignment in the NCBI Taxonomy database (taxa 341701 and 31600) but it is better classified as SLCMV.</p> <p>These results are described in a paper by Crespo-Bellido et al. (2021) https://doi.org/10.1128/JVI.00541-21</p>
Data from: The Cumulative Indel Model: fast and accurate statistical evolutionary alignment
Sequence alignment is essential for phylogenetic and molecular evolution inference, as well as in many other areas of bioinformatics and evolutionary biology. Inaccurate alignments can lead to severe biases in most downstream statistical analyses. Statistical alignment based on probabilistic models of sequence evolution addresses these issues by replacing heuristic score functions with evolutionary model-based probabilities. However, score-based aligners and fixed-alignment phylogenetic approaches are still more prevalent than methods based on evolutionary indel models, mostly due to computational convenience. Here, I present new techniques for improving the accuracy and speed of statistical evolutionary alignment. The "cumulative indel model" approximates realistic evolutionary indel dynamics using differential equations. "Adaptive banding" reduces the computational demand of most alignment algorithms without requiring prior knowledge of divergence levels or pseudo-optimal alignments. Using simulations, I show that these methods lead to fast and accurate pairwise alignment inference. Also, I show that it is possible, with these methods, to align and infer evolutionary parameters from a single long synteny block (approximately 530kbp) between the human and chimp genomes. The cumulative indel model and adaptive banding can therefore improve the performance of alignment and phylogenetic methods.
How to Align and Merge Chunks in Metashape
<p>Instructional video explaining how to align and merge two half-models to form a single, complete 3D model. https://youtu.be/RFWx5zAghko</p>
ScienceDex guides
Understand access before you commit
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.