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1,199 results for “Alignement”
Dataset associated with manuscript "Magnetosphere-ionosphere coupling via prescribed field-aligned current simulated by the TIEGCM"
<p>The dataset is associated with the manuscript "Magnetosphere-ionosphere coupling via prescribed field-aligned current simulated by the TIEGCM". It is based on simulations using the NCAR Thermosphere-Ionosphere Electrodynamics General Circulation Model (TIEGCM) and comparing the thermosphere-ionosphere response during 28-30 May, 2010 geomagnetic storm due to different realizations of magnetosphere-ionosphere (MI) coupling in the model. Results are presented using for MI coupling the Assimilative Mapping of Ionospheric Electrodynamics (AMIE), the empirical Weimer ion convection, and fitted field-aligned current based on observations from the Active Magnetosphere and Planetary Electrodynamics Response Experiment (AMPERE). The output includes among others high latitude quantities of auroral ionization rates, field-aligned current, electric potential, hemispheric integrated Joule heating, and middle and low-latitude zonal mean neutral wind, density, composition, ionospheric Nmf2, TEC and equatorial vertical drift.</p>
Evolutionary "crowdsourcing": alignment of fitness landscapes allows for cross-species adaptation of a horizontally transferred gene
<p>This repository accompanies the publication of <i><strong>Evolutionary "crowdsourcing": alignment of fitness landscapes allows for cross-species adaptation of a horizontally transferred gene</strong></i> by Kosterlitz et. al. This research project explores the cross-species adaptation of a horizontally transferred gene through evolutionary "crowdsourcing." The repository provides all relevant data, code, and figures associated with the publication, enabling users to replicate the results and explore the findings in-depth.</p>
Datasets for paper "Explorative characterization and taxonomy-aligned comparison of alterations in lipids and other biomolecules in Antarctic bacteria grown at different temperatures"
<p>Temperature significantly impacts bacterial physiology, metabolism, and cell chemistry. In this study, we analyzed lipids and total cellular biochemical profile of seventy-four fast-growing Antarctic bacteria grown at different temperatures. Fatty acid diversity and temperature-induced alterations aligned with bacterial classification - Gram-groups, phylum, genus, and species. Total lipid content, varied from 4% to 19% of cell dry weight, was genus- and species-specific. Most bacteria increased lipid content at lower temperatures. The effect of temperature on the profile was complex and more specie-specific, while some common for all bacteria responses were recorded. Gram-negative bacteria adjusted unsaturation and acyl chain length. Gram-positive bacteria adjusted methyl branching (anteiso-/iso-), chain length, and unsaturation. Fourier transform infrared spectroscopy analysis revealed Gram-, genus-, and specie-specific changes in the total cellular biochemical profile triggered by temperature fluctuations. The most significant temperature related alterations detected on all taxonomy levels were recorded for mixed region 1500-900 cm-1, specifically the band at 1083 cm−1 related to phosphodiester groups mainly from phospholipids (for Gram-negative bacteria) and teichoic /lipoteichoic acids (for Gram-positive bacteria). Some changes in protein region were detected for few genera, while lipid region remained relatively stable despite the temperature fluctuations.</p>
Two new species of Aphyllon from northeastern Mexico: Sequence alignments and phylogenetic trees
<p>Plants originally identified as <em>Aphyllon ludovicianum</em> that occur near Monterrey, Nuevo Leon, and Cuatro Ciénegas Bolson, Coahuila, Mexico, were found to not align with the protologue of that species, the close relative <em>A. multiflorum,</em> or any other species of <em>Aphyllon</em>. Following a detailed study of floral morphology, geographic range, host species, and phylogenetic position using dry herbarium specimens, field study and georeferenced color photographs, we propose the new binomials <em>Aphyllon spectabile </em>for the plants from Nuevo Leon and <em>Aphyllon gypsophilum</em> for the plants from Coahuila, Mexico. This increases the taxonomic diversity of <em>Aphyllon</em> to 27 species plus ten additional subspecies. <em>Gymnosperma glutinosum</em> and two species of <em>Xanthisma</em> were reported for the first time as a host species for the genus <em>Aphyllon</em>. We also provide an updated key to <em>Aphyllon</em> in Mexico. </p>
Data and Codes for "Graphene-Based Quantum Hall Interferometer with Self-Aligned Side Gates"
<p>Data and Codes for "Graphene-Based Quantum Hall Interferometer with Self-Aligned Side Gates"</p>
Alignment of geophysical fields: a differential geometry perspective
<p>This is the document for the code mentioned in "Alignment of geophysical fields: a differential geometry perspective".</p> <p> </p> <p>(To save time, steps 1,2,3,4 can be skipped since the data is already saved in the corresponding filefolder)</p> <p> </p> <p><strong>1,GENERATE ENSEMBLE MEMBERS</strong> : run getens_doublevortex_256.py</p> <p><strong>2,GENERATE THE TRUTH </strong> : run gettruth_doublevortex_256.py</p> <p> </p> <p><strong>3,BEFORE MORPHING</strong> : run exp/get_dataens.py and exp/get_dataobs.py</p> <p><strong>4,MORPH THE ENSEMBLE </strong> : run exp/get_morphed.py</p> <p> </p> <p><strong>5,BEFORE DA </strong> : run exp/get_ens_LR.py and exp/get_truth_LR.py</p> <p><strong>6,DA </strong> : run exp/EnKF_direct.py and exp/EnKF_morphed.py</p> <p><strong>7,PLOT DA RESULTS </strong> : run exp/plt_comparemean.py and exp/plt_compare_member.py</p> <p> </p> <p><strong>8,MORPH WITH PLAIN T#(10000 steps) </strong> : run exp/get_morphed_noDiffGeo.py</p> <p><strong>9,MORPH WITH PLAIN T#(6000 steps) </strong> : run exp/get_morphed_noDiffGeo2.py</p> <p> </p> <p><strong>10,PLOT MORPHED ENSEMBLE MEMBERS </strong> : run exp/ensemble_morphed/figs/plt_main.py</p> <p><strong>11,PLOT MORPHED ENSEMBLE MEMBER WITH PLAIN T# </strong>: run exp/ensemble_morphed_noDiffGEo/figs/plt_main.py and exp/ensemble_morphed_noDiffGEo2/figs/plt_main.py</p>
Pereira et al snakeworms DNA alignment Supplementary_File_1.nex
<p>Pereira et al snakeworms DNA alignment Supplementary File 1 </p>
Observation of Electrical Alignment Signatures in An Isolated Thunderstorm by Dual-Polarized Phased Array Weather Radar and the Relationship with Intracloud Lightning Flash Rate
<div> <p>The data of the Dual-polarized Phased Array Weather Radar (DP-PAWR), from 2019-08-20 16:10:15 to16:41:04 on August 20, 2019. </p> <p> </p> </div>
Data from: Alignment of COI haplotypes from museum samples of Diptera of forensic importance
<p>Necrophagous Diptera are the most important group of insects used for the purposes of forensic entomology. While the most utilized fly family in this context is the family Calliphoridae, there is a number of other families, which can be of a great importance during real case investigations. This article analyses the necrophagous flies of all families recorded from 160 real cases in Switzerland in between 1993-2007. A total of 56 species belonging to 16 families was identified with Calliphoridae being the most dominant family (90,63 % of all cases), followed by Muscidae (26,25 %), Sarcophagidae (19,38 %), Phoridae (14,38 %) and Fanniidae (12,50 %). For specimens that were difficult to identify morphologically, a new PCR primer has been specifically designed for the amplification of a short, informative COI barcode in degraded museum samples of forensically important Diptera taxa. The richest family in terms of species was the family Muscidae with 16 species. <em>Fannia fuscula</em> and <em>Fannia monilis</em> were recorded from human cadavers for the first time. The study highlights the importance of different fly families in forensic investigation, enhancing our comprehension of their prevalence and dispersion in real cases in Central Europe. The results pave the way for additional exploration, especially regarding the involvement of less frequently observed species in forensic entomology.</p>
Nexus file of alignment for phylogeny of Philopteroides s. lat.
Open the record for dataset details and reuse information.
Supplementary material to "Aligning business processes with regulatory requirements"
<p>Bibliographic collection from Web of Science (March 8, 2024), ScienceDirect (March 8, 2024).</p> <p>The below query is a compositie of 4 queries and yields 42 results </p> <p>https://www.webofscience.com/wos/woscc/summary/88d17377-0bb9-4db5-97d1-bf866c373e6f-ce98ba0a/relevance/1</p> <p>The savedrecs.bib file was created after selecting "full records" on export.</p> <p>Also included is the resulting excelfile containing identified literature slr_logbook.xlsx</p>
Splam: a deep-learning-based splice site predictor that improves spliced alignments
<p><span>The process of splicing messenger RNA to remove introns plays a central role in creating genes and gene variants. Here we describe Splam, a novel method for predicting splice junctions in DNA based on deep residual convolutional neural networks. Unlike some previous models, Splam looks at a relatively limited window of 400 base pairs flanking each splice site, motivated by the observation that the biological process of splicing relies primarily on signals within this window. Additionally, Splam introduces the idea of training the network on donor and acceptor pairs together, based on the principle that the splicing machinery recognizes both ends of each intron at once. We compare Splam’s accuracy to recent state-of-the-art splice site prediction methods, particularly SpliceAI, another method that uses deep neural networks. Our results show that Splam is consistently more accurate than SpliceAI, with an overall accuracy of 96% at predicting human splice junctions. Splam generalizes even to non-human species, including distant ones like the flowering plant <em>Arabidopsis thaliana</em>. Finally, we demonstrate the use of Splam on a novel application: processing the spliced alignments of RNA-seq data to identify and eliminate errors. We show that when used in this manner, Splam yields substantial improvements in the accuracy of downstream transcriptome analysis of both poly(A) and ribo-depleted RNA-seq libraries. Overall, Splam offers a faster and more accurate approach to detecting splice junctions, while also providing a reliable and efficient solution for cleaning up erroneous spliced alignments. </span></p>
Aligned DNA sequence matrix for phylogenetic analyses in the article "Systematics of the Dendropsophus leucophyllatus species group (Anura, Hylidae) from the Chocó region of Ecuador, with description of a new species"
<p>Aligned DNA sequence matrix for phylogenetic analyses of the article "Systematics of the <em>Dendropsophus leucophyllatus</em> species group (Anura, Hylidae) from the Chocó region of Ecuador, with description of a new species"</p> <p>The matrix is in NEXUS format and has 7691 bp and 203 terminals.</p> <p>Partitions are as follows:</p> <div> <div>charset 12S = 1-996;</div> <div> </div> <div>charset CO1codonPos1 = 997-1639\3;</div> <div>charset CO1codonPos2 = 998-1640\3;</div> <div>charset CO1codonPos3 = 999-1638\3;</div> <div> </div> <div>charset ND1nonCoding = 1641- 1713 2675- 2796 ;</div> <div>charset ND1codonPos1 = 1714-2674\3;</div> <div>charset ND1codonPos2 = 1715-2672\3;</div> <div>charset ND1codonPos3 = 1716-2673\3;</div> <div> </div> <div>charset CytbcodonPos1 = 2798-3686\3;</div> <div>charset CytbcodonPos2 = 2799-3687\3;</div> <div>charset CytbcodonPos3 = 2797-3685\3;</div> <div> </div> <div>charset RhodcodonPos1 = 3689-4001\3;</div> <div>charset RhodcodonPos2 = 3690-4002\3;</div> <div>charset RhodcodonPos3 = 3688-4003\3;</div> <div> </div> <div>charset TYRcodonPos1 = 4005-4539\3;</div> <div>charset TYRcodonPos2 = 4006-4537\3;</div> <div>charset TYRcodonPos3 = 4004-4538\3;</div> <div> </div> <div>charset RAG1codonPos1 = 4542-4965\3;</div> <div>charset RAG1codonPos2 = 4540-4966\3;</div> <div>charset RAG1codonPos3 = 4541-4964\3;</div> <div> </div> <div>charset POMCcodonPos1 = 4967-5441\3;</div> <div>charset POMCcodonPos2 = 4968-5439\3;</div> <div>charset POMCcodonPos3 = 4969-5440\3;</div> <div> </div> <div>charset SIAH1codonPos1 = 5443-5836\3;</div> <div>charset SIAH1codonPos2 = 5444-5837\3;</div> <div>charset SIAH1codonPos3 = 5442-5838\3;</div> <div> </div> <div>charset 16S_rec = 5839-7695;</div> </div>
Dataset and code related to the publication "Aligning heat pump operation with market signals: A win-win scenario for the electricity market and its actors?"
<h3>General remarks</h3> <p>This dataset and code was developed and used for the publication</p> <blockquote> <p><em>E. Sperber, C. Schimeczek, U. Frey, K. K. Cao, V. Bertsch: Aligning heat pump operation with market signals: A win-win scenario for the electricity market and its actors? In: Energy Reports, Volume 13, June 2025, pp. 491-513, https://doi.org/10.1016/j.egyr.2024.12.028<br></em></p> </blockquote> <h3>Data description</h3> <p>The dataset "<em>heat_pump_results.zip</em>" includes all relevant results underlying the above publication. </p> <p>The data is organized according to the scenarios considered in the analysis. Therefore, each folder is labelled according to the scenario structure, starting with the building efficiency scenario ("BAU" / "EFF"), followed by the PV scenario ("no-PV" / "with-PV"), the HP operation scenario ("ModFlex_V", "ModFlex_F", "HighFlex_V"), the simulation year (2030 / 2040) and the weather year (2017 / 2019 / 2023).</p> <p>Within each result directory per scenario, the data is further structured according to the results at the market level ("AMIRIS") and at the user level ("GAMS" and "INFLEX"). The "INFLEX" directory contains results for the inflexible reference operation, while the "GAMS" directory contains results for the cost-minimized heat pump operation at the level of building types. The data at the user level is further structured by location. Data is given in hourly resolution.</p> <p>The scenario evaluation indicators presented in the publication, as well as other indicators, are summarized in the "MPI" directory.</p> <p>Abbreviations used:</p> <ul> <li>HP: heat pump</li> <li>SH: space heating</li> <li>DHW: domestic hot water</li> <li>AW: air/water</li> <li>BW: brine/water</li> <li>PV: photovoltaic</li> <li>Ti: indoor air temperature</li> <li>Ttes: temperature of domestic hot water storage tank</li> </ul> <h3>Code description</h3> <p>The code to generate the results is given in "<em>heat_pump_workflow.zip</em>". Please follow the instructions in the README.md that you can find in this archive.</p> <h3>Conctact</h3> <p>Please contact Evelyn Sperber at evelyn.sperber@dlr.de if you have any questions.</p>
JuDig aligned corpus
<p>Corpus of Book of abstracts South Slavic Languages in the Digital Environment, 21-23 November 2024 published in English and one of the South Slavic languages. 60 documents are aligned: Introduction, 4 invited talks, 51 abstracts, and 4 workshop descriptions. In total 1129 aligned segments is published. Many forms are available: TXT, XML, TMX (Translation Memory exchange), and annotated corpus for TXM software.</p> <p><a href="https://judig.jerteh.rs/images/knjige/JUDIG-2024-book%20of%20abstracts.pdf">Book of abstracts in English</a> </p> <p><a href="https://judig.jerteh.rs/images/knjige/JUDIG-2024-knjiga%20rezimea.pdf">Book of abstracts in South Slavic Languages</a></p>
Confocal images from: Cell density, alignment, and orientation correlate with C-signal-dependent gene expression during Myxococcus xanthus development
<p>Starving <em>Myxococcus xanthus</em> bacteria use short-range C-signaling to coordinate their movements and construct multicellular mounds, which mature into fruiting bodies as rods differentiate into spherical spores. Differentiation requires efficient C-signaling to drive the expression of developmental genes, but how the arrangement of cells within nascent fruiting bodies (NFBs) affects C-signaling is not fully understood. Here, we used confocal microscopy and cell segmentation to visualize and quantify the arrangement, morphology, and gene expression of cells near the bottom of NFBs at much higher resolution than previously achieved. We discovered that "transitioning cells" (TCs), intermediate in morphology between rods and spores, comprised 10 to 15% of the total population. Spores appeared midway between the center and the edge of NFBs early in their development and near the center as maturation progressed. The developmental pattern as well as C-signal-dependent gene expression in TCs and spores were correlated with cell density, the alignment of neighboring rods, and the tangential orientation of rods early in the development of NFBs. These dynamic radial patterns support a model in which the arrangement of cells within the NFBs affects C-signaling efficiency to regulate precisely the expression of developmental genes and cellular differentiation in space and time. Developmental patterns in other bacterial biofilms may likewise rely on short-range signaling to communicate multiple aspects of cellular arrangement, analogous to juxtacrine and paracrine signaling during animal development.</p>
ddRAD-seq alignment data for Unionid mussels
<p><span><span><span><span><span><span><span><span><span><span><span><span><span>North American watersheds contain the world's highest diversity of freshwater mussels (Unionoida), and up to 40 species can co-occur in a single riffle. They collectively exhibit little evidence for ecological differentiation during the long-lived, benthic phase of their life cycle. In contrast, their brief parasitic larval phase involves the infection of a wide diversity of fish hosts. Gravid female mussels have evolved multiple methods for increasing the probability of infecting a host fish. Some species use a passive broadcast strategy: placing high numbers of larvae in the water column and relying on chance encounters with potential hosts for infection. Most species have a proactive strategy that entails the use of prey-mimetic lures to change the behavior of the hosts, <i>i.e.</i>, eliciting a feeding response through which they become infected. Gravid females collectively produce two main lure types: a mantle tissue lure (on the female's body) and a brood lure, containing infective larvae, that she releases into the external environment. In this study, we used a phylogenomic approach (ddRAD-seq) to place the diversity of infection strategies used by 54 North American lampsiline mussels into an evolutionary context. Ancestral state reconstruction recovered evidence for the early evolution of mantle lures in this clade, with brood lures and broadcast infection strategies both being independently derived twice. The most common infection strategy, occurring in our largest ingroup clade, is a mixed one in which mimetic mantle lures are apparently the predominant infection mechanism, but gravid females also release simple, non-mimetic brood lures at the end of the season. This mixed infection strategy clade shows some evidence of an increase in diversification rate and most members use bass (<i>Micropterus</i> & <i>Ambloplites spp</i>.) as their predominant fish hosts. Broad linkage between infection strategies and predominant fish host genera is also seen in other lampsiline clades: worm-like mantle lures of <i>Toxolasma spp. </i>with sunfish (<i>Lepomis spp.</i>); insect larvae-like brood lures (<i>Ptychobranchus spp.</i>), or mantle lures (<i>Medionidus</i> spp., <i>Obivaria</i>spp.), or mantle lures combined with host capture (<i>Epioblasma</i> spp.) with a spectrum of darter (<i>Etheostoma </i>& <i>Percina</i><i>spp.</i>) and sculpin (<i>Cottus spp.</i>) hosts, and tethered brood lures (<i>Hamiota</i> spp.) with bass (<i>Micropterus</i> & <i>Ambloplites spp</i>.). Our phylogenetic results confirm that discrete lampsiline mussel clades exhibit considerable specialization in the primary fish host clades their larvae parasitize, and in the host infection strategies they employ to do so. They are also consistent with the hypothesis that larval resource partitioning of fish hosts is an important factor in maintaining species diversity in mussel assemblages. We conclude that taking their larval ecology and host-infection mechanisms into account, lampsiline mussels may be legitimately viewed as a cryptic adaptive radiation.</span></span></span></span></span></span></span></span></span></span></span></span></span></p>
FIGURE 9. Maximum likelihood phylogenetic tree with 100 bootstraps using the aligned 16,409 in Two new species of Rhinogobius (Gobiiformes: Oxudercidae) from Palawan, Philippines, with their phylogenetic placement
FIGURE 9. Maximum likelihood phylogenetic tree with 100 bootstraps using the aligned 16,409 bp of mitochondrial genomes in Rhinogobius including the two new species, R. estrellae and R. tandikan, with Tridentiger kuroiwae as an outgroup taxon. Material sequenced in the present study are shown with the catalogue numbers of the vouchers (beginning with NSMT-P, URM- P, or WPU-PPC-P) and sequences from the International Nucleotide Sequence Database are shown with the accession numbers (R. cliffordpopei, R. duospilus, and R. leavelli). The scale bar indicates 0.02 substitutions per site. Pictures shown along with the species names are of the specimens with an asterisk.
FIGURE 22 in Corrections to "Padial et al. (2014) Molecular systematics of terraranas (Anura: Brachycephaloidea) with an assessment of the effects of alignment and optimality criteria"
FIGURE 22. Schematic representation of the new family- and genus-level taxonomy of Brachycephaloidea presented in this study as derived from the results of tree-alignment + parsimony phylogenetic analyses of nucleotide sequences. The placement and affinities of Dischidodactylus and Niceforonia are based on morphological synapomorphies (see text).
Alignement and phylogenetic tree of 106 Lepidoptera
<p>We used both published and de novo sequences from one mitochondrial gene and seven nuclear genes, representing a total length of 7433 bp to infer a molecular phylogeny for 106 lepidopteran species.</p> <p>Müllerian mimicry is a positive interspecific interaction, whereby co-occurring defended prey species share a common aposematic signal. In Lepidoptera, aposematic species typically harbour conspicuous opaque wing colour patterns with convergent optical properties among co-mimetic species. Surprisingly, some aposematic mimetic species have partially transparent wings, raising the questions of whether optical properties of transparent patches are also convergent, and of how transparency is achieved. Here we conducted a comparative study of wing optics, micro and nanostructures in neotropical mimetic clearwing Lepidoptera, using spectrophotometry and microscopy imaging. We show that transparency, as perceived by predators, is convergent among co-mimics. Underlying micro- and nanostructures are also convergent despite a large structural diversity. We reveal that while transparency is primarily produced by microstructure modifications, nanostructures largely influence light transmission, maybe enabling additional fine-tuning in transmission properties. This study shows that transparency might not only enable camouflage but can also be part of aposematic signals.</p>
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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
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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.