Yang-Baxter deformations of the AdS4×CP3AdS_4\times\mathbb{CP}^3 superstring sigma model

The gravity dual of $\beta$-deformed ABJM theory can be obtained by a TsT transformation of $AdS_4\times\mathbb{CP}^3$. We present a supercoset construction of $\mathbb{CP}^3$ to obtain this gravity dual theory as a Yang-Baxter deformation. This is done by selecting a convenient combination of Cartan generators in order to get an Abelian $r$-matrix satisfying the classical Yang-Baxter equation. Our results provide another illustration of the relation between Abelian $r$-matrices and TsT transformations.Comment: 15 pages; v2: references added; v3: more references added, minor corrections, published versio

Arecibon planetaarisen tutkan Maan lähiasteroidihavainnot: 2017 joulukuu - 2019 joulukuu

We successfully observed 191 near-Earth asteroids using the Arecibo Observatory's S-band planetary radar system from 2017 December through 2019 December. We present radar cross sections for 167 asteroids; circular-polarization ratios for 112 asteroids based on Doppler-echo-power spectra measurements; and radar albedos, constraints on size and spin periods, and surface-feature and shape evaluation for 37 selected asteroids using delay-Doppler radar images with a range resolution of 75 m or finer. Out of 33 asteroids with an estimated effective diameter of at least 200 m and sufficient image quality to give clues of the shape, at least 4 (∼12%) are binary asteroids, including 1 equal-mass binary asteroid, 2017 YE5, and at least 10 (∼30%) are contact-binary asteroids. For 5 out of 112 asteroids with reliable measurements in both circular polarizations, we measured circular-polarization ratios greater than 1.0, which could indicate that they are E-type asteroids, while the mean and the 1σ standard deviation were 0.37 ± 0.23. Further, we find a mean opposite-sense circular-polarization radar albedo of 0.21 ± 0.11 for 41 asteroids (0.19 ± 0.06 for 11 S-complex asteroids). We identified two asteroids, 2011 WN15 and (505657) 2014 SR339, as possible metal-rich objects based on their unusually high radar albedos, and discuss possible evidence of water ice in 2017 YE5.Peer reviewe

Sulfated Zirconia-Catalyzed Synthesis of 3,4-Dihydropyrimidin-2(1H)-ones (DHPMs) Under Solventless Conditions: Competitive Multicomponent Biginelli vs. Hantzsch Reactions

The catalytic ability of ZrO2/SO42- to promote solventless three-componentcondensation reactions of a diversity of aromatic aldehydes, urea or thoiurea and ethylacetoacetate was studied. Products resulting from Hantzsch and/or Biginelli multi-component reactions are obtained in the presence of solid acid catalysts using the samereactants but different temperature conditions. The sulfated zirconia catalyst can berecovered and recycled in subsequent reactions with a gradual decrease of activity

nextstrain/nextclade: 3.0.0-alpha.1

<p>| ⚠️ | This is a pre-release. It can contain bugs and significant changes which are not yet finalized. Changes may appear without notice. We recommend to try the pre-releases to learn about upcoming features. For important projects, use stable releases. | |:---:|:---|</p> <p>For changes compared to the previous final release version, please refer to "Unreleased" section in <a href="https://github.com/nextstrain/nextclade/blob/ff02c1e0a2cff7c73f787166b4487f5e7b479c0a/CHANGELOG.md">CHANGELOG.md</a></p&gt

nextstrain/nextclade: 3.0.0-alpha.2

<p>| ⚠️ | This is a pre-release. It can contain bugs and significant changes which are not yet finalized. Changes may appear without notice. We recommend to try the pre-releases to learn about upcoming features. For important projects, use stable releases. | |:---:|:---|</p> <p>For changes compared to the previous final release version, please refer to "Unreleased" section in <a href="https://github.com/nextstrain/nextclade/blob/4ba4fdd0a10fb2dff22af8416c351c831f50d11d/CHANGELOG.md">CHANGELOG.md</a></p&gt

nextstrain/nextclade: 3.0.0

<h2>Unreleased</h2> <p>We are happy to present a major release of Nextclade, containing new features and bug fixes.</p> <blockquote> <p>⚠️ This release contains breaking changes which may require your attention.</p> </blockquote> <p>Useful links:</p> <ul> <li><a href="https://clades.nextstrain.org">Nextclade Web v3</a></li> <li><a href="https://v2.clades.nextstrain.org">Nextclade Web v2</a> - if you need the old version, e.g. if you have custom v2 datasets</li> <li><a href="https://github.com/nextstrain/nextclade/releases">Nextclade CLI releases</a> - all versions</li> <li><a href="https://docs.nextstrain.org/projects/nextclade/en/stable/index.html">Nextclade user documentation</a> - for detailed instructions on how to use Nextclade Web and Nextclade CLI</li> <li><a href="https://github.com/nextstrain/nextclade_data/blob/master/docs/dataset-curation-guide.md">Nextclade dataset curation guide</a> - if you have a custom Nextclade dataset or want to create one</li> <li><a href="https://github.com/nextstrain/nextclade">Nextclade source code repository</a> - for contributors to Nextclade software (code, bug reports, feature requests etc.)</li> <li><a href="https://github.com/nextstrain/nextclade_data">Nextclade data repository</a> - for contributors to Nextclade datasets (add new datasets, update existing ones, report bugs, etc.)</li> <li><a href="https://github.com/nextstrain/nextclade/issues">Nextclade software issues</a> - to report bugs and ask questions about Nextclade software</li> <li><a href="https://github.com/nextstrain/nextclade_data/issues">Nextclade data issues</a> - to report bugs and ask questions about Nextclade datasets</li> <li><a href="https://discussion.nextstrain.org">Nextstrain discussion forum</a> - for general discussion and questions about Nextstrain</li> </ul> <h3>BREAKING CHANGES</h3> <p>This section briefly lists breaking changes in Nextclade v3 compared to Nextclade v2. Please see <a href="https://docs.nextstrain.org/projects/nextclade/en/stable/user/migration-v3.html">Nextclade v3 migration guide</a> (<a href="https://github.com/nextstrain/nextclade/blob/master/docs/user/migration-v3.md">alternative link</a>) for a detailed description of each breaking change and of possible migration paths.</p> <ol> <li>Nextalign CLI is removed, because Nextclade CLI can now do everything that Nextalign v2 did</li> <li>Potentially different alignment and translation output due to changes in the seed alignment algorithm. Some of the alignment parameters are removed. Default parameters of new parameters might need to be adjusted.</li> <li>Potentially different tree output due to a new tree builder algorithm.</li> <li>Dataset file format and dataset names have changed.</li> <li>Some CLI arguments for individual input files are removed.</li> <li>Some output files are removed</li> <li>Genome annotation CLI argument is renamed</li> <li>URL parameters in Nextclade Web have changed</li> <li>CDS instead of genes</li> </ol> <p>The sections below list all changes - breaking and non-breaking. The breaking changes are denoted with word <code>[BREAKING]</code>.</p> <p>If you encounter problems during migration, or breaking changes not mentioned in this document, please report it to the developers by <a href="https://github.com/nextstrain/nextclade/issues/new?title=%5Bv3%5D">opening a new GitHub issue</a>.</p> <h3>General changes</h3> <h4>[BREAKING] Alignment</h4> <p>The seed matching algorithm was rewritten to be more robust and handle sequences with higher diversity. For example, RSV-A can now be aligned against RSV-B.</p> <p>Parameters <code>minSeeds</code>, <code>seedLength</code>, <code>seedSpacing</code>, <code>minMatchRate</code>, <code>mismatchesAllowed</code>, <code>maxIndel</code> no longer have any effect and are removed.</p> <p>New parameters <code>kmerLength</code>, <code>kmerDistance</code>, <code>minMatchLength</code>, <code>allowedMismatches</code>, <code>windowSize</code> are added.</p> <p>Default values should work for sequences with a diversity of up to X%. For sequences with higher diversity, the parameters may need to be adjusted.</p> <p>For short sequences, the threshold length to use full-matrix alignment is now determined based on <code>kmerLength</code> instead of the removed <code>seedLength</code>. The coefficient is adjusted to roughly match the old final value.</p> <h4>Genome annotation</h4> <h5>Replace genes with CDSes</h5> <p>Nextclade now treats genes only as containers for CDSes ("CDS" is <a href="https://en.wikipedia.org/wiki/Coding_region">coding sequence</a>). CDSes are the main unit of translation and a basis for AA mutations now. A gene can contain multiple CDSes, but they are handled independently.</p> <h5>Handle fragmentation of genetic features</h5> <p>A CDS can consist of multiple fragments. These fragments are extracted from the full nucleotide genome independently and joined together (in the order provided in the genome annotation) to form the nucleotide sequence of the CDS. The CDS is then translated and the resulting polypeptides are analyzed (mutations are detected etc.). This implementation allows to handle slippage (e.g. <em>ORF1ab</em> in coronaviruses) and splicing (e.g. <em>tat</em> and <em>rev</em> in HIV-1).</p> <h5>Handle circular genomes</h5> <p>If genome annotation describes a CDS fragment as circular (wrapping around origin), Nextclade splits it into multiple linear (non-wrapping) fragments. The translation and analysis is then performed as if it was a linear genome.</p> <p>Nextclade follows the <a href="https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md#circular-genomes">GFF3 specification</a>. Please refer to it for how to describe circular features.</p> <h5>Parse regions, genes and CDSes from GFF3 file</h5> <p>The GFF3 file parser has been augmented to support all the types of genetic features necessary for Nextclade to operate. There are still feature types which Nextclade ignores. We can consider supporting more types as scientific need arises.</p> <h4>Phylogenetic tree placement</h4> <p>Nextclade v3 now has the ability to phylogenetically resolve relationships between input sequences, where v2 would only attach each query sequence independently to the reference tree. Nextclade v3 thus may produce trees that are different from the trees produced in Nextclade v2.</p> <p>Please read the <a href="https://docs.nextstrain.org/projects/nextclade/en/stable/user/algorithm/05-phylogenetic-placement.html">Phylogenetic placement</a> section in the documentation for more details.</p> <h4>Don't count mutations to ambiguous nucleotides as reversions</h4> <p>We no longer treat mutations to ambiguous nucleotides as reversions, i.e. if the attachment node has a mutation mutated with respect to reference and the query sequence is ambiguous we previously counted this as a reversion. This change only affects "private mutation" QC score and the classification of private mutations into "reversion substitution" and "unlabeled substitution".</p> <h3>Changes in Nextclade Web</h3> <h4>Dataset autosuggestion</h4> <p>Nextclade Web can now optionally suggest the most appropriate dataset(s) for user-provided input sequences. Drop your sequences and click "Suggest" to try out this feature.</p> <h4>Genome annotation widget</h4> <p>Following changes in genome annotation handling, the genome annotations widget in Nextclade Web now shows CDS fragments instead of genes.</p> <h4>CDS selector widget in Nextclade Web</h4> <p>The gene selector dropdown in Nextclade Web's results table has been transformed into a more general genetic feature selector. It shows the hierarchy of genetic features if there are nested features. Otherwise, the list is flat, to save screen space. It shows types of each of the genetic feature (gene, CDS or protein) as colorful badges. The menu is searchable, which is useful for mpox and other large viruses with many genes. Only CDSes can be selected currently, but we may extend this in the future to more feature types.</p> <h4>Show ambiguous nucleotides in sequence views</h4> <p>Nucleotide sequence views (in the results table) now also show colored markers for ambiguous nucleotides (non-ACTGN).</p> <h4>Improve website navigation</h4> <p>The row of buttons, containing "Back", "Tree" and other buttons is removed. Instead, different sections of the web application are always accessible via the main navigation bar.</p> <p>The "Export" ("Download") and "Settings" sections are moved to dedicated pages.</p> <h4>[BREAKING] Changed and removed some of the URL parameters</h4> <p>Due to changes in the dataset format and input files, the URL parameters have the following changes:</p> <ul> <li><code>input-root-seq</code> renamed to <code>input-ref</code></li> <li><code>input-gene-map</code> renamed to <code>input-annotation</code></li> <li><code>input-pathogen-json</code> added</li> <li><code>input-qc-config</code> removed</li> <li><code>input-pcr-primers</code> removed</li> <li><code>input-virus-properties</code> removed</li> <li><code>dataset-reference</code> removed</li> </ul> <h4>[BREAKING] Removed some redundant output files</h4> <p>The <code>nextclade.errors.csv</code> and <code>nextclade.insertions.csv</code> files are removed and no longer appear in the "Export" dialog, nor are they included into the <code>nextclade.zip</code> archive of all outputs.</p> <p>Errors and insertions are now included in the <code>nextclade.csv</code> and <code>nextclade.tsv</code> files.</p> <h4>Auspice updated from v2.45.2 to v2.51.0</h4> <p>The Auspice tree viewer component is updated from version 2.45.2 to 2.51.0. See the <a href="https://github.com/nextstrain/auspice/releases">Auspice releases</a> or <a href="https://github.com/nextstrain/auspice/compare/v2.45.2...v2.51.0#diff-06572a96a58dc510037d5efa622f9bec8519bc1beab13c9f251e97e657a9d4ed">changelog</a>.</p> <h3>Changes in Nextclade CLI</h3> <h4>[BREAKING] Nextalign CLI is removed</h4> <p>Nextalign CLI is no longer provided as a standalone application along with Nextclade CLI v3 because Nextclade now has all the features that distinguished Nextalign. This means there's only one set of command line arguments to remember. Nextclade CLI runs the same algorithms, accepts same the inputs and provides the same outputs as v2 Nextalign, plus some more. For most use-cases, the CLI interface and the input and output files should be the same or very similar.</p> <h4>[BREAKING] Some alignment parameters are removed</h4> <p>Due to changes in the seed alignment algorithm, the following parameters are no longer used and the corresponding CLI arguments and JSON fields under <code>alignmentParams</code> in <code>pathogen.json</code> (previously <code>virus_properties.json</code>) were removed:</p> <pre><code>--seed-length --seed-spacing --max-indel --min-match-rate --min-seeds --mismatches-allowed </code></pre> <p>The following new alignment parameters were added:</p> <pre><code>--allowed-mismatches --kmer-distance --kmer-length --min-match-length --min-seed-cover --max-alignment-attempts --max-band-area --window-size </code></pre> <h4>[BREAKING] Some CLI arguments for individual input files are removed</h4> <p>Due to changes in the dataset format the following CLI arguments were removed:</p> <pre><code>--input-virus-properties --input-qc-config --input-pcr-primers </code></pre> <p>in favor of <code>--input-pathogen-json</code>.</p> <h4>[BREAKING] Some CLI arguments for output files are removed</h4> <p>The arguments <code>--output-errors</code> and <code>--output-insertions</code> have been removed. Their information is now included in <code>--output-csv</code> and <code>--output-tsv</code>.</p> <h4>[BREAKING] Genome annotation CLI argument is renamed</h4> <p>The argument <code>--input-gene-map</code> renamed to <code>--input-annotation</code>. The short form <code>-m</code> remains unchanged.</p> <h4>[Breaking] Translation selection CLI argument is renamed</h4> <p>The argument <code>--genes</code> is renamed to <code>--cds-selection</code>. The short form <code>-g</code> remains unchanged.</p> <h4>Newick tree output</h4> <p>Nextclade can now also export the tree in Newick format via the <code>--output-tree-nwk</code> argument.</p> <h4>Optional input files</h4> <p>Most input files and files inside datasets are now optional. This simplifies dataset creation and maintenance and allows for step-by-step, incremental extension of them. You can start only with a reference sequence, which will only allow for alignment and very basic mutation calling in Nextclade, and later you can add more functionality. Optional input files also enable the removal of Nextalign CLI.</p> <p>If you maintain a custom dataset or want to try creating one - refer to our <a href="https://github.com/nextstrain/nextclade_data/blob/master/docs/dataset-curation-guide.md">Dataset curation guide</a>. Community contributed datasets are welcome!</p> <h4>Added flag for disabling the new tree builder</h4> <p>The old phylogenetic tree placement behavior can be restored by adding the <code>--without-greedy-tree-builder</code> flag.</p> <h4>New arguments in <code>dataset list</code> command</h4> <p>The new argument <code>--only-names</code> allows to print a concise list of dataset names:</p> <pre><code>nextclade dataset list --only-names </code></pre> <p>The new argument <code>--search</code> allows to search datasets using substring match with dataset name, dataset friendly name, reference name or reference accession:</p> <pre><code>nextclade dataset list --search=flu </code></pre> <p>The argument <code>--json</code> allows to output a JSON object instead of the table. You can write it into a file and to postprocess it:</p> <pre><code>nextclade dataset list --json > "dataset_list.json" nextclade dataset list --json | jq '.[] | select(.path | startswith("nextstrain/sars-cov-2")) | .attributes' </code></pre> <h4>New subcommand: <code>sort</code></h4> <p>The <code>sort</code> subcommand takes your sequences in FASTA format and outputs sequences grouped by dataset in the form of a directory tree. Each subdirectory corresponds to a dataset and contains an output FASTA file with only sequences that are detected to be similar to the reference sequence in this dataset.</p> <p>Example usage:</p> <pre><code>nextclade sort --output-dir="out/sort/" --output-results-tsv="out/sort.tsv" "input.fasta" </code></pre> <p>This can be useful for splitting FASTA files containing sequences which belong to different pathogens, strains or segments, for example for separating flu HA and NA segments.</p> <h4>New subcommand: <code>read-annotation</code></h4> <p>The <code>read-annotation</code> subcommand takes a GFF3 file and displays how features are arranged hierarchically as viewed by Nextclade. This is useful for Nextclade developers and dataset creators to verify (and debug) how Nextclade understand genetic features from a particular GFF3 file.</p> <p>Example usage:</p> <pre><code>nextclade read-annotation genome_annotation.gff3 </code></pre> <p>Type <code>nextclade read-annotation --help</code> for description of arguments.</p> <h3>Performance improvements</h3> <h4>Nextclade web now twice as fast when processing many sequences</h4> <p>Nextclade Web now uses multithreading more effectively. This results in faster processing of large fastas on computers with more than one processor. The speedup is around 2 for 1000 SARS-CoV-2 sequences on a multi-core machine.</p> <h3>Internal changes</h3> <h4>Ensure type safety across programming language boundaries</h4> <p>The new features caused changes in major internal data structures and made them more complex. We now generate JSON schema and Typescript typings from Rust code. This allows to find mismatches between parts written in different languages, and to avoid bugs related to data types.</p> <h4>Make positions and ranges in different coord spaces type-safe</h4> <p>The change in genome annotation handling had significant consequences for coordinate spaces Nextclade is using internally (e.g. alignment space vs reference space, nuc space vs aa space, global nuc space vs nuc space local to a CDS). In order to make coordinate transforms safer, we introduced new <code>Position</code> and <code>Range</code> types, different for each space. This prevents mixing up coordinates in different spaces.</p> <h2>Instructions</h2> <p> Nextclade CLI & Nextalign CLI can be downloaded from the links in the "Assets" section just below. Click "Show all" at the bottom of the "Assets" section to show more download options. Note the difference between "nextalign" and "nextclade" files as well as differences in operating systems and computer architectures.</p> <p> Nextclade Web is available at <a href="https://clades.nextstrain.org">https://clades.nextstrain.org</a></p> <p> Docker images are available at <a href="https://hub.docker.com/r/nextstrain/nextclade">DockerHub</a></p> <p> To understand how it all works, make sure to read the <a href="https://docs.nextstrain.org/projects/nextclade">Documentation</a></p&gt