724 skills found · Page 1 of 25
getmaxun / Maxun🔥 The open-source no-code platform for web scraping, crawling, search and AI data extraction • Turn websites into structured APIs in minutes 🔥
NAalytics / Assemblies Of Putative SARS CoV2 Spike Encoding MRNA Sequences For Vaccines BNT 162b2 And MRNA 1273RNA vaccines have become a key tool in moving forward through the challenges raised both in the current pandemic and in numerous other public health and medical challenges. With the rollout of vaccines for COVID-19, these synthetic mRNAs have become broadly distributed RNA species in numerous human populations. Despite their ubiquity, sequences are not always available for such RNAs. Standard methods facilitate such sequencing. In this note, we provide experimental sequence information for the RNA components of the initial Moderna (https://pubmed.ncbi.nlm.nih.gov/32756549/) and Pfizer/BioNTech (https://pubmed.ncbi.nlm.nih.gov/33301246/) COVID-19 vaccines, allowing a working assembly of the former and a confirmation of previously reported sequence information for the latter RNA. Sharing of sequence information for broadly used therapeutics has the benefit of allowing any researchers or clinicians using sequencing approaches to rapidly identify such sequences as therapeutic-derived rather than host or infectious in origin. For this work, RNAs were obtained as discards from the small portions of vaccine doses that remained in vials after immunization; such portions would have been required to be otherwise discarded and were analyzed under FDA authorization for research use. To obtain the small amounts of RNA needed for characterization, vaccine remnants were phenol-chloroform extracted using TRIzol Reagent (Invitrogen), with intactness assessed by Agilent 2100 Bioanalyzer before and after extraction. Although our analysis mainly focused on RNAs obtained as soon as possible following discard, we also analyzed samples which had been refrigerated (~4 ℃) for up to 42 days with and without the addition of EDTA. Interestingly a substantial fraction of the RNA remained intact in these preparations. We note that the formulation of the vaccines includes numerous key chemical components which are quite possibly unstable under these conditions-- so these data certainly do not suggest that the vaccine as a biological agent is stable. But it is of interest that chemical stability of RNA itself is not sufficient to preclude eventual development of vaccines with a much less involved cold-chain storage and transportation. For further analysis, the initial RNAs were fragmented by heating to 94℃, primed with a random hexamer-tailed adaptor, amplified through a template-switch protocol (Takara SMARTerer Stranded RNA-seq kit), and sequenced using a MiSeq instrument (Illumina) with paired end 78-per end sequencing. As a reference material in specific assays, we included RNA of known concentration and sequence (from bacteriophage MS2). From these data, we obtained partial information on strandedness and a set of segments that could be used for assembly. This was particularly useful for the Moderna vaccine, for which the original vaccine RNA sequence was not available at the time our study was carried out. Contigs encoding full-length spikes were assembled from the Moderna and Pfizer datasets. The Pfizer/BioNTech data [Figure 1] verified the reported sequence for that vaccine (https://berthub.eu/articles/posts/reverse-engineering-source-code-of-the-biontech-pfizer-vaccine/), while the Moderna sequence [Figure 2] could not be checked against a published reference. RNA preparations lacking dsRNA are desirable in generating vaccine formulations as these will minimize an otherwise dramatic biological (and nonspecific) response that vertebrates have to double stranded character in RNA (https://www.nature.com/articles/nrd.2017.243). In the sequence data that we analyzed, we found that the vast majority of reads were from the expected sense strand. In addition, the minority of antisense reads appeared different from sense reads in lacking the characteristic extensions expected from the template switching protocol. Examining only the reads with an evident template switch (as an indicator for strand-of-origin), we observed that both vaccines overwhelmingly yielded sense reads (>99.99%). Independent sequencing assays and other experimental measurements are ongoing and will be needed to determine whether this template-switched sense read fraction in the SmarterSeq protocol indeed represents the actual dsRNA content in the original material. This work provides an initial assessment of two RNAs that are now a part of the human ecosystem and that are likely to appear in numerous other high throughput RNA-seq studies in which a fraction of the individuals may have previously been vaccinated. ProtoAcknowledgements: Thanks to our colleagues for help and suggestions (Nimit Jain, Emily Greenwald, Lamia Wahba, William Wang, Amisha Kumar, Sameer Sundrani, David Lipman, Bijoyita Roy). Figure 1: Spike-encoding contig assembled from BioNTech/Pfizer BNT-162b2 vaccine. Although the full coding region is included, the nature of the methodology used for sequencing and assembly is such that the assembled contig could lack some sequence from the ends of the RNA. Within the assembled sequence, this hypothetical sequence shows a perfect match to the corresponding sequence from documents available online derived from manufacturer communications with the World Health Organization [as reported by https://berthub.eu/articles/posts/reverse-engineering-source-code-of-the-biontech-pfizer-vaccine/]. The 5’ end for the assembly matches the start site noted in these documents, while the read-based assembly lacks an interrupted polyA tail (A30(GCATATGACT)A70) that is expected to be present in the mRNA.
LeeeSe / MessAuto自动提取Mac平台的短信和邮箱验证码；Automatic extraction of 2FA codes from iMassage and Mail App for Mac platform
cased / KitThe toolkit for AI devtools context engineering. Build with codebase mapping, symbol extraction, and many kinds of code search.
MaLeLabTs / RegexGeneratorThis project contains the source code of a tool for generating regular expressions for text extraction: 1. automatically, 2. based only on examples of the desired behavior, 3. without any external hint about how the target regex should look like
thunlp / DocREDDataset and codes for ACL 2019 DocRED: A Large-Scale Document-Level Relation Extraction Dataset.
wenwenyu / PICK PytorchCode for the paper "PICK: Processing Key Information Extraction from Documents using Improved Graph Learning-Convolutional Networks" (ICPR 2020)
norman / BabosaA library for creating slugs. Babosa is an extraction and improvement of the string code from FriendlyId, intended to help developers create similar libraries or plugins.
gkiril / Oie ResourcesA curated list of Open Information Extraction (OIE) resources: papers, code, data, etc.
gemengtju / Tutorial SeparationThis repo summarizes the tutorials, datasets, papers, codes and tools for speech separation and speaker extraction task. You are kindly invited to pull requests.
rxn4chemistry / RxnmapperRXNMapper: Unsupervised attention-guided atom-mapping. Code complementing our Science Advances publication on "Extraction of organic chemistry grammar from unsupervised learning of chemical reactions" (https://advances.sciencemag.org/content/7/15/eabe4166).
wala / Graph4codeGraphGen4Code: a toolkit for creating code knowledge graphs based on WALA code analysis and extraction of documentation and forum content.
sicaril / BaymaxToolsBaymaxTools is a feature code extraction and search plug-in for x64dbg debugger. it is convenient to extract the signature of the specified instruction and the number of occurrences of the signature in the search module.
ruidan / Unsupervised Aspect ExtractionCode for acl2017 paper "An unsupervised neural attention model for aspect extraction"
Lydorn / Polygonization By Frame Field LearningThis repository contains the code for our fast polygonal building extraction from overhead images pipeline.
midoxnet / MapperplusMapperPlus facilitates the extraction of source code from a collection of targets that have publicly exposed .js.map files.
thunlp / Chinese NRESource code for ACL 2019 paper "Chinese Relation Extraction with Multi-Grained Information and External Linguistic Knowledge"
thunlp / PL MarkerSource code for "Packed Levitated Marker for Entity and Relation Extraction"
nicobailon / Pi Web AccessWeb search and content extraction extension for Pi coding agent
iqiukp / KPCA MATLABMATLAB code for dimensionality reduction, feature extraction, fault detection, and fault diagnosis using Kernel Principal Component Analysis (KPCA).
