luguenth's Stars
cobalamin/obsidian-remarkable
Integrates the reMarkable tablet into an Obsidian workflow by letting users quickly capture and insert their drawings.
Kompakkt/Extender
Extension system for modularizing instances of Kompakkt
IIIF-Commons/manifesto
IIIF Presentation API client and server utility library.
isadorasophia/murder
Murder is a pixel art ECS game engine.
Annoraaq/grid-engine
A grid based movement engine compatible with Phaser3.
leomfn/lent
Borrow anything
gitbutlerapp/gitbutler
The GitButler version control client, backed by Git, powered by Tauri/Rust/Svelte
cheeaun/life
Life - a timeline of important events in my life
AndyTheFactory/newspaper4k
📰 Newspaper4k a fork of the beloved Newspaper3k. Extraction of articles, titles, and metadata from news websites.
MeoMix/symbiants
Ant Colony Sim + Daily Mental Health Exercises
luguenth/mediatheke
CorentinJ/Real-Time-Voice-Cloning
Clone a voice in 5 seconds to generate arbitrary speech in real-time
wagtail/wagtail
A Django content management system focused on flexibility and user experience
opentofu/manifesto
The OpenTF Manifesto expresses concern over HashiCorp's switch of the Terraform license from open-source to the Business Source License (BSL) and calls for the tool's return to a truly open-source license.
seapagan/fastapi-template
Configurable template for a FastAPI application, with Authentication and User integration.
zylon-ai/private-gpt
Interact with your documents using the power of GPT, 100% privately, no data leaks
mx4k/RNDplus4free
"Plus" Inhalte der RND.de Zeitungen aus dem Quelltext auslesen und in die Seite einfügen.
Significant-Gravitas/AutoGPT
AutoGPT is the vision of accessible AI for everyone, to use and to build on. Our mission is to provide the tools, so that you can focus on what matters.
codezeit/Komplano
leomfn/RuPyks
Experimental Rubiks cube program
techgaun/active-forks
Find active github forks of a repo https://git.io/vSnrC
actualbudget/actual
A local-first personal finance app
symfony/symfony
The Symfony PHP framework
luguenth/Mautic-Monitor-Client
A monitoring tool for Mautic instances. You need to install the Corresponding API Plugin for Mautic https://github.com/luguenth/Mautic-Monitor-API-Plugin
mar-muel/local-geocode
Simple library for efficient geocoding without making API calls
api-platform/api-platform
🕸️ Create REST and GraphQL APIs, scaffold Jamstack webapps, stream changes in real-time.
NAalytics/Assemblies-of-putative-SARS-CoV2-spike-encoding-mRNA-sequences-for-vaccines-BNT-162b2-and-mRNA-1273
RNA 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.
rust-embedded/rust-raspberrypi-OS-tutorials
:books: Learn to write an embedded OS in Rust :crab:
open-discourse/open-discourse
Open Discourse is the first fully comprehensive corpus of the plenary proceedings of the federal German Parliament (Bundestag).
p2pu/course-in-a-box
An open-source project for creating online courses, built by P2PU