Pinned Repositories
buildroot
Configure and build dahliaOS
flatpak.dart
flatpak library in dart via ffi
iso9660
This library is a simple implementation of the iso9660 filesystem standard.
nothing_archive
This repository contains firmware files for Nothing Phone 1, 2, 2a, 2a plus and CMF Phone 1. The firmware files are sourced from the official OTA servers and are mirrored here for archival purposes.
pangolin-linux
pangolin desktop running on linux systems
trident
The magic kernel manager for ubuntu based distros and WSL2 written in dart.
tv_downloader
ubuntumainline
script for installing the latest mainline kernel on ubuntu and ubuntu based distros
unsafeexambrowser
vlot_eindproject
Eindproject: Intelligent sensorarray voor binnenklimaatmetingen
quintenvandamme's Repositories
quintenvandamme/nothing_archive
This repository contains firmware files for Nothing Phone 1, 2, 2a, 2a plus and CMF Phone 1. The firmware files are sourced from the official OTA servers and are mirrored here for archival purposes.
quintenvandamme/unsafeexambrowser
quintenvandamme/pangolin-linux
pangolin desktop running on linux systems
quintenvandamme/ubuntumainline
script for installing the latest mainline kernel on ubuntu and ubuntu based distros
quintenvandamme/trident
The magic kernel manager for ubuntu based distros and WSL2 written in dart.
quintenvandamme/OpenZCS
An open source version of the ZCS programming language in zeqOS Chabazite
quintenvandamme/dart-sdk-riscv64
The dart sdk for riscv64
quintenvandamme/quintenvandamme.github.io
personal website
quintenvandamme/buildroot
Configure and build dahliaOS Linux-based builds on docker
quintenvandamme/tv_downloader
quintenvandamme/vlot_eindproject
Eindproject: Intelligent sensorarray voor binnenklimaatmetingen
quintenvandamme/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.
quintenvandamme/book
The Rust Programming Language
quintenvandamme/cosmic-epoch
Next generation Cosmic desktop environment
quintenvandamme/distroware.gitlab.io
Distroware open archive. Manual bidirectional mirror of https://gitlab.com/Distroware/distroware.gitlab.io
quintenvandamme/documentation
Documentation for dahliaOS
quintenvandamme/documentation-2
📘 Nextcloud documentation
quintenvandamme/dotnet9x
Backport of .NET 2.0 - 3.5 to Windows 9x
quintenvandamme/duckduckgo-help-pages
DuckDuckGo Help Pages
quintenvandamme/engine
The Flutter engine
quintenvandamme/ephemeral
A private-by-default, always-incognito browser for elementary OS
quintenvandamme/fastfetch
Like neofetch, but much faster because written mostly in C.
quintenvandamme/getwindows11.tech
For the website
quintenvandamme/mainline-builder
The script builder for ubuntumainline
quintenvandamme/nextra
The Next.js Static Site Generator
quintenvandamme/pangolin_desktop
Pangolin Desktop UI shell, designed for dahliaOS, written in Flutter.
quintenvandamme/quintenvandamme
quintenvandamme/supabase
The open source Firebase alternative. Follow to stay updated about our public Beta.
quintenvandamme/unix-time
simple c++ program that converts current time to unix time
quintenvandamme/utopia
The comfy compositor