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afid

A highly parallel application for Rayleigh-Benard and Taylor-Couette flows

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.

bss2022_dedalus_examples

cdcs

An open-source MATLAB® ADMM solver for partially decomposable conic optimization programs.

chang_liu.github.io

channelflow

Channelflow is a software system for numerical analysis of the incompressible fluid flow in channel geometries, written in C++ and MPI-parallelized.

cliu124.github.io

Github Pages template for academic personal websites, forked from mmistakes/minimal-mistakes

coleso

Collection of exact solutions for verification of numerical algorithms for simulation of compressible flows

coral

Parallel spectral solver for partial differential equations in the plane layer geometry.

couette

crazepony-firmware-none

Crazepony flight control source code with no RTOS.

crazepony-gitbook

Gitbook about quadcopter and crazepony.

crazepony.github.io

The web site of Crazepony.

d3

Bring data to life with SVG, Canvas and HTML. :bar_chart::chart_with_upwards_trend::tada:

dcm-imu

The DCM-IMU algorithm is designed for fusing low-cost triaxial MEMS gyroscope and accelerometer measurements. An extended Kalman filter is used to estimate attitude in direction cosine matrix (DCM) formation and gyroscope biases online. A variable measurement covariance method is implemented for acceleration measurements to ensure robustness against temporarily non-gravitational accelerations which usually induce errors to attitude estimate in ordinary IMU-algorithms. The code and data will be added after related scientific work is published and open source publication is approved.

dedalus

A flexible framework for solving PDEs with modern spectral methods.

dedalus_codes

In this repository I collect python scripts for the numerical framework Dedalus 3.

dedalus_example

dmsuite

A collection of spectral collocation differentiation matrices

fftw3

DO NOT CHECK OUT THESE FILES FROM GITHUB UNLESS YOU KNOW WHAT YOU ARE DOING. (See below.)

gait-tracking-with-x-imu

hita

Matlab code for the spectral analysis of homogenous isotropic turbulence

ibamr_uconn

imufusion

EKF IMU Fusion Algorithms

inara

Tools to create JOSS/JOSE publishing artifacts

intsostools

Plug-in to SOSTOOLS for Integral Inequalities

jhu-dissertation-mwe

JHU Dissertation LaTeX mwe

kronic

Koopman Reduced-Order Nonlinear Identification and Control

learn-git

A demonstration repository for learning how to use git and github

lesgo

The Large-Eddy Simulation framework from the Turbulence Research Group at Johns Hopkins University