sfmajors373

Secure-Private-AI-Facebook-Scholarship-KeyStone-project

Secure & Private AI Facebook Scholarship-KeyStone Project

Climate-Change-Datasets

Here is a list of Climate Change Public Datasets 🌦🌪🌫🌀💧🌊

Computer-Architecture-Two

Computer Architecture - Peripherals: Network, DMA, Storage, Graphcis

FourthBrain

This is a collection of live coding exercises, homework assignments and the like created during my experience with Fourth Brain

FourthBrainBreastCancer

This is our final project for Fourth Brain

intel_30_days_of_Udacity

Participation in the Intel Edge AI Udacity Scholarship 30 days of Udacity challenge

LambdaCSA-Syllabus

LatexCookbook

LongArmQuiltingFrame

Plans to make an open source long arm quilting frame from aluminum v-channel

Resume

sfmajors373/FourthBrainBreastCancer

This is our final project for Fourth Brain

sfmajors373/Resume

sfmajors373/artillery-detection

Capstone project for FourthBrain MLOps course in which I train and deploy a machine learning model to detect heavy artillery/bombing damage to buildings

sfmajors373/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.

sfmajors373/CMakeTest

sfmajors373/CppNanoDegree

sfmajors373/CppND-Memory-Management-Chatbot

sfmajors373/CppND-Program-a-Concurrent-Traffic-Simulation

The final project for the Udacity C++ Nanodegree Concurrency course

sfmajors373/CppND-RoutePlanning

Udacity C++ project 1. Using A* to plan a route from OpenStreetMaps

sfmajors373/CppND-System-Monitor

Student repository for the CppND OOP course project

sfmajors373/CppNDCapstone

Capstone for C++ Nanodegree

sfmajors373/damage-assessment

sfmajors373/DVC-testing

sfmajors373/ml-monitoring

A demo of Prometheus+Grafana for monitoring an ML model served with FastAPI.

sfmajors373/MLO4

MLOps assignments, projects, stuffs

sfmajors373/portfolio

Portfolio

sfmajors373/portfolio-hydejack

sfmajors373/portfolio-hydejack-gh

sfmajors373/SensorFusionND

Coursework for Sensor Fusion NanoDegree from Udacity

sfmajors373/SFND_2D_Feature_Matching

sfmajors373/SFND_3D_Feature_Matching

Udacity Sensor Fusion NanoDegree Computer Vision and Lidar Course Project

sfmajors373/SFND_3D_TTC

sfmajors373/SFND_Lidar_Obstacle_Detection

Sensor Fusion NanoDegree Course 1 project: Lidar Obstacle Detection

sfmajors373/SFND_radar

sfmajors373/SFND_Unscented_Kalman_Filter

sfmajors373/software-dev-for-mlops-101

Set up your local environment to do some real Machine Learning Operations software development, just like pro MLOps practitioners.

sfmajors373/Syria-First-Stage

sfmajors373/tech-interviews

Materials for Technical Interviews at TeamSense

sfmajors373/vimrc

Vimrc

sfmajors373/xView2_baseline

Baseline localization and classification models for the xView 2 challenge.