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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.
ambuda-org / AmbudaMain application code for Ambuda, a breakthrough Sanskrit library (ambuda.org)
prip-lab / MSU LatentAFISA system for identifying latent fingerprints. Created at Michigan State University by Anil K. Jain, Kai Cao, Dinh-Luan Nguyen, and Cori Tymoszek.
premaseem / DesignPatternsJava9This repository has all 23 GOF design patterns coded in Java 9 with around 50+ working project code used for Video Course by Packt Publication with title "Learn Design Patterns with Java " authored by "Aseem Jain". The link of the course is
cchudant / 100 Days Of ML CodeMy attempt at solving https://github.com/Avik-Jain/100-Days-Of-ML-Code
Apress / Deep Learning For Natural Language ProcessingSource Code for 'Deep Learning for Natural Language Processing' by Palash Goyal, Sumit Pandey and Karan Jain
MrBriit / FLASK End To End Zomato Restaurant Price Prediction And Deployment# **ABSTRACT** Main Objective: The main agenda of this project is: Perform extensive Exploratory Data Analysis(EDA) on the Zomato Dataset. Build an appropriate Machine Learning Model that will help various Zomato Restaurants to predict their respective Ratings based on certain features DEPLOY the Machine learning model via Flask that can be used to make live predictions of restaurants ratings A step by step guide is attached to this documnet as well as a video explanation of each concpet. Zomato is one of the best online food delivery apps which gives the users the ratings and the reviews on restaurants all over india.These ratings and the Reviews are considered as one of the most important deciding factors which determine how good a restaurant is. We will therefore use the real time Data set with variuos features a user would look into regarding a restaurant. We will be considering Banglore City in this analysis. Content The basic idea of analyzing the Zomato dataset is to get a fair idea about the factors affecting the establishment of different types of restaurant at different places in Bengaluru, aggregate rating of each restaurant, Bengaluru being one such city has more than 12,000 restaurants with restaurants serving dishes from all over the world. With each day new restaurants opening the industry has’nt been saturated yet and the demand is increasing day by day. Inspite of increasing demand it however has become difficult for new restaurants to compete with established restaurants. Most of them serving the same food. Bengaluru being an IT capital of India. Most of the people here are dependent mainly on the restaurant food as they don’t have time to cook for themselves. With such an overwhelming demand of restaurants it has therefore become important to study the demography of a location. What kind of a food is more popular in a locality. Do the entire locality loves vegetarian food. If yes then is that locality populated by a particular sect of people for eg. Jain, Marwaris, Gujaratis who are mostly vegetarian. These kind of analysis can be done using the data, by studying the factors such as • Location of the restaurant • Approx Price of food • Theme based restaurant or not • Which locality of that city serves that cuisines with maximum number of restaurants • The needs of people who are striving to get the best cuisine of the neighborhood • Is a particular neighborhood famous for its own kind of food. “Just so that you have a good meal the next time you step out” The data is accurate to that available on the zomato website until 15 March 2019. The data was scraped from Zomato in two phase. After going through the structure of the website I found that for each neighborhood there are 6-7 category of restaurants viz. Buffet, Cafes, Delivery, Desserts, Dine-out, Drinks & nightlife, Pubs and bars. Phase I, In Phase I of extraction only the URL, name and address of the restaurant were extracted which were visible on the front page. The URl's for each of the restaurants on the zomato were recorded in the csv file so that later the data can be extracted individually for each restaurant. This made the extraction process easier and reduced the extra load on my machine. The data for each neighborhood and each category can be found here Phase II, In Phase II the recorded data for each restaurant and each category was read and data for each restaurant was scraped individually. 15 variables were scraped in this phase. For each of the neighborhood and for each category their onlineorder, booktable, rate, votes, phone, location, resttype, dishliked, cuisines, approxcost(for two people), reviewslist, menu_item was extracted. See section 5 for more details about the variables. Acknowledgements The data scraped was entirely for educational purposes only. Note that I don’t claim any copyright for the data. All copyrights for the data is owned by Zomato Media Pvt. Ltd.. Source: Kaggle
Apress / Pro Apache JmeterSource code for 'Pro Apache JMeter' by Sai Matam and Jagdeep Jain
RestComm / Jain SleeThe World's #1 Open Source JAIN-SLEE (JSLEE) 1.1 Implementation
EkType / JainiJainī is a Devanāgarī and Latin typeface based on the calligraphic style of the Jain Kalpasūtra manuscripts.
absmall / P2This program implements the P^2 algorithm as documented in "The P-Square Algorithm for Dynamic Calculation of Percentiles and Histograms without Storing Observations," Communications of the ACM, October 1985 by R. Jain and I. Chlamtac. Both the point method and histogram method are implemented.
avikj / SnapStitchBuilt by Avik Jain, Anish Nag, Sahas Dendukuri, Hari Senthilkumar, and Rishi Upadhyay at Angelhack Silicon Valley 2017.
atishay / Atishay.github.ioAtishay Jain's personal website
jainqq-org / JLORJain Literature Open Repository
rachitiitr / Conda101This "Conda Tutorial" is part of the quest to navigate your "Software Engineer Career" into "Senior Developer" and "Lead Developer" Roles. Join Rachit Jain in his journey as he learns and shares his knowledge from a University Student to a Senior Software Engineer.
clvrai / AgileOfficial implementation of "Know Your Action Set: Learning Action Relations for Reinforcement Learning", Jain et al., ICLR 2022.
Apress / Linux Containers VirtualizationSource Code for 'Linux Containers and Virtualization' by Shashank Mohan Jain
nzery / Easysip基于sip协议的android通话客户端，协议栈jain-sip 媒体库使用webrtc
Apress / Intro Transformers NlpSource Code for 'Introduction to Transformers for NLP' by Shashank Mohan Jain
tusharjain1082 / DiaryJournal.NetDiaryJournal.Net is an open source and free desktop and laptop software from Tushar Jain for all kinds of writers, book and story writing, educational, notes keeping, journal and diary. for latest Visual Studio 2022, Windows 10/11 and .Net 8.0. includes precompiled application ready to use.
