victordit's Repositories
victordit/AliceBundle
A Symfony bundle to manage fixtures with Alice and Faker.
victordit/anonymizer
Universal tool to anonymize database. GDPR (General Data Protection Regulation) data protection act supporting tool.
victordit/Aoe_Scheduler
Cron Scheduler Module for Magento
victordit/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.
victordit/bash_completion_extended
Extend bash_completion for support php-cli applications like composer or n98-magerun.phar
victordit/BL_CustomGrid
Enhanced Admin Grids extension for Magento.New 1.0.0 version under development. WIP version is now available for testing. Project on hold due to a long-lasting lack of time - sorry to all the issues awaiting an answer ! (will answer as soon / much as possible)
victordit/E-MailPreview
This extension enables the merchants and developers to preview mail templates from the backend with real data.
victordit/flag-icon-css
:flags: A collection of all country flags in SVG — plus the CSS for easier integration
victordit/gitignore
A collection of useful .gitignore templates
victordit/importexportfree
Improve default Magento 2 Import / Export features - cron jobs, CSV , XML , JSON , Excel , mapping of any format, Google Sheet, data and price modification, improved speed and a lot more!
victordit/jQuery-Dependent-Fields
Show/hide a form field based on another form field
victordit/magento-configurable-simple
Enhancement to Magento to allow simple product prices to be used instead of the default special-case configurable product prices
victordit/magento-events-cheat-sheet
victordit/magento-export-tiny-database
Script with the ability to generated a reduced database dump
victordit/magento1_devtools
Magento tools for developers
victordit/magento2
Prior to making any Submission(s), you must sign an Adobe Contributor License Agreement, available here at: https://opensource.adobe.com/cla.html. All Submissions you make to Adobe Inc. and its affiliates, assigns and subsidiaries (collectively “Adobe”) are subject to the terms of the Adobe Contributor License Agreement.
victordit/magento2-create-admin-grid-CURD-operations
Here We Create Collection Grid , Edit/Add Grid Row And Installer In Magento2
victordit/magento2-easy-template-path-hints
Magento 2 Easy Template Path Hints
victordit/magento2-google-address-lookup
Provides an address lookup service on a Magento 2 store powered by the Google Places API
victordit/magento2-marketplace
Magento2 multi-vendor marketplace module
victordit/magentostudyguide.com
Study materials for all who are interested to take the Magento Certified Developer exam. You can see the project live at: http://www.magestudyguide.com/
victordit/MagePsycho_Easypathhints
Easy Template Path Hints extension is used to turn on the template path hints for frontend & backend with ease in a secured way. Moreover it's joomla way of turning on the template path hints.
victordit/merge-and-share-wp
Wordpress Plugin for merge images and share on social
victordit/NelmioApiDocBundle
Generates documentation for your REST API from annotations
victordit/Pombo-0.0.7
victordit/regenerate-catalog-urls
This extension adds console commands to be able to regenerate; a product rewrite URL based on its url path; a category rewrite URL based on its url path; a category URL path based on its URL key and its parent categories.
victordit/Sylius
eCommerce PHP framework built on top of Symfony with component-based architecture and format-agnostic rendering. (HTML/JSON/XML)
victordit/SyliusCmsPlugin
Content management system for eCommerce apps created on Sylius platform. Build with Sylius code quality, flexibility, BDD.
victordit/WaPoNe_StatusStaticBlocksManager
A Magento extension to schedule CMS blocks enabling/disabling
victordit/wmdlogincheck
The Login check control for Magento 1