Yuu Eguci's Projects
Want to practice angular-cli + SPA + MPA + i18n + import different external css files in each component.
Try to use Azure DevOps for free.
This app was made cuz I wanted to try to use pygame library. You can put floors and chairs. All graphics were what I made.
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 โ) 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 94โ, 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 5โ 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.
Create banks and their branches master.
Smt I modularized what I wanted to do before executing Python script.
๐ In this repository, I tried to study Bootstrap 5.1 and making calendar design without any libraries such as FullCalendar.
The repository that is for the bootstrap test on the GitHub Pages.
Tried to use Python web server library, bottle. Janken app.
๐ โ๏ธ Python 3.10 + Box + OAuth 2.0 Demonstration!
Wanna try Vue.js. What to make? Will reproduce Carsensor app's design with bootstrap. Why bootstrap? Well simple is the best.
Character making tool for CoC TRPG, using Python3 and tkinter.
Skype Bot for supporting CoC TRPG.
Try to play with Cognitive Services!! [Cognitive Services] [OpenCV] [Numpy]
This program posts Pull Request using api.github.com. It is worth using when you want to notify only about the PRs about project release.
๐ช This is my first cookiecutter that contains some files what I always prepare when making a new Python repository. The cookiecutter is now growing... I wish I can continuously upgrade it.
Cookie hockey uwp pie
Generic framework for making dialog plays. So enjoyed to create this.
Cassettes for dialog-framework.
โ๐ฝโ๐ฝ ๐ ๐ณ ๐ณ Python 3.10 + Django v4 + Yarn + Nuxt v2 + Nginx + Docker + GitHub Actions + CI/CD | Nuxt.js ใไฝฟใใฆใผใใ Django ใไฝฟใใฆใผใใฉใใตใผใใฏใตใใคใไฝฟใใใใญใผใใใ Nginx ใไฝฟใฃใฆ Django ใจ Nuxt.js ใๅใใกใคใณใง้
ไฟกใใใผใใใใจ Docker ใฏๅฝ็ถไฝฟใใใ
Docker Image for Redmine
๐ GitHub Actions ใไฝฟใฃใฆ ECR -> ECS ใใใญใคใใใใใ ๐ณ
My first GUI app, supporting effort leveling about Pokemon.
This app is what was remade Effort Leveling Support of tkinter, that was my first Python app, using Eel library.
๐ flower-stuff-easy-web project - back-end side. python, Django, json, tensorflow, flake8.
๐ณ Dev environment for flower-stuff-easy-web project. It starts Vue and Django projects in Docker containers.
๐ท flower-stuff-easy-web project - front-end side. vue, GitHub Pages, CI/CD, Standard JS.
๐ This repository was exported to python-mate organization. ๐ป FlowerStuff project; this repository is for experiment. This repository was constructed to enable each member be able to fetch other members' experiment results and to share them. And to each member be able to execute them on the Google Colaboratory.
๐ฏ Flutter + Dart ็ฅๆฅใฎๅฑฑใฎๆฅใซใใชใใจใชใไธๆฅใงใขใใชใใฃใไฝใฃใฆใฟใฃใใฃใฆใใชใงๅฎๆใใๆงๆ ผ่จบๆญ + ใชในในใกใฎใขใญใ็ฒพๆฒน้ธใณใขใใชใ iOS & Android