Pinned Repositories
awesome-awesomeness
A curated list of awesome awesomeness
awesome-opensource-apps
:house::information_source: Curated list of awesome open source crafted web & mobile applications - Learn, Fork, Contribute & Most Importantly Enjoy!
awesome-wechat-weapp
微信小程序开发资源汇总 :100:
BluestNight
A dark theme with blue accents for Hugo. Provides multiple configuration options and overrides.
FeelUOwn
trying to be a user-friendly and hackable music player
GameCore
能快速开发出游戏的游戏引擎，本来是如鹏网的GameCore游戏引擎，我对它封装，便于自己用
learn-anything
Organize world's knowledge, explore connections and curate learning paths
Python-100-Days
Python - 100天从新手到大师
tuchang.github.io
tuchang's Repositories
tuchang/tuchang.github.io
tuchang/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.
tuchang/baiduyun-1
一个免费开源的网盘下载助手
tuchang/bean-of-the-wild
Remake of Rune game mechanics from The Legend of Zelda - Breath of The Wild
tuchang/build-your-own-x
🤓 Build your own (insert technology here)
tuchang/CnC_Remastered_Collection
tuchang/Communion
tuchang/copilot-docs
Documentation for GitHub Copilot
tuchang/CTF-All-In-One
CTF竞赛权威指南
tuchang/dailycheck
tuchang/eladmin
项目基于 Spring Boot 2.1.0 、 Jpa、 Spring Security、redis、Vue的前后端分离的后台管理系统，项目采用分模块开发方式， 权限控制采用 RBAC，支持数据字典与数据权限管理，支持一键生成前后端代码，支持动态路由
tuchang/fucking-algorithm
刷算法全靠套路，认准 labuladong 就够了！English version supported! Crack LeetCode, not only how, but also why.
tuchang/gallery
Flutter Gallery
tuchang/graph-note-of-greek-myth
希腊神话读书笔记
tuchang/halo
✍ An excellent open source blog publishing application. | 一个优秀的开源博客发布应用。
tuchang/lightweight-gan
Implementation of 'lightweight' GAN, proposed in ICLR 2021, in Pytorch. High resolution image generations that can be trained within a day or two
tuchang/logseq-graph-of-greek-myth
tuchang/MockingBird
🚀AI拟声: 5秒内克隆您的声音并生成任意语音内容 Clone a voice in 5 seconds to generate arbitrary speech in real-time
tuchang/open-event-frontend
The frontend for the Open Event API Server
tuchang/open-event-server
The Open Event Organizer Server to Manage Events http://open-event-api.herokuapp.com
tuchang/portfolio-template
A Web Developer Portfolio Template
tuchang/samples
A collection of Flutter examples and demos.
tuchang/SearchTT
Twitter crawler based on python
tuchang/spleeter
Deezer source separation library including pretrained models.
tuchang/spring-master-class
An updated introduction to the Spring Framework 5. Become an Expert understanding the core features of Spring In Depth. You would write Unit Tests, AOP, JDBC and JPA code during the course. Includes introductions to Spring Boot, JPA, Eclipse, Maven, JUnit and Mockito.
tuchang/system-design-primer
Learn how to design large-scale systems. Prep for the system design interview. Includes Anki flashcards.
tuchang/taichi
Parallel programming for everyone.
tuchang/vdhcoapp
Companion application for Video DownloadHelper browser add-on
tuchang/weh
Toolkit to save time when developing a browser add-on for Firefox, Chrome, Edge, Opera and Vivaldi
tuchang/widevinedump