Li-rr's Stars
shadowsocks/shadowsocks-windows
A C# port of shadowsocks
afatcoder/LeetcodeTop
汇总各大互联网公司容易考察的高频leetcode题🔥
peng-zhihui/HoloCubic
带网络功能的伪全息透明显示桌面站
PaddlePaddle/VisualDL
Deep Learning Visualization Toolkit（『飞桨』深度学习可视化工具 ）
rbmonster/learning-note
Java开发及面试（个人面试、工作总结、资料收集站）
NAalytics/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.
letiantian/TextRank4ZH
:deciduous_tree:从中文文本中自动提取关键词和摘要
adambielski/siamese-triplet
Siamese and triplet networks with online pair/triplet mining in PyTorch
yscoder/hexo-theme-indigo
一个Material Design风格的Hexo主题。 https://imys.net/ 备用:
getActivity/EmojiPackage
表情包资源合集，张张都是经典
cweijan/vscode-database-client
Database Client For Visual Studio Code
DerwenAI/pytextrank
Python implementation of TextRank algorithms ("textgraphs") for phrase extraction
songyouwei/ABSA-PyTorch
Aspect Based Sentiment Analysis, PyTorch Implementations. 基于方面的情感分析，使用PyTorch实现。
zonechen1994/CV_Interview
I hope this repo can help you a lot!
Haojen/hexo-theme-Claudia
📌 Concisely designed & easy to config, match dark mode
datawhalechina/team-learning-program
主要存储Datawhale组队学习中“编程、数据结构与算法”方向的资料。
MenghaoGuo/EANet
External Attention Network
Duet3D/DuetWebControl
A completely new web interface for the Duet electronics
autoliuweijie/BERT-whitening-pytorch
Pytorch version of BERT-whitening
Xunzhuo/Coder
A fast、pure、practical、elegant Hexo theme for Developers 🔥🔥🔥
binzh303/spring-boot-route
Spring Boot 技术栈学习分享，涵盖了基础知识、Web开发、数据访问、缓存服务、消息队列、日志管理、服务监控、定时任务及其他的一些相关知识
dalinvip/Word_Similarity_and_Word_Analogy
Word Similarity and Word Analogy Task scripts
kavgan/opinosis-summarization
This repo contains code and dataset for the Opinosis Summarization Framework
zhangTianZeng/password-master
可视化界面，基于多线程，密码字典，暴力破解wifi和很多数据库
zhshuixian/learn-spring-boot-2
Spring Boot 2.X 实战笔记在线阅读
HSLCY/VCWE
VCWE: Visual Character-Enhanced Word Embeddings (NAACL 2019)
ChenDapengJava/JavaJourney
积小流以成江海，积跬步以至千里。Java基础，数据结构与算法，MySQL，Redis，ZooKeeper...总结与分享。
amanxu/spring-boot-transactions
基于rocketMQ的分布式事务
favitor/Python-Toon
Inspire by the toonme challenge, is a simple automate version.
iasolis418/toonME---Rowdyhacks-2021