Pinned Repositories
7d-mall-microservice
7d电商微服务-极客时间「高楼的性能工程实战课」专栏项目
ar
Autoregressive process modeling tools in header-only C++
Bear
Bear is a tool that generates a compilation database for clang tooling.
c99sh
A shebang-friendly script for "interpreting" single C99, C11, and C++ files, including rcfile support.
colmap
COLMAP - Structure-from-Motion and Multi-View Stereo
entt
Gaming meets modern C++ - a fast and reliable entity component system (ECS) and much more
ESIO
The ExaScale IO (ESIO) library provides simple, high throughput input and output of structured data sets using parallel HDF5. ESIO is designed to support reading and writing turbulence simulation restart files within C, C++, and modern Fortran applications.
Fastapi-jewels-tutorial
Repo for my youtube tutorial
fff
📁 A simple file manager written in bash.
gxb-core
GXChain Blockchain implementation
Tiancheng-Luo's Repositories
Tiancheng-Luo/Algorithms
A collection of algorithms and data structures
Tiancheng-Luo/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.
Tiancheng-Luo/bdwgc
The Boehm-Demers-Weiser conservative C/C++ Garbage Collector (libgc, bdwgc, boehm-gc)
Tiancheng-Luo/bmx-mode
Action-paced Windows Batch-file editing, powered by GNU Emacs!
Tiancheng-Luo/C-OOP-Concepts-Apply-C-OOP-Concepts-On-Real-C-Projects
Tiancheng-Luo/calcite-test
Test code for apache calcite
Tiancheng-Luo/convex_adversarial
A method for training neural networks that are provably robust to adversarial attacks.
Tiancheng-Luo/Cosette
Cosette is an automated SQL solver.
Tiancheng-Luo/CtCI-6th-Edition
Cracking the Coding Interview 6th Ed. Solutions
Tiancheng-Luo/diff-match-patch
Diff Match Patch is a high-performance library in multiple languages that manipulates plain text.
Tiancheng-Luo/easyexcel
快速、简单避免OOM的java处理Excel工具
Tiancheng-Luo/flagser
Computing homology of directed flag complexes (based on https://github.com/Ripser/ripser). Online version: https://homepages.abdn.ac.uk/neurotopology/flagser.html
Tiancheng-Luo/frames-only-mode
Make emacs play nicely with tiling window managers by setting it up to use frames rather than windows
Tiancheng-Luo/Java
All Algorithms implemented in Java
Tiancheng-Luo/libatomic_ops
The atomic_ops project (Atomic memory update operations portable implementation)
Tiancheng-Luo/libredblack
Copy of RedBlack Balanced Tree Searching and Sorting Library - http://libredblack.sourceforge.net/
Tiancheng-Luo/nanogui
Minimalistic C++/Python GUI library for OpenGL, GLES2/3, Metal, and WebAssembly/WebGL
Tiancheng-Luo/nginx-handbook-projects
Project codes used in "The NGINX Handbook"
Tiancheng-Luo/offline-wikipedia
Demo of how something like Wikipedia could be offline-first
Tiancheng-Luo/org-marginalia
Highlight text; write margin notes (marginalia) for any text files in a separate Org file
Tiancheng-Luo/pig
↥ ↥ ↥ 点击关注更新,基于 Spring Cloud 2020 、Spring Boot 2.4、 OAuth2 的 RBAC 权限管理系统
Tiancheng-Luo/regexgen
Generate regular expressions that match a set of strings
Tiancheng-Luo/ripser
Ripser: efficient computation of Vietoris–Rips persistence barcodes
Tiancheng-Luo/shell2http
Executing shell commands via HTTP server
Tiancheng-Luo/SmarterStreaming
业内为数不多致力于极致体验的超强全自研跨平台(windows/android/iOS)流媒体内核,通过模块化自由组合,支持实时RTMP推流、RTSP推流、RTMP播放器、RTSP播放器、录像、多路流媒体转发、音视频导播、动态视频合成、音频混音、直播互动、内置轻量级RTSP服务等,比快更快,业界真正靠谱的超低延迟直播SDK(1秒内,低延迟模式下200~400ms)。
Tiancheng-Luo/symbol-overlay
Highlight symbols with keymap-enabled overlays
Tiancheng-Luo/vscode-javadoc-tools
This is an extension for VSCode that allows user to generate javadoc comments for all methods within a class
Tiancheng-Luo/write-music
visualise sentence length
Tiancheng-Luo/wvp-GB28181
WEB VIDEO PLATFORM是一个基于GB28181-2016标准实现的网络视频平台,负责实现核心信令与设备管理后台部分,支持NAT穿透,支持海康、大华、宇视等品牌的IPC、NVR、DVR接入。 流媒体服务基于ZLMediaKit-https://github.com/xiongziliang/ZLMediaKit 前端展示基于MediaServerUI-https://gitee.com/kkkkk5G/MediaServerUI/tree/gb28181/
Tiancheng-Luo/yaku
A lightweight promise library