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ImageOptim / GifskiGIF encoder based on libimagequant (pngquant). Squeezes maximum possible quality from the awful GIF format.
NAalytics / Assemblies Of Putative SARS CoV2 Spike Encoding MRNA Sequences For Vaccines BNT 162b2 And MRNA 1273RNA 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.
facebookresearch / DenoiserReal Time Speech Enhancement in the Waveform Domain (Interspeech 2020)We provide a PyTorch implementation of the paper Real Time Speech Enhancement in the Waveform Domain. In which, we present a causal speech enhancement model working on the raw waveform that runs in real-time on a laptop CPU. The proposed model is based on an encoder-decoder architecture with skip-connections. It is optimized on both time and frequency domains, using multiple loss functions. Empirical evidence shows that it is capable of removing various kinds of background noise including stationary and non-stationary noises, as well as room reverb. Additionally, we suggest a set of data augmentation techniques applied directly on the raw waveform which further improve model performance and its generalization abilities.
mbzuai-oryx / Video ChatGPT[ACL 2024 🔥] Video-ChatGPT is a video conversation model capable of generating meaningful conversation about videos. It combines the capabilities of LLMs with a pretrained visual encoder adapted for spatiotemporal video representation. We also introduce a rigorous 'Quantitative Evaluation Benchmarking' for video-based conversational models.
bheinzerling / BpembPre-trained subword embeddings in 275 languages, based on Byte-Pair Encoding (BPE)
yuval-alaluf / Restyle EncoderOfficial Implementation for "ReStyle: A Residual-Based StyleGAN Encoder via Iterative Refinement" (ICCV 2021) https://arxiv.org/abs/2104.02699
antimatter15 / WhammyA real time javascript webm encoder based on a canvas hack
PrithivirajDamodaran / FlashRankLite & Super-fast re-ranking for your search & retrieval pipelines. Supports SoTA Listwise and Pairwise reranking based on LLMs and cross-encoders and more. Created by Prithivi Da, open for PRs & Collaborations.
hila-chefer / Transformer MM Explainability[ICCV 2021- Oral] Official PyTorch implementation for Generic Attention-model Explainability for Interpreting Bi-Modal and Encoder-Decoder Transformers, a novel method to visualize any Transformer-based network. Including examples for DETR, VQA.
evanw / KiwiA schema-based binary format for efficiently encoding trees of data
flatgeobuf / FlatgeobufA performant binary encoding for geographic data based on flatbuffers
webtorrent / Wormhole CryptoStreaming encryption for Wormhole.app, based on Encrypted Content-Encoding for HTTP (RFC 8188)
sinovation / ZENA BERT-based Chinese Text Encoder Enhanced by N-gram Representations
NightFurySL2001 / CJK Character CountProgram that counts the amount of CJK characters based on Unicode ranges and Chinese encoding standards 字体汉字计数软件
jinliming2 / Chrome CharsetAn extension used to modify the page default encoding for Chromium 55+ based browsers.
OpenVisualCloud / SVT HEVCSVT HEVC encoder. Scalable Video Technology (SVT) is a software-based video coding technology that is highly optimized for Intel® Xeon® processors. Using the open source SVT-HEVC encoder, it is possible to spread video encoding processing across multiple Intel® Xeon® processors to achieve a real advantage of processing efficiency.
oddity-ai / Video RsVideo readers, writers, muxers, encoders and decoders for Rust based on ffmpeg libraries.
facebookresearch / KeypointNeRFKeypointNeRF Generalizing Image-based Volumetric Avatars using Relative Spatial Encoding of Keypoints
nbadal / Android Gif EncoderAn animated GIF encoder for Android, without any native code required. Based on the J2ME encoder by Alessandro La Rosa with the addition of dirty rectangle support.
xplip / PixelResearch code for pixel-based encoders of language (PIXEL)
