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Masks, sanitizers, and social distancing gadgets: The COVID tech that dominated CES 2021

Mashable

With virtual booths and digital portals taking the place of convention center halls and showcases, CES in the time of coronavirus looked different. So did some of the tech. COVID-oriented tech products stood out at this year's CES. Some brands debuted new products made for the pandemic, others found that items they'd been working on all along now have newfound applications and relevance. But is "COVID tech" really necessary? After all, the best way to slow the spread of the virus is to practice social distancing and wear a face mask, which can be as simple as a bandana or a repurposed old T-shirt -- fundamentally low-tech strategies.


Returning as Intel CEO, prodigal son Pat Gelsinger faces daunting challenges

ZDNet

This week, Intel announced CEO Bob Swan will be replaced by VMware CEO Pat Gelsinger. Facing stronger competitive challenges, Intel has struggled. Recently, the company has come under pressure by activist investors to make significant changes. Wednesday brought one such change. Gelsinger is no stranger to Intel.


AIs that read sentences can also spot virus mutations

MIT Technology Review

In a study published in Science today, Berger and her colleagues pull several of these strands together and use NLP to predict mutations that allow viruses to avoid being detected by antibodies in the human immune system, a process known as viral immune escape. The basic idea is that the interpretation of a virus by an immune system is analogous to the interpretation of a sentence by a human. "It's a neat paper, building off the momentum of previous work," says Ali Madani, a scientist at Salesforce, who is using NLP to predict protein sequences. Berger's team uses two different linguistic concepts: grammar and semantics (or meaning). The genetic or evolutionary fitness of a virus--characteristics such as how good it is at infecting a host--can be interpreted in terms of grammatical correctness.


The language of a virus

Science

Uncovering connections between seemingly unrelated branches of science might accelerate research in one branch by using the methods developed in the other branch as stepping stones. On page 284 of this issue, Hie et al. ([ 1 ][1]) provide an elegant example of such unexpected connections. The authors have uncovered a parallel between the properties of a virus and its interpretation by the host immune system and the properties of a sentence in natural language and its interpretation by a human. By leveraging an extensive natural language processing (NLP) toolbox ([ 2 ][2], [ 3 ][3]) developed over the years, they have come up with a powerful new method for the identification of mutations that allow a virus to escape from recognition by neutralizing antibodies. In 1950, Alan Turing predicted that machines will eventually compete with men in “intellectual fields” and suggested that one possible way forward would be to build a machine that can be taught to understand and speak English ([ 4 ][4]). This was, and still is, an ambitious goal. It is clear that language grammar can provide a formal skeleton for building sentences, but how can machines be trained to infer the meanings? In natural language, there are many ways to express the same idea, and yet small changes in expression can often change the meaning. Linguistics developed a way of quantifying the similarity of meaning (semantics). Specifically, it was proposed that words that are used in the same context are likely to have similar meanings ([ 5 ][5], [ 6 ][6]). This distributional hypothesis became a key feature for the computational technique in NLP, known as word (semantic) embedding. The main idea is to characterize words as vectors that represent distributional properties in a large amount of language data and then embed these sparse, high-dimensional vectors into more manageable, low-dimensional space in a distance-preserving manner. By the distributional hypothesis, this technique should group words that have similar semantics together in the embedding space. Hie et al. proposed that viruses can also be thought to have a grammar and semantics. Intuitively, the grammar describes which sequences make specific viruses (or their parts). Biologically, a viral protein sequence should have all the properties needed to invade a host, multiply, and continue invading another host. Thus, in some way, the grammar represents the fitness of a virus. With enough data, current machine learning approaches can be used to learn this sequence-based fitness function. ![Figure][7] Predicting immune escape The constrained semantic change search algorithm obtains semantic embeddings of all mutated protein sequences using bidirectional long short-term memory (LSTM). The sequences are ranked according to the combined score of the semantic change (the distance of a mutation from the original sequence) and fitness (the probability that a mutation appears in viral sequences). GRAPHIC: V. ALTOUNIAN/SCIENCE But what would be the meaning (semantics) of a virus? Hie et al. suggested that the semantics of a virus should be defined in terms of its recognition by immune systems. Specifically, viruses with different semantics would require a different state of the immune system (for example, different antibodies) to be recognized. The authors hypothesized that semantic embeddings allow sequences that require different immune responses to be uncovered. In this context, words represent protein sequences (or protein fragments), and recognition of such protein fragments is the task performed by the immune system. To escape immune responses, viral genomes can become mutated so that the virus evolves to no longer be recognized by the immune system. However, a virus that acquires a mutation that compromises its function (and thus fitness) will not survive. Using the NLP analogy, immune escape will be achieved by the mutations that change the semantics of the virus while maintaining its grammaticality so that the virus will remain infectious but escape the immune system. On the basis of this idea, Hie et al. developed a new approach, called constrained semantic change search (CSCS). Computationally, the goal of CSCS is to identify mutations that confer high fitness and substantial semantic changes at the same time (see the figure). The immune escape scores are computed by combining the two quantities. The search algorithm builds on a powerful deep learning technique for language modeling, called long short-term memory (LSTM), to obtain semantic embeddings of all mutated sequences and rank the sequences according to their immune escape scores in the embedded space. The semantic changes correspond to the distance of the mutated sequences to the original sequence in the semantic embedding, and its “grammaticality” (or fitness) is estimated by the probability that the mutation appears in viral sequences. The immune escape scores can then be computed by simultaneously considering both the semantic distance and fitness probability. Hie et al. confirmed their hypothesis for the correspondence of grammaticality and semantics to fitness and immune response in three viral proteins: influenza A hemagglutinin (HA), HIV-1 envelope (Env), and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Spike. For the analogy of semantics to immune response, they found that clusters of semantically similar viruses were in good correspondence with virus subtypes, host, or both, confirming that the language model can extract functional meanings from protein sequences. The clustering patterns also revealed interspecies transmissibility and antigenic similarity. The correspondence of grammaticality to fitness was assessed more directly by using deep mutational scans evaluated for replication fitness (for HA and Env) or binding (for Spike). The combined model was tested against experimentally verified mutations that allow for immue escape. Scoring each amino acid residue with CSCS, the authors uncovered viral protein regions that are significantly enriched with escape potential: the head of HA for influenza, the V1/V2 hypervariable regions for HIV Env, and the receptor-binding domain (RBD) and amino-terminal domain for SARS-CoV-2 Spike. The language of viral evolution and escape proposed by Hie et al. provides a powerful framework for predicting mutations that lead to viral escape. However, interesting questions remain. Further extending the natural language analogy, it is notable that individuals can interpret the same English sentence differently depending on their past experience and the fluency in the language. Similarly, immune response differs between individuals depending on factors such as past pathogenic exposures and overall “strength” of the immune system. It will be interesting to see whether the proposed approach can be adapted to provide a “personalized” view of the language of virus evolution. 1. [↵][8]1. B. Hie, 2. E. Zhong, 3. B. Berger, 4. B. Bryson , Science 371, 284 (2021). [OpenUrl][9][Abstract/FREE Full Text][10] 2. [↵][11]1. L. Yann, 2. Y. Bengio, 3. G. Hinton , Nature 521, 436 (2015). [OpenUrl][12][CrossRef][13][PubMed][14] 3. [↵][15]1. T. Young, 2. D. Hazarika, 3. S. Poria, 4. E. Cambria , IEEE Comput. Intell. Mag. 13, 55 (2018). [OpenUrl][16] 4. [↵][17]1. A. Turing , Mind LIX, 433 (1950). 5. [↵][18]1. Z. S. Harris , Word 10, 146 (1954). [OpenUrl][19][CrossRef][20][PubMed][21] 6. [↵][22]1. J. R. Firth , in Studies in Linguistic Analysis (1957), pp. 1–32. Acknowledgments: The authors are supported by the Intramural Research Programs of the National Library of Medicine at the National Institutes of Health, USA. [1]: #ref-1 [2]: #ref-2 [3]: #ref-3 [4]: #ref-4 [5]: #ref-5 [6]: #ref-6 [7]: pending:yes [8]: #xref-ref-1-1 "View reference 1 in text" [9]: {openurl}?query=rft.jtitle%253DScience%26rft.stitle%253DScience%26rft.aulast%253DHie%26rft.auinit1%253DB.%26rft.volume%253D371%26rft.issue%253D6526%26rft.spage%253D284%26rft.epage%253D288%26rft.atitle%253DLearning%2Bthe%2Blanguage%2Bof%2Bviral%2Bevolution%2Band%2Bescape%26rft_id%253Dinfo%253Adoi%252F10.1126%252Fscience.abd7331%26rft.genre%253Darticle%26rft_val_fmt%253Dinfo%253Aofi%252Ffmt%253Akev%253Amtx%253Ajournal%26ctx_ver%253DZ39.88-2004%26url_ver%253DZ39.88-2004%26url_ctx_fmt%253Dinfo%253Aofi%252Ffmt%253Akev%253Amtx%253Actx [10]: /lookup/ijlink/YTozOntzOjQ6InBhdGgiO3M6MTQ6Ii9sb29rdXAvaWpsaW5rIjtzOjU6InF1ZXJ5IjthOjQ6e3M6ODoibGlua1R5cGUiO3M6NDoiQUJTVCI7czoxMToiam91cm5hbENvZGUiO3M6Mzoic2NpIjtzOjU6InJlc2lkIjtzOjEyOiIzNzEvNjUyNi8yODQiO3M6NDoiYXRvbSI7czoyMjoiL3NjaS8zNzEvNjUyNi8yMzMuYXRvbSI7fXM6ODoiZnJhZ21lbnQiO3M6MDoiIjt9 [11]: #xref-ref-2-1 "View reference 2 in text" [12]: {openurl}?query=rft.jtitle%253DNature%26rft.volume%253D521%26rft.spage%253D436%26rft_id%253Dinfo%253Adoi%252F10.1038%252Fnature14539%26rft_id%253Dinfo%253Apmid%252F26017442%26rft.genre%253Darticle%26rft_val_fmt%253Dinfo%253Aofi%252Ffmt%253Akev%253Amtx%253Ajournal%26ctx_ver%253DZ39.88-2004%26url_ver%253DZ39.88-2004%26url_ctx_fmt%253Dinfo%253Aofi%252Ffmt%253Akev%253Amtx%253Actx [13]: /lookup/external-ref?access_num=10.1038/nature14539&link_type=DOI [14]: /lookup/external-ref?access_num=26017442&link_type=MED&atom=%2Fsci%2F371%2F6526%2F233.atom [15]: #xref-ref-3-1 "View reference 3 in text" [16]: {openurl}?query=rft.jtitle%253DIEEE%2BComput.%2BIntell.%2BMag.%26rft.volume%253D13%26rft.spage%253D55%26rft.genre%253Darticle%26rft_val_fmt%253Dinfo%253Aofi%252Ffmt%253Akev%253Amtx%253Ajournal%26ctx_ver%253DZ39.88-2004%26url_ver%253DZ39.88-2004%26url_ctx_fmt%253Dinfo%253Aofi%252Ffmt%253Akev%253Amtx%253Actx [17]: #xref-ref-4-1 "View reference 4 in text" [18]: #xref-ref-5-1 "View reference 5 in text" [19]: {openurl}?query=rft.jtitle%253DWord%26rft.volume%253D10%26rft.spage%253D146%26rft_id%253Dinfo%253Adoi%252F10.1080%252F00437956.1954.11659520%26rft_id%253Dinfo%253Apmid%252F32513867%26rft.genre%253Darticle%26rft_val_fmt%253Dinfo%253Aofi%252Ffmt%253Akev%253Amtx%253Ajournal%26ctx_ver%253DZ39.88-2004%26url_ver%253DZ39.88-2004%26url_ctx_fmt%253Dinfo%253Aofi%252Ffmt%253Akev%253Amtx%253Actx [20]: /lookup/external-ref?access_num=10.1080/00437956.1954.11659520&link_type=DOI [21]: /lookup/external-ref?access_num=32513867&link_type=MED&atom=%2Fsci%2F371%2F6526%2F233.atom [22]: #xref-ref-6-1 "View reference 6 in text"


Phylodynamics for cell biologists

Science

Advances in experimental approaches for single-cell analysis allow in situ sequencing, genomic barcoding, and mapping of cell lineages within tissues and organisms. Large amounts of data have thus accumulated and present an analytical challenge. Stadler et al. recognized the need for conceptual and computational approaches to fully exploit these technological advances for the understanding of normal and disease states. The authors review ideas taken from phylodynamics of infectious disease and show how similar tree-building techniques can be applied to monitoring changes in somatic cell lineages for applications ranging from development and differentiation to cancer biology. Science , this issue p. [eaah6266][1] ### BACKGROUND The birth, death, and diversification of individuals are events that drive biological processes across all scales. This is true whether the individuals in question represent nucleic acids, cells, whole organisms, populations, or species. The ancestral relationships of individuals can be visualized as branching trees or phylogenies, which are long-established representations in the fields of evolution, ecology, and epidemiology. Molecular phylogenetics is the discipline concerned with the reconstruction of such trees from gene or genome sequence data. The shape and size of such phylogenies depend on the past birth and death processes that generated them, and in phylodynamics, mathematical models are used to infer and quantify the dynamical behavior of biological populations from ancestral relationships. New technological advances in genetics and cell biology have led to a growing body of data about the molecular state and ancestry of individual cells in multicellular organisms. Ideas from phylogenetics and phylodynamics are being applied to these data to investigate many questions in tissue formation and tumorigenesis. ### ADVANCES Trees offer a valuable framework for tracing cell division and change through time, beginning with individual ancestral stem cells or fertilized eggs and resulting in complex tissues, tumors, or whole organisms (see the figure). They also provide the basis for computational and statistical methods with which to analyze data from cell biology. Our Review explains how “tree-thinking” and phylodynamics can be beneficial to the interpretation of empirical data pertaining to the individual cells of multicellular organisms. We summarize some recent research questions in developmental and cancer biology and briefly introduce the new technologies that allow us to observe the spatiotemporal histories of cell division and change. We provide an overview of the various and sometimes confusing ways in which graphical models, based on or represented by trees, have been applied in cell biology. To provide conceptual clarity, we outline four distinct graphical representations of the history of cell division and differentiation in multicellular organisms. We highlight that cells from an organism cannot be always treated as statistically independent observations but instead are often correlated because of phylogenetic history, and we explain how this can cause difficulties when attempting to infer dynamical behavior from experimental single-cell data. We introduce simple ecological null models for cell populations and illustrate some potential pitfalls in hypothesis testing and the need for quantitative phylodynamic models that explicitly incorporate the dependencies caused by shared ancestry. ### OUTLOOK We expect the rapid growth in the number of cell-level phylogenies to continue, a trend enhanced by ongoing technological advances in cell lineage tracing, genomic barcoding, and in situ sequencing. In particular, we anticipate the generation of exciting datasets that combine phenotypic measurements for individual cells (such as through transcriptome sequencing) with high-resolution reconstructions of the ancestry of the sampled cells. These developments will offer new ways to study developmental, oncogenic, and immunological processes but will require new and appropriate conceptual and computational tools. We discuss how models from phylogenetics and phylodynamics will benefit the interpretation of the data sets generated in the foreseeable future and will aid the development of statistical tests that exploit, and are robust to, cell shared ancestry. We hope that our discussion will initiate the integration of cell-level phylodynamic approaches into experimental and theoretical studies of development, cancer, and immunology. We sketch out some of the theoretical advances that will be required to analyze complex spatiotemporal cell dynamics and encourage explorations of these new directions. Powerful new statistical and computational tools are essential if we are to exploit fully the wealth of new experimental data being generated in cell biology. ![Figure][2] Multicellular organisms develop from a single fertilized egg. The division, apoptosis, and differentiation of cells can be displayed in a development tree, with the fertilized egg being the root of the tree. The development of any particular tissue within an organism can be traced as a subtree of the full developmental tree. Subtrees that represent cancer tumors or B cell clones may exhibit rapid growth and genetic change. Here, we illustrate the developmental tree of a human and expand the subtree representing haematopoiesis (blood formation) in the bone marrow. Stem cells in the bone marrow differentiate, giving rise to the numerous blood cell types in humans. The structure of the tree that underlies haematopoiesis and the formation of all tissues is unclear. Phylogenetic and phylodynamic tools can help to describe and statistically explore questions about this cell differentiation process. Multicellular organisms are composed of cells connected by ancestry and descent from progenitor cells. The dynamics of cell birth, death, and inheritance within an organism give rise to the fundamental processes of development, differentiation, and cancer. Technical advances in molecular biology now allow us to study cellular composition, ancestry, and evolution at the resolution of individual cells within an organism or tissue. Here, we take a phylogenetic and phylodynamic approach to single-cell biology. We explain how “tree thinking” is important to the interpretation of the growing body of cell-level data and how ecological null models can benefit statistical hypothesis testing. Experimental progress in cell biology should be accompanied by theoretical developments if we are to exploit fully the dynamical information in single-cell data. [1]: /lookup/doi/10.1126/science.aah6266 [2]: pending:yes


Learning the language of viral evolution and escape

Science

Viral mutations that evade neutralizing antibodies, an occurrence known as viral escape, can occur and may impede the development of vaccines. To predict which mutations may lead to viral escape, Hie et al. used a machine learning technique for natural language processing with two components: grammar (or syntax) and meaning (or semantics) (see the Perspective by Kim and Przytycka). Three different unsupervised language models were constructed for influenza A hemagglutinin, HIV-1 envelope glycoprotein, and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike glycoprotein. Semantic landscapes for these viruses predicted viral escape mutations that produce sequences that are syntactically and/or grammatically correct but effectively different in semantics and thus able to evade the immune system. Science , this issue p. [284][1]; see also p. [233][2] The ability for viruses to mutate and evade the human immune system and cause infection, called viral escape, remains an obstacle to antiviral and vaccine development. Understanding the complex rules that govern escape could inform therapeutic design. We modeled viral escape with machine learning algorithms originally developed for human natural language. We identified escape mutations as those that preserve viral infectivity but cause a virus to look different to the immune system, akin to word changes that preserve a sentence’s grammaticality but change its meaning. With this approach, language models of influenza hemagglutinin, HIV-1 envelope glycoprotein (HIV Env), and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Spike viral proteins can accurately predict structural escape patterns using sequence data alone. Our study represents a promising conceptual bridge between natural language and viral evolution. [1]: /lookup/doi/10.1126/science.abd7331 [2]: /lookup/doi/10.1126/science.abf6894


Samsung launches new flagship Galaxy S21 range

Daily Mail - Science & tech

Samsung has unveiled its latest range of flagship smartphones, with three models ranging in price from £769 ($799) to £1,149 ($1,199). The S21 range from the South Korean tech giant features an entry-level model, the mid-range Plus, and the Ultra – which is the first S Series phone to be compatible with the Samsung's S-Pen stylus. The stand-out feature on all three devices is the upgraded rear camera system, which was heavily leaked ahead of today's announcement and features night and portrait mode as well as its 100x'space zoom'. Pre-orders of the handsets open today, and the phones will be available as of January 29. The Ultra also comes with S-pen compatibility, the first Galaxy device to do so.


These five AI developments will shape 2021 and beyond

MIT Technology Review

The year 2020 was profoundly challenging for citizens, companies, and governments around the world. As covid-19 spread, requiring far-reaching health and safety restrictions, artificial intelligence (AI) applications played a crucial role in saving lives and fostering economic resilience. Research and development (R&D) to enhance core AI capabilities, from autonomous driving and natural language processing to quantum computing, continued unabated. Baidu was at the forefront of many important AI breakthroughs in 2020. This article outlines five significant advances with implications for combating covid-19 as well as transforming the future of our economies and society.


Check your health at the door: This high-tech doorbell shown at CES 2021 can check your temperature

USATODAY - Tech Top Stories

A new doorbell shown at CES 2021 does more than capture an image of who's at your front step: it will also check whether they have a fever. The makers of the Ettie claim the device is the first video doorbell that combines temperature checks, image recording and real-time alerts. The doorbell uses a built-in infrared sensor to check a visitor's temperature, then logs the data along with their image, date and time to a corresponding app. Plott, the company behind the app, says the doorbell can help with contact tracing amid the COVID-19 pandemic. It is also capable of tracking headcount and will alert users if they've reached peak capacity in a space. The doorbell is slated to launch later in 2021 at a price of $300.


Forehead scanners result in a large number of false, study warns

Daily Mail - Science & tech

Thermal screening to spot people infected with coronavirus is more reliable when scanning the eyeball and fingertip than taking body or forehead measurements. Experts in human physiology published a scientific article on the usefulness of thermometers which scan a person's skin to detect a fever. They say the current process is fundamentally flawed and produces a large number of false negatives, as well as some false positives, and also because not all people infected with the coronavirus develop a fever. A fever is defined as a temperature of greater than or equal to 100.4F (38 C) if spotted outside of a healthcare environment. In healthcare settings, such as a hospital, a fever is technically defined as anything greater than or equal to 100.0F (37.8 C).