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  • 1
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    Annual Reviews
    In:  EPIC3Annual Review of Marine Science, Annual Reviews, 16(1), pp. 513-536, ISSN: 1941-1405
    Publication Date: 2024-01-31
    Description: 〈jats:p〉 For decades, multiple-driver/stressor research has examined interactions among drivers that will undergo large changes in the future: temperature, pH, nutrients, oxygen, pathogens, and more. However, the most commonly used experimental designs—present-versus-future and ANOVA—fail to contribute to general understanding or predictive power. Linking experimental design to process-based mathematical models would help us predict how ecosystems will behave in novel environmental conditions. We review a range of experimental designs and assess the best experimental path toward a predictive ecology. Full factorial response surface, fractional factorial, quadratic response surface, custom, space-filling, and especially optimal and sequential/adaptive designs can help us achieve more valuable scientific goals. Experiments using these designs are challenging to perform with long-lived organisms or at the community and ecosystem levels. But they remain our most promising path toward linking experiments and theory in multiple-driver research and making accurate, useful predictions. 〈/jats:p〉
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , peerRev
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  • 2
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    Annual Reviews
    In:  EPIC3Annual Review of Marine Science, Annual Reviews, 16(1), pp. 417-441, ISSN: 1941-1405
    Publication Date: 2024-03-01
    Description: The genus Phaeocystis is globally distributed, with blooms commonly occurring on continental shelves. This unusual phytoplankter has two major morphologies: solitary cells and cells embedded in a gelatinous matrix. Only colonies form blooms. Their large size (commonly 2 mm but up to 3 cm) and mucilaginous envelope allow the colonies to escape predation, but data are inconsistent as to whether colonies are grazed. Cultured Phaeocystis can also inhibit the growth of co-occurring phytoplankton or the feeding of potential grazers. Colonies and solitary cells use nitrate as a nitrogen source, although solitary cells can also grow on ammonium. Phaeocystis colonies might be a major contributor to carbon flux to depth, but in most cases, colonies are rapidly remineralized in the upper 300 m. The occurrence of large Phaeocystis blooms is often associated with environments with low and highly variable light and high nitrate levels, with Phaeocystis antarctica blooms being linked additionally to high iron availability. Emerging results indicate that different clones of Phaeocystis have substantial genetic plasticity, which may explain its appearance in a variety of environments. Given the evidence of Phaeocystis appearing in new systems, this trend will likely continue in the near future.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , peerRev
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  • 3
    Publication Date: 2023-02-28
    Description: © The Author(s), 2023. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Timmermans, M.-L., & Toole, J. The Arctic Ocean’s Beaufort Gyre. Annual Review of Marine Science, 15(1), (2023): 223-248, https://doi.org/10.1146/annurev-marine-032122-012034.
    Description: The Arctic Ocean's Beaufort Gyre is a dominant feature of the Arctic system, a prominent indicator of climate change, and possibly a control factor for high-latitude climate. The state of knowledge of the wind-driven Beaufort Gyre is reviewed here, including its forcing, relationship to sea-ice cover, source waters, circulation, and energetics. Recent decades have seen pronounced change in all elements of the Beaufort Gyre system. Sea-ice losses have accompanied an intensification of the gyre circulation and increasing heat and freshwater content. Present understanding of these changes is evaluated, and time series of heat and freshwater content are updated to include the most recent observations.
    Description: Support was provided by the National Science Foundation Office of Polar Programs and the Office of Naval Research.
    Keywords: Arctic Ocean ; Beaufort Gyre ; Circulation ; Sea ice ; Freshwater ; Ocean heat content
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 4
    Publication Date: 2022-10-27
    Description: This paper is not subject to U.S. copyright. The definitive version was published in Sherwood, C. R., van Dongeren, A., Doyle, J., Hegermiller, C. A., Hsu, T.-J., Kalra, T. S., Olabarrieta, M., Penko, A. M., Rafati, Y., Roelvink, D., van der Lugt, M., Veeramony, J., & Warner, J. C. Modeling the morphodynamics of coastal responses to extreme events: what shape are we in? Annual Review of Marine Science, 14, (2022): 457–492, https://doi.org/10.1146/annurev-marine-032221-090215.
    Description: This review focuses on recent advances in process-based numerical models of the impact of extreme storms on sandy coasts. Driven by larger-scale models of meteorology and hydrodynamics, these models simulate morphodynamics across the Sallenger storm-impact scale, including swash,collision, overwash, and inundation. Models are becoming both wider (as more processes are added) and deeper (as detailed physics replaces earlier parameterizations). Algorithms for wave-induced flows and sediment transport under shoaling waves are among the recent developments. Community and open-source models have become the norm. Observations of initial conditions (topography, land cover, and sediment characteristics) have become more detailed, and improvements in tropical cyclone and wave models provide forcing (winds, waves, surge, and upland flow) that is better resolved and more accurate, yielding commensurate improvements in model skill. We foresee that future storm-impact models will increasingly resolve individual waves, apply data assimilation, and be used in ensemble modeling modes to predict uncertainties.
    Description: All authors except D.R. were partially supported by the IFMSIP project, funded by US Office of Naval Research grant PE 0601153N under contracts N00014-17-1-2459 (Deltares), N00014-18-1-2785 (University of Delaware), N0001419WX00733 (US Naval Research Laboratory, Monterey), N0001418WX01447 (US Naval Research Laboratory, Stennis Space Center), and N0001418IP00016 (US Geological Survey). C.R.S., C.A.H., T.S.K., and J.C.W. were supported by the US Geological Survey Coastal/Marine Hazards and Resources Program. A.v.D. and M.v.d.L. were supported by the Deltares Strategic Research project Quantifying Flood Hazards and Impacts. M.O. acknowledges support from National Science Foundation project OCE-1554892.
    Keywords: Coastal morphodynamics ; Extreme storms ; Coastal modeling ; Sandy coasts ; Waves ; Sediment transport
    Repository Name: Woods Hole Open Access Server
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  • 5
    Publication Date: 2024-02-07
    Description: Organic matter (OM) plays a significant role in the formation of oxygen minimum zones (OMZs) and associated biogeochemical cycling. OM supply processes to the OMZ include physical transport, particle formation, and sinking as well as active transport by migrating zooplankton and nekton. In addition to the availability of oxygen and other electron acceptors, the remineralization rate of OM is controlled by its biochemical quality. Enhanced microbial respiration of OM can induce anoxic microzones in an otherwise oxygenated water column. Reduced OM degradation under low-oxygen conditions, on the other hand, may increase the CO2 storage time in the ocean. Understanding the interdependencies between OM and oxygen cycling is of high relevance for an ocean facing deoxygenation as a consequence of global warming. In this review, we describe OM fluxes into and cycling within two large OMZs associated with eastern boundary upwelling systems that differ greatly in the extent of oxygen loss: the highly oxygen-depleted OMZ in the tropical South Pacific and the moderately hypoxic OMZ in the tropical North Atlantic. We summarize new findings from a large German collaborative research project, Collaborative Research Center 754 (SFB 754), and identify knowledge gaps and future research priorities.
    Type: Article , PeerReviewed , info:eu-repo/semantics/article
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  • 6
    Publication Date: 2024-02-07
    Description: The colonization of land by plants generated opportunities for the rise of new heterotrophic life forms, including humankind. A unique event underpinned this massive change to earth ecosystems-the advent of eukaryotic green algae. Today, an abundant marine green algal group, the prasinophytes, alongside prasinodermophytes and nonmarine chlorophyte algae, is facilitating insights into plant developments. Genome-level data allow identification of conserved proteins and protein families with extensive modifications, losses, or gains and expansion patterns that connect to niche specialization and diversification. Here, we contextualize attributes according to Viridiplantae evolutionary relationships, starting with orthologous protein families, and then focusing on key elements with marked differentiation, resulting in patchy distributions across green algae and plants. We place attention on peptidoglycan biosynthesis, important for plastid division and walls; phytochrome photosensors that are master regulators in plants; and carbohydrate-active enzymes, essential to all manner of carbohydratebiotransformations. Together with advances in algal model systems, these areas are ripe for discovering molecular roles and innovations within and across plant and algal lineages
    Type: Article , PeerReviewed
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  • 7
    Publication Date: 2021-08-20
    Description: Species tree estimation is a basic part of many biological research projects, ranging from answering basic evolutionary questions (e.g., how did a group of species adapt to their environments?) to addressing questions in functional biology. Yet, species tree estimation is very challenging, due to processes such as incomplete lineage sorting, gene duplication and loss, horizontal gene transfer, and hybridization, which can make gene trees differ from each other and from the overall evolutionary history of the species. Over the last 10–20 years, there has been tremendous growth in methods and mathematical theory for estimating species trees and phylogenetic networks, and some of these methods are now in wide use. In this survey, we provide an overview of the current state of the art, identify the limitations of existing methods and theory, and propose additional research problems and directions. Expected final online publication date for the Annual Review of Ecology, Evolution, and Systematics, Volume 52 is November 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    Print ISSN: 1543-592X
    Electronic ISSN: 1545-2069
    Topics: Biology
    Published by Annual Reviews
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  • 8
    Publication Date: 2021-08-20
    Description: In this article, we review the nascent literature on the transmission of negative policy rates. We discuss the theory of how the transmission depends on bank balance sheets, and how this changes once policy rates become negative. We review the growing evidence that negative policy rates are special because the pass-through to banks’ retail deposit rates is hindered by a zero lower bound. We summarize existing research on the impact of negative rates on banks’ lending and securities portfolios as well as their consequences for the real economy. Finally, we discuss the role of different initial conditions when the policy rate becomes negative, and potential interactions between negative policy rates and other unconventional monetary policies. Expected final online publication date for the Annual Review of Financial Economics, Volume 13 is November 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    Print ISSN: 1941-1367
    Electronic ISSN: 1941-1375
    Topics: Economics
    Published by Annual Reviews
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  • 9
    Publication Date: 2021-08-20
    Description: Bacterial stress-signaling alarmones are important components of a protective network against diverse stresses such as nutrient starvation and antibiotic assault. pppGpp and ppGpp, collectively (p)ppGpp, have well-documented regulatory roles in gene expression and protein translation. Recent work has highlighted another key function of (p)ppGpp: inducing rapid and coordinated changes in cellular metabolism by regulating enzymatic activities, especially those involved in purine nucleotide synthesis. Failure of metabolic regulation by (p)ppGpp results in the loss of coordination between metabolic and macromolecular processes, leading to cellular toxicity. In this review, we document how (p)ppGpp and newly characterized nucleotides pGpp and (p)ppApp directly regulate these enzymatic targets for metabolic remodeling. We examine targets’ common determinants for alarmone interaction as well as their evolutionary diversification. We highlight classical and emerging themes in nucleotide signaling, including oligomerization and allostery along with metabolic interconversion and crosstalk, illustrating how they allow optimized bacterial adaptation to their environmental niches. Expected final online publication date for the Annual Review of Genetics, Volume 55 is November 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    Print ISSN: 0066-4197
    Electronic ISSN: 1545-2948
    Topics: Biology
    Published by Annual Reviews
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  • 10
    Publication Date: 2021-08-20
    Description: The large-scale dynamics of ocean oxygenation have changed dramatically throughout Earth's history, in step with major changes in the abundance of O2 in the atmosphere and changes to marine nutrient availability. A comprehensive mechanistic understanding of this history requires insights from oceanography, marine geology, geochemistry, geomicrobiology, evolutionary ecology, and Earth system modeling. Here, we attempt to synthesize the major features of evolving ocean oxygenation on Earth through more than 3 billion years of planetary history. We review the fundamental first-order controls on ocean oxygen distribution and summarize the current understanding of the history of ocean oxygenation on Earth from empirical and theoretical perspectives—integrating geochemical reconstructions of oceanic and atmospheric chemistry, genomic constraints on evolving microbial metabolism, and mechanistic biogeochemical models. These changes are used to illustrate primary regimes of large-scale ocean oxygenation and to highlight feedbacks that can act to stabilize and destabilize the ocean–atmosphere system in anoxic, low-oxygen, and high-oxygen states. Expected final online publication date for the Annual Review of Marine Science, Volume 14 is January 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    Print ISSN: 1941-1405
    Electronic ISSN: 1941-0611
    Topics: Biology , Geosciences
    Published by Annual Reviews
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  • 11
    Publication Date: 2021-08-20
    Description: The SUP05 clade of gammaproteobacteria (Thioglobaceae) comprises both primary producers and primary consumers of organic carbon in the oceans. Host-associated autotrophs are a principal source of carbon and other nutrients for deep-sea eukaryotes at hydrothermal vents, and their free-living relatives are a primary source of organic matter in seawater at vents and in marine oxygen minimum zones. Similar to other abundant marine heterotrophs, such as SAR11 and Roseobacter, heterotrophic Thioglobaceae use the dilute pool of osmolytes produced by phytoplankton for growth, including methylated amines and sulfonates. Heterotrophic members are common throughout the ocean, and autotrophic members are abundant at hydrothermal vents and in anoxic waters; combined, they can account for more than 50% of the total bacterial community. Studies of both cultured and uncultured representatives from this diverse family are providing novel insights into the shifting biogeochemical roles of autotrophic and heterotrophic bacteria that cross oxic–anoxic boundary layers in the ocean. Expected final online publication date for the Annual Review of Marine Science, Volume 14 is January 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    Print ISSN: 1941-1405
    Electronic ISSN: 1941-0611
    Topics: Biology , Geosciences
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  • 12
    Publication Date: 2021-08-20
    Description: Beyond the better-studied carbohydrates and the macronutrients nitrogen and phosphorus, a remaining 20 or so elements are essential for life and have distinct geographical distributions, making them of keen interest to ecologists. Here, I provide a framework for understanding how shortfalls in micronutrients like iodine, copper, and zinc can regulate individual fitness, abundance, and ecosystem function. With a special focus on sodium, I show how simple experiments manipulating biogeochemistry can reveal why many of the variables that ecologists study vary so dramatically from place to place. I conclude with a discussion of how the Anthropocene's changing temperature, precipitation, and atmospheric CO2 levels are contributing to nutrient dilution (decreases in the nutrient quality at the base of food webs). Expected final online publication date for the Annual Review of Ecology, Evolution, and Systematics, Volume 52 is November 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    Print ISSN: 1543-592X
    Electronic ISSN: 1545-2069
    Topics: Biology
    Published by Annual Reviews
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  • 13
    Publication Date: 2021-08-20
    Description: A key Earth system science question is the role of atmospheric deposition in supplying vital nutrients to the phytoplankton that form the base of marine food webs. Industrial and vehicular pollution, wildfires, volcanoes, biogenic debris, and desert dust all carry nutrients within their plumes throughout the globe. In remote ocean ecosystems, aerosol deposition represents an essential new source of nutrients for primary production. The large spatiotemporal variability in aerosols from myriad sources combined with the differential responses of marine biota to changing fluxes makes it crucially important to understand where, when, and how much nutrients from the atmosphere enter marine ecosystems. This review brings together existing literature, experimental evidence of impacts, and new atmospheric nutrient observations that can be compared with atmospheric and ocean biogeochemistry modeling. We evaluate the contribution and spatiotemporal variability of nutrient-bearing aerosols from desert dust, wildfire, volcanic, and anthropogenic sources, including the organic component, deposition fluxes, and oceanic impacts. Expected final online publication date for the Annual Review of Marine Science, Volume 14 is January 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    Print ISSN: 1941-1405
    Electronic ISSN: 1941-0611
    Topics: Biology , Geosciences
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  • 14
    Publication Date: 2021-08-20
    Description: When a phenological shift affects a demographic vital rate such as survival or reproduction, the altered vital rate may or may not have population-level consequences. We review the evidence that climate change affects populations by shifting species’ phenologies, emphasizing the importance of demographic life-history theory. We find many examples of phenological shifts having both positive and negative consequences for vital rates. Yet, few studies link phenological shifts to changes in vital rates known to drive population dynamics, especially in plants. When this link is made, results are largely consistent with life-history theory: Phenological shifts have population-level consequences when they affect survival in longer-lived organisms and reproduction in shorter-lived organisms. However, there are just as many cases in which demographic mechanisms buffer population growth from phenologically induced changes in vital rates. We provide recommendations for future research aiming to understand the complex relationships among climate, phenology, and demography, which will help to elucidate the extent to which phenological shifts actually alter population persistence. Expected final online publication date for the Annual Review of Ecology, Evolution, and Systematics, Volume 52 is November 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    Print ISSN: 1543-592X
    Electronic ISSN: 1545-2069
    Topics: Biology
    Published by Annual Reviews
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  • 15
    Publication Date: 2021-08-20
    Description: Marine ecosystems are increasingly impacted by global environmental changes, including warming temperatures, deoxygenation, and ocean acidification. Marine scientists recognize intuitively that these environmental changes are translated into community changes via organismal physiology. However, physiology remains a black box in many ecological studies, and coexisting species in a community are often assumed to respond similarly to environmental stressors. Here, we emphasize how greater attention to physiology can improve our ability to predict the emergent effects of ocean change. In particular, understanding shifts in the intensity and outcome of species interactions such as competition and predation requires a sharpened focus on physiological variation among community members and the energetic demands and trophic mismatches generated by environmental changes. Our review also highlights how key species interactions that are sensitive to environmental change can operate as ecological leverage points through which small changes in abiotic conditions are amplified into large changes in marine ecosystems. Expected final online publication date for the Annual Review of Marine Science, Volume 14 is January 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    Print ISSN: 1941-1405
    Electronic ISSN: 1941-0611
    Topics: Biology , Geosciences
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  • 16
    Publication Date: 2021-08-20
    Description: CRISPR-Cas adaptive immune systems in bacteria and archaea utilize short CRISPR RNAs (crRNAs) to guide sequence-specific recognition and clearance of foreign genetic material. Multiple crRNAs are stored together in a compact format called a CRISPR array that is transcribed and processed into the individual crRNAs. While the exact processing mechanisms vary widely, some CRISPR-Cas systems, including those encoding the Cas9 nuclease, rely on a trans-activating crRNA (tracrRNA). The tracrRNA was discovered in 2011 and was quickly co-opted to create single-guide RNAs as core components of CRISPR-Cas9 technologies. Since then, further studies have uncovered processes extending beyond the traditional role of tracrRNA in crRNA biogenesis, revealed Cas nucleases besides Cas9 that are dependent on tracrRNAs, and established new applications based on tracrRNA engineering. In this review, we describe the biology of the tracrRNA and how its ongoing characterization has garnered new insights into prokaryotic immune defense and enabled key technological advances. Expected final online publication date for the Annual Review of Genetics, Volume 55 is November 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    Print ISSN: 0066-4197
    Electronic ISSN: 1545-2948
    Topics: Biology
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  • 17
    Publication Date: 2021-08-20
    Description: A small subset of marine microbial enzymes and surface transporters have a disproportionately important influence on the cycling of carbon and nutrients in the global ocean. As a result, they largely determine marine biological productivity and have been the focus of considerable research attention from microbial oceanographers. Like all biological catalysts, the activity of these keystone biomolecules is subject to control by temperature and pH, leaving the crucial ecosystem functions they support potentially vulnerable to anthropogenic environmental change. We summarize and discuss both consensus and conflicting evidence on the effects of sea surface warming and ocean acidification for five of these critical enzymes [carbonic anhydrase, ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO), nitrogenase, nitrate reductase, and ammonia monooxygenase] and one important transporter (proteorhodopsin). Finally, we forecast how the responses of these few but essential biocatalysts to ongoing global change processes may ultimately help to shape the microbial communities and biogeochemical cycles of the future greenhouse ocean. Expected final online publication date for the Annual Review of Marine Science, Volume 14 is January 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    Print ISSN: 1941-1405
    Electronic ISSN: 1941-0611
    Topics: Biology , Geosciences
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  • 18
    Publication Date: 2021-08-20
    Description: State-owned investors (SOIs), including sovereign wealth funds and public pension funds, have $27 trillion in assets under management in 2020, making these funds the third largest group of asset owners globally. SOIs have become the largest and are among the most important private equity investors, and they are key investors in other alternative asset investments such as real estate, infrastructure, and hedge funds. SOIs are also leaders in promoting environmental, social, and governance policies and corporate social responsibility policies in investee companies. We document the rise of SOIs, assess their current investment policies, and describe how their state ownership both constrains and enhances their investment opportunity sets. We survey the most impactful recent academic research on sovereign wealth funds, public pension funds, and their closest financial analogs, private pension funds. We also introduce a new Governance-Sustainability-Resilience Scoreboard for SOIs and survey research examining their role in promoting good corporate governance. Expected final online publication date for the Annual Review of Financial Economics, Volume 13 is November 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    Print ISSN: 1941-1367
    Electronic ISSN: 1941-1375
    Topics: Economics
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  • 19
    Publication Date: 2021-08-20
    Description: With the discovery of the incredible diversity of neurons, Cajal and coworkers laid the foundation of modern neuroscience. Neuron types are not only structural units of nervous systems but also evolutionary units, because their identities are encoded in the genome. With the advent of high-throughput cellular transcriptomics, neuronal identities can be characterized and compared systematically across species. The comparison of neurons in mammals, reptiles, and birds indicates that the mammalian cerebral cortex is a mosaic of deeply conserved and recently evolved neuron types. Using the cerebral cortex as a case study, this review illustrates how comparing neuron types across species is key to reconciling observations on neural development, neuroanatomy, circuit wiring, and physiology for an integrated understanding of brain evolution. Expected final online publication date for the Annual Review of Cell and Developmental Biology, Volume 37 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    Print ISSN: 1081-0706
    Electronic ISSN: 1530-8995
    Topics: Biology , Medicine
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  • 20
    Publication Date: 2021-08-20
    Description: A statistical model is a class of probability distributions assumed to contain the true distribution generating the data. In parametric models, the distributions are indexed by a finite-dimensional parameter characterizing the scientific question of interest. Semiparametric models describe the distributions in terms of a finite-dimensional parameter and an infinite-dimensional component, offering more flexibility. Ordinarily, the statistical model represents distributions for the full data intended to be collected. When elements of these full data are missing, the goal is to make valid inference on the full-data-model parameter using the observed data. In a series of fundamental works, Robins, Rotnitzky, and colleagues derived the class of observed-data estimators under a semiparametric model assuming that the missingness mechanism is at random, which leads to practical, robust methodology for many familiar data-analytic challenges. This article reviews semiparametric theory and the key steps in this derivation. Expected final online publication date for the Annual Review of Statistics, Volume 9 is March 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    Print ISSN: 2326-8298
    Electronic ISSN: 2326-831X
    Topics: Mathematics
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  • 21
    Publication Date: 2021-08-20
    Description: For centuries, mathematicians and, later, statisticians, have found natural research and employment opportunities in the realm of insurance. By definition, insurance offers financial cover against unforeseen events that involve an important component of randomness, and consequently, probability theory and mathematical statistics enter insurance modeling in a fundamental way. In recent years, a data deluge, coupled with ever-advancing information technology and the birth of data science, has revolutionized or is about to revolutionize most areas of actuarial science as well as insurance practice. We discuss parts of this evolution and, in the case of non-life insurance, show how a combination of classical tools from statistics, such as generalized linear models and, e.g., neural networks contribute to better understanding and analysis of actuarial data. We further review areas of actuarial science where the cross fertilization between stochastics and insurance holds promise for both sides. Of course, the vastness of the field of insurance limits our choice of topics; we mainly focus on topics closer to our main areas of research. Expected final online publication date for the Annual Review of Statistics, Volume 9 is March 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    Print ISSN: 2326-8298
    Electronic ISSN: 2326-831X
    Topics: Mathematics
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  • 22
    Publication Date: 2021-08-20
    Description: Aging is a major risk factor for multiple diseases. Understanding the underlying mechanisms of aging would help to delay and prevent age-associated diseases. Short-lived model organisms have been extensively used to study the mechanisms of aging. However, these short-lived species may be missing the longevity mechanisms that are needed to extend the lifespan of an already long-lived species such as humans. Unconventional long-lived animal species are an excellent resource to uncover novel mechanisms of longevity and disease resistance. Here, we review mechanisms that evolved in nonmodel vertebrate species to counteract age-associated diseases. Some antiaging mechanisms are conserved across species; however, various nonmodel species also evolved unique mechanisms to delay aging and prevent disease. This variety of antiaging mechanisms has evolved due to the remarkably diverse habitats and behaviors of these species. We propose that exploring a wider range of unconventional vertebrates will provide important resources to study antiaging mechanisms that are potentially applicable to humans. Expected final online publication date for the Annual Review of Genetics, Volume 55 is November 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    Print ISSN: 0066-4197
    Electronic ISSN: 1545-2948
    Topics: Biology
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  • 23
    Publication Date: 2021-08-20
    Description: Studies of cetacean evolution using genetics and other biomolecules have come a long way—from the use of allozymes and short sequences of mitochondrial or nuclear DNA to the assembly of full nuclear genomes and characterization of proteins and lipids. Cetacean research has also advanced from using only contemporary samples to analyzing samples dating back thousands of years, and to retrieving data from indirect environmental sources, including water or sediments. Combined, these studies have profoundly deepened our understanding of the origin of cetaceans; their adaptation and speciation processes; and of the past population change, migration, and admixture events that gave rise to the diversity of cetaceans found today. Expected final online publication date for the Annual Review of Ecology, Evolution, and Systematics, Volume 52 is November 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    Print ISSN: 1543-592X
    Electronic ISSN: 1545-2069
    Topics: Biology
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  • 24
    Publication Date: 2021-08-20
    Description: Many large marine predators make excursions from surface waters to the deep ocean below 200 m. Moreover, the ability to access meso- and bathypelagic habitats has evolved independently across marine mammals, reptiles, birds, teleost fishes, and elasmobranchs. Theoretical and empirical evidence suggests a number of plausible functional hypotheses for deep-diving behavior. Developing ways to test among these hypotheses will, however, require new ways to quantify animal behavior and biophysical oceanographic processes at coherent spatiotemporal scales. Current knowledge gaps include quantifying ecological links between surface waters and mesopelagic habitats and the value of ecosystem services provided by biomass in the ocean twilight zone. Growing pressure for ocean twilight zone fisheries creates an urgent need to understand the importance of the deep pelagic ocean to large marine predators. Expected final online publication date for the Annual Review of Marine Science, Volume 14 is January 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    Print ISSN: 1941-1405
    Electronic ISSN: 1941-0611
    Topics: Biology , Geosciences
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  • 25
    Publication Date: 2021-03-30
    Description: The faithful and timely copying of DNA by molecular machines known as replisomes depends on a disparate suite of enzymes and scaffolding factors working together in a highly orchestrated manner. Large, dynamic protein–nucleic acid assemblies that selectively morph between distinct conformations and compositional states underpin this critical cellular process. In this article, we discuss recent progress outlining the physical basis of replisome construction and progression in eukaryotes. Expected final online publication date for the Annual Review of Biochemistry, Volume 90 is June 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    Print ISSN: 0066-4154
    Electronic ISSN: 1545-4509
    Topics: Biology , Chemistry and Pharmacology
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  • 26
    Publication Date: 2021-03-29
    Description: Microbiomes are complex and ubiquitous networks of microorganisms whose seemingly limitless chemical transformations could be harnessed to benefit agriculture, medicine, and biotechnology. The spatial and temporal changes in microbiome composition and function are influenced by a multitude of molecular and ecological factors. This complexity yields both versatility and challenges in designing synthetic microbiomes and perturbing natural microbiomes in controlled, predictable ways. In this review, we describe factors that give rise to emergent spatial and temporal microbiome properties and the meta-omics and computational modeling tools that can be used to understand microbiomes at the cellular and system levels. We also describe strategies for designing and engineering microbiomes to enhance or build novel functions. Throughout the review,we discuss key knowledge and technology gaps for elucidating the networks and deciphering key control points for microbiome engineering, and highlight examples where multiple omics and modeling approaches can be integrated to address these gaps. Expected final online publication date for the Annual Review of Biomedical Engineering, Volume 23 is June 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    Print ISSN: 1523-9829
    Electronic ISSN: 1545-4274
    Topics: Medicine , Technology
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  • 27
    Publication Date: 2021-03-29
    Description: The remarkable diversity of specialized metabolites produced by plants has inspired several decades of research and nucleated a long list of theories to guide empirical ecological studies. However, analytical constraints and the lack of untargeted processing workflows have long precluded comprehensive metabolite profiling and, consequently, the collection of the critical currencies to test theory predictions for the ecological functions of plant metabolic diversity. Developments in mass spectrometry (MS) metabolomics have revolutionized the large-scale inventory and annotation of chemicals from biospecimens. Hence, the next generation of MS metabolomics propelled by new bioinformatics developments provides a long-awaited framework to revisit metabolism-centered ecological questions, much like the advances in next-generation sequencing of the last two decades impacted all research horizons in genomics. Here, we review advances in plant (computational) metabolomics to foster hypothesis formulation from complex metabolome data. Additionally, we reflect on how next-generation metabolomics could reinvigorate the testing of long-standing theories on plant metabolic diversity. Expected final online publication date for the Annual Review of Plant Biology, Volume 72 is May 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    Print ISSN: 1543-5008
    Electronic ISSN: 1545-2123
    Topics: Biology
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  • 28
    Publication Date: 2021-03-29
    Description: Optobiochemical control of protein activities allows the investigation of protein functions in living cells with high spatiotemporal resolution. Over the last two decades, numerous natural photosensory domains have been characterized and synthetic domains engineered and assembled into photoregulatory systems to control protein function with light.Here, we review the field of optobiochemistry, categorizing photosensory domains by chromophore, describing photoregulatory systems by mechanism of action, and discussing protein classes frequently investigated using optical methods. We also present examples of how spatial or temporal control of proteins in living cells has provided new insights not possible with traditional biochemical or cell biological techniques. Expected final online publication date for the Annual Review of Biochemistry, Volume 90 is June 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    Print ISSN: 0066-4154
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    Topics: Biology , Chemistry and Pharmacology
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  • 29
    Publication Date: 2021-03-29
    Description: Codon-dependent translation underlies genetics and phylogenetic inferences, but its origins pose two challenges. Prevailing narratives cannot account for the fact that aminoacyl-tRNA synthetases (aaRSs), which translate the genetic code, must collectively enforce the rules used to assemble themselves. Nor can they explain how specific assignments arose from rudimentary differentiation between ancestral aaRSs and corresponding transfer RNAs (tRNAs). Experimental deconstruction of the two aaRS superfamilies created new experimental tools with which to analyze the emergence of the code. Amino acid and tRNA substrate recognition are linked to phase transfer free energies of amino acids and arise largely from aaRS class-specific differences in secondary structure. Sensitivity to protein folding rules endowed ancestral aaRS–tRNA pairs with the feedback necessary to rapidly compare alternative genetic codes and coding sequences. These and other experimental data suggest that the aaRS bidirectional genetic ancestry stabilized the differentiation and interdependence required to initiate and elaborate the genetic coding table. Expected final online publication date for the Annual Review of Biochemistry, Volume 90 is June 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    Print ISSN: 0066-4154
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    Topics: Biology , Chemistry and Pharmacology
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  • 30
    Publication Date: 2021-03-29
    Description: Nucleosomes wrap DNA and impede access for the machinery of transcription. The core histones that constitute nucleosomes are subject to a diversity of posttranslational modifications, or marks, that impact the transcription of genes. Their functions have sometimes been difficult to infer because the enzymes that write and read them are complex, multifunctional proteins. Here, we examine the evidence for the functions of marks and argue that the major marks perform a fairly small number of roles in either promoting transcription or preventing it. Acetylations and phosphorylations on the histone core disrupt histone-DNA contacts and/or destabilize nucleosomes to promote transcription. Ubiquitylations stimulate methylations that provide a scaffold for either the formation of silencing complexes or resistance to those complexes, and carry a memory of the transcriptional state. Tail phosphorylations deconstruct silencing complexes in particular contexts. We speculate that these fairly simple roles form the basis of transcriptional regulation by histone marks. Expected final online publication date for the Annual Review of Genomics and Human Genetics Volume 22 is August 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    Print ISSN: 1527-8204
    Electronic ISSN: 1545-293X
    Topics: Biology
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  • 31
    Publication Date: 2021-03-30
    Description: In 1961, Jacob and Monod proposed the operon model of gene regulation. At the model's core was the modular assembly of regulators, operators, and structural genes. To illustrate the composability of these elements, Jacob and Monod linked phenotypic diversity to the architectures of regulatory circuits. In this review, we examine how the circuit blueprints imagined by Jacob and Monod laid the foundation for the first synthetic gene networks that launched the field of synthetic biology in 2000. We discuss the influences of the operon model and its broader theoretical framework on the first generation of synthetic biological circuits, which were predominantly transcriptional and posttranscriptional circuits. We also describe how recent advances in molecular biology beyond the operon model—namely, programmable DNA- and RNA-binding molecules as well as models of epigenetic and posttranslational regulation—are expanding the synthetic biology toolkit and enabling the design of more complex biological circuits. Expected final online publication date for the Annual Review of Biochemistry, Volume 90 is June 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    Print ISSN: 0066-4154
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    Topics: Biology , Chemistry and Pharmacology
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  • 32
    Publication Date: 2021-03-23
    Description: Salicylic acid (SA) is an essential plant defense hormone that promotes immunity against biotrophic and semibiotrophic pathogens. It plays crucial roles in basal defense and the amplification of local immune responses, as well as the establishment of systemic acquired resistance. During the past three decades, immense progress has been made in understanding the biosynthesis, homeostasis, perception, and functions of SA. This review summarizes the current knowledge regarding SA in plant immunity and other biological processes. We highlight recent breakthroughs that substantially advanced our understanding of how SA is biosynthesized from isochorismate, how it is perceived, and how SA receptors regulate different aspects of plant immunity. Some key questions in SA biosynthesis and signaling, such as how SA is produced via another intermediate benzoic acid and how SA affects the activities of its receptors in the transcriptional regulation of defense genes, remain to be addressed. Expected final online publication date for the Annual Review of Plant Biology, Volume 72 is May 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    Print ISSN: 1543-5008
    Electronic ISSN: 1545-2123
    Topics: Biology
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  • 33
    Publication Date: 2021-03-23
    Description: The perception of light signals by the phytochrome family of photoreceptors has a crucial influence on almost all aspects of growth and development throughout a plant's life cycle. The holistic regulatory networks orchestrated by phytochromes, including conformational switching, subcellular localization, direct protein-protein interactions, transcriptional and posttranscriptional regulations, and translational and posttranslational controls to promote photomorphogenesis, are highly coordinated and regulated at multiple levels. During the past decade, advances using innovative approaches have substantially broadened our understanding of the sophisticated mechanisms underlying the phytochrome-mediated light signaling pathways. This review discusses and summarizes these discoveries of the role of the modular structure of phytochromes, phytochrome-interacting proteins, and their functions; the reciprocal modulation of both positive and negative regulators in phytochrome signaling; the regulatory roles of phytochromes in transcriptional activities, alternative splicing, and translational regulation; and the kinases and E3 ligases that modulate PHYTOCHROME INTERACTING FACTORs to optimize photomorphogenesis. Expected final online publication date for the Annual Review of Plant Biology, Volume 72 is May 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    Print ISSN: 1543-5008
    Electronic ISSN: 1545-2123
    Topics: Biology
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  • 34
    Publication Date: 2021-03-23
    Description: Jupiter's Galilean satellite Io is one of the most remarkable objects in our Solar System. The tidal heating Io undergoes through its orbital resonance with Europa and Ganymede has resulted in a body rich in active silicate volcanism. Over the past decades, Io has been observed from ground-based and Earth-orbiting telescopes and by several spacecraft. In this review we summarize the progress made toward our understanding of the physical and chemical processes related to Io and its environment since the Galileo era. Io science has been revolutionized by the use of adaptive optics techniques on large, 8- to 10-m telescopes. The resultant ever-increasing database, mapping the size, style, and spatial distribution of Io's diverse volcanoes, has improved our understanding of Io's interior structure, its likely composition, and the tidal heating process. Additionally, new observations of Io's atmosphere obtained with these large optical/infrared telescopes and the Atacama Large Millimeter/submillimeter Array reveal the presence of volcanic plumes, the (at times) near-collapse of Io's atmosphere during eclipse, and the interactions of plumes with the sublimation atmosphere. ▪ Extensive new data sets of Io at ultraviolet, mid- to near-infrared, and radio wavelengths have been gathered since the Galileo era. ▪ New data and models inform us about tidal heating, surface properties, and magma composition across Io—although key questions remain. ▪ Atmospheric observations indicate a dominant sublimation-supported component and reinforce the presence of stealth volcanism. ▪ Observations of volcanic plumes show high gas velocities (up to ∼1 km/s) and their effect on Io's atmosphere. Expected final online publication date for the Annual Review of Earth and Planetary Sciences, Volume 49 is May 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    Print ISSN: 0084-6597
    Electronic ISSN: 1545-4495
    Topics: Geosciences , Physics
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  • 35
    Publication Date: 2021-03-22
    Description: Specialized features of vasculature in the central nervous system greatly limit therapeutic treatment options for many neuropathologies. Focused ultrasound, in combination with circulating microbubbles, can be used to transiently and noninvasively increase cerebrovascular permeability with a high level of spatial precision. For minutes to hours following sonication, drugs can be administered systemically to extravasate in the targeted brain regions and exert a therapeutic effect, after which permeability returns to baseline levels. With the wide range of therapeutic agents that can be delivered using this approach and the growing clinical need, focused ultrasound and microbubble (FUS+MB) exposure in the brain has entered human testing to assess safety. This review outlines the use of FUS+MB-mediated cerebrovascular permeability enhancement as a drug delivery technique, details several technical and biological considerations of this approach, summarizes results from the clinical trials conducted to date, and discusses the future direction of the field. Expected final online publication date for the Annual Review of Biomedical Engineering, Volume 23 is June 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    Print ISSN: 1523-9829
    Electronic ISSN: 1545-4274
    Topics: Medicine , Technology
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  • 36
    Publication Date: 2021-03-22
    Description: Plants have an extraordinary diversity of transcription machineries, including five nuclear DNA-dependent RNA polymerases. Four of these enzymes are dedicated to the production of long noncoding RNAs (lncRNAs), which are ribonucleic acids with functions independent of their protein-coding potential. lncRNAs display a broad range of lengths and structures, but they are distinct from the small RNA guides of RNA interference (RNAi) pathways. lncRNAs frequently serve as structural, catalytic, or regulatory molecules for gene expression. They can affect all elements of genes, including promoters, untranslated regions, exons, introns, and terminators, controlling gene expression at various levels, including modifying chromatin accessibility, transcription, splicing, and translation. Certain lncRNAs protect genome integrity, while others respond to environmental cues like temperature, drought, nutrients, and pathogens. In this review, we explain the challenge of defining lncRNAs, introduce the machineries responsible for their production, and organize this knowledge by viewing the functions of lncRNAs throughout the structure of a typical plant gene. Expected final online publication date for the Annual Review of Plant Biology, Volume 72 is May 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    Print ISSN: 1543-5008
    Electronic ISSN: 1545-2123
    Topics: Biology
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  • 37
    Publication Date: 2021-02-01
    Description: The problem of planning for a robot that operates in environments containing a large number of objects, taking actions to move itself through the world as well as to change the state of the objects, is known as task and motion planning (TAMP). TAMP problems contain elements of discrete task planning, discrete–continuous mathematical programming, and continuous motion planning and thus cannot be effectively addressed by any of these fields directly. In this article, we define a class of TAMP problems and survey algorithms for solving them, characterizing the solution methods in terms of their strategies for solving the continuous-space subproblems and their techniques for integrating the discrete and continuous components of the search. Expected final online publication date for the Annual Review of Control, Robotics, and Autonomous Systems, Volume 4 is May 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    Electronic ISSN: 2573-5144
    Topics: Electrical Engineering, Measurement and Control Technology
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  • 38
    Publication Date: 2021-02-01
    Description: Multiple sclerosis (MS) is a chronic disease that is characterized by the inappropriate invasion of lymphocytes and monocytes into the central nervous system (CNS), where they orchestrate the demyelination of axons, leading to physical and cognitive disability. There are many reasons immunologists should be interested in MS. Aside from the fact that there is still significant unmet need for patients living with the progressive form of the disease, MS is a case study for how immune cells cross CNS barriers and subsequently interact with specialized tissue parenchymal cells. In this review, we describe the types of immune cells that infiltrate the CNS and then describe interactions between immune cells and glial cells in different types of lesions. Lastly, we provide evidence for CNS-compartmentalized immune cells and speculate on how this impacts disease progression for MS patients. Expected final online publication date for the Annual Review of Immunology, Volume 39 is April 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    Print ISSN: 0732-0582
    Electronic ISSN: 1545-3278
    Topics: Biology , Medicine
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  • 39
    Publication Date: 2021-03-22
    Description: Paleogeography is the study of the changing surface of Earth through time. Driven by plate tectonics, the configuration of the continents and ocean basins has been in constant flux. Plate tectonics pushes the land surface upward or pulls it apart, causing its collapse. All the while, the unrelenting forces of climate and weather slowly reduce mountains to sand and mud and redistribute these sediments to the sea. This article reviews the changing paleogeography of the past 600 million years. It describes the broad patterns of Phanerozoic paleogeography as well as many of the specific paleogeographic events that have shaped the modern continents and ocean basins. The focus is on the changing latitudinal distribution of the continents, fluctuations in sea level, the opening and closing of oceanic seaways, mountain building, and how these paleogeographic changes have affected global climate, ocean circulation, and the evolution of life. This review presents an atlas of 114 paleogeographic maps that illustrate how Earth's surface has evolved during the past 600 million years. During that time interval, Earth has witnessed the formation and breakup of two supercontinents: Pannotia and Pangea. The continents have been transformed from low-lying flooded platforms to high-standing land areas crisscrossed by the scars of past continental collisions. Oceans have opened and closed, and then opened again in a seemingly never-ending cycle. ▪ The changing configuration of the continents and ocean basins during the past 750 million years is illustrated in 114 paleogeographic maps. ▪ These maps describe how the surface of Earth has been continually modified by mountain building and erosion. ▪ The changing paleogeography has affected global climate, ocean circulation, and the evolution of life. ▪ The data and methods used to produce the maps are described in detail. Expected final online publication date for the Annual Review of Earth and Planetary Sciences, Volume 49 is May 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    Print ISSN: 0084-6597
    Electronic ISSN: 1545-4495
    Topics: Geosciences , Physics
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  • 40
    Publication Date: 2021-03-22
    Description: As a frontal node in the primate social brain, the medial prefrontal cortex (MPFC) plays a critical role in coordinating one's own behavior with respect to that of others. Current literature demonstrates that single neurons in the MPFC encode behavior-related variables such as intentions, actions, and rewards, specifically for self and other, and that the MPFC comes into play when reflecting upon oneself and others. The social moderator account of MPFC function can explain maladaptive social cognition in people with autism spectrum disorder, which tips the balance in favor of self-centered perspectives rather than taking into consideration the perspective of others. Several strands of evidence suggest a hypothesis that the MPFC represents different other mental models, depending on the context at hand, to better predict others’ emotions and behaviors. This hypothesis also accounts for aberrant MPFC activity in autistic individuals while they are mentalizing others. Expected final online publication date for the Annual Review of Neuroscience, Volume 44 is July 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    Print ISSN: 0147-006X
    Electronic ISSN: 1545-4126
    Topics: Biology , Medicine
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  • 41
    Publication Date: 2021-03-22
    Description: The Cassini-Huygens mission that explored the Saturn system during the period 2004–2017 revolutionized our understanding of Titan, the only known moon with a dense atmosphere and the only body, besides Earth, with stable surface liquids. Its predominantly nitrogen atmosphere also contains a few percent of methane that is photolyzed on short geological timescales to form ethane and more complex organic molecules. The presence of a significant amount of methane and 40Ar, the decay product of 40K, argues for exchange processes from the interior to the surface. Here we review the information that constrains Titan's interior structure. Gravity and orbital data suggest that Titan is an ocean world, which implies differentiation into a hydrosphere and a rocky core. The mass and gravity data complemented by equations of state constrain the ocean density and composition as well as the hydrosphere thickness. We present end-member models, review the dynamics of each layer, and discuss the global evolution consistent with the Cassini-Huygens data. ▪ Titan is the only moon with a dense atmosphere where organic molecules are synthesized and have sedimented at the surface. ▪ The Cassini-Huygens mission demonstrated that Titan is an ocean world with an internal water shell and liquid hydrocarbon seas at the poles. ▪ Interactions between water, rock, and organics may have occurred during most of Titan's evolution, which has strong astrobiological implications. ▪ Data collected by the Dragonfly mission and comparison with the JUpiter ICy moons Explorer (JUICE) data for Ganymede will further reveal Titan's astrobiology potential. Expected final online publication date for the Annual Review of Earth and Planetary Sciences, Volume 49 is May 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    Print ISSN: 0084-6597
    Electronic ISSN: 1545-4495
    Topics: Geosciences , Physics
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  • 42
    Publication Date: 2021-03-24
    Description: Here, the research field of nanoplasmonic sensors is placed under scrutiny, with focus on affinity-based detection using refractive index changes. This review describes how nanostructured plasmonic sensors can deliver unique advantages compared to the established surface plasmon resonance technique, where a planar metal surface is used. At the same time, it shows that these features are actually only useful in quite specific situations. Recent trends in the field are also discussed and some devices that claim extraordinary performance are questioned. It is argued that the most important challenges are related to limited receptor affinity and nonspecific binding rather than instrumental performance. Although some nanoplasmonic sensors may be useful in certain situations, it seems likely that conventional surface plasmon resonance will continue to dominate biomolecular interaction analysis. For detection of analytes in complex samples, plasmonics may be an important tool, but probably not in the form of direct refractometric detection. Expected final online publication date for the Annual Review of Analytical Chemistry, Volume 14 is June 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    Print ISSN: 1936-1327
    Electronic ISSN: 1936-1335
    Topics: Chemistry and Pharmacology
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  • 43
    Publication Date: 2021-03-24
    Description: Advances in the instrumentation and signal processing for simultaneously acquired electroencephalography and functional magnetic resonance imaging (EEG-fMRI) have enabled new ways to observe the spatiotemporal neural dynamics of the human brain. Central to the utility of EEG-fMRI neuroimaging systems are the methods for fusing the two data streams, with machine learning playing a key role. These methods can be dichotomized into those that are symmetric and asymmetric in terms of how the two modalities inform the fusion. Studies using these methods have shown that fusion yields new insights into brain function that are not possible when each modality is acquired separately. As technology improves and methods for fusion become more sophisticated, the future of EEG-fMRI for noninvasive measurement of brain dynamics includes mesoscale mapping at ultrahigh magnetic resonance fields, targeted perturbation-based neuroimaging, and using deep learning to uncover nonlinear representations that link the electrophysiological and hemodynamic measurements. Expected final online publication date for the Annual Review of Neuroscience, Volume 44 is July 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    Print ISSN: 0147-006X
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    Topics: Biology , Medicine
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  • 44
    Publication Date: 2021-03-10
    Description: Studies of biological systems and materials, together with recent experimental and theoretical advances in colloidal and nanoscale materials, have shown how nonequilibrium forcing can be used to modulate organization in many novel ways. In this review, we focus on how an accounting of energy dissipation, using the tools of stochastic thermodynamics, can constrain and provide intuition for the correlations and configurations that emerge in a nonequilibrium process. We anticipate that the frameworks reviewed here can provide a starting point to address some of the unique phenomenology seen in biophysical systems and potentially replicate them in synthetic materials.
    Print ISSN: 1947-5454
    Electronic ISSN: 1947-5462
    Topics: Physics
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  • 45
    Publication Date: 2021-03-10
    Description: The recent development of artificially fabricated van der Waals nanostructures makes it possible to design and control the symmetry of solids and to find novel physical properties and related functionalities. A characteristic physical property reflecting such symmetry breaking is the nonlinear response, which is typically studied as the second harmonic generation of light, although studies have recently expanded to include various transport phenomena. An important aspect of nonlinear transport for modern condensed matter physics is that it is not only a unique functionality of noncentrosymmetric systems but also an emergent property reflecting underlying physics such as spin–orbit interaction, superconductivity, magnetism, and band geometry/topology. In this article, we review the nonlinear electrical transport in noncentrosymmetric van der Waals nanostructures obtained by exfoliation, nano-structure fabrication, or the application of an electric field, in particular, nonreciprocal transport resulting from inversion symmetry breaking and the bulk photovoltaic effect in nanomaterials without conventional p- n junctions.
    Print ISSN: 1947-5454
    Electronic ISSN: 1947-5462
    Topics: Physics
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  • 46
    Publication Date: 2021-03-12
    Description: The ability of cells to generate mechanical forces, but also to sense, adapt to, and respond to mechanical signals, is crucial for many developmental, postnatal homeostatic, and pathophysiological processes. However, the molecular mechanisms underlying cellular mechanotransduction have remained elusive for many decades, as techniques to visualize and quantify molecular forces across individual proteins in cells were missing. The development of genetically encoded molecular tension sensors now allows the quantification of piconewton-scale forces that act upon distinct molecules in living cells and even whole organisms. In this review, we discuss the physical principles, advantages, and limitations of this increasingly popular method. By highlighting current examples from the literature, we demonstrate how molecular tension sensors can be utilized to obtain access to previously unappreciated biophysical parameters that define the propagation of mechanical forces on molecular scales. We discuss how the methodology can be further developed and provide a perspective on how the technique could be applied to uncover entirely novel aspects of mechanobiology in the future. Expected final online publication date for the Annual Review of Biophysics, Volume 50 is May 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    Print ISSN: 1936-122X
    Electronic ISSN: 1936-1238
    Topics: Biology , Physics
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  • 47
    Publication Date: 2021-03-10
    Description: The thermally activated creep motion of an elastic interface weakly driven on a disordered landscape is one of the best examples of glassy universal dynamics. Its understanding has evolved over the past 30 years thanks to a fruitful interplay among elegant scaling arguments, sophisticated analytical calculations, efficient optimization algorithms, and creative experiments. In this article, starting from the pioneer arguments, we review the main theoretical and experimental results that lead to the current physical picture of the creep regime. In particular, we discuss recent works unveiling the collective nature of such ultraslow motion in terms of elementary activated events. We show that these events control the mean velocity of the interface and cluster into “creep avalanches” statistically similar to the deterministic avalanches observed at the depinning critical threshold. The associated spatiotemporal patterns of activated events have been recently observed in experiments with magnetic domain walls. The emergent physical picture is expected to be relevant for a large family of disordered systems presenting thermally activated dynamics.
    Print ISSN: 1947-5454
    Electronic ISSN: 1947-5462
    Topics: Physics
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  • 48
    Publication Date: 2021-03-26
    Description: The large number of ion channels found in all nervous systems poses fundamental questions concerning how the characteristic intrinsic properties of single neurons are determined by the specific subsets of channels they express. All neurons display many different ion channels with overlapping voltage- and time-dependent properties. We speculate that these overlapping properties promote resilience in neuronal function. Individual neurons of the same cell type show variability in ion channel conductance densities even though they can generate reliable and similar behavior. This complicates a simple assignment of function to any conductance and is associated with variable responses of neurons of the same cell type to perturbations, deletions, and pharmacological manipulation. Ion channel genes often show strong positively correlated expression, which may result from the molecular and developmental rules that determine which ion channels are expressed in a given cell type. Expected final online publication date for the Annual Review of Neuroscience, Volume 44 is July 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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    Topics: Biology , Medicine
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  • 49
    Publication Date: 2021-03-26
    Description: The human microbiome encodes a second genome that dwarfs the genetic capacity of the host. Microbiota-derived small molecules can directly target human cells and their receptors or indirectly modulate host responses through functional interactions with other microbes in their ecological niche. Their biochemical complexity has profound implications for nutrition, immune system development, disease progression, and drug metabolism, as well as the variation in these processes that exists between individuals. While the species composition of the human microbiome has been deeply explored, detailed mechanistic studies linking specific microbial molecules to host phenotypes are still nascent. In this review, we discuss challenges in decoding these interaction networks, which require interdisciplinary approaches that combine chemical biology, microbiology, immunology, genetics, analytical chemistry, bioinformatics, and synthetic biology. We highlight important classes of microbiota-derived small molecules and notable examples. An understanding of these molecular mechanisms is central to realizing the potential of precision microbiome editing in health, disease, and therapeutic responses. Expected final online publication date for the Annual Review of Biochemistry, Volume 90 is June 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    Print ISSN: 0066-4154
    Electronic ISSN: 1545-4509
    Topics: Biology , Chemistry and Pharmacology
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  • 50
    Publication Date: 2021-03-15
    Description: The development of massively parallel sequencing–based genomic sequencing tests has increased genetic test availability and access. The field and practice of genetic counseling have adapted in response to this paradigm-shifting technology and the subsequent transition to practicing genomic medicine. While the key elements defining genetic counseling remain relevant, genetic counseling service delivery models and practice settings have evolved. Genetic counselors are addressing the challenges of direct-to-consumer and consumer-driven genetic testing, and genetic counseling training programs are responding to the ongoing increased demand for genetic counseling services across a broadening range of contexts. The need to diversify both the patient and participant groups with access to genetic information, as well as the field of genetic counseling, is at the forefront of research and training program initiatives. Genetic counselors are key stakeholders in the genomics era, and their contributions are essential to effectively and equitably deliver precision medicine. Expected final online publication date for the Annual Review of Genomics and Human Genetics Volume 22 is August 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    Print ISSN: 1527-8204
    Electronic ISSN: 1545-293X
    Topics: Biology
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  • 51
    Publication Date: 2021-03-12
    Description: As the professional antigen-presenting cells of the immune system, dendritic cells (DCs) sense the microenvironment and shape the ensuing adaptive immune response. DCs can induce both immune activation and immune tolerance according to the peripheral cues. Recent work has established that DCs comprise of several phenotypically and functionally heterogeneous subsets that differentially regulate T lymphocyte differentiation. This review summarizes both mouse and human DC subset phenotypes, development, diversification, and function. We focus on advances in our understanding of how different DC subsets regulate distinct CD4+ T helper (Th) cell differentiation, including Th1, Th2, Th17, T follicular helper, and T regulatory cells. We review DC subset intrinsic properties, local tissue microenvironments, and other immune cells that together determine Th cell differentiation during homeostasis and inflammation. Expected final online publication date for the Annual Review of Immunology, Volume 39 is April 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    Print ISSN: 0732-0582
    Electronic ISSN: 1545-3278
    Topics: Biology , Medicine
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  • 52
    Publication Date: 2021-03-09
    Description: Developmental and environmental signals converge on cell cycle machinery to achieve proper and flexible organogenesis under changing environments. Studies on the plant cell cycle began 30 years ago, and accumulated research has revealed many links between internal and external factors and the cell cycle. In this review, we focus on how phytohormones and environmental signals regulate the cell cycle to enable plants to cope with a fluctuating environment. After introducing key cell cycle regulators, we first discuss how phytohormones and their synergy are important for regulating cell cycle progression and how environmental factors positively and negatively affect cell division. We then focus on the well-studied example of stress-induced G2 arrest and view the current model from an evolutionary perspective. Finally, we discuss the mechanisms controlling the transition from the mitotic cycle to the endocycle, which greatly contributes to cell enlargement and resultant organ growth in plants. Expected final online publication date for the Annual Review of Plant Biology, Volume 72 is May 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    Print ISSN: 1543-5008
    Electronic ISSN: 1545-2123
    Topics: Biology
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  • 53
    Publication Date: 2021-03-09
    Description: Nucleotide-binding domain leucine-rich repeat receptors (NLRs) play important roles in the innate immune systems of both plants and animals. Recent breakthroughs in NLR biochemistry and biophysics have revolutionized our understanding of how NLR proteins function in plant immunity. In this review, we summarize the latest findings in plant NLR biology and draw direct comparisons to NLRs of animals. We discuss different mechanisms by which NLRs recognize their ligands in plants and animals. The discovery of plant NLR resistosomes that assemble in a comparable way to animal inflammasomes reinforces the striking similarities between the formation of plant and animal NLR complexes. Furthermore, we discuss the mechanisms by which plant NLRs mediate immune responses and draw comparisons to similar mechanisms identified in animals. Finally, we summarize the current knowledge of the complex genetic architecture formed by NLRs in plants and animals and the roles of NLRs beyond pathogen detection. Expected final online publication date for the Annual Review of Plant Biology, Volume 72 is May 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    Print ISSN: 1543-5008
    Electronic ISSN: 1545-2123
    Topics: Biology
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  • 54
    Publication Date: 2021-03-23
    Description: Recreating human organ–level function in vitro is a rapidly evolving field that integrates tissue engineering, stem cell biology, and microfluidic technology to produce 3D organoids. A critical component of all organs is the vasculature. Herein, we discuss general strategies to create vascularized organoids, including common source materials, and survey previous work using vascularized organoids to recreate specific organ functions and simulate tumor progression. Vascularization is not only an essential component of individual organ function but also responsible for coupling the fate of all organs and their functions. While some success in coupling two or more organs together on a single platform has been demonstrated, we argue that the future of vascularized organoid technology lies in creating organoid systems complete with tissue-specific microvasculature and in coupling multiple organs through a dynamic vascular network to create systems that can respond to changing physiological conditions. Expected final online publication date for the Annual Review of Biomedical Engineering, Volume 23 is June 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    Print ISSN: 1523-9829
    Electronic ISSN: 1545-4274
    Topics: Medicine , Technology
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  • 55
    Publication Date: 2021-03-23
    Description: Opioids such as morphine and oxycodone are analgesics frequently prescribed for the treatment of moderate or severe pain. Unfortunately, these medications are associated with exceptionally high abuse potentials and often cause fatal side effects, mainly through the μ-opioid receptor (MOR). Efforts to discover novel, safer, and more efficacious analgesics targeting MOR have encountered challenges. In this review, we summarize alternative strategies and targets that could be used to develop safer nonopioid analgesics. A molecular understanding of G protein–coupled receptor activation and signaling has illuminated not only the complexities of receptor pharmacology but also the potential for pathway-selective agonists and allosteric modulators as safer medications. The availability of structures of pain-related receptors, in combination with high-throughput computational tools, has accelerated the discovery of multitarget ligands with promising pharmacological profiles. Emerging clinical evidence also supports the notion that drugs targeting peripheral opioid receptors have potential as improved analgesic agents. Expected final online publication date for the Annual Review of Biochemistry, Volume 90 is June 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    Print ISSN: 0066-4154
    Electronic ISSN: 1545-4509
    Topics: Biology , Chemistry and Pharmacology
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  • 56
    Publication Date: 2021-03-23
    Description: Throughout Earth's history, CO2 is thought to have exerted a fundamental control on environmental change. Here we review and revise CO2 reconstructions from boron isotopes in carbonates and carbon isotopes in organic matter over the major climate transition of the past 66 million years. We find close coupling between CO2 and climate throughout the Cenozoic, with peak CO2 levels of ∼1,500 ppm in the Eocene greenhouse, decreasing to ∼550 ppm in the Miocene, and falling further into ice age world of the Plio–Pleistocene. Around two-thirds of Cenozoic CO2 drawdown is explained by an increase in the ratio of alkalinity to dissolved inorganic carbon, likely linked to a change in the balance of weathering to outgassing, with the remaining one-third due to changing ocean temperature and major ion composition. Earth system climate sensitivity is explored and may vary between different time intervals. The Cenozoic CO2 record highlights the truly geological scale of anthropogenic CO2 change: Current CO2 levels were last seen around 3 million years ago, and major cuts in emissions are required to prevent a return to the CO2 levels of the Miocene or Eocene in the coming century. ▪ CO2 reconstructions over the past 66 Myr from boron isotopes and alkenones are reviewed and re-evaluated. ▪ CO2 estimates from the different proxies show close agreement, yielding a consistent picture of the evolution of the ocean-atmosphere CO2 system over the Cenozoic. ▪ CO2 and climate are coupled throughout the past 66 Myr, providing broad constraints on Earth system climate sensitivity. ▪ Twenty-first-century carbon emissions have the potential to return CO2 to levels not seen since the much warmer climates of Earth's distant past. Expected final online publication date for the Annual Review of Earth and Planetary Sciences, Volume 49 is May 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    Print ISSN: 0084-6597
    Electronic ISSN: 1545-4495
    Topics: Geosciences , Physics
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  • 57
    Publication Date: 2021-03-23
    Description: A renaissance of interest in crystallographic shear structures and our recent work in this remarkable class of materials inspired this review. We first summarize the geometrical aspects of shear plane formation and possible transformations in ReO3, rutile, and perovskite-based structures. Then we provide a mechanistic overview of crystallographic shear formation, plane ordering, and propagation. Next we describe the energetics of planar defect formation and interaction, equilibria between point and extended defect structures, and thermodynamic stability of shear compounds. Finally, we emphasize the remaining challenges and propose future directions in this exciting area. Expected final online publication date for the Annual Review of Materials Science, Volume 51 is July 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    Print ISSN: 1531-7331
    Electronic ISSN: 1545-4118
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
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  • 58
    Publication Date: 2021-03-26
    Description: Field-flow fractionation (FFF) is a family of techniques that was created especially for separating and characterizing macromolecules, nanoparticles, and micrometer-sized analytes. It is coming of age as new nanomaterials, polymers, composites, and biohybrids with remarkable properties are introduced and new analytical challenges arise due to synthesis heterogeneities and the motivation to correlate analyte properties with observed performance. Appreciation of the complexity of biological, pharmaceutical, and food systems and the need to monitor multiple components across many size scales have also contributed to FFF's growth. This review highlights recent advances in FFF capabilities, instrumentation, and applications that feature the unique characteristics of different FFF techniques in determining a variety of information, such as averages and distributions in size, composition, shape, architecture, and microstructure and in investigating transformations and function. Expected final online publication date for the Annual Review of Analytical Chemistry, Volume 14 is June 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    Print ISSN: 1936-1327
    Electronic ISSN: 1936-1335
    Topics: Chemistry and Pharmacology
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  • 59
    Publication Date: 2021-03-26
    Description: Polymers that simultaneously transport electrons and ions are paramount to drive the technological advances necessary for next-generation electrochemical devices, including energy storage devices and bioelectronics. However, efforts to describe the motion of ions or electrons separately within polymeric systems become inaccurate when both species are present. Herein, we highlight the basic transport equations necessary to rationalize mixed transport and the multiscale materials properties that influence their transport coefficients. Potential figures of merit that enable a suitable performance benchmark in mixed conducting systems independent of end application are discussed. Practical design and implementation of mixed conducting polymers require an understanding of the evolving nature of structure and transport with ionic and electronic carrier density to capture the dynamic disorder inherent in polymeric materials. Expected final online publication date for the Annual Review of Materials Science, Volume 51 is July 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    Print ISSN: 1531-7331
    Electronic ISSN: 1545-4118
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
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  • 60
    Publication Date: 2021-03-26
    Description: Telemedicine is perhaps the most rapidly growing area in health care. Approximately 15 million Americans receive medical assistance remotely every year. Yet rural communities face significant challenges in securing subspecialist care. In the United States, 25% of the population resides in rural areas, where less than 15% of physicians work. Current surgery residency programs do not adequately prepare surgeons for rural practice. Telementoring, wherein a remote expert guides a less experienced caregiver, has been proposed to address this challenge. Nonetheless, existing mentoring technologies are not widely available to rural communities, due to a lack of infrastructure and mentor availability. For this reason, some clinicians prefer simpler and more reliable technologies. This article presents past and current telementoring systems, with a focus on rural settings, and proposes a set of requirements for such systems. We conclude with a perspective on the future telementoring systems and the integration of artificial intelligence within those systems. Expected final online publication date for the Annual Review of Biomedical Engineering, Volume 23 is June 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    Print ISSN: 1523-9829
    Electronic ISSN: 1545-4274
    Topics: Medicine , Technology
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  • 61
    Publication Date: 2021-03-26
    Description: Influenza virus RNA-dependent RNA polymerase (FluPol) transcribes the viral RNA genome in the infected cell nucleus. In the 1970s, researchers showed that viral transcription depends on host RNA polymerase II (RNAP II) activity and subsequently that FluPol snatches capped oligomers from nascent RNAP II transcripts to prime its own transcription. Exactly how this occurs remains elusive. Here, we review recent advances in the mechanistic understanding of FluPol transcription and early events in RNAP II transcription that are relevant to cap-snatching. We describe the known direct interactions between FluPol and the RNAP II C-terminal domain and summarize the transcription-related host factors that have been found to interact with FluPol. We also discuss open questions regarding how FluPol may be targeted to actively transcribing RNAP II and the exact context and timing of cap-snatching, which is presumed to occur after cap completion but before the cap is sequestered by the nuclear cap-binding complex. Expected final online publication date for the Annual Review of Biochemistry, Volume 90 is June 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    Print ISSN: 0066-4154
    Electronic ISSN: 1545-4509
    Topics: Biology , Chemistry and Pharmacology
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  • 62
    Publication Date: 2021-03-17
    Description: Single-cell approaches are quickly changing our view on biological systems by increasing the spatiotemporal resolution of our analyses to the level of the individual cell. The field of plant biology has fully embraced single-cell transcriptomics and is rapidly expanding the portfolio of available technologies and applications. In this review, we give an overview of the main advances in plant single-cell transcriptomics over the past few years and provide the reader with an accessible guideline covering all steps, from sample preparation to data analysis. We end by offering a glimpse of how these technologies will shape and accelerate plant-specific research in the near future. Expected final online publication date for the Annual Review of Plant Biology, Volume 72 is May 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    Print ISSN: 1543-5008
    Electronic ISSN: 1545-2123
    Topics: Biology
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  • 63
    Publication Date: 2021-03-17
    Description: Many of our daily activities, such as riding a bike to work or reading a book in a noisy cafe, and highly skilled activities, such as a professional playing a tennis match or a violin concerto, depend upon the ability of the brain to quickly make moment-to-moment adjustments to our behavior in response to the results of our actions. Particularly, they depend upon the ability of the neocortex to integrate the information provided by the sensory organs (bottom-up information) with internally generated signals such as expectations or attentional signals (top-down information). This integration occurs in pyramidal cells (PCs) and their long apical dendrite, which branches extensively into a dendritic tuft in layer 1 (L1). The outermost layer of the neocortex, L1 is highly conserved across cortical areas and species. Importantly, L1 is the predominant input layer for top-down information, relayed by a rich, dense mesh of long-range projections that provide signals to the tuft branches of the PCs. Here, we discuss recent progress in our understanding of the composition of L1 and review evidence that L1 processing contributes to functions such as sensory perception, cross-modal integration, controlling states of consciousness, attention, and learning. Expected final online publication date for the Annual Review of Neuroscience, Volume 44 is July 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    Print ISSN: 0147-006X
    Electronic ISSN: 1545-4126
    Topics: Biology , Medicine
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  • 64
    Publication Date: 2021-03-15
    Description: Myelination of axons provides the structural basis for rapid saltatory impulse propagation along vertebrate fiber tracts, a well-established neurophysiological concept. However, myelinating oligodendrocytes and Schwann cells serve additional functions in neuronal energy metabolism that are remarkably similar to those of axon-ensheathing glial cells in unmyelinated invertebrates. Here we discuss myelin evolution and physiological glial functions, beginning with the role of ensheathing glia in preventing ephaptic coupling, axoglial metabolic support, and eliminating oxidative radicals. In both vertebrates and invertebrates, axoglial interactions are bidirectional, serving to regulate cell fate, nerve conduction, and behavioral performance. One key step in the evolution of compact myelin in the vertebrate lineage was the emergence of the open reading frame for myelin basic protein within another gene. Several other proteins were neofunctionalized as myelin constituents and help maintain a healthy nervous system. Myelination in vertebrates became a major prerequisite of inhabiting new ecological niches. Expected final online publication date for the Annual Review of Neuroscience, Volume 44 is July 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    Print ISSN: 0147-006X
    Electronic ISSN: 1545-4126
    Topics: Biology , Medicine
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  • 65
    Publication Date: 2021-03-17
    Description: The central theme of this review is the dynamic interaction between information selection and learning. We pose a fundamental question about this interaction: How do we learn what features of our experiences are worth learning about? In humans, this process depends on attention and memory, two cognitive functions that together constrain representations of the world to features that are relevant for goal attainment. Recent evidence suggests that the representations shaped by attention and memory are themselves inferred from experience with each task. We review this evidence and place it in the context of work that has explicitly characterized representation learning as statistical inference. We discuss how inference can be scaled to real-world decisions by approximating beliefs based on a small number of experiences. Finally, we highlight some implications of this inference process for human decision-making in social environments. Expected final online publication date for the Annual Review of Neuroscience, Volume 44 is July 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    Print ISSN: 0147-006X
    Electronic ISSN: 1545-4126
    Topics: Biology , Medicine
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  • 66
    Publication Date: 2021-03-17
    Description: The dense reconstruction of neuronal wiring diagrams from volumetric electron microscopy data has the potential to generate fundamentally new insights into mechanisms of information processing and storage in neuronal circuits. Zebrafish provide unique opportunities for dynamical connectomics approaches that combine reconstructions of wiring diagrams with measurements of neuronal population activity and behavior. Such approaches have the power to reveal higher-order structure in wiring diagrams that cannot be detected by sparse sampling of connectivity and that is essential for neuronal computations. In the brain stem, recurrently connected neuronal modules were identified that can account for slow, low-dimensional dynamics in an integrator circuit. In the spinal cord, connectivity specifies functional differences between premotor interneurons. In the olfactory bulb, tuning-dependent connectivity implements a whitening transformation that is based on the selective suppression of responses to overrepresented stimulus features. These findings illustrate the potential of dynamical connectomics in zebrafish to analyze the circuit mechanisms underlying higher-order neuronal computations. Expected final online publication date for the Annual Review of Neuroscience, Volume 44 is July 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    Print ISSN: 0147-006X
    Electronic ISSN: 1545-4126
    Topics: Biology , Medicine
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  • 67
    Publication Date: 2021-03-15
    Description: Over the past decade, genomic analyses of single cells—the fundamental units of life—have become possible. Single-cell DNA sequencing has shed light on biological questions that were previously inaccessible across diverse fields of research, including somatic mutagenesis, organismal development, genome function, and microbiology. Single-cell DNA sequencing also promises significant future biomedical and clinical impact, spanning oncology, fertility, and beyond. While single-cell approaches that profile RNA and protein have greatly expanded our understanding of cellular diversity, many fundamental questions in biology and important biomedical applications require analysis of the DNA of single cells. Here, we review the applications and biological questions for which single-cell DNA sequencing is uniquely suited or required. We include a discussion of the fields that will be impacted by single-cell DNA sequencing as the technology continues to advance. Expected final online publication date for the Annual Review of Genomics and Human Genetics Volume 22 is August 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    Print ISSN: 1527-8204
    Electronic ISSN: 1545-293X
    Topics: Biology
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  • 68
    Publication Date: 2021-03-15
    Description: Cells receive enormous amounts of information from their environment. How they act on this information—by migrating, expressing genes, or relaying signals to other cells—comprises much of the regulatory and self-organizational complexity found across biology. The “parts list” involved in cell signaling is generally well established, but how do these parts work together to decode signals and produce appropriate responses? This fundamental question is increasingly being addressed with optogenetic tools: light-sensitive proteins that enable biologists to manipulate the interaction, localization, and activity state of proteins with high spatial and temporal precision. In this review, we summarize how optogenetics is being used in the pursuit of an answer to this question, outlining the current suite of optogenetic tools available to the researcher and calling attention to studies that increase our understanding of and improve our ability to engineer biology. Expected final online publication date for the Annual Review of Biomedical Engineering, Volume 23 is June 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    Print ISSN: 1523-9829
    Electronic ISSN: 1545-4274
    Topics: Medicine , Technology
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  • 69
    Publication Date: 2021-02-03
    Description: Notch signaling is a conserved system of communication between adjacent cells, influencing numerous cell fate decisions in the development of multicellular organisms. Aberrant signaling is also implicated in many human pathologies. At its core, Notch has a mechanotransduction module that decodes receptor–ligand engagement at the cell surface under force to permit proteolytic cleavage of the receptor, leading to the release of the Notch intracellular domain (NICD). NICD enters the nucleus and acts as a transcriptional effector to regulate expression of Notch-responsive genes. In this article, we review and integrate current understanding of the detailed molecular basis for Notch signal transduction, highlighting quantitative, structural, and dynamic features of this developmentally central signaling mechanism. We discuss the implications of this mechanistic understanding for the functionality of the signaling pathway in different molecular and cellular contexts. Expected final online publication date for the Annual Review of Biophysics, Volume 50 is May 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    Print ISSN: 1936-122X
    Electronic ISSN: 1936-1238
    Topics: Biology , Physics
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  • 70
    Publication Date: 2021-02-03
    Description: Primary immunodeficiency diseases (PIDs) are a rapidly growing, heterogeneous group of genetically determined diseases characterized by defects in the immune system. While individually rare, collectively PIDs affect between 1/1,000 and 1/5,000 people worldwide. The clinical manifestations of PIDs vary from susceptibility to infections to autoimmunity and bone marrow failure. Our understanding of the human immune response has advanced by investigation and discovery of genetic mechanisms of PIDs. Studying patients with isolated genetic variants in proteins that participate in complex signaling pathways has led to an enhanced understanding of host response to infection, and mechanisms of autoimmunity and autoinflammation. Identifying genetic mechanisms of PIDs not only furthers immunological knowledge but also benefits patients by dictating targeted therapies or hematopoietic stem cell transplantation. Here, we highlight several of these areas in the field of primary immunodeficiency, with a focus on the most recent advances. Expected final online publication date for the Annual Review of Immunology, Volume 39 is April 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    Print ISSN: 0732-0582
    Electronic ISSN: 1545-3278
    Topics: Biology , Medicine
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  • 71
    Publication Date: 2021-02-03
    Description: Biophysics experiments performed at single-molecule resolution provide exceptional insight into the structural details and dynamic behavior of biological systems. However, extracting this information from the corresponding experimental data unequivocally requires applying a biophysical model. In this review, we discuss how to use probability theory to apply these models to single-molecule data. Many current single-molecule data analysis methods apply parts of probability theory, sometimes unknowingly, and thus miss out on the full set of benefits provided by this self-consistent framework. The full application of probability theory involves a process called Bayesian inference that fully accounts for the uncertainties inherent to single-molecule experiments. Additionally, using Bayesian inference provides a scientifically rigorous method of incorporating information from multiple experiments into a single analysis and finding the best biophysical model for an experiment without the risk of overfitting the data. These benefits make the Bayesian approach ideal for analyzing any type of single-molecule experiment. Expected final online publication date for the Annual Review of Biophysics, Volume 50 is May 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    Print ISSN: 1936-122X
    Electronic ISSN: 1936-1238
    Topics: Biology , Physics
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  • 72
    Publication Date: 2021-02-08
    Description: Members of the mitochondrial carrier family [solute carrier family 25 (SLC25)] transport nucleotides, amino acids, carboxylic acids, fatty acids, inorganic ions, and vitamins across the mitochondrial inner membrane. They are important for many cellular processes, such as oxidative phosphorylation of lipids and sugars, amino acid metabolism, macromolecular synthesis, ion homeostasis, cellular regulation, and differentiation. Here, we describe the functional elements of the transport mechanism of mitochondrial carriers, consisting of one central substrate-binding site and two gates with salt-bridge networks on either side of the carrier. Binding of the substrate during import causes three gate elements to rotate inward, forming the cytoplasmic network and closing access to the substrate-binding site from the intermembrane space. Simultaneously, three core elements rock outward, disrupting the matrix network and opening the substrate-binding site to the matrix side of the membrane. During export, substrate binding triggers conformational changes involving the same elements but operating in reverse. Expected final online publication date for the Annual Review of Biochemistry, Volume 90 is June 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    Print ISSN: 0066-4154
    Electronic ISSN: 1545-4509
    Topics: Biology , Chemistry and Pharmacology
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  • 73
    Publication Date: 2021-02-08
    Description: The preparation of extremely thin samples, which are required for high-resolution electron microscopy, poses extreme risk of damaging biological macromolecules due to interactions with the air-water interface. Although the rapid increase in the number of published structures initially gave little indication that this was a problem, the search for methods that substantially mitigate this hazard is now intensifying. The two main approaches under investigation are ( a) immobilizating particles onto structure-friendly support films and ( b) reducing the length of time during which such interactions may occur. While there is little possibility of outrunning diffusion to the interface, intentional passivation of the interface may slow the process of adsorption and denaturation. In addition, growing attention is being given to gaining more effective control of the thickness of the sample prior to vitrification. Expected final online publication date for the Annual Review of Biochemistry, Volume 90 is June 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    Print ISSN: 0066-4154
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    Topics: Biology , Chemistry and Pharmacology
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  • 74
    Publication Date: 2021-02-08
    Description: For many infections and almost all vaccines, neutralizing-antibody-mediated immunity is the primary basis and best functional correlate of immunological protection. Durable long-term humoral immunity is mediated by antibodies secreted by plasma cells that preexist subsequent exposures and by memory B cells that rapidly respond to infections once they have occurred. In the midst of the current pandemic of coronavirus disease 2019, it is important to define our current understanding of the unique roles of memory B cells and plasma cells in immunity and the factors that control the formation and persistence of these cell types. This fundamental knowledge is the basis to interpret findings from natural infections and vaccines. Here, we review transcriptional and metabolic programs that promote and support B cell fates and functions, suggesting points at which these pathways do and do not intersect. Expected final online publication date for the Annual Review of Immunology, Volume 39 is April 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    Print ISSN: 0732-0582
    Electronic ISSN: 1545-3278
    Topics: Biology , Medicine
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  • 75
    Publication Date: 2021-02-08
    Description: DNA double-strand breaks pose a serious threat to genome stability. In vertebrates, these breaks are predominantly repaired by nonhomologous end joining (NHEJ), which pairs DNA ends in a multiprotein synaptic complex to promote their direct ligation. NHEJ is a highly versatile pathway that uses an array of processing enzymes to modify damaged DNA ends and enable their ligation. The mechanisms of end synapsis and end processing have important implications for genome stability. Rapid and stable synapsis is necessary to limit chromosome translocations that result from the mispairing of DNA ends. Furthermore, end processing must be tightly regulated to minimize mutations at the break site. Here, we review our current mechanistic understanding of vertebrate NHEJ, with a particular focus on end synapsis and processing. Expected final online publication date for the Annual Review of Biochemistry, Volume 90 is June 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    Print ISSN: 0066-4154
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    Topics: Biology , Chemistry and Pharmacology
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  • 76
    Publication Date: 2021-02-08
    Description: During the approximately 5 days of Drosophila neurogenesis (late embryogenesis to the beginning of pupation), a limited number of neural stem cells produce approximately 200,000 neurons comprising hundreds of cell types. To build a functional nervous system, neuronal types need to be produced in the proper places, appropriate numbers, and correct times. We discuss how neural stem cells (neuroblasts) obtain so-called area codes for their positions in the nervous system (spatial patterning) and how they keep time to sequentially produce neurons with unique fates (temporal patterning). We focus on specific examples that demonstrate how a relatively simple patterning system (Notch) can be used reiteratively to generate different neuronal types. We also speculate on how different modes of temporal patterning that operate over short versus long time periods might be linked. We end by discussing how specification programs are integrated and lead to the terminal features of different neuronal types. Expected final online publication date for the Annual Review of Neuroscience, Volume 44 is July 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    Print ISSN: 0147-006X
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    Topics: Biology , Medicine
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  • 77
    Publication Date: 2021-02-09
    Description: Classically, skin was considered a mere structural barrier protecting organisms from a diversity of environmental insults. In recent decades, the cutaneous immune system has become recognized as a complex immunologic barrier involved in both antimicrobial immunity and homeostatic processes like wound healing. To sense a variety of chemical, mechanical, and thermal stimuli, the skin harbors one of the most sophisticated sensory networks in the body. However, recent studies suggest that the cutaneous nervous system is highly integrated with the immune system to encode specific sensations into evolutionarily conserved protective behaviors. In addition to directly sensing pathogens, neurons employ novel neuroimmune mechanisms to provide host immunity. Therefore, given that sensation underlies various physiologies through increasingly complex reflex arcs, a much more dynamic picture is emerging of the skin as a truly systemic organ with highly coordinated physical, immunologic, and neural functions in barrier immunology. Expected final online publication date for the Annual Review of Immunology, Volume 39 is April 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    Print ISSN: 0732-0582
    Electronic ISSN: 1545-3278
    Topics: Biology , Medicine
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  • 78
    Publication Date: 2021-02-09
    Description: G-quadruplexes have raised considerable interest during the past years for the development of therapies against cancer. These noncanonical structures of DNA may be found in telomeres and/or oncogene promoters, and it has been observed that the stabilization of such G-quadruplexes may disturb tumor cell growth. Nevertheless, the mechanisms leading to folding and stabilization of these G-quadruplexes are still not well established, and they are the focus of much current work in this field. In seminal works, stabilization was observed to be produced by cations. However, subsequent studies showed that different kinds of small molecules, from planar and nonplanar organic molecules to square-planar and octahedral metal complexes, may also lead to the stabilization of G-quadruplexes. Thus, the comprehension and rationalization of the interaction of these small molecules with G-quadruplexes are also important topics of current interest in medical applications. To shed light on the questions arising from the literature on the formation of G-quadruplexes, their stabilization, and their interaction with small molecules, synergies between experimental studies and computational works are needed. In this review, we mainly focus on in silico approaches and provide a broad compilation of different leading studies carried out to date by different computational methods. We divide these methods into two main categories: ( a) classical methods, which allow for long-timescale molecular dynamics simulations and the corresponding analysis of dynamical information, and ( b) quantum methods (semiempirical, quantum mechanics/molecular mechanics, and density functional theory methods), which allow for the explicit simulation of the electronic structure of the system but, in general, are not capable of being used in long-timescale molecular dynamics simulations and, therefore, give a more static picture of the relevant processes. Expected final online publication date for the Annual Review of Biophysics, Volume 50 is May 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    Print ISSN: 1936-122X
    Electronic ISSN: 1936-1238
    Topics: Biology , Physics
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  • 79
    Publication Date: 2021-02-08
    Description: Improvements in understanding the neurobiological basis of mental illness have unfortunately not translated into major advances in treatment. At this point, it is clear that psychiatric disorders are exceedingly complex and that, in order to account for and leverage this complexity, we need to collect longitudinal datasets from much larger and more diverse samples than is practical using traditional methods. We discuss how smartphone-based research methods have the potential to dramatically advance our understanding of the neuroscience of mental health. This, we expect, will take the form of complementing lab-based hard neuroscience research with dense sampling of cognitive tests, clinical questionnaires, passive data from smartphone sensors, and experience-sampling data as people go about their daily lives. Theory- and data-driven approaches can help make sense of these rich data sets, and the combination of computational tools and the big data that smartphones make possible has great potential value for researchers wishing to understand how aspects of brain function give rise to, or emerge from, states of mental health and illness. Expected final online publication date for the Annual Review of Neuroscience, Volume 44 is July 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    Print ISSN: 0147-006X
    Electronic ISSN: 1545-4126
    Topics: Biology , Medicine
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  • 80
    Publication Date: 2021-02-08
    Description: The immune system of the central nervous system (CNS) consists primarily of innate immune cells. These are highly specialized macrophages found either in the parenchyma, called microglia, or at the CNS interfaces, such as leptomeningeal, perivascular, and choroid plexus macrophages. While they were primarily thought of as phagocytes, their function extends well beyond simple removal of cell debris during development and diseases. Brain-resident innate immune cells were found to be plastic, long-lived, and host to an outstanding number of risk genes for multiple pathologies. As a result, they are now considered the most suitable targets for modulating CNS diseases. Additionally, recent single-cell technologies enhanced our molecular understanding of their origins, fates, interactomes, and functional cell states during health and perturbation. Here, we review the current state of our understanding and challenges of the myeloid cell biology in the CNS and treatment options for related diseases. Expected final online publication date for the Annual Review of Immunology, Volume 39 is April 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    Print ISSN: 0732-0582
    Electronic ISSN: 1545-3278
    Topics: Biology , Medicine
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  • 81
    Publication Date: 2021-02-16
    Description: Our understanding of the interactions between the nuclear and mitochondrial genomes is becoming increasingly important as they are extensively involved in establishing early development and developmental progression. Evidence from various biological systems indicates the interdependency between the genomes, which requires a high degree of compatibility and synchrony to ensure effective cellular function throughout development and in the resultant offspring. During development, waves of DNA demethylation, de novo methylation, and maintenance methylation act on the nuclear genome and typify oogenesis and pre- and postimplantation development. At the same time, significant changes in mitochondrial DNA copy number influence the metabolic status of the developing organism in a typically cell-type-specific manner. Collectively, at any given stage in development, these actions establish genomic balance that ensures each developmental milestone is met and that the organism's program for life is established.
    Print ISSN: 2165-8102
    Electronic ISSN: 2165-8110
    Topics: Biology
    Published by Annual Reviews
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  • 82
    Publication Date: 2021-02-16
    Description: Antimicrobial resistance (AMR) is a threat to animal and human health. Antimicrobial use has been identified as a major driver of AMR, and reductions in use are a focal point of interventions to reduce resistance. Accordingly, stakeholders in human health and livestock production have implemented antimicrobial stewardship programs aimed at reducing use. Thus far, these efforts have yielded variable impacts on AMR. Furthermore, scientific advances are prompting an expansion and more nuanced appreciation of the many nonantibiotic factors that drive AMR, as well as how these factors vary across systems, geographies, and contexts. Given these trends, we propose a framework to prioritize AMR interventions. We use this framework to evaluate the impact of interventions that focus on antimicrobial use. We conclude by suggesting that priorities be expanded to include greater consideration of host–microbial interactions that dictate AMR, as well as anthropogenic and environmental systems that promote dissemination of AMR.
    Print ISSN: 2165-8102
    Electronic ISSN: 2165-8110
    Topics: Biology
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  • 83
    Publication Date: 2021-02-16
    Print ISSN: 2165-8102
    Electronic ISSN: 2165-8110
    Topics: Biology
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  • 84
    Publication Date: 2021-02-03
    Description: A common way to represent a system's dynamics is to specify how the state evolves in time. An alternative viewpoint is to specify how functions of the state evolve in time. This evolution of functions is governed by a linear operator called the Koopman operator, whose spectral properties reveal intrinsic features of a system. For instance, its eigenfunctions determine coordinates in which the dynamics evolve linearly. This review discusses the theoretical foundations of Koopman operator methods, as well as numerical methods developed over the past two decades to approximate the Koopman operator from data, for systems both with and without actuation. We pay special attention to ergodic systems, for which especially effective numerical methods are available. For nonlinear systems with an affine control input, the Koopman formalism leads naturally to systems that are bilinear in the state and the input, and this structure can be leveraged for the design of controllers and estimators. Expected final online publication date for the Annual Review of Control, Robotics, and Autonomous Systems, Volume 4 is May 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    Electronic ISSN: 2573-5144
    Topics: Electrical Engineering, Measurement and Control Technology
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  • 85
    Publication Date: 2021-02-03
    Description: The air transportation system connects the world through the transport of goods and people. However, operational inefficiencies such as flight delays and cancellations are prevalent, resulting in economic and environmental impacts. In the first part of this article, we review recent advances in using network analysis techniques to model the interdependencies observed in the air transportation system and to understand the role of airports in connecting populations, serving air traffic demand, and spreading delays. In the second part, we present some of our recent work on using operational data to build dynamical system models of air traffic delay networks. We show that Markov jump linear system models capture many of the salient characteristics of these networked systems. We illustrate how these models can be validated and then used to analyze system properties such as stability and to design optimal control strategies that limit the propagation of disruptions in air traffic networks. Expected final online publication date for the Annual Review of Control, Robotics, and Autonomous Systems, Volume 4 is May 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    Electronic ISSN: 2573-5144
    Topics: Electrical Engineering, Measurement and Control Technology
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  • 86
    Publication Date: 2021-02-03
    Description: Type 2 immunity helps protect the host from infection, but it also plays key roles in tissue homeostasis, metabolism, and repair. Unfortunately, inappropriate type 2 immune reactions may lead to allergy and asthma. Group 2 innate lymphoid cells (ILC2s) in the lungs respond rapidly to local environmental cues, such as the release of epithelium-derived type 2 initiator cytokines/alarmins, producing type 2 effector cytokines such as IL-4, IL-5, and IL-13 in response to tissue damage and infection. ILC2s are associated with the severity of allergic asthma, and experimental models of lung inflammation have shown how they act as playmakers, receiving signals variously from stromal and immune cells as well as the nervous system and then disseminating cytokine cues to elicit effector functions and potentiate CD4+ T helper cell activation, both of which characterize the pathology of allergic asthma. Recent breakthroughs identifying stromal- and neuronal-derived microenvironmental cues that regulate ILC2s, along with studies recognizing the potential plasticity of ILC2s, have improved our understanding of the immunoregulation of asthma and opened new avenues for drug discovery. Expected final online publication date for the Annual Review of Immunology, Volume 39 is April 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    Print ISSN: 0732-0582
    Electronic ISSN: 1545-3278
    Topics: Biology , Medicine
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  • 87
    Publication Date: 2021-02-03
    Description: Comparative neuroscience is entering the era of big data. New high-throughput methods and data-sharing initiatives have resulted in the availability of large, digital data sets containing many types of data from ever more species. Here, we present a framework for exploiting the new possibilities offered. The multimodality of the data allows vertical translations, which are comparisons of different aspects of brain organization within a single species and across scales. Horizontal translations compare particular aspects of brain organization across species, often by building abstract feature spaces. Combining vertical and horizontal translations allows for more sophisticated comparisons, including relating principles of brain organization across species by contrasting horizontal translations, and for making formal predictions of unobtainable data based on observed results in a model species. Expected final online publication date for the Annual Review of Neuroscience, Volume 44 is July 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    Print ISSN: 0147-006X
    Electronic ISSN: 1545-4126
    Topics: Biology , Medicine
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  • 88
    Publication Date: 2021-02-12
    Description: Aquaporins function as water and neutral solute channels, signaling hubs, disease virulence factors, and metabolon components. We consider plant aquaporins that transport ions compared to some animal counterparts. These are candidates for important, as yet unidentified, cation and anion channels in plasma, tonoplast, and symbiotic membranes. For those individual isoforms that transport ions, water, and gases, the permeability spans 12 orders of magnitude. This requires tight regulation of selectivity via protein interactions and posttranslational modifications. A phosphorylation-dependent switch between ion and water permeation in AtPIP2;1 might be explained by coupling between the gates of the four monomer water channels and the central pore of the tetramer. We consider the potential for coupling between ion and water fluxes that could form the basis of an electroosmotic transducer. A grand challenge in understanding the roles of ion transporting aquaporins is their multifunctional modes that are dependent on location, stress, time, and development. Expected final online publication date for the Annual Review of Plant Biology, Volume 72 is May 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    Print ISSN: 1543-5008
    Electronic ISSN: 1545-2123
    Topics: Biology
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  • 89
    Publication Date: 2021-04-16
    Description: Microengineering advances have enabled the development of perfusable, endothelialized models of the microvasculature that recapitulate the unique biological and biophysical conditions of the microcirculation in vivo. Indeed, at that size scale (
    Print ISSN: 1523-9829
    Electronic ISSN: 1545-4274
    Topics: Medicine , Technology
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  • 90
    Publication Date: 2021-04-16
    Description: Neurons in the brain represent information in their collective activity. The fidelity of this neural population code depends on whether and how variability in the response of one neuron is shared with other neurons. Two decades of studies have investigated the influence of these noise correlations on the properties of neural coding. We provide an overview of the theoretical developments on the topic. Using simple, qualitative, and general arguments, we discuss, categorize, and relate the various published results. We emphasize the relevance of the fine structure of noise correlation, and we present a new approach to the issue. Throughout this review, we emphasize a geometrical picture of how noise correlations impact the neural code. Expected final online publication date for the Annual Review of Neuroscience, Volume 44 is July 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    Print ISSN: 0147-006X
    Electronic ISSN: 1545-4126
    Topics: Biology , Medicine
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  • 91
    Publication Date: 2021-04-16
    Description: Gene therapy makes it possible to engineer chimeric antigen receptors (CARs) to create T cells that target specific diseases. However, current approaches require elaborate and expensive protocols to manufacture engineered T cells ex vivo, putting this therapy beyond the reach of many patients who might benefit. A solution could be to program T cells in vivo. Here, we evaluate the clinical need for in situ CAR T cell programming, compare competing technologies, review current progress, and provide a perspective on the long-term impact of this emerging and rapidly flourishing biotechnology field. Expected final online publication date for the Annual Review of Biomedical Engineering, Volume 23 is June 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    Print ISSN: 1523-9829
    Electronic ISSN: 1545-4274
    Topics: Medicine , Technology
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  • 92
    Publication Date: 2021-04-16
    Description: What changes in neural architecture account for the emergence and expansion of dexterity in primates? Dexterity, or skill in performing motor tasks, depends on the ability to generate highly fractionated patterns of muscle activity. It also involves the spatiotemporal coordination of activity in proximal and distal muscles across multiple joints. Many motor skills require the generation of complex movement sequences that are only acquired and refined through extensive practice. Improvements in dexterity have enabled primates to manufacture and use tools and humans to engage in skilled motor behaviors such as typing, dance, musical performance, and sports. Our analysis leads to the following synthesis: The neural substrate that endows primates with their enhanced motor capabilities is due, in part, to ( a) major organizational changes in the primary motor cortex and ( b) the proliferation of output pathways from other areas of the cerebral cortex, especially from the motor areas on the medial wall of the hemisphere. Expected final online publication date for the Annual Review of Neuroscience, Volume 44 is July 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    Print ISSN: 0147-006X
    Electronic ISSN: 1545-4126
    Topics: Biology , Medicine
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  • 93
    Publication Date: 2021-04-14
    Description: The rise of antibiotic-resistant strains of bacterial pathogens has necessitated the development of new therapeutics. Antimicrobial peptides (AMPs) are a class of compounds with potentially attractive therapeutic properties, including the ability to target specific groups of bacteria. In nature, AMPs exhibit remarkable structural and functional diversity, which may be further enhanced through genetic engineering, high-throughput screening, and chemical modification strategies. In this review, we discuss the molecular mechanisms underlying AMP selectivity and highlight recent computational and experimental efforts to design selectively targeting AMPs. While there has been an extensive effort to find broadly active and highly potent AMPs, it remains challenging to design targeting peptides to discriminate between different bacteria on the basis of physicochemical properties. We also review approaches for measuring AMP activity, point out the challenges faced in assaying for selectivity, and discuss the potential for increasing AMP diversity through chemical modifications. Expected final online publication date for the Annual Review of Biomedical Engineering, Volume 23 is June 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    Print ISSN: 1523-9829
    Electronic ISSN: 1545-4274
    Topics: Medicine , Technology
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  • 94
    Publication Date: 2021-04-29
    Description: The mouse, as a model organism to study the brain, gives us unprecedented experimental access to the mammalian cerebral cortex. By determining the cortex's cellular composition, revealing the interaction between its different components, and systematically perturbing these components, we are obtaining mechanistic insight into some of the most basic properties of cortical function. In this review, we describe recent advances in our understanding of how circuits of cortical neurons implement computations, as revealed by the study of mouse primary visual cortex. Further, we discuss how studying the mouse has broadened our understanding of the range of computations performed by visual cortex. Finally, we address how future approaches will fulfill the promise of the mouse in elucidating fundamental operations of cortex. Expected final online publication date for the Annual Review of Neuroscience, Volume 44 is July 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    Print ISSN: 0147-006X
    Electronic ISSN: 1545-4126
    Topics: Biology , Medicine
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  • 95
    Publication Date: 2021-04-26
    Description: We provide an overview of the relationship between financial networks and systemic risk. We present a taxonomy of different types of systemic risk, differentiating between direct externalities between financial organizations (e.g., defaults, correlated portfolios, fire sales), and perceptions and feedback effects (e.g., bank runs, credit freezes). We also discuss optimal regulation and bailouts, measurements of systemic risk and financial centrality, choices by banks regarding their portfolios and partnerships, and the changing nature of financial networks. Expected final online publication date for the Annual Review of Economics, Volume 13 is August 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    Print ISSN: 1941-1383
    Electronic ISSN: 1941-1391
    Topics: Economics
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  • 96
    Publication Date: 2021-04-26
    Description: Tissue-resident macrophages are present in most tissues with developmental, self-renewal, or functional attributes that do not easily fit into a textbook picture of a plastic and multifunctional macrophage originating from hematopoietic stem cells; nor does it fit a pro- versus anti-inflammatory paradigm. This review presents and discusses current knowledge on the developmental biology of macrophages from an evolutionary perspective focused on the function of macrophages, which may aid in study of developmental, inflammatory, tumoral, and degenerative diseases. We also propose a framework to investigate the functions of macrophages in vivo and discuss how inherited germline and somatic mutations may contribute to the roles of macrophages in diseases.
    Print ISSN: 0732-0582
    Electronic ISSN: 1545-3278
    Topics: Biology , Medicine
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  • 97
    Publication Date: 2021-04-26
    Description: Measurement of biological systems containing biomolecules and bioparticles is a key task in the fields of analytical chemistry, biology, and medicine. Driven by the complex nature of biological systems and unprecedented amounts of measurement data, artificial intelligence (AI) in measurement science has rapidly advanced from the use of silicon-based machine learning (ML) for data mining to the development of molecular computing with improved sensitivity and accuracy. This review presents an overview of fundamental ML methodologies and discusses their applications in disease diagnostics, biomarker discovery, and imaging analysis. We next provide the working principles of molecular computing using logic gates and arithmetical devices, which can be employed for in situ detection, computation, and signal transduction for biological systems. This review concludes by summarizing the strengths and limitations of AI-involved biological measurement in fundamental and applied research. Expected final online publication date for the Annual Review of Analytical Chemistry, Volume 14 is June 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    Print ISSN: 1936-1327
    Electronic ISSN: 1936-1335
    Topics: Chemistry and Pharmacology
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  • 98
    Publication Date: 2021-04-26
    Description: The gametophyte represents the sexual phase in the alternation of generations in plants; the other, nonsexual phase is the sporophyte. Here, we review the evolutionary origins of the male gametophyte among land plants and, in particular, its ontogenesis in flowering plants. The highly reduced male gametophyte of angiosperm plants is a two- or three-celled pollen grain. Its task is the production of two male gametes and their transport to the female gametophyte, the embryo sac, where double fertilization takes place. We describe two phases of pollen ontogenesis—a developmental phase leading to the differentiation of the male germline and the formation of a mature pollen grain and a functional phase representing the pollen tube growth, beginning with the landing of the pollen grain on the stigma and ending with double fertilization. We highlight recent advances in the complex regulatory mechanisms involved, including posttranscriptional regulation and transcript storage, intracellular metabolic signaling, pollen cell wall structure and synthesis, protein secretion, and phased cell–cell communication within the reproductive tissues. Expected final online publication date for the Annual Review of Plant Biology, Volume 72 is May 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    Print ISSN: 1543-5008
    Electronic ISSN: 1545-2123
    Topics: Biology
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  • 99
    Publication Date: 2021-04-28
    Description: Diploidy has profound implications for population genetics and susceptibility to genetic diseases. Although two copies are present for most genes in the human genome, they are not necessarily both active or active at the same level in a given individual. Genomic imprinting, resulting in exclusive or biased expression in favor of the allele of paternal or maternal origin, is now believed to affect hundreds of human genes. A far greater number of genes display unequal expression of gene copies due to cis-acting genetic variants that perturb gene expression. The availability of data generated by RNA sequencing applied to large numbers of individuals and tissue types has generated unprecedented opportunities to assess the contribution of genetic variation to allelic imbalance in gene expression. Here we review the insights gained through the analysis of these data about the extent of the genetic contribution to allelic expression imbalance, the tools and statistical models for gene expression imbalance, and what the results obtained reveal about the contribution of genetic variants that alter gene expression to complex human diseases and phenotypes. Expected final online publication date for the Annual Review of Biomedical Data Science, Volume 4 is July 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    Electronic ISSN: 2574-3414
    Topics: Computer Science , Medicine
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  • 100
    Publication Date: 2021-04-26
    Description: An imbalance in the microbiota may contribute to many human illnesses, which has prompted efforts to rebalance it by targeting the microbes themselves. However, by supplying the habitat, the host wields a prominent influence over microbial growth at body surfaces, raising the possibility that rebalancing the microbiota by targeting our immune system would be a viable alternative. Host control mechanisms that sculpt the microbial habitat form a functional unit with the microbiota, termed microbiota-nourishing immunity, that confers colonization resistance against pathogens. The host components of microbiota-nourishing immunity can be viewed as habitat filters that select for microbial traits licensing growth and survival in host habitat patches. Here we review current knowledge of how host-derived habitat filters shape the size, species composition, and spatial heterogeneity of the microbiota and discuss whether these host control mechanisms could be harnessed for developing approaches to rebalance microbial communities during dysbiosis.
    Print ISSN: 0732-0582
    Electronic ISSN: 1545-3278
    Topics: Biology , Medicine
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