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  1. Dynamics of Bacteriorhodopsin in the Dark-Adapted State from Solution Nuclear Magnetic Resonance Spectroscopy 

    Kooijman, Laurens; Schuster, Matthias; Baumann, Christian; et al. (2020)
    Angewandte Chemie. International Edition
    To achieve efficient proton pumping in the light-driven proton pump bacteriorhodopsin (bR), the protein must be tightly coupled to the retinal to rapidly convert retinal isomerization into protein structural rearrangements. Methyl group dynamics of bR embedded in lipid nanodiscs were determined in the dark-adapted state, and were found to be mostly well ordered at the cytosolic side. Methyl groups in the M145A mutant of bR, which displays ...
    Journal Article
  2. Stratospheric influence on ECMWF sub-seasonal forecast skill for energy-industry-relevant surface weather in European countries 

    Bueeler, Dominik; Beerli, Remo; Wernli, Heini; et al. (2020)
    Quarterly Journal of the Royal Meteorological Society
    Meteorologists in the energy industry increasingly draw upon the potential for enhanced sub-seasonal predictability of European surface weather following anomalous states of the winter stratospheric polar vortex (SPV). How the link between the SPV and the large-scale tropospheric flow translates into forecast skill for surface weather in individual countries - a spatial scale that is particularly relevant for the energy industry - remains ...
    Journal Article
  3. Inflection point in climatic suitability of insect pest species in Europe suggests non-linear responses to climate change 

    Gruenig, Marc; Calanca, Pierluigi; Mazzi, Dominique; et al. (2020)
    Global Change Biology
    Climate change and globalization affect the suitable conditions for agricultural crops and insect pests, threatening future food security. It remains unknown whether shifts in species' climatic suitability will be linear or rather non-linear, with crop exposure to pests suddenly increasing when a critical temperature threshold is crossed. Moreover, uncertainty of forecasts can arise because of the modelling approach based either on species ...
    Journal Article
  4. Morphologic analysis of the subtalar joint using statistical shape modeling 

    Krahenbuhl, Nicola; Lenz, Amy L.; Lisonbee, Rich J.; et al. (2020)
    Journal of orthopaedic research : a journal for musculoskeletal investigation
    Weightbearing computed tomography (WBCT) enables visualization of the foot and ankle as patients stand under load. Clinical measurements of WBCT images are generally limited to two-dimensions, which reduces the ability to quantify complex morphology of individual osseous structures as well as the alignment between two or more bones. The shape and orientation of the healthy/normal subtalar joint, in particular, is not well-understood, which ...
    Journal Article
  5. Model-Based Reconstruction of Large Three-Dimensional Optoacoustic Datasets 

    Ding, Lu; Razansky, Daniel; Dean-Ben, Xose Luis (2020)
    IEEE Transactions on Medical Imaging
    Iterative model-based algorithms are known to enable more accurate and quantitative optoacoustic (photoacoustic) tomographic reconstructions than standard back-projection methods. However, three-dimensional (3D) model-based inversion is often hampered by high computational complexity and memory overhead. Parallel implementations on a graphics processing unit (GPU) have been shown to efficiently reduce the memory requirements by on-the-fly ...
    Journal Article
  6. Cell Types of the Human Retina and Its Organoids at Single-Cell Resolution 

    Cowan C.S.; Renner M.; De Gennaro M.; et al. (2020)
    © 2020 The Author(s) Human organoids recapitulating the cell-type diversity and function of their target organ are valuable for basic and translational research. We developed light-sensitive human retinal organoids with multiple nuclear and synaptic layers and functional synapses. We sequenced the RNA of 285,441 single cells from these organoids at seven developmental time points and from the periphery, fovea, pigment epithelium and choroid ...
    Journal Article
  7. High-Dimensional T Helper Cell Profiling Reveals a Broad Diversity of Stably Committed Effector States and Uncovers Interlineage Relationships 

    Tortola L.; Jacobs A.; Pohlmeier L.; et al. (2020)
    © 2020 Elsevier Inc. CD4+ T helper (Th) cells orchestrate immune responses. Tortola et al. characterize Th cell cytokine responses by CyTOF and unveil the plethora of Th cell sublineages. They highlight the predisposition of Th17 cells to acquire a Th2-cell phenotype after challenge and the contribution of “ex-Th17”-Th2 cells in neutrophilic asthma.
    Journal Article
  8. Structural Basis for Helicase-Polymerase Coupling in the SARS-CoV-2 Replication-Transcription Complex 

    Chen J.; Malone B.; Llewellyn E.; et al. (2020)
    © 2020 Elsevier Inc. Chen et al. present cryo-EM structures of the SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) holoenzyme (nsp7/nsp8/nsp12) containing an RNA template product in complex with the viral helicase (nsp13). The work provides insight into assembly and function of the multi-subunit protein machine and how it might be targeted therapeutically to treat COVID-19.
    Journal Article
  9. Arctic Amplification: A Rapid Response to Radiative Forcing 

    Previdi M.; Janoski T.P.; Chiodo G.; et al. (2020)
    Geophysical Research Letters
    ©2020. American Geophysical Union. All Rights Reserved. Arctic amplification (AA) of surface warming is a prominent feature of anthropogenic climate change with important implications for human and natural systems. Despite its importance, the underlying causes of AA are not fully understood. Here, analyzing coupled climate model simulations, we show that AA develops rapidly (within the first few months) following an instantaneous quadrupling ...
    Journal Article
  10. 3D-Printed Biocompatible Scaffolds with Built-In Nanoplasmonic Sensors 

    Garcia-Astrain, Clara; Lenzi, Elisa; Jimenez de Aberasturi, Dorleta; et al. (2020)
    Advanced functional materials
    3D printing strategies have acquired great relevance toward the design of 3D scaffolds with precise macroporous structures, for supported mammalian cell growth. Despite advances in 3D model designs, there is still a shortage of detection tools to precisely monitor in situ cell behavior in 3D, thereby allowing a better understanding of the progression of diseases or to test the efficacy of drugs in a more realistic microenvironment. Even ...
    Journal Article
  11. The impact of segmentation on whole-lung functional MRI quantification: Repeatability and reproducibility from multiple human observers and an artificial neural network 

    Willers, Corin; Bauman, Grzegorz; Andermatt, Simon; et al. (2020)
    Magnetic Resonance in Medicine
    Purpose To investigate the repeatability and reproducibility of lung segmentation and their impact on the quantitative outcomes from functional pulmonary MRI. Additionally, to validate an artificial neural network (ANN) to accelerate whole-lung quantification. Method Ten healthy children and 25 children with cystic fibrosis underwent matrix pencil decomposition MRI (MP-MRI). Impaired relative fractional ventilation (R-FV) and relative ...
    Journal Article
  12. Calibrating Environmental DNA Metabarcoding to Conventional Surveys for Measuring Fish Species Richness 

    McElroy M.E.; Dressler T.L.; Titcomb G.C.; et al. (2020)
    Frontiers in Ecology and Evolution
    © Copyright © 2020 McElroy, Dressler, Titcomb, Wilson, Deiner, Dudley, Eliason, Evans, Gaines, Lafferty, Lamberti, Li, Lodge, Love, Mahon, Pfrender, Renshaw, Selkoe and Jerde. The ability to properly identify species present in a landscape is foundational to ecology and essential for natural resource management and conservation. However, many species are often unaccounted for due to ineffective direct capture and visual surveys, especially ...
    Journal Article
  13. Nanoscale Force Sensing of an Ultrafast Nonlinear Optical Response 

    Schumacher Z.; Rejali R.; Pachlatko R.; et al. (2020)
    Proceedings of the National Academy of Sciences of the United States of America
    © 2020 National Academy of Sciences. All rights reserved. The nonlinear optical response of a material is a sensitive probe of electronic and structural dynamics under strong light fields. The induced microscopic polarizations are usually detected via their far-field light emission, thus limiting spatial resolution. Several powerful near-field techniques circumvent this limitation by employing local nanoscale scatterers; however, their ...
    Journal Article
  14. How Food Affects Colonization Resistance Against Enteropathogenic Bacteria 

    Kreuzer M.; Hardt W.D. (2020)
    Annual review of microbiology
    Food has a major impact on all aspects of health. Recent data suggest that food composition can also affect susceptibility to infections by enteropathogenic bacteria. Here, we discuss how food may alter the microbiota as well as mucosal defenses and how this can affect infection. Salmonella Typhimurium diarrhea serves as a paradigm, and complementary evidence comes from other pathogens. We discuss the effects of food composition on ...
    Journal Article
  15. Linking Molecular Behavior to Macroscopic Properties in Ideal Dynamic Covalent Networks 

    Marco-Dufort B.; Iten R.; Tibbitt M.W. (2020)
    Journal of the American Chemical Society
    Dynamic covalent networks (DCvNs) are increasingly used in advanced materials design with applications ranging from recyclable thermosets to self-healing hydrogels. However, the relationship between the underlying chemistry at the junctions of DCvNs and their macroscopic properties is still not fully understood. In this work, we constructed a robust framework to predict how complex network behavior in DCvNs emerges from the chemical ...
    Journal Article
  16. Global quieting of high-frequency seismic noise due to COVID-19 pandemic lockdown measures 

    Lecocq T.; Hicks S.P.; Van Noten K.; et al. (2020)
    Copyright © 2020 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works. Human activity causes vibrations that propagate into the ground as high-frequency seismic waves. Measures to mitigate the coronavirus disease 2019 (COVID-19) pandemic caused widespread changes in human activity, leading to a months-long reduction in seismic noise of up to ...
    Journal Article
  17. What Configuration of the Atmospheric Circulation Drives Extreme Net and Total Moisture Transport Into the Arctic 

    Papritz L.; Dunn-Sigouin E. (2020)
    Geophysical Research Letters
    ©2020. American Geophysical Union. All Rights Reserved. Previous work highlighted different configurations of the atmospheric circulation causing moisture transport into the Arctic and contributing to surface warming. Here, we clarify the configurations leading to extreme wintertime events of zonal-mean net and total (sum of absolute values of poleward and equatorward) moisture transports by comparing feature-based weather system diagnostics ...
    Journal Article
  18. The Global-Mean Precipitation Response to CO<inf>2</inf>-Induced Warming in CMIP6 Models 

    Pendergrass A.G. (2020)
    Geophysical Research Letters
    ©2020. The Authors. We examine the response of globally averaged precipitation to global warming—the hydrologic sensitivity (HS)—in the Coupled Model Intercomparison Project phase 6 (CMIP6) multi-model ensemble. Multi-model mean HS is 2.5% K−1 (ranging from 2.1–3.1% K−1 across models), a modest decrease compared to CMIP5 (where it was 2.6% K−1). This new set of simulations is used as an out-of-sample test for observational constraints on ...
    Journal Article
  19. Flagellar kinematics reveals the role of environment in shaping sperm motility 

    Guasto J.S.; Estrada J.B.; Menolascina F.; et al. (2020)
    Interface: Journal of the Royal Society
    Swimming spermatozoa from diverse organisms often have very similar morphologies, yet different motilities as a result of differences in the flagellar waveforms used for propulsion. The origin of these differences has remained largely unknown. Using high-speed video microscopy and mathematical analysis of flagellar shape dynamics, we quantitatively compare sperm flagellar waveforms from marine invertebrates to humans by means of a novel ...
    Journal Article
  20. Metalign: efficient alignment-based metagenomic profiling via containment min hash 

    LaPierre N.; Alser M.; Eskin E.; et al. (2020)
    Genome biology
    Metagenomic profiling, predicting the presence and relative abundances of microbes in a sample, is a critical first step in microbiome analysis. Alignment-based approaches are often considered accurate yet computationally infeasible. Here, we present a novel method, Metalign, that performs efficient and accurate alignment-based metagenomic profiling. We use a novel containment min hash approach to pre-filter the reference database prior ...
    Journal Article

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