Understanding the structural determinants of a protein's biochemical properties, such as activity and stability, is a major challenge in biology and medicine. Comparing computer simulations of protein variants with different biochemical properties is an increasingly powerful means to drive progress. However, success often hinges on dimensionality reduction algorithms for simplifying the complex ensemble of structures each variant adopts. Unfortunately, common algorithms rely on potentially misleading assumptions about what structural features are important, such as emphasizing larger geometric changes over smaller ones. Here we present DiffNets, self-supervised autoencoders that avoid such assumptions, and automatically identify the relevant features, by requiring that the low-dimensional representations they learn are sufficient to predict the biochemical differences between protein variants. For example, DiffNets automatically identify subtle structural signatures that predict the relative stabilities of β-lactamase variants and duty ratios of myosin isoforms. DiffNets should also be applicable to understanding other perturbations, such as ligand binding.Assessment of the cumulative incidence of SARS-CoV-2 infections is critical for monitoring the course and extent of the COVID-19 epidemic. Here, we report estimated seroprevalence in the French population and the proportion of infected individuals who developed neutralising antibodies at three points throughout the first epidemic wave. Testing 11,000 residual specimens for anti-SARS-CoV-2 IgG and neutralising antibodies, we find nationwide seroprevalence of 0.41% (95% CI 0.05-0.88) mid-March, 4.14% (95% CI 3.31-4.99) mid-April and 4.93% (95% CI 4.02-5.89) mid-May 2020. Approximately 70% of seropositive individuals have detectable neutralising antibodies. Infection fatality rate is 0.84% (95% CI 0.70-1.03) and increases exponentially with age. These results confirm that the nationwide lockdown substantially curbed transmission and that the vast majority of the French population remained susceptible to SARS-CoV-2 in May 2020. Our study shows the progression of the first epidemic wave and provides a framework to inform the ongoing public health response as viral transmission continues globally.Study of human disease remains challenging due to convoluted disease etiologies and complex molecular mechanisms at genetic, genomic, and proteomic levels. Many machine learning-based methods have been developed and widely used to alleviate some analytic challenges in complex human disease studies. While enjoying the modeling flexibility and robustness, these model frameworks suffer from non-transparency and difficulty in interpreting each individual feature due to their sophisticated algorithms. However, identifying important biomarkers is a critical pursuit towards assisting researchers to establish novel hypotheses regarding prevention, diagnosis and treatment of complex human diseases. Herein, we propose a Permutation-based Feature Importance Test (PermFIT) for estimating and testing the feature importance, and for assisting interpretation of individual feature in complex frameworks, including deep neural networks, random forests, and support vector machines. PermFIT (available at https//github.com/SkadiEye/deepTL ) is implemented in a computationally efficient manner, without model refitting. We conduct extensive numerical studies under various scenarios, and show that PermFIT not only yields valid statistical inference, but also improves the prediction accuracy of machine learning models. With the application to the Cancer Genome Atlas kidney tumor data and the HITChip atlas data, PermFIT demonstrates its practical usage in identifying important biomarkers and boosting model prediction performance.Manipulation of excitons via coherent light-matter interaction is a promising approach for quantum state engineering and ultrafast optical modulation. Various excitation pathways in the excitonic multilevel systems provide controllability more efficient than that in the two-level system. Galunisertib Smad inhibitor However, these control schemes have been restricted to limited control-light wavelengths and cryogenic temperatures. Here, we report that lead halide perovskites can lift these restrictions owing to their multiband structure induced by strong spin-orbit coupling. Using CsPbBr3 perovskite nanocrystals, we observe an anomalous enhancement of the exciton energy shift at room temperature with increasing control-light wavelength from the visible to near-infrared region. The enhancement occurs because the interconduction band transitions between spin-orbit split states have large dipole moments and induce a crossover from the two-level optical Stark effect to the three-level Autler-Townes effect. Our finding establishes a basis for efficient coherent optical manipulation of excitons utilizing energy states with large spin-orbit splitting.Highly monodisperse colloidal InAs quantum dots (QDs) with superior optoelectronic properties are promising candidates for various applications, including infrared photodetectors and photovoltaics. Recently, a synthetic process involving continuous injection has been introduced to synthesize uniformly sized InAs QDs. Still, synthetic efforts to increase the particle size of over 5 nm often suffer from growth suppression. Secondary nucleation or interparticle ripening during the growth accompanies the inhomogeneity in size as well. In this study, we propose a growth model for the continuous synthetic processing of colloidal InAs QDs based on molecular diffusion. The experimentally validated model demonstrates how precursor solution injection reduces monomer flux, limiting particle growth during synthesis. As predicted by our model, we control the diffusion dynamics by tuning reaction volume, precursor concentration, and injection rate of precursor. Through diffusion-dynamics-control in the continuous process, we synthesize the InAs QDs with a size over 9.0-nm (1Smax of 1600 nm) with a narrow size distribution (12.2%). Diffusion-dynamics-controlled synthesis presented in this study effectively manages the monomer flux and thus overcome monomer-reactivity-originating size limit of nanocrystal growth in solution.