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Abstract Polygenic scores (PGSs) offer the ability to predict genetic risk for complex diseases across the life course; a key benefit over short-term prediction models. To produce risk estimates relevant to clinical and public health decision-making, it is important to account for varying effects due to age and sex. Here, we develop a novel framework to estimate country-, age-, and sex-specific estimates of cumulative incidence stratified by PGS for 18 high-burden diseases. We integrate PGS associations from seven studies in four countries (N = 1,197,129) with disease incidences from the Global Burden of Disease. PGS has a significant sex-specific effect for asthma, hip osteoarthritis, gout, coronary heart disease and type 2 diabetes (T2D), with all but T2D exhibiting a larger effect in men. PGS has a larger effect in younger individuals for 13 diseases, with effects decreasing linearly with age. We show for breast cancer that, relative to individuals in the bottom 20% of polygenic risk, the top 5% attain an absolute risk for screening eligibility 16.3 years earlier. Our framework increases the generalizability of results from biobank studies and the accuracy of absolute risk estimates by appropriately accounting for age- and sex-specific PGS effects. Our results highlight the potential of PGS as a screening tool which may assist in the early prevention of common diseases.

Abstract One of the key challenges for spintronic and quantum technologies is to achieve active control of the spin angular momentum of electrons in nanoscale materials on ultrafast, femtosecond timescales. While conventional ferromagnetic materials and materials supporting spin texture suffer both from conceptional limitations in miniaturization and inefficiency of optical and electronic manipulation, non-magnetic centrosymmetric layered materials with hidden spin polarization may offer an alternative pathway to manipulate the spin degree of freedom by external stimuli. Here we demonstrate an approach for generating transient spin polarization on a femtosecond timescale in the otherwise spin-unpolarized band structure of the centrosymmetric 2H-stacked group VI transition metal dichalcogenide WSe2. Using ultrafast optical excitation of a fullerene layer grown on top of WSe2, we trigger an ultrafast interlayer electron transfer from the fullerene layer into the WSe2 crystal. The resulting transient charging of the C60/WSe2 interface leads to a substantial interfacial electric field that by means of spin-layer-valley locking ultimately creates ultrafast spin polarization without the need of an external magnetic field. Our findings open a novel pathway for true optical engineering of spin functionalities such as the sub-picosecond generation and manipulation of ultrafast spin currents in 2D heterostructures.

Abstract Synthetic Chromosome Rearrangement and Modification by LoxP-mediated Evolution (SCRaMbLE) is a promising tool to study genomic rearrangements. However, the potential of SCRaMbLE to study genomic rearrangements is currently hindered, because a strain containing all 16 synthetic chromosomes is not yet available. Here, we construct SparLox83R, a yeast strain containing 83 loxPsym sites distributed across all 16 chromosomes. SCRaMbLE of SparLox83R produces versatile genome-wide genomic rearrangements, including inter-chromosomal events. Moreover, when combined with synthetic chromosomes, SCRaMbLE of hetero-diploids with SparLox83R leads to increased diversity of genomic rearrangements and relatively faster evolution of traits compared to hetero-diploids only with wild-type chromosomes. Analysis of the SCRaMbLEd strain with increased tolerance to nocodazole demonstrates that genomic rearrangements can perturb the transcriptome and 3D genome structure and consequently impact phenotypes. In summary, a genome with sparsely distributed loxPsym sites can serve as a powerful tool for studying the consequence of genomic rearrangements and accelerating strain engineering in Saccharomyces cerevisiae.

Abstract The genome of an organism is inherited from its ancestor and continues to evolve over time, however, the extent to which the current version could be altered remains unknown. To probe the genome plasticity of Saccharomyces cerevisiae, here we replace the native left arm of chromosome XII (chrXIIL) with a linear artificial chromosome harboring small sets of reconstructed genes. We find that as few as 12 genes are sufficient for cell viability, whereas 25 genes are required to recover the partial fitness defects observed in the 12-gene strain. Next, we demonstrate that these genes can be reconstructed individually using synthetic regulatory sequences and recoded open-reading frames with a “one-amino-acid-one-codon” strategy to remain functional. Finally, a synthetic neochromsome with the reconstructed genes is assembled which could substitute chrXIIL for viability. Together, our work not only highlights the high plasticity of yeast genome, but also illustrates the possibility of making functional eukaryotic chromosomes from entirely artificial sequences.

Abstract Mobilized peripheral blood is increasingly used instead of bone marrow as a source of autologous hematopoietic stem/progenitor cells for ex vivo gene therapy. Here, we present an unplanned exploratory analysis evaluating the hematopoietic reconstitution kinetics, engraftment and clonality in 13 pediatric Wiskott-Aldrich syndrome patients treated with autologous lentiviral-vector transduced hematopoietic stem/progenitor cells derived from mobilized peripheral blood (n = 7), bone marrow (n = 5) or the combination of the two sources (n = 1). 8 out of 13 gene therapy patients were enrolled in an open-label, non-randomized, phase 1/2 clinical study (NCT01515462) and the remaining 5 patients were treated under expanded access programs. Although mobilized peripheral blood- and bone marrow- hematopoietic stem/progenitor cells display similar capability of being gene-corrected, maintaining the engineered grafts up to 3 years after gene therapy, mobilized peripheral blood-gene therapy group shows faster neutrophil and platelet recovery, higher number of engrafted clones and increased gene correction in the myeloid lineage which correlate with higher amount of primitive and myeloid progenitors contained in hematopoietic stem/progenitor cells derived from mobilized peripheral blood. In vitro differentiation and transplantation studies in mice confirm that primitive hematopoietic stem/progenitor cells from both sources have comparable engraftment and multilineage differentiation potential. Altogether, our analyses reveal that the differential behavior after gene therapy of hematopoietic stem/progenitor cells derived from either bone marrow or mobilized peripheral blood is mainly due to the distinct cell composition rather than functional differences of the infused cell products, providing new frames of references for clinical interpretation of hematopoietic stem/progenitor cell transplantation outcome.

LATS1/2 kinases are reported to be tumour suppressors in many cancers. Here the authors show that conditional deletion of LATS1/2 in the mature mouse luminal mammary epithelium leads to luminal-basal plasticity and development of basal-like carcinomas.

The spectrally narrow photoluminescence lines occurring in transition metal dichalcogenides (TMD) heterostructures at low temperature have been attributed to interlayer excitons (IXs) localized by the moiré potential between the TMD layers. Here, the authors show that these lines are present even when the moiré potential is suppressed by inserting an hBN spacer between the TMD layers.

Genetic association studies for rare variants suffer from lack of power and thus there is a need for methods to improve rare variant discovery. Here, the authors present functionally informed association tests with increased statistical power to aid discovery and interpretation of rare variants.

Most neuroimaging studies are associated with a broad range analytic and methodological choices that the researcher needs to make, but every choice might lead to different answers, and evaluating all possible analytic choices is computationally challenging. Here, authors present a framework that maps the space of analysis by creating a low-dimensional space and using a Bayesian optimization to navigate it.

Large amounts of interaction data are collected by messaging apps, mobile phone carriers, and social media. Creţu et al. propose a behavioral profiling attack model and show that the stability of people’s interaction networks over time can allow individuals to be re-identified in interaction datasets.

Elastic strain is being increasingly employed to enhance the catalytic properties of mixed ion-electron conducting oxides. However, its effect on oxygen storage capacity is not well established. Here, we fabricate ultrathin, coherently strained films of CeO2-δ between 5.6% biaxial compression and 2.1% tension. In situ ambient pressure X-ray photoelectron spectroscopy reveals up to a fourfold enhancement in equilibrium oxygen storage capacity under both compression and tension. This non-monotonic variation with strain departs from the conventional wisdom based on a chemical expansion dominated behaviour. Through depth profiling, film thickness variations and a coupled photoemission-thermodynamic analysis of space-charge effects, we show that the enhanced reducibility is not dominated by interfacial effects. On the basis of ab initio calculations of oxygen vacancy formation incorporating defect interactions and vibrational contributions, we suggest that the non-monotonicity arises from the tetragonal distortion under large biaxial strain. These results may guide the rational engineering of multilayer and core-shell oxide nanomaterials.

Deep learning is becoming a popular approach for understanding biological processes but can be hard to adapt to new questions. Here, the authors develop Janggu, a python library that aims to ease data acquisition and model evaluation and facilitate deep learning applications in genomics.

While inorganic semiconductors are well-studied for their solar-to-fuel energy conversion abilities, organic materials receive far less attention. Here, authors prepare linear conjugated polymers as H2 evolution photocatalysts and rationalize photocatalytic activities with fundamental properties.

The unique contributions of different frontoparietal networks (FPNs) in cognition remains unclear. Here, authors use neuroadaptive Bayesian optimization to identify cognitive tasks that segregate dorsal and ventral FPNs and reveal complex many-to-many mappings between cognitive tasks and FPNs.

Owing to their layered nature, transition metal dichalcogenides possess an anisotropic electronic structure whose impact on carrier dynamics is not fully known. Here, the authors use X-ray spectroscopy to unveil the electronic coupling and attosecond dynamics in SnS2, a prototypical van der Waals layered crystal.

The surface oxygen storage capacity is an important metric of catalytic activity, but its dependence on strain is not well characterized. Here, the authors show the surface oxygen nonstoichiometry in coherently strained CeO2-δ films increases non-monotonically with biaxial strain.