Drakethorsen8197

Modeling human diseases as networks simplify complex multi-cellular processes, helps understand patterns in noisy data that humans cannot find, and thereby improves precision in prediction. Using Inflammatory Bowel Disease (IBD) as an example, here we outline an unbiased AI-assisted approach for target identification and validation. A network was built in which clusters of genes are connected by directed edges that highlight asymmetric Boolean relationships. Using machine-learning, a path of continuum states was pinpointed, which most effectively predicted disease outcome. This path was enriched in gene-clusters that maintain the integrity of the gut epithelial barrier. We exploit this insight to prioritize one target, choose appropriate pre-clinical murine models for target validation and design patient-derived organoid models. Potential for treatment efficacy is confirmed in patient-derived organoids using multivariate analyses. This AI-assisted approach identifies a first-in-class gut barrier-protective agent in IBD and predicted Phase-III success of candidate agents.The gymnosperm Welwitschia mirabilis belongs to the ancient, enigmatic gnetophyte lineage. It is a unique desert plant with extreme longevity and two ever-elongating leaves. We present a chromosome-level assembly of its genome (6.8 Gb/1 C) together with methylome and transcriptome data to explore its astonishing biology. We also present a refined, high-quality assembly of Gnetum montanum to enhance our understanding of gnetophyte genome evolution. The Welwitschia genome has been shaped by a lineage-specific ancient, whole genome duplication (~86 million years ago) and more recently (1-2 million years) by bursts of retrotransposon activity. High levels of cytosine methylation (particularly at CHH motifs) are associated with retrotransposons, whilst long-term deamination has resulted in an exceptionally GC-poor genome. Changes in copy number and/or expression of gene families and transcription factors (e.g. R2R3MYB, SAUR) controlling cell growth, differentiation and metabolism underpin the plant's longevity and tolerance to temperature, nutrient and water stress.The quantum Hall effect is the seminal example of topological protection, as charge carriers are transmitted through one-dimensional edge channels where backscattering is prohibited. Graphene has made its marks as an exceptional platform to reveal new facets of this remarkable property. However, in conventional Hall bar geometries, topological protection of graphene edge channels is found regrettably less robust than in high mobility semi-conductors. Here, we explore graphene quantum Hall regime at the local scale, using a scanning gate microscope. We reveal the detrimental influence of antidots along the graphene edges, mediating backscattering towards upstream edge channels, hence triggering topological breakdown. Combined with simulations, our experimental results provide further insights into graphene quantum Hall channels vulnerability. In turn, this may ease future developments towards precise manipulation of topologically protected edge channels hosted in various types of two-dimensional crystals.The nonlocal electron-phonon couplings in organic semiconductors responsible for the fluctuation of intermolecular transfer integrals has been the center of interest recently. Several irreconcilable scenarios coexist for the description of the nonlocal electron-phonon coupling, such as phonon-assisted transport, transient localization, and band-like transport. Through a nearly exact numerical study for the carrier mobility of the Holstein-Peierls model using the matrix product states approach, we locate the phonon-assisted transport, transient localization and band-like regimes as a function of the transfer integral (V) and the nonlocal electron-phonon couplings (ΔV), and their distinct transport behaviors are analyzed by carrier mobility, mean free path, optical conductivity and one-particle spectral function. We also identify an "intermediate regime" where none of the established pictures applies, and the generally perceived hopping regime is found to be at a very limited end in the proposed regime paradigm.Lipoproteins serve diverse functions in the bacterial cell and some are essential for survival. Some lipoproteins are adjuvants eliciting responses from the innate immune system of the host. The growing list of membrane enzymes responsible for lipoprotein synthesis includes the recently discovered lipoprotein intramolecular transacylase, Lit. Lit creates a lipoprotein that is less immunogenic, possibly enabling the bacteria to gain a foothold in the host by stealth. Here, we report the crystal structure of the Lit enzyme from Bacillus cereus and describe its mechanism of action. Lit consists of four transmembrane helices with an extracellular cap. Conserved residues map to the cap-membrane interface. They include two catalytic histidines that function to effect unimolecular transacylation. The reaction involves acyl transfer from the sn-2 position of the glyceryl moiety to the amino group on the N-terminal cysteine of the substrate via an 8-membered ring intermediate. Transacylation takes place in a confined aromatic residue-rich environment that likely evolved to bring distant moieties on the substrate into proximity and proper orientation for catalysis.Tuberous Sclerosis Complex (TSC) is caused by TSC1 or TSC2 mutations, resulting in hyperactivation of the mechanistic target of rapamycin complex 1 (mTORC1). Transcription factor EB (TFEB), a master regulator of lysosome biogenesis, is negatively regulated by mTORC1 through a RAG GTPase-dependent phosphorylation. Here we show that lysosomal biogenesis is increased in TSC-associated renal tumors, pulmonary lymphangioleiomyomatosis, kidneys from Tsc2+/- mice, and TSC1/2-deficient cells via a TFEB-dependent mechanism. Interestingly, in TSC1/2-deficient cells, TFEB is hypo-phosphorylated at mTORC1-dependent sites, indicating that mTORC1 is unable to phosphorylate TFEB in the absence of the TSC1/2 complex. Importantly, overexpression of folliculin (FLCN), a GTPase activating protein for RAGC, increases TFEB phosphorylation at the mTORC1 sites in TSC2-deficient cells. Overexpression of constitutively active RAGC is sufficient to relocalize TFEB to the cytoplasm. These findings establish the TSC proteins as critical regulators of lysosomal biogenesis via TFEB and RAGC and identify TFEB as a driver of the proliferation of TSC2-deficient cells.Magnetic skyrmions are nanoscale spin textures touted as next-generation computing elements. When subjected to lateral currents, skyrmions move at considerable speeds. Their topological charge results in an additional transverse deflection known as the skyrmion Hall effect (SkHE). While promising, their dynamic phenomenology with current, skyrmion size, geometric effects and disorder remain to be established. Here we report on the ensemble dynamics of individual skyrmions forming dense arrays in Pt/Co/MgO wires by examining over 20,000 instances of motion across currents and fields. The skyrmion speed reaches 24 m/s in the plastic flow regime and is surprisingly robust to positional and size variations. Meanwhile, the SkHE saturates at ∼22∘, is substantially reshaped by the wire edge, and crucially increases weakly with skyrmion size. Particle model simulations suggest that the SkHE size dependence - contrary to analytical predictions - arises from the interplay of intrinsic and pinning-driven effects. These results establish a robust framework to harness SkHE and achieve high-throughput skyrmion motion in wire devices.Homology-directed repair (HDR), a critical DNA repair pathway in mammalian cells, is complex, leading to multiple outcomes with different impacts on genomic integrity. However, the factors that control these different outcomes are often not well understood. Here we show that SWS1-SWSAP1-SPIDR controls distinct types of HDR. Despite their requirement for stable assembly of RAD51 recombinase at DNA damage sites, these proteins are not essential for intra-chromosomal HDR, providing insight into why patients and mice with mutations are viable. However, SWS1-SWSAP1-SPIDR is critical for inter-homolog HDR, the first mitotic factor identified specifically for this function. Furthermore, SWS1-SWSAP1-SPIDR drives the high level of sister-chromatid exchange, promotes long-range loss of heterozygosity often involved with cancer initiation, and impels the poor growth of BLM helicase-deficient cells. The relevance of these genetic interactions is evident as SWSAP1 loss prolongs Blm-mutant embryo survival, suggesting a possible druggable target for the treatment of Bloom syndrome.India has the world's highest number of undernourished children and the largest school feeding program, the Mid-Day Meal (MDM) scheme. As school feeding programs target children outside the highest-return "first 1000-days" window, they have not been included in the global agenda to address stunting. School meals benefit education and nutrition in participants, but no studies have examined whether benefits carry over to their children. Using nationally representative data on mothers and their children spanning 1993 to 2016, we assess whether MDM supports intergenerational improvements in child linear growth. Here we report that height-for-age z-score (HAZ) among children born to mothers with full MDM exposure was greater (+0.40 SD) than that in children born to non-exposed mothers. Associations were stronger in low socioeconomic strata and likely work through women's education, fertility, and health service utilization. MDM was associated with 13-32% of the HAZ improvement in India from 2006 to 2016.Does higher socioeconomic status predict decreased prosocial behavior? Methodological issues such as the reliance of survey studies on self-reported measures of prosociality, the insufficient control of relative incentives in experiments, and the use of non-random samples, have prevented researchers from ruling out that there is a negative association between socioeconomic status (SES) and prosociality. selleck chemicals llc Here, we present results from a field experiment on the willingness of unaware individuals of different SES to undertake an effortful prosocial task-returning a misdelivered letter. Specifically, using the rental or sale value of homes as indicators of SES, we randomly selected households of high and low SES and misdelivered envelopes to them. Despite controlling for numerous covariates and performing a series of ancillary tests, we fail to find any evidence that higher SES predicts decreased prosocial behavior. Instead, we find that misdelivered letters are substantially more likely to be returned from high rather than low SES households.We describe a case of posthumously diagnosed MIRAGE syndrome (Myelodysplasia, Infection, Restriction of growth, Adrenal hypoplasia, Genital problems, and Enteropathy) in a girl with a new pathogenic SAMD9 variant (p.F437S), who was initially considered to have familial dysautonomia (FD)-like disease due to increased levels of catecholamine metabolites. Functional analyses of F437S-SAMD9 were performed, showing characteristics of disease-causing variants. This new SAMD9 variant (p.F437S) also causes MIRAGE syndrome.