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Dynamic in-situ reconstruction of active site circulators for photo-Fenton-like reactions
Carbohydrate intake and activation of gastric acid secretion decrease gastric estrogen secretion
Large-scale biosynthetic analysis of human microbiomes reveals diverse protective ribosomal peptides
Genomic and metabolomic insights into the antimicrobial compounds and plant growth-promoting potential of Bacillus velezensis B115
Mechanism of quiescent nanoplastic formation from semicrystalline polymers
Gender differences in L1 vertebral strength in adults 50+ using automated CT-based finite element analysis
Cell-cycle dependent DNA repair and replication unifies patterns of chromosome instability
Abstract Chromosomal instability (CIN) is pervasive in human tumours and often leads to structural or numerical chromosomal aberrations. Somatic structural variants (SVs) are intimately related to copy number alterations but the two types of variant are often studied independently. Additionally, despite numerous studies on detecting various SV patterns, there are still no general quantitative models of SV generation. To address this issue, we develop a computational cell-cycle model for the generation of SVs from end-joining repair and replication after double-strand break formation. Our model provides quantitative information on the relationship between breakage fusion bridge cycle, chromothripsis, seismic amplification, and extra-chromosomal circular DNA. Given whole-genome sequencing data, the model also allows us to infer important parameters in SV generation with Bayesian inference. Our quantitative framework unifies disparate genomic patterns resulted from CIN, provides a null mutational model for SV, and reveals deeper insights into the impact of genome rearrangement on tumour evolution.
Tailoring adversarial attacks on deep neural networks for targeted class manipulation using DeepFool algorithm
Abstract The susceptibility of deep neural networks (DNNs) to adversarial attacks undermines their reliability across numerous applications, underscoring the necessity for an in-depth exploration of these vulnerabilities and the formulation of robust defense strategies. The DeepFool algorithm by Moosavi-Dezfooli et al. (2016) represents a pivotal step in identifying minimal perturbations required to induce misclassification of input images. Nonetheless, its generic methodology falls short in scenarios necessitating targeted interventions. Additionally, previous research studies have predominantly concentrated on the success rate of attacks without adequately addressing the consequential distortion of images, the maintenance of image quality, or the confidence threshold required for misclassification. To bridge these gaps, we introduce the Enhanced Targeted DeepFool (ET DeepFool) algorithm, an evolution of DeepFool that not only facilitates the specification of desired misclassification targets but also incorporates a configurable minimum confidence score. Our empirical investigations demonstrate the superiority of this refined approach in maintaining the integrity of images and minimizing perturbations across a variety of DNN architectures. Unlike previous iterations, such as the Targeted DeepFool by Gajjar et al. (2022), our method grants unparalleled control over the perturbation process, enabling precise manipulation of model responses. Preliminary outcomes reveal that certain models, including AlexNet and the advanced Vision Transformer, display commendable robustness to such manipulations. This discovery of varying levels of model robustness, as unveiled through our confidence level adjustments, could have far-reaching implications for the field of image recognition. Our code is available at https://github.com/FazleLabib/et_deepfool
PIP2-mediated oligomerization of the endosomal sodium/proton exchanger NHE9
Abstract The strict exchange of Na+ for H+ ions across cell membranes is a reaction carried out in almost every cell. Na+/H+ exchangers that perform this task are physiological homodimers, and whilst the ion transporting domain is highly conserved, their dimerization differs. The Na+/H+ exchanger NhaA from Escherichia coli has a weak dimerization interface mediated by a β-hairpin domain and with dimer retention dependent on cardiolipin. Similarly, organellar Na+/H+ exchangers NHE6, NHE7 and NHE9 also contain β-hairpin domains and recent analysis of Equus caballus NHE9 indicated PIP2 lipids could bind at the dimer interface. However, structural validation of the predicted lipid-mediated oligomerization has been lacking. Here, we report cryo-EM structures of E. coli NhaA and E. caballus NHE9 in complex with cardiolipin and phosphatidylinositol-3,5-bisphosphate PI(3,5)P2 lipids binding at their respective dimer interfaces. We further show how the endosomal specific PI(3,5)P2 lipid stabilizes the NHE9 homodimer and enhances transport activity. Indeed, we show that NHE9 is active in endosomes, but not at the plasma membrane where the PI(3,5)P2 lipid is absent. Thus, specific lipids can regulate Na+/H+ exchange activity by stabilizing dimerization in response to either cell specific cues or upon trafficking to their correct membrane location.
Poor sleep quality was associated with increased plasma aldosterone concentration in community dwellers, a cross-sectional study
Muscle-specific Ryanodine receptor 1 properties underlie limb-girdle muscular dystrophy 2B/R2 progression
Transcriptomic and metabolomic insights into flavor variations in wild and cultivated Agaricus bisporus
PinMyMetal: a hybrid learning system to accurately model transition metal binding sites in macromolecules
Green infrastructure site prioritization to improve urban flood resilience in Monterrey and Brussels using a decision support model
Abstract Green infrastructure (GI) has been increasingly associated with urban flood resilience as it provides benefits in protecting communities from flood dangers and improving socio-economic capabilities. In order to optimize the GI advantages, it is necessary to engage in strategic prioritizing of implementation areas, considering local conditions. Despite a growing interest in connecting GI and flood resilience, there is still a lack of strategic-oriented GI planning models aimed at enhancing urban flood resilience. This study has introduced the Flood Resilience-based Urban Green Infrastructure Site Priority (FRUGISP) model, which employs a GIS-based multi-criteria assessment to determine the urban regions that should be prioritized for the implementation of GI systems, based on their flood resilience levels. The model was used to map the priority areas in Monterrey, Mexico, and Brussels, Belgium. Despite their distinct features, both cities face flood challenges. The results showed regions of utmost importance based on the flood resilience index and land availability for GI implementation. The model has the potential to be applied to other urban areas grappling with flood issues, providing guidance to decision-makers in selecting high-priority locations for GI projects. This approach can effectively address the difficulties posed by urban floods, ensuring the resilience of urban areas.
A 2D hybrid perovskite ferroelectric with switchable polarization and photoelectric robustness down to monolayer
Abstract The continuous dimensional scaling of semiconductor and logic photoelectric device requires ferroelectrics to possess robust photoelectric activity and switchable polarization at the nanoscale. However, traditional ferroelectrics such as oxide perovskites generally suffer from relatively large bandgap and deteriorated ferroelectricity in ultrathin forms, while the polarization in many transition metal dichalcogenides is related to inter-layer effects, leading to ferroelectricity that only exists in flakes with a certain layer number and particular stacking forms. The associated challenging fabrication and high-cost synthesis of inorganic ferroelectrics currently render mass industrial production of ultrathin ferroelectric semiconductors impossible. Here with (isopentylammonium)2(ethylammonium)2Pb3I10, we report an organic-inorganic hybrid perovskite nanoflake with cheap solution synthesis, switchable polarization, a narrow bandgap (1.86 eV to 2.21 eV form bulk to monolayer), and robust photoelectric properties down to the monolayer. The present work reveals the great potential of 2D hybrid perovskite ferroelectrics as low-cost ferroelectric semiconductors at the nanoscale.
Exploring the applicability of “One-Size-Fits-All” road transport decarbonization strategies: a participatory energy systems modeling comparison of urban and non-urban municipalities
Abstract Despite the key role that local authorities play in shaping energy policies and implementing action plans, their level of involvement has been insufficiently examined. This study aims to assess how different socio-geographical factors impact the adoption of fossil-free vehicle technologies and fuels for private cars, buses, and trucks. Using a participatory energy systems modeling approach, this study explores the cost-optimal decarbonization of road transport in four urban and non-urban Swedish municipalities. By collaborating with local authorities, socio-technical scenarios are modeled to reflect climate actions, resources and infrastructure availability, as well as travel patterns. The findings reveal a preference for lower upfront costs in urban areas with shorter trip distances, leading to a higher small-size battery electric vehicles (BEVs) share. Conversely, in non-urban areas with longer trip distances, fuel economy, fuel cost, as well as operation and maintenance costs outweigh upfront costs, increasing average-size BEVs share. Buses and trucks also experience a growing BEVs and fuel cell vehicles (FCEVs) share, driven by their typically high annual mileage. Biofuels play an intermediate role until BEVs and FCEVs are reduced in cost. Tailoring decarbonization strategies to local contexts is essential for maximum effectiveness, balancing national and regional climate goals with urban and non-urban challenges.