Stepwise reduction of an asymmetric π-expanded pyracylene towards the crystalline radical trianion.

The chemical reduction of a pyracylene-hexa--hexabenzocoronene-(HBC)-fused nanographene TPP was investigated with K and Rb metals to reveal its multi-electron acceptor abilities. The reaction of TPP with the above alkali metals, monitored by UV-vis-NIR and H NMR spectroscopy, evidenced the stepwise reduction process. The use of different solvents and secondary ligands enabled isolation of single crystals of three different reduced states of TPP with 1, 2, and 3 electrons added to its π-system.

Using Energetic Information Quantities from Density Functional Theory to Simultaneously Identify Both Covalent and Noncovalent Interactions.

Covalent bonding and noncovalent interactions are important chemical concepts and how to identify them has been of current interest in the literature. Within the framework of density functional theory (DFT), we recently proposed a few qualitative descriptors to categorize different types of interactions with Pauli energy and its derivatives. In this work, we expand the scope by including the quantities derived from energetic information, which were recently proposed and thoroughly investigated by us from the framework of information-theoretic approach (ITA) in DFT.

Quantum Broadcast Channel Simulation via Multipartite Convex Splitting.

We show that the communication cost of quantum broadcast channel simulation under free entanglement assistance between the sender and the receivers is asymptotically characterized by an efficiently computable single-letter formula in terms of the channel's multipartite mutual information. Our core contribution is a new one-shot achievability result for multipartite quantum state splitting via multipartite convex splitting. As part of this, we face a general instance of the quantum joint typicality problem with arbitrarily overlapping marginals.

Deep learning for augmented process monitoring of scalable perovskite thin-film fabrication.

Reproducible large-area fabrication is one of the remaining challenges for the commercialization of perovskite photovoltaics. Imaging methods augmented with deep learning (DL) enable in-line detection of spatial or temporal inconsistencies and predict the impact of observed changes on device performance. In this work, we showcase three use cases of how DL augments complex experimental data analysis of the large-area perovskite thin film formation, even on moderate-sized datasets.

Electro-driven direct lithium extraction from geothermal brines to generate battery-grade lithium hydroxide.

As Li-ion batteries are increasingly being deployed in electric vehicles and grid-level energy storage, the demand for Li is growing rapidly. Extracting lithium from alternative aqueous sources such as geothermal brines plays an important role in meeting this demand. Electrochemical intercalation emerges as a promising Li extraction technology due to its ability to offer high selectivity for Li and its avoidance of harsh chemical regenerants.

Kohn-Sham inversion for open-shell systems.

Methods based on density-functional theory usually treat open-shell atoms and molecules within the spin-unrestricted Kohn-Sham (KS) formalism, which breaks symmetries in real and spin space. Symmetry breaking is possible because the KS Hamiltonian operator does not need to exhibit the full symmetry of the physical Hamiltonian operator, but only the symmetry of the spin density, which is generally lower. Symmetry breaking leads to spin contamination and prevents a proper classification of the KS wave function with respect to the symmetries of the physical electron system.

Modeling tumor dynamics and predicting response to chemo-, targeted-, and immune-therapies in a murine model of pancreatic cancer.

We seek to establish a parsimonious mathematical framework for understanding the interaction and dynamics of the response of pancreatic cancer to the NGC triple chemotherapy regimen (mNab-paclitaxel, gemcitabine, and cisplatin), stromal-targeting drugs (calcipotriol and losartan), and an immune checkpoint inhibitor (anti-PD-L1). We developed a set of ordinary differential equations describing changes in tumor size (growth and regression) under the influence of five cocktails of treatments. Model calibration relies on three tumor volume measurements obtained over a 14-day period in a genetically engineered pancreatic cancer model (KrasLSLG12D-Trp53LSLR172H-Pdx1-Cre).

Evaluating Variational Quantum Eigensolver Approaches for Simplified Models of Molecular Systems: A Case Study on Protocatechuic Acid.

The Variational Quantum Eigensolver (VQE) is a hybrid algorithm that combines quantum and classical computing to determine the ground-state energy of molecular systems. In this context, this study applies VQE to investigate the ground state of protocatechuic acid, analyzing its performance with various Ansatzes and active spaces. Subsequently, all VQE results were compared to those obtained with the CISD and FCI methods.

Mode of Metal Ligation Governs Inhibition of Carboxypeptidase A.

Carboxypeptidase is a Zn-dependent protease that specifically recognises and hydrolyses peptides with a hydrophobic side chain at the C-terminal residue. According to hydrolysis mechanisms proposed in the literature, catalysis requires a water molecule to be close to the Zn ion so as to be activated as a nucleophile. Among small molecules that resemble the slowly hydrolysed Gly-Tyr peptide, which have been previously designed as inhibitors and characterised structurally, a variant with the terminal amino acid in a D-configuration has been the most effective.

Curvilinear incidence models for parity in the entire fertility range for cancers of the breast, ovary, and endometrium: A follow-up of the Norwegian 1960 Census.

The protective effect of parity has been demonstrated for cancer of the breast, ovary, and endometrium but no studies have estimated the effect of each subsequent birth in women with 10 or more children or grand-grand parity women, nor compared the linear relationship of the three cancers sites. Here, we aim to explore these relationships based on the Norwegian 1960 Census. The question of parity in present marriage was answered by 385,816 women born 1870-1915, a period with high fertility.

SEAD reference panel with 22,134 haplotypes boosts rare variant imputation and genome-wide association analysis in Asian populations.

Limited whole genome sequencing (WGS) studies in Asian populations result in a lack of representative reference panels, thus hindering the discovery of ancestry-specific variants. Here, we present the South and East Asian reference Database (SEAD) panel ( https://imputationserver.westlake.

DMRIntTk: Integrating different DMR sets based on density peak clustering.

Background: Identifying differentially methylated regions (DMRs) is a basic task in DNA methylation analysis. However, due to the different strategies adopted, different DMR sets will be predicted on the same dataset, which poses a challenge in selecting a reliable and comprehensive DMR set for downstream analysis.

Results: Here, we develop DMRIntTk, a toolkit for integrating DMR sets predicted by different methods on a same dataset.

Parallelization of particle-based reaction-diffusion simulations using MPI.

Particle-based reaction-diffusion models offer a high-resolution alternative to the continuum reaction-diffusion approach, capturing the discrete and volume-excluding nature of molecules undergoing stochastic dynamics. These methods are thus uniquely capable of simulating explicit self-assembly of particles into higher-order structures like filaments, spherical cages, or heterogeneous macromolecular complexes, which are ubiquitous across living systems and in materials design. The disadvantage of these high-resolution methods is their increased computational cost.

Dynamics of SARS-CoV-2 lineages in children and adults in 2021 and 2022.

Purpose: We aimed to describe SARS-CoV-2 lineages and diversity in children and adults in Estonia and similarity to travel-related cases and neighbouring countries.

Methods: SARS-CoV-2 sequences in 2021-2022 from a nationwide study were included. The proportion of predominant lineages in Estonian regions and among travel-related cases was described by multinomial logistic regression.

Effects of combined exposure to PM, O, and NO on health risks of different disease populations in the Beijing-Tianjin-Hebei region.

Air pollution adversely affects people's health. Under the current background of compound air pollution in China, the emission reduction potential of air pollution control has significantly decreased, and there are few studies on multi-pollutant emission reduction and synergistic effects. PM, O, and NO have caused the enormous disease burden and health risks.

Addressing the Evolution of Cardenolide Formation in Iridoid-Synthesizing Plants: Site-Directed Mutagenesis of PRISEs (Progesterone-5β-Reductase/Iridoid Synthase-like Enzymes) of Plantago Species.

Enzymes capable of processing a variety of compounds enable plants to adapt to diverse environmental conditions. PRISEs (progesterone-5β-reductase/iridoid synthase-like enzymes), examples of such substrate-promiscuous enzymes, are involved in iridoid and cardenolide pathways and demonstrate notable substrate promiscuity by reducing the activated C=C double bonds of plant-borne and exogenous 1,4-enones. In this study, we identified PRISE genes in () and (), and the corresponding enzymes were determined to share a sequence identity of 95%.

Exploring CRISPR-Cas9 HNH-Domain-Catalyzed DNA Cleavage Using Accelerated Quantum Mechanical Molecular Mechanical Free Energy Simulation.

The target DNA (tDNA) cleavage catalyzed by the CRISPR Cas9 enzyme is a critical step in the Cas9-based genome editing technologies. Previously, the tDNA cleavage from an active SpyCas9 enzyme conformation was modeled by Palermo and co-workers (Nierzwicki et al., , 912) using ab initio quantum mechanical molecular mechanical (ai-QM/MM) free energy simulations, where the free energy barrier was found to be more favorable than that from a pseudoactive enzyme conformation.

Antioxidant effect, DNA-binding, and transport of the flavonoid acacetin influenced by the presence of redox-active Cu(II) ion: Spectroscopic and in silico study.

Acacetin (AC) is a natural polyphenol from the group of flavonoids. It is well established that the behavior of flavonoids depends on the presence of redox-active substances; therefore, we aim to investigate their biological activity following the interaction with Cu(II) ion. Our study demonstrates that AC can effectively bind Cu(II) ions, as confirmed by UV-Vis and EPR spectroscopy as well as DFT calculations.

Workflow for practical quantum chemical calculations with a quantum phase estimation algorithm: electronic ground and π-π* excited states of benzene and its derivatives.

Quantum computers are expected to perform full-configuration interaction calculations with less computational resources compared to classical ones, thanks to the use of quantum phase estimation (QPE) algorithms. However, only a limited number of QPE-based quantum chemical calculations have been reported even for numerical simulations on a classical computer, and the practical workflow for the QPE computation has not yet been established. In this paper, we report the QPE simulations of the electronic ground and the π-π* excited singlet state of benzene and its chloro- and nitro-derivatives as the representative industrially important systems, with the aid of GPGPU acceleration of quantum circuit simulations.

A deep learning approach to real-time Markov modeling of ion channel gating.

The patch-clamp technique allows us to eavesdrop the gating behavior of individual ion channels with unprecedented temporal resolution. The signals arise from conformational changes of the channel protein as it makes rapid transitions between conducting and non-conducting states. However, unambiguous analysis of single-channel datasets is challenging given the inadvertently low signal-to-noise ratio as well as signal distortions caused by low-pass filtering.

What are microsatellites and how to choose the best tool: a user-friendly review of SSR and 74 SSR mining tools.

Microsatellites, also known as SSR or STR, are essential molecular markers in genomic research, playing crucial roles in genetic mapping, population genetics, and evolutionary studies. Their applications range from plant breeding to forensics, highlighting their diverse utility across disciplines. Despite their widespread use, traditional methods for SSR analysis are often laborious and time-consuming, requiring significant resources and expertise.

The use of assistive technology to promote practical skills in persons with autism spectrum disorder and intellectual disabilities: A systematic review.

Persons with autism spectrum disorder (ASD) and/or intellectual disability (ID) have difficulties in planning, organising and coping with change, which impedes the learning of daily living skills (DLSs), social participation and self-management across different environmental settings. Assistive technologies (ATs) is a broad term encompassing devices and services designed to support individuals with disabilities, and if used in a self-controlled manner, they may contribute inclusion in all domains of participation. This comprehensive literature review aims to critically assess and unify existing research that investigates the use of assistive technology within the practical domain for individuals with ASD and/or ID.

ChIP-Rx: Arabidopsis Chromatin Profiling Using Quantitative ChIP-Seq.

Chromatin immunoprecipitation followed by deep sequencing (ChIP-seq) is widely used to probe the chromatin landscape of transcription factors, chromatin components, and associated proteins. Conventional ChIP normalization procedures robustly allow estimating differences in local enrichment across genomic regions. Yet, inter-sample comparisons can be biased by technical variability and biological differences.