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Novel strategy for whole-genome sequencing of hepatitis A virus using NGS illumina technology and phylogenetic comparison with partial VP1/2A genomic region

Selective adsorption mechanism of a new combined collector on the surfaces of quartz and potassium feldspar

This study presents a novel methodology for the separation of quartz and feldspar under neutral and weakly alkaline conditions. Ethyl-bis(dodecyl dimethyl ammonium bromide) (Gemini) is introduced as a new collector in the flotation process, combined with sodium oleate (NaOL) to enhance separation efficiency. The investigation focuses on the adsorption mechanism of these combined collectors on mineral surfaces. While the individual collectors, Gemini and NaOL, were ineffective in differentiating between quartz and feldspar, their combination resulted in significantly improved separation outcomes. Flotation tests indicated that at a pulp pH of 7, with Gemini and NaOL at concentrations of 12 × 10−5 mol l−1 and molar ratios of 1:1 and 1:2, the flotation recovery of quartz was 46.51% and 40.57% higher than that of potassium feldspar, respectively. Zeta potential measurements, Fourier transform infrared spectroscopy, x-ray photoelectron spectroscopy analyses, and molecular dynamics simulations demonstrate that the Gemini collector predominantly influences the flotation performance of quartz and feldspar. NaOL molecules do not directly adsorb onto the quartz surface; instead, they co-adsorb via electrostatic interactions with Gemini, which minimally affects the interaction dynamics. In contrast, NaOL preferentially adsorbs onto the aluminum, silicon, and other reactive sites on the feldspar surface through its –COO functional group, leading to competitive adsorption with Gemini and consequently diminishing Gemini’s effectiveness on feldspar. This study elucidates the selective separation mechanism of quartz and feldspar using Gemini and NaOL and aims to provide insights into employing combined collectors in diverse separation scenarios to enhance quartz quality.

Compliance with smoke-free laws in hospitality venues in Ethiopia: A cross-sectional observational study in 10 cities

Background The 2019 Ethiopia’s comprehensive tobacco control proclamation mandates 100% smoke-free public places and workplaces. Despite the proclamation, compliance remains uncertain, particularly at hospitality venues (HVs). The aim of this study was to evaluate the extent of compliance with smoke-free laws in HVs and to also understand the factors associated with non-compliance. Methods This cross-sectional observational study was conducted in 10 cities in Ethiopia—Addis Ababa, Adama, Assosa, Bahir Dar, Dire Dawa, Gambella, Harar, Hawassa, Jigjiga, and Semera-Logia -between December 5th and 28th, 2022. Data were collected electronically using smartphones, utilizing a pre-tested, standardized checklist and covert observation. The subjects were selected through multi-stage cluster sampling. A total of 1,370 HVs (hotels, restaurants, bars, bars and restaurants, café and restaurants, butcher houses and restaurants, groceries, and nightclubs/ lounges) were observed. Specific and composite compliance indicators were computed for indoor and outdoor spaces. Poisson regression analyses identified factors associated with indoor active smoking and non-compliance. Statistical significance was set at P<0.05. Data were analyzed using SPSS version 26. Results Among the 1,370 HVs included in this study, 1,368 had indoor spaces, 327 had both indoor and outdoor spaces, and two had only outdoor spaces. Active smoking was observed in 32.2% (95% CI:30–35) of indoor HVs, with the highest rates in nightclubs/lounges (68.6%) and bars (65.7%). Semera-Logia reported the highest prevalence of active smoking (70.4%). Adherence with ‘no smoking’ signage was low (35.2%), while ashtrays, lighters, and designated smoking areas (DSAs) were rarely present. Outdoor active smoking was observed in 46.5% (95% CI:41–52) of HVs. Only 12.8% of indoor spaces were fully adherent to the smoke-free law requirements. Venues in Semera-Logia were over twice as likely to have active smoking (adjusted prevalence ratio [aPR]: 2.71; 95% CI: 2.00–3.66) compared to Addis Ababa. Bars and nightclubs/lounges had significantly higher prevalence of active smoking than cafés/restaurants. ‘No smoking’ signs were associated with reduced prevalence of indoor active smoking (aPR: 0.77; 95% CI: 0.67–0.89), while smoking within a 10-meter range (aPR: 2.67; 95% CI: 2.13–3.32), the presence of lighters (aPR: 1.69; 95% CI: 1.41–2.02), and the sale of tobacco products (aPR: 1.58; 95% CI: 1.34–1.86) were all associated with higher prevalence of indoor active smoking. Conclusion Compliance with ‘no active smoking’ and adherence to smoke-free laws in HVs remain low, particularly in bars, nightclubs/lounges, and Semera-Logia, with high rates of active smoking both indoors and outdoors. Enhanced enforcement and targeted are needed to educate the public and HV owners about the risks of SHS and the importance of tobacco control laws.

Within-project and cross-project defect prediction based on model averaging

Multi-center decomposition of molecular densities: A numerical perspective

In this study, we analyze various Iterative Stockholder Analysis (ISA) methods for molecular density partitioning, focusing on the numerical performance of the recently proposed Linear approximation of Iterative Stockholder Analysis (LISA) model [Benda et al., J. Chem. Phys. 156, 164107 (2022)]. We first provide a systematic derivation of various iterative solvers to find the unique LISA solution. In a subsequent systematic numerical study, we evaluate their performance on 48 organic and inorganic, neutral and charged molecules and also compare LISA to two other well-known ISA variants: the Gaussian iterative stockholder analysis and Minimum Basis Iterative Stockholder analysis (MBIS). The study reveals that LISA-family methods can offer a numerically more efficient approach with better accuracy compared to the two comparative methods. Moreover, the well-known issue with the MBIS method, where atomic charges obtained for negatively charged molecules are anomalously negative, is not observed in LISA-family methods. Despite the fact that LISA occasionally exhibits elevated entropy as a consequence of the absence of more diffuse basis functions, this issue can be readily mitigated by incorporating additional or integrating supplementary basis functions within the LISA framework. This research provides the foundation for future studies on the efficiency and chemical accuracy of molecular density partitioning schemes.

Isolation and characterization of 24 phages infecting the plant growth-promoting rhizobacterium Klebsiella sp. M5al

Bacteriophages largely impact bacterial communities via lysis, gene transfer, and metabolic reprogramming and thus are increasingly thought to alter nutrient and energy cycling across many of Earth’s ecosystems. However, there are few model systems to mechanistically and quantitatively study phage-bacteria interactions, especially in soil systems. Here, we isolated, sequenced, and genomically characterized 24 novel phages infecting Klebsiella sp. M5al, a plant growth-promoting, nonencapsulated rhizosphere-associated bacterium, and compared many of their features against all 565 sequenced, dsDNA Klebsiella phage genomes. Taxonomic analyses revealed that these Klebsiella phages belong to three known phage families (Autographiviridae, Drexlerviridae, and Straboviridae) and two newly proposed phage families (Candidatus Mavericviridae and Ca. Rivulusviridae). At the phage family level, we found that core genes were often phage-centric proteins, such as structural proteins for the phage head and tail and DNA packaging proteins. In contrast, genes involved in transcription, translation, or hypothetical proteins were commonly not shared or flexible genes. Ecologically, we assessed the phages’ ubiquity in recent large-scale metagenomic datasets, which revealed they were not widespread, as well as a possible direct role in reprogramming specific metabolisms during infection by screening their genomes for phage-encoded auxiliary metabolic genes (AMGs). Even though AMGs are common in the environmental literature, only one of our phage families, Straboviridae, contained AMGs, and the types of AMGs were correlated at the genus level. Host range phenotyping revealed the phages had a wide range of infectivity, infecting between 1–14 of our 22 bacterial strain panel that included pathogenic Klebsiella and Raoultella strains. This indicates that not all capsule-independent Klebsiella phages have broad host ranges. Together, these isolates, with corresponding genome, AMG, and host range analyses, help build the Klebsiella model system for studying phage-host interactions of rhizosphere-associated bacteria.

Leuconostoc lactis strain APC 3969 produces a new variant of cyclic bacteriocin leucocyclicin Q and displays potent anti-Clostridium perfringens activity

Adsorption of methanol on cationic cobalt clusters in the gas phase

Knowledge about the adsorption and activation of methanol on metal catalysts is essential to obtain insights into the conversion of methanol to sustainable chemicals. In this work, the adsorption of methanol on Con+ (n = 1–60) clusters is investigated using low-pressure collision cell experiments in combination with time-of-flight mass spectrometry. Experiments are conducted using both methanol and deuterated methanol in order to examine potential isotope effects and to gain insights into the reaction mechanism. Kinetic data and Rice–Ramsperger–Kassel–Marcus calculations indicate the absence of methanol desorption for n < 10 cluster sizes, suggesting dissociative chemisorption of methanol for those sizes. For larger clusters, the reaction involves a combination of association and desorption, with a pronounced size dependence of the corresponding reaction rates. This size dependence is anti-correlated with the promotion energy of an electron from an occupied frontier orbital to the lowest unoccupied d-state.

Controls on concentrations and clumped isotopologues of vehicle exhaust methane

Methane emissions from vehicle exhaust, as a source of methane, are often overlooked. However, in areas with high vehicle activity, the emissions can be substantial. There is a notable lack of characterization regarding the variable concentrations and isotopic signatures of methane in vehicle exhaust. This gap in knowledge limits our understanding of the mechanisms of methane production in vehicles and the factors controlling concentration variations and isotopic fractionation, which also makes it difficult to identify and reduce methane emissions from vehicle exhaust. This study characterized the methane concentration ([CH4]), methane-to-ethane ratio (C2:C1), methane carbon and hydrogen isotopes (δ13C and δD), and methane clumped isotopologues (Δ13CH3D and Δ12CH2D2) of the vehicle exhaust methane endmember. [CH4] varied widely from below 1 ppm to more than 3000 ppm, potentially influenced by vehicle maintenance and operational phases. Ethane concentrations ([C2H6]) correlated with [CH4], yet C2:C1 varied significantly from 0.1% to 18.3%. The δ13C and δD values of exhaust methane were less negative than those of natural gas. A large portion of samples showed a positive linear relationship between [CH4], δ13C from -22‰ to -11‰, and δD values from -170‰ to -120‰, while their clumped isotopologues exhibit ~0.8‰ clumping in Δ13CH3D and ~-2.4‰ anti-clumping in Δ12CH2D2. A small portion of the samples exhibited distinct isotopic characteristics, with their δ13C and δD values either becoming significantly more positive or aligning closer to the composition of ambient air, while their Δ12CH2D2 values showed a marked increase, reaching between +25‰ to +33‰. These concentration and isotope characteristics show trends that can be explained by a combination of processes, including 1) methane formation in the engine, 2) methane combustion in the engine, 3) methane oxidation by the catalytic converter, and 4) mixing with air. The observed isotopic fractionation can be explained by thermo equilibrium and Rayleigh fractionations. These processes, elucidated through isotopic and clumped isotopologue analyses, underscore the intricate dynamics and controls of vehicular methane emissions.

Author Correction: Temporal dynamics of uncertainty and prediction error in musical improvisation across different periods

Liouville-space response theory in the self-consistent field approximation

We present a second-quantization based Liouville-space formulation of response theory for non-eigenstates of unperturbed Hamiltonian in the single-determinant self-consistent field framework, where we include a time-independent relaxation superoperator in the Liouville equation of motion. This density-based formulation uses quantities and concepts similar to those introduced in established wave function-based forms of approximate-state response theory, and we discuss how the wave function-based class of theory relates to the present more general treatment. We also discuss various aspects of the present methodology, including its opportunities and limitations/challenges, and outline future work.

Epidemiology, literacy, risk factors, and clinical status of oral cancer in East Africa: A scoping review

Background Oral cancer (OC) is a topical public health issue in East Africa due to increasing incidence of the disease. Public health efforts to address the oral cancer burden depends largely on the available empirical evidence. Hence, this scoping review aims to map the existing empirical evidence on oral cancer in East African countries. Methods The Preferred Reporting Items for Systematic Review and Meta-analysis Extension for Scoping Reviews (PRISMA-ScR) was used as a guideline for reporting this scoping review. Additionally, we ensured quality assessment of the methodology and reporting process of this study using the AMSTAR 2 checklist. We conducted a systematic search of nine research databases on 17th November 2023, and reviewed studies published in English from year 2000 to 17th November 2023. The team developed data extraction form and data extraction was done by two reviewers. Thematic analyses were conducted manually and presented in texts, tables and flow chart. Results Only 30 full manuscripts were included in this review. Twenty-nine out of 30 studies were either hospital- or clinic-based while two were community-based. Only four studies showed gaps and obvious disparities in awareness and knowledge levels across East Africa, however, higher levels of awareness were reported among dentists and dental patients relative to the general population. Most neoplasms were presented and diagnosed late. The review finding also highlighted the significant impact of Toombak use on the oral microbiome composition, potentially contributing to oral cancer risks. Further, this review elucidated the prognostic relevance of PD-L1 expression at the invasive tumor front and microbial composition, with Candida correlating with adverse prognosis and Malassezia showing associations with improved survival rates. Also, Toombak usage, tumor staging, and mucosal field alterations emerged as predictors of local recurrence, while lymph node involvement and extranodal extension were associated with regional recurrence among Sudanese cohorts. Finally, a few studies undertook an evaluation of instrument validity for OC detection, revealing promising outcomes concerning diagnostic accuracy and instrument reliability. Conclusions There is a dire need for targeted interventions and early detection strategies tailored to the unique epidemiological and clinical profiles of oral and maxillofacial tumors in East Africa. Public health interventions aimed at curbing the prevalence of Toombak use and promoting healthier lifestyle choices to reduce the oral diseases incidence in Sudan and other regions where these behaviors are prevalent remain germane.

Author Correction: Wild Andean camelids promote rapid ecosystem development after glacier retreat

High-energy irradiation of matrix isolated acetic acid yields a ·CH3⋯CO2 complex: A spectroscopic and <i>ab initio</i> study

The mechanism of the chemical transformations of isolated small organic molecules induced by high-energy radiation is of basic interest for astrophysics and astrochemistry. In this work, we first applied a combination of electron paramagnetic resonance (EPR) and Fourier-transform infrared (FTIR) spectroscopy to identify the products of the radiation-induced transformations of isolated CH3COOH and CD3COOH molecules. As revealed by EPR, ·CH3 (or ·CD3) is the principal primary radical generated from acetic acid in solid argon and xenon, while the FTIR results suggest that this radical is trapped mainly in the form of the ·CH3⋯CO2 radical–molecule complex. The assignment of this previously unknown complex was based on the complexation-induced shifts of the absorption bands corresponding to CH3OPLA and CO2bend vibration modes, confirmed by analysis of the kinetic curves, photochemical behavior, and comparison with the results of ab initio computations at the spin-unrestricted coupled-cluster singles, doubles, and perturbative triples level of theory. Most likely, the complex in matrices adopts the geometry close to the theoretically predicted structure with Cs symmetry stabilized by the C⋯C and O⋯H interactions. It was suggested that the complex could be produced via the intermediate formation of a CH3COOH+· radical cation deprotonating to the CH3COO· radical, which promptly decomposed to ·CH3 + CO2 fragments. We believe that the results obtained in this study may contribute to a better understanding of the processing of acetic acid molecules in astrophysically relevant ices under high-energy irradiation and give a valuable insight into the understanding of weak intermolecular interactions involving radicals relevant to atmospheric chemistry, combustion, and carbon dioxide conversion.

Impact of COVID-19 on admission and in-hospital mortality of patients with acute myocardial infarction in Korea: An interrupted time series analysis

Objectives The purpose of this study is to investigate the impact of COVID-19 on admission and in-hospital mortality of patients with acute myocardial infarction (AMI). Methods We constructed a dataset of monthly hospitalizations and mortality of inpatients with AMI from January 2017 to December 2021 utilizing the National Health Insurance Claims Data which covers nearly the entire population. Using an interrupted time series (ITS), we investigated how COVID-19 affected hospitalizations and in-hospital deaths of patients with AMI. Results During the study period, the average age of patients with AMI was 65.2–65.8 years, and the ratio of men to women was higher, with 73.0–75.3% of patients being men and 24.7–27.0% being women. ITS analysis showed that admission rates of patients with AMI decreased one per 100,000 population due to COVID-19 (P&lt;0.001). Reductions in admission rates were greatest among men, those aged 55 and older, and people with medical aid. COVID-19 did not affect inpatient mortality (p = 0.9608), but in-hospital mortality decreased from 12% to 7% in the medical aid group. Conclusion Overall, we found that COVID-19 had an impact on admission rates of patients with AMI but did not have a significant impact on in-hospital mortality. However, we also found differential impacts by sex, age, and socioeconomic status, indicating some may be more vulnerable. This highlights the importance of identifying and supporting these vulnerable populations to prevent poorer health outcomes.

Intradermally injected abobotulinumtoxinA administered preemptively before surgery alleviates post-surgical pain and normalizes behavior in a translational animal model

Rubber wear: Experiment and theory

We study the wear rate (mass loss per unit sliding distance) of a tire tread rubber compound sliding on concrete paver surfaces under dry and wet conditions, at different nominal contact pressures of σ0 = 0.12, 0.29, and 0.43 MPa, and sliding velocities ranging from v = 1 μm s−1 to 1 cm s−1. We find that the wear rate is proportional to the normal force and remains independent of the sliding speed. Sliding in water and soapy water results in significantly lower wear rates compared to dry conditions. The experimental data are analyzed using a theory that predicts wear rates and wear particle size distributions consistent with the experimental observations.

Identification of novel proteins associated with intelligence by integrating genome-wide association data and human brain proteomics

While genome-wide association studies (GWAS) have identified genetic variants associated with intelligence, their biological mechanisms remain largely unexplored. This study aimed to bridge this gap by integrating intelligence GWAS data with human brain proteomics and transcriptomics. We conducted proteome-wide (PWAS) and transcriptome-wide (TWAS) association studies, along with enrichment and protein-protein interaction (PPI) network analyses. PWAS identified 44 genes in the human brain proteome that influence intelligence through protein abundance regulation (FDR P &lt;  0.05). Causal analysis revealed 36 genes, including GPX1, involved in the cis-regulation of protein abundance (P &lt;  0.05). In independent PWAS analyses, 17 genes were validated, and 10 showed a positive correlation with intelligence (P &lt;  0.05). TWAS revealed significant SNP-based heritability for mRNA in 28 proteins, and cis-regulation of mRNA levels for 20 genes was nominally associated with intelligence (FDR P &lt;  0.05). This study identifies key genes that bridge genetic variants and protein-level mechanisms of intelligence, providing novel insights into its biological pathways and potential therapeutic targets.

Vertical structure of subsurface marine heatwaves in a shallow nearshore upwelling system

Abstract Marine heatwaves (MHWs) are increasing in frequency and intensity globally and are among the greatest threats to marine ecosystems. However, limited studies have characterized subsurface MHWs, particularly in shallow waters. We utilized nearly two decades of full water-column (~ 10 m) observations from a unique automated profiler in central California to characterize, for the first time, the vertical structure of MHWs in a shallow nearshore upwelling system. We found MHWs have similar average durations and intensities across all depths, but there were ~ 17% more bottom MHW days than surface MHW days. Nearly one third of bottom MHWs occurred independently of surface MHWs, indicating that satellites miss a significant fraction of events. MHWs showed distinct seasonality with more frequent and intense events during the fall/winter when weak stratification allowed for MHWs to occupy a larger portion of the water column and persist longer. During summer, strong stratification limited the vertical extent of MHWs, leading to surface- and bottom-trapped events with shorter durations and intensities. Additionally, MHW initiation and termination across depths was consistently linked to anomalously low and high coastal upwelling, respectively. This study highlights the need for expansion of subsurface monitoring of MHWs globally amid a warming planet.

Accurate prediction of electron correlation energies of topological atoms by delta learning from the Müller approximation

FFLUX is a polarizable machine-learning force field that deploys pre-trained kernel-based models of quantum topological properties in molecular dynamics simulations. Despite a track record of successful applications, this unconventional force field still uses Lennard-Jones parameters to account for dispersion effects when performing in-bulk simulations. However, optimal Lennard-Jones parameters are system-dependent and not easy to calibrate. Fortunately, physics-informed dispersion energies can be obtained from the two-particle density matrix (2PDM) of any system using correlated wavefunctions. The only challenge is that the 2PDM is a humongous object whose calculation is very time-consuming and memory-greedy. In this proof-of-concept study, we utilize the Δ-learning method to address both problems using a small set of water trimers. More specifically, we obtain pure two-electron correlation energies with the aug-cc-pVDZ basis set at the cost of Müller-approximated 2PDM calculated at a very small basis set, 6-31+G(d). We also benchmark different Δ-learning tasks designed by changing the baseline and target method and/or the basis set. Our experiments suggest that two-electron correlation energies of weakly relaxed water trimers can be accurately predicted via Δ-learning with a maximum absolute error of 1.30 ± 0.32 kJ/mol traded against a colossal computational speed-up of roughly 40 times.