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Bilinguals often show evidence of cross language influences, such as facilitation in processing cognates. Here we use computational methods for analyzing spontaneous English texts written by hundreds of speakers of different L1s, at different levels of English proficiency, to investigate writers' preference for using cognates over alternative word choices. We focus on English, since a majority of its lexicon is either of Romance or Germanic origin, allowing an investigation of the preference of speakers of Germanic and Romance L1s towards cognates between their L1 and English. Results show that L2 writers tend to prefer English cognates, and that this tendency is weaker as English proficiency level increases, suggesting diminishing effects of CLI. However, a comparison of the L2 writers with native English writers shows general overuse of cognates only for the Germanic, but not the Romance, L1 speakers, most likely due to the register of argumentative writing. [ABSTRACT FROM AUTHOR]

Directed evolution, rational design and statistical methods are used for improving the capacity of toluene 4-monooxygenase (T4MO) to produce a potent antioxidant, hydroxytyrosol. The studies have shown that T4MO variants are improved for hydroxytyrosol biosynthesis by improving 2-phenylethanol (PEA) oxidation rate and integrating a substitution allowing hydroxytyrosol formation.

Sex differences in longevity may reflect sex-specific costs of intrasexual competition and reproductive effort. As male rhesus macaques experience greater intrasexual competition and die younger, we predicted that males would experience greater oxidative stress than females and that oxidative stress would reflect sex-specific measures of reproductive effort. Males, relative to females, had higher concentrations of 8-OHdG andmalondialdehyde, which aremarkers of DNA oxidative damage and lipid peroxidation, respectively. Older macaques had lower 8-OHdG levels than younger ones, suggesting that oxidative stress decreases in parallel with known age-related declines in reproductive investment. Among males, a recent period of social instability affected oxidative status:males who attacked others at higher rates had higher 8-OHdG levels. Multiparous lactating females with daughters had higher 8-OHdG levels than those with sons. No differences in antioxidant capacity were found. These results lend initial support for the use of oxidative stress markers to assess trade-offs between reproductive effort and somatic maintenance in primates. [ABSTRACT FROM AUTHOR]

We study mathematically a method for discovering which gene is related to a cell characteristic (“phenotype”) of interest. The method is based on RNA interference – a molecular process for gene deactivation – and on coupling the phenotype with cell fluorescence. A small number of candidate genes are thus isolated, and then tested individually. We model probabilistically this process, prove a limit theorem for its outcome, and derive operational guidelines for maximizing the probability of successful gene discovery. [ABSTRACT FROM AUTHOR]

Most existing methods for improving protein activity are laborious and costly, as they either require knowledge of protein structure or involve expression and screening of a vast number of protein mutants. We describe here a successful first application of a novel approach, which requires no structural knowledge and is shown to significantly reduce the number of mutants that need to be screened. In the first phase of this study, around 7000 mutants were screened through standard directed evolution, yielding a 230-fold improvement in activity relative to the wild type. Using sequence analysis and site-directed mutagenesis, an additional single mutant was then produced, with 500-fold improved activity. In the second phase, a novel statistical method for protein improvement was used; building on data from the first phase, only 11 targeted additional mutants were produced through site-directed mutagenesis, and the best among them achieved a >1500-fold improvement in activity over the wild type. Thus, the statistical model underlying the experiment was validated, and its predictions were shown to reduce laboratory labor and resources.The ISME Journal (2008) 2, 171–179; doi:10.1038/ismej.2007.100; published online 22 November 2007 [ABSTRACT FROM AUTHOR]

Background: Metabolic dysfunction-associated steatotic liver disease (MASLD) is associated with an unhealthy lifestyle. However, there is limited prospective evidence regarding the association between combined lifestyle factors and MASLD. This study aims to test the association of a combination of lifestyle components, expressed as a healthy lifestyle index (HLI), and unhealthful eating behavior habits with MASLD, insulin resistance (IR), liver fibrosis, and metabolic dysfunction-associated steatohepatitis., Methods: A prospective cohort study was conducted among participants of metabolic and hepatic screening surveys. MASLD was evaluated by ultrasonography or controlled attenuation parameter at 2 time points to assess new-onset, persistence, or remission, and IR was estimated by homeostasis model assessment. Presumed liver fibrosis and metabolic dysfunction-associated steatohepatitis were evaluated using FibroMax biomarkers. The HLI was calculated as the sum of 4 lifestyle components: nonsmoking, healthy weight, healthy diet, and physical activity., Results: The final cohort included 315 subjects with 6.7 years of follow-up, 40-70 years old. In multivariable analyses, a favorable lifestyle (≥3 components) was independently associated with lower odds of new-onset MASLD (OR = 0.42; 95% CI: 0.19-0.90). Similarly, a favorable lifestyle was associated with lower odds of new-onset/persistent (vs. never/remission) MASLD and IR, respectively (OR = 0.49; 95% CI: 0.30-0.80; OR = 0.40; 95% CI: 0.24-0.66). There was a dose-response association between HLI and new-onset/persistent MASLD and IR. A favorable lifestyle was associated with lower odds of new-onset metabolic dysfunction-associated steatohepatitis (OR = 0.50; 95% CI: 0.27-0.95). Adjusting for HLI, unhealthful eating behavior habits were associated with higher odds of MASLD prevalence (OR = 1.81; 95% CI: 1.07-3.06)., Conclusions: Adherence to a healthy lifestyle is prospectively associated with lower odds of MASLD, markers of liver damage, and IR. A holistic approach that considers overall lifestyle and eating behavior may be useful for preventing MASLD., (Copyright © 2024 The Author(s). Published by Wolters Kluwer Health, Inc. on behalf of the American Association for the Study of Liver Diseases.)

Statement of Problem: As part of the growing digitization of the dental field, clinicians are looking for ways to simplify digital workflow, reduce chairside time, and provide new work patterns for future applications. Whether scanning with a multifunctional apparatus (MFA) scan body results in improved scanning is unclear., Purpose: The purpose of this in vitro study was to compare the horizontal, vertical, and angular deviations with the MFA scan body with a commercially available scan body (SBIO)., Material and Methods: Sixteen identically printed edentulous maxillary models were used to plan two Ø3.8×11.5-mm implants in the right maxillary first molar and left maxillary central incisor locations. Two implants in each model were installed using a surgical guide. The models were scanned using an intraoral scanner with MFA and then rescanned twice, with SBIO using the intraoral scanner and a laboratory 3D scanner. The implants were digitally positioned according to the scanned MFA and SBIO locations in standard tessellation language (STL) files. These STL files were superimposed on the reference laboratory 3D scanner STL files. Linear measurements included implant apex/cervical horizontal/vertical deviations, as well as implant axis angular deviations. Normality was evaluated with the Shapiro-Wilk test. Paired samples t tests (2 sided) were used for the mean SBIO-MFA deviation difference. To compare the molar/incisor sites, paired samples Wilcoxon tests were used (α=.05 for all tests)., Results: No statistically significant differences were found between the MFA/ SBIO deviations, for each of the 10 sites × deviation combinations (P>.05). Overall, the lowest endpoint of the 95% confidence intervals among the 8 linear measurement comparisons was -0.107 mm (coronal vertical deviation, right maxillary first molar site) and -0.30 degrees between the 2 angular measurement comparisons., Conclusions: The current in vitro study demonstrated high accuracy for the novel MFA device, similar to that of the standard SBIO scan body. Furthermore, the current study offers an alternative technique to evaluate the accuracy of implant placement by using scanning and back programming over the traditional postplacement cone beam computed tomography (CBCT) scanning., (Copyright © 2024 Editorial Council for The Journal of Prosthetic Dentistry. Published by Elsevier Inc. All rights reserved.)

Directed evolution has emerged as an important tool for engineering proteins with improved or novel properties. Because of their inherent reliance on randomness, directed evolution protocols are amenable to probabilistic modeling and analysis. This chapter summarizes and reviews in a nonmathematical way some of the probabilistic works related to directed evolution, with particular focus on three of the most widely used methods: saturation mutagenesis, error-prone PCR, and in vitro recombination. The ultimate aim is to provide the reader with practical information to guide the planning and design of directed evolution studies. Importantly, the applications and locations of freely available computational resources to assist with this process are described in detail.