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  1. The ongoing COVID-19 pandemic continues to infect people worldwide, and the virus continues to evolve in significant ways which can pose challenges to the efficiency of available vaccines and therapeutic drugs and cause future pandemic. Therefore, it is important to investigate the binding and interaction of ACE2 with different RBD variants. A comparative study using all-atom MD simulations was conducted on ACE2 binding with 8 different RBD variants, including N501Y, E484K, P479S, T478I, S477N, N439K, K417N and N501YE484K- K417N on RBD. Based on the RMSD, RMSF, and DSSP results, overall the binding of RBD variants with ACE2 is stable, and the secondary structure of RBD and ACE2 are consistent after the point mutation. Besides that, a similar buried surface area, a consistent binding interface and a similar amount of hydrogen bonds formed between RBD and ACE2 although the exact residue pairs on the binding interface were modified. The change of binding free energy from point mutation was predicted using the free energy perturbation (FEP) method. It is found that N501Y, N439K, and K417N can strengthen the binding of RBD with ACE2, while E484K and P479S weaken the binding, and S477N and T478I have negligible effect on the binding. Point mutations modified the dynamic correlation of residues in RBD based on the dihedral angle covariance matrix calculation. Doing dynamic network analysis, a common intrinsic network community extending from the tail of RBD to central, then to the binding interface region was found, which could communicate the dynamics in the binding interface region to the tail thus to the other sections of S protein. The result can supply unique methodology and molecular insight on studying the molecular structure and dynamics of possible future pandemics and design novel drugs. 
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    Free, publicly-accessible full text available October 5, 2024
  2. Abstract

    Breast cancer has emerged as the most life-threatening disease among women around the world. Early detection and treatment of breast cancer are thought to reduce the need for surgery and boost the survival rate. The Magnetic Resonance Imaging (MRI) segmentation techniques for breast cancer diagnosis are investigated in this article. Kapur’s entropy-based multilevel thresholding is used in this study to determine optimal values for breast DCE-MRI lesion segmentation using Gorilla Troops Optimization (GTO). An improved GTO, is developed by incorporating Rotational opposition based-learning (RBL) into GTO called (GTORBL) and applied it to the same problem. The proposed approaches are tested on 20 patients’ T2 Weighted Sagittal (T2 WS) DCE-MRI 100 slices. The proposed approaches are compared with Tunicate Swarm Algorithm (TSA), Particle Swarm Optimization (PSO), Arithmetic Optimization Algorithm (AOA), Slime Mould Algorithm (SMA), Multi-verse Optimization (MVO), Hidden Markov Random Field (HMRF), Improved Markov Random Field (IMRF), and Conventional Markov Random Field (CMRF). The Dice Similarity Coefficient (DSC), sensitivity, and accuracy of the proposed GTO-based approach is achieved$$87.04\%$$87.04%,$$90.96\%$$90.96%, and$$98.13\%$$98.13%respectively. Another proposed GTORBL-based segmentation method achieves accuracy values of$$99.31\%$$99.31%, sensitivity of$$95.45\%$$95.45%, and DSC of$$91.54\%$$91.54%. The one-way ANOVA test followed by Tukey HSD and Wilcoxon Signed Rank Test are used to examine the results. Furthermore, Multi-Criteria Decision Making is used to evaluate overall performance focused on sensitivity, accuracy, false-positive rate, precision, specificity,$$F_1$$F1-score, Geometric-Mean, and DSC. According to both quantitative and qualitative findings, the proposed strategies outperform other compared methodologies.

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  3. Introduction: Essential genes are essential for the survival of various species. These genes are a family linked to critical cellular activities for species survival. These genes are coded for proteins that regulate central metabolism, gene translation, deoxyribonucleic acid replication, and fundamental cellular structure and facilitate intracellular and extracellular transport. Essential genes preserve crucial genomics information that may hold the key to a detailed knowledge of life and evolution. Essential gene studies have long been regarded as a vital topic in computational biology due to their relevance. An essential gene is composed of adenine, guanine, cytosine, and thymine and its various combinations. Methods: This paper presents a novel method of extracting information on the stationary patterns of nucleotides such as adenine, guanine, cytosine, and thymine in each gene. For this purpose, some co-occurrence matrices are derived that provide the statistical distribution of stationary patterns of nucleotides in the genes, which is helpful in establishing the relationship between the nucleotides. For extracting discriminant features from each co-occurrence matrix, energy, entropy, homogeneity, contrast, and dissimilarity features are computed, which are extracted from all co-occurrence matrices and then concatenated to form a feature vector representing each essential gene. Finally, supervised machine learning algorithms are applied for essential gene classification based on the extracted fixed-dimensional feature vectors. Results: For comparison, some existing state-of-the-art feature representation techniques such as Shannon entropy (SE), Hurst exponent (HE), fractal dimension (FD), and their combinations have been utilized. Discussion: An extensive experiment has been performed for classifying the essential genes of five species that show the robustness and effectiveness of the proposed methodology. 
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    Free, publicly-accessible full text available April 20, 2024
  4. Bonomo, Robert A. (Ed.)
    ABSTRACT Microbial diversity is reduced in the gut microbiota of animals and humans treated with selective serotonin reuptake inhibitors (SSRIs) and tricyclic antidepressants (TCAs). The mechanisms driving the changes in microbial composition, while largely unknown, is critical to understand considering that the gut microbiota plays important roles in drug metabolism and brain function. Using Escherichia coli , we show that the SSRI fluoxetine and the TCA amitriptyline exert strong selection pressure for enhanced efflux activity of the AcrAB-TolC pump, a member of the resistance-nodulation-cell division (RND) superfamily of transporters. Sequencing spontaneous fluoxetine- and amitriptyline-resistant mutants revealed mutations in marR and lon, negative regulators of AcrAB-TolC expression. In line with the broad specificity of AcrAB-TolC pumps these mutants conferred resistance to several classes of antibiotics. We show that the converse also occurs, as spontaneous chloramphenicol-resistant mutants displayed cross-resistance to SSRIs and TCAs. Chemical-genomic screens identified deletions in marR and lon, confirming the results observed for the spontaneous resistant mutants. In addition, deletions in 35 genes with no known role in drug resistance were identified that conferred cross-resistance to antibiotics and several displayed enhanced efflux activities. These results indicate that combinations of specific antidepressants and antibiotics may have important effects when both are used simultaneously or successively as they can impose selection for common mechanisms of resistance. Our work suggests that selection for enhanced efflux activities is an important factor to consider in understanding the microbial diversity changes associated with antidepressant treatments. IMPORTANCE Antidepressants are prescribed broadly for psychiatric conditions to alter neuronal levels of synaptic neurotransmitters such as serotonin and norepinephrine. Two categories of antidepressants are selective serotonin reuptake inhibitors (SSRIs) and tricyclic antidepressants (TCAs); both are among the most prescribed drugs in the United States. While it is well-established that antidepressants inhibit reuptake of neurotransmitters there is evidence that they also impact microbial diversity in the gastrointestinal tract. However, the mechanisms and therefore biological and clinical effects remain obscure. We demonstrate antidepressants may influence microbial diversity through strong selection for mutant bacteria with increased AcrAB-TolC activity, an efflux pump that removes antibiotics from cells. Furthermore, we identify a new group of genes that contribute to cross-resistance between antidepressants and antibiotics, several act by regulating efflux activity, underscoring overlapping mechanisms. Overall, this work provides new insights into bacterial responses to antidepressants important for understanding antidepressant treatment effects. 
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    Free, publicly-accessible full text available December 20, 2023
  5. High-throughput microfluidics-based assays can potentially increase the speed and quality of yeast replicative lifespan measurements. One major challenge is to efficiently convert large volumes of time-lapse images into quantitative measurements of cellular lifespans. Here, we address this challenge by prototyping an algorithm that can track cellular division events through family trees of cells. We generated a null distribution using single cells inside microfluidic traps. Based on this null distribution, we prototyped a maximum likelihood algorithm for cell tracking between images at different time-points. We inferred cell family trees through a likelihood based trace-back method. The branching patterns of the cell family trees are then used to infer replicative lifespan of the yeast mother cells. The longest branch of a cell family tree represents the full trajectory of a yeast mother cell. The replicative lifespan of this mother cell can be counted as the number of bifurcating branches of this family tree. In addition, we prototyped a different approach based on summing cells area which improved the replicative lifespan estimation significantly. These generic methods have the potential to accelerate the efficiency and expand the range of quantitative measurement of yeast replicative aging experiments. 
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  6. Frantz, Kyle (Ed.)
    In-person undergraduate research experiences (UREs) promote students’ integration into careers in life science research. In 2020, the COVID-19 pandemic prompted institutions hosting summer URE programs to offer them remotely, raising questions about whether undergraduates who participate in remote research can experience scientific integration and whether they might perceive doing research less favorably (i.e., not beneficial or too costly). To address these questions, we examined indicators of scientific integration and perceptions of the benefits and costs of doing research among students who participated in remote life science URE programs in Summer 2020. We found that students experienced gains in scientific self-efficacy pre- to post-URE, similar to results reported for in-person UREs. We also found that students experienced gains in scientific identity, graduate and career intentions, and perceptions of the benefits of doing research only if they started their remote UREs at lower levels on these variables. Collectively, students did not change in their perceptions of the costs of doing research despite the challenges of working remotely. Yet students who started with low cost perceptions increased in these perceptions. These findings indicate that remote UREs can support students’ self-efficacy development, but may otherwise be limited in their potential to promote scientific integration. 
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    Free, publicly-accessible full text available June 1, 2024
  7. null (Ed.)
    Replicative lifespan (RLS) of the budding yeast is the number of mother cell divisions until senescence and is instrumental to understanding mechanisms of cellular aging. Recent research has shown that replicative aging is heterogeneous, which argues for mixture modeling. The mixture model is a statistical method to infer subpopulations of the heterogeneous population. Mixture modeling is a relatively underdeveloped area in the study of cellular aging. There is no open access software currently available that assists extensive comparison among mixture modeling methods. To address these needs, we developed an R package called fitmix that facilitates the computation of well-known distributions utilized for RLS data and other lifetime datasets. This package can generate a group of functions for the estimation of probability distributions and simulation of random observations from well-known finite mixture models including Gompertz, Log-logistic, Log-normal, and Weibull models. To estimate and compute the maximum likelihood estimates of the model parameters, the Expectation–Maximization (EM) algorithm is employed. 
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