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Hossain, J.

Publications and source records attributed to Hossain, J..

6 recordsLinked to original sources

Attention-Guided Multimodal Neuroimaging Fusion Network for Modeling Brain Aging Pattern

Brain age prediction from neuroimaging data provides critical insights into neurodevelopmental trajectories and neurodegenerative processes. However, effectively leveraging complementary structural and functional brain information for accurate prediction remains a major challenge. In this study, we propose an Attention-guided Multimodal brain Age prediction Network (AMAge-Net), a novel framework that integrates resting-state functional MRI (fMRI) and structural MRI (sMRI) to enhance brain age estimation. In AMAge-Net, functional features are captured from fMRI through a hierarchical Graph Attention Network, while structural features are learned from sMRI via a 3D DenseNet architecture. To enable effective cross-modal integration, AMAge-Net incorporates a Multi-Head Cross-Attention mechanism followed by a Gated Fusion Module, allowing the model to dynamically prioritize the most informative features from each modality, thereby improving interpretability and predictive accuracy. Evaluation on the Cam-CAN dataset (652 participants, aged 18-89) demonstrates that AMAge-Net outperforms state-of-the-art unimodal and multimodal baselines, achieving a mean absolute error (MAE) of 5.09, root mean square error (RMSE) of 6.52, R2 of 0.87, and Pearson correlation (PCC) of 0.94. The proposed model further demonstrates robust generalization, achieving an MAE of 4.29, RMSE of 5.59, R2 of 0.58, and PCC of 0.77 on the independent OASIS-3 dataset. Comparative and ablation studies further confirm the effectiveness of the proposed fusion strategy and modality-specific encoders. Beyond predictive performance, AMAge-Net highlights interpretable brain regions that provide insights into the mechanisms of functional and structural brain aging, while gender-specific analyses reveal distinct aging trajectories between males and females. These findings establish AMAge-Net as a powerful and interpretable approach to brain age estimation, advancing efforts to characterize healthy aging and detect early deviations associated with neurological and psychiatric disorders. Author summaryEstimating the biological age of the brain from imaging data offers a window into normal development, healthy aging, and the early stages of disease. A major challenge is how to combine information from structural scans, which show brain anatomy, and functional scans, which capture brain activity. Here, we present a new computational framework that integrates both types of data to improve the accuracy and interpretability of brain age prediction. Applied to two independent, large-scale lifespan magnetic resonance imaging datasets of individuals spanning early adulthood to late life, our framework produced highly accurate predictions and consistently outperformed existing methods. Beyond predictive performance, the model highlighted brain regions that appear especially important for age-related changes, and it revealed distinct aging patterns between men and women. These findings provide a powerful and interpretable tool for studying how the brain changes across the lifespan, with potential applications in detecting early deviations linked to neurological and psychiatric disorders.

neuroscience↗

Deep learning-based codon optimization with large-scale synonymous variant datasets enables generalized tunable protein expression

Increasing recombinant protein expression is of broad interest in industrial biotechnology, synthetic biology, and basic research. Codon optimization is an important step in heterologous gene expression that can have dramatic effects on protein expression level. Several codon optimization strategies have been developed to enhance expression, but these are largely based on bulk usage of highly frequent codons in the host genome, and can produce unreliable results. Here, we develop deep contextual language models that learn the codon usage rules from natural protein coding sequences across members of the Enterobacterales order. We then fine-tune these models with over 150,000 functional expression measurements of synonymous coding sequences from three proteins to predict expression in E. coli. We find that our models recapitulate natural context-specific patterns of codon usage and can accurately predict expression levels across synonymous sequences. Finally, we show that expression predictions can generalize across proteins unseen during training, allowing for in silico design of gene sequences for optimal expression. Our approach provides a novel and reliable method for tuning gene expression with many potential applications in biotechnology and biomanufacturing.

synthetic biology↗

Bivalent mRNA vaccine improves antibody-mediated neutralization of many SARS-CoV-2 Omicron lineage variants

The early Omicron lineage variants evolved and gave rise to diverging lineages that fueled the COVID-19 pandemic in 2022. Bivalent mRNA vaccines, designed to broaden protection against circulating and future variants, were authorized by the U.S. Food and Drug Administration (FDA) in August 2022 and recommended by the U.S. Centers for Disease Control and Prevention (CDC) in September 2022. The impact of bivalent vaccination on eliciting neutralizing antibodies against homologous BA.4/BA.5 viruses as well as emerging heterologous viruses needs to be analyzed. In this study, we analyze the neutralizing activity of sera collected after a third dose of vaccination (2-6 weeks post monovalent booster) or a fourth dose of vaccination (2-7 weeks post bivalent booster) against 10 predominant/recent Omicron lineage viruses including BA.1, BA.2, BA.5, BA.2.75, BA.2.75.2, BN.1, BQ.1, BQ.1.1, XBB, and XBB.1. The bivalent booster vaccination enhanced neutralizing antibody titers against all Omicron lineage viruses tested, including a 10-fold increase in neutralization of BQ.1 and BQ.1.1 viruses that predominated in the U.S. during the last two months of 2022. Overall, the data indicate the bivalent vaccine booster strengthens protection against Omicron lineage variants that evolved from BA.5 and BA.2 progenitors.

microbiology↗

Differential neutralization and inhibition of SARS-CoV-2 variants by antibodies elicited by COVID-19 mRNA vaccines

IntroductoryThe evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has resulted in the emergence of many new variant lineages that have exacerbated the COVID-19 pandemic. Some of those variants were designated as variants of concern/interest (VOC/VOI) by national or international authorities based on many factors including their potential impact on vaccines. To ascertain and rank the risk of VOCs and VOIs, we analyzed their ability to escape from vaccine-induced antibodies. The variants showed differential reductions in neutralization and replication titers by post-vaccination sera. Although the Omicron variant showed the most escape from neutralization, sera collected after a third dose of vaccine (booster sera) retained moderate neutralizing activity against that variant. Therefore, vaccination remains the most effective strategy to combat the COVID-19 pandemic.

microbiology↗

SARS-CoV-2 susceptibility of cell lines and substrates commonly used in diagnosis and isolation of influenza and other viruses

Coinfection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and other viruses is inevitable as the COVID-19 pandemic continues. This study aimed to evaluate cell lines commonly used in virus diagnosis and isolation for their susceptibility to SARS-CoV-2. While multiple kidney cell lines from monkeys were susceptible and permissive to SARS-CoV-2, many cell types derived from human, dog, mink, cat, mouse, or chicken were not. Analysis of MDCK cells, which are most commonly used for surveillance and study of influenza viruses, demonstrated that they were insusceptible to SARS-CoV-2 and that the cellular barrier to productive infection was due to low expression level of the angiotensin converting enzyme 2 (ACE2) receptor and lower receptor affinity to SARS-CoV-2 spike, which could be overcome by over-expression of canine ACE2 in trans. Moreover, SARS-CoV-2 cell tropism did not appear to be affected by a D614G mutation in the spike protein.

microbiology↗

SARS-CoV-2 spike D614G variant confers enhanced replication and transmissibility

During the evolution of SARS-CoV-2 in humans a D614G substitution in the spike (S) protein emerged and became the predominant circulating variant (S-614G) of the COVID-19 pandemic1. However, whether the increasing prevalence of the S-614G variant represents a fitness advantage that improves replication and/or transmission in humans or is merely due to founder effects remains elusive. Here, we generated isogenic SARS-CoV-2 variants and demonstrate that the S-614G variant has (i) enhanced binding to human ACE2, (ii) increased replication in primary human bronchial and nasal airway epithelial cultures as well as in a novel human ACE2 knock-in mouse model, and (iii) markedly increased replication and transmissibility in hamster and ferret models of SARS-CoV-2 infection. Collectively, our data show that while the S-614G substitution results in subtle increases in binding and replication in vitro, it provides a real competitive advantage in vivo, particularly during the transmission bottle neck, providing an explanation for the global predominance of S-614G variant among the SARS-CoV-2 viruses currently circulating.

microbiology↗