Article
Immunology
Anne Inderbitzin, Tom Loosli, Lennart Opitz, Peter Rusert, Karin J. Metzner
Summary: The main obstacle to curing HIV-1 is the latent reservoir. Understanding the mechanism of HIV-1 latency and reactivation through CD4(+) T cell models is crucial. Recent studies have used transcriptome analysis to identify differentially expressed genes in latently- and reactivated HIV-1 infected cells, providing insights into HIV-1 latency.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Medicine, Research & Experimental
Yik Lim Kok, Valentina Vongrad, Sandra E. Chaudron, Mohaned Shilaih, Christine Leemann, Kathrin Neumann, Katharina Kusejko, Francesca Di Giallonardo, Herbert Kuster, Dominique L. Braun, Roger D. Kouyos, Huldrych F. Gunthard, Karin J. Metzner
Summary: Characteristics of HIV-1 integration sites are established as early as during primary infection and are found in both resting and activated CD4(+) T cells. HIV-1 integration sites preferentially occur in specific genes and highly expressed genes, regardless of the activation state of CD4(+) T cells. The preference for cancer-related genes is more prominent at later stages of HIV-1 infection.
Article
Immunology
Mark Mensink, Thi Ngoc Minh Tran, Esther A. Zaal, Ellen Schrama, Celia R. Berkers, Jannie Borst, Sander de Kivit
Summary: CD4(+) T cells play a role in immune responses depending on the environment and stage, with nutrient availability also impacting their functionality. TNFR2 has been identified as key in regulating T cells, particularly Tregs. This study provides new evidence for the role of TNFR2 in metabolic regulation.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Immunology
Xiao-Peng Dai, Feng-Ying Wu, Cheng Cui, Xue-Jiao Liao, Yan-Mei Jiao, Chao Zhang, Jin-Wen Song, Xing Fan, Ji-Yuan Zhang, Qing He, Fu-Sheng Wang
Summary: Platelet-T cell aggregates play a critical role in maintaining inflammation in chronic HIV-1 infection. The formation of platelet-CD4(+) T cell aggregates was increased in treatment-naive HIV-1-infected individuals compared to healthy controls. Higher levels of these aggregates were associated with HIV-1 permissiveness and immune activation during HIV-1 infection.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Cell Biology
Hannah L. Itell, Daryl Humes, Julie Overbaugh
Summary: This study identifies new ISGs that inhibit HIV and confirms the role of certain factors in IFN restriction in T cells. The findings demonstrate the multifaceted nature of IFN restriction against HIV and establish a screening model for identifying HIV-restricting ISGs.
Review
Immunology
Constance Renault, Nicolas Veyrenche, Franck Mennechet, Anne-Sophie Bedin, Jean-Pierre Routy, Philippe Van de Perre, Jacques Reynes, Edouard Tuaillon
Summary: Th17 cells play a crucial role in defending against pathogens at mucosal barriers, but they are also vulnerable to HIV-1 infection and depletion from gut mucosal sites. The imbalance caused by the loss of Th17 cells impairs cytokine production and leads to damage in the gut mucosal barrier, promoting HIV-1 disease progression. The expression of specific receptors by Th17 cells contributes to their susceptibility to HIV infection. Moreover, Th17 cells serve as long-lived viral reservoirs in HIV patients receiving antiretroviral therapy.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Ecology
Khashiff K. Miranda, Brooke L. Weigel, Sophie J. McCoy, Catherine A. Pfister
Summary: Disturbance affects the spatial distribution of primary producers and can lead to cascading effects on ecosystem function. In the lower-intertidal zone of rocky shores in the Pacific Northwest, wave energy creates a mosaic-like distribution between surfgrass meadows and kelp-dominated macroalgal forests. Experimental removal of surfgrass monocultures led to an increase in diversity, biomass, and net primary productivity in the resulting macroalgal assemblage, enhancing carbon turnover and potential for carbon sequestration.
Article
Biochemistry & Molecular Biology
Mohammad Fayyad-Kazan, Redouane Rouas, Makram Merimi, Mehdi Najar, Bassam Badran, Philippe Lewalle, Hussein Fayyad-Kazan
Summary: CD4(+)CD25(+) FOXP3(+) regulatory T cells are important in suppressing immune reactions, but difficult to distinguish from conventional CD4(+) T cells. This study identifies differentially transcribed genes between Tregs and conventional T cells using qRT-PCR and bioinformatics analysis, providing new molecular targets for understanding Tregs' function and isolation.
NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS
(2023)
Article
Multidisciplinary Sciences
Sung Min Choi, Hi Jung Park, Eun A. Choi, Kyeong Cheon Jung, Jae Il Lee
Summary: The study identified a diverse subset of circulating DP cells, including naive cells and various subpopulations with multiple potential functions such as CD4 CTL-, Eomes(+) Tr1-, Th2-, Th17-, Tfh-, Treg-, CD8 CTL-, and innate-like cells. In addition, flow cytometry analysis showed that a substantial number of naive DP T cells express CD8 alpha beta and CD8 alpha alpha, while subsets with high levels of CD4 co-receptor express helper and regulatory functions. Conversely, subsets with high CD8 co-receptor expression in the CD4(lo)CD8(hi) population display characteristics of CD8 CTL- and innate-like properties.
SCIENTIFIC REPORTS
(2021)
Review
Immunology
Jarrod York, Kavitha Gowrishankar, Kenneth Micklethwaite, Sarah Palmer, Anthony L. Cunningham, Najla Nasr
Summary: Despite the effectiveness of ART in reducing morbidity and mortality associated with HIV infection, the latent HIV reservoir remains a major barrier to immune clearance and HIV cure. CAR T cell therapies, involving genetically engineered T cells, offer promising potential in targeting HIV-infected cells and have shown efficacy, safety, and long-term persistence in peripheral blood.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Multidisciplinary Sciences
Allison M. Meadows, Kim Han, Komudi Singh, Antonio Murgia, Ben D. McNally, James A. West, Rebecca D. Huffstutler, Tiffany M. Powell-Wiley, Yvonne Baumer, Julian L. Griffin, Michael N. Sack
Summary: Caloric deprivation interventions such as intermittent fasting and caloric restriction have positive effects on metabolic and inflammatory diseases. When subjected to a 24-hour fast, both innate and adaptive immune cell responsiveness is reduced, and this effect can be transferred through serum. Metabolomic and lipidomic analysis of serum extracted after a 24-hour fast and re-feeding revealed metabolite-sensing GPCRs as crucial mediators of fasting-mediated immune modulation. The elevated levels of N-arachidonylglycine (NAGly), a putative GPR18 ligand, during fasting attenuate CD4(+)T cell responsiveness and reduce inflammatory cytokines levels in obese subjects, suggesting its role in regulating nutrient-level dependent inflammation associated with metabolic disease.
Article
Virology
Jacob K. Files, Sarah Sterrett, Sebastian Henostroza, Christopher Fucile, Kevin Maroney, Tim Fram, Simon Mallal, Spyros Kalams, Jonathan Carlson, Alexander Rosenberg, Nathan Erdmann, Anju Bansal, Paul A. Goepfert
Summary: HLA-II-associated viral adaptation reduces CD4(+) T-cell responses in HIV-1 vaccine recipients, potentially affecting HIV-specific antibody production and vaccine efficacy.
JOURNAL OF VIROLOGY
(2022)
Article
Public, Environmental & Occupational Health
Shi Zou, Yuting Tan, Yanni Xiang, Yang Liu, Qi Zhu, Songjie Wu, Wei Guo, Mingqi Luo, Ling Shen, Ke Liang
Summary: This study found a significant increase in CD4 and CD8 double-positive (DP) T cells in patients with HIV/TB coinfection. Additionally, these DP T cells also expressed more cytotoxic markers. This suggests that DP T cells may play an important immune role in HIV/TB infection.
FRONTIERS IN PUBLIC HEALTH
(2022)
Article
Microbiology
Helene Bauby, Christopher C. Ward, Rupert Hugh-White, Chad M. Swanson, Reiner Schulz, Caroline Goujon, Michael H. Malim
Summary: The interaction between HIV-1 and CD4(+) T cells have been studied through transcriptomics analysis, unveiling global changes in gene expression. The viral accessory protein Vpr plays a crucial role in these gene expression changes, highlighting its significance in infection and pathogenesis. This finding sheds new light on the interplay between HIV-1 and its host at the cellular level.
Article
Immunology
Chenfeng He, Michael J. Malone, Ben S. Wendel, Ke-Yue Ma, Daniel Del Alcazar, David B. Weiner, Philip L. De Jager, Perla M. Del Rio-Estrada, Yuria Ablanedo-Terrazas, Gustavo Reyes-Teran, Laura F. Su, Ning Jiang
Summary: Follicular-helper T cells, a vital part of adaptive immunity, have complex and plastic functions, but study limitations have hindered a comprehensive understanding. CXCR3-expressing T-FH cells in chronic infection show abnormal accumulation in lymphoid tissues, suggesting potential functional differences that may enhance defense.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Biology
Phasit Charoenkwan, Chonlatip Pipattanaboon, Chanin Nantasenamat, Md Mehedi Hasan, Mohammad Ali Moni, Pietro Lio, Watshara Shoombuatong
Summary: Despite existing cancer therapies, the development of new and effective treatments is necessary to address the ongoing cancer recurrence and new cases. This study proposes a new machine learning-based approach, PSRTTCA, for improving the identification and characterization of tumor T cell antigens (TTCAs) based on their primary sequences.
COMPUTERS IN BIOLOGY AND MEDICINE
(2023)
Article
Biochemistry & Molecular Biology
Valentina Granata, Isabel Pagani, Emanuela Morenghi, Maria Lucia Schiavone, Alessandra Lezzi, Silvia Ghezzi, Elisa Vicenzi, Guido Poli, Cristina Sobacchi
Summary: Preliminary evidence suggests an interaction between NBAS and NBAS-related functions and SARS-CoV-2 in infected cells, as observed in the early time points after infection of human lung epithelial cell line Calu3.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biotechnology & Applied Microbiology
Sadia Afrin Bristy, Md Arju Hossain, Md Imran Hasan, S. M. Hasan Mahmud, Mohammad Ali Moni, Md Habibur Rahman
Summary: Moraxella catarrhalis is a unique bacterium in humans, acting as a symbiotic organism while also causing mucosal infections. It is a major contributor to acute middle ear infections in children, and its resistance to multiple drugs poses a challenge in treatment. This study used a computational approach to understand the processes leading to antibiotic resistance in M. catarrhalis by analyzing 12 strains from the NCBI-Genome database. The study found 74 antimicrobial-resistant genes and explored their interaction network, revealing their involvement in antibiotic inactivation, target replacement, alteration, and efflux pump processes. Several genes, such as rpoB, atpA, fusA, groEL, and rpoL, were identified as potential therapeutic targets for novel medications. Overall, this study provides valuable insights into the antimicrobial resistance system of M. catarrhalis.
BRIEFINGS IN FUNCTIONAL GENOMICS
(2023)
Article
Biology
Md Arju Hossain, Md Habibur Rahman, Habiba Sultana, Asif Ahsan, Saiful Islam Rayhan, Md Imran Hasan, Md Sohel, Pratul Dipta Somadder, Mohammad Ali Moni
Summary: The study aimed to investigate the pharmacological mechanism behind apigenin's role in the synergetic effects of COVID-19 to the progression of HIV patients. The research found that apigenin has strong interactions with certain key proteins and its pharmacokinetic features suggest it is an effective therapeutic agent. However, more in vitro and in vivo studies are needed to validate these findings.
COMPUTERS IN BIOLOGY AND MEDICINE
(2023)
Article
Biology
Md. Ali Hossain, Tania Akter Asa, Md. Rabiul Auwul, Md. Aktaruzzaman, Md. Mahfizur Rahman, M. Zahidur Rahman, Mohammad Ali Moni
Summary: This study aimed to understand the influence of smoking on COVID-19 infected patients by analyzing the transcriptomics data of lung epithelial cells. The analysis revealed dysregulated genes and pathways associated with smoking and COVID-19 infection. The network analysis identified key proteins overlapping between smoking and COVID-19, and the gene ontology and pathways analysis suggested potential therapeutic targets for smoking individuals with COVID-19.
COMPUTERS IN BIOLOGY AND MEDICINE
(2023)
Article
Clinical Neurology
Anita Sathyanarayanan, Tamara T. Mueller, Mohammad Ali Moni, Katja Schueler, Bernhard T. Baune, Pietro Lio, Divya Mehta
Summary: This review summarizes the methods for discovering biologically meaningful biomarkers for diagnosis, treatment, and prognosis by combining multi-omics data. It discusses conventional and state-of-the-art statistical and machine learning approaches, as well as the role of biological model systems and in silico multi-omics model designs in clinical translation of psychiatric research. Challenges and future applications of multi-omics integration in psychiatric research are also discussed.
EUROPEAN NEUROPSYCHOPHARMACOLOGY
(2023)
Article
Computer Science, Artificial Intelligence
Taima Rahman Mim, Maliha Amatullah, Sadia Afreen, Mohammad Abu Yousuf, Shahadat Uddin, Salem A. Alyami, Khondokar Fida Hasan, Mohammad Ali Moni
Summary: Human Activity Recognition (HAR) is a valuable research field for clinical applications, where machine learning algorithms play a significant role. The proposed Gated Recurrent Unit-Inception (GRU-INC) model effectively utilizes both temporal and spatial information of time-series data, achieving high F1-scores on various publicly available datasets. The combination of GRU with Attention Mechanism and Inception module with Convolutional Block Attention Module (CBAM) contributes to the superior recognition rate and lower computational cost of the GRU-INC model. This framework has the potential to be applied in activity-associated clinical and rehabilitation applications.
EXPERT SYSTEMS WITH APPLICATIONS
(2023)
Article
Biochemical Research Methods
Pietro Bongini, Franco Scarselli, Monica Bianchini, Giovanna Maria Dimitri, Niccolo Pancino, Pietro Lio
Summary: Drug side-effects have a significant impact on public health, care system costs, and drug discovery processes. Predicting the probability of side-effects before their occurrence is crucial to reduce this impact, especially in drug discovery. By integrating heterogeneous data into a graph dataset, this study successfully utilizes Graph Neural Networks (GNNs) to predict drug side-effects, showing promising results. The experimental results highlight the significance of utilizing relationships between data entities and suggest potential future developments in this field.
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
(2023)
Article
Computer Science, Artificial Intelligence
Md Shofiqul Islam, Khondokar Fida Hasan, Sunjida Sultana, Shahadat Uddin, Pietro Lio', Julian M. W. Quinn, Mohammad Ali Moni
Summary: We propose a hybrid hierarchical attention-based bidirectional recurrent neural network with dilated CNN (HARDC) method for arrhythmia classification. This method fully exploits the dilated CNN and bidirectional recurrent neural network unit (BiGRU-BiLSTM) architecture to generate fusion features, improving the model's performance for prediction. By combining the fusion features with a dilated CNN and a hierarchical attention mechanism, the trained HARDC model showed significantly improved classification results and interpretability of feature extraction on the PhysioNet 2017 challenge dataset.
Article
Computer Science, Artificial Intelligence
Md. Alamin Talukder, Md. Manowarul Islam, Md. Ashraf Uddin, Arnisha Akhter, Md. Alamgir Jalil Pramanik, Sunil Aryal, Muhammad Ali Abdulllah Almoyad, Khondokar Fida Hasan, Mohammad Ali Moni
Summary: Brain tumors are fatal and devastating, reducing life expectancy significantly. Accurate diagnosis is crucial for treatment plans. Manual analysis of MRI data is challenging and time-consuming, calling for a reliable deep learning model.
EXPERT SYSTEMS WITH APPLICATIONS
(2023)
Article
Computer Science, Hardware & Architecture
Md. Monirul Islam, Mohammod Abul Kashem, Salem A. Alyami, Mohammad Ali Moni
Summary: This paper presents an IoT framework for aquaculture that allows real-time monitoring and effective control of water-related parameters. The proposed system utilizes sensors and an Arduino microcontroller to collect and store data in an IoT cloud platform. The collected data is then analyzed using various machine learning algorithms, with Random Forest achieving the highest performance scores. The study also includes hardware details of the IoT system and calculates biochemical and chemical oxygen demands.
MICROPROCESSORS AND MICROSYSTEMS
(2023)
Article
Genetics & Heredity
Rabea Khatun, Maksuda Akter, Md. Manowarul Islam, Md. Ashraf Uddin, Md. Alamin Talukder, Joarder Kamruzzaman, Akm Azad, Bikash Kumar Paul, Muhammad Ali Abdulllah Almoyad, Sunil Aryal, Mohammad Ali Moni
Summary: This article proposes an ensemble rank-based feature selection method and classifier to address the challenge of high-dimensional data in cancer diagnosis. The method efficiently discovers the most relevant and useful features by aggregating rankings from different selection methods. The results show high accuracy on multiple datasets and the study identifies a subset of the most important cancer-causing genes and demonstrates their significance.
Article
Computer Science, Information Systems
Nuruzzaman Faruqui, Mohammad Abu Yousuf, Md Whaiduzzaman, A. K. M. Azad, Salem A. Alyami, Pietro Lio, Muhammad Ashad Kabir, Mohammad Ali Moni
Summary: The Internet of Medical Things (IoMT) has become an attractive target for cybercriminals due to its market value and rapid growth. However, IoMT devices have limited computational capabilities, making them vulnerable to cyber-attacks. To address this, a novel Intrusion Detection System (IDS) called SafetyMed is proposed, which combines Convolutional Neural Networks (CNN) and Long Short-Term Memory (LSTM) networks to defend against intrusion from sequential and grid data. SafetyMed has shown high detection rates and accuracy, making it a potential game-changer in vulnerable sectors like the medical industry.
Article
Chemistry, Medicinal
Isabel Pagani, Linda Ottoboni, Paola Panina-Bordignon, Gianvito Martino, Guido Poli, Sarah Taylor, Jeremy E. Turnbull, Edwin Yates, Elisa Vicenzi
Summary: This study investigates the effects of chemically modified heparin derivatives with reduced anticoagulant activities on ZIKV infection, and finds that they can prevent cell death and inhibit ZIKV replication in infected neural progenitor cells. The combination of heparin with Sofosbuvir shows a synergistic effect.
Article
Health Care Sciences & Services
Md. Martuza Ahamad, Sakifa Aktar, Md. Jamal Uddin, Md. Rashed-Al-Mahfuz, A. K. M. Azad, Shahadat Uddin, Salem A. Alyami, Iqbal H. Sarker, Asaduzzaman Khan, Pietro Lio, Julian M. W. Quinn, Mohammad Ali Moni
Summary: Good vaccine safety and reliability are crucial for countering infectious diseases effectively. This study aims to reduce adverse reactions to COVID-19 vaccines by identifying common factors through patient data analysis and classification. Patient medical histories and postvaccination effects were examined, and statistical and machine learning approaches were used. The analysis revealed that prior illnesses, hospital admissions, and SARS-CoV-2 reinfection were significantly associated with poor patient reactions.
