Article
Biochemical Research Methods
Sander N. Goossens, Tim H. Heupink, Elise De Vos, Anzaan Dippenaar, Margaretha De Vos, Rob Warren, Annelies Van Rie
Summary: The study evaluated the performance of the variant calling tool LoFreq in detecting minor variants in Mycobacterium tuberculosis next generation sequencing data. LoFreq showed high precision and sensitivity in detecting various types and frequencies of minor variants. It can successfully detect minor variant populations and reduce false positive variants due to sequencing errors. The findings can guide future studies in determining the depth of sequencing and the limit of detection in whole genome sequencing data of M. tuberculosis.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Multidisciplinary Sciences
Zhixing Feng, Jose C. Clemente, Brandon Wong, Eric E. Schadt
Summary: Cellular genetic heterogeneity is common across biological conditions, yet high error rates in long-read sequencing technologies limit their application to this subject. iGDA is introduced as a tool for accurate detection and phasing of minor variants, enabling precise haplotype reconstruction.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Binsheng Gong, Ira W. Deveson, Timothy Mercer, Donald J. Johann, Wendell Jones, Weida Tong, Joshua Xu
Summary: This study evaluated the analytical performance of five industry-leading ctDNA assays and demonstrated their high accuracy and reproducibility. By using tailor-made reference samples and assessing multiple key variables, this study provides a valuable dataset for ultra-deep ctDNA sequencing technology.
Article
Immunology
Wei-You Li, Szu-Wei Huang, Sheng-Fan Wang, Hsin-Fu Liu, Chih-Hung Chou, Shang-Jung Wu, Hsien-Da Huang, Po-Liang Lu, Cathy S. J. Fann, Marcelo Chen, Yen-Hsu Chen, Yi-Ming Arthur Chen
Summary: This study introduced phylogenetic tree results as forensic evidence in HIV-1 transmission cases in Taiwan. The analysis helped identify transmission sources in lawsuits, but limitations such as delayed sampling time and data interpretation were observed.
JOURNAL OF MICROBIOLOGY IMMUNOLOGY AND INFECTION
(2021)
Article
Parasitology
A. A. Morrison, U. Chaudhry, L. Andrews, L. Melville, S. R. Doyle, N. D. Sargison, D. J. Bartley
Summary: The study on benzimidazole (BZ) resistance in Haemonchus contortus through reciprocal genetic crosses revealed a potential difference in resistance phenotype depending on whether the resistant allele is paternally or maternally inherited. These findings provide new insight into the inheritance of BZ resistance in H. contortus and prompt further investigation.
INTERNATIONAL JOURNAL FOR PARASITOLOGY-DRUGS AND DRUG RESISTANCE
(2022)
Review
Biochemistry & Molecular Biology
Martje G. Pauly, Norbert Brueggemann, Stephanie Efthymiou, Anne Groezinger, Sokhna Haissatou Diaw, Viorica Chelban, Valentina Turchetti, Barbara Vona, Vera Tadic, Henry Houlden, Alexander Muenchau, Katja Lohmann
Summary: VPS13D gene defects are associated with spastic ataxia or spastic paraplegia. We report two patients with intronic pathogenic variants, including one patient with severe spastic ataxia and tremor and another patient with late-onset spastic paraplegia. Altered splicing and disrupted mitochondrial integrity were confirmed, and deep brain stimulation resulted in significant improvement in tremor for the first patient. This study highlights the importance of searching for mutations outside canonical splice sites to avoid missing a genetic diagnosis in disorders with diverse presentations.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemical Research Methods
Yongzhuang Liu, Yalin Huang, Guohua Wang, Yadong Wang
Summary: Short read whole genome sequencing is widely used in human genetic studies and clinical practices for detecting structural variants, but accurate detection is challenging. This study introduces a novel deep learning-based approach, DeepSVFilter, for filtering structural variants in short read whole genome sequencing data.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Biology
Yunfan Fu, Justin Bedo, Anthony T. Papenfuss, Alan F. Rubin
Summary: In this study, a linear regression-based predictor was extended to improve the prediction of amino acid variant impacts by incorporating data from alanine scanning. The results showed that the improvement in model performance is closely related to the correlation between DMS and AS results.
Article
Computer Science, Artificial Intelligence
Justin Engelmann, Alice D. McTrusty, Ian J. C. MacCormick, Emma Pead, Amos Storkey, Miguel O. Bernabeu
Summary: This study proposes an improved deep learning model for recognizing multiple retinal diseases under more realistic conditions and uses global explainability methods to identify the relevant regions in ultra-widefield (UWF) images. The model performs well in distinguishing between healthy and diseased retinas and identifies the posterior pole as the most important region.
NATURE MACHINE INTELLIGENCE
(2022)
Review
Biochemical Research Methods
Ninon Burgos, Simona Bottani, Johann Faouzi, Elina Thibeau-Sutre, Olivier Colliot
Summary: Deep learning is increasingly utilized in medicine, particularly in the study of brain disorders. By leveraging various data modalities, deep learning algorithms can enhance the understanding of brain diseases and provide guidance for clinical practices.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Computer Science, Hardware & Architecture
Prosanta Gope, Pradip Kumar Sharma, Biplab Sikdar
Summary: This article proposes a machine-learning-based ultra-light-weight data aggregation scheme for smart grids that does not require a secret key to be maintained for communicating with the aggregator. The scheme utilizes embedded PUFs to generate unique random responses for ensuring the privacy of metering data, and collaborative learning is used to optimize the performance of the scheme.
IEEE WIRELESS COMMUNICATIONS
(2022)
Review
Computer Science, Artificial Intelligence
Majid Bahramian, Recep Kaan Dereli, Wanqing Zhao, Matteo Giberti, Eoin Casey
Summary: Increasing energy efficiency in wastewater treatment plants is crucial and exploiting data science and modelling, as well as deploying sensors and artificial intelligence, can help achieve this goal. Artificial Neural Networks (ANN) is the most popular standalone model for WWTP modelling, followed by Decision Trees (DT), Fuzzy Logic (FL), Genetic algorithm (GA), and Support Vector Machine (SVM). Hybrid models, especially the Machine Learning (ML)-metaheuristic, demonstrate better performance than standalone models. Industrial deployment is still lacking, and future research should focus on enhancing collaboration between interested parties for more effective implementation.
EXPERT SYSTEMS WITH APPLICATIONS
(2023)
Article
Engineering, Electrical & Electronic
Fouzi Harrou, Tuoyuan Cheng, Ying Sun, TorOve Leiknes, Noreddine Ghaffour
Summary: Energy consumption is crucial for the global costs of wastewater treatment plants (WWTPs), and modeling and forecasting it has become a critical factor in WWTP design. This article focuses on providing short-term forecasting of WWTP energy consumption using data-driven soft sensors, comparing ten different methods and finding that ARIMA performs slightly better. The use of adaptive deep learning-based soft sensors is expected to enhance the capabilities of deep models to accurately follow future data trends.
IEEE SENSORS JOURNAL
(2021)
Article
Energy & Fuels
Binghan Cui, Han Wang, Renlong Li, Lizhi Xiang, Huaian Zhao, Rang Xiao, Sai Li, Zheng Liu, Geping Yin, Xinqun Cheng, Yulin Ma, Hua Huo, Pengjian Zuo, Taolin Lu, Jingying Xie, Chunyu Du
Summary: Accurately predicting battery performance is crucial for battery management. A mechanism and data-driven fusion model is developed in this study to predict charging capacity and energy curves of batteries under different working conditions, achieving high accuracy and robustness, and also enabling battery fault detection.
Article
Clinical Neurology
Amie W. Hsia, Marie L. Luby, Richard Leigh, John K. Lynch, Zurab Nadareishvili, Richard T. Benson, Chandni Kalaria, Shannon P. Burton, Larry Latour
Summary: Patients with minor acute ischemic stroke (mAIS) who received IV tPA treatment showed more frequent MRI targets compared to untreated patients, even in those without clearly disabling deficits.
Article
Infectious Diseases
Cristina Andres, Alejandra Gonzalez-Sanchez, Moraima Jimenez, Ester Marquez-Algaba, Maria Pinana, Candela Fernandez-Naval, Juliana Esperalba, Narcis Saubi, Josep Quer, Ariadna Rando-Segura, Marta Miarons, Maria Gema Codina, Isabel Ruiz-Camps, Tomas Pumarola, Pau Abrisqueta, Andres Anton
Summary: This study aimed to monitor the early emergence of genetic mutations related to reduced susceptibility to monoclonal antibody (mAb)-based treatment in immunocompromised patients with long-term viral excretion. The results showed that most cases were infected with the Omicron variant, and mutations associated with mAb therapy resistance were detected in some patients. This highlights the importance of monitoring for drug resistance mutations in immunocompromised patients and the community.
CLINICAL MICROBIOLOGY AND INFECTION
(2023)
Article
Geriatrics & Gerontology
Marta Del Pozo-Valero, Marta Corton, Rosario Lopez-Rodriguez, Ignacio Mahillo-Fernandez, Javier Ruiz-Hornillos, Pablo Minguez, Cristina Villaverde, Maria Elena Perez-Tomas, Maria Barreda-Sanchez, Esther Mancebo, Estela Paz-Artal, Encarna Guillen-Navarro, Berta Almoguera, Carmen Ayuso
Summary: This study reveals the association between clonal hematopoiesis and mortality in COVID-19 patients, particularly showing a significant correlation between pathogenic/likely pathogenic clonal hematopoiesis and mortality in the 75-84 age group.
Article
Microbiology
Pilar Somovilla, Carlos Garcia-Crespo, Brenda Martinez-Gonzalez, Maria Eugenia Soria, Ana Isabel de Avila, Isabel Gallego, Pablo Minguez, Antoni Duran-Pastor, Cristina Ferrer-Orta, Llanos Salar-Vidal, Mario Esteban-Munoz, Sonia Zuniga, Isabel Sola, Luis Enjuanes, Jaime Esteban, Ricardo Fernandez-Roblas, Ignacio Gadea, Jordi Gomez, Nuria Verdaguer, Esteban Domingo, Celia Perales
Summary: We report that ribavirin has an inhibitory and mutagenic activity on SARS-CoV-2-infected Vero cells, with a therapeutic index higher than 10. Deep sequencing analysis shows an increase in mutations, but not deletions, and modification of diversity indices in the presence of ribavirin. The major mutation types enhanced by ribavirin are A -> G and U -> C transitions, opposite to the dominant G -> A and C -> U transitions observed in most RNA viruses. The implications of ribavirin's inhibitory activity and atypical mutational bias on SARS-CoV-2 for the search for synergistic anti-COVID-19 lethal mutagen combinations are discussed.
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY
(2023)
Article
Biochemistry & Molecular Biology
Josep Gregori, Marta Ibanez-Lligona, Josep Quer
Summary: The rapid evolution of a viral quasispecies in a host, especially during treatment, is compared to the slow evolution of a natural ecosystem. Methods to quantify the evolution of a quasispecies are introduced and simulated examples are given. The correlation between the proposed indices is also discussed and a clinical case is used to demonstrate the efficacy of the proposed methods.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Multidisciplinary Sciences
Erola Pairo-Castineira, Konrad Rawlik, Andrew D. Bretherick, Ting Qi, Yang Wu, Isar Nassiri, Glenn A. McConkey, Marie Zechner, Lucija Klaric, Fiona Griffiths, Wilna Oosthuyzen, Athanasios Kousathanas, Anne Richmond, Jonathan Millar, Clark D. Russell, Tomas Malinauskas, Ryan Thwaites, Kirstie Morrice, Sean Keating, David Maslove, Alistair Nichol, Malcolm G. Semple, Julian Knight, Manu Shankar-Hari, Charlotte Summers, Charles Hinds, Peter Horby, Lowell Ling, Danny McAuley, Hugh Montgomery, Peter J. M. Openshaw, Colin Begg, Timothy Walsh, Albert Tenesa, Carlos Flores, Jose A. Riancho, Augusto Rojas-Martinez, Pablo Lapunzina, Jian Yang, Chris P. Ponting, James F. Wilson, Veronique Vitart, Malak Abedalthagafi, Andre D. Luchessi, Esteban J. Parra, Raquel Cruz, Angel Carracedo, Angie Fawkes, Lee Murphy, Kathy Rowan, Alexandre C. Pereira, Andy Law, Benjamin Fairfax, Sara Clohisey Hendry, J. Kenneth Baillie
Summary: This study analyzed genetic data from 24,202 severe COVID-19 cases and identified potentially druggable targets, including inflammatory signaling, monocyte-macrophage activation and endothelial permeability, immunometabolism, and host factors required for viral entry and replication.
Review
Virology
Marta Ibanez-Lligona, Sergi Colomer-Castell, Alejandra Gonzalez-Sanchez, Josep Gregori, Carolina Campos, Damir Garcia-Cehic, Cristina Andres, Maria Pinana, Tomas Pumarola, Francisco Rodriguez-Frias, Andres Anton, Josep Quer
Summary: Viruses are the major cause of epidemics and pandemics, and high-throughput next-generation sequencing technologies based on metagenomics can detect new infectious genomes and properly diagnose certain diseases. However, these techniques require a large amount of genetic material and involve complex bioinformatic analyses.
Article
Immunology
Carlos Garcia-Crespo, Irene Francisco-Recuero, Isabel Gallego, Marina Camblor-Murube, Maria Eugenia Soria, Ana Lopez-Lopez, Ana Isabel de avila, Antonio Madejon, Javier Garcia-Samaniego, Esteban Domingo, Aurora Sanchez-Pacheco, Celia Perales
Summary: This study found that hepatitis C virus (HCV) infection leads to cellular epigenetic modifications, which may be related to the development of liver cancer. The levels of H3Ser10ph, AURKB, and H4K20m3 in the infected cells significantly decreased after infection with high fitness HCV. This could be due to either an early increase in the number of infected cells or a larger number of replicating RNA molecules per cell in high fitness HCV infection.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2023)
Article
Multidisciplinary Sciences
Ascension Ariza-Mateos, Carlos Briones, Celia Perales, Maria Teresa Bayo-Jimenez, Esteban Domingo, Jordi Gomez
Summary: The entry of a virus into the host cell alters intracellular molecular relationships, leading to the recovery of ancient cellular activities. Viruses can be used as archaeological tools to identify unexpressed activities in non-infected cells, opening new perspectives for molecular biology.
ANNALS OF THE NEW YORK ACADEMY OF SCIENCES
(2023)
Article
Microbiology
Brenda Martinez-Gonzalez, Isabel Gallego, Josep Gregori, Maria Eugenia Soria, Pilar Somovilla, Ana Isabel de Avila, Carlos Garcia-Crespo, Antoni Duran-Pastor, Carlos Briones, Jordi Gomez, Josep Quer, Esteban Domingo, Celia Perales
Summary: In this study, we report the mild mutagenic activity of sofosbuvir (SOF) for hepatitis C virus (HCV). Serial passages of HCV in the presence of SOF led to increased C & RARR; U transitions in the mutant spectra, indicating its potential as a mild mutagen. This activity was dependent on the fitness of the HCV population and may contribute to its antiviral efficacy.
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY
(2023)
Review
Neurosciences
Ascension Ariza-Mateos, Carlos Briones, Celia Perales, Francisco Sobrino, Esteban Domingo, Jordi Gomez
Summary: Studies with RNA enzymes and protein enzymes have identified structural elements in cellular mRNAs and viral RNAs that have common structural folds and may have an ancient and common origin. The term 'mRNA archaeology' refers to the search for these ancient RNA elements, which can provide insights into early evolutionary developments. These RNA elements may have developed as biological signals with structural and functional relevance, coexisting with the linear information of nucleic acid molecules.
JOURNAL OF PHYSIOLOGY-LONDON
(2023)
Review
Immunology
Francisco Rodriguez-Frias, Ariadna Rando-Segura, Josep Quer
Summary: Hepatitis is a complex inflammation of the liver, primarily caused by hepatotropic viruses, but can also be influenced by other pathogens, metabolic disorders, or autoimmune reactions. In 2022, an unknown etiology of severe acute hepatitis in previously healthy young children, with cases requiring liver transplantation, drew global attention. The co-occurrence with COVID-19 may be a contributing factor to this acute hepatitis.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Meritxell Llorens-Revull, Brenda Martinez-Gonzalez, Josep Quer, Juan Ignacio Esteban, Gonzalo Nunez-Moreno, Pablo Minguez, Idoia Burgui, Ricardo Ramos-Ruiz, Maria Eugenia Soria, Angie Rico, Mar Riveiro-Barciela, Silvia Sauleda, Maria Piron, Irene Corrales, Francesc E. Borras, Francisco Rodriguez-Frias, Ariadna Rando, Clara Ramirez-Serra, Silvia Camos, Esteban Domingo, Marta Bes, Celia Perales, Maria Isabel Costafreda
Summary: MicroRNAs (miRNAs) encapsulated in extracellular vesicles (EVs) have potential as diagnostic and prognostic biomarkers. This study aimed to find a reliable EV isolation method for miRNA sequencing, suitable for clinical applications. Results showed that SEC yielded the highest amount of EVs with good reproducibility, while GRAD and SEC+GRAD resulted in purer EV preparations. The NEBNext library exhibited the highest reproducibility in miRNA recovery and diversity. Therefore, combining GRAD EV isolation with NEBNext library preparation is suitable for miRNA detection using plasma samples.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Medicine, General & Internal
Jesus Rivera-Esteban, Alba Jimenez-Masip, Sergio Munoz-Martinez, Salvador Augustin, Rafael A. Guerrero, Pablo Gabriel-Medina, Roser Ferrer-Costa, Francisco Rodriguez-Frias, Elisabet Turu, Andres Marco, Juan M. Pericas
Summary: Metabolic disorders, including MASLD, are highly prevalent among inmates. The prevalence of significant fibrosis seems notably higher than that of the general population, underscoring the need for targeted screening programs and therapeutic interventions in the incarcerated population.
JOURNAL OF CLINICAL MEDICINE
(2023)