Review
Infectious Diseases
Rimjhim Kanaujia, Manisha Biswal, Archana Angrup, Pallab Ray
Summary: The study aimed to evaluate and compare the diagnostic efficacy of metagenomic NGS (mNGS) for bacterial meningoencephalitis (BM/E) diagnosis. The analysis showed that mNGS had moderate diagnostic accuracy in diagnosing BM/E from cerebrospinal fluid specimens, and it can be particularly helpful in cases with undiagnosed BM/E.
EUROPEAN JOURNAL OF CLINICAL MICROBIOLOGY & INFECTIOUS DISEASES
(2022)
Review
Biochemistry & Molecular Biology
Domenico Tierno, Gabriele Grassi, Serena Scomersi, Marina Bortul, Daniele Generali, Fabrizio Zanconati, Bruna Scaggiante
Summary: The poor survival of triple-negative breast cancer (TNBC) is attributed to its aggressive behavior, large heterogeneity, and high risk of recurrence. Next-generation sequencing (NGS) has been used to investigate the molecular characteristics of TNBC, revealing recurrent pathogenic alterations in TP53, immunocheckpoint response genes, and PIK3CA and DNA repair pathways. NGS has also identified potential personalized treatments and novel biomarkers such as AURKA, MYC, and JARID2 mutations. Additionally, NGS studies have identified ethnicity-specific alterations in African and African American TNBC, including EZH2 overexpression, BRCA1 alterations, and a BRCA2-delaAAGA mutation. The development of long-read sequencing methods and their combination with optimized short-read techniques hold promise for improving the efficiency of NGS approaches in future clinical use.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Immunology
Fengxiang Huang, Haoran Wang, Ruiping Qiao, Qiang Peng, Chang Zhao, Lijun Miao
Summary: This study evaluated the diagnostic accuracy of metagenomic next-generation sequencing (mNGS) and GeneXpert Mycobacterium tuberculosis (MTB) for identifying tuberculous pleurisy and analyzing the microbial profiles of both tuberculous and non-tuberculous pleural effusions. The results showed that both tests had high specificity and positive predictive value for detecting tuberculous pleurisy, along with comparable sensitivity. Additionally, mNGS analysis revealed valuable insights into the microbial profiles of both types of pleural effusions.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2023)
Editorial Material
Hematology
Michael Nagler, Henning Nilius
Summary: Gallo et al. examined the impact of implementing a clinical decision support tool across multiple hospitals. This study highlights three crucial steps to unleash the potential of next-generation diagnostic instruments: (a) integrating diagnostic information from various sources, (b) ensuring accurate development and validation through well-designed clinical studies, and (c) seamlessly integrating them into clinical practice.
BRITISH JOURNAL OF HAEMATOLOGY
(2023)
Article
Microbiology
Choon-Mee Kim, Dong-Min Kim, Na Ra Yun
Summary: This study evaluated the accuracy of different antibody tests for scrub typhus, revealing that the sensitivity and specificity of each test were unsatisfactory. There is an urgent need to develop more highly sensitive and specific tests.
JOURNAL OF CLINICAL MICROBIOLOGY
(2021)
Article
Medicine, General & Internal
Daniel Mukadi-Bamuleka, Junior Bulabula-Penge, Bart K. M. Jacobs, Anja De Weggheleire, Francois Edidi-Atani, Fabrice Mambu-Mbika, Anais Legand, John D. Klena, Peter N. Fonjungo, Placide Mbala-Kingebeni, Sheila Makiala-Mandanda, Masahiro Kajihara, Ayato Takada, Joel M. Montgomery, Pierre Formenty, Jean-Jacques Muyembe-Tamfum, Kevin K. Arien, Johan van Griensven, Steve Ahuka-Mundeke, Study Grp
Summary: This study evaluated the performance of four rapid diagnostic tests (RDTs) for Ebola virus disease (EVD) detection. The sensitivity of the RDTs did not meet the desired levels set by the World Health Organization, but the specificity was satisfactory. Among the RDTs evaluated, QuickNavi-EbolaTM and OraQuick(R) Ebola Rapid Antigen Test showed the most favorable profiles and can be used as frontline tests for screening suspected cases.
Article
Oncology
Karoline Andersen, Kasper Holm, Mette Tranberg, Cecilie Lebech Pedersen, Sara Bonlokke, Torben Steiniche, Berit Andersen, Magnus Stougaard
Summary: This study demonstrates the use of a targeted HPV next generation sequencing (NGS) panel for cervical cancer screening. The targeted panel shows similar sensitivity and specificity to commercial HPV assays, but also provides additional advantages such as specific detection of all relevant HPV types and identification of viral integration and variants.
Review
Clinical Neurology
Arba Francesco, Rinaldi Chiara, Boulouis Gregoire, Fainardi Enrico, Charidimou Andreas, Morotti Andrea
Summary: The study evaluated the diagnostic accuracy of NCCT markers in identifying hematoma expansion in patients with primary intracerebral hemorrhage, finding that the diagnostic accuracy of these markers remains suboptimal for implementation in clinical trials. This analysis may help in better tailoring patients' selection for hematoma expansion targeted trials.
INTERNATIONAL JOURNAL OF STROKE
(2022)
Article
Infectious Diseases
Masato Inaba, Yuki Higashimoto, Yoko Toyama, Tomoya Horiguchi, Masaya Hibino, Mitsunaga Iwata, Kazuyoshi Imaizumi, Yohei Doi
Summary: The study demonstrates that RT-LAMP has a diagnostic accuracy comparable to RT-qPCR in the early phase of COVID-19, until the 9th day after symptom onset. However, after the 10th day, the positivity rate of RT-LAMP significantly decreases, suggesting its limitations in diagnosing COVID-19 in later stages of the disease.
INTERNATIONAL JOURNAL OF INFECTIOUS DISEASES
(2021)
Article
Pathology
J. Lippert, S. Bonlokke, A. Utke, B. R. Knudsen, B. S. Sorensen, T. Steiniche, M. Stougaard
Summary: The study demonstrates that targeted NGS is effective in detecting and genotyping HPV in both FFPE biopsies and plasma samples. This method provides early diagnosis and prognosis for cervical cancer progression, enhancing recovery and survival potential for patients.
EXPERIMENTAL AND MOLECULAR PATHOLOGY
(2021)
Article
Multidisciplinary Sciences
Martha M. C. Elwenspoek, Joni Jackson, Rachel O'Donnell, Anthony Sinobas, Sarah Dawson, Hazel Everitt, Peter Gillett, Alastair D. Hay, Deborah L. Lane, Susan Mallett, Gerry Robins, Jessica C. Watson, Hayley E. Jones, Penny Whiting
Summary: Diagnosing celiac disease can be challenging, but targeted testing based on symptoms and genetic factors can improve case-finding rates. Some indicators may suggest a higher likelihood of having celiac disease.
Article
Infectious Diseases
Hanwen Cheng, Haoyu Wu, Ni Tan, Zhuojie Liu, Ning Wang, Ningyi Chen, Chunhai Li
Summary: This study investigates the diagnostic efficacy of metagenomic next-generation sequencing (mNGS) in spinal infections. The findings reveal that mNGS has higher sensitivity and negative predictive value compared to culture, and outperforms culture in diagnosing Mycobacterium tuberculosis infections. The results provide compelling clinical evidence for the enhanced diagnostic efficacy of mNGS in spinal infections.
INFECTION AND DRUG RESISTANCE
(2023)
Article
Mathematical & Computational Biology
Kevin J. Wilson, S. Faye Williamson, A. Joy Allen, Cameron J. Williams, Thomas P. Hellyer, B. Clare Lendrem
Summary: This article proposes a novel Bayesian approach to determine the sample size for the diagnostic accuracy study, utilizing information from the analytical validity stage. The approach uses assurance to calculate the required sample size based on the target width of a posterior probability interval and allows for the choice of using or disregarding the data from the analytical validity study. Sensitivity analyses and evaluations of prior-data conflict are performed to assess the robustness of the proposed method. The results demonstrate that the assurance-based approach can reduce the required sample size when suitable prior information is available.
STATISTICS IN MEDICINE
(2022)
Article
Infectious Diseases
Hongxia Duan, Xuan Li, Aihong Mei, Ping Li, Yang Liu, Xiaofeng Li, Weiwei Li, Changhui Wang, Shuanshuan Xie
Summary: The study found that mNGS had a higher sensitivity than the traditional method, especially in blood, bronchoalveolar lavage fluid and sputum samples. The positive mNGS group had a higher hospital stay and 28-day mortality, with age being significant in multivariate logistic analyses of positive results of mNGS.
BMC INFECTIOUS DISEASES
(2021)
Article
Infectious Diseases
Thomas R. Fanshawe, Rebecca K. Judge, Sam Mort, Christopher C. Butler, Gail N. Hayward
Summary: Given the lack of accurate rapid diagnostics for UTI in women, guidelines have been developed to support appropriate antibiotic prescribing, but some guidelines have not been validated. A study was conducted to validate the diagnostic accuracy of two guidelines: Public Health England (GW-1263) and Scottish Intercollegiate Guidelines Network (SIGN160). The results demonstrate the potential for diagnostic error when using these guidelines for managing uncomplicated UTI and making antimicrobial prescribing decisions.
JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY
(2023)
Article
Biochemical Research Methods
Giacomo Baruzzo, Giulia Cesaro, Barbara Di Camillo
Summary: scSeqComm is a computational method for identifying and quantifying intercellular and intracellular signaling from scRNA-seq data, while providing functional characterization of cellular communication. The method enhances the reliability and robustness of the results by considering both intercellular and intracellular signaling evidence.
Editorial Material
Biochemical Research Methods
Barbara Di Camillo, Giuseppe Nicosia
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
(2022)
Article
Biochemistry & Molecular Biology
Silvia Ceschi, Michele Berselli, Marta Cozzaglio, Mery Giantin, Stefano Toppo, Barbara Spolaore, Claudia Sissi
Summary: The study identified Vimentin as a binder with nanomolar affinity for G4 repeats, suggesting its role in regulating gene expression at core promoters during cell development and migration by reshaping the local higher-order genome topology.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Genetics & Heredity
Enrico Lavezzo, Monia Pacenti, Laura Manuto, Caterina Boldrin, Margherita Cattai, Marco Grazioli, Federico Bianca, Margherita Sartori, Federico Caldart, Gioele Castelli, Michele Nicoletti, Eleonora Nieddu, Elisa Salvadoretti, Beatrice Labella, Ludovico Fava, Maria Cristina Vanuzzo, Vittoria Lisi, Maria Antonello, Carmela Ileana Grimaldi, Chiara Zulian, Claudia Del Vecchio, Mario Plebani, Andrea Padoan, Daniela Maria Cirillo, Alessandra R. Brazzale, Giovanni Tonon, Stefano Toppo, Ilaria Dorigatti, Andrea Crisanti
Summary: The study investigated the long-term antibody persistence in previously infected individuals and the extent of antibody-mediated protection against different SARS-CoV-2 variants in vaccinated and unvaccinated subjects.
Article
Multidisciplinary Sciences
Claudia Del Vecchio, Bethan Cracknell Daniels, Giuseppina Brancaccio, Alessandra Rosalba Brazzale, Enrico Lavezzo, Constanze Ciavarella, Francesco Onelia, Elisa Franchin, Laura Manuto, Federico Bianca, Vito Cianci, Anna Maria Cattelan, Ilaria Dorigatti, Stefano Toppo, Andrea Crisanti
Summary: Antigen tests are widely used for COVID-19 population testing, but they have limitations in detecting variant strains of the virus. Molecular testing should be retained alongside antigen testing for surveillance purposes to improve detection accuracy.
NATURE COMMUNICATIONS
(2022)
Article
Biochemical Research Methods
Marco Cappellato, Giacomo Baruzzo, Barbara Di Camillo
Summary: The development of high throughput DNA sequencing techniques has facilitated the study of complex microbial systems. Differential abundance analysis has led to important conclusions in various fields, but the lack of known biological truth makes validating the results challenging.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Medical Informatics
Erica Tavazzi, Roberto Gatta, Mauro Vallati, Stefano Cotti Piccinelli, Massimiliano Filosto, Alessandro Padovani, Maurizio Castellano, Barbara Di Camillo
Summary: In this study, the evolution trajectories of ALS patients were investigated using Process Mining techniques, revealing differences in disease progression based on patients' characteristics. The study found that most patients start without impairments, and impairment of Walking/Self-care abilities is the most common initial symptom. Spinal onset increases the risk of experiencing the loss of Walking/Self-care ability as the first impairment, and older age at onset corresponds to a faster progression to death. The comparison between the trial population and the clinical cohort showed similarities in the natural progression of the disease, but differences in observed trajectories potentially due to trial scheduling and recruitment criteria.
BMC MEDICAL INFORMATICS AND DECISION MAKING
(2023)
Article
Biochemistry & Molecular Biology
Barbara Di Camillo, Lucia Puricelli, Elisabetta Iori, Gianna Maria Toffolo, Paolo Tessari, Giorgio Arrigoni
Summary: Protein turnover rate is crucial for cellular functions and dysregulation of protein degradation can lead to various diseases. Studying protein synthesis and degradation rates is important to understand the pathophysiology of diseases. This study used a dynamic-SILAC approach to investigate protein turnover and abundance in a cellular model of diabetic nephropathy, identifying several proteins with altered turnover and abundance between diabetic nephropathic subjects and controls. These proteins could potentially serve as biomarkers or therapeutic targets for diabetic complications. The data obtained also provide valuable information on protein half-lives in human fibroblasts and contribute to basic cell biology.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Biochemical Research Methods
Emilio Ispano, Federico Bianca, Enrico Lavezzo, Stefano Toppo
Summary: Predicting protein function is a major challenge, and traditional methods can be resource-intensive and time-consuming. Automated protein function prediction techniques, especially those using machine learning, have shown promise in providing faster and cost-effective alternatives. Recent research has focused on improving prediction accuracy using machine learning, with the goal of closing the gap between predicted and experimental evidence.
CURRENT BIOINFORMATICS
(2023)
Article
Surgery
Gaya Spolverato, Matteo Fassan, Giulia Capelli, Melania Scarpa, Silvia Negro, Valentina Chiminazzo, Andromachi Kotsafti, Imerio Angriman, Michela Campi, Ottavia De Simoni, Cesare Ruffolo, Stepanyan Astghik, Chiara Vignotto, Federico Scognamiglio, Giulia Becherucci, Giorgio Rivella, Francesco Marchegiani, Luca Facci, Francesca Bergamo, Stefano Brignola, Gianluca Businello, Vincenza Guzzardo, Luca Dal Santo, Roberta Salmaso, Marco Massani, Anna Pozza, Ivana Cataldo, Tommaso Stecca, Angelo Paolo Dei Tos, Vittorina Zagonel, Pierluigi Pilati, Boris Franzato, Antonio Scapinello, Giovanni Pirozzolo, Alfonso Recordare, Roberto Merenda, Giovanni Bordignon, Silvio Guerriero, Chiara Romiti, Giuseppe Portale, Chiara Cipollari, Maurizio Zizzo, Andrea Porzionato, Marco Agostini, Francesco Cavallin, Barbara Di Camillo, Romeo Bardini, Isacco Maretto, Ignazio Castagliuolo, Salvatore Pucciarelli, Marco Scarpa
Summary: This study evaluated the sex differences in the immune microenvironment of rectal cancer patients and found that male patients had more frequent oncogene mutations associated with lower expression of T-cell activation genes, while female patients had more Th1 cells and cytotoxic T cells in the healthy mucosa, suggesting a potentially better immune response to the tumor.
INTERNATIONAL JOURNAL OF SURGERY
(2023)
Article
Medicine, General & Internal
Luca Emanuele Bossi, Cassandra Palumbo, Alessandra Trojani, Agostina Melluso, Barbara Di Camillo, Alessandro Beghini, Luca Maria Sarnataro, Roberto Cairoli
Summary: This study aimed to investigate the causes of continuous deep fluctuations in ALC in an untreated CLL patient who has had a favorable prognosis since diagnosis. The patient has chosen to adopt a vegetarian and fruitarian diet, along with prolonged fasting. Transcriptome profiling analysis revealed nine differentially expressed genes between the patient and other untreated CLL patients, providing potential insights into the role of fasting and gene expression in sustaining the lymphocytosis trend.
MEDICINA-LITHUANIA
(2023)
Article
Multidisciplinary Sciences
Massimo Bellato, Marco Cappellato, Francesca Longhin, Claudia Del Vecchio, Giuseppina Brancaccio, Anna Maria Cattelan, Paola Brun, Claudio Salaris, Ignazio Castagliuolo, Barbara Di Camillo
Summary: This study investigates the respiratory tract microbial communities of COVID-19 patients using 16S rDNA sequencing and aims to identify microbial signatures predictive of disease progression to intubation.
SCIENTIFIC REPORTS
(2023)
Article
Biochemical Research Methods
Federico Bianca, Emilio Ispano, Ermanno Gazzola, Enrico Lavezzo, Paolo Fontana, Stefano Toppo
Summary: FunTaxIS-lite is a tool that addresses the complex challenge of defining the full domain of protein functions belonging to an organism by specifying constraints based on taxon. It extends the constraints of Gene Ontology terms, reducing errors in function predictions and assisting in correcting inconsistent protein annotations.
Article
Veterinary Sciences
Giada Innocente, Ilaria Patuzzi, Tommaso Furlanello, Barbara Di Camillo, Luca Bargelloni, Maria Cecilia Giron, Sonia Facchin, Edoardo Savarino, Mirko Azzolin, Barbara Simionati
Summary: Fecal microbiota transplantation (FMT) is a promising approach for decreasing disease activity in canine chronic enteropathies (CE), but the relationship between remission mechanisms and microbiome changes is not yet elucidated. This study aimed to report the clinical effects of oral freeze-dried FMT in CE dogs by comparing the fecal microbiomes of pre-FMT CE-affected dogs, post-FMT dogs, and healthy dogs. Diversity analysis, differential abundance analysis, and machine learning algorithms were applied to investigate the differences in microbiome composition. Clinical improvement was observed in 74% of CE-affected dogs, with a significant decrease in Disease Activity Index. Each receiver showed variations in microbiome composition after FMT, indicating the need for further research on different healing patterns of microbiome changes.
VETERINARY SCIENCES
(2022)
