Review
Medical Laboratory Technology
Peter Schlattmann
Summary: This tutorial explains how to conduct a meta-analysis of diagnostic test accuracy studies based on 2x2 tables from primary studies. It discusses univariate methods for analyzing sensitivity and specificity, as well as logistic regression models for sensitivity with and without random effects. The use of diagnostic odds ratios (DOR) to assess publication bias is also covered. Additionally, bivariate random effects models are recommended, along with the construction of summary receiver operating characteristic (sROC) curves using a regression model. The tutorial includes instructions on performing the necessary calculations using the R software and provides an example meta-analysis of studies on Procalcitonin as a diagnostic marker for sepsis.
CLINICAL CHEMISTRY AND LABORATORY MEDICINE
(2023)
Article
Allergy
Bernardo Sousa-Pinto, Isabel Tarrio, Kimberly G. Blumenthal, Luis Araujo, Luis Filipe Azevedo, Luis Delgado, Joao Almedia Fonseca
Summary: The diagnostic accuracy of skin tests and specific IgE quantification in identifying patients reporting a penicillin/B-lactam allergy is low, with low sensitivity and high specificity. More research is needed to assess the role of these tests in stratifying patients for delabeling.
JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY
(2021)
Review
Infectious Diseases
Basilua Andre Muzembo, Kei Kitahara, Anusuya Debnath, Keinosuke Okamoto, Shin-Ichi Miyoshi
Summary: This study systematically evaluated the accuracy of cholera rapid diagnostic tests (RDTs) and found that they have moderate sensitivity and specificity, especially when enriched with alkaline peptone water (APW). Although they are less useful for clinical management, the current generation of RDTs can be valuable for surveillance efforts if used in a principled manner.
CLINICAL MICROBIOLOGY AND INFECTION
(2022)
Review
Parasitology
Lachlan Fairley, Samuel Smith, Shalisa Maisrikrod, Lars Henning
Summary: This study analyzed the accuracy of various diagnostic tests in detecting Burkholderia pseudomallei infection. The results showed that immunofluorescence assay, polymerase chain reaction, and lateral flow immunoassay have moderate sensitivity and specificity. Serological tests have higher sensitivity but lower specificity compared to direct detection methods.
Review
Medicine, General & Internal
Juan Jeferson Vilca-Alosilla, Mayron Antonio Candia-Puma, Katiusca Coronel-Monje, Luis Daniel Goyzueta-Mamani, Alexsandro Sobreira Galdino, Ricardo Andrez Machado-de-Avila, Rodolfo Cordeiro Giunchetti, Eduardo Antonio Ferraz Coelho, Miguel Angel Chavez-Fumagalli
Summary: This paper presents a systematic review and meta-analysis evaluating the reliability of COVID-19 diagnostic tests. Ninety-nine scientific articles were analyzed to assess the specificity and sensitivity of these tests. Molecular tests, such as RT-PCR and CRISPR, performed better in terms of accuracy compared to serological tests. The study highlights the need to improve the performance of these diagnostic tests to effectively control COVID-19 outbreaks.
Review
Medicine, General & Internal
Basilua Andre Muzembo, Kei Kitahara, Ayumu Ohno, Anusuya Debnath, Keinosuke Okamoto, Shin-Ichi Miyoshi
Summary: This meta-analysis assessed the diagnostic accuracy of cholera rapid tests for detecting Vibrio cholerae O1, finding moderate sensitivity and specificity. Sensitivity was higher in African studies, while specificity was higher in Asian studies. Overall, cholera RDTs have moderate performance for detecting Vibrio cholerae O1 compared to culture or PCR.
Review
Public, Environmental & Occupational Health
Beatriz Boger, Mariana M. Fachi, Raquel O. Vilhena, Alexandre F. Cobre, Fernanda S. Tonin, Roberto Pontarolo
Summary: This study systematically reviewed the accuracy parameters of different diagnostic methods for detecting SARS-CoV-2, finding that computed tomography has high sensitivity but low specificity, while the combination of IgM and IgG antibodies showed promising results. The research also indicated that RT-PCR remains the gold standard for diagnosing COVID-19 in sputum samples, but combining different diagnostic methods can improve accuracy.
AMERICAN JOURNAL OF INFECTION CONTROL
(2021)
Review
Infectious Diseases
Constance Dubois, Pierre R. Smeesters, Yacine Refes, Corinne Levy, Philippe Bidet, Robert Cohen, Martin Chalumeau, Julie Toubiana, Jeremie F. Cohen
Summary: This study evaluated the accuracy of RNATs in patients with pharyngitis, showing a high sensitivity of 97.5% and specificity of 95.1%. RNATs were found to be more sensitive than RADTs, with equal specificity. The authors suggest that RNATs may be used as stand-alone tests for diagnosing group A streptococcus pharyngitis.
CLINICAL MICROBIOLOGY AND INFECTION
(2021)
Review
Medicine, General & Internal
Maniya Arshadi, Fatemeh Fardsanei, Behnaz Deihim, Zahra Farshadzadeh, Farhad Nikkhahi, Farima Khalili, Giovanni Sotgiu, Amir Hashem Shahidi Bonjar, Rosella Centis, Giovanni Battista Migliori, Mohammad Javad Nasiri, Mehdi Mirsaeidi
Summary: This study evaluated the accuracy of rapid antigen tests (RATs) in diagnosing COVID-19. The results showed that RATs had high sensitivity and specificity compared to the reference test (real-time PCR), making them suitable for early detection and resource-limited countries.
FRONTIERS IN MEDICINE
(2022)
Review
Multidisciplinary Sciences
Yonas Yimam, Mehdi Mohebali, Mohammad Javad Abbaszadeh Afshar
Summary: This study compared the diagnostic performance of a new ultrasensitive rapid diagnostic test (us-RDT) and a conventional rapid diagnostic test (co-RDT) for detecting malaria. The results showed that us-RDT had higher sensitivity, especially in asymptomatic individuals and low transmission areas.
Article
Gastroenterology & Hepatology
Ferenc Emil Mozes, Jenny A. Lee, Emmanuel Anandraj Selvaraj, Arjun Narayan Ajmer Jayaswal, Michael Trauner, Jerome Boursier, Celine Fournier, Katharina Staufer, Rudolf E. Stauber, Elisabetta Bugianesi, Ramy Younes, Silvia Gaia, Monica Lupsor-Platon, Salvatore Petta, Toshihide Shima, Takeshi Okanoue, Sanjiv Mahadeva, Wah-Kheong Chan, Peter J. Eddowes, Gideon M. Hirschfield, Philip Noel Newsome, Vincent Wai-Sun Wong, Victor de Ledinghen, Jiangao Fan, Feng Shen, Jeremy F. Cobbold, Yoshio Sumida, Akira Okajima, Joern M. Schattenberg, Christian Labenz, Won Kim, Myoung Seok Lee, Johannes Wiegand, Thomas Karlas, Yusuf Yilmaz, Guruprasad Padur Aithal, Naaventhan Palaniyappan, Christophe Cassinotto, Sandeep Aggarwal, Harshit Garg, Geraldine J. Ooi, Atsushi Nakajima, Masato Yoneda, Marianne Ziol, Nathalie Barget, Andreas Geier, Theresa Tuthill, M. Julia Brosnan, Quentin Mark Anstee, Stefan Neubauer, Stephen A. Harrison, Patrick M. Bossuyt, Michael Pavlides
Summary: Liver biopsy is still necessary for fibrosis staging in patients with non-alcoholic fatty liver disease. This study evaluated the diagnostic performance of liver stiffness measurement, FIB-4 Index, and NAFLD Fibrosis Score, and showed that sequential combinations of markers can reduce the need for liver biopsies.
Article
Clinical Neurology
Nicole Ruebsamen, Stephanie Pape, Stefan Konigorski, Antonia Zapf, Gerta Ruecker, Andre Karch
Summary: This study conducted a network meta-analysis to compare the diagnostic accuracies of cerebrospinal fluid and blood biomarkers for sporadic Creutzfeldt-Jakob disease (sCJD) in specialized care settings. The results showed that RT-QuIC and NfL were the most sensitive biomarkers, and RT-QuIC was the most specific biomarker. However, there was high heterogeneity in accuracy estimates between studies.
EUROPEAN JOURNAL OF NEUROLOGY
(2022)
Review
Public, Environmental & Occupational Health
Celestin Danwang, Jean Jacques Noubiap, Jacob Souopgui, Jean Gaudart, Jean Cyr Yombi, Annie Robert
Summary: This study is the first systematic review to estimate the diagnostic performance of malaria tests on non-invasively collected specimens. PCR-based diagnosis using saliva and urine samples should only be considered when blood samples cannot be collected. The performance of rapid diagnostic testing in urine is limited, especially in terms of sensitivity. Further improvements are needed for malaria testing on non-invasively collected specimens.
Review
Medicine, General & Internal
David Fawkner-Corbett, Gail Hayward, Mohammed Alkhmees, Ann Van den Bruel, Jose M. Ordonez-Mena, Gea A. Holtman
Summary: The study aimed to determine the diagnostic accuracy of four blood tests (white cell count (WCC), neutrophil count or percentage, C reactive protein (CRP), and/or procalcitonin) for childhood appendicitis. The results showed that WCC or ANC were the best single blood tests for ruling-out pediatric appendicitis, and the combination of WCC and CRP improved accuracy. These findings have implications for clinical practice.
Review
Medicine, General & Internal
Mayron Antonio Candia-Puma, Laura Yesenia Machaca-Luque, Brychs Milagros Roque-Pumahuanca, Alexsandro Sobreira Galdino, Rodolfo Cordeiro Giunchetti, Eduardo Antonio Ferraz Coelho, Miguel Angel Chavez-Fumagalli
Summary: This systematic review and meta-analysis examined the accuracy of diagnostic tests for Chagas disease over a thirty-year period. The results showed that ELISA and qPCR techniques had higher accuracy in diagnosing chronic and acute phases of the disease, respectively. Future studies should focus on developing new diagnostic approaches for Chagas disease.
Article
Genetics & Heredity
Yiannis Goutzelas, Panagiota Kontou, Zissis Mamuris, Pantelis Bagos, Theologia Sarafidou
Summary: This study performed a meta-analysis of gene expression data in adipose tissue to identify differentially expressed genes between obese and non-obese subjects. The results revealed 821 differentially expressed genes and reconstructed a protein-protein interactions network, suggesting their involvement in RNA and energy metabolism pathways.
Article
Environmental Sciences
Anastasios Sepetis, Paraskevi N. Zaza, Fotios Rizos, Pantelis G. Bagos
Summary: The healthcare sector produces a significant amount of waste annually, and it is crucial to have effective waste management systems to protect public health. This study investigated the factors affecting healthcare waste in Greek public hospitals and found that individual-hospital characteristics have an impact on waste generation. The study provides prediction models and suggests specific actions to reduce healthcare waste and associated costs.
INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH
(2022)
Article
Genetics & Heredity
Tzoulia-Maria Tsalazidou-Founta, Evangelia A. Stasi, Maria Samara, Yorgos Mertzanis, Maria Papathanassiou, Pantelis G. Bagos, Spyros Psaroudas, Vasiliki Spyrou, Yorgos Lazarou, Athanasios Tragos, Yannis Tsaknakis, Elpida Grigoriadou, Athanasios Korakis, Maria Satra, Charalambos Billinis
Summary: This study estimated the population size, genetic status, and gene flow of brown bear sub-populations in three National Parks in Greece. The results showed high levels of inbreeding in some sub-populations and a distinct genetic structure in one sub-population. Significant gene flow was also observed between certain sub-populations.
Review
Medicine, General & Internal
Anastasia Tapari, Georgia G. Braliou, Maria Papaefthimiou, Helen Mavriki, Panagiota Kontou, Georgios K. Nikolopoulos, Pantelis G. Bagos
Summary: This article conducts a systematic review and meta-analysis of antigen-based diagnostic tests for COVID-19, comparing different methods and performance. The findings suggest that the performance of tests varies based on sample sources and rapid methods, emphasizing the influence of viral load on test sensitivity.
Article
Biology
Ioannis A. Tamposis, Georgios A. Manios, Theodosia Charitou, Konstantina E. Vennou, Panagiota Kontou, Pantelis G. Bagos
Summary: MAGE is an open-source Python package designed for meta-analysis and functional enrichment analysis of gene expression data. It includes various functions for analysis and visualization, and is available as both a standalone version and a webserver.
Article
Genetics & Heredity
Theodosia Charitou, Panagiota Kontou, Ioannis A. Tamposis, Georgios A. Pavlopoulos, Georgia G. Braliou, Pantelis G. Bagos
Summary: This study examines the relationship between drugs, genes, and COVID-19 susceptibility. It suggests that genetic factors may influence the clinical manifestation of COVID-19, especially in patients with comorbidities.
PHARMACOGENOMICS JOURNAL
(2022)
Article
Oncology
Robert Carreras-Torres, Andre E. Kim, Yi Lin, Virginia Diez-Obrero, Stephanie A. Bien, Conghui Qu, Jun Wang, Niki Dimou, Elom K. Aglago, Demetrius Albanes, Volker Arndt, James W. Baurley, Sonja I. Berndt, Stephane Bezieau, D. Timothy Bishop, Emmanouil Bouras, Hermann Brenner, Arif Budiarto, Peter T. Campbell, Graham Casey, Andrew T. Chan, Jenny Chang-Claude, Xuechen Chen, David Conti, Christopher H. Dampier, Matthew A. M. Devall, David A. Drew, Jane C. Figueiredo, Steven Gallinger, Graham G. Giles, Stephen B. Gruber, Andrea Gsur, Marc J. Gunter, Tabitha A. Harrison, Akihisa Hidaka, Michael Hoffmeister, Jeroen R. Huyghe, Mark A. Jenkins, Kristina M. Jordahl, Eric Kawaguchi, Temitope O. Keku, Anshul Kundaje, Loic Le Marchand, Juan Pablo Lewinger, Li Li, Bharuno Mahesworo, John L. Morrison, Neil Murphy, Hongmei Nan, Rami Nassir, Polly A. Newcomb, Mireia Obon-Santacana, Shuj Ogino, Jennifer Ose, Rish K. Pai, Julie R. Palmer, Nikos Papadimitriou, Bens Pardamean, Anita R. Peoples, Paul D. P. Pharoah, Elizabeth A. Platz, Gad Rennert, Edward Ruiz-Narvaez, Lori C. Sakoda, Peter C. Scacheri, Stephanie L. Schmit, Robert E. Schoen, Anna Shcherbina, Martha L. Slattery, Mariana C. Stern, Yu-Ru Su, Catherine M. Tangen, Duncan C. Thomas, Yu Tian, Konstantinos K. Tsilidis, Cornelia M. Ulrich, Fräuronzel J. B. van Duijnhoven, Bethany Van Guelpen, Kala Visvanathan, Pavel Vodicka, Tjeng Wawan Cenggoro, Stephanie J. Weinstein, Emily White, Alicja Wolk, Michael O. Woods, Li Hsu, Ulrike Peters, Victor Moreno, W. James Gauderman
Summary: A genome-wide interaction scan revealed novel genetic loci associated with the risk of colorectal cancer in relation to smoking. The identified loci were found to be involved in tumor suppression and immune response. These findings have important implications for potential prevention treatments.
CANCER EPIDEMIOLOGY BIOMARKERS & PREVENTION
(2023)
Review
Oncology
Maria Papathanassiou, Ioannis Tamposis, Kalliopi K. K. Exarchou-Kouveli, Panagiota I. I. Kontou, Anna Tzortzi de Paz, Lampros Mitrakas, Maria Samara, Pantelis G. G. Bagos, Vassilios Tzortzis, Panagiotis J. J. Vlachostergios
Summary: The effectiveness or ineffectiveness of immunotherapy after prior use of anti-PD1/PD-L1 or/and anti-CTLA monoclonal antibodies is still largely unknown.
FRONTIERS IN ONCOLOGY
(2022)
Review
Medicine, General & Internal
Georgia V. Kapoula, Konstantina E. Vennou, Pantelis G. Bagos
Summary: This study conducted a systematic review and meta-analysis to assess the association between seasonal influenza vaccination and pneumococcal vaccination with SARS-CoV-2 infection and its clinical outcomes. The results showed that both influenza and pneumococcal vaccination were associated with a lower risk of SARS-CoV-2 infection. However, there was no evidence to support the association between vaccination and harder endpoints such as ICU admission and death.
Article
Education & Educational Research
Zoi Kourti, Christos-Apostolos Michalakopoulos, Pantelis G. G. Bagos, Efrosyni-Alkisti Paraskevopoulou-Kollia
Summary: This study investigates the development of Computational Thinking (CT) skills in preschool age children by assessing their readiness and exploring the perspectives of parents and preschool teachers. The research findings indicate that preschool children show a high level of readiness for CT activities, although parents express concerns. Additionally, the study reveals that the use of personal computers in kindergarten varies among teachers, with their attitudes towards CT introduction being mainly neutral.
EDUCATION SCIENCES
(2023)
Review
Health Care Sciences & Services
Pelagia Soultatou, Stamatis Vardaros, Pantelis G. Bagos
Summary: This article aims to review the evidence generated over the past two decades (2003-2023), identifying the main policy gaps in school health services and health education curricula in Greece and providing a concrete policy plan. The findings suggest that school health services are not school-based but a function of the primary health care system, and health education has a constantly changing position in school curricula. The study also highlights deficiencies in schoolteachers' training, coordination, and leadership. The article provides a set of policy measures towards the reform and integration of school health with health education.
Article
Oncology
Niki Dimou, Andre E. Kim, Orlagh Flanagan, Neil Murphy, Virginia Diez-Obrero, Anna Shcherbina, Elom K. Aglago, Emmanouil Bouras, Peter T. Campbell, Graham Casey, Steven Gallinger, Stephen B. Gruber, Mark A. Jenkins, Yi Lin, Victor Moreno, Edward Ruiz-Narvaez, Mariana C. Stern, Yu Tian, Kostas K. Tsilidis, Volker Arndt, Elizabeth L. Barry, James W. Baurley, Sonja I. Berndt, Stephane Bezieau, Stephanie A. Bien, D. Timothy Bishop, Hermann Brenner, Arif Budiarto, Robert Carreras-Torres, Tjeng Wawan Cenggoro, Andrew T. Chan, Jenny Chang-Claude, Stephen J. Chanock, Xuechen Chen, David V. Conti, Christopher H. Dampier, Matthew Devall, David A. Drew, Jane C. Figueiredo, Graham G. Giles, Andrea Gsur, Tabitha A. Harrison, Akihisa Hidaka, Michael Hoffmeister, Jeroen R. Huyghe, Kristina Jordahl, Eric Kawaguchi, Temitope O. Keku, Susanna C. Larsson, Loic Le Marchand, Juan Pablo Lewinger, Li Li, Bharuno Mahesworo, John Morrison, Polly A. Newcomb, Christina C. Newton, Mireia Obon-Santacana, Jennifer Ose, Rish K. Pai, Julie R. Palmer, Nikos Papadimitriou, Bens Pardamean, Anita R. Peoples, Paul D. P. Pharoah, Elizabeth A. Platz, John D. Potter, Gad Rennert, Peter C. Scacheri, Robert E. Schoen, Yu-Ru Su, Catherine M. Tangen, Stephen N. Thibodeau, Duncan C. Thomas, Cornelia M. Ulrich, Caroline Y. Um, Franzel J. B. van Duijnhoven, Kala Visvanathan, Pavel Vodicka, Ludmila Vodickova, Emily White, Alicja Wolk, Michael O. Woods, Conghui Qu, Anshul Kundaje, Li Hsu, W. James Gauderman, Marc J. Gunter, Ulrike Peters
Summary: Diabetes is a risk factor for colorectal cancer, but the mechanisms and genetic variants affecting this relationship are still unclear. Through genome-wide gene-environment interaction analysis, it was found that variations in insulin signaling gene (SLC30A8) and immune function gene (LRCH1) may modify the association between diabetes and colorectal cancer risk.
BRITISH JOURNAL OF CANCER
(2023)
Article
Biochemistry & Molecular Biology
Marina Petsana, Ahmed F. Roumia, Pantelis G. Bagos, Haralabia Boleti, Georgia G. Braliou
Summary: The aim of this study was to retrieve the entire spectrum of Kinetoplastea protein sequences containing the PX module, predict their structures, and identify evolutionary conserved and unique traits. A new Kinetoplastea_PX pHMM was constructed using a combination of protein IDs from two searches. The study identified the unique PX-Pkinase domain architecture in Trypanosoma spp. and suggests the potential use of Kinetoplastea PX-proteins as targets for anti-parasitic drug design.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Nutrition & Dietetics
Maria Papaefthimiou, Panagiota I. Kontou, Pantelis G. Bagos, Georgia G. Braliou
Summary: This study aimed to investigate the effects of stevia leaf extracts or glycosides on oxidative stress markers in diseased rats. The results demonstrated that stevia leaf extracts restored oxidative stress markers to a higher extent compared to pure glycosides. Rats with diabetes mellitus showed the strongest restorative response to stevia leaf extract administration. These findings suggest that stevia leaf extract may have protective effects against various diseases through its antioxidant properties.
Article
Biochemical Research Methods
Evangelos Karatzas, Fotis A. Baltoumas, Eleni Aplakidou, Panagiota Kontou, Panos Stathopoulos, Leonidas Stefanis, Pantelis G. Bagos, Georgios A. Pavlopoulos
Summary: This article introduces Flame (v2.0), a web tool that combines and visualizes results from popular functional enrichment applications. Flame utilizes aGOtool, g: Profiler, WebGestalt, and Enrichr pipelines to present their outputs separately or in combination. It offers interactive plots for intuitive representations and easier interpretation.
