Article
Immunology
Yi-Qiang Lin, Ya-Ling Gao, Mao Wang, Shui-Di Yan, Li-Rong Lin
Summary: This study investigates the clinical characteristics of patients with false-positive HIV screening test results and identifies potential diseases unrelated to HIV. Characterization of these patients can help in interpreting HIV screening test results.
INTERNATIONAL IMMUNOPHARMACOLOGY
(2022)
Article
Biochemical Research Methods
Daniel P. Zolg, Siegfried Gessulat, Carmen Paschke, Michael Graber, Magnus Rathke-Kuhnert, Florian Seefried, Kai Fitzemeier, Frank Berg, Daniel Lopez-Ferrer, David Horn, Christoph Henrich, Andreas Huhmer, Bernard Delanghe, Martin Frejno
Summary: INFERYS rescoring utilizes deep learning for accurate prediction of peptide fragment ion intensities, enhancing the scoring accuracy of Sequest HT search engine results. By combining intensity-based scores with classical search engine scores, this approach leads to improved peptide spectrum match and identification numbers in proteomic data analysis.
RAPID COMMUNICATIONS IN MASS SPECTROMETRY
(2021)
Article
Forestry
Mihai Dragomir, Silvia Tofana, Diana Dragomir, Aurel Mihail Titu, Daniela Popescu
Summary: The article presents a complete approach for assessing the adoption of circular economy in the wood industry. Through questionnaire survey and statistical analysis, the article concludes that the wood industry has made good progress in circular economy and proposes recommendations to further promote the maturity of current circular approaches.
Article
Obstetrics & Gynecology
Madison Miller, Rachel Cevigney, Mariam Ayyash, Majid Shaman, Monica Kole
Summary: A retrospective cohort study compared the occurrence of false-positive HIV test results in pregnant patients before and during the COVID-19 pandemic. The study found a significantly higher frequency of false-positive results during COVID-19, which was associated with SARS-CoV-2 seropositivity. However, when patients with positive SARS-CoV-2 PCR test results preceding the false-positive HIV results were excluded, the difference in frequency between the cohorts became non-significant.
OBSTETRICS AND GYNECOLOGY
(2023)
Article
Medicine, General & Internal
Xiang-Qi Kong, Yong-Jing Wang, Zan-Xi Fang, Tian-Ci Yang, Man-Li Tong
Summary: Real-time reverse transcription-polymerase chain reaction (RT-PCR) is the gold standard for diagnosing COVID-19, but it may yield false-positive results. This study reports a case of positive nucleic acid test during routine screening, which was later determined to be due to vaccine contamination. It raises awareness of false-positive RT-PCR results for SARS-CoV-2, particularly among vaccinators, and provides suggestions to prevent such incidents from recurring.
FRONTIERS IN MEDICINE
(2022)
Article
Virology
Michael J. Wilson, Dominic Sparkes, Chloe Myers, Anna A. Smielewska, Mir Mubariz Husain, Christopher Smith, Kathryn J. Rolfe, Hongyi Zhang, Hamid Jalal
Summary: Confirmatory testing is necessary to reduce false positives, but can lead to delays in results. Establishing a threshold for confirmatory testing can streamline the process and improve accuracy when needed.
JOURNAL OF CLINICAL VIROLOGY
(2021)
Article
Psychiatry
Noa Katz Shroitman, Einat Peles, Sharona Even-Tov, Shaul Schreiber, Oren Tene
Summary: Patients with schizophrenia treated with long-term injectable risperidone may falsely test positive for fentanyl in rapid commercial screening kits, highlighting the potential for inaccurate results regarding fentanyl misuse in clinical settings.
PSYCHIATRY RESEARCH
(2021)
Article
Biochemical Research Methods
John A. Cormican, Yehor Horokhovskyi, Wai Tuck Soh, Michele Mishto, Juliane Liepe
Summary: This article introduces a method of rescoring mass spectrometry search results using spectral predictors, which can increase the identification rate of peptide spectrum matches. This method is particularly effective in immunopeptidomics and has potential benefits for the identification of noncanonical peptides.
MOLECULAR & CELLULAR PROTEOMICS
(2022)
Article
Oncology
Blanca Lumbreras, Lucy Anne Parker, Juan Pablo Caballero-Romeu, Luis Gomez-Perez, Marta Puig-Garcia, Maite Lopez-Garrigos, Nuria Garcia, Ildefonso Hernandez-Aguado
Summary: In a prospective cohort study, we found a high rate of false-positive results (46.6%) in prostate-specific antigen (PSA) testing in clinical practice, with age, alcohol intake, and urinary tract infection being associated factors. False-negative results were less common (3.7%) and were associated with diabetes mellitus. This study provides important information for shared decision making in clinical practice.
Article
Public, Environmental & Occupational Health
Yannick Galipeau, Abishek Xavier, Aaron Dyks, Curtis Cooper, Marc-Andre Langlois
Summary: Efficient and rapid identification of active SARS-CoV-2 infections is crucial for monitoring and controlling the spread of the virus. Nucleic acid testing and rapid antigen tests are widely used methods. This case report highlights the occurrence of sustained false positive results, which were ruled out by alternative testing methods. It emphasizes the importance of using alternative tests to confirm results in case of false positives and the need for broader awareness in healthcare and public health communities.
FRONTIERS IN PUBLIC HEALTH
(2023)
Article
Management
Asma Zare, Alireza Choobineh, Hamidreza Mokarami, Mehdi Jahangiri
Summary: The study developed a tool with 26 items in six domains, including tactile sensation, dexterity, grip strength, fitting, reliability and hand hygiene. The tool demonstrated good validity and reliability, providing a comprehensive assessment of the ergonomic and safety status of medical gloves.
JOURNAL OF NURSING MANAGEMENT
(2021)
Review
Chemistry, Analytical
So-Hee Kim, So-Young Lee, Unji Kim, Se-Wook Oh
Summary: This review outlines several techniques for reducing false-positive LAMP results before and after amplification. Organic additives or pullulan can be used to decrease nonspecific amplification before amplification. Uracil-DNA-glycosylase and the hot-start effect with gold nanoparticles can eliminate carry-over contamination and reduce nonspecific amplification after amplification. The use of guide RNA and colorimetric change in DNAzyme can accurately confirm amplification results.
ANALYTICA CHIMICA ACTA
(2023)
Article
Immunology
Laura G. Alfie, Yesica S. Longueira, Monica Pippo, Leonel Cruces, Maria F. Quiroga, Gabriela Turk, Natalia Laufer
Summary: This study evaluated the occurrence of false-positive HIV serology results among individuals with COVID-19 diagnosis and in vaccinated individuals. The results showed a higher occurrence of HIV false-positive results among individuals with detectable SARS-CoV-2 antibodies.
Article
Engineering, Chemical
C. Kroesche, K. Budde, M. Malow
Summary: The study reveals that the poly-chlorosilanes do not exhibit oxidizing properties in the UN Test O.2 due to their high affinity to oxygen, with false-positive results attributed to the presence of cellulose as the test substance. This information imposes limitations on the classification of these substances in the internationally used UN Test O.2.
JOURNAL OF LOSS PREVENTION IN THE PROCESS INDUSTRIES
(2021)
Article
Radiology, Nuclear Medicine & Medical Imaging
Yan Liu, Lulu Yang, Hui Xu, Yiyuan Yang, Yiqian Liang, Aimin Yang, Xiaojiang Tang, Shengkai Lei, Ioannis Christakis, Pornpeera Jitpratoom, Jianjun Xue
Summary: Tc-99m-MIBI SPECT/CT parathyroid imaging has good sensitivity and high specificity in accurately locating hyperparathyroidism. The accuracy of localization is positively correlated with lesion weight and parathyroid hormone levels. Lightweight lesions are the main source of false-negative results in Tc-99m-MIBI SPECT/CT parathyroid imaging.
QUANTITATIVE IMAGING IN MEDICINE AND SURGERY
(2023)
Article
Plant Sciences
Pan Gong, Michiel Bontinck, Kirin Demuynck, Jolien De Block, Kris Gevaert, Dominique Eeckhout, Geert Persiau, Stijn Aesaert, Griet Coussens, Mieke Van Lijsebettens, Laurens Pauwels, Geert De Jaeger, Dirk Inze, Hilde Nelissen
Summary: SAMBA has been identified as a plant-specific regulator of the anaphase-promoting complex/cyclosome (APC/C) in Arabidopsis and maize. Two samba genome edited mutants in maize showed growth defects, with samba-1 representing a knockout allele and samba-3 producing a truncated protein that still interacted with APC/C but with altered activity. This suggests a dosage-dependent role for SAMBA in controlling developmental processes.
Article
Chemistry, Analytical
Maxime Gavage, Kaatje Van Vlierberghe, Marc Dieu, Patsy Renard, Thierry Arnould, Marc De Loose, Kris Gevaert, Nathalie Gillard, Christof Van Poucke
Summary: This study has successfully developed a robust method for detecting and quantifying multiple allergens in food, ensuring the safety of allergic consumers. The combination of specific incurred test materials, standard addition strategy, and stable isotope-labeled concatemer has provided the method with sufficient sensitivity and reliability.
JOURNAL OF AOAC INTERNATIONAL
(2022)
Article
Biochemistry & Molecular Biology
Petra Van Damme, Camilla Osberg, Veronique Jonckheere, Nina Glomnes, Kris Gevaert, Thomas Arnesen, Henriette Aksnes
Summary: N-terminal acetylation of proteins is a conserved modification in eukaryotes, and the yeast Saccharomyces cerevisiae is a valuable model for studying this process. The bulk of N-terminal acetylation in S. cerevisiae is catalyzed by NatA, NatB, and NatC. In this study, the authors identified 57 yeast NatC substrates using a combination of techniques. They also uncovered some non-NatC NAT activity, suggesting redundancy between NatC and NatE/Naa50. Furthermore, the authors demonstrated the evolutionary conservation of NatC from yeast to humans and its potential implications for studying pathogenic variants. Overall, this work provides valuable insights into NatC-mediated N-terminal acetylation.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2023)
Article
Biochemical Research Methods
Elke Debrie, Milan Malfait, Ralf Gabriels, Arthur Declerq, Adriaan Sticker, Lennart Martens, Lieven Clement
Summary: Reliable peptide identification is crucial in MS-based proteomics, and the TDA method is widely used for estimating the FDR. However, the assumptions of TDA are often not verified in practice, which can result in poor FDR control and negatively impact downstream data analysis. To address this issue, the TargetDecoy package is introduced, providing necessary functionality to assess the quality and assumptions of TDA for a given set of PSMs.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Biochemical Research Methods
Ralf Gabriels, Arthur Declercq, Robbin Bouwmeester, Sven Degroeve, Lennart Martens
Summary: There are various output file formats from proteomics search engines, but the lack of standardized formats makes it difficult to process peptide-spectrum matches (PSMs) and PSM files downstream. This article presents psm_utils, a Python package that can handle various PSM file formats and provides a unified and user-friendly interface. It includes a Python API, a command line interface, and a web application for interconverting PSM files and retrieving basic PSM statistics.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Oncology
Ana Teresa Pinto, Ana Beatriz Machado, Hugo Osorio, Marta Laranjeiro Pinto, Rui Vitorino, Goncalo Justino, Catia Santa, Flavia Castro, Tania Cruz, Carla Rodrigues, Jorge Lima, Jose Luis R. Sousa, Ana Patricia Cardoso, Rita Figueira, Armanda Monteiro, Margarida Marques, Bruno Manadas, Jarne Pauwels, Kris Gevaert, Marc Mareel, Sonia Rocha, Tiago Duarte, Maria Jose Oliveira
Summary: Resistance to radiotherapy is a major problem in cancer treatment. Investigating the response of macrophages to ionizing radiation could help overcome tumor radio resistance.
Article
Biochemistry & Molecular Biology
Patrick Willems, Valerie Van Ruyskensvelde, Takanori Maruta, Robin Pottie, Alvaro D. Fernandez-Fernandez, Jarne Pauwels, Matthew A. Hannah, Kris Gevaert, Frank Van Breusegem, Katrien Van der Kelen
Summary: Alternative splicing is an important gene regulatory process in plants, and its inhibition can alleviate cell death and enhance tolerance to oxidative stress.
FREE RADICAL BIOLOGY AND MEDICINE
(2023)
Article
Chemistry, Analytical
Maxime Gavage, Kaatje Van Vlierberghe, Marc Dieu, Patsy Renard, Thierry Arnould, Kris Gevaert, Marc De Loose, Christof Van Poucke, Anne-Catherine Huet, Nathalie Gillard
Summary: This interlaboratory study evaluated the potential of MS for food allergen detection and quantification using a standard addition quantification strategy and a stable isotope-labeled concatemer as an internal standard. Nine laboratories participated in the study and were able to detect allergens with sufficient sensitivity, although egg detection was more challenging. The encouraging results of this study contribute to harmonization among laboratories testing for allergens.
JOURNAL OF AOAC INTERNATIONAL
(2023)
Article
Biochemical Research Methods
Benjamin A. Neely, Viktoria Dorfer, Lennart Martens, Isabell Bludau, Robbin Bouwmeester, Sven Degroeve, Eric W. Deutsch, Siegfried Gessulat, Lukas Kaell, Pawel Palczynski, Samuel H. Payne, Tobias Greisager Rehfeldt, Tobias Schmidt, Veit Schwaemmle, Julian Uszkoreit, Juan Antonio Vizcaino, Mathias Wilhelm, Magnus Palmblad
Summary: In recent years, machine learning has made significant progress in modeling mass spectrometry data for proteomics analysis. A workshop was conducted to evaluate and explore machine learning applications in multidimensional mass spectrometry-based proteomics analysis. The workshop helped identify knowledge gaps, define needs, and discuss the possibilities, challenges, and future opportunities. The summary of the discussions conveys excitement about the potential of machine learning in proteomics and aims to inspire future research.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Biochemical Research Methods
Tine Claeys, Maxime Menu, Robbin Bouwmeester, Kris Gevaert, Lennart Martens
Summary: Using data from 183 public human data sets, a machine learning model was trained to identify tissue and cell-type specific protein patterns. The model achieved high accuracy in predicting tissues (98%) and cell types (99%) based on protein abundance. The results provide valuable insights into tissue-specific proteins and can be applied to various downstream applications.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Multidisciplinary Sciences
Andreia Ferreira, Evy Timmerman, An Staes, Marnik Vuylsteke, Louis De Muynck, Kris Gevaert
Summary: By using affinity-enrichment mass spectrometry, we identified novel potential protein ligands that may interact with (3S-)HS. Our dataset expands the repertoire of proteins that depend on 3S-HS in (patho)physiological conditions, providing new insights into the molecular mechanisms involved.
Article
Biochemical Research Methods
Pieter Verschaffelt, Alessandro Tanca, Marcello Abbondio, Tim van den Bossche, Tibo Vande Moortele, Peter Dawyndt, Lennart Martens, Bart Mesuere
Summary: Unipept Desktop 2.0 is the latest version of the Unipept Desktop tool, which now supports the analysis of metaproteogenomics datasets. It allows for the automatic construction of targeted protein reference databases for improved taxonomic and functional resolution. By limiting the proteins in the database, (meta)proteogenomic analyses can also be performed with better control and privacy. A case study using human gut metaproteome dataset and matched 16S rRNA gene sequencing data is presented as a proof of concept.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Multidisciplinary Sciences
Tine Claeys, Tim van den Bossche, Yasset Perez-Riverol, Kris Gevaert, Juan Antonio Vizcaino, Lennart Martens
Summary: Public proteomics data often lack essential metadata, but lesSDRF provides a tool to simplify the process of metadata annotation and ensure that the data has lasting impact beyond its initial publication.
NATURE COMMUNICATIONS
(2023)
Article
Biochemical Research Methods
Ralf Gabriels, Arthur Declercq, Robbin Bouwmeester, Sven Degroeve, Lennart Martens
Summary: This study introduces a Python package called psm_utils, which can read and write various proteomics search engine output file formats and handle peptide-spectrum matches (PSMs) and PSM lists in a unified data structure. The package includes a Python API and command line interface, as well as a user-friendly web application for converting PSM files and retrieving basic PSM statistics.
JOURNAL OF PROTEOME RESEARCH
(2023)