Editorial Material
Oncology
Mateus Trinconi Cunha, Vinicius Jardim Carvalho, Rafael Maffei Loureiro, Carlos Eduardo Brantis-de-Carvalho, Murilo Bicudo Cintra, Gilberto de Castro Junior
Summary: The commentary highlights potential issues with predictor selection, cross-validation method, and lack of final testing in a research article, which may lead to overfitting and overestimation of performance metrics.
JOURNAL FOR IMMUNOTHERAPY OF CANCER
(2021)
Letter
Oncology
Abigail Goodman, Jose Velazquez-Vega, Jeffrey Olson
Summary: This study reviewed the WHO 2021 Classification of Tumors of the Central Nervous System terminology to determine the applicable components for updating the guideline on progressive glioblastoma. The research concluded that glioblastoma, IDH-wildtype WHO grade 4 is the closest category to the tumors referred to as glioblastoma in the 2016 WHO classification. As a result, this term was chosen to replace glioblastoma in the updated guideline on the role of neuropathology in managing progressive glioblastoma.
JOURNAL OF NEURO-ONCOLOGY
(2022)
Editorial Material
Oncology
Raphael Colle, Thierry Andre, Yves Menu
Summary: The article highlights that early tumor shrinkage and depth of response predict prognosis in colorectal cancer patients treated with immune checkpoint inhibitors, but no cases of pseudoprogression were observed. Discrepancies with other studies may be due to differences in radiological evaluation criteria and timing of imaging.
JOURNAL FOR IMMUNOTHERAPY OF CANCER
(2021)
Editorial Material
Oncology
Rivka R. Colen, Christian Rolfo, Murat Ak, Mira Ayoub, Sara Ahmed, Nabil Elshafeey, Priyadarshini Mamindla, Pascal O. Zinn, Chaan Ng, Raghu Vikram, Spyridon Bakas, Christine B. Peterson, Jordi Rodon Ahnert, Vivek Subbiah, Daniel D. Karp, Bettzy Stephen, Joud Hajjar, Aung Naing
Summary: In our study, we focused on predicting immunotherapy response in patients with rare cancers using radiomics analysis. By selecting appropriate feature selection and classifier methods, avoiding overfitting, checking for multicollinearity among features, and performing 10-fold cross-validation, we achieved effective predictive performance for our radiomics models.
JOURNAL FOR IMMUNOTHERAPY OF CANCER
(2021)
Letter
Computer Science, Interdisciplinary Applications
Antonio Fernandez-Cano
Summary: This paper discusses the current phenomenon of "publish or perish" in academia, highlighting the consequences and questioning the role of scientific journals and the effectiveness of peer review. It calls for improvements in the field of scientific information and communication.
Article
Oncology
Niloofar Faraji, Shahab Aali, Mahsa Motiei, Sahand Sadat Mansouri
Summary: The role of large language models (LLM) in medical and biomedical sciences is important, and AI models like ChatGPT have the potential to assist in research and clinical practice. However, it is crucial to recognize that these models should be used in conjunction with human expertise and judgment, and not as a replacement for the knowledge and experience of healthcare professionals and researchers in the field.
JOURNAL OF CANCER RESEARCH AND CLINICAL ONCOLOGY
(2023)
Article
Biochemical Research Methods
Jing Chen, Lindsey J. Leach, Zewei Luo
Summary: Mapping quantitative trait loci (QTL) in autotetraploid species is a timely and challenging task. Two papers by Wu and his colleagues proposed statistical methods for QTL mapping in these species, but have been criticized for fundamental conceptual errors from statistical and genetic perspectives.
BRIEFINGS IN BIOINFORMATICS
(2021)
Letter
Biochemical Research Methods
Hansi Zheng, Xiaoman Li, Haiyan Hu
Summary: The authors of the BASiNET tool claim that the survey paper 'A systematic evaluation of computational tools for lncRNA identification' incorrectly evaluates the BASiNET tool. However, in this rebuttal, it is pointed out that the survey paper indeed evaluates the BASiNET tool correctly and explains why the evaluation should not be carried out as suggested by the BASiNET authors.
BRIEFINGS IN BIOINFORMATICS
(2022)
Letter
Computer Science, Interdisciplinary Applications
Gangan Prathap
Summary: In this Letter to the Editor, the dimensionless citation indicators h/P, p/P, and i/P are extended to the case of fractional counting by introducing the concepts of Hirsch h-index, performance index of Prathap, and impact value measured by the ratio of citations to publications.
Letter
Gastroenterology & Hepatology
Per Cajander, Taher Omari, Harry Scheinin, Mika Scheinin, Johanna Savilampi
Summary: It is important to consider the impact of anesthetic agents on esophageal function testing. Dexmedetomidine has been found to affect primary peristalsis in esophageal manometry, and in the case reports by Toaz et al., secondary peristalsis during FLIP panometry was also affected. This may be due to a specific pharmacodynamic effect, with a transient direct alpha 2-mediated effect on esophageal smooth muscle, associated with a high plasma concentration before sympathetic inhibition begins.
NEUROGASTROENTEROLOGY AND MOTILITY
(2023)
Article
Public, Environmental & Occupational Health
S. Eliza Dunn, Jennifer E. Reed, Christoph Neumann
Summary: The article on the global distribution of acute unintentional pesticide poisoning emphasized the importance of evaluating this issue, but there may be an overestimation in the numbers provided. Understanding the benefits of these chemistries is also crucial for a comprehensive evaluation.
Letter
Computer Science, Interdisciplinary Applications
Gangan Prathap
Summary: The research proposes an additive rule based on dimensionality and conservation rules to determine the appropriate cumulative h-index of a complex set of partial-sets.
Letter
Anesthesiology
Rui Liu, Ruizhao Lyu, Menghao Wu, Yumo Jing, Jianhua Wang
Summary: This article reviews a study on ultrasound-guided regional blocks in clavicle surgery and its effects on anesthesia and postoperative outcomes. However, there are concerns regarding the defined population, undefined fracture types, and unclear method of measuring the diaphragm, which may affect the accurate interpretation of the results.
JOURNAL OF CLINICAL MONITORING AND COMPUTING
(2023)
Article
Engineering, Environmental
Suraj Gupta, Diana Aga, Amy Pruden, Liqing Zhang, Peter Vikesland
Summary: The advancement of new data acquisition and handling techniques has enabled researchers to use machine learning techniques for analyzing complex environmental systems, leading to more comprehensive approaches in environmental monitoring. The current applications of ML algorithms in Environmental Science and Engineering include metagenomic data analysis for antimicrobial resistance, nontarget analysis for environmental pollutant profiling, and anomaly detection in continuous data from engineered water systems.
ENVIRONMENTAL SCIENCE & TECHNOLOGY
(2021)
Letter
Biochemical Research Methods
Emily L. Leventhal, Andrea R. Daamen, Peter E. Lipsky
Summary: Developing molecular profiles to predict clinical features of SLE from blood transcriptomic data can assist in personalized treatment. A web tool was created to aid clinicians in therapeutic decision making and predict clinical features associated with SLE. However, the tool did not perform well enough to replace the standard kidney biopsy as a diagnostic procedure.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Environmental Sciences
Johan Gustafsson, Jessica Legradi, Marja H. Lamoree, Lillemor Asplund, Pim E. G. Leonards
Summary: This study is the first to focus on the effects of OH-PBDEs at the metabolite level in vivo and uses metabolomics to investigate the metabolic effects of exposure to OH-PBDEs. The results suggest that OH-PBDEs may disrupt energy metabolism, neurotoxicity, and potential immunotoxicity, and different compounds have different metabolic effects.
SCIENCE OF THE TOTAL ENVIRONMENT
(2023)
Article
Environmental Sciences
Elvis D. Okoffo, Cassandra Rauert, Kevin V. Thomas
Summary: This study investigated the mass concentrations and removal rates of plastic particles above 1 μm in municipal wastewater treatment plants in Australia, providing valuable information on the pollution level and distribution characteristics of plastic polymers in these plants.
SCIENCE OF THE TOTAL ENVIRONMENT
(2023)
Article
Environmental Sciences
Maurice de Jonker, Pim E. G. Leonards, Marja H. Lamoree, Sicco H. Brandsma
Summary: A novel method using AP-MALDI coupled with qTOF-MS was developed for fast-screening analysis of additives in electronics and plastic consumer products. A GNP-doped target plate was developed to simplify sample preparation and increase sample throughput. The method showed high desorption/ionization capability for low molecular weight molecules and identified 56 additives in various products. The identification of certain additives in plastic toys suggests their recycling from electronic waste.
Article
Engineering, Environmental
Benilde Bonnefille, Oskar Karlsson, May Britt Rian, Rubhana Raqib, Faruque Parvez, Stefano Papazian, M. Sirajul Islam, Jonathan W. Martin
Summary: This study analyzed water samples from urban and rural rivers in Dhaka, Bangladesh using nontarget mass spectrometry with open-source workflows. The results revealed over 20,000 unique molecular features correlated with urban pollution sources, mainly from uncontrolled urban drainage. Additionally, several unknown compounds associated with an urban source were identified using in silico structure prediction. The findings provide important insights for water pollution monitoring and further wastewater treatment initiatives.
ENVIRONMENTAL SCIENCE & TECHNOLOGY
(2023)
Article
Engineering, Environmental
Phong H. N. Vo, Brett R. Hamilton, Roger A. Wepf, Trent A. Key, Thi Minh Hong Nguyen, Phong K. Thai, Kevin Thomas, Jochen F. Mueller
Summary: This study used DESI MSI to analyze the vertical distribution of PFAS in a concrete core from an AFFF-impacted FTG, and the results were consistent with the conventional method of core sidewall drilling. DESI MSI can provide detailed mass distribution at a higher resolution.
ENVIRONMENTAL SCIENCE & TECHNOLOGY LETTERS
(2023)
Article
Environmental Sciences
Katja M. Shimko, Jake W. O'Brien, Xialu Lin, Benjamin J. Tscharke, Kevin Thomas
Summary: Wastewater analysis shows potential in tracking the use of performance- and image-enhancing drugs in communities, but the stability of samples after sampling is currently unknown. This study conducted stability experiments on 52 biomarkers of such drugs in wastewater, testing different conditions including pretreatments, sample preservation methods, and temperatures. The results indicate that filtration and acidification to pH 2 are the optimal preservation methods, with stability ranging from medium to high for up to 200 days. Additionally, a calculator was provided to assist in sample collection and archiving.
Article
Environmental Sciences
Pradeep Dewapriya, Nikolaos Rousis, Cassandra Rauert, Nikolaos S. Thomaidis, Kevin V. Thomas
Summary: Urban stormwater runoff is a major source of water pollution caused by a large mixture of chemicals. The pollutant profile of stormwater samples collected from an Australian creek was analyzed using high-resolution mass spectrometry and chemometric tools. The study identified compounds such as nonpolymeric surfactants, plastic additives, rubber and resin-related products, and natural products in the stormwater. The prioritization workflow used in this study proved to be an effective tool for assessing key stormwater-related compounds and determining their environmental effects.
Article
Chemistry, Analytical
Denice van Herwerden, Jake W. O'Brien, Sascha Lege, Bob W. J. Pirok, Kevin V. Thomas, Saer Samanipour
Summary: Clean high-resolution mass spectra are crucial for the successful structural elucidation of unknown features in non-target analysis workflows. An algorithm combining time domain and mass domain information is presented for spectral deconvolution, achieving high true positive rates and reduction rates in real samples. The combination of correlation analysis and the cumulative neutral loss model proved to be the most effective for fragment deconvolution.
ANALYTICAL CHEMISTRY
(2023)
Article
Engineering, Environmental
Kalliroi Sdougkou, Hongyu Xie, Stefano Papazian, Beinilde Bonnefille, Ingvar A. Bergdahl, Jonathan W. Martin
Summary: Chemical exposomics in human plasma was enhanced by an optimized phospholipid removal step that increased targeted method sensitivity while also revealing >13,000 new molecular features by LC-HRMS non-targeted acquisition. The method validated a chemical exposomics protocol with an optimized phospholipid-removal step prior to targeted and non-targeted liquid chromatography high-resolution mass spectrometry. The method allows for the detection of a wide range of substances in human plasma, including previously undetectable ones, and can support large-scale studies of the exposome.
ENVIRONMENTAL SCIENCE & TECHNOLOGY
(2023)
Article
Engineering, Environmental
Pradeep Dewapriya, Sandra Nilsson, Sara Ghorbani Gorji, Jake W. O'Brien, Jennifer Braunig, Maria Jose Gomez Ramos, Eric Donaldson, Saer Samanipour, Jonathan W. Martin, Jochen F. Mueller, Sarit L. Kaserzon, Kevin V. Thomas
Summary: Leaching of PFASs from Australian firefighting training grounds has resulted in extensive contamination. A study identified various PFAS classes in cattle's blood exposed to contaminated groundwater and discovered novel PFASs. Results suggest that targeting only major PFASs underestimates the toxicological risks associated with exposure.
ENVIRONMENTAL SCIENCE & TECHNOLOGY
(2023)
Article
Medicine, Legal
Jennifer L. Bonetti, Ruben F. Kranenburg, Esmee Schoonderwoerd, Saer Samanipour, Arian C. van Asten
Summary: Chemometric analysis of mass spectral data has become increasingly popular for differentiating positional isomers of novel psychoactive substances. However, generating a large and robust dataset for chemometric isomer identification is time consuming and impractical for forensic laboratories. To address this issue, three sets of isomers were analyzed using multiple GC-MS instruments at three laboratories, and the dataset was split into training and validation sets. An optimized model was developed, achieving 100% accuracy in isomer identification. These models eliminate the need for reference drug standards and specific instrument datasets.
FORENSIC SCIENCE INTERNATIONAL
(2023)
Article
Engineering, Environmental
Zhe Wang, Jochen F. Mueller, Jake W. O'Brien, Jack Thompson, Benjamin J. Tscharke, Rory Verhagen, Qiuda Zheng, Jeremy Prichard, Wayne Hall, Keith Humphreys, Kevin Thomas, Phong K. Thai
Summary: This study used wastewater-based epidemiology to estimate the consumption of licit and illicit drugs in an Australian prison. The findings showed that the average consumption of common illicit drugs in the prison was significantly lower than in the community population. The study also suggested potential illicit buprenorphine consumption in the prison, and noted changes in drug use under different security conditions.
Review
Environmental Sciences
Juliane Hollender, Emma L. Schymanski, Lutz Ahrens, Nikiforos Alygizakis, Frederic Been, Lubertus Bijlsma, Andrea M. Brunner, Alberto Celma, Aurelie Fildier, Qiuguo Fu, Pablo Gago-Ferrero, Ruben Gil-Solsona, Peter Haglund, Martin Hansen, Sarit Kaserzon, Anneli Kruve, Marja Lamoree, Christelle Margoum, Jeroen Meijer, Sylvain Merel, Cassandra Rauert, Pawel Rostkowski, Saer Samanipour, Bastian Schulze, Tobias Schulze, Randolph R. Singh, Jaroslav Slobodnik, Teresa Steininger-Mairinger, Nikolaos S. Thomaidis, Anne Togola, Katrin Vorkamp, Emmanuelle Vulliet, Linyan Zhu, Martin Krauss
Summary: The increasing production and use of chemicals have led to a growing interest in understanding their impact on ecosystems and human health through suspect and non-target screening (NTS). To promote effective implementation of NTS, more harmonisation is needed. The NORMAN Association has prepared a guidance document to provide guidance on conducting high-quality NTS studies and interpreting data while addressing the challenges and pitfalls of these techniques. The document covers various steps of NTS, from sampling and analysis to data evaluation and reporting, and also introduces analytical methods, processing techniques, and databases commonly used in NTS workflows.
ENVIRONMENTAL SCIENCES EUROPE
(2023)
