Article
Radiology, Nuclear Medicine & Medical Imaging
Sae Nakamura, Madoka Sakai, Natsuki Ishizaka, Kazuki Mayumi, Tomotaka Kinoshita, Shinya Akamatsu, Takayuki Nishikata, Shunpei Tanabe, Hisashi Nakano, Satoshi Tanabe, Takeshi Takizawa, Takumi Yamada, Hironori Sakai, Motoki Kaidu, Ryuta Sasamoto, Hiroyuki Ishikawa, Satoru Utsunomiya
Summary: This study successfully created and evaluated deep learning-based models to detect and classify errors in multi-leaf collimator modeling parameters in volumetric modulated radiation therapy (VMAT). The accuracy of the models depends on the magnitude of the errors, treatment site, and the degree of mimicked measurement doses.
JOURNAL OF APPLIED CLINICAL MEDICAL PHYSICS
(2023)
Article
Oncology
Wenliang Yu, Chengjian Xiao, Jiayi Xu, Juebin Jin, Xiance Jin, Lanxiao Shen
Summary: This study used deep learning models to predict the voxel-based dose distribution for postoperative cervical cancer patients undergoing volumetric modulated arc therapy. A total of 254 patients were included in the study, and two deep learning networks were adapted for training and testing. The results showed that the deep learning models had good prediction accuracy. The automatic dose prediction time was 5 to 10 minutes, which was about one-eighth to one-tenth of the manual optimization time.
TECHNOLOGY IN CANCER RESEARCH & TREATMENT
(2023)
Article
Radiology, Nuclear Medicine & Medical Imaging
Maude Gondre, Fanny Marsolat, Jean Bourhis, Francois Bochud, Raphael Moeckli
Summary: The study commissioned and evaluated the MC dose calculation algorithm for CyberKnife with MLC, showing good agreement in measurements but underestimating the delivered dose by an average of 1.5%. The MC model is recommended for use in heterogeneous regions and shallow-seated tumors.
JOURNAL OF APPLIED CLINICAL MEDICAL PHYSICS
(2022)
Article
Oncology
Davide Franceschini, Luca Cozzi, Antonella Fogliata, Beatrice Marini, Luciana Di Cristina, Luca Dominici, Ruggero Spoto, Ciro Franzese, Pierina Navarria, Tiziana Comito, Giacomo Reggiori, Stefano Tomatis, Marta Scorsetti
Summary: The study investigated the performance of a narrow-scope knowledge-based RapidPlan model for intensity-modulated proton therapy and volumetric modulated arc therapy plans applied to pleural mesothelioma patients. The results showed that IMPT plans outperformed VMAT plans for all organs at risk (OARs). RP-based planning enables the automation of part of the optimization process and harmonization of dose-volume results. Using an RP-based approach can simplify the optimization workflow without impacting the plan quality for these complex treatment indications.
RADIATION ONCOLOGY
(2022)
Article
Oncology
Fady Samir, Talaat M. Meaz, Fathi AEl Hussiny, Ahmed A. Ahmed, Amr A. Mahmoud, Tamer Refaat, Ahmed Gawish, Mohamed Abouegylah
Summary: The study compared four techniques in prostate treatment to find the preferred technique. Plans were created for 30 prostate cancer patients using different techniques, and the quality of the plans was assessed by comparing target coverage, organs at risk, monitor units, homogeneity, and conformity among the techniques.
JOURNAL OF CANCER RESEARCH AND CLINICAL ONCOLOGY
(2023)
Article
Oncology
Shengpeng Jiang, Yi Xue, Ming Li, Chengwen Yang, Daguang Zhang, Qingxin Wang, Jing Wang, Jie Chen, Jinqiang You, Zhiyong Yuan, Xiaochun Wang, Xiaodong Zhang, Wei Wang
Summary: This study investigated the use of artificial intelligence-based automated treatment planning to generate high-quality postmastectomy VMAT plans. The automated plans showed significant improvements in target volume uniformity and conformity, as well as dose to the heart and lungs compared to manual clinical plans.
FRONTIERS IN ONCOLOGY
(2022)
Article
Medicine, General & Internal
Kazuhiro Ohtakara, Kojiro Suzuki
Summary: This study aimed to determine the optimal dose distribution for VMARS of brain metastases, especially regarding dose inhomogeneity of the gross tumor volume (GTV). The results showed that a very inhomogeneous GTV dose is the most suitable option for SRS of BMs in terms of superior dose conformity, minimizing the dose of surrounding normal tissue, and appropriate dose spillage margin. However, excessive dose inhomogeneity may lead to surrounding brain injury.
CUREUS JOURNAL OF MEDICAL SCIENCE
(2023)
Article
Radiology, Nuclear Medicine & Medical Imaging
Ann Van Esch, Antti Kulmala, Ronan Rochford, Juha Kauppinen, Ari Harju
Summary: By enhancing the modeling of the multileaf collimator (MLC) in the dose calculation algorithms, the accuracy of dose calculation can be significantly improved. This study demonstrates that the enhanced MLC model effectively resolves discrepancies and provides excellent agreements with measurements.
Article
Oncology
Chengqiang Li, Cheng Tao, Tong Bai, Zhenjiang Li, Ying Tong, Jian Zhu, Yong Yin, Jie Lu
Summary: This study compared the beam complexity and monitor unit efficiency of two different VMAT delivery technologies for left-sided breast cancer and nasopharyngeal carcinoma patients, finding that each system had its own advantages and disadvantages. Therefore, beam complexity should be taken into consideration in developing further methodologies for optimizing VMAT autoplanning.
Article
Oncology
Mingli Wang, Huikuan Gu, Jiang Hu, Jian Liang, Sisi Xu, Zhenyu Qi
Summary: This study aimed to investigate if a highly refined DVH prediction model can enhance the accuracy and reliability of knowledge-based VMAT planning for cervical cancer. The results demonstrated that the refined model significantly improved prediction ability and subsequently the consistency and quality of VMAT plans.
RADIATION ONCOLOGY
(2021)
Article
Radiology, Nuclear Medicine & Medical Imaging
Phillip D. H. Wall, Jonas D. Fontenot
Summary: This study successfully explored the feasibility of an optimization framework for maximizing predicted QA outcomes while maintaining dosimetric quality of plans. By utilizing SVM model and QAO framework, predicted GPRs were improved with minimal impact on dose, indicating potential for future optimization incorporating QA endpoints.
PHYSICA MEDICA-EUROPEAN JOURNAL OF MEDICAL PHYSICS
(2021)
Article
Oncology
Alparslan Serarslan, Yalcin Dastan, Telat Aksu, Rana Elif Yildiz, Bilge Gursel, Deniz Meydan, Nilguen Ozbek Okumus
Summary: A new technique called 90 degrees angled collimated dynamic IMRT (A-IMRT) was developed to better protect organs at risk (OARs) by turning the collimator angle to 90 degrees. Compared to conventional dynamic IMRT (C-IMRT), A-IMRT significantly reduced the dose constraints exceeded for the bladder, rectum, and bilateral femoral heads.
Article
Oncology
Emily Keit, Casey Liveringhouse, Nicholas Figura, Joseph Weygand, Maria L. Sandoval, Genevieve Garcia, Julia Peters, Michael Nieder, Rawan Faramand, Farhad Khimani, Sungjune Kim, Timothy J. Robinson, Peter A. S. Johnstone, Jose Penagaricano, Kujtim Latifi
Summary: This study describes a new method of delivering high-dose total body irradiation (TBI) using VMAT technology and compares dosimetric outcomes with helical tomotherapy (HT) treatment. The study found that VMAT technique can achieve lower lung doses compared to HT treatment and demonstrate the possibility of selective organ-at-risk (OAR) sparing to reduce TBI-related morbidity and mortality.
TECHNOLOGY IN CANCER RESEARCH & TREATMENT
(2023)
Article
Engineering, Biomedical
Pinar Dursun, Masoud Zarepisheh, Gourav Jhanwar, Joseph O. Deasy
Summary: The proposed method utilizes a sequential convex programming algorithm to solve the non-convex VMAT problem efficiently, with both local and global search strategies. The algorithm demonstrates good performance in clinical cases.
PHYSICS IN MEDICINE AND BIOLOGY
(2021)
Article
Oncology
Mikko Mankinen, Tuomas Viren, Jan Seppala, Heikki Hakkarainen, Tuomas Koivumaki
Summary: In this study, the effects of respiratory motion on planned dose in free-breathing right-sided whole-breast irradiation were studied through simulating hypofractionated VMAT treatment courses. The results showed that respiratory motion perturbed PTV coverage decreased, but changes to doses of organs at risk were not clinically significant, and 5mm margins were sufficient to account for respiratory motion.
RADIATION ONCOLOGY
(2022)
Article
Cell Biology
Caleb A. Dawson, Bhupinder Pal, Francois Vaillant, Luke C. Gandolfo, Zhaoyuan Liu, Camille Bleriot, Florent Ginhoux, Gordon K. Smyth, Geoffrey J. Lindeman, Scott N. Mueller, Anne C. Rios, Jane E. Visvader
NATURE CELL BIOLOGY
(2020)
Article
Rheumatology
Andrew D. Foers, Alexandra L. Garnham, Gordon K. Smyth, Susanna M. Proudman, Lesley Cheng, Andrew F. Hill, Ken C. Pang, Ian P. Wicks
JOURNAL OF RHEUMATOLOGY
(2020)
Article
Multidisciplinary Sciences
Wing Fuk Chan, Hannah D. Coughlan, Jie H. S. Zhou, Christine R. Keenan, Naiara G. Bediaga, Philip D. Hodgkin, Gordon K. Smyth, Timothy M. Johanson, Rhys S. Allan
Summary: The study elucidated the chromosome conformational changes in B lymphocytes as they differentiate into plasma cells, indicating that these changes occur prior to cell division and may guide the gene expression necessary for differentiation.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Andrew D. Foers, Alexandra L. Garnham, Simon Chatfield, Gordon K. Smyth, Lesley Cheng, Andrew F. Hill, Ian P. Wicks, Ken C. Pang
Summary: In rheumatoid arthritis, extracellular vesicles are associated with joint inflammation and destruction. Through sequencing EV miRNAs in synovial fluid from RA patients, differences between joints with high- and low-grade inflammation were identified, suggesting a role in regulating inflammation-related genes. EV miRNAs have the potential to modulate inflammation and contribute to RA pathophysiology.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Oncology
Emily Durie, Emma Nicholson, Chloe Anthias, Emma M. Dunne, Mike Potter, Mark Ethell, Christina Messiou, Joy Brennan, Sally Eagle, James Talbot, Gregory Smyth, Westley Ingram, Frank Saran, Henry C. Mandeville
Summary: The retrospective study evaluated 74 adult patients treated with forward-planned intensity modulated radiotherapy technique for total body irradiation (TBI), showing that this treatment method has lower rates of idiopathic interstitial pneumonitis and chronic kidney disease compared to the literature.
RADIOTHERAPY AND ONCOLOGY
(2021)
Article
Developmental Biology
Zoe L. Grant, Peter F. Hickey, Waruni Abeysekera, Lachlan Whitehead, Sabrina M. Lewis, Robert C. A. Symons, Tracey M. Baldwin, Daniela Amann-Zalcenstein, Alexandra L. Garnham, Gordon K. Smyth, Tim Thomas, Anne K. Voss, Leigh Coultas
Summary: The histone acetyltransferase HBO1 plays a crucial role in blood vessel development, with its impairment leading to defects in developmental sprouting angiogenesis and pathological EC overgrowth in the retinal endothelium. Loss of HBO1 results in an increased abundance of tip cells, hindering efficient tip cell migration and causing EC overcrowding in the retinal sprouting front.
Article
Oncology
G. Smyth, S. Mowat, K. Chia, K. Robinson, K. Warren-Oseni, L. C. Welsh, I Blasiak-Wal, H. C. Mandeville
Summary: This study aimed to evaluate the safety and accuracy of using CSI-VMAT in a commercially available treatment planning system. The initial clinical experience showed that the technique is feasible for patients undergoing craniospinal irradiation, with the limitation being the available beam overlap length in the neck.
Article
Multidisciplinary Sciences
Dimitra Zotos, Isaak Quast, Connie S. N. Li-Wai-Suen, Craig I. McKenzie, Marcus J. Robinson, Andrey Kan, Gordon K. Smyth, Philip D. Hodgkin, David M. Tarlinton
Summary: IL-21 plays a crucial role in promoting cell cycle progression within the germinal centre (GC) light zone, facilitating release from the G1 cell cycle stage. This cytokine is essential for establishing normal zone representation and preventing cell accumulation in the G1 cell cycle stage in the GC LZ, highlighting its importance in antibody affinity maturation.
NATURE COMMUNICATIONS
(2021)
Article
Oncology
Joerg Lehmann, Mohammad Hussein, Miriam A. Barry, Shankar Siva, Alisha Moore, Michael Chu, Patricia Diez, David J. Eaton, Jeffrey Harwood, Peta Lonski, Elizabeth Claridge Mackonis, Carole Meehan, Rushil Patel, Xenia Ray, Maddison Shaw, Justin Shepherd, Gregory Smyth, Therese S. Standen, Brindha Subramanian, Peter B. Greer, Catharine H. Clark
Summary: This study aims to improve the quality of radiation therapy and patient outcomes by assessing institutions' ability to detect errors through routine Patient Specific Quality Assurance (PSQA). A new audit concept is needed as existing dosimetry audits may not catch all errors. The study evaluates institutions' ability to detect errors by embedding deliberately introduced edits into radiation treatment plans.
RADIOTHERAPY AND ONCOLOGY
(2022)
Article
Multidisciplinary Sciences
Yunshun Chen, Bhupinder Pal, Geoffrey J. Lindeman, Jane E. Visvader, Gordon K. Smyth
Summary: This article extends our understanding of the development mechanism of breast cancer by providing quality control thresholds, processed data objects, complete cell annotation, and R code for analysis of a large-scale single-cell RNA expression atlas.
Article
Cell Biology
Johannes Wichmann, Catherine Pitt, Samantha Eccles, Alexandra L. Garnham, Connie S. N. Li-Wai-Suen, Rose May, Elizabeth Allan, Stephen Wilcox, Marco J. Herold, Gordon K. Smyth, Brendon J. Monahan, Tim Thomas, Anne K. Voss
Summary: Histone acetylation is crucial for chromatin conformation and gene transcription, and TIP60 is a key enzyme involved in this process. Loss of TIP60 leads to cell growth arrest and abnormal chromosome alignment during mitosis. However, cell survival is not affected. TIP60 is essential for the acetylation of H2AZ at lysine 7 and plays a role in the activation of transcription for thousands of genes, including those involved in metabolism.
CELL DEATH & DISEASE
(2022)
Article
Multidisciplinary Sciences
Wing Fuk Chan, Hannah D. Coughlan, Yunshun Chen, Christine R. Keenan, Gordon K. Smyth, Andrew C. Perkins, Timothy M. Johanson, Rhys S. Allan
Summary: By coupling the catalytic domain of DNA demethylating enzyme TET1 with transcriptional activators (TETact), the authors have developed an improved activation system that can induce transcription of stably silenced genes. The TETact system is applicable in various cell types and has the ability to reactivate embryonic haemoglobin genes in non-erythroid cells. It is expected that TETact will have significant implications in functional studies, genetic screens, and potential therapeutics.
NATURE COMMUNICATIONS
(2022)
Article
Immunology
Hesham D. D. Abdulla, Raed Alserihi, Christoffer Flensburg, Waruni Abeysekera, Meng-Xiao Luo, Daniel H. D. Gray, Xiaodong Liu, Gordon K. K. Smyth, Warren S. S. Alexander, Ian J. J. Majewski, Matthew P. P. McCormack
Summary: Abdulla et al. demonstrate that the LMO2 transcription factor promotes the development of T-lymphoblastic leukemia by inhibiting thymocyte competition in a transgenic mouse model.
JOURNAL OF EXPERIMENTAL MEDICINE
(2023)
Article
Biochemical Research Methods
Mengbo Li, Gordon K. Smyth
Summary: Mass spectrometry proteomics in biomedical research suffers from the problem of missing values in peptides. Many analysis strategies have been proposed to distinguish different types of missing values and estimate detection probabilities. A logit-linear function is used to accurately model the detection probability, showing that missing values are related to peptide intensity. A probability model is developed to infer the distribution of unobserved intensities from observed values.
Article
Biochemistry & Molecular Biology
Pedro L. Baldoni, Yunshun Chen, Soroor Hediyeh-zadeh, Yang Liao, Xueyi Dong, Matthew E. Ritchie, Wei Shi, Gordon K. Smyth
Summary: Differential expression analysis of RNA-seq is commonly used in bioinformatics. However, transcript-level quantifications are more uncertain due to the ambiguity of sequence reads. To address this issue, a new method is proposed to estimate the overdispersion caused by read-to-transcript ambiguity and generate scaled transcript counts, which improves the efficiency and accuracy of differential analysis.
NUCLEIC ACIDS RESEARCH
(2023)