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| http://dx.doi.org/10.1016/j.jtocrr.2020.100004 | DOI Listing |
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A compendium of Amplification-Related Gain Of Sensitivity genes in human cancer.
Nat Commun
January 2025
European Research Institute for the Biology of Ageing, University Medical Center Groningen, Groningen, Netherlands.
While the effect of amplification-induced oncogene expression in cancer is known, the impact of copy-number gains on "bystander" genes is less understood. We create a comprehensive map of dosage compensation in cancer by integrating expression and copy number profiles from over 8000 tumors in The Cancer Genome Atlas and cell lines from the Cancer Cell Line Encyclopedia. Additionally, we analyze 17 cancer open reading frame screens to identify genes toxic to cancer cells when overexpressed.
View Article and Find Full Text PDFIntegrating representation learning, permutation, and optimization to detect lineage-related gene expression patterns.
Nat Commun
January 2025
Laboratory for Information and Decision Systems, Massachusetts Institute of Technology, Cambridge, MA, USA.
Recent barcoding technologies allow reconstructing lineage trees while capturing paired single-cell RNA-sequencing (scRNA-seq) data. Such datasets provide opportunities to compare gene expression memory maintenance through lineage branching and pinpoint critical genes in these processes. Here we develop Permutation, Optimization, and Representation learning based single Cell gene Expression and Lineage ANalysis (PORCELAN) to identify lineage-informative genes or subtrees where lineage and expression are tightly coupled.
View Article and Find Full Text PDFPrediction of Radiation Therapy Induced Cardiovascular Toxicity from Pretreatment CT Images in Patients with Thoracic Malignancy via an Optimal Biomarker Approach.
Acad Radiol
January 2025
Medical Image Processing Group, 602 Goddard building, 3710 Hamilton Walk, Department of Radiology, University of Pennsylvania, Philadelphia, PA 19104 (M.L., M.A., J.K.U., Y.T., C.W., N.P., S.M., D.A.T.). Electronic address:
Rationale And Objectives: Cardiovascular toxicity is a well-known complication of thoracic radiation therapy (RT), leading to increased morbidity and mortality, but existing techniques to predict cardiovascular toxicity have limitations. Predictive biomarkers of cardiovascular toxicity may help to maximize patient outcomes.
Methods: The machine learning optimal biomarker (OBM) method was employed to predict development of cardiotoxicity (based on serial echocardiographic measurements of left ventricular ejection fraction and longitudinal strain) from computed tomography (CT) images in patients with thoracic malignancy undergoing RT.
Polymicrobial empyema in a patient with lung adenocarcinomacontaining .
BMJ Case Rep
January 2025
Thoracic Medicine and Surgery, Temple University Hospital, Philadelphia, Pennsylvania, USA.
A man in his 60s with advanced COPD and lung adenocarcinoma presented with sepsis and acute hypoxaemic respiratory failure. Imaging revealed bilateral pleural effusions, and he was found to have a polymicrobial empyema which included Despite appropriate treatment, he continued to deteriorate and ultimately died of sepsis. species, typically benign constituents of the oral microbiota, rarely can instigate pleuropulmonary infections, especially in immunocompromised individuals.
View Article and Find Full Text PDFInteractive segmentation for accurately isolating metastatic lesions from low-resolution, large-size bone scintigrams.
Phys Med Biol
January 2025
Charles Sturt University, Albury-Wodonga, NSW, Albury, New South Wales, 2640, AUSTRALIA.
Bone is a common site for the metastasis of malignant tumors, and Single Photon Emission Computed Tomography (SPECT) is widely used to detect these metastases. Accurate delineation of metastatic bone lesions in SPECT images is essential for developing treatment plans. However, current clinical practices rely on manual delineation by physicians, which is prone to variability and subjective interpretation.
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