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TopoQual polishes circular consensus sequencing data and accurately predicts quality scores.
BMC Bioinformatics
January 2025
Auburn University, Auburn, AL, 36849, USA.
Background: Pacific Biosciences (PacBio) circular consensus sequencing (CCS), also known as high fidelity (HiFi) technology, has revolutionized modern genomics by producing long (10 + kb) and highly accurate reads. This is achieved by sequencing circularized DNA molecules multiple times and combining them into a consensus sequence. Currently, the accuracy and quality value estimation provided by HiFi technology are more than sufficient for applications such as genome assembly and germline variant calling.
View Article and Find Full Text PDFDeep Radiogenomics Sequencing for Breast Tumor Gene-Phenotype Decoding Using Dynamic Contrast Magnetic Resonance Imaging.
Mol Imaging Biol
January 2025
Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, CH-1211, Geneva, Switzerland.
Purpose: We aim to perform radiogenomic profiling of breast cancer tumors using dynamic contrast magnetic resonance imaging (MRI) for the estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor 2 (HER2) genes.
Methods: The dataset used in the current study consists of imaging data of 922 biopsy-confirmed invasive breast cancer patients with ER, PR, and HER2 gene mutation status. Breast MR images, including a T1-weighted pre-contrast sequence and three post-contrast sequences, were enrolled for analysis.
Single and multitarget stereotactic radiosurgery (SRS) with single isocenter in the treatment of multiple brain metastases (BM): institutional experience.
Clin Transl Oncol
January 2025
Department of Radiation Oncology, HM Hospitales, Madrid, Spain.
Introduction: SRS for the treatment of limited brain metastases (BM) is widely accepted, but there are still limitations in the management of numerous BM. Frameless single-isocenter multitarget SRS is a novel technique that allows for rapid treatment delivery to multiple BM. We report our preliminary clinical, dosimetric, and patient´s shifts outcomes with this technique.
View Article and Find Full Text PDFThe integral role of in brain function: from neurogenesis to synaptic plasticity and social behavior.
Acta Neurobiol Exp (Wars)
January 2025
Laboratory of Animal Models, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland.
The phosphatase and tensin homolog deleted on chromosome 10 (PTEN) gene is a critical tumor suppressor that plays an essential role in the development and functionality of the central nervous system. Located on chromosome 10 in humans and chromosome 19 in mice, PTEN encodes a protein that regulates cellular processes such as division, proliferation, growth, and survival by antagonizing the PI3K‑Akt‑mTOR signaling pathway. In neurons, PTEN dephosphorylates phosphatidylinositol‑3,4,5‑trisphosphate (PIP3) to PIP2, thereby modulating key signaling cascades involved in neurogenesis, neuronal migration, and synaptic plasticity.
View Article and Find Full Text PDFCorrecting mitochondrial loss mitigates NOTCH1-related aortopathy in mice.
Nat Cardiovasc Res
January 2025
Shanghai Fifth People's Hospital and Institutes of Biomedical Sciences Zhongshan Hospital, Shanghai Medical College, Fudan University, Shanghai, China.
Loss-of-function mutations in NOTCH1 were previously linked to thoracic aortopathy, a condition for which non-surgical treatment options are limited. Based on clinical proteome analysis, we hypothesized that mitochondrial fusion and biogenesis in aortic smooth muscle cells (SMCs) are crucial for regulating the progression of NOTCH1-related aortopathy. Here we demonstrate that SMC-specific Notch1 knockout mice develop aortic pathology, including stiffening, dilation and focal dissection.
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