Motivation: In microarray studies gene discovery based on fold-change values is often misleading because error variability for each gene is heterogeneous under different biological conditions and intensity ranges. Several statistical testing methods for differential gene expression have been suggested, but some of these approaches are underpowered and result in high false positive rates because within-gene variance estimates are based on a small number of replicated arrays.
Results: We propose to use local-pooled-error (LPE) estimates and robust statistical tests for evaluating significance of each gene's differential expression. Our LPE estimation is based on pooling errors within genes and between replicate arrays for genes in which expression values are similar. We have applied our LPE method to compare gene expression in naïve and activated CD8+ T-cells. Our results show that the LPE method effectively identifies significant differential-expression patterns with a small number of replicated arrays.
Availability: The methodology is implemented with S-PLUS and R functions available at http://hesweb1.med.virginia.edu/bioinformatics
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http://dx.doi.org/10.1093/bioinformatics/btg264 | DOI Listing |
J Cardiothorac Surg
January 2025
Division of Thoracic Surgery, LMU University Hospital, LMU Munich and Asklepios Lung Clinic, Gauting, Germany.
Background: Lymph node upstaging represents a quality criterion for standardized lymphadenectomy in lung cancer surgery. The aim of the study was to compare whether the quality of standardized lymphadenectomy in lung cancer surgery is comparable in minimally invasive (video-assisted thoracoscopic surgery) and the open approach (thoracotomy). Furthermore, factors associated with lymph node upstaging were assessed, as was its impact on overall survival and progression-free survival.
View Article and Find Full Text PDFMed Phys
January 2025
Department of Radiology, Mayo Clinic, Rochester, Minnesota, USA.
Background: The spatial resolution of new, photon counting detector (PCD) CT scanners is limited by the size of the focal spot. Smaller, brighter focal spots would melt the tungsten focal track of a conventional X-ray source.
Purpose: To propose focal spot multiplexing (FSM), an architecture to improve the power of small focal spots and thereby enable higher resolution clinical PCD CT.
Sci Rep
January 2025
School of Life Sciences, College of Agriculture, Engineering and Science, University of KwaZulu-Natal (Westville Campus), Private Bag X 54001, Durban, 4000, South Africa.
Declining soil health and productivity are key challenges faced by sugarcane small-scale growers in South Africa. Incorporating Vicia sativa and Vicia villosa as cover crops can improve soil health by enhancing nutrient-cycling enzyme activities and nitrogen (N) contributions while promoting the presence of beneficial bacteria in the rhizosphere. A greenhouse experiment was conducted to evaluate the chemical and biological inputs of V.
View Article and Find Full Text PDFSci Rep
January 2025
State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, Beijing Key Laboratory of Carcinogenesis and Translational Research, Department of Pathology, Peking University Cancer Hospital and Institute, 52 Fucheng Road, Haidian District, Beijing, 100142, China.
Delta-like protein (DLL3) is a novel therapeutic target. DLL3 expression in gastroenteropancreatic neuroendocrine tumors (GEP-NECs) is poorly understood, complicating the distinction between well-differentiated neuroendocrine tumors G3 (NET G3) and poorly differentiated NEC. DLL3 immunohistochemistry (IHC) was performed on 248 primary GEP-NECs, correlating with clinicopathological parameters, NE markers, PD-L1, Ki67 index, and prognosis.
View Article and Find Full Text PDFJ Atheroscler Thromb
January 2025
Department of Neurology, National Cerebral and Cardiovascular Center.
Aim: Branch atheromatous disease (BAD), characterized by the occlusion of perforating branches near the orifice of a parent artery, often develops early neurological deterioration because the mechanisms underlying BAD remain unclear. Abnormal wall shear stress (WSS) is strongly associated with endothelial dysfunction and plaque growth or rupture. Therefore, we hypothesized that computational fluid dynamics (CFD) modeling could detect differences in WSS between BAD and small-vessel occlusion (SVO), both of which result from perforating artery occlusion/stenosis.
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