A filter-based feature selection approach for identifying potential biomarkers for lung cancer

Background: Lung cancer is the leading cause of death from cancer in the world and its treatment is dependant on the type and stage of cancer detected in the patient. Molecular biomarkers that can characterize the cancer phenotype are thus a key tool in planning a therapeutic response. A common protocol for identifying such biomarkers is to employ genomic microarray analysis to find genes that show differential expression according to disease state or type. Data-mining techniques such as feature selection are often used to isolate, from among a large manifold of genes with differential expression, those specific genes whose differential expression patterns are of optimal value in phenotypic differentiation. One such technique, Biomarker Identifier (BMI), has been developed to identify features with the ability to distinguish between two data groups of interest, which is thus highly applicable for such studies. Results: Microarray data with validated genes was used to evaluate the utility of BMI in identifying markers for lung cancer. This data set contains a set of 129 gene expression profiles from large-airway epithelial cells (60 samples from smokers with lung cancer and 69 from smokers without lung cancer) and 7 genes from this data have been confirmed to be differentially expressed by quantitative PCR. Using this data set, BMI was compared with various well-known feature selection methods and was found to be more successful than other methods in finding useful genes to classify cancerous samples. Also it is evident that genes selected by BMI (given the same number of genes and classification algorithms) showed better discriminative power than those from the original study. After pathway analysis on the selected genes by BMI, we have been able to correlate the selected genes with well-known cancer-related pathways. Conclusions: Our results show that BMI can be used to analyze microarray data and to find useful genes for classifying samples. Pathway analysis suggests that BMI is successful in identifying biomarker-quality cancer-related genes from the data

Effect of exposure energy dose on lateral resolution and flexural strength of three-dimensionally printed dental zirconia.

PURPOSE This study aims to evaluate the effects of exposure energy on the lateral resolution and mechanical strength of dental zirconia manufactured using digital light processing (DLP). MATERIALS AND METHODS A zirconia suspension and a custom top-down DLP printer were used for in-office manufacturing. The viscosity of the suspension and uniformity of the exposed light intensity were controlled. Based on the exposure energy dose delivered to each layer, the specimens were classified into three groups: low-energy (LE), medium-energy (ME), and high-energy (HE). For each energy group, a simplified molar cube was used to measure the widths of the outline (Xo and Yo) and isthmus (Xi and Yi), and a bar-shaped specimen of the sintered body was tested. A Kruskal-Wallis test for the lateral resolution and one-way analysis of variance for the mechanical strength were performed (α = .05). RESULTS The zirconia green bodies of the ME group showed better lateral resolution than those of the LE and HE groups (both P < .001). Regarding the flexural strength of the sintered bodies, the ME group had the highest mean value, whereas the LE group had the lowest mean value (both P < .05). The ME group exhibited fewer agglomerates than the LE group, with no distinctive interlayer pores or surface defects. CONCLUSION Based on these findings, the lateral resolution of the green body and flexural strength of the sintered body of dental zirconia could be affected by the exposure energy dose during DLP. The exposure energy should be optimized when fabricating DLP-based dental zirconia

Optimization of coupling between photonic crystal resonator and curved microfiber

The evanescent coupling from a photonic crystal resonator to a micron-thick optical fiber is investigated in detail by using a 3D-FDTD method. Properly designed photonic crystal cavity and taper structures are proposed, and optimal operating conditions are found to enhance the coupling strength while suppressing other cavity losses including the coupling to the slab propagating mode and to the higher-order fiber mode. In simulation, the coupling into the fundamental fiber mode is discriminated from other cavity losses by spatial and parity filtering of the FDTD results. The coupling efficiency of more than 80% into the fundamental fiber mode together with a total Q factor of 5,200 is achieved for the fiber diameter of 1.0 um and the air gap of 200 nm between the fiber and the cavity.Comment: 6 pages, 6 figure

SSASS: Semi-Supervised Approach for Stenosis Segmentation

Coronary artery stenosis is a critical health risk, and its precise identification in Coronary Angiography (CAG) can significantly aid medical practitioners in accurately evaluating the severity of a patient's condition. The complexity of coronary artery structures combined with the inherent noise in X-ray images poses a considerable challenge to this task. To tackle these obstacles, we introduce a semi-supervised approach for cardiovascular stenosis segmentation. Our strategy begins with data augmentation, specifically tailored to replicate the structural characteristics of coronary arteries. We then apply a pseudo-label-based semi-supervised learning technique that leverages the data generated through our augmentation process. Impressively, our approach demonstrated an exceptional performance in the Automatic Region-based Coronary Artery Disease diagnostics using x-ray angiography imagEs (ARCADE) Stenosis Detection Algorithm challenge by utilizing a single model instead of relying on an ensemble of multiple models. This success emphasizes our method's capability and efficiency in providing an automated solution for accurately assessing stenosis severity from medical imaging data.Comment: MICCAI 2023 Conference ARCADE Challeng

MPSeg : Multi-Phase strategy for coronary artery Segmentation

Accurate segmentation of coronary arteries is a pivotal process in assessing cardiovascular diseases. However, the intricate structure of the cardiovascular system presents significant challenges for automatic segmentation, especially when utilizing methodologies like the SYNTAX Score, which relies extensively on detailed structural information for precise risk stratification. To address these difficulties and cater to this need, we present MPSeg, an innovative multi-phase strategy designed for coronary artery segmentation. Our approach specifically accommodates these structural complexities and adheres to the principles of the SYNTAX Score. Initially, our method segregates vessels into two categories based on their unique morphological characteristics: Left Coronary Artery (LCA) and Right Coronary Artery (RCA). Specialized ensemble models are then deployed for each category to execute the challenging segmentation task. Due to LCA's higher complexity over RCA, a refinement model is utilized to scrutinize and correct initial class predictions on segmented areas. Notably, our approach demonstrated exceptional effectiveness when evaluated in the Automatic Region-based Coronary Artery Disease diagnostics using x-ray angiography imagEs (ARCADE) Segmentation Detection Algorithm challenge at MICCAI 2023.Comment: MICCAI 2023 Conference ARCADE Challeng

Acinetobacter baumannii invades epithelial cells and outer membrane protein A mediates interactions with epithelial cells

<p>Abstract</p> <p>Background</p> <p><it>Acinetobacter baumannii </it>is a nosocomial pathogen of increasing importance, but the pathogenic mechanism of this microorganism has not been fully explored. This study investigated the potential of <it>A. baumannii </it>to invade epithelial cells and determined the role of <it>A. baumannii </it>outer membrane protein A (AbOmpA) in interactions with epithelial cells.</p> <p>Results</p> <p><it>A. baumannii </it>invaded epithelial cells by a zipper-like mechanism, which is associated with microfilament- and microtubule-dependent uptake mechanisms. Internalized bacteria were located in the membrane-bound vacuoles. Pretreatment of recombinant AbOmpA significantly inhibited the adherence to and invasion of <it>A. baumannii </it>in epithelial cells. Cell invasion of isogenic AbOmpA^-mutant significantly decreased as compared with wild-type bacteria. In a murine pneumonia model, wild-type bacteria exhibited a severe lung pathology and induced a high bacterial burden in blood, whereas AbOmpA^-mutant was rarely detected in blood.</p> <p>Conclusion</p> <p><it>A. baumannii </it>adheres to and invades epithelial cells. AbOmpA plays a major role in the interactions with epithelial cells. These findings contribute to the understanding of <it>A. baumannii </it>pathogenesis in the early stage of bacterial infection.</p

Increased Immunoendocrine Cells in Intestinal Mucosa of Postinfectious Irritable Bowel Syndrome Patients 3 Years after Acute Shigella Infection - An Observation in a Small Case Control Study

PURPOSE: Postinfectiously irritable bowel syndrome (PI-IBS) develops in 3-30% of individuals with bacterial gastroenteritis. Recent studies demonstrated increases in inflammatory components in gut mucosa of PI-IBS patients even after complete resolution of infection. We aimed to investigate histological changes in colon and rectum of PI-IBS subjects after long term period of infection. MATERIALS AND METHODS: We recruited PI-IBS subjects who had been diagnosed IBS after complete resolution of enteritis caused by shigellosis outbreak 3 years earlier. We compared unmatched four groups, PI-IBS (n = 4), non PI-IBS (n = 7), D-IBS (n = 7, diarrhea predominant type) and healthy controls (n = 10). All of them underwent colonoscopic biopsy at three areas, including descending colon (DC), sigmoid colon (SC) and rectum, which were assessed for 5-hydroxytryptamine (5-HT)/peptide YY (PYY)-containing enterochromaffin (EC) cell, intraepithelial (IEL) and lamina propria T lymphocyte (CD3), CD8 lymphocytes, mast cells and CD68/calprotectin+ macrophages. RESULTS: All subjects had no structural or gross abnormalities at colonoscopy. In PI-IBS, 5-HT containing EC cells, PYY containing EC cells, IELs, CD3 lymphocytes, CD8 lymphocytes, mast cells, and CD68 + macrophages were increased compared to control (p < 0.05). In D-IBS, PYY containing EC cells, IELs, and CD3 lymphocytes were increased compared to control (p < 0.05). In PI-IBS, 5-HT containing EC cells tended to increase and PYY containing EC cells, CD8 lymphocytes, mast cells, and CD68+ macrophages were increased compared to non PI-IBS (p < 0.05). Calprotectin + marcrophages were decreased in PI-IBS, non PI-IBS and IBS compared to control. CONCLUSION: The immunoendocrine cells were sporadically increased in PI-IBS, non PI-IBS and D-IBS compared with control. Our findings in a very small number of patients suggest that mucosal inflammation may play a role in long-term PI-IBS, and that other sub-groups of IBS and larger scale studies are needed to confirm this observation.ope

Vav1 inhibits RANKL-induced osteoclast differentiation and bone resorption

Vav1 is a Rho/Rac guanine nucleotide exchange factor primarily expressed in hematopoietic cells. In this study, we investigated the potential role of Vav1 in osteoclast (OC) differentiation by comparing the ability of bone marrow mononuclear cells (BMMCs) obtained from Vav1-deficient (Vav1−/−) and wild-type (WT) mice to differentiate into mature OCs upon stimulation with macrophage colony stimulating factor and receptor activator of nuclear kappa B ligand in vitro. Our results suggested that Vav1 deficiency promoted the differentiation of BMMCs into OCs, as indicated by the increased expression of tartrate-resistant acid phosphatase, cathepsin K, and calcitonin receptor. Therefore, Vav1 may play a negative role in OC differentiation. This hypothesis was supported by the observation of more OCs in the femurs of Vav1−/− mice than in WT mice. Furthermore, the bone status of Vav1−/− mice was analyzed in situ and the femurs of Vav1−/− mice appeared abnormal, with poor bone density and fewer number of trabeculae. In addition, Vav1-deficient OCs showed stronger adhesion to vitronectin, an αvβ3 integrin ligand important in bone resorption. Thus, Vav1 may inhibit OC differentiation and protect against bone resorption