A visual analysis approach and the developed supporting technology provide a comprehensive solution for analyzing large and complex integrated genomic and biomedical data. This paper presents a methodology that is implemented as an interactive visual analysis technology for extracting knowledge from complex genetic and clinical data and then visualizing it in a meaningful and interpretable way. By synergizing the domain knowledge into development and analysis processes, we have developed a comprehensive tool that supports a seamless patient-to-patient analysis, from an overview of the patient population in the similarity space to the detailed views of genes. The system consists of multiple components enabling the complete analysis process, including data mining, interactive visualization, analytical views, and gene comparison. We demonstrate our approach with medical scientists on a case study of childhood cancer patients on how they use the tool to confirm existing hypotheses and to discover new scientific insights.
Data Display ; Data Mining ; Humans ; Precursor Cell Lymphoblastic Leukemia-Lymphoma

The epithelial-mesenchymal transition (EMT) is one mechanism by which cells with mesenchymal features can be generated and is a fundamental event in morphogenesis. Recently, invasion and metastasis of cancer cells from the primary tumor are now thought to be initiated by the developmental process termed the EMT, whereby epithelial cells lose cell polarity and cell-cell interactions, and gain mesenchymal phenotypes with increased migratory and invasive properties. The EMT is believed to be an important step in metastasis and is implicated in cancer progression, although the influence of the EMT in clinical specimens has been debated. This review presents the recent results of two cell surface proteins, the functions and underlying mechanisms of which have recently begun to be demonstrated, as novel regulators of the molecular networks that induce the EMT and cancer progression.
Cell Polarity ; Epithelial Cells ; Epithelial-Mesenchymal Transition* ; Membrane Proteins* ; Membranes* ; Morphogenesis ; Neoplasm Metastasis ; Phenotype

After the initial enthusiasm of the human genome project, it became clear that without additional data pertaining to the epigenome, i.e., how the genome is marked at specific developmental periods, in different tissues, as well as across individuals and species-the promise of the genome sequencing project in understanding biology cannot be fulfilled. This realization prompted several large-scale efforts to map the epigenome, most notably the Encyclopedia of DNA Elements (ENCODE) project. While there is essentially a single genome in an individual, there are hundreds of epigenomes, corresponding to various types of epigenomic marks at different developmental times and in multiple tissue types. Unprecedented advances in next-generation sequencing (NGS) technologies, by virtue of low cost and high speeds that continue to improve at a rate beyond what is anticipated by Moore's law for computer hardware technologies, have revolutionized molecular biology and genetics research, and have in turn prompted innovative ways to reduce the problem of measuring cellular events involving DNA or RNA into a sequencing problem. In this article, we provide a brief overview of the epigenome, the various types of epigenomic data afforded by NGS, and some of the novel discoveries yielded by the epigenomics projects. We also provide ample references for the reader to get in-depth information on these topics.
Biology ; Computers ; DNA ; Epigenomics* ; Genetics ; Genome ; Human Genome Project ; Jurisprudence ; Methylation ; Molecular Biology ; RNA ; Virtues

No abstract available.

No abstract available.

Eosinophilic gastroenteritis (EGE) is a rare disease characterized by focal or diffuse eosinophilic infiltration of the gastrointestinal tract, especially the stomach and duodenum. EGE has vague, nonspecific symptoms, including nausea, vomiting, abdominal pain, diarrhea, weight loss, ascites, and malabsorption. Here, we report a patient with EGE presenting with concurrent acute pancreatitis and ascites. A 68-year-old woman was admitted with abdominal pain, nausea, vomiting, and watery diarrhea. Laboratory findings revealed elevated serum titers of amylase, lipase, and peripheral blood eosinophil count. An abdominopelvic computed tomography scan showed a normal pancreas, moderate amount of ascites, and duodenal thickening. A esophagogastroduodenoscopy showed patchy erythematous mucosal lesions in the 2nd portion of the duodenum. Biopsies from the duodenum indicated eosinophilic infiltration in the lamina propria. The patient was successfully treated with prednisolone and montelukast. Despite its unusual occurrence, EGE may be considered in the differential diagnosis of unexplained acute pancreatitis, especially in a patient with duodenal edema on imaging or peripheral eosinophilia.
Acute Disease ; Aged ; Ascites/*etiology ; Enteritis/*complications ; Eosinophilia/*complications ; Female ; Gastritis/*complications ; Humans ; Pancreatitis/*etiology ; Tomography, X-Ray Computed

BACKGROUND/AIMS: The objective of our study was to identify useful computed tomography (CT) findings for differentiating fundal type adenomyomatosis from localized chronic cholecystitis involving the fundus of the gallbladder. METHODS: We retrospectively identified cases of 41 patients with pathologically proven adenomyomatosis (n=21) or chronic cholecystitis (n=20) who had fundal thickening of the gallbladder on preoperative abdominal CT. Analysis of the CT findings included evaluation of the thickness, contour, border, intralesional cystic area, adjacent gallbladder wall thickening, presence of inner layer enhancement, enhancement grade, enhancement pattern, and presence of stones. Statistical analyses were performed using the Mann-Whitney U test and Fisher exact test. RESULTS: Oval contour, inner layer enhancement and intralesional cystic area were more frequently noted in adenomyomatosis than in chronic cholecystitis (p<0.05 for each finding). Flat contour and adjacent gallbladder wall thickening were more frequently observed in chronic cholecystitis than in adenomyomatosis. No differences between adenomyomatosis and chronic cholecystitis in terms of the thickness, enhancement grade, enhancement pattern and presence of stones were apparent. CONCLUSIONS: CT may help to differentiate fundal type adenomyomatosis from localized chronic cholecystitis involving the fundus of the gallbladder.
Adenomyoma/*pathology/radiography ; Adult ; Aged ; Cholecystitis/*pathology/radiography ; Chronic Disease ; Diagnosis, Differential ; Female ; Gallbladder ; Gallbladder Neoplasms/*pathology/radiography ; Humans ; Male ; Middle Aged ; Retrospective Studies ; Tomography, X-Ray Computed

BACKGROUND/AIMS: Endoscopic ultrasound-guided fine needle aspiration (EUS-FNA) is useful for the pathological diagnosis of pancreatic masses, but patients are susceptible to severe bleeding and perforation. Because the incidence and severity of these complications have not been fully evaluated. METHODS: We aimed to evaluate severe bleeding and perforation after EUS-FNA for pancreatic masses using large-scale data derived from a Japanese nationwide administrative database. RESULTS: In total, 3,090 consecutive patients from 212 low- to high-volume hospitals were analyzed. Severe bleeding requiring transfusion or endoscopic treatment occurred in seven patients (0.23%), and no perforation was observed. No patient mortality was recorded within 30 days of EUS-FNA. The rate of severe bleeding in low-volume hospitals was significantly higher than that in medium- and high-volume hospitals (0.48% vs 0.10%, p=0.045). CONCLUSIONS: Severe bleeding and perforation following EUS-FNA for pancreatic masses are rare, and the procedure is safe.
Blood Transfusion/statistics & numerical data ; Endoscopic Ultrasound-Guided Fine Needle Aspiration/*adverse effects ; Female ; Fibrinolytic Agents/adverse effects ; Gastrointestinal Hemorrhage/*etiology ; Humans ; Intestinal Perforation/*etiology ; Male ; Middle Aged ; Pancreatic Neoplasms/*pathology

Renal cell carcinoma is extremely uncommon in children. But this neoplasm should be considered in the differential diagnosis of hematuria and/or abdominal mass in children. We present a case of renal cell carcinoma in an 11-year-old girl which was confirmed pathologically.
Carcinoma, Renal Cell* ; Child ; Diagnosis, Differential ; Female ; Hematuria ; Humans

Primary localized amyloidosis is a rare disease. A 75-year-old woman with a history of intermittent right-sided renal colic and hematuria had a stricture of lower ureter which was suspected to be caused by tumor or fibrosis. Intraoperative frozen biopsy of the ureter showed no evidence of malignancy. So we report a case of primary amyloidosis of the ureter which was treated successfully with segmental resection and end to end anastomosis.
Aged ; Amyloidosis* ; Biopsy ; Constriction, Pathologic ; Female ; Fibrosis ; Hematuria ; Humans ; Rare Diseases ; Renal Colic ; Ureter*