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Biomedical subjects

Yasunori Yamamoto

Publications and source records attributed to Yasunori Yamamoto.

11 recordsLinked to original sources
PubMed2006

Biomedical knowledge navigation by literature clustering.

There is an urgent need for a system that facilitates surveys by biomedical researchers and the subsequent formulation of hypotheses based on the knowledge stored in literature. One approach is to cluster papers discussing a topic of interest and reveal its sub-topics that allow researchers to acquire an overview of the topic. We developed such a system called McSyBi. It accepts a set of citation data retrieved with PubMed and hierarchically and non-hierarchically clusters them based on the titles and the abstracts using statistical and natural language processing methods. A novel point is that McSyBi allows its users to change the clustering by entering a MeSH term or UMLS Semantic Type, and therefore they can see a set of citation data from multiple aspects. We evaluated McSyBi quantitatively and qualitatively: clustering of 27 sets of citation data (40643 different papers) and scrutiny of several resultant clusters. While non-hierarchical clustering provides us with an overview of the target topic, hierarchical clustering allows us to see more details and relationships among citation data. McSyBi is freely available at http://textlens.hgc.jp/McSyBi/.

Artificial Intelligence↗
PubMed2005

Characterization of H5N1 influenza A viruses isolated during the 2003-2004 influenza outbreaks in Japan.

In Japan, between the end of December 2003 and March 2004, four outbreaks of acute, highly transmissible and lethal disease occurred in birds in three prefectures separated by 150-450 km, involving three chicken farms and a group of chickens raised as pets. The cause of each outbreak was an H5N1 influenza A virus-the first highly pathogenic virus to be isolated from the outbreaks in Japan since 1925. The H5N1 virus was also isolated from dead crows, apparently infected by contact with virus-contaminated material. These H5N1 viruses were antigenically similar to each other, but could be differentiated from other H5 viruses, including those isolated from Hong Kong in 1997 and 2003, by use of a panel of monoclonal antibodies in hemagglutination inhibition assays. Genetically, the H5N1 viruses in Japan were closely related to each other in all genes and were genetically closely related to a single isolate of genotype V that was isolated in 2003 in the Guandong Province of mainland China (A/chicken/Shantou/4231/2003). The virulence of the index isolate (A/chicken/Yamaguchi/7/2004) was studied in chickens and mice. Chickens intravenously or intranasally inoculated with the isolate died within 1 or 3 days of inoculation, respectively. In mice, although this virus replicated well in the lung without prior adaptation and spread to the brain, the dose lethal to 50% of the mice was 5 x 10(5) 50% egg infectious doses (EID50), which is less pathogenic than the Hong Kong 1997 H5N1 viruses isolated from humans. Our findings indicate that the H5N1 viruses associated with the influenza outbreaks in chickens in Japan were genotypically closely related to an H5N1 virus isolated from chicken in China in 2003 (genotype V), but were different from those prevalent in southeastern Asia in 2003-2004 (i.e., genotype Z) and that these highly pathogenic viruses can be transmitted to crows, which are highly susceptible to these viruses.

Animals↗
PubMed2005

Epidemiology, pathology, and immunohistochemistry of layer hens naturally affected with H5N1 highly pathogenic avian influenza in Japan.

Epidemiology, pathology, and immunohistochemistry were investigated in layer hens affected with H5N1 highly pathogenic avian influenza, which occurred for the first time in 79 years in Japan. The farm, which had a total of 34,640 chickens, experienced up to 43.3% mortality before the chickens were depopulated. Clinically, the affected chickens exhibited mortality without apparent clinical signs. Histologically, hepatocytic necrosis; necrosis of ellipsoids and follicles with fibrin in the spleen; necrosis with glial nodules in the brain stem, cerebrum, and cerebellum; necrosis of acinar cells in the pancreas; and necrosis of lymphoid tissues in intestinal lamina propria were seen. Occasionally, mild bronchiolitis, degeneration of smooth muscle fibers in the cecum, and mild tubulonephrosis were noted. Immunohistochemically, influenza virus antigens were detected often in the liver and spleen, heart, intestine, gizzard, proventriculus, and oviduct. In addition, antigens were seen also in the brain, kidney, pancreas, and ovary, but seldom in the lung and trachea. Virus antigen was mainly detected in the capillary endothelium and parenchymal cells. This suggests that virus excretion from the respiratory tract was not as prevalent as that from the digestive tract in the present cases.

Animals↗
PubMed2004

Direct binding of the human homologue of the Drosophila disc large tumor suppressor gene to seven-pass transmembrane proteins, tumor endothelial marker 5 (TEM5), and a novel TEM5-like protein.

The human homologue of the Drosophila discs large tumor suppressor gene (hDlg) is a member of the membrane-associated guanylate kinase family with three PSD-95/Dlg/ZO-1 (PDZ) domains. hDlg has been shown to bind tumor suppressor proteins, adenomatous polyposis coli (APC) and protein tyrosine phosphatase and tensin homologue (PTEN), and several viral oncoproteins, and has been implicated in the negative regulation of cell proliferation. hDlg has furthermore been shown to localize at the plasma membrane of synapses and to scaffold cell surface receptors and channels. In epithelial cells, hDlg localizes at the basolateral plasma membrane, but its localization mechanism is unknown. We searched here for a transmembrane protein that directly bound to hDlg. hDlg bound tumor endothelial marker 5 (TEM5), a seven-pass transmembrane protein that is homologous to the family B of G-protein-coupled receptors (GPCRs). TEM5 has previously been reported to display elevated expression during tumor angiogenesis and neoangiogenesis. The PDZ domains of hDlg bound the C-terminal PDZ-binding motif of TEM5. The expression of TEM5 was detected in endothelial cells of embryonic liver, where hDlg colocalized with TEM5. hDlg furthermore bound a novel seven-pass transmembrane protein, which was homologous to TEM5, and was named here a TEM5-like protein (TEM5-like). These results suggest that hDlg localizes at the plasma membrane through TEM5 and TEM5-like and furthermore scaffolds these GPCRs in endothelial cells during tumor angiogenesis and neoangiogenesis.

Adaptor Proteins, Signal Transducing↗
PubMed2004

Vmac: a novel protein associated with vimentin-type intermediate filament in podocytes of rat kidney.

Vimentin-type intermediate filaments (IFs) play an important role in cytoskeletal organization and cell morphology. We identified here a novel protein associated with vimentin-type IFs and named it vimentin-type IF-associated coiled-coil protein (Vmac). Vmac consists of 171 amino acids with a calculated Mr of 18,844 and has a coiled-coil domain in its N-terminal region and the PDZ-binding tetrapeptide consensus motif in its C-terminal region. Northern blotting showed that the Vmac mRNA was expressed in many rat tissues examined but most abundantly expressed in the kidney. Immunofluorescence microscopy revealed that Vmac was highly concentrated at podocytes of renal glomeruli. Podocytes are highly specialized epithelial cells characterized by a large cell body and numerous foot processes, and express vimentin-type IFs that are distributed in the cell body and the major processes. Immunoelectron microscopy revealed that Vmac was associated with vimentin-type IFs of podocytes. These results indicate that Vmac is a novel protein associated with vimentin-type IF in podocytes of rat kidney.

Amino Acid Sequence↗
PubMed2003

Latency and persistence of bovine herpesvirus type 4, strain B11-41, in bovine nervous tissues.

Three cattle were experimentally infected with bovine herpesvirus type 4 (BoHV-4), strain B11-41, isolated from the spinal cord of a cow, and monitored for clinical symptoms. None of them showed any clinical signs except increases of leukocyte numbers in two of them, and the body temperature remained normal throughout the experiment. Antibody titers against BoHV-4 continuously increased for one month and were maintained at a high level for more than 1 year by enzyme-linked immunosorbent assay (ELISA). The virus was isolated only from serum and peripheral blood leukocytes (PBL) of one cow in the early stage of infection, but the viral genome was detected in PBL continuously by PCR. When they were euthanized, the viral genome was detected in the lymph nodes and nervous tissues such as medulla, spinal cord, and trigeminal ganglion. These results indicate that cattle are infected with the virus latently and persistently, and the latency site would be in the tissues of the central nervous system as well as lymphoid tissues. When a seroepidemiological survey was performed on antibodies to BoHV-4 among cattle in Japan by ELISA, the rate of antibody-positive cattle was 8.9% and they were found irregularly on certain farms.

Animals↗
PubMed2002

Localization of mLin-7 at nectin-based cell-cell junctions.

In C. elegans, lin-7 as well as lin-2/lin-10 is involved in the proper localization of the LET-23 receptor tyrosine kinase that regulates vulval induction. The mammalian homologue, mLin-7, forms a ternary complex with the mammalian homologues of LIN-2 and LIN-10 and localizes at cell-cell junctions in epithelial cells, but the mechanism of this localization of mLin-7 is unknown. Nectin is an immunoglobulin-like cell-cell adhesion molecule that is involved in organization of adherens and tight junctions in epithelial cells. Nectin is indirectly associated with the cadherin-catenin system and the actin cytoskeleton through afadin, an actin filament-binding protein. We showed here that mLin-7 localized at the nectin-based cell-cell junctions. This localization of mLin-7 required the interaction of nectin with afadin, but not the cadherin-catenin system or the actin cytoskeleton. mLin-7 did not directly interact with nectin or afadin. The results indicate that mLin-7 localizes at cell-cell junctions through the nectin-afadin system.

Actin Cytoskeleton↗