Evola: Ortholog database of all human genes in H-InvDB with manual curation of phylogenetic trees.

Orthologs are genes in different species that evolved from a common ancestral gene by speciation. Currently, with the rapid growth of transcriptome data of various species, more reliable orthology information is prerequisite for further studies. However, detection of orthologs could be erroneous if pairwise distance-based methods, such as reciprocal BLAST searches, are utilized. Thus, as a sub-database of H-InvDB, an integrated database of annotated human genes (http://h-invitational.jp/), we constructed a fully curated database of evolutionary features of human genes, called 'Evola'. In the process of the ortholog detection, computational analysis based on conserved genome synteny and transcript sequence similarity was followed by manual curation by researchers examining phylogenetic trees. In total, 18 968 human genes have orthologs among 11 vertebrates (chimpanzee, mouse, cow, chicken, zebrafish, etc.), either computationally detected or manually curated orthologs. Evola provides amino acid sequence alignments and phylogenetic trees of orthologs and homologs. In 'd(N)/d(S) view', natural selection on genes can be analyzed between human and other species. In 'Locus maps', all transcript variants and their exon/intron structures can be compared among orthologous gene loci. We expect the Evola to serve as a comprehensive and reliable database to be utilized in comparative analyses for obtaining new knowledge about human genes. Evola is available at http://www.h-invitational.jp/evola/.

An empirical evaluation of electronic annotation tools for Twitter data.

Despite a growing number of natural language processing shared-tasks dedicated to the use of Twitter data, there is currently no ad-hoc annotation tool for the purpose. During the 6th edition of BLAH, after a short review of 19 generic annotation tools, we adapted GATE and TextAE for annotating Twitter timelines. Although none of the tools reviewed allow the annotation of all information inherent of Twitter timelines, a few may be suitable provided the willingness by annotators to compromise on some functionality.

Expression of MUC1 and MUC2 mucins in gastric carcinomas: its relationship with the prognosis of the patients.

Our previous immunohistochemical studies for the expression of MUC1 mucin antigen (which was detected by monoclonal antibody DF3) and MUC2 mucin antigen (which was detected by polyclonal antibody anti-MRP) in pancreatic and intrahepatic bile duct tumors demonstrated that invasive carcinoma with poor outcome showed a pattern of MUC1+ and MUC2- expression, whereas many of the noninvasive tumors with favorable outcome showed a pattern of MUC1- and MUC2+ expression. To clarify the relationship between the expression of these mucin antigens and the biological properties of gastric cancers, the expression of MUC1 and MUC2 mucin antigens was examined immunohistochemically in 136 patients with gastric cancer invading the submucosa or the deeper layer, and the survival of the antigen-positive and antigen-negative patient groups was compared using the Kaplan-Meier method. For MUC1 mucin expression, different glycoforms of MUC1 were examined using four monoclonal antibodies (NCL-MUC-1-CORE, DF3, MY.1E12, and HMFG-1). The patients with MUC1+ mucin antigen staining in the carcinoma showed significantly worse survival than those with MUC1- mucin antigen staining. In contrast, the patients with MUC2+ mucin antigen staining in the carcinoma showed significantly better survival than those with MUC2- mucin antigen staining. In conclusion, MUC1 antigen expression was associated with a poor outcome in patients with gastric cancer, irrespective of its glycosylation status, and MUC1 is thus considered to be a useful prognostic factor for poor outcome in patients. In contrast, MUC2 antigen expression is a prognostic factor associated with a favorable outcome in patients. In addition, combined evaluation of the MUC1 and MUC2 mucin staining is clinically useful to predict outcome in patients with gastric cancer.

Difference in incidence and transmission mode of methicillin-resistant Staphylococcus aureus among surgery, orthopedics, and pediatrics wards: a prospective study at a university hospital.

The incidence and circumstances of colonization by methicillin-resistant Staphylococcus aureus were prospectively investigated. Among 404 patients, 15 (3.7%) were carriers on admission, and 43 (10.6%) became colonized, mainly after surgical operation. A different mode of transmission was suggested in each ward.

Biosynthesis of IL-8 and endothelin-1,2 by immortal simian virus 40 tsA-transformed human endothelial cells.

Immortal human umbilical cord vein endothelial cells (HUVEC-SV40) established in our laboratory by gene transfection of plasmid pSVts58neo were analyzed for their biological activities. The growth and cellular viability of these immortal cells were temperature dependent. Typical bioactive products of endothelial cells, IL-8 and endothelins, were released into the culture medium as in the case of mortal cells. The production of IL-8 was temperature dependent and significantly increased in cells incubated at 37 degrees C as compared with those incubated at 33 degrees C. Such a temperature dependence was not observed in endothelin production. Stimulation of cells with both TNF-alpha and IFN-gamma increased the biosynthesis of IL-8 or endothelins significantly (p<0.05). From these results, it became clear that immortal HUVEC-SV40 cells also secrete IL-8 or endothelins in the same manner as mortal cells, and that they react to the stimulation by cytokines to promote IL-8 or endothelin production.

Role of thymidine phosphorylase in Fas-induced apoptosis.

Thymidine phosphorylase (TP) has chemotactic and angiogenic activity in vitro, and it promotes tumor growth and inhibits apoptosis in vivo. It plays a key role in the invasiveness and metastasis of TP-expressing solid tumors. KB/TP cells transfected with a TP cDNA have been shown to be resistant to hypoxia-induced apoptosis, suggesting that TP has effects on tumor growth and cell death independent of its effects on angiogenesis. However, the mechanisms of cell death inhibition by TP are unknown. In the present study, we demonstrate that caspase-8 is cleaved in control transfectant KB cells early on during Fas-induced apoptosis. Caspase-8 activation leads to the loss of mitochondrial membrane potential, followed by the release of cytochrome c, the activation of caspase-3, and apoptosis. In contrast, Fas-induced caspase-8 cleavage is inhibited in KB/TP cells, which lead to inhibition of the downstream apoptotic cascade and inhibition of apoptosis. These findings indicate that TP plays an important role in intracellular apoptotic signal transduction in the Fas-induced apoptotic pathway. Therefore, inhibition of TP may suppress the progression of TP-overexpressing solid tumors by inducing apoptosis.

The migration of lymphocytes across the vascular endothelium in lymph nodes: a scanning electron microscopic study.

Endothelial cells of Postcapillary Venules (PCV) and the passage of lymphocytes through the wall of PCV were investigated with Scanning Electron Microscope (SEM) in mesenteric lymph nodes of rats. Individual endothelial cells of PCV in the lymph node did not have flat surface or were not typically cubic, but swelled at the central part assuming a foot ball-like shape. Circulating lymphocytes are considered to migrate into lymphatic tissues through the wall of PCV from the blood stream. Two hypotheses, inter-endothelial cell passage and intra-endothelial cell passage, have been proposed. The three-dimensional studies on lymphocytes passing the wall with SEM confirmed that migrating lymphocytes pushes their way through the intercellular space with pressing the adjoining endothelial cells from beginning to end, supporting the former hypothesis. Invasion of lymphocytes into endothelial cells were not observed.

[Clinical and genetic study on human cancer--gastric cancer].

The relationship between gastrointestinal cancers and genetic influence was investigated. The subjects examined were 1211 cancer cases and 781 non-cancer cases registered to the 1st Department of Surgery of Kagoshima University Hospital from 1972 to 1980. The results were as follows: 1. Malignant cases were found in 266/1211 (22.0%) in the families of cancer probandus. Incidence was significantly (P less than 0.01) higher than that [130/781 (16.6%)] in those of non-cancer probandus. 2. Malignant cases were found in 79/356 (22.2%) in the families of gastric cancer probandus and in 51/189 (27.0%) in those of colo-rectal cancer probandus. 3. The relationship between cancer probandus and malignant cases in the families was classified according to the vertical relationship (grandparents-parents-uncle and aunt-probandus-children) and the horizontal relationship (probandus-siblings-cousin). 4. Incidence in the vertical relationships (159/266: 59.8%) was higher than that in the horizontal relationships (107/266: 40.2%). Incidence of the vertical relationships of female cancer probandus (gastric cancer: 70.4%, esophageal cancer: 55.7%, clorectal cancer: 73.9%) was significantly (P less than 0.05) higher than that in those of male cancer probandus. 5. Incidence of blood B type in male gastric cancer group tended to be less when compared with the control group (P less than 0.05). 6. Incidence of smoking habits in esophageal cancer group (82.2%) and the lung cancer group (63.4%) was significantly (P less than 0.01) higher than that in the control group (46.0%). 7. Incidence of drinking habits in the male esophageal cancer group (84.2%) was significantly (P less than 0.01) higher than that in the control group (53.0%).

[A case of advanced esophageal cancer successfully treated by concurrent use of radiotherapy and low-dose CDDP and continuous infusion of 5-FU].

A 75-year-old male patient with advanced esophageal cancer was treated by radiotherapy and chemotherapy. External radiotherapy was performed by the field in field method. A total dose of 60 Gy was used in the small field (7 x 5 cm) (2.4 Gy/f and 25 f/5 wks) and a total dose of 45 Gy in the large field (14 x 6 cm) (1.8 Gy/f, 25 f/5 wks). Concurrent chemotherapy was performed at the 2nd and 5th weeks of the radiation therapy. In this chemotherapy of CDDP plus 5-FU, CDDP (25 mg/day) was given on days 1,3 and 5 of the week and 5-FU (500 mg/day) was given for 5 days by continuous infusion for the same week. By this treatment, a complete response (CR) was obtained, and no serious side effects were observed. After 1 year and 6 months, he is alive with no evidence of recurrence.

[Experimental study on cisplatin microspheres incorporated in polylactic acid and polyethylene glycol acid].

Cisplatin incorporated into polylactic acid/polyethylene glycol acid blend polymeric microspheres was prepared as a dosage (CDDP-MS) by the solvent evaporation method in an oil-in-oil emulsion system. When CDDP-MS was preserved in phosphate-buffer saline, the dissolution rate of cisplatin from CDDP-MS was 14% after one day, 25% after 5 days, 33% after 7 days, 66% after 21 days and 85% after 30 days. CDDP-MS and CDDP aqueous solution (CDDP-SOL) were intraperitoneally administered to compare the tissue distribution of cisplatin in 42 rats each. On days 0.5, 1, 5, 7, 14 and 21, omentum, lung, liver and kidney were removed, and the CDDP concentration was measured. The CDDP concentration of the CDDP-MS group was maintained at a high level in the omentum for a long time. On the other hand, the CDDP level of CDDP-MS group was low in the lung, liver and kidney, compared with the CDDP-SOL group. Consequently, it was suggested that CDDP-MS is useful as a carrier in a drug delivery system, since it improves the burst effect and releases CDDP for a long time without serious side effects.

[Experimental study of cisplatin microspheres incorporated in polylactic acid and polyethylene glycol acid on peritoneal carcinomatosis in rats].

Cisplatin incorporated into polylactic acid/polyethylene glycol acid blend polymeric microspheres was prepared as a dosage (CDDP-MS) by solvent evaporation method in oil-in-oil emulsion system. CDDP-MS and CDDP aqueous solutions (CDDP-SOL) were intraperitoneally administered to compare the tissue distribution of CDDP in 72 rats each. On 0.5, 1, 7, 14, 21 and 30 days, the omentum, lung, liver and kidney were removed, and the CDDP concentration was measured. The CDDP concentration of CDDP-MS group was maintained at a high level in the omentum for a long time. On the other hand, the CDDP level of the CDDP-MS group was low in the lung, liver and kidney, compared with the CDDP-SOL group. Additionally, acute toxicity of anticancer drug in CDDP-MS group was reduced, compared with CDDP-SOL. The effects of CDDP-MS, CDDP-SOL, empty-MS and non-therapy group on survival time were compared using intraperitoneally administered Yoshida sarcoma. The survival time in CDDP-MS, CDDP-SOL, non-therapy and empty-MS group were 43 +/- 24, 11.7 +/- 4.7, 9.8 +/- 1.1, and 7.8 +/- 1.1 days each. Consequently, it was suggested that CDDP-MS is useful as a tool in loco-regional chemotherapy using drug delivery system.

[A study on the changes in the tracheo-bronchial mucosa after esophagectomy for esophageal cancer; with special reference to the influence of neck and upper mediastinal lymph node dissections].

The tracheo-bronchial mucosa of 27 surgical patients with esophageal cancer was examined by bronchofiberscope postoperatively, and the changes of the mucosa were divided into four grades, i.e., GI: no change or slight redness only (7 cases), GII: Severe redness or erosion (7 cases), GIII: Ulcer formation (11 cases) and GIV: Necrosis of the mucosa (2 cases). All the GI-III changes were reversible. However, GIV change was irreversible. The biopsy specimens were taken from the mucosa of the tracheal bifurcation on the 7th postoperative day, showing squamous metaplasia in 9 of 13 patients. Bilateral modified neck and upper mediastinal lymph node dissections were performed in 18 of 27 patients. The change of the mucosa was judged as GIII or IV in 12 of 18 patients (67%), whereas the change was less significant in the remaining 6 patients. Namely, the degree of mucosal change did not necessarily correspond with the extent of lymph node dissection. The changes of the mucosa were considered to be brought about not only by tracheo-bronchial ischemia but also by injurious effects on the pulmonary parenchyma following aggressive lymph node dissection. The assessment of the degree of the mucosal change might be a useful indicator for postoperative management of esophageal cancer patients.

[Significance of preservation of tracheal proper sheath at the time of cervical and upper mediastinal lymph node dissection for thoracic esophageal cancer].

Extended lymph node dissection in the neck and upper mediastinum often brings about postoperative pulmonary complications. Since September 1987, we have performed this type of lymph node dissection in 18 patients paying special attention to the preservation of tracheal proper sheath along with left bronchial artery and autonomic nerve branches. We compared their postoperative respiratory and circulatory outcomes with those of 17 patients in whom lymph node dissection was carried out without consideration for these aspects. Tracheal mucosal damage, respiratory functional parameters such as PaO2, AaDO2 and Qs/Qp and actual incidence of pneumonia significantly improved in recent cases undergoing meticulous dissection in the neck and upper mediastinum. However, neither circulatory dynamics nor incidences of recurrent nerve palsy and arrhythmia showed a significant improvement. The postoperative period required for reappearance of cough reflex was shorter in this group of patients, but the difference was not significant. The results indicated that pulmonary disorders occurring frequently after extended lymph node dissection for thoracic esophageal cancer was able to be well controlled by meticulous dissection procedure as mentioned above.

[Evaluation of nutritional status in patients with esophageal cancer by measurement of sternocleidomastoid, rectus abdominis and quadriceps muscles on ultrasound imaging].

To assess the nutritional status of the patients with esophageal cancer, we measured the areas of sternocleidomastoid and rectus abdominis muscles (SMA, RAMA) on real time ultrasound imaging and calculated muscle index (MI = (SMA+RAMA/Height)). Eighty-three patients with esophageal cancer were included in the present study. Preoperatively, significant Spearman's coefficients were found between MI and the percentage of standard arm circumference (R = 0.52) and between MI and the percentage of standard arm muscle circumference (R = 0.51). Postoperatively, patients with wide muscle area showed high values of prealbumin, transferrin and fibronectin. To study the changes after surgery, we also measured the area of quadriceps muscle in patients with esophageal cancer. The areas of quadriceps muscle in patients with dysphagia were much diminished than in those without dysphagia. Measurement of areas of muscles such as SMA, RAMA and quadriceps muscle was proved to be a useful procedure in evaluating the nutritional status of patients with esophageal cancer.

[Postoperative changes in acute phase protein in patients with esophageal cancer].

Thirty-three patients with esophageal cancer were studied to assess the relationship between nutritional state and the acute phase protein responses. Blood samples taken preoperatively and days 1, 4, 7 and 14 after operation were analyzed for C-reactive protein, fibrinogen, alpha 1-antitrypsin, alpha 1-acid glycoprotein and haptoglobin. Significant Spearman's coefficients were found between percent of ideal body weight (IBW) and alpha 1-acid glycoprotein (r = -0.42), between prealbumin and alpha 1-anti-trypsin (r = -0.55), and between retinol-binding protein and alpha 1-antitrypsin (r = -0.51). Postoperatively, the levels of C-reactive protein, fibrinogen, alpha 1-anti-trypsin and alpha 1-acid glycoprotein were significantly lower in the poorly nourished group than in the other groups. The changes of acute phase proteins in the immediate postoperative period were affected by the preoperative nutritional state, and were less marked in the poorly nourished patients. Between two groups of patients in whom lymph node dissection was carried out in 2 or 3 areas, no significant differences were observed in the acute phase protein responses postoperatively. The measurement of acute phase proteins is very important in assessing the body defense capacity of the patient, but it should be noted that the changes may be affected by several factors including malnutrition.

Genome sequence of a mesophilic hydrogenotrophic methanogen Methanocella paludicola, the first cultivated representative of the order Methanocellales.

We report complete genome sequence of a mesophilic hydrogenotrophic methanogen Methanocella paludicola, the first cultured representative of the order Methanocellales once recognized as an uncultured key archaeal group for methane emission in rice fields. The genome sequence of M. paludicola consists of a single circular chromosome of 2,957,635 bp containing 3004 protein-coding sequences (CDS). Genes for most of the functions known in the methanogenic archaea were identified, e.g. a full complement of hydrogenases and methanogenesis enzymes. The mixotrophic growth of M. paludicola was clarified by the genomic characterization and re-examined by the subsequent growth experiments. Comparative genome analysis with the previously reported genome sequence of RC-I(MRE50), which was metagenomically reconstructed, demonstrated that about 70% of M. paludicola CDSs were genetically related with RC-I(MRE50) CDSs. These CDSs included the genes involved in hydrogenotrophic methane production, incomplete TCA cycle, assimilatory sulfate reduction and so on. However, the genetic components for the carbon and nitrogen fixation and antioxidant system were different between the two Methanocellales genomes. The difference is likely associated with the physiological variability between M. paludicola and RC-I(MRE50), further suggesting the genomic and physiological diversity of the Methanocellales methanogens. Comparative genome analysis among the previously determined methanogen genomes points to the genome-wide relatedness of the Methanocellales methanogens to the orders Methanosarcinales and Methanomicrobiales methanogens in terms of the genetic repertoire. Meanwhile, the unique evolutionary history of the Methanocellales methanogens is also traced in an aspect by the comparative genome analysis among the methanogens.