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.

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.

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.

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.

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/.

Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana.

We present here the annotation of the complete genome of rice Oryza sativa L. ssp. japonica cultivar Nipponbare. All functional annotations for proteins and non-protein-coding RNA (npRNA) candidates were manually curated. Functions were identified or inferred in 19,969 (70%) of the proteins, and 131 possible npRNAs (including 58 antisense transcripts) were found. Almost 5000 annotated protein-coding genes were found to be disrupted in insertional mutant lines, which will accelerate future experimental validation of the annotations. The rice loci were determined by using cDNA sequences obtained from rice and other representative cereals. Our conservative estimate based on these loci and an extrapolation suggested that the gene number of rice is approximately 32,000, which is smaller than previous estimates. We conducted comparative analyses between rice and Arabidopsis thaliana and found that both genomes possessed several lineage-specific genes, which might account for the observed differences between these species, while they had similar sets of predicted functional domains among the protein sequences. A system to control translational efficiency seems to be conserved across large evolutionary distances. Moreover, the evolutionary process of protein-coding genes was examined. Our results suggest that natural selection may have played a role for duplicated genes in both species, so that duplication was suppressed or favored in a manner that depended on the function of a gene.

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.

Cholangiolocellular carcinoma of the liver: CT and MR findings.

The authors report two cases of surgically proved cholangiolocellular carcinoma of the liver. Marked contrast enhancement was observed at the periphery of the tumor on CTs and MRIs obtained during the hepatic arterial and portal venous phases, with concentric filling on the delayed images. On T1-weighted and T2-weighted MRIs, the tumor was, respectively, hypointense and hyperintense, with a central hypointense area. Therefore, helical CT and MRI features of these cholangiolocellular carcinomas were thought to be similar to those of cholangiocarcinoma.

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.

MUC-1 mucin expression in invasive areas of intraductal papillary mucinous tumors of the pancreas.

The expression of MUC-1 mucin (membrane-associated mucin) and MUC-2 mucin (secretory mucin) were immunohistochemically examined in 46 invasive ductal carcinomas (IDC) and 16 intraductal papillary mucinous tumors (IPMT) of the pancreas. Intraductal papillary mucinous tumors usually reveal expansive growth. However, of the 16 IPMT examined in the present study, three showed an invasive growth pattern, which was similar to 'mucinous carcinoma', around the non-invasive growth areas. Of 46 IDC, MUC-1 mucin detected by monoclonal antibodies, DF3 and MY.1E12, was expressed in 44 cases (96%) and in 45 cases (98%), respectively, whereas MUC-2 mucin detected by polyclonal antibody, anti-MRP, was not expressed in any of the cases (0%). In contrast, in the non-invasive growth areas of the 16 IPMT, MUC-1 mucin detected by DF3 and MY.1E12 was expressed in four cases (25%) and in six cases (38%), respectively, whereas MUC-2 mucin detected by anti-MRP was expressed in 13 cases (81%). The invasive growth areas of the three IPMT showed positive expression of MUC-1 mucins detected by DF3 and MY.1E12, although the non-invasive growth areas showed negative expression of MUC-1 mucins, except for their focal positive expression in one of the three cases. These findings indicate that the invasive growth areas of IPMT acquire a characteristic of MUC-1 mucin expression that is usually seen in IDC.

Lymphoepithelial cysts of the pancreas: demonstration of lipid component using CT and MRI.

We present two cases of surgically proven lymphoepithelial cyst (LEC) of the pancreas that had a lipid component visualized by CT and MRI. Identification of this component in a pancreatic cystic lesion is a key to favor the diagnosis of LEC or splenic epidermoid cyst over other cystic lesions when the lesion is noted in an elderly patient.

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.

[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 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.

Novel functional polymers: poly(dimethylsiloxane)-polyamide multiblock copolymer. V. The interaction between biomolecules and the surface of aramid-silicone resins.

Multiblock copolymers consisting of aromatic polyamide(aramid) and poly(dimethylsiloxane) (PDMS) aramid-silicone resins (PASs) were synthesized by low temperature solution polycondensation, and PAS films were prepared by casting from an N,N'-dimethylacetamide solution. In this study, we investigated bovine serum albumin (BSA) adsorption, L929 cell adhesion, and tissue reaction on the surface of PAS in order to clarify the interaction between PAS and biomolecules. It was found that the amount of adsorbed biomolecules on PAS was extremely low in contrast with those on aramid and nylon films, and it was comparable to SILASTIC 500-1 film. This suppression of adsorption of biomolecules onto PAS seemed to be due to the low surface free energy of the outermost surface of PAS, where PDMS block was condensed.

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.

[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.

[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.