[A case of corrosive gastritis caused by accidental ingestion of calcium chloride that resulted in gastric stenosis and penetration].

A Japanese woman in her 40s came to our emergency room with vomiting and upper abdominal pain after drinking a bottle of milk tea at home. She had a history of bipolar disorder. Blood tests revealed hypercalcemia (calcium level of 18.6mg/dl). Abdominal computed tomography depicted thickening of the gastric wall and hyperabsorbed material in the stomach. Upper gastroduodenal endoscopy showed extreme mucosal redness from the gastric body to the pylorus. The hypercalcemia improved with intravenous infusion of zoledronic acid. The patient had not been taking any medication that could have caused hypercalcemia. Later, her father drank the same bottle of milk tea at home and developed upper abdominal pain. He was admitted to the hospital because of vomiting, and computed tomography showed hyperabsorbed material in the stomach, as in his daughter's case. Computed tomography of the bottle of milk tea revealed a highly absorbent substance. The bottle was sent to the forensics laboratory for testing, and it was found to contain calcium chloride. Thus both patients had consumed a beverage containing calcium chloride, and corrosive gastritis was diagnosed. Despite fasting and intravenous drip therapy, the first patient underwent a total gastrectomy because of severe stenosis and perforation of the gastric lumen.

ChIP-Atlas: a data-mining suite powered by full integration of public ChIP-seq data.

We have fully integrated public chromatin chromatin immunoprecipitation sequencing (ChIP-seq) and DNase-seq data (n > 70,000) derived from six representative model organisms (human, mouse, rat, fruit fly, nematode, and budding yeast), and have devised a data-mining platform-designated ChIP-Atlas (http://chip-atlas.org). ChIP-Atlas is able to show alignment and peak-call results for all public ChIP-seq and DNase-seq data archived in the NCBI Sequence Read Archive (SRA), which encompasses data derived from GEO, ArrayExpress, DDBJ, ENCODE, Roadmap Epigenomics, and the scientific literature. All peak-call data are integrated to visualize multiple histone modifications and binding sites of transcriptional regulators (TRs) at given genomic loci. The integrated data can be further analyzed to show TR-gene and TR-TR interactions, as well as to examine enrichment of protein binding for given multiple genomic coordinates or gene names. ChIP-Atlas is superior to other platforms in terms of data number and functionality for data mining across thousands of ChIP-seq experiments, and it provides insight into gene regulatory networks and epigenetic mechanisms.

MACON: a web tool for computing DNA methylation data obtained by the Illumina Infinium Human DNA methylation BeadArray.

AIM: Bioinformatics analysis for Illumina Infinium Human DNA methylation BeadArray is essential, but still remains difficult task for many experimental researchers. We here aimed to develop a browser-accessible bioinformatics tool for analyzing the BeadArray data. MATERIALS & METHODS: The tool was established as an analytical pipeline using R, Perl and Python programming languages. RESULTS: We introduced a method that groups neighboring probes into a genomic block, which facilitated efficient identification of densely methylated/unmethylated regions. The tool, MACON, provided probe filtering, ß-mixture quantile normalization, grouping into genomic blocks, annotation and production of a data subset. CONCLUSION: MACON allows researchers to analyze the BeadArray data using a web browser ( http://epigenome.ncc.go.jp/macon ).

DNA Data Bank of Japan.

The DNA Data Bank of Japan (DDBJ) (http://www.ddbj.nig.ac.jp) has been providing public data services for thirty years (since 1987). We are collecting nucleotide sequence data from researchers as a member of the International Nucleotide Sequence Database Collaboration (INSDC, http://www.insdc.org), in collaboration with the US National Center for Biotechnology Information (NCBI) and European Bioinformatics Institute (EBI). The DDBJ Center also services Japanese Genotype-phenotype Archive (JGA), with the National Bioscience Database Center to collect human-subjected data from Japanese researchers. Here, we report our database activities for INSDC and JGA over the past year, and introduce retrieval and analytical services running on our supercomputer system and their recent modifications. Furthermore, with the Database Center for Life Science, the DDBJ Center improves semantic web technologies to integrate and to share biological data, for providing the RDF version of the sequence data.

DNA data bank of Japan (DDBJ) progress report.

The DNA Data Bank of Japan Center (DDBJ Center; http://www.ddbj.nig.ac.jp) maintains and provides public archival, retrieval and analytical services for biological information. The contents of the DDBJ databases are shared with the US National Center for Biotechnology Information (NCBI) and the European Bioinformatics Institute (EBI) within the framework of the International Nucleotide Sequence Database Collaboration (INSDC). Since 2013, the DDBJ Center has been operating the Japanese Genotype-phenotype Archive (JGA) in collaboration with the National Bioscience Database Center (NBDC) in Japan. In addition, the DDBJ Center develops semantic web technologies for data integration and sharing in collaboration with the Database Center for Life Science (DBCLS) in Japan. This paper briefly reports on the activities of the DDBJ Center over the past year including submissions to databases and improvements in our services for data retrieval, analysis, and integration.

Clinicopathological factors affecting survival and recurrence after initial hepatectomy in non-B non-C hepatocellular carcinoma patients with comparison to hepatitis B or C virus.

We evaluated clinicopathological factors affecting survival and recurrence after initial hepatectomy in non-B non-C (NBNC) hepatocellular carcinoma (HCC) patients with comparison to hepatitis B or C virus, paying attention to relationship between alcohol consumption and histopathological findings. The medical records on the 201HCC patients who underwent initial hepatectomy between January 2000 and April 2013 were retrospectively reviewed. NBNC patients had higher prevalence of hypertension (47.4%), diabetes mellitus (35.5%), alcohol consumption (>20 g/day) (61.8%), and preserved liver function than hepatitis B or C patients. The 5-year survival rate of NBNC patients (74.1%) was significantly better than hepatitis B (49.1%) or C (65.0%) patients (NBNC versus B, P = 0.031). Among the NBNC patients, there was no relationship between alcohol consumption and clinicopathological findings including nonalcoholic fatty liver disease activity score (NAS). However, the 5-year OS and RFS rates in the alcohol-unrelated NBNC patients tend to be better than in the alcohol-related. By multivariate analysis, independent factors for OS in NBNC patients were Child-Pugh B/C, intrahepatic metastasis (im), and extrahepatic recurrence. NBNC patients, who were highly associated with lifestyle-related disease and preserved liver function, had significantly better prognosis compared to hepatitis B/C patients; however, there was no association between alcohol consumption and histopathological findings.

[A case of jejunal malignant melanoma diagnosed by enteroscopy and pre-operative biopsy].

We report a case of 72-year-old man found to have a primary malignant melanoma in the jejunum. The patient was noted to be anemic and had lower abdominal pain on his visit to the Department of Gastroenterology. However, an upper gastrointestinal series and colonofiberscopic examination revealed no abnormalities. After clinical examinations, the radiological workup, which included CT, X-ray of the small intestine and single-balloon enteroscopy, revealed an intraluminal polypoid tumor, with a patchy light gray and black pattern. Pre-operative biopsy specimens revealed a malignant melanoma. Segmental intestinal resection with regional lymph node dissection was performed. The tumor size was 7.0×9.5×5.8cm. Nodal metastasis was seen only in the mesenteric node draining from the tumor-bearing intestinal segment (stage IIIa). Adjuvant chemotherapy with dacarbazine, nimustine hydrochloride and vincristine sulfate was performed, and the patient was able to recover his level of activity of daily living for 6 months.

Occurrence, horizontal transfer and degeneration of VDE intein family in Saccharomycete yeasts.

VDE is a homing endonuclease gene originally discovered as an intervening element in VMA1s of Saccharomyces cerevisiae. There have been two independent subfamilies of VDE, one from S. cerevisiae strain X2180-1A and the other from Saccharomyces sp. DH1-1A in the host VMA1 gene, and they share the identity of 96.3%. In order to search the occurrence, intra/interspecies transfer and molecular degeneration of VDE, complete sequences of VMA1 in 10 strains of S. cerevisiae, eight species of saccharomycete yeasts, Candida glabrata and Kluyveromyces lactis were determined. We found that six of 10 S. cerevisiae strains contain VDEs 99.7-100% identical to that of the strain X2180-1A, one has no VDE, whereas the other three harbour VDEs 100% identical to that of the strain DH1-1A. S. carlsbergensis has two VMA1s, one being 99.8% identical to that of the strain X2180-1A with VDE 100% identical to that of the strain DH1-1A and the other containing the same VMA1 in S. pastorianus with no VDE. This and other evidence indicates that intra/interspecies transmissions of VDEs have occurred among saccharomycete yeasts. Phylogenetic analyses of VMA1 and VDE suggest that the S. cerevisiae VDEs had branched earlier than other VDEs from an ancestral VDE and had invaded into the host loci as relatively late events. The two VDEs seemed to degenerate in individual host loci, retaining their splicing capacity intact. The degeneration of the endonuclease domains was distinct and, if compared, its apparent rate was much faster than that of the protein-splicing domains.

Malignant fibrous histiocytoma arising from the renal capsule.

Malignant fibrous histiocytoma (MFH) arising from the renal capsule is a rare tumor. We report a case of 55-year-old man with this tumor. Radiological imaging, including magnetic resonance (MR) imaging, was helpful in the differential diagnosis between MFH of the renal capsule and other renal tumors. In particular, a hypo-intense area identified on T(2)-weighted images reflecting the fibrous component was identified as an important characteristic of renal MFH.

Expression and regulation of gp130 messenger ribonucleic acid in cultured immature rat Sertoli cells.

The expression of glycoprotein 130 (gp130) was studied in rat primary Sertoli cells by Northern blot analysis. Gp130 mRNA of 9.0 and 7.5 kb were detected in a variety of rat tissues including the testis. Gp130 mRNAs were detected in isolated, immature Sertoli cells. The levels of gp130 were significantly stimulated by the addition of interleukin-1-beta (IL-1-beta) or interleukin-6 (IL-6) but not by the addition of follicle-stimulating hormone (FSH). IL-6 activates intracellular signaling by binding with a receptor consisting of an 80-kDa ligand-binding protein, IL-6 receptor (IL-6R), and a second 130-kDa protein, gp130. As previously reported, expression of IL-6R mRNA in rat Sertoli cells was stimulated not only by IL-1-beta and IL-6 but also by FSH. In contrast, gp130 mRNA expression was not stimulated by FSH in our analysis. These data suggest that gp130 expression may be regulated by more than 1 mechanism and that production of gp130 and IL-6R, the 2 components of the IL-6 receptor system, may be regulated, at least in part, by a different pathway.