Database for crude drugs and Kampo medicine.

A wiki-based repository for crude drugs and Kampo medicine is introduced. It provides taxonomic and chemical information for 158 crude drugs and 348 prescriptions of the traditional Kampo medicine in Japan, which is a variation of ancient Chinese medicine. The system is built on MediaWiki with extensions for inline page search and for sending user-input elements to the server. These functions together realize implementation of word checks and data integration at the user-level. In this scheme, any user can participate in creating an integrated database with controlled vocabularies on the wiki system. Our implementation and data are accessible at http://metabolomics.jp/wiki/.

Large cell neuroendocrine carcinoma of the gallbladder: long survival achieved by multimodal treatment.

Large cell neuroendocrine carcinoma of the gall-bladder is a rare disease in which the prognosis worsens with size. We report a case of large cell neuroendocrine carcinoma of the gallbladder in a 64-year-old woman who presented with a right upper quadrant mass whose longest diameter was 11.5 cm; the mass was initially considered to be unresectable because of probable invasion to the main portal vein and biliary tract. The patient received multi-modal treatment, consisting of intraarterial chemotherapy, three-dimensional radiation therapy, right trisegmentectomy, and gamma-knife irradiation (for brain metastases). She has survived for 69 months since the initial diagnosis and has shown no signs of recurrence at 35 months after the last gamma-knife irradiation for brain metastases. This result suggests that multimodal treatment including surgery, chemotherapy, and radiation therapy achieved a good response and led to long survival.

Feasibility and efficacy of single photon emission computed tomography-based three-dimensional conformal radiotherapy for hepatocellular carcinoma 8 cm or more with portal vein tumor thrombus in combination with transcatheter arterial chemoembolization.

PURPOSE: To assess the feasibility and efficacy of single photon emission computed tomography-based three-dimensional conformal radiotherapy (SPECT-B 3D-CRT) for large hepatocellular carcinoma (HCC) with portal vein tumor thrombus (PVTT). METHODS AND MATERIALS: HCC patients with PVTT in the first branch or main trunk, 8 cm or greater in size, were admitted to the study. SPECT, using Tc-99m-galactosyl human serum albumin, was used in radiation treatment planning to explore the optimal irradiation beam angle. SPECT enabled the minimum possible irradiation of functional liver (FL). Clinical target volume (CTV) included the main tumor and PVTT. SPECT-B 3D-CRT targeted the CTV to a total dose of 45 Gy/18 fractions. HCC outside the CTV was treated by transcatheter arterial chemoembolization (TACE). RESULTS: Nineteen cases were enrolled in this study. The mean maximum dimension, mean CTV, and mean dose to FL were 11.0 cm (range, 8.0-20.0), 435 cm(3) (range, 60-2,535), and 1,102 cGy (range, 691-1,695), respectively. Follow-up SPECT demonstrated radiation-induced dysfunctional liver. Despite the inclusion of 6 cases of Child-Pugh B or C, no patients experienced Grade 3 or worse radiation-induced liver disease. The cumulative non-progression rates of PVTT and PVTT plus main tumor were 78.0 and 43.2%, respectively. Survival rates at 1 and 2 years were 47.4 and 23.7%, respectively. CONCLUSIONS: SPECT-B 3D-CRT with TACE appears to be tolerable to cirrhotic liver and to provide promising prognosis for patients with HCC sized 8 cm or more, in comparison with previous treatment methods. A longer follow-up period is required to evaluate these findings.

MassBank: a public repository for sharing mass spectral data for life sciences.

MassBank is the first public repository of mass spectra of small chemical compounds for life sciences (<3000 Da). The database contains 605 electron-ionization mass spectrometry (EI-MS), 137 fast atom bombardment MS and 9276 electrospray ionization (ESI)-MS(n) data of 2337 authentic compounds of metabolites, 11 545 EI-MS and 834 other-MS data of 10,286 volatile natural and synthetic compounds, and 3045 ESI-MS(2) data of 679 synthetic drugs contributed by 16 research groups (January 2010). ESI-MS(2) data were analyzed under nonstandardized, independent experimental conditions. MassBank is a distributed database. Each research group provides data from its own MassBank data servers distributed on the Internet. MassBank users can access either all of the MassBank data or a subset of the data by specifying one or more experimental conditions. In a spectral search to retrieve mass spectra similar to a query mass spectrum, the similarity score is calculated by a weighted cosine correlation in which weighting exponents on peak intensity and the mass-to-charge ratio are optimized to the ESI-MS(2) data. MassBank also provides a merged spectrum for each compound prepared by merging the analyzed ESI-MS(2) data on an identical compound under different collision-induced dissociation conditions. Data merging has significantly improved the precision of the identification of a chemical compound by 21-23% at a similarity score of 0.6. Thus, MassBank is useful for the identification of chemical compounds and the publication of experimental data.

Single photon emission computed tomography-based three-dimensional conformal radiotherapy for hepatocellular carcinoma with portal vein tumor thrombus.

PURPOSE: To evaluate the safety and efficacy of three-dimensional conformal radiotherapy (3D-CRT) using single photon emission computed tomography (SPECT) in unresectable hepatocellular carcinoma (HCC) with portal vein tumor thrombus (PVTT). METHODS AND MATERIALS: Patients with HCC with PVTT in the first branch and/or main trunk were selected for this study. The optimal beam directions for 3D-CRT were explored using a Tc-99m-galactosyl human serum albumin SPECT image for guidance. The SPECT image was classified as either wedge type or localized type. The clinical target volume to a total dose of 45 or 50 Gy per 18-20 fractions included the main tumor and PVTT in the wedge type and PVTT alone in the localized type. RESULTS: Twenty-six patients were enrolled: 18 with wedge type and 8 with localized type. Mean tumor size was 7.1 cm (range, 4.4-12.3 cm). Clinical target volumes of wedge type vs. localized type were 111.2 cm(3) vs. 48.4 cm(3) (p = 0.010), respectively. Mean dose to normal liver and mean dose to functional liver were 1185 cGy and 988 cGy (p = 0.001) in wedge type and 1046 cGy and 1043 cGy (p = 0.658) in localized type, respectively. Despite an incidence of Child-Pugh B and C of 57.7%, no patients experienced radiation-induced liver disease. The progression of PVTT was inhibited, with an incidence of 92.2%; survival rates at 1 and 2 years were 44% and 30%, respectively. CONCLUSION: Single photon emission computed tomography-based 3D-CRT enables irradiation of both the main tumor and PVTT with low toxicity and promising survival.

Search extension transforms Wiki into a relational system: a case for flavonoid metabolite database.

BACKGROUND: In computer science, database systems are based on the relational model founded by Edgar Codd in 1970. On the other hand, in the area of biology the word 'database' often refers to loosely formatted, very large text files. Although such bio-databases may describe conflicts or ambiguities (e.g. a protein pair do and do not interact, or unknown parameters) in a positive sense, the flexibility of the data format sacrifices a systematic query mechanism equivalent to the widely used SQL. RESULTS: To overcome this disadvantage, we propose embeddable string-search commands on a Wiki-based system and designed a half-formatted database. As proof of principle, a database of flavonoid with 6902 molecular structures from over 1687 plant species was implemented on MediaWiki, the background system of Wikipedia. Registered users can describe any information in an arbitrary format. Structured part is subject to text-string searches to realize relational operations. The system was written in PHP language as the extension of MediaWiki. All modifications are open-source and publicly available. CONCLUSION: This scheme benefits from both the free-formatted Wiki style and the concise and structured relational-database style. MediaWiki supports multi-user environments for document management, and the cost for database maintenance is alleviated.