Gateways to the FANTOM5 promoter level mammalian expression atlas

The FANTOM5 project investigates transcription initiation activities in more than 1,000 human and mouse primary cells, cell lines and tissues using CAGE. Based on manual curation of sample information and development of an ontology for sample classification, we assemble the resulting data into a centralized data resource (http://fantom.gsc.riken.jp/5/). This resource contains web-based tools and data-access points for the research community to search and extract data related to samples, genes, promoter activities, transcription factors and enhancers across the FANTOM5 atlas. Electronic supplementary material The online version of this article (doi:10.1186/s13059-014-0560-6) contains supplementary material, which is available to authorized users

Long-term results of curative intraluminal high dose rate brachytherapy for endobronchial carcinoma

<p>Abstract</p> <p>Background</p> <p>The treatment strategy of central lung tumors is not established. Intraluminal brachytherapy (ILBT) is widely used for palliative treatment of endobronchial tumors, however, it is also a promising option for curative treatment with limited data. This study evaluates the results after ILBT for endobronchial carcinoma.</p> <p>Method</p> <p>Sixteen-endobronchial carcinoma of 13 patients treated with ILBT in curative intent for 2000 to 2008 were retrospectively reviewed. ILBT using high dose rate 192 iridium thin wire system was performed with 5 Gy/fraction at mucosal surface. The patient age ranged from 57 to 82 years old with median 75 years old. The 16 lesions consisted of 13 central endobronchial cancers including 7 roentgenographically occult lung cancers and 3 of tracheal cancers. Of them, 10 lesions were treated with ILBT of median 20 Gy combined with external beam radiation therapy of median 45 Gy and 6 lesions were treated with ILBT alone of median 25 Gy.</p> <p>Results</p> <p>Median follow-up time was 32.5 months. Two-year survival rate and local control rate were 92.3% and 86.2%, respectively. Local recurrences were observed in 2 lesions. Three patients died due to lung cancer (1 patient) and intercurrent disease (2 patients). Complications greater than grade 2 were not observed except for one grade 3 dyspnea.</p> <p>Conclusions</p> <p>ILBT combined with or without EBRT might be a curative treatment option in inoperable endobronchial carcinoma patients with tolerable complication.</p

Mechanism of enhancement effect of carbon-beam irradiation combined with chemo-therapeutic agants on two cell lines with different radiosensitivities and different p53 status in vitro

Particle Therapy Co-Operative Group 4

National survey of radiation oncologists practice patterns regarding hormone-naïve prostate cancer with bone metastases

Objective: To explore radiation oncologists’ attitudes and practice patterns of radiotherapy for hormone-naïve prostate cancer with bone metastases in Japan.Methods: An internet-based survey was distributed to board-certified radiation oncologists of the Japanese Society of Radiation Oncology. Three hypothetical cases were assumed: hormone-naïve prostate cancer with single, three or multiple non-symptomatic bone metastases. The respondents described their attitude regarding such cases, treatment methods and the radiotherapy dosefractionation that they would recommend.Results: Among the 1013 board-certified radiation oncologists in Japan, 373 (36.8%) responded to the questionnaire. Most of the respondents (85.0%) believed that radiotherapy may be applicable as a primary treatment for hormone-naïve prostate cancer with bone metastases in some circumstances. For Case 1 (single bone metastasis), 55.0% of the respondents recommendedradiotherapy for the prostate and bone metastasis. For Case 2 (three bone metastases), only 24.4% recommended radiotherapy for all lesions, and 31.4% recommended radiotherapy for the prostate only. For Case 3 (multiple bone metastases), 49.1% of the respondents stated that there was no indication for radiotherapy. However, 34% of the respondents still preferred to administerradiotherapy for the prostate. The radiotherapy techniques and dose fractionations varied widely among the respondents

The effects of PSA kinetics on the outcome of hypofractionated salvage radiotherapy for biochemical recurrence of prostate cancer after prostatectomy

The feasibility and efficacy of hypofractionated salvage radiotherapy (HS-RT) for prostate cancer (PC) with biochemical recurrence (BR) after prostatectomy, and the usefulness of prostate-specific antigen (PSA) kinetics as apredictor of BR, were evaluated in 38 patients who received HS-RT without androgen deprivation therapy between May 2009 and January 2017. Their median age, PSA level and PSA doubling time (PSA-DT) at the start of HS-RTwere 68 (53–74) years, 0.28 (0.20–0.79) ng/ml and 7.7 (2.3–38.5) months, respectively. A total dose of 60 Gy in 20 fractions (three times a week) was three-dimensionally delivered to the prostate bed. After a median follow-upof 62 (30–100) months, 19 (50%) patients developed a second BR after HS-RT, but only 1 patient died before the last follow-up. The 5-year overall survival and BR-free survival rates were 97.1 and 47.4%, respectively. Late grade 2gastrointestinal and genitourinary morbidities were observed in 0 and 5 (13%) patients, respectively. The PSA level as well as pathological T-stage and surgical margin status were regarded as significant predictive factors for a secondBR by multivariate analysis. BR developed within 6 months after HS-RT in 11 (85%) of 13 patients with a PSADT < 10 months compared with 1 (17%) of 6 with a PSA-DT ≥ 10 months (median time to BR: 3 vs 14 months,P < 0.05). Despite the small number of patients, our HS-RT protocol seems feasible, and PSA kinetics may be useful for predicting the risk of BR and determining the appropriate follow-up schedule

Carbon-ion Radiotherapy for Prostate Cancer: Analysis of Morbidities and Change in Health-related Quality of Life.

AIM: To prospectively evaluate the feasibility of carbon-ion radiotherapy (C-ion RT) for prostate cancer using a new compact-sized accelerator. PATIENTS AND METHODS: Seventy-six patients underwent C-ion RT at our center using a recommended dose fractionation of 57.6 GyE in 16 fractions established at the National Institute of Radiological Sciences. Health-related Quality of Life (HRQOL) assessment was also performed using the Medical Outcome Study 8-items Short Form Health Survey (SF-8) questionnaire. RESULTS: The median follow-up time was 51 months (range=8-58 months). Grade 2 gastrointestinal and genitourinary complications developed in 1 (1.3%) and 5 (6.6%) patients, respectively. Recurrences occurred in 4 patients, and the 4-year biochemical relapse-free rate was 94.6%. The HRQOL scores after C-ion RT were objectively well-maintained. CONCLUSION: Irrespective of the small number of patients of the study, C-ion RT for prostate cancer using the first commercial-based accelerator reproduced the toxicity outcomes at the NIRS

Supporting Information

Supporting information for a research artile "A highly contiguous genome assembly of red perilla (Perilla frutescens) domesticated in Japan". Table S1. Statistics of the contigs generated by Hifiasm. Table S2. AGP file (scaffolds_FINAL.agp) generated by SALSA2 describing the contig assignment of each scaffold. Table S3. Length and the components of 20 pseudochromosomes. Table S4. Summary of the gene annotation of each of the three methods. Figure S1. Merqury assembly spectrum plots of haplotype 1 (hap1) and haplotype 2 (hap2). Figure S2. Dot-plot alignment between the draft scaffolds (indicated as “s”) (longest 25 scaffolds; scaffold_1–25) and reference PF40 genome assembly. Blue dots represent +/+ strand alignments and red dots represent +/- strand alignments. Figure S3. Hi-C contact map of the draft scaffolds (indicated as “s”) generated by SALSA2.</p