Search

Highlights: [•] Methane emission differs significantly among cultivars but not between the late- and early-maturing groups. [•] Short flooding duration in the cultivation of early-maturing cultivars did not effectively reduce CH4 emissions during the rice growing season. [•] Methane fluxes were significantly correlated with methanogen and methanotroph abundances but not with any of the apparent plant growth characteristics. [•] Selection of low-CH4 emitting cultivars with high productivity is a promising strategy to reduce CH4 emissions in paddy soils. [ABSTRACT FROM AUTHOR]

Conclusions: p16 immunohistochemistry (IHC) status correlated with less exposure to smoking and/or alcohol in Korean patients with locally advanced tonsillar squamous cell carcinoma (TSCC), and was an independent prognostic factor for survival. Objective: TSCC is more likely to be human papillomavirus (HPV)-positive than other head and neck squamous cell carcinoma (HNSCC) subtypes. The objective of this study was to ascertain the HPV status of TSCC in Korean patients and to determine its relationship with clinical parameters and prognosis. Methods: The locally advanced TSCCs of 79 patients who were treated between 2000 and 2008 were tested by p16 IHC and HPV in situ hybridization (ISH) with a tissue microarray. Results: Sixty-three patients (80%) were positive for p16 IHC, while 54 (68%) were positive by HPV ISH. p16 IHC status correlated significantly with lower exposure to smoking and alcohol ( p < 0.05) but did not correlate with T and N stage classification, histological differentiation, age, or gender. The p16-positive group had a significantly higher 5-year overall survival rate in comparison with the p16-negative group (78% vs 63%, hazard ratio (HR) = 0.347, 95% CI = 0.14, 95% C p = 0.025). p16 IHC was a favorable independent prognostic factor for overall survival, even after adjustment for age and T stage (HR = 0.283, 95% CI = 0.103, 95% p = 0.015). [ABSTRACT FROM AUTHOR]

Abstract: Plastic-film greenhouse (hereafter, greenhouse) vegetable production by temporarily flooding for crop rotation with rice is used as a countermeasure to reduce salt build-up, specifically in flooded rice production systems in Korea. However, flood waters are still observed to contain large amounts of soluble phosphorus (P) enhancing fresh water eutrophication rate. We hypothesized that the addition of liming materials containing high calcium (Ca) content can convert water-soluble P (W-P) into lesser soluble forms reducing P release into off-field water bodies. An incubation study was conducted to select the best liming material, using Ca(OH)2, CaCO3, and CaSO4·2H2O (hereafter, gypsum) mixed with a salt-accumulated soil at a rate 10g Cakg−1. Calcium hydroxide was found to be the most effective in reducing W-P concentration in the incubation test. Thus, Ca(OH)2 was applied at rates of 0, 2, 4, and 8 Mgha−1 before transplanting rice (Oryza sativa) into a paddy field and temporarily successively planted from vegetables grown in greenhouse. Addition of Ca(OH)2 significantly reduced total P (T-P) and dissolved reactive P (DRP) concentrations in the flooded water and T-P, DRP and unreactive P (UP) in the leachate collected at −60cm soil depth. The reduction of P leaching and runoff loss by amending Ca(OH)2 was mainly affected by the conversion of W-P into calcium bound P (Ca-P) forms. Liming improved soil pH and other nutrient conditions. Conclusively, Ca(OH)2 could be a good material to reduce P release and restore nutrient balance in a vegetable–rice crop rotation under greenhouse condition. [Copyright &y& Elsevier]

Fertilization with urea can lead to a loss of carbon dioxide (CO 2 ) that was fixed during the industrial production process. The extent of atmospheric CO 2 removal from urea manufacturing was estimated by the Industrial Processes and Product Use sector (IPPU sector). On its basis, the Intergovernmental Panel on Climate Change (IPCC) has proposed a value of 0.2 Mg C per Mg urea (available in 2006 revised IPCC guidelines for greenhouse gas inventories), which is the mass fractions of C in urea, as the CO 2 emission coefficient from urea for the agricultural sector. Notably, due to the possibility of bicarbonate leaching to waters, all C in urea might not get released as CO 2 to the atmosphere. Hence, in order to provide an accurate value of the CO 2 emission coefficient from applied urea in the rice ecosystem, the CO 2 emission factors were characterized under different levels of 13 C-urea applied paddy field in the current study. The total CO 2 fluxes and rice grain yields increased significantly with increasing urea application (110–130 kg N ha −1 ) and thereafter, decreased. However, with increasing 13 C-urea application, a significant and proportional increase of the 13 CO 2 C emissions from 13 C-urea was also observed. From the relationships between urea application levels and 13 CO 2 C fluxes from 13 C-urea, the CO 2 C emission factor from urea was estimated to range between 0.0143 and 0.0156 Mg C per Mg urea. Thus, the CO 2 C emission factor of this study is less than that of the value proposed by IPCC. Therefore, for the first time, we propose to revise the current IPCC guideline value of CO 2 C emission factor from urea as 0.0143–0.0156 Mg C per Mg urea for Korean paddy soils. [ABSTRACT FROM AUTHOR]

We present the first Korean individual genome sequence (SJK) and analysis results. The diploid genome of a Korean male was sequenced to 28.95-fold redundancy using the Illumina paired-end sequencing method. SJK covered 99.9% of the NCBI human reference genome. We identified 420,083 novel single nucleotide polymorphisms (SNPs) that are not in the dbSNP database. Despite a close similarity, significant differences were observed between the Chinese genome (YH), the only other Asian genome available, and SJK: (1) 39.87% (1,371,239 out of 3,439,107) SNPs were SJK-specific (49.51% against Venter's, 46.94% against Watson's, and 44.17% against the Yoruba genomes); (2) 99.5% (22,495 out of 22,605) of short indels (< 4 bp) discovered on the same loci had the same size and type as YH; and (3) 11.3% (331 out of 2920) deletion structural variants were SJK-specific. Even after attempting to map unmapped reads of SJK to unanchored NCBI scaffolds, HGSV, and available personal genomes, there were still 5.77% SJK reads that could not be mapped. All these findings indicate that the overall genetic differences among individuals from closely related ethnic groups may be significant. Hence, constructing reference genomes for minor socio-ethnic groups will be useful for massive individual genome sequencing.

Conclusion: Surgical treatment of carotid invasion may give an improved 2-year survival in selected patients without significant morbidity., Objective: To evaluate survival outcomes in patients with head and neck squamous cell carcinomas invading the carotid artery., Patients and Methods: At the time of carotid invasion, 23 patients underwent surgery (n=11), chemoradiotherapy (n=6), or palliation (n=6). Surgical methods included carotid resection and ligation (n=5), carotid resection and reconstruction with saphenous vein (n=4), and peeling (n=2). Survival outcomes among different treatments were compared., Results: None of the 11 surgical patients experienced perioperative mortality or major neurologic complications. Three of these patients survived, but two had recurrent disease at last follow-up; their 2-year overall survival and disease-free survival rates were 24.5% and 18.2%, respectively. In contrast, all patients treated with chemoradiation or palliation died within 15 months. Median survival time was 16.5 months in the surgery group, 11.5 months in the chemoradiation group, and 3 months in the palliation group (p=0.025).

Unlabelled: High tumor uptake of (18)F-FDG is associated with an unfavorable outcome in cancer patients. We evaluated pretreatment (18)F-FDG uptake as guidance for the primary treatment modality in patients with squamous cell carcinoma (SCC) of the oropharynx., Methods: Fifty-two consecutive patients with newly diagnosed resectable SCC of the oropharynx underwent (18)F-FDG PET before treatment. Primary treatment modalities consisted of surgical resection plus radiotherapy (RT) (surgery group, n=31) or radical RT plus chemotherapy (RT group, n=21). The sex, age, tumor stage, histologic grade, TNM classification, treatment strategy, and maximum standardized uptake value (SUV) categories were analyzed for association with local control (LC) and disease-free survival (DFS). The median follow-up of the surviving patients was 36 mo., Results: The median SUV was significantly higher in the 11 patients who failed treatment than that in the remaining controlled patients (8.0 vs. 5.4; P=0.021). Patients having tumors with a high SUV > 6.0 had poorer LC and DFS (P<0.05). In multivariate analysis, the SUV remained an independent determinant of LC and DFS (P<0.05). Patients with a SUV > 6.0 in the surgery group had a higher 3-y DFS than that in the RT group (78% vs. 33%; P=0.043)., Conclusion: Pretreatment tumor (18)F-FDG uptake represents an independent prognostic factor in patients with oropharyngeal SCC. Patients with high (18)F-FDG uptake may be better treated by surgery followed by RT with or without chemotherapy, which needs to be verified by a prospective randomized study.

The GSTP1 and NQO1 have been reported to be associated with an increased risk for smoking related head and neck squamous cell carcinoma (HNSCC). The purpose of this study was to determine the effect of these metabolic gene polymorphisms on the risk of HNSCC. The study population included 294 histologically confirmed HNSCC cases and 333 controls without cancer. Genotyping analysis of the GSTP1 Ile105Val and NQO1 Trp139Arg genes was performed by polymerase chain reaction-based techniques on DNA prepared from peripheral blood. The Mantel-Haenszel chi2 test was used for statistical analysis. The allele frequencies of the GSTP1 and NQO1 polymorphisms were not statistically significant between cases and controls. In analyzing the association between smoking amounts and genetic polymorphisms, GSTP1 and NQO1 polymorphisms were associated with cigarette smoking amounts in cases. G allele containing genotypes in GSTP1 and T allele containing genotypes in NQO1 were associated with a tobacco dose-dependent increase in risk of HNSCC and these genotype distributions were statistically significant (p<0.05). We found that the GSTP1 105Val allele and NQO1 139Arg allele were associated with tobacco dose-dependent increase in risk of HNSCC. GSTP1 and NQO1 genotype polymorphisms may play an important role in the development of smoking related HNSCC.

Background: The BRAF(V600E) mutation, the most common genetic alteration reported in papillary thyroid carcinoma, has been associated with poor prognostic factors., Aim: To determine whether the presence of the BRAF(V600E) mutation is associated with poor prognosis in Korean patients with conventional papillary thyroid microcarcinoma (micro-PTC)., Patients and Methods: DNA was extracted from paraffin-embedded thyroid tumour specimens taken from 60 patients with conventional micro-PTC, as well as from nine patients with follicular variant papillary carcinoma, six with nodular hyperplasia, four with follicular carcinoma (including one with Hürthle cell carcinoma), four with follicular adenoma (including two with Hürthle cell adenoma) and one each with medullary carcinoma, poorly differentiated carcinoma and anaplastic carcinoma. The presence of the BRAF(V600E) mutation was determined by polymerase chain reaction (PCR) amplification of exon 15 followed by direct sequencing., Results: The BRAF(V600E) mutation was detected in tumour samples from 31 of 60 conventional micro-PTC patients (52%), but was not detected in patients with other types of thyroid tumours. The age distribution, tumour size, extrathyroid extension, multifocality and staging did not differ significantly between patients with and without the BRAF(V600E) mutation., Conclusion: In Korean patients with conventional micro-PTC, the presence of the BRAF(V600E) mutation was not significantly associated with prognostic factors.