Whole-Genome Sequencing of the NARO World Rice Core Collection (WRC) as the Basis for Diversity and Association Studies.

Genebanks provide access to diverse materials for crop improvement. To utilize and evaluate them effectively, core collections, such as the World Rice Core Collection (WRC) in the Genebank at the National Agriculture and Food Research Organization, have been developed. Because the WRC consists of 69 accessions with a high degree of genetic diversity, it has been used for >300 projects. To allow deeper investigation of existing WRC data and to further promote research using Genebank rice accessions, we performed whole-genome resequencing of these 69 accessions, examining their sequence variation by mapping against the Oryza sativa ssp. japonica Nipponbare genome. We obtained a total of 2,805,329 single nucleotide polymorphisms (SNPs) and 357,639 insertion-deletions. Based on the principal component analysis and population structure analysis of these data, the WRC can be classified into three major groups. We applied TASUKE, a multiple genome browser to visualize the different WRC genome sequences, and classified haplotype groups of genes affecting seed characteristics and heading date. TASUKE thus provides access to WRC genotypes as a tool for reverse genetics. We examined the suitability of the compact WRC population for genome-wide association studies (GWASs). Heading date, affected by a large number of quantitative trait loci (QTLs), was not associated with known genes, but several seed-related phenotypes were associated with known genes. Thus, for QTLs of strong effect, the compact WRC performed well in GWAS. This information enables us to understand genetic diversity in 37,000 rice accessions maintained in the Genebank and to find genes associated with different phenotypes. The sequence data have been deposited in DNA Data Bank of Japan Sequence Read Archive (DRA) (Supplementary Table S1).

Impact of treatment planning with deformable image registration on dose distribution for carbon-ion beam lung treatment using a fixed irradiation port and rotating couch.

OBJECTIVE: When using a fixed irradiation port, treatment couch rotation is necessary to increase beam angle selection. We evaluated dose variations associated with positional morphological changes to organs. METHODS: We retrospectively chose the data sets of ten patients with lung cancer who underwent respiratory-gated CT at three different couch rotation angles (0°, 20° and -20°). The respective CT data sets are referred to as CT0, CT20 and CT-20. Three treatment plans were generated as follows: in Plan 1, all compensating bolus designs and dose distributions were calculated using CT0. To evaluate the rotation effect without considering morphology changes, in Plan 2, the compensating boli designed using CT0 were applied to the CT±20 images. Plan 3 involved compensating boli designed using the CT±20 images. The accumulated dose distributions were calculated using deformable image registration (DIR). RESULTS: A sufficient prescribed dose was calculated for the planning target volume (PTV) in Plan 1 [minimum dose received by a volume ≥95% (D95) > 95.8%]. By contrast, Plan 2 showed degraded dose conformation to the PTV (D95 > 90%) owing to mismatch of the bolus design to the morphological positional changes in the respective CT. The dose assessment results of Plan 3 were very close to those of Plan 1. CONCLUSION: Dose distribution is significantly affected by whether or not positional organ morphology changes are factored into dose planning. ADVANCES IN KNOWLEDGE: In treatment planning using multiple CT scans with different couch positions, it is mandatory to calculate the accumulated dose using DIR.

Pharmacokinetic and pharmacodynamic investigation of irinotecan hydrochloride in pediatric patients with recurrent or progressive solid tumors.

OBJECTIVE: A multicenter Phase I/II study of Irinotecan hydrochloride (CPT-11; 40-45 mg/m(2)/dose) was conducted for the treatment of refractory pediatric solid tumors. The pharmacokinetics of CPT-11 and its metabolites were characterized using both traditional noncompartmental analysis and population pharmacokinetics using NONMEM VI; pharmacokinetic pharmacodynamic relationships of SN-38 with indices of toxicity were also evaluated. METHOD: 11 patients between 3 and 18 years were enrolled. Pharmacokinetic parameters and consideration of relevant covariates (performance status (PS), BSA, corrected body weight (CBW), exponent of 3/4 on weight, etc.) were evaluated. Relationships between pharmacokinetic parameters of SN-38 and percentage change from baseline in patient biochemical response data were investigated via regression analysis. RESULT: CPT-11 exhibited a mean clearance (CL) of 15.31 +/- 5.95 (l/h) (13.06 +/- 3.58 (l/hr/m(2))) and AUC(0-inf) of 3547.0 +/- 1406.5 (ng x h/ml); the AUC ratio of parent CPT-11 to SN-38 was 5.0%. Based on the population pharmacokinetic analysis, decreasing PS was significantly dependent on reduction in CL of CPT-11 (p < 0.001). The final model for CPT-11 are as follows: CL (l/h) = 1.31 x CBW(0.75) (omegaCL = 21.7%), Vss (l) = 2.66 x CBW (omegaVss = 21.2%), Vc (l) = 1.13 x CBW, inter-compartment CL (l/h) = 0.257 x CBW(0.75). Percentage changes of leucocyte and neutrophil count within a first month treatment were significantly correlated with Cmax of SN-38 (r = 0.78 and r = 0.74) and AUC0-2 of SN-38 (r = 0.73 and r = 0.73). CONCLUSION: Pharmacokinetic parameters were similar to results published in several past reports. An allometric scaling of CBW(0.75) would seem to provide a good index of dosage requirement of CPT-11 in pediatric patients.

An improved glycerin-jelly mounting procedure for permanent preparations of helminth eggs.

Many attempts have been undertaken to make permanent preparations of helminth eggs. However, the resulting preparations either lacked durability or tended to deform thin-shelled eggs, such as those of the hookworm. To overcome these drawbacks, we have modified 2 aspects of the glycerin-jelly mounting procedure. First, we gradually changed the media in which the helminth eggs soaked, from 10% formalin via water to a 70% ethanol and 5% glycerin solution. It took 10 days, which is much longer than the time required for the processes previously reported. Second, we used a hole slide glass instead of a slide glass. Eggs of 11 species of helminths have been prepared with this procedure, and have kept their morphology without apparent change for more than 4 yr.

Long-term results of Tokyo Children's Cancer Study Group trials for childhood acute lymphoblastic leukemia, 1984-1999.

We report the long-term results of Tokyo Children's Cancer Study Group's studies L84-11, L89-12, L92-13, and L95-14 for 1846 children with acute lymphoblastic leukemia, which were conducted between 1984 and 1999. The value of event-free survival (EFS)+/-s.e. was 67.2+/-2.2% at 10 years in L84-11, which was not improved in the following two studies, and eventually improved to 75.0+/-1.8% at 10 years in L95-14 study. The lower EFS of the L89-12 reflected a high rate of induction failure because of infection and delayed remission in very high-risk patients. The L92-13 study was characterized by short maintenance therapy; it resulted in poor EFS, particularly in the standard-risk (SR) group and boys. Females did significantly better than males in EFS in the early three studies. The gender difference was not significant in overall survival, partly because >60% of the males survived after the testicular relapse. Randomized studies in the former three protocols revealed that intermediate- or high-dose methotrexate therapy significantly reduced the testicular relapse rate. In the L95-14 study, gender difference disappeared in EFS. Contrary to the results of larger-scale studies, the randomized control study in the L95-14 reconfirmed with updated data that dexamethasone 8 mg/m(2) had no advantage over prednisolone 60 mg/m(2) in the SR and intermediate-risk groups. Prophylactic cranial irradiation was assigned to 100, 80, 44, and 44% of the patients in the studies, respectively. Isolated central nervous system relapse rates decreased to <2% in the last two trials. Secondary brain tumors developed in 12 patients at 8-22 years after cranial irradiation. Improvement of the remission induction rates and the complete omission of irradiation are currently main objectives in our studies.

Administration of dietary fish oil capsules in healthy middle-aged Japanese men with a high level of fish consumption.

The nutritional effects of fish oil, which is rich in the n-3 polyunsaturated fatty acids, have been reported. In this randomized, placebo-controlled, double-blind, crossover study, we evaluated the effects of dietary fish oil capsules on the hematological parameters of healthy middle-aged Japanese men with a high level of fish oil consumption. Over a 4-week period, subjects were administered five fish oil or olive oil (placebo) capsules with every meal (1,260 mg eicosapentaenoic acid and 540 mg docosahexaenoic acid/day). There was a 4-week washout period between the treatment phases. The results did not demonstrate a decrease in plasma triacylglycerol, cholesterol, low-density lipoprotein cholesterol, and whole-blood viscosity. Further, no changes in the fatty acid composition of plasma and erythrocyte phospholipids were noted. These results suggested that the supplementation of fish oil might be effective only for those subjects who have a lower level of fish oil consumption.

Characterization of Hawaiian isolates of Cymbidium mosaic virus (CymMV) co-infecting Dendrobium orchid.

We report here the isolation and characterization of three distinct isolates of Cymbidium mosaic virus (CymMV) co-infecting Dendrobium orchid in Hawaii. Isolates 1 and 2 were phylogenetically distinct from previously reported CymMV isolates. However, isolate 3 was highly similar to previously reported CymMV sequences and could be localised to CymMV subgroup A. Isolate 2 localised to CymMV subgroup B. Thus, we report here the first full-length CymMV subgroup B isolate. Isolate 1 represents a recombination event between isolates 2 and 3. Infectivity assays revealed that all three isolates are functional and individually infectious in both Dendrobium and indicator species.

Association between high signal intensity in the posterior disc attachment seen on T2 weighted fat-suppressed images and temporomandibular joint pain.

OBJECTIVES: We sought to determine whether high signal intensity in the posterior disc attachment (PDA) seen on T2 weighted fat-suppressed MRI is associated with temporomandibular joint (TMJ) pain and joint pathology. METHODS: This study was based on 283 TMJs of 177 patients (31 males and 146 females, mean age 32.7 years) with TMJ disorders showing anterior disc displacement. MRI evaluation included assessment of signal intensity in the PDA and TMJ status (disc displacement with reduction, disc displacement without reduction and disc displacement with bone changes). Clinical criteria that were considered positive indicators of TMJ pain included the presence of pre-auricular pain during palpation, jaw function and assisted or unassisted mandibular opening. Association of signal intensity in the PDA with joint pain and TMJ status was analysed using chi2 test. RESULTS: Joint pain was reported in 47 (77.0%) out of 61 joints with high signal intensity in the PDA and in 97 (43.7%) out of 222 joints with low signal intensity in the PDA (P<0.0001). High signal intensity in the PDA correlated closely with more advanced joint pathology. In joints with anterior disc displacement with bone changes, TMJ pain was more commonly reported in joints with high signal intensity in the PDA than with low signal intensity in the PDA (P<0.0001). CONCLUSIONS: High signal intensity in the PDA on T2 weighted fat-suppressed MRI is associated with TMJ pain in TMJ disorders with anterior disc displacement with bone changes in the mandibular condyles.

Carotid artery calcification seen on panoramic dental radiographs in the Asian population in Japan.

OBJECTIVES: To determine the frequency of carotid artery calcification (CAC) seen on panoramic dental radiographs, the relationship between the condition and a history of cerebral infarction (CI), and the history of the risk factors of CI in patients in Japan. METHODS: A total of 2374 individuals whose panoramic radiographs were obtained at their first consultation were reviewed. RESULT: CAC was found in 95 subjects (4.0%) and was found at a higher frequency in patients with a history of CI than in those without a history of CI. The modifiable risk factors (a history of hypertension, diabetes and hypercholesterolaemia) and CAC showed significant relationship in the chi(2) test for pairwise comparison. When age and gender were added and all of these risk factors were considered simultaneously in the multiple logistic regression analysis, age and history of hypercholesterolaemia remained statistically significant. CONCLUSIONS: CAC may be seen on panoramic dental radiographs and is related to the patients' general history of CI, and the risk factors of CI in the Asian population in Japan.

The relationship of bone marrow edema pattern in the mandibular condyle with joint pain in patients with temporomandibular joint disorders: longitudinal study with MR imaging.

The purpose of this study was to investigate the course of bone marrow edema pattern (decreased signal intensity on T1- or proton-density-weighted images and increased signal intensity on T2-weighted fat-suppressed images) in the mandibular condyle after improvement in clinical symptoms, and to clarify its relationship with temporomandibular joint (TMJ) pain. This study was based on 14 joints of 11 patients (all female, mean age 37.5 years) with TMJ disorders showing condylar bone marrow edema pattern on initial magnetic resonance (MR) images. All joints were re-evaluated clinically and using MR images after relief of joint pain following arthrocentesis combined with non-surgical treatment. The time interval between the initial and follow-up MR images ranged from 14 to 27 months (mean 17 months). Of the 14 joints, 4 joints (28.6%) showed a normal bone marrow signal, whereas 10 joints (71.4%) showed persistent bone marrow edema pattern on follow-up MR images (P = 0.125). Therefore, the reduction in TMJ pain did not correlate with resolution of bone marrow edema pattern in most joints. The results of this study suggest that the bone marrow edema pattern in the mandibular condyle does not always contribute to the occurrence of joint pain in patients with TMJ disorders.

Genetic parameter estimates of meat quality traits in Duroc pigs selected for average daily gain, longissimus muscle area, backfat thickness, and intramuscular fat content.

Using a multitrait animal model BLUP, selection was conducted over seven generations for growth rate (ADG), real-time ultrasound LM area (LMA), backfat thickness (BF), and intramuscular fat content (IMF) to develop a new line of purebred Duroc pigs with enhanced meat production and meat quality. This selection experiment examined 543 slaughtered pigs (394 barrows and 153 gilts) from the first to the seventh generation for meat quality traits. Further, electric impedance and collagen content of loin meat were measured from the fourth to sixth generation. The present study was intended to estimate genetic parameters of the correlated traits of tenderness (TEND), meat color (pork color standard: PCS; lightness = L*), drip loss (DL), cooking loss (CL), pH (PH), electric impedance (IMP), and collagen (COL) of the LM, and the genetic trends of these traits. Respective heritability estimates for IMF, TEND, DL, CL, PCS, L*, PH, IMP, and COL were 0.39, 0.45, 0.14, 0.09, 0.18, 0.16, 0.07, 0.22, and 0.23. Genetic correlations of IMF with ADG and BF were low and positive, but low and negative with LMA. Tenderness was correlated negatively with ADG (-0.44) and BF (-0.59), but positively correlated with LMA (0.32). The genetic correlation between LMA and DL was positive and high (0.64). The genetic correlations of TEND with IMF and COL were low (-0.09 and 0.26, respectively), but a moderate genetic correlation (0.43) between COL and IMF was estimated, suggesting related increases of IMF and connective tissue. Genetic correlations among meat quality traits suggested that when IMF increases, the water holding capacity improves. Genetic trends of meat quality traits showed increased IMF and lighter meat color.

Involvement of retinoic acid-inducible gene-I in the IFN-{gamma}/STAT1 signalling pathway in BEAS-2B cells.

Bronchial epithelial cells play an important role in airway host defence, and interferon (IFN)-gamma controls immune reactions by regulating the expression of various genes in bronchial epithelial cells. Signal transducer and activator of transcription 1 (STAT1) is the key transcriptional factor in IFN-gamma signalling. Retinoic acid-inducible gene-I (RIG-I) is a member of the DExH box family of proteins and designated a putative RNA helicase. RNA helicases play diverse roles in regulation of gene expression and cellular functions, and RIG-I is implicated in antiviral responses. The aim of the present study was to investigate the effect of IFN-gamma on RIG-I expression in a cell line derived from human bronchial epithelial cells, BEAS-2B. Induction of RIG-I in response to IFN-gamma was found in BEAS-2B cells. Induction of RIG-I by IFN-gamma was also demonstrated in another pulmonary epithelial cell line, NCI-H292. Transfection of BEAS-2B cells with RIG-I complementary DNA resulted in the upregulation of STAT1. Induction of IFN-gamma-inducible protein 10 by IFN-gamma was enhanced in the cells overexpressing RIG-I. It is concluded that retinoic acid-inducible gene-I may play an important role in the regulation of immunological reactions in bronchial epithelial cells elicited by interferon-gamma.

Intussusception in neonates: analysis of 14 Japanese patients.

OBJECTIVE: To clarify the clinical features and pathogenesis of intussusception in neonates. METHODS: Fourteen neonates were diagnosed with intussusception between June 1974 and January 2001. Patients were divided into two groups according to whether or not signs were present on the first day of life. The clinical features were interrelated with the pathological findings. RESULTS: All six patients in the group whose signs were present on the first day of life also had intestinal atresia or malrotation. Among patients whose signs began less than 24 h after birth, five of eight patients suffered hypoxia. Moreover, it was very difficult to establish the diagnosis of intussusception, particularly in the group of late-onset type intussusception. CONCLUSIONS: Hypoxic events may play a crucial aetiologic role in the pathogenesis of late-onset neonatal intussusception.

In vitro characterization of the relationship between the Q-angle and the lateral component of the quadriceps force.

Although the Q-angle is routinely measured, the relationship between the Q-angle and the lateral component of the quadriceps force acting on the patella is unknown. Five cadaver knees were flexed on a knee simulator with a normal Q-angle, and flexed after increasing and decreasing the Q-angle by shifting the quadriceps origin laterally and medially, respectively. The motion of the femur, tibia and patella was tracked from 20 to 90 degrees of flexion using electromagnetic sensors. The motion of landmarks used to quantify the Q-angle was tracked to determine the 'dynamic Q-angle' during flexion. The lateral component of the force applied by the actuator secured to the quadriceps tendon was also quantified throughout flexion. Increasing the initial Q-angle significantly (p < 0.05) increased the dynamic Q-angle and the lateral force exerted through the quadriceps tendon throughout flexion. Decreasing the initial Q-angle significantly decreased the dynamic Q-angle at 90 degrees of flexion and significantly decreased the lateral force exerted through the quadriceps tendon from 20 to 40 degrees of flexion. Even though the dynamic Q-angle changes during flexion, an abnormally large initial Q-angle can be an indicator of an abnormally large lateral force acting on the patella during flexion.

Involvement of adenosine A1 receptors in forced walking stress-induced analgesia in mice.

We investigated the involvement of adenosine receptors on forced walking stress-induced analgesia using a formalin-induced paw-licking test in male mice. Exposure to forced walking stress for 6 h showed stress-induced analgesia in the second phase (10-30 min), but not in the first phase (0-10 min). In the second phase, forced walking stress-induced analgesia was blocked by theophylline, a nonselective adenosine-receptor antagonist and DPCPX, an adenosine A1-receptor antagonist, but not ZM 241385, an adenosine A2A-receptor antagonist. These findings suggest that adenosine A1 receptors are involved in the analgesic mechanism activated by the forced walking stress.

Interleukin-1beta stimulates galectin-9 expression in human astrocytes.

Galectin-9 is an eosinophil chemoattractant produced by activated T lymphocytes. We have addressed expression of galectin-9 in normal human astrocytes in culture. Expression of galectin-9 mRNA and protein were examined by reverse transcription-polymerase chain reaction (RT-PCR), Western blotting, and immunofluorescent staining. Interleukin-1beta (IL-1beta) was found to enhance the galectin-9 expression in time- and concentration-dependent manners. Galectin-9 protein was detected in the membrane fraction, 105 000 x g precipitate, and immunofluorescent staining revealed diffuse cellular and perinuclear distributions. Dexamethasone pretreatment almost completely suppressed the production. We conclude that astrocytes produce galectin-9 in response to the stimulation with IL-1beta, and this may contribute to inflammatory reactions in the CNS.

Effect of calcium antagonists, calcium channel blockers and calmodulin inhibitors on the growth and encystation of Entamoeba histolytica and E. invadens.

The effects of calcium antagonists, calcium channel blockers, and calmodulin inhibitors on the growth of Entamoeba histolytica and the growth and encystation of Entamoeba invadens were examined. Calcium chelators ethyleneglycol bis (beta-aminoethyl ether)-N,N'-tetraacetate (EGTA) and ethylene-diaminetetraacetate (EDTA) inhibited the growth of both Entamoeba and also the encystation of E. invadens in a dose-dependent manner, with EDTA being more effective than EGTA. A putative antagonist of intracellular calcium flux, 8-(N,N-diethylamino) octyl-3,4,5-trimethoxybenzoate (TMB-8) also inhibited both growth and encystation, with the E. histolytica being more sensitive than E. invadens, and with the growth of E. invadens being more sensitive than encystation. The slow Na+-Ca2+ channel blockers bepridil and verapamil inhibited both growth and encystation. Bepridil was more effective than verapamil. The calmodulin (CaM) inhibitors, W-7 (N-(6-aminohexyl)-chloro-1-naphtalene sulphonamide) and trifluoperazine (TFP), were also inhibitory for both the growth and encystation; TFP was more effective than W-7, and encystation was more sensitive than growth in E. invadens. These results indicate that extracellular calcium ions, amebic intracellular calcium flux, calcium channels, and a CaM-dependent process contribute to the growth and encystation of Entamoeba.

Laparoscopic adhesiolysis for recurrent small bowel obstruction: long-term follow-up.

BACKGROUND: Recurrent small bowel obstruction caused by postoperative adhesions has traditionally been treated by conventional laparotomy, but laparoscopic management of acute small bowel obstruction has been reported. The aim of this study was to assess the long-term efficacy and clinical outcome of laparoscopic adhesiolysis for recurrent small bowel obstruction. METHODS: After conservative treatment, elective laparoscopic treatment was attempted in 17 patients hospitalized for recurrent small bowel obstruction after abdominal or pelvic surgery. RESULTS: Postoperative adhesions were identified laparoscopically in all patients. Laparoscopic treatment was possible in 14 patients (82.4%). Conversion to laparotomy was required for 3 patients (17.6%) because of intestinal perforation (n = 1) or a convoluted mass of adherent bowel (n = 2). Long-term follow-up was possible in 16 patients. Two recurrences of small bowel obstructions were noted over a mean follow-up period of 61.7 months. CONCLUSIONS: Laparoscopic adhesiolysis is a safe and effective treatment for recurrent small bowel obstruction. Conversion to laparotomy should be considered in patients with dense adhesions.

Q-angle influences tibiofemoral and patellofemoral kinematics.

Numerous surgical procedures have been developed to correct patellar tracking and improve patellofemoral symptoms by altering the Q-angle (the angle between the quadriceps load vector and the patellar tendon load vector). The influence of the Q-angle on knee kinematics has yet to be specifically quantified, however. In vitro knee simulation was performed to relate the Q-angle to tibiofemoral and patellofemoral kinematics. Six cadaver knees were tested by applying simulated hamstrings, quadriceps and hip loads to induce knee flexion. The knees were tested with a normal alignment, after increasing the Q-angle and after decreasing the Q-angle. Increasing the Q-angle significantly shifted the patella laterally from 20 degrees to 60 degrees of knee flexion, tilted the patella medially from 20 degrees to 80 degrees of flexion, and rotated the patella medially from 20 degrees to 50 degrees of flexion. Decreasing the Q-angle significantly tilted the patella laterally at 20 degrees and from 50 degrees to 80 degrees of flexion, rotated the tibia externally from 30 degrees to 60 degrees of flexion, and increased the tibiofemoral varus orientation from 40 degrees to 90 degrees of flexion. The results show that an increase in the Q-angle could lead to lateral patellar dislocation or increased lateral patellofemoral contact pressures. A Q-angle decrease may not shift the patella medially, but could increase the medial tibiofemoral contact pressure by increasing the varus orientation.

Soluble interleukin-6 receptor alpha inhibits the cytokine-Induced fractalkine/CX3CL1 expression in human vascular endothelial cells in culture.

Soluble form of IL-6 receptor alpha (sIL-6R) is known to serve as an agonist, without exogenous IL-6, on endothelial cells which do not express IL-6R but have only IL-6 receptor beta chain, gp130. We investigated the effect of sIL-6R on fractalkine expression in human umbilical vein endothelial cells (HUVECs) in culture. sIL-6R markedly inhibited HUVEC fractalkine/CX3CL1 expression induced by interleukin (IL)-1alpha, tumor necrosis factor (TNF)-alpha, or interferon (IFN)-gamma. IL-1alpha-induced fractalkine expression was inhibited by sIL-6R in time- and concentration-dependent manners. The experiment using actinomycin D indicated that sIL-6R lowered the stability of fractalkine mRNA. The inhibitory effect of sIL-6R was reversed by anti-gp130 neutralizing antibody. sIL-6R inhibited adhesion of mononuclear cells (MNCs) to HUVEC monolayers stimulated with IFN-gamma, but it did not inhibit the adhesion to monolayers stimulated with IL-1alpha. MNC chemotactic activity of conditioned medium of HUVEC stimulated with IL-1alpha or IFN-gamma was inhibited by co-treatment with sIL-6R. sIL-6R may play a regulatory role in immune responses by modulating the interaction between leukocytes and the vascular endothelium.