Region-specific DNA hydroxymethylation along the malignant progression of IDH-mutant gliomas

The majority of low-grade isocitrate dehydrogenase-mutant (IDHmt) gliomas undergo malignant progression (MP), but their underlying mechanism remains unclear. IDHmt gliomas exhibit global DNA methylation, and our previous report suggested that MP could be partly attributed to passive demethylation caused by accelerated cell cycles. However, during MP, there is also active demethylation mediated by ten-eleven translocation, such as DNA hydroxymethylation. Hydroxymethylation is reported to potentially contribute to gene expression regulation, but its role in MP remains under investigation. Therefore, we conducted a comprehensive analysis of hydroxymethylation during MP of IDHmt astrocytoma. Five primary/malignantly progressed IDHmt astrocytoma pairs were analyzed with oxidative bisulfite and the Infinium EPIC methylation array, detecting 5-hydroxymethyl cytosine at over 850,000 locations for region-specific hydroxymethylation assessment. Notably, we observed significant sharing of hydroxymethylated genomic regions during MP across the samples. Hydroxymethylated CpGs were enriched in open sea and intergenic regions (p < 0.001), and genes undergoing hydroxymethylation were significantly associated with cancer-related signaling pathways. RNA sequencing data integration identified 91 genes with significant positive/negative hydroxymethylation-expression correlations. Functional analysis suggested that positively correlated genes are involved in cell-cycle promotion, while negatively correlated ones are associated with antineoplastic functions. Analyses of The Cancer Genome Atlas clinical data on glioma were in line with these findings. Motif-enrichment analysis suggested the potential involvement of the transcription factor KLF4 in hydroxymethylation-based gene regulation. Our findings shed light on the significance of region-specific DNA hydroxymethylation in glioma MP and suggest its potential role in cancer-related gene expression and IDHmt glioma malignancy.

Transcriptomic and epigenetic dissection of spinal ependymoma (SP-EPN) identifies clinically relevant subtypes enriched for tumors with and without NF2 mutation

Ependymomas encompass multiple clinically relevant tumor types based on localization and molecular profiles. Tumors of the methylation class "spinal ependymoma" (SP-EPN) represent the most common intramedullary neoplasms in children and adults. However, their developmental origin is ill-defined, molecular data are scarce, and the potential heterogeneity within SP-EPN remains unexplored. The only known recurrent genetic events in SP-EPN are loss of chromosome 22q and NF2 mutations, but neither types and frequency of these alterations nor their clinical relevance have been described in a large, epigenetically defined series. Transcriptomic (n = 72), epigenetic (n = 225), genetic (n = 134), and clinical data (n = 112) were integrated for a detailed molecular overview on SP-EPN. Additionally, we mapped SP-EPN transcriptomes to developmental atlases of the developing and adult spinal cord to uncover potential developmental origins of these tumors. The integration of transcriptomic ependymoma data with single-cell atlases of the spinal cord revealed that SP-EPN display the highest similarities to mature adult ependymal cells. Unsupervised hierarchical clustering of transcriptomic data together with integrated analysis of methylation profiles identified two molecular SP-EPN subtypes. Subtype A tumors primarily carried previously known germline or sporadic NF2 mutations together with 22q loss (bi-allelic NF2 loss), resulting in decreased NF2 expression. Furthermore, they more often presented as multilocular disease and demonstrated a significantly reduced progression-free survival as compared to SP-EP subtype B. In contrast, subtype B predominantly contained samples without NF2 mutation detected in sequencing together with 22q loss (monoallelic NF2 loss). These tumors showed regular NF2 expression but more extensive global copy number alterations. Based on integrated molecular profiling of a large multi-center cohort, we identified two distinct SP-EPN subtypes with important implications for genetic counseling, patient surveillance, and drug development priorities.

EPEN-27. Epigenetic dissection of spinal ependymomas (SP-EPN) separates tumors with and withoutNF2 mutation

Ependymomas encompass multiple, clinically relevant tumor types based on localization, genetic alterations, and epigenetic and transcriptomic profiles. Tumors belonging to the methylation class of spinal ependymoma (SP-EPN) represent the most common intramedullary neoplasms in children and adults. However, molecular data of SP-EPN are scarce, and clear treatment recommendations are lacking. The only known recurrent genetic events in SP-EPN are loss of chromosome 22q and NF2 mutations. Yet, it remains unclear whether SP-EPN with germline or sporadic NF2 mutations or with NF2 wild type status differ clinically or molecularly. To provide a comprehensive molecular profile of SP-EPN, we integrated epigenetic, genomic, transcriptomic, and histological analyses of up to 237 cases. Clustering of methylation data revealed two distinct molecular SP-EPN subtypes. The distribution of NF2 mutated cases differed significantly across these subtypes (p <0.0001): The vast majority of tumors harboring either a previously known NF2 germline mutation or a sporadic mutation were assigned to subtypes A, whereas subtype B tumors mainly contained NF2 wild type sequences. In addition, subtype A tumors showed a lower frequency of MGMT promoter methylation (p= 0.018) and contained almost all pediatric patients of the cohort. Whole-exome sequencing (30 cases) identified numerous mutations in NF2 wild type and mutated tumors. Mutated genes in NF2 wild type tumors were enriched for genes associated with cell cycle and cytoskeleton. RNA sequencing revealed two distinct transcriptional groups with upregulation of proliferative genes in one group and upregulation of cilial genes in the other group. The molecular subtypes displayed subtle, but significant differences in the appearance of histopathological characteristics, such as surfaces, inflammation, and hyalinized vessels. Investigation of clinical parameters is ongoing and will complete the picture of SP-EPN heterogeneity as an important basis for future clinical decision-making.

High-power laser experiment forming a supercritical collisionless shock in a magnetized uniform plasma at rest

We present an experimental method to generate quasiperpendicular supercritical magnetized collisionless shocks. In our experiment, ambient nitrogen (N) plasma is at rest and well magnetized, and it has uniform mass density. The plasma is pushed by laser-driven ablation aluminum (Al) plasma. Streaked optical pyrometry and spatially resolved laser collective Thomson scattering clarify structures of plasma density and temperatures, which are compared with one-dimensional particle-in-cell simulations. It is indicated that just after the laser irradiation, the Al plasma is magnetized by a self-generated Biermann battery field, and the plasma slaps the incident N plasma. The compressed external field in the N plasma reflects N ions, leading to counterstreaming magnetized N flows. Namely, we identify the edge of the reflected N ions. Such interacting plasmas form a magnetized collisionless shock.

EPCO-01. MOLECULAR PROFILING OF SPINAL CORD EPENDYMOMA

BACKGROUND

Ependymomas are currently classified into 9 subgroups by DNA methylation profiles. Although spinal cord ependymoma (SP-EPN) is distinct from other tumors, diversity within SP-EPN is still unclear. Here, we used transcriptomic and epigenomic profiles to investigate the diversity among Japanese SP-EPN cases.

MATERIALS AND METHODS

We analyzed 57 SP-EPN patients (32 males and 25 females, aged from 18 to 78 years, median: 52), including two cases of neurofibromatosis type 2, five cases of grade 3 (WHO grade). We obtained transcriptome (RNA-seq) and DNA methylation (Infinium Methylation EPIC array) data from fresh frozen specimens of SP-EPN resected at the University of Tokyo Hospital and our collaborative groups.

RESULTS

Three cases had a previous intracranial ependymoma operation. Hierarchical clustering of the DNA methylation data showed that these three cases of intracranial origin as a different cluster from spinal origin. The 45 grade 2 spinal ependymoma showed a relatively homogenous methylation pattern. However, the methylation status of HOX gene cluster regions is compatible with the segment of origin, which reflects the cells of origins are derived after the determination of segment identity. RNA sequencing of 57 cases revealed two subgroups within grade 2. Gene ontology analysis of differentially expressed genes suggested the difference in metabolic state such as rRNA translation and mitochondrial respiration between the two expression subgroups.

CONCLUSION

Epigenetic analysis indicated the accurate body segment origin of SP-EPN. We observed that metabolic states could divide grade 2 spinal cord ependymoma into 2 subgroups and will present the relationship to clinicopathological information.

Genetic and epigenetic basis of hepatoblastoma diversity

Hepatoblastoma (HB) is the most common pediatric liver malignancy; however, hereditary predisposition and acquired molecular aberrations related to HB clinicopathological diversity are not well understood. Here, we perform an integrative genomic profiling of 163 pediatric liver tumors (154 HBs and nine hepatocellular carcinomas) based on the data acquired from a cohort study (JPLT-2). The total number of somatic mutations is precious low (0.52/Mb on exonic regions) but correlated with age at diagnosis. Telomerase reverse transcriptase (TERT) promoter mutations are prevalent in the tween HBs, selective in the transitional liver cell tumor (TLCT, > 8 years old). DNA methylation profiling reveals that classical HBs are characterized by the specific hypomethylated enhancers, which are enriched with binding sites for ASCL2, a regulatory transcription factor for definitive endoderm in Wnt-pathway. Prolonged upregulation of ASCL2, as well as fetal-liver-like methylation patterns of IGF2 promoters, suggests their "cell of origin" derived from the premature hepatoblast, similar to intestinal epithelial cells, which are highly proliferative. Systematic molecular profiling of HB is a promising approach for understanding the epigenetic drivers of hepatoblast carcinogenesis and deriving clues for risk stratification.

PATH-33. EPIGENOMIC ANALYSIS OF SPINAL EPENDYMOMA

BACKGROUND

Ependymomas commonly occur in the fourth ventricle and the spinal cord. Gross total resection, age and WHO grade are known prognostic factors. Ependymomas are currently classified into 9 distinct subgroups by DNA methylation profile analysis. Spinal cord ependymoma is distinct from other subgroups. To investigate heterogeneity within spinal cord ependymoma, we examined DNA methylation profiles.

MATERIALS AND METHODS

We used Infinium MethylationEPIC array (illumina) to obtain DNA methylation data from frozen specimens of spinal ependymoma resected at the University of Tokyo, Osaka City University, and Tokyo Metropolitan Neurological Hospital. Japan Pediatric Molecular Neuro-Oncology Group provided methylation data for 11 reported cases. Cluster analysis was performed using Cluster3.0.

RESULTS

We analyzed 34 patients, 21 male and 13 female, aged from 18 to 76 years (median 50.5 years), including 2 cases with neurofibromatosis type 2. WHO grade was grade_3 in 2 cases and grade_2 in others. Clustering of the DNA methylation data showed that WHO grade_3 cases tended to be classified into a subgroup distinct from other cases.

CONCLUSION

This is the largest DNA methylation profiling study on spinal cord ependymoma to date. The study may suggest a new subgroup correlated with higher WHO grade.

A novel sensitive detection method for DNA methylation in circulating free DNA of pancreatic cancer

Despite recent advances in clinical treatment, pancreatic cancer remains a highly lethal malignancy. In order to improve the survival rate of patients with pancreatic cancer, the development of non-invasive diagnostic methods using effective biomarkers is urgently needed. Here, we developed a highly sensitive method to detect DNA methylation in cell-free (cf)DNA samples based on the enrichment of methyl-CpG binding (MBD) protein coupled with a digital PCR method (MBD–ddPCR). Five DNA methylation markers for the diagnosis of pancreatic cancer were identified through DNA methylation microarray analysis in 37 pancreatic cancers. The sensitivity and specificity of the five markers were validated in another independent cohort of pancreatic cancers (100% and 100%, respectively; n = 46) as well as in The Cancer Genome Atlas data set (96% and 90%, respectively; n = 137). MBD–ddPCR analysis revealed that DNA methylation in at least one of the five markers was detected in 23 (49%) samples of cfDNA from 47 patients with pancreatic cancer. Further, a combination of DNA methylation markers and the KRAS mutation status improved the diagnostic capability of this method (sensitivity and specificity, 68% and 86%, respectively). Genome-wide MBD-sequencing analysis in cancer tissues and corresponding cfDNA revealed that more than 80% of methylated regions were overlapping; DNA methylation profiles of cancerous tissues and cfDNA significantly correlated with each other (R = 0.97). Our data indicate that newly developed MBD–ddPCR is a sensitive method to detect cfDNA methylation and that using five marker genes plus KRAS mutations may be useful for the detection of pancreatic cancers.

Defined lifestyle and germline factors predispose Asian populations to gastric cancer

Germline and environmental effects on the development of gastric cancers (GC) and their ethnic differences have been poorly understood. Here, we performed genomic-scale trans-ethnic analysis of 531 GCs (319 Asian and 212 non-Asians). There was one distinct GC subclass with clear alcohol-associated mutation signature and strong Asian specificity, almost all of which were attributable to alcohol intake behavior, smoking habit, and Asian-specific defective ALDH2 allele. Alcohol-related GCs have low mutation burden and characteristic immunological profiles. In addition, we found frequent (7.4%) germline CDH1 variants among Japanese GCs, most of which were attributed to a few recurrent single-nucleotide variants shared by Japanese and Koreans, suggesting the existence of common ancestral events among East Asians. Specifically, approximately one-fifth of diffuse-type GCs were attributable to the combination of alcohol intake and defective ALDH2 allele or to CDH1 variants. These results revealed uncharacterized impacts of germline variants and lifestyles in the high incidence areas.

Disturbance of the Front Region of Magnetic Reconnection Outflow Jets due to the Lower-Hybrid Drift Instability

A 3D fully kinetic simulation shows that the lower-hybrid drift instability disturbs the front of magnetic reconnection outflow jets and additionally causes energy dissipation. The result is very consistent with a disturbance observed at the dipolarization front (DF) in Earth's magnetotail by the Magnetospheric Multiscale (MMS) mission. A fully kinetic dispersion relation solver, validated by the MMS observations, further predicts that the disturbance of the reconnection jet front could occur over different parameter regimes in space plasmas including Earth's DF and solar flares.

Base-Resolution Analysis of 5-Hydroxymethylcytosine by One-Pot Bisulfite-Free Chemical Conversion with Peroxotungstate

5-Hydroxymethylcytosine (^hmC) is an essential intermediate in the active DNA demethylation pathway. Here we report a new base-resolution method for measuring ^hmC by combining peroxotungstate-mediated oxidation and sequencing analysis. We reveal that an oxidized product of ^hmC, trihydroxylated thymine (^thT), tolerated the incorporation of dATP as a substrate in the process of DNA polymerase elongation. By comparing the results of Sanger sequencing before and after the oxidation, we observed that ^hmC sites on single-stranded DNAs could be discriminated from unmethylated cytosines. We found that a thermal cycle condition during peroxotungstate treatment enhanced the oxidation reaction of ^hmC in double-stranded DNA. Furthermore, Illumina sequencing analysis of ^hmC-containing synthetic genome fragments enabled us to identify simultaneously the positions of ^hmC in base resolution. This bisulfite-free simple ^hmC detection technique could facilitate the acquisition of epigenomic information.

Erratum: Intracellular amyloid β oligomers impair organelle transport and induce dendritic spine loss in primary neurons

The original version of this article unfortunately contained a mistake in the presentation of Fig. 1 in both the PDF and HTML versions of this manuscript [1]. In the right panel of the corrected Fig. 1d, the images of Mock cells, which were visualized with GFP and stained with Abeta oligomer-specific antibody 11A1, were replaced with those of APPWT cells, and instead the images of APPWT cells were replaced with those of Mock cells. These images had been incorrectly placed in the original Fig. 1. The correct version of Fig. 1 is presented below.

A silicon carbide room-temperature single-photon source

Over the past few years, single-photon generation has been realized in numerous systems: single molecules, quantum dots, diamond colour centres and others. The generation and detection of single photons play a central role in the experimental foundation of quantum mechanics and measurement theory. An efficient and high-quality single-photon source is needed to implement quantum key distribution, quantum repeaters and photonic quantum information processing. Here we report the identification and formation of ultrabright, room-temperature, photostable single-photon sources in a device-friendly material, silicon carbide (SiC). The source is composed of an intrinsic defect, known as the carbon antisite-vacancy pair, created by carefully optimized electron irradiation and annealing of ultrapure SiC. An extreme brightness (2×10(6) counts s(-1)) resulting from polarization rules and a high quantum efficiency is obtained in the bulk without resorting to the use of a cavity or plasmonic structure. This may benefit future integrated quantum photonic devices.

Early and late outcomes of inflammatory abdominal aortic aneurysms: comparison with the outcomes after open surgical and endovascular aneurysm repair in literature reviews

AIM

The aim of this study was to analyze the clinical characteristics, operative management and early and late outcomes of Inflammatory abdominal aortic aneurysms (IAAAs) in our vascular service, retrospectively and to compare with the outcomes of open and endovascular aneurysm repair (EVAR) in the patients with IAAAs in literature reviews.

METHODS

Between January 1990 and December 2011, this series included twenty-four patients with IAAAs who underwent surgical treatment. The mean length of follow-up was 37.6 months (range 3-108). Kaplan-Meier life tables were used to calculate survival rate.

RESULTS

Fifteen patients (60%) were symptomatic including 3 patients with hydronephrosis. Seven patients with severe symptoms underwent emergency operations. Twenty four patients underwent open surgical AAA repair. The 30 - day mortality rates were 0%. All patients had successful post operative courses and followed as outpatients in an elective situation. The ten year cumulative survival rate was 70%. The early and late mortality was the same for open repair compared to non-inflammatory AAA.

CONCLUSIONS

IAAA compared with non-IAAA is associated with a higher incidence of preoperative morbidity, however operative mortality rates are lower. EVAR has lower early operative mortality rates, however, there are some problems such as remaining periaortic fibrosis and hydronephrosis in approximately half of IAAA patients after EVAR.

Morphological and topological transformation of membrane vesicles

Liposomes are micro-compartments made of lipid bilayer membranes withcharacteristics quite similar to those of biological membranes. To formartificial cell-like structures, we generated liposomes that containedsubunit proteins of cytoskeletons: tubulin or actin. Spherical liposomeswere transformed into bipolar or cell-like shapes by mechanical forcesgenerated by the polymerization of encapsulated subunits of microtubules.Disk- or dumbbell-shaped liposomes were developed by the polymerizationof encapsulated actin. Dynamic processes of morphological transformationsof liposomes were visualized by high intensity dark-field lightmicroscopy.Topological changes, such as fusion and division of membrane vesicles,play an essential role in cellular activities. To investigate themechanism of these processes, we visualized in real time the liposomesundergoing topological transformation. A variety of novel topologicaltransformations were found, including the opening-up of liposomes and thedirect expulsion of inner vesicles.

Abstract P1-15-11: The Kampo medicine Goshajinkigan prevents docetaxel-related peripheral neuropathy in breast cancer patients

Background: Although taxanes have become a key chemotherapeutic drug in breast cancer treatment. Taxanes inhibit the growth of cancer cells by disrupting the functioning of their microtubules; however, the microtubules of nerve cells are also affected by this process, which can cause neurological disorders. The Kampo medicine Goshajinkigan (GJG) is a traditional Japanese medicine that is used for the treatment of several neurological symptoms including pain and numbness, GJG is comprised of 10 herbs, each of which contains numerous active ingredients. Recently, GJG has been reported to prevent anticancer drug-induced peripheral neuropathy in colorectal cancer. We performed the present prospective randomized study to confirm the effects of GJG and mecobalamin (B12) against docetaxel (DOC)-associated peripheral neurotoxicity in breast cancer patients.

Patients and method: Between May 2007 and April 2011, 60 breast cancer patients were treated with DOC. Thirty-three patients (GJG group) received oral administration of 7.5 g/day GJG and 27 patients (B12 group) received oral administration of 1500 μg/day B12. The patients were treated with TC (75mg/m2 docetaxel and 600 mg/m2 cyclophosphamide) every 3 weeks for 4 cycles, docetaxel alone (100mg/m2) every 3 weeks for 4 cycles, and XT (900mg/m2 capecitabine administered orally twice a day on days 1–14 plus 60 mg/m2 docetaxel) every 3 weeks for 6 cycles. Peripheral neuropathy was evaluated during every course according to DEB-NTC (Neurotoxicity Criteria of Debiopharm), Common Terminology Criteria for Adverse Events (NCI-CTC) ver.3.0, and a visual analogue scale (VAS).

Results: The median age of the GJG group was 58 years old (35 to 70 years old), the B12 group was 55 years old (33 to 69 years old), and they were all females. For the regimens, in the GJG group, TC, DOC only, and XT were administered in 19 cases, 13 cases and 1 case, respectively. In the B12 group, they were 15 cases, 11 cases and 12 cases, respectively. The cumulative dose of DOC was 338.5 mg/m2 in the GJG group, and 340 mg/m2 in the B12 group. Peripheral neuropathy occurred significantly less frequently in the GJG group (39.3%) than the B12 group (88.9%) (p &lt; 0.01). In the GJG group, grade 1 DEB-NTC was observed in 2 cases, grade 2 in 5 cases and grade 3 in 5 cases. Grade 1 NCI-CTC was observed in 7 cases, grade 2 in 6 cases. In the B12 group, grades 1, 2 and 3 DEB-NTC were observed in one case, 12 cases and 12 cases, respectively; and grades 1, 2 and 3 NCI-CTC were observed in 11 cases, 12 cases and one case. The mean VAS scores for numbness after chemotherapy were 2.7 in the GJG group and 4.9 in the B12 group (p &lt; 0.01). The incidence of grade 2/3 peripheral neuropathy was lower in the GJG group than the B12 group. Peripheral neuropathy was significantly controlled in the GJG group.

Conclusion: The present study is the first prospective control study to prove the efficacy of GJG against docetaxel-induced peripheral neuropathy in breast cancer patients. Our findings suggest that DOC-associated peripheral neurotoxicity can be suppressed by the administration of GJG. It will be necessary to confirm the usefulness of GJG in larger prospective studies.

Citation Information: Cancer Res 2012;72(24 Suppl):Abstract nr P1-15-11.

Negative-U system of carbon vacancy in 4H-SiC

Using electron paramagnetic resonance (EPR), energy levels of the carbon vacancy (V(C)) in 4H-SiC and its negative-U properties have been determined. Combining EPR and deep-level transient spectroscopy we show that the two most common defects in as-grown 4H-SiC--the Z(1/2) lifetime-limiting defect and the EH(7) deep defect--are related to the double acceptor (2-|0) and single donor (0|+) levels of V(C), respectively.

The unique correlation between anti-mutagenicity of human saliva and change in body weight

The purpose of this study was to investigate the effect of weight reduction on the anti-mutagenicity of human saliva. Subjects were 16 male college judo players. The anti-mutagenicity of the saliva was measured using the umu test. There was an inhibiting effect of the saliva on the mutagenicity of AF-2. However, a modifying effect of the saliva on Trp-P-1 was not observed. On the day before a competition and 7 days after the competition, the inhibiting capacity of the saliva for the mutagenicity of AF-2 decreased and increased in two non-weight reduction and two weight reduction groups, respectively.However, on the day before the competition, the changed body weights (r=-0.77, p<0.01) and BMI (r=-0.77, p<0.01) were significantly correlated with that of the inhibiting capacity of the saliva for the mutagenicity of AF-2. In addition, the BMI at 20 days before the competition was not significantly but markedly correlated with it (r=0.50, p=0.057). At 7 days after the competition, however, these correlations were not found.These findings suggest a unique correlation between the anti-mutagenicity of human saliva and body weight or BMI.

Changes in physical characteristics, hematological parameters and nutrients and food intake during weight reduction in judoists

We studied changes in physical characteristics: body composition; muscle and physical strength; hematological parameters; and nutrients and food intake in 22 male college judoists who were losing weight purposefully. Nutritional parameters in blood, such as triglycerides, decreased immediately before matches and rebounded after matches. Free fatty acid increased before matches and returned to previous levels 10 days after matches. IgM and complements decreased before matches and did not return to previous levels even 10 days after matches. These changes were noted in the marked weight reduction group (weight lost / body weight before weight reduction, weight reduction rate≥6%). In contrast, creatine kinase increased before matches in the slight and moderate weight reduction groups (weight reduction rate< 3%, 3≤and<6%, respectively). The marked weight reduction group showed no changes in creatine kinase, however, indicating inadequate exercise due to excessive weight reduction. Muscle strength (grip) and nutrients and food intake decreased significantly before matches. These changes were noted in the marked weight reduction group. These findings suggested that a weight reduction rate of 6% or more adversely affected the performance and health of the judoist.

Comparison between chest digital tomosynthesis and CT as a screening method to detect artificial pulmonary nodules: a phantom study

OBJECTIVES

The objective of this study was to evaluate the imaging capabilities of chest digital tomosynthesis (DT) as a screening method for the detection of artificial pulmonary nodules, and to compare its efficiency with that of CT.

METHODS

DT and CT were used to detect artificial pulmonary nodules (5 mm and 8 mm in diameter, ground-glass opacities) placed in a chest phantom. Using a three-dimensional filtered back-projection algorithm at acquisition angles of 8°, 20°, 30° and 40°, DT images of the desired layer thicknesses were reconstructed from the image data acquired during a single tomographic scan. Both standard and sharp CT reconstruction kernels were used, and the detectability index (DI) valves computed for both the DT scan acquisition angles and CT reconstruction kernel types were considered. For the observer study, we examined 50 samples of artificial pulmonary nodules using both DT and CT imaging. On the basis of evaluations made by five thoracic radiologists, a jackknife free-response receiver operating characteristic (JAFROC) study was performed to compare and assess the differences in detection accuracy between CT and DT imaging.

RESULTS

For each increased acquisition angle, DI obtained by DT imaging was similar to that obtained by CT imaging. The difference in the observer-averaged JAFROC figure of merit for the five readings was 0.0363 (95% confidence interval: -0.18, 0.26; F=0.101; p=0.75).

CONCLUSION

With the advantages of a decreased radiation dose and the practical accessibility of examination, DT may be a useful alternative to CT for the detection of artificial pulmonary nodules.

Hybrid quantum circuit with a superconducting qubit coupled to a spin ensemble

We report the experimental realization of a hybrid quantum circuit combining a superconducting qubit and an ensemble of electronic spins. The qubit, of the transmon type, is coherently coupled to the spin ensemble consisting of nitrogen-vacancy centers in a diamond crystal via a frequency-tunable superconducting resonator acting as a quantum bus. Using this circuit, we prepare a superposition of the qubit states that we store into collective excitations of the spin ensemble and retrieve back into the qubit later on. These results constitute a proof of concept of spin-ensemble based quantum memory for superconducting qubits.

Preparation of YBa2Cu3O7-δ Superconductor by Sol-Gel Method and Fiber Drawing

Superconducting YBa2Cu3O7-δ, ceramic pieces and fibers were prepared through a sol-gel route from ametal acetate aqueous solution of controlled pH. Concentrating the starting solution by evaporating the solvent provided a transparent viscous sol, from which gel fibers could be drawn. Further concentrating of the viscous solution led to formation of gel pieces. Conversion of gel fibers and pieces to superconductors were investigated in terms of precipitating crystalline species and electrical conductivities.

Knee osteoarthritis, knee joint pain and aging in relation to increasing serum hyaluronan level in the Japanese population

OBJECTIVE

To investigate relationship between serum hyaluronan (HA) level and the presence and severity of radiographic knee osteoarthritis (OA) as well as degree of knee pain in Japanese population.

DESIGN

A total of 616 volunteers participated in this study. Based on the Kellgren-Lawrence (K-L) grade, participants were radiographically classified into three groups: Normal (K-L grade 0 or 1), Moderate (grade 2) and Severe (grade 3 or 4). The degree of knee pain was quantified by visual analogue scale (VAS) and Knee injury and Osteoarthritis Outcome Score (KOOS) Pain. Serum HA levels were compared among the Normal, Moderate and Severe groups, and the relationship between serum HA level and the severity of knee OA was analyzed after age, sex and body mass index (BMI) were adjusted. In addition, the correlation between serum HA level and the degree of knee pain was analyzed in each group.

RESULTS

Regarding relationship between serum HA level and the severity of radiographic knee OA, serum HA levels of the Moderate and Severe groups were significantly higher than in the Normal group (P<0.001). Furthermore, serum HA level correlated with the severity of radiographic knee OA (r=0.289, P<0.001) after adjusting for age, sex and BMI. Serum HA level correlated with VAS of knee pain and/or KOOS Pain in the Normal and Moderate groups.

CONCLUSION

Serum HA level has the potential to be useful for the diagnosis of the presence and severity of knee OA.

First-principles study of blue silicate phosphors

First-principles calculations were performed to investigate the optical property of blue silicate phosphor, CMS:Eu. The optical absorption property is discussed based on electronic band structure and density of states. Our calculation results indicate that hybridization of the wavefunction plays an important role for nonradiative migration of electrons and holes. The calculated optical absorption spectrum could reproduce the optical features of the experimental excitation spectrum. It is also demonstrated that a practical approach using computational materials screening is effective in phosphor materials development.

Population-genetic nature of copy number variations in the human genome

Copy number variations (CNVs) are universal genetic variations, and their association with disease has been increasingly recognized. We designed high-density microarrays for CNVs, and detected 3000–4000 CNVs (4–6% of the genomic sequence) per population that included CNVs previously missed because of smaller sizes and residing in segmental duplications. The patterns of CNVs across individuals were surprisingly simple at the kilo-base scale, suggesting the applicability of a simple genetic analysis for these genetic loci. We utilized the probabilistic theory to determine integer copy numbers of CNVs and employed a recently developed phasing tool to estimate the population frequencies of integer copy number alleles and CNV–SNP haplotypes. The results showed a tendency toward a lower frequency of CNV alleles and that most of our CNVs were explained only by zero-, one- and two-copy alleles. Using the estimated population frequencies, we found several CNV regions with exceptionally high population differentiation. Investigation of CNV–SNP linkage disequilibrium (LD) for 500–900 bi- and multi-allelic CNVs per population revealed that previous conflicting reports on bi-allelic LD were unexpectedly consistent and explained by an LD increase correlated with deletion-allele frequencies. Typically, the bi-allelic LD was lower than SNP–SNP LD, whereas the multi-allelic LD was somewhat stronger than the bi-allelic LD. After further investigation of tag SNPs for CNVs, we conclude that the customary tagging strategy for disease association studies can be applicable for common deletion CNVs, but direct interrogation is needed for other types of CNVs.

Detection and Separation of Two Kinds of Acidic Arginine Amidases from Boar Sperm Using Lima Bean Trypsin Inhibitor and Aprotinin Affinity Adsorptions

Two kinds of acidic arginine amidase activity were found in boar sperm. One enzyme was separated by a treatment consisting of lima bean trypsin inhibitor (LBTI) affinity adsorption and elution. The other enzyme was separated by aprotinin affinity adsorption and elution through the same solutions as those used for first enzyme; the two enzymes provisionally named boar sperm acidic arginine amidases 1 (BSAA-1) and 2 (BSAA-2), respectively. The amidolytic activity of BSAA-1 was increased by high concentrations of calcium chloride, while the activity of BSAA-2 was independent of calcium chloride. Their behavior with LBTI and aprotinin, and profiles of their substrate specificities, were also different. The affinity of LBTI to BSAA-1 was approximately 14 times higher than that to BSAA-2.

Effect of Sample Collection Site on Semen Parameters of Healthy Young Volunteers

The effect of sample collection site on semen parameters in ten men aged between 22 and 24 years was investigated. Sperm was collected at two sites: in a university hospital restroom for general use and in a one-person hospital room. Samples were collected from the same individual twice, with an interval of two weeks between collections. Semen parameters for the two sites were compared. Samples were collected after a minimum of three days and not longer than seven days of sexual abstinence. Sperm concentration did not differ significantly between the university hospital restroom location (86.8 +/- 25.4 x 10(6)/ml; mean +/- standard deviation) and the private hospital room (97.1 +/- 72.0 x 10(6)/ml). There was no difference in the total motile sperm count or daily sperm production between the collection sites. These results suggest that the collection site has little effect on semen parameters.

INDIVIDUAL VARIATION IN SEMEN PARAMETERS OF HEALTHY YOUNG VOLUNTEERS

Individual variation in semen parameters was investigated in healthy young volunteers. Semen samples were collected approximately once a month over a one-year period for a total of 93 samples (5 to 10 samples per subject) from 12 volunteers in their twenties. Semen analysis was carried out according to the WHO Manual. The amount of variation in each semen variable was calculated for each subject by dividing the maximum value by the minimum value. The results showed that the semen volume varied by 1.9+/-0.8 fold (1.3 to 4.2 fold), the sperm concentration by 4.8+/-4.3 fold (1.5 to 17.2 fold), the percentage of sperm with forward progression by 2.8+/-1.4 fold (1.6 to 6.4 fold), the percentage of sperm with rapid linear progression by 3.4+/-2.6 fold (1.7 to 10.9 fold), the percentage of sperm with normal morphology by 1.9+/-0.4 fold (1.3 to 2.4 fold), and the percentage of live sperm by 1.5+/-0.4 fold (1.1 to 2.6 fold). A between-group comparison showed significant differences in all of the variables except the percentage of sperm with normal morphology. These results suggest multiple and considerable semen analyses are needed when evaluating semen parameters.

Feasibility and toxicity of docetaxel before or after fluorouracil, epirubicin, and cyclophosphamide as adjuvant chemotherapy for early-stage breast cancer

604

Background: As adjuvant chemotherapy for breast cancer, the addition of docetaxel to regimens containing anthracyline has been shown to be effective. However, tolerance and safety associated with the administration order of the two drugs have not been evaluated. Methods: Breast cancer patients with node-positive or high-risk patients with node-negative were eligible. The treatment completion rate and toxicity were evaluated in 2 arms who underwent a total of 6 courses of the following regimens: Arm A: 3 courses of fluorouracil 500 mg/m2, epirubicin 100 mg/m2 and cyclophosphamide 500 mg/m2 (FEC100: q3w) followed by 3 courses of docetaxel (DOC100: 100 mg/m2, q3w); and Arm B: 3 courses of DOC100 (q3w) followed by 3 courses of FEC100 (q3w). Results: June 2006 to April 2008, 42 patients were registered. To the present, analysis has been completed in 21 patients in arm A and 21 in arm B. The mean age of patients was 49.1 years and 53.8 years, respectively. In arm A, the stage of cancer was 1 in 4 patients, 2a in 10, and 2b in 7, in arm B, the stage of cancer was 1 in 3 patients, 2a in 9, and 2b in 9. The adjuvant chemotherapy completion rate was 100 % for arm A and 95.2 % for arm B. The relative dose intensity (RDI) was 94.2 % for FEC100 and 97.8 % for DOC100 in arm A, and 98.9 % for DOC100 and 95.2 % for FEC100 in arm B. In arm A, grade 3 or higher hematological toxicity was observed in 9 patients, and febrile neutropenia developed in 3 patients with FEC100. In arm B, grade 3 or higher hematological toxicity was observed in 7 patients, but febrile neutropenia was not noted in any patients. Grade 3 or higher non-hematological toxicity was observed with FEC100 in 2 patients each in the two arms. Grade 1 or 2 edema developed in 11 patients with DOC100 in the two arms. Conclusions: In both arm A and B, adverse events associated with FEC100 were frequently observed but spontaneously recovered, or adequate management was possible by supportive therapy. Adverse events associated with DOC100 were mild. The regimens in both arms A and B were safe regarding adjuvant chemotherapy for early stage breast cancer. However, DOC100 followed by FEC100 may be more tolerable and effective.

No significant financial relationships to disclose.

The oro-ileal transit of cellulose

The effects of cellulose and the interindividual variations on the transit time in the small intestine remain unclear, but no previous study has to date taken these factors into sufficient consideration. We assessed the oro-ileal transit time and the recovery percentage of cellulose in the terminal ileum looking at interindividual variations. Seven healthy males received 100 mL of a dietary fiber-free basal diet with 5 g cellulose and 5 g of polyethylene glycol 4000. The ileal contents were aspirated every 30 min via an experimental tube placed in the terminal ileum to assess the oro-ileal transit time and the recovery percentage of cellulose. The mean percentage (with standard deviation) of the amounts of cellulose collected in the terminal ileum was 98.4%+/- 16.5% (ranging from 67.4% to 114.5%) with a coefficient variation of 16.8%. The average times (in hours) taken for 20%, 40%, 60%, and 80% of cellulose to reach the terminal ileum were 5.5 +/- 1.1, 6.7 +/- 0.7, 8.5 +/- 1.3, and 8.8 +/- 1.2, respectively, with large interindividual variations. In conclusion, the averaged recovery percentage of cellulose in the terminal ileum was approximately 100%, in accordance with the present generally accepted definition of dietary fiber. However, there were large interindividual variations in the oro-ileal transit time and the percentage of cellulose recovered.

Effects of long-term training on neutrophil function in male university judoists

OBJECTIVES

To clarify the effects of high-intensity and high-frequency long-term/chronic training on neutrophil function and serum levels of myogenic enzymes in male university judoists.

METHODS

The subjects were 24 male judoists who had stopped judo training for 6 months and then restarted their training. The following parameters were examined before and after a 2 h unified exercise loading (UEL) at the beginning of the restarted quotidian training (pre-training) and at 2 months, 4 months and 6 months thereafter: myogenic enzymes, neutrophil and leucocyte counts, and neutrophil phagocytic activity (PA) and oxidative burst activity as a measure of reactive oxygen species (ROS) production capability.

RESULTS

Myogenic enzymes that were measured after UEL at all four points significantly increased except for creatine kinase at the 2-month point (p<0.01 in each) and neutrophil counts significantly increased after UEL at the pre-training, 2-month and 4-month points (p<0.01 in each), but these changes became smaller from the 2-month point. PA significantly decreased after UEL at the pre-training and 2-month points (p<0.01 in each), but no change was seen at the 4-month and 6-month points. On the other hand, no change in ROS production per cell after UEL was seen at the pre-training point, but it significantly increased after UEL at the 2-month, 4-month and 6-month points (p<0.01 in each).

CONCLUSION

The changing rate of the levels of UEL-mediated myogenic enzymes, neutrophil mobilisation and neutrophil function was seen to decrease at the 2-month, 4-month and 6-month assessments, compared with the pre-training point: these may comprise at least some of the long-term training effects.

Effects of rugby sevens matches on human neutrophil-related non-specific immunity

AIMS

To evaluate the influences of the accumulative effect of two consecutive rugby sevens matches (Sevens) on aspects of human neutrophil-related non-specific immunity.

METHODS

In seven players participating in the Japan Sevens, neutrophil reactive oxygen species (ROS) production capability and phagocytic activity were measured using flow cytometry, and serum opsonic activity (SOA) was assessed by measuring neutrophil ROS using the peak height of lucigenin-dependent chemiluminescence before and after two consecutive matches.

RESULTS

ROS showed no change immediately after the first match, and had significantly (P<0.05) increased 4 h later, but showed a decrease after the second match. Phagocytic activity showed no change immediately after the first match, but had significantly (P<0.01) decreased 4 h later, and showed a further decrease after the second match, although it was not significant. SOA significantly (P<0.01) increased after the first match, and still maintained its high 4 h later, but decreased after the second match. ROS production capability, phagocytic activity and SOA significantly (P<0.01) decreased after the second match.

CONCLUSIONS

When rugby players play two consecutive Sevens matches, the exercise loading is thought to be hard, similar to that experienced during a marathon race and intensive or long training in a training camp, although the expected changes were not seen after the first match. Differences between after the first and the second matches may be due to the "cumulative effect".

The coalescence time of sampled genes in the structured coalescent model

The aim of this article is to investigate the distribution of the coalescence time (T) for sampled genes in the structured coalescent. We obtain some exact solutions for small samples and approximate distributions for n sampled genes in strong and weak migration. We also conduct computer simulation to evaluate efficiencies of these approximations and show the dependency of the distribution of the coalescence time on the geographical structure and the intensity of migration. In a panmictic population, we prove that the conditional distribution of the coalescence time given the number of segregating sites (S) among sampled genes is given by the weighted mean of the convolution of gamma distributions. We also study the joint distribution of T and S in the structured coalescent model and show some exact solutions.

Tracer clearance in radionuclide cisternography in patients with spontaneous intracranial hypotension

We semiquantitatively analysed radionuclide cisternography in three patients with spontaneous cerebrospinal fluid (CSF) leakage diagnosed by typical symptoms and magnetic resonance imaging findings before and several months after treatment with epidural blood patch. Radioactivity in the whole CSF space was measured immediately after and at 1, 5, 7 and 24 h after intrathecal injection of (111)In-diethylenetriaminepentaacetic acid (DTPA). Initial findings included the vague appearance of leakage in the thoracic spine in two patients, early bladder filling at 1 h in one and a lack of tracer filling into the high cranial convexity in all three. The radioactivity count rapidly decreased within several hours after injection and reached 20% of the initial value at 24 h. In contrast, no rapid decrease was observed after treatment and more than 50% of tracer remained at 24 h after injection. Semiquantitative analysis of tracer clearance may provide additional information in the diagnosis of CSF leakage, especially with no obvious qualitative findings.

Weight loss effect of dietary diacylglycerol in obese dogs

Obesity in dogs and cats have been increasingly recognized in recent years. Because obesity underlies various diseases, pet owners and veterinarians have an important responsibility to help animals lose weight and maintain their health. Diet therapy, however, is typically based on limited calorie intake and animals may suffer stress from hunger and this is also a concern to animal owners. For this reason, many clients drop out of weight control programmes. In the present study, we focused on dietary diacylglycerol (DAG) as a potentially effective ingredient for canine weight control without caloric restriction. We replaced a portion of the fat in dog food with either DAG or triacylglycerol (TAG), referred to as DAG or TAG diets here, and fed overweight beagle dogs (body condition score of 4 or higher) with either the DAG or TAG diet for a 6-week period. Results indicated that, even though the food composition other than fat type were identical, dogs fed the DAG diet showed a statistically significant reduction in body weight averaging a 2.3% reduction within 6 weeks while the TAG-fed dogs maintained their obese body weights. In addition, the DAG group also showed a reduction in body fat content, serum triglyceride and total cholesterol concentrations. These results suggest the possibility of developing a pet food using DAG to control weight and serum lipid levels without compromising caloric intake.

Identification of the carbon antisite-vacancy pair in 4H-SiC

The metastability of vacancies was theoretically predicted for several compound semiconductors alongside their transformation into the antisite-vacancy pair counterpart; however, no experiment to date has unambiguously confirmed the existence of antisite-vacancy pairs. Using electron paramagnetic resonance and first principles calculations we identify the S15 center as the carbon antisite-vacancy pair in the negative charge state (C(Si)V-(C)) in 4H-SiC. We suggest that this defect is a strong carrier-compensating center in n-type or high-purity semi-insulating SiC.

Divacancy in 4H-SiC

Electron paramagnetic resonance and ab initio supercell calculations suggest that the P6/P7 centers, which were previously assigned to the photoexcited triplet states of the carbon vacancy-antisite pairs in the double positive charge state, are related to the triplet ground states of the neutral divacancy. The spin density is found to be located mainly on three nearest C neighbors of the silicon vacancy, whereas it is negligible on the nearest Si neighbors of the carbon vacancy.