All-sky LIGO search for periodic gravitational waves in the early fifth-science-run data

We report on an all-sky search with the LIGO detectors for periodic gravitational waves in the frequency range 50-1100 Hz and with the frequency's time derivative in the range -5 x 10{-9}-0 Hz s{-1}. Data from the first eight months of the fifth LIGO science run (S5) have been used in this search, which is based on a semicoherent method (PowerFlux) of summing strain power. Observing no evidence of periodic gravitational radiation, we report 95% confidence-level upper limits on radiation emitted by any unknown isolated rotating neutron stars within the search range. Strain limits below 10{-24} are obtained over a 200-Hz band, and the sensitivity improvement over previous searches increases the spatial volume sampled by an average factor of about 100 over the entire search band. For a neutron star with nominal equatorial ellipticity of 10{-6}, the search is sensitive to distances as great as 500 pc.

All-sky LIGO search for periodic gravitational waves in the early fifth-science-run data

We report on an all-sky search with the LIGO detectors for periodic gravitational waves in the frequency range 50-1100 Hz and with the frequency's time derivative in the range -5 x 10{-9}-0 Hz s{-1}. Data from the first eight months of the fifth LIGO science run (S5) have been used in this search, which is based on a semicoherent method (PowerFlux) of summing strain power. Observing no evidence of periodic gravitational radiation, we report 95% confidence-level upper limits on radiation emitted by any unknown isolated rotating neutron stars within the search range. Strain limits below 10{-24} are obtained over a 200-Hz band, and the sensitivity improvement over previous searches increases the spatial volume sampled by an average factor of about 100 over the entire search band. For a neutron star with nominal equatorial ellipticity of 10{-6}, the search is sensitive to distances as great as 500 pc.

All-sky LIGO search for periodic gravitational waves in the early fifth-science-run data

We report on an all-sky search with the LIGO detectors for periodic gravitational waves in the frequency range 50-1100 Hz and with the frequency's time derivative in the range -5 x 10{-9}-0 Hz s{-1}. Data from the first eight months of the fifth LIGO science run (S5) have been used in this search, which is based on a semicoherent method (PowerFlux) of summing strain power. Observing no evidence of periodic gravitational radiation, we report 95% confidence-level upper limits on radiation emitted by any unknown isolated rotating neutron stars within the search range. Strain limits below 10{-24} are obtained over a 200-Hz band, and the sensitivity improvement over previous searches increases the spatial volume sampled by an average factor of about 100 over the entire search band. For a neutron star with nominal equatorial ellipticity of 10{-6}, the search is sensitive to distances as great as 500 pc.

All-sky LIGO search for periodic gravitational waves in the early fifth-science-run data

We report on an all-sky search with the LIGO detectors for periodic gravitational waves in the frequency range 50-1100 Hz and with the frequency's time derivative in the range -5 x 10{-9}-0 Hz s{-1}. Data from the first eight months of the fifth LIGO science run (S5) have been used in this search, which is based on a semicoherent method (PowerFlux) of summing strain power. Observing no evidence of periodic gravitational radiation, we report 95% confidence-level upper limits on radiation emitted by any unknown isolated rotating neutron stars within the search range. Strain limits below 10{-24} are obtained over a 200-Hz band, and the sensitivity improvement over previous searches increases the spatial volume sampled by an average factor of about 100 over the entire search band. For a neutron star with nominal equatorial ellipticity of 10{-6}, the search is sensitive to distances as great as 500 pc.

Search for gravitational-wave bursts from soft gamma repeaters

We present a LIGO search for short-duration gravitational waves (GWs) associated with soft gamma ray repeater (SGR) bursts. This is the first search sensitive to neutron star f modes, usually considered the most efficient GW emitting modes. We find no evidence of GWs associated with any SGR burst in a sample consisting of the 27 Dec. 2004 giant flare from SGR 1806-20 and 190 lesser events from SGR 1806-20 and SGR 1900+14. The unprecedented sensitivity of the detectors allows us to set the most stringent limits on transient GW amplitudes published to date. We find upper limit estimates on the model-dependent isotropic GW emission energies (at a nominal distance of 10 kpc) between 3x10;{45} and 9x10;{52} erg depending on waveform type, detector antenna factors and noise characteristics at the time of the burst. These upper limits are within the theoretically predicted range of some SGR models.

Dynamic change in phosphorylated platelet-derived growth factor receptor in peripheral blood leukocytes following docetaxel therapy predicts progression-free and overall survival in prostate cancer

In a placebo-controlled randomised study of the platelet-derived growth factor receptor (PDGFR) inhibitor imatinib mesylate and docetaxel in metastatic prostate cancer with bone metastases (n=116), no significant differences in progression-free and overall survival were observed. To evaluate pharmacodynamic correlates of outcomes, we assessed the association of plasma platelet-derived growth factor (PDGF) isoform kinetics and PDGFR inhibition with progression-free and overall survival by individual treatment arm. We found that in the docetaxel–placebo arm alone, the probability of decrease in PDGFR phosphorylation (Pr-Decr-pPDGFR) above 0.5 (vs ⩽0.5) was associated with a sharp increase in all measured plasma PDGF isoforms (P=0.006 for AA, 0.002 for BB, 0.045 for AB); a decreased median progression-free survival of 3.3 months vs 6.8 months (hazard ratio (HR) 2.5; P=0.006 in log-rank test) and an inferior median overall survival of 20 months vs >30 months (HR 3.1; P=0.04 in log-rank test). By contrast, in the docetaxel plus imatinib arm, the association of Pr-Decr-pPDGFR >0.5 with a rise in plasma PDGF isoform concentrations and inferior survival was not observed. The data suggest that dynamic changes in PDGFR phosphorylation in peripheral blood leukocytes predict docetaxel efficacy. Rising plasma PDGF concentrations may explain and/or mark docetaxel resistance. Validation and mechanistic studies addressing these unexpected findings should anticipate a confounding influence of concurrent PDGFR inhibitor therapy.

Differential gene expression in preoperative study of selenium and vitamin E chemoprevention in prostate cancer

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Background: To identify genes that distinguish between treatments, tumor types, and their interaction, we undertook a microarray analysis of tissue in a preoperative chemoprevention study of L-selenomethionine (SeMet) and vitamin E (VE) in prostate cancer. Methods: Forty-eight men with prostate cancer were enrolled in a single-institution, double-blind, placebo-controlled trial that randomized patients into four groups receiving 200 μg SeMet, 400 IU VE, a combination of the two, or placebo (see 2006 ASCO abstract 1007). All patients also received a multivitamin and vitamin C (250 mg) daily. Modeled on the Selenium and Vitamin E Cancer Prevention Trial, this study included patients scheduled for prostatectomy within 3 to 6 wk of registration who had a prostate-specific antigen level <10 ng/mL within 3 mo of registration, clinical stage T1c/T2 disease, and a Gleason score =7. From core biopsy specimens, we isolated cancerous and noncancerous cells, tumor-adjacent stroma, and non-tumor adjacent stroma of 38 evaluable radical prostatectomy specimens using laser capture microdissection. The cDNA hybridized to oligonucleotide microarrays was generated from extracted RNA, which had undergone two rounds of linear amplification. Expression levels were extracted using the positional-dependent nearest-neighbor model, and after ANOVA model analysis, effects were contrasted using the approximate z-test with statistic z. The beta-uniform mixture model was used to analyze p values and control the false discovery rate. Ingenuity Pathway Analysis followed. Results: Differentially expressed genes were selected that were common in the combination and selenium arms or in the combination and VE arms: unique in tumor-69 in combination and selenium, 71 in combination and VE; unique in stroma-64 in combination and selenium, 45 in combination and VE; unique in normal tissue-48 in combination and selenium, 38 in combination and VE. Conclusions: This work demonstrates that gene expression may be correlated with specific therapeutic interventions, and this analysis indicates that dietary antioxidants modulate gene expression in human prostate cancer cells and pathways relevant to prostate carcinogenesis.

No significant financial relationships to disclose.

Coordinated modulation of sonic hedgehog (Shh) signaling and androgen receptor (AR) in the prostate tumor microenvironment by chemo-hormonal therapy

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Background: Shh and androgen signaling are implicated experimentally in prostate development, regeneration and neoplastic progression. We assessed expression of components of these pathways in pretreated and control high risk prostate cancers (PCa) in a hypothesis generating search for an association with resistance to therapy. Methods: Sixty-four men with high risk PCa were randomized to receive either complete androgen ablation (AA) or AA and ketoconazole, adriamycin, vinblastine and estramustine (KAVE) for 16 weeks followed by radical prostatectomy (RP). We constructed 3 tissue microarrays from RP specimens of: a) (AA) 26 men pretreated with AA, b) (CH) 27 men pretreated with AA + KAVE and c) (Control) 26 untreated men matched for clinical stage, biopsy Gleason Score and PSA. A total of 3,178 cores were obtained [median cores: 36 (range 18–90), median blocks: 5 (range 3–9) per specimen]. Immunohistochemical expression of Shh pathway components (Shh, patched, smoothened, gli2) and AR were assessed in the tumor epithelium and stroma and recorded as percentage of cells exhibiting staining. A mixed model was used for fitting the correlated data (multiple observations from a subject). Pearson’s correlations between biomarkers were calculated based on mean expression. Results: Shh signaling, as indicated by mean expression (standard deviation) of nuclear gli2, was observed in the residual tumor epithelium [AA: 79.9 (17.4), CH: 85.7 (12.2)] and adjacent stroma [ AA: 43 (18.2),CH: 53 (16.4)] following treatment, in parallel (0.78 by Pearson’s correlation), and higher than in untreated control tumor epithelium [39.9 (20.6)] and stroma [22.9 (15.2)] (P<.0001). Smoothened and Shh were expressed accordingly. AR expression was lower in the treated tumor epithelium [AA: 47.3 (20.8), CH: 46.8 (21.1)] (P<.0001), with a trend toward increased stromal AR [AA: 8.6 (10.4), CH: 10.5 (8.2)] compared to control tumor epithelium [60.1 (24.1)] and stroma [6.4 (11.7)]. Conclusions: Shh and androgen pathways are modulated in a manner that suggests they behave in a compensatory fashion, and are determinants of response to therapy. These data support the hypothesis that the tumor microenvironment is implicated in PCa therapy resistance.

No significant financial relationships to disclose.

Distribution and characteristics of hepatitis B virus genotype C subgenotypes in China

Genetic diversity within the same hepatitis B virus (HBV) genotype indicates the presence of several subgenotypes. We have found that genotype C is the most common in China, and this study aimed to determine the geographical distribution and characteristics of HBV-C subgenotypes in the country. A cohort of 534 patients with chronic HBV genotype C infection, collected across China, was analysed by nucleotide sequencing or polymerase chain reaction-restriction fragment length polymorphism. HBV-C1/Cs (n = 112, 21%) and HBV-C2/Ce (n = 397, 74%) were the most common HBV-C subgenotypes and showed different geographical distribution in China. No significant differences were found between patients infected with HBV-C1 and HBV-C2 when comparing liver function tests, hepatitis B e antigen positive rate and clinical manifestations. We identified two other types of HBV-C provisionally designated as HBV-CD1 and HBV-CD2, which have particular virological features and clustered in one geographic area. These two types of C/D hybrids have emerged through recombination with genotype D and encode serotype ayw2 hepatitis B surface antigen. In conclusion, there are at least four subtypes of HBV genotype C: subgenotypes C1, C2 and two types of C/D recombinants CD1 and CD2 in China, which have a distinct geographic distribution. Whether HBV-C subgenotypes differ in their impact on liver disease progression requires prospective studies.

Application of gene shaving and mixture models to cluster microarray gene expression data

Researchers are frequently faced with the analysis of microarray data of a relatively large number of genes using a small number of tissue samples. We examine the application of two statistical methods for clustering such microarray expression data: EMMIX-GENE and GeneClust. EMMIX-GENE is a mixture-model based clustering approach, designed primarily to cluster tissue samples on the basis of the genes. GeneClust is an implementation of the gene shaving methodology, motivated by research to identify distinct sets of genes for which variation in expression could be related to a biological property of the tissue samples. We illustrate the use of these two methods in the analysis of Affymetrix oligonucleotide arrays of well-known data sets from colon tissue samples with and without tumors, and of tumor tissue samples from patients with leukemia. Although the two approaches have been developed from different perspectives, the results demonstrate a clear correspondence between gene clusters produced by GeneClust and EMMIX-GENE for the colon tissue data. It is demonstrated, for the case of ribosomal proteins and smooth muscle genes in the colon data set, that both methods can classify genes into co-regulated families. It is further demonstrated that tissue types (tumor and normal) can be separated on the basis of subtle distributed patterns of genes. Application to the leukemia tissue data produces a division of tissues corresponding closely to the external classification, acute myeloid leukemia (AML) and acute lymphoblastic leukemia (ALL), for both methods. In addition, we also identify genes specific for the subgroup of ALL-Tcell samples. Overall, we find that the gene shaving method produces gene clusters at great speed; allows variable cluster sizes and can incorporate partial or full supervision; and finds clusters of genes in which the gene expression varies greatly over the tissue samples while maintaining a high level of coherence between the gene expression profiles. The intent of the EMMIX-GENE method is to cluster the tissue samples. It performs a filtering step that results in a subset of relevant genes, followed by gene clustering, and then tissue clustering, and is favorable in its accuracy of ranking the clusters produced.

Application of Gene Shaving and Mixture Models to Cluster Microarray Gene Expression Data

Researchers are frequently faced with the analysis of microarray data of a relatively large number of genes using a small number of tissue samples. We examine the application of two statistical methods for clustering such microarray expression data: EMMIX-GENE and GeneClust. EMMIX-GENE is a mixture-model based clustering approach, designed primarily to cluster tissue samples on the basis of the genes. GeneClust is an implementation of the gene shaving methodology, motivated by research to identify distinct sets of genes for which variation in expression could be related to a biological property of the tissue samples. We illustrate the use of these two methods in the analysis of Affymetrix oligonucleotide arrays of well-known data sets from colon tissue samples with and without tumors, and of tumor tissue samples from patients with leukemia. Although the two approaches have been developed from different perspectives, the results demonstrate a clear correspondence between gene clusters produced by GeneClust and EMMIX-GENE for the colon tissue data. It is demonstrated, for the case of ribosomal proteins and smooth muscle genes in the colon data set, that both methods can classify genes into co-regulated families. It is further demonstrated that tissue types (tumor and normal) can be separated on the basis of subtle distributed patterns of genes. Application to the leukemia tissue data produces a division of tissues corresponding closely to the external classification, acute myeloid meukemia (AML) and acute lymphoblastic leukemia (ALL), for both methods. In addition, we also identify genes specific for the subgroup of ALL-Tcell samples. Overall, we find that the gene shaving method produces gene clusters at great speed; allows variable cluster sizes and can incorporate partial or full supervision; and finds clusters of genes in which the gene expression varies greatly over the tissue samples while maintaining a high level of coherence between the gene expression profiles. The intent of the EMMIX-GENE method is to cluster the tissue samples. It performs a filtering step that results in a subset of relevant genes, followed by gene clustering, and then tissue clustering, and is favorable in its accuracy of ranking the clusters produced.

Biological activities of a recombinant adenovirus p53 (SCH 58500) administered by hepatic arterial infusion in a Phase 1 colorectal cancer trial

The major focus of intrahepatic arterial (IHA) administration of adenoviruses (Ad) has been on safety. Currently, there is little published data on the biological responses to Ad when administered via this route. As part of a Phase I study, we evaluated biological responses to a replication-defective adenovirus encoding the p53 transgene (SCH 58500) when administered by hepatic arterial infusion to patients with primarily colorectal cancer metastatic to the liver. In analyzing biological responses to the Ad vector, we found that both total and neutralizing Ad antibodies increased weeks after SCH 58500 infusion. The fold increase in antibody titers was not dependent on SCH 58500 dosage. The proinflammatory cytokine interleukin-6 (IL-6) transiently peaked within 6 h of dosing. The cytokine sTNF-R2 showed elevation by 24 h post-treatment, and fold increases were directly related to SCH 58500 doses. Cytokines TNF-alpha, IL-1beta, and sTNF-R1 showed no increased levels over 24 h. Predose antibody levels did not appear to predict transduction, nor did serum Ad neutralizing factor (SNF). Delivery of SCH 58500 to tumor tissue occurred, though we found distribution more predominantly in liver tissues, as opposed to tumors. RT-PCR showed significantly higher expression levels (P<0.0001, ANOVA) for adenovirus type 2 and 5 receptor (CAR) in liver tissues, suggesting a correlation with transduction. Evidence of tumor-specific apoptotic activity was provided by laser scanning cytometry, which determined a coincidence of elevated nuclear p53 protein expression with apoptosis in patient tissue. IHA administration of a replication defective adenovirus is a feasible mode of delivery, allowing for exogenous transfer of the p53 gene into target tissues, with evidence of functional p53. Limited and transient inflammatory responses to the drug occurred, but pre-existing immunity to Ad did not preclude SCH 58500 delivery.

CD8+ tumor-infiltrating lymphocytes as a statistically significant marker of disease recurrence and survival in transitional cell carcinoma patients

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Background: Superficial transitional cell carcinoma (TCC) is an immune-responsive tumor evidenced by immunotherapy trials with BCG demonstrating improved survival. In contrast, more advanced muscle-invasive TCC is not considered an immunologically active tumor. Yet, host immune functions that may have a clinical impact on the biologic activity of these more invasive tumors have not been systemically evaluated. CD8+ T-cells are responsible for cytotoxicity and potential tumor eradication by interaction with antigen plus human leukocyte antigens (HLA). A clear association between intratumoral CD8+ T-cells and clinical outcome has not been established in TCC. Methods: We performed pathological, immunohistochemical and RT-PCR analyses of 69 TCC patient samples that were obtained with appropriate informed consent on an Institutional Review Board (IRB)-approved protocol. The samples were studied for pathological stage, tumor-associated antigen expression, class I HLA expression, and CD8+ intratumoral T-cells. Systemic CD8+ T-cells from one patient with positive CD8+ intratumoral T-cells were studied by tetramer analyses for reactivity against the NY-ESO-1 tumor antigen expressed on the patient’s tumor. Results: In a subset analysis, advanced TCC (pT2, pT3 and pT4) patients who had higher numbers of CD8+ tumor infiltrating lymphocytes (TILs) had a greater disease-free survival (p = 0.0002) and overall survival (p = 0.011) than similarly staged TCC patients with lower numbers of CD8+ TILs. In the multivariate analyses, CD8+ TILs (p = 0.04) and tumor stage (p < 0.001) were significant risk factors to predict overall survival. Furthermore, a CD8+ T-cell clone derived from one patient demonstrated strong recognition of the tumor antigen NY-ESO-1. Conclusions: This is the first report, to our knowledge, that CD8+ TILs is an important prognostic indicator for patients with advanced TCC. Investigational immunotherapy strategies to evoke CD8+ T-cell responses are warranted in patients with advanced TCC.

[Table: see text]

Development of a Compound-Specific Carbon Isotope Analysis Method for Atmospheric Formaldehyde via NaHSO3 and Cysteamine Derivatization

A novel method has been developed for the compound-specific carbon isotope analysis of atmospheric formaldehyde using gas chromatography/combustion/isotope ratio mass spectrometry (GC/C/IRMS). The method allows the determination of the delta13C value for atmospheric formaldehyde at nanogram levels with higher precision and lower detection limit. In the present work, atmospheric formaldehyde was collected using NaHSO3-coated Sep-Pak silica gel cartridges, washed out by water, then derivatized by cysteamine of known delta13C value, and the delta13C value of its derivative (thiazolidine) determined by GC/C/IRMS. Finally, the delta13C value of atmospheric formaldehyde could be calculated by a simple mass balance equation between formaldehyde, cysteamine, and thiazolidine. Using three formaldehydes with different delta13C values, calibration experiments were carried out over large ranges of formaldehyde concentrations. The carbon isotope analysis method achieved excellent reproducibility and high accuracy. There was no carbon isotopic fractionation throughout the derivatization processes. The differences in the carbon isotopic compositions of thiazolidine between the measured and predicted values were always <0.5 per thousand, within the specifications of the GC/C/IRMS system. The present method was also compared with the previous 2,4-dinitrophenylhydrazine derivatization method, and this method could be performed with lower analytical error and detection limit. Using this method, four 6-h ambient atmospheric formaldehyde samples were consecutively collected from 8 to 9 March 2005. The results showed that the delta13C values of atmospheric formaldehyde were different during the daytime and nighttime. This method proved suitable for the routine operation and may provide additional insight on sources and sinks of atmospheric formaldehyde.

Upper limits on a stochastic background of gravitational waves

The Laser Interferometer Gravitational-Wave Observatory has performed a third science run with much improved sensitivities of all three interferometers. We present an analysis of approximately 200 hours of data acquired during this run, used to search for a stochastic background of gravitational radiation. We place upper bounds on the energy density stored as gravitational radiation for three different spectral power laws. For the flat spectrum, our limit of omega0 < 8.4 x 10(-4) in the 69-156 Hz band is approximately 10(5) times lower than the previous result in this frequency range.

Geographic distribution, virologic and clinical characteristics of hepatitis B virus genotypes in China

The significance of hepatitis B virus (HBV) genotypes for the heterogeneity of chronic HBV infection and severity of liver disease is not well understood. The aim of this study was to determine the distribution and virologic characteristics of HBV genotypes in China and possible association with the diversity of liver disease. The study includes 1096 chronic HBV carriers from nine provinces in China. We collected clinical and laboratory data and analysed the HBV strains in sera by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and nucleotide sequencing techniques. The most common HBV genotypes were B (41%) and C (53%), while genotypes A and D were also found. A North-South divide was identified in genotype B and C distribution - genotype C was predominant in northern China, while genotype B was more prevalent in southern provinces. Patients with genotype B were younger than those with genotype C, and had a lower prevalence of HBeAg - 65%vs 72%, respectively (P = 0.03). However, the severity of liver disease did not differ significantly between patients infected with genotype B or C - neither when comparing liver function tests (1024 patients), nor hepatic inflammation and fibrosis (264 patients). Amongst 47 patients with genotype D (by PCR-RFLP), 37 (79%) were infected with a new subtype (designated Dc), having a recombination fragment from genotype C precore/core region. This is the first large-scale HBV genotype study from China and convincing documentation of the North-to-South gradient of genotypes C vs B in this country. HBV DNA recombination over the surface and precore/core genes increases the diversity of HBV strains and may have diagnostic and clinical implications.