Network integration meets network dynamics

Molecular interaction networks provide a window on the workings of the cell. However, combining various types of networks into one coherent large-scale dynamic model remains a formidable challenge. A recent paper in BMC Systems Biology describes a promising step in this direction

Epstein–Barr virus antibody level and gastric cancer risk in Korea: a nested case–control study

BACKGROUND: Few cohort studies have investigated Epstein-Barr virus (EBV) infection before the occurrence of gastric cancer. METHODS: Among 14 440 cohort participants, 100 incident gastric cancer cases were individually matched to two controls. Epstein-Barr virus antibodies IgG and IgA against viral capsid antigen (VCA), EBV nuclear antigen (EBNA) antibody IgG, and early antigen (EA) antibody IgG were measured using enzyme immunoassays (EIAs). RESULTS: The highest titres of VCA IgG (odds ratio (OR): 1.37, 95% confidence interval (CI): 0.62-3.06) or EBNA IgG (OR: 0.87, 95% CI: 0.51-1.46) were not associated with gastric cancer risk. CONCLUSION: Higher levels of VCA IgG or EBNA IgG were not associated with increased risk of gastric adenocarcinoma in Koreans.Akiba S, 2008, CANCER SCI, V99, P195, DOI 10.1111/j.1349-7006.2007.00674.xKoshiol J, 2007, BRIT J CANCER, V97, P1567, DOI 10.1038/sj.bjc.6604063Tedeschi R, 2007, AM J EPIDEMIOL, V165, P134, DOI 10.1093/aje/kwj332Gwack J, 2006, BRIT J CANCER, V95, P639, DOI 10.1038/sj.bjc.6603309Ouburg S, 2005, EUR J GASTROEN HEPAT, V17, P1213Chan D, 2005, J RES PRACT INF TECH, V37, P267HERRERAGOEPFERT R, 2005, WORLD J GASTROENTERO, V11, P6096CORREA P, 2004, GASTRIC CANCER, V7, P9Macsween KF, 2003, LANCET INFECT DIS, V3, P131Gartner BC, 2003, CLIN DIAGN LAB IMMUN, V10, P78, DOI 10.1128/CDLI.10.1.78-82.2003Burgess DE, 2002, BRIT J CANCER, V86, P702, DOI 10.1038/sj/bjc/6600107YOO KY, 2002, ASIAN PAC J CANCER P, V3, P85Chien YC, 2001, NEW ENGL J MED, V345, P1877Bruu AL, 2000, CLIN DIAGN LAB IMMUN, V7, P451Shinkura R, 2000, J MED VIROL, V60, P411Akre O, 1999, INT J CANCER, V82, P1Tokunaga M, 1998, CANCER EPIDEM BIOMAR, V7, P449*IARC, 1997, EPSTEINBARR VIR KAP, V8LEVINE PH, 1995, INT J CANCER, V60, P642LEHTINEN T, 1993, CANCER CAUSE CONTROL, V4, P187GESER A, 1982, INT J CANCER, V29, P397

Worksite health screening programs for predicting the development of Metabolic Syndrome in middle-aged employees: a five-year follow-up study

<p>Abstract</p> <p>Background</p> <p>Metabolic syndrome (MetS) management programs conventionally focus on the adults having MetS. However, risk assessment for MetS development is also important for many adults potentially at risk but do not yet fulfill MetS criteria at screening. Therefore, we conducted this follow-up study to explore whether initial screening records can be efficiently applied on the prediction of the MetS occurrence in healthy middle-aged employees.</p> <p>Methods</p> <p>Utilizing health examination data, a five-year follow-up observational study was conducted for 1384 middle-aged Taiwanese employees not fulfilling MetS criteria. Data analyzed included: gender, age, MetS components, uric acid, insulin, liver enzymes, sonographic fatty liver, hepatovirus infections and lifestyle factors. Multivariate logistic regression was used to estimate the adjusted odds ratios (OR) and 95% confidence interval (CI) of risk for MetS development. The synergistic index (SI) values and their confidence intervals of risk factor combinations were calculated; and were used to estimate the interacting effects of coupling MetS components on MetS development.</p> <p>Results</p> <p>Within five years, 13% (175 out of 1384) participants fulfilled MetS criteria. The ORs for MetS development among adults initially having one or two MetS components were 2.8 and 7.3, respectively (both p < 0.01), versus the adults having zero MetS component count at screening. Central obesity carried an OR of 7.5 (p < 0.01), which far exceeded other risk factors (all ORs < 2.7). Synergistic effects on MetS development existed between coupling MetS components: 1. High blood pressure plus low-HDL demonstrated an OR of 11.7 (p < 0.01) for MetS development and an SI of 4.7 (95% CI, 2.1-10.9). 2. High blood pressure plus hyperglycemia had an OR of 7.9 (p < 0.01), and an SI of 2.7 (95% CI, 1.2-6.4).</p> <p>Conclusion</p> <p>MetS component count and combination can be used in predicting MetS development for participants potentially at risk. Worksite MetS screening programs simultaneously allow for finding out cases and for assessing risk of MetS development.</p

Oncogenic CagA Promotes Gastric Cancer Risk via Activating ERK Signaling Pathways: A Nested Case-Control Study

Background: CagA cellular interaction via activation of the ERK signaling pathway may be a starting point in the development of gastric cancer. This study aimed to evaluate whether genes involved in ERK downstream signaling pathways activated by CagA are susceptible genetic markers for gastric cancer. Methods: In the discovery phase, a total of 580 SNPs within +/-5 kbp of 30 candidate genes were genotyped to examine an association with gastric cancer risk in the Korean Multi-center Cancer Cohort (100 incident gastric cancer case-control sets). The most significant SNPs (raw or permutated p value??0.02) identified in the discovery analysis were re-evaluated in the extension phase using unconditional logistic regression model (400 gastric cancer case-control sets). Combined analyses including pooled-and meta-analysis were conducted to summarize all the results. Results: 24 SNPs in eight genes (ERK, Dock180, C3G, Rap1, Src, CrkL, Mek and Crk) were significantly associated with gastric cancer risk in the individual SNP analyses in the discovery phase (p??0.05). In the extension analyses, ERK rs5999749, Dock180 rs4635002 and C3G rs7853122 showed marginally significant gene-dose effects for gastric cancer. Consistently, final combined analysis presented the SNPs as significantly associated with gastric cancer risk (OR = 1.56, [95% CI: 1.19-2.06], OR = 0.61, [95% CI: 0.43-0.87], OR = 0.59, [95% CI: 0.54-0.76], respectively). Conclusions: Our findings suggest that ERK rs5999749, Dock180 rs4635002 and C3G rs7853122 are genetic determinants in gastric carcinogenesis

Hypoxic gene expression in chronic hepatitis B virus infected patients is not observed in state-of-the-art in vitro and mouse infection models

Hepatitis B virus (HBV) is the leading cause of hepatocellular carcinoma (HCC) worldwide. The prolyl hydroxylase domain (PHD)-hypoxia inducible factor (HIF) pathway is a key mammalian oxygen sensing pathway and is frequently perturbed by pathological states including infection and inflammation. We discovered a significant upregulation of hypoxia regulated gene transcripts in patients with chronic hepatitis B (CHB) in the absence of liver cirrhosis. We used state-of-the-art in vitro and in vivo HBV infection models to evaluate a role for HBV infection and the viral regulatory protein HBx to drive HIF-signalling. HBx had no significant impact on HIF expression or associated transcriptional activity under normoxic or hypoxic conditions. Furthermore, we found no evidence of hypoxia gene expression in HBV de novo infection, HBV infected human liver chimeric mice or transgenic mice with integrated HBV genome. Collectively, our data show clear evidence of hypoxia gene induction in CHB that is not recapitulated in existing models for acute HBV infection, suggesting a role for inflammatory mediators in promoting hypoxia gene expression

Stable Field Emitters for a Miniature X-ray Tube Using Carbon Nanotube Drop Drying on a Flat Metal Tip

Stable carbon nanotube (CNT) field emitters for a vacuum-sealed miniature X-ray tube have been fabricated. The field emitters with a uniform CNT coating are prepared by a simple drop drying of a CNT mixture solution that is composed of chemically modified multi-walled CNTs, silver nanoparticles, and isopropyl alcohol on flat tungsten tips. A highly thermal- and electrical-conductive silver layer strongly attaches CNTs to the tungsten tips. Consequently, the field emitters exhibit good electron emission stability: continuous electron emission of around 100 μA at 2.3 V/μm has stably lasted over 40 h even at non-high vacuum ambient (~10−3 Pa)

Measurement of the Forward-Backward Asymmetry in the B -> K(*) mu+ mu- Decay and First Observation of the Bs -> phi mu+ mu- Decay

We reconstruct the rare decays $B^+ \to K^+\mu^+\mu^-$, $B^0 \to K^{*}(892)^0\mu^+\mu^-$, and $B^0_s \to \phi(1020)\mu^+\mu^-$ in a data sample corresponding to $4.4 {\rm fb^{-1}}$ collected in $p\bar{p}$ collisions at $\sqrt{s}=1.96 {\rm TeV}$ by the CDF II detector at the Fermilab Tevatron Collider. Using $121 \pm 16$ $B^+ \to K^+\mu^+\mu^-$ and $101 \pm 12$ $B^0 \to K^{*0}\mu^+\mu^-$ decays we report the branching ratios. In addition, we report the measurement of the differential branching ratio and the muon forward-backward asymmetry in the $B^+$ and $B^0$ decay modes, and the $K^{*0}$ longitudinal polarization in the $B^0$ decay mode with respect to the squared dimuon mass. These are consistent with the theoretical prediction from the standard model, and most recent determinations from other experiments and of comparable accuracy. We also report the first observation of the $B^0_s \to \phi\mu^+\mu^- decay and measure its branching ratio${\mathcal{B}}(B^0_s \to \phi\mu^+\mu^-) = [1.44 \pm 0.33 \pm 0.46] \times 10^{-6}$using$27 \pm 6$signal events. This is currently the most rare$B^0_s$ decay observed.Comment: 7 pages, 2 figures, 3 tables. Submitted to Phys. Rev. Let

Measurements of the properties of Lambda_c(2595), Lambda_c(2625), Sigma_c(2455), and Sigma_c(2520) baryons

We report measurements of the resonance properties of Lambda_c(2595)+ and Lambda_c(2625)+ baryons in their decays to Lambda_c+ pi+ pi- as well as Sigma_c(2455)++,0 and Sigma_c(2520)++,0 baryons in their decays to Lambda_c+ pi+/- final states. These measurements are performed using data corresponding to 5.2/fb of integrated luminosity from ppbar collisions at sqrt(s) = 1.96 TeV, collected with the CDF II detector at the Fermilab Tevatron. Exploiting the largest available charmed baryon sample, we measure masses and decay widths with uncertainties comparable to the world averages for Sigma_c states, and significantly smaller uncertainties than the world averages for excited Lambda_c+ states.Comment: added one reference and one table, changed order of figures, 17 pages, 15 figure

Investigation of Semiconductor Quantum Dots for Waveguide Electroabsorption Modulator

In this work, we investigated the use of 10-layer InAs quantum dot (QD) as active region of an electroabsorption modulator (EAM). The QD-EAM is a p-i-n ridge waveguide structure with intrinsic layer thickness of 0.4 μm, width of 10 μm, and length of 1.0 mm. Photocurrent measurement reveals a Stark shift of ~5 meV (~7 nm) at reverse bias of 3 V (75 kV/cm) and broadening of the resonance peak due to field ionization of electrons and holes was observed for E-field larger than 25 kV/cm. Investigation at wavelength range of 1,300–1320 nm reveals that the largest absorption change occurs at 1317 nm. Optical transmission measurement at this wavelength shows insertion loss of ~8 dB, and extinction ratio of ~5 dB at reverse bias of 5 V. Consequently, methods to improve the performance of the QD-EAM are proposed. We believe that QDs are promising for EAM and the performance of QD-EAM will improve with increasing research efforts