Simpson's paradox - aggregating and partitioning populations in health disparities of lung cancer patients

It is well known that non-small cell lung cancer (NSCLC) is a heterogeneous group of diseases. Previous studies have demonstrated genetic variation among different ethnic groups in the epidermal growth factor receptor (EGFR) in NSCLC. Research by our group and others has recently shown a lower frequency of EGFR mutations in African Americans with NSCLC, as compared to their White counterparts. In this study, we use our original study data of EGFR pathway genetics in African American NSCLC as an example to illustrate that univariate analyses based on aggregation versus partition of data leads to contradictory results, in order to emphasize the importance of controlling statistical confounding. We further investigate analytic approaches in logistic regression for data with separation, as is the case in our example data set, and apply appropriate methods to identify predictors of EGFR mutation. Our simulation shows that with separated or nearly separated data, penalized maximum likelihood (PML) produces estimates with smallest bias and approximately maintains the nominal value with statistical power equal to or better than that from maximum likelihood and exact conditional likelihood methods. Application of the PML method in our example data set shows that race and EGFR-FISH are independently significant predictors of EGFR mutation.

Age-related changes in the default mode network are more advanced in Alzheimer disease

OBJECTIVE

To investigate age-related default mode network (DMN) connectivity in a large cognitively normal elderly cohort and in patients with Alzheimer disease (AD) compared with age-, gender-, and education-matched controls.

METHODS

We analyzed task-free-fMRI data with both independent component analysis and seed-based analysis to identify anterior and posterior DMNs. We investigated age-related changes in connectivity in a sample of 341 cognitively normal subjects. We then compared 28 patients with AD with 56 cognitively normal noncarriers of the APOE ε4 allele matched for age, education, and gender.

RESULTS

The anterior DMN shows age-associated increases and decreases in fontal lobe connectivity, whereas the posterior DMN shows mainly age-associated declines in connectivity throughout. Relative to matched cognitively normal controls, subjects with AD display an accelerated pattern of the age-associated changes described above, except that the declines in frontal lobe connectivity did not reach statistical significance. These changes survive atrophy correction and are correlated with cognitive performance.

CONCLUSIONS

The results of this study indicate that the DMN abnormalities observed in patients with AD represent an accelerated aging pattern of connectivity compared with matched controls.

Rheological Properties of Neat and Calcium Carbonate Particles Filled Polypropylene Blends under Axial Vibration Force Field

Structures, working mechanism, data collecting and processing methods of the self-made multifunctional all-electronic rheometer for polymer composites were introduced in detail. The validity of this equipment was proved by deriving the apparent shear viscosity expression under axial vibration condition and comparing the results obtained from both this self-made rheometer and Rosand Rh7D capillary rheometer at steady state. With this equipment, the effects of calcium carbonate weight fraction, particle size and vibration parameters on apparent shear viscosity of calcium carbonate filled propylene composites were investigated. The results show that: the apparent shear viscosity of the composites increases with the filled particle concentration. However, it is seldom affected by particle size within certain a range of shear rate. While the apparent shear viscosity increases with the decrease of particle size at moderate shear rate. Besides, the apparent shear viscosity declines rapidly with the increasing vibration amplitude. However it exhibits a cosinoidal or sinusoidal trend as vibration frequency increases and peaks at the resonant frequency of the composites.

Lower Temperature Plasticizing and Extrusion of Polymer in Spherical Screw Extruder under Vibration Force Field

Physical and mathematical model for polymer plasticizing in proposed electromagnetic dynamic spherical screw extruder were developed to explore polymer plasticizing and molding mechanism at lower temperature under vibration force field. Polymer plasticizing mechanism was studied by deriving the mathematical expressions of energy consumed and the polymer flow. The energy consumed in polymer plasticizing was depicted in terms of vibrating dissipation, polymer deformation, shear and friction energy. LDPE was used as an objective material and extruded by the extruder with the electromagnetic excitation and spherical screw. The experimental results show the good agreement with theoretical calculations. Both of them show that: Polymer processing temperature and energy consumption decrease significantly while the plasticizing rate is increased over 60% by introducing the vibration force field. The research offers experimental and theoretical references as well as the evaluation method for optimizing the polymer processing parameters and designing the vibration induced equipment.

Anti-sports anaemia effects of verbascoside and martynoside in mice

This paper aims to investigate the effects of verbascoside and martynoside isolated from PEDICULARIS DOLICHOCYMBA on sports anaemia. Forty mice were divided into four groups: Group R (control group, nonsupplemented and maintained at rest), Group E (nonsupplemented and undergoing exercise), Group VE (supplemented with verbascoside 10 mg/kg per day and undergoing exercise), and Group ME (supplemented with martynoside 10 mg/kg per day and undergoing exercise). After 5 weeks intensive swimming exercises, we measured the RBC count, the hemoglobin concentration, the hematocrit (Hct), the mean corpuscular hemoglobin concentration (MCHC) and the mean corpuscular hemoglobin (MCH). We studied the shapes of RBC and measured the plasma malonyldialdehyde (MDA). We found Group E showed lower RBC, hemoglobin and Hct levels, higher MCHC, MCH, plasma MDA levels and the abnormally shaped RBCs percentage than Groups R, VE and ME. Group ME showed lower RBC and Hct levels, higher MCH, plasma MDA levels and the abnormally shaped RBCs percentage than Group VE. The results indicated that verbascoside and martynoside have the potential of antagonizing sports anaemia, the mechanism of this effect might be related to preventing RBC from free radical damage. Moreover, verbascoside was found to be more active than martynoside.

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.

The global atmospheric environment for the next generation

Air quality, ecosystem exposure to nitrogen deposition, and climate change are intimately coupled problems: we assess changes in the global atmospheric environment between 2000 and 2030 using 26 state-of-the-art global atmospheric chemistry models and three different emissions scenarios. The first (CLE) scenario reflects implementation of current air quality legislation around the world, while the second (MFR) represents a more optimistic case in which all currently feasible technologies are applied to achieve maximum emission reductions. We contrast these scenarios with the more pessimistic IPCC SRES A2 scenario. Ensemble simulations for the year 2000 are consistent among models and show a reasonable agreement with surface ozone, wet deposition, and NO2 satellite observations. Large parts of the world are currently exposed to high ozone concentrations and high deposition of nitrogen to ecosystems. By 2030, global surface ozone is calculated to increase globally by 1.5 +/- 1.2 ppb (CLE) and 4.3 +/- 2.2 ppb (A2), using the ensemble mean model results and associated +/-1 sigma standard deviations. Only the progressive MFR scenario will reduce ozone, by -2.3 +/- 1.1 ppb. Climate change is expected to modify surface ozone by -0.8 +/- 0.6 ppb, with larger decreases over sea than over land. Radiative forcing by ozone increases by 63 +/- 15 and 155 +/- 37 mW m(-2) for CLE and A2, respectively, and decreases by -45 +/- 15 mW m(-2) for MFR. We compute that at present 10.1% of the global natural terrestrial ecosystems are exposed to nitrogen deposition above a critical load of 1 g N m(-2) yr(-1). These percentages increase by 2030 to 15.8% (CLE), 10.5% (MFR), and 25% (A2). This study shows the importance of enforcing current worldwide air quality legislation and the major benefits of going further. Nonattainment of these air quality policy objectives, such as expressed by the SRES-A2 scenario, would further degrade the global atmospheric environment.

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.

Dynamical variability in the modelling of chemistry–climate interactions

We have used a version of the Met Office's climate model, into which we have introduced schemes for atmospheric chemistry, to study chemistry-dynamics-climate interactions. We have considered the variability of the stratospheric polar vortex, whose behaviour influences stratospheric ozone loss and will affect ozone recovery. In particular, we analyse the dynamical control of high latitude ozone in a model version which includes an assimilation of the equatorial quasi-biennial oscillation (QBO), demonstrating the stability of the linear relation between vortex strength and high latitude ozone. We discuss the effect of interactive model ozone on polar stratospheric cloud (PSC) area/volume and winter-spring stratospheric ozone loss in the northern hemisphere. In general we find larger polar ozone losses calculated in those model integrations in which modelled ozone is used interactively in the radiation scheme, even though we underestimate the slope of the ozone loss per PSC volume relation derived from observations. We have also looked at the influence of changing stratosphere-to-troposphere exchange on the tropospheric oxidizing capacity and, in particular, have considered the variability of tropospheric composition under different climate regimes (El Niño/La Niña, etc.). Focusing on the UT/LS, we show the response of ozone to El Niño in two different model set-ups (tropospheric/ stratospheric). In the stratospheric model set-up we find a distinct signal in the lower tropical stratosphere, which shows an anti-correlation between the Niño 3 index and the ozone column amount. In contrast ozone generally increases in the upper troposphere of the tropospheric model set-up after an El Niño. Understanding future trends in stratospheric ozone and tropospheric oxidizing capacity requires an understanding of natural variability, which we explore here.

Characterization and identification of the Detroit River mystery oil spill (2002)

In this paper, a case study of the Detroit River mystery oil spill (2002) is presented that demonstrates the utility of detailed and integrated oil fingerprinting in investigating unknown or suspected oil spills. The detailed diagnostic oil fingerprinting techniques include determination of hydrocarbon groups and semi-quantitative product screening, analysis of oil-characteristic biomarkers and the extended suite of parent and alkylated polycyclic aromatic hydrocarbons (PAHs), and quantitative determination of a variety of diagnostic ratios of "source-specific marker" compounds. The detailed chemical fingerprinting data and results highlight the followings: (1) The spill samples were largely composed of used lube oil mixed with smaller portion of diesel fuel. (2) The diesel in the samples had been weathered and degraded. (3) Sample 3 collected from N. Boblo Island on 14 April was more weathered (most probably caused by more evaporation and water-washing) than samples 1 and 2. (4) All fingerprinting results clearly demonstrated oils in three samples were the same, and they came from the same source. (5) Most PAH compounds were from the diesel portion in the spill samples, while the biomarker compounds were largely from the lube oil. (6) Input of pyrogenic PAHs to the spill samples was clearly demonstrated. The pyrogenic PAHs were most probably produced from combustion and motor lubrication processes, and the lube oil in these spill samples was waste lube oil.

The effect of astragapolysaccharide on the lymphocyte proliferation and airway inflammation in sensitized mice

In order to investigate the regulating role of Astragapolysaccharide (APS) in the mice model of asthmatic airway inflammation, the airway eosinophil number, spleen T lymphocyte proliferation, level of IL-2 production and their relationships were studied in sensitized mice and sensitized mice treated with different concentrations of APS. The results showed that the number of eosinophils as well as lymphocytes in the airway of the sensitized animals were significantly increased, and a marked positive correlation between the inflammation cells and spleen T lymphocyte proliferation was found. Moreover, there was a positive correlation between inflammation cells and the level of IL-2 production. The APS of given dosage could significantly reduce the number of eosinophils in the airway of the sensitized animals. At the same time the level of IL-2 secreted by spleen T lymphocytes stimulated with ConA was also significantly decreased and there was a marked positive correlation between them. Our results suggested that APS of given dosage could prevent antigen-induced the number of eosinophils infiltrating into the airway of sensitized mice and inhibit the proliferation and activation of lymphocyte and IL-2 production. Through its immuno-regulating effect, APS can be helpful in the treatment of asthma.

Role of tumor-associated gangliosides in cancer progression

Neuroectodermic tumors can mostly be characterized by the presence of tumor-associated glycosphingolipid antigens, such as gangliosides, defined by monoclonal antibodies. Recently, cumulative evidence indicates that gangliosides modify the biological effects of several trophic factors, in vitro and in vivo, as well as the mitogenic signaling cascade that these factors generate. The functional roles of gangliosides in tumor progression can be revisited: (i) ganglioside antigens on the cell surface, or shed from the cells, act as immunosuppressors, as typically observed for the suppression of cytotoxic T cells and dendritic cells, (ii) certain gangliosides, such as GD3 or GM2, promote tumor-associated angiogenesis, (iii) gangliosides strongly regulate cell adhesion/motility and thus initiate tumor metastasis, (iv) ganglioside antigens are directly connected with transducer molecules in microdomains to initiate adhesion coupled with signaling, and (v) ganglioside antigens and their catabolites are modulators of signal transduction through interaction with tyrosine kinases associated with growth factor receptors or other protein kinases. Given the potential importance of these sialylated gangliosides and their modulating biological behavior in vivo, further studies on the role of gangliosides are warranted.

Innovative cancer vaccine strategies based on the identification of tumour-associated antigens

The identification of tumour-associated antigens has opened up new approaches to cancer immunotherapy. While past research focused on CD8+ cytotoxic T-cell responses, accumulating evidence suggests that CD4+ T cells also play an important role in orchestrating the host immune response against cancer. In this article, we summarise new strategies for the identification of major histocompatibility complex (MHC) class II-associated tumour antigens and discuss the importance of engaging both CD4+ and CD8+ T cells in cancer immunotherapy. The cloning of MHC class I- or class II-associated antigens has made it possible to develop synthetic and recombinant cancer vaccines that express specific tumour antigens. There are three major types of synthetic and recombinant cancer vaccines: recombinant viral and bacterial vaccines; naked DNA or RNA vaccines; and recombinant protein and peptide vaccines. In this article, we also discuss a new generation of recombinant cancer vaccines, 'self-replicating' DNA and RNA vaccines. Studies on the mechanisms of 'self-replicating' nucleic acid vaccines revealed that the enhanced immunogenicity was not due to an enhanced antigen expression, suggesting that the quantitative difference may not be as important as the qualitative difference in antigen presentation. The presence of the RNA replicase in the 'self-replicating' nucleic acid vaccines mimics alphavirus infection, which triggers the innate antiviral pathways of the host cells. Studies on how viral and cellular modulators of the innate antiviral pathways affect vaccine function should provide molecular insights crucial to future vaccine design.

Regulation of yeast actin cytoskeleton-regulatory complex Pan1p/Sla1p/End3p by serine/threonine kinase Prk1p

The serine/threonine kinase Prk1p is known to be involved in the regulation of the actin cytoskeleton organization in budding yeast. One possible function of Prk1p is the negative regulation of Pan1p, an actin patch regulatory protein that forms a complex in vivo with at least two other proteins, Sla1p and End3p. In this report, we identified Sla1p as another substrate for Prk1p. The phosphorylation of Sla1p by Prk1p was established in vitro with the use of immunoprecipitated Prk1p and in vivo with the use of PRK1 overexpression, and was further supported by the finding that immunoprecipitated Sla1p contained PRK1- and ARK1-dependent kinase activities. Stable complex formation between Prk1p and Sla1p/Pan1p in vivo could be observed once the phosphorylation reaction was blocked by mutation in the catalytic site of Prk1p. Elevation of Prk1p activities in wild-type cells resulted in a number of deficiencies, including those in colocalization of Pan1p and Sla1p, endocytosis, and cell wall morphogenesis, likely attributable to a disintegration of the Pan1p/Sla1p/End3p complex. These results lend a strong support to the model that the phosphorylation of the Pan1p/Sla1p/End3p complex by Prk1p is one of the important mechanisms by which the organization and functions of the actin cytoskeleton are regulated.