Nonlinear dust-acoustic structures in space plasmas with superthermal electrons,positrons, and ions

Some features of nonlinear dust-acoustic (DA) structures are investigated in a space plasma consisting of superthermal electrons, positrons, and positive ions in the presence of negatively charged dust grains with finite-temperature by employing a pseudo-potential technique in a hydrodynamic model. For this purpose, it is assumed that the electrons, positrons, and ions obey a kappa-like (κ) distribution in the background of adiabatic dust population. In the linear analysis, it is found that the dispersion relation yield two positive DA branches, i.e., the slow and fast DA waves. The upper branch (fast DA waves) corresponds to the case in which both (negatively charged) dust particles and (positively charged) ion species oscillate in phase with electrons and positrons. On the other hand, the lower branch (slow DA waves) corresponds to the case in which only dust particles oscillate in phase with electrons and positrons, while ion species are in antiphase with them. On the other hand, the fully nonlinear analysis shows that the existence domain of solitons and their characteristics depend strongly on the dust charge, ion charge, dust temperature, and the spectral index κ. It is found that the minimum/maximum Mach number increases as the spectral index κ increases. Also, it is found that only solitons with negative polarity can propagate and that their amplitudes increase as the parameter κ increases. Furthermore, the domain of Mach number shifts to the lower values, when the value of the dust charge Z _d increases. Moreover, it is found that the Mach number increases with an increase in the dust temperature. Our analysis confirms that, in space plasmas with highly charged dusts, the presence of superthermal particles (electrons, positrons, and ions) may facilitate the formation of DA solitary waves. Particularly, in two cases of hydrogen ions H⁺ (Z _i = 1) and doubly ionized Helium atoms He²⁺ (Z _i = 2), the mentioned results are the same. Additionally, the mentioned dusty plasma does not support DA solitons with positive polarity (compressive solitons). Furthermore, our analysis confirms that DA double layers cannot exist in such a system. Moreover, the positron density has not a considerable effect on the behavior of DA solitons in our model.     

Exact calculations of average power for the Benjamini-Hochberg procedure

Exact analytic expressions are developed for the average power of the Benjamini and Hochberg false discovery control procedure. The result is based on explicit computation of the joint probability distribution of the total number of rejections and the number of false rejections, and expressed in terms of the cumulative distribution functions of the p-values of the hypotheses. An example of analytic evaluation of the average power is given. The result is confirmed by numerical experiments and applied to a meta-analysis of three clinical studies in mammography.     

Off-center spherical model for dosimetry calculations in chick brain tissue

This paper presents calculations for the electric field and absorbed power density distribution in chick brain tissue inside a test tube, using an off-center spherical model. It is shown that the off-center spherical model overcomes many of the limitations of the concentric spherical model, and permits a more realistic modeling of the brain tissue as it sits in the bottom of the test tube surrounded by buffer solution. The effect of the unequal amount of buffer solution above the upper and below the lower surfaces of the brain is analyzed. The field distribution is obtained in terms of a rapidly converging series of zonal harmonics. A method that permits the expansion of spherical harmonics about an off-center origin in terms of spherical harmonics at the origin is developed to calculate in closed form the electric field distribution. Numerical results are presented for the absorbed power density distribution at a carrier frequency of 147 MHz. It is shown that the absorbed power density increases toward the bottom of the brain surface. Scaling relations are developed by keeping the electric field intensity in the brain tissue the same at two different frequencies. Scaling relations inside, as well as outside, the brain surface are given. The scaling relation distribution is calculated as a function of position, and compared to the scaling relations obtained in the concentric spherical model. It is shown that the off-center spherical model yields scaling ratios in the brain tissue that lie between the extreme values predicted by the concentric and isolated spherical models.     

Empirical power and sample size calculations for cluster-randomized and cluster-randomized crossover studies

In recent years, the number of studies using a cluster-randomized design has grown dramatically. In addition, the cluster-randomized crossover design has been touted as a methodological advance that can increase efficiency of cluster-randomized studies in certain situations. While the cluster-randomized crossover trial has become a popular tool, standards of design, analysis, reporting and implementation have not been established for this emergent design. We address one particular aspect of cluster-randomized and cluster-randomized crossover trial design: estimating statistical power. We present a general framework for estimating power via simulation in cluster-randomized studies with or without one or more crossover periods. We have implemented this framework in the clusterPower software package for R, freely available online from the Comprehensive R Archive Network. Our simulation framework is easy to implement and users may customize the methods used for data analysis. We give four examples of using the software in practice. The clusterPower package could play an important role in the design of future cluster-randomized and cluster-randomized crossover studies. This work is the first to establish a universal method for calculating power for both cluster-randomized and cluster-randomized clinical trials. More research is needed to develop standardized and recommended methodology for cluster-randomized crossover studies.     

Comparisons of calculations with PARTRAC and NOREC: transport of electrons in liquid water

Monte Carlo computer models that simulate the detailed, event-by-event transport of electrons in liquid water are valuable for the interpretation and understanding of findings in radiation chemistry and radiation biology. Because of the paucity of experimental data, such efforts must rely on theoretical principles and considerable judgment in their development. Experimental verification of numerical input is possible to only a limited extent. Indirect support for model validity can be gained from a comparison of details between two independently developed computer codes as well as the observable results calculated with them. In this study, we compare the transport properties of electrons in liquid water using two such models, PARTRAC and NOREC. Both use interaction cross sections based on plane-wave Born approximations and a numerical parameterization of the complex dielectric response function for the liquid. The models are described and compared, and their similarities and differences are highlighted. Recent developments in the field are discussed and taken into account. The calculated stopping powers, W values, and slab penetration characteristics are in good agreement with one another and with other independent sources.     

SPCalc: A web-based calculator for sample size and power calculations in micro-array studies

Calculation of the appropriate sample size in planning microarray studies is important because sample collection can be expensive and time-consuming. Sample-size calculation is also a challenging issue for microarray studies because the number of genes is far larger than the number of samples so that traditional methods of sample-size calculation cannot be directly applied. To help investigators answer the question of how many samples are needed in their microarray studies, we developed a user-friendly web-based calculator, SPCalc, for calculating sample size and power for a variety of commonly used experimental designs, including completely randomized treatmentcontrol design, matched-pairs design, multiple-treatment design having an isolated treatment effect, and randomized block design. AVAILABILITY: The web-based calculator SPCalc is publicly available at http://www.biostat.harvard.edu /people/faculty/mltlee/webfront-r.html.     

Comparative proteome analysis of breast cancer and adjacent normal breast tissues in human

Two-dimensional polyacrylamide gel assisted laser desorption/ionization electrophoresis （2D-PAGE） and matrixtandem time-of-flight mass spectrometry （MALDI-TOF/TOF-MS）, incorporated with online database searching, were performed to investigate differential proteins of breast cancer and adjacent normal breast tissues. Considering that serum albumin is abundantly presented in normal control samples, 15 differential spots detected in 11 out of 12 （91.7%） breast cancer samples were identified by online SIENA-2DPAGE database searching and MALDI-TOF/TOF-MS analysis. The results indicate that pathological changes of breast cancer are concerned with augmentation of substance metabolism, promotion of proteolytic activity, decline of activity of some inhibitors of enzymes, and so on. Some important proteins involved in the pathological process of breast cancer with changed expression may be useful biomarkers, such as alpha-l-antitrypsin, EF- 1-beta, cathepsin D, TCTP, SMT3A, RPS12, and PSMA1, among which SMT3A, RPSl2, and PSMA1 were first reported for breast cancer in this study.     

Glutamine synthetase isozymes in elasmobranch brain and liver tissues

Glutamine synthetase is present as isozymic forms in the elasmobranchs Squalus acanthias (dogfish shark) and Dasyatis sabina (stingray). Subcellular fractionation of elasmobranch brain and liver tissue shows the enzyme to be predominantly cytosolic in the former tissue and mitochondrial in the latter. For the cytosolic brain enzyme, the subunit Mr equals 42,000 in the stingray and 45,000 in the shark, as determined by sodium dodecyl sulfate-gel electrophoresis/Western blotting. The subunit Mr = 45,000 and 47,000, respectively, for stingray and dogfish mitochondrial liver enzymes. Translation of total brain RNA from both species gives immunoprecipitable nascent peptides of the same size as their respective mature enzymes. However, in liver tissue, translation of glutamine synthetase mRNA yields peptides of higher Mr than that of the mature enzymes. In dogfish liver, Mr = 50,000 for the translation product and, in stingray liver, Mr = 48,000. This suggests that the translocation of the enzyme into liver mitochondria may be via a signal or leader sequence mechanism. The larger liver isozyme of elasmobranch glutamine synthetase is found in kidney where it is also known to be mitochondrial. The smaller cytosolic isozyme occurs in retina, heart, gill, and rectal gland tissue as well as in brain.     

Selecting tagging SNPs for association studies using power calculations from genotype data

Recent studies have indicated that linkage disequilibrium (LD) between single nucleotide polymorphism (SNP) markers can be used to derive a reduced set of tagging SNPs (tSNPs) for genetic association studies. Previous strategies for identifying tSNPs have focused on LD measures or haplotype diversity, but the statistical power to detect disease-associated variants using tSNPs in genetic studies has not been fully characterized. We propose a new approach of selecting tSNPs based on determining the set of SNPs with the highest power to detect association. Two-locus genotype frequencies are used in the power calculations. To show utility, we applied this power method to a large number of SNPs that had been genotyped in Caucasian samples. We demonstrate that a significant reduction in genotyping efforts can be achieved although the reduction depends on genotypic relative risk, inheritance mode and the prevalence of disease in the human population. The tSNP sets identified by our method are remarkably robust to changes in the disease model when small relative risk and additive mode of inheritance are employed. We have also evaluated the ability of the method to detect unidentified SNPs. Our findings have important implications in applying tSNPs from different data sources in association studies.     

Selection for environmental variation: a statistical analysis and power calculations to detect response

Data from uterine capacity in rabbits (litter size) were analyzed to determine whether the environmental variance was partly genetically determined. The fit of a classical homogeneous variance mixed linear (HOM) model and that of a genetically structured heterogeneous variance mixed linear (HET) model were compared. Various methods to assess the quality of fit favor the HET model. The posterior mean (95% posterior interval) of the additive genetic variance affecting the environmental variance was 0.16 (0.10; 0.25) and the corresponding number for the coefficient of correlation between genes affecting mean and variance was -0.74 (-0.90;-0.52). It is argued that stronger support for the HET model than that derived from statistical analysis of data would be provided by a successful selection experiment designed to modify the environmental variance. A simple selection criterion is suggested (average squared deviation from the mean of repeated records within individuals) and its predicted response and variance under the HET model are derived. This is used to determine the appropriate size and length of a selection experiment designed to change the environmental variance. Results from the analytical expressions are compared with those obtained using simulation. There is good agreement provided selection intensity is not intense.     

Progression of thanatophagy in cadaver brain and heart tissues

Autophagy is an evolutionarily conserved catabolic process for maintaining cellular homeostasis during both normal and stress conditions. Metabolic reprogramming in tissues of dead bodies is inevitable due to chronic ischemia and nutrient deprivation, which are well-known features that stimulate autophagy. Currently, it is not fully elucidated whether postmortem autophagy, also known as thanatophagy, occurs in dead bodies is a function of the time of death. In this study, we tested the hypothesis that thanatophagy would increase in proportion to time elapsed since death for tissues collected from cadavers. Brain and heart tissue from corpses at different time intervals after death were analyzed by Western blot. Densitometry analysis demonstrated that thanatophagy occurred in a manner that was dependent on the time of death. The autophagy-associated proteins, LC3 II, p62, Beclin-1 and Atg7, increased in a time-dependent manner in heart tissues. A potent inducer of autophagy, BNIP3, decreased in the heart tissues as time of death increased, whereas the protein levels increased in brain tissues. However, there was no expression of BNIP3 at extended postmortem intervals in both brain and heart samples. Collectively, the present study demonstrates for the first time that thanatophagy occurs in brain and heart tissues of cadavers in a time-dependent manner. Further, our data suggest that cerebral thanatophagy may occur in a Beclin-1- independent manner. This unprecedented study provides potential insight into thanatophagy as a novel method for the estimation of the time of death in criminal investigationsAbstract: Autophagy is an evolutionarily conserved catabolic process for maintaining cellular homeostasis during both normal and stress conditions. Metabolic reprogramming in tissues of dead bodies is inevitable due to chronic ischemia and nutrient deprivation, which are well-known features that stimulate autophagy. Currently, it is not fully elucidated whether postmortem autophagy, also known as thanatophagy, occurs in dead bodies is a function of the time of death. In this study, we tested the hypothesis that thanatophagy would increase in proportion to time elapsed since death for tissues collected from cadavers. Brain and heart tissue from corpses at different time intervals after death were analyzed by Western blot. Densitometry analysis demonstrated that thanatophagy occurred in a manner that was dependent on the time of death. The autophagy-associated proteins, LC3 II, p62, Beclin-1 and Atg7, increased in a time-dependent manner in heart tissues. A potent inducer of autophagy, BNIP3, decreased in the heart tissues as time of death increased, whereas the protein levels increased in brain tissues. However, there was no expression of BNIP3 at extended postmortem intervals in both brain and heart samples. Collectively, the present study demonstrates for the first time that thanatophagy occurs in brain and heart tissues of cadavers in a time-dependent manner. Further, our data suggest that cerebral thanatophagy may occur in a Beclin-1- independent manner. This unprecedented study provides potential insight into thanatophagy as a novel method for the estimation of the time of death in criminal investigations     

Roles of steroid sulfatase in brain and other tissues

Steroid sulfatase (EC 3.1.6.2) is an important enzyme involved in steroid hormone metabolism. It catalyzes the hydrolysis of steroid sulfates into their unconjugated forms. This action rapidly changes their physiological and biochemical properties, especially in brain and neural tissue. As a result, any imbalance in steroid sulfatase activity may remarkably influence physiological levels of active steroid hormones with serious consequences. Despite that the structure of the enzyme has been completely resolved there is still not enough information about the regulation of its expression and action in various tissues. In the past few years research into the enzyme properties and regulations has been strongly driven by the discovery of its putative role in the indirect stimulation of the growth of hormone-dependent tumors of the breast and prostate.     

GLUT 5 is not over-expressed in breast cancer cells and patient breast cancer tissues

F18 2-Fluoro 2-deoxyglucose (FDG) has been the gold standard in positron emission tomography (PET) oncologic imaging since its introduction into the clinics several years ago. Seeking to complement FDG in the diagnosis of breast cancer using radio labeled fructose based analogs, we investigated the expression of the chief fructose transporter-GLUT 5 in breast cancer cells and human tissues. Our results indicate that GLUT 5 is not over-expressed in breast cancer tissues as assessed by an extensive immunohistochemistry study. RT-PCR studies showed that the GLUT 5 mRNA was present at minimal amounts in breast cancer cell lines. Further knocking down the expression of GLUT 5 in breast cancer cells using RNA interference did not affect the fructose uptake in these cell lines. Taken together these results are consistent with GLUT 5 not being essential for fructose uptake in breast cancer cells and tissues.     

Exercise induces autophagy in peripheral tissues and in the brain

We recently identified physical exercise as a newly defined inducer of autophagy in vivo. Exercise induced autophagy in multiple organs involved in metabolic regulation, such as muscle, liver, pancreas and adipose tissue. To study the physiological role of exercise-induced autophagy, we generated mice with a knock-in nonphosphorylatable mutation in BCL2 (Thr69Ala, Ser70Ala and Ser84Ala) (BCL2 AAA) that are defective in exercise- and starvation-induced autophagy but not in basal autophagy. We found that BCL2 AAA mice could not run on a treadmill as long as wild-type mice, and did not undergo exercise-mediated increases in skeletal glucose muscle uptake. Unlike wild-type mice, the BCL2 AAA mice failed to reverse high-fat diet-induced glucose intolerance after 8 weeks of exercise training, possibly due to defects in signaling pathways that regulate muscle glucose uptake and metabolism during exercise. Together, these findings suggested a hitherto unknown important role of autophagy in mediating exercise-induced metabolic benefits. In the present addendum, we show that treadmill exercise also induces autophagy in the cerebral cortex of adult mice. This observation raises the intriguing question of whether autophagy may in part mediate the beneficial effects of exercise in neurodegeneration, adult neurogenesis and improved cognitive function.