P-value based analysis for shared controls design in genome-wide association studies

An appealing genome-wide association study design compares one large control group against several disease samples. A pioneering study by the Wellcome Trust Case Control Consortium that employed such a design has identified multiple susceptibility regions, many of which have been independently replicated. While reusing a control sample provides effective utilization of data, it also creates correlation between association statistics across diseases. An observation of a large association statistic for one of the diseases may greatly increase chances of observing a spuriously large association for a different disease. Accounting for the correlation is also particularly important when screening for SNPs that might be involved in a set of diseases with overlapping etiology. We describe methods that correct association statistics for dependency due to shared controls, and we describe ways to obtain a measure of overall evidence and to combine association signals across multiple diseases. The methods we describe require no access to individual subject data, instead, they efficiently utilize information contained in P-values for association reported for individual diseases. P-value based combined tests for association are flexible and essentially as powerful as the approach based on aggregating the individual subject data.     

Dosimetric feasibility of cone-beam CT-based treatment planning compared to CT-based treatment planning

PURPOSE: Cone-beam computed tomography (CBCT) images are currently used for positioning verification. However, it is yet unknown whether CBCT could be used in dose calculation for replanning in adaptive radiation therapy. This study investigates the dosimetric feasibility of CBCT-based treatment planning. METHODS AND MATERIALS: Hounsfield unit (HU) values and profiles of Catphan, homogeneous/inhomogeneous phantoms, and various tissue regions of patients in CBCT images were compared to those in CT. The dosimetric consequence of the HU variation was investigated by comparing CBCT-based treatment plans to conventional CT-based plans for both phantoms and patients. RESULTS: The maximum HU difference between CBCT and CT of Catphan was 34 HU in the Teflon. The differences in other materials were less than 10 HU. The profiles for the homogeneous phantoms in CBCT displayed reduced HU values up to 150 HU in the peripheral regions compared to those in CT. The scatter and artifacts in CBCT became severe surrounding inhomogeneous tissues with reduced HU values up to 200 HU. The MU/cGy differences were less than 1% for most phantom cases. The isodose distributions between CBCT-based and CT-based plans agreed very well. However, the discrepancy was larger when CBCT was scanned without a bowtie filter than with bowtie filter. Also, up to 3% dosimetric error was observed in the plans for the inhomogeneous phantom. In the patient studies, the discrepancies of isodose lines between CT-based and CBCT-based plans, both 3D and IMRT, were less than 2 mm. Again, larger discrepancy occurred for the lung cancer patients. CONCLUSION: This study demonstrated the feasibility of CBCT-based treatment planning. CBCT-based treatment plans were dosimetrically comparable to CT-based treatment plans. Dosimetric data in the inhomogeneous tissue regions should be carefully validated.     

Static and dynamic standing balance: test-retest reliability and reference values in 9 to 10 year old children

Introduction Based on the literature, reliability reports and normative data for bilateral stance assessments in elementary schoolchildren are limited. The present study was designed to report test-retest reliability and reference values for postural stability in 9 to 10 years old schoolchildren using the Balance Master system.Materials and methods Twenty children participated in the reproducibility study (mean age 10.1±0.7) including test and retest measurement with a one-week interval. The modified clinical test of sensory interaction on balance (mCTSIB) quantified children’s static standing balance. The test for the limits of stability (LOS) measured dynamic standing balance. The study sample to determine reference values consisted of 99 children (mean age 9.8±0.5).Results The ICCs for inter-item reliability of the four sensory conditions of the mCTSIB showed fair to excellent reliability (ICCs between 0.62 and 0.80). The reproducibility between test and retest was non-significant for the condition ‘firm surface with eyes closed’ (ICC of 0.37), fair to good for the three other sensory conditions (ICCs between 0.59 and 0.68), and excellent for the composite sway velocity (ICC of 0.77). For all LOS parameters, the significant ICCs showed fair to good reproducibility (ICCs between 0.44 and 0.62), with the exception of the non-significant ICC for the composite reaction time. The ICCs for the separate LOS parameters showed fair to good and excellent reliability for nine parameters (ICCs between 0.46 and 0.81), while 11 separate LOS scores did not demonstrate significant ICCs.Discussion Analysing reference values, girls performed better on all the composite balance parameters compared to boys, with the exception of reaction time and movement velocity. No differences were found on standing balance scores between 9 and 10 year olds.Conclusion In conclusion, the Balance Master showed fair to good reliability for most postural parameters in 9 to 10 year olds. The current data on postural control in children aged 9 to 10 years are relevant for research in other domains within the clinical field, like obesitas and developmental coordination disorder or in relation to back pain prevalence at early age.     

Dynamics of hepatic enzyme activity following birth asphyxia

Aim: To investigate: 1) the occurrence of hypoxic hepatitis in full-term infants after birth asphyxia, 2) the temporal enzyme pattern in asphyxiated newborn infants, and 3) whether the degree of hypoxic hepatitis, as reflected by the rise in aminotransferase, correlates with the severity of the asphyxia and CNS symptomatology. Methods: Serum aminotransferases, lactate dehydrogenase, gamma-glutamyl transferase, total and conjugated bilirubin, cholinesterase activity, albumin, international normalized ratio (INR), and nucleated red blood cell count were prospectively measured in full-term asphyxiated newborn infants (n=26). Samples were collected three times during the first 72 h and once between days 6 and 12 after birth. Samples from healthy newborns (n=56), collected 24-172 h after birth, served as controls. Results: In 12 of the 26 asphyxiated infants, a serum alanine aminotransferase (S-ALAT) pattern compatible with hypoxic hepatitis was found. Five infants showed increased S-ALAT activity but with a different pattern. Similar patterns were seen in serum aspartate aminotransferase (S-ASAT). S-ALAT and -ASAT concentrations 0-72 h after birth correlated significantly with severity of hypoxic-ischaemic encephalopathy.
Conclusion: Birth asphyxia can induce an enzyme pattern in serum compatible to hypoxic hepatitis. There seems to be a correlation between aminotransferases in serum and the extent of CNS injury.     

Total peroxyl radical-trapping ability and anti-oxidant vitamins of the umbilical venous plasma and the placenta in pre-eclampsia

AIM: Our purpose was to investigate lipid peroxide levels, total peroxyl radical-trapping anti-oxidative parameter (TRAP) values, and anti-oxidant vitamin levels in umbilical venous plasma and placental tissues, and to evaluate their roles in the pathophysiology of pre-eclampsia. METHODS: Samples of umbilical venous plasma and placental tissue homogenates were obtained from 23 normal and 18 pre-eclamptic women at between 33 and 40 weeks' gestation. The enzyme-linked immunosorbent assay method was used to assay alpha-tumor necrosis factor (TNF-alpha), and lipid peroxide levels were measured by thiobarbituric acid reaction. The TRAP values were measured using the modified Wayner's method. Ascorbic acid, retinol alpha-tocopherol and gamma-tocopherol were measured by high performance liquid chromatography. RESULTS: Levels of TNF-alpha in placental tissue homogenates of women with pre-eclampsia were significantly higher than those of women with normal pregnancy (21.4 +/- 3.39 v. 10.3 +/- 1.06 pg/mL, P < 0.05). Lipid peroxide levels in umbilical venous plasma and placental tissue homogenates of women with pre-eclampsia were significantly higher than those of women with normal pregnancy (10.3 +/- 1.1 v. 5.85 +/- 0.53, P < 0.01, 5.14 +/- 0.40 v. 3.99 +/- 0.33 nmol/mg protein, P < 0.05, respectively). The TRAP values in umbilical venous plasma and placental tissue homogenates of women with pre-eclampsia were significantly lower than those of women with normal pregnancy (0.39 +/- 0.02 v. 0.45 +/- 0.02, P < 0.05, 0.27 +/- 0.02 v. 0.34 +/- 0.03 mM, P < 0.05, respectively). Ascorbic acid levels in umbilical venous plasma and placental tissue homogenates of women with pre-eclampsia were significantly lower than those of women with normal pregnancy (325.4 +/- 50.4 v. 543 +/- 73.8, P < 0.05, 219.0 +/- 21.0 v. 333.3 +/- 32.6 nmol/mL, P < 0.05, respectively). CONCLUSIONS: The above results suggest that increased oxidative stress in the placenta is involved in the pathophysiology of pre-eclampsia, and ascorbic acid may act as an important preventative factor in the development of pre-eclampsia.     

Quantification of immunohistochemistry--issues concerning methods, utility and semiquantitative assessment II

Immunohistochemistry is entering its fourth decade of use on formalin‐fixed paraffin‐embedded tissues. Over this period the method has evolved to become a major part of the practice of diagnostic surgical pathology worldwide. From the beginning immunohistochemistry has been adapted to provide a range of markers of cell lineage and tissue type, with particular application to the diagnosis and classification of tumours. In this modality immunohistochemical methods were employed simply as ‘special stains’, the results of which were evaluated qualitatively by the pathologist, as for any other stain. More recently, attention has shifted to the demonstration of prognostic markers in tumour cells, driven by the advent of molecular biology and the discovery of numerous regulatory molecules, coupled with manufacture of the corresponding specific antibodies. Immunohistochemistry has rapidly adapted to this new use, but in so doing the demand for quantification has become paramount; it is no longer enough that the ‘stain’ is there; rather it is a question of ‘How much is there?’. This review explores the limitations of immunohistochemistry when employed in a semiquantitative mode, and explores the possibility of fulfilling the full potential of immunohistochemistry, as a true quantitative immunoassay applied in a tissue section environment.     

Development of a commercial cigarette "market map" comparison methodology for evaluating new or non-conventional cigarettes

A "market map" comparison methodology for cigarette smoke chemistry yields is presented. Federal Trade Commission machine-method smoke chemistry was determined for a range of filtered cigarettes from the US marketplace. These data were used to develop illustrative market maps for each smoke constituent as analytical tools for comparing new or non-conventional cigarettes to a sampling of the broader range of marketplace cigarettes. Each market map contained best-estimate "market-means," showing the relationship between commercial cigarette constituent and tar yields, and yield "market ranges" defined by prediction intervals. These market map means and ranges are the basis for comparing new cigarette smoke yields to those of conventional cigarettes. The potential utility of market maps for evaluating differences in smoke chemistry was demonstrated with 1R4F and 2R4F Kentucky reference cigarettes, an Accord cigarette, and an Advance cigarette. Conventional cigarette tobacco nicotine, nitrate, soluble ammonia, and tobacco specific nitrosamine levels are reported. Differences among conventional cigarette constituent yields at similar tar levels were explained in part by the chemical composition range of those cigarette tobaccos. The study also included a comparison of smoke constituent yields and in vitro smoke cytotoxicity and mutagenicity assay results for the 1R4F Kentucky reference cigarette and its replacement 2R4F. Significant smoke yield differences were noted for lead, NNK, and NNN. The majority of their smoke constituent yields were within the market range developed from the sampled conventional cigarettes. Within the sensitivity and specificity of the in vitro bioassays used, smoke toxic activity differences for the two reference cigarettes were not statistically significant. These results add to the limited information available for the 2R4F reference cigarette.     

Evaluation of the antioxidant activity of wheatgrass (Triticum aestivum L.) as a function of growth under different conditions

The antioxidant activity of wheatgrass, which is consumed as a dietary supplement, was estimated at different levels. The methods employed include FRAP (ferric reducing antioxidant power), ABTS (2,2'-azobis-3-ethylbenzthiazoline-6-sulfonic acid) and DPPH (1,1'-diphenyl-2-picrylhydrazyl) assays. Aqueous and ethanol extracts of wheatgrass grown under different conditions over a period of 6, 7, 8, 10 and 15 days were used. Lipid peroxidation and oxygen radical absorbance capacity (ORAC) were determined and utilized to check the potency of a few selected extracts. Different conditions used for growth were (1) tap water, (2) tap water with nutrients, (3) soil and tap water, and (4) soil with nutrients. For comparison, a commercially available wheatgrass tablet was analysed. To explain the reasons behind the observed differences, the total phenolic and flavonoid contents of the extracts were measured. These contents increased with growth under all the conditions. The ethanol extracts were found to have a higher phenolic and flavonoid content than the aqueous extracts. The highest FRAP values occurred on day 15 of growth under condition 4, the values being 0.463 and 0.573 mmol of ascorbic acid and Trolox equivalents/100 g fresh wheatgrass for aqueous and ethanol extracts, respectively. In the aqueous extracts no specific trend was observed with the DPPH assay for the different conditions nor for the growth period. In the case of ethanol extracts, however, it increased with the growth period and the wheatgrass grown in condition 4 was found to be the most effective. These extracts were also found to inhibit significantly ascorbate-Fe2+ induced lipid peroxidation in rat liver mitochondria. The ORAC values of aqueous and ethanol extracts of day 10 with condition 4 were found to be 39.9 and 48.2, respectively, being higher than those reported for many natural extracts or vegetables.