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IR microspectroscopy: potential applications in cervical cancer screening.

Screening exfoliative cytology for early dysplastic cells reduces incidence and mortality from squamous carcinoma of the cervix. In the developed world, screening programmes have adopted a 3-5 years recall system. In its absence, cervical cancer would be the second most common female cancer in these regions; instead, it is currently eleventh. However, there exist a number of limitations to the smear test even given the removal of contaminants using liquid-based cytology. It is prohibitively expensive, labour-intensive and subject to inaccuracies that give rise to significant numbers of false negatives. There remains a need for novel approaches to allow efficient and objective interrogation of exfoliative cytology. Methods that variously exploit infrared (IR) microspectroscopy are one possibility. Using IR microspectroscopy, an integrated 'biochemical-cell fingerprint' of the lipid, protein and carbohydrate composition of a biomolecular entity may be derived in the form of a spectrum via vibrational transitions of individual chemical bonds. Powerful statistical approaches (e.g. principal component analysis) now facilitate the interrogation of large amounts of spectroscopic data to allow the extraction of what may be small but extremely significant biomarker differences between disease-free and pre-malignant or malignant samples. An increasing wealth of literature points to the ability of IR microspectroscopy to allow the segregation of cells based on their disease status. We review the current evidence supporting its diagnostic potential in cancer biology.

Female↗

Power in randomized group comparisons: the value of adding a single intermediate time point to a traditional pretest-posttest design.

Adding a pretest as a covariate to a randomized posttest-only design increases statistical power, as does the addition of intermediate time points to a randomized pretest-posttest design. Although typically 5 waves of data are required in this instance to produce meaningful gains in power, a 3-wave intensive design allows the evaluation of the straight-line growth model and may reduce the effect of missing data. The authors identify the statistically most powerful method of data analysis in the 3-wave intensive design. If straight-line growth is assumed, the pretest-posttest slope must assume fairly extreme values for the intermediate time point to increase power beyond the standard analysis of covariance on the posttest with the pretest as covariate, ignoring the intermediate time point.

Humans↗

Inferring the historical patterns of biological evolution.

Phylogenetic trees describe the pattern of descent amongst a group of species. With the rapid accumulation of DNA sequence data, more and more phylogenies are being constructed based upon sequence comparisons. The combination of these phylogenies with powerful new statistical approaches for the analysis of biological evolution is challenging widely held beliefs about the history and evolution of life on Earth.

Animals↗

The application of statistical physics to evolutionary biology.

A number of fundamental mathematical models of the evolutionary process exhibit dynamics that can be difficult to understand analytically. Here we show that a precise mathematical analogy can be drawn between certain evolutionary and thermodynamic systems, allowing application of the powerful machinery of statistical physics to analysis of a family of evolutionary models. Analytical results that follow directly from this approach include the steady-state distribution of fixed genotypes and the load in finite populations. The analogy with statistical physics also reveals that, contrary to a basic tenet of the nearly neutral theory of molecular evolution, the frequencies of adaptive and deleterious substitutions at steady state are equal. Finally, just as the free energy function quantitatively characterizes the balance between energy and entropy, a free fitness function provides an analytical expression for the balance between natural selection and stochastic drift.

Adaptation, Biological↗

Early impairment of systolic and diastolic function in asymptomatic HIV-positive patients: a multicenter echocardiographic and echo-Doppler study. The Gruppo Italiano Per lo Studio Cardiologico dei Pazienti Affetti da AIDS.

Human immunodeficiency virus (HIV) possesses an intrinsic cardiopathogenic action that may be detected even in the early stages of HIV disease. To assess an early impairment of systolic and diastolic function in asymptomatic HIV-positive patients (CD4+ > or = 600/mm3), we performed a multicenter echocardiographic and echo-Doppler trial on 1236 asymptomatic NYHA class I HIV-positive patients (885 M and 351 F; mean age 28 years) compared with 1230 healthy subjects (922 M and 308 F; mean age 30 years). The sample size was established considering, as null hypothesis, a difference less than 10% in the values of the principal echocardiographic and echo-Doppler parameters between groups with a 90% statistical power (alpha = 0.01; beta = 0.10). Analysis of echocardiographic and echo-Doppler data revealed a reduction of 19.7% in ejection fraction, an increase of 55.7% in wall motion score, a reduction of 34.6% in the E/A ratio, and an increase of 19.7% in the isovolumetric relaxation time in HIV-positive subjects compared with healthy controls (p < 0.001). Baseline electrocardiographic alterations were observed in 707 (57.2%) HIV-positive subjects and in 169 (13.7%) of the subjects of the control group (p < 0.001). The results of our study have demonstrated that in asymptomatic HIV-positive subjects a significant impairment of systolic and diastolic function may be detected by echocardiographic and echo-Doppler examination, confirming an early involvement of the heart in HIV disease.

Adult↗

High density lipoprotein cholesterol increases with living altitude.

BACKGROUND: The relationship between high density lipoprotein cholesterol (HDL) serum level and the altitude at which people live is controversial. METHODS: A cross-sectional study was carried out in the adult population (30-64 years) of the Island of El Hierro (Canary Islands, Spain). In all, 594 individuals representative of the El Hierro population for gender, age, district and the altitude at which they lived were included. The factors measured included HDL, living altitude, body mass index (BMI), smoking habits, alcohol consumption, diabetes, menopause in women, and physical activity and dietary habits. RESULTS: The HDL showed a correlation with living altitude (r = 0.14, P < 0.01) and with BMI (r = -0.19, P < 0.01). Smokers had lower HDL levels than ex-smokers and non-smokers (P < 0.05). Men who were moderate drinkers had higher HDL levels than heavy or mild drinkers and non-drinkers (P < 0.01). Physical activity was only related to HDL in men with levels >1.52 mmol/l, who walked on the average more than the rest (P < 0.05). Variables not showing the expected relationship with HDL were diabetes and the menopause in women (probably due to a low statistical power of their subsamples). Regression analysis, with HDL as dependent variable showed that the association between HDL and altitude persists when taking altitude as a categorical or a continuous variable. CONCLUSIONS: High density lipoprotein cholesterol levels are linearly and significantly increased when living at a higher altitude. This fact should be taken into account when comparing cardiovascular risk in populations living at different altitudes.

Adult↗

Analysis of rodent growth data in toxicology studies.

To evaluate compound-related effects on the growth of rodents, body weight and food consumption data are commonly collected either weekly or biweekly in toxicology studies. Body weight gain, food consumption relative to body weight, and efficiency of food utilization can be derived from body weight and food consumption for each animal in an attempt to better understand the compound-related effects. These five parameters are commonly analyzed in toxicology studies for each sex using a one-factor analysis of variance (ANOVA) at each collection point. The objective of this manuscript is to present an alternative approach to the evaluation of compound-related effects on body weight and food consumption data from both subchronic and chronic rodent toxicology studies. This approach is to perform a repeated-measures ANOVA on a selected set of parameters and analysis intervals. Compared with a standard one-factor ANOVA, this approach uses a statistical analysis method that has greater power and reduces the number of false-positive claims, and consequently provides a succinct yet comprehensive summary of the compound-related effects. Data from a mouse carcinogenicity study are included to illustrate this repeated-measures ANOVA approach to analyzing growth data in contrast with the one-factor ANOVA approach.

Analysis of Variance↗

Hospital Outcomes Project for the Elderly (HOPE): rationale and design for a prospective pooled analysis.

OBJECTIVE: To describe a collaborative investigation that is based on a series of six clinical studies aimed at reducing functional decline in the acutely-ill hospitalized elderly. DESIGN: A prospective, multicenter pooled analysis project involving collection of a common set of data from a group of related but distinct intervention trials with similar objectives. SETTING: Five university-affiliated hospitals and one community hospital. PARTICIPANTS: Elderly patients (age minimums from 65 to 75 years) admitted for a range of acute illnesses. INTERVENTIONS: Site-specific interventions include exercise and physical therapy; developing and implementing methods to improve detection and evaluation of delirious patients; a multidisciplinary geriatric care unit; a multidisciplinary intervention implemented in-hospital that includes some post-discharge care; and a nursing-centered geriatric care program. MAIN OUTCOME MEASURE: Functional status. CONCLUSION: The prospective, multicenter design of the Hospital Outcomes Project for the Elderly (HOPE) provides an innovative approach for analysis of hospital outcomes in the elderly. Although differences in study populations and interventions exist, qualitative comparisons across sites will enhance generalizability and will provide a great opportunity to examine consistency among the sites. The HOPE pooled analysis project will impart greater statistical power to detect the primary and secondary outcomes compared with previous single-center trials that have assessed interventions related to functional decline in the hospitalized elderly.

Activities of Daily Living↗

Repeatability of measures of inflammatory cell number in bronchial biopsies in atopic asthma.

Airway pathology is increasingly considered to be a major outcome in asthma research. The aim of this study was to examine the intra-observer, within-section and between-biopsy repeatability, together with the implications for statistical power of a computerized quantitative analysis of inflammatory cell numbers in the lamina propria in bronchial biopsy specimens from atopic asthmatic subjects. Thirty six atopic adults (aged 19-40 yrs) with mild to moderate asthma (baseline forced expiratory volume in one second (FEV1) > or =50% of predicted value, methacholine (PC20) range 0.02-18.2 mg x mL[-1]) at various levels of treatment (25 subjects on inhaled steroids) entered the study. Biopsies were taken from the (sub)segmental carinae of the right lower and middle lobe and from the main carina. Specimens were snap-frozen and immunohistochemical staining was performed on cryostat sections with monoclonal antibodies against: (secreted) eosinophil cationic protein (EG1, EG2), mast cell tryptase (AA1), CD45, CD22, CD4, CD8, CD25, and CD45RO. Using a computerized system, the number of positively stained cells in the lamina propria was counted. When considering all cell types together, satisfactory intraclass correlation coefficients (ICC) values were obtained for intra-observer, within-section and between-biopsy repeatability, being 0.90, 0.80 and 0.81, respectively. The analysis of repeatability for individual cell types revealed ICC values ranging 0.47-0.82 for intra-observer, 0.44-0.76 for within-section and 0.37-0.67 for between-biopsy repeatability. The results imply that a sample-size between eight and 25 subjects is needed to detect at least one doubling difference in cell number per 0.1 mm2 for a particular inflammatory cell type in a study, using a within-group design with alpha=0.05 and power of 0.80. A sample-size of 13-48 subjects per group is required to detect the same difference between the groups in a parallel design.

Adult↗

Drotrecogin alfa (activated): a pharmacoeconomic review of its use in severe sepsis.

Drotrecogin alfa (activated) [Xigris] (DAA), the recombinant form of human activated protein C, is approved as an adjunctive therapy for patients with severe sepsis (sepsis associated with > or = 1 organ system failure [OSF]). In the international, randomised, double-blind, placebo-controlled PROWESS (Recombinant Human Activated Protein C Worldwide Evaluation in Severe Sepsis) study, the absolute reduction in 28-day all-cause mortality with intravenous DAA 24 micro g/kg/h for 96 hours plus conventional care versus conventional care alone was 6.1%. Although lacking statistical power, a prospectively planned subgroup analysis of this study suggested that the absolute reduction in mortality increased in patients with a baseline APACHE (Acute Physiology and Chronic Health Evaluation) II score of > or = 25 or > or = 2 OSFs, with no clear treatment effect in patients with an APACHE II score of < or = 24 or 1 OSF. Three fully published cost-effectiveness/cost-utility models of DAA plus conventional care relative to conventional care alone adopted a national healthcare payer's and/or societal perspective in North America. The base-case (baseline) discounted incremental cost per life-year gained (LYG) with DAA for all patients with severe sepsis was $US15,801-33,300 (year of costing 2000-2002). The results were more favourable for patients with an APACHE II score of > or = 25 ($US10,833-19,723 per LYG), but considerably worse for patients with an APACHE II score of < or = 24 based on a post hoc reanalysis by the US FDA. Among several fully or partly published cost-effectiveness/cost-utility models that adopted a national healthcare payer's perspective in continental Western European countries, the base-case (baseline) undiscounted incremental cost per LYG was broadly similar and more favourable for patients with > or = 2 OSFs (9660-11,300 euros; year of costing/publication 1998/1999, 2000, 2002 or 2003) than for all patients with severe sepsis (13,436-15,071 euros) in those studies that reported both analyses. The DAA acquisition cost accounts for up to 95% of the additional cost of using the drug. In conclusion, DAA is a major advance in the treatment of severe sepsis, based on the significant mortality reduction observed in the PROWESS study. From a hospital/hospital pharmacy perspective, the drug is associated with a high acquisition cost and a small increase in other short-term costs. From a societal or national healthcare payer's perspective, however, its administration to patients who meet the PROWESS study inclusion criteria, especially individuals with more severe disease (e.g APACHE II score of > or =25 and/or > or = 2 OSFs), has a lifetime cost-effectiveness profile that compares well to that of many widely accepted therapies.

Anti-Infective Agents↗

A comparative study of usefulness of quantitative parameters in the description of cardiotocogram records.

This study was an attempt to choose the optimized set of the features obtained from cardiotocogram records, which could explain in the best way the variability of foetal acid-base status parameters at labour. We prepared a package of the procedures in FORTRAN language which provides the possibilities for automatic detection and recognition of the long-term variability such as accelerations and decelerations and assessing some parameters connected with short-term variability (among other things oscillation bandwidth and number of baseline crossings). The acquired variables were subjected to multivariate statistical analysis to estimate the predictive power of a particular parameter. We used the described method to predict the variation of the foetal scalp blood pH and base deficit. This let us construct a set of variables which explains the maximal part of the variability of gasometric parameters. It affords possibilities for the estimation of the relative power of a particular component calculated from the cardiotocogram pattern. We obtain 41.7% of the explained variance for pH and 38.3% for base deficit.

Female↗

Meta-analysis of over 8,000 individuals from Hawai'i and Samoa for genetic associations to cardiometabolic phenotypes.

Although genome-wide association studies (GWAS) now routinely reveal genetic associations and biological insights in millions of individuals, underrepresentation of global populations, such as those from Polynesia, continue to persist. These exclusions, often driven by logistical challenges and lack of data, prevent systematic identification of population-enriched associations, such as the association of the missense variant at the CREBRF locus to BMI and type 2 diabetes discovered commonly occurring in Polynesian populations due to its rarity in global populations. Armed with the recently updated TOPMed imputation panel that could benefit studies in diverse populations that previously had poorer imputation performance, we performed the first GWAS of Native Hawaiians and largest to date of Polynesian-ancestry populations (combined N up to 8,461) to identify population-enriched associations for 13 adiposity and cardiometabolic traits available across both cohorts: BMI, fasting glucose, fasting insulin, HDL, height, hip circumference, HOMA-IR, LDL, T2D, total cholesterol, triglycerides, waist circumference, and waist-hip ratio. We found 25 trait-loci associations that met genome-wide significance: 20 previously reported or known associations and 5 associations newly confirmed via meta-analysis. In particular, with improved statistical power, we were able to confirm the suspected association between the missense CREBRF variant with fasting glucose levels. The remaining 4 potentially novel loci-trait associations for BMI, LDL, and waist-hip ratio, however, were not replicated in multi-ethnic datasets from All-of-Us despite having reasonable power to replicate. The lack of Polynesian-enriched findings outside of the CREBRF locus informs the bounds of the effect sizes or frequency of any enriched variants, and suggests that further expansion of cohort sizes from this region of the world and improved imputation references specific to these populations are needed to identify more population-enriched associations.

Journal Article↗

Tangles in smears of granulomatous lymphadenitis--a clue to the diagnosis.

OBJECTIVE: To assess the significance and nature of tangles in fine needle aspiration biopsy (FNAB) smears of granulomatous lymphadenitis. METHODS: The study group included 45 cases of clinically suspected granulomatous lymphadenitis particularly of tuberculous origin in which a cytologic diagnosis of granulomatous lymphadenitis (GL) was made on FNAB material. Smears of 21 lymph node aspirates without cytologic evidence of granulomatous disease (NGL) were included as a control group. One case with double pathology was excluded. All smears were fixed in 95% alcohol and stained with haematoxylin and eosin. Tangles were defined as a meshwork of haematoxyphilic string-like material occurring in a tangle in an otherwise well preserved smear. A score was given for the distribution (0-3) and density (1-3) of the tangles on the count of 10 high power fields for each aspirate. Statistical analysis was done by the Mann Whitney U test. RESULTS: Tangles were present in 41 of 45 (91%) GL and 7 of 21 (33%) NGL. The differences were statistically significant (p = 0.0008 and 0.0001 for distribution and density respectively). Six of the seven (84%) NGL with tangles were either cytologically diagnostic or suspicious of malignancy with 5 (71%) showing features of non-Hodgkin's lymphoma. The tangles were positive for nuclear stains (Feulgen) and originated in the nuclei of both lymphocytes and epithelioid cells, probably due to easy fragility of altered nuclear material. CONCLUSION: The presence of tangles in smears should raise the possibility of GL in the absence of a malignancy, specifically a lymphoma. This becomes an important diagnostic clue especially in situations where epithelioid histiocytes, the hall mark of GL, are sparse or absent in cytologic material.

Biopsy, Needle↗

Development of a 17-plex microsatellite polymerase chain reaction kit for genotyping horses.

AIM: To describe the development and performance of the new horse genotyping kit. METHODS: Highly discriminatory 17-Plex horse genotyping kit was designed by adding the fifth dye to the StockMarks kit for genotyping horses and taking advantage of the new instrument platforms. This was accomplished by using a new set of five fluorescent dyes developed by Applied Biosystems (DS-31), with four of the dyes used to label the forward amplification primers (6-FAM, VIC, NED, and PET) in each primer set. RESULTS: The new equine kit contained five extra loci (ASB17, LEX3, HMS1, CA425, and ASB23) in addition to the 12 original loci (VHL20, HTG4, AHT4, HMS7, HTG6, HMS6, HTG7, HMS3, AHT5, ASB2, HTG10, and HMS2) recommended by the International Society for Animal Genetics. The kit performed well on different instrument platforms (ABI PRISM 377, 310, and 3100 instruments) and across wide ranges of DNA template concentrations (1-10 ng). These 17 loci were combined and amplified in a single polymerase chain reaction (PCR) cycle, which dramatically improved the power of statistical tests for pedigree analysis while reducing the time and work required to perform such tests. An in-lane size standard labeled with the fifth dye (LIZ) provided accurate size determination for genotyping. CONCLUSION: The new 17-Plex horse kit, designed to improve the laboratory efficiency by genotyping more markers in a shorter time, has 17 primer sets labeled with new fluorescent dyes, which can be amplified in one PCR cycle and genotyped in one run on a high-throughput instruments.

Animals↗

The Allan factor: a new model of mathematical interpretation of heart rate variability in stable coronary artery disease. Preliminary results.

INTRODUCTION: The current analysis of heart rate variability (HRV) is one of the noninvasive methods of cardiovascular system assessment. The quantitative characteristics of the RR interval sequence and its dynamics are still under development as regards measurement techniques and development of new HRV interpretation models. The practical clinical application of the standard measurements is still insufficient and improvement of sensitivity and specificity of HRV parameters is needed. AIM: To assess a novel mathematical model of HRV interpretation and compare it with standard HRV measurements for patients with stable coronary artery disease (CAD), based on the virtual instrumentation technique. METHODS: The study group consisted of 24 patients with CAD confirmed by coronary angiography and a control group of 15 volunteers. Short-term electrocardiographic signals were recorded by a computer system and analysed for estimation of several HRV descriptors in time, frequency and combined time-frequency domains. Calculations included standard HRV measures and the Allan factor, a parameter based on the Haar wavelet transform. RESULTS: None of the investigated measurements derived from power spectral analysis has shown a statistically significant difference between healthy controls and patients with CAD, with the exception of rMSSD (Wilcoxon test: supine position *p=0.0018, erect position p=0.0708; discriminant function analysis: supine position *p=0.0069, erect position p=0.7851). Compared with standard HRV variables, the Allan factor better discriminated patients with CAD from healthy subjects (Wilcoxon test: supine position *p=0.0172, erect position *p=0.0001; discriminant function analysis: supine position p=0.8962, erect position *p=0.0200). CONCLUSIONS: The observations related to the novel parameter based on combined time and frequency domains may provide better quantitative measurements of heart rate variability in patients with coronary artery disease and require further investigations to assess their sensitivity and specificity.

Adult↗

Power of the classical twin design revisited.

Statistical power of the classical twin design was revisited. The approximate sampling variances of a least-squares estimate of the heritability in a univariate analysis and estimate of the genetic correlation coefficient in a bivariate analysis were derived analytically for the ACE model. Statistical power to detect additive genetic variation under the ACE model was derived analytically for least-squares, goodness-of-fit and maximum likelihood-based test statistics. The noncentrality parameter for the likelihood ratio test statistic is shown to be a simple function of the MZ and DZ intraclass correlation coefficients and the proportion of MZ and DZ twin pairs in the sample. All theoretical results were validated using simulation. The derived expressions can be used to calculate power of the classical twin design in a simple and rapid manner.

Analysis of Variance↗

Haplotype sharing analysis using mantel statistics.

OBJECTIVE: The potential value of haplotypes has attracted widespread interest in the mapping of complex traits. Haplotype sharing methods take the linkage disequilibrium information between multiple markers into account, and may have good power to detect predisposing genes. We present a new approach based on Mantel statistics for spacetime clustering, which is developed in order to improve the power of haplotype sharing analysis for gene mapping in complex disease. METHODS: The new statistic correlates genetic similarity and phenotypic similarity across pairs of haplotypes for case-only and case-control studies. The genetic similarity is measured as the shared length between haplotypes around a putative disease locus. The phenotypic similarity is measured as the mean-corrected cross-product based on the respective phenotypes. We analyzed two tests for statistical significance with respect to type I error: (1) assuming asymptotic normality, and (2) using a Monte Carlo permutation procedure. The results were compared to the chi(2) test for association based on 3-marker haplotypes. RESULTS: The results of the type I error rates for the Mantel statistics using the permutational procedure yielded pointwise valid tests. The approach based on the assumption of asymptotic normality was seriously liberal. CONCLUSION: Power comparisons showed that the Mantel statistics were better than or equal to the chi(2) test for all simulated disease models.

Case-Control Studies↗

Compartments within the lymph node cortex of calves and adult cattle differ in the distribution of leukocyte populations: an immunohistochemical study using computer-assisted morphometric analysis.

The combination of an immunohistochemical technique and a panel of monoclonal antibodies was used to investigate the presence of leukocyte populations in the distal jejunal lymph node of 3-4 week old calves and adult cattle. The application of computer-assisted morphometric analysis enabled information to be obtained on the distribution of leukocyte populations in lymphoid compartments of the lymph node cortex. Semi-quantitative estimates of the areas of staining in histological sections showed that calves possessed significantly fewer B-cells and CD4+ cells in the outer cortex and significantly fewer T-cells (CD4+, CD8+ and gamma delta T-cells) in the deep cortex. These findings were interpreted to be a possible consequence of immunosuppression resulting from the passive transfer of maternal immunity in colostrum. The presence of some B-cell follicles in the region defined as the deep cortex suggested the on-going differentiation of this predominantly T-cell compartment. The larger presence of interdigitating cells (IDC) in the deep cortex of calves than adults was suggested by significantly larger CD1+ populations and it was argued that this could be the result of the confrontation with exogenous antigen faced by calves in early postnatal life. Antigen presenting populations, pan MHC II+ and MHC II DQ+ populations, were increased in all compartments of calf lymph nodes but were not significantly different from the populations in adult lymph nodes. Variance component analysis of the data generated in the present study showed that the image analysis technique was an effective and statistically powerful approach to investigate leukocyte populations within the specific microenvironments of the lymph node.

Age Factors↗