Serum IL-6: a candidate biomarker for intracranial pressure elevation following isolated traumatic brain injury.

BACKGROUND: Increased intracranial pressure (ICP) is a serious, life-threatening, secondary event following traumatic brain injury (TBI). In many cases, ICP rises in a delayed fashion, reaching a maximal level 48-96 hours after the initial insult. While pressure catheters can be implanted to monitor ICP, there is no clinically proven method for determining a patient's risk for developing this pathology. METHODS: In the present study, we employed antibody array and Luminex-based screening methods to interrogate the levels of inflammatory cytokines in the serum of healthy volunteers and in severe TBI patients (GCS RESULTS: Consistent with previous reports, we observed sustained increases in IL-6 levels in TBI patients irrespective of their ICP status. However, the group of patients who subsequently experienced ICP >or= 25 mm Hg had significantly higher IL-6 levels within the first 17 hours of injury as compared to the patients whose ICP remained 128 pg/ml correctly identified 85% of isolated TBI patients who subsequently developed elevated ICP, and values between these cut-off values correctly identified 75% of all patients whose ICP remained CONCLUSIONS: Our results suggest that serum IL-6 can be used for the differential diagnosis of elevated ICP in isolated TBI.

Nonlinear tests for genetic studies of complex disease

Linkage and association studies are major analytical tools to search for susceptibility genes for complex diseases. With the availability of large collection of single nucleotide polymorphisms (SNPs) and the rapid progresses for high throughput genotyping technologies, together with the ambitious goals of the International HapMap Project, genetic markers covering the whole genome will be available for genome-wide linkage and association studies. In order not to inflate the type I error rate in performing genome-wide linkage and association studies, multiple adjustment for the significant level for each independent linkage and/or association test is required, and this has led to the suggestion of genome-wide significant cut-off as low as 5 × 10 −7. Almost no linkage and/or association study can meet such a stringent threshold by the standard statistical methods. Developing new statistics with high power is urgently needed to tackle this problem. This dissertation proposes and explores a class of novel test statistics that can be used in both population-based and family-based genetic data by employing a completely new strategy, which uses nonlinear transformation of the sample means to construct test statistics for linkage and association studies. Extensive simulation studies are used to illustrate the properties of the nonlinear test statistics. Power calculations are performed using both analytical and empirical methods. Finally, real data sets are analyzed with the nonlinear test statistics. Results show that the nonlinear test statistics have correct type I error rates, and most of the studied nonlinear test statistics have higher power than the standard chi-square test. This dissertation introduces a new idea to design novel test statistics with high power and might open new ways to mapping susceptibility genes for complex diseases. ^

An empirical evaluation of the Random Forests classifier models for variable selection in a large-scale lung cancer case-control study

Random Forests™ is reported to be one of the most accurate classification algorithms in complex data analysis. It shows excellent performance even when most predictors are noisy and the number of variables is much larger than the number of observations. In this thesis Random Forests was applied to a large-scale lung cancer case-control study. A novel way of automatically selecting prognostic factors was proposed. Also, synthetic positive control was used to validate Random Forests method. Throughout this study we showed that Random Forests can deal with large number of weak input variables without overfitting. It can account for non-additive interactions between these input variables. Random Forests can also be used for variable selection without being adversely affected by collinearities. ^ Random Forests can deal with the large-scale data sets without rigorous data preprocessing. It has robust variable importance ranking measure. Proposed is a novel variable selection method in context of Random Forests that uses the data noise level as the cut-off value to determine the subset of the important predictors. This new approach enhanced the ability of the Random Forests algorithm to automatically identify important predictors for complex data. The cut-off value can also be adjusted based on the results of the synthetic positive control experiments. ^ When the data set had high variables to observations ratio, Random Forests complemented the established logistic regression. This study suggested that Random Forests is recommended for such high dimensionality data. One can use Random Forests to select the important variables and then use logistic regression or Random Forests itself to estimate the effect size of the predictors and to classify new observations. ^ We also found that the mean decrease of accuracy is a more reliable variable ranking measurement than mean decrease of Gini. ^

Body mass index of Vietnamese children ages 6--15 years old

Childhood overweight can increase the risk of chronic diseases later in life. To determine the prevalence, trends and determinants of overweight among children ages 6-15 years old in Vietnam, we assessed data on body mass index (BMI) and demographic and socio-economic characteristics obtained from the 1992 Vietnam Living Standard Survey (1992 VLSS), the 1997 Vietnam Living Standard Survey (1997 VLSS), and the 2000 General Nutrition Survey (2000 GNS). These surveys used multi-stage cluster sample designs to produce nationally representative samples of Vietnamese children ages 6-15 years in 1992-1993, 1997-1998 and 2000. BMI classification was determined using cut-off values set by the International Obesity Task Force (IOTF). The mean prevalence of at risk of overweight and overweight among Vietnamese children rapidly increased from 0.4% in 1992 to 2.0% in 2000, along with a high prevalence of underweight (33.4% in 2000). Increases in weight, height and BMI varied according to gender, area of residence and socioeconomic status. Age, areas of residence and education of the household head are statistically significant predictors of at risk of overweight and overweight. This study identified the prevalence and trends of weight among children crucial to understanding the prevention of child overweight in Vietnam. ^

The information bottleneck method for genome-wide association studies

In population studies, most current methods focus on identifying one outcome-related SNP at a time by testing for differences of genotype frequencies between disease and healthy groups or among different population groups. However, testing a great number of SNPs simultaneously has a problem of multiple testing and will give false-positive results. Although, this problem can be effectively dealt with through several approaches such as Bonferroni correction, permutation testing and false discovery rates, patterns of the joint effects by several genes, each with weak effect, might not be able to be determined. With the availability of high-throughput genotyping technology, searching for multiple scattered SNPs over the whole genome and modeling their joint effect on the target variable has become possible. Exhaustive search of all SNP subsets is computationally infeasible for millions of SNPs in a genome-wide study. Several effective feature selection methods combined with classification functions have been proposed to search for an optimal SNP subset among big data sets where the number of feature SNPs far exceeds the number of observations. ^ In this study, we take two steps to achieve the goal. First we selected 1000 SNPs through an effective filter method and then we performed a feature selection wrapped around a classifier to identify an optimal SNP subset for predicting disease. And also we developed a novel classification method-sequential information bottleneck method wrapped inside different search algorithms to identify an optimal subset of SNPs for classifying the outcome variable. This new method was compared with the classical linear discriminant analysis in terms of classification performance. Finally, we performed chi-square test to look at the relationship between each SNP and disease from another point of view. ^ In general, our results show that filtering features using harmononic mean of sensitivity and specificity(HMSS) through linear discriminant analysis (LDA) is better than using LDA training accuracy or mutual information in our study. Our results also demonstrate that exhaustive search of a small subset with one SNP, two SNPs or 3 SNP subset based on best 100 composite 2-SNPs can find an optimal subset and further inclusion of more SNPs through heuristic algorithm doesn't always increase the performance of SNP subsets. Although sequential forward floating selection can be applied to prevent from the nesting effect of forward selection, it does not always out-perform the latter due to overfitting from observing more complex subset states. ^ Our results also indicate that HMSS as a criterion to evaluate the classification ability of a function can be used in imbalanced data without modifying the original dataset as against classification accuracy. Our four studies suggest that Sequential Information Bottleneck(sIB), a new unsupervised technique, can be adopted to predict the outcome and its ability to detect the target status is superior to the traditional LDA in the study. ^ From our results we can see that the best test probability-HMSS for predicting CVD, stroke,CAD and psoriasis through sIB is 0.59406, 0.641815, 0.645315 and 0.678658, respectively. In terms of group prediction accuracy, the highest test accuracy of sIB for diagnosing a normal status among controls can reach 0.708999, 0.863216, 0.639918 and 0.850275 respectively in the four studies if the test accuracy among cases is required to be not less than 0.4. On the other hand, the highest test accuracy of sIB for diagnosing a disease among cases can reach 0.748644, 0.789916, 0.705701 and 0.749436 respectively in the four studies if the test accuracy among controls is required to be at least 0.4. ^ A further genome-wide association study through Chi square test shows that there are no significant SNPs detected at the cut-off level 9.09451E-08 in the Framingham heart study of CVD. Study results in WTCCC can only detect two significant SNPs that are associated with CAD. In the genome-wide study of psoriasis most of top 20 SNP markers with impressive classification accuracy are also significantly associated with the disease through chi-square test at the cut-off value 1.11E-07. ^ Although our classification methods can achieve high accuracy in the study, complete descriptions of those classification results(95% confidence interval or statistical test of differences) require more cost-effective methods or efficient computing system, both of which can't be accomplished currently in our genome-wide study. We should also note that the purpose of this study is to identify subsets of SNPs with high prediction ability and those SNPs with good discriminant power are not necessary to be causal markers for the disease.^

Mean corpuscular volume as a marker for adherence to antiretroviral therapy among HIV infected children and adolescents in Uganda

Mean corpuscular volume, which is an inexpensive and widely available measure to assess, increases in HIV infected individuals receiving zidovudine and stavudine raising the hypothesis that it could be used as a surrogate for adherence.^ The aim of this study was to examine the association between mean corpuscular volume and adherence to antiretroviral therapy among HIV infected children and adolescents aged 0–19 years in Uganda as well as the extent to which changes in mean corpuscular volume predict adherence as determined by virologic suppression.^ The investigator retrospectively reviewed and analyzed secondary data of 158 HIV infected children and adolescents aged 0–19 years who initiated antiretroviral therapy under an observational cohort at the Baylor College of Medicine Children's Foundation - Uganda. Viral suppression was used as the gold standard for monitoring adherence and defined as viral load of < 400 copies/ml at 24 and 48 weeks. ^ Patients were at least 48 weeks on therapy, age 0.2–18.4 years, 54.4% female, 82.3% on zidovudine based regimen, 92% WHO stage III at initiation of therapy, median pre therapy MCV 80.6 fl (70.3–98.3 fl), median CD4% 10.2% (0.3%–28.0%), and mean pre therapy viral load 407,712.9 ± 270,413.9 copies/ml. For both 24 and 48 weeks of antiretroviral therapy, patients with viral suppression had a greater mean percentage change in mean corpuscular volume (15.1% ± 8.4 vs. 11.1% ± 7.8 and 2.3% ± 13.2 vs. -2.7% ± 10.5 respectively). The mean percentage change in mean corpuscular volume was greater in the first 24 weeks of therapy for patients with and without viral suppression (15.1% ± 8.4 vs. 2.3% ± 13.2 and 11.1% ± 7.8 vs. -2.7% ± 10.5 respectively). In the multivariate logistic regression model, percentage change in mean corpuscular volume ≥ 20% was significantly associated with viral suppression (adjusted OR 4.0; CI 1.2–13.3; p value 0.02). The ability of percentage changes in MCV to correctly identify children and adolescents with viral suppression was higher at a cut off of ≥ 20% (90.7%; sensitivity, 31.7%) than at ≥ 9% (82.9%; sensitivity, 78.9%). Negative predictive value was lower at ≥ 20% change (25%; specificity, 84.8%) than at ≥ 9% change (33.3%; specificity, 39.4%).^ Mean corpuscular volume is a useful marker of adherence among children and adolescents with viral suppression. ^

Plasma homocysteine levels and Alzheimer's Disease: A systematic review

Objective. To systematically review studies published in English on the relationship between plasma total homocysteine (Hcy) levels and the clinical and/or postmortem diagnosis of Alzheimer's disease (AD) in subjects who are over 60 years old.^ Method. Medline, PubMed, PsycINFO and Academic Search Premier, were searched by using the keywords "homocysteine", "Alzheimer disease" and "dementia", and "cognitive disorders". In addition, relevant articles in PubMed using the "related articles" link and by cross-referencing were identified. The study design, study setting and study population, sample size, the diagnostic criteria of the National Institute of Neurological and Communicative Disorders and Stroke (NINCDS) and the Alzheimer's Disease and Related Disorders Association (ADRDA), and description of how Hcy levels were measured or defined had to have been clearly stated. Empirical investigations reporting quantitative data on the epidemiology of the relationship between plasma total Hcy (exposure factor) and AD (outcome) were included in the systematic review.^ Results. A total of 7 studies, which included a total of 2,989 subjects, out of 388 potential articles met the inclusion criteria: four case control and three cohort studies were identified. All 7 studies had association statistics, such as the odds ratio (OR), the relative rates (RR), and the hazard ratio (HR) of AD, examined using multivariate and logistic regression analyses. Three case - comparison studies: Clarke et al. (1998) (OR: 4.5, 95% CI.: 2.2 - 9.2); McIlroy et al. (2002) (OR: 2.9, 95% CI.: 1.00–8.1); Quadri et al. (2004) (OR: 3.7, 95% CI.: 1.1 - 13.1), and two cohort studies: Seshadri et al. (2002) (RR: 1.8, 95% CI.: 1.3 - 2.5); Ravaglia et al. (2005) (HR: 2.1, 95% CI.: 1.7 - 3.8) found a significant association between serum total Hcy and AD. One case-comparison study, Miller et al. (2002) (OR: 2.2, 95% C.I.: 0.3 -16), and one cohort study, Luchsinger et al. (2004) (HR: 1.4, 95% C.I.: 0.7 - 2.3) failed to reject H0.^ Conclusions. The purpose of this review is to provide a thorough analysis of studies that examined the relationship between Hcy levels and AD. Five studies showed a positive statistically significant association between elevated total Hcy values and AD but the association was not statistically significant in two studies. Further research is needed in order to establish evidence of the strong, consistent association between serum total Hcy and AD as well as the presence of the appropriate temporal relationship. To answer these questions, it is important to conduct more prospective studies that examine the occurrence of AD in individuals with and without elevated Hcy values at baseline. In addition, the international standardization of measurements and cut-off points for plasma Hcy levels across laboratories is a critical issue to be addressed for the conduct of future studies on the topic.^

Expression study of the atherosclerosis mouse aorta reveals significant disturbance of calcium signaling pathway

Atherosclerosis is a complex disease resulting from interactions of genetic and environmental risk factors leading to heart failure and stroke. Using an atherosclerotic mouse model (ldlr-/-, apobec1-/- designated as LDb), we performed microarray analysis to identify candidate genes and pathways, which are most perturbed in changes in the following risk factors: genetics (control C57BL/6 vs. LDb mice), shearstress (lesion-prone vs. lesion-resistant regions in LDb mice), diet (chow vs. high fat fed LDb mice) and age (2-month-old vs. 8-month old LDb mice). ^ Atherosclerotic lesion quantification and lipid profile studies were performed to assess the disease phenotype. A microarray study was performed on lesion-prone and lesion-resistant regions of each aorta. Briefly, 32 male C57BL/6 and LDb mice (n =16/each) were fed on either chow or high fat diet, sacrificed at 2- and 8-months old, and RNA isolated from the aortic lesion-prone and aortic lesion-resistant segments. Using 64 Affymetrix Murine 430 2.0 chips, we profiled differentially expressed genes with the cut off value of FDR ≤ 0.15 for t-test, and q <0.0001 for the ANOVA. The data were normalized using two normalization methods---invariant probe sets (Loess) and Quantile normalization, the statistical analysis was performed using t-tests and ANOVA, and pathway characterization was done using Pathway Express (Wayne State). The result identified the calcium signaling pathway as the most significant overrepresented pathway, followed by focal adhesion. In the calcium signaling pathway, 56 genes were found to be significantly differentially expressed out of 180 genes listed in the KEGG calcium signaling pathway. Nineteen of these genes were consistently identified by both statistical tests, 11 of which were unique to the test, and 26 were unique to the ANOVA test, using the cutoffs noted above. ^ In conclusion, this finding suggested that hypercholesterolemia drives the disease progression by altering the expression of calcium channels and regulators which subsequently results in cell differentiation, growth, adhesion, cytoskeletal change and death. Clinically, this pathway may serve as an important target for future therapeutic intervention, and thus the calcium signaling pathway may serve as an important target for future diagnostic and therapeutic intervention. ^

Secondary analysis of effectivness of tinidazole-containing-quadruple eradication therapy in asymptomatic H. pylori infected children in El Paso

Helicobacter pylori infection is frequently acquired during childhood. This microorganism is known to cause gastritis, and duodenal ulcer in pediatric patients, however most children remain completely asymptomatic to the infection. Currently there is no consensus in favor of treatment of H. pylori infection in asymptomatic children. The firstline of treatment for this population is triple medication therapy including two antibacterial agents and one proton pump inhibitor for a 2 week duration course. Decreased eradication rate of less than 75% has been documented with the use of this first-line therapy but novel tinidazole-containing quadruple sequential therapies seem worth investigating. None of the previous studies on such therapy has been done in the United States of America. As part of an iron deficiency anemia study in asymptomatic H. pylori infected children of El Paso, Texas, we conducted a secondary data analysis of study data collected in this trial to assess the effectiveness of this tinidazole-containing sequential quadruple therapy compared to placebo on clearing the infection. Subjects were selected from a group of asymptomatic children identified through household visits to 11,365 randomly selected dwelling units. After obtaining parental consent and child assent a total of 1,821 children 3-10 years of age were screened and 235 were positive to a novel urine immunoglobulin class G antibodies test for H. pylori infection and confirmed as infected using a 13C urea breath test, using a hydrolysis urea rate >10 μg/min as cut-off value. Out of those, 119 study subjects had a complete physical exam and baseline blood work and were randomly allocated to four groups, two of which received active H. pylori eradication medication alone or in combination with iron, while the other two received iron only or placebo only. Follow up visits to their houses were done to assess compliance and occurrence of adverse events and at 45+ days post-treatment, a second urea breath test was performed to assess their infection status. The effectiveness was primarily assessed on intent to treat basis (i.e., according to their treatment allocation), and the proportion of those who cleared their infection using a cut-off value >10 μg/min of for urea hydrolysis rate, was the primary outcome. Also we conducted analysis on a per-protocol basis and according to the cytotoxin associated gene A product of the H. pylori infection status. Also we compared the rate of adverse events across the two arms. On intent-to-treat and per-protocol analyses, 44.3% and 52.9%, respectively, of the children receiving the novel quadruple sequential eradication cleared their infection compared to 12.2% and 15.4% in the arms receiving iron or placebo only, respectively. Such differences were statistically significant (p<0.001). The study medications were well accepted and safe. In conclusion, we found in this study population, of mostly asymptomatically H. pylori infected children, living in the US along the border with Mexico, that the quadruple sequential eradication therapy cleared the infection in only half of the children receiving this treatment. Research is needed to assess the antimicrobial susceptibility of the strains of H. pylori infecting this population to formulate more effective therapies. ^

Is depression associated with insulin resistance? A systematic review

Studies suggest that depression affects glucose metabolism, and therefore is a risk factor for insulin resistance. The association between depression and insulin resistance has been investigated in a number of studies, but there is no agreement on the results. The objective of this study is to survey the epidemiological studies, identify the ones that measured the association of depression (as exposure) with insulin resistance (as outcome), and perform a systematic review to assess the reliability and strength of the association. For high quality reporting, and assessment, this systematic review used the outlined procedures, guidelines and recommendations for reviews in health care, suggested by the Centre for Reviews and Dissemination, along with recommendations from the STROBE group (Strengthening the Reporting of Observational Studies in Epidemiology). Ovid MEDLINE 1996 to April Week 1 2010, was used to identify the relevant epidemiological studies. To identify the most relevant set of articles for this systematic review, a set of inclusion and exclusion criteria were applied. Six studies that met the specific criteria were selected. Key information from identified studies was tabulated, and the methodological quality, internal and external validity, and the strength of the evidence of the selected studies were assessed. The result from the tabulated data of the reviewed studies indicates that the studies either did not apply a case definition for insulin resistance in their investigation, or did not state a specific value for the index used to define insulin resistance. The quality assessment of the reviewed studies indicates that to assess the association between insulin resistance and depression, specifying a case definition for insulin resistance is important. The case definition for insulin resistance is defined by the World Health Organization and the European Group for the Study of Insulin Resistance as the insulin sensitivity index of the lowest quartile or lowest decile of a general population, respectively. Three studies defined the percentile cut-off point for insulin resistance, but did not give the insulin sensitivity index value. In these cases, it is not possible to compare the results. Three other studies did not define the cut-off point for insulin resistance. In these cases, it is hard to confirm the existence of insulin resistance. In conclusion, to convincingly answer our question, future studies need to adopt a clear case definition, define a percentile cut-off point and reference population, and give value of the insulin resistance measure at the specified percentile.^

A STUDY TO INVESTIGATE DIET DIVERSITY AS A NUTRITION ASSESSMENT INSTRUMENT

Nutrient intake and specific food item data from 24-hour dietary recalls were utilized to study the relationship between measures of diet diversity and dietary adequacy in a population of white females of child-bearing age and socioeconomic subgroups of that population. As the basis of the diet diversity measures, twelve food groups were constructed from the 24-hour recall data and the number of unique foods per food group counted and weighted according to specified weighting schemes. Utilizing these food groups, nine diet diversity indices were developed.^ Sensitivity/specificity analysis was used to determine the ability of varying levels of selected diet diversity indices to identify individuals above and below preselected intakes of different nutrients. The true prevalence proportions, sensitivity and specificity, false positive and false negative rates, and positive predictive values observed at the selected levels of diet diversity indices were investigated in relation to the objectives and resources of a variety of nutrition improvement programs. Diet diversity indices constructed from the total population data were evaluated as screening tools for respondent nutrient intakes in each of the socioeconomic subgroups as well.^ The results of the sensitivity/specificity analysis demonstrated that the false positive rate, the false negative rate, or both were too high at each diversity cut-off level to validate the widespread use of any of the diversity indices in the dietary assessment of the study population. Although diet diversity has been shown to be highly correlated with the intakes of a number of nutrients, the diet diversity indices constructed in this study did not adequately represent nutrient intakes in the diet as reported, in this study, intakes as reported in the 24-hour dietary recall. Specific cut-off levels of selected diversity indices might have limited application in some nutrition programs. The results were applicable to the sensitivity/specificity analyses in the socioeconomic subgroups as well as in the total population. ^

THE APPLICATION OF PATH ANALYSIS TO ASSESSMENT OF IRON NUTRITIONAL STATUS IN MAN

Path analysis has been applied to components of the iron metabolic system with the intent of suggesting an integrated procedure for better evaluating iron nutritional status at the community level. The primary variables of interest in this study were (1) iron stores, (2) total iron-binding capacity, (3) serum ferritin, (4) serum iron, (5) transferrin saturation, and (6) hemoglobin concentration. Correlation coefficients for relationships among these variables were obtained from published literature and postulated in a series of models using measures of those variables that are feasible to include in a community nutritional survey. Models were built upon known information about the metabolism of iron and were limited by what had been reported in the literature in terms of correlation coefficients or quantitative relationships. Data were pooled from various studies and correlations of the same bivariate relationships were averaged after z- transformations. Correlation matrices were then constructed by transforming the average values back into correlation coefficients. The results of path analysis in this study indicate that hemoglobin is not a good indicator of early iron deficiency. It does not account for variance in iron stores. On the other hand, 91% of the variance in iron stores is explained by serum ferritin and total iron-binding capacity. In addition, the magnitude of the path coefficient (.78) of the serum ferritin-iron stores relationship signifies that serum ferritin is the most important predictor of iron stores in the proposed model. Finally, drawing upon known relations among variables and the amount of variance explained in path models, it is suggested that the following blood measures should be made in assessing community iron deficiency: (1) serum ferritin, (2) total iron-binding capacity, (3) serum iron, (4) transferrin saturation, and (5) hemoglobin concentration. These measures (with acceptable ranges and cut-off points) could make possible the complete evaluation of all three stages of iron deficiency in those persons surveyed at the community level. ^