Metabolomics Insights in Early Childhood Caries

Dental caries is characterized by a dysbiotic shift at the biofilm-tooth surface interface, yet comprehensive biochemical characterizations of the biofilm are scant. We used metabolomics to identify biochemical features of the supragingival biofilm associated with early childhood caries (ECC) prevalence and severity. The study's analytical sample comprised 289 children ages 3 to 5 (51% with ECC) who attended public preschools in North Carolina and were enrolled in a community-based cross-sectional study of early childhood oral health. Clinical examinations were conducted by calibrated examiners in community locations using International Caries Detection and Classification System (ICDAS) criteria. Supragingival plaque collected from the facial/buccal surfaces of all primary teeth in the upper-left quadrant was analyzed using ultra-performance liquid chromatography-tandem mass spectrometry. Associations between individual metabolites and 18 clinical traits (based on different ECC definitions and sets of tooth surfaces) were quantified using Brownian distance correlations (dCor) and linear regression modeling of log₂-transformed values, applying a false discovery rate multiple testing correction. A tree-based pipeline optimization tool (TPOT)-machine learning process was used to identify the best-fitting ECC classification metabolite model. There were 503 named metabolites identified, including microbial, host, and exogenous biochemicals. Most significant ECC-metabolite associations were positive (i.e., upregulations/enrichments). The localized ECC case definition (ICDAS ≥1 caries experience within the surfaces from which plaque was collected) had the strongest correlation with the metabolome (dCor P = 8 × 10^-3). Sixteen metabolites were significantly associated with ECC after multiple testing correction, including fucose (P = 3.0 × 10^-6) and N-acetylneuraminate (p = 6.8 × 10^-6) with higher ECC prevalence, as well as catechin (P = 4.7 × 10^-6) and epicatechin (P = 2.9 × 10^-6) with lower. Catechin, epicatechin, imidazole propionate, fucose, 9,10-DiHOME, and N-acetylneuraminate were among the top 15 metabolites in terms of ECC classification importance in the automated TPOT model. These supragingival biofilm metabolite findings provide novel insights in ECC biology and can serve as the basis for the development of measures of disease activity or risk assessment.

Electrophysiology-based stratification of pancreatic tumorigenicity by label-free single-cell impedance cytometry

Pancreatic ductal adenocarcinoma (PDAC) is an aggressive cancer lacking specific biomarkers that can be correlated to disease onset, promotion and progression. To assess whether tumor cell electrophysiology may serve as a marker for PDAC tumorigenicity, we use multi-frequency impedance cytometry at high throughput (∼350 cells/s) to measure the electrical phenotype of single PDAC tumor cells from xenografts, which are derived from primary pancreatic tumors versus those from liver metastases of different patients. A novel phase contrast metric based on variations in the high and low frequency impedance phase responses that is related to electrophysiology of the cell interior is found to be systematically altered as a function of tumorigenicity. PDAC cells of higher tumorigenicity exhibited lowered interior conductivity and enhanced permittivity, which is validated by the dielectrophoresis on the respective cell types. Using genetic analysis, we suggest the role of dysregulated Na⁺ transport and removal of Ca²⁺ ions from the cytoplasm on key oncogenic KRAS-driven processes that may be responsible for lowering of the interior cell conductivity. We envision that impedance cytometry can serve as a tool to quantify phenotypic heterogeneity for rapidly stratifying tumorigenicity. It can also aid in protocols for dielectrophoretic isolation of cells with a particular phenotype for prognostic studies on patient survival and to tailor therapy selection to specific patients.

How to increase our belief in discovered statistical interactions via large-scale association studies?

The understanding that differences in biological epistasis may impact disease risk, diagnosis, or disease management stands in wide contrast to the unavailability of widely accepted large-scale epistasis analysis protocols. Several choices in the analysis workflow will impact false-positive and false-negative rates. One of these choices relates to the exploitation of particular modelling or testing strategies. The strengths and limitations of these need to be well understood, as well as the contexts in which these hold. This will contribute to determining the potentially complementary value of epistasis detection workflows and is expected to increase replication success with biological relevance. In this contribution, we take a recently introduced regression-based epistasis detection tool as a leading example to review the key elements that need to be considered to fully appreciate the value of analytical epistasis detection performance assessments. We point out unresolved hurdles and give our perspectives towards overcoming these.

Data science approaches to pharmacogenetics

Pharmacogenetic studies rely on applied statistics to evaluate genetic data describing natural variation in response to pharmacotherapeutics such as drugs and vaccines. In the beginning, these studies were based on candidate gene approaches that specifically focused on efficacy or adverse events correlated with variants of single genes. This hypothesis driven method required the researcher to have a priori knowledge of which genes or gene sets to investigate. According to rational design, the focus of these studies has been on drug metabolizing enzymes, drug transporters, and drug targets. As technology has progressed, these studies have transitioned to hypothesis-free explorations where markers across the entire genome can be measured in large scale, population based, genome-wide association studies (GWAS). This enables identification of novel genetic biomarkers, therapeutic targets, and analysis of gene-gene interactions, which may reveal molecular mechanisms of drug activities. Ultimately, the challenge is to utilize gene-drug associations to create dosing algorithms based individual genotypes, which will guide physicians and ensure they prescribe the correct dose of the correct drug the first time eliminating trial-and-error and adverse events. We review here basic concepts and applications of data science to the genetic analysis of pharmacologic outcomes.

Epiregulin (EREG) and human V-ATPase (TCIRG1): genetic variation, ethnicity and pulmonary tuberculosis susceptibility in Guinea-Bissau and The Gambia

We analyzed two West African samples (Guinea-Bissau: n=289 cases and 322 controls; The Gambia: n=240 cases and 248 controls) to evaluate single-nucleotide polymorphisms (SNPs) in Epiregulin (EREG) and V-ATPase (T-cell immune regulator 1 (TCIRG1)) using single and multilocus analyses to determine whether previously described associations with pulmonary tuberculosis (PTB) in Vietnamese and Italians would replicate in African populations. We did not detect any significant single locus or haplotype associations in either sample. We also performed exploratory pairwise interaction analyses using Visualization of Statistical Epistasis Networks (ViSEN), a novel method to detect only interactions among multiple variables, to elucidate possible interaction effects between SNPs and demographic factors. Although we found no strong evidence of marginal effects, there were several significant pairwise interactions that were identified in either the Guinea-Bissau or the Gambian samples, two of which replicated across populations. Our results indicate that the effects of EREG and TCIRG1 variants on PTB susceptibility, to the extent that they exist, are dependent on gene-gene interactions in West African populations as detected with ViSEN. In addition, epistatic effects are likely to be influenced by inter- and intra-population differences in genetic or environmental context and/or the mycobacterial lineages causing disease.

Entropy-based information gain approaches to detect and to characterize gene-gene and gene-environment interactions/correlations of complex diseases

For complex diseases, the relationship between genotypes, environment factors, and phenotype is usually complex and nonlinear. Our understanding of the genetic architecture of diseases has considerably increased over the last years. However, both conceptually and methodologically, detecting gene-gene and gene-environment interactions remains a challenge, despite the existence of a number of efficient methods. One method that offers great promises but has not yet been widely applied to genomic data is the entropy-based approach of information theory. In this article, we first develop entropy-based test statistics to identify two-way and higher order gene-gene and gene-environment interactions. We then apply these methods to a bladder cancer data set and thereby test their power and identify strengths and weaknesses. For two-way interactions, we propose an information gain (IG) approach based on mutual information. For three-ways and higher order interactions, an interaction IG approach is used. In both cases, we develop one-dimensional test statistics to analyze sparse data. Compared to the naive chi-square test, the test statistics we develop have similar or higher power and is robust. Applying it to the bladder cancer data set allowed to investigate the complex interactions between DNA repair gene single nucleotide polymorphisms, smoking status, and bladder cancer susceptibility. Although not yet widely applied, entropy-based approaches appear as a useful tool for detecting gene-gene and gene-environment interactions. The test statistics we develop add to a growing body methodologies that will gradually shed light on the complex architecture of common diseases.

Integrated analysis of genetic and proteomic data identifies biomarkers associated with adverse events following smallpox vaccination

Complex clinical outcomes, such as adverse reaction to vaccination, arise from the concerted interactions among the myriad components of a biological system. Therefore, comprehensive etiological models can be developed only through the integrated study of multiple types of experimental data. In this study, we apply this paradigm to high-dimensional genetic and proteomic data collected to elucidate the mechanisms underlying the development of adverse events (AEs) in patients after smallpox vaccination. As vaccination was successful in all of the patients under study, the AE outcomes reported likely represent the result of interactions among immune system components that result in excessive or prolonged immune stimulation. In this study, we examined 1442 genetic variables (single nucleotide polymorphisms) and 108 proteomic variables (serum cytokine concentrations) to model AE risk. To accomplish this daunting analytical task, we employed the Random Forests (RF) method to filter the most important attributes, then we used the selected attributes to build a final decision tree model. This strategy is well suited to integrated analysis, as relevant attributes may be selected from categorical or continuous data. Importantly, RF is a natural approach for studying the type of gene-gene, gene-protein and protein-protein interactions we hypothesize to be involved in the development of clinical AEs. RF importance scores for particular attributes take interactions into account, and there may be interactions across data types. Combining information from previous studies on AEs related to smallpox vaccination with the genetic and proteomic attributes identified by RF, we built a comprehensive model of AE development that includes the cytokines intercellular adhesion molecule-1 (ICAM-1 or CD54), interleukin-10 (IL-10), and colony stimulating factor-3 (CSF-3 or G-CSF) and a genetic polymorphism in the cytokine gene interleukin-4 (IL4). The biological factors included in the model support our hypothesized mechanism for the development of AEs involving prolonged stimulation of inflammatory pathways and an imbalance of normal tissue damage repair pathways. This study shows the utility of RF for such analytical tasks, while both enhancing and reinforcing our working model of AE development after smallpox vaccination.

Neuromuscular excitability changes in the vastus medialis following anterior cruciate ligament reconstruction

PURPOSE

Quadriceps weakness following anterior cruciate ligament reconstruction (ACLR) is prevalent despite intensive rehabilitation. Diminished neuromuscular excitability is one potential factor that may limit muscular recovery following injury or surgery. The H-reflex provides a measure of alpha motorneuron (neuromuscular) excitability in the sensory-motor pathway of the respective muscle and nerve. To date the vastus medialis (VM) and soleus (SOL) H-reflexes have been examined primarily in control subjects with induced knee joint effusion. This prospective, randomized clinical trial evaluated the affect of ACLR, utilizing hamsting (HS) or bone-patellar tendon-bone (BTB) autograft, on VM and SOL H-reflex latency and amplitude in twenty subjects.

METHODS

Preoperatively bilateral VM and SOL H-reflex tests were conducted. VM and SOL H-reflexes were subsequently conducted on the involved lower extremity at 1 and 3 months post surgery. At each test session subjects completed visual analog scales and knee girth was measured.

RESULTS

The VM H-reflex amplitude increased in the HS group at 3 months compared to 1-month post surgery (p<.05). Significant changes over time were also noted in the visual analog pain and functional scales and the mid-patella girth.

CONCLUSIONS

The increased VM H-reflex amplitude at 3 months following HS autograft ACLR demonstrates an increase in VM neuromuscular excitability. Increased VM neuromuscular excitability was not evident in patients following BTB reconstruction. The increased neuromuscular excitability, observed only in the HS group, warrants consideration when selecting graft type for patients with extensive preoperative quadriceps dysfunction.

The Pathway Less Traveled: Moving from Candidate Genes to Candidate Pathways in the Analysis of Genome-Wide Data from Large Scale Pharmacogenetic Association Studies

The candidate gene approach to pharmacogenetics is hypothesis driven, and anchored in biological plausibility. Whole genome scanning is hypothesis generating, and it may lead to new biology. While both approaches are important, the scientific community is rapidly reallocating resources toward the latter. We propose a step-wise approach to large-scale pharmacogenetic association studies that begins with candidate genes, then uses a pathway-based intermediate step, to inform subsequent analyses of data generated through whole genome scanning. Novel computational strategies are explored in the context of two clinically relevant examples, cholesterol synthesis and lipid signaling.

Evaporative cooling feature selection for genotypic data involving interactions

MOTIVATION

The development of genome-wide capabilities for genotyping has led to the practical problem of identifying the minimum subset of genetic variants relevant to the classification of a phenotype. This challenge is especially difficult in the presence of attribute interactions, noise and small sample size.

METHODS

Analogous to the physical mechanism of evaporation, we introduce an evaporative cooling (EC) feature selection algorithm that seeks to obtain a subset of attributes with the optimum information temperature (i.e. the least noise). EC uses an attribute quality measure analogous to thermodynamic free energy that combines Relief-F and mutual information to evaporate (i.e. remove) noise features, leaving behind a subset of attributes that contain DNA sequence variations associated with a given phenotype.

RESULTS

EC is able to identify functional sequence variations that involve interactions (epistasis) between other sequence variations that influence their association with the phenotype. This ability is demonstrated on simulated genotypic data with attribute interactions and on real genotypic data from individuals who experienced adverse events following smallpox vaccination. The EC formalism allows us to combine information entropy, energy and temperature into a single information free energy attribute quality measure that balances interaction and main effects.

AVAILABILITY

Open source software, written in Java, is freely available upon request.

Gender-specific correlations of plasminogen activator inhibitor-1 and tissue plasminogen activator levels with cardiovascular disease-related traits

BACKGROUND

The purpose of this study was to examine the correlations between plasma levels of plasminogen activator inhibitor-1 (PAI-1) and tissue plasminogen activator (t-PA) and cardiovascular disease-related traits in a general population and whether these correlations differed between females and males.

METHODS

Plasma PAI-1 and t-PA antigen levels and C-reactive protein (CRP), HDL-cholesterol, triglycerides, total cholesterol, systolic blood pressure, diastolic blood pressure, urinary albumin excretion, and glucose were measured in the population-based PREVEND study in Groningen, the Netherlands (n = 2527).

RESULTS

Except for CRP and total cholesterol levels, all traits were significantly different between gender (P < 0.001). PAI-1 levels were correlated with all measured cardiovascular disease-related traits (P < 0.01) in both females and males. Except for urinary albumin excretion, similar results, albeit less significant, were found for t-PA levels. Age-adjusted correlations between PAI-1 and CRP, triglycerides, total cholesterol, systolic blood pressure, and diastolic blood pressure differed significantly between females and males (P < 0.01). Many of the gender differences were predominantly present between premenopausal females and males.

CONCLUSION

PAI-1 and t-PA levels were correlated with cardiovascular disease-related traits in subjects obtained from the general population and several of these correlations differed across gender. The correlations found in the present study suggest the presence of coordinated patterns of cardiovascular risk factors and indicate which traits might influence PAI-1 and t-PA levels and thereby provide a framework and potential tool for therapeutic intervention to reduce thromboembolic events in the general population.

Hybrid grammar-based approach to nonlinear dynamical system identification from biological time series

We introduce a grammar-based hybrid approach to reverse engineering nonlinear ordinary differential equation models from observed time series. This hybrid approach combines a genetic algorithm to search the space of model architectures with a Kalman filter to estimate the model parameters. Domain-specific knowledge is used in a context-free grammar to restrict the search space for the functional form of the target model. We find that the hybrid approach outperforms a pure evolutionary algorithm method, and we observe features in the evolution of the dynamical models that correspond with the emergence of favorable model components. We apply the hybrid method to both artificially generated time series and experimentally observed protein levels from subjects who received the smallpox vaccine. From the observed data, we infer a cytokine protein interaction network for an individual's response to the smallpox vaccine.

A novel method to identify gene–gene effects in nuclear families: the MDR-PDT

It is now well recognized that gene-gene and gene-environment interactions are important in complex diseases, and statistical methods to detect interactions are becoming widespread. Traditional parametric approaches are limited in their ability to detect high-order interactions and handle sparse data, and standard stepwise procedures may miss interactions that occur in the absence of detectable main effects. To address these limitations, the multifactor dimensionality reduction (MDR) method [Ritchie et al., 2001: Am J Hum Genet 69:138-147] was developed. The MDR is well-suited for examining high-order interactions and detecting interactions without main effects. The MDR was originally designed to analyze balanced case-control data. The analysis can use family data, but requires a single matched pair be selected from each family. This may be a discordant sib pair, or may be constructed from triad data when parents are available. To take advantage of additional affected and unaffected siblings requires a test statistic that measures the association of genotype with disease in general nuclear families. We have developed a novel test, the MDR-PDT, by merging the MDR method with the genotype-Pedigree Disequilibrium Test (geno-PDT)[Martin et al., 2003: Genet Epidemiol 25:203-213]. MDR-PDT allows identification of single-locus effects or joint effects of multiple loci in families of diverse structure. We present simulations to demonstrate the validity of the test and evaluate its power. To examine its applicability to real data, we applied the MDR-PDT to data from candidate genes for Alzheimer disease (AD) in a large family dataset. These results show the utility of the MDR-PDT for understanding the genetics of complex diseases.

Analysis of the RELN gene as a genetic risk factor for autism

Several genome-wide screens have indicated the presence of an autism susceptibility locus within the distal long arm of chromosome 7 (7q). Mapping at 7q22 within this region is the candidate gene reelin (RELN). RELN encodes a signaling protein that plays a pivotal role in the migration of several neuronal cell types and in the development of neural connections. Given these neurodevelopmental functions, recent reports that RELN influences genetic risk for autism are of significant interest. The total data set consists of 218 Caucasian families collected by our group, 85 Caucasian families collected by AGRE, and 68 Caucasian families collected at Tufts University were tested for genetic association of RELN variants to autism. Markers included five single-nucleotide polymorphisms (SNPs) and a repeat in the 5'-untranslated region (5'-UTR). Tests for association in Duke and AGRE families were also performed on four additional SNPs in the genes PSMC2 and ORC5L, which flank RELN. Family-based association analyses (PDT, Geno-PDT, and FBAT) were used to test for association of single-locus markers and multilocus haplotypes with autism. The most significant association identified from this combined data set was for the 5'-UTR repeat (PDT P-value=0.002). These analyses show the potential of RELN as an important contributor to genetic risk in autism.

Practical means for the study of electron correlation in atoms

Electron correlation is basic to the understanding of a diverse range of physical and chemical phenomena, yet, there have been no direct measurements of the correlated motion of electrons. Measurement of the correlated momenta of atomic electrons is possible via electron-impact double ionization provided that the ionizing collisions are both impulsive and binary, and the three-body scattering mechanism is known. The results reported here satisfy these conditions, and a practical means for the study of atomic electron correlation through measurement of two-electron momentum densities is presented.

Multifactor-dimensionality reduction shows a two-locus interaction associated with Type 2 diabetes mellitus

AIMS/HYPOTHESIS

Type 2 diabetes mellitus is a complex genetic disease, which results from interactions between multiple genes and environmental factors without any single factor having strong independent effects. This study was done to identify gene to gene interactions which could be associated with the risk of Type 2 diabetes.

METHODS

We genotyped 23 different loci in the 15 candidate genes of Type 2 diabetes in 504 unrelated Type 2 diabetic patients and 133 non-diabetic control subjects. We analysed gene to gene interactions among 23 polymorphic loci using the multifactor-dimensionality reduction (MDR) method, which has been shown to be effective for detecting and characterising gene to gene interactions in case-control studies with relatively small samples.

RESULTS

The MDR analysis showed a significant gene to gene interaction between the Ala55Val polymorphism in the uncoupling protein 2 gene ( UCP2) and the 161C>T polymorphism in the exon 6 of peroxisome proliferator-activated receptor gamma ( PPARgamma) gene. This interaction showed the maximum consistency and minimum prediction error among all gene to gene interaction models evaluated. Moreover, the combination of the UCP2 55 Ala/Val heterozygote and the PPARgamma 161 C/C homozygote was associated with a reduced risk of Type 2 diabetes (odds ratio: 0.51, 95% CI: 0.34 to 0.77, p=0.0016).

CONCLUSIONS/INTERPRETATION

Using the MDR method, we showed a two-locus interaction between the UCP2 and PPARgamma genes among 23 loci in the candidate genes of Type 2 diabetes. The determination of such genotype combinations contributing to Type 2 diabetes mellitus could provide a new tool for identifying high-risk individuals.

The effect of the median nerve compression test on median nerve conduction across the carpal tunnel

INTRODUCTION

We conducted an experimental, single-blind research study to determine the efficacy of using the median nerve compression test (MNCT) to improve the sensitivity and specificity of median nerve motor and sensory latencies for the diagnosis of carpal tunnel syndrome (CTS). We expected post-MNCT latencies to be prolonged in the CTS group.

METHODS

A convenience sample of 18 subjects aged 18-65 was enrolled in this study. The CTS group consisted of 9 subjects with 14 hands tested having clinical signs and symptoms of CTS and normal baseline latency measures. The control group consisted of 9 gender- and age-matched (+/- 3 years) subjects with 14 hands tested. Three standard distal sensory latencies (DSL) and one distal motor latency (DML) were obtained, then repeated after application of the MNCT.

RESULTS

No significant differences in latencies were found between groups (p = 0.76) or within subjects (p = 0.74) after application of the MNCT. There was less than 10% increase in sensitivities of post-MNCT latencies.

DISCUSSION AND CONCLUSION

We found that the MNCT did not cause a meaningful increase in sensitivity or specificity of latencies for the diagnosis of CTS. The use of the MNCT as a method to prolong standard latencies is not recommended.

A comparison of combinatorial partitioning and linear regression for the detection of epistatic effects of the ACE I/D and PAI-1 4G/5G polymorphisms on plasma PAI-1 levels

The detection and characterization of epistasis or non-additive gene-gene interactions remains a statistical challenge in genetic epidemiology. The recently developed combinatorial partitioning method (CPM) may overcome some of the limitations of linear regression for the exploratory analysis of non-additive epistatic effects. The goal of this study was to compare CPM with linear regression analysis for the exploratory analysis of non-additive interactive effects of the angiotensin converting enzyme (ACE) insertion/deletion (I/D) and plasminogen activator inhibitor 1 (PAI-1) 4G/5G polymorphisms on plasma PAI-1 levels in a sample of 50 unrelated African Americans and 117 unrelated Caucasians. Using linear regression, we documented the additive effects of the ACE and PAI-1 genes on plasma PAI-1 levels in African American females (R(2) = 0.10), African American males (R(2) = 0.16), Caucasian females (R(2) = 0.11), and Caucasian males (R2 = 0.09). Using CPM, we found evidence for non-additive effects of the ACE and PAI-1 genes in both African American females (R(2) = 0.22) and African American males (R(2) = 0.24) but not in Caucasian females (R(2) = 0.10) or Caucasian males (R(2) = 0.11). The results of this exploratory data analysis support previous experimental, clinical, and epidemiological studies that have proposed as a working hypothesis that the ACE gene mediates interaction effects of the fibrinolytic and renin-angiotensin systems on plasma levels of PAI-1.

The relationship between plasma t-PA and PAI-1 levels is dependent on epistatic effects of the ACE I/D and PAI-1 4G/5G polymorphisms

Thrombus formation and degradation is partly due to a complex interplay between tissue-type plasminogen activator (t-PA) and plasminogen activator inhibitor 1 (PAI-1). There is accumulating evidence that plasma levels of t-PA and PAI-1 may be influenced by an interaction between the fibrinolytic and renin-angiotensin systems. The goal of this study was to conduct an exploratory data analysis to determine whether there is evidence that the relationship (i.e. correlation) between plasma t-PA and PAI-1 is influenced by interactive effects of the angiotensin converting enzyme (ACE) insertion/deletion (I/D) and plasminogen activator inhibitor 1 (PAI-1) 4G/5G polymorphisms in a sample of 50 unrelated African Americans and 117 unrelated Caucasians. In a single-locus analysis, no evidence for heterogeneity of plasma t-PA and PAI-1 correlations among either ACE I/D or PAI-1 4G/5G genotypes was detected. However, using the combinatorial partitioning method for exploratory data analysis, we identified evidence that is suggestive of heterogeneity of plasma t-PA and PAI-1 correlations among multilocus ACE I/D and PAI-1 4G/5G genotypes in African American females, Caucasian females, Caucasian males, but not African American males. From these results, we propose as a working hypothesis that the correlation between plasma t-PA and PAI-1 may be dependent on epistatic effects of the ACE I/D and PAI-1 4G/5G polymorphisms. This study supports the idea that interactions between the fibrinolytic and renin-angiotensin systems play an important role in the genetic architecture of plasma t-PA and PAI-1.

Improved power of sib-pair linkage analysis using measures of complex trait dynamics

The influence of epistasis on a quantitative trait can reduce the power of linkage analysis to identify the underlying loci. In the present study, we simulated a complex trait derived from a dynamic one-locus gene expression system with epistasis arising from feedback regulation and tested the power of sib-pair linkage analysis methods for detecting the underlying quantitative trait locus (QTL). Using this simple genetic architecture, we demonstrate that the power of sib-pair linkage analysis can be greatly improved if measures of complex trait dynamics are considered.

Epidural analgesia compared with intravenous morphine patient-controlled analgesia: postoperative outcome measures after mastectomy with immediate TRAM flap breast reconstruction

BACKGROUND AND OBJECTIVES

Epidural analgesia has been shown to provide superior pain control compared with intravenous (IV) opioids after major surgical procedures. In this study, we compared the effect of epidural analgesia and IV morphine patient-controlled analgesia (PCA) on pain relief, duration of hospitalization, oral nutrition, ambulation, and side effects in patients undergoing a major surgical procedure (i.e., unilateral mastectomy with immediate transverse rectus abdominis musculocutaneous flap reconstruction).

METHODS

Eighteen patients were prospectively randomized to receive either epidural analgesia or PCA during the postoperative period. The intensity of pain was assessed daily by a 100-mm visual analog scale. The total length of hospital stay, time to ambulation, and time to oral nutrition were recorded.

RESULTS

The epidural group had significantly lower pain scores at 3 evaluation times through postoperative day number 4 (P < .05). The total length of hospitalization for the epidural group (median, 101 hours) was significantly less than the PCA group (median, 126 hours; P = .0498). The time to first ambulation, time to first bowel sounds, time to tolerating oral nutrition, incidence of nausea/vomiting or pruritus, and time to first flatus were not statistically different between the groups.

CONCLUSIONS

These results show that epidural analgesia compared with PCA offered improved pain control after breast reconstruction with immediate transverse rectus abdominis musculocutaneous flap reconstruction. It also resulted in a 25-hour reduction in time of hospitalization.

Test-retest reliability of the ulnar F-wave minimum latency versus ulnar distal motor latency in healthy adults

BACKGROUND AND PURPOSE

The purposes of this study were to explore reliability of the ulnar F-wave minimum latency (Fmin) and the ulnar distal motor latency (DML) and to contrast those levels of reliability in order to reveal whether physiologic lability is the primary contributor to unwanted variability in Fmin measurements.

SUBJECTS AND METHODS

Fmin and DML in the Abductor Digiti Minimi muscle were measured bilaterally by two raters in 50 healthy adults (n = 100 hands, 70 male, 30 female) with 3-14 days between testing sessions.

RESULTS

Intrarater reliability (ICC 3,1) for the Fmin was 0.89 with a standard error of the measurement (SEM) of 0.77 msec. Interrater reliability (ICC 2,1) for the Fmin was 0.80 with a SEM of 1.04 msec. Intrarater reliability (ICC 3,1) for the DML was 0.71 with a SEM of 0.18 msec. Interrater reliability (ICC 2,1) for the DML was 0.76 with a SEM of 0.19 msec.

DISCUSSION AND CONCLUSIONS

Contrary to our hypothesis, the Fmin had a higher reliability than the DML. The DML did not display the high reliability other investigators have reported. We conclude the Fmin is a reliable measurement when 10 supramaximal stimulations are administered to healthy, young to middle-aged adult subjects. However, no inferences were made regarding relative levels of psychologic lability for the two latencies.

How many frogs does it take to leap around the Americas? Comments on Anderson and Gillam

In modeling the colonization of the Americas, Anderson and Gillam (2000) employ size estimates for vanguard forager bands that are of dubious reproductive viability in light of human incest prohibitions and variable sex ratios at birth.

Flexural wave propagation velocity and bone mineral density in females with and without tibial bone stress injuries

STUDY DESIGN

Case-control nonexperimental design.

OBJECTIVES

To compare flexural wave propagation velocity (FWPV) and tibial bone mineral density (BMD) in women with and without tibial bone stress injuries (BSIs).

BACKGROUND

Physical therapists, particularly in military and sports medicine settings, routinely diagnose and manage stress fractures or bone stress injuries. Improved methods of preparticipation quantification of tibial strength may provide markers of BSI risk and thus potentially reduce morbidity.

METHODS AND MEASURES

Bone mineral density, FWPV, bone geometry, and historical variables were collected from 14 subjects diagnosed with tibial BSIs and 14 age-matched controls; all 28 were undergoing military training.

RESULTS

No difference was found between groups in FWPV and tibial BMD when analyzed with t tests (post hoc power = 0.89 and 0.81, respectively). Furthermore, no difference was found in tibial length, tibial width, femoral neck BMD, and lumbar spine BMD among the groups. There were no differences between the 2 groups in smoking history, birth control pill use, and onset of menarche. Finally, sensitivity and positive likelihood ratios for FWPV (0.14 and 0.63), tibial BMD (0.0 and 0.0), and lumbar BMD (0.18 and 2.0) were low, while specificity was high (0.77, 0.93, and 0.91, respectively).

CONCLUSION

Current bone analysis devices and methods may not be sensitive enough to detect differences in tibial material and structure; local stresses on bone may be more important in the development of BSIs than the overall structural stiffness.

Effect of time of day on intraindividual variability in ambulatory blood pressure

The aim of this study was to determine whether intraindividual blood pressure (BP) variability, measured by noninvasive ambulatory monitoring, differs between the active (daytime) and inactive (nighttime) periods of the day. We obtained ambulatory BP recordings in 143 healthy adults (95 men, 48 women) from Rochester, Minnesota. Readings were obtained every 10 min for a 24-h period. We calculated the standard deviation of each individual's BP readings about the means for the active period and for the inactive period as measures of intraindividual BP variability. In men, mean within-individual standard deviations for both systolic (SBP) and diastolic blood pressure (DBP) were significantly greater during the inactive period than during the active period (for SBP: 10.3 +/- 2.1 v 11.9 +/- 2.7, P < .0001; for DBP: 8.8 +/- 2.0 v 9.7 +/- 2.5, P = .0027). In women, the mean within-individual standard deviation for SBP did not differ significantly between the active and inactive periods (9.7 +/- 2.2 v 10.3 +/- 2.4, P = 0.225) but for DBP was significantly greater during the inactive period than during the active period (8.1 +/- 2.0 v 9.2 +/- 2.3, P = .020). Statistically significant predictors of intraindividual BP variability included measures of age and body size, metabolic traits, neuroendocrine traits, erythrocyte cation traits, and renal function traits. This study demonstrates that intraindividual BP variability, as measured by noninvasive ambulatory monitoring, is as great or greater during the inactive period as during the active period of the day.

Detection of linear and nonlinear dependencies in time series using the method of surrogate data in S-PLUS

A general implementation of the method of surrogate data in the S programming language for use with the S-PLUS statistical package is presented. We illustrate the application of the S functions to testing hypotheses about a human heart rate time series and demonstrate that there is evidence for both linear and nonlinear dependencies. We expect these S functions will be useful for the application of the method of surrogate data to the analysis of biomedical time series using the S-PLUS statistical software package.

The biophysical effects of ultrasound on median nerve distal latencies

PURPOSE

Previous studies have documented the lack of ultrasound's non-thermal effects on nerve conduction using frequencies of 1 MHz and 870 kHz. The analyses and conclusions were reached, despite only one study incorporating pulsed ultrasound. The purpose of this study was to determine the biophysical effects of continuous wave (CW) and pulsed wave (PW) ultrasound on median nerve motor and sensory latencies using common frequencies of 1.0 and 3.0 MHz.

SUBJECTS

Fifteen healthy subjects (8 males, 7 females, age = 23.5 + 4.44 yrs, height = 171.2 + 10.7 cm, weight = 67.5 + 7.9 kg) without a history of neurological or musculoskeletal injury to their non-dominant arm volunteered for testing.

METHODS AND MATERIALS

Subjects were exposed in counterbalanced order to five ultrasound treatment conditions: (1) 1 MHz, 1.0 W/cm2, 8 min., (2) 1 MHz, 1.0 W/cm2, 50% PW, 8 min., (3) 3.0 MHz, 1.0 W/cm2, CW, 8 min., (4) 3.0 MHz, 1.0 W/cm2, 50% PW, 8 min., (5) placebo, 0.0 W/cm2, 8 min. Dependent measures for motor and sensory latencies, and subcutaneous temperatures were taken pretreatment, at 2, 4 and 6 minutes during treatment, and immediately post-treatment. Separate two within repeated measures ANOVA were used for each dependent measure.

RESULTS

Analysis revealed significant interactions for motor latencies [F (16,224) = 52.77, p < .001], sensory latencies [F (16,224) = 41.10, p < .001], and subcutaneous temperatures [F (16,224) = 52.77, p < .001]. Tukey's HSD post hoc analyses confirmed that nerve latencies responded similarly to subcutaneous temperature changes during and after ultrasound treatment.

CONCLUSIONS

Alterations in nerve latencies from ultrasound on healthy nerves appeared to be related to temperature changes induced by ultrasound's thermal effects, and not by non-thermal or mechanical effects.

Predictors of interindividual variation in ambulatory blood pressure and their time or activity dependence

The objectives of this study were to determine whether total interindividual variation in blood pressure (BP) differs between inactive and active hours of the day, to identify predictors of interindividual variation in BP, and to assess whether variation associated with any of these identified predictors is greater (or less) during inactive hours than during active hours of the day. We obtained ambulatory BP recordings over 20 consecutive hours (12 active, out of bed [daytime]; and 8 inactive, in bed [nighttime]) in a sample of 240 unrelated, non-Hispanic white adults (138 men; 102 women). We estimated total interindividual variation in BP, and the percentage of interindividual variation associated with measures of age and body size, metabolic traits, catecholamines, erythrocyte cation transport, and renal function. We used linear regression to assess changes in the hourly estimates of total interindividual variation and in variation attributable to each set of predictor traits over the 20 h. In both men and women, total interindividual variation in systolic BP was significantly greater (not less) during inactive hours than during active hours. In addition, in women, total interindividual variation in diastolic BP was as great during inactive hours as during active hours. Each set of traits considered predicted a statistically significant percentage of interindividual variation in BP. None of the sets of traits predicted a greater percentage of interindividual variation during the inactive hours than during the active hours. Measures of age and body size, catecholamines, cation transport and renal function traits predicted significantly less interindividual variation during inactive hours than during active hours of the day. That total interindividual variation in BP is as great or greater during inactive hours than during active hours of the day emphasizes the potential for differences in nighttime BP to contribute to the development of cardiovascular disease. In as much as the predictors of interindividual variation in BP differ between the daytime and nighttime, the causes of variation during these two times may also differ.

Test-retest reliability of the ulnar F-wave minimum latency in normal adults

BACKGROUND AND PURPOSE

The purpose of this study was to measure the test-retest reliability of the ulnar F-wave minimum latency (Fmin) in normal adults. A reliable Fmin measure allows clinicians to ascribe changes in latency to true changes in a subject and not merely random daily variation.

SUBJECTS AND METHODS

Fmin in the Abductor Digiti Minimi muscle was measured bilaterally in 49 healthy adults (n = 98) with a three day separation between tests.

RESULTS

The Fmin reliability estimate as measured by intraclass correlation coefficient (3,1) was 0.59 with a standard error of measurement (SEM) of 1.3 msec. A paired t-test showed no significant difference (t = 1.7, df = 97, p > 0.05) between the mean scores from the two testing sessions.

DISCUSSION AND CONCLUSIONS

We found moderate reliability and relatively low precision (high SEM) in Fmin scores taken from healthy individuals on two separate days. Strict adherence to our protocol and an acceptable overall precision of measurements (as measured by mean scores) suggest the contributions of rater and instrument error were low in our study. We conclude that 1) valid clinical interpretation of minimum F-wave latency findings is questionable because the Fmin measurement appears to have only moderate reliability, and 2) the lability of the phenomenon itself is the most likely contributor to variability in the Fmin latencies. Further research is warranted before electrophysiologists may be justified in attributing small changes in the Fmin to actual changes in the subject.

Diabetes research in an American Indian community

PURPOSE

To describe field experiences of a nurse-led team conducting collaborative research on diabetes with an American Indian community. Diabetes is of epidemic proportions among Indians. Methodological reports can assist nurse researchers to make important contributions to Indian health and diabetes care.

ORGANIZING FRAMEWORK

Wax's stages of fieldwork: Initiation, fieldwork, post-field work. SCOPE AND METHOD: Report of key research experiences from all phases of a study with an Indian community (1988-1996). Based on review of classic literature, field notes, and team meetings.

FINDINGS

Methodological literature on research with Indians and cultural tutelage by Indians were helpful but neither sufficient nor infallible. A long period of investigator presence in the community before beginning the research was extremely useful. The need for researchers to explain their presence and the contribution of research to the community was ongoing.

CONCLUSIONS

Wax's conception of field work as a dialectic process was supported. A collaborative, community focus and willingness to spend much time acquiring cultural knowledge can facilitate successful research on Indian health.

Effects of strength training on strength development and joint position sense in functionally unstable ankles

OBJECTIVE

To examine the effects of ankle-strengthening exercises on joint position sense and strength development in subjects with functionally unstable ankles.

DESIGN AND SETTING

Subjects were randomly assigned to a training or control group. The training group participated in a 6-week strength-training protocol using rubber tubing 3 times a week throughout the training period. The control group did not participate in the strength-training protocol.

SUBJECTS

Twenty healthy college students (10 females, 10 males, age = 20.6 +/- 2.23 years; ht = 176.40 +/- 7.14 cm; wt = 74.18 +/- 10.17 kg) with a history of functional ankle instability volunteered to participate in this study.

MEASUREMENTS

We pretested and posttested dorsiflexor and evertor isometric strength with a handheld dynamometer and collected joint position sense (JPS) data at 20 degrees for inversion and plantar flexion and at 10 degrees for eversion and dorsiflexion.

RESULTS

Statistical tests for strength and JPS revealed significant group-by-time interactions for dorsiflexion strength, eversion strength, inversion JPS, and plantar flexion JPS. Simple main-effects testing revealed improvements in training group strength and JPS at posttesting. There were no significant effects for eversion JPS, but the group main effect for dorsiflexion JPS was significant, with the experimental group having better scores than the control group.

CONCLUSIONS

Ankle-strengthening exercises improved strength, inversion JPS, dorsiflexion JPS, and plantar flexion JPS in subjects with functionally unstable ankles.

Soft-tissue complications of intra-arterial chemotherapy for extremity sarcomas

High-grade sarcomas have a high rate of local recurrence as well as distant metastases. This has led to the development of intra-arterial chemotherapy (IAC) as part of a multimodal approach to control local disease and/or reduce the extent of surgical resection. Intra-arterial catheters are positioned by an interventional radiologist into the feeding vessels of the tumor. Adriamycin and 5-fluorodeoxyuridine are infused intra-arterially. Cisplatinum, with or without granulocyte colony stimulating factor, is given systemically. Patients usually experience acute self-limited soft-tissue inflammation in the treated area. In our experience of 118 patients, 3 patients experienced soft-tissue necrosis that required excision and reconstruction. The first was treated for synovial sarcoma of a metatarsal. After IAC with Adriamycin, she sloughed the skin, subcutaneous tissue, and some of the posterior compartment musculature of her calf. This tissue was debrided. A gastrocnemius flap and skin graft were used for coverage. She is free of disease and ambulatory. The second patient was treated with IAC Adriamycin for a radial head chondrosarcoma. She developed soft-tissue slough, which became infected with Pseudomonas. She required extensive debridement of the skin, subcutaneous tissue, and muscle, and was subsequently reconstructed with a latissimus flap and a split-thickness skin graft (STSG). She later developed a local recurrence requiring amputation. The latissimus was elevated and used to cover the distal stump. She also is free of disease. The third patient was treated with IAC Adriamycin for Ewing's sarcoma of the right femur. This was complicated by fat necrosis and persistent pain. Subsequent radiotherapy only worsened her symptoms. She underwent wide excision and muscle flap/STSG repair, which relieved her pain. She is currently ambulatory and free of disease. In conclusion, as the use of IAC continues, its complications may become more common. Our experience with this previously unknown entity is illustrated and therapeutic options are discussed.

Dexamethasone stimulates leptin release from human adipocytes: unexpected inhibition by insulin

In the present study we have examined the effect of dexamethasone on ob gene mRNA expression and leptin release from isolated human subcutaneous adipocytes. Dexamethasone stimulated leptin release from cultured adipocytes in a time- and dose-dependent manner. A two-fold increase in leptin release was detectable by 36 h of treatment with 10(-7) M dexamethasone. Leptin release was preceded by a significant 83 +/- 30% increase in ob mRNA after 24 h exposure to the compound. Co-incubation of cells with dexamethasone (10(-7) M) and insulin (10(-7) or 10(-9) M) completely blocked the dexamethasone-stimulated increase in ob mRNA and leptin release. These data demonstrate that insulin and glucocorticoids regulate leptin synthesis and release from human adipocytes in vitro.

The role of the apolipoprotein E polymorphism in the prediction of coronary artery disease age of onset

We investigated the role of the apolipoprotein (Apo) E polymorphism in the prediction of CAD age of onset in a sample of unrelated living male (n = 65) and female (n = 54) Caucasian subjects diagnosed with CAD. Cumulative distributions of age at the first diagnosis of CAD were estimated for each Apo E genotype and tested for homogeneity using the log-rank test. The Apo epsilon 33 genotype was used as a reference group for all hypothesis tests. Analyses were performed separately in males and females. We found evidence suggesting that the presence of the Apo epsilon 32 genotype in males is associated with a significantly earlier CAD age of onset. These results suggest that the Apo E polymorphism may be a gender-specific predictor of CAD age of onset.