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PubMed2006

Phylogenetic analysis of major African genotype (Af2) of JC virus: Implications for origin and dispersals of modern Africans.

Both mtDNA and the Y chromosome have been used to investigate how modern humans dispersed within and out of Africa. This issue can also be studied using the JC virus (JCV) genotype, a novel marker with which to trace human migrations. Africa is mainly occupied by two genotypes of JCV, designated Af1 and Af2. Af1 is localized to central/western Africa, while Af2 is spread throughout Africa and in neighboring areas of Asia and Europe. It was recently suggested that Af1 represents the ancestral type of JCV, which agrees with the African origin of modern humans. To better understand the origin of modern Africans, we examined the phylogenetic relationships among Af2 isolates worldwide. A neighbor-joining phylogenetic tree was constructed based on the complete JCV DNA sequences of 51 Af2 isolates from Africa and neighboring areas. According to the resultant tree, Af2 isolates diverged into two major clusters, designated Af2-a and -b, with high bootstrap probabilities. Af2-a contained isolates mainly from South Africa, while Af2-b contained those from the other parts of Africa and neighboring regions of Asia and Europe. These findings suggest that Af2-carrying Africans diverged into two groups, one carrying Af2-a and the other carrying Af2-b; and that the former moved to southern Africa, while the latter dispersed throughout Africa and to neighboring regions of Asia and Europe. The present findings are discussed with reference to relevant findings in genetic and linguistic studies.

Africa↗
PubMed2005

Sparse multifocal stimuli for the detection of multiple sclerosis.

We compared the diagnostic capabilities of contrast reversal and sparse pattern pulse stimulation for dichoptic multifocal visual evoked potentials (mfVEPs) measured in normal subjects and multiple sclerosis (MS) patients. Multifocal responses were obtained from 27 normal subjects and 50 relapsing-remitting patients, 26 of whom had experienced optic neuritis (ON+). The patient groups were matched for length of disease and number of clinical attacks. Compared with the responses of normal subjects those of MS patients had significantly smaller response amplitudes, lower signal-to-noise ratios, more complex response waveforms, and longer response delays. The effects were larger for sparser stimuli. Sensitivities and specificities for the different stimulus types were estimated from receiver operator characteristic (ROC) plots. Bootstrap estimates of the accuracies of the ROCs for the most promising measure, the template delays, indicated the sparsest stimulus would deliver 92% sensitivity at a false-positive rate of 0%. In contrast, at 92% sensitivity the conventional mfVEP stimulus misdiagnosed more than 20% of the normal population. The results were similar for patients with no history of ON (ON-). In performing well in patients with no history of ON, the sparse mfVEPs seem to measure progressive damage associated with axon and gray matter losses rather than damage associated with a history of serious inflammation.

Adult↗
PubMed1994

Serial contrast-enhanced magnetic resonance imaging in patients with early relapsing-remitting multiple sclerosis: implications for treatment trials.

Serial monthly contrast-enhanced MRIs were performed in 10 early relapsing-remitting patients with multiple sclerosis and 2 patients with chronic progressive disease for a period of 12 to 55 months. MRI was performed at 1.5 T using contiguous 5-mm slices with pre- and postgadolinium-diethylenetriamine pentaacetic acid (Gd-DTPA) T1-weighted and T2-weighted images. New and total number of Gd-DTPA-enhancing lesions were numbered and counted and lesion areas were correlated to an increase of > or = 0.5 in Expanded Disability Status Scale (EDSS) scores. The frequency of enhancing lesions varied from patient to patient; however, there was a correlation between a burst of enhancing lesion number and area above the individual's mean lesion frequency to an increase in EDSS score. A bootstrap analysis of the lesion count was performed to develop a statistical basis for determining population sizes for treatment trials. These results provide a basis for the potential use of contrast-enhanced MRI as a primary outcome measure in phase II treatment trials involving patients with relapsing-remitting MS.

Adult↗
PubMed2002

Brain expansion in the chick embryo initiated by experimentally produced occlusion of the spinal neurocoel.

The brain expands in the early chick embryo from pressure generated by accumulation of cerebrospinal fluid (CSF) in a closed neural tube. The sealing of the neural tube occurs as the result of occlusion of the spinal neurocoel rostral to and before closure of the posterior neuropore. We have previously demonstrated the dependence of normal brain expansion upon intraluminal pressure. We had yet to demonstrate, however, that brain expansion actually depends upon natural occlusion of the spinal neurocoel. To demonstrate such dependence, we experimentally occluded the spinal neurocoels of embryos 5 hr younger than stage 11 embryos (in which occlusion of the neurocoel occurs naturally). The stage 10 chick embryos were cultured ex ovo and critically staged, and their spinal neurocoels were occluded using microcautery. All embryos were photographed immediately and at 5, 12, and 24 hr after cautery. Serial sections were made of selected embryos, in which the areas of both the brain and the head were measured. Wilcoxon-Mann-Whitney rank-sum nonparametric tests, Hodges-Lehmann estimators, bootstrapping techniques, and resampling randomization tests were used to determine whether the increases in the brain and head areas for the experimental embryos were significantly different from those of the control embryos during three distinct intervals of expansion: 0-5, 5-12, and 0-12 hr. From 0 to 5 hr, the brains of the precociously occluded embryos expanded significantly more than the brains of the non-occluded controls. From 5 to 12 hr, the brains of the embryos with naturally occluded neurocoels grew significantly larger than the brains of the embryos with precociously occluded neurocoels. At 12 hr, there appeared to be no difference in brain size for these two groups. We conclude that the data support the hypothesis that brain expansion is directly dependent upon occlusion of the spinal neurocoel.

Animals↗
PubMed2005

Recovery of cDNAs encoding ribosomal proteins S9 and L26 from Aedes albopictus mosquito cells and identification of their homologs in the malaria vector, Anopheles gambiae.

We used PCR-based approaches to obtain the full-length cDNA sequences encoding ribosomal protein (Rp) S9 and L26 from a mosquito (Aedes albopictus) C7-10 cell line. The deduced mosquito RpS9 protein has a mass of 22,826 Da and a pI of 11.41, while RpL26 had a mass of 17,442 Da and a pI of 11.52. Both cDNAs initiated with the 5'-polypyrimidine motif characteristic of ribosomal protein transcripts. Using the Aedes protein and nucleic acid sequences, we identified rpS9 and rpL26 as single copy genes in the Anopheles gambiae genome. In An. gambiae, the RpS9 coding region was distributed over 3 exons, spanning 2.6 kb, but the Anopheles rpL26 protein coding region lacked introns. The Aedes and Anopheles RpS9 and RpL26 proteins shared 96 and 92% identity, respectively. Despite low numbers of parsimony-informative amino acid substitutions, phylogenies based on the ribosomal protein sequences accurately group the Aedes and Anopheles proteins with high bootstrap values.

Aedes↗
PubMed2006

Short-term prediction of mortality in patients with systemic lupus erythematosus: classification of outcomes using random forests.

OBJECTIVE: To identify demographic and clinical characteristics that classify patients with systemic lupus erythematosus (SLE) at risk for in-hospital mortality. METHODS: Patients hospitalized in California from 1996 to 2000 with a principal diagnosis of SLE (N = 3,839) were identified from a state hospitalization database. As candidate predictors of mortality, we used patient demographic characteristics; the presence or absence of 40 different clinical conditions listed among the discharge diagnoses; and 2 summary indexes derived from the discharge diagnoses, the Charlson Index and the SLE Comorbidity Index. Predictors of patients at increased risk of mortality were identified and validated using random forests, a statistical procedure that is a generalization of single classification trees. Random forests use bootstrapped samples of patients and randomly selected subsets of predictors to create individual classification trees, and this process is repeated to generate multiple trees (a forest). Classification is then done by majority vote across all trees. RESULTS: Of the 3,839 patients, 109 died during hospitalization. Selecting from all available predictors, the random forests had excellent predictive accuracy for classification of death. The mean classification error rate, averaged over 10 forests of 500 trees each, was 11.9%. The most important predictors were the Charlson Index, respiratory failure, SLE Comorbidity Index, age, sepsis, nephritis, and thrombocytopenia. CONCLUSION: Information on clinical diagnoses can be used to accurately predict mortality among hospitalized patients with SLE. Random forests represent a useful technique to identify the most important predictors from a larger (often much larger) number and to validate the classification.

Adult↗
PubMed2003

Motor protein control of ion flux is an early step in embryonic left-right asymmetry.

The invariant left-right asymmetry of animal body plans raises fascinating questions in cell, developmental, evolutionary, and neuro-biology. While intermediate mechanisms (e.g., asymmetric gene expression) have been well-characterized, very early steps remain elusive. Recent studies suggested a candidate for the origins of asymmetry: rotary movement of extracellular morphogens by cilia during gastrulation. This model is intellectually satisfying, because it bootstraps asymmetry from the intrinsic biochemical chirality of cilia. However, conceptual and practical problems remain with this hypothesis, and the genetic data is consistent with a different mechanism. Based on wide-ranging data on ion fluxes and motor protein action in a number of species, a model is proposed whereby laterality is generated much earlier, by asymmetric transport of ions, which results in pH/voltage gradients across the midline. These asymmetries are in turn generated by a new candidate for "step 1": asymmetric localization of electrogenic proteins by cytoplasmic motors.

Animals↗
PubMed2005

A simple test of the homogeneity of risk difference in sparse data: an application to a multicenter study.

In this paper, we focus discussion on testing the homogeneity of risk difference for sparse data, in which we have few patients in each stratum, but a moderate or large number of strata. When the number of patients per treatment within strata is small (2 to 5 patients), none of test procedures proposed previously for testing the homogeneity of risk difference for sparse data can really perform well. On the basis of bootstrap methods, we develop a simple test procedure that can improve the power of the previous test procedures. Using Monte Carlo simulations, we demonstrate that the test procedure developed here can perform reasonable well with respect to Type I error even when the number of patients per stratum for each treatment is as small as two patients. We evaluate and study the power of the proposed test procedure in a variety of situations. We also include a comparison of the performance between the test statistics proposed elsewhere and the test procedure developed here. Finally, we briefly discuss the limitation of using the proposed test procedure. We use the data comparing two chemotherapy treatments in patients with multiple myeloma to illustrate the use of the proposed test procedure.

Computer Simulation↗
PubMed2006

Model-based clustering of binary longitudinal atopic dermatitis disease histories by latent class mixture models.

Atopic dermatitis is a skin disease which affects mainly children, has a very strong genetical component, and manifests itself clinically as flexural excema in connection with torturing itching. The course of disease is notoriously changeable and runs in phases, therefore it is difficult to predict the future course of disease. To improve prediction it would be interesting to identify clusters of children with different disease histories because this would shed light on common genetic and environmental risk factors. We use, relying on previous work of Nagin, a Latent class mixture model to estimate, in a data-dependent and model-based fashion, a clustering of typical binary atopic dermatitis disease histories in children. The data were collected from 1990 to 1997 in the so called MAS-study, a prospective cohort study of 1314 children in five German cities. The original method of Nagin is extended in two different aspects, first we use bootstrap confidence intervals to account for uncertainty in curve fitting, and second, we propose to model covariates for cluster membership by Anderson's Stereotype regression model. We feel that the Latent class mixture model is a valuable tool for assessing the course of atopic dermatitis, yielding a wealth of communicable and graphically displayable results.

Algorithms↗
PubMed2005

A class of goodness of fit tests for a copula based on bivariate right-censored data.

The copula of a bivariate distribution, constructed by making marginal transformations of each component, captures all the information in the bivariate distribution about the dependence between two variables. For frailty models for bivariate data the choice of a family of distributions for the random frailty corresponds to the choice of a parametric family for the copula. A class of tests of the hypothesis that the copula is in a given parametric family, with unspecified association parameter, based on bivariate right censored data is proposed. These tests are based on first making marginal Kaplan-Meier transformations of the data and then comparing a non-parametric estimate of the copula to an estimate based on the assumed family of models. A number of options are available for choosing the scale and the distance measure for this comparison. Significance levels of the test are found by a modified bootstrap procedure. The procedure is used to check the appropriateness of a gamma or a positive stable frailty model in a set of survival data on Danish twins.

Algorithms↗
PubMed2005

Monitoring complex media fermentations with near-infrared spectroscopy: comparison of different variable selection methods.

Near-infrared spectroscopy (NIRS) is known to be a suitable technique for rapid fermentation monitoring. Industrial fermentation media are complex, both chemically (ill-defined composition) and physically (multiphase sample matrix), which poses an additional challenge to the development of robust NIRS calibration models. We investigated the use of NIRS for at-line monitoring of the concentration of clavulanic acid during an industrial fermentation. An industrial strain of Streptomyces clavuligerus was cultivated at 200-L scale for the production of clavulanic acid. Partial least squares (PLS) regression was used to develop calibration models between spectral and analytical data. In this work, two different variable selection methods, genetic algorithms (GA) and PLS-bootstrap, were studied and compared with models built using all the spectral variables. Calibration models for clavulanic acid concentration performed well both on internal and external validation. The two variable selection methods improved the predictive ability of the models up to 20%, relative to the calibration model built using the whole spectra.

Algorithms↗
PubMed2005

Short-term cost effectiveness and long-term cost analysis comparing laparoscopic Nissen fundoplication with proton-pump inhibitor maintenance for gastro-oesophageal reflux disease.

BACKGROUND: This study examined the short-term cost-effectiveness and long-term cost of laparoscopic Nissen fundoplication (LNF) versus maintenance proton-pump inhibitor (PPI) medication for severe gastro-oesophageal reflux disease (GORD) based on a randomized clinical trial. METHODS: Costs and outcomes for 12 months were obtained from the first 100 patients in the trial. Detailed costing was performed using resource use data from hospital records and general practitioners' notes. Short-term incremental cost-effectiveness ratios, calculated as the cost difference divided by the effectiveness difference between LNF and PPI therapy, were analysed using net benefit and bootstrap approaches. Long-term cost was examined using sensitivity analyses incorporating published data from other large series. RESULTS: The incremental cost of LNF compared with PPI therapy per additional patient returned to a physiologically normal acid score (less than 13.9) at 3 months was pound5515 (95 per cent confidence interval (c.i.) pound3655 to pound13 400) and the incremental cost per point improvement in combined Gastro-Intestinal and Psychological Well-being score at 12 months was pound293 (90 per cent c.i. pound149 to pound5250). On average, LNF cost pound2247 (95 per cent c.i. pound2020 to pound2473) more than PPI therapy in year 1 and broke even in year 8. Break-even was highly sensitive to hospital unit costs but less sensitive to PPI ingestion rate after LNF, LNF reoperation rate, PPI relapse rate, future PPI price, PPI dose escalation and discount rate. CONCLUSION: From a National Health Service perspective, LNF may be cost-saving after 8 years compared with maintenance PPI therapy for the treatment of GORD.

Cost-Benefit Analysis↗
PubMed2006

Phylogeny of the Schisandraceae based on cpDNA mat-K and rpL16 intron data.

The chloroplast mat-K region and rpL16 intron region were sequenced for 14 species of Schisandraceae, representing both genera Kadsura Kaempf. ex Juss. and Schisandra Michx, to discuss the phylogeny of this family. Analyses were performed both in separate and combined sequence data sets (including the rbc-L sequence), with Illicium angustispealum A. C. Smith as the out-group. The results showed that the Schisandraceae are monophyletic. In all the analyses, Schisandra propinqua var. chinensis Oliva and Schisandra plena A. C. Smith were nested within Kadsura, which implies that the genera Kadsura and Schisandra are closely related. They might have originated from a common ancestor, but then evolved via different routes. The result inferred from the combined data showed a greater resolution within Schisandra than those from the two separate data sets. High bootstrap values supported the monophyly of most subgenera according to Law's system (1996). A combination of morphological, anatomical, and chemical analyses indicates that S. chinensis and S. rubriflora may be the primitive taxa in Schisandra.

DNA, Chloroplast↗
PubMed2002

The relevance of prostatectomy findings for brachytherapy selection in patients with localized prostate carcinoma.

BACKGROUND: The efficacy of brachytherapy for patients with localized prostate carcinoma depends on adequate radiotherapeutic coverage of the primary tumor and its subclinical extraprostatic extensions. Predictive models based on pretherapy factors may be useful to estimate the likelihood for clinically relevant extraprostatic disease and may be incorporated into selection criteria for this procedure. METHODS: Multivariate logistic regression model building was performed using pretherapy factors in 2905 surgically staged patients with localized prostate carcinoma to estimate the probability of seminal vesicle and/or lymph node involvement. Bootstrap methods were employed to assess the stability of the final model parameters and to determine the sensitivity and specificity of the final model. RESULTS: Clinical tumor classification, biopsy Gleason score groupings, and serum prostate specific antigen (PSA) levels were associated with seminal vesicle and/or pelvic lymph node involvement. These factors were incorporated into a multivariate model that predicted for these adverse histopathologic features. Allowing for up to a 10% likelihood for seminal vesicle and/or pelvic lymph node involvement, patients with tumors classified as T1c-T2a, Gleason scores of 2-6, and PSA < or = 16 ng/mL; or with tumors classified as T1c-T2a, Gleason scores of 7-10, and PSA < or = 4 ng/mL; or with tumors classified as T2b-T2c, Gleason scores of 2-6, and PSA < or = 6 ng/mL would be potential candidates for brachytherapy alone. CONCLUSIONS: The predictive model presented may provide criteria whereby an adequately performed prostate brachytherapy procedure is expected to encompass the intraprostatic and adjacent extraprostatic disease. Prostate brachytherapy alone may be considered in these circumstances, whereas the addition of external beam radiotherapy may be reserved for patients with disease that is apt to extend beyond the brachytherapy target volume.

Brachytherapy↗
PubMed2002

A comprehensive and novel predictive modeling technique using detailed pathology factors in men with localized prostate carcinoma.

BACKGROUND: The purpose of the current study was to evaluate modeling strategies using sextant core prostate biopsy specimen data that would best predict biochemical control in patients with localized prostate carcinoma treated with permanent prostate brachytherapy (PPB). METHODS: One thousand four hundred seventy-seven patients underwent PPB between 1992 and 2000. The authors restricted analysis to those patients who had sextant biopsies (n = 1073). A central pathology review was undertaken on all specimens. Treatment consisted of PPB with either I-125 or Pd-103 prescribed to 144 Gy or 140 Gy, respectively. Two hundred twenty-eight patients (21%) received PPB in combination with external radiotherapy and 333 patients (31%) received neoadjuvant hormones. In addition to clinical stage, biopsy Gleason sum, and pretreatment prostate specific antigen (pretx-PSA), the following detailed biopsy variables were considered: mean percentage of cancer in an involved core; maximum percentage of cancer; mean primary and secondary Gleason grades; maximum Gleason grade (primary or secondary); percentage of cancer in the apex, mid, and base; percent of cores positive; maximum primary and secondary Gleason grades in apex, mid, and base; maximum percent cancer in apex, mid, and base; maximum Gleason grade in apex, mid, and base; maximum primary Gleason grade; and maximum secondary Gleason grade. In all, 23 biopsy variables were considered. Four modeling strategies were compared. As a base model, the authors considered the pretx-PSA, clinical stage, and biopsy Gleason sum as predictors. For the second model, the authors added percent of cores positive. The third modeling strategy was to use stepwise variable selection to select only those variables (from the total pool of 26) that were statistically significant. The fourth strategy was to apply principal components analysis, which has theoretical advantages over the other strategies. Principal components analysis creates component scores that account for maximum variance in the predictors. RESULTS: The median followup of the study cohort was 36 months (range, 6-92), and the Kattan modification of the American Society for Therapeutic Radiology and Oncology (ASTRO) definition was used to define PSA freedom from recurrence (PSA-FFR). The four models were compared in their ability to predict PSA-FFR as measured by the Somers D rank correlation coefficient. The Somers D rank correlation coefficients were then corrected for optimism with use of bootstrapping. The results for the four models were 0.32, 0.34, 0.37, and 0.39, respectively. CONCLUSIONS: The current study shows that the use of principal components analysis with additional pathology data is a more discriminating model in predicting outcome in prostate carcinoma than other conventional methods and can also be used to model outcome predictions for patients treated with radical prostatectomy and external beam.

Adult↗
PubMed2003

Cost-effectiveness and lung cancer clinical trials.

BACKGROUND: Lung cancer is the leading cause of cancer death in the U.S., with an estimated annual economic burden of $5 billion. Clinical trials offer innovative therapeutic options with potentially better outcomes, but their effects on health care costs are disputed. METHODS: The authors analyzed the 1-year facility-based treatment cost and survival of 336 newly diagnosed nonsmall cell lung cancer patients who were deemed eligible for clinical trials between 1994 and 1998 at the Karmanos Cancer Institute. The incremental cost-effectiveness ratio (ICER) of clinical trial treatments with adjustment for confounders was calculated along with its 95% confidence interval (CI) using the bootstrap resampling method. RESULTS: Of the 336 patients, 76 (22.6%) were treated on clinical trials. Trial participation was associated significantly with race (P < 0.01), gender (P = 0.01), age (P = 0.02), and insurance type (P = 0.02). The average 1-year cost for trial enrollees was $41,734 with a median survival of 1.3 years, whereas the average 1-year cost for nonenrollees was $34,191 with a median survival period of 0.9 years. Differences in survival and 1-year cost between enrollees and nonenrollees were significant when controlling for age, race, gender, insurance, stage, performance status, and comorbidities. The ICER for trial participation after adjustment for confounders was $9741 per life year saved (95% CI, $3089-$19,149). CONCLUSIONS: Enrollment in lung cancer clinical trials was found to be associated with improved survival at a moderate incremental cost. Cancer 2003;98:1491-6.

Adult↗
PubMed2006

Comparative assessment of the 1992 and 2002 pathologic T3 substages for the prediction of biochemical recurrence after radical prostatectomy.

BACKGROUND: The objective of this study was to compare the ability of the 1992 American Joint Committee on Cancer (AJCC) TNM staging system for nonorgan-confined prostate carcinoma (PCa) (pathologic T3 [pT3a], pT3b,and pT3c) to predict biochemical recurrence (BCR) after radical prostatectomy with its revision from 1997/2002 (pT3a and pT3b). METHODS: The authors analyzed prospectively collected data from 971 consecutive patients with pT3 tumors who underwent radical prostatectomy alone at a single institution. According to the 1992 AJCC substages, 494 patients had pT3a PCa (51%), 85 patients had pT3b PCa (9%), 302 patients had pT3c PCa (31%) and 91 patients had pT3 PCa (9%) with metastatic lymph node invasion (LNI). Kaplan-Meier and Cox proportional hazards regression analyses were employed to assess the BCR rate using the preoperative prostate-specific antigen (PSA) level, surgical margin (SM) status, pathologic Gleason score, and LNI. The predictive accuracy of this "base" model was compared with models that added either the AJCC 1992 or the AJCC 1997/2002 staging definitions. RESULTS: BCR was observed in 345 patients (36%). The actuarial 5-year recurrence-free probability for patients with AJCC 1992 pT3a, pT3b, and pT3c PCa was 69%, 42%, and 33%, respectively, and differed significantly between men with pT3a tumors and men with pT3b tumors (log-rank test; P < 0.0005). In Cox regression analyses, the 1992 substages were associated significantly with BCR after controlling for PSA, SM status, Gleason grade, and LNI (P < 0.0005). The predictive accuracy of the base model (bootstrap-corrected concordance index, 0.739) was improved after addition of the 1992 TNM staging criteria (concordance index, 0.747). However, predictive accuracy was similar for the model that included the 1997/2002 substages (concordance index, 0.746). CONCLUSIONS: Substaging of pT3 tumors according to the less complex 1997/2002 pT3 classification improved the predictive accuracy of the BCR rate virtually to the same extent as the more detailed 1992 classification. Therefore, the current data favor the use of the 1997/2002 pT3 substaging system.

Biomarkers, Tumor↗