A novel computational biostatistics approach implies impaired dephosphorylation of growth factor receptors as associated with severity of autism.

The prevalence of autism spectrum disorders (ASDs) has increased 20-fold over the past 50 years to >1% of US children. Although twin studies attest to a high degree of heritability, the genetic risk factors are still poorly understood. We analyzed data from two independent populations using u-statistics for genetically structured wide-locus data and added data from unrelated controls to explore epistasis. To account for systematic, but disease-unrelated differences in (non-randomized) genome-wide association studies (GWAS), a correlation between P-values and minor allele frequency with low granularity data and for conducting multiple tests in overlapping genetic regions, we present a novel study-specific criterion for 'genome-wide significance'. From recent results in a comorbid disease, childhood absence epilepsy, we had hypothesized that axonal guidance and calcium signaling are involved in autism as well. Enrichment of the results in both studies with related genes confirms this hypothesis. Additional ASD-specific variations identified in this study suggest protracted growth factor signaling as causing more severe forms of ASD. Another cluster of related genes suggests chloride and potassium ion channels as additional ASD-specific drug targets. The involvement of growth factors suggests the time of accelerated neuronal growth and pruning at 9-24 months of age as the period during which treatment with ion channel modulators would be most effective in preventing progression to more severe forms of autism. By extension, the same computational biostatistics approach could yield profound insights into the etiology of many common diseases from the genetic data collected over the last decade.

Women's health measures in two North Carolina regions sampled from the Basic Automated Birth Yearbook (BABY) datasets: experimental findings, methodological limits and future directions.

PURPOSE: To compare selected characteristics in two North Carolina counties to document women's health services at the geographical extremes of the state. METHODS: Using aggregated 2004 data obtained from the North Carolina State Center for Health Statistics, obstetric and perinatal characteristics were experimentally analyzed for the westernmost and easternmost counties in North Carolina (Cherokee and Dare County, respectively). FINDINGS: During the experiment period, 489 infants were delivered in Dare County (population 33,518), while 259 births were recorded in Cherokee County (population 25,289). Prenatal care was established by most women in both counties by the second gestational month. Women in Cherokee County were younger and less educated at delivery than women in Dare County, and smoking prevalence was higher in Cherokee County than in Dare County (31.3% vs 12.9%; p <0.01). Cherokee County infants required assisted ventilation and other medical interventions more often than babies born in Dare County (p <0.01) yet significantly fewer cesarean deliveries were performed in Cherokee County than Dare County (25.5% vs 35.2%; p = 0.04). CONCLUSION: This pilot study showed a significantly higher rate of tobacco use, and lower maternal education level in Cherokee County was associated with a higher incidence of multiple maternal complications and neonatal interventions compared to Dare County. Interestingly, the cesarean delivery rate was lower in Cherokee County despite these factors. We found < 10% of babies born in the study regions required any neonatal intervention. Early and almost universal access to prenatal care did not appear to be a problem at either site. Our preliminary comparison identified important limitations in this government-sponsored dataset that rendered logistic regression analysis methodologically impossible. Changes in process could improve surveillance based on patient-level data and facilitate multivariate analysis. Specific interventions to optimize women's health services form the basis of future experimental research, including larger regional populations.

Comparison of centrifugation- and noncentrifugation-based techniques for recovery of motile human sperm in assisted reproduction.

To compare standard density gradient centrifugation sperm preparation with a novel non-centrifugation-based dual-chamber capillary dish in efficiency for motile human sperm separation, approximately 3 mL fresh ejaculate specimens was obtained from 21 men (median age = 32 years. range 26-42 years) undergoing infertility evaluation. For each specimen, half of the sample was processed with a standard 45%/90% density gradient preparation (PureSperm. Nidacon International, Gothenburg, Sweden) followed by semen analysis. The other half was incubated in the Zech glass capillary dish (Astromedtec, Salzburg, Austria) consisting of 2 concentric wells overlaid by a U-ring and coverglass. After approximately 3 h, a 1-mL sample was taken from the central chamber and analyzed. Percentage motile sperm recovery, absolute (motile) cell number, and path velocities were compared for spermatozoa obtained from both methods. Both techniques reduced overall sperm concentration while enriching specimens with more motile spermatozoa. A trend towards higher % recovery of motile spermatozoa (p = .264) was observed with the Zech device, but at a cost of fewer absolute numbers of higher velocity cells (p = .004). The Zech device, therefore, localized a very small population of motile sperm without exposure to centrifugation stress, which has been considered potentially harmful to spermatozoa. This technique could theoretically improve efficiency by reducing time required to identify motile cells in in vitro fertilization where intracytoplasmic sperm injection is planned. However, refinements in incubation interval and suspension volumes are needed before this technique can be considered comparable to the density gradient method in recovering sperm for use in intrauterine insemination.

A statistically valid alternative to the TDT.

OBJECTIVE: To present an alternative linkage test to the transmission/disequilibrium test (TDT) which is conservative under the null hypothesis and generally more powerful under alternatives. METHODS: The exact distribution of the TDT is examined under both the null hypothesis and relevant alternatives. The TDT is rewritten in an alternate form based on the contributions from each of the three relevant parental mating types. This makes it possible to show that a particular term in the estimate is an exact tie and thus to rewrite the estimate without this term and to replace the multinomial 'variance estimate' of Spielman et al. [Am J Hum Genet 1993;52:506-516] by the binomial variance. RESULTS: The resulting test is shown to be a stratified McNemar test (SMN). The significance level attained by the SMN is shown to be conservative when compared to the asymptotic chi(2) distribution, while the TDT often exceeds the nominal level alpha. Under alternatives, the proposed test is shown to be typically more powerful than the TDT. CONCLUSION: The properties of the TDT as a statistical test have never been fully investigated. The proposed test replaces the heuristically motivated TDT by a formally derived test, which is also computationally simple.

Effect on treatment outcome of coinfection with SEN viruses in patients with hepatitis C.

The newly discovered SEN D and SEN H viruses are transmitted parenterally and can cause post-transfusion hepatitis. We assessed whether coinfection of patients with chronic hepatitis C and SEN D or SEN H correlates with the outcome of treatment with interferon and ribavirin. Of 31 patients with hepatitis C studied, six were positive for SEN D and seven for SEN H (one was positive for both). All of those positive for SEN D and five of those positive for SEN H failed to respond to therapy. Overall response (RNA titre and alanine aminotransferase concentration after treatment) was lower in SEN-infected patients than uninfected patients (p=0.025). We conclude that coinfection with SEN viruses is frequent in chronic hepatitis C patients and might adversely affect the outcome of treatment with interferon and ribavirin.

Immune and clinical responses in patients with metastatic melanoma to CD34(+) progenitor-derived dendritic cell vaccine.

Immunization to multiple defined tumor antigens for specific immune therapy of human cancer has thus far proven difficult. Eighteen HLA A*0201(+) patients with metastatic melanoma received injections s.c. of CD34(+)progenitor-derived autologous dendritic cells (DCs), which included Langerhans cells. DCs were pulsed with peptides derived from four melanoma antigens [(MelAgs) MelanA/MART-1, tyrosinase, MAGE-3, and gp100], as well as influenza matrix peptide (Flu-MP) and keyhole limpet hemocyanin (KLH) as control antigens. Overall immunological effects were assessed by comparing response profiles using marginal likelihood scores. DC injections were well tolerated except for progressive vitiligo in two patients. DCs induced an immune response to control antigens (KLH, Flu-MP) in 16 of 18 patients. An enhanced immune response to one or more MelAgs was seen in these same 16 patients, including 10 patients who responded to >2 MelAgs. The two patients failing to respond to both control and tumor antigens experienced rapid tumor progression. Of 17 patients with evaluable disease, 6 of 7 patients with immunity to two or less MelAgs had progressive disease 10 weeks after study entry, in contrast to tumor progression in only 1 of 10 patients with immunity to >2 MelAgs. Regression of >1 tumor metastases were observed in seven of these patients. The overall immunity to MelAgs after DC vaccination is associated with clinical outcome (P = 0.015).

A new approach to adjust for multivariate confounders in small randomized studies applied to dendritic cell vaccination data.

In small studies, randomization alone is unlikely to eliminate confounding. In linear models, confounding can be addressed by including additional dependent variables, adding covariates, or stratifying the data for the analysis. When the functional relation between observed variables and underlying (latent) factors is unknown, however, methods based on ranks may be more appropriate than ANOVA. It is demonstrated, how the marginal likelihood principle can be used to provide objective and intrinsically valid procedures to adjust for (multiple) confounders when the assumptions of the linear model cannot be justified.

The protective effect of condoms and nonoxynol-9 against HIV infection.

OBJECTIVES: Whether or not spermicides can reduce the risk of human immunodeficiency virus (HIV) transmission remains an important question for the control of heterosexual HIV transmission. The authors provide estimates from a reanalysis of one of the few observational studies on the efficacy of condoms and spermicides, used separately and together, per vaginal contact. METHODS: In this reanalysis, three different models were used to assess the efficacy of spermicides and condoms: linear (Pearl index), exponential (maximum likelihood), and monotonic (marginal likelihood). RESULTS: Reported use of barrier methods among 27,432 contacts was as follows: condoms plus nonoxynol-9, 39%; condoms alone, 25%; nonoxynol-9 alone, 24%; and unprotected, 11%. Under all three models, the results indicate a strong protective effect for spermicidal suppositories. The Pearl index indicated that spermicide alone is apparently efficacious, but the efficacy per contact cannot be quantified with this approach. Maximum likelihood estimates for the efficacy of nonoxynol-9 alone and condoms (with or without nonoxynol-9) were 100% (95% confidence interval [CI95] = 43%, 100%) and 92% (95% CI95 = 79%, 100%), respectively. CONCLUSIONS: The data from this observational study suggest that spermicides may be efficacious in reducing the risk of HIV transmission.

Reporting sexual risk behavior for HIV: a practical risk index and a method for improving risk indices.

OBJECTIVES: As a means of enhancing public health efforts to control sexual transmission of human immunodeficiency virus (HIV), methods were developed to report on risk behavior in a manner that is comparable and widely interpretable. METHODS: An elementary sexual behavior risk index (the vaginal episode equivalent index) that is in accord with some of the essential knowledge about sexual transmission of HIV is described, and a multivariate ordinal risk (MOR) method that can be used to improve such risk indices is introduced. RESULTS: An example shows that these approaches are applicable to observational studies of seroconversion. CONCLUSIONS: The MOR represents a powerful new tool to develop valid comparable measures of sexual risk behavior and, thereby, to advance HIV prevention research.

Different behavior of human osteoblast-like cells isolated from normal and heterotopic bone In vitro.

In this study, a characterization of human bone-forming cells responsible for heterotopic ossification was carried out in vitro. The biological and biochemical cell characteristics of the heterotopic osteoblast-like (HOB) cells were compared with those of orthotopic osteoblast-like (OB) cells from normal bone and stromal bone marrow cells believed to contain a subpopulation of osteogenic precursor cells. We found that HOB's from the spongiosa of heterotopic ossification required less time until the beginning of migration and the achievement of confluence in vitro compared with OBs from femoral shaft spongiosa. The fraction of mitotically active cells assessed by a clonogenic assay was higher as well in HOB cells. The in vitro studies of mitogenesis and the efficiency of colony formation of osteogenic cells indicate that with increasing differentiation and relative age they become more dependent on growth factors in the medium, otherwise the morphology of osteoblast-like cells changes and they pass irreversibly into the postmitotic stage of the cell cycle. The activity of the alkaline phosphatase is distinctly higher in the HOB than in the OB cells, HOB cells exhibit a lower level of osteocalcin expression compared with OB cells. No significant difference was found between OB and HOB cells in the amount of procollagen of type I sequestered by the cells. After 30 days, HOB and OB cells formed a mineralized matrix on exposure to 2 mM beta-glycerophosphate. Since HOBs were isolated from heterotopic bone that had developed within 3-6 months after hip surgery, the differences in cellular behavior compared with OBs may be attributed to the relatively young age of HOB cells.

[Epidemiology of HIV in Germany (status: 30 June 1995)--transmission among heterosexuals and value of HIV screening programs]. / Epidemiologie von HIV in Deutschland (Stand: 30.6.95)--Ausbreitung unter Heterosexuellen und Aussagekraft von HIV-Screening-Programmen.

As compared to the earlier publication [1], the current publication further refines the figures published for the first time 1988-90 by the author [2,3] and adds additional sources. Sample sizes for and feasibility of anonymous unlinked testing (AUT) are discussed in greater detail.

Polymerase chain reaction monitoring reduces the incidence of cytomegalovirus disease and the duration and side effects of antiviral therapy after bone marrow transplantation.

Culture-based preemptive therapy with ganciclovir was shown to reduce the incidence of cytomegalovirus (CMV) disease after bone marrow transplantation (BMT). Culture techniques did not detect CMV in 12% to 13% of patients before the onset of CMV disease. In a prospective study, 71 patients either received preemptive therapy based on polymerase chain reaction (PCR) technique (37 patients) or on culture assays (34 patients). In both groups, therapy was continued until clinical signs disappeared and PCR negativity was documented. Twenty-two patients in the PCR group and 15 patients in the culture group received antiviral therapy. PCR allowed detection of the virus (median day, +32 v day +49; P = .006) and introduction of antiviral therapy (median day, +44 v day +54; P = .02) earlier than did culture assays. The incidences of CMV disease (2 of 37 v 8 of 34 in PCR group v culture group, respectively; P = .02) and CMV-associated mortality (0 of 37 v 5 of 34 in PCR group v culture group, respectively; P = .02) were decreased, and the duration of ganciclovir therapy (P < .001) was shorter in the PCR-monitored group. Incidence and median duration of severe neutropenia (less than 500/microL) were lower in the PCR group (two v eight episodes, P = .02; median duration, 1.5 v 5 days, P = .04), as was the incidence of nonviral infections during/after antiviral therapy (2 of 37 v 9 of 34; P = .012). Thus, preemptive therapy based on more sensitive detection methods such as the PCR assay reduces the incidence of CMV disease and CMV-related mortality. Additionally, stopping and withholding antiviral therapy in a PCR-negative patient is safe and allows reduction of the duration and side effects of antiviral therapy.

[Epidemiology of HIV in Germany]. / Epidemiologie von HIV in Deutschland.

In many developing countries, HIV is predominantly distributed among heterosexuals. This has given rise to the concern that similar patterns are to be expected in Europe. The current publication discusses different methods for estimation of the number of people infected. The figures published for the first time 1988-1990 by the author (1,2) are refined and consequences are discussed. It is demonstrated that legalizing drugs may reduce the import of HIV into the heterosexual population and that using condoms and spermicides in the first three months of a partnership may prevent the spread of HIV, while anonymous unlinked testing (AUT) is neither necessary for assessing the spread of HIV nor can it provide reliable estimates within a reasonable period of time.

Backcalculation of the number infected with human immunodeficiency virus in Germany.

The method of backcalculation was used to estimate the cumulative number of human immunodeficiency virus type 1 (HIV-1)-infected adults in Germany from reporting delay-corrected surveillance data on acquired immunodeficiency syndrome (AIDS) in the pretreatment era. Using different backcalculation approaches with various incubation period distributions, a plausible range of 13,100 to 23,900 HIV-1-infected adults as of December 31, 1984, was calculated. Estimates of the number infected at more recent times were subject to much greater uncertainty. On average, the cumulative incidences calculated by the nonparametric backprojection method are about 15% lower than the results from the step function model. Nonparametric backprojection with the Hessol incubation distribution suggests a declining HIV infection rate after 1985, as might be expected from German health policies. This distribution is derived from cohorts of homosexual men, the main fraction of German AIDS cases.

A structured visual language for a knowledge-based front-end to statistical analysis systems in biomedical research.

Within the last few years, several knowledge-based systems for statistical analysis systems have been proposed (see Refs. 1-4 for references). Most of these systems provide so-called 'natural-language' interfaces for acquisition and application of meta-data. Since graphics have been very efficient in displaying results (e.g., as scatter, QQ and residual plots), some attempts have been made (cf. Refs. 5,6) to use graphics also to display knowledge of the statistical strategy. In the present paper I will concentrate on the visualization of knowledge of the experimental design and its impacts on the design of a structured visual syntax language for acquisition and application of this knowledge in the field of biomedical research.