A robust numerical algorithm for studying biomolecular transport processes

We present a numerical algorithm that is well suited for the study of biomolecular transport processes. In the algorithm a continuous Markov process is discretized as a jump process and the jump rates are derived from local solutions of the continuous system. Consequently, the algorithm has two advantages over standard numerical methods: (1) it preserves detailed balance for equilibrium processes, (2) it is able to handle discontinuous potentials. The formulation of the algorithm also allows us to calculate the effective diffusion coefficient or, equivalently, the randomness parameter. We provide several simple examples of how to implement the algorithm. All the MATLAB functions files needed to reproduce the results presented in the article are available from www.amath.unc.edu/Faculty/telston/matlab_functions.     

A whole-genome screen of a quantitative trait of age-related maculopathy in sibships from the Beaver Dam Eye Study

Age-related maculopathy (ARM) is a leading cause of visual impairment among the elderly in Western populations. To identify ARM-susceptibility loci, we genotyped a subset of subjects from the Beaver Dam (WI) Eye Study and performed a model-free genomewide linkage analysis for markers linked to a quantitative measure of ARM. We initially genotyped 345 autosomal markers in 325 individuals (N=263 sib pairs) from 102 pedigrees. Ten regions suggestive of linkage with ARM were observed on chromosomes 3, 5, 6, 12, 15, and 16. Prior to fine mapping, the most significant regions were an 18-cM region on chromosome 12, near D12S1300 (P=.0159); a region on chromosome 3, near D3S1763, with a P value of.0062; and a 6-cM region on chromosome 16, near D16S769, with a P value of.0086. After expanding our analysis to include 25 additional fine-mapping markers, we found that a 14-cM region on chromosome 12, near D12S346 (located at 106.89 cM), showed the strongest indication of linkage, with a P value of.004. Three other regions, on chromosomes 5, 6, and 15, that were nominally significant at P< or =.01 are also appropriate for fine mapping.     

Genome-wide linkage scan for genes affecting longitudinal trends in systolic blood pressure

Only one genome scan to date has attempted to make use of the longitudinal data available in the Framingham Heart Study, and this attempt yielded evidence of linkage to a gene for mean systolic blood pressure. We show how the additional information available in these longitudinal data can be utilized to examine linkages for not only mean systolic blood pressure (SBP), but also for its trend with age and its variability. Prior to linkage analysis, individuals treated for hypertension were adjusted to account for right-censoring of SBP. Regressions on age were fitted to obtain orthogonal measures of slope, curvature, and residual variance of SBP that were then used as dependent variables in the model-free linkage program SIBPAL. We included mean age, gender, and cohort as covariates in the analysis. To improve power, sibling pairs were weighted for informativity using weights derived from both the marker and trait. The most significant results from our analyses were found on chromosomes 12, 15, and 17 for mean SBP, and chromosome 20 for both SBP slope and curvature.     

An audit of 'equivocal' (C3) and 'suspicious' (C4) categories in fine needle aspiration cytology of the breast

An audit of 'equivocal' (C3) and 'suspicious' (C4) categories in fine needle aspiration cytology of the breast
We have audited the frequency of use and outcome of the 'equivocal/atypia probably benign' (C3) and 'suspicious of malignancy' (C4) category for breast cytology in our Unit. A total of 14 935 cytological specimens were reported by at least one of the three pathologists with a special interest in breast pathology, according to five categories of the NHSBSP guidelines for cytology reporting, 1992; 3.7% (555 cases) and 3.9% (587 cases) of cases were classified as equivocal (C3) and suspicious (C4), respectively, giving a total rate (C3 + C4) of 7.6%. Of the C3 cases, 68% were subsequently benign and 32% were malignant. Of the C4 cases, 19% were subsequently benign and 81% malignant. The commonest benign lesions in both categories were fibroadenomas (7.6% of C3 and 19.8% of C4), fibrocystic change (14.3% of C3 and 12.5% of C4), radial scars (6.2% of C3 and 10.4% of C4) and papillomas (6.2% of C3 and 6.3% of C4). Of the malignant lesions (particularly those classified as C3), a high proportion were low grade or special type cancers. The categories of atypia probably benign (C3) and suspicious of malignancy (C4) in breast cytology provide a strategy for classification of problematic or uncertain cases; this maintains the predictive value of the benign (C2) and malignant (C5) categories, and allows separation of these difficult cases into clinically useful groups with differing probabilities of malignancy.     

The finite polygenic mixed model: An alternative formulation for the mixed model of inheritance

This paper presents a mixed model of inheritance with a finite number of polygenic loci. This model leads to a likelihood that can be calculated using efficient algorithms developed for oligogenic models. For comparison, likelihood profiles were obtained for the finite polygenic mixed model, the usual mixed model, with exact and approximate calculations, and for a class D regressive model. The profiles for the finite polygenic mixed model were closest to the profiles for the usual mixed model with exact calculations.     

Staging breast cancer: role of bone scanning.

Bone scans using technetium-99m phosphate complexes and a rectilinear scanner were carried out on 192 women with primary operable breast cancer four to six weeks after operation. The lymph node status of all these patients was assessed histologically from triple node biopsy specimens. Only nine patients had positive scans, although 94 patients had histological evidence that the tumour had already spread beyond the confines of the breast. Bone scanning, although accurate as a prognostic guide, is helpful only in a very few cases, and serves mainly to confirm prognostic information obtained more simply and less extensively by histological examination of lymph node biopsy specimens.     

Pathogenicity testing of shellfish hatchery bacterial isolates on Pacific oyster Crassostrea gigas larvae

Bacterial diseases are a major cause of larval mortality in shellfish hatcheries. Even with proper sanitation measures, bacterial pathogens cannot be eliminated in all cases. The pathogenicity of bacteria isolated from Pacific Northwest shellfish hatcheries to Pacific oyster Crassostrea gigas larvae was investigated. We found 3 highly pathogenic strains and 1 mildly pathogenic strain among 33 isolates tested. These strains appear to be members of the genus Vibrio. Although there have been many studies of bivalve bacterial pathogens, a standard method to assess bacterial pathogenicity in bivalve larvae is needed. Thus, we developed 2 methods using either 15 ml conical tubes or tissue culture plates that were employed for rapidly screening bacterial strains for pathogenicity to Pacific oyster larvae. The tissue culture plates worked well for screening both mildly pathogenic strains and LD50 (lethal dose) assays. This method allowed for non-intrusive and non-destructive observation of the oyster larvae with a dissecting microscope. The LD50 for the 3 highly pathogenic strains ranged between 1.6 and 3.6 x 10(4) colony forming units (CFU) ml(-1) after 24 h and between 3.2 x 102 and 1.9 x 10(3) CFU ml(-1) after 48 h.     

A century of biometrical genetics

We briefly review the major contribution of biometrics to genetics over the last century (population genetic models, familial correlations, segregation analysis, and gene mapping) and current areas of active research and then speculate about what problems will be tackled in the next century.     

On estimating the heterozygosity and polymorphism information content value

The polymorphism information content (PIC) value is commonly used in genetics as a measure of polymorphism for a marker locus used in linkage analysis. In this communication we have derived the uniformly minimum variance unbiased estimator of PIC along with its exact variance. We have also calculated the exact variance of the maximum likelihood estimator of PIC which is asymptotically an unbiased estimator. In order to find this variance we have derived a recursive formula to calculate the moments of any polynomial in a set of variables that are multinomially distributed.