Biomedical subjects

S A Fernández

Publications and source records attributed to S A Fernández.

4 recordsLinked to original sources

PubMed2002

Technical note: determining peeling order using sparse matrix algorithms.

To study the effect of individual genes by segregation or linkage analyses, the likelihood of the model needs to be evaluated. The likelihood can be computed efficiently using the Elston-Stewart algorithm. This algorithm involves summing over the unobserved genotypes in the pedigree, which is called peeling. An important aspect of this algorithm is to determine the order of peeling to maximize efficiency. This paper shows how determining peeling order is related to a problem in solving systems of symmetric sparse linear equations. It also shows how algorithms developed to efficiently solve those systems, can be used to determine the optimal order of peeling in the Elston-Stewart algorithm.

Algorithms↗

PubMed1992

Transfer of the tibialis anterior for calcaneus deformity in myelodysplasia.

We evaluated the results of transfer of the tibialis anterior in the management of calcaneus deformity in young patients who had myelodysplasia; fifteen patients (twenty-two feet) were operated on between 1978 and 1985. The neural deficit was at the fourth and fifth lumbar levels. The average age at the time of the operation was seven years and two months (range, two to nineteen years). The average age at the latest follow-up was thirteen years (range, five to twenty-four years). The average duration of follow-up was five years and ten months (range, two to eleven years). Seventeen feet (twelve patients) had a good result (no ulceration of the heel or osteomyelitis and correction of the calcaneus deformity), and five feet (three patients) had a poor result (persistent ulceration, signs of osteomyelitis, recurrent or persistent calcaneus deformity, or the need for additional operative intervention). Children who were less than five years old had a better outcome, as determined by the Fisher exact test (p less than 0.5).

Adolescent↗

PubMed1990

Neural tube defects: a study in Puerto Rico.

Recent literature reports an apparent decline in the incidence of neural tube defects throughout the world. A revision of stillbirth certificates and surgical reports of closure procedures for open neural tube defects was done in order to establish the incidence and its trend during a nine year period in Puerto Rico. The current prevalence of the syndrome was estimated using the death certificates in addition to the fore-mentioned surgical reports. Our results indicate that Puerto Rico carries probably the highest incidence of the US territories and that the trend is not declining one.

Cohort Studies↗

PubMedDate not supplied

Sampling genotypes in large pedigrees with loops.

Markov chain Monte Carlo (MCMC) methods have been proposed to overcome computational problems in linkage and segregation analyses. This approach involves sampling genotypes at the marker and trait loci. Scalar-Gibbs is easy to implement, and it is widely used in genetics. However, the Markov chain that corresponds to scalar-Gibbs may not be irreducible when the marker locus has more than two alleles, and even when the chain is irreducible, mixing has been observed to be slow. These problems do not arise if the genotypes are sampled jointly from the entire pedigree. This paper proposes a method to jointly sample genotypes. The method combines the Elston-Stewart algorithm and iterative peeling, and is called the ESIP sampler. For a hypothetical pedigree, genotype probabilities are estimated from samples obtained using ESIP and also scalar-Gibbs. Approximate probabilities were also obtained by iterative peeling. Comparisons of these with exact genotypic probabilities obtained by the Elston-Stewart algorithm showed that ESIP and iterative peeling yielded genotypic probabilities that were very close to the exact values. Nevertheless, estimated probabilities from scalar-Gibbs with a chain of length 235 000, including a burn-in of 200 000 steps, were less accurate than probabilities estimated using ESIP with a chain of length 10 000, with a burn-in of 5 000 steps. The effective chain size (ECS) was estimated from the last 25 000 elements of the chain of length 125 000. For one of the ESIP samplers, the ECS ranged from 21 579 to 22 741, while for the scalar-Gibbs sampler, the ECS ranged from 64 to 671. Genotype probabilities were also estimated for a large real pedigree consisting of 3 223 individuals. For this pedigree, it is not feasible to obtain exact genotype probabilities by the Elston-Stewart algorithm. ESIP and iterative peeling yielded very similar results. However, results from scalar-Gibbs were less accurate.

Algorithms↗