Biomedical subjects

P D Jarvis

Publications and source records attributed to P D Jarvis.

8 recordsLinked to original sources

PubMed2006

Using the tangle: a consistent construction of phylogenetic distance matrices for quartets.

Distance based algorithms are a common technique in the construction of phylogenetic trees from taxonomic sequence data. The first step in the implementation of these algorithms is the calculation of a pairwise distance matrix to give a measure of the evolutionary change between any pair of the extant taxa. A standard technique is to use the log det formula to construct pairwise distances from aligned sequence data. We review a distance measure valid for the most general models, and show how the log det formula can be used as an estimator thereof. We then show that the foundation upon which the log det formula is constructed can be generalized to produce a previously unknown estimator which improves the consistency of the distance matrices constructed from the log det formula. This distance estimator provides a consistent technique for constructing quartets from phylogenetic sequence data under the assumption of the most general Markov model of sequence evolution.

Algorithms↗

PubMed2005

A base-pairing model of duplex formation. I. Watson-Crick pairing geometries.

We present a base-pairing model of oligonucleotide duplex formation and show in detail its equivalence to the nearest-neighbor dimer methods from fits to free energy of duplex formation data for short DNA-DNA and DNA-RNA hybrids containing only Watson-Crick pairs. For completeness, the corresponding RNA-RNA parameters are included. In this approach, the connection between rank-deficient polymer and rank-determinant oligonucleotide parameter sets for DNA duplexes is transparent. The method is generalized to include RNA-DNA hybrids where the rank-deficient model with 11 dimer parameters in fact provides slightly improved predictions relative to the standard method with 16 independent dimer parameters (DeltaG mean errors of 4.5 and 5.4%, respectively).

Base Pairing↗

PubMed2005

Entanglement invariants and phylogenetic branching.

It is possible to consider stochastic models of sequence evolution in phylogenetics in the context of a dynamical tensor description inspired from physics. Approaching the problem in this framework allows for the well developed methods of mathematical physics to be exploited in the biological arena. We present the tensor description of the homogeneous continuous time Markov chain model of phylogenetics with branching events generated by dynamical operations. Standard results from phylogenetics are shown to be derivable from the tensor framework. We summarize a powerful approach to entanglement measures in quantum physics and present its relevance to phylogenetic analysis. Entanglement measures are found to give distance measures that are equivalent to, and expand upon, those already known in phylogenetics. In particular we make the connection between the group invariant functions of phylogenetic data and phylogenetic distance functions. We introduce a new distance measure valid for three taxa based on the group invariant function known in physics as the "tangle". All work is presented for the homogeneous continuous time Markov chain model with arbitrary rate matrices.

Evolution, Molecular↗

PubMed2004

An algebraic model of RNA duplex formation.

We propose a simple algebraic description of the two-body interactions of bases in RNA thermodynamics showing in detail qualitative equivalence with conventional nearest-neighbor models. The process of obtaining base content, polymer, and oligomer parameters is illustrated, and for duplexes containing Watson-Crick pairs, fits to oligonucleotide duplex heat-of-formation data are shown to be statistically equivalent to existing models.

Base Pairing↗

PubMed1998

A supersymmetric model for the evolution of the genetic code.

A model is presented for the structure and evolution of the eukaryotic and vertebrate mitochondrial genetic codes, based on the representation theory of the Lie superalgebra A(5,0) approximately sl(6/1). A key role is played by pyrimidine and purine exchange symmetries in codon quartets.

Animals↗

PubMed1995

Evaluation of acute scrotum in the emergency department.

A 2-year retrospective review of 238 cases of acute scrotal pain encountered in a children's hospital emergency department is presented. The incidences of testicular torsion, torsion of a testicular appendage, and epididymitis were 16%, 46%, and 35%, respectively. Testicular salvage was critically dependent on the interval between onset of pain and surgical intervention. No testis likely to have been viable at the time of presentation was "lost." The diagnostic error rate on first encounter was 7%, resulting in 10 negative scrotal explorations. With the exception of cases of far-advanced necrotic testes, both color Doppler ultrasound and radioisotope imaging were highly specific diagnostic modalities. Thirty-nine percent of the children with epididymitis who underwent investigation were found to have either structural or functional urinary tract abnormalities. Noninvasive urodynamic studies appear to be useful screening modalities in older children with epididymitis.

Acute Disease↗

PubMed1995

Relative microbial resistance of gastric, ileal and cecal bladder augmentation in the rat.

PURPOSE: Bladder resistance to bacterial infection after gastrocystoplasty, ileocystoplasty and cecocystoplasty was investigated in the rat. MATERIALS AND METHODS: Bladders were infected with Escherichia coli 6 to 13 months after augmentation and urine culture was obtained weekly for 3 months. RESULTS: No differences were observed in the number of infected animals within each group or electrolyte data among groups. The number of animals infected after surgery but before E. coli challenge was lowest in the gastrocystoplasty group. Bladder stones formed only in ileocystoplasty and cecocystoplasty groups. No group had a change in urinary pH. CONCLUSIONS: Gastrocystoplasty may be associated with a lower incidence of spontaneous infection and stone formation. An aggressive infection protocol may have masked differences in susceptibility to infection. Since urinary pH was unchanged after gastrocystoplasty, use of the rat may not be appropriate for augmentation studies.

Animals↗

PubMedDate not supplied

The genetic code as a periodic table: algebraic aspects.

The systematics of indices of physico-chemical properties of codons and amino acids across the genetic code are examined. Using a simple numerical labelling scheme for nucleic acid bases, A=(-1,0), C=(0,-1), G=(0,1), U=(1,0), data can be fitted as low order polynomials of the six coordinates in the 64-dimensional codon weight space. The work confirms and extends the recent studies by Siemion et al. (1995. BioSystems 36, 231-238) of the conformational parameters. Fundamental patterns in the data such as codon periodicities, and related harmonics and reflection symmetries, are here associated with the structure of the set of basis monomials chosen for fitting. Results are plotted using the Siemion one-step mutation ring scheme, and variants thereof. The connections between the present work, and recent studies of the genetic code structure using dynamical symmetry algebras, are pointed out.

Amino Acids↗