Patrick L. Williams

Phylogeny determination using dynamically weighted parsimony method.

Publisher Summary This chapter presents various methods for assigning two kinds of weights plus a method for evaluating trees given the weights. A character is a nucleotide position, and a character state is the particular nucleotide in that position. There are two kinds of weighting. The first is character weighting in which the weight or importance to be given to any position may differ from that given to other positions. These weights are stored in a character weight vector, sometimes referred to hereafter simply as the C vector. Dynamic weighting means altering the values of the C vector and/or the T matrix as a consequence of the results of the previous pass. With these new sets of weights, researchers make another pass repeating the search for the best tree. The user has the option of starting subsequent passes using either the seed tree or the best tree of the previous pass. Whether the result is more likely correct than when unweighted parsimony is used has not been proved. It ought to be true in principle, but the improvement might be marginal.

The isolated perfused porcine skin flap: III. Percutaneous absorption pharmacokinetics of organophosphates, steroids, benzoic acid, and caffeine

The isolated perfused porcine skin flap (IPPSF) has been developed as an alternative in vitro tool for examining the pharmacokinetics and mechanisms of percutaneous absorption. In this study, dosing solutions of seven 14C-radiolabeled compounds representing three chemical classes--organic acid/base [benzoic acid (B), caffeine (C)], organophosphate (OP) pesticides (diisopropylfluorophosphidate, malathion, parathion), and steroid hormones (progesterone, testosterone)--were prepared in ethanol and applied topically at a surface concentration of 40 micrograms cm-2 to the IPPSF. A three-compartment pharmacokinetic model used to stimulate mass transfer from the surface (C1), diffusion through epidermis and dermis (C2), and transfer into the capillary perfusate (C3), was developed based on flux through the IPPSF from 0 to 8 hr. This basic model accurately stimulated measured IPPSF fluxes for five of seven compounds, including the OPs and steroids. The model was modified to simulate the shunting of drug to fast and slow release pathways, which occurred for B 3-4 hr postapplication, and to account for flow-dependent flux increases seen for C at 6 hr postapplication. The latter may be due to a direct pharmacologic effect, since C is a known vasodilator. Extrapolated (to 6 days) areas under the curve from the model simulations were compared with in vivo percutaneous absorption estimates, obtained from 6-day excretion studies in pigs. The in vivo-in vitro correlation, based on simple linear regression across compounds, was excellent (R2 = 0.88, R = 0.94, p less than 0.002). These results suggest that xenobiotic penetration in the 8-hr IPPSF experiments is highly predictive of in vivo absorption totals (6-day studies). In addition, since pig and human skin are similar physiologically and pharmacologically, the IPPSF may eventually have applications in formulating human dermal risk assessment models.

Finding the Minimal Change in a Given Tree

It is a common task in biology to determine the genealogy of species, populations, people, or genes and estimate the condition of the ancestral forms. That is often done for molecules such as proteins and nucleic acids. There are many procedures. I address here only the parsimony procedures which ask, “ How can I account for the descent of these various sequences from a common ancestor with the fewest number of changes?” The general problem being addressed is as follows. One has a set of s sequences, each sequence being a linear string of letters from some alphabet. In molecular biology the sequences are either proteins, of which there are 20 letters (amino acids), or nucleic acids, of which there are 4 letters (nucleotides). We assume that the sequences have been aligned by some method so that they are all of the same length, t. It is assumed that these s sequences arose from a common ancestral sequence by a branching process that is properly described as a strictly bifurcating tree, that is, as a graph in which there is one and only one path connecting any two nodes on the tree. The tree has s tips (exterior nodes of degree one), one for each of the s sequences and s — 2 interior nodes of degree three, plus one node of degree two, called the root, that is the ultimate ancestor, the node at which the branching process began. The edges connecting two adjacent nodes are called branches. The task is to discover for any given tree topology, the minimum amount of change, and its nature, on each branch.

Percutaneous absorption, dermatopharmacokinetics and related bio-transformation studies of carbaryl, lindane, malathion, and parathion in isolated perfused porcine skin.

The percutaneous absorption of topically applied pesticides is a primary route for systemic exposure and potential toxicity. The isolated perfused porcine skin flap (IPPSF) is an in vitro model for studying percutaneous absorption of xenobiotics as well as cutaneous metabolism and toxicity in an anatomically intact viable skin preparation. In the present studies, percutaneous absorption of four different pesticides, carbaryl (C), lindane (L), malathion (M), and parathion (P), was assessed topically in an ethanol vehicle. A 4-compartment pharmacokinetic model was utilized to model their absorption profile. The order of absorption was C > P > L > M for the 8-h experimental period, but C > L > P > M for a model-extrapolated 6-day prediction. Metabolism of C and P was also assessed by high performance liquid chromatography (HPLC). The HPLC results indicate a significant first-pass effect for both pesticides after topical application, with parathion being metabolized to paraoxon and para-nitrophenol and carbaryl to naphthol. In addition, comparison of the metabolic data of P with previous results underscores the difference between non-recirculating and recirculating IPPSF systems in xenobiotic metabolism studies.

Effect of hyperthermia on cisplatin and carboplatin disposition in the isolated, perfused tumour and skin flap

The effect of hyperthermia on the disposition of platinum (Pt) from cisplatin (CDDP) and carboplatin (CBDCA) in the isolated, perfused tumour and skin flap (IPTSF) was evaluated. Flaps (n = 4/treatment) were perfused with 3.0 micrograms CDDP or 15 micrograms CBDCA/ml perfusion medium at a rate of 1 ml/min for 3 h. Two-hour (CDDP experiments) or 3 h (CBDCA experiments) washout phases were then performed. The disposition kinetics of free Pt were characterized using a four-compartment, physiologically relevant, pharmacokinetic model. Hyperthermia (HT) may have enhanced the mobility of Pt but it did not increase total Pt mass in the tissue compartments in CDDP experiments. Conversely, HT significantly increased Pt mass in the fixed, non-tumour tissue compartment (p < 0.05) in CBDCA experiments. While a similar trend was noted in the fixed, tumour tissue compartment of CBDCA-treated flaps, the difference was not significant (p = 0.17). Total tissue Pt mass was significantly greater in CDDP compared with CBDCA experiments (p < 0.05). In conclusion, HT alters the disposition of Pt from CDDP and CBDCA under conditions of constant rate infusion. Further characterization of factors influencing drug disposition to non-tumour and tumour tissues can be systematically accomplished using the IPTSF.

Cutaneous metabolism of isosorbide dinitrate after transdermal administration in isolated perfused porcine skin

Abstract The purpose of this study was to determine whether isosorbide dinitrate (ISDN) was metabolized by the skin during transdermal delivery. In order to assess this, the isolated perfused porcine skin flap (IPPSF) was utilized since this in vitro model possesses a viable epidermis and intact vasculature, two attributes ideal for studying the biotransformation of a vasoactive drug. ISDN transdermal systems (20 cm 2 ) were applied onto IPPSFs and the venous efflux sampled repeatedly over 16 h. ISDN, isosorbide-2-mononitrate (IS-2-MN), and isosorbide-5-mononitrate (IS-5-MN) fluxes were determined using gas chromatography. Approximately 14% of parent ISDN was metabolized to IS-2-MN and 10% to IS-5-MN. These observations are important as they indicate that a fraction of ISDN is biotransformed during transdermal delivery.

Effect of hyperthermia on cisplatin (CDDP) disposition to isolated perfused skin

Hyperthermia has previously been postulated to enhance tissue uptake of systemically administered chemotherapeutic drugs. Normothermic (36.2 degrees C) and hyperthermic (42.1 degrees C) isolated perfused porcine skin flaps (IPPSF) were infused with cisplatin (CDDP) to assess any influence of heat on drug disposition to skin. A three-compartment physiologically relevant model was employed to interpret kinetically the measured arterial and venous flux profiles. Additionally, non-parametric methods were applied to these data in an effort to confirm the propriety of the model. Results of both approaches suggest that heat does not increase tissue uptake of CDDP after infusion in isolated perfused skin, although it does increase the mobility of CDDP as evidenced by shorter transit times through the IPPSF. These findings are similar to those seen in skin in vivo, but do not predict the enhanced in vivo uptake seen with hyperthermia in more highly perfused tissues.

Effect of whole body hyperthermia on carboplatin disposition and toxicity in dogs.

Fifty dogs with refractory or disseminated spontaneous tumours were evaluated in two independent phase I studies using either carboplatin (CBDCA) alone or CBDCA plus whole body hyperthermia (WBH). CBDCA was administered as a 30 min infusion at the onset of the plateau phase of WBH in dogs receiving combined treatment. Serum samples were collected and drug disposition was determined in both treatment groups. The dose-effect relationship was mathematically described with a logistic regression model developed from categorical toxicity data accumulated throughout the first two treatment courses in all dogs. The maximum tolerated dose (MTD) was defined as that dose which resulted in a 50% probability of achieving moderate or severe toxicity. The only toxicities observed were neutropenia and thrombocytopenia, which were dose-dependent. The nadir occurred between 7 and 14 days following treatment. A significant decrease in the area under the serum CBDCA versus time curve for dogs undergoing WBH was consistent with increased tissue binding of the drug as well as increased urinary eliminations. Serum AUC values determined following the first course of treatment were predictive of subsequent toxicity in both treatment groups. The MTD (95%CI) for CBDCA and CBDCA/WBH were estimated to be 318(44) and 239(51) mg/M2 respectively (p = 0.08). A randomized phase II evaluation should be initiated to determine if a therapeutic gain can be achieved using combined CBDCA and WBH. Further refinement of the CBDCA dose in such a trial should be based on both pharmacokinetic parameters and normal tissue response.

Effect of hyperthermia on the in vitro hydrolysis of melphalan

The pharmacokinetics of melphalan was investigated at 37 degrees C and 42 degrees C in vitro in canine and porcine plasma to assess heat-induced changes in the in vivo rate of melphalan hydrolysis. Melphalan concentrations were assayed using HPLC. Rate of spontaneous hydrolysis of melphalan at 42 degrees C was increased 1.5-fold in canine and 1.9-fold in porcine plasma. These results should be considered when interpreting in vivo disposition studies.

Effect of tumor presence on cisplatin and carboplatin: disposition in the isolated, perfused tumor and skin flap

The purpose of this study was to evaluate the disposition of elemental platinum (Pt) derived from cisplatin (CDDP) or carboplatin (CBDCA) in the isolated, perfused tumor and skin flap (IPTSF). Flaps were perfused with either 3.0 μg CDDP/ml perfusion medium (n=4 tumor,n=4 control) or 15 μg CBDCA/ml (n=4 tumor,n=3 control) at a rate of 1 ml/min for 3 h. A 2-h (CDDP experiments) or 3-h (CBDCA experiments) washout phase using undosed medium was then performed. The disposition kinetics of free (ultrafilterable) Pt were characterized using a four-compartment physiologically relevant pharmacokinetic model. A tumor effect on the disposition of Pt was noted in that the Pt mass from CDDP in the central and mobile tissue compartments was greater in tumor flaps than in control flaps (P<0.05). Similar trends were noted in CBDCA-treated flaps, but these were not significant. The Pt mass in the fixed tumor and non-tumor tissue compartments was significantly greater when Pt was derived from CDDP than when it was derived from CBDCA (P<0.05). A linear relationship existed between the estimated micrograms of Pt in the flaps from both CDDP and CBDCA and the cross-sectional vascular resistance of the flaps at 30 (CDDP,r=0.78; CBDCA,r=0.89) and 60 min (CDDP,r=0.65; CBDCA,r=0.85) of perfusion. We conclude that the IPTSF is a useful model for evaluating the disposition of Pt drugs in tumor and non-tumor tissue and that tumor presence alters the disposition of CDDP.