Christopher M. Triggs

Interpreting DNA Mixtures in Structured Populations

DNA profiles from multiple-contributor samples are interpreted by comparing the probabilities of the profiles under alternative propositions. The propositions may specify some known contributors to the sample and may also specify a number of unknown contributors. The probability of the alleles carried by the set of people, known or unknown, depends on the allelic frequencies and also upon any relationships among the people. Membership of the same subpopulation implies a relationship from a shared evolutionary history, and this effect has been incorporated into the probabilities. This acknowledgment of the effects of population structure requires account to be taken of all people in a subpopulation who are typed, whether or not they contributed to the sample.

Dietary factors in chronic inflammation: Food tolerances and intolerances of a New Zealand Caucasian Crohn's disease population

Diet is known to play a major role in the symptoms of the inflammatory bowel disease, Crohns disease (CD). Although no single diet is appropriate to all individuals, most CD patients are aware of foods that provide adverse or beneficial effects. This study seeks to categorise foods in relation to their effects on symptoms of CD, in a New Zealand Caucasian population. Four hundred and forty-six subjects from two different centres in New Zealand were recruited into the study. An extensive dietary questionnaire (257 food items in 15 groups) recorded self-reported dietary tolerances and intolerances. Across each of the food groups, there were statistically significant differences among responses to foods. A two-dimensional graphical summary enabled stratification of foods according to the probability that they will be either beneficial or detrimental. A small number of foods are frequently considered to be beneficial, including white fish, salmon and tuna, gluten-free products, oatmeal, bananas, boiled potatoes, sweet potatoes (kumara), pumpkin, soya milk, goats milk and yoghurt. Foods that are typically considered detrimental include grapefruit, chilli or chilli sauce, corn and corn products, peanuts, cream, salami, curried foods, cola drinks, high energy drinks, beer, and red wine. For a number of the food items, the same item that was beneficial for one group of subjects was detrimental to others; in particular soya milk, goats milk, yoghurt, oatmeal, kiwifruit, prunes, apple, broccoli, cauliflower, linseed, pumpkin seed, sunflower seed, ginger and ginger products, beef, lamb, liver, and oily fish. It was not possible to identify a specific group of food items that should be avoided by all CD patients. The wide range of detrimental items suggests that dietary maintenance of remission is likely to be difficult, and to exclude a substantial number of foods. Personalised diets may be especially important to these individuals.

The adsorption of heterocyclic aromatic amines by model dietary fibres with contrasting compositions

It is often recommended that consumption of dietary fibre should in increased to protect against colorectal cancer. However, although more than 95% of dietary fibre is contributed by whole plant cell walls, very little experimental work has been done using whole plant cell walls. These may protect by adsorbing carcinogens, thus lowering their effective concentration in the alimentary tract, and by carrying the carcinogens out of the body in the faeces. However, plant cell walls vary widely in their composition and physical properties, and not all cell walls will necessarily have protective properties. We therefore isolated 4 plant cell-wall preparations with contrasting compositions as models of the types of cell walls that occur in the diet. We investigated the abilities of these preparations to adsorb in vitro 6 heterocyclic aromatic amines (HAAs). HAAs occur in the human diet and several are colon carcinogens, at least in rats. We found that the ability of the HAAs to adsorb to the plant cell walls increased with increasing hydrophobicity of the HAA, measured as the calculated logarithm of the partition coefficient between 1-octanol and water (C logP). A cell-wall preparation containing mainly the walls of parenchyma cells (the most common cell type in food plants) had only poor adsorptive ability. A cell-wall preparation from commercial cork had the best adsorptive ability. This preparation was the most hydrophobic of those examined because the cell walls contained the polymer, suberin, together with associated waxes. The preparation modelled suberized cell walls which occur in the diet, for example in potato skins. The other two cell-wall preparations contained another hydrophobic polymer, lignin, and had intermediate adsorptive abilities which were not significantly different from one another. These preparations modelled lignified cell walls which occur in the diet, for example in wheat bran. Our results indicate that suberized and lignified cell walls may be important in protecting against colorectal cancer.

A replicated comparison of cross-company and within-company effort estimation models using the ISBSG database

Four years ago was the last time the ISBSG database was used to compare the effort prediction accuracy between cross-company and within-company cost models. Since then more than 2,000 projects have been volunteered to this database, which may have changed the trends previously observed. This paper therefore replicates a previous study by investigating how successful a cross-company cost model is: i) to estimate effort for projects that belong to a single company and were not used to build the cross-company model; ii) compared to a within-company cost model. Our within-company data set had data on 184 software projects from a single company and our cross-company data set employed data on 672 software projects. Our results did not corroborate those from the previous study, showing that predictions based on the within-company model were not significantly more accurate than those based on the cross-company model. We analysed the data using forward stepwise regression

A comparison of adjustment methods to test the robustness of an STR DNA database comprised of 24 European populations

An aim of the European Network of Forensic Science Institutes (ENFSI) is to produce a DNA database of second generation multiplex (SGM) STR profiles that is representative of the resident cosmopolitan populations. To achieve this, data were collected from 24 different populations. All of the data were combined to form one database of 5700 profiles from which allele proportions were calculated. The robustness of this combined European database was tested by estimating parameter d for every DNA profile, where d=log(10)(Pm(c)/Pm(E)) Pm(c) is the match probability of the profile calculated from its cognate database and Pm(E) is the match probability of the combined European database. Overall there was a small tendency for Pm(c)>Pm(E) primarily because of sampling bias. This bias was removed by the simple expediency of applying an adjustment factor to the calculation of Pm(E). These were selected from the Balding size bias correction, the Balding and Nichols Fst correction, a minimum allele proportion (between 0.01 and 0.02), an upper bound of a 95% confidence interval (CI) and a lower bound on the genotype match probability. It was demonstrated that a single European database is a feasible proposition. A combination of different adjustment methods can be used to ensure that the result is conservative relative to the cognate database, and their effect measured by parameter d.

The Hodrick-Prescott Filter, a Generalization, and a New Procedure for Extracting an Empirical Cycle from a Series

This paper proposes a novel derivation of the Hodrick-Prescott (HP) minimization problem which leads to a generalization of the Hodrick-Prescott filter. The main result is the development of a new filter to extract a localized maximum-likelihood estimate of the cycle from a series. This new filter, the multivariate normal cyclical (MNC) filter, makes only a general assumption about the cyclical nature of the series. The output from this filtering procedure is from a nonlinear optimization routine.

Adsorption of a hydrophobic mutagen to cereal brans and cereal bran dietary fibres

The abilities of brans from the cereals barley, oats, maize, rice, and wheat to adsorb in vitro the hydrophobic, environmental mutagen 1,8-dinitropyrene (DNP) were investigated using a mutagenicity assay. These brans were obtained from known cultivars using defined milling conditions and were chemically characterised. The abilities of total and insoluble dietary fibre preparations obtained from these brans to adsorb DNP were also investigated. The predicted weight of each bran required to adsorb 50% of the added DNP was used to compare the adsorptive abilities of the different brans. The brans were ranked in the order (most effective to least effective): rice, wheat, maize, barley, and oats. The adsorptive abilities of the dietary fibre preparations were not significantly different from the bran from which they were prepared. However, if the dietary fibres (cell walls) were the only components adsorbing the DNP, we would have expected the dietary fibre preparations to have adsorbed more DNP than the equivalent unextracted bran. This suggests that other components, probably starch, also adsorb DNP in the unextracted brans. It is not known why brans from different cereal species differ in adsorptive ability but the lignified cell walls in wheat bran may be important in conferring good adsorptive properties to this bran. The possible relationship between adsorptive ability and ability of the bran from a particular species to protect against colorectal cancer is discussed.

The effects of soluble-fiber polysaccharides on the adsorption of a hydrophobic carcinogen to an insoluble dietary fiber

Dietary fiber is believed to decrease the incidence of colorectal cancer, but not all types of fiber are equally protective. Dietary fibers may be divided broadly into insoluble and soluble fibers, and there is evidence from animal experiments that the latter not only fails to protect against colorectal cancer but may enhance its development. Adsorption of carcinogens to insoluble dietary fiber in the intestinal tract is one of the mechanisms by which dietary fiber is believed to protect against colorectal cancer. In previous in vitro experiments, we showed that the hydrophobic carcinogen 1,8-dinitropyrene (DNP) adsorbs to insoluble plant cell wall components (insoluble dietary fibers). Soluble polysaccharides (pectic polysaccharides) extracted from the walls of parenchyma cells of dicotyledonous plants were found to maintain DNP in aqueous solutions and decrease its adsorption to insoluble wall components. In the present study, we examined a commercial preparation of pectin and seven other soluble-fiber polysaccharides with diverse structures for their effects on the distribution of DNP. Many of these are used as emulsifiers and stabilizers in the food industry. They all maintained DNP in aqueous solution and decreased its adsorption to alpha-cellulose, which we used as an example of an insoluble dietary fiber. Gum arabic was the most effective and kappa-carrageenan the least. The capacity of the polysaccharides to act as emulsifiers and stabilizers may explain their effects on DNP distribution. The monosaccharide glucose and the disaccharide cellobiose had no effect on the distribution of DNP. These results indicate three possible mechanisms by which soluble-fiber polysaccharides may enhance the development of colorectal cancer. First, because they reduce the ability of insoluble dietary fibers to adsorb hydrophobic carcinogens, more carcinogens may enter the colon maintained in solution than adsorbed onto insoluble fibers. Second, if soluble-fiber polysaccharides are maintaining hydrophobic carcinogens in solution and these polysaccharides are degraded by bacterial enzymes in the colon, then the carcinogens may come out of solution and be deposited onto the mucosal surface of the colon. Third, soluble-fiber polysaccharides may cross the intestinal epithelium and carry with them carcinogens maintained in solution. These studies have important consequences for nutrition, because soluble-fiber polysaccharides represent a common component of foods.

On the relation between conditional independence models determined by finite distributive lattices and by directed acyclic graphs

The relations among the classes of multivariate conditional independence models determined by directed acyclic graphs (DAG), undirected graphs (UDG), decomposable graphs (DEC), and finite distributive lattices (LCI) are investigated. First, LCI models that admit positive joint densities are characterized in terms of an appropriate factorization of the density. This factorization is then recognized as a particular form of the recursive factorization that characterizes DAG models, thereby establishing that the LCI models comprise a subclass of the class of DAG models. Precisely, the class of LCI models coincides with the subclass of transitive DAG models. Furthermore, the class of LCI models has nontrivial intersection with the class of DEC models. A series of examples illustrating these relations are presented.

Prenatally undernourished rats show increased preference for wheel running v. lever pressing for food in a choice task.

Maternal nutrition during pregnancy has a significant influence in establishing patterns of metabolism and postnatal behaviours in offspring, and therefore shapes their risk of developing disorders in later life. Although it is well established that a mismatch between food consumption and energy expenditure leads to obesity and metabolic dysregulation, little research has investigated the biological origin of such behaviour. We conducted the present experiments to investigate effects of early-life nutrition on preference between wheel running and lever pressing for food during adult life. To address this issue we employed a well-established experimental approach in the rat which has shown that offspring of mothers undernourished during pregnancy develop obesity and metabolic disorders when kept under standard laboratory conditions. Using this experimental approach, two studies were conducted where offspring of ad libitum-fed dams and dams undernourished throughout pregnancy were given the choice between wheel running and pressing a response lever for food. Across subsequent conditions, the rate at which the response lever provided food was varied from 0.22 to 6.0 (study 1) and 0.19 to 3.0 (study 2) pellets per min. Compared with the control group, offspring from dams undernourished during pregnancy showed a consistently greater preference for running over lever pressing for food throughout both experiments of the study. The results of the present study provide experimental evidence that a mothers nutrition during pregnancy can result in a long-term shift in her offsprings lifestyle choices that are relevant to obesity prevention. Such a shift, if endorsed, will have substantial and wide-ranging health consequences throughout the lifespan.