We have applied the polymerase chain-reaction (PCR) technique to benign and malignant squamous tumours of the pharynx and larynx and to nasal inverted papillomas to detect evidence of infection with human papillomavirus (HPV) 6 and 11. Each of these lesions tended to be infected with either or both of these but the prevalence of infection when compared with that of histologically normal biopsies from the nasopharynx was not significantly increased.

The free energy of solvation can play an important or even dominant role in the accurate prediction of binding affinities and various other molecular-scale interaction phenomena critical to the study of biochemical processes. Many research applications for solvation modeling, such as fragment-based drug design, require algorithms that are both accurate and computationally inexpensive. We have developed a calculation of solvation free energy which runs fast enough for interactive applications, functions for a wide range of chemical species relevant to simulating molecules for biological and pharmaceutical applications, and is readily extended when data for new species becomes available. We have also demonstrated that the incorporation of ab initio data provides necessary access to sufficient reference data for a broad range of chemical features. Our empirical model, including an electrostatic term and a different set of atom types, demonstrates improvements over a previous, solvent-accessible surface area-only model by Wang et al. when fit to identical training sets (mean absolute error of 0.513 kcal/mol versus the 0.538 kcal/mol reported by Wang). The incorporation of ab initio solvation free energies provides a significant increase in the breadth of chemical features for which the model can be applied by introducing classes of compounds for which little or no experimental data is available. The increased breadth and the speed of this solvation model allow for conformational minimization, conformational search, and ligand binding free energy calculations that economically account for the complex interplay of bonded, nonbonded, and solvation free energies as conformations with varying solvent-accessible surfaces are sampled.

In a clinicopathological study of granulomatous prostatitis, we have found two distinct histological patterns. Approximately one third of cases consisted of localized, often elongated or stellate lesions, resembling rheumatoid nodules. Where clinical details were available, most of these cases had a history of previous transurethral resection. The remaining cases showed more diffuse involvement of the prostate, with lesions centred on ducts and glands, and were not associated with previous prostatic surgery or systemic illness. Immunohistochemical studies of the associated inflammatory infiltrate showed an apparently random distribution of T- and B-lymphocytes in the former group, while in the latter group there was a concentration of T-cells in and around damaged ducts and glands, suggesting a possible immune-mediated destruction of these structures.

Peutz-Jeghers syndrome is characterized by multiple polyps throughout the gastrointestinal tract in association with mucocutaneous pigmentation. Small bowel polyps in the syndrome may exhibit epithelial misplacement, into the submucosa, the muscularis propria, and even the subserosa. The authors demonstrate two patients in whom there is also misplacement of dysplastic epithelium into the submucosa and muscularis propria of the small bowel. Epithelial misplacement is recognized to mimic invasive malignancy. Such mimicry is heightened substantially when the misplaced epithelium is dysplastic. Correct interpretation of the histologic changes is aided by the use of special stains, which demonstrate the associated lamina propria and the lack of a desmoplastic response, and immunohistochemistry, which shows that the misplaced dysplastic epithelium is accompanied by non-neoplastic mucosa. There is an increased prevalence of gastrointestinal malignancy in Peutz-Jeghers syndrome. However, the presence of perplexing histologic features, caused by epithelial misplacement, especially when some of that epithelium is dysplastic, in small bowel polyps at least has the potential for the overdiagnosis of malignancy in the syndrome.

The success of molecular fragment-based design depends critically on the ability to make predictions of binding poses and of affinity ranking for compounds assembled by linking fragments. The SAMPL3 Challenge provides a unique opportunity to evaluate the performance of a state-of-the-art fragment-based design methodology with respect to these requirements. In this article, we present results derived from linking fragments to predict affinity and pose in the SAMPL3 Challenge. The goal is to demonstrate how incorporating different aspects of modeling protein-ligand interactions impact the accuracy of the predictions, including protein dielectric models, charged versus neutral ligands, ΔΔGs solvation energies, and induced conformational stress. The core method is based on annealing of chemical potential in a Grand Canonical Monte Carlo (GC/MC) simulation. By imposing an initially very high chemical potential and then automatically running a sequence of simulations at successively decreasing chemical potentials, the GC/MC simulation efficiently discovers statistical distributions of bound fragment locations and orientations not found reliably without the annealing. This method accounts for configurational entropy, the role of bound water molecules, and results in a prediction of all the locations on the protein that have any affinity for the fragment. Disregarding any of these factors in affinity-rank prediction leads to significantly worse correlation with experimentally-determined free energies of binding. We relate three important conclusions from this challenge as applied to GC/MC: (1) modeling neutral ligands--regardless of the charged state in the active site--produced better affinity ranking than using charged ligands, although, in both cases, the poses were almost exactly overlaid; (2) simulating explicit water molecules in the GC/MC gave better affinity and pose predictions; and (3) applying a ΔΔGs solvation correction further improved the ranking of the neutral ligands. Using the GC/MC method under a variety of parameters in the blinded SAMPL3 Challenge provided important insights to the relevant parameters and boundaries in predicting binding affinities using simulated annealing of chemical potential calculations.

As measurement of absolute glomerular size is difficult we developed a method of assessing glomerular size that was simple and practical and could be used to compare the kidneys in different groups of patients. Using a semi-automatic image analyser, the cross-sectional area of 100 randomly-selected glomeruli, outlined by Bowman's capsule, was measured on sections of kidneys taken at necropsy. The mean of the logarithms of the largest 25 areas was calculated. The method was applied to compare control kidneys (53) with the kidneys in acromegalics (20), in patients with one kidney (10) and in patients with asymmetrical kidneys (12). Kidneys were heavier in the three test groups than in controls. Glomerular sizes were similar in controls and in acromegalics but were larger in single and disparate kidneys. There was a relationship between glomerular size and kidney weight within the control group and across the four groups taken together. This only partly accounted for the observed differences in glomerular size between the groups. Histological comparison of the acromegalic and single kidneys showed more global glomerulosclerosis in single kidneys and also segmental lesions, mainly at the glomerular hilum, only in the single kidneys. These findings show that renal enlargement occurs in acromegaly and in single and disparate kidneys but is accompanied by markedly different glomerular features. This implies different mechanisms for the renal enlargement. The method of assessing glomerular size is useful in the study of these and other conditions affecting the kidney.

In conclusion, we demonstrated that NAT1, SULT1A1 and SULT1A3 are present in human prostate and that both enzyme classes significantly contribute to the activation of N-hydroxylated heterocyclic amines to DNA-damaging species in this tissue. Variation in expression levels, in combination with dietary and/or environmental exposure to carcinogens, could be influential in determining individual susceptibility to prostate cancer.

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