Classification of highly unbalanced CYP450 data of drugs using cost sensitive machine learning techniques

In this paper, we study the classifications of unbalanced data sets of drugs. As an example we chose a data set of 2D6 inhibitors of cytochrome P450. The human cytochrome P450 2D6 isoform plays a key role in the metabolism of many drugs in the preclinical drug discovery process. We have collected a data set from annotated public data and calculated physicochemical properties with chemoinformatics methods. On top of this data, we have built classifiers based on machine learning methods. Data sets with different class distributions lead to the effect that conventional machine learning methods are biased toward the larger class. To overcome this problem and to obtain sensitive but also accurate classifiers we combine machine learning and feature selection methods with techniques addressing the problem of unbalanced classification, such as oversampling and threshold moving. We have used our own implementation of a support vector machine algorithm as well as the maximum entropy method. Our feature selection is based on the unsupervised McCabe method. The classification results from our test set are compared structurally with compounds from the training set. We show that the applied algorithms enable the effective high throughput in silico classification of potential drug candidates.

Localization of Hyaluronic Acid in the Seminal Vesicles of the Miniature Pig

We studied the detailed localization of hyaluronic acid in the seminal vesicles of the miniature pig, using hyaluronic acid-binding protein as a specific histochemical probe at the ultrastructural level. According to the results, the basolateral surface of the plasma membrane of the glandular epithelial cells, was found to contain hyaluronan. However, abundantly present was hyaluronan in the subepithelial connective tissue, in particular, in the extracellular matrix surrounding the fibroblasts, smooth muscle cells, small blood vessels and capillaries. The substance was also observed in the surface coat of the plasma membrane of the fibroblasts, but not in that of the smooth muscle cells. The findings suggest that hyaluronan in the seminal vesicles of the miniature pig is synthesized onto the surface coat of the plasma membrane of the fibroblasts, is contributed to the extracellular matrix, and consequently concentrates in the subepithelial connective tissue. The substance may particularly be involved in a variety of cellular functions to maintain morphological organization as well as to regulate physiological homeostasis in the reproductive organ of this species, rather than participate in sperm functions.

Measurement of the Gerasimov-Drell-Hearn Integrand for 2H from 200 to 800 MeV

A measurement of the helicity dependence of the total inclusive photoabsorption cross section on the deuteron was carried out at MAMI (Mainz) in the energy range 200<Egamma<800 MeV. The experiment used a 4pi detection system, a circularly polarized tagged photon beam and a frozen-spin target which provided longitudinally polarized deuterons. The contribution to the Gerasimov-Drell-Hearn sum rule for the deuteron determined from the data is 407+/-20(stat)+/-24(syst) mu b for 200<Egamma<800 MeV.

Current concepts in the diagnosis and management of metabolic complications of HIV infection and its therapy

Changes in fat distribution, dyslipidemia, disordered glucose metabolism, and lactic acidosis have emerged as significant challenges to the treatment of human immunodeficiency virus (HIV) infection. Over the past decade, numerous investigations have been conducted to better define these conditions, identify risk factors associated with their development, and test potential therapeutic interventions. The lack of standardized diagnostic criteria, as well as disparate study populations and research methods, have led to conflicting data regarding the diagnosis and treatment of metabolic and body shape disorders associated with HIV infection. On the basis of a review of the medical literature published and/or data presented before April 2006, we have prepared a guide to assist the clinician in the detection and management of these complications.

Dactinomycin (A) and vincristine (V) with or without cyclophosphamide (C) and radiation therapy (RT) for newly diagnosed patients with low-risk embryonal/botryoid rhabdomyosarcoma (RMS). An IRS-V report from the Soft Tissue Sarcoma Committee of the Children’s Oncology Group (STS COG)

9001

Background: The STS COG defines patients with low-risk RMS as those with localized tumors of embryonal histology that occur in favorable sites or occur in unfavorable sites and are grossly resected. Intergroup Rhabdomyosarcoma Studies (IRS)-III (1984–1991) and -IV (1991–1997) found that these patients had a 5-year failure-free survival (FFS) of 83% and an overall survival of 95%. Methods: Two subsets were identified for the IRS-V low-risk RMS study (D9602) (1997–2004) based on the hypothesis that they required different treatment intensities to achieve similar excellent outcomes. Patients assigned to Subset A (Stage [Sg] 1 Group [Gp] I/IIA, Sg 1 Gp III orbit, Sg 2 Gp I) received VA (cumulative doses over 1 year of treatment: V: 54 mg/m2, A: 24 mg/kg) ± local RT. Patients assigned to Subset B (Sg 2 Gp IIB/C, Sg 1 Gp III non-orbit, Sg 2 Gp II, Sg 3 Gp I/II) received VA + C (C: 28.6 g/m2) ± RT. The RT dose was reduced to 36 Gy (instead of 41.4 Gy on IRS-IV) for Gp IIA patients and to 45 Gy (instead of 50.4 or 59.4 Gy on IRS-IV) for Gp III orbit patients. The primary endpoint was FFS. Results: Estimated 3-yr FFS was 89% (95% CI 84%, 93%) for Subset A (n=263) and 89% (95% CI 77%, 95%) for Subset B (n=79). Median follow-up was 2.9 years. Estimated 3-yr FFS was 80% (95% CI 64%, 89%; n=59) for patients with Sg 1 Gp IIA disease and 88% (95% CI 77%, 94%; n=76) for Gp III orbit disease. Conclusions: There is not evidence to suggest that outcome for these patients differs from outcomes observed in similar patients treated on IRS-III and IRS-IV.

No significant financial relationships to disclose.

Cytochemical Localization of Glycoconjugates in the Secretory Epithelial Cells Lining the Prostate Gland of the Miniature Pig

The aim of the study was to emphasize several specific functional aspects of the mammalian prostate gland. In this connection, the subcellular localization and characterization of glycoconjugates in the secretory epithelial cells were examined that line the prostate gland of the miniature pig, using cytochemistry, including lectin-gold methods. The results verified a diversified pattern of glycoconjugates in the structures of the secretory cells. The secretory granules and the free surface coat of the plasma membrane contained several sugar moieties such as alpha-D-Man, alpha-D-Glc, alpha-L-Fuc, beta-D-Gal, GalNAc, GlcNAc and NeuAc (sialic acid), whereas the Golgi apparatus exhibited GlcNAc and sialic acid residues. In addition, the cisterns of the endoplasmic reticulum showed alpha-D-Man and alpha-D-Glc moieties. It seems likely that the secretory glycoconjugates demonstrated contribute to favourable conditions for fertilization.

Morphological, histochemical and immunohistochemical characterization of secretory production of the ciliary glands in the porcine eyelid

In addition to performing general histology and cytology of the ciliary glands of the miniature pig, we studied the localization of glycoconjugates and beta-defensins in these glands with the use of carbohydrate histochemical and immunohistochemical methods. The secretory cells of the glands were equipped with non-homogeneous secretory granules, a well-developed Golgi apparatus and rough endoplasmic reticulum. The secretory epithelium and luminal secretion of the glands contained large amounts of neutral and acidic glycoconjugates with various saccharide residues (alpha-L-Fuc, beta-D-Gal, alpha-D-GalNAc and sialic acid). The sebaceous glands and tarsal glands also exhibited positive reactions to most of the histochemical methods. Additionally, the antimicrobial peptide group of beta-defensins was demonstrated to be products of the ciliary glands, as well as the sebaceous glands and tarsal glands. The results obtained are discussed with regard to the specific function of the ciliary glandular secretions. These secretory products may be related to the moistening and general protection of the skin surface of the eyelid and ocular surface.