The rectus abdominis muscle advancement flap as a salvage option for chest wall reconstruction.

We describe a previously unreported technique of advancing the rectus abdominis muscle superiorly, based on the deep inferior epigastric artery, to cover a lower anterior chest wall defect. This technique represents an important salvage option for chest wall reconstruction and affords a great deal of intra-operative flexibility.

Relationship of thyroid transcription factor 1 to EGFR status in non-small-cell lung cancer.

BACKGROUND: Activating mutations of the epidermal growth factor receptor (EGFR) gene are known to drive a proportion of non-small-cell lung cancers. Identification of lung cancers harbouring such mutations can lead to effective treatment using one of the agents that targets and blocks egfr-mediated signalling. METHODS: All specimens received at the BC Cancer Agency (Vancouver) for EGFR testing were prospectively identified and catalogued, together with clinical information and EGFR status, over a 14-month period. RESULTS: Specimens from 586 patients were received for EGFR testing, and EGFR status was reported for 509 patients. No relationship between specimen type or site of origin and EGFR test failure rate was identified. Concurrent immunohistochemical (ihc) status for thyroid transcription factor 1 (ttf1) was available for 309 patients. The negative predictive value of ttf1-negative status by ihc was 94.2% for predicting negative EGFR status. CONCLUSIONS: In patients with limited tissue available for testing, a surrogate for EGFR status would aid in timely management. Immunohistochemistry for ttf1 is readily available and correlates highly with EGFR status. In conjunction with genetic assays, ttf1 could be used to optimize an EGFR testing strategy.

Polyethylene glycol-drug ester conjugates for prolonged retention of small inhaled drugs in the lung.

Typically, inhaled drugs are rapidly absorbed into the bloodstream, which results in systemic side effects and a brief residence time in the lungs. PEGylation was evaluated as a novel strategy for prolonging the retention of small inhaled molecules in the pulmonary tissue. Hydrolysable ester conjugates of PEG1000, PEG2000, 2000, PEG3400 and prednisolone, a model drug cleared from the lungs within a few minutes, were synthesised and thoroughly characterised. The conjugates were stable in buffers with hydrolysis half-lives ranging from 1h to 70 h, depending on the pH and level of substitution. With the exception of PEG3400-prednisolone, conjugates did not induce a significant lactate dehydrogenase (LDH) release from Calu-3 cells after a 20 h exposure. Following nebulisation to isolated perfused rat lungs (IPRL), the PEG2000 and mPEG2000 conjugates reduced the maximum prednisolone concentration in the perfusate (Cmax) by 3.0 and 2.2 fold, respectively. Moreover, while prednisolone was undetectable in the perfusion solution beyond 20 min when the free drug was administered, prednisolone concentrations were still quantifiable after 40 min following delivery of the conjugates. This study is the first to demonstrate hydrolysable PEG drug ester conjugates are a promising approach for optimising the pharmacokinetic profile of small drugs delivered by inhalation.

Adverse outcome analyses of observational data: assessing cardiovascular risk in HIV disease.

Clinical decisions are ideally based on randomized trials but must often rely on observational data analyses, which are less straightforward and more influenced by methodology. The authors, from a series of expert roundtables convened by the Forum for Collaborative HIV Research on the use of observational studies to assess cardiovascular disease risk in human immunodeficiency virus infection, recommend that clinicians who review or interpret epidemiological publications consider 7 key statistical issues: (1) clear explanation of confounding and adjustment; (2) handling and impact of missing data; (3) consistency and clinical relevance of outcome measurements and covariate risk factors; (4) multivariate modeling techniques including time-dependent variables; (5) how multiple testing is addressed; (6) distinction between statistical and clinical significance; and (7) need for confirmation from independent databases. Recommendations to permit better understanding of potential methodological limitations include both responsible public access to de-identified source data, where permitted, and exploration of novel statistical methods.

The association of folate, zinc and antioxidant intake with sperm aneuploidy in healthy non-smoking men.

BACKGROUND: Little is known about the effect of paternal nutrition on aneuploidy in sperm. We investigated the association of normal dietary and supplement intake of folate, zinc and antioxidants (vitamin C, vitamin E and beta-carotene) with the frequency of aneuploidy in human sperm. METHODS: Sperm samples from 89 healthy, non-smoking men from a non-clinical setting were analysed for aneuploidy using fluorescent in situ hybridization with probes for chromosomes X, Y and 21. Daily total intake (diet and supplements) for zinc, folate, vitamin C, vitamin E and beta-carotene was derived from a food frequency questionnaire. Potential confounders were obtained from a self-administered questionnaire. RESULTS: After adjusting for covariates, men with high folate intake (>75th percentile) had lower frequencies of sperm with disomies X, 21, sex nullisomy, and a lower aggregate measure of sperm aneuploidy (P

The effects of body fat on pulmonary function and gas exchange in cynomolgus monkeys.

Obesity adversely affects lung function in humans often reducing arterial blood oxygenation. To determine if obesity adversely affects lung function in cynomolgus monkeys, which is a species that is often used for pulmonary research, pulmonary mechanics, ventilation, functional residual capacity (FRC), and arterial blood gases were measured using spontaneous respiration and on mechanical ventilation with room air or 100% O(2). Body fat percentage was measured by dual energy X-ray absorption. Blood leptin levels were measured by radioimmune assay. Obese monkeys breathed faster with lower tidal volume, but pulmonary resistance and dynamic lung compliance did not change with body fat. FRC and blood leptin were, respectively, negatively and positively correlated with percent body fat. FRC correlated moderately with ventilatory parameters and strongly with arterial oxygen tension, alveolar-arterial oxygen difference and venous admixture. Therefore, obesity in cynomolgus monkeys had marked, deleterious effects on FRC, ventilation and arterial oxygenation. Obesity may be an important confounding variable in lung function studies in primates.

Cystic fibrosis screening in newborns: results from existing programs.

Newborn screening for cystic fibrosis (CF) provides early identification and initiation of treatment to infants with this fatal and often misdiagnosed genetic disease. Although reports of health benefits continue to mount from decade-old screening programs in Wisconsin, France, and Australia, newborn screening for CF is still a highly debated topic in genetic policy development. This article summarizes the literature published between May 2000 and April 2001 regarding the health benefits, risks, cost-effectiveness, and programmatic issues of newborn screening for CF. The literature consistently shows evidence of benefits and lack of harm from newborn screening for CF.

Genomic organization of the X-linked inhibitor of apoptosis and identification of a novel testis-specific transcript.

Here we report the genomic organization and mapping of the X-linked inhibitor of apoptosis gene (BIRC4, also known as XIAP and hILP) and the identification of a closely related transcript. BIRC4 is located on Xq25 and is composed of seven exons. The intron/exon structure is highly conserved between the mouse homologue and its human counterpart. Four bands cross-react with a BIRC4 coding region probe on a genomic Southern blot. One of these cross-reactive bands encodes an intronless gene that expresses a 2.2-kb transcript solely in the testis. This testis-specific transcript contains a putative open reading frame (ORF) that is homologous to the carboxy-terminal end of BIRC4; overexpression of this ORF shows protective effects against BAX-induced apoptosis.

Statistical decoding of potent pools based on chemical structure.

Pooling experiments are used as a cost-effective approach for screening chemical compounds as part of the drug discovery process in pharmaceutical companies. When a biologically potent pool is found, the goal is to decode the pool, i.e., to determine which of the individual compounds are potent. We propose augmenting the data on pooled testing with information on the chemical structure of compounds in order to complete the decoding process. This proposal is based on the well-known relationship between biological potency of a compound and its chemical structure. Application to real data from a drug discovery process at GlaxoSmithKline reveals a 100% increase in hit rate, namely, the number of potent compounds identified divided by the number of tests required.

Assessment of visually lossless irreversible image compression: comparison of three methods by using an image-comparison workstation.

PURPOSE: To determine the degree of irreversible image compression detectable in conservative viewing conditions. MATERIALS AND METHODS: An image-comparison workstation, which alternately displayed two registered and magnified versions of an image, was used to study observer detection of image degradation introduced by irreversible compression. Five observers evaluated 20 16-bit posteroanterior digital chest radiographs compressed with Joint Photographic Experts Group (JPEG) or wavelet-based trellis-coded quantization (WTCQ) algorithms at compression ratios of 8:1-128:1 and x2 magnification by using (a) traditional two-alternative forced choice; (b) original-revealed two-alternative forced choice, in which the noncompressed image is identified to the observer; and (c) a resolution-metric method of matching test images to degraded reference images. RESULTS: The visually lossless threshold was between 8:1 and 16:1 for four observers. JPEG compression resulted in performance as good as that with WTCQ compression at these ratios. The original-revealed forced-choice method was faster and as sensitive as the two-alternative forced-choice method. The resolution-metric results were robust and provided information on performance above visually lossless levels. CONCLUSION: The image-comparison workstation is a versatile tool for comparative assessment of image quality. At x2 magnification, images compressed with either JPEG or WTCQ algorithms were indistinguishable from unaltered original images for most observers at compression ratios between 8:1 and 16:1, indicating that 10:1 compression is acceptable for primary image interpretation.

Analysis of a large structure/biological activity data set using recursive partitioning.

Combinatorial chemistry and high-throughput screening are revolutionizing the process of lead discovery in the pharmaceutical industry. Large numbers of structures and vast quantities of biological assay data are quickly being accumulated, overwhelming traditional structure/activity relationship (SAR) analysis technologies. Recursive partitioning is a method for statistically determining rules that classify objects into similar categories or, in this case, structures into groups of molecules with similar potencies. SCAM is a computer program implemented to make extremely efficient use of this methodology. Depending on the size of the data set, rules explaining biological data can be determined interactively. An example data set of 1650 monoamine oxidase inhibitors exemplifies the method, yielding substructural rules and leading to general classifications of these inhibitors. The method scales linearly with the number of descriptors, so hundreds of thousands of structures can be analyzed utilizing thousands to millions of molecular descriptors. There are currently no methods to deal with statistical analysis problems of this size. An important aspect of this analysis is the ability to deal with mixtures, i.e., identify SAR rules for classes of compounds in the same data set that might be binding in different ways. Most current quantitative structure/activity relationship methods require that the compounds follow a single mechanism. Advantages and limitations of this methodology are presented.

Eotaxin and nitric oxide production as markers of inflammation in allergic cynomolgus monkeys.

BACKGROUND: Cynomolgus monkeys have a natural hypersensitivity to Ascaris suum antigen. Inhalation of antigen produces immediate and delayed allergic reactions and an influx of inflammatory cells into the lungs. This study investigated the production of nitric oxide (NO) and the chemokine eotaxin during this allergic response. The effect of bronchoscopy alone on lung inflammatory cells was also investigated along with the time course of the eosinophil influx into the lung. METHODS: Allergic cynomolgus monkeys were challenged with antigen. Bronchoalveolar lavage (BAL) was performed before and after challenge, and end-tidal NO was measured before and 24 h after challenge. Eotaxin was measured in the BAL fluid 6, 24 and 72 h after challenge. One group of animals was treated with dexamethasone before challenge to block the influx of cells into the lung. RESULTS: BLA alone induced an influx of neutrophils, but not eosinophils, into the lung 24 h later. A single antigen challenge produced a marked increase in BAL eosinophils that was apparent at 6 h but increased at 72 h after challenge. The increase at 6 h was largely blocked by dexamethasone. Three antigen challenges produced elevated BAL eosinophil levels that persisted for at least 8 weeks. Eotaxin levels rose dramatically 6 h after challenge and remained the same after 24 h. By 72 h, the eotaxin levels had returned to baseline. The increase in eotaxin at 6 h was nonsignificantly reduced by dexamethasone. Exhaled NO levels doubled 24 h after challenge and were not affected by dexamethasone. CONCLUSIONS: Eotaxin and NO production were increased after airway challenge in allergic monkeys. The rise in NO was not blocked by dexamethasone. The effects of bronchoscopy on the BAL can be avoided by using alternate lungs on consecutive occasions. Eosinophils persist in the BAL for many weeks after antigen challenge.

Automated pharmacophore identification for large chemical data sets.

The identification of three-dimensional pharmacophores from large, heterogeneous data sets is still an unsolved problem. We developed a novel program, SCAMPI (statistical classification of activities of molecules for pharmacophore identification), for this purpose by combining a fast conformation search with recursive partitioning, a data-mining technique, which can easily handle large data sets. The pharmacophore identification process is designed to run recursively, and the conformation spaces are resampled under the constraints of the evolving pharmacophore model. This program is capable of deriving pharmacophores from a data set of 1000-2000 compounds, with thousands of conformations generated for each compound and in less than 1 day of computational time. For two test data sets, the identified pharmacophores are consistent with the known results from the literature.

Genomic organization and physical map of the human inhibitors of apoptosis: HIAP1 and HIAP2.

We report the genomic organization, mapping, and tissue distribution of the human inhibitors of apoptosis, HIAP1 and HIAP2. HIAP1 is 8.7 kb in length and is contained within eight coding and two non-coding (5'UTR) exons. The 4.5-kb HIAP2 message is contained within eight coding region exons and a single 5'UTR exon. The HIAP1 and HIAP2 genes lie in tandem on Chromosome (Chr) 11 (q22-23) with the intergenic distance being approximately 7 kb. The tissue distributions of HIAP1 and HIAP2 appear similar although the relative expression of HIAP1 is generally higher. Expression is highest in the kidney, small intestine, liver, and lung and lowest in tissues of the central nervous system.

Short duration anaesthesia with medetomidine and ketamine in cynomolgus monkeys.

Cynomolgus monkeys were anaesthetized with either intramuscular ketamine (10 mg/kg or intramuscular ketamine 2 mg/kg and medetomidine 50 microg/kg. Various physiological measurements were made once the animals were safe to handle and again 10 min later. Cardiovascular and respiratory function were well maintained with both regimens but the heart rate was lower and arterial-alveolar carbon dioxide gradient was higher in the animals that received medetomidine. In those animals that received medetomidine, atipamezole was given to reverse the medetomidine but there was no difference in recovery times between the two regimens. Anaesthesia was not entirely reliable with medetomidine/ketamine and we recommend caution when using this mixture.

Use of recursive partitioning in the sequential screening of G-protein-coupled receptors.

High-throughput screening (HTS) is changing as more compounds and better assay techniques become available. HTS is also generating a large amount of data. There is a need to rationalize the HTS process, because, in some cases, the screening of all available compounds is not economically feasible. In addition to the selection of promising compounds, there is a need to learn from the data that we collect. In this paper, we use a data-mining method, recursive partitioning, to help uncover and understand structure-activity relations and to help biology and chemistry experts make better decisions on which compounds to screen next and better characterize. The sequential-screening process is presented and the results of applying that process to 14 G-protein-coupled receptor assays are reported.

Discovery 99: accelerate and improve the drug discovery process. 26-29 April 1999, San Diego, CA, USA.

The stated purpose of this conference was the examination of emerging technologies for drug discovery. The meeting was divided into numerous pre- and post-conferences and tracks. A pre-conference workshop examined enabling software and business strategies. Nine tracks covered natural products, high-throughput screening, bioinformatics, proteomics/functional genomics, pharmacogenomics, combichem, chemoinformatics and assay methods. A post-conference symposium covered ADME-toxicology screening. In short, the gamut of drug discovery.