Object-oriented Technology for Compressor Simulation

An object-oriented basis for interdisciplinary compressor simulation can, in principle, overcome several barriers associated with the traditional structured (procedural) development approach. This paper presents the results of a research effort with the objective to explore the repercussions on design, analysis, and implementation of a compressor model in an object oriented (OO) language, and to examine the ability of the OO system design to accommodate computational fluid dynamics (CFD) code for compressor performance prediction. Three fundamental results are that: (1) the selection of the object oriented language is not the central issue; enhanced (interdisciplinary) analysis capability derives from a broader focus on object-oriented technology; (2) object-oriented designs will produce more effective and reusable computer programs when the technology is applied to issues involving complex system inter-relationships (more so than when addressing the complex physics of an isolated discipline); and (3) the concept of disposable prototypes is effective for exploratory research programs, but this requires organizations to have a commensurate long-term perspective. This work also suggests that interdisciplinary simulation can be effectively accomplished (over several levels of fidelity) with a mixed language treatment (i.e., FORTRAN-C++), reinforcing the notion the OO technology implementation into simulations is a 'journey' in which the syntax can, by design, continuously evolve

Spectroscopic probe for in vivo measurement of raman signals

An optical probe is disclosed which is suitable for rapidly measuring Raman spectra in vivo. The probe is designed to minimize interfering Raman and fluorescence signals generated within the probe itself. In addition, the probe design is compact, making it particularly suited for use in confined spaces such as body cavities. In one embodiment, the probe is employed to detect tissue abnormalities such as cervical cancers and precancers.Board of Regents, University of Texas Syste

Absolute quantitative real-time polymerase chain reaction for the measurement of human papillomavirus E7 mRNA in cervical cytobrush specimens

BACKGROUND: Few reports of the utilization of an accurate, cost-effective means for measuring HPV oncogene transcripts have been published. Several papers have reported the use of relative quantitation or more expensive Taqman methods. Here, we report a method of absolute quantitative real-time PCR utilizing SYBR-green fluorescence for the measurement of HPV E7 expression in cervical cytobrush specimens. RESULTS: The construction of a standard curve based on the serial dilution of an E7-containing plasmid was the key for being able to accurately compare measurements between cervical samples. The assay was highly reproducible with an overall coefficient of variation of 10.4%. CONCLUSION: The use of highly reproducible and accurate SYBR-based real-time polymerase chain reaction (PCR) assays instead of performing Taqman-type assays allows low-cost, high-throughput analysis of viral mRNA expression. The development of such assays will help in refining the current screening programs for HPV-related carcinomas

Human papillomavirus infection in women with and without cervical cancer in Ibadan, Nigeria

<p>Abstract</p> <p>Background</p> <p>Concerns have been raised that the proportion of cervical cancer preventable by human papillomavirus (HPV) 16/18 vaccines might be lower in sub-Saharan Africa than elsewhere.</p> <p>Method</p> <p>In order to study the relative carcinogenicity of HPV types in Nigeria, as well as to estimate the vaccine-preventable proportion of invasive cervical cancer (ICC) in the country, we compared HPV type prevalence among 932 women from the general population of Ibadan, Nigeria, with that among a series of 75 ICC cases diagnosed in the same city. For all samples, a GP5+/6+ PCR based assay was used for the detection of 44 genital HPV types.</p> <p>Results</p> <p>In the general population, 245 (26.3%, 95% confidence interval (CI) 23.5% - 29.2%) women were HPV-positive, among whom the prevalence of HPV35 and HPV16 were equally frequent (12.2%, 95% CI 8.4% - 17.0%). In ICC, however, HPV16 predominated strongly (67.6% of 68 HPV-positive cases), with the next most common types being 18 (10.3%, 95% CI 4.2% - 20.1%), 35, 45 and 56 (each 5.9%, 95% CI 1.6% - 14.4%). Comparing among HPV-positive women only, HPV16 and 18 were over-represented in ICC <it>versus </it>the general population (prevalence ratios 5.52, 95% CI 3.7 - 8.3 and 1.4, 95% CI 0.6 - 3.3, respectively). Other high-risk HPV types, as well as low-risk and multiple HPV infections were less common in HPV-positive women with ICC than from the general population.</p> <p>Conclusions</p> <p>Our study confirms that in Nigeria, as elsewhere, women infected with HPV16 and 18 are at higher risk of developing ICC than those infected with other high-risk types, and that current HPV16/18 vaccines have enormous potential to reduce cervical cancer in the region.</p

The performance of human papillomavirus high-risk DNA testing in the screening and diagnostic settings.

OBJECTIVE: We sought to evaluate the performance of the human papillomavirus high-risk DNA test in patients 30 years and older. MATERIALS AND METHODS: Screening (n=835) and diagnosis (n=518) groups were defined based on prior Papanicolaou smear results as part of a clinical trial for cervical cancer detection. We compared the Hybrid Capture II (HCII) test result with the worst histologic report. We used cervical intraepithelial neoplasia (CIN) 2/3 or worse as the reference of disease. We calculated sensitivities, specificities, positive and negative likelihood ratios (LR+ and LR-), receiver operating characteristic (ROC) curves, and areas under the ROC curves for the HCII test. We also considered alternative strategies, including Papanicolaou smear, a combination of Papanicolaou smear and the HCII test, a sequence of Papanicolaou smear followed by the HCII test, and a sequence of the HCII test followed by Papanicolaou smear. RESULTS: For the screening group, the sensitivity was 0.69 and the specificity was 0.93; the area under the ROC curve was 0.81. The LR+ and LR- were 10.24 and 0.34, respectively. For the diagnosis group, the sensitivity was 0.88 and the specificity was 0.78; the area under the ROC curve was 0.83. The LR+ and LR- were 4.06 and 0.14, respectively. Sequential testing showed little or no improvement over the combination testing. CONCLUSIONS: The HCII test in the screening group had a greater LR+ for the detection of CIN 2/3 or worse. HCII testing may be an additional screening tool for cervical cancer in women 30 years and older

Using LongSAGE to Detect Biomarkers of Cervical Cancer Potentially Amenable to Optical Contrast Agent Labelling

Sixteen longSAGE libraries from four different clinical stages of cervical intraepithelial neoplasia have enabled us to identify novel cell-surface biomarkers indicative of CIN stage. By comparing gene expression profiles of cervical tissue at early and advanced stages of CIN, several genes are identified to be novel genetic markers. We present fifty-six cell-surface gene products differentially expressed during progression of CIN. These cell surface proteins are being examined to establish their capacity for optical contrast agent binding. Contrast agent visualization will allow real-time assessment of the physiological state of the disease process bringing vast benefit to cancer care. The data discussed in this publication have been submitted to NCBIs Gene Expression Omnibus (GEO, http://www.ncbi.nlm.nih.gov/geo/) and are accessible through GEO Series accession number GSE6252

Comprehensive serial analysis of gene expression of the cervical transcriptome

<p>Abstract</p> <p>Background</p> <p>More than half of the approximately 500,000 women diagnosed with cervical cancer worldwide each year will die from this disease. Investigation of genes expressed in precancer lesions compared to those expressed in normal cervical epithelium will yield insight into the early stages of disease. As such, establishing a baseline from which to compare to, is critical in elucidating the abnormal biology of disease. In this study we examine the normal cervical tissue transcriptome and investigate the similarities and differences in relation to CIN III by Long-SAGE (L-SAGE).</p> <p>Results</p> <p>We have sequenced 691,390 tags from four L-SAGE libraries increasing the existing gene expression data on cervical tissue by 20 fold. One-hundred and eighteen unique tags were highly expressed in normal cervical tissue and 107 of them mapped to unique genes, most belong to the ribosomal, calcium-binding and keratinizing gene families. We assessed these genes for aberrant expression in CIN III and five genes showed altered expression. In addition, we have identified twelve unique HPV 16 SAGE tags in the CIN III libraries absent in the normal libraries.</p> <p>Conclusion</p> <p>Establishing a baseline of gene expression in normal cervical tissue is key for identifying changes in cancer. We demonstrate the utility of this baseline data by identifying genes with aberrant expression in CIN III when compared to normal tissue.</p

Incorporating PET information in radiation therapy planning

PET scanning, because of its impressive sensitivity and accuracy, is being incorporated into the standard staging workup for many cancers. These include lung cancer, lymphomas, head and neck cancers, and oesophageal cancers. PET often provides incremental information about the patient’s disease status, adding to the data obtained from structural imaging methods, such as, CT scan or MRI. PET commonly upstages patients into more advanced disease categories. Incorporation of PET information into the radiotherapy planning process has the potential to reduce the risks of geographic miss and can help minimise unnecessary irradiation of normal tissues. The best means of incorporating PET information into radiotherapy planning is uncertain, and considerable effort is being expended in this area of research

Up regulation in gene expression of chromatin remodelling factors in cervical intraepithelial neoplasia

<p>Abstract</p> <p>Background</p> <p>The highest rates of cervical cancer are found in developing countries. Frontline monitoring has reduced these rates in developed countries and present day screening programs primarily identify precancerous lesions termed cervical intraepithelial neoplasias (CIN). CIN lesions described as mild dysplasia (CIN I) are likely to spontaneously regress while CIN III lesions (severe dysplasia) are likely to progress if untreated. Thoughtful consideration of gene expression changes paralleling the progressive pre invasive neoplastic development will yield insight into the key casual events involved in cervical cancer development.</p> <p>Results</p> <p>In this study, we have identified gene expression changes across 16 cervical cases (CIN I, CIN II, CIN III and normal cervical epithelium) using the unbiased long serial analysis of gene expression (L-SAGE) method. The 16 L-SAGE libraries were sequenced to the level of 2,481,387 tags, creating the largest SAGE data collection for cervical tissue worldwide. We have identified 222 genes differentially expressed between normal cervical tissue and CIN III. Many of these genes influence biological functions characteristic of cancer, such as cell death, cell growth/proliferation and cellular movement. Evaluation of these genes through network interactions identified multiple candidates that influence regulation of cellular transcription through chromatin remodelling (<it>SMARCC1</it>, <it>NCOR1</it>, <it>MRFAP1 </it>and <it>MORF4L2</it>). Further, these expression events are focused at the critical junction in disease development of moderate dysplasia (CIN II) indicating a role for chromatin remodelling as part of cervical cancer development.</p> <p>Conclusion</p> <p>We have created a valuable publically available resource for the study of gene expression in precancerous cervical lesions. Our results indicate deregulation of the chromatin remodelling complex components and its influencing factors occur in the development of CIN lesions. The increase in SWI/SNF stabilizing molecule <it>SMARCC1 </it>and other novel genes has not been previously illustrated as events in the early stages of dysplasia development and thus not only provides novel candidate markers for screening but a biological function for targeting treatment.</p

Synthetic Retinoid Interventions and Outcomes in People with Cancer or Potentially Malignant Disorders of the Upper Aerodigestive Tract: A Systematic Review and Meta-analysis

Background & Aims: Retinoids may have a role in the chemoprevention of potentially malignant disorders of the upper aerodigestive tract. Therefore, we conducted a systematic review of randomised controlled trials to examine the effect of synthetic retinoid interventions in people with cancer or potentially malignant disorders of the upper digestive tract. Methods: We searched five electronic databases and reference lists to locate all eligible trials and analysed trial quality. Outcome measures were all-cause and cancer mortality, disease-free survival, second primary cancer, cancer and potentially malignant disorder recurrence and progression to cancer. Results of individual trials were combined by use of random-effects meta-analyses. Results & Conclusions: We identified 17 15 trials, eightnine in people with upper aerodigestive tract cancer and seven eight in people with potentially malignant disorders, respectively. The results provide little evidence that retinoids have a beneficial effect on disease-free survival (OR=0.74, 95% CI =0.51, 1.09), all cause mortality (OR = 1.28, 95% confidence interval [CI] =1.00 to 1.65), disease-free survival (OR=0.74, 95% CI =0.51, 1.09), recurrence of cancer (OR = 1.47, 95% CI = 0.95, 2.26), development of second primary cancers (OR = 0.96, 95% CI = 0.76, 1.20) or the progression to malignancy (OR = 0.69, 95% CIs = 0.22, 2.15). There was even a suggestion of harm for some outcomes. There was also a suggestion that retinoids may decrease the recurrence of potentially malignant disorders (OR = 0.22, 95% CIs = 0.03, 1.34). For now there is no evidence to support the use of retinoids in people with upper aerodigestive tract cancer