Comparison of the Aptima HIV-1 Quant Dx Assay with the COBAS\uae AmpliPrep/COBAS\uae TaqMan\uae HIV-1 v2.0 Test for HIV-1 Viral Load Quantification in Plasma Samples from HIV-1-Infected Patients.

Background and aims: HIV\u20101 RNA viral load (VL) in plasma samples of HIV\u20101\u2013positive patients is used to assess the level of viral replication, the risk of disease progression, and the response and efficacy to antiretroviral treatment. Knowing the performance of different tests for HIV\u20101 RNA detection is, therefore, important for clinical care. This study compared the performance of the recently introduced Aptima HIV\u20101 Quant Dx assay (Hologic, Inc) and the standard COBAS AmpliPrep/COBAS TaqMan HIV\u20101 v2.0 Test (CAP/CTM2) (Roche Molecular System, Inc) for HIV\u20101 RNA quantitation. Methods: Assay performance was assessed using 335 clinical samples, a standard HIV\u20101 low VL panel, and 2 diluted samples from well\u2010characterized patients infected with different HIV\u20101 subtypes tested in 5 replicates over 3 days. All samples were tested on both assays to evaluate inter\u2010assay agreement, both qualitatively and quantitively. Altogether, we evaluated assay sensitivity, linearity, accuracy, precision, repeatability, and reproducibility. Results: Assay agreement for qualitative results in 335 clinical samples was fair (80.6%). Correlation of quantitative assay results (n = 164) was excellent (R2 = 0.97), with 96.3% of the results within the 95% limit of assay agreement ( 120.42 to +0.86 log), and 98.8% within 1 log of each other. Aptima\u2010HIV\u20101 yielded results, on average, 0.22 log higher than CAP/CTM2. Both assays accurately quantitated the HIV\u20101 standard at low VL (R2 65 0.94), with all samples within 0.5 log of the target. Conclusion: Aptima\u2010HIV\u20101 assay demonstrated sensitivity, accuracy, reproducibility, and precision for the detection and quantitation of HIV\u20101 RNA across a wide dynamic range of VLs. Its performance, together with full automation and high throughput, suggests that Aptima\u2010HIV\u20101 could be a suitable assay for reliable monitoring of HIV\u20101 VL in patients undergoing treatment

Development of C-TILDA: A modified TILDA method for reservoir quantification in long term treated patients infected with subtype C HIV-1

A better characterization of the HIV reservoir is pivotal for the development of effective eradication strategies. Accurate quantification of the latent reservoir remains challenging. Starting from a regular blood draw, the Tat/Rev induced limiting dilution assay (TILDA) combines serial dilution of CD4+ T cells with a PCR-based detection of HIV-1 spliced mRNA produced upon cell stimulation. Here we adapted the original protocol for HIV-1 subtype B to detect tat/rev mRNAs transcribed from reactivated latently infected cells in long term suppressed patients infected with HIV-1 subtype C. Given the heterogeneity of global HIV epidemiology, it is pivotal to develop assays with optimal performances also in patients infected with non-B subtypes. We observed that, in these patients infected with subtype C virus, the HIV reservoir quantified by TILDA correlates with both the time of virological suppression and CD4/CD8 ratio

Gene expression meta-analysis identifies metastatic pathways and transcription factors in breast cancer

<p>Abstract</p> <p>Background</p> <p>Metastasis is believed to progress in several steps including different pathways but the determination and understanding of these mechanisms is still fragmentary. Microarray analysis of gene expression patterns in breast tumors has been used to predict outcome in recent studies. Besides classification of outcome, these global expression patterns may reflect biological mechanisms involved in metastasis of breast cancer. Our purpose has been to investigate pathways and transcription factors involved in metastasis by use of gene expression data sets.</p> <p>Methods</p> <p>We have analyzed 8 publicly available gene expression data sets. A global approach, "gene set enrichment analysis" as well as an approach focusing on a subset of significantly differently regulated genes, GenMAPP, has been applied to rank pathway gene sets according to differential regulation in metastasizing tumors compared to non-metastasizing tumors. Meta-analysis has been used to determine overrepresentation of pathways and transcription factors targets, concordant deregulated in metastasizing breast tumors, in several data sets.</p> <p>Results</p> <p>The major findings are up-regulation of cell cycle pathways and a metabolic shift towards glucose metabolism reflected in several pathways in metastasizing tumors. Growth factor pathways seem to play dual roles; EGF and PDGF pathways are decreased, while VEGF and sex-hormone pathways are increased in tumors that metastasize. Furthermore, migration, proteasome, immune system, angiogenesis, DNA repair and several signal transduction pathways are associated to metastasis. Finally several transcription factors e.g. E2F, NFY, and YY1 are identified as being involved in metastasis.</p> <p>Conclusion</p> <p>By pathway meta-analysis many biological mechanisms beyond major characteristics such as proliferation are identified. Transcription factor analysis identifies a number of key factors that support central pathways. Several previously proposed treatment targets are identified and several new pathways that may constitute new targets are identified.</p

Obesity and prevalence of chronic diseases in the 1999–2000 Italian National Health Survey

<p>Abstract</p> <p>Background</p> <p>There is consistent evidence that obesity is a correlate of mortality. Less information is available about the relation between body weight and the prevalence of diseases. We investigated the prevalence of overweight and obesity and their relationship with 14 groups of chronic diseases in a Mediterranean population using data from the Italian National Survey collected in 1999–2000.</p> <p>Methods</p> <p>A sample of 52,300 families was randomly selected using a complex stratified multistage design, within strata of geographical areas, municipalities, and household sizes, to produce estimates representative of the whole Italian population. Data were collected by civil servants both with an interview and a self-reported questionnaire.</p> <p>Results</p> <p>The present study documents an increase in the prevalence of overweight among Italian adults in the last decades and an increased prevalence of several chronic conditions in obese or overweight individuals. A general pattern of a positive association between excess weight and chronic disease was observed for both sexes. The ratio of the prevalences of cardiovascular diseases, diabetes and chronic respiratory diseases was higher in obese versus normal-weight individuals in the age group under 45 years.</p> <p>Conclusion</p> <p>To reduce the prevalence of chronic diseases a policy promoting a healthier individual lifestyle is becoming more and more desirable.</p

Expression signatures of TP53 mutations in serous ovarian cancers

<p>Abstract</p> <p>Background</p> <p>Mutations in the <it>TP53 </it>gene are extremely common and occur very early in the progression of serous ovarian cancers. Gene expression patterns that relate to mutational status may provide insight into the etiology and biology of the disease.</p> <p>Methods</p> <p>The <it>TP53 </it>coding region was sequenced in 89 frozen serous ovarian cancers, 40 early stage (I/II) and 49 advanced stage (III/IV). Affymetrix U133A expression data was used to define gene expression patterns by mutation, type of mutation, and cancer stage.</p> <p>Results</p> <p>Missense or chain terminating (null) mutations in <it>TP53 </it>were found in 59/89 (66%) ovarian cancers. Early stage cancers had a significantly higher rate of null mutations than late stage disease (38% vs. 8%, p < 0.03). In advanced stage cases, mutations were more prevalent in short term survivors than long term survivors (81% vs. 30%, p = 0.0004). Gene expression patterns had a robust ability to predict <it>TP53 </it>status within training data. By using early versus late stage disease for out of sample predictions, the signature derived from early stage cancers could accurately (86%) predict mutation status of late stage cancers.</p> <p>Conclusions</p> <p>This represents the first attempt to define a genomic signature of <it>TP53 </it>mutation in ovarian cancer. Patterns of gene expression characteristic of <it>TP53 </it>mutation could be discerned and included several genes that are known p53 targets or have been described in the context of expression signatures of <it>TP53 </it>mutation in breast cancer.</p

A Prognostic Model for Estimating the Time to Virologic Failure in HIV-1 Infected Patients Undergoing a New Combination Antiretroviral Therapy Regimen

<p>Abstract</p> <p>Background</p> <p>HIV-1 genotypic susceptibility scores (GSSs) were proven to be significant prognostic factors of fixed time-point virologic outcomes after combination antiretroviral therapy (cART) switch/initiation. However, their relative-hazard for the time to virologic failure has not been thoroughly investigated, and an expert system that is able to predict how long a new cART regimen will remain effective has never been designed.</p> <p>Methods</p> <p>We analyzed patients of the Italian ARCA cohort starting a new cART from 1999 onwards either after virologic failure or as treatment-naïve. The time to virologic failure was the endpoint, from the 90^thday after treatment start, defined as the first HIV-1 RNA > 400 copies/ml, censoring at last available HIV-1 RNA before treatment discontinuation. We assessed the relative hazard/importance of GSSs according to distinct interpretation systems (Rega, ANRS and HIVdb) and other covariates by means of Cox regression and random survival forests (RSF). Prediction models were validated via the bootstrap and c-index measure.</p> <p>Results</p> <p>The dataset included 2337 regimens from 2182 patients, of which 733 were previously treatment-naïve. We observed 1067 virologic failures over 2820 persons-years. Multivariable analysis revealed that low GSSs of cART were independently associated with the hazard of a virologic failure, along with several other covariates. Evaluation of predictive performance yielded a modest ability of the Cox regression to predict the virologic endpoint (c-index≈0.70), while RSF showed a better performance (c-index≈0.73, p < 0.0001 vs. Cox regression). Variable importance according to RSF was concordant with the Cox hazards.</p> <p>Conclusions</p> <p>GSSs of cART and several other covariates were investigated using linear and non-linear survival analysis. RSF models are a promising approach for the development of a reliable system that predicts time to virologic failure better than Cox regression. Such models might represent a significant improvement over the current methods for monitoring and optimization of cART.</p

Gender differences in the use of cardiovascular interventions in HIV-positive persons; the D:A:D Study

Peer reviewe

Effects of feed additives on rumen fungi

International audienc

Prevalence of sub-clinical vertebral fractures in HIV-infected patients.

Although the increased prevalence of low bone mineral density among HIV-infected patients has raised concern for increased fracture risk, few investigations have evaluated fracture rates. Increasing evidence indicates that HIV patients are at higher risk of osteoporotic fractures compared to the general population. This is a very important issue, because fragility fractures are complications with a significant prognostic value. Our study performed lateral spine X-ray to assess the prevalence of sub-clinical vertebral fractures in 202 HIV patients. Factors associated with vertebral fractures were also investigated. The prevalence of vertebral fractures was significantly high (23.3%): 14 subjects had SDI (spine deformity index)= 1, 22 SDI=2-3 and 11 SDI >4. Differences in the prevalence of vertebral fractures between naive and ART experienced patients was 18% vs. 24%, respectively. Furthermore, patients had a high prevalence of severe and multiple fractures; in 19 patients (40%) fractures involved multiple vertebrae. Patients with vertebral fractures were significantly older, with renal insufficiency and steroid use more frequently than subjects with no fractures. Our data suggest that the prevalence of vertebral fractures in HIV infection may be higher than expected, and lateral spine X-ray has a role in the screening of bone disease, at least in patients with a significant risk of fragility fractures