A perspective for biomedical data integration: Design of databases for flow cytometry

<p>Abstract</p> <p>Background</p> <p>The integration of biomedical information is essential for tackling medical problems. We describe a data model in the domain of flow cytometry (FC) allowing for massive management, analysis and integration with other laboratory and clinical information. The paper is concerned with the proper translation of the Flow Cytometry Standard (FCS) into a relational database schema, in a way that facilitates end users at either doing research on FC or studying specific cases of patients undergone FC analysis</p> <p>Results</p> <p>The proposed database schema provides integration of data originating from diverse acquisition settings, organized in a way that allows syntactically simple queries that provide results significantly faster than the conventional implementations of the FCS standard. The proposed schema can potentially achieve up to 8 orders of magnitude reduction in query complexity and up to 2 orders of magnitude reduction in response time for data originating from flow cytometers that record 256 colours. This is mainly achieved by managing to maintain an almost constant number of data-mining procedures regardless of the size and complexity of the stored information.</p> <p>Conclusion</p> <p>It is evident that using single-file data storage standards for the design of databases without any structural transformations significantly limits the flexibility of databases. Analysis of the requirements of a specific domain for integration and massive data processing can provide the necessary schema modifications that will unlock the additional functionality of a relational database.</p

Tumoral and non-tumoral trachea stenoses: evaluation with three-dimensional CT and virtual bronchoscopy

<p>Abstract</p> <p>Background</p> <p>We evaluated the ability of 3D-CT and virtual bronchoscopy to estimate trachea stenosis in comparison to conventional axial CT and fiberoptic bronchoscopy, with a view to assist thoracic surgeons in depicting the anatomical characteristics of tracheal strictures.</p> <p>Methods</p> <p>Spiral CT was performed in 16 patients with suspected tracheal stenoses and in 5 normal subjects. Tracheal stenoses due to an endoluminal neoplasm were detected in 13 patients, whilst post-intubation tracheal stricture was observed in the other 3 patients. Multiplanar reformatting (MPR), volume rendering techniques (VRT) and virtual endoscopy (VE) for trachea evaluation were applied and findings were compared to axial CT and fiberoptic bronchoscopy. The accuracy of the procedure in describing the localization and degree of stenosis was tested by two radiologists in a blinded controlled trial.</p> <p>Results</p> <p>The imaging modalities tested showed the same stenoses as the ones detected by flexible bronchoscopy and achieved accurate and non-invasive morphological characterization of the strictures, as well as additional information about the extraluminal extent of the disease. No statistically significant difference was observed between the bronchoscopic findings and the results of axial CT estimations (P = 1.0). No statistically significant differences were observed between bronchoscopic findings and the MPR, VRT and VE image evaluations (P = 0.705, 0.414 and 0.414 respectively).</p> <p>Conclusion</p> <p>CT and computed generated images may provide a high fidelity, noninvasive and reproducible evaluation of the trachea compared to bronchoscopy. They may play a role in assessment of airway patency distal to high-grade stenoses, and represent a reliable alternative method for patients not amenable to conventional bronchoscopy.</p

Ureteropelvic Junction Obstruction: An Innovative Approach Combining Metallic Approach Combining Metallic Stenting and Virtual Endoscopy

Purpose: We report our experience with auto-expandable metallic stents for treating ureteropelvic junction obstruction

Factors affecting the long-term response to tacrolimus in renal transplant patients: Pharmacokinetic and pharmacogenetic approach

<p><b>Background:</b> The aim of our study was to determine the impact of CYP3A5*1 and CYP3A5*3 on the kinetics of tacrolimus in renal transplant recipients.</p> <p><b>Material and methods: </b>Forty kidney recipients were selected to participate. Maintenance scheme consisted of tacrolimus, a purine inhibitor and a steroid. CYP3A5 genotyping was performed with PCR and RFLP. Pharmacokinetic model was developed with Linear Regression and General Linear Model repeated measures approach. The impact of sex, CYP3A5*1 allele, age at transplantation, hepatic and renal function on tacrolimus kinetics was examined.</p> <p><b>Results:</b> The frequency of CYP3A5*3/*3 and CYP3A5*1/*3 genotype was 35/40 and 5/40, respectively. No CYP3A5*1/*1 was detected. CYP3A5*1 variant was associated with significant lower TAC dose adjusted concentration at 3, 6, 12 and 36 months after transplantation. Hepatic and renal function showed a significant effect on tacrolimus dose adjusted concentration 3 months after transplantation (p=0.000 and 0.028, respectively). Sex did not show a significant impact on tacrolimus kinetics. Carriers of CYP3A5*1 allele had lower predicted measures for tacrolimus dose adjusted concentration and higher predicted measures for volume of distribution.</p> <p><b>Conclusion:</b> We proved that CYP3A5*1 carriers need higher tacrolimus dose than CYP3A5*3 homozygotes to achieve the target blood concentration.</p

Investigation of realistic PET simulations incorporating tumor patient's specificity using anthropomorphic models : creation of an oncology database

International audienceThe GATE Monte Carlo simulation toolkit is used for the implementation of realistic PET simulations incorporating tumor heterogeneous activity distributions. The reconstructed patient images include noise from the acquisition process, imaging system's performance restrictions and have limited spatial resolution. For those reasons, the measured intensity cannot be simply introduced in GATE simulations, to reproduce clinical data. Investigation of the heterogeneity distribution within tumors applying partial volume correction (PVC) algorithms was assessed. The purpose of the present study was to create a simulated oncology database based on clinical data with realistic intratumor uptake heterogeneity properties