PATRIC, the bacterial bioinformatics database and analysis resource

The Pathosystems Resource Integration Center (PATRIC) is the all-bacterial Bioinformatics Resource Center (BRC) (http://www.patricbrc.org). A joint effort by two of the original National Institute of Allergy and Infectious Diseases-funded BRCs, PATRIC provides researchers with an online resource that stores and integrates a variety of data types [e.g. genomics, transcriptomics, protein-protein interactions (PPIs), three-dimensional protein structures and sequence typing data] and associated metadata. Datatypes are summarized for individual genomes and across taxonomic levels. All genomes in PATRIC, currently more than 10 000, are consistently annotated using RAST, the Rapid Annotations using Subsystems Technology. Summaries of different data types are also provided for individual genes, where comparisons of different annotations are available, and also include available transcriptomic data. PATRIC provides a variety of ways for researchers to find data of interest and a private workspace where they can store both genomic and gene associations, and their own private data. Both private and public data can be analyzed together using a suite of tools to perform comparative genomic or transcriptomic analysis. PATRIC also includes integrated information related to disease and PPIs. All the data and integrated analysis and visualization tools are freely available. This manuscript describes updates to the PATRIC since its initial report in the 2007 NAR Database Issu

Örneğe dayalı sorgulama ile uydu görüntü içeriğinin etkileşimli sınıflandırılması

In our attempt to construct a semantic filter for satellite image content, we have built a software that allows user to indicate a few number of image regions that contains a specific geographical object, such as, a bridge, and to retrieve similar objects on the same satellite image. We are particularly interested in performing a data analysis approach based on user interaction. User can guide the classification procedure by interaction and visual observation of the results. We have applied a two step procedure for this and preliminary results show that we eliminate many true negatives while keeping most of the true positives.M.S. - Master of Scienc

CA242 and total antioxidant levels in comparison to CEA and CA 19-9 in colorectal cancer

We investigated the levels of CEA, CA 242,CA 19-9 and the total antioxidant status in 45 patients with colorectal cancer. Blood samples were obtained from 24 patients in the early postoperative phase, 16 patients in the late postoperative phase and 5 patients with recurrent disease. Statistical significances were calculated in each group by the Mann-Whitney U test. No meaningful difference was observed between the control and early or late postoperative groups. However, serum CEA levels were significantly different between the control and recurrent groups (p < 0.001). A meaningful difference was also observed between the recurrent and early (p < 0.001) and late postoperative (p = 0.015) groups, respectively. Our study shows that CEA is the only tumor marker that can be used in monitoring colorectal cancer patients

Utility of CEA in the diagnosis of patients with cancer

Serum CEA levels in patients with malignant tumors (n = 536) were investigated by using two cut-off values (> 2.5 ng/ml and >10 ng/ml). In the control group and cancer patients the mean values for serum CEA were 1.67 +/- 0.99 ng/ml and 160.43 +/- 1317.86 ng/ml, respectively. Although the specificity was high, the sensitivity of the test was poor for both cut-off values. The sensitivity was 42 % for breast cancer, 33.3 % for lung cancer and 16.7 % for gastrointestinal malignancies. Increasing the cut-off value from 2.5 ng/ml to 10 ng/ml resulted in a lower sensitivity. Our data shows that CEA should not be used as a diagnostic test in cancer patients independently. However, recording the percentage rise in a series of multiple measurements may predict disease recurrence