Optimization by Monte Carlo method of photon fluence from the X-ray beam spectrum in a bimodal tomographic system.

A bimodal tomographic system with a RTW MCBM 65B-50Mo X-ray tube and a XPAD3s semiconductor camera that contains 8 bars, each one with 67,200 hybrid pixels are modeled in GEANT4 simulation code. Several conical X-ray spectra were simulated, particularly a spectrum with a peak energy of 17.4 keV used in tomography on small animals. Three phantoms located in the tomographic center were added to the simulation to evaluate the image quality and its magnification based on the simulation of different photon fluences and the rotation effect of the tomographic system with an average angular velocity of 360o per minute. The images were recorded and analyzed in 2D through ROOT software toolkit in virtual XPAD3 detector. The quantitative method 20-80% of the maximum intensity of radiation was used for obtain the contouring of the phantoms, this method is used in radiotherapy and radiodiagnosis imaging. For this purpose, the images were taken to DICOM format in order to estimate the optical density of the contours and to evaluate the optimum and minimum photon fluence to be used in the tomographic system in order to reduce the absorbed doses in the individuals. This study allowed to determine the optimal fluence to validate it with realistic fluences used in the tomographic prototype ClearPET /XPAD-CT and to make an intercomparison with the absorbed doses measured with detectors located in the tomographic center.

DNA sequence recognition by hybridization to short oligomers: experimental verification of the method on the E. coli genome.

A newly developed method for sequence recognition by hybridization to short oligomers is verified for the first time in genome-scale experiments. The experiments involved hybridization of 15,328 randomly selected 2-kb genomic clones of Escherichia coli with 997 short oligomer probes to detect complementary oligomers within the clones. Lists of oligomers detected within individual clones were compiled into a database. The database was then searched using known E. coli sequences as queries. The goal was to recognize the clones that are identical or similar to the query sequences. A total of 76 putative recognitions were tested in two separate but complementary recognition experiments. The results indicate high specificity of recognition. Current and prospective applications of this novel method are discussed.

Genome-scale DNA sequence recognition by hybridization to short oligomers.

Recently developed hybridization technology (Drmanac et al. 1994) enables economical large-scale detection of short oligomers within DNA fragments. The newly developed recognition method (Milosavljevic 1995b) enables comparison of lists of oligomers detected within DNA fragments against known DNA sequences. We here describe an experiment involving a set of 4,513 distinct genomic E.coli clones of average length 2kb, each hybridized with 636 randomly selected short oligomer probes. High hybridization signal with a particular probe was used as an indication of the presence of a complementary oligomer in the particular clone. For each clone, a list of oligomers with highest hybridization signals was compiled. The database consisting of 4,513 oligomer lists was then searched using known E.coli sequences as queries in an attempt to identify the clones that match the query sequence. Out of a total of 11 clones that were recognized at highest significance level by our method, 8 were single-pass sequenced from both ends. The single-pass sequenced ends were then compared against the query sequences. The sequence comparisons confirmed 7 out of the total of 8 examined recognitions. This experiment represents the first successful example of genome-scale sequence recognition based on hybridization data.