Thermodynamic parameters for DNA sequences with dangling ends.

The thermodynamic contributions to duplex formation of all 32 possible single-nucleotide dangling ends on a Watson-Crick pair are reported. In most instances, dangling ends are stabilizing with free energy contributions ranging from +0.48 (GT(A)) to-0.96 kcal/mol (). In comparison, Watson-Crick nearest-neighbor increments range from -0. 58 (TA/AT) to -2.24 (GC/CG) kcal/mol. Hence, in some cases, a dangling end contributes as much to duplex stability as a Watson-Crick A-T base pair. The implications of these results for DNA probe design are discussed. Analysis of the sequence dependence of dangling-end stabilities show that the nature of the closing base pair largely determines the stabilization. For a given closing base pair, however, adenine dangling ends are always more or equally as stable as the other dangling nucleotides. Moreover, 5' dangling ends are more or equally as stabilizing as their 3' counterparts. Comparison of DNA with RNA dangling-end motifs shows that DNA motifs with 5' dangling ends contribute to stability equally or more than their RNA counterparts. Conversely, RNA 3' dangling ends contribute to stability equally or more than their DNA counterparts. This data set has been incorporated into a DNA secondary structure prediction algorithm (DNA MFOLD) (http://mfold2.wustl.edu/mfold/dna/for m1.cgi) as well as a DNA hybridization prediction algorithm (HYTHERtrade mark) (http://jsl1.chem.wayne.edu/Hyther/hythermenu .html).

Effect of image compression of digital lateral cephalograms on the reproducibility of cephalometric points.

OBJECTIVES: To evaluate the influence of JPEG quality factors 100, 80 and 60 on the reproducibility of identification of cephalometric points on images of lateral cephalograms, compared with the Digital Imaging and Communications in Medicine (DICOM) format. METHODS: The sample was composed of 30 images of digital lateral cephalograms obtained from 30 individuals (15 males and 15 females) on a phosphor plate system in DICOM format. The images were converted to JPEG with quality factors 100, 80 and 60 with the aid of software, adding up to 90 images. The 120 images (DICOM, JPEG 100, 80 and 60) were blinded and 12 cephalometric points were identified on each image by three calibrated orthodontists, using the x-y coordinate system, on a cephalometric software. RESULTS: The results revealed that identification of cephalometric points was highly reproducible, except for the point Orbitale (Or) on the x-axis. The different file formats did not present a statistically significant difference. CONCLUSIONS: JPEG images of lateral cephalograms with quality factors 100, 80 and 60 did not present alterations in the reproducibility of identification of cephalometric points compared with the DICOM format. Good reproducibility was achieved for the 12 points, except for point Or on the x-axis.

Evaluation of optical density of the midpalatal suture 3 months after surgically assisted rapid maxillary expansion.

OBJECTIVES: This study evaluated new bone formation at the midpalatal suture after surgically assisted rapid maxillary expansion (SARME) by optical density analysis. METHODS: The study population consisted of 18 patients, 10 males and 8 females. All patients presented maxillary atresia with posterior crossbite and were submitted to SARME. Maxillary occlusal radiographs were taken at three stages (before SARME, immediately after SARME and after 3 months). Three patients did not attend the session at the 3-month period for achievement of the occlusal radiography and thus were excluded, leading to a final sample of 15 patients. Two regions were selected and analysed at each stage. Region A measured 8 x 1 mm(2) and was located 1.2 cm from the tangent to the maxillary central incisors at the region of the midpalatal suture. Region B measured 5 x 9 mm(2) and was located 4.3 cm from the tangent to the maxillary central incisors at the region of the midpalatal suture. An aluminium scale (step wedge) with eight steps varying from 1 mm to 8 mm was adapted at the end of the films. Radiographs were taken on a Spectro 70X machine (Dabi Atlante, Ribeirão Preto, Brazil) set at 70 kVp and 10 mA with an exposure time of 1.0 s. Radiographs were scanned using a Power Look 1000 scanner (Umax, Taiwan, China) and a computer Dimension E510 (Dell Computer, Taiwan, China). Optical density analysis was performed after digitization of radiographs using the software Image Tool (UTHSCSA, San Antonio, TX). RESULTS: Statistical analysis of region A revealed statistically significant differences between Stages I and II (P=0.0001), Stages II and III (P=0.0001) and Stages I and III (P=0.0003). In region B, statistically significant differences were observed between Stages I and II, I and III and II and III (P=0.0018, P=0.0003 and P=0.0003, respectively). CONCLUSIONS: Optical density analysis improves post-treatment control of SARME procedures by surgeons and orthodontists. After 3 months, new bone formation at the midpalatal suture is not complete.