Improving the protein fold recognition accuracy of a reduced state-space hidden Markov model

Fold recognition is a challenging field strongly associated with protein function determination, which is crucial for biologists and the pharmaceutical industry. Hidden Markov models (HMMs) have been widely used for this purpose. In this paper we demonstrate how the fold recognition performance of a recently introduced HMM with a reduced state-space topology can be improved. Our method employs an efficient architecture and a low complexity training algorithm based on likelihood maximization. The fold recognition performance of the model is further improved in two steps. In the first step we use a smaller model architecture based on the {E,H,L} alphabet instead of the DSSP secondary structure alphabet. In the second step secondary structure information (predicted or true) is additionally used in scoring the test set sequences. The Protein Data Bank and the annotation of the SCOP database are used for the training and evaluation of the proposed methodology. The results show that the fold recognition accuracy is substantially improved in both steps. Specifically, it is increased by 2.9% in the first step to 22%. In the second step it further increases and reaches up to 30% when predicted secondary structure information is additionally used and it increases even more and reaches up to 34.7% when we use the true secondary structure. The major advantage of the proposed improvements is that the fold recognition performance is substantially increased while the size of the model and the computational complexity of scoring are decreased.     

Parietal foramina with cleidocranial dysplasia is caused by mutation in MSX2

The combination of skull defects in the form of enlarged parietal foramina (PFM) and deficient ossification of the clavicles is known as parietal foramina with cleidocranial dysplasia (PFMCCD). It is considered to be distinct from classical cleidocranial dysplasia (CCD) and is listed as a separate OMIM entry (168550). So far, only two families have been reported and the molecular basis of the disorder is unknown. We present a third family with PFMCCD, comprising four affected individuals in three generations, and demonstrate that a heterozygous tetranucleotide duplication in the MSX2 homeobox gene (505_508dupATTG) segregates with the phenotype. PFMCCD is indeed aetiologically distinct from CCD, which is caused by mutations in the RUNX2 gene, but allelic with isolated PFM, in which MSX2 mutations were previously identified. Our observations highlight the role of MSX2 in clavicular development and the importance of radiological examination of the clavicles in subjects with PFM.     

Ultrasound Findings of an Intratesticular Varicocele. Report of a New Case and Review of the Literature

The authors present a new case of intratesticular varicocele(ITV). The ultrasound findings on gray-scale and color Doppler imaging as well as the pertinent clinical manifestations are discussed. A review of the literature is also presented. According to our knowledge only 34 cases of ITV have been reported in the literature and the clinical significance of this lesion is not yet well established. This is the first reported case of infertility caused by a solely ITV, showing that the clinical implications of this entity may be more significant than previously thought.     

Endovascular repair for thoracic aortic disease: tertiary single-center experience in northwestern Greece

The purpose of this article is to report the initial experience with endovascular repair of thoracic aortic disease in a single tertiary vascular unit in northwestern Greece. Between 2003 and 2005, 16 patients were treated with endovascular techniques for various pathologies of the descending thoracic aorta. Twelve patients were treated electively and four emergently. Operative and follow-up data for a mean time of 18.4 months were retrospectively collected and analyzed. Primary technical success was obtained in 14 (87.5%) cases. No early or late deaths occurred, and there was no major operation-related complication. No paraplegia was observed in our patients. Stent graft-related complications occurred in 18.75% (one type 2 and two type 3 endoleaks), but they all had a favorable outcome. No further problems have been reported in any of our patients. Endovascular stent graft repair for diseases of the thoracic aorta seems to be a promising alternative to open surgery, especially for high-risk patients. Long-term results are needed to confirm the early benefit of this treatment option with regard to morbidity and mortality rates. The potential of this technique to be applicable even in relatively small, tertiary vascular centers might be of great benefit to patients.     

Feasibility of using real-time MRI to measure joint kinematics in 1.5T and open-bore 0.5T systems

PURPOSE: To test the feasibility and accuracy of measuring joint motion with real-time MRI in a 1.5T scanner and in a 0.5T open-bore scanner and to assess the dependence of measurement accuracy on movement speed. MATERIALS AND METHODS: We developed an MRI-compatible motion phantom to evaluate the accuracy of tracking bone positions with real-time MRI for varying movement speeds. The measurement error was determined by comparing phantom positions estimated from real-time MRI to those measured using optical motion capture techniques. To assess the feasibility of measuring in vivo joint motion, we calculated 2D knee joint kinematics during knee extension in six subjects and compared them to previously reported measurements. RESULTS: Measurement accuracy decreased as the phantom's movement speed increased. The measurement accuracy was within 2 mm for velocities up to 217 mm/s in the 1.5T scanner and 38 mm/s in the 0.5T scanner. We measured knee joint kinematics with small intraobserver variation (variance of 0.8 degrees for rotation and 3.6% of patellar width for translation). CONCLUSION: Our results suggest that real-time MRI can be used to measure joint kinematics when 2 mm accuracy is sufficient. They can also be used to prescribe the speed of joint motion necessary to achieve certain measurement accuracy.