Biomedical subjects

Zafer Aydin

Publications and source records attributed to Zafer Aydin.

4 recordsLinked to original sources

PubMed2006

Protein secondary structure prediction for a single-sequence using hidden semi-Markov models.

BACKGROUND: The accuracy of protein secondary structure prediction has been improving steadily towards the 88% estimated theoretical limit. There are two types of prediction algorithms: Single-sequence prediction algorithms imply that information about other (homologous) proteins is not available, while algorithms of the second type imply that information about homologous proteins is available, and use it intensively. The single-sequence algorithms could make an important contribution to studies of proteins with no detected homologs, however the accuracy of protein secondary structure prediction from a single-sequence is not as high as when the additional evolutionary information is present. RESULTS: In this paper, we further refine and extend the hidden semi-Markov model (HSMM) initially considered in the BSPSS algorithm. We introduce an improved residue dependency model by considering the patterns of statistically significant amino acid correlation at structural segment borders. We also derive models that specialize on different sections of the dependency structure and incorporate them into HSMM. In addition, we implement an iterative training method to refine estimates of HSMM parameters. The three-state-per-residue accuracy and other accuracy measures of the new method, IPSSP, are shown to be comparable or better than ones for BSPSS as well as for PSIPRED, tested under the single-sequence condition. CONCLUSIONS: We have shown that new dependency models and training methods bring further improvements to single-sequence protein secondary structure prediction. The results are obtained under cross-validation conditions using a dataset with no pair of sequences having significant sequence similarity. As new sequences are added to the database it is possible to augment the dependency structure and obtain even higher accuracy. Current and future advances should contribute to the improvement of function prediction for orphan proteins inscrutable to current similarity search methods.

Algorithms↗

PubMed2005

Schwannoma of the conus medullaris.

We report a rare case of schwannoma of the conus medullaris. A 38-year-old female presented with pain and numbness in her lower limbs. Magnetic resonance imaging confirmed a heterogenous tumour of the conus medullaris. A subtotal resection was performed and histology confirmed schwannoma. The literature regarding these rare tumours, and their cell of origin, is reviewed.

Adult↗

PubMed2005

Electron microscopic study of the progeny of ependymal stem cells in the normal and injured spinal cord.

BACKGROUND: Spinal cord injury (SCI) is a common and often irreversible lesion that can incapacitate patients. Precursor cells in the spinal cord proliferate in response to trauma, and this proliferation can be enhanced by exogenous stimuli such as specific growth factors. In the present study, we examined electron microscopic detection of the proliferation, distribution, and phenotypic fate of these precursor cells in the injured adult rat spinal cord. METHODS: Adult female Sprague-Dawley rats weighing 250 to 300 g were divided into 3 groups. The first group consisted of spinal cord-injured animals with application of a 2.4-g clip extradurally around the spinal cord at the T1 level. A 26-g clip was applied in the second group. The third group included normal uninjured animals. Rats were sacrificed at 3 days, 3 weeks, and 6 weeks after injury. A segment of the spinal cord, 0.4 cm in length, encompassing the injury site was removed and was prepared for electron microscopy. RESULTS: Three days after mild injury (2.4-g clip), ependymal cells had begun to proliferate and had migrated from the central canal. They had a tendency to surround perivascular spaces close to the axons. The central canal rostral to the lesion site was widely dilated at 6 weeks postoperative in the moderately injured groups (26-g clip). The layer of ependymal cells lining the dilated canal showed reduction in cell height. Traumatic syringomyelic cavities were observed in all of the animals. There was an active proliferative response of the ependymal cells to injury. Large clusters of displaced ependymal cells associated with the dilated central canal were observed. Rests of ependymal cells were observed remote from the central canal with a tendency to form rosettes and accessory lumina 6 weeks after trauma. Fascicles of 3 to 8 fibers enclosed within an ependymal cell were a common finding among the ependymal clusters. There were also debris and some ependymal cells in the lumen. CONCLUSION: Trauma induces active proliferation of precursor cells in the ependymal region. These cells may replace neural tissue lost to SCI and may assist in axonal regeneration.

Animals↗

PubMed2005

Primary intradural extramedullary hydatid cyst.

Spinal hydatid cysts account for 1% of all cases of hydatid disease; primary intradural hydatid cysts are uncommon. We present a case of pathologically confirmed intradural spinal cyst hydatid in an otherwise healthy patient who showed no other evidence of systemic hydatid cyst disease. The patient presented with back pain, paraparesis, and weakness. An intradural extramedullary cystic lesion was identified with magnetic resonance imaging and was shown to be a hydatid cyst by histopathologic examination after surgical removal. To our knowledge, this is the 25th case of hydatid cyst at an intradural extramedullary location reported in the literature.

Adult↗