Biomedical subjects

Kyung-Hoon Kim

Publications and source records attributed to Kyung-Hoon Kim.

7 recordsLinked to original sources

PubMed2005

CLAGen: a tool for clustering and annotating gene sequences using a suffix tree algorithm.

Most multiple gene sequence alignment methods rely on conventions regarding the score of a multiple alignment in pairwise fashion. Therefore, as the number of sequences increases, the runtime of sequencing expands exponentially. In order to solve the problem, this paper presents a multiple sequence alignment method using a linear-time suffix tree algorithm to cluster similar sequences at one time without pairwise alignment. After searching for common subsequences, cross-matching common subsequences were generated, and sometimes inexact matching was found. So, a procedure aimed at masking the inexact cross-matching pairs was suggested here. In addition, BLAST was combined with a clustering tool in order to annotate the clusters generated by suffix tree clustering. The proposed method for clustering and annotating genes consists of the following steps: (1) construction of a suffix tree; (2) searching and overlapping common subsequences; (3) grouping subsequence pairs; (4) masking cross-matching pairs; (5) clustering gene sequences; (6) annotating gene clusters by the BLAST search. The performance of the proposed system, CLAGen, was successfully evaluated with 42 gene sequences in a TCA cycle (a citrate cycle) of bacteria. The system generated 11 clusters and found the longest subsequences of each cluster, which are biologically significant.

Algorithms↗

PubMed2005

Cervical facet joint injections in the neck and shoulder pain.

The effects from cervical facet joint injections in those patients who have been complaining cervical zygapophyseal joint pain were compared. The patients were diagnosed originally as myofascial pain syndrome (MPS), cervical herniated nucleus pulposus (HNP), and whiplash-associated disorders (WAD). Patients with the zygapophyseal joints pain of C5-6 and C6-7 were classified by their pain origin as MPS, HNP, and WAD. All patients had been undergone cervical zygapophyseal joints injections with the mixture of lidocaine and triamcinolone unilaterally or bilaterally through the posterior approach under C-arm imaging guide. The therapeutic effects were compared with reduction of numeric rating scale (NRS) of pain before and immediately after blockade and symptom-free periods in each group after 12 months. Symptom durations before injections were 16.1+/-9.6, 4.6+/-1.9 and 4.1+/-1.1 months in each MPS, HNP, and WAD groups. The reductions of NRS immediately after the blockade among the three groups were not different. However, the symptom-free duration after blockade lasted longer in the HNP group than the other two groups. In patients with cervical zygapophyseal pain syndromes, the analgesic effect from cervical facet joint blocks lasted longer in cervical HNP than MPS or WAD.

Adolescent↗

PubMed2005

Indigo carmine for the selective endoscopic intervertebral nuclectomy.

This study was undertaken to prove that the selectively infiltrated parts of nucleus pulposus with indigo carmine was degenerated parts of nucleus pulposus. This study was done, between August and October 2002, in 5 patients, who received endoscopic discectomy, due to intervertebral disc herniation. Discogram was done with mixture of indigo carmine and radioactive dye. Blue discolored part was removed through endoscope, and small undiscolored part was removed together for the control. The two parts were stained with hematoxylin and eosin and compared under the microscope. Undiscolored part was normal nucleus pulposus, composed of chondrocytes with a matrix of type II collagen and proteoglycan, mainly aggrecan. However, in discolored part, slits with destruction of collagen fiber array and ingrowth of vessel and nerve were observed. Using indigo carmine in endoscopic discectomy gives us selective removal of degenerated disc.

Chondrocytes↗

PubMed2005

Percutaneous vertebroplasty and facet joint block.

It is surprising that about 24% of patients with benign osteoporotic vertebral fracture die within a year from respiratory infection and urinary tract infection because of coughing and voiding difficulties, depending on the sites of compression fractures. We reviewed 500 patients on whom percutaneous vertebroplasty (PVP) was performed, at 612 levels in terms of patient selection, operation technique, medication, and clinical outcomes during the follow-up course for 2 yr study period. To confirm the most painful level among the multiple fracture sites, physical examination after facet joint block under the fluoroscope was the most reliable method. The mean total lumbar spine fracture threshold of bone mineral density was 0.81+/-0.05 g/cm2. The mean changes of numeric rating scale scores, Oswestry Disability Index except sex life, and Karnofsky performance status were -72.00, -83.50 and +60.62% in the osteoporosis group and -51.89, -45.02, and 69.03% in the tumor group. Complications related to the procedure were lateral spinal cord damage, transient paresthesia and transient hypotension. PVP with facet joint block is a profitable method for the vertebral compression fracture because of low risk and short duration of procedure with a high chance to result in pain relief and early mobilization.

Aged↗

PubMed2004

Distinct roles for p53, p27Kip1, and p21Cip1 during tumor development.

Mutations in p53 and reduced expression of the Cdk inhibitor p27Kip1 are frequently observed in a wide variety of human cancers, but it is not known whether alterations in these tumor suppressors interact to influence tumor progression. To address this, we measured tumor latency and spectrum in p53 and p27 single and compound mutant mice. p53-/- (null) mice developed T-cell lymphomas and soft-tissue sarcomas, while p27-/- mice developed adenomas of the pituitary and lung, but with much longer latency. The latency for tumor development in p53-/- p27-/- and p53-/- p27+/- compound mutant mice was significantly reduced, by 15-30%, compared to single mutant p53-/- mice. The tumor spectrum in the compound mutants was similar to that of p53-/- mice, and additional tumors of diverse histotypes. In tumors from p53-/- mice, p27 protein levels were reduced to a greater extent than were mRNA levels, indicating that p27 is downregulated in tumors at the transcriptional as well as post-transcriptional levels. In contrast, mice deficient in another Cdk inhibitor p21Cip1, which is also a transcriptional target and effector of p53, showed only a marginal increase in tumor predisposition in response to ENU treatment. Thus, downregulation of p27 is a common feature in p53-/- tumors. Germline deletion of one or both alleles of p27 accelerates tumor development and associated mortality in p53-/- mice, indicating potent synergy between loss of p27 and p53. Although p21 is functionally similar to both p53 and p27, it plays a lesser role in tumor suppression. These results further highlight the highly cooperative nature of p27 and its central role in tumor suppression.

Animals↗

PubMed2002

Pathway-specific tumor suppression. Reduction of p27 accelerates gastrointestinal tumorigenesis in Apc mutant mice, but not in Smad3 mutant mice.

Expression of the cyclin-dependent kinase inhibitor p27(Kip1) (p27) is frequently reduced in human colorectal cancer, and this correlates with poor patient prognosis. To clarify the role of p27 in gastrointestinal (GI) cancer, we measured p27 expression, as well as the effect of germline deletion of p27, in 3 different mouse models of GI neoplasia. p27 expression was frequently reduced in GI tumors arising in 1,2-dimethylhydrazine (DMH) treated mice, and in Apc mutant Min/+ mice, but not in GI tumors arising in Smad3 mutant mice. Germline deletion of p27 resulted in accelerated tumor development and increased tumor cell proliferation in both DMH treated and Min/+ mice, but not in Smad3 mutant mice. p27 deficiency also led to increased adenoma to adenocarcinoma progression. These results indicate that reduction of p27 cooperates with mutations in Apc but not in Smad3 during GI tumorigenesis. Thus, tumor suppression by p27 is contingent on the specific oncogenic pathway that drives tumor development.

1,2-Dimethylhydrazine↗

PubMed2002

Detection of JC virus type 1 in peripheral lymphocytes, brain and cerebrospinal fluid from two Korean AIDS patients with progressive multifocal leukoencephalopathy.

The human polyomavirus JC virus (JCV) is the etiologic agent of the fatal demyelinating central nervous system disease progressive multifocal leukoencephalopathy (PML), which occurs in 4-7% of AIDS patients. Two Korean AIDS patients with PML were assayed for JCV, and the virus was genotyped by polymerase chain reaction, DNA sequencing and phylogenetic analysis. Using immunohistochemical analysis, we also examined the distribution of JCV antigen in the brains of the patients. The JCV genome was detected in peripheral lymphocytes, brain and cerebrospinal fluid from these Korean PML patients. Although type 2 is the most common genotype in Asia, the genotype of the JCV in these two AIDS patients was characterized as type 1, which is of European origin. We found that JCV antigen was selectively detected in oligodendrocytes and astrocytes of the brains from these patients. Compared to the prototype type 1 (Mad-1), two different nucleotides (G-->C) in the KOR-1 strain identified here were found at positions 2488 and 2490 of the major capsid protein VP1 gene. In summary, this is the first report of PML in Korean AIDS patients; it is also the first isolation of JCV type 1 in PML in East Asians.

AIDS-Related Opportunistic Infections↗