In silico approach to calculate the transcript capacity

We sought the novel concept, transcript capacity (TC) and analyzed TC. Our approach to estimate TC was through an in silico method. TC refers to the capacity that a transcript exerts in a cell as enzyme or protein function after translation. We used the genome-wide association study (GWAS) beta effect and transcription level in RNA-sequencing to estimate TC. The trait was body fat percent and the transcript reads were obtained from the human protein atlas. The assumption was that the GWAS beta effect is the gene’s effect and TC was related to the corresponding gene effect and transcript reads. Further, we surveyed gene ontology (GO) in the highest TC and the lowest TC genes. The most frequent GOs with the highest TC were neuronal-related and cell projection organization related. The most frequent GOs with the lowest TC were wound-healing related and embryo development related. We expect that our analysis contributes to estimating TC in the diverse species and playing a benevolent role to the new bioinformatic analysis.

Should Cerebral Angiography Be Avoided within Three Hours after Subarachnoid Hemorrhage?

OBJECTIVE: While the risk of aneurysmal rebleeding induced by catheter cerebral angiography is a serious concern and can delay angiography for a few hours after a subarachnoid hemorrhage (SAH), current angiographic technology and techniques have been much improved. Therefore, this study investigated the risk of aneurysmal rebleeding when using a recent angiographic technique immediately after SAH.METHODS: Patients with acute SAH underwent immediate catheter angiography on admission. A four-vessel examination was conducted using a biplane digital subtraction angiography (DSA) system that applied a low injection rate and small volume of a diluted contrast, along with appropriate control of hypertension. Intra-angiographic aneurysmal rebleeding was diagnosed in cases of extravasation of the contrast medium during angiography or increased intracranial bleeding evident in flat-panel detector computed tomography scans.RESULTS: In-hospital recurrent hemorrhages before definitive treatment to obliterate the ruptured aneurysm occurred in 11 of 266 patients (4.1%). Following a univariate analysis, a multivariate analysis using a logistic regression analysis revealed that modified Fisher grade 4 was a statistically significant risk factor for an in-hospital recurrent hemorrhage (p =0.032). Cerebral angiography after SAH was performed on 88 patients ≤3 hours, 74 patients between 3–6 hours, and 104 patients >6 hours. None of the time intervals showed any cases of intra-angiographic rebleeding. Moreover, even though the DSA ≤3 hours group included more patients with a poor clinical grade and modified Fisher grade 4, no case of aneurysmal rebleeding occurred during erebral angiography.CONCLUSION: Despite the high risk of aneurysmal rebleeding within a few hours after SAH, emergency cerebral angiography after SAH can be acceptable without increasing the risk of intra-angiographic rebleeding when using current angiographic techniques and equipment.

Should Cerebral Angiography Be Avoided within Three Hours after Subarachnoid Hemorrhage?

OBJECTIVE: While the risk of aneurysmal rebleeding induced by catheter cerebral angiography is a serious concern and can delay angiography for a few hours after a subarachnoid hemorrhage (SAH), current angiographic technology and techniques have been much improved. Therefore, this study investigated the risk of aneurysmal rebleeding when using a recent angiographic technique immediately after SAH. METHODS: Patients with acute SAH underwent immediate catheter angiography on admission. A four-vessel examination was conducted using a biplane digital subtraction angiography (DSA) system that applied a low injection rate and small volume of a diluted contrast, along with appropriate control of hypertension. Intra-angiographic aneurysmal rebleeding was diagnosed in cases of extravasation of the contrast medium during angiography or increased intracranial bleeding evident in flat-panel detector computed tomography scans. RESULTS: In-hospital recurrent hemorrhages before definitive treatment to obliterate the ruptured aneurysm occurred in 11 of 266 patients (4.1%). Following a univariate analysis, a multivariate analysis using a logistic regression analysis revealed that modified Fisher grade 4 was a statistically significant risk factor for an in-hospital recurrent hemorrhage (p =0.032). Cerebral angiography after SAH was performed on 88 patients ≤3 hours, 74 patients between 3–6 hours, and 104 patients >6 hours. None of the time intervals showed any cases of intra-angiographic rebleeding. Moreover, even though the DSA ≤3 hours group included more patients with a poor clinical grade and modified Fisher grade 4, no case of aneurysmal rebleeding occurred during erebral angiography. CONCLUSION: Despite the high risk of aneurysmal rebleeding within a few hours after SAH, emergency cerebral angiography after SAH can be acceptable without increasing the risk of intra-angiographic rebleeding when using current angiographic techniques and equipment.

Genome-Wide Association Studies Associated with Backfat Thickness in Landrace and Yorkshire Pigs

Although pork quality traits are important commercially, genome-wide association studies (GWASs) have not well considered Landrace and Yorkshire pigs worldwide. Landrace and Yorkshire pigs are important pork-providing breeds. Although quantitative trait loci of pigs are well-developed, significant genes in GWASs of pigs in Korea must be studied. Through a GWAS using the PLINK program, study of the significant genes in Korean pigs was performed. We conducted a GWAS and surveyed the gene ontology (GO) terms associated with the backfat thickness (BF) trait of these pigs. We included the breed information (Yorkshire and Landrace pigs) as a covariate. The significant genes after false discovery rate (<0.01) correction were AFG1L, SCAI, RIMS1, and SPDEF. The major GO terms for the top 5% of genes were related to neuronal genes, cell morphogenesis and actin cytoskeleton organization. The neuronal genes were previously reported as being associated with backfat thickness. However, the genes in our results were novel, and they included ZNF280D, BAIAP2, LRTM2, GABRA5, PCDH15, HERC1, DTNBP1, SLIT2, TRAPPC9, NGFR, APBB2, RBPJ, and ABL2. These novel genes might have roles in important cellular and physiological functions related to BF accumulation. The genes related to cell morphogenesis were NOX4, MKLN1, ZNF280D, BAIAP2, DNAAF1, LRTM2, PCDH15, NGFR, RBPJ, MYH9, APBB2, DTNBP1, TRIM62, and SLIT2. The genes that belonged to actin cytoskeleton organization were MKLN1, BAIAP2, PCDH15, BCAS3, MYH9, DTNBP1, ABL2, ADD2, and SLIT2.

Estimation of the Genetic Substitution Rate of Hanwoo and Holstein Cattle Using Whole Genome Sequencing Data

Despite the importance of mutation rate, some difficulties exist in estimating it. Next-generation sequencing (NGS) data yields large numbers of single-nucleotide polymorphisms, which can make it feasible to estimate substitution rates. The genetic substitution rates of Hanwoo and Holstein cattle were estimated using NGS data. Our main findings was to calculate the gene's substitution rates. Through estimation of genetic substitution rates, we found: diving region of altered substitution density exists. This region may indicate a boundary between protected and unprotected genes. The protected region is mainly associated with the gene ontology terms of regulatory genes. The genes that distinguish Hanwoo from Holstein in terms of substitution rate predominantly have gene ontology terms related to blood and circulatory system. This might imply that Hanwoo and Holstein evolved with dissimilar mutation rates and processes after domestication. The difference in meat quality between Hanwoo and Holstein could originate from differential evolution of the genes related to these blood and circulatory system ontology terms.

The Usage of an SNP-SNP Relationship Matrix for Best Linear Unbiased Prediction (BLUP) Analysis Using a Community-Based Cohort Study

Best linear unbiased prediction (BLUP) has been used to estimate the fixed effects and random effects of complex traits. Traditionally, genomic relationship matrix-based (GRM) and random marker-based BLUP analyses are prevalent to estimate the genetic values of complex traits. We used three methods: GRM-based prediction (G-BLUP), random marker-based prediction using an identity matrix (so-called single-nucleotide polymorphism [SNP]-BLUP), and SNP-SNP variance-covariance matrix (so-called SNP-GBLUP). We used 35,675 SNPs and R package "rrBLUP" for the BLUP analysis. The SNP-SNP relationship matrix was calculated using the GRM and Sherman-Morrison-Woodbury lemma. The SNP-GBLUP result was very similar to G-BLUP in the prediction of genetic values. However, there were many discrepancies between SNP-BLUP and the other two BLUPs. SNP-GBLUP has the merit to be able to predict genetic values through SNP effects.

Anterior Choroidal Artery Aneurysm Surgery: Ischemic Complications and Clinical Outcomes Revisited

OBJECTIVE: Surgical results for anterior choroidal artery (AChA) aneurysms have previously been reported as unsatisfactory due to inadvertent occlusion of the AChA, while the low incidence of AChA aneurysms hampers the accumulation of surgical experience. The authors reviewed their related surgical experience to document the ischemic complications and surgical outcomes. METHODS: Identification of the AChA at its origin by rigorous visual scrutiny, careful microdissection, and meticulous clip placement to avoid the AChA origin are all crucial surgical maneuvers. A retrospective review of a surgical series of 62 consecutive cases of an AChA aneurysm between 2004 and 2012 was performed. RESULTS: All patients, except for five (8.1%) with a small residual neck, showed complete aneurysm obliteration in postoperative angiographic evaluations. There was no incidence of procedure-related permanent AChA syndrome or oculomotor nerve palsy, while three (4.8%) patients suffered from transient AChA syndrome. The clinical outcomes [the 3-month modified Rankin Scale (mRS)] of the patients were related to their preoperative World Federation of Neurologic Surgeons (WFNS) grade. As regards the 3-month mRS, significant differences were found between patients with an unruptured aneurysm (WFNS grade 0; n=20), good-grade subarachnoid hemorrhage (WFNS grade 1-3; n=30), and poor-grade subarachnoid hemorrhage (WFNS grade 4-5; n=4). CONCLUSION: In surgical treatment of AChA aneurysms, a risk of AChA insufficiency can be minimized by taking every precaution to preserve the AChA patency and intraoperative monitoring. In addition, the surgical outcome is primarily determined by the preoperative clinical state.

Clinical Manifestation and Differential Diagnosis of Thyroid Follicular Neoplasm / 대한이비인후과학회지

BACKGROUND AND OBJECTIVES: A preoperative differential diagnosis between follicular adenoma and follicular carcinoma of thyroid is very difficult, and the standard basis for distinction is the presence of capsular and/or vascular invasion. In this study, we analyzed the findings of preoperative tests and clinical features to facilitate the differential diagnosis and treatment of the follicular neoplasm. SUBJECTS AND METHOD: A retrospective review of medical records was carried out on 104 patients who had undergone thyroid surgery and had been diagnosed with thyroid follicular adenoma or carcinoma from 1995 through 2004. The final pathologic diagnosis was compared to the various clinical data including the result of fine needle aspiration cytology (FNAC) and ultrasonographic findings. RESULTS: Of total 104 cases, 82 were follicular adenoma and 22 were follicular carcinoma. The incidence of carcinoma was significantly higher in male than in female. The result of FNAC were divided into 6 cytodiagnostic groups, namely, inadequate, colloid nodule without atypia, colloid nodule with atypia, follicular neoplasm without atypia, follicular neoplasm with atypia, or highly suspicious malignancy. The incidence of carcinoma was significantly higher in the groups with atypia such as colloid nodule with atypia, follicular neoplasm with atypia, and highly suspicious malignancy than in the groups without atypia. The incidence of follicular carcinoma was significantly higher in ill-defined marginal cases. Calcification on ultrasonography also indicated the possibility of malignancy. CONCLUSION: The incidence of follicular carcinoma was significantly high in male patients, atypia in FNAC, and ill-defined margin and calcification on ultrasonography.

Differential Regulation of Antioxidant Enzymes during Monocyte Differentiation / 대한면역학회지

Antioxidant enzymes levels were determined in monocytes during phorbol myristate acetate (PMA)-induced differentiation. PMA induced the differentiation of a human monocytic leukemia cell line THP-1 into macrophage-like cells as indicated by activity of acid phosphatase and morphological changes. The level of Mn-superoxide dismutase (SOD) was selectively increased in PMA-treated THP-1 cells after one day of culture, while the levels of Cu/Zn-SOD and catalase were progressively decreased by Western blot analysis. In contrast, levels of Cu/Zn-SOD and catalase protein and enzyme activitiy remained unchanged in THP-1 cells after transforming growth factor-p, treatment. Cu/Zn-SOD is oxidatively inactivated by exposure to H,O, which is produced by PMA-treated THP-1 cells, and then the inactivated enzyme undergoes proteolysis and fragmentation as analyzed by radiolabeled method. Thus monocytes have a coordinated system for synthesis and degradation of antioxidant enzymes during PMA-induced differentiation.