We developed the BaSDAS (Barcode-Seq Data Analysis System), a GUI-based pooled knockout screening data analysis system, to facilitate the analysis of pooled knockout screen data easily and effectively by researchers with limited bioinformatics skills. The BaSDAS supports the analysis of various pooled screening libraries, including yeast, human, and mouse libraries, and provides many useful statistical and visualization functions with a user-friendly web interface for convenience. We expect that BaSDAS will be a useful tool for the analysis of genome-wide screening data and will support the development of novel drugs based on functional genomics information.

We developed the BaSDAS (Barcode-Seq Data Analysis System), a GUI-based pooled knockout screening data analysis system, to facilitate the analysis of pooled knockout screen data easily and effectively by researchers with limited bioinformatics skills. The BaSDAS supports the analysis of various pooled screening libraries, including yeast, human, and mouse libraries, and provides many useful statistical and visualization functions with a user-friendly web interface for convenience. We expect that BaSDAS will be a useful tool for the analysis of genome-wide screening data and will support the development of novel drugs based on functional genomics information.

BACKGROUND: Vincristine-induced peripheral neuropathy is a major dose limiting side effect and thus effective therapeutic strategy is required. In this study, we investigated the antinociceptive effect of memantine and morphine on a vincristine-induced peripheral neuropathy model in rats. METHODS: Male Sprague-Dawley rats weighing 220-240 g were used in all experiments. Rats subsequently received daily intraperitoneal injections of either vincristine sulfate (0.1 ml/kg/day) or saline (0.1 ml/kg/day) over 12 days, immediately following behavioral testing. For assessment of mechanical allodynia, mechanical stimuli using von Frey filament was applied to the paw to measure withdrawal threshold. The effects of N-methyl-D-aspartate receptors antagonist (memantine; 2.5, 5, 10 mg/kg intraperitoneal), opioid agonist (morphine; 2.5, 5, 10 mg/kg intraperitoneal) and vehicle (saline) on vicristine-induced neuropathy were evaluated. RESULTS: Mechanical allodynia developed over the course of ten daily injections of vincristine relative to groups receiving saline at the same time. Morphine abolished the reduction in paw withdrawal threshold compared to vehicle and produced dose-responsiveness. Only the highest dose of memantine (10 mg/kg) was able to increase paw withdrawal threshold compared to vehicle. CONCLUSIONS: Systemic morphine and memantine have an antinociceptive effect on the vincristine-induced peripheral neuropathy model in rats. These results suggest morphine and memantine may be an alternative approach for the treatment of vincristine-induced peripheral neuropathic pain.
Animals ; Humans ; Hyperalgesia ; Injections, Intraperitoneal ; Male ; Memantine ; Morphine ; Neuralgia ; Peripheral Nervous System Diseases ; Rats ; Rats, Sprague-Dawley ; Receptors, N-Methyl-D-Aspartate ; Vincristine

Acute renal failure is a rare complication of acute pyelonephritis. Therefore, acute pyelonephritis is not usually considered in the differential diagnosis of acute renal failure. However, it is important to consider this entity because of potential for recovery of renal function if appropriate early antibiotics are instituted. We report a case of biopsy proven acute pyelonephritis which was manifested as acute renal failure. A 38 year old women was admitted to this hospital owing to abdominal distension and generalized edema. On admission she was started on hemodialysis because of severe hyperkalemia and marked uremic sypmtoms. She had pyuria and hematuria, but no organism was isolated at urine. We initially don't know the cause of renal failure. She was improved with antimicrobial therapy and hemodialysis. A kidney biopsy was performed on the 26th hospital day because of persistent proteinuria. Microscopic examination revealed focal tubular atrophy, necrosis or loss with heavy infilteration of leukocytes and histocytes in interstitium. Atrophic tubules contain pus casts. The patient was treated with ciprofloxacin for 4 weeks. At about 2 month follow up, proteinuria completely disappeared and serum creatinine level decreased to 1.0 mg/dL.
Acute Kidney Injury* ; Adult ; Anti-Bacterial Agents ; Atrophy ; Biopsy ; Ciprofloxacin ; Creatinine ; Diagnosis, Differential ; Edema ; Female ; Follow-Up Studies ; Hematuria ; Humans ; Hyperkalemia ; Kidney ; Leukocytes ; Necrosis ; Proteinuria ; Pyelonephritis* ; Pyuria ; Renal Dialysis ; Renal Insufficiency ; Suppuration

We report the CT findings of four cases of squamous cell carcinoma, paying special attention to the epicenter of the lesion and the pattern of bony destruction. All four patients had a past history of chronic otitis media. Squamous cell carcinoma affected mainly the hypotympanum and inferior wall of the external auditary canal, and in all cases revealed an irregular pattern of bony destruction. Irregular destruction of the tegmen tympani occurred in two cases. In cases of squamous cell carcinoma, CT findings suggesting involvement of the promontary are usually noted.
Carcinoma, Squamous Cell* ; Humans ; Otitis Media ; Temporal Bone*

Understanding complex relationships among heterogeneous biological data is one of the fundamental goals in biology. In most cases, diverse biological data are stored in relational databases, such as MySQL and Oracle, which store data in multiple tables and then infer relationships by multiple-join statements. Recently, a new type of database, called the graph-based database, was developed to natively represent various kinds of complex relationships, and it is widely used among computer science communities and IT industries. Here, we demonstrate the feasibility of using a graph-based database for complex biological relationships by comparing the performance between MySQL and Neo4j, one of the most widely used graph databases. We collected various biological data (protein-protein interaction, drug-target, gene-disease, etc.) from several existing sources, removed duplicate and redundant data, and finally constructed a graph database containing 114,550 nodes and 82,674,321 relationships. When we tested the query execution performance of MySQL versus Neo4j, we found that Neo4j outperformed MySQL in all cases. While Neo4j exhibited a very fast response for various queries, MySQL exhibited latent or unfinished responses for complex queries with multiple-join statements. These results show that using graph-based databases, such as Neo4j, is an efficient way to store complex biological relationships. Moreover, querying a graph database in diverse ways has the potential to reveal novel relationships among heterogeneous biological data.
Biology ; Data Mining

PURPOSE: Atopic dermatitis is often accompanied by food allergies which occur through skin barrier defects. Especially Staphylococcus aureus colonization can exacerbate skin barrier defects that cause sensitization and increase specific IgE (sIgE) to food. We investigated the association between skin colonization and food sIgE changes in children with atopic dermatitis. METHODS: Atopic dermatitis was diagnosed by a pediatric allergist in patients between 3 months and 3 years of age. Total IgE and sIgE to egg white, cow's milk, wheat, and peanuts were taken. Eosinophil count and eosinophil cationic protein were also taken. Comparisons were done between the groups with and without S. aureus colonization. RESULTS: It was found that 50.3% of the 294 enrolled patients had S. aureus colonization on lesional skin. Statistically significant sensitization to wheat and peanut were increased with S. aureus colonization. Statistically significant increases in sIgE (above cutoff level) were also found in egg white, milk, wheat and peanut. Higher S. aureus colony counts also increased sIgE of all foods. Methicillin-resistant S. aureus showed no statistical difference compared to methicillin-susceptible S. aureus in severity and sIgE levels. CONCLUSION: S. aureus colonization increases the risk of food sensitization in children with atopic dermatitis.
Arachis ; Child* ; Colon* ; Dermatitis, Atopic* ; Egg White ; Eosinophil Cationic Protein ; Eosinophils ; Food Hypersensitivity ; Humans ; Immunoglobulin E ; Methicillin Resistance ; Milk ; Skin ; Staphylococcus aureus* ; Staphylococcus* ; Triticum

PURPOSE: To document the radiologic characteristics of Korean Gaucher disease. MATERIALS AND METHODS: Fifteen bone marrow biopsy and laboratory data confirmed Gaucher disease patients (age 1 -21, mean 10.9 yr) wereundertaken plain X ray and MRI. Number of type I were 10, type II, 2, type III, 3. Seven were splenectomized oninitial evaluation or during follow up. Five enzyme treated patient were undertaken follow-up MR examinationduring 6 -40 month with 6 month interval. Conventional T1 and T2WI of spine and femur was performed and FMPSPGR inand out of phase image was also done. Volume of liver and spleen were measured, and bone marrow infiltration andpresence of infarction were scored according to 6 scale scoring system. Clinical data were also reviewed andcorrelated with the MR findings. RESULTS: Marrow infiltration was noted in 71.4% of all patients in MRI, while itwas in 45.7% with plain radiography. Type I group showed marrow infiltration in all but one cases, which wasparallel with ages, SGPT, and presence of osteopenia, reversely correlated with spleen size. Severe bonecomplications (infarction or fracture) were noted in 7 of 10 type I group, and 6 patients showed severe growthretardation (below 3rd percentile). Follow up MR examination of 5 patient showed decrease in liver and spleen sizefirst without bone change until 6 months. There showed bone regeneration in 2 patient 1 year after, and increasedfat signal in one patient 3.5 years after. In and out of phase images couldn't help in quantifying fatcomposition in bone marrow. CONCLUSION: Korean Gaucher patients revealed as more severe skeletal complicationsthan others reported from Western groups. MR examination is a effective modality to evaluate and monitor ofGaucher patients.
Alanine Transaminase ; Biopsy ; Bone Diseases, Metabolic ; Bone Marrow ; Bone Regeneration ; Femur ; Follow-Up Studies ; Gaucher Disease* ; Humans ; Infarction ; Liver ; Magnetic Resonance Imaging ; Metabolism ; Radiography ; Spine ; Spleen

PURPOSE: To report drug-resistant fungal keratitis that was treated with voriconazole. CASE SUMMARY: A 31-year-old man was admitted to hospital because of ocular pain, conjunctival injection, and visual weakness 7 days after LASIK surgery. At that time, his vision was counting finger at 30 cm and he presented with corneal epithelial defects, stromal infiltration, and inflammation in the anterior chamber of his eye. He was transferred to our hospital because his infection was resistant to gatifloxacin, tobramycin, amphotericin B, and natamycin eyedrops. At the time of transfer, his vision was counting finger at 30 cm and he presented with corneal epithelial defects, stromal infiltration, and hypopyon. He was treated with topical 2% voriconazole every 2 hours and the lesion improved. However, the hypopyon recurred after 12 days. He was then treated with intracameral voriconazole injection (50 microgram/0.1 cc) and topical 5% voriconazole every hour causing the hypopyon to disappear. His vision improved from counting finger to 20/40 six months after this treatment.
Adult ; Amphotericin B ; Anterior Chamber ; Eye ; Fingers ; Fluoroquinolones ; Humans ; Inflammation ; Keratectomy, Subepithelial, Laser-Assisted ; Keratitis ; Keratomileusis, Laser In Situ ; Natamycin ; Ophthalmic Solutions ; Pyrimidines ; Tobramycin ; Triazoles ; Vision, Ocular

BACKGROUND: Waist circumference is one of the key components of metabolic syndrome. Recent studies demonstrated that the reproductive profile was associated with metabolic syndrome in postmenopausal women. This study focused on the association between central obesity and age at first childbirth. It also considered other factors associated with central obesity in postmenopausal women. METHODS: This study was based on the 2013–2015 Korean National Health and Nutrition Examination Survey and involved 3,143 naturally postmenopausal women. These women were divided into three groups according to their age at first childbirth: 19 years or younger (n=252), 20–29 years (n=2,695), and 30 years or older (n=196). Multivariate analysis using logistic regression was performed to evaluate the effects of various reproductive factors, including other confounding factors. RESULTS: During adjustment for confounding factors, in the early age at first childbirth group, odds ratios (95% confidence intervals) for central obesity decreased. In the final model, younger age at first childbirth was not significantly related to central obesity (waist circumference more than 85 cm) in naturally postmenopausal women after adjusting for other confounding factors. CONCLUSION: Younger age at first childbirth was not significantly associated with central obesity after adjustment for confounding factors.
Female ; Humans ; Logistic Models ; Menopause ; Multivariate Analysis ; Nutrition Surveys* ; Obesity, Abdominal* ; Odds Ratio ; Parturition* ; Waist Circumference