Introduction of the Korea BioData Station (K-BDS) for sharing biological data

A wave of new technologies has created opportunities for the cost-effective generation of high-throughput profiles of biological systems, foreshadowing a "data-driven science" era. The large variety of data available from biological research is also a rich resource that can be used for innovative endeavors. However, we are facing considerable challenges in big data deposition, integration, and translation due to the complexity of biological data and its production at unprecedented exponential rates. To address these problems, in 2020, the Korean government officially announced a national strategy to collect and manage the biological data produced through national R&D fund allocations and provide the collected data to researchers. To this end, the Korea Bioinformation Center (KOBIC) developed a new biological data repository, the Korea BioData Station (K-BDS), for sharing data from individual researchers and research programs to create a data-driven biological study environment. The K-BDS is dedicated to providing free open access to a suite of featured data resources in support of worldwide activities in both academia and industry.

Inhibition of melanogenesis by sodium 2-mercaptoethanesulfonate

Sodium 2-mercaptoethanesulfonate (mesna) is a protective agent that is widely used in medicine because of its antioxidant effects. Recently, reactive oxygen species (ROS) were shown to increase pigmentation. Thus, ROS scavengers and inhibitors of ROS production may suppress melanogenesis. Forkhead box-O3a (FoxO3a) is an antimelanogenic factor that mediates ROS-induced skin pigmentation. In this study, we aimed to investigate the whitening effect of mesna and the signaling mechanism mediating this effect. Human melanoma (MNT-1) cells were used in this study. mRNA and protein expression were measured by real-time quantitative PCR and Western blotting analysis to track changes in FoxO3a-related signals induced by mesna. An immunofluorescence assay was performed to determine the nuclear translocation of FoxO3a. When MNT-1 melanoma cells were treated with mesna, melanin production and secretion decreased. These effects were accompanied by increases in FoxO3a activation and nuclear translocation, resulting in downregulation of four master genes of melanogenesis: MITF, TYR, TRP1, and TRP2. We found that mesna, an antioxidant and radical scavenger, suppresses melanin production and may therefore be a useful agent for the clinical treatment of hyperpigmentation disorders.

Inhibition of melanogenesis by sodium 2-mercaptoethanesulfonate

Sodium 2-mercaptoethanesulfonate (mesna) is a protective agent that is widely used in medicine because of its antioxidant effects. Recently, reactive oxygen species (ROS) were shown to increase pigmentation. Thus, ROS scavengers and inhibitors of ROS production may suppress melanogenesis. Forkhead box-O3a (FoxO3a) is an antimelanogenic factor that mediates ROS-induced skin pigmentation. In this study, we aimed to investigate the whitening effect of mesna and the signaling mechanism mediating this effect. Human melanoma (MNT-1) cells were used in this study. mRNA and protein expression were measured by real-time quantitative PCR and Western blotting analysis to track changes in FoxO3a-related signals induced by mesna. An immunofluorescence assay was performed to determine the nuclear translocation of FoxO3a. When MNT-1 melanoma cells were treated with mesna, melanin production and secretion decreased. These effects were accompanied by increases in FoxO3a activation and nuclear translocation, resulting in downregulation of four master genes of melanogenesis: MITF, TYR, TRP1, and TRP2. We found that mesna, an antioxidant and radical scavenger, suppresses melanin production and may therefore be a useful agent for the clinical treatment of hyperpigmentation disorders.

Comparison of the MGISEQ-2000 and Illumina HiSeq 4000 sequencing platforms for RNA sequencing

Currently, Illumina sequencers are the globally leading sequencing platform in the next-generation sequencing market. Recently, MGI Tech launched a series of new sequencers, including the MGISEQ-2000, which promise to deliver high-quality sequencing data faster and at lower prices than Illumina’s sequencers. In this study, we compared the performance of two major sequencers (MGISEQ-2000 and HiSeq 4000) to test whether the MGISEQ-2000 sequencer delivers high-quality sequence data as suggested. We performed RNA sequencing of four human colon cancer samples with the two platforms, and compared the sequencing quality and expression values. The data produced from the MGISEQ-2000 and HiSeq 4000 showed high concordance, with Pearson correlation coefficients ranging from 0.98 to 0.99. Various quality control (QC) analyses showed that the MGISEQ-2000 data fulfilled the required QC measures. Our study suggests that the performance of the MGISEQ-2000 is comparable to that of the HiSeq 4000 and that the MGISEQ-2000 can be a useful platform for sequencing.

Polydeoxyribonucleotides Improve Diabetic Wound Healing in Mouse Animal Model for Experimental Validation

BACKGROUND: Wound healing mechanisms is believed to have effects similar to wound healing disorders in diabetic patients, including abnormal inflammatory cells, angiogenesis disorders, and reduced collagen synthesis. Therefore, reestablishment of structural and promoted angiogenesis could be beneficial to promote wound healing process. OBJECTIVE: Therefore, we investigated whether the polydeoxyribonucleotide (PDRN) that was self-production in Korea, could be useful as an intradermal injection for promoting wound healing. Also, we validate for wound healing effect of PDRN using healing-impaired (db/db) mice. METHODS: In this study, we confirmed the effects of PDRN by creating wound models in in vitro and in vivo model. Using an in vitro wound healing assay, we observed that PDRN stimulated closure of wounded monolayers of human fibroblast cells. PDRN (8.25 mg/ml) or phosphate-buffered saline (0.9% NaCl) was injected once daily into the dermis adjacent to the wound for 12 days after skin injury. RESULTS: Time course observations revealed that mice treated with PDRN showed accelerated wound closure and epidermal and dermal regeneration, enhanced angiogenesis. The wound area and depth decreased at 3, 6, 9, and 12 days after skin injury. Histological evaluation showed an increase of vascular endothelial growth factor, CD31, and collagen fibers in the PDRN group compared with the control group, indicating that PDRN was effective in the treatment of delayed wound healing caused by diabetes. CONCLUSION: This study suggests that our PDRN has a wound healing effect in transgenic animal models with cells and diabetes through angiogenesis.

Effects of cholesterol levels on outcomes of out-of-hospital cardiac arrest: a cross-sectional study

OBJECTIVE: High cholesterol level is a risk factor for coronary artery disease, and coronary artery disease is a major risk factor for out-of-hospital cardiac arrest (OHCA). However, the effect of cholesterol level on outcomes of OHCA has been poorly studied. This study aimed to determine the effect of cholesterol level on outcomes of OHCA.METHODS: This cross-sectional study used the CAPTURES (Cardiac Arrest Pursuit Trial with Unique Registration and Epidemiologic Surveillance) project database in Korea. Multivariable conditional logistic regression analysis was performed to estimate the effect of cholesterol level on outcomes in OHCA.RESULTS: In all, 584 cases of OHCA were analyzed; those with cholesterol levels <120 mg/dL were classified as having low total cholesterol (TC) (n=197), those with levels ranging from 120–199 mg/dL as middle TC (n=322), and those with ≥200 mg/dL as high TC (n=65). Compared to low TC, more patients with middle TC and high TC survived to discharge (9.1% vs. 22.0% and 26.2%, respectively, P=0.001). The good cerebral performance category also increased in that order (4.1 % vs. 14.6% and 23.1%, respectively, P≤0.001). Comparing middle TC and high TC with low TC, adjusted odds ratios (95% confidence intervals) were 1.97 (1.06 to 3.64) and 2.53 (1.08 to 5.92) for survival to discharge, respectively, and 2.53 (1.07 to 5.98) and 4.73 (1.63 to 13.71) for good neurological recovery, respectively.CONCLUSION: Higher cholesterol is associated with better outcomes in OHCA; cholesterol level is a good predictor of outcomes of OHCA.

Reduction of the Isolated Anterior Wall of the Maxillary Sinus Fracture with Double Urinary Balloon Catheters and Fibrin Glue

BACKGROUND: Conservative treatment is performed for isolated anterior wall of the maxillary sinus fractures, in many cases when the fracture is clinically not severe and asymptomatic. Despite the absence of symptoms, complications such as sinusitis, rhinitis, and chronic purulent secretion may develop; therefore, successful reduction is required. We attempted to reduce the risk of complications using an alternative technique: reduction of the fracture with two urinary balloon catheters inserted through the maxillary ostium and fixation using fibrin glue, which minimizes the damage to the bony fragments and sinus mucosa. METHODS: In this study, 38 patients who were diagnosed with an isolated anterior wall of the maxillary sinus fracture at our hospital between January 2014 and January 2017 were enrolled. The fracture site was exposed via the Caldwell-Luc approach followed by reduction through the insertion of two urinary balloon catheters using a nasal endoscope and fixation with fibrin glue. The sex, cause of fracture, physical examination, and presence of complications were examined and patient's medical records and facial bone computed tomography scans were analyzed. RESULTS: Radiological evaluation showed that there was no evidence of collapsed reduction fragments. Although some patients had remaining symptoms of hypoesthesia (15%; 3 patients), there were no complications such as infection, rhinitis, sinusitis, and chronic purulent secretion at the surgical site. CONCLUSION: In this study, we present an alternative surgical technique using two urinary balloon catheters and fibrin glue for the successful reconstruction of an isolated anterior wall of the maxillary sinus fracture. This technique enables precise restoration with a reduced risk of complications.

Gold thread implantation promotes hair growth in human and mice / 한국실험동물학회지

Thread-embedding therapy has been widely applied for cosmetic purposes such as wrinkle reduction and skin tightening. Particularly, gold thread was reported to support connective tissue regeneration, but, its role in hair biology remains largely unknown due to lack of investigation. When we implanted gold thread and Happy Lift™ in human patient for facial lifting, we unexpectedly found an increase of hair regrowth in spite of no use of hair growth medications. When embedded into the depilated dorsal skin of mice, gold thread or polyglycolic acid (PGA) thread, similarly to 5% minoxidil, significantly increased the number of hair follicles on day 14 after implantation. And, hair re-growth promotion in the gold threadimplanted mice were significantly higher than that in PGA thread group on day 11 after depilation. In particular, the skin tissue of gold thread-implanted mice showed stronger PCNA staining and higher collagen density compared with control mice. These results indicate that gold thread implantation can be an effective way to promote hair re-growth although further confirmatory study is needed for more information on therapeutic mechanisms and long-term safety.

Tattoo Granuloma Restricted to Red Dyes

No abstract available.

A ChIP-Seq Data Analysis Pipeline Based on Bioconductor Packages

Nowadays, huge volumes of chromatin immunoprecipitation-sequencing (ChIP-Seq) data are generated to increase the knowledge on DNA-protein interactions in the cell, and accordingly, many tools have been developed for ChIP-Seq analysis. Here, we provide an example of a streamlined workflow for ChIP-Seq data analysis composed of only four packages in Bioconductor: dada2, QuasR, mosaics, and ChIPseeker. ‘dada2’ performs trimming of the high-throughput sequencing data. ‘QuasR’ and ‘mosaics’ perform quality control and mapping of the input reads to the reference genome and peak calling, respectively. Finally, ‘ChIPseeker’ performs annotation and visualization of the called peaks. This workflow runs well independently of operating systems (e.g., Windows, Mac, or Linux) and processes the input fastq files into various results in one run. R code is available at github: https://github.com/ddhb/Workflow_of_Chipseq.git.

Non-negligible Occurrence of Errors in Gender Description in Public Data Sets

Due to advances in omics technologies, numerous genome-wide studies on human samples have been published, and most of the omics data with the associated clinical information are available in public repositories, such as Gene Expression Omnibus and ArrayExpress. While analyzing several public datasets, we observed that errors in gender information occur quite often in public datasets. When we analyzed the gender description and the methylation patterns of gender-specific probes (glucose-6-phosphate dehydrogenase [G6PD], ephrin-B1 [EFNB1], and testis specific protein, Y-linked 2 [TSPY2]) in 5,611 samples produced using Infinium 450K HumanMethylation arrays, we found that 19 samples from 7 datasets were erroneously described. We also analyzed 1,819 samples produced using the Affymetrix U133Plus2 array using several gender-specific genes (X (inactive)-specific transcript [XIST], eukaryotic translation initiation factor 1A, Y-linked [EIF1AY], and DEAD [Asp-Glu-Ala-Asp] box polypeptide 3, Y-linked [DDDX3Y]) and found that 40 samples from 3 datasets were erroneously described. We suggest that the users of public datasets should not expect that the data are error-free and, whenever possible, that they should check the consistency of the data.

Sebaceoma Arising from Nevus Sebaceous with Early Focal Carcinomatous Area

No abstract available.

Simultaneous Determination and Recognition Analysis of Coumarins in Angelica decursiva and Peucedanum praeruptorum by HPLC-DAD

Peucedani Radix is the root of Angelica decursiva Franchet et Savatier (=Peucedanum decursivum Maximowicz) or Peucedanum praeruptorum Dunn in several Asian countries. The coumarins contained in Peucedani Radix were quantitatively analyzed using HPLC-DAD to develop a simultaneous determination for the quality control of A. decursiva and P. praeruptorum. For quantitative analysis, four major coumarins contained in these medicinal plants were assessed. Nodakenin (1), nodakenetin (2), praeruptorin A (3), and praeruptorin B (4) were separated with a Phenomenex Luna C18 column (5 µm, 4.6 × 250 mm) under the gradient conditions using distilled water with 0.1% phosphoric acid and acetonitrile with 0.1% phosphoric acid as the mobile phase, at a flow rate of 1.0 ml/min and a detection wavelength of 330 nm. This method was fully validated for linearity, accuracy, precision, recovery, and limit of detection and quantification. As a result, A. decursiva and P. praeruptorum were clearly classified by the quantification of four major coumarins in extracts. Also, the pattern recognition analysis based on HPLC indicates that all of the samples were largely clustered into two groups. Therefore, it is possible to distinguish between A. decursiva and P. praeruptorum and contribute to quality control.

Inferior Blow-Out Fracture Reduction Using Two Urinary Balloon Catheters

BACKGROUND: The reduction of orbital blowout fracture primarily aims to normalize the extra-ocular movement by returning the herniated orbital soft tissue into the original position, and to prevent enophthalmos by normalizing the orbital cavity volume. We introduce a balloon catheter-assisted orbital floor reduction technique. METHODS: A retrospective review was performed for all patients with orbital floor fracture who underwent the technique described in the main body of this text. Medical records were reviewed for demographic data, clinical presentation and course, degree of enophthalmos, intraorbital volume on computed tomography scan, and postoperative outcomes. The enophthalmos and intraorbital volume of the injured site were compared to the uninjured eye and orbit. RESULTS: The review identified 14 patients (11 male, 3 female). The mean preoperative difference in en-exopthalmos was 2.13 mm, while the mean orbital volume was 116%. The mean postoperative difference in en-exophthalmos had improved to 0.61 mm with a mean orbital volume of 101.85%. At the time of catheter removal at 10 days, three patients experienced diplopia (n=1), extra-ocular movement disorder (1), or enophthalmos (1). All of these had resolved by the 6-month follow-up visit. CONCLUSION: Balloon catheter-assisted reduction of the orbital floor fractures was associated with improvements in intraorbital volume and enopthalmos in the 14 patients. Notable complications included diplopia, enophthalmos, and limited extra-ocular movement, all of which were transient in the early postoperative period and had resolved by 6-month follow up.

Cytotoxicity and anti-inflammatory effects of root bark extracts of Acanthopanax henryi / 中国天然药物

AIM@#To investigate the cytotoxicity, anti-inflammatory activity, and action mechanism of root bark extracts of Acanthopanax henryi.@*METHOD@#The hot methanol extract of the root bark of A. henryi was subjected to XAD-4 column chromatography eluting with a gradient of methanol in water. The cytotoxicity and anti-inflammatory effects of the MeOH fractions were evaluated on the inhibition on lipopolysaccharide (LPS)-induced nitric oxide, prostaglandin E2, interleukin-1β, and interleukin-6 production in RAW 264.7 macrophages.@*RESULTS@#The 80% MeOH fraction was a better inhibitor of LPS-induced NO, PGE2, IL-1β, and IL-6 production, and expression of inducible nitric oxide synthase (iNOS) at the protein levels in a concentration-dependent manner.@*CONCLUSION@#The 80% MeOH fraction of A. henryi root bark has significant anti-inflammatory activity. This provides a pharmacological basis for clinical application for the treatment of inflammation.

Reconstruction Techniques for Tissue Defects Formed after Preauricular Sinus Excision

BACKGROUND: Preauricular sinuses are congenital abnormalities caused by a failure of fusion of the primitive tubercles from which the pinna is formed. When persistent or recurring inflammation occurs, surgical excision of the infected tissue should be considered. Preauricular defects inevitably occur as a result of excisions and are often difficult to resolve with a simple suture; a more effective reconstruction technique is required for treating these defects. METHODS: After total excision of a preauricular sinus, the defect was closed by a plastic surgeon. Based on the depth of the defect and the degree of tension when apposing the wound margins, the surgeon determined whether to use primary closure or a posterior auricular flap. RESULTS: A total of 28 cases were examined. In 5 cases, including 2 reoperations for dehiscence after primary repair, reconstruction was performed using posterior auricular transposition flaps. In 16 cases of primary closure, the defects were closed using simple sutures, and in 7 cases, closure was performed after wide undermining. CONCLUSIONS: If a preauricular defect is limited to the subcutaneous layer and the margins can be easily approximated, primary closure by only simple suturing may be used to perform the repair. If the defect is deep enough to expose the perichondrium or if there is tension when apposing the wound margins, wide undermining should be performed before primary closure. If the extent of the excision exposes cartilage, the procedure follows dehiscence of the primary repair, or the tissue is not sufficiently healthy, the surgeon should use a posterior auricular flap.

Apocrine Hidrocystoma of the Cheek

No abstract available.

Management of Infections with Rapidly Growing Mycobacteria after Unexpected Complications of Skin and Subcutaneous Surgical Procedures

BACKGROUND: Infection caused by rapidly growing mycobacteria (RGM) is not uncommon, and the prevalence of RGM infection has been increasing. Clinical diagnosis is difficult because there are no characteristic clinical features. There is also no standard antibiotic regimen for treating RGM infection. A small series of patients with RGM infections was studied to examine their treatments and outcomes. METHODS: A total of 5 patients who had developed postoperative infections from January 2009 to December 2010 were retrospectively reviewed. Patients were initially screened using a mycobacteria rapid screening test (polymerase chain reaction [PCR]-reverse blot hybridization assay). To confirm mycobacterial infection, specimens were cultured for nontuberculous mycobacteria and analyzed by 16 S ribosomal RNA and rpoB gene PCR. RESULTS: The patients were treated with intravenous antibiotics during hospitalization, and oral antibiotics were administered after discharge. The mean duration of follow-up was 9 months, and all patients were completely cured of infection with a regimen of a combination of antibiotics plus surgical treatment. Although none of the patients developed recurrence, there were complications at the site of infection, including hypertrophic scarring, pigmentation, and disfigurement. CONCLUSIONS: Combination antibiotic therapy plus drainage of surgical abscesses appeared to be effective for the RGM infections seen in our patients. Although neither the exact dosage nor a standardized regimen has been firmly established, we propose that our treatment can provide an option for the management of rapidly growing mycobacterial infection.

Immediate Operation in Pediatric White-eye Blowout Fracture

PURPOSE: 'White-eye blowout' fracture is often occur in young patients and defined as blow out fracture with little or no clinical sign of soft tissue trauma such as edema, ecchymosis, but with marked motility restrictions in vertical gaze. In this conditions, immediate operation is essential. We reported the clinical investigation study of these cases about clinical symptoms and radiologic findings and introduce our experiences about immediate operations in 'white-eye blowout' fractures. METHODS: From January 2008 to December 2009, nine pediatric patients who were diagnosed as pure white-eye blowout fractures were involved this study. Patients with other facial bone fractures or with poor general medical condition were excluded. In all cases, we performed immediate operation within 48 hours. RESULTS: All patients had diplopia, vertical gaze restriction or systemic symptoms. Six patients had nausea, vomiting and syncope caused by oculocardiac reflex. In all patients, preoperative symptoms were improved after immediate operation. There were no postoperative complications such as infection, hematoma or wound dehiscence. CONCLUSION: When we meet the young patients with history of periocular trauma, with little or no soft tissue trauma signs, but with marked vertical gaze restriction or general symptoms caused by oculocardiac reflex, we should immediately examine by facial bone computed tomography and refer the patient to ophthalmologist for ophthalmic evaluations. If patient is diagnosed as orbital floor fracture with entrapped muscle or soft tissue, the earlier surgical reduction get better clinical outcomes.

Glomus Tumor in Subcutaneous Layerof Forearm : A Case Report

PURPOSE: Glomus tumor is rare benign neoplasm arising from the normal glomus, which is a neuromyoarterial apparatus, usually seen in the nail bed of fingers. Concerning about the origin, there were few written reports about extra-digit glomus tumor of elderly patient. MATERIALS AND METHODS: A 69-year-old man presented with severe pain and tenderness localized to the distal dorsal portion of forearm for 5 years. The pain was sudden in onset resting several seconds, cold frequently exacerbated these symptoms. So much pain was caused by touching the sensitive area that the patient was quite reluctant to have the maneuver repeated. The clinical suspicion of glomus tumor was made and the lesion was completely excised. Glomus tumor was confirmed by the pathologist. RESULTS: After the operation, patient didn't complain of his symptoms anymore and there was no evidence of recurrence during 6 months follow-up period. CONCLUSIONS: We report a rare case of glomus tumor arising in subcutaneous layer of forearm with elderly patient.