Estimation of the journal distance of Genomics & Informatics from other bioinformatics-driven journals, 2003-2018

This study explored the trends of Genomics & Informatics during the period of 2003-2018 in comparison with 11 other scholarly journals: BMC Bioinformatics, Algorithms for Molecular Biology: AMB, BMC Systems Biology, Journal of Computational Biology, Briefings in Bioinformatics, BMC Genomics, Nucleic Acids Research, American Journal of Human Genetics, Oncogenesis, Disease Markers, and Microarrays. In total, 22,423 research articles were reviewed. Content analysis was the main method employed in the current research. The results were interpreted using descriptive analysis, a clustering analysis, word embedding, and deep learning techniques. Trends are discussed for the 12 journals, both individually and collectively. This is an extension of our previous study (PMCID: PMC6808643).

Correlation between Sleep and C-reactive Protein of Patients in Amnestic Mild Cognitive Impairment and Alzheimer’s Dementia

Objective@#Sleep affects systemic inflammation and amyloid deposition, and sleep disturbance is known to be a risk factor for cognitive decline. To date, literatures on the relationship between peripheral inflammatory markers and sleep in Alzheimer’s de-mentia and mild cognitive impairment patients have been scarce. The aim of this study was to determine the correlation between sleep and C-reactive protein (CRP) in Alzheimer’s dementia and amnestic mild cognitive impairment patients. @*Methods@#A total of 81 patients were divided in to four groups: amyloid negative healthy control, amyloid negative amnestic mild cognitive impairment, amyloid positive amnestic mild cognitive impairment, and amyloid positive Alzheimer’s dementia.Demographic data and cognitive measurement through the Consortium to Establish a Registry for Alzheimer’s Disease were conducted. Amyloid positivity status was attained through positron emission tomography scans using [18F]-flutemetamol. The quality of sleep was evaluated by the sleep item of Korean Neuropsychiatric Inventory (K-NPI-SLEEP), and peripheral blood tests were conducted to measure CRP. @*Results@#There was no statistically difference in CRP levels or K-NPI-SLEEP scores among four groups. Moreover, there was no association between K-NPI-SLEEP and CRP in four groups. @*Conclusion@#Since K-NPI-SLEEP score shows overall, subjective sleep problems, further follow-up studies in consideration for objective sleep studies to unravel the relationship of peripheral inflammatory markers and sleep in amnestic mild cognitive impairment and Alzheimer’s dementia patients.

Organizing an in-class hackathon to correct PDF-to-text conversion errors of Genomics & Informatics 1.0

This paper describes a community effort to improve earlier versions of the full-text corpus of Genomics & Informatics by semi-automatically detecting and correcting PDF-to-text conversion errors and optical character recognition errors during the first hackathon of Genomics & Informatics Annotation Hackathon (GIAH) event. Extracting text from multi-column biomedical documents such as Genomics & Informatics is known to be notoriously difficult. The hackathon was piloted as part of a coding competition of the ELTEC College of Engineering at Ewha Womans University in order to enable researchers and students to create or annotate their own versions of the Genomics & Informatics corpus, to gain and create knowledge about corpus linguistics, and simultaneously to acquire tangible and transferable skills. The proposed projects during the hackathon harness an internal database containing different versions of the corpus and annotations.

Organizing an in-class hackathon to correct PDF-to-text conversion errors of Genomics & Informatics 1.0

This paper describes a community effort to improve earlier versions of the full-text corpus of Genomics & Informatics by semi-automatically detecting and correcting PDF-to-text conversion errors and optical character recognition errors during the first hackathon of Genomics & Informatics Annotation Hackathon (GIAH) event. Extracting text from multi-column biomedical documents such as Genomics & Informatics is known to be notoriously difficult. The hackathon was piloted as part of a coding competition of the ELTEC College of Engineering at Ewha Womans University in order to enable researchers and students to create or annotate their own versions of the Genomics & Informatics corpus, to gain and create knowledge about corpus linguistics, and simultaneously to acquire tangible and transferable skills. The proposed projects during the hackathon harness an internal database containing different versions of the corpus and annotations.

Association between Glycemic Control in Patients with Diabetes and Mental Health Variables Including Depression / 우울ㆍ조울병

Background@#The purpose of this study was to measure several mental health variables according to HbA1c level and examine their relationship among diabetic patients. @*Methods@#Total 89 outpatients who attended diabetes education program at St. Vincent’s Hospital, The Catholic University of Korea College of Medicine, were enrolled this study. The Beck Depression Inventory (BDI), State-Trait Anxiety Inventory, Stress Response Inventory (SRI), abbreviated version of World Health Organization Quality of Life assessment instrument (WHOQOL-BREF), Insomnia Severity Index, and Epworth Sleepiness Scale (ESS) were administered to all patients. Significant differences between groups were assessed by t-test and chi-squared test. Pearson correlation and multiple linear regression analyses were used to identify the variables that affect HbA1c levels. @*Results@#The well-controlled group had a significantly lower BDI score than the poorly controlled group. The wellcontrolled group also showed significantly lower SRI and ESS. HbA1c, BDI, SRI, and ESS were positively correlated. Duration and BDI were the only variables affecting HbA1c levels. @*Conclusion@#Emphasis should be given to the identification and management of mental health problems, including especially depressive symptoms in patients with diabetes.

The Reliability and Validity of the Korean Version of Behavioral Activation for Depression Scale / 신경정신의학

OBJECTIVES: The Behavioral Activation of Depression Scale (BADS) has been reported to be a valid tool for assessing the different behavioral aspects of depression, such as activation, rumination or avoidance, and functional impairment. The aim of this study was to assess the reliability and validity of the Korean version of BADS (K-BADS). METHODS: A sample of 196 outpatients completed the K-BADS and the data were analyzed for internal consistency and factor structures. An additional 51 outpatients re-filled the K-BADS after two weeks for the test-retest reliability. To test for the validity, the Hospital Anxiety and Depression Scale (HADS), Working Alliance Inventory (WAI), Drug Attitude Inventory-10 (DAI-10), and Mindfulness Attention Awareness Scale (MAAS) were administered. RESULTS: Internal consistency of K-BADS was good (Cronbach's alpha=0.843) and principal component factor analysis revealed the four-factor structure. The K-BADS showed a reasonable test-retest reliability (r=0.863, p<0.001). The total score of K-BADS correlated significantly with the total scores of the HADS depression (r=−0.694) and HADS anxiety (r=−0.681). No correlations were found between the K-BADS and the K-WAI (r=0.170) and between the K-BADS and the K-DAI-10 (r=0.311). CONCLUSION: The K-BADS is a reliable and valid instrument for measuring the behavioral activation for depression in Korean patients with depressive symptoms.

Association between Smoking and the Progression of Computed Tomography Findings in Chronic Pancreatitis

BACKGROUND/AIMS: Smoking and alcohol intake are two well-known risk factors for chronic pancreatitis. However, there are few studies examining the association between smoking and changes in computed tomography (CT) findings in chronic pancreatitis. The authors evaluated associations between smoking, drinking and the progression of calcification on CT in chronic pancreatitis. METHODS: In this retrospective study, 59 patients with chronic pancreatitis who had undergone initial and follow-up CT between January 2002 and September 2010 were included. Progression of calcification among CT findings was compared according to the amount of alcohol intake and smoking. RESULTS: The median duration of follow-up was 51.6 months (range, 17.1 to 112.7 months). At initial CT findings, there was pancreatic calcification in 35 patients (59.3%). In the follow-up CT, progression of calcification was observed in 37 patients (62.7%). Progression of calcification was more common in smokers according to the multivariate analysis (odds ratio [OR], 9.987; p=0.006). The amount of smoking was a significant predictor for progression of calcification in the multivariate analysis (OR, 6.051 in less than 1 pack per day smokers; OR, 36.562 in more than 1 pack per day smokers; p=0.008). CONCLUSIONS: Continued smoking accelerates pancreatic calcification, and the amount of smoking is associated with the progression of calcification in chronic pancreatitis.

Changes in Causative Pathogens of Acute Cholangitis and Their Antimicrobial Susceptibility over a Period of 6 Years / 대한소화기학회지

BACKGROUND/AIMS: We evaluated changes of causative pathogen in acute cholangitis and their antimicrobial susceptibility over six years and differences between community-acquired and hospital-acquired acute cholangitis at our institution. METHODS: Medical records of 1,596 patients with acute cholangitis and biliary drainage between August 2006 and August 2012 were reviewed retrospectively. Cases were divided according to time: period 1 (August 2006-December 2008, n=645, 40.4%), period 2 (January 2009-August 2012, n=951, 59.6%). Cases were divided according to community-acquired cholangitis (n=1,397, 87.5%) and hospital-acquired cholangitis (n=199, 12.5%). Causative pathogens and antimicrobial susceptibility were investigated in each group. RESULTS: Causative pathogen was isolated from bile culture in 1,520 out of 1,596 cases (95.2%). The three most frequently isolated Gram-negative bacteria were extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli (n=485, 30.4%), E. coli (n=237, 13.2%), and Citrobacter freundii (n=110, 6.9%). Between periods 1 and 2, prevalence of ESBL-producing E. coli and Klebsiella pneumoniae did not show significant change (36.7% vs. 32.1%, p=0.073; 6.6% vs. 6.2%, p=0.732). C. freundii showed a significant increase from period 1 to period 2 (1.7% vs. 13.2%, p=0.000). In both time periods, imipenem was the antimicrobial agent showing the highest rate of susceptibility (93.3% vs. 93.9%, p=0.783). Higher prevalence of ESBL-producing E. coli and C. freundii was observed in the hospital-acquired cholangitis group (52.1% vs. 31.2%, p=0.000; 15.9% vs. 7.3%, p=0.001). CONCLUSIONS: The most common causative pathogen of acute cholangitis was ESBL-producing E. coli. Prevalence of C. freundii increased over the time period. Imipenem should be reserved as an alternative for resistant pathogens.

Osteogenic Response of Human Osteoblasts Derived from Mandible and Maxilla: A Preliminary Study

Radiation Exposure of the Hand and Chest during C-arm Fluoroscopy-Guided Procedures

BACKGROUND: The C-arm fluoroscope is an essential tool for the intervention of pain. The aim of this study was to investigate the radiation exposure experienced by the hand and chest of pain physicians during C-arm fluoroscopy-guided procedures. METHODS: This is a prospective study about radiation exposure to physicians during transforaminal epidural steroid injection (TFESI) and medial branch block (MBB). Four pain physicians were involved in this study. Data about effective dose (ED) at each physician's right hand and left side of the chest, exposure time, radiation absorbed dose (RAD), and the distance from the center of the X-ray field to the physician during X-ray scanning were collected. RESULTS: Three hundred and fifteen cases were included for this study. Demographic data showed no significant differences among the physicians in the TFESIs and MBBs. In the TFESI group, there was a significant difference between the ED at the hand and chest in all the physicians. In physician A, B and C, the ED at the chest was more than the ED at the hand. The distance from the center of the X-ray field to physician A was more than that of the other physicians, and for the exposure time, the ED and RAD in physician A was less than that of the other physicians. In the MBB group, there was no difference in the ED at the hand and chest, except for physician D. The distance from the center of the X-ray field to physician A was more than that of the other physicians and the exposure time in physician A was less than that of the other physicians. CONCLUSIONS: In conclusion, the distance from the radiation source, position of the hand, experience and technique can correlate with the radiation dose.

Pretreatment of magnesium sulphate improves intubating conditions of rapid sequence tracheal intubation using alfentanil, propofol, and rocuronium: a randomized trial / 대한마취과학회지

BACKGROUND: We investigated the effects of a magnesium sulfate pretreatment on intubating conditions and cardiovascular responses during rapid sequence tracheal intubation (RSI) in this double-blind randomized study. METHODS: Adult patients (n = 154) were randomly allocated to a rocuronium-0.6, rocuronium-0.9, or magnesium group. The magnesium group was pretreated with 50 mg/kg MgSO4, and the other two groups received the same volume of isotonic saline. Anesthesia was induced with alfentanil, propofol, and either 0.6 mg/kg (rocuronium-0.6 and magnesium groups) or 0.9 mg/kg (rocuronium-0.9 group) rocuronium. An anesthesiologist, blinded to the group assignments, performed RSI and assessed the intubating conditions. Systolic arterial pressure (SAP) and heart rate (HR) were recorded before the magnesium sulfate or normal saline was administered, before anesthesia induction, before intubation, and every minute after intubation for 5 min. RESULTS: Airway features were similar among the three groups. The intubating conditions were improved significantly in the magnesium group (P 0.05). No hypertensive episode occurred during the immediate post-intubation period in the magnesium group (P = 0.001), and tachycardia occurred most frequently in the rocuronium-0.6 group (P < 0.05). CONCLUSIONS: MgSO4 administered prior to RSI using alfentanil, propofol, and rocuronium may improve intubating conditions and prevent post-intubation hypertension.

A Case of Clonorchiasis Presenting as Common Bile Duct Mass / 대한소화기학회지

No abstract available.

Reunion of the Rabbit Superior Oblique Tendon After Weakening Procedures

PURPOSE: To investigate the degree of reunion in rabbit eyes of the superior oblique tendon after several surgical weakening procedures. METHODS: A total of 32 rabbits (64 eyes) were used in this study. The rabbits were randomly assigned to four groups, eight rabbits (16 eyes) in the tenotomy group, eight rabbits (16 eyes) in the tenectomy group, eight rabbits (16 eyes) in the disinsertion group and eight rabbits (16 eyes) in the recession group. The degree of reunion or reattachment of the superior oblique tendon on the globe were examined on four eyes in each group at postoperative weeks two, four, six and eight. RESULTS: At eight weeks, the newly created insertion site remained at the same site in all eyes in the recession group, and the distal end of the superior oblique tendon was reattached at the medial border of the superior rectus muscle in all four eyes in the tenotomy and disinsertion groups, and in three of four eyes in the tenectomy group. CONCLUSIONS: From this experimental study, it was speculated that superior oblique recession is more effective than other superior oblique weakening procedures. This result could be helpful in the prediction of time of recurrence for superior oblique overaction after superior oblique weakening procedures.

The Effect of Preoperative Subconjunctival Injection of Mitomycin C and Triamcinolone in Recurrent Pterygium

PURPOSE: To evaluate the effect of a preoperative subconjunctival injection of mitomycin C or triamcinolone in patients with recurrent pterygium. METHODS: The records of 50 eyes of 50 patients who received excision of recurrent pterygium between June 2006 and January 2007 were reviewed. The recurrence rate and postoperative fibrovascular growth were compared in the preoperative subconjunctival mitomycin C, or triamcinolone injection group and non-treated control group. Additionally, the quantitative expression level of the transforming growth factor-beta1, -beta2 (TGF-beta1, -beta2), connective tissue growth factor (CTGF), and vascular endothelial growth factor (VEGF) in excised sample of the pterygium was assessed. RESULTS: There was no statistically significant difference in the recurrence rate and the relative gene expression level of growth factors in the triamcinolone group and the mitomycin group when compared with the non-treated control group. Postoperative fibrovascular proliferation was more severe in the triamcinolone group than other groups. CONCLUSIONS: Subconjunctival mitomycin C or triamcinolone as adjunctive therapy before pterygium excision did not influence the recurrence rate of pterygium.

Intestinal Amyloidosis Treated with High-Dose Steroids and Azathioprine: A Case Report / 대한소화기내시경학회지

Amyloidosis is a rare disease characterized by deposition and accumulation of insoluble fibrils in various organs and tissues. Variations in the precursor proteins composing each fibril account for the diverse character of amyloidosis. Amyloidosis light chain (AL) and amyloid A amyloidosis (AA) are two clinical entities representative of this diversity. We present a case of a 58-year-old woman presenting with refractory diarrhea and abdominal pain. She was ultimately diagnosed with intestinal amyloidosis diffusely involving the small and large intestines. Even though a definitive therapeutic strategy has not been established for gastrointestinal amyloidosis, this particular patient has been successfully managed with high-dose steroids and azathioprine.

Improvement of Pulmonary Function after Administration of Azithromycin in a Patient with Bronchiolitis Obliterans: a Case Report / 결핵및호흡기질환

Bronchiolitis obliterans (BO) is a serious noninfectious complication following an allogeneic bone marrow transplant (BMT). A 21-year-old female received an allogeneic BMT as a treatment for myelodyplastic syndrome. Four months after the BMT, progressive dyspnea developed and BO was also diagnosed by a lung biopsy. The patient was administered steroid and immunosuppressive agents for 1 year but there was no improvement in pulmonary function. Azithromycin was prescribed (500 mg q.d. for 3 days followed by 250 mg three time a week) because macrolides might decrease the inflammatory reaction leading to BO. The patient's pulmonary function improved after administration of azithromycin for 1 year. The forced expiratory volume in a one second (FEV1) increase was 220 mL (28.2%) and the forced vital capacity (FVC) increase was 460 mL (25.7%). We report the improvement in the pulmonary function after the administration of azithromycin for 1 year in a patient with BO after a BMT.