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1.  Second Complete Remission of Relapsed Stage IV Non-Small Cell Lung Cancer Following Retreatment 
Non-small cell lung cancer (NSCLC) is the leading cause of cancer related deaths. Most patients were presented with advanced disease at the time of diagnosis. In advanced NSCLC, it is almost impossible to anticipate complete remission by using only cytotoxic chemotherapy or molecularly targeted agents. In our case, two patients were diagnosed as advanced NSCLC and received chemotherapy. They achieved complete response (CR). After finishing treatment, disease recurred. They were retreated with the same regimens and achieved second CR. Until now, they have received each regimen, continuously, and the CR state has been maintained.
PMCID: PMC3510290  PMID: 23227080
Carcinoma, Non-Small-Cell Lung; Remission Induction; Retreatment; Maintenance Chemotherapy
2.  Prevalence of Anti-Ganglioside Antibodies and Their Clinical Correlates with Guillain-Barré Syndrome in Korea: A Nationwide Multicenter Study 
Background and Purpose
No previous studies have investigated the relationship between various anti-ganglioside antibodies and the clinical characteristics of Guillain-Barré syndrome (GBS) in Korea. The aim of this study was to determine the prevalence and types of anti-ganglioside antibodies in Korean GBS patients, and to identify their clinical significance.
Serum was collected from patients during the acute phase of GBS at 20 university-based hospitals in Korea. The clinical and laboratory findings were reviewed and compared with the detected types of anti-ganglioside antibody.
Among 119 patients, 60 were positive for immunoglobulin G (IgG) or immunoglobulin M antibodies against any type of ganglioside (50%). The most frequent type was IgG anti-GM1 antibody (47%), followed by IgG anti-GT1a (38%), IgG anti-GD1a (25%), and IgG anti-GQ1b (8%) antibodies. Anti-GM1-antibody positivity was strongly correlated with the presence of preceding gastrointestinal infection, absence of sensory symptoms or signs, and absence of cranial nerve involvement. Patients with anti-GD1a antibody were younger, predominantly male, and had more facial nerve involvement than the antibody-negative group. Anti-GT1a-antibody positivity was more frequently associated with bulbar weakness and was highly associated with ophthalmoplegia when coupled with the coexisting anti-GQ1b antibody. Despite the presence of clinical features of acute motor axonal neuropathy (AMAN), 68% of anti-GM1- or anti-GD1a-antibody-positive cases of GBS were diagnosed with acute inflammatory demyelinating polyradiculoneuropathy (AIDP) by a single electrophysiological study.
Anti-ganglioside antibodies were frequently found in the serum of Korean GBS patients, and each antibody was correlated strongly with the various clinical manifestations. Nevertheless, without an anti-ganglioside antibody assay, in Korea AMAN is frequently misdiagnosed as AIDP by single electrophysiological studies.
PMCID: PMC4017025  PMID: 24829594
Guillain-Barré syndrome; ganglioside; antibodies; Korea; acute motor axonal neuropathy
3.  Silver nanoparticles modify VEGF signaling pathway and mucus hypersecretion in allergic airway inflammation 
The anti-inflammatory action of silver nanoparticles (NPs) has been reported in a murine model of asthma in a previous study. But more specific mechanisms of silver NPs in an attenuation of allergic airway inflammation have not yet been established. Vascular and mucous changes are believed to contribute largely in pathophysiology in asthma. Among various factors related to vascular changes, vascular endothelial growth factor (VEGF) plays a pivotal role in vascular changes in asthma. Mucin proteins MUC5AC and MUC5B have been implicated as markers of goblet cell metaplasia in lung pathologies. The aim of this study was to investigate the effects of silver NPs on VEGF signaling pathways and mucus hypersecretion. Ovalbumin (OVA)-inhaled female BALBc mice were used to evaluate the role of silver NPs and the related molecular mechanisms in allergic airway disease. In this study, with an OVA-induced murine model of allergic airway disease, it was found that the increased levels of hypoxia-inducible factor (HIF)-1α, VEGF, phosphatidylinositol-3 kinase (PI3K) and phosphorylated-Akt levels, and mucous glycoprotein expression (Muc5ac) in lung tissues were substantially decreased by the administration of silver NPs. In summary, silver NPs substantially suppressed mucus hypersecretion and PI3K/HIF-1α/VEGF signaling pathway in an allergic airway inflammation.
PMCID: PMC3310409  PMID: 22457593
allergic airway disease; hypoxia inducible factor-1α; vascular endothelial growth factor
4.  Comparison on the Efficacy of Disinfectants Used in Automated Endoscope Reprocessors: PHMB-DBAC versus Orthophthalaldehyde 
Clinical Endoscopy  2011;44(2):109-115.
Since endoscopes are reusable apparatus classified as semicritical item, thorough reprocessing to achieve high-level disinfection is of utmost importance to prevent spread of infection. To improve disinfection efficacy and safety, disinfectants and endoscope reprocessors are continuously evolving. This study aimed to compare the efficacy of the combination of polyhexamethylenebiguanide hydrochloride-alkyldimethylbenzylammonium chloride (PHMB-DBAC) and orthophthalaldehyde (OPA) used respectively in ultrasonographic cleaning incorporated automated endoscope reprocessors: COOLENDO (APEX Korea) or OER-A (Olympus Optical).
A total of 86 flexible upper endoscopes were randomly reprocessed with either COOLENDO/PHMB-DBAC or OER-A/OPA. Culture samplings were done at two sites (endoscope tip and working channel) which were later incubated on blood agar plate. Bacterial colonies were counted and identified.
The culture-positive rate at the endoscope tip and working channel was 0% and 2.33% for COOLENDO/PHMB-DBAC and 4.65% and 0% for OER-A/OPA. Staphylococcus hominis was cultured from one endoscope reprocessed with COOLENDO/PHMB-DBAC and Pseudomonas putida was isolated from two endoscopes reprocessed with OER-A/OPA.
The reprocessing efficacy of COOLENDO/PHMB-DBAC was non-inferior to that of OER-A/OPA (p=0.032; confidence interval, -0.042 to 0.042). During the study period, significant side effect of PHMB-DBAC was not observed.
PMCID: PMC3363059  PMID: 22741121
Endoscope reprocessing; Disinfectants; High-level disinfection
5.  Ordinary kriging approach to predicting long-term particulate matter concentrations in seven major Korean cities 
Cohort studies of associations between air pollution and health have used exposure prediction approaches to estimate individual-level concentrations. A common prediction method used in Korean cohort studies is ordinary kriging. In this study, performance of ordinary kriging models for long-term particulate matter less than or equal to 10 μm in diameter (PM10) concentrations in seven major Korean cities was investigated with a focus on spatial prediction ability.
We obtained hourly PM10 data for 2010 at 226 urban-ambient monitoring sites in South Korea and computed annual average PM10 concentrations at each site. Given the annual averages, we developed ordinary kriging prediction models for each of the seven major cities and for the entire country by using an exponential covariance reference model and a maximum likelihood estimation method. For model evaluation, cross-validation was performed and mean square error and R-squared (R2) statistics were computed.
Mean annual average PM10 concentrations in the seven major cities ranged between 45.5 and 66.0 μg/m3 (standard deviation=2.40 and 9.51 μg/m3, respectively). Cross-validated R2 values in Seoul and Busan were 0.31 and 0.23, respectively, whereas the other five cities had R2 values of zero. The national model produced a higher crossvalidated R2 (0.36) than those for the city-specific models.
In general, the ordinary kriging models performed poorly for the seven major cities and the entire country of South Korea, but the model performance was better in the national model. To improve model performance, future studies should examine different prediction approaches that incorporate PM10 source characteristics.
PMCID: PMC4178540  PMID: 25262773
Exposure prediction; Health effect; Kriging; Long-term exposure; Particulate matter
6.  Abnormal Activation of the Social Brain Network in Children with Autism Spectrum Disorder: An fMRI Study 
Psychiatry Investigation  2014;12(1):37-45.
The aim of this study is to investigate abnormal findings of social brain network in Korean children with autism spectrum disorder (ASD) compared with typically developing children (TDC).
Functional magnetic resonance imaging (fMRI) was performed to examine brain activations during the processing of emotional faces (happy, fearful, and neutral) in 17 children with ASD, 24 TDC.
When emotional face stimuli were given to children with ASD, various areas of the social brain relevant to social cognition showed reduced activation. Specifically, ASD children exhibited less activation in the right amygdala (AMY), right superior temporal sulcus (STS) and right inferior frontal gyrus (IFG) than TDC group when fearful faces were shown. Activation of left insular cortex and right IFG in response to happy faces was less in the ASD group. Similar findings were also found in left superior insular gyrus and right insula in case of neutral stimulation.
These findings suggest that children with ASD have different processing of social and emotional experience at the neural level. In other words, the deficit of social cognition in ASD could be explained by the deterioration of the capacity for visual analysis of emotional faces, the subsequent inner imitation through mirror neuron system (MNS), and the ability to transmit it to the limbic system and to process the transmitted emotion.
PMCID: PMC4310919
Autism spectrum disorder; Social brain network; Social cognition; fMRI
7.  Is elective inguinal radiotherapy necessary for locally advanced rectal adenocarcinoma invading anal canal? 
We investigated whether routine elective irradiation of a clinically negative inguinal node (IGN) is necessary for patients with locally advanced distal rectal cancer and anal canal invasion (ACI).
We reviewed retrospectively 1,246 patients with locally advanced rectal adenocarcinoma managed using preoperative or postoperative chemoradiotherapy and radical surgery between 2001 and 2011. The patients’ IGN was clinically negative at presentation and IGN irradiation was not performed. ACI was defined as the lower edge of the tumor being within 3 cm of the anal verge. Patients were divided into two groups, those with ACI (n = 189, 15.2%) and without ACI (n = 1,057, 84.8%).
The follow-up period was a median of 66 months (range, 3–142 months). Among the 1,246 patients, 10 developed IGN recurrence; 7 with ACI and 3 without ACI. The actuarial IGN recurrence rate at 5 years was 0.7%; 3.5% and 0.2% in patients with and without ACI, respectively (p < 0.001). Isolated IGN recurrence occurred in three patients, all of whom had ACI tumors. These three patients received curative intent local treatments, and one was alive with no evidence of disease 10 years after IGN recurrence. Salvage treatments in the other two patients controlled successfully the IGN recurrence for >5 years, but they developed second malignancy or pelvic and distant recurrences. Seven patients with non-isolated IGN recurrence died of disease at 5–22 months after IGN recurrence.
The low IGN recurrence rate even with ACI and the feasibility of salvage of isolated IGN recurrence indicated that routine elective IGN irradiation is not necessary for rectal cancer with ACI.
PMCID: PMC4299686  PMID: 25533887
Rectal cancer; Radiotherapy; Inguinal lymph node; Anal canal invasion
8.  Differences in the clinical and radiological characteristics of lung-involved toxocariasis between toxocariasis with eosinophilia and those without eosinophilia 
Journal of Thoracic Disease  2014;6(12):1757-1764.
Previously, most studies did not discuss about the characteristics of lung-involved toxocariasis without eosinophilia. However, the patients are not always accompanied by eosinophilia, so it is necessary to learn about the clinical and radiologic features that may predict pulmonary toxocariasis without eosinophilia. In addition, we also want to check the differences in characteristics between the two groups based on the presence of eosinophilia.
We investigated patients from October 2009 to February 2014 with antibody against Toxocara positive using enzyme-linked immunosorbent assay (ELISA), abnormal chest X-ray, and computed tomography (CT) findings. This retrospective study included patients diagnosed as toxocariasis with pulmonary involvement, using the results of laboratory findings, symptoms, and CT at the time of diagnosis.
Out of 88 patients, 78% were male and 22% were female; and the mean age was 51 years. The mean eosinophil fraction in peripheral blood was 11.8%. The most common chest CT findings of patients with eosinophilia were nodules plus ground glass opacity (GGO) pattern, and nodules were found in patients with no eosinophilia. Pure GGO was the most common predominant subtype in GGO lesions of patients with eosinophilia. In terms of anatomical distribution, random distribution was seen more in patients with eosinophilia than those without eosinophilia, with statistically significance (P=0.042). In patients who underwent additional CT scans, 44% of those with eosinophilia had migrating lesions and had significant differences from patients without eosinophilia (P=0.008).
There were no significant differences in lesion characteristics with the exception of random anatomic distribution between patients with and without eosinophilia. However, there was a significant difference between the fixation and migration of the lesion in patients with and without eosinophilia.
PMCID: PMC4283343  PMID: 25589970
Computed tomography (CT); eosinophilia; lung disease; Toxocara canis (T. canis); toxocariasis
9.  Colonic lipoma covered by hyperplastic epithelium: Case report 
Colonic lipomas are submucosal nonepithelial tumors covered by intact or eroded mucosa. In rare cases, alterations in the mucosa covering a lipoma include hyperplasia, adenoma, atrophy, ulceration, and necrosis. Here, we report a case of a colonic lipoma covered by hyperplastic epithelium in a 68-year-old woman. Based on the colonoscopy findings, a snare polypectomy was performed for a presumptive diagnosis of an epithelial lesion; however, the histological examination revealed a colonic submucosal lipoma with overlying hyperplastic epithelium.
PMCID: PMC3845912  PMID: 24303482
Lipoma; Colonic lipomas; Hyperplastic; Colonoscopy
10.  Low-mass-ion discriminant equation: A new concept for colorectal cancer screening 
Blood metabolites can be detected as low-mass ions (LMIs) by mass spectrometry (MS). These LMIs may reflect the pathological changes in metabolism that occur as part of a disease state, such as cancer. We constructed a LMI discriminant equation (LOME) to investigate whether systematic LMI profiling might be applied to cancer screening. LMI information including m/z and mass peak intensity was obtained by five independent MALDI-MS analyses, using 1,127 sera collected from healthy individuals and cancer patients with colorectal cancer (CRC), breast cancer (BRC), gastric cancer (GC) and other types of cancer. Using a two-stage principal component analysis to determine weighting factors for individual LMIs and a two-stage LMI selection procedure, we selected a total of 104 and 23 major LMIs by the LOME algorithms for separating CRC from control and rest of cancer samples, respectively. CRC LOME demonstrated excellent discriminating power in a validation set (sensitivity/specificity: 93.21%/96.47%). Furthermore, in a fecal occult blood test (FOBT) of available validation samples, the discriminating power of CRC LOME was much stronger (sensitivity/specificity: 94.79%/97.96%) than that of the FOBT (sensitivity/specificity: 50.00%/100.0%), which is the standard CRC screening tool. The robust discriminating power of the LOME scheme was reconfirmed in screens for BRC (sensitivity/specificity: 92.45%/96.57%) and GC (sensitivity/specificity: 93.18%/98.85%). Our study demonstrates that LOMEs might be powerful noninvasive diagnostic tools with high sensitivity/specificity in cancer screening. The use of LOMEs could potentially enable screening for multiple diseases (including different types of cancer) from a single sampling of LMI information.
PMCID: PMC4233965  PMID: 24096867
serum profiling; MALDI-TOF mass spectrometry; pattern recognition
11.  Boerhaave’s syndrome during bowel preparation with polyethylene glycol in a patient with postpolypectomy bleeding 
Boerhaave’s syndrome is spontaneous rupture of the esophagus, a rare condition with high mortality that occurs most often after forceful vomiting. Polyethylene glycol (PEG) solution is the most common preparation used for colonoscopy. Since large volumes have to be ingested, PEG may induce severe vomiting or retching. However, Boerhaave’s syndrome has rarely been reported as a potential problem related to PEG solution. We report a case of spontaneous esophageal rupture due to violent vomiting during bowel preparation with PEG solution in a patient with postpolypectomy bleeding.
PMCID: PMC3653029  PMID: 23678383
Esophageal perforation; Colonoscopy; Polyethylene glycols
12.  Therapeutic potential of Gastrodia elata Blume for the treatment of Alzheimer's disease☆ 
Neural Regeneration Research  2013;8(12):1061-1070.
Several studies have demonstrated that the Chinese herb Gastrodia elata Blume can protect against amyloid beta-peptide (Aβ)-induced cell death. To investigate the possible therapeutic effects of Gastrodia elata Blume on Alzheimer's disease, we established a rat model of Alzheimer's disease by injecting Aβ25-35 into bilateral hippocampi. These rats were intragastrically administered 500 or 1 000 mg/kg Gastrodia elata Blume per day for 52 consecutive days. Morris water maze tests showed that Gastrodia elata Blume treatment significantly improved the spatial memory of Alzheimer's disease rats. Congo red staining revealed that Gastrodia elata Blume significantly reduced the number of amyloid deposits in the hippocampus of these rats. Western blot analysis showed that choline acetyltransferase expression in the medial septum and hippocampus was significantly increased by the treatment of Gastrodia elata Blume, while Ellman method showed significant decrease in the activity of acetylcholinesterase in all three regions (prefrontal cortex, medial septum and hippocampus). These findings suggest that long-term administration of Gastrodia elata Blume has therapeutic potential for Alzheimer's disease.
PMCID: PMC4145891  PMID: 25206400
neural regeneration; neuroprotective effect; Traditional Chinese medicine; Gastrodia elata Blume; Alzheimer's disease; Morris water maze test; choline acetyltransferase; acetylcholinesterase; grants-supported paper; neuroregeneration
13.  S-Adenosyl Methionine Prevents Endothelial Dysfunction by Inducing Heme Oxygenase-1 in Vascular Endothelial Cells 
Molecules and Cells  2013;36(4):376-384.
S-adenosyl methionine (SAM) is a key intermediate in the metabolism of sulfur amino acids and is a major methyl donor in the cell. Although the low plasma level of SAM has been associated with atherosclerosis, the effect of SAM administration on atherosclerosis is not known. Endothelial dysfunction is an early prerequisite for atherosclerosis. This study was undertaken to investigate the possible preventive effect of SAM on endothelial dysfunction and the molecular mechanism of its action. SAM treatment prevented endothelial dysfunction in high fat diet (HFD)-fed rats. In cultured human aortic endothelial cells, linoleic acid (LA) increased and SAM decreased cell apoptosis and endoplasmic reticulum stress. Both LA and SAM increased heme oxygenase-1 (HO-1) expression in an NF-E2-related factor 2-dependent manner. However, knockdown of HO-1 reversed only the SAM-induced preventive effect of cell apoptosis. The LA-induced HO-1 expression was dependent on PPARα, whereas SAM induced HO-1 in a PPAR-independent manner. These data demonstrate that SAM treatment prevents endothelial dysfunction in HFD-fed animals by inducing HO-1 in vascular endothelial cells. In cultured endothelial cells, SAM-induced HO-1 was responsible for the observed prevention of cell apoptosis. We propose that SAM treatment may represent a new therapeutic strategy for atherosclerosis.
PMCID: PMC3887983  PMID: 24046187
endoplasmic reticulum stress; endothelial dysfunction; heme oxygenase-1; S-adenosyl methionine; vascular endothelial cell
14.  Prognostic significance of gelsolin and MMP12 in Langerhans cell histiocytosis 
The Korean Journal of Hematology  2012;47(4):267-272.
Gelsolin and matrix metalloproteinase 12 (MMP12) expression has been reported in Langerhans cell histiocytosis (LCH), but the clinical significance of this expression is unknown. We investigated the associations of these proteins with clinical manifestations in patients diagnosed with LCH.
We performed a retrospective analysis of clinical data from patients diagnosed with LCH and followed up between 1998 and 2008. Available formalin-fixed, paraffin-embedded specimens were used for gelsolin and MMP12 immunohistochemical staining. We analyzed the expression levels of these proteins and their associations with LCH clinical features.
Specimens from 36 patients (20 males, 16 females) with a diagnosis of LCH based on CD1a positivity with clinical manifestations were available for immunohistochemical staining. Median patient age was 62 months (range, 5 to 207). The expression of gelsolin varied; it was high in 17 patients (47.2%), low in 11 patients (30.6%), and absent in 8 patients (22.2%). The high gelsolin expression group had a higher tendency for multi-organ and risk organ involvement, although the trend was not statistically significant. MMP12 was detected only in 7 patients (19.4%) who showed multi-system involvement (P=0.018) and lower event-free survival (P=0.002) in comparison to patients with negative MMP12 staining.
Gelsolin and MMP12 expression may be associated with the clinical course of LCH, and MMP12 expression may be particularly associated with severe LCH. Further studies of larger populations are needed to define the precise role and significance of gelsolin and MMP12 in the pathogenesis of LCH.
PMCID: PMC3538798  PMID: 23320005
Histiocytosis; Langerhans cells; Immunohistochemistry; Gelsolin; Matrix Metalloproteinase 12
15.  Identification of DNA Aptamers toward Epithelial Cell Adhesion Molecule via Cell-SELEX 
Molecules and Cells  2014;37(10):742-746.
The epithelial cell adhesion molecule (EpCAM, also known as CD326) is a transmembrane glycoprotein that is specifically detected in most adenocarcinomas and cancer stem cells. In this study, we performed a Cell systematic evolution of ligands by exponential enrichment (SELEX) experiment to isolate the aptamers against EpCAM. After seven round of Cell SELEX, we identified several aptamer candidates. Among the selected aptamers, EP166 specifically binds to cells expressing EpCAM with an equilibrium dissociation constant (Kd) in a micromolar range. On the other hand, it did not bind to negative control cells. Moreover, EP166 binds to J1ES cells, a mouse embryonic stem cell line. Therefore, the isolated aptamers against EpCAM could be used as a stem cell marker or in other applications in both stem cell and cancer studies.
PMCID: PMC4213765  PMID: 25266702
aptamer; EpCAM; SELEX; stem cell marker
16.  Childhood trauma and adult interpersonal relationship problems in patients with depression and anxiety disorders 
Although a plethora of studies have delineated the relationship between childhood trauma and onset, symptom severity, and course of depression and anxiety disorders, there has been little evidence that childhood trauma may lead to interpersonal problems among adult patients with depression and anxiety disorders. Given the lack of prior research in this area, we aimed to investigate characteristics of interpersonal problems in adult patients who had suffered various types of abuse and neglect in childhood.
A total of 325 outpatients diagnosed with depression and anxiety disorders completed questionnaires on socio-demographic variables, different forms of childhood trauma, and current interpersonal problems. The Childhood Trauma Questionnaire (CTQ) was used to measure five different forms of childhood trauma (emotional abuse, emotional neglect, physical abuse, physical neglect, and sexual abuse) and the short form of the Korean-Inventory of Interpersonal Problems Circumplex Scale (KIIP-SC) was used to assess current interpersonal problems. We dichotomized patients into two groups (abused and non-abused groups) based on CTQ score and investigated the relationship of five different types of childhood trauma and interpersonal problems in adult patients with depression and anxiety disorders using multiple regression analysis.
Different types of childhood abuse and neglect appeared to have a significant influence on distinct symptom dimensions such as depression, state-trait anxiety, and anxiety sensitivity. In the final regression model, emotional abuse, emotional neglect, and sexual abuse during childhood were significantly associated with general interpersonal distress and several specific areas of interpersonal problems in adulthood. No association was found between childhood physical neglect and current general interpersonal distress.
Childhood emotional trauma has more influence on interpersonal problems in adult patients with depression and anxiety disorders than childhood physical trauma. A history of childhood physical abuse is related to dominant interpersonal patterns rather than submissive interpersonal patterns in adulthood. These findings provide preliminary evidence that childhood trauma might substantially contribute to interpersonal problems in adulthood.
PMCID: PMC4304140  PMID: 25648979
Childhood trauma; Interpersonal relationship; Depression; Anxiety
17.  Identification of Degenerate Nuclei and Development of a SCAR Marker for Flammulina velutipes 
PLoS ONE  2014;9(9):e107207.
Flammulina velutipes is one of the major edible mushrooms in the world. Recently, abnormalities that have a negative impact on crop production have been reported in this mushroom. These symptoms include slow vegetative growth, a compact mycelial mat, and few or even no fruiting bodies. The morphologies and fruiting capabilities of monokaryons of wild-type and degenerate strains that arose through arthrospore formation were investigated through test crossing. Only one monokaryotic group of the degenerate strains and its hybrid strains showed abnormal phenotypes. Because the monokaryotic arthrospore has the same nucleus as the parent strain, these results indicated that only one aberrant nucleus of the two nuclei in the degenerate strain was responsible for the degeneracy. A sequence-characterized amplified region marker that is linked to the degenerate monokaryon was identified based on a polymorphic sequence that was generated using random primers. Comparative analyses revealed the presence of a degenerate-specific genomic region in a telomere, which arose via the transfer of a genomic fragment harboring a putative helicase gene. Our findings have narrowed down the potential molecular targets responsible for this phenotype for future studies and have provided a marker for the detection of degenerate strains.
PMCID: PMC4164608  PMID: 25221949
18.  Positive matrix factorization of a 32-month series of daily PM2.5 speciation data with incorporation of temperature stratification 
This study presents source apportionment results for PM2.5 from applying positive matrix factorization (PMF) to a 32-month series of daily PM2.5 compositional data from Denver, CO, including concentrations of sulfate, nitrate, bulk elemental carbon (EC) and organic carbon (OC), and 51 organic molecular markers (OMMs). An optimum 8-factor solution was determined primarily based on the interpretability of the PMF results and rate of matching factors from bootstrapped PMF solutions with those from the base case solution. These eight factors were identified as inorganic ion, n-alkane, EC/sterane, light n-alkane/polycyclic aromatic hydrocarbon (PAH), medium alkane/alkanoic acid, PAH, winter/methoxyphenol and summer/odd n-alkane. The inorganic ion factor dominated the reconstructed PM2.5 mass (sulfate + nitrate + EC + OC) in cold periods (daily average temperature < 10 °C; 43.7% of reconstructed PM2.5 mass) whereas the summer/odd n-alkane factor dominated in hot periods (> 20 °C; 53.1%). The two factors had comparable relative contributions of 26.5% and 27.1% in warm periods with temperatures between 10 °C and 20 °C. Each of the seven factors resolved in a previous study (Dutton et al., 2010b) using a 1-year data set from the same location matches one factor from the current work based on comparing factor profiles. Six out of the seven matched pairs of factors are linked to similar source classes as suggested by the strong correlations between factor contributions (r = 0.89 − 0.98). Temperature-stratified source apportionment was conducted for three subsets of the data in the current study, corresponding to the cold, warm and hot periods mentioned above. The cold period (7-factor) solution exhibited a similar distribution of reconstructed PM2.5 mass as the full data set solution. The factor contributions of the warm period (7-factor) solution were well correlated with those from the full data set solution (r = 0.76 − 0.99). However, the reconstructed PM2.5 mass was distributed more to inorganic ion, n-alkane and medium alkane/alkanoic acid factors in the warm period solution than in the full data set solution. For the hot period (6-factor) solution, PM2.5 mass distribution was quite different from that of the full data set solution, as illustrated by regression slopes as low as 0.2 and as high as 4.8 of each matched pair of factors across the two solutions.
PMCID: PMC4159165  PMID: 25214809
Source apportionment; Positive matrix factorization; Organic molecular markers; Temperature-stratified; Reconstructed PM2.5 mass
19.  Intra-urban spatial variability and uncertainty assessment of PM2.5 sources based on carbonaceous species 
To identify the sources of PM2.5 – bound carbonaceous species and examine the spatial variability of source contributions in the Denver metropolitan area, positive matrix factorization (PMF) was applied to one year of every sixth day ambient PM2.5 compositional data, including elemental carbon (EC), organic carbon (OC), and 32 organic molecular markers, from four sites (two residential and two near-traffic). Statistics (median, inner quantiles and 5th – 95th percentiles range) of factor contributions, expressed as reconstructed carbonaceous mass (EC + OC), were estimated from PMF solutions of replicate datasets generated by using a stationary block bootstrap technique. A seven-factor solution was resolved for a set of data pooled across the four sites, as it gave the most interpretable results and had the highest rate of neural network factor matching (76.9%). Identified factors were primarily associated with high plant wax, summertime emission, diesel vehicle emission, fossil fuel combustion, motor vehicle emission, lubricating oil combustion and wood burning. Pearson correlation coefficients (r) and coefficients of divergence (COD) were used to assess spatial variability of factor contributions. The summertime emission factor exhibited the highest spatial correlation (r = 0.74 – 0.88) and lowest CODs (0.32 – 0.38) among all resolved factors; while the three traffic dominated factors (diesel vehicle emission, motor vehicle emission and lubricating oil combustion) showed lower correlations (r = 0.47 – 0.55) and higher CODs (0.41 – 0.53) on average. Average total EC and OC mass were apportioned to each factor and showed a similar distribution across the four sites. Modeling uncertainties were defined as the 5th – 95th percentile range of the factor contributions derived from valid bootstrap PMF solutions, and were highly correlated with the median factor contribution in each factor (r = 0.77 – 0.98). Source apportionment was also performed on site specific datasets; the results exhibited similar factor profiles and temporal variation in factor contribution as those obtained for the pooled dataset, indicating that the four sites are primarily influenced by similar types of sources. On the other hand, differences were observed in absolute factor contributions between PMF solutions for the pooled versus site-specific datasets, likely due to the large uncertainties in EC and OC factor profiles derived from the site specific datasets with limited numbers of observations.
PMCID: PMC4159203  PMID: 25214808
Source apportionment; Positive matrix factorization; Bootstrap; Uncertainty; Spatial variability
20.  Inhibition of matrix metalloproteinases expression in human dental pulp cells by all-trans retinoic acid 
All-trans retinoic acid (ATRA) inhibits matrix metalloproteinase (MMP)-2 and MMP-9 in synovial fibroblasts, skin fibroblasts, bronchoalveolar lavage cells and cancer cells, but activates MMP-9 in neuroblast and leukemia cells. Very little is known regarding whether ATRA can activate or inhibit MMPs in human dental pulp cells (HDPCs). The purpose of this study was to determine the effects of ATRA on the production and secretion of MMP-2 and -9 in HDPCs. The productions and messenger RNA (mRNA) expressions of MMP-2 and -9 were accessed by gelatin zymography and real-time polymerase chain reaction (PCR), respectively. ATRA was found to decrease MMP-2 level in a dose-dependent manner. Significant reduction in MMP-2 mRNA expression was also observed in HDPCs treated with 25 µmol⋅L−1 ATRA. However, HDPCs treated with ATRA had no effect on the pattern of MMP-9 produced or secreted in either cell extracts or conditioned medium fractions. Taken together, ATRA had an inhibitory effect on MMP-2 expression in HDPCs, which suggests that ATRA could be a candidate as a medicament which could control the inflammation of pulp tissue in vital pulp therapy and regenerative endodontics.
PMCID: PMC4170145  PMID: 24008270
all-trans retinoic acid; human dental pulp cell; matrix metalloproteinase; zymography
21.  Expression of colSR Genes Increased in the rpf Mutants of Xanthomonas oryzae pv. oryzae KACC10859 
The Plant Pathology Journal  2014;30(3):304-309.
The rpf genes and colSXOO1207/colRXOO1208 were known to require for virulence of Xanthomonas oryzae pv. oryzae (Xoo). In Xoo KACC10331 genome, two more colS/colR genes, colSXOO3534 (raxH)/colRXOO3535 (raxR) and colSXOO3762/colRXOO3763 were annotated. The colSXOO3534/colRXOO3535 were known to control AvrXa21 activity and functions of colSXOO3762/colRXOO3763 were unknown in Xoo. To characterize the relationship between rpf and colS/colR genes, expression of colS/colR genes in Rpf mutants of Xoo were analyzed with quantitative reverse transcription PCR (qRT-PCR). Expressions of all three colS/colR genes increased in the rpfF mutant in which DSF synthesis is defective. Expression of colSXOO1207/colRXOO1208, colSXOO3534/colRXOO3535 and colSXOO3762/colRXOO3763 increased 2, 2–7, 3–13 folds respectively. Expression of colSXOO3534 and colSXOO3762 also increased 2–4 folds in the rpfG mutant in which the signal from DSF is no longer transferred to down-stream. Expression of the other colS/colR genes was not significantly changed in the rpfG mutant compared to the wild type. Since RpfF and RpfG are responsible for DSF synthesis and signal transfer from DSF to down-stream to regulate virulence gene expression, these results suggest that the DSF and DSF-mediated signal regulate negatively three colS/colR genes in Xoo.
PMCID: PMC4181107  PMID: 25289017
ColS/ColR; Rpf; virulence regulation; Xanthomonas oryzae pv. oryzae
22.  Identification and Functional Analysis of Pheromone and Receptor Genes in the B3 Mating Locus of Pleurotus eryngii 
PLoS ONE  2014;9(8):e104693.
Pleurotus eryngii has recently become a major cultivated mushroom; it uses tetrapolar heterothallism as a part of its reproductive process. Sexual development progresses only when the A and B mating types are compatible. Such mating incompatibility occasionally limits the efficiency of breeding programs in which crossing within loci-shared strains or backcrossing strategies are employed. Therefore, understanding the mating system in edible mushroom fungi will help provide a short cut in the development of new strains. We isolated and identified pheromone and receptor genes in the B3 locus of P. eryngii and performed a functional analysis of the genes in the mating process by transformation. A genomic DNA library was constructed to map the entire mating-type locus. The B3 locus was found to contain four pheromone precursor genes and four receptor genes. Remarkably, receptor PESTE3.3.1 has just 34 amino acid residues in its C-terminal cytoplasmic region; therefore, it seems likely to be a receptor-like gene. Real-time quantitative RT-PCR (real-time qRT-PCR) revealed that most pheromone and receptor genes showed significantly higher expression in monokaryotic cells than dikaryotic cells. The pheromone genes PEphb3.1 and PEphb3.3 and the receptor gene PESTE3.3.1 were transformed into P5 (A3B4). The transformants were mated with a tester strain (A4B4), and the progeny showed clamp connections and a normal fruiting body, which indicates the proposed role of these genes in mating and fruiting processes. This result also confirms that PESTE3.3.1 is a receptor gene. In this study, we identified pheromone and receptor genes in the B3 locus of P. eryngii and found that some of those genes appear to play a role in the mating and fruiting processes. These results might help elucidate the mechanism of fruiting differentiation and improve breeding efficiency.
PMCID: PMC4136793  PMID: 25133513
23.  Quantitative PCR for Etiologic Diagnosis of Methicillin-Resistant Staphylococcus aureus Pneumonia in Intensive Care Unit 
Ventilator-associated pneumonia (VAP) requires prompt and appropriate treatment. Since methicillin-resistant Staphylococcus aureus (MRSA) is a frequent pathogen in VAP, rapid identification of it, is pivotal. Our aim was to evaluate the utility of quantitative polymerase chain reaction (qPCR) as a useful method for etiologic diagnoses of MRSA pneumonia.
We performed qPCR for mecA, S. aureus-specific femA-SA, and S. epidermidis-specific femA-SE genes from bronchoalveolar lavage or bronchial washing samples obtained from clinically-suspected VAP. Molecular identification of MRSA was based on the presence of the mecA and femA-SA gene, with the absence of the femA-SE gene. To compensate for the experimental and clinical conditions, we spiked an internal control in the course of DNA extraction. We estimated number of colony-forming units per mL (CFU/mL) of MRSA samples through a standard curve of a serially-diluted reference MRSA strain. We compared the threshold cycle (Ct) value with the microbiologic results of MRSA.
We obtained the mecA gene standard curve, which showed the detection limit of the mecA gene to be 100 fg, which corresponds to a copy number of 30. We chose cut-off Ct values of 27.94 (equivalent to 1×104 CFU/mL) and 21.78 (equivalent to 1×105 CFU/mL). The sensitivity and specificity of our assay were 88.9% and 88.9% respectively, when compared with quantitative cultures.
Our results were valuable for diagnosing and identifying pathogens involved in VAP. We believe our modified qPCR is an appropriate tool for the rapid diagnosis of clinical pathogens regarding patients in the intensive care unit.
PMCID: PMC3510279  PMID: 23227069
Methicillin-Resistant Staphylococcus aureus; Real-Time Polymerase Chain Reaction; Pneumonia, Ventilator-Associated
24.  Postprandial glucose-lowering effects of fermented red ginseng in subjects with impaired fasting glucose or type 2 diabetes: a randomized, double-blind, placebo-controlled clinical trial 
Red ginseng is prepared by steaming raw ginseng, a process believed to increase the pharmacological efficacy. Further bioconversion of red ginseng through fermentation is known to increase its intestinal absorption and bioactivity, and bioconversion diminishes the toxicity of red ginseng’s metabolite. This study was conducted to investigate the effects of daily supplementation with fermented red ginseng (FRG) on glycemic status in subjects with impaired fasting glucose or type 2 diabetes.
This study was a four-week long, randomized, double-blind, placebo-controlled trial. Forty-two subjects with impaired fasting glucose or type 2 diabetes were randomly allocated to two groups assigned to consume either the placebo or fermented red ginseng (FRG) three times per day for four weeks. Fasting and postprandial glucose profiles during meal tolerance tests were assessed before and after the intervention.
FRG supplementation led to a significant reduction in postprandial glucose levels and led to an increase in postprandial insulin levels compared to the placebo group. There was a consistently significant improvement in the glucose area under the curve (AUC) in the FRG group. However, fasting glucose, insulin, and lipid profiles were not different from the placebo group.
Daily supplementation with FRG lowered postprandial glucose levels in subjects with impaired fasting glucose or type 2 diabetes.
Trial registration NCT01826409
PMCID: PMC4227112  PMID: 25015735
Fermented red ginseng; Type 2 diabetes; Impaired fasting glucose; Postprandial glucose

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