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1.  KNOW-KT (KoreaN cohort study for outcome in patients with kidney transplantation: a 9-year longitudinal cohort study): study rationale and methodology 
BMC Nephrology  2014;15:77.
Background
Asian patients undergoing kidney transplantation (KT) generally have better renal allograft survival and a lower burden of cardiovascular disease than those of other racial groups. The KNOW-KT aims to explore allograft survival rate, cardiovascular events, and metabolic profiles and to elucidate the risk factors in Korean KT patients.
Methods
KNOW-KT is a multicenter, observational cohort study encompassing 8 transplant centers in the Republic of Korea. KNOW-KT will enroll 1,000 KT recipients between 2012 and 2015 and follow them up to 9 years. At the time of KT and at pre-specified intervals, clinical information, laboratory test results, and functional and imaging studies on cardiovascular disease and metabolic complications will be recorded. Comorbid status will be assessed by the age-adjusted Charlson co-morbidity index. Medication adherence and information on quality of life (QoL) will be monitored periodically. The QoL will be assessed by the Kidney Disease Quality of Life Short Form. Donors will include both living donors and deceased donors whose status will be assessed by the Kidney Donor Risk Index. Primary endpoints include graft loss and patient mortality. Secondary endpoints include renal functional deterioration (a decrease in eGFR to <30 mL/min/1.73 m2), acute rejection, cardiovascular event, albuminuria, new-onset diabetes after transplant, and QoL. Data on other adverse outcomes including episodes of infection, malignancy, recurrence of original renal disease, fracture, and hospitalization will also be collected. A bio-bank has been established for the acquisition of DNA, RNA, and protein from serum and urine samples of recipients at regular intervals. Bio-samples from donors will also be collected at the time of KT. KNOW-KT was registered in an international clinical trial registry (NCT02042963 at http://www.clinicaltrials.gov) on January 20th, 2014.
Conclusion
The KNOW-KT, the first large-scale cohort study in Asian KT patients, is expected to represent the Asian KT population and provide information on their natural course, complications, and risk factors for complications.
doi:10.1186/1471-2369-15-77
PMCID: PMC4022441  PMID: 24884405
Cohort study; Complication; Kidney transplantation; KNOW-KT; Risk factor
2.  Risk of secondary cancers from scattered radiation during intensity-modulated radiotherapies for hepatocellular carcinoma 
Purpose
To evaluate and compare the risks of secondary cancers from therapeutic doses received by patients with hepatocellular carcinoma (HCC) during intensity-modulated radiotherapy (IMRT), volumetric arc therapy (VMAT), and tomotherapy (TOMO).
Methods
Treatments for five patients with hepatocellular carcinoma (HCC) were planned using IMRT, VMAT, and TOMO. Based on the Biological Effects of Ionizing Radiation VII method, the excess relative risk (ERR), excess absolute risk (EAR), and lifetime attributable risk (LAR) were evaluated from therapeutic doses, which were measured using radiophotoluminescence glass dosimeters (RPLGDs) for each organ inside a humanoid phantom.
Results
The average organ equivalent doses (OEDs) of 5 patients were measured as 0.23, 1.18, 0.91, 0.95, 0.97, 0.24, and 0.20 Gy for the thyroid, lung, stomach, liver, small intestine, prostate (or ovary), and rectum, respectively. From the OED measurements, LAR incidence were calculated as 83, 46, 22, 30, 2 and 6 per 104 person for the lung, stomach, normal liver, small intestine, prostate (or ovary), and rectum.
Conclusions
We estimated the secondary cancer risks at various organs for patients with HCC who received different treatment modalities. We found that HCC treatment is associated with a high secondary cancer risk in the lung and stomach.
doi:10.1186/1748-717X-9-109
PMCID: PMC4030012  PMID: 24886163
HCC; IMRT; VMAT; Tomotherapy; Radiophotoluminescence; OED; EAR; ERR; LAR
3.  A Conserved Mechanism for Binding of p53 DNA-Binding Domain and Anti-Apoptotic Bcl-2 Family Proteins 
Molecules and Cells  2014;37(3):264-269.
The molecular interaction between tumor suppressor p53 and the anti-apoptotic Bcl-2 family proteins plays an essential role in the transcription-independent apoptotic pathway of p53. In this study, we investigated the binding of p53 DNA-binding domain (p53DBD) with the anti-apoptotic Bcl-2 family proteins, Bcl-w, Mcl-1, and Bcl-2, using GST pull-down assay and NMR spectroscopy. The GST pull-down assays and NMR experiments demonstrated the direct binding of the p53DBD with Bcl-w, Mcl-1, and Bcl-2. Further, NMR chemical shift perturbation data showed that Bcl-w and Mcl-1 bind to the positively charged DNA-binding surface of p53DBD. Noticeably, the refined structural models of the complexes between p53DBD and Bcl-w, Mcl-1, and Bcl-2 showed that the binding mode of p53DBD is highly conserved among the anti-apoptotic Bcl-2 family proteins. Furthermore, the chemical shift perturbations on Bcl-w, Mcl-1, and Bcl-2 induced by p53DBD binding occurred not only at the p53DBD-binding acidic region but also at the BH3 peptide-binding pocket, which suggests an allosteric conformational change similar to that observed in Bcl-XL. Taken altogether, our results revealed a structural basis for a conserved binding mechanism between p53DBD and the anti-apoptotic Bcl-2 family proteins, which shed light on to the molecular understanding of the transcription-independent apoptosis pathway of p53.
doi:10.14348/molcells.2014.0001
PMCID: PMC3969048  PMID: 24646834
apoptosis; Bcl-2 family proteins; binding mechanism; DNA-binding domain; p53
4.  Risk of second cancer from scattered radiation of intensity-modulated radiotherapies with lung cancer 
Purpose
To compare the risk of secondary cancer from scattered and leakage doses following intensity-modulated radiotherapy (IMRT), volumetric arc therapy (VMAT) and tomotherapy (TOMO) in patients with lung cancer.
Methods
IMRT, VMAT and TOMO were planned for five lung cancer patients. Organ equivalent doses (OEDs) are estimated from the measured corresponding secondary doses during irradiation at various points 20 to 80 cm from the iso-center by using radio-photoluminescence glass dosimeter (RPLGD).
Results
The secondary dose per Gy from IMRT, VMAT and TOMO for lung cancer, measured 20 to 80 cm from the iso-center, are 0.02~2.03, 0.03~1.35 and 0.04~0.46 cGy, respectively. The mean values of relative OED of secondary dose of VMAT and TOMO, which is normalized by IMRT, ranged between 88.63% and 41.59% revealing 88.63% and 41.59% for thyroid, 82.33% and 41.85% for pancreas, 77.97% and 49.41% for bowel, 73.42% and 72.55% for rectum, 74.16% and 81.51% for prostate. The secondary dose and OED from TOMO became similar to those from IMRT and VMAT as the distance from the field edge increased.
Conclusions
OED based estimation suggests that the secondary cancer risk from TOMO is less than or comparable to the risks from conventional IMRT and VMAT.
doi:10.1186/1748-717X-8-47
PMCID: PMC3599921  PMID: 23452670
IMRT; VMAT; TOMOTHERAPY; Radio-photoluminescence; Secondary dose; OED
5.  Large-scale replication and heterogeneity in Parkinson disease genetic loci 
Sharma, Manu | Ioannidis, John P.A. | Aasly, Jan O. | Annesi, Grazia | Brice, Alexis | Van Broeckhoven, Christine | Bertram, Lars | Bozi, Maria | Crosiers, David | Clarke, Carl | Facheris, Maurizio | Farrer, Matthew | Garraux, Gaetan | Gispert, Suzana | Auburger, Georg | Vilariño-Güell, Carles | Hadjigeorgiou, Georgios M. | Hicks, Andrew A. | Hattori, Nobutaka | Jeon, Beom | Lesage, Suzanne | Lill, Christina M. | Lin, Juei-Jueng | Lynch, Timothy | Lichtner, Peter | Lang, Anthony E. | Mok, Vincent | Jasinska-Myga, Barbara | Mellick, George D. | Morrison, Karen E. | Opala, Grzegorz | Pramstaller, Peter P. | Pichler, Irene | Park, Sung Sup | Quattrone, Aldo | Rogaeva, Ekaterina | Ross, Owen A. | Stefanis, Leonidas | Stockton, Joanne D. | Satake, Wataru | Silburn, Peter A. | Theuns, Jessie | Tan, Eng-King | Toda, Tatsushi | Tomiyama, Hiroyuki | Uitti, Ryan J. | Wirdefeldt, Karin | Wszolek, Zbigniew | Xiromerisiou, Georgia | Yueh, Kuo-Chu | Zhao, Yi | Gasser, Thomas | Maraganore, Demetrius | Krüger, Rejko | Boyle, R.S | Sellbach, A | O'Sullivan, J.D. | Sutherland, G.T. | Siebert, G.A | Dissanayaka, N.N.W | Van Broeckhoven, Christine | Theuns, Jessie | Crosiers, David | Pickut, Barbara | Engelborghs, Sebastiaan | Meeus, Bram | De Deyn, Peter P. | Cras, Patrick | Rogaeva, Ekaterina | Lang, Anthony E | Agid, Y | Anheim, M | Bonnet, A-M | Borg, M | Brice, A | Broussolle, E | Corvol, JC | Damier, P | Destée, A | Dürr, A | Durif, F | Lesage, S | Lohmann, E | Pollak, P | Rascol, O | Tison, F | Tranchant, C | Viallet, F | Vidailhet, M | Tzourio, Christophe | Amouyel, Philippe | Loriot, Marie-Anne | Mutez, Eugénie | Duflot, Aurélie | Legendre, Jean-Philippe | Waucquier, Nawal | Gasser, Thomas | Riess, Olaf | Berg, Daniela | Schulte, Claudia | Klein, Christine | Djarmati, Ana | Hagenah, Johann | Lohmann, Katja | Auburger, Georg | Hilker, Rüdiger | van de Loo, Simone | Dardiotis, Efthimios | Tsimourtou, Vaia | Ralli, Styliani | Kountra, Persa | Patramani, Gianna | Vogiatzi, Cristina | Hattori, Nobutaka | Tomiyama, Hiroyuki | Funayama, Manabu | Yoshino, Hiroyo | Li, Yuanzhe | Imamichi, Yoko | Toda, Tatsushi | Satake, Wataru | Lynch, Tim | Gibson, J. Mark | Valente, Enza Maria | Ferraris, Alessandro | Dallapiccola, Bruno | Ialongo, Tamara | Brighina, Laura | Corradi, Barbara | Piolti, Roberto | Tarantino, Patrizia | Annesi, Ferdinanda | Jeon, Beom S. | Park, Sung-Sup | Aasly, J | Opala, Grzegorz | Jasinska-Myga, Barbara | Klodowska-Duda, Gabriela | Boczarska-Jedynak, Magdalena | Tan, Eng King | Belin, Andrea Carmine | Olson, Lars | Galter, Dagmar | Westerlund, Marie | Sydow, Olof | Nilsson, Christer | Puschmann, Andreas | Lin, JJ | Maraganore, Demetrius M. | Ahlskog, J, Eric | de Andrade, Mariza | Lesnick, Timothy G. | Rocca, Walter A. | Checkoway, Harvey | Ross, Owen A | Wszolek, Zbigniew K. | Uitti, Ryan J.
Neurology  2012;79(7):659-667.
Objective:
Eleven genetic loci have reached genome-wide significance in a recent meta-analysis of genome-wide association studies in Parkinson disease (PD) based on populations of Caucasian descent. The extent to which these genetic effects are consistent across different populations is unknown.
Methods:
Investigators from the Genetic Epidemiology of Parkinson's Disease Consortium were invited to participate in the study. A total of 11 SNPs were genotyped in 8,750 cases and 8,955 controls. Fixed as well as random effects models were used to provide the summary risk estimates for these variants. We evaluated between-study heterogeneity and heterogeneity between populations of different ancestry.
Results:
In the overall analysis, single nucleotide polymorphisms (SNPs) in 9 loci showed significant associations with protective per-allele odds ratios of 0.78–0.87 (LAMP3, BST1, and MAPT) and susceptibility per-allele odds ratios of 1.14–1.43 (STK39, GAK, SNCA, LRRK2, SYT11, and HIP1R). For 5 of the 9 replicated SNPs there was nominally significant between-site heterogeneity in the effect sizes (I2 estimates ranged from 39% to 48%). Subgroup analysis by ethnicity showed significantly stronger effects for the BST1 (rs11724635) in Asian vs Caucasian populations and similar effects for SNCA, LRRK2, LAMP3, HIP1R, and STK39 in Asian and Caucasian populations, while MAPT rs2942168 and SYT11 rs34372695 were monomorphic in the Asian population, highlighting the role of population-specific heterogeneity in PD.
Conclusion:
Our study allows insight to understand the distribution of newly identified genetic factors contributing to PD and shows that large-scale evaluation in diverse populations is important to understand the role of population-specific heterogeneity. Neurology® 2012;79:659–667
doi:10.1212/WNL.0b013e318264e353
PMCID: PMC3414661  PMID: 22786590
6.  Case of Small Bowel Perforation due to Enteropathy-Type T-Cell Lymphoma 
Yonsei Medical Journal  2009;50(6):859-861.
Enteropathy-type T-cell lymphoma (ETTL) is a rare disease with a poor prognosis. According to the World Health Organization (WHO) classification, it is a subtype of the peripheral T-cell lymphomas. This disease is associated with gluten-sensitive enteropathy, has a high risk of intestinal perforation and obstruction, and is refractory to chemotherapeutic treatment. We report the case of a 73-year-old woman who was diagnosed with enteropathy-type T-cell lymphoma of the small intestine, which was positive for the markers of cytotoxic T cells, CD3, CD8, and CD56, on immunohistochemical staining after resection of the perforated terminal ileum.
doi:10.3349/ymj.2009.50.6.859
PMCID: PMC2796418  PMID: 20046432
Enteropathy-type T-cell lymphoma; celiac disease; intestinal perforation
7.  An improved algorithm for respiration signal extraction from electrocardiogram measured by conductive textile electrodes using instantaneous frequency estimation 
In this paper, an improved algorithm for the extraction of respiration signal from the electrocardiogram (ECG) in home healthcare is proposed. The whole system consists of two-lead electrocardiogram acquisition using conductive textile electrodes located in bed, baseline fluctuation elimination, R-wave detection, adjustment of sudden change in R-wave area using moving average, and optimal lead selection. In order to solve the problems of previous algorithms for the ECG-derived respiration (EDR) signal acquisition, we are proposing a method for the optimal lead selection. An optimal EDR signal among the three EDR signals derived from each lead (and arctangent of their ratio) is selected by estimating the instantaneous frequency using the Hilbert transform, and then choosing the signal with minimum variation of the instantaneous frequency. The proposed algorithm was tested on 15 male subjects, and we obtained satisfactory respiration signals that showed high correlation (r2 > 0.8) with the signal acquired from the chest-belt respiration sensor.
doi:10.1007/s11517-007-0302-y
PMCID: PMC2668578  PMID: 18210178
Home healthcare; Conductive textile electrodes in bed; ECG-derived respiration; Instantaneous frequency; Hilbert transform
8.  Prevalence of Systemic Lupus Erythematosus in South Korea: An Administrative Database Study 
Journal of Epidemiology  2014;24(4):295-303.
Background
Systemic lupus erythematosus (SLE) is a rare autoimmune disease for which a population-based survey on the prevalence of the disease in South Korea has not yet been conducted. Our goal was to estimate the nationwide prevalence of SLE.
Methods
The International Classification of Diseases, Tenth Revision (ICD-10) code for SLE diagnosis—M32—was tentatively given when patients were suspected to have SLE before 2009. As such, the positive predictive value (PPV) of the M32 code shown in medical bills reflecting true SLE was uncertain. We attempted to estimate the prevalence of SLE in South Korea using national administrative database data from 2004–2006. We approximated the actual number of SLE patients by analyzing a list of SLE-coded patients provided by the National Health Insurance (NHI) and Health Insurance Review and Assessment Service. Prevalence was estimated by multiplying the PPV of the M32 diagnostic code by the number of patients receiving the code. The PPV was determined by three methods: direct investigation of the medical records of patients randomly selected from the SLE-coded patients list; assessment of all SLE patients treated at 56 selected hospitals in South Korea; and extrapolation from sub-groups at a single institute to the sub-groups of the national NHI data.
Results
The estimated number of national SLE cases was between 9000 and 11 000, depending on the method of ascertainment, corresponding to a prevalence of 18.8–21.7 per 100 000 people.
Conclusions
This is the first report of a nationwide prevalence survey of SLE in South Korea. National databases may serve as a resource for epidemiologic studies of rare autoimmune diseases like SLE.
doi:10.2188/jea.JE20120204
PMCID: PMC4074634  PMID: 24857955
systemic lupus erythematosus; prevalence; epidemiology
9.  First Korean Case of Mycobacterium arupense Tenosynovitis 
Annals of Laboratory Medicine  2014;34(4):321-324.
doi:10.3343/alm.2014.34.4.321
PMCID: PMC4071191  PMID: 24982839
10.  Depression and Anxiety in People with Epilepsy 
Many recent epidemiological studies have found the prevalence of depression and anxiety to be higher in people with epilepsy (PWE) than in people without epilepsy. Furthermore, people with depression or anxiety have been more likely to suffer from epilepsy than those without depression or anxiety. Almost one-third of PWE suffer from depression and anxiety, which is similar to the prevalence of drug-refractory epilepsy. Various brain areas, including the frontal, temporal, and limbic regions, are associated with the biological pathogenesis of depression in PWE. It has been suggested that structural abnormalities, monoamine pathways, cerebral glucose metabolism, the hypothalamic-pituitary-adrenal axis, and interleukin-1b are associated with the pathogenesis of depression in PWE. The amygdala and the hippocampus are important anatomical structures related to anxiety, and γ-aminobutyric acid and serotonin are associated with its pathogenesis. Depression and anxiety may lead to suicidal ideation or attempts and feelings of stigmatization. These experiences are also likely to increase the adverse effects associated with antiepileptic drugs and have been related to poor responses to pharmacological and surgical treatments. Ultimately, the quality of life is likely to be worse in PWE with depression and anxiety than in PWE without these disorders, which makes the early detection and appropriate management of depression and anxiety in PWE indispensable. Simple screening instruments may be helpful for in this regard, particularly in busy epilepsy clinics. Although both medical and psychobehavioral therapies may ameliorate these conditions, randomized controlled trials are needed to confirm that.
doi:10.3988/jcn.2014.10.3.175
PMCID: PMC4101093  PMID: 25045369
epilepsy; depression; anxiety
11.  Resting energy expenditure is not associated with disease activity in women with rheumatoid arthritis: cross-sectional study 
Background/Aims
Increased resting energy expenditure (REE) in rheumatoid arthritis (RA) patients is thought to be caused by hypermetabolism associated with production of proinflammatory cytokines. Our aim in the present study was to explore the possible association between REE and disease activity in females with RA.
Methods
A total of 499 female RA patients were recruited to this cross-sectional study assessing REE scores on disease activity indices (the routine assessment of patient index data 3 [RAPID3], the disease activity score 28, and the clinical/simplified disease activity index [CDAI/SDAI]) and the levels of RA-associated autoantibodies (rheumatoid factor and anticyclic citrullinated peptide [anti-CCP] antibodies). Age-matched healthy female controls (n = 131) were also enrolled.
Results
REE did not differ between RA patients (all patients, and those in remission or not) and controls, or between RA patients in remission or not (p > 0.05 for all comparisons). Increased REE in total RA patients was associated with younger age and a higher body mass index (BMI) (p < 0.001 and p < 0.001, respectively), but not with disease activity index scores on any of RAPID3, CDAI, or SDAI. BMI was the only clinical parameter exhibiting a significant relationship with REE quartiles (Q1 to Q4; p < 0.001); none of disease duration, functional status, or anti-CCP antibody titer in RA patients was significantly related to REE, based on analysis of covariance.
Conclusions
We found no association between REE and disease activity in RA patients, implying that energy metabolism in RA patients might be independent of RA-associated systemic inflammation.
doi:10.3904/kjim.2014.29.4.516
PMCID: PMC4101599  PMID: 25045300
Arthritis, rheumatoid; Resting energy expenditure; Disease activity index
12.  A Case Report of Preoperative and Postoperative 7.0T Brain MRI in a Patient with a Small Cell Glioblastoma 
Journal of Korean Medical Science  2014;29(7):1012-1017.
A 45-yr-old female patient was admitted with one-month history of headache and progressive left hemiparesis. Brain magnetic resonance imaging (MRI) demonstrated a mass lesion in her right frontal lobe. Her brain tumor was confirmed as a small cell glioblastoma. Her follow-up brain MRI, taken at 8 months after her initial surgery demonstrated tumor recurrence in the right frontal lobe. Contrast-enhanced 7.0T brain magnetic resonance imaging (MRI) was safely performed before surgery and at the time of recurrence. Compared with 1.5T and 3.0T brain MRI, 7.0T MRI showed sharpened images of the brain tumor contexture with detailed anatomical information. The fused images of 7.0T and 1.5T brain MRI taken at the time of recurrence demonstrated no significant discrepancy in the positions of the anterior and the posterior commissures. It is suggested that 7.0T MRI can be safely utilized for better images of the maligant gliomas before and after surgery.
Graphical Abstract
doi:10.3346/jkms.2014.29.7.1012
PMCID: PMC4101769  PMID: 25045237
Pre- and post-operative 7.0T MRI; Small Cell Glioblastoma
13.  Clinical Significance of Non-Alcoholic Fatty Liver Disease as a Risk Factor for Prehypertension 
Journal of Korean Medical Science  2014;29(7):973-979.
Previous epidemiologic studies have shown the clinical association between non-alcoholic fatty liver disease (NAFLD) and cardiovascular disease (CVD). However, there is only limited information about the effect of NAFLD on the development of hypertension. Accordingly, we investigated the clinical association between NAFLD and prehypertension. A prospective cohort study was conducted on the 11,350 Korean men without prehypertension for 5 yr. The incidences of prehypertension were evaluated, and Cox proportional hazard model was used to measure the hazard ratios (HRs) for the development of prehypertension according to the degree of NAFLD (normal, mild, moderate to severe). The incidence of prehypertension increased according to NAFLD states (normal: 55.5%, mild: 63.7%, moderate to severe: 70.3%, P<0.001). Even after adjusting for multiple covariates, the HRs (95% confidence interval) for prehypertension were higher in the mild group (1.18; 1.07-1.31) and moderate to severe group (1.62; 1.21-2.17), compared to normal group, respectively (P for trend <0.001). The development of prehypertension is more potentially associated with the more progressive NAFLD than normal and milder state. These findings suggest the clinical significance of NAFLD as one of risk factors for prehypertension.
doi:10.3346/jkms.2014.29.7.973
PMCID: PMC4101786  PMID: 25045230
Non-Alcoholic Fatty Liver Disease; Blood Pressure; Prehypertension
14.  Posterior Reversible Encephalopathy Syndrome Due to Hyponatremia 
Journal of Epilepsy Research  2014;4(1):31-33.
Posterior reversible encephalopathy syndrome (PRES) is characterized by variable associations of seizure activity, consciousness impairment, headaches, visual abnormalities, nausea/vomiting, and focal neurological signs. The PRES may occur in diverse situations. The findings on neuroimaging in PRES are often symmetric and predominate edema in the white matter of the brain areas perfused by the posterior brain circulation, which is reversible when the underlying cause is treated. We report the case of PRES in normotensive patient with hyponatremia.
PMCID: PMC4066623  PMID: 24977130
Posterior reversible encephalopathy syndrome; Hyponatremia; Cerebral autoregulation; Seizure
15.  Modeling and Estimation of Kinetic Parameters and Replicative Fitness of HIV-1 from Flow-Cytometry-Based Growth Competition Experiments 
Bulletin of mathematical biology  2008;70(6):1749-1771.
Growth competition assays have been developed to quantify the relative fitness of HIV-1 mutants. In this article, we develop mathematical models to describe viral/cellular dynamic interactions in the assay system from which the competitive fitness indices or parameters are defined. In our previous HIV-viral fitness experiments, the concentration of uninfected target cells was assumed to be constant (Wu et al., 2006). But this may not be true in some experiments. In addition, dual infection may frequently occur in viral fitness experiments and may not be ignorable. Here, we relax these two assumptions and extend our earlier viral fitness model (Wu et al., 2006). The resulting models then become nonlinear ODE systems for which closed-form solutions are not achievable. In the new model, the viral relative fitness is a function of time since it depends on the target cell concentration. First, we studied the structure identifiability of the nonlinear ODE models. The identifiability analysis showed that all parameters in the proposed models are identifiable from the flow-cytometry-based experimental data that we collected. We then employed a global optimization approach (the differential evolution algorithm) to directly estimate the kinetic parameters as well as the relative fitness index in the nonlinear ODE models using nonlinear least square regression based on the experimental data. Practical identifiability was investigated via Monte Carlo simulations.
doi:10.1007/s11538-008-9323-4
PMCID: PMC4065495  PMID: 18648886
Differential evolution; Global optimization; HIV/AIDS; Model identifiability; Ordinary differential equation (ODE); Statistical inverse problem; Viral fitness
16.  MyD88 signaling is not essential for induction of antigen-specific B cell responses but is indispensable for protection against Streptococcus pneumoniae infection following oral vaccination with attenuated Salmonella expressing PspA antigen 
Toll-like receptors (TLRs) directly induce innate host defense responses, but the mechanisms of TLR-mediated adaptive immunity remain subject to debate. In this study, we clarified a role of TLR-mediated innate immunity for induction of adaptive immunity by oral vaccination with a live recombinant attenuated Salmonella enteric serovar typhimurium vaccine (RASV) strain expressing Streptococcus pneumoniae surface protein A (PspA) antigen. Of note, oral or intranasal vaccination with RASV expressing PspA resulted in identical or even significantly higher levels of PspA-specific IgG and IgA responses in the systemic and mucosal compartments of MyD88−/− mice of either BALB/c or C57BL/6 background when compared with those of wild-type mice. Although PspA-specific CD4+ T cell proliferation in the MyD88−/− mice was minimal, depletion of CD4+ T cells abolished PspA-specific IgG and IgA responses in the MyD88−/− mice of BALB/c background. Of most interest, MyD88−/− mice that possessed high levels of PspA-specific IgG and IgA responses but minimal levels of CD4+ T cell responses died earlier than non-vaccinated and vaccinated wild-type mice following intravenous or intranasal challenge with virulent S. pneumoniae. Taken together, these results suggest that innate immunity activated by MyD88 signals might not be necessary for antigen-specific antibody induction in both systemic and mucosal sites but is critical for protection following oral vaccination with attenuated Salmonella expressing PspA.
PMCID: PMC4063294  PMID: 18941235
Oral; Vaccination; Salmonella; MyD88; Innate Immunity; Mucosal Immunity
17.  Therapeutic effect of anti-C-X-C motif chemokine 10 (CXCL10) antibody on C protein-induced myositis mouse 
Arthritis Research & Therapy  2014;16(3):R126.
Introduction
C-X-C motif chemokine 10 (CXCL10) is a chemokine that plays a critical role in the infiltration of T cells in autoimmune diseases and is reported to be expressed in muscle tissue of polymyositis. To determine the therapeutic efficacy of CXCL10 blockade, we investigated the role of CXCL10 and the effect of anti-CXCL10 antibody treatment in C protein-induced myositis (CIM), an animal model of polymyositis.
Methods
CIM was induced with human skeletal muscle C protein fragment in female C57BL/6 mice. Immunohistochemistry of CXCL10 and C-X-C motif chemokine receptor 3 (CXCR3) and measurement of serum CXCL10 were performed. Cell surface markers and interferon-gamma (IFN-γ) and tumor necrosis factor-alpha (TNF-α) in CIM lymph node cells was investigated by flow cytometry. Mice with CIM were treated with anti-CXCL10 antibody or control antibody (anti-RVG1) and the inflammation in muscle tissue was assessed.
Results
Immunohistochemistry showed increased expression of CXCL10 and CXCR3 in the inflammatory lesions of muscle in CIM. Especially, CD8+ T cells invading myofiber expressed CXCR3. Serum level of CXCL10 was increased in CIM compared to the level in normal mice (normal mouse, 14.3 ± 5.3 pg/ml vs. CIM, 368.5 ± 135.6 pg/ml, P < 0.001). CXCR3 positivity in CD8+ T cells was increased compared to that of CD4+ T cells in the lymph node cells of CIM (CXCR3+ among CD8+ T cell, 65.9 ± 2.1% vs. CXCR3+ among CD4+ T cell, 23.5 ± 4.7%, P <0.001). Moreover, IFN-γ+ cells were increased among CXCR3+CD8+ T cells compared to CXCR3–CD8+ T cells (CXCR3+CD8+ T cell, 28.0 ± 4.2% vs. CXCR3-CD8+ T cell, 9.5 ± 1.5%, P = 0.016). Migration of lymph node cells was increased in response to CXCL10 (chemotactic index was 1.91 ± 0.45). CIM mice treated with anti-CXCL10 antibody showed a lower inflammation score in muscles than those with anti-RVG1 (median, anti-CXCL10 treatment group, 0.625 vs. anti-RVG1 treatment group, 1.25, P = 0.007).
Conclusions
CXCL10/CXCR3 expression was increased in the inflammation of CIM model and its blockade suppressed inflammation in muscle.
doi:10.1186/ar4583
PMCID: PMC4095607  PMID: 24939012
18.  Incidence and predictors of morphometric vertebral fractures in patients with ankylosing spondylitis 
Arthritis Research & Therapy  2014;16(3):R124.
Introduction
Ankylosing spondylitis (AS) is associated with an increased incidence of vertebral fractures (VFs); however the actual incidence and predictors of morphometric VFs are unknown. The present study examined the incidence and predictors of new VFs in a large AS cohort.
Methods
In total, 298 AS patients who fulfilled the modified New York criteria were enrolled and spinal radiographs were evaluated biennially. Clinical and laboratory data and radiographic progression were assessed according to the Bath AS Disease Activity Index, erythrocyte sedimentation rate, C-reactive protein (CRP), and the Stoke AS spine score (SASSS). VF was defined according to the Genant criteria. The incidence of VFs at 2 and 4 years was evaluated using the Kaplan-Meier method. The age-specific standardized prevalence ratio (SPR) for AS patients in comparison with the general population was calculated.
Results
Of 298 patients, 31 (10.8%) had previous VFs at baseline. A total of 30 new VFs occurred in 26 patients over 4 years. The incidence of morphometric VFs was 4.7% at 2 years and 13.6% at 4 years. Multivariate logistic regression analysis showed that previous VFs at baseline and increased CRP levels at 2 years were predictors of new VFs (odds ratio (OR) =12.8, 95% confidence interval (CI) = 3.6-45.3 and OR = 5.4, 95% CI = 1.4–15.9). The age-specific specific standardized prevalence ratio of morphometric VFs in AS was 3.3 (95% CI 2.1–4.5).
Conclusions
The incidence of morphometric VFs increased in AS. Previous VFs and increased CRP levels predicted future VFs. Further studies are needed to identify the effects of treatment interventions on the prevention of new VFs.
doi:10.1186/ar4581
PMCID: PMC4095597  PMID: 24935156
19.  Innate immunity mediated by MyD88 signal is not essential for induction of LPS-specific B cell responses but is indispensable for protection against Salmonella enterica serovar Typhymurium infection1 
Salmonella organisms are gram-negative and facultative anaerobic bacteria that cause typhoid fever in humans. In this study, we evaluated LPS-specific adaptive immunity in innate immune-deficient mice after oral administration of attenuated S. enterica serovar Typhymurium (S. Typhimurium) strains. Of interest, identical levels of LPS-specific IgG and IgA antibodies were elicited in the systemic (i.e., serum and spleen) and mucosal (i.e., fecal extract and small intestine) compartments of wild-type, TLR4−/−, and MyD88−/− mice following oral vaccination with recombinant attenuated S. Typhimurium (RASV). Depletion of CD4+ T cells during RASV vaccination completely abrogated the generation of LPS-specific antibodies in MyD88−/− mice. In addition, mRNA expression levels of a B-cell activating factor of the TNF family (BAFF) were significantly increased in the spleens of MyD88−/− mice after oral administration, implying that T cell–independent B cell switching might be also enhanced in the MyD88 signal-deficient condition. Of most interest, orally vaccinated MyD88−/− mice that possessed high levels of LPS-specific IgG and IgA, which had neutralizing effect against Salmonella, died earlier than non-vaccinated wild-type mice following lethal oral challenge with virulent Salmonella species. These results suggest that innate immunity mediated by MyD88 signal is dispensable for induction of LPS-specific antibody responses following oral administration of attenuated Salmonella strains but indispensable for efficient protection.
doi:10.4049/jimmunol.0801980
PMCID: PMC4049229  PMID: 19201885
Mucosa; Vaccination; Salmonella; MyD88; innate immunity
20.  Identification and Characterization of a Ginsenoside-Transforming β-Glucosidase from Pseudonocardia sp. Gsoil 1536 and Its Application for Enhanced Production of Minor Ginsenoside Rg2(S) 
PLoS ONE  2014;9(6):e96914.
The ginsenoside Rg2(S), which is one of the pharmaceutical components of ginseng, is known to have neuroprotective, anti-inflammation, and anti-diabetic effects. However, the usage of ginsenoside Rg2(S) is restricted owing to the small amounts found in white and red ginseng. To enhance the production of ginsenoside Rg2(S) as a 100 gram unit with high specificity, yield, and purity, an enzymatic bioconversion method was developed to adopt the recombinant glycoside hydrolase (BglPC28), which is a ginsenoside-transforming recombinant β-glucosidase from Pseudonocardia sp. strain Gsoil 1536. The gene, termed bglPC28, encoding β-glucosidase (BglPC28) belonging to the glycoside hydrolase family 3 was cloned. bglPC28 consists of 2,232 bp (743 amino acid residues) with a predicted molecular mass of 78,975 Da. This enzyme was overexpressed in Escherichia coli BL21(DE3) using a GST-fused pGEX 4T-1 vector system. The optimum conditions of the recombinant BglPC28 were pH 7.0 and 37°C. BglPC28 can effectively transform the ginsenoside Re to Rg2(S); the Km values of PNPG and Re were 6.36±1.10 and 1.42±0.13 mM, respectively, and the Vmax values were 40.0±2.55 and 5.62±0.21 µmol min−1 mg−1 of protein, respectively. A scaled-up biotransformation reaction was performed in a 10 L jar fermenter at pH 7.0 and 30°C for 12 hours with a concentration of 20 mg/ml of ginsenoside Re from American ginseng roots. Finally, 113 g of Rg2(S) was produced from 150 g of Re with 84.0±1.1% chromatographic purity. These results suggest that this enzymatic method could be usefully exploited in the preparation of ginsenoside Rg2(S) in the cosmetics, functional food, and pharmaceutical industries.
doi:10.1371/journal.pone.0096914
PMCID: PMC4049585  PMID: 24911166
21.  Principal Interactions Analysis for Repeated Measures Data: Application to Gene-Gene, Gene-Environment Interactions 
Statistics in medicine  2012;31(22):2531-2551.
Many existing cohorts with longitudinal data on environmental exposures, occupational history, lifestyle/behavioral characteristics and health outcomes have collected genetic data in recent years. In this paper, we consider the problem of modeling gene-gene, gene-environment interactions with repeated measures data on a quantitative trait. We review possibilities of using classical models proposed by Tukey (1949) and Mandel (1961) using the cell means of a two-way classification array for such data. Whereas these models are effective for detecting interactions in presence of main effects, they fail miserably if the interaction structure is misspecified. We explore a more robust class of interaction models that are based on a singular value decomposition of the cell means residual matrix after fitting the additive main effect terms. This class of additive main effects and multiplicative interaction (AMMI) models (Gollob, 1968) provide useful summaries for subject-specific and time-varying effects as represented in terms of their contribution to the leading eigenvalues of the interaction matrix. It also makes the interaction structure more amenable to geometric representation. We call this analysis “Principal Interactions Analysis” (PIA). While the paper primarily focusses on a cell-mean based analysis of repeated measures outcome, we also introduce resampling-based methods that appropriately recognize the unbalanced and longitudinal nature of the data instead of reducing the response to cell-means. The proposed methods are illustrated by using data from the Normative Aging Study, a longitudinal cohort study of Boston area veterans since 1963. We carry out simulation studies under an array of classical interaction models and common epistasis models to illustrate the properties of the PIA procedure in comparison to the classical alternatives.
doi:10.1002/sim.5315
PMCID: PMC4046647  PMID: 22415818
biplot; column interaction; eigenvalue; epistasis; intraclass correlation; likelihood-ratio test; non-additivity; permutation tests; pseudo F-test; row interaction; singular vector; Wishart matrix
22.  Environmental Risk Score as a New Tool to Examine Multi-Pollutants in Epidemiologic Research: An Example from the NHANES Study Using Serum Lipid Levels 
PLoS ONE  2014;9(6):e98632.
Objective
A growing body of evidence suggests that environmental pollutants, such as heavy metals, persistent organic pollutants and plasticizers play an important role in the development of chronic diseases. Most epidemiologic studies have examined environmental pollutants individually, but in real life, we are exposed to multi-pollutants and pollution mixtures, not single pollutants. Although multi-pollutant approaches have been recognized recently, challenges exist such as how to estimate the risk of adverse health responses from multi-pollutants. We propose an “Environmental Risk Score (ERS)” as a new simple tool to examine the risk of exposure to multi-pollutants in epidemiologic research.
Methods and Results
We examined 134 environmental pollutants in relation to serum lipids (total cholesterol, high-density lipoprotein cholesterol (HDL), low-density lipoprotein cholesterol (LDL) and triglycerides) using data from the National Health and Nutrition Examination Survey between 1999 and 2006. Using a two-stage approach, stage-1 for discovery (n = 10818) and stage-2 for validation (n = 4615), we identified 13 associated pollutants for total cholesterol, 9 for HDL, 5 for LDL and 27 for triglycerides with adjustment for sociodemographic factors, body mass index and serum nutrient levels. Using the regression coefficients (weights) from joint analyses of the combined data and exposure concentrations, ERS were computed as a weighted sum of the pollutant levels. We computed ERS for multiple lipid outcomes examined individually (single-phenotype approach) or together (multi-phenotype approach). Although the contributions of ERS to overall risk predictions for lipid outcomes were modest, we found relatively stronger associations between ERS and lipid outcomes than with individual pollutants. The magnitudes of the observed associations for ERS were comparable to or stronger than those for socio-demographic factors or BMI.
Conclusions
This study suggests ERS is a promising tool for characterizing disease risk from multi-pollutant exposures. This new approach supports the need for moving from a single-pollutant to a multi-pollutant framework.
doi:10.1371/journal.pone.0098632
PMCID: PMC4047033  PMID: 24901996
23.  MEMS-based Force-clamp Analysis of the Role of Body Stiffness in C. elegans Touch Sensation 
Touch is enabled by mechanoreceptor neurons in the skin and plays an essential role in our everyday lives, but is among the least understood of our five basic senses. Force applied to the skin deforms these neurons and activates ion channels within them. Despite the importance of the mechanics of the skin in determining mechanoreceptor neuron deformation and ultimately touch sensation, the role of mechanics in touch sensitivity is poorly understood. Here, we use the model organism Caenorhabditis elegans to directly test the hypothesis that body mechanics modulate touch sensitivity. We demonstrate a microelectromechanical system (MEMS)-based force clamp that can apply calibrated forces to freely crawling C. elegans worms and measure touch-evoked avoidance responses. This approach reveals that wild-type animals sense forces < 1 μN and indentation depths < 1 μm. We use both genetic manipulation of the skin and optogenetic modulation of body wall muscles to alter body mechanics. We find that small changes in body stiffness dramatically affect force sensitivity, while having only modest effects on indentation sensitivity. We investigate the theoretical body deformation predicted under applied force and conclude that local mechanical loads induce inward bending deformation of the skin to drive touch sensation in C. elegans.
doi:10.1039/c3ib20293c
PMCID: PMC3701114  PMID: 23598612
Mechanotransduction; touch; biomechanics; C. elegans; piezoresistor; MEMS cantilever; optogenetics; cuticle; touch receptor neurons; behavior
24.  Effect of micro-vibration culture system on embryo development 
Purpose
Micro-vibration culture system was examined to determine the effects on mouse and human embryo development and possible improvement of clinical outcomes in poor responders.
Materials and methods
The embryonic development rates and cell numbers of blastocysts were compared between a static culture group (n = 178) and a micro-vibration culture group (n = 181) in mice. The embryonic development rates and clinical results were compared between a static culture group (n = 159 cycles) and a micro-vibration culture group (n = 166 cycles) in poor responders. A micro-vibrator was set at a frequency of 42 Hz, 5 s/60 min duration for mouse and human embryo development.
Results
The embryonic development rate was significantly improved in the micro-vibration culture group in mice (p < 0.05). The cell numbers of mouse blastocysts were significantly higher in the micro-vibration group than in the static culture group (p < 0.05). In the poor responders, the rate of high grade embryos was not significantly improved in the micro-vibration culture group on day 3. However, the optimal embryonic development rate on day 5 was improved in the micro-vibration group, and the total pregnancy rate and implantation rate were significantly higher in the micro-vibration group than in the static culture group (p < 0.05).
Conclusions
Micro-vibration culture methods have a beneficial effect on embryonic development in mouse embryos. In poor responders, the embryo development rate was improved to a limited extent under the micro-vibration culture conditions, but the clinical results were significantly improved.
doi:10.1007/s10815-013-0007-0
PMCID: PMC3696450  PMID: 23657828
Embryo culture; Micro-vibration; Static culture; Dynamic culture
25.  Popliteal Artery Pseudoaneurysm after Anterior Cruciate Ligament Re-Revision Using a Rigidfix Cross Pin 
Knee Surgery & Related Research  2014;26(2):121-124.
Popliteal artery injury is a very rare complication of anterior cruciate ligament (ACL) reconstruction. The authors experienced a case of popliteal arterial pseudoaneurysm after re-revision of ACL reconstruction using Rigidfix for femoral tunnel fixation. Pseudoaneurysm was detected in knee magnetic resonance imaging, which caused pain, limit of motion, common peroneal nerve palsy, leg swelling and symptoms similar to compartment syndrome. After excision and re-anastomosis of the popliteal artery using a greater saphenous vein graft, all symptoms were resolved within 3 months except for common peroneal nerve palsy. So we report on this case with a review of the literature.
doi:10.5792/ksrr.2014.26.2.121
PMCID: PMC4061407  PMID: 24944979
Knee; Anterior cruciate ligament; Popliteal artery; Psedoaneurysm

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