Publications by authors named "Eric Oh"

13 Publications

  • Page 1 of 1

Improved generalized raking estimators to address dependent covariate and failure-time outcome error.

Biom J 2021 Jun 11;63(5):1006-1027. Epub 2021 Mar 11.

Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania, Philadelphia, PA, USA.

Biomedical studies that use electronic health records (EHR) data for inference are often subject to bias due to measurement error. The measurement error present in EHR data is typically complex, consisting of errors of unknown functional form in covariates and the outcome, which can be dependent. To address the bias resulting from such errors, generalized raking has recently been proposed as a robust method that yields consistent estimates without the need to model the error structure. We provide rationale for why these previously proposed raking estimators can be expected to be inefficient in failure-time outcome settings involving misclassification of the event indicator. We propose raking estimators that utilize multiple imputation, to impute either the target variables or auxiliary variables, to improve the efficiency. We also consider outcome-dependent sampling designs and investigate their impact on the efficiency of the raking estimators, either with or without multiple imputation. We present an extensive numerical study to examine the performance of the proposed estimators across various measurement error settings. We then apply the proposed methods to our motivating setting, in which we seek to analyze HIV outcomes in an observational cohort with EHR data from the Vanderbilt Comprehensive Care Clinic.
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http://dx.doi.org/10.1002/bimj.202000187DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8211389PMC
June 2021

The carbon isotope ratios of nonessential amino acids identify sugar-sweetened beverage (SSB) consumers in a 12-wk inpatient feeding study of 32 men with varying SSB and meat exposures.

Am J Clin Nutr 2021 05;113(5):1256-1264

Institute of Arctic Biology, Department of Biology and Wildlife, University of Alaska Fairbanks, Fairbanks, AK, USA.

Background: The carbon isotope ratios (CIRs) of individual amino acids (AAs) may provide more sensitive and specific biomarkers of sugar-sweetened beverages (SSBs) than total tissue CIR. Because CIRs turn over slowly, long-term controlled-feeding studies are needed in their evaluation.

Objective: We assessed the responses of plasma and RBC CIRAA's to SSB and meat intake in a 12-wk inpatient feeding study.

Methods: Thirty-two men (aged 46.2 ± 10.5 y) completed the feeding study at the National Institute of Diabetes and Digestive and Kidney Diseases in Phoenix, Arizona. The effects of SSB, meat, and fish intake on plasma and RBC CIRAA's were evaluated in a balanced factorial design with each dietary variable either present or absent in a common weight-maintaining, macronutrient-balanced diet. Fasting blood samples were collected biweekly from baseline. Dietary effects on the postfeeding CIR of 5 nonessential AAs (CIRNEAA's) and 4 essential AAs (CIREAA's) were analyzed using multivariable regression.

Results: In plasma, 4 of 5 CIRNEAA's increased with SSB intake. Of these, the CIRAla was the most sensitive (β = 2.81, SE = 0.38) to SSB intake and was not affected by meat or fish intake. In RBCs, all 5 CIRNEAA's increased with SSBs but had smaller effect sizes than in plasma. All plasma CIREAA's increased with meat intake (but not SSB or fish intake), and the CIRLeu was the most sensitive (β = 1.26, SE = 0.23). CIRs of leucine and valine also increased with meat intake in RBCs. Estimates of turnover suggest that CIRAA's in plasma, but not RBCs, were in equilibrium with the diets by the end of the study.

Conclusions: The results of this study in men support CIRNEAA's as potential biomarkers of SSB intake and suggest CIREAA's as potential biomarkers of meat intake in US diets. This trial was registered at clinicaltrials.gov/ct2/show/NCT01237093 as NCT01237093.
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http://dx.doi.org/10.1093/ajcn/nqaa374DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8106756PMC
May 2021

Raking and regression calibration: Methods to address bias from correlated covariate and time-to-event error.

Stat Med 2021 02 2;40(3):631-649. Epub 2020 Nov 2.

Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania, Philadelphia, Pennsylvania, USA.

Medical studies that depend on electronic health records (EHR) data are often subject to measurement error, as the data are not collected to support research questions under study. These data errors, if not accounted for in study analyses, can obscure or cause spurious associations between patient exposures and disease risk. Methodology to address covariate measurement error has been well developed; however, time-to-event error has also been shown to cause significant bias, but methods to address it are relatively underdeveloped. More generally, it is possible to observe errors in both the covariate and the time-to-event outcome that are correlated. We propose regression calibration (RC) estimators to simultaneously address correlated error in the covariates and the censored event time. Although RC can perform well in many settings with covariate measurement error, it is biased for nonlinear regression models, such as the Cox model. Thus, we additionally propose raking estimators which are consistent estimators of the parameter defined by the population estimating equation. Raking can improve upon RC in certain settings with failure-time data, require no explicit modeling of the error structure, and can be utilized under outcome-dependent sampling designs. We discuss features of the underlying estimation problem that affect the degree of improvement the raking estimator has over the RC approach. Detailed simulation studies are presented to examine the performance of the proposed estimators under varying levels of signal, error, and censoring. The methodology is illustrated on observational EHR data on HIV outcomes from the Vanderbilt Comprehensive Care Clinic.
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http://dx.doi.org/10.1002/sim.8793DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7874496PMC
February 2021

COVID-19 and cardiac arrhythmias.

Heart Rhythm 2020 Sep 22;17(9):1439-1444. Epub 2020 Jun 22.

Division of Cardiovascular Medicine, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania. Electronic address:

Background: Early studies suggest that coronavirus disease 2019 (COVID-19) is associated with a high incidence of cardiac arrhythmias. Severe acute respiratory syndrome coronavirus 2 infection may cause injury to cardiac myocytes and increase arrhythmia risk.

Objectives: The purpose of this study was to evaluate the risk of cardiac arrest and arrhythmias including incident atrial fibrillation (AF), bradyarrhythmias, and nonsustained ventricular tachycardia (NSVT) in a large urban population hospitalized for COVID-19. We also evaluated correlations between the presence of these arrhythmias and mortality.

Methods: We reviewed the characteristics of all patients with COVID-19 admitted to our center over a 9-week period. Throughout hospitalization, we evaluated the incidence of cardiac arrests, arrhythmias, and inpatient mortality. We also used logistic regression to evaluate age, sex, race, body mass index, prevalent cardiovascular disease, diabetes, hypertension, chronic kidney disease, and intensive care unit (ICU) status as potential risk factors for each arrhythmia.

Results: Among 700 patients (mean age 50 ± 18 years; 45% men; 71% African American; 11% received ICU care), there were 9 cardiac arrests, 25 incident AF events, 9 clinically significant bradyarrhythmias, and 10 NSVTs. All cardiac arrests occurred in patients admitted to the ICU. In addition, admission to the ICU was associated with incident AF (odds ratio [OR] 4.68; 95% confidence interval [CI] 1.66-13.18) and NSVT (OR 8.92; 95% CI 1.73-46.06) after multivariable adjustment. Also, age and incident AF (OR 1.05; 95% CI 1.02-1.09) and prevalent heart failure and bradyarrhythmias (OR 9.75; 95% CI 1.95-48.65) were independently associated. Only cardiac arrests were associated with acute in-hospital mortality.

Conclusion: Cardiac arrests and arrhythmias are likely the consequence of systemic illness and not solely the direct effects of COVID-19 infection.
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http://dx.doi.org/10.1016/j.hrthm.2020.06.016DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7307518PMC
September 2020

Associations of plasma, RBCs, and hair carbon and nitrogen isotope ratios with fish, meat, and sugar-sweetened beverage intake in a 12-wk inpatient feeding study.

Am J Clin Nutr 2019 12;110(6):1306-1315

Center for Alaska Native Health Research, Institute of Arctic Biology, Department of Biology and Wildlife, University of Alaska Fairbanks, Fairbanks, AK, USA.

Background: Naturally occurring carbon and nitrogen stable isotope ratios [13C/12C (CIR) and 15N/14N (NIR)] are promising dietary biomarkers. As these candidate biomarkers have long tissue residence times, long-term feeding studies are needed for their evaluation.

Objective: Our aim was to evaluate plasma, RBCs, and hair CIR and NIR as biomarkers of fish, meat, and sugar-sweetened beverage (SSB) intake in a 12-wk dietary intervention.

Methods: Thirty-two men (aged 46.2 ± 10.5 y; BMI: 27.2 ± 4.0 kg/m2) underwent a 12-wk inpatient dietary intervention at the National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) in Phoenix, Arizona. The effects of fish, meat, and SSB intake on CIR and NIR were evaluated using a balanced factorial design, with each intake factor at 2 levels (present/absent) in a common, background diet (50% carbohydrate, 30% fat, 20% protein). Fasting blood samples were taken biweekly from baseline, and hair samples were collected at baseline and postintervention. Data were analyzed using multivariable regression.

Results: The postintervention CIR of plasma was elevated when diets included meat (β = 0.89, 95% CI: 0.73,1.05) and SSBs (β = 0.48, 95% CI: 0.32, 0.64). The postintervention NIR of plasma was elevated when diets included fish (β = 0.85, 95% CI: 0.64, 1.05) and meat (β = 0.61, 95% CI: 0.42, 0.8). Results were similar for RBCs and hair. Postintervention RBC CIR and NIR had strong associations with baseline, suggesting that turnover to the intervention diets was incomplete after 12 wk. Estimates of isotopic turnover rate further confirmed incomplete turnover of RBCs.

Conclusions: CIR was associated with meat and SSBs, and more strongly with meat. NIR was associated with fish and meat, and more strongly with fish. Overall, CIR and NIR discriminated between dietary fish and meat, and to a lesser extent SSBs, indicating their potential utility as biomarkers of intake in US diets. Approaches to make these biomarkers more specific are needed. This trial was registered at clinicaltrials.gov as NCT01237093.
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http://dx.doi.org/10.1093/ajcn/nqz208DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6885477PMC
December 2019

Considerations for analysis of time-to-event outcomes measured with error: Bias and correction with SIMEX.

Stat Med 2018 04 29;37(8):1276-1289. Epub 2017 Nov 29.

Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, U.S.A.

For time-to-event outcomes, a rich literature exists on the bias introduced by covariate measurement error in regression models, such as the Cox model, and methods of analysis to address this bias. By comparison, less attention has been given to understanding the impact or addressing errors in the failure time outcome. For many diseases, the timing of an event of interest (such as progression-free survival or time to AIDS progression) can be difficult to assess or reliant on self-report and therefore prone to measurement error. For linear models, it is well known that random errors in the outcome variable do not bias regression estimates. With nonlinear models, however, even random error or misclassification can introduce bias into estimated parameters. We compare the performance of 2 common regression models, the Cox and Weibull models, in the setting of measurement error in the failure time outcome. We introduce an extension of the SIMEX method to correct for bias in hazard ratio estimates from the Cox model and discuss other analysis options to address measurement error in the response. A formula to estimate the bias induced into the hazard ratio by classical measurement error in the event time for a log-linear survival model is presented. Detailed numerical studies are presented to examine the performance of the proposed SIMEX method under varying levels and parametric forms of the error in the outcome. We further illustrate the method with observational data on HIV outcomes from the Vanderbilt Comprehensive Care Clinic.
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http://dx.doi.org/10.1002/sim.7554DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5810403PMC
April 2018

Public engagement with scientific evidence in health: A qualitative study among primary-care patients in an urban population.

Public Underst Sci 2016 07 9;25(5):612-26. Epub 2014 Dec 9.

Perelman School of Medicine, University of Pennsylvania, USA.

The purpose of this study is to explore the experience and perspective of patients regarding scientific evidence in health and the degree that this information impacts health behavior and medical decision making. A focus group study was conducted. Participants were recruited from an urban primary-care practice. The focus group discussions were audio-recorded, transcribed verbatim, and coded by two independent investigators. Emergent themes were identified. Participants (n = 30) ranged in age from 30 to 79 years, 60% were female, 77% were black, and 50% had at least some college experience. Three thematic areas informed a wide range in level of interest regarding scientific study design and result information: (1) scientific literacy, (2) medical decision making style, and (3) impact of culture and community on decision making. Our findings indicate that communication strategies that incorporate key elements of scientific study design, methods, and results will most effectively translate findings from comparative effectiveness research to patient-informed decision making regarding evidence-based health interventions.
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http://dx.doi.org/10.1177/0963662514560489DOI Listing
July 2016

Prefrontal cortical kappa-opioid receptor modulation of local neurotransmission and conditioned place aversion.

Neuropsychopharmacology 2013 Aug 29;38(9):1770-9. Epub 2013 Mar 29.

Integrative Neuroscience Section, Integrative Neuroscience Branch, National Institute on Drug Abuse, Baltimore, MD, USA.

Kappa-opioid receptors (KORs) are important for motivation and other medial prefrontal cortex (mPFC)-dependent behaviors. Although KORs are present in the mPFC, their role in regulating transmission in this brain region and their contribution to KOR-mediated aversion are not known. Using in vivo microdialysis in rats and mice, we demonstrate that intra-mPFC administration of the selective KOR agonist U69,593 decreased local dopamine (DA) overflow, while reverse dialysis of the KOR antagonist nor-Binaltorphimine (nor-BNI) enhanced mPFC DA overflow. Extracellular amino-acid levels were also affected by KORs, as U69,593 reduced glutamate and GABA levels driven by the glutamate reuptake blocker, l-trans-pyrrolidine-2,4-dicarboxylate. Whole-cell recordings from mPFC layer V pyramidal neurons revealed that U69,593 decreased the frequency, but not amplitude, of glutamatergic mini EPSPs. To determine whether KOR regulation of mPFC DA overflow was mediated by KOR on DA terminals, we utilized a Cre recombinase-driven mouse line lacking KOR in DA neurons. In these mice, basal DA release or uptake was unaltered relative to controls, but attenuation of mPFC DA overflow by local U69,593 was not observed, indicating KOR acts directly on mPFC DA terminals to locally inhibit DA levels. Conditioning procedures were then used to determine whether mPFC KOR signaling was necessary for KOR-mediated aversion. U69,593-mediated conditioned place aversion was blocked by intra-mPFC nor-BNI microinjection. These findings demonstrate that mPFC KORs negatively regulate DA and amino-acid neurotransmission, and are necessary for KOR-mediated aversion.
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http://dx.doi.org/10.1038/npp.2013.76DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3717537PMC
August 2013

Alleviation of neuropathic pain hypersensitivity by inhibiting neuronal pentraxin 1 in the rostral ventromedial medulla.

J Neurosci 2012 Sep;32(36):12431-6

Integrative Neuroscience Branch, National Institute on Drug Abuse, NIH, Baltimore, Maryland 21224, USA.

Peripheral nerve injury causes spontaneous and long-lasting pain, hyperalgesia, and allodynia. Excitatory amino acid receptor-dependent increases in descending facilitatory drive from the brainstem rostral ventromedial medulla (RVM) contribute to injury-evoked hypersensitivity. Although increased excitability likely reflects changes in synaptic efficacy, the cellular mechanisms underlying injury-induced synaptic plasticity are poorly understood. Neuronal pentraxin 1 (NP1), a protein with exclusive CNS expression, is implicated in synaptogenesis and AMPA receptor recruitment to immature synapses. Its role in the adult brain and in descending pain facilitation is unknown. Here, we use the spared nerve injury (SNI) model in rodents to examine this issue. We show that SNI increases RVM NP1 expression and constitutive deletion or silencing NP1 in the RVM, before or after SNI, attenuates allodynia and hyperalgesia in rats. Selective rescue of RVM NP1 expression restores behavioral hypersensitivity of knock-out mice, demonstrating a key role of RVM NP1 in the pathogenesis of neuropathic pain.
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http://dx.doi.org/10.1523/JNEUROSCI.2730-12.2012DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3457630PMC
September 2012

Effect of sinus membrane perforation on dental implant integration: a retrospective study on 128 patients.

Implant Dent 2011 Feb;20(1):13-9

Division of Oral and Maxillofacial Surgery, Montefiore Medical Center, Bronx, NY 10467, USA.

A common complication of sinus augmentation is perforation of the sinus membrane during augmentation and/or implant placement. This retrospective study examines the effect of sinus membrane perforation with regard to graft survival and implant integration. A total of 175 sinuses were augmented with 115 of the membranes being reported intact at the time of surgery. A total of three infections occurred in patients who sustained perforated sinuses and one infection occurred in a patient who had an intact sinus. All four infections resolved after culture sensitivity and placement of the patient on an appropriate antibiotic for 10 days. Of 438 dental implants placed in the augmented sinuses, five implants failed, four of which were associated with perforated sinuses and and which was not associated with a perforated grafted sinus.
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http://dx.doi.org/10.1097/ID.0b013e3182061a73DOI Listing
February 2011

Novel insights into iron metabolism by integrating deletome and transcriptome analysis in an iron deficiency model of the yeast Saccharomyces cerevisiae.

BMC Genomics 2009 Mar 25;10:130. Epub 2009 Mar 25.

Department of Nutritional Sciences and Toxicology, University of California, Berkeley, California 94720, USA.

Background: Iron-deficiency anemia is the most prevalent form of anemia world-wide. The yeast Saccharomyces cerevisiae has been used as a model of cellular iron deficiency, in part because many of its cellular pathways are conserved. To better understand how cells respond to changes in iron availability, we profiled the yeast genome with a parallel analysis of homozygous deletion mutants to identify essential components and cellular processes required for optimal growth under iron-limited conditions. To complement this analysis, we compared those genes identified as important for fitness to those that were differentially-expressed in the same conditions. The resulting analysis provides a global perspective on the cellular processes involved in iron metabolism.

Results: Using functional profiling, we identified several genes known to be involved in high affinity iron uptake, in addition to novel genes that may play a role in iron metabolism. Our results provide support for the primary involvement in iron homeostasis of vacuolar and endosomal compartments, as well as vesicular transport to and from these compartments. We also observed an unexpected importance of the peroxisome for growth in iron-limited media. Although these components were essential for growth in low-iron conditions, most of them were not differentially-expressed. Genes with altered expression in iron deficiency were mainly associated with iron uptake and transport mechanisms, with little overlap with those that were functionally required. To better understand this relationship, we used expression-profiling of selected mutants that exhibited slow growth in iron-deficient conditions, and as a result, obtained additional insight into the roles of CTI6, DAP1, MRS4 and YHR045W in iron metabolism.

Conclusion: Comparison between functional and gene expression data in iron deficiency highlighted the complementary utility of these two approaches to identify important functional components. This should be taken into consideration when designing and analyzing data from these type of studies. We used this and other published data to develop a molecular interaction network of iron metabolism in yeast.
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http://dx.doi.org/10.1186/1471-2164-10-130DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2669097PMC
March 2009

Supersensitivity to amphetamine in protein kinase-C interacting protein/HINT1 knockout mice.

Neuropsychopharmacology 2007 Aug 3;32(8):1774-82. Epub 2007 Jan 3.

Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD 21201, USA.

Protein kinase C interacting protein/histidine triad nucleotide binding protein 1 (PKCI/HINT1) is a member of the histidine triad protein family. Although this protein is widely expressed in the mammalian brain including mesocorticolimbic and mesostriatal regions, its physiological function in CNS remains unknown. Recent microarray studies reported decreased mRNA expression of PKCI/HINT1 in the frontal cortex of individuals with schizophrenia, suggesting the possible involvement of this protein in the pathophysiology of the disease. In view of the documented link between dopamine (DA) transmission and schizophrenia, the present study used behavioral and neurochemical approaches to examine the influence of constitutive PKCI/HINT1 deletion upon: (i) basal and amphetamine (AMPH)-evoked locomotor activity; (ii) DA dynamics in the dorsal striatum, and (iii) postsynaptic DA receptor function. PKCI/HINT1(-/-) (KO) mice displayed lower spontaneous locomotion relative to wild-type (WT) controls. Acute AMPH administration significantly increased locomotor activity in WT mice; nonetheless, the effect was enhanced in KO mice. Quantitative microdialysis studies revealed no alteration in basal DA dynamics in the striatum or nucleus accumbens of KO mice. The ability of acute AMPH to increase DA levels was unaltered indicating that function in presynaptic DA neurotransmission in these regions do not underlie the behavioral phenotype of KO mice. In contrast to WT mice, systemic administration of the direct-acting DA receptor agonist apomorphine (10 mg/kg) significantly increased locomotor activity in KO mice suggesting that postsynaptic DA function is altered in these animals. These results demonstrate an important role of PKCI/HINT1 in modulating the behavioral response to AMPH. Furthermore, they indicate that the absence of this protein may be associated with dysregulation of postsynaptic DA transmission.
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http://dx.doi.org/10.1038/sj.npp.1301301DOI Listing
August 2007

Spectroscopic and biochemical characterization of heme binding to yeast Dap1p and mouse PGRMC1p.

Biochemistry 2005 Dec;44(50):16729-36

Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, USA.

Yeast damage-associated response protein (Dap1p) and mouse progesterone receptor membrane component-1 protein (mPGRMC1p) belong to a highly conserved class of putative membrane-associated progesterone binding proteins (MAPR), with Dap1p and inner zone antigen (IZA), the rat homologue of mPGRMC1p, recently being reported to bind heme. While primary structure analysis reveals similarities to the cytochrome b(5) motif, neither of the two axial histidines responsible for ligation to the heme is present in any of the MAPR proteins. In this paper, EPR, MCD, CD, UV-vis, and general biochemical methods have been used to characterize the nature of heme binding in both Dap1p and a His-tagged, membrane anchor-truncated mPGRMC1p. As isolated, Dap1p is a tetramer which can be converted to a dimer upon addition of 150 mM salt. The heme is noncovalently attached, with a maximal, in vitro, heme loading of approximately 30%, for both proteins. CD and fluorescence spectroscopies indicate a well-ordered structure, suggesting the low level of heme loading is probably not due to improperly folded protein. EPR confirmed a five-coordinate, high-spin, ferric resting state for both proteins, indicating one axial amino acid ligand, in contrast to the six-coordinate, low-spin, ferric state of cytochrome b(5). The MCD spectrum confirmed this conclusion for Dap1p and indicated the axial ligand is most likely a tyrosine and not a histidine, or a cysteine; however, an aspartic acid residue could not be conclusively ruled out. Potential axial ligands, which are conserved in all MAPRs, were mutated (Y78F, D118A, and Y138F) and purified to homogeneity. The Y78F and D118A mutants were found to bind heme; however, Y138F did not. This result is consistent with the MCD data and indicates that Tyr138 is most likely the axial ligand to the heme in Dap1p.
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http://dx.doi.org/10.1021/bi0511585DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2577039PMC
December 2005
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