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Find video protocols related to scientific articles indexed in Pubmed.
Influenza Vaccine Prevents Medically-Attended Influenza-Associated Acute Respiratory Illness in Adults 50 Years or Older.
J. Infect. Dis.
PUBLISHED: 10-23-2014
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?There are few estimates of influenza vaccine effectiveness in preventing serious outcomes in older adults.
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A note on the relationships between multiple imputation, maximum likelihood and fully Bayesian methods for missing responses in linear regression models.
Stat Interface
PUBLISHED: 10-14-2014
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Multiple Imputation, Maximum Likelihood and Fully Bayesian methods are the three most commonly used model-based approaches in missing data problems. Although it is easy to show that when the responses are missing at random (MAR), the complete case analysis is unbiased and efficient, the aforementioned methods are still commonly used in practice for this setting. To examine the performance of and relationships between these three methods in this setting, we derive and investigate small sample and asymptotic expressions of the estimates and standard errors, and fully examine how these estimates are related for the three approaches in the linear regression model when the responses are MAR. We show that when the responses are MAR in the linear model, the estimates of the regression coefficients using these three methods are asymptotically equivalent to the complete case estimates under general conditions. One simulation and a real data set from a liver cancer clinical trial are given to compare the properties of these methods when the responses are MAR.
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Immune Responses to Pertussis Antigens in Infants and Toddlers after Immunization with Multicomponent Acellular Pertussis Vaccine.
Clin. Vaccine Immunol.
PUBLISHED: 09-26-2014
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Given the resurgence of pertussis despite high vaccination rates with the diphtheria-tetanus-acellular pertussis (DTaP) vaccine, a better understanding of vaccine-induced immune responses to Bordetella pertussis (B. pertussis) is needed. We investigated the antibody, cell-mediated, and cytokine responses to B. pertussis antigens in children who received the primary vaccination series (at 2, 4, and 6 months) and first booster vaccination (at 15-18 months) with 5-component acellular pertussis (aP) vaccine. The majority of subjects demonstrated 4-fold increase in antibody titer to all four pertussis antigens (pertussis toxin[PT], pertactin[PRN], filamentous hemagglutinin[FHA], and fimbriae[FIM]) following the primary series and booster vaccination. Following the primary vaccine series, the majority of subjects (52-67%) mounted a positive T-cell proliferative response (stimulation index ?3) to PT and PRN antigens, while few subjects (7-12%) mounted positive proliferative responses to FHA and FIM. One month after booster vaccination (age 16-19 months), our study revealed significant increase in IFN-? production in response to PT and FIM antigens, significant increase in IL-2 production with PT, FHA, and PRN antigens, and lack of significant IL-4 secretion with any of the antigens. While previous reports documented a mixed Th1/Th2 or Th2-skewed response to DTaP vaccine in children, our data suggest that following the first DTaP booster, children aged 16-19 months have a cytokine profile consistent with a Th1 response, which is known to be essential for clearance of pertussis infection. To better define aP-induced immune responses following the booster vaccine, further studies are needed to assess cytokine responses pre- and post-booster in DTaP recipients.
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MSEA: detection and quantification of mutation hotspots through mutation set enrichment analysis.
Genome Biol.
PUBLISHED: 08-21-2014
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Many cancer genes form mutation hotspots that disrupt their functional domains or active sites, leading to gain- or loss-of-function. We propose a mutation set enrichment analysis (MSEA) implemented by two novel methods, MSEA-clust and MSEA-domain, to predict cancer genes based on mutation hotspot patterns. MSEA methods are evaluated by both simulated and real cancer data. We find approximately 51% of the eligible known cancer genes form detectable mutation hotspots. Application of MSEA in eight cancers reveals a total of 82 genes with mutation hotspots, including well-studied cancer genes, known cancer genes re-found in new cancer types, and novel cancer genes.
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Validating drug repurposing signals using electronic health records: a case study of metformin associated with reduced cancer mortality.
J Am Med Inform Assoc
PUBLISHED: 07-24-2014
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Drug repurposing, which finds new indications for existing drugs, has received great attention recently. The goal of our work is to assess the feasibility of using electronic health records (EHRs) and automated informatics methods to efficiently validate a recent drug repurposing association of metformin with reduced cancer mortality.
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A novel approach to supporting relationship-centered care through electronic health record ergonomic training in preclerkship medical education.
Acad Med
PUBLISHED: 05-16-2014
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How can physicians incorporate the electronic health record (EHR) into clinical practice in a relationship-enhancing fashion ("EHR ergonomics")?
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Joint modeling of longitudinal and survival data with missing and left-censored time-varying covariates.
Stat Med
PUBLISHED: 05-02-2014
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We propose a joint model for longitudinal and survival data with time-varying covariates subject to detection limits and intermittent missingness at random. The model is motivated by data from the Multicenter AIDS Cohort Study (MACS), in which HIV+ subjects have viral load and CD4 cell count measured at repeated visits along with survival data. We model the longitudinal component using a normal linear mixed model, modeling the trajectory of CD4 cell count by regressing on viral load, and other covariates. The viral load data are subject to both left censoring because of detection limits (17%) and intermittent missingness (27%). The survival component of the joint model is a Cox model with time-dependent covariates for death because of AIDS. The longitudinal and survival models are linked using the trajectory function of the linear mixed model. A Bayesian analysis is conducted on the MACS data using the proposed joint model. The proposed method is shown to improve the precision of estimates when compared with alternative methods. Copyright © 2014 John Wiley & Sons, Ltd.
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A Bayesian Approach for the Cox Proportional Hazards Model with Covariates Subject to Detection Limit.
Int J Stat Med Res
PUBLISHED: 04-29-2014
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The research on biomarkers has been limited in its effectiveness because biomarker levels can only be measured within the thresholds of assays and laboratory instruments, a challenge referred to as a detection limit (DL) problem. In this paper, we propose a Bayesian approach to the Cox proportional hazards model with explanatory variables subject to lower, upper, or interval DLs. We demonstrate that by formulating the time-to-event outcome using the Poisson density with counting process notation, implementing the proposed approach in the OpenBUGS and JAGS is straightforward. We have conducted extensive simulations to compare the proposed Bayesian approach to the other four commonly used methods and to evaluate its robustness with respect to the distribution assumption of the biomarkers. The proposed Bayesian approach and other methods were applied to an acute lung injury study, in which a panel of cytokine biomarkers was studied for the biomarkers' association with ventilation-free survival.
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Quantifying the average of the time-varying hazard ratio via a class of transformations.
Lifetime Data Anal
PUBLISHED: 02-04-2014
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The hazard ratio derived from the Cox model is a commonly used summary statistic to quantify a treatment effect with a time-to-event outcome. The proportional hazards assumption of the Cox model, however, is frequently violated in practice and many alternative models have been proposed in the statistical literature. Unfortunately, the regression coefficients obtained from different models are often not directly comparable. To overcome this problem, we propose a family of weighted hazard ratio measures that are based on the marginal survival curves or marginal hazard functions, and can be estimated using readily available output from various modeling approaches. The proposed transformation family includes the transformations considered by Schemper et al. (Statist Med 28:2473-2489, 2009) as special cases. In addition, we propose a novel estimate of the weighted hazard ratio based on the maximum departure from the null hypothesis within the transformation family, and develop a Kolmogorov[Formula: see text]Smirnov type of test statistic based on this estimate. Simulation studies show that when the hazard functions of two groups either converge or diverge, this new estimate yields a more powerful test than tests based on the individual transformations recommended in Schemper et al. (Statist Med 28:2473-2489, 2009), with a similar magnitude of power loss when the hazards cross. The proposed estimates and test statistics are applied to a colorectal cancer clinical trial.
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Dichotomous effects of exposure to bivalirudin in patients undergoing percutaneous coronary intervention on protease-activated receptor-mediated platelet activation.
J. Thromb. Thrombolysis
PUBLISHED: 10-18-2013
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Bivalirudin is a direct thrombin inhibitor that is increasingly used in percutaneous coronary intervention (PCI) and has been previously shown to lack inherent platelet activation. Thrombin works through activation of protease activated receptor-1 (PAR1) and PAR4 on human platelets to initiate signaling cascades leading to platelet aggregation. Despite the increasing usage of bivalirudin, the effects on platelet function have not been well defined. Bivalirudin exposure during PCI was therefore assessed for its potential short-term effects on washed platelet function through PAR1 and PAR4. Bivalirudin significantly inhibited low-dose thrombin-mediated platelet aggregation, dense granule secretion, integrin ?IIb?3 activation and Rap1 activation and high dose thrombin-mediated dense granule secretion and Rap1 activation. Exposure to bivalirudin did not alter PAR1 or 4 agonist peptide (PAR1-AP or PAR4-AP) induced aggregation, dense granule secretion, integrin glycoprotein IIbIIIa activation or Rap1 activation. However, exposure to bivalirudin significantly potentiated surface expression of P-selectin following stimulation with high dose thrombin and PAR1-AP, and both low and high dose PAR4-AP. Hence, our data are the first to show that exposure to bivalirudin increased P-selectin expression with certain conditions demonstrating that bivalirudin can increase inherent platelet activity.
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Medical decision support using machine learning for early detection of late-onset neonatal sepsis.
J Am Med Inform Assoc
PUBLISHED: 09-16-2013
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The objective was to develop non-invasive predictive models for late-onset neonatal sepsis from off-the-shelf medical data and electronic medical records (EMR).
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Assessing adolescent asthma symptoms and adherence using mobile phones.
J. Med. Internet Res.
PUBLISHED: 05-04-2013
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Self-report is the most common method of measuring medication adherence but is influenced by recall error and response bias, and it typically does not provide insight into the causes of poor adherence. Ecological momentary assessment (EMA) of health behaviors using mobile phones offers a promising alternative to assessing adherence and collecting related data that can be clinically useful for adherence problem solving.
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An assessment of pharmacists readiness for paperless labeling: a national survey.
J Am Med Inform Assoc
PUBLISHED: 03-23-2013
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To assess the state of readiness for the adoption of paperless labeling among a nationally representative sample of pharmacies, including chain pharmacies, independent retail pharmacies, hospitals, and other rural or urban dispensing sites.
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Bayesian gamma frailty models for survival data with semi-competing risks and treatment switching.
Lifetime Data Anal
PUBLISHED: 03-16-2013
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Motivated from a colorectal cancer study, we propose a class of frailty semi-competing risks survival models to account for the dependence between disease progression time, survival time, and treatment switching. Properties of the proposed models are examined and an efficient Gibbs sampling algorithm using the collapsed Gibbs technique is developed. A Bayesian procedure for assessing the treatment effect is also proposed. The deviance information criterion (DIC) with an appropriate deviance function and Logarithm of the pseudomarginal likelihood (LPML) are constructed for model comparison. A simulation study is conducted to examine the empirical performance of DIC and LPML and as well as the posterior estimates. The proposed method is further applied to analyze data from a colorectal cancer study.
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Bayesian modeling and inference for clinical trials with partial retrieved data following dropout.
Stat Med
PUBLISHED: 03-08-2013
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In randomized clinical trials, it is common that patients may stop taking their assigned treatments and then switch to a standard treatment (standard of care available to the patient) but not the treatments under investigation. Although the availability of limited retrieved data on patients who switch to standard treatment, called off-protocol data, could be highly valuable in assessing the associated treatment effect with the experimental therapy, it leads to a complex data structure requiring the development of models that link the information of per-protocol data with the off-protocol data. In this paper, we develop a novel Bayesian method to jointly model longitudinal treatment measurements under various dropout scenarios. Specifically, we propose a multivariate normal mixed-effects model for repeated measurements from the assigned treatments and the standard treatment, a multivariate logistic regression model for those stopping the assigned treatments, logistic regression models for those starting a standard treatment off protocol, and a conditional multivariate logistic regression model for completely withdrawing from the study. We assume that withdrawing from the study is non-ignorable, but intermittent missingness is assumed to be at random. We examine various properties of the proposed model. We develop an efficient Markov chain Monte Carlo sampling algorithm. We analyze in detail via the proposed method a real dataset from a clinical trial. Copyright © 2013 John Wiley & Sons, Ltd.
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Effectiveness of influenza vaccine for preventing laboratory-confirmed influenza hospitalizations in adults, 2011-2012 influenza season.
Clin. Infect. Dis.
PUBLISHED: 02-28-2013
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During the 2011-2012 influenza season, we enrolled hospitalized adults with acute respiratory illness and tested each for influenza using reverse transcription polymerase chain reaction. Influenza vaccination was verified in 35% (6/17) of adults with influenza-associated hospitalizations compared to 64% (97/152) of test-negative controls; adjusted vaccine effectiveness was 71.4% (95% confidence interval, 17.1%-94.9%).
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Estimating treatment effects with treatment switching via semicompeting risks models: an application to a colorectal cancer study.
Biometrika
PUBLISHED: 12-29-2011
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Treatment switching is a frequent occurrence in clinical trials, where, during the course of the trial, patients who fail on the control treatment may change to the experimental treatment. Analysing the data without accounting for switching yields highly biased and inefficient estimates of the treatment effect. In this paper, we propose a novel class of semiparametric semicompeting risks transition survival models to accommodate treatment switches. Theoretical properties of the proposed model are examined and an efficient expectation-maximization algorithm is derived for obtaining the maximum likelihood estimates. Simulation studies are conducted to demonstrate the superiority of the model compared with the intent-to-treat analysis and other methods proposed in the literature. The proposed method is applied to data from a colorectal cancer clinical trial.
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The financial impact of health information exchange on emergency department care.
J Am Med Inform Assoc
PUBLISHED: 11-04-2011
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To examine the financial impact health information exchange (HIE) in emergency departments (EDs).
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Extracting and integrating data from entire electronic health records for detecting colorectal cancer cases.
AMIA Annu Symp Proc
PUBLISHED: 10-22-2011
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Identification of a cohort of patients with specific diseases is an important step for clinical research that is based on electronic health records (EHRs). Informatics approaches combining structured EHR data, such as billing records, with narrative text data have demonstrated utility for such tasks. This paper describes an algorithm combining machine learning and natural language processing to detect patients with colorectal cancer (CRC) from entire EHRs at Vanderbilt University Hospital. We developed a general case detection method that consists of two steps: 1) extraction of positive CRC concepts from all clinical notes (document-level concept identification); and 2) determination of CRC cases using aggregated information from both clinical narratives and structured billing data (patient-level case determination). For each step, we compared performance of rule-based and machine-learning-based approaches. Using a manually reviewed data set containing 300 possible CRC patients (150 for training and 150 for testing), we showed that our method achieved F-measures of 0.996 for document level concept identification, and 0.93 for patient level case detection.
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Health information exchange usage in emergency departments and clinics: the who, what, and why.
J Am Med Inform Assoc
PUBLISHED: 08-18-2011
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Health information exchange (HIE) systems are being developed across the nation. Understanding approaches taken by existing successful exchanges can help new exchange efforts determine goals and plan implementations. The goal of this study was to explore characteristics of use and users of a successful regional HIE.
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User perspectives on the usability of a regional health information exchange.
J Am Med Inform Assoc
PUBLISHED: 05-27-2011
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We assessed the usability of a health information exchange (HIE) in a densely populated metropolitan region. This grant-funded HIE had been deployed rapidly to address the imminent needs of the patient population and the need to draw wider participation from regional entities.
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Effectiveness of non-adjuvanted pandemic influenza A vaccines for preventing pandemic influenza acute respiratory illness visits in 4 U.S. communities.
PLoS ONE
PUBLISHED: 05-26-2011
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We estimated the effectiveness of four monovalent pandemic influenza A (H1N1) vaccines (three unadjuvanted inactivated, one live attenuated) available in the U.S. during the pandemic. Patients with acute respiratory illness presenting to inpatient and outpatient facilities affiliated with four collaborating institutions were prospectively recruited, consented, and tested for influenza. Analyses were restricted to October 2009 through April 2010, when pandemic vaccine was available. Patients testing positive for pandemic influenza by real-time RT-PCR were cases; those testing negative were controls. Vaccine effectiveness was estimated in logistic regression models adjusted for study community, patient age, timing of illness, insurance status, enrollment site, and presence of high-risk medical conditions. Pandemic virus was detected in 1,011 (15%) of 6,757 enrolled patients. Fifteen (1%) of 1,011 influenza positive cases and 1,042 (18%) of 5,746 test-negative controls had record-verified pandemic vaccination >14 days prior to illness onset. Adjusted effectiveness (95% confidence interval) for pandemic vaccines combined was 56% (23%, 75%). Adjusted effectiveness for inactivated vaccines alone (79% of total) was 62% (25%, 81%) overall and 32% (-92%, 76%), 89% (15%, 99%), and -6% (-231%, 66%) in those aged 0.5 to 9, 10 to 49, and 50+ years, respectively. Effectiveness for the live attenuated vaccine in those aged 2 to 49 years was only demonstrated if vaccination >7 rather than >14 days prior to illness onset was considered (61%? 12%, 82%). Inactivated non-adjuvanted pandemic vaccines offered significant protection against confirmed pandemic influenza-associated medical care visits in young adults.
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Effectiveness of seasonal vaccine in preventing confirmed influenza-associated hospitalizations in community dwelling older adults.
J. Infect. Dis.
PUBLISHED: 01-10-2011
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Current evidence supporting the effectiveness of influenza vaccine in preventing hospitalizations in older adults is insufficient.
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Specialized Pediatric Growth Charts For Electronic Health Record Systems: the example of Down syndrome.
AMIA Annu Symp Proc
PUBLISHED: 11-13-2010
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Electronic health record (EHR) systems serving pediatric populations typically incorporate growth charts to help healthcare providers monitor childrens growth. Currently, easily implementable growth charts are not available for subpopulations having growth that differs from the population as a whole, such as children with Down syndrome. This manuscript describes an approach for generating subpopulation-specific growth charts meeting requirements for implementation into EHR systems, using as an example weights for children with Down syndrome. Gender-specific growth curves were generated from 2358 weight values obtained from 331 patients with Down syndrome from July 2001 until March 2005. The project generated printable curves and computable data tables formatted according to growth chart standards set forth by the Centers for Disease Control and Prevention to facilitate implementation into EHR systems. This approach will help developers implementing growth charts and provides actual data tables for monitoring growth in children with Down syndrome.
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Impact of generic substitution decision support on electronic prescribing behavior.
J Am Med Inform Assoc
PUBLISHED: 10-22-2010
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To evaluate the impact of generic substitution decision support on electronic (e-) prescribing of generic medications.
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Human metapneumovirus in hospitalized children in Amman, Jordan.
J. Med. Virol.
PUBLISHED: 04-27-2010
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Human metapneumovirus (HMPV) has recently been identified as an important cause of acute respiratory infections (ARI) in children worldwide. However, there is little systematic data on its frequency and importance as a cause of ARI in the Middle East. We conducted a viral surveillance study in children <5 years of age admitted with respiratory symptoms and/or fever at two major tertiary care hospitals in Amman, Jordan from 1/18-3/29/07. Nose and throat swabs were collected and tested for HMPV and other respiratory viruses by real-time RT-PCR. A total of 743 subjects were enrolled. Forty-four (6%) subjects were positive for HMPV, 467 (64%) were positive for RSV and 13 (1.3%) had co-infection with both HMPV and RSV. The frequency of HMPV in January, February, and March was 4.1%, 3.0%, and 11.9% respectively. Clinical features associated with HMPV infection were similar to those of other respiratory viruses, except children with HMPV were more likely to present with fever than children not infected with HMPV. Children with HMPV and RSV co-infection were administered supplemental oxygen and were admitted to the ICU more frequently than children infected with HMPV alone or RSV alone, though these differences did not reach statistical significance. We conclude that HMPV is an important cause of acute respiratory infections in children in Amman, Jordan. Longer surveillance studies are needed to better understand the seasonal epidemiology of HMPV and to assess if co-infection with HMPV and RSV leads to more severe illness.
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Missing covariate data in medical research: to impute is better than to ignore.
J Clin Epidemiol
PUBLISHED: 03-24-2010
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We compared popular methods to handle missing data with multiple imputation (a more sophisticated method that preserves data).
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Assessment of parental acceptance of a potential cytomegalovirus vaccine for adolescent females.
Vaccine
PUBLISHED: 02-25-2010
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The development of a vaccine against cytomegalovirus (CMV) has been designated as a high priority and adolescent females are a likely target population for CMV vaccination. A self-administered, internet-based survey was developed using constructs from the Health Belief Model to identify factors that may be associated with parental acceptance of a CMV vaccine for their adolescent daughters. Data from 516 parents were analyzed, the majority of whom were female, white, and college educated. Parental acceptance of a CMV vaccine was generally high. Perceived benefits of vaccine were independently associated with vaccine acceptance while history of previous vaccine refusal, concerns about safety and cost of the vaccine were negatively associated. These findings provide initial data on factors that are likely to influence parental acceptance of a CMV vaccine for adolescent girls.
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Burden of respiratory syncytial virus in hospitalized infants and young children in Amman, Jordan.
Scand. J. Infect. Dis.
PUBLISHED: 01-27-2010
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Acute respiratory infections (ARI) play a major role in hospitalizations in the Middle East, but the specific viral causes are unknown. We conducted prospective viral surveillance in children <5 y of age admitted with ARI and/or fever at 2 dissimilar hospitals in Amman, Jordan during peak respiratory syncytial virus (RSV) season. We collected prospective clinical and demographic data and obtained nose/throat swabs for testing for RSV by real-time polymerase chain reaction (RT-PCR). We obtained clinical and laboratory data for 728/743 (98%) subjects enrolled. The childrens median age was 4.3 months, 58.4% were males, 87% were breastfed, 4% attended day care, 67% were exposed to smokers, 7% were admitted to the intensive care unit, and 0.7% died (n = 5). Out of 728 subjects, 467 (64%) tested positive by RT-PCR for RSV. Comparing RSV-positive with RSV-negative subjects, the RSV-positive subjects had lower median age (3.6 vs 6.4 months, p < 0.001) and fewer males (55% vs 64%, p = 0.02). RSV-positive children had higher rates of oxygen use (72% vs 42%, p < 0.001), a longer hospital stay (5 vs 4 days, p = 0.001), and higher hospital charges (US$538 vs US$431, p < 0.001) than RSV-negative children. In young hospitalized Jordanian infants, the medical and financial burden of RSV was found to be high. Effective preventive measures, such as an RSV vaccine, would have a significant beneficial impact.
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Role of inflammation and oxidative stress in atrial fibrillation.
Heart Rhythm
PUBLISHED: 06-28-2009
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Atrial fibrillation (AF) is the most common arrhythmia seen in clinical practice. Increasing evidence indicates that inflammation and oxidative stress contribute to the pathogenesis of AF, but their role remains poorly defined. In addition, whether inflammation and oxidative stress are associated with particular types of AF is unclear.
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Adjustment for missingness using auxiliary information in semiparametric regression.
Biometrics
PUBLISHED: 05-07-2009
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In this article, we study the estimation of mean response and regression coefficient in semiparametric regression problems when response variable is subject to nonrandom missingness. When the missingness is independent of the response conditional on high-dimensional auxiliary information, the parametric approach may misspecify the relationship between covariates and response while the nonparametric approach is infeasible because of the curse of dimensionality. To overcome this, we study a model-based approach to condense the auxiliary information and estimate the parameters of interest nonparametrically on the condensed covariate space. Our estimators possess the double robustness property, i.e., they are consistent whenever the model for the response given auxiliary covariates or the model for the missingness given auxiliary covariate is correct. We conduct a number of simulations to compare the numerical performance between our estimators and other existing estimators in the current missing data literature, including the propensity score approach and the inverse probability weighted estimating equation. A set of real data is used to illustrate our approach.
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Dealing with missing predictor values when applying clinical prediction models.
Clin. Chem.
PUBLISHED: 03-12-2009
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Prediction models combine patient characteristics and test results to predict the presence of a disease or the occurrence of an event in the future. In the event that test results (predictor) are unavailable, a strategy is needed to help users applying a prediction model to deal with such missing values. We evaluated 6 strategies to deal with missing values.
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Human rhinovirus C associated with wheezing in hospitalised children in the Middle East.
J. Clin. Virol.
PUBLISHED: 03-03-2009
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Few studies have investigated the disease burden and genetic diversity of human rhinoviruses (HRVs) in developing countries.
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Influenza in older adults: impact of vaccination of school children.
Vaccine
PUBLISHED: 01-20-2009
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The extent to which immunizing school children reduce the burden of influenza in adults is controversial. We enrolled a systematic sample of adults > or = 50 years hospitalized with respiratory symptoms in two counties, one with and one without a school-based immunization program. We tested all subjects for influenza by polymerase chain reaction. Hospitalizations per 1000 adults aged > or = 50 years were 1.28 (95% CI 0.59, 2.04) in the intervention county and 1.53 (95% CI 0.71, 2.34) in the control county. These rates did not differ significantly except in the subgroup aged 50 -- 64 years where rates in the intervention county were significantly lower.
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A study of transportability of an existing smoking status detection module across institutions.
AMIA Annu Symp Proc
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Electronic Medical Records (EMRs) are valuable resources for clinical observational studies. Smoking status of a patient is one of the key factors for many diseases, but it is often embedded in narrative text. Natural language processing (NLP) systems have been developed for this specific task, such as the smoking status detection module in the clinical Text Analysis and Knowledge Extraction System (cTAKES). This study examined transportability of the smoking module in cTAKES on the Vanderbilt University Hospitals EMR data. Our evaluation demonstrated that modest effort of change is necessary to achieve desirable performance. We modified the system by filtering notes, annotating new data for training the machine learning classifier, and adding rules to the rule-based classifiers. Our results showed that the customized module achieved significantly higher F-measures at all levels of classification (i.e., sentence, document, patient) compared to the direct application of the cTAKES module to the Vanderbilt data.
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A Bayesian Approach for Generalized Linear Models with Explanatory Biomarker Measurement Variables Subject to Detection Limit - an Application to Acute Lung Injury.
J Appl Stat
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Biomarkers have the potential to improve our understanding of disease diagnosis and prognosis. Biomarker levels that fall below the assay detection limits (DLs), however, compromise the application of biomarkers in research and practice. Most existing methods to handle non-detects focus on a scenario in which the response variable is subject to detection limit; only a few methods consider explanatory variables when dealing with DLs. We propose a Bayesian approach for generalized linear models with explanatory variables subject to lower, upper, or interval DLs. In simulation studies, we compared the proposed Bayesian approach to four commonly used methods in a logistic regression model with explanatory variable measurements subject to DL. We also applied the Bayesian approach and other four methods in a real study, in which a panel of cytokine biomarkers was studied for their association with acute lung injury (ALI). We found that IL8 was associated with a moderate increase in risk for ALI in the model based on the proposed Bayesian approach.
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Pentoxifylline lowers plasminogen activator inhibitor 1 levels in obese individuals: a pilot study.
Angiology
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Plasminogen activator inhibitor 1 (PAI-1), the primary inhibitor of fibrinolysis and C-reactive protein (CRP), is a predictor of myocardial infarction. Both are upregulated by tumor necrosis factor-alpha (TNF-?) within the obese population. This pilot study tested the hypothesis that TNF-? blockade with pentoxifylline lowers PAI-1 and high-sensitivity CRP (hsCRP) in obese individuals. Twenty participants were treated with pentoxifylline for 8 weeks. A proportional odds model was used to compare the change in PAI-1 and CRP in the pentoxifylline and placebo groups. Plasminogen activator inhibitor 1, but not hsCRP levels, decreased over the 8-week period of the study (P = .025 and P = NS). There was significant dropout of participants due to drug tolerability. These findings suggest that these markers of cardiovascular risk are differentially regulated in obesity and that PAI-1 levels can be reduced by pentoxifylline in this population.
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Suboptimal inhibition of platelet cyclooxygenase-1 by aspirin in metabolic syndrome.
Hypertension
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Interindividual variation in the ability of aspirin to inhibit platelet cyclooxygenase-1 (COX-1) could account for some on-treatment cardiovascular events. Here, we sought to determine whether there are clinical phenotypes that are associated with a suboptimal pharmacological effect of aspirin. In a prospective, 2-week study, we evaluated the effect of aspirin (81 mg) on platelet COX-1 in 135 patients with stable coronary artery disease by measuring serum thromboxane B(2) (sTxB(2)) as an indicator of inhibition of platelet COX-1. A nested randomized study compared enteric-coated with immediate-release formulations of aspirin. We found that sTxB(2) was systematically higher among the 83 patients with metabolic syndrome than among the 52 patients without (median: 4.0 versus 3.02 ng/mL; P=0.013). Twelve patients (14%) with metabolic syndrome, but none without metabolic syndrome, had sTxB(2) levels consistent with inadequate inhibition of COX (sTxB(2) ?13 ng/mL). In linear regression models, metabolic syndrome (but none of its individual components) significantly associated with higher levels of log-transformed sTxB(2) (P=0.006). Higher levels of sTxB(2) associated with greater residual platelet function measured by aggregometry-based methods. Among the randomized subset, sTxB(2) levels were systematically higher among patients receiving enteric-coated aspirin. Last, urinary 11-dehydro thromboxane B(2) did not correlate with sTxB(2), suggesting that the former should not be used to quantitate aspirins pharmacological effect on platelets. In conclusion, metabolic syndrome, which places patients at high risk for thrombotic cardiovascular events, strongly and uniquely associates with less effective inhibition of platelet COX-1 by aspirin.
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Novel Nanostructured Paper with Ultra-High Transparency and Ultra-High Haze for Solar Cells.
Nano Lett.
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Solar cell substrates require high optical transparency, but also prefer high optical haze to increase the light scattering and consequently the absorption in the active materials. Unfortunately there is a tradeoff between these optical properties, which is exemplified by common transparent paper substrates exhibiting a transparency of about 90% yet a low optical haze (< 20%). In this work we introduce a novel transparent paper made of wood fibers that display both ultra-high optical transparency (~96%) and ultra-high haze (~60%), thus delivering an optimal substrate design for solar cell devices. Compared to previously demonstrated nanopaper composed of wood-based cellulose nanofibers, our novel transparent paper has better dual performance in transmittance and haze, but also is fabricated at a much lower cost. This high-performance, low-cost transparent paper is a potentially revolutionary material that may influence a new generation of environmentally friendly printed electronics.
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What is Visualize?

JoVE Visualize is a tool created to match the last 5 years of PubMed publications to methods in JoVE's video library.

How does it work?

We use abstracts found on PubMed and match them to JoVE videos to create a list of 10 to 30 related methods videos.

Video X seems to be unrelated to Abstract Y...

In developing our video relationships, we compare around 5 million PubMed articles to our library of over 4,500 methods videos. In some cases the language used in the PubMed abstracts makes matching that content to a JoVE video difficult. In other cases, there happens not to be any content in our video library that is relevant to the topic of a given abstract. In these cases, our algorithms are trying their best to display videos with relevant content, which can sometimes result in matched videos with only a slight relation.