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Search Results: 1 - 10 of 186351 matches for " James E. Baker "
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Evolution of the cluster abundance in non-Gaussian models
James Robinson,Jonathan E. Baker
Physics , 1999, DOI: 10.1046/j.1365-8711.2000.03109.x
Abstract: We carry out N-body simulations of several non-Gaussian structure formation models, including Peebles' isocurvature cold dark matter model, cosmic string models, and a model with primordial voids. We compare the evolution of the cluster mass function in these simulations with that predicted by a modified version of the Press-Schechter formalism. We find that the Press-Schechter formula can accurately fit the cluster evolution over a wide range of redshifts for all of the models considered, with typical errors in the mass function of less than 25%, considerably smaller than the amount by which predictions for different models may differ. This work demonstrates that the Press-Schechter formalism can be used to place strong model independent constraints on non-Gaussianity in the universe.
RNAi-induced silencing of embryonic tryptophan oxygenase in the Pyralid moth, Plodia interpunctella
Jeffrey A. Fabrick,Michael R. Kanost,James E. Baker
Journal of Insect Science , 2004,
Abstract: Gene silencing through the introduction of double-stranded RNA (RNA interference, RNAi) provides a powerful tool for the elucidation of gene function in many systems, including those where genomics and proteomics are incomplete. The use of RNAi technology for gene silencing in Lepidoptera has lacked significant attention compared to other systems. To demonstrate that RNAi can be utilized in the lepidopteran, Plodia interpunctella, we cloned a cDNA for tryptophan oxygenase, and showed that silencing of tryptophan oxygenase through RNAi during embryonic development resulted in loss of eye-color pigmentation. The complete amino acid sequence of Plodia tryptophan oxygenase can be accessed through NCBI Protein Database under NCBI Accession # AY427951.
Effects of Smoking and Cessation on Subclinical Arterial Disease: A Substudy of a Randomized Controlled Trial
Heather M. Johnson, Megan E. Piper, Timothy B. Baker, Michael C. Fiore, James H. Stein
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0035332
Abstract: Background The mechanisms by which smoking cessation reduces cardiovascular disease risk are unclear. We evaluated longitudinal changes in carotid intima-media thickness among current smokers enrolled in a prospective, randomized smoking cessation clinical trial. Methodology/Principal Findings Subjects were enrolled in a randomized, double-blind, placebo-controlled trial of 5 smoking cessation pharmacotherapies and underwent carotid ultrasonography with carotid intima-media thickness measurement. Subjects were classified as continuously abstinent (biochemically confirmed abstinence at 6 months, 1 year, and 3 years post-quit attempt), intermittently abstinent (reported smoking at one of the three time points), or smoked continuously (reported smoking at all three time points). The primary endpoint was the absolute change (mm) in carotid intima-media thickness (ΔCIMTmax) before randomization and 3 years after the target quit date. Pearson correlations were calculated and multivariable regression models (controlling for baseline CIMTmax and research site) were analyzed. Among 795 subjects (45.2±10.6 years old, 58.5% female), 189 (23.8%) were continuously abstinent, 373 (46.9%) smoked continuously, and 233 (29.3%) were abstinent intermittently. There was a greater increase in carotid intima-media thickness among subjects who were continuously abstinent than among those who smoked continuously (p = 0.020), but not intermittently (p = 0.310). Antihypertensive medication use (p = 0.001) and research site (p<0.001) independently predicted ΔCIMTmax – not smoking status. The greatest increase in carotid intima-media thickness among continuous abstainers was related to increases in body-mass index (p = 0.043). Conclusions/Significance Smoking status did not independently predict ΔCIMTmax; increasing body-mass index and antihypertensive medication use were the most important independent predictors. The rapid reduction in cardiovascular disease events observed with smoking cessation is unlikely to be mediated by changes in subclinical atherosclerosis burden. Trial Registration ClinicalTrials.gov NCT00332644
A versatile toolkit for high throughput functional genomics with Trichoderma reesei
André Schuster, Kenneth S Bruno, James R Collett, Scott E Baker, Bernhard Seiboth, Christian P Kubicek, Monika Schmoll
Biotechnology for Biofuels , 2012, DOI: 10.1186/1754-6834-5-1
Abstract: Aiming at high efficiency and high throughput methods, we present here a construction kit for gene knock out in T. reesei. We provide a primer database for gene deletion using the pyr4, amdS and hph selection markers. For high throughput generation of gene knock outs, we constructed vectors using yeast mediated recombination and then transformed a T. reesei strain deficient in non-homologous end joining (NHEJ) by spore electroporation. This NHEJ-defect was subsequently removed by crossing of mutants with a sexually competent strain derived from the parental strain, QM9414.Using this strategy and the materials provided, high throughput gene deletion in T. reesei becomes feasible. Moreover, with the application of sexual development, the NHEJ-defect can be removed efficiently and without the need for additional selection markers. The same advantages apply for the construction of multiple mutants by crossing of strains with different gene deletions, which is now possible with considerably less hands-on time and minimal screening effort compared to a transformation approach. Consequently this toolkit can considerably boost research towards efficient exploitation of the resources of T. reesei for cellulase expression and hence second generation biofuel production.The increasing awareness of the limited availability of fossil fuels along with the environmental problems caused by their application initiated considerable research efforts towards clean and sustainable biofuels [1-3]. Thereby, the cellulases required to degrade cellulosic plant materials into small building blocks, which can be metabolized by yeast or other microbes to ethanol or hydrocarbon biofuel precursors, respectively, are one major focus of investigation [4]. Trichoderma reesei (Hypocrea jecorina) is currently the most efficient producer of enzyme mixtures for degradation of plant materials [5]. The cellulases produced by this fungus are utilized for diverse industrial processes, from biobleaching of t
Electrocardiographic Changes Associated with Smoking and Smoking Cessation: Outcomes from a Randomized Controlled Trial
Adam D. Gepner, Megan E. Piper, Miguel A. Leal, Asha Asthana, Michael C. Fiore, Timothy B. Baker, James H. Stein
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0062311
Abstract: Introduction Cardiovascular disease (CVD) can be detected and quantified by analysis of the electrocardiogram (ECG); however the effects of smoking and smoking cessation on the ECG have not been characterized. Methods Standard 12-lead ECGs were performed at baseline and 3 years after subjects enrolled in a prospective, randomized, placebo-controlled clinical trial of smoking cessation pharmacotherapies. ECGs were interpreted using the Minnesota Code ECG Classification. The effects of (i) smoking burden on the prevalence of ECG findings at baseline, and (ii) smoking and smoking cessation on ECG changes after 3 years were investigated by multivariable and multinomial regression analyses. Results At baseline, 532 smokers were (mean [SD]) 43.3 (11.5) years old, smoked 20.6 (7.9) cigarettes/day, with a smoking burden of 26.7 (18.6) pack-years. Major and minor ECG criteria were identified in 87 (16.4%) and 131 (24.6%) of subjects, respectively. After adjusting for demographic data and known CVD risk factors, higher pack-years was associated with major ECG abnormalities (p = 0.02), but current cigarettes/day (p = 0.23) was not. After 3 years, 42.9% of subjects were abstinent from smoking. New major and minor ECG criteria were observed in 7.2% and 15.6% of subjects respectively, but in similar numbers of abstinent subjects and continuing smokers (p>0.2 for both). Continuing smokers showed significant reduction in current smoking (–8.4 [8.8] cigarettes/day, p<0.001) compared to baseline. Conclusions In conclusion, major ECG abnormalities are independently associated with lifetime smoking burden. After 3 years, smoking cessation was not associated with a decrease in ECG abnormalities, although cigarettes smoked/day decreased among continuing smokers.
Electromagnetic Nanoscale Metrology Based on Entropy Production and Fluctuations
James Baker-Jarvis
Entropy , 2008, DOI: 10.3390/e10040411
Abstract: The goal in this paper is to show how many high-frequency electromagnetic metrology areas can be understood and formulated in terms of entropy evolution, production, and fluctuations. This may be important in nanotechnology where an understanding of fluctuations of thermal and electromagnetic energy and the effects of nonequilibrium are particularly important. The approach used here is based on a new derivation of an entropy evolution equation using an exact Liouville-based statistical-mechanical theory rooted in the Robertson-Zwanzig-Mori formulations. The analysis begins by developing an exact equation for entropy rate in terms of time correlations of the microscopic entropy rate. This equation is an exact fluctuation-dissipation relationship. We then define the entropy and its production for electromagnetic driving, both in the time and frequency domains, and apply this to study dielectric and magnetic material measurements, magnetic relaxation, cavity resonance, noise, measuring Boltzmann’s constant, and power measurements.
Limitations of Improved Nitrogen Management to Reduce Nitrate Leaching and Increase Use Efficiency
James L. Baker
The Scientific World Journal , 2001, DOI: 10.1100/tsw.2001.457
Evaluation of a Metabolic Cotton Seedling Emergence Model  [PDF]
Dennis C. Gitz III, Jeffrey T. Baker, James R. Mahan
American Journal of Plant Sciences (AJPS) , 2015, DOI: 10.4236/ajps.2015.611172
Abstract: A model for cotton seedling emergence (MaGi) based on malate synthase kinetics was evaluated. Cotton seeds were planted through the early spring and into typical planting times for the areas. Soil temperatures at seed depth were used as inputs into MaGi and a commonly used seedling emergence model based on heat unit accumulation (DD60). Time to 50% emergence was calculated and compared with predicted emergence using MaGi and DD60. MaGi yielded predictive capability without the need to resort to lengthy experimentation required by traditional methods. The results suggest that a physiological or semi-empirical approach incorporating both enzyme kinetics and whole plant temperature responses would be useful for rapidly constructing seedling emergence models.
Treatment with clopidogrel and proton pump inhibitors in combination: a review of emerging evidence  [PDF]
David A. Johnson, Danial E. Baker
Open Journal of Internal Medicine (OJIM) , 2011, DOI: 10.4236/ojim.2011.13011
Abstract: Proton pump inhibitors often are prescribed in combination with clopidogrel to decrease risk of gastrointestinal bleeding after acute coronary syndrome. Clopidogrel is a prodrug that has to be metabolized in the liver to generate the active metabolite. Both medications are metabolized largely by the CYP2C19 enzyme; therefore, concerns exist that a drug-drug interaction during concomitant treatment with clopidogrel and a proton pump inhibitor may result in reduction of platelet inhibition. We have reviewed observational and randomized control studies that have evaluated the potential influence of proton pump inhibitors on the platelet inhibitory effect of clopidogrel, along with cardiovascular outcomes. We also have summarized regulatory and academic guidelines for treatment of patients in which concomitant therapy with clopidogrel and proton pump inhibitors may be indicated. Confounding issues, including differential effects of individual proton pump inhibitors on the pharmacodynamics of clopidogrel and variation in clopidogrel metabolism mediated by CYP2C19 gene polymorphisms, also are discussed.
Emergency Department Discharge Instructions: Lessons Learned through Developing New Patient Education Materials
Danielle M. McCarthy,Kirsten G. Engel,Barbara A. Buckley,Victoria E. Forth,Michael J. Schmidt,James G. Adams,David W. Baker
Emergency Medicine International , 2012, DOI: 10.1155/2012/306859
Abstract: Our multidisciplinary team developed a new set of discharge instructions for five common emergency department diagnoses using recommended tools for creating literacy-appropriate and patient-centered education materials. We found that the recommended tools for document creation were essential in constructing the new instructions. However, while the tools were necessary, they were not sufficient. This paper describes the insights gained and lessons learned in this document creation process. 1. Introduction Ninety million Americans have difficulty understanding their own medical care [1]. A large number of studies document that health-related materials exceed the average users reading ability [2]. Within the emergency medicine literature, studies have demonstrated that emergency department (ED) populations are particularly at risk for limited literacy and numeracy [3, 4]. Adding to the problem, print discharge instructions are not written at appropriate reading levels [5–7] and ED patients frequently do not understand their discharge instructions [6, 8–11]. The decision to discharge a patient from the ED is complex and multifactorial; however, once that decision has been made, it is important that patients understand how to properly continue their care at home. In comparison to other aspects of their visit, ED patients have more difficulty understanding their discharge instructions and home care plan than any other component of their visit [12]. In fact, several studies have evaluated patient comprehension of discharge instructions in the days following discharge and have found that up to 78% of patients has an incomplete understanding of their instructions [11, 12]. The patient’s ability to comprehend instructions has many implications, not only for the health of the individual, but also for the healthcare system, as patients with poor comprehension are at increased risk for adverse events and increased healthcare utilization [13]. Unfortunately, the high rates of poor comprehension have not encouraged significant changes in the printed materials provided by the ED [14]. Nearly every discharged patient receives instructions upon leaving the ED, but these instructions vary widely. The instructions may be hand written or preformulated. The instructions might be based on an individual physician’s notion of “what a patient needs to know” or may have been created by a third-party commercial entity. Regardless of the source of information, individual ED clinicians have no simple means of assessing if a patient will understand the content, if the content
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