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Search Results: 1 - 10 of 3619 matches for " Midori Kato-Maeda "
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Model of the Effects of Improving TB Diagnosis on Infection Dynamics in Differing Demographic and HIV-Prevalence Scenarios  [PDF]
Allison S. Rhines, Midori Kato-Maeda, Marcus W. Feldman
Journal of Tuberculosis Research (JTR) , 2015, DOI: 10.4236/jtr.2015.31001
Abstract: This paper seeks to examine the sensitivity of tuberculosis transmission (TB) dynamics to the rate at which infectious individuals with active TB begin a TB treatment course, and therefore cease to be infectious to others. We model this by varying both the rate at which individuals are diagnosed and begin treatment, and the demographic conditions in which the epidemic occurs. An agestructured deterministic ordinary differential equation model is used to study the sensitivity of TB transmission dynamics to the implementation of a more effective diagnostic such as Xpert MTB/ RIF in a high HIV prevalence setting. Sensitivity analysis of the effectiveness of the diagnostic (λ) shows the interim disease dynamics in three demographic scenarios defined by differences in HIV prevalence and age structure at a constant transmission rate. In the near future, we expect the diagnostic to have the most effect in areas of high HIV prevalence. In the long term, we expect the diagnostic to have the most significant impact at high transmission rates regardless of HIV prevalence and age structure.
Likelihood-Based Inference for Discretely Observed Birth-Death-Shift Processes, with Applications to Evolution of Mobile Genetic Elements
Jason Xu,Peter Guttorp,Midori Kato-Maeda,Vladimir N. Minin
Quantitative Biology , 2014,
Abstract: Continuous-time birth-death-shift (BDS) processes are frequently used in stochastic modeling, with many applications in ecology and epidemiology. In particular, such processes can model evolutionary dynamics of transposable elements - important genetic markers in molecular epidemiology. Estimation of the effects of individual covariates on the birth, death, and shift rates of the process can be accomplished by analyzing patient data, but inferring these rates in a discretely and unevenly observed setting presents computational challenges. We propose a mutli-type branching process approximation to BDS processes and develop a corresponding expectation maximization (EM) algorithm, where we use spectral techniques to reduce calculation of expected sufficient statistics to low dimensional integration. These techniques yield an efficient and robust optimization routine for inferring the rates of the BDS process, and apply more broadly to multi-type branching processes where rates can depend on many covariates. After rigorously testing our methodology in simulation studies, we apply our method to study intrapatient time evolution of IS6110 transposable element, a frequently used element during estimation of epidemiological clusters of Mycobacterium tuberculosis infections.
Fitting birth-death processes to panel data with applications to bacterial DNA fingerprinting
Charles R. Doss,Marc A. Suchard,Ian Holmes,Midori Kato-Maeda,Vladimir N. Minin
Quantitative Biology , 2010, DOI: 10.1214/13-AOAS673
Abstract: Continuous-time linear birth-death-immigration (BDI) processes are frequently used in ecology and epidemiology to model stochastic dynamics of the population of interest. In clinical settings, multiple birth-death processes can describe disease trajectories of individual patients, allowing for estimation of the effects of individual covariates on the birth and death rates of the process. Such estimation is usually accomplished by analyzing patient data collected at unevenly spaced time points, referred to as panel data in the biostatistics literature. Fitting linear BDI processes to panel data is a nontrivial optimization problem because birth and death rates can be functions of many parameters related to the covariates of interest. We propose a novel expectation--maximization (EM) algorithm for fitting linear BDI models with covariates to panel data. We derive a closed-form expression for the joint generating function of some of the BDI process statistics and use this generating function to reduce the E-step of the EM algorithm, as well as calculation of the Fisher information, to one-dimensional integration. This analytical technique yields a computationally efficient and robust optimization algorithm that we implemented in an open-source R package. We apply our method to DNA fingerprinting of Mycobacterium tuberculosis, the causative agent of tuberculosis, to study intrapatient time evolution of IS6110 copy number, a genetic marker frequently used during estimation of epidemiological clusters of Mycobacterium tuberculosis infections. Our analysis reveals previously undocumented differences in IS6110 birth-death rates among three major lineages of Mycobacterium tuberculosis, which has important implications for epidemiologists that use IS6110 for DNA fingerprinting of Mycobacterium tuberculosis.
Impact of Isoniazid Resistance-Conferring Mutations on the Clinical Presentation of Isoniazid Monoresistant Tuberculosis
Raymund Dantes, John Metcalfe, Elizabeth Kim, Midori Kato-Maeda, Philip C. Hopewell, Masae Kawamura, Payam Nahid, Adithya Cattamanchi
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0037956
Abstract: Background Specific isoniazid (INH) resistance conferring mutations have been shown to impact the likelihood of tuberculosis (TB) transmission. However, their role in the clinical presentation and outcomes of TB has not been evaluated. Methods We included all cases of culture-confirmed, INH monoresistant tuberculosis reported to the San Francisco Department of Public Health Tuberculosis Control Section from October 1992 through October 2005. For cases with stored culture isolates, we used polymerase chain reaction (PCR) testing and gene sequencing to identify INH resistance-conferring mutations, and compared genotypic and phenotypic characteristics. Results Among 101 consecutive cases of INH monoresistant TB in San Francisco 19 (19%) had isolates with a katG mutation other than S315T; 38 (38%) had isolates with the katG S315T mutation, 29 (29%) had isolates with a inhA-15;c-t promoter mutation, and 15 (15%) had isolates with other mutations. The katG S315T mutation was independently associated with high-level INH resistance (risk ratio [RR] 1.56, 95% confidence interval [CI] 1.07–2.27), and the inhA-15;c-t promoter mutation was inversely associated with high-level INH resistance (RR 0.43, 95% CI 0.21–0.89). However, specific INH resistance-conferring mutations were not associated with the clinical severity or outcomes of INH monoresistant TB cases. Conclusion These data suggest that INH resistance-conferring mutations do not impact the clinical presentation of TB.
Pyrazinamide Resistance, Mycobacterium tuberculosis Lineage and Treatment Outcomes in San Francisco, California
Jonathan M. Budzik, Leah G. Jarlsberg, Julie Higashi, Jennifer Grinsdale, Phil C. Hopewell, Midori Kato-Maeda, Payam Nahid
PLOS ONE , 2014, DOI: 10.1371/journal.pone.0095645
Abstract: Background Pyrazinamide (PZA) is a first line agent for the treatment of active tuberculosis. PZA is also considered a potent companion drug for newer regimens under development. There are limited data on the demographic, clinical, and pathogen characteristics of PZA resistant tuberculosis. Methods Using a retrospective cohort study design, we evaluated all PZA resistant M. tuberculosis (M.tb) and M. bovis cases reported in San Francisco from 1991 to 2011. Demographic, clinical, and molecular data were analyzed. M.tb lineage was determined for all PZA resistant strains and compared to PZA susceptible strains. Results PZA resistance was identified in 1.8% (50 of 2,842) of mycobacterial isolates tested, corresponding to a case rate of 0.3 per 100,000 in the population. Monoresistant PZA infection was associated with the Hispanic population ([OR], 6.3; 95% [CI], 1.97–20.16) and 48% of cases were due to M. bovis. Infection with monoresistant PZA was also associated with extrapulmonary disease ([OR], 6.0; 95% [CI], 2.70–13.26). There was no statistically significant difference between treatment failure and mortality rates in patients infected with PZA monoresistance compared to pansusceptible controls (4% vs. 8%, p = 0.51), or those with PZA and MDR resistance (PZA-MDR) compared to MDR controls (18% vs. 29%, p = 0.40). PZA resistance was not associated with M.tb lineage. Conclusions Across two decades of comprehensive epidemiologic data on tuberculosis in San Francisco County, PZA resistance was uncommon. PZA resistance caused predominantly extrapulmonary disease and was more common in Hispanics compared to other ethnicities, with nearly half the cases attributed to M. bovis. No association was found between PZA monoresistance and M.tb lineage. Treatment outcomes were not adversely influenced by the presence of PZA resistance.
The Role of Speciation in Positive Lowenstein-Jensen Culture Isolates from a High Tuberculosis Burden Country
William Worodria, Jillian Anderson, Adithya Cattamanchi, J. Lucian Davis, Saskia den Boon, Alfred Andama, Samuel D. Yoo, Moses Joloba, Laurence Huang, Midori Kato-Maeda
PLOS ONE , 2011, DOI: 10.1371/journal.pone.0027017
Abstract: Objective To determine the need for routine speciation of positive Lowenstein-Jensen mycobacterial cultures in HIV-infected patients suspected of having pulmonary tuberculosis at Mulago Hospital in Kampala, Uganda. Methods Sputum and bronchoalveolar lavage Lowenstein-Jensen mycobacterial culture isolates from consecutive, HIV-infected patients admitted to Mulago Hospital with 2 weeks or more of cough were subjected to IS6110 PCR and rpoB genetic analysis to determine the presence of Mycobacterium tuberculosis complex (MTBC) and non-tuberculous mycobacteria (NTM). Results Eighty (100%) mycobacterial cultures from 65 patients were confirmed to be members of MTBC. Subsequent analysis of the cultures from 54 patients by PCR and sequence analyses to identify co-infection with NTM confirmed the presence of MTBC as well as the presence of Micrococcus luteus (n = 4), Janibacter spp. (n = 1) and six cultures had organisms that could not be identified. Conclusions Presumptive diagnosis of tuberculosis on the basis of a positive Lowenstein-Jensen culture is sufficient in HIV-infected Ugandans suspected of having tuberculosis. Routine molecular confirmation of positive Lowenstein-Jensen cultures is unnecessary in this low resource setting.
Influence of M. tuberculosis Lineage Variability within a Clinical Trial for Pulmonary Tuberculosis
Payam Nahid,Erin E. Bliven,Elizabeth Y. Kim,William R. Mac Kenzie,Jason E. Stout,Lois Diem,John L. Johnson,Sebastien Gagneux,Philip C. Hopewell,Midori Kato-Maeda
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0010753
Abstract: Recent studies suggest that M. tuberculosis lineage and host genetics interact to impact how active tuberculosis presents clinically. We determined the phylogenetic lineages of M. tuberculosis isolates from participants enrolled in the Tuberculosis Trials Consortium Study 28, conducted in Brazil, Canada, South Africa, Spain, Uganda and the United States, and secondarily explored the relationship between lineage, clinical presentation and response to treatment. Large sequence polymorphisms and single nucleotide polymorphisms were analyzed to determine lineage and sublineage of isolates. Of 306 isolates genotyped, 246 (80.4%) belonged to the Euro-American lineage, with sublineage 724 predominating at African sites (99/192, 51.5%), and the Euro-American strains other than 724 predominating at non-African sites (89/114, 78.1%). Uneven distribution of lineages across regions limited our ability to discern significant associations, nonetheless, in univariate analyses, Euro-American sublineage 724 was associated with more severe disease at baseline, and along with the East Asian lineage was associated with lower bacteriologic conversion after 8 weeks of treatment. Disease presentation and response to drug treatment varied by lineage, but these associations were no longer statistically significant after adjustment for other variables associated with week-8 culture status.
Use of Whole Genome Sequencing to Determine the Microevolution of Mycobacterium tuberculosis during an Outbreak
Midori Kato-Maeda, Christine Ho, Ben Passarelli, Niaz Banaei, Jennifer Grinsdale, Laura Flores, Jillian Anderson, Megan Murray, Graham Rose, L. Masae Kawamura, Nader Pourmand, Muhammad A. Tariq, Sebastien Gagneux, Philip C. Hopewell
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0058235
Abstract: Rationale Current tools available to study the molecular epidemiology of tuberculosis do not provide information about the directionality and sequence of transmission for tuberculosis cases occurring over a short period of time, such as during an outbreak. Recently, whole genome sequencing has been used to study molecular epidemiology of Mycobacterium tuberculosis over short time periods. Objective To describe the microevolution of M. tuberculosis during an outbreak caused by one drug-susceptible strain. Method and Measurements We included 9 patients with tuberculosis diagnosed during a period of 22 months, from a population-based study of the molecular epidemiology in San Francisco. Whole genome sequencing was performed using Illumina’s sequencing by synthesis technology. A custom program written in Python was used to determine single nucleotide polymorphisms which were confirmed by PCR product Sanger sequencing. Main results We obtained an average of 95.7% (94.1–96.9%) coverage for each isolate and an average fold read depth of 73 (1 to 250). We found 7 single nucleotide polymorphisms among the 9 isolates. The single nucleotide polymorphisms data confirmed all except one known epidemiological link. The outbreak strain resulted in 5 bacterial variants originating from the index case A1 with 0–2 mutations per transmission event that resulted in a secondary case. Conclusions Whole genome sequencing analysis from a recent outbreak of tuberculosis enabled us to identify microevolutionary events observable during transmission, to determine 0–2 single nucleotide polymorphisms per transmission event that resulted in a secondary case, and to identify new epidemiologic links in the chain of transmission.
Synthesis and Spectroscopic Properties of Ferrocenyl Derivative Containing Donor and Acceptor Groups  [PDF]
Makoto Minato, Chiharu Sorai, Takashi Ito, Masashi Kiguchi, Midori Kato
International Journal of Organic Chemistry (IJOC) , 2017, DOI: 10.4236/ijoc.2017.73022
Abstract: Much interest has been devoted to organometallic NLO materials. We have become interested in exploring the utility of ferrocenyl group as the conjugating bridge. Thus, we synthesized 1-{{[1,3-(5-methylbenzo)dithiol]-2-yli- dene}methyl}-1’-[2-(p-nitrophenyl)-(E)-ethenyl]ferrocene (1). This new ferrocenyl compound has a donor and an acceptor group in 1,1’-positions. Investigations of the solvatochromic property of the compound revealed that it has polarized structure in a polar solvent, such as DMF. SHG efficiency of the compound was estimated by an SHEW (second-harmonic generation with the evanescent wave) method.
On characters and formal degrees of discrete series of affine Hecke algebras of classical types
Dan Ciubotaru,Midori Kato,Syu Kato
Mathematics , 2010,
Abstract: We address two fundamental questions in the representation theory of affine Hecke algebras of classical types. One is an inductive algorithm to compute characters of tempered modules, and the other is the determination of the constants in the formal degrees of discrete series (in the form conjectured by Reeder \cite{Re}). The former is completely different than the Lusztig-Shoji algorithm \cite{Sh, L}, and it is more effective in a number of cases. The main idea in our proof is to introduce a new family of representations which behave like tempered modules, but for which it is easier to analyze the effect of parameter specializations. Our proof also requires a comparison of the $C^{\ast}$-theoretic results of Opdam, Delorme, Slooten, Solleveld \cite{O, DO, Sl2, OSa, OS}, and the geometric construction from \cite{K1,K2,CK}.
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