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Search Results: 1 - 10 of 9852 matches for " Scott Dryden-Peterson "
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Cotrimoxazole Prophylaxis and Risk of Severe Anemia or Severe Neutropenia in HAART-Exposed, HIV-Uninfected Infants
Scott Dryden-Peterson, Oluwemimo Jayeoba, Michael D. Hughes, Haruna Jibril, Kenneth McIntosh, Taolo A. Modise, Aida Asmelash, Kathleen M. Powis, Max Essex, Roger L. Shapiro, Shahin Lockman
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0074171
Abstract: Background Prophylactic cotrimoxazole is recommended for infants born to HIV-infected mothers. However, cotrimoxazole may increase the risk of severe anemia or neutropenia. Methods We compared the proportion of HIV-exposed uninfected (HIV-EU) infants experiencing incident severe anemia (and separately, severe neutropenia) between a prospective cohort receiving prophylactic cotrimoxazole from 1 to 6 months vs. infants from two prior trials who did not receive cotrimoxazole. Infants were from rural and urban communities in southern Botswana. Results A total of 1705 HIV-EU infants were included. Among these 645 (37.8%) were fed with iron-supplemented formula from birth. Severe anemia developed in 87 (5.1%) infants, and severe neutropenia in 164 (9.6%) infants. In an analysis stratified by infant feeding method, there were no significant differences in the risk of severe anemia by prophylactic cotrimoxazole exposure–risk difference, ?0.69% (95% confidence interval [CI] ?2.1 to 0.76%). Findings were similar in multivariable analysis, adjusted odds ratio (aOR) 0.35 (95% CI 0.07 to 1.65). There were also no significant differences observed for severe neutropenia by cotrimoxazole exposure, risk difference 2.0% (95% CI ?1.3 to 5.2%) and aOR 0.80 (95% CI 0.33 to 1.93). Conclusions Severe anemia and severe neutropenia were infrequent among HIV-exposed uninfected infants receiving cotrimoxazole from 1–6 months of age. Concerns regarding hematologic toxicity should not limit the use of prophylactic cotrimoxazole in HIV-exposed uninfected infants. ClinicalTrials.gov Registration Numbers NCT01086878 (http://clinicaltrials.gov/show/NCT010868?78), NCT00197587 (http://clinicaltrials.gov/show/NCT001975?87), and NCT00270296 (http://clinicaltrials.gov/show/NCT002702?96).
Effectiveness of the Standard WHO Recommended Retreatment Regimen (Category II) for Tuberculosis in Kampala, Uganda: A Prospective Cohort Study
Edward C. Jones-López equal contributor ,Irene Ayakaka equal contributor,Jonathan Levin,Nancy Reilly,Francis Mumbowa,Scott Dryden-Peterson,Grace Nyakoojo,Kevin Fennelly,Beth Temple,Susan Nakubulwa,Moses L. Joloba,Alphonse Okwera,Kathleen D. Eisenach,Ruth McNerney,Alison M. Elliott,Jerrold J. Ellner,Peter G. Smith,Roy D. Mugerwa
PLOS Medicine , 2011, DOI: 10.1371/journal.pmed.1000427
Abstract: Background Each year, 10%–20% of patients with tuberculosis (TB) in low- and middle-income countries present with previously treated TB and are empirically started on a World Health Organization (WHO)-recommended standardized retreatment regimen. The effectiveness of this retreatment regimen has not been systematically evaluated. Methods and Findings From July 2003 to January 2007, we enrolled smear-positive, pulmonary TB patients into a prospective cohort to study treatment outcomes and mortality during and after treatment with the standardized retreatment regimen. Median time of follow-up was 21 months (interquartile range 12–33 months). A total of 29/148 (20%) HIV-uninfected and 37/140 (26%) HIV-infected patients had an unsuccessful treatment outcome. In a multiple logistic regression analysis to adjust for confounding, factors associated with an unsuccessful treatment outcome were poor adherence (adjusted odds ratio [aOR] associated with missing half or more of scheduled doses 2.39; 95% confidence interval (CI) 1.10–5.22), HIV infection (2.16; 1.01–4.61), age (aOR for 10-year increase 1.59; 1.13–2.25), and duration of TB symptoms (aOR for 1-month increase 1.12; 1.04–1.20). All patients with multidrug-resistant TB had an unsuccessful treatment outcome. HIV-infected individuals were more likely to die than HIV-uninfected individuals (p<0.0001). Multidrug-resistant TB at enrolment was the only common risk factor for death during follow-up for both HIV-infected (adjusted hazard ratio [aHR] 17.9; 6.0–53.4) and HIV-uninfected (14.7; 4.1–52.2) individuals. Other risk factors for death during follow-up among HIV-infected patients were CD4<50 cells/ml and no antiretroviral treatment (aHR 7.4, compared to patients with CD4≥200; 3.0–18.8) and Karnofsky score <70 (2.1; 1.1–4.1); and among HIV-uninfected patients were poor adherence (missing half or more of doses) (3.5; 1.1–10.6) and duration of TB symptoms (aHR for a 1-month increase 1.9; 1.0–3.5). Conclusions The recommended regimen for retreatment TB in Uganda yields an unacceptable proportion of unsuccessful outcomes. There is a need to evaluate new treatment strategies in these patients. Please see later in the article for the Editors' Summary
The complexity of simplicity
Scott N Peterson, Claire M Fraser
Genome Biology , 2001, DOI: 10.1186/gb-2001-2-2-comment2002
Abstract: Attempts to define life have touched nearly every scientific discipline and have been a long-standing subject in philosophy. Even when limited to the realm of biology, the definitions of life fall short of universal agreement and remain a widely debated subject. The practice of reductionism, whereby life is considered solely from the perspective of the genetic material, also generates controversy and complications. Many of these complications have been appreciated recently as a result of the large-scale application of whole-genome sequencing to microbes. The specific issue we discuss here is an attempt to define the minimum number of genes or functions necessary to support cellular life. The appeal of this subject lies largely in the fact that it represents a fundamental question in biology.We have approached the concept of a 'minimal genome' in a manner not unlike that taken by physicists interested in understanding the nature of the universe: we have relied on an underlying assumption or guiding force that states that a simple set of rules must exist. The difficulty lies in finding the proper way to strip away the outer layers of complexity in order to uncover what is truly general and therefore satisfactorily describes all things. It is our belief that some set of basic parameters and principles are common to all cellular life on this planet. On the surface, especially in the age of genomics, it would appear that we will indeed be able to draw inferences and define commonalities. The advent of whole-genome shotgun sequencing [1] has changed biology in ways that we will not fully appreciate for many years to come. Advances in functional genomics, structural genomics and computational biology have also contributed greatly to our ability to make 'sense' of the huge quantities of DNA sequence data being generated. As we begin to apply these methodologies to the question of the minimal genome, we are faced with new perspectives which emphasize that, like any good scie
Nephele: genotyping via complete composition vectors and MapReduce
Marc E Colosimo, Matthew W Peterson, Scott Mardis, Lynette Hirschman
Source Code for Biology and Medicine , 2011, DOI: 10.1186/1751-0473-6-13
Abstract: Nephele is a suite of tools that uses the complete composition vector algorithm to represent each sequence in the dataset as a vector derived from its constituent k-mers by passing the need for multiple sequence alignment, and affinity propagation clustering to group the sequences into genotypes based on a distance measure over the vectors. Our methods produce results that correlate well with expert-defined clades or genotypes, at a fraction of the computational cost of traditional phylogenetic methods run on traditional hardware. Nephele can use the open-source Hadoop implementation of MapReduce to parallelize execution using multiple compute nodes. We were able to generate a neighbour-joined tree of over 10,000 16S samples in less than 2 hours.We conclude that using Nephele can substantially decrease the processing time required for generating genotype trees of tens to hundreds of organisms at genome scale sequence coverage.In the post-genomic era, as sequencing becomes ever cheaper and more routine, biological sequence analysis has provided many useful tools for the study and combat of infectious disease. These tools, which can include both experimental and computational methods, are important for molecular epidemiological studies [1-3], vaccine development [4-6], and microbial forensics [7-9]. One such method is genotyping, the grouping of samples based on their genetic sequence. This can be done experimentally [10-12] or computationally, either by identifying genetic signatures (nucleotide substrings which are only found in a single group of sequences) [13], or on the basis of genetic distance among the sequences [14-16]. These methods allow a researcher to split a group of sequences into distinct partitions for further analysis. In a forensics context, genotyping a sequence can yield clues on where the sequence comes from. In surveillance, genotyping can be used to examine the evolutionary footprint of a pathogen, for example, to identify areas where certain v
Predicting the distribution of a parasite using the ecological niche model, GARP
Haverkost, Terry R.;Gardner, Scott L.;Townsend Peterson, A.;
Revista mexicana de biodiversidad , 2010,
Abstract: the ecological niche of a parasite exists only at the nexus of certain abiotic and biotic conditions suitable for both the definitive and intermediate hosts. however, the life cycles of most parasites are not known, or are poorly known, and using known ranges of hosts to find endemic parasitic infections has been difficult. however, with ecological niche modeling, we can create potential range maps using known localities of infection. testing the validity of such maps requires knowledge of the localities of other parasites with common history. here, we find that the ecological niche of a tapeworm parasite of voles, paranoplocephala macrocephala (cestoda: anoplocephalidae), allows prediction of the presence (in ecological and geographic space) of 19 related parasite species from 3 genera in 23 different hosts throughout the nearctic. these results give credence to the idea that this group shares similar life cycle requirements despite phylogenetic distance. this work further validates ecological niche modeling as a means by which to predict occurrence of parasites when not all facets of the life cycle are confirmed. such inductive methods create the opportunity for deducing potential reservoir or intermediate hosts, and complementing studies of parasite biodiversity and community ecology.
Predicting the distribution of a parasite using the ecological niche model, GARP Predicción de la distribución de un parásito usando el modelo de nicho ecológico, GARP
Terry R. Haverkost,Scott L. Gardner,A. Townsend Peterson
Revista mexicana de biodiversidad , 2010,
Abstract: The ecological niche of a parasite exists only at the nexus of certain abiotic and biotic conditions suitable for both the definitive and intermediate hosts. However, the life cycles of most parasites are not known, or are poorly known, and using known ranges of hosts to find endemic parasitic infections has been difficult. However, with ecological niche modeling, we can create potential range maps using known localities of infection. Testing the validity of such maps requires knowledge of the localities of other parasites with common history. Here, we find that the ecological niche of a tapeworm parasite of voles, Paranoplocephala macrocephala (Cestoda: Anoplocephalidae), allows prediction of the presence (in ecological and geographic space) of 19 related parasite species from 3 genera in 23 different hosts throughout the Nearctic. These results give credence to the idea that this group shares similar life cycle requirements despite phylogenetic distance. This work further validates ecological niche modeling as a means by which to predict occurrence of parasites when not all facets of the life cycle are confirmed. Such inductive methods create the opportunity for deducing potential reservoir or intermediate hosts, and complementing studies of parasite biodiversity and community ecology. El nicho ecológico de un parásito existe sólo cuando coinciden condiciones abióticas y bióticas necesarias para los hospederos definitivos e intermediarios. No obstante, los ciclos de vida de la mayoría de los parásitos son poco conocidos; el usar áreas de distribución de hospederos para encontrar áreas endémicas de parasitismo ha resultado difícil. Con el modelado de nicho, se pueden producir mapas del área de distribución potencial con base en sitios conocidos de presencia. Para probar la validez de estos mapas, se requiere el conocimiento de sitios de presencia de otros parásitos relacionados. En este estudio, encontramos que el nicho ecológico de un gusano parásito de ratones, Paranoplocephala macrocephala (Cestoda: Anoplocephalidae) permite predecir la presencia de 19 especies relacionadas de parásitos de 3 géneros en 23 diferentes hospederos a través del Neártico. Estos resultados apoyan la idea de que este grupo comparte una historia filogenética común que se refleja en nichos compartidos y que el modelado de nichos ofrece una manera de predecir la presencia de parásitos aunque no se conozcan todos los detalles de su ciclo de vida. Estos métodos permiten deducir reservorios u hospederos para estos parásitos.
Treatment of complicated skin and soft-tissue infections caused by resistant bacteria: value of linezolid, tigecycline, daptomycin and vancomycin
Christian Eckmann, Matthew Dryden
European Journal of Medical Research , 2010, DOI: 10.1186/2047-783x-15-12-554
Abstract: Tigecycline is an alternative in polymicrobial infections except by diabetic foot infections. Daptomycin might be a treatment option for cases of cSSTI with MRSA bacteremia. cSSTI caused by resistant Gram-negative bacteria are a matter of great concern. The development of new antibiotics in this area is an urgent priority to avoid the risk of a postantibiotic era with no antimicrobial treatment options. An individual approach for every single patient is mandatory to evaluate the optimal antimicrobial treatment regimen.Skin and soft tissue infections (SSTI) are amongst the most common bacterial infections in humans. They represent one of the most common indications for antibiotic treatment and represent about 10% of hospital admissions in the US [1]. Amongst the broad spectrum of skin and soft tissue infections treatment is mainly delivered out of hospital. SSTI have a broad range of aetiology, clinical manifestation and severity [2,3]. At one end of the spectrum the outcome may be spontaneous resolution without antibiotics, but at the other end it may present with sepsis with lethal outcome. SSTI at 10% is the third most frequent focus for severe sepsis or septic shock, after pneumonia (5560%) and abdominal infections (25%) [4].This review aims to discuss the currently available antibiotics active against resistant bacteria (primarily MRSA, VRE, ESBL-producing bacteria and carbapenem-resistant strains) in terms of mechanisms of action, eradication rates and most important clinical outcome.The classification of skin and soft tissue infections is often confusing. Specific SSTI can be sub-categorised according to the causative microbial agents, the main tissue layer affected (i.e. skin, subcutis, fascia and muscle) or according to clinical signs and symptoms. It is to be differentiated, whether the infection is localised or generalised. Useful classifications are those which differentiate SSTI according to urgency of surgical intervention [5,6]. Three categories can be
Isospectral Finiteness of Hyperbolic Orbisurfaces
Emily B. Dryden
Mathematics , 2004,
Abstract: We discuss questions of isospectrality for hyperbolic orbisurfaces, examining the relationship between the geometry of an orbisurface and its Laplace spectrum. We show that certain hyperbolic orbisurfaces cannot be isospectral, where the obstructions involve the number of singular points and genera of our orbisurfaces. Using a version of the Selberg Trace Formula for hyperbolic orbisurfaces, we show that the Laplace spectrum determines the length spectrum and the orders of the singular points, up to finitely many possibilities. Conversely, knowledge of the length spectrum and the orders of the singular points determines the Laplace spectrum. This partial generalization of Huber's theorem is used to prove that isospectral sets of hyperbolic orbisurfaces have finite cardinality, generalizing a result of McKean for Riemann surfaces.
Statistical analysis on high-dimensional spheres and shape spaces
Ian L. Dryden
Mathematics , 2005, DOI: 10.1214/009053605000000264
Abstract: We consider the statistical analysis of data on high-dimensional spheres and shape spaces. The work is of particular relevance to applications where high-dimensional data are available--a commonly encountered situation in many disciplines. First the uniform measure on the infinite-dimensional sphere is reviewed, together with connections with Wiener measure. We then discuss densities of Gaussian measures with respect to Wiener measure. Some nonuniform distributions on infinite-dimensional spheres and shape spaces are introduced, and special cases which have important practical consequences are considered. We focus on the high-dimensional real and complex Bingham, uniform, von Mises-Fisher, Fisher-Bingham and the real and complex Watson distributions. Asymptotic distributions in the cases where dimension and sample size are large are discussed. Approximations for practical maximum likelihood based inference are considered, and in particular we discuss an application to brain shape modeling.
Collars and partitions of hyperbolic cone-surfaces
Emily B. Dryden,Hugo Parlier
Mathematics , 2004, DOI: 10.1007/s10711-007-9172-6
Abstract: For compact Riemann surfaces, the collar theorem and Bers' partition theorem are major tools for working with simple closed geodesics. The main goal of this paper is to prove similar theorems for hyperbolic cone-surfaces. Hyperbolic two-dimensional orbifolds are a particular case of such surfaces. We consider all cone angles to be strictly less than $\pi$ to be able to consider partitions.
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