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Search Results: 1 - 10 of 231370 matches for " Michael G. Rosenberg "
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MixtureTree: a program for constructing phylogeny
Shu-Chuan Chen, Michael S Rosenberg, Bruce G Lindsay
BMC Bioinformatics , 2011, DOI: 10.1186/1471-2105-12-111
Abstract: The MixtureTree program written in C++ is a Linux based package. The User's Guide and source codes will be available at http://math.asu.edu/~scchen/MixtureTree.html webciteThe efficiency of the mixture algorithm is relatively higher than some classical methods, such as Neighbor-Joining method, Maximum Parsimony method and Maximum Likelihood method. The shortcoming of the mixture tree algorithms, for example timing consuming, can be improved by implementing other revised Expectation-Maximization(EM) algorithms instead of the traditional EM algorithm.Methods for constructing a phylogeny given a set of the DNA sequences is always a popular topic in both biological and statistical research. Many classical methods are popular, such as Neighbor-Joining (NJ) method, Maximum Parsimony (MP) method, Maximum Likelihood (ML) method, and Bayesian (MCMC) approaches ([1] and [2]). There are also many programs which implement these methods, including PHYLIP [3], PAUP [4], and MEGA [5]. Chen and Lindsay introduced a mixture likelihood algorithm as a novel and natural way to deal with such problems because the distribution of offsprings' sequence is a mixture of parental distributions [6]. Unlike the classic methods, this approach uses the frequencies of each sequence within the population to help reconstructing the phylogeny from binary sequences. The model proposed by Chen and Lindsay [6] was done mathematically, as a first step, and that it should not be particularly problematic with most SNPs are bi-allelic with only a very small proportion (well less than 1% and probably less than 0.1%) tri-allelic or quad-allelic ([7] and [8]). The algorithm uses a K-component bernoulli mixture to model binary sequences. It is well-known that when the parameter takes values in an infinite dimensional space, the maximum likelihood estimation often fails. To overcome the above issue, we can first maximize over a constrained subspace of the parameter space then relax the constraint as the sample s
Decay Kinetics of HIV-1 Specific T Cell Responses in Vertically HIV-1 Exposed Seronegative Infants
Sara J. Holditch,Esper G. Kallas,Michael G. Rosenberg,Douglas F. Nixon
Frontiers in Immunology , 2012, DOI: 10.3389/fimmu.2011.00094
Abstract: Objective: The majority of infants born, in developed countries, to HIV-1 positive women are exposed to the HIV-1 virus in utero or peri/post-partum, but are born uninfected. We, and others, have previously shown HIV-1 specific T cell responses in HIV-1 exposed seronegative (HESN) neonates/infants. Our objective in this study was to examine the rate of decay in their HIV-1 specific T cell response over time from birth. Design: Cross-sectional and longitudinal studies of HIV-1 specific T cell responses in HESN infants were performed. Methods: Peripheral blood mononuclear cells (PBMC) were isolated from 18 HIV-1 DNA PCR negative infants born to HIV-1 infected mothers receiving care at the Jacobi Medical Center, Bronx, NY, USA. PBMC were examined for T cell responses to HIV-1 antigens by interferon-gamma (IFN-γ) ELISPOT. Results: PBMC from 15 HESN neonates/infants were analyzed. We observed a decay of HIV-1 specific T cell responses from birth at a rate of ?0.599 spot forming unit/106 cells per day, with a median half-life decay rate of 21.38 weeks (13.39–115.8). Conclusion: Our results support the dynamic nature of T cell immunity in the context of a developing immune system. The disparate rate of decay with studies of adults placed on antiretroviral drugs suggests that antigen specific T cell responses are driven by the natural rate of decay of the T cell sub-populations themselves.
Demographic History of European Populations of Arabidopsis thaliana
Olivier Fran?ois ,Michael G. B. Blum,Mattias Jakobsson,Noah A. Rosenberg
PLOS Genetics , 2008, DOI: 10.1371/journal.pgen.1000075
Abstract: The model plant species Arabidopsis thaliana is successful at colonizing land that has recently undergone human-mediated disturbance. To investigate the prehistoric spread of A. thaliana, we applied approximate Bayesian computation and explicit spatial modeling to 76 European accessions sequenced at 876 nuclear loci. We find evidence that a major migration wave occurred from east to west, affecting most of the sampled individuals. The longitudinal gradient appears to result from the plant having spread in Europe from the east ~10,000 years ago, with a rate of westward spread of ~0.9 km/year. This wave-of-advance model is consistent with a natural colonization from an eastern glacial refugium that overwhelmed ancient western lineages. However, the speed and time frame of the model also suggest that the migration of A. thaliana into Europe may have accompanied the spread of agriculture during the Neolithic transition.
Low Friction Traction for Cervical Spine Dislocation  [PDF]
Lior Merom, Michael Soudry, Nahum Rosenberg
Open Journal of Clinical Diagnostics (OJCD) , 2015, DOI: 10.4236/ojcd.2015.53019
Abstract: In order to reduce the magnitude of the force applied to skull for treatment of acute cervical spine dislocation, we developed a method of skeletal traction based on reduction of friction forces under the patient’s head. Traction force was applied to sculls of five patients with cervical fracture-dislocations. A difference in friction interface between the patient’s head and shoulder girdle was created. The traction weight required for the reduction of the vertebral dislocation was significantly lower than an expected minimal traction weight in the commonly used techniques (p = 0.013). The presented method permits an effective and safe reduction of dislocated cervical vertebra by a relatively low traction force.
Stem diameter and rotational stability in revision total hip arthroplasty: a biomechanical analysis
R Michael Meneghini, Nadim J Hallab, Richard A Berger, Joshua J Jacobs, Wayne G Paprosky, Aaron G Rosenberg
Journal of Orthopaedic Surgery and Research , 2006, DOI: 10.1186/1749-799x-1-5
Abstract: Twenty-four cadaveric femoral specimens were implanted with a fully porous-coated stem. Two different diameters were tested and the stems were implanted at multiple contact lengths without proximal bone support. Each specimen underwent torsional testing to failure and rotational micromotion was measured at the implant-bone interface.The larger stem diameter demonstrated a greater torsional stability for a given length of cortical contact (p ≤ 0.05). Decreasing length of diaphyseal contact length was associated with less torsional stability. Torsional resistance was inconsistent at 2 cm of depth.Larger stem diameters frequently used in revisions may be associated with less diaphyseal contact length to achieve equivalent rotational stability compared to smaller diameter stems. Furthermore, a minimum of 3 cm or 4 cm of diaphyseal contact with a porous-coated stem should be achieved in proximal femoral bone deficiency and will likely be dependent on the stem diameter utilized at the time of surgery.Proximal femoral bone loss during revision total hip arthroplasty is a common and challenging problem. Aseptic loosening and osteolysis may cause significant periprosthetic femoral bone destruction, often necessitating bypass of the deficient proximal femur to obtain stable fixation in the distal diaphysis [1-3]. The fixation should provide adequate initial implant stability to minimize micromotion and facilitate osseous ingrowth of the host bone into the prosthesis. In this setting of proximal bone loss, inadequate length of diaphyseal contact has been shown to correlate with a high clinical failure rate [1]. As a consequence, a minimum of 4 cm to 6 cm of diaphyseal contact length has been recommended and is associated with improved clinical results and a lower failure rate [1].Clinical and biomechanical studies suggest that clinical failure of the femoral component is likely due to torsional forces applied to the prosthesis [4-8]. Femoral construct properties that may affec
A Generalized Formula for Converting Chi-Square Tests to Effect Sizes for Meta-Analysis
Michael S. Rosenberg
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0010059
Abstract: The common formula used for converting a chi-square test into a correlation coefficient for use as an effect size in meta-analysis has a hidden assumption which may be violated in specific instances, leading to an overestimation of the effect size. A corrected formula is provided.
Evolutionary distance estimation and fidelity of pair wise sequence alignment
Michael S Rosenberg
BMC Bioinformatics , 2005, DOI: 10.1186/1471-2105-6-102
Abstract: Under the studied conditions, distance estimation was relatively unaffected by alignment error (50% or more of the sites incorrectly aligned) as long as 50% or more of the sites were identical among the sequences (observed P-distance < 0.5). Beyond this threshold, the alignment procedure artificially inflates the apparent sequence identity, skewing distance estimates, and creating alignments that are essentially indistinguishable from random data. This general result was independent of substitution model, sequence length, and insertion and deletion size and rate.Examination of the estimated sequence identity may yield some guidance as to the accuracy of the alignment. Inaccurate alignments are expected to have large effects on analyses dependent on site specificity, but analyses that depend on evolutionary distance may be somewhat robust to alignment error as long as fewer than half of the sites have diverged.Evolutionary distance, the number of substitutions per site separating a pair of homologous sequences since they diverged from their common ancestral sequence, is an extremely important measure in molecular evolution and comparative genomics. It is used for a wide variety of purposes, ranging from phylogenetic analysis [1,2], to estimating times of divergence [3,4], the tempo and mode of evolutionary change [5], and functional constraints [6,7]. Evolutionary distance estimation is often one of the first steps in high-throughput sequence analysis; errors in these estimates may have wide-ranging consequences on downstream analyses and conclusions.There are many ways to estimate evolutionary distance; accuracy of various methods tends to be dependent on proper specification of the substitution model and sequence length [8,9]. One factor that has not been well examined with respect to evolutionary distance estimation, however, is alignment (although see [10-12]). Sequence alignment is an extremely common analytical tool used in comparative genomics. The purpose of
Multiple sequence alignment accuracy and evolutionary distance estimation
Michael S Rosenberg
BMC Bioinformatics , 2005, DOI: 10.1186/1471-2105-6-278
Abstract: The maximal gain in alignment accuracy was found not when the third sequence is directly intermediate between the initial two sequences, but rather when it perfectly subdivides the branch leading from the root of the tree to one of the original sequences (making it half as close to one sequence as the other). Evolutionary distance estimation in the multiple alignment framework, however, is largely unrelated to alignment accuracy and rather is dependent on the position of the third sequence; the closer the branch leading to the third sequence is to the root of the tree, the larger the estimated distance between the first two sequences.The bias in distance estimation appears to be a direct result of the standard greedy progressive algorithm used by many multiple alignment methods. These results have implications for choosing new taxa and genomes to sequence when resources are limited.DNA sequence alignment is a common step in molecular evolutionary analysis. Aligned sequences are used for many purposes, including estimation of patterns of divergence, selection, the tempo and mode of evolutionary change, identification of functional elements and constraints, and phylogenetic history, just to name a few. Alignments are a hypothesis of site homology; as evolutionary distance among sequences increases, alignments are known to become less accurate [1-7]. The effect of alignment accuracy on downstream analysis in comparative genomics and bioinformatics is largely an unexplored topic, although some empirical studies have attempted to examine this with respect to functional element identification [8,9] and phylogenetic analysis [10-16].Multiple sequence alignment, the alignment of more than two sequences, is generally thought to lead to more accurate alignments than simple pair wise alignments [4]. There are numerous approaches to multiple alignment, although most are based in some way on a progressive alignment algorithm [17,18] where similar sequences are aligned first and
MySSP: Non-stationary evolutionary sequence simulation, including indels
Michael S. Rosenberg
Evolutionary Bioinformatics , 2005,
Abstract: MySSP is a new program for the simulation of DNA sequence evolution across a phylogenetic tree. Although many programs are available for sequence simulation, MySSP is unique in its inclusion of indels, flexibility in allowing for non-stationary patterns, and output of ancestral sequences. Some of these features can individually be found in existing programs, but have not all have been previously available in a single package.
Contextual Cross-Referencing of Species Names for Fiddler Crabs (Genus Uca): An Experiment in Cyber-Taxonomy
Michael S. Rosenberg
PLOS ONE , 2014, DOI: 10.1371/journal.pone.0101704
Abstract: Cyber-taxonomy of name usage has focused primarily on producing authoritative lists of names or cross-linking names and data across disparate databases. A feature missing from much of this work is the recording and analysis of the context in which a name was used—context which can be critical for understanding not only what name an author used, but to which currently recognized species they actually refer. An experiment on recording contextual information associated with name usage was conducted for the fiddler crabs (genus Uca). Data from approximately one quarter of all publications that mention fiddler crabs, including 95% of those published prior to 1924 and 67% of those published prior to 1976, have currently been recorded in a database. Approaches and difficulties in recording and analyzing the context of name use are discussed. These results are not meant to be a full solution, rather to highlight problems which have not been previously investigated and may act as a springboard for broader approaches and discussion. Some data on the accessibility of the literature, including in particular electronic forms of publication, are also presented. The resulting data has been integrated for general browsing into the website http://www.fiddlercrab.info; the raw data and code used to construct the website is available at https://github.com/msrosenberg/fiddlercr?ab.info.
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