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Search Results: 1 - 10 of 7618 matches for " Joel Thompson "
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Intergenic subset organization within a set of geographically-defined viral sequences from the 2009 H1N1 influenza A pandemic  [PDF]
William A. Thompson, Joel K. Weltman
American Journal of Molecular Biology (AJMB) , 2012, DOI: 10.4236/ajmb.2012.21004
Abstract: We report a bioinformatic analysis of the datasets of sequences of all ten genes from the 2009 H1N1 influenza A pandemic in the state of Wisconsin. The gene with the greatest summed information entropy was found to be the hemagglutinin (HA) gene. Based upon the viral ID identifier of the HA gene sequence, the sequences of all of the genes were sorted into two subsets, depending upon whether the nucleotide occupying the position of maximum entropy, position 658 of the HA sequence, was either A or U. It was found that the information entropy (H) distributions of subsets differed significantly from each other, from H distributions of randomly generated subsets and from the H distributions of the complete datasets of each gene. Mutual information (MI) values facilitated identification of nine nucleotide positions, distributed over seven of the influenza genes, at which the nucleotide subsets were disjoint, or almost disjoint. Nucleotide frequencies at these nine positions were used to compute mutual information values that subsequently served as weighting factors for edges in a graph net-work. Seven of the nucleotide positions in the graph network are sites of synonymous mutations. Three of these sites of synonymous mutation are within a single gene, the M1 gene, which occupied the position of greatest graph centrality. It is proposed that these bioinformatic and network graph results may reflect alterations in M1-mediated viral packaging and exteriorization, known to be susceptible to synonymous mutations.
Knots and k-width
Joel Hass,J. Hyam Rubinstein,Abigail Thompson
Mathematics , 2006,
Abstract: We investigate several integer invariants of curves in 3-space. We demonstrate relationships of these invariants to crossing number and to total curvature.
Stabilization of Heegaard splittings
Joel Hass,Abigail Thompson,William Thurston
Mathematics , 2008, DOI: 10.2140/gt.2009.13.2029
Abstract: For each g greater than one there is a 3-manifold with two genus g Heegaard splittings that require g stabilizations to become equivalent. Previously known examples required at most one stabilization. Control of families of Heegaard surfaces is obtained through a deformation to harmonic maps.
The number of surfaces of fixed genus in an alternating link complement
Joel Hass,Abigail Thompson,Anastasiia Tsvietkova
Mathematics , 2015,
Abstract: Let $L$ be a prime alternating link with $n$ crossings. We show that for each fixed $g$, the number of genus $g$ incompressible surfaces in the complement of $L$ is bounded by a polynomial in $n$. Previous bounds were exponential in $n$.
Jacobsen/Paris-Trousseau Syndrome: Report of a Case with Emphasis on Platelet’s Light Microscopic and Ultrastructure Findings  [PDF]
Michael Losos, Basil M. Kahwash, Miriam Conces, Joel Thompson, Riten Kumar, Samir B. Kahwash
Open Journal of Pathology (OJPathology) , 2016, DOI: 10.4236/ojpathology.2016.61002
Abstract: Jacobsen syndrome (JS) is a rare, inherited disorder, characterized by facial and skull dysmorphism, mental retardation, and platelet abnormalities. Paris-Trousseau syndrome (PTS) is a platelet function disorder that may be encountered in patients affected by JS. PTS is manifested by a mild lifelong bleeding tendency. Morphologically, the presence of large fused platelet alpha granules is characteristic. We present a case of Jacobsen syndrome in a child and highlight the typical morphologic and ultrastructure findings of platelets.
Thompson, W.A. et al. Decimative Multiplication of Entropy Arrays, with Application to Influenza. Entropy, 2009, 11, 351-359
William A. Thompson,Andy Martwick,Joel K. Weltman
Entropy , 2009, DOI: 10.3390/e110300384
Abstract: The sentence sixth line from the end of paragraph two on page 355, “The second synonymous mutation was another G=>A transition at position 600 that converted the CAG codon to CAA, without change of encoded amino acid.”
Information Entropy of Influenza A Segment 7
William A. Thompson,Shaohua Fan,Joel K. Weltman
Entropy , 2008, DOI: 10.3390/e10040736
Abstract: Information entropy (H) is a measure of uncertainty at each position within in a sequence of nucleotides.H was used to characterize a set of influenza A segment 7 nucleotide sequences. Nucleotide locations of high entropy were identified near the 5’ start of all of the sequences and the sequences were assigned to subsets according to synonymous nucleotide variants at those positions: either uracil at position six (U6), cytosine at position six (C6), adenine (A12) at position 12, guanine at position 12 (G12), adenine at position 15 (A15) or cytosine (C15) at position 15. H values were found to be correlated/corresponding (Kendall tau) along the lengths of the nucleotide segments of the subset pairs at each position. However, the H values of each subset of sequences were statistically distinguishable from those of the other member of the pair (Kolmogorov-Smirnov test). The joint probability of uncorrelated distributions of U6 and C6 sequences to viral subtypes and to viral host species was 34 times greater than for the A12:G12 subset pair and 214 times greater than for the A15:C15 pair. This result indicates that the high entropy position six of segment 7 is either a reporter or a sentinel location. The fact that not one of the H5N1 sequences in the dataset was a member of the C6 subset, but all 125 H5N1 sequences are members of the U6 subset suggests a non-random sentinel function.
Decimative Multiplication of Entropy Arrays, with Application to Influenza
William A. Thompson,Andy Martwick,Joel K. Weltman
Entropy , 2009, DOI: 10.3390/e11030351
Abstract: The use of the digital signal processing procedure of decimation is introduced as a tool to detect patterns of information entropy distribution and is applied to information entropy in influenza A segment 7. Decimation was able to reveal patterns of entropy accumulation in archival and emerging segment 7 sequences that were not apparent in the complete, undecimated data. The low entropy accumulation along the first 25% of segment 7, revealed by the three frames of decimation, may be a sign of regulation at both protein and RNA levels to conserve important viral functions. Low segment 7 entropy values from the 2009 H1N1 swine flu pandemic suggests either that: (1) the viruses causing the current outbreak have convergently evolved to their low entropy state or (2) more likely, not enough time has yet passed for the entropy to accumulate. Because of its dependence upon the periodicity of the codon, the decimative procedure should be generalizable to any biological system.
Winnowing DNA for Rare Sequences: Highly Specific Sequence and Methylation Based Enrichment
Jason D. Thompson, Gosuke Shibahara, Sweta Rajan, Joel Pel, Andre Marziali
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0031597
Abstract: Rare mutations in cell populations are known to be hallmarks of many diseases and cancers. Similarly, differential DNA methylation patterns arise in rare cell populations with diagnostic potential such as fetal cells circulating in maternal blood. Unfortunately, the frequency of alleles with diagnostic potential, relative to wild-type background sequence, is often well below the frequency of errors in currently available methods for sequence analysis, including very high throughput DNA sequencing. We demonstrate a DNA preparation and purification method that through non-linear electrophoretic separation in media containing oligonucleotide probes, achieves 10,000 fold enrichment of target DNA with single nucleotide specificity, and 100 fold enrichment of unmodified methylated DNA differing from the background by the methylation of a single cytosine residue.
Population Level Analysis of Evolved Mutations Underlying Improvements in Plant Hemicellulose and Cellulose Fermentation by Clostridium phytofermentans
Supratim Mukherjee, Lynmarie K. Thompson, Stephen Godin, Wendy Schackwitz, Anna Lipzen, Joel Martin, Jeffrey L. Blanchard
PLOS ONE , 2014, DOI: 10.1371/journal.pone.0086731
Abstract: Background The complexity of plant cell walls creates many challenges for microbial decomposition. Clostridium phytofermentans, an anaerobic bacterium isolated from forest soil, directly breaks down and utilizes many plant cell wall carbohydrates. The objective of this research is to understand constraints on rates of plant decomposition by Clostridium phytofermentans and identify molecular mechanisms that may overcome these limitations. Results Experimental evolution via repeated serial transfers during exponential growth was used to select for C. phytofermentans genotypes that grow more rapidly on cellobiose, cellulose and xylan. To identify the underlying mutations an average of 13,600,000 paired-end reads were generated per population resulting in ~300 fold coverage of each site in the genome. Mutations with allele frequencies of 5% or greater could be identified with statistical confidence. Many mutations are in carbohydrate-related genes including the promoter regions of glycoside hydrolases and amino acid substitutions in ABC transport proteins involved in carbohydrate uptake, signal transduction sensors that detect specific carbohydrates, proteins that affect the export of extracellular enzymes, and regulators of unknown specificity. Structural modeling of the ABC transporter complex proteins suggests that mutations in these genes may alter the recognition of carbohydrates by substrate-binding proteins and communication between the intercellular face of the transmembrane and the ATPase binding proteins. Conclusions Experimental evolution was effective in identifying molecular constraints on the rate of hemicellulose and cellulose fermentation and selected for putative gain of function mutations that do not typically appear in traditional molecular genetic screens. The results reveal new strategies for evolving and engineering microorganisms for faster growth on plant carbohydrates.
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