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Title
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Undecanoic Acid, Lauric Acid, and N-Tridecanoic Acid Inhibit Escherichia coli Persistence and Biofilm Formation
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Date
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2021,
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Description
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Persister cell formation and biofilms of pathogens are extensively involved in the development of chronic infectious diseases. Eradicating...
Show morePersister cell formation and biofilms of pathogens are extensively involved in the development of chronic infectious diseases. Eradicating persister cells is challenging, owing to their tolerance to conventional antibiotics, which cannot kill cells in a metabolically dormant state. A high frequency of persisters in biofilms makes inactivating biofilm cells more difficult, because the biofilm matrix inhibits antibiotic penetration. Fatty acids may be promising candidates as antipersister or antibiofilm agents, because some fatty acids exhibit antimicrobial effects. We previously reported that fatty acid ethyl esters effectively inhibit Escherichia coli persister formation by regulating an antitoxin. In this study, we screened a fatty acid library consisting of 65 different fatty acid molecules for altered persister formation. We found that undecanoic acid, lauric acid, and N-tridecanoic acid inhibited E. coli BW25113 persister cell formation by 25-, 58-, and 44-fold, respectively. Similarly, these fatty acids repressed persisters of enterohemorrhagic E. coli EDL933. These fatty acids were all medium-chain saturated forms. Furthermore, the fatty acids repressed Enterohemorrhagic E. coli (EHEC) biofilm formation (for example, by 8-fold for lauric acid) without having antimicrobial activity. This study demonstrates that medium-chain saturated fatty acids can serve as antipersister and antibiofilm agents that may be applied to treat bacterial infections.
Sponsorship: NIH-R15AI130988; NSF REU-1757989
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Title
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Geometry of Higher-Order Markov Chains, AS2012 Special Volume, part 1: This issue includes a second series of papers from talks, posters and collaborations resulting from and
inspired by the Algebraic Statistics in the Alleghenies Conference at Penn State, which took place in July
2012.
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Date
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2012, 2012
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Description
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We determine an explicit Gr ?obner basis, consisting of linear forms and determinantal quadrics, for the prime ideal of Raftery’s mixture...
Show moreWe determine an explicit Gr ?obner basis, consisting of linear forms and determinantal quadrics, for the prime ideal of Raftery’s mixture transition distribution model for Markov chains. When the states are binary, the corresponding projective variety is a linear space, the model itself consists of two simplices in a cross-polytope, and the likelihood function typically has two local maxima. In the general non-binary case, the model corresponds to a cone over a Segre variety.
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Collection
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Journal of Algebraic Statistics
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Title
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Properties of semi-elementary imsets as sums of elementary imsets
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Date
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2011, 2011
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Description
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We study properties of semi-elementary imsets and elementary imsets introduced by Studeny [10]. The rules of the semi-graphoid axiom ...
Show moreWe study properties of semi-elementary imsets and elementary imsets introduced by Studeny [10]. The rules of the semi-graphoid axiom (decomposition, weak union and contraction) for conditional independence statements can be translated into a simple identity among three semi-elementary imsets. By recursively applying the identity, any semi-elementary imset can be written as a sum of elementary imsets, which we call a representation of the semi-elementary imset. A semi-elementary imset has many representations. We study properties of the set of possible representations of a semi-elementary imset and prove that all representations are connected by relations among four elementary imsets.
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Collection
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Journal of Algebraic Statistics
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Title
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Connectivity for 3 x 3 x K contingency tables
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Description
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We consider an exact sequential conditional test for three-way conditional test of no interaction. At each time τ, the test uses as the...
Show moreWe consider an exact sequential conditional test for three-way conditional test of no interaction. At each time τ, the test uses as the conditional inference frame the set F(Hτ) of all tables with the same three two-way marginal tables as the obtained table Hτ . For 3 × 3 × K tables, we propose a method to construct F(Hτ) from F(Hτ−1). This enables us to perform efficiently the sequential exact conditional test. The subset Sτ of F (Hτ ) consisting of s + Hτ − Hτ −1 for s ∈ F(Hτ−1) contains Hτ , where the operations + and − are defined elementwise. Our argument is based on the minimal Markov basis for 3 × 3 × K contingency tables and we give a minimal subset M of some Markov basis which has the property that F (Hτ ) = {s − m | s ∈ Sτ , m ∈ M}.
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Collection
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Journal of Algebraic Statistics
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Title
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FAST AUTOMATIC BAYESIAN CUBATURE USING MATCHING KERNELS AND DESIGNS
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Date
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2019, 2019-12-20
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Publisher
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Chicago
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Description
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Automatic cubatures approximate multidimensional integrals to user-specified...
Show moreAutomatic cubatures approximate multidimensional integrals to user-specified
error tolerances. In many real-world integration problems, the analytical solution is
either unavailable or difficult to compute. To overcome this, one can use numerical
algorithms that approximately estimate the value of the integral.
For high dimensional integrals, quasi-Monte Carlo (QMC) methods are very
popular. QMC methods are equal-weight quadrature rules where the quadrature
points are chosen deterministically, unlike Monte Carlo (MC) methods where the
points are chosen randomly. The families of integration lattice nodes and digital nets
are the most popular quadrature points used. These methods consider the integrand
to be a deterministic function. An alternate approach, called Bayesian cubature,
postulates the integrand to be an instance of a Gaussian stochastic process.
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Title
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Environmental Monitoring of University Archives and Special Collections
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Date
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2020,
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Description
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This is the final report and analysis of activities conducted as part of Environmental Monitoring of University Archives and Special...
Show moreThis is the final report and analysis of activities conducted as part of Environmental Monitoring of University Archives and Special Collections, a project funded by a Preservation Assistance Grant from the National Endowment of the Humanities (PG-263471-19). This grant was awarded to support the first evercsystematic environmental monitoring of the UASC spaces. This report includes a summary of the collected data, analysis of the data, and potential future activities to be undertaken as a result of the grant activities and the data collected.
Sponsorship: National Endowment For The Humanities, Preservation Assistance Grants for Smaller Institutions
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Title
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Detecting epistasis via Markov bases
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Date
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2011, 2011
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Description
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Rapid research progress in genotyping techniques have allowed large genome-wide association studies. Existing methods often focus on...
Show moreRapid research progress in genotyping techniques have allowed large genome-wide association studies. Existing methods often focus on determining associations between single loci and a specific phenotype. However, a particular phenotype is usually the result of complex relationships between multiple loci and the environment. In this paper, we describe a two-stage method for detecting epistasis by combining the traditionally used single-locus search with a search for multiway interactions. Our method is based on an extended version of Fisher’s exact test. To perform this test, a Markov chain is constructed on the space of multidimensional contingency tables using the elements of a Markov basis as moves. We test our method on simulated data and compare it to a two-stage logistic regression method and to a fully Bayesian method, showing that we are able to detect the interacting loci when other methods fail to do so. Finally, we apply our method to a genome-wide data set consisting of 685 dogs and identify epistasis associated with canine hair length for four pairs of single nucleotide polymorphisms (SNPs).
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Collection
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Journal of Algebraic Statistics
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