Search results
Pages
- Title
- Editorial, "Cell-Free Synthetic Biology": Synthetic Biology Meets Cell-Free Protein Synthesis
- Date
- 2019,
- Publisher
- MDPI
- Description
-
Sponsorship: NIH R15AI130988
- Title
- Leveraging the flexibility of Islandora to create a dual-use digital repository
- Date
- 2021, 2021
- Publisher
- Henry Stewart Publications
- Collection
- Journal of Digital Media Management
- Title
- From Critical to Transformative Pedagogy in Architectural Education
- Date
- 2019, 2019
- Publisher
- Association of Collegiate Schools of Architecture, Washington, DC
- Collection
- 2019 ACSA/EAAE Teachers Conference Proceeding
- Title
- German Spritzdekor Ceramics, 1928-1936: A Degenerate Art
- Date
- 2018
- Publisher
- IIT Press
- Description
-
An exhibition catalog for an exhibit housed in Galvin Library's Kemper Gallery from April to Septmeber, 2017. The exhibition was comprised of...
Show moreAn exhibition catalog for an exhibit housed in Galvin Library's Kemper Gallery from April to Septmeber, 2017. The exhibition was comprised of German airbrushed ceramics from the collection of Maral and Rolf Achilles. Ghazal Hashemi designed the Spritzdekor web site and this pdf catalog. All photographs are by Allen Bourgeois.
Sponsorship: Funding for this catalog was provided by grants from the Walter and Karla Goldschmidt Foundation and Richard H. Driehaus.
Show less
- Title
- Algorithms for Discrete Data in Statistics and Operations Research
- Date
- 2021-11-19, 2021-12
- Publisher
- ProQuest, https://www.proquest.com/docview/2622985712
- Description
-
Sponsorship: The Air Force Office of Scientific Research's grant FA9550-14-1-0141 supported Prof. Petrović's and my initial...
Show moreSponsorship: The Air Force Office of Scientific Research's grant FA9550-14-1-0141 supported Prof. Petrović's and my initial work on this project.
Show less
- Title
- The Landings in North Africa November 1942
- Creator
- Moran, Charles
- Date
- 1993, 1993
- Publisher
- Naval Historical Center, Dept. of the Navy,
- Description
-
Donated to the Paul V. Galvin Library by IIT Naval ROTC
- Title
- Undecanoic Acid, Lauric Acid, and N-Tridecanoic Acid Inhibit Escherichia coli Persistence and Biofilm Formation
- Date
- 2021,
- Description
-
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
Show less
- Title
- Engineering Ethics in China
- Creator
- Zhang, Hengli, Davis, Michael
- Date
- 2018
- Description
-
This article describes China’s century-long concern...
Show moreThis article describes China’s century-long concern with the professional ethics of engineers, especially a succession of codes of engineering ethics going back at least to 1933. This description is the result both of our own archival research and of “philosophical history”, the application of concepts from the philosophy of professions to the facts historians (or we) have discovered. Engineers, historians, social scientists, and philosophers of technology, as well as students of professional ethics, should find this description interesting. It certainly provides a reason to wonder whether those who write about codes of professional ethics as if they were an Anglo-American export unlikely to put down roots elsewhere might have overlooked many early codes outside English-speaking countries. While code writers in China plainly learned from Western codes, the Chinese codes were not mere copies of their Western counterparts. Indeed, the Chinese codes sometimes differed inventively from Western codes in form (for example, being wholly positive) or content (for example, protecting local culture).
Show less - Collection
- Business and Professional Ethics Journal
- Title
- 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.
- Date
- 2012, 2012
- Description
-
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.
Show less - Collection
- Journal of Algebraic Statistics
- Title
- Phylogenetic invariants for group-based models, 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.
- Date
- 2012, 2012
- Description
-
In this paper we investigate properties of algebraic varieties representing group-based phylogenetic models. We propose a method of generating...
Show moreIn this paper we investigate properties of algebraic varieties representing group-based phylogenetic models. We propose a method of generating many phylogenetic invariants. We prove that we obtain all invariants for any tree for the two-state Jukes-Cantor model. We conjecture that for a large class of models our method can give all phylogenetic invariants for any tree. We show that for 3-Kimura our conjecture is equivalent to the conjecture of Sturmfels and Sullivant [22, Conjecture 2]. This, combined with the results in [22], would make it possible to determine all phylogenetic invariants for any tree for 3-Kimura model, and also other phylogenetic models. Next we give the (first) examples of non-normal varieties associated to general group-based model for an abelian group. Following Kubjas [17] we prove that for many group-based models varieties associated to trees with the same number of leaves do not have to be deformation equivalent.
Show less - Collection
- Journal of Algebraic Statistics
- Title
- An Iterative Method Converging to a Positive Solution of Certain Systems of Polynomial Equations
- Date
- 2011, 2011
- Description
-
We present a numerical algorithm for finding real non-negative solutions to a certain class of polynomial equations. Our methods are based on...
Show moreWe present a numerical algorithm for finding real non-negative solutions to a certain class of polynomial equations. Our methods are based on the expectation maximization and iterative proportional fitting algorithms, which are used in statistics to find maximum likelihood parameters for certain classes of statistical models. Since our algorithm works by iteratively improving an approximate solution, we find approximate solutions in the cases when there are no exact solutions, such as overconstrained systems.
Show less - Collection
- Journal of Algebraic Statistics
- Title
- Properties of semi-elementary imsets as sums of elementary imsets
- Date
- 2011, 2011
- Description
-
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.
Show less - Collection
- Journal of Algebraic Statistics
- Title
- Hilbert Polynomial of the Kimura 3-Parameter Model, 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.
- Description
-
In [2] Buczyn ́ska and Wi ́sniewski showed that the Hilbert polynomial of the algebraic variety associated to the Jukes-Cantor binary model on...
Show moreIn [2] Buczyn ́ska and Wi ́sniewski showed that the Hilbert polynomial of the algebraic variety associated to the Jukes-Cantor binary model on a trivalent tree depends only on the number of leaves of the tree and not on its shape. We ask if this can be generalized to other group-based models. The Jukes-Cantor binary model has Z2 as the underlying group. We consider the Kimura 3-parameter model with Z2 × Z2 as the underlying group. We show that the generalization of the statement about the Hilbert polynomials to the Kimura 3-parameter model is not possible as the Hilbert polynomial depends on the shape of a trivalent tree.
Show less - Collection
- Journal of Algebraic Statistics
- Title
- Connectivity for 3 x 3 x K contingency tables
- Description
-
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}.
Show less - Collection
- Journal of Algebraic Statistics
- Title
- FAST AUTOMATIC BAYESIAN CUBATURE USING MATCHING KERNELS AND DESIGNS
- Date
- 2019, 2019-12-20
- Publisher
- Chicago
- Description
-
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.
Show less
- Title
- Environmental Monitoring of University Archives and Special Collections
- Date
- 2020,
- Description
-
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
Show less
- Title
- The Waste of Parts Capstone Examples
- Date
- 2020,
- Description
-
The Waste of Parts is a prototype board game finished for my Digital Humanities Capstone Elective
- Title
- Detecting epistasis via Markov bases
- Date
- 2011, 2011
- Description
-
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).
Show less - Collection
- Journal of Algebraic Statistics
- Title
- Open Problems on Connectivity of Fibers with Positive Margins in Multi-dimensional Contingency Tables
- Date
- 2010, 2010
- Description
-
Diaconis-Sturmfels developed an algorithm for sampling from conditional distributions for a statistical model of discrete exponential families...
Show moreDiaconis-Sturmfels developed an algorithm for sampling from conditional distributions for a statistical model of discrete exponential families, based on the algebraic theory of toric ideals. This algorithm is applied to categorical data analysis through the notion of Markov bases. Initiated with its application to Markov chain Monte Carlo approach for testing statistical fitting of the given model, many researchers have extensively studied the structure of Markov bases for models in computational algebraic statistics. In the Markov chain Monte Carlo approach for testing statistical fitting of the given model, a Markov basis is a set of moves connecting all contingency tables satisfying the given margins. Despite the computational advances, there are applied problems where one may never be able to compute a Markov basis. In general, the number of elements in a minimal Markov basis for a model can be exponentially many. Thus, it is important to compute a reduced number of moves which connect all tables instead of computing a Markov basis. In some cases, such as logistic regression, positive margins are shown to allow a set of Markov connecting moves that are much simpler than the full Markov basis. Such a set is called a Markov subbasis with assumption of positive margins. In this paper we summarize some computations of and open problems on Markov subbases for contingency tables with assumption of positive margins under specific models as well as develop algebraic methods for studying connectivity of Markov moves with margin positivity to develop Markov sampling methods for exact conditional inference in statistical models where the Markov basis is hard to compute.
Show less - Collection
- Journal of Algebraic Statistics
- Title
- Generalized Fréchet Bounds for Cell Entries in Multidimensional Contingency Tables, Special Volume in honor of memory of S.E.Fienberg
- Description
-
We consider the lattice, L, of all subsets of a multidimensional contingency table and establish the properties of monotonicity and...
Show moreWe consider the lattice, L, of all subsets of a multidimensional contingency table and establish the properties of monotonicity and supermodularity for the marginalization function, n(·), on L. We derive from the supermodularity of n(·) some generalized Fr ́echet inequalities comple- menting and extending inequalities of Dobra and Fienberg. Further, we construct new monotonic and supermodular functions from n(·), and we remark on the connection between supermodularity and some correlation inequalities for probability distributions on lattices. We also apply an inequal- ity of Ky Fan to derive a new approach to Fr ́echet inequalities for multidimensional contingency tables.
Show less - Collection
- Journal of Algebraic Statistics