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Title: Connectivity for 3 x 3 x K contingency tables
Creator: Sumi, Toshio, 2012
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}.
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Collection: Journal of Algebraic Statistics

Title: Matrix Completion for the Independence Model
Creator: Kubjas, Kaie, Rosen, Zvi
Description: We investigate the problem of completing partial matrices to rank-one matrices in the standard simplex ∆mn−1. The motivation for studying this...
Show moreWe investigate the problem of completing partial matrices to rank-one matrices in the standard simplex ∆mn−1. The motivation for studying this problem comes from statistics: A lack of eligible completion can provide a falsification test for partial observations to come from the independence model. For each pattern of specified entries, we give equations and inequalities which are satisfied if and only if an eligible completion exists. We also describe the set of valid completions, and we optimize over this set.
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Collection: Journal of Algebraic Statistics

Title: One example of general unidentifiable tensors
Creator: Chiantini, Luca, Mella, Massimiliano, Ottaviani, Giorgio
Description: Abstract. Theidentifiabilityofparametersinaprobabilisticmodelisacrucialnotioninstatistical inference. We prove that a general tensor of rank 8...
Show moreAbstract. Theidentifiabilityofparametersinaprobabilisticmodelisacrucialnotioninstatistical inference. We prove that a general tensor of rank 8 in C3 ⊗ C6 ⊗ C6 has at least 6 decompositions as sum of simple tensors, so it is not 8-identifiable. This is the highest known example of balanced tensors of dimension 3, which are not k-identifiable, when k is smaller than the generic rank.
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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.
Creator: Kubjas, Kaie, inspired by the Algebraic Statistics in the Alleghenies Conference at Penn State, which took place in July
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.
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Collection: Journal of Algebraic Statistics

Title: Semantics and further Use-Cases and Evaluation of the C-Saw language
Creator: Zhu, Henry, Zhao, Junyong, Sultana, Nik
Date: 2023-03-09
Description: This report provides supplementary technical details to the conference paper that introduced C-Saw, a language for expressing software...
Show moreThis report provides supplementary technical details to the conference paper that introduced C-Saw, a language for expressing software architecture patterns. This report provides additional examples of using C-Saw, supplementary evaluation details, and it defines the formal semantics of the language.
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Title: Experimental Design and Analysis
Creator: Seltman, Howard J.
Date: 2018-07-11
Description: Experimental Design and Analysis textbook originally written for use in 36-309/749, Experimental Design for Behavioral and Social Sciences at...
Show moreExperimental Design and Analysis textbook originally written for use in 36-309/749, Experimental Design for Behavioral and Social Sciences at Carnegie Mellon University.
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Title: Experimental Design and Analysis data files
Creator: Seltman, Howard J.
Date: 2018-07-11
Description: Data files for use with the Experimental Design and Analysis textbook.

Title: Optimizing Cell-Free Protein Synthesis for Increased Yield and Activity of Colicins
Creator: Jin, Xing, Kightlinger, Weston, Hong, Seok Hoon
Date: 2019
Publisher: MDPI
Description: Colicins are antimicrobial proteins produced by Escherichia coli that hold great promise as viable complements or alternatives to antibiotics....
Show moreColicins are antimicrobial proteins produced by Escherichia coli that hold great promise as viable complements or alternatives to antibiotics. Cell-free protein synthesis (CFPS) is a useful production platform for toxic proteins because it eliminates the need to maintain cell viability, a common problem in cell-based production. Previously, we demonstrated that colicins produced by CFPS based on crude Escherichia coli lysates are e?ective in eradicating antibiotic-tolerant bacteria known as persisters. However, we also found that some colicins have poor solubility or low cell-killing activity. In this study, we improved the solubility of colicin M from 16% to nearly 100% by producing it in chaperone-enriched E. coli extracts, resulting in enhanced cell-killing activity. We also improved the cytotoxicity of colicin E3 by adding or co-expressing the E3 immunity protein during the CFPS reaction, suggesting that the E3 immunity protein enhances colicin E3 activity in addition to protecting the host strain. Finally, we con?rmed our previous ?nding that active colicins can be rapidly synthesized by observing colicin E1 production over time in CFPS. Within three hours of CFPS incubation, colicin E1 reached its maximum production yield and maintained high cytotoxicity during longer incubations up to 20 h. Taken together, our ?ndings indicate that colicin production can be easily optimized for improved solubility and activity using the CFPS platform.
Sponsorship: NIH R15AI130988
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Title: "China's unwritten code of engineering ethics": Table list (1), China's unwritten code of engineering ethics: Table list (1)
Creator: Davis, Michael, Wei, Lina
Date: 2019-08-02, 2019-08-02

Title: Fostering personal finance engagement with a habit building app
Creator: Hapner, Bridget
Date: 2022-11-04
Description: Master's Project focused on developing a concept for a personal finance literacy app.

Title: Experimental Design and Analysis
Creator: Seltman, Howard J.
Date: 2018-07-11
Description: Experimental Design and Analysis textbook originally written for use in 36-309/749, Experimental Design for Behavioral and Social Sciences at...
Show moreExperimental Design and Analysis textbook originally written for use in 36-309/749, Experimental Design for Behavioral and Social Sciences at Carnegie Mellon University.
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Title: Controlling biofilms using synthetic biology approaches
Creator: Fang, Kuili, Park, Oh-Jin, Hong, Seok Hoon
Date: 2020
Description: Bacterial biofilms are formed by the complex but ordered regulation of intra- or inter-cellular communication, environmentally responsive gene...
Show moreBacterial biofilms are formed by the complex but ordered regulation of intra- or inter-cellular communication, environmentally responsive gene expression, and secretion of extracellular polymeric substances. Given the robust nature of bio?lms due to the non-growing nature of bio?lm bacteria and the physical barrier provided by the extracellular matrix, eradicating bio?lms is a very di?cult task to accomplish with conventional antibiotic or disinfectant treatments. Synthetic biology holds substantial promise for controlling bio?lms by improving and expanding existing biological tools, introducing novel functions to the system, and re-conceptualizing gene regulation. This review summarizes synthetic biology approaches used to eradicate bio?lms via protein engineering of bio?lm-related enzymes, utilization of synthetic genetic circuits, and the development of functional living agents. Synthetic biology also enables bene?cial applications of bio?lms through the production of biomaterials and patterning bio?lms with speci?c temporal and spatial structures. Advances in synthetic biology will add novel bio?lm functionalities for future therapeutic, biomanufacturing, and environmental applications.
Sponsorship: NIH-R15AI130988, NSF CBET-1917130
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Title: Engineering Escherichia coli to produce and secrete colicins for rapid and selective biofilm cell killing
Creator: Jin, Xing, An, Sungjun, Kightlinger, Weston, Zhou, Jiacheng, Hong, Seok Hoon
Date: 2021
Description: Bacterial biofilms are associated with chronic infectious diseases and are highly resistant to conventional antibiotics. Antimicrobial...
Show moreBacterial biofilms are associated with chronic infectious diseases and are highly resistant to conventional antibiotics. Antimicrobial bacteriocins are alternatives to conventional antibiotics and are characterized by unique cell-killing mechanisms, including pore formation on cell membranes, nuclease activity, and cell wall synthesis inhibition. Here, we used cell-free protein synthesis to rapidly evaluate the antibiofilm activities of colicins E1, E2, and E3. We found that E2 (with DNase activity) most effectively killed target biofilm cells (i.e., the K361 strain) while leaving nontargeted biofilms intact. We then engineered probiotic Escherichia coli microorganisms with genetic circuits to controllably synthesize and secrete colicin E2, which successfully inhibited biofilms and killed preformed indicator biofilms. Our findings suggest that colicins rapidly and selectively kill target biofilm cells in multispecies biofilms and demonstrate the potential of using microorganisms engineered to produce antimicrobial colicin proteins as live therapeutic strategies to treat biofilm-associated infections.
Sponsorship: NIH-R15AI130988
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Title: Continuous Generalization of 2’s Complement Arithmetic
Creator: Patel, Shivam
Date: 2022-11-26

Title: Editorial, "Cell-Free Synthetic Biology": Synthetic Biology Meets Cell-Free Protein Synthesis
Creator: Hong, Seok Hoon
Date: 2019
Publisher: MDPI
Description: Sponsorship: NIH R15AI130988

Title: Incorporation of non-standard amino acids into proteins: challenges, recent achievements, and emerging applications
Creator: Jin, Xing, Park Oh-Jin, Hong, Seok Hoon
Date: 2019
Description: The natural genetic code only allows for 20 standard amino acids in protein translation, but genetic code reprogramming enables the...
Show moreThe natural genetic code only allows for 20 standard amino acids in protein translation, but genetic code reprogramming enables the incorporation of non-standard amino acids (NSAAs). Proteins containing NSAAs provide enhanced or novel properties and open diverse applications. With increased attention to the recent advancements in synthetic biology, various improved and novel methods have been developed to incorporate single and multiple distinct NSAAs into proteins. However, various challenges remain in regard to NSAA incorporation, such as low yield and misincorporation. In this review, we summarize the recent efforts to improve NSAA incorporation by utilizing orthogonal translational system optimization, cell-free protein synthesis, genomically recoded organisms, artificial codon boxes, quadruplet codons, and orthogonal ribosomes, before closing with a discussion of the emerging applications of NSAA incorporation.
Sponsorship: NIH R15AI130988
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Title: Undecanoic Acid, Lauric Acid, and N-Tridecanoic Acid Inhibit Escherichia coli Persistence and Biofilm Formation
Creator: Jin, Xing, Zhou, Jiacheng, Richey, Gabriella, Wang, Mengya, Hong, Sung Min Choi, Hong, Seok Hoon
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
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Title: Priming Movie Product Placements: New Insights from a Cross-National Case Study
Creator: Balasubramanian,Siva K, Gistri, Giacomo
Date: 44354, 44327
Publisher: Taylor & Francis
Description: The paucity of research on priming product placements and insights from practitioners (Study 1) motivated our investigation into how and when...
Show moreThe paucity of research on priming product placements and insights from practitioners (Study 1) motivated our investigation into how and when priming works in movie placements. Study 2 explores the impact of media priming (a media story announcing a movie placement before the movie’s release) and ad priming (a similar ad announcement) on recall through contrasts with no priming (control). US students watched a movie in a theatre after such priming for a subtle or a prominent placement. When compared to no priming, both media priming and ad priming enhanced recall for the subtle placement; no difference in recall performance emerged between no priming and either type of priming for the prominent placement. Contrast tests comparing media priming and ad priming indicated no differences in recall for either subtle or prominent placement. Study 3 replicated these recall findings with Italian moviegoers, and supported additional hypotheses and propositions for brand attitude. For the subtle (prominent) placement, attitude did not change (decreased) when comparing either media priming or ad priming with no priming. Contrast tests comparing media priming and ad priming indicated no differences in attitude outcomes, for either subtle or prominent placement. Using no priming as a baseline for comparison, the converging conclusion is that any type of priming improves (does not change) recall and does not change (worsens) attitude for subtle (prominent) placements. Overall, results do not support priming for prominent placements; selective use of any type of priming for subtle placements appears appropriate to improve recall outcomes.
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Collection: International Journal of Advertising

Title: “Broader Impacts” or “Responsible Research and Innovation”? A Comparison of Two Criteria for Funding Research in Science and Engineering
Creator: Davis, Michael, Laas, Kelly
Date: 2013-10, 2013-10
Publisher: Springer
Description: Our subject is how the experience of Americans with a certain funding criterion, “broader impacts” (and some similar criteria) may help in...
Show moreOur subject is how the experience of Americans with a certain funding criterion, “broader impacts” (and some similar criteria) may help in efforts to turn the European concept of Responsible Research and Innovation (RRI) into a useful guide to funding Europe’s scientific and technical research. We believe this comparison may also be as enlightening for Americans concerned with revising research policy. We have organized our report around René Von Schomberg’s definition of RRI, since it seems both to cover what the European research group to which we belong is interested in and to be the only widely accepted definition of RRI. According to Von Schomberg, RRI: “… is a transparent, interactive process by which societal actors and innovators become mutually responsive to each other with a view to the (ethical) acceptability, sustainability and societal desirability of the innovation process and its marketable products (in order to allow a proper embedding of scientific and technological advances in our society).” While RRI seeks fundamental changes in the way research is conducted, Broader Impacts is more concerned with more peripheral aspects of research: widening participation of disadvantaged groups, recruiting the next generation of scientists, increasing the speed with which results are used, and so on. Nevertheless, an examination of the broadening of funding criteria over the last four decades suggests that National Science Foundation has been moving in the direction of RRI.
Sponsorship: European Community’s Seventh Framework Programme grant number 321400.
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Title: Occupational exposure to diisocyanates, Criteria for a recommended standard...occupational exposure to diisocyanates
Date: 2016-11-03, 1978-09
Publisher: National Institute for Occupational Safety and Health

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