85 research outputs found
Genomics and epigenomics using 2D nanopores
No full textDNA methylation is an epigenetic modification caused by the addition of a methyl group to DNA and heavily involved in gene expression and regulation, thereby critical to the progression of diseases such as cancer. In this work we show that detection and localization of DNA methylation can be achieved with nanopore sensors made of two-dimensional (2D) materials such as graphene and MoS. We label each DNA methylated site with a methyl-CpG binding domain protein (MBD1), and combine molecular dynamics simulations with electronic transport calculations to investigate the translocation of the methylated DNA-MBD1 complex through 2D material nanopores under external voltage biases. The passage of the MBD1-labeled methylation site through the pore is identified by dips in the current blockage induced by the DNA strand, as well as by peaks in the transverse electronic sheet current across the 2D layer. The positions of the methylation sites can be clearly recognized by the relative positions of the dips in the recorded ionic current blockade and large deviations in the transverse sheet conductances. We define the spatial resolution of the 2D material nanopore device as the minimal distance between two methylation sites identified within a single measurement, which is 15 base pairs by ionic current recognition, but as low as 10 base pairs by transverse electronic conductance detection, indicating better resolution with this latter technique. The present approach opens a new route for precise and efficient profiling of DNA methylation. Finally we propose techniques to improve the signal-to-noise (SNR) ratio in 2D solid state nanopores. In graphene, we demonstrate that the hydrophobic nature of the material can be utilized to introduce a ``step-wise'' translocation of a stretched ssDNA in a graphene nanopore, which can be used to detect bases via transverse sheet current. We also propose an information-theoretic approach to improve the SNR of the system by using matched filtering, which could possibly be used for real time base calling in solid state nanopores.Submission published under a 24 month embargo labeled 'U of I Access', the embargo will last until 2020-08-01The student, Aditya Sarathy, accepted the attached license on 2018-07-09 at 12:53.The student, Aditya Sarathy, submitted this Dissertation for approval on 2018-07-09 at 12:59.This Dissertation was approved for publication on 2018-07-09 at 16:07.DSpace SAF Submission Ingestion Package generated from Vireo submission #12776 on 2018-09-27 at 11:18:30Made available in DSpace on 2018-09-27T16:30:27Z (GMT). No. of bitstreams: 2
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Previous issue date: 2018-07-09Embargo set by: Seth Robbins for item 107786
Lift date: 2020-09-27T16:30:34Z
Reason: Author requested U of Illinois access only (OA after 2yrs) in Vireo ETD systemEmbargo set by: Seth Robbins for item 107786
Lift date: 2020-09-27T16:31:43Z
Reason: Author requested U of Illinois access only (OA after 2yrs) in Vireo ETD systemEmbargo set by: Seth Robbins for item 107786
Lift date: 2020-09-27T16:34:29Z
Reason: Author requested U of Illinois access only (OA after 2yrs) in Vireo ETD systemU of I Only Restriction Lifted for Item 107786 on 2020-09-28T09:15:24Z
An Innovative Leadership Effectiveness Measure: Applied Analytic Indicators of High-Consequence Industry Performance
No full textLeadership effectiveness in high-consequence industries has more than a bottom-line fiscal impact; it is linked to critical issues of human safety. Performance, productivity and overall quality of service have to be managed with focus on improvement in systemic safety while simultaneously maintaining a viable and profitable organization. This premise is specifically foremost in the leadership of airline organizations. The Airline Quality Rating has become a recognized and lauded indicator of airline performance in the United States. A valid case is presented herein to confirm that the Airline Quality Rating’s applied analytic methodology effectively provides a tool for assessing organizational leadership. These results provide a benchmark for global adoption in the world airline industry
Bulk viscous string cosmological models in f(R) gravity
No full textIn this paper, we derive f(R) gravity field equations with the help of a spatially homogeneous and anisotropic Bianchi type-III space–time, in the presence of a bulk viscous fluid, containing one-dimensional cosmic strings. Here we obtained the solutions of the field equations, both in the presence and in the absence of cosmic strings, under some specific plausible physical conditions. In particular, cosmological models with bulk viscous strings in f(R) theory of gravity are obtained by using the special law of variation for Hubble’s parameter proposed by Berman (Nuovo Cimento, B74, 182 (1983)). Various physical and kinematical properties of the models are also discussed.The accepted manuscript in pdf format is listed with the files at the bottom of this page. The presentation of the authors' names and (or) special characters in the title of the manuscript may differ slightly between what is listed on this page and what is listed in the pdf file of the accepted manuscript; that in the pdf file of the accepted manuscript is what was submitted by the author
Assessing usability of full-body immersion in an interactive virtual reality environment
No full text2020 Summer.Includes bibliographical references.Improving immersion and playability has a direct impact on the effectiveness of certain Virtual Reality applications. This project looks at understanding how to develop an immersive soccer application with the intention to measure skills, particularly for the use of assessment and health promotion. This project will show the requirements to create a top-down immersive experience with commodity devices. The particular system serves the simulation of a soccer training environment to evade opponents, pass to teammates, and score goals with the objective of measuring the difficulty of single, double, and triple tasks. It is expected that the performance will go down as the level of tasks increases. This hypothesis is extremely relevant as it provides a system that could serve as an assessment tool for people with concussions to return to play (with an OK by a physician) or to promote exercise to non-athletes. This thesis provides all the necessary steps to explain the high-level details of highly immersive applications while providing a future-path for human-subject experiments
New insights into the pore development mechanism of layered hydroxides upon thermal activation
No full textabstract: Layered double hydroxides (LDHs), also known as hydrotalcite-like materials, are extensively used as precursors for the preparation of (photo-)catalysts, electrodes, magnetic materials, sorbents, etc. The synthesis typically involves the transformation to the corresponding mixed metal oxide via calcination, resulting in atomically dispersed mixed metal oxides (MMOs). This process alters the porosity of the materials, with crucial implications for the performance in many applications. Yet, the mechanisms of pore formation and collapse are poorly understood. Combining an integrated in situ and ex situ characterization approach, here we follow the evolution of porosity changes during the thermal decomposition of LDHs integrating different divalent (Mg, Ni) and trivalent (Al, Ga) metals. Variations in porous properties determined by high-resolution argon sorption are linked to the morphological and compositional changes in the samples by in situ transmission electron microscopy coupled with energy dispersive X-ray spectroscopy, which is facilitated by the synthesis of well crystallized LDHs of large crystal size. The observations are correlated with the phase changes identified by X-ray diffraction, the mass losses evidenced by thermogravimetric analysis, the structural changes determined by infrared and nuclear magnetic resonance spectroscopy, and the pore connectivity analyzed by positron annihilation spectroscopy. The findings show that the multimetallic nature of the LDH governs the size and distribution (geometry, location, and connectivity) of the mesopores developed, which is controlled by the crystallization of the MMO phase, providing key insights for the improved design of porous mixed metal oxides
Author Correction:SciPy 1.0: fundamental algorithms for scientific computing in Python (Nature Methods, (2020), 10.1038/s41592-019-0686-2)
No full textIn the version of this article initially published online, the corresponding author designation was missing for Matt Haberland and Tyler Reddy. The affiliation for Evgeni Burovski was given as Higher School of Economics; the correct affiliation is National Research University, Higher School of Economics. In Box 1, “SciPy is an open-source package that builds on the strengths of Python and Numeric, providing a wide range of fast scientific and numeric functionality” was used as the box title; this has been moved to the beginning of the box text and a new title has been provided: “Excerpt from the SciPy 0.1 release announcement (typos corrected), posted 20 August 2001 on the Python-list mailing list.” From the original first sentence of this box, “(text following the % symbol indicates that a typo in the original text has been corrected in the version reproduced here)” has been deleted, and “% hanker to Hankel” and “% Netwon to Newton” have been deleted from the ends of the special functions row and the optimization row, respectively. In the first sentence of the ndimage section of Box 2, “nonlinear filter” has been changed to plural. At the end of the first paragraph of the section “SciPy matures,” “The library was expanded carefully, with the patience affordable in open-source projects and via best practices common in industry” has been changed to “The library was expanded carefully, with the patience affordable in open-source projects and via best practices, which are increasingly common in the scientific Python ecosystem and industry.” In Table 2, “Inequality constraint” has been changed to plural. In the “Nonlinear optimization: global minimization” section, “scipy.optimize.differentialevolution” had been changed to “scipy.optimize.differential_evolution.” In the first sentence of the section “Maintainers and contributors,” “SciPy developer guide” has been changed to “SciPy contributor guide” and the URL has been changed from http://scipy.github.io/devdocs/dev/core-dev/index. html to https://scipy.github.io/devdocs/dev/contributor/contributor_toc.html. In Table 2, entries in the first column have been changed from capitalized to lower-case. Finally, a URL in the second paragraph of the Discussion has been changed from https://scholar.google. com/scholar?q=SciPy to https://scholar.google.com/scholar?cites=2086009121748039507. The errors have been corrected in the print, HTML and PDF versions of the article. SciPy 1.0 Contributors Aditya Vijaykumar, Alessandro Pietro Bardelli, Alex Rothberg, Andreas Hilboll, Andreas Kloeckner, Anthony Scopatz, Antony Lee, Ariel Rokem, C. Nathan Woods, Chad Fulton, Charles Masson, Christian Häggström, Clark Fitzgerald, David A. Nicholson, David R. Hagen, Dmitrii V. Pasechnik, Emanuele Olivetti, Eric Martin, Eric Wieser, Fabrice Silva, Felix Lenders, Florian Wilhelm, G. Young, Gavin A. Price, Gert-Ludwig Ingold, Gregory E. Allen, Gregory R. Lee, Hervé Audren, Irvin Probst, Jörg P. Dietrich, Jacob Silterra, James T Webber, Janko Slavič, Joel Nothman, Johannes Buchner, Johannes Kulick, Johannes L. Schönberger, José Vinícius de Miranda Cardoso, Joscha Reimer, Joseph Harrington, Juan Luis Cano Rodríguez, Juan Nunez-Iglesias, Justin Kuczynski, Kevin Tritz, Martin Thoma, Matthew Newville, Matthias Kümmerer, Maximilian Bolingbroke, Michael Tartre, Mikhail Pak, Nathaniel J. Smith, Nikolai Nowaczyk, Nikolay Shebanov, Oleksandr Pavlyk, Per A. Brodtkorb, Perry Lee, Robert T. McGibbon, Roman Feldbauer, Sam Lewis, Sam Tygier, Scott Sievert, Sebastiano Vigna, Stefan Peterson, Surhud More, Tadeusz Pudlik, Takuya Oshima, Thomas J. Pingel, Thomas P. Robitaille, Thomas Spura, Thouis R. Jones, Tim Cera, Tim Leslie, Tiziano Zito, Tom Krauss, Utkarsh Upadhyay, Yaroslav O. Halchenko and Yoshiki Vázquez-Baeza.</p
Combinatorial methods in algorithms and complexity theory
No full textTheoretical Computer Science has connections to several areas of mathematics and one of the more prominent of these connections is to combinatorics. Indeed, many problems in this subject are often very combinatorial in nature. These problems have either used existing techniques from combinatorics or have given rise to new combinatorial techniques. This dissertation is a collection of the study of some such problems.
1. We recover a result by Abbe, Shpilka and Wigderson which states that a Reed-Muller code of rate 1 - Theta((log^r n)/n) can be recovered from o((log^((r-1)/2))/n) randomly chosen errors in a stronger way. Namely, we show that the set of corrupted locations in the message can be recovered just from the syndrome of the message. Among the techniques are the study of tensor decomposition over finite fields and an algorithm to find the roots of a space of low degree polynomials.
2. We show that it is NP-hard to properly 2-color a k-uniform (k - O(sqrt{k}))-rainbow colorable hypergraph. In particular, we show that it is NP-hard to properly 2-color a 4-uniform -rainbow colorable hypergraph. We further extend this using a notion of almost rainbow colorability. We show that given a k-uniform hypergraph where there is a -coloring of the vertices such that every edge gets (k - 3sqrt{ck})-colors, it is NP-hard to properly c-color it. Among the techniques are topological methods to lower bound the chromatic number of certain hypergraphs and a theorem of Sarkaria on the chromatic number of the generalized Kneser hypergraph.
3. We show that the discrepancy of a regular hypergraph can be bounded in terms of its spectral information. Let H subset 2^{[n]} be a t-regular hypergraph where |H| >= n, and M be the |H| x n incidence matrix. Define . We show that the discrepancy of H is at most O(sqrt{t} + lambda). In particular, this shows that for every t, the discrepancy of a random t-regular hypergraph on m > = n hyperedges has discrepancy O(sqrt{t}) with high probability as n grows. This bound also comes with an efficient algorithm that takes as input and outputs a coloring that has the guaranteed discrepancy.
4. We show that every q-ary error-correcting code of distance 1 - q^{-1} - epsilon^2 can be punctured to rate tilde{Omega}((epsilon)/(log q)) so that it is (O_{rho,delta}(q),delta,rho)-zero-error list-decodable. In particular, this shows that there are Reed-Solomon codes that are zero-error list-recoverable beyond the Johnson radius. This immediately improves the degree bound for unbalanced expanders obtained from randomly punctured Reed-Solomon codesPh.D.Includes bibliographical reference
Predicting Human Fetal Drug Exposure Through Maternal‐Fetal PBPK Modeling and In Vitro or Ex Vivo Studies
No full textThis is the peer reviewed version of the following article: [Predicting Human Fetal Drug Exposure Through Maternal‐Fetal PBPK Modeling and In Vitro or Ex Vivo Studies. The Journal of Clinical Pharmacology 62, S1 (2022)], which has been published in final form at https://doi.org/10.1002/jcph.2117. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Use of Self-Archived Versions: https://authorservices.wiley.com/author-resources/Journal-Authors/licensing/self-archiving.html#3. Deposited by shareyourpaper.org and openaccessbutton.org. We've taken reasonable steps to ensure this content doesn't violate copyright. However, if you think it does you can request a takedown by emailing [email protected]
Characterization of Series Arcs in LVdc Microgrids
No full textThis paper provides an empirical study on series arc behavior in low voltage dc microgrids. The response of an R-L-C dc microgrid abstraction towards series arcs is studied experimentally for varying grid inductance, dc voltages, load capacitances and load currents. In order to account for the stochastic nature of arcs, experiments are repeated multiple times under similar conditions to gain statistical significance. Thereby, insight on percentage occurrence and burn time of initiated series arcs is provided. Load side voltage response is studied to gain insight on the expected peak drop and fall time. This empirical evidence was judged to be a necessary requirement in developing a novel series arc extinguishing method from load side power electronic devices.DC systems, Energy conversion & Storag
UNDERSTANDING THE QUALITY OF PANSHARPENING - A LAB STUDY
No full textAtlantic Innovation Fund (AIF) of the Atlantic Canada Opportunities Agency (ACOA)SCI(E)ARTICLE10747-7558
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