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Item Action of the Mazur pattern up to topological concordance(arXiv, 2024) Manchester, AlexIn the '80s, Freedman showed that the Whitehead doubling operator acts trivally up to topological concordance. On the other hand, Akbulut showed that the Whitehead doubling operator acts nontrivially up to smooth concordance. The Mazur pattern is a natural candidate for a satellite operator which acts by the identity up to topological concordance but not up to smooth concordance. Recently there has been a resurgence of study of the action of the Mazur pattern up to concordance in the smooth and topological categories. Examples showing that the Mazur pattern does not act by the identity up to smooth concordance have been given by Cochran--Franklin--Hedden--Horn and Collins. In this paper, we give evidence that the Mazur pattern acts by the identity up to topological concordance. In particular, we show that two satellite operators $P_{K_0,\eta_0}$ and $P_{K_1,\eta_1}$ with $\eta_0$ and $\eta_1$ freely homotopic have the same action on the topological concordance group modulo the subgroup of $(1)$-solvable knots, which gives evidence that they act in the same way up to topological concordance. In particular, the Mazur pattern and the identity operator are related in this way, and so this is evidence for the topological side of the analogy to the Whitehead doubling operator. We give additional evidence that they have the same action on the full topological concordance group by showing that up to topological concordance they cannot be distinguished by Casson-Gordon invariants or metabelian $\rho$-invariants.Item Application of a fully polynomial randomized approximation scheme (FPRAS) to infrastructure system reliability assessments(8/6/2017) Fu, Bowen; Dueñas-Osorio, LeonardoNetworked systems make the reliability assessment of critical infrastructure computationally challenging given the combinatorial nature of system-level states. Several methods from numerical schemes to analytical approaches, such as Monte Carlo Simulation (MCS) and recursive decomposition algorithms (RDA), respectively, have been applied to this stochastic network problem. Despite progress over several decades, the problem remains open because of its intrinsic computational complexity. As the structural facilities of infrastructure systems continue to in terconnect in network forms, their study steers analysts to develop system reliability assessment methods based on graph theory and network science. A fully polynomial randomized approximation scheme (FPRAS) based on Karger’s graph contraction algorithm is an approximating method for reliability evaluation, which has a unique property rarely exploited in engineering reliability: that by performing a number of experiments in polynomial time (as a function of system size), it provides an a priori theoretical guarantee that the reliability estimate falls into the ϵ-neighborhood of its true value with (1−δ) confidence. We build upon the FPRAS ideas to develop an s-t reliability version that has practical appeal. Focusing on the relevant-cut enumeration stage of the FPRAS, we find correlations between the recurrence frequencies of links in minimum cuts within the randomization phase of the contraction algorithm, and typical network topological properties. We employ LASSO regression analysis to approximate the relationship between link recurrence frequencies and such topological metrics. With the topology-informed link recurrence frequencies, obtained at a much lower computational cost, we use a new biased contraction probability yielding 16.9% more distinct minimum cuts (MinCuts) than the original random contraction scheme. The biased contraction scheme proposed here can significantly improve the efficiency of reliability evaluation of networked infrastructure systems, while supporting infrastructure systems design, maintenance and restoration given its ability to offer error guarantees, which are ideal for future prescriptive guidelines in practice.Item Resilience-informed infrastructure network dismantling(2022-09-13) Fu, Bowen; Dueñas-Osorio, LeonardoLarge-scale networked infrastructure systems contribute significantly to modern society. Highly intra- and interconnnected systems enable communities to be more productive, at the expense of becoming more vulnerable to extreme events, cascading failures, and operational demands, including random failures and even targeted attacks. The resilience of infrastructure systems against common but random failure and rare but intentional attacks is critical for safe communities, as it covers multiple other types of contingencies in between. Network dismantling is a process to make the network dysfunctional by removi ng a fraction of components, which provides insights for robustness and resilience under many events, from common to rare. In particular, to protect networks from uncertain dismantling, we need to understand how to optimally fragment networks into small clusters by removing a fraction of their assets with minimal cost. Approximation methods are desirable because finding the optimal dismantling strategy is NP-hard, thus impractical on infrastructure networks. First attempts rely on iterative removal of the nodes with the highest adaptive importance, either from basic centralities, such as degree and betweeness, or from some more advanced metrics like collective influence. However, the additive nature of such methods fails to capture the synergistic nature of the dismantling problem. An algorithm connecting network dismantling problems with network decycling problems, identifies better the collective dismantling set. Other recent strategies add realism by adopting nonuniform node remo val costs, and applying a bisecting algorithm based on weighted spectral approximations iteratively. Despite these efforts, the combinatorial optimization nature of the network dismantling problem still requires global solutions, even if approximated. Additionally, the cost to remove components is the only factor considered in most previous methods. Network resilience, which can inform what to protect from dismantling to facilitate recovery, is seldom included as part of the cost. In this work, we propose a method employing Karger`s contraction algorithm and node-transferring heuristic optimization to approximate the optimal dismantling set, considering both component removal cost and network resilience after dismantling. The proposed method, resilDism, obtains good performance compared to state-of-the-art network dismantling methods, and provides valuable insights to guide network design and resilience enhancement in practice.Item Morphological diversity of extracellular vesicles revealed by cryo-electron microscopy(Rice University, 2022-10-01) Kapoor, Kshipra S.Introduction: Exosomes are extracellular vesicles 80-150 nm in diameter, containing proteins, mRNAs, microRNAs, and lipids reflecting the parent cell. While there has been an extensive characterization of the cargo incorporated in exosomes, a detailed morphological analysis of exosomes purified by various isolation techniques has not been performed. Objective: We aimed to determine the heterogeneity of exosomes morphology and if such morphological features are conserved across sample types. Methods: Our study used Cryogenic Electron Microscopy (Cryo-EM) to examine exosome size and morphology. Results: Our results revealed significant diversity in extracellular vesicle morphology independent of the isolation method, suggesting that morphological subpopulations of these vesicles exist. Based on their shape, our analysis classified exosomes into seven categories. In addition, we developed a semi-automatic image analysis framework to accurately characterize exosome attributes and distribution to facilitate reliable quantification of specific bio-nanoparticle features in Cryo-EM micrographs. Conclusions: Morphological features of exosomes inform their biophysical properties, which influence both biodistribution and biological activity in vivo. Our data demonstrating the innate morphological diversity of exosomes may have implications for improving the specificity and precision of exosome-delivered therapeutics. Conflict of interest: R.K. and MD Anderson Cancer Center hold patents in exosome biology and are stock equity holders in Codiak Biosciences Inc. R.K. is a consultant and a scientific advisor of Codiak Biosciences Inc.Item Morphological diversity of extracellular vesicles revealed by cryo-electron microscopy(ASEMV/AAEV, 10/1/2022) Kapoor, Kshipra S.; McAndrews, Kathleen M.; Biswal, Lisa S.; Kalluri, RaghuIntroduction: Exosomes are extracellular vesicles 80-150 nm in diameter, containing proteins, mRNAs, microRNAs, and lipids reflecting the parent cell. While there has been an extensive characterization of the cargo incorporated in exosomes, a detailed morphological analysis of exosomes purified by various isolation techniques has not been performed. Objective: We aimed to determine the heterogeneity of exosomes morphology and if such morphological features are conserved across sample types. Methods: Our study used Cryogenic Electron Microscopy (Cryo-EM) to examine exosome size and morphology. Results: Our results revealed significant diversity in extracellular vesicle morphology independent of the isolation method, suggesting that morphological subpopulations of these vesicles exist. Based on their shape, our analysis classified exosomes into seven categories. In addition, we developed a semi-automatic image analysis framework to accurately characterize exosome attributes and distribution to facilitate reliable quantification of specific bio-nanoparticle features in Cryo-EM micrographs. Conclusions: Morphological features of exosomes inform their biophysical properties, which influence both biodistribution and biological activity in vivo. Our data demonstrating the innate morphological diversity of exosomes may have implications for improving the specificity and precision of exosome-delivered therapeutics. Conflict of interest: R.K. and MD Anderson Cancer Center hold patents in exosome biology and are stock equity holders in Codiak Biosciences Inc. R.K. is a consultant and a scientific advisor of Codiak Biosciences Inc.Item Autocorrelation Reflectivity of Mars(Wiley, 2020) Deng, Sizhuang; Levander, AlanThe seismic structure of the Martian interior can shed light on the formation and dynamic evolution of the planet and our solar system. The deployment of the seismograph carried by the InSight mission provides a means to study Martian internal structure. We used ambient noise autocorrelation to analyze the available vertical component seismic data to recover the reflectivity beneath the Insight lander. We identify the noise that is approximately periodic with the Martian sol as daily lander operations and the diurnal variation in Martian weather and tides. To investigate the seismic discontinuities at different depths, the autocorrelograms are filtered and stacked into different frequency bands. We observe prominent reflection signals probably corresponding to the Martian Moho, the olivine-wadsleyite transition in the mantle, and the core-mantle boundary in the stacked autocorrelograms. We estimate the depths of these boundaries as ~35, 1,110–1,170, and 1,520–1,600 km, consistent with other estimates.Item Demonstration of Piecewise Cubic Polynomial Fitting on Mesoscale Tester Data(Rice University, 2020) Mehta, Shail Maharshi; De Santos, Diego Ricardo; Sridhar, Shweta; Aguayo, Veronica Cristina; Meraz, Carlos Alberto; Mikos, Mary; Grande-Allen, K. Jane; BioengineeringAnimation of piecewise cubic polynomial fitting to data from a replicate of 1:15 PDMS performed in order to obtain stress values at exact increments of strainItem Parts List, Prices, and Links for Commercial Components of Mesoscale Testing Device(Rice University, 2020) Mehta, Shail Maharshi; De Santos, Diego Ricardo; Sridhar, Shweta; Aguayo, Veronica Cristina; Meraz, Carlos Alberto; Mikos, Mary; Grande-Allen, K. Jane; BioengineeringFile displaying names, prices, quantities, and purchasing links of commercial components of mesoscale testing deviceItem Print and CAD Files for Mesoscale Testing Device(Rice University, 2020) Mehta, Shail Maharshi; De Santos, Diego Ricardo; Sridhar, Shweta; Aguayo, Veronica Cristina; Meraz, Carlos Alberto; Mikos, Mary; Grande-Allen, K. Jane; BioengineeringFolder containing 3D-printable components of mesoscale testing deviceItem Tracking Demonstration Video of 1:10 PDMS from Mesoscale Testing Device on Fluorescence Microscope(Rice University, 2020) Mehta, Shail Maharshi; De Santos, Diego Ricardo; Sridhar, Shweta; Aguayo, Veronica Cristina; Meraz, Carlos Alberto; Mikos, Mary; Grande-Allen, K. Jane; BioengineeringEdge tracking output from testing video taken using a fluorescence microscope at 10x magnification of 1:15 PDMS. Yellow lines indicate tracking pathsItem Pixel Selection Demonstration Video of 1:15 PDMS from Mesoscale Testing Device(Rice University, 2020) Mehta, Shail Maharshi; De Santos, Diego Ricardo; Sridhar, Shweta; Aguayo, Veronica Cristina; Meraz, Carlos Alberto; Mikos, Mary; Grande-Allen, K. Jane; BioengineeringTesting video taken using a stereomicroscope at 0.63x magnification of 1:15 PDMS demonstrating which pixels are selected as belonging to points to be tracked in yellow. Only every other pixel was checked for the appropriate color to reduce processing timeItem Tracking Demonstration Video of 1:15 PDMS from Mesoscale Testing Device(Rice University, 2020) Mehta, Shail Maharshi; De Santos, Diego Ricardo; Sridhar, Shweta; Aguayo, Veronica Cristina; Meraz, Carlos Alberto; Mikos, Mary; Grande-Allen, K. Jane; BioengineeringPoint tracking output from testing video taken using a stereomicroscope at 0.63x magnification of 1:15 PDMS. Yellow lines indicate tracking paths. One red line directly connects the center points of the sample-attached and static element points. The other red line indicates where the sample-attached point would have been without the presence of a sample. The difference between the endpoints of these lines is the deflection, shown using blue linesItem Pixel Selection Demonstration Video of 1:10 PDMS from Mesoscale Testing Device on Fluorescence Microscope(Rice University, 2020) Mehta, Shail Maharshi; De Santos, Diego Ricardo; Sridhar, Shweta; Aguayo, Veronica Cristina; Meraz, Carlos Alberto; Mikos, Mary; Grande-Allen, K. Jane; BioengineeringTesting video taken using a fluorescence microscope at 10x magnification of 1:10 PDMS demonstrating which pixels are selected as belonging to edges to be tracked in yellow. Only every other pixel was checked for the appropriate color to reduce processing timeItem Simulating Transport and Adsorption of Organic Contaminants in 3D Porous Activated Carbon Block Media(2019) Kim, Jun; Morgott, Amanda; Wu, Ziqi; Hopaluk, Liane; Miles, Michael; Stoner, William; Li, QilinTo evaluate the organic contaminants removal performance of hollow cylindrical block-shaped porous activated carbon media, COMSOL Multiphysics® simulation software with Chemical Engineering module was used. The study clearly demonstrates how each organic compound in a steady-state fluid is dynamically transported in the three-dimensional porous media and removed by adsorption. The simulated adsorption results are compared to the experimental test data for validation. Axisymmetric geometry in COMSOL gives better simulation accuracy and faster computation than full three-dimensional geometry due to higher element quality and lower volume/area ratio. Based on 5% breakthrough (95% removal) line, the COMSOL simulations have only 0.9-2.9% discrepancy from the actual data, while a classical two-dimensional rapid-small-scale column test (RSSCT) model method has 39.8-782.2%. The COMSOL Multiphysics® model used in this transport/adsorption study successfully demonstrated not only flow patterns in the modulated reactor but also chemical concentration changes in the full-scale porous adsorbent structure.Item Origin and Early Differentiation of Carbon and Associated Life-Essential Volatile Elements on Earth(Cambridge University Press, 2019) Dasgupta, Rajdeep; Grewal, Damanveer S.; Orcutt, Beth N.; Daniel, Isabelle; Dasgupta, RajdeepThis chapter reviews what is known about the fate of carbon during early differentiation of inner solar system planets. It reviews the nature of carbon fractionation in a magma ocean as compared to the core, mantle, and atmosphere, and how this may have varied between planetary bodies in the solar system. It discusses whether magma ocean processes could have established the present-day budget of carbon in Earth’s bulk silicate, and also reviews possibilities for the early temporal evolution of the mantle carbon budget through core formation, later veneer addition, and magma ocean crystallization processes.Item Simple ultraviolet microscope using off-the-shelf components for point-of-care diagnostics.(Rice University, 2019-02-12) Wong, Cindy; BioengineeringAt the primary care setting, where there are often no or minimal laboratories, examinations often consist of self-testing and rapid diagnostics. Because of this, medical devices must be simple, robust, and easy to operate. To address these concerns, an alternate fluorescence microscope design uses ultraviolet (UV) excitation, since fluorescent dyes that are excitable in the visible region are also excitable by UV. This may allow for the removal of typical excitation, emission, and dichroic filters as optical components absorb UV wavelengths and UV is not detected by silicon based detectors. Additionally, UV has a very low penetration into samples, which may allow for controlling the depth of excitation, and thus the imaging volume. Based on these ideas, we developed a simple fluorescence microscope built completely from off-the-shelf components that uses UV to image fluorescently stained samples. The simple opto-mechanical design of the system may allow it to be more compact and easy to use, as well as decrease the overall cost of the diagnostic device. For biological validation, we imaged whole blood stained with acridine orange and performed a two-part white blood cell differential count.Item Book review: Barnstorming the Prairies: How Aerial Vision Shaped the Midwest, by Jason Weems(Rice University, 2018) LaFlamme, Marcel; University of Nebraska PressItem On the Problem of the Namesake(Rice University, 2016-02) LaFlamme, Marcel; American Anthropological AssociationItem What Happened, or, Impasses and Future Horizons for an Open Anthropology of Work(Rice University, 2018-06) Brown, Nina; LaFlamme, Marcel; Lyon, Sarah; American Anthropological AssociationItem Rescoping research through student-librarian collaboration: Lessons from the Fondren Fellows program(2018) LaFlamme, Marcel; Kipphut-Smith, Shannon; Association of College and Research LibrariesAcademic library professionals increasingly see student workers as full coparticipants in the design and delivery of library resources and services. For some librarians, this perspective grows out of a commitment to critical and feminist pedagogy,1 while for others, greater reliance on student workers in the face of flat or contracting budgets has led to the pragmatic realization that the “skills of student workers could be leveraged to advance the library in unexpected and invaluable ways.”2 This article examines how collaboration with students can take librarian-initiated research in new directions, drawing on the experiences of the coauthors (a library staff member and a graduate student) as part of the Fondren Fellows program at Rice University’s Fondren Library.
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