2020 Summer Research and Scholarship
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MicroWorkshop | Robotics – May 27, 2020, 11:00am (PST)
MicroWorkshop | Atmospheric and Climate Sciences – June 24, 2020, 11:00AM (PST)
MicroWorkshop | Computational Biology – July 10, 2020 11:00AM (PST)
MicroWorkshop | Computational Imaging – July 15, 2020 11:00AM (PST)
MicroWorkshop | Big Problems in Circuit Design – July 22, 2020 11:00AM (PST)
MicroWorkshop | Biomedical Device Design – July 29, 2020 11:00AM (PST)
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Invisible, Inevitable and Toxic
There's a new book encouraging stronger policies to ensure that people act with greater caution around creating and maintaining toxic landscapes.
In Inevitably Toxic: Historical Perspectives on Contamination, Exposure, and Expertise, editors/ authors Vivien Hamilton (history of science professor, Harvey Mudd), Brinda Sarathy (Pitzer) and Janet Farrell Brodie (Claremont Graduate University) present a collection of essays that consider exposure of humans to toxic environments that often appear innocuous.
Deep-Sea Surprise
As a shallow-water biologist, Catherine McFadden's usual method of coral specimen collection is via SCUBA [...]
Fulbright en Español
In his lab at Harvey Mudd College, chemistry professor David Vosburg seeks to make medicinally [...]
Libeskind-Hadas, Wu, HMC Students Publish Bioinformatics Paper
Research related to the evolution of genes and species being conducted at Harvey Mudd College by professors of computer science Ran Libeskind-Hadas and Yi-Chieh "Jessica" [...]
Researchers Seek Better Software Testing Techniques
Software systems in programmable items—from household appliances to cars and planes—must be reliable and high quality to avoid inconvenient or disastrous consequences. In order to [...]
Harvey Mudd Ranks High in U.S. News and World Report 2021
Harvey Mudd College ranked No. 2 for undergraduate engineering programs in U.S. News & World Report's Best Colleges 2021, maintaining the same spot as last year. Harvey [...]
Interdisciplinary Research on Gene Histories Accepted to ACM Conference
In pursuit of developing models and algorithms for reconstructing gene histories across multiple species, Harvey Mudd College researchers have completed a paper that has been [...]
The Social Rules Project ​From national policies to the most minute technical design standards, social rules are the constraints that make coordinated human activity possible. The Social Rules Project is an educational initiative at Harvey Mudd College that reveals how social rules, or "institutions," shape our planet and our lives. Program Director: Paul F. Steinberg 2014 - Ongoing Humanities, Social Sciences, and the Arts
Water exit dynamics of jumping archer fish: Integrating two-phase flow large-eddy simulation with experimental measurements Archer fish jumping for prey capture are capable of achieving accelerations that can reach 12 times gravitational from a stationary start at the free surface. This behavior is associated with nontrivial production of hydrodynamic thrust. In this work, we numerically investigate the hydrodynamic and aerodynamic performance of a jumping smallscale archer fish (Toxotes microlepis) to elucidate the propulsive mechanisms that contribute to the rapid acceleration and the considerable jump accuracy. We conduct high-fidelity, two-phase flow, large-eddy simulation (LES) of an anatomically realistic archer fish using detailed jump kinematics in water, through the water/air interface, and in air. The complex fish body kinematics are reconstructed using high-speed imaging. The LES results during the water phase of the jump are compared with particle image velocimetry measurements of a live jumping archer fish, and excellent agreement is found. The numerical simulations further enable detailed analysis of the flow dynamics and elucidate for the first time the dynamics of the coherent vortical structures in both the water and air phases. In particular, the pectoral fins are shown to contribute to the initial spike in acceleration before water exit and to enhance the overall jumping performance of the fish.
Ali Khosronejad, Leah Mendelson, Alexandra H. Techet, Seokkoo Kang, Dionysios Angelidis, Fotis Sotiropoulos 2020 Engineering
Dynamic Control of Probabilistic Simple Temporal Networks The controllability of a temporal network is defined as an agent's ability to navigate around the uncertainty in its schedule and is well-studied for certain networks of temporal constraints. However, many interesting real-world problems can be better represented as Probabilistic Simple Temporal Networks (PSTNs) in which the uncertain durations are represented using potentially-unbounded probability density functions. This can make it inherently impossible to control for all eventualities. In this paper, we propose two new dynamic con-trollability algorithms that attempt to maximize the likelihood of successfully executing a schedule within a PSTN. The first approach, which we call MIN-LOSS DC, finds a dynamic scheduling strategy that minimizes loss of control by using a conflict-directed search to decide where to sacrifice the control in a way that optimizes overall success. The second approach , which we call MAX-GAIN DC, works in the other direction: it finds a dynamically controllable schedule and then attempts to progressively strengthen it by capturing additional uncertainty. Our approaches are the first known that work by finding maximally dynamically controllable schedules. We empirically compare our approaches against two existing PSTN offline dispatch approaches and one online approach and show that our MIN-LOSS DC algorithm outper-forms the others in terms of maximizing execution success while maintaining competitive runtimes. James C. Boerkoel Jr., Lindsay Popowski, Michael Gao 2020 Computer Science
María Acuña. Poesía descalza. Granada: Valparaíso Ediciones, 2020. (Barefoot Poetry) In 2007, the Congress of Deputies in Spain approved the Law of Historical Memory. The law sought to redress wrongs experienced by victims on both sides of the Spanish Civil War (1936-1939) and condemned the Franco regime. Since then, exhumation of the repressed past has witnessed a burgeoning. Restoration ought to include not just notables like Federico García Lorca but also the unsung voices that played a quiet yet relevant role. Within this context, I have edited the unpublished poetry of María Acuña (1928-1994). Poesía descalza is the first volume to come out. The first woman to wear pants in her village, to smoke in public, among the few to give birth out of wedlock when the Church sanctioned the harshening dictatorship, she cuts a striking figure across the somber Francoist years. My research draws on her poetry to reconstruct the postwar female experience. Women's creativity under Franco, regional lives too often neglected, must be acknowledged and written into Spain's intellectual history. Isabel Balseiro 2020 Humanities, Social Sciences, and the Arts
Decomposable Probability-of-Success Metrics in Algorithmic Search Previous studies have used a specific success metric within an algorithmic search framework to prove machine learning impossibility results. However, this specific success metric prevents us from applying these results on other forms of machine learning, e.g. transfer learning. We define decomposable metrics as a category of success metrics for search problems which can be expressed as a linear operation on a probability distribution to solve this issue. Using an arbitrary decomposable metric to measure the success of a search, we demonstrate theorems which bound success in various ways, generalizing several existing results in the literature. George D. Montañez, Tyler Sam, Jake Williams, Abel Tadesse, Huey Sun 2020 Computer Science
Minimal Complexity Requirements for Proteins and Other How complex do proteins (and other multi-part recognition systems) need to be? Using an informationtheoretic framework, we characterize the information costs of recognition tasks and the information capacity of combinatorial recognition systems, to determine minimum complexity requirements for systems performing such tasks. Reducing the recognition task to a finite set of binary constraints, we determine the sizes of minimal equivalent constraint sets using a form of distinguishability, and show how the representation of constraint sets as binary circuits or decision trees also results in minimum constraint set size requirements. We upper-bound the number of configurations a recognition system can distinguish between as a function of the number of parts it contains, which we use to determine the minimum number of parts needed to accomplish a given recognition task. Lastly, we apply our framework to DNA-binding proteins and derive estimates for the minimum number of amino acids needed to accomplish binding tasks of a given complexity. George D. Montañez, Laina Sanders, Howard Deshong 2020 Computer Science
Virtue as a framework for the design and use of artificial intelligence Practitioners are seeking information and ethical guidance related to the design and utilization of artificial intelligence (AI) across a variety of applications. Developments at Google illustrate the potential good of AI as well as potential concerns. In this article, we use Google to create a context that demonstrates the relevance of virtue for the ethical design and use of AI. We describe a set of ethical challenges encountered by Google and introduce virtue as a framework for ethical decision making that can be applied broadly to numerous organizations. We also examine support for virtue in ethical decision making as well as its power in attracting and retaining the employees who develop AI and the customers who use it. To conclude, we apply the virtue framework to Google's AI challenges and offer suggestions for its use in other organizations. George D. Montañez, Mitchell J. Neubert 2020 Computer Science
Mathematics for Human Flourishing For mathematician Francis Su, a society without mathematical affection is like a city without concerts, parks, or museums. To miss out on mathematics is to live without experiencing some of humanity's most beautiful ideas. In this profound book, written for a wide audience but especially for those disenchanted by their past experiences, an award-winning mathematician and educator weaves parables, puzzles, and personal reflections to show how mathematics meets basic human desires—such as for play, beauty, freedom, justice, and love—and cultivates virtues essential for human flourishing. These desires and virtues, and the stories told here, reveal how mathematics is intimately tied to being human. Some lessons emerge from those who have struggled, including philosopher Simone Weil, whose own mathematical contributions were overshadowed by her brother's, and Christopher Jackson, who discovered mathematics as an inmate in a federal prison. Christopher's letters to the author appear throughout the book and show how this intellectual pursuit can—and must—be open to all. Francis Su; With Reflections by Christopher Jackson 2020 Mathematics
How do I design a chemical reaction to do useful work? Reinvigorating general chemistry by connecting chemistry and society Insights and methods from the chemical sciences are directly relevant to global challenges such as climate change, renewable energy generation and storage, water purification, and food production. However, these connections are often opaque to students in general chemistry courses, who may get lost in the weeds of stoichiometry, VSEPR, and gas laws, and fail to see the relevance of their studies to their lives and their communities. Herein we describe a redesigned first-year undergraduate chemistry course that grounds chemical content in relevant societal applications. Students engage in collaborative, inquiry-based learning through an adapted POGIL methodology, and the highly structured class activities help students learn soft skills that enable success in higher education. Significant course revisions sometimes face resistance from key stakeholders, including students, faculty, and administration. We offer a case study in framing broader disciplinary concerns through the lens of institutional values to increase buy-in among key stakeholders. Katherine M. Van Heuvelen, G. William Daub, Lelia N. Hawkins, Adam R. Johnson, Hal Van Ryswyk, David A. Vosburg 2020 Chemistry
Evolutionary implications of analyses of complete mitochondrial genomes across order Zoantharia (Cnidaria: Hexacorallia) Cnidarians are early‐diverging metazoans, but evolutionary aspects of some taxa are still poorly understood, as in the order Zoantharia (Anthozoa: Hexacorallia). Zoantharians have been divided into two suborders based on the arrangement of the fifth septae as complete (Macrocnemina) or incomplete (Brachycnemina). Previous molecular phylogenetic analyses have indicated the need for re‐evaluation as Macrocnemina has been found to be paraphyletic. Despite many phylogenetic studies, the recovery of complete mitochondrial genomes (mt‐genomes) for systematic and evolutionary studies of zoantharians has been limited. The present study represents the first to sequence the complete mt‐genomes of members of eight of nine zoantharian families. Although all examined mt‐genomes had the same gene order arrangement, there were variations among mt‐genomes' sizes, nucleotide substitution rates, and introns. Only two species did not have the cox1 intron, which harbors a gene coding a homing endonuclease of the LAGLIDADG type. Our mitogenomic analyses also showed relatively high nucleotide diversity in mt‐DNA regions other than the standard regions traditionally considered for DNA barcoding of this group. Phylogenetic analyses using 13 mt‐genome protein‐coding genes recovered a fully resolved tree with clear separation between macrocnemic representatives. Ancestral state reconstruction analyses revealed three main transitions in arrangement of the marginal musculature through the evolutionary history of the order. An "early" transition from reticulate mesogleal to a cteniform endodermal arrangement was followed by transitions that occurred in the common ancestor of the Brachycnemina and family Hydrozoanthidae. Our results indicate the need for clarification of higher‐level phylogeny and taxonomy of Zoantharia. Angelo Poliseno, Maria Eduarda Alves Santos, Hiroki Kise, Brooks Macdonald, Andrea M. Quattrini, James Davis Reimer, Catherine S. McFadden 2020 Biology
Cryptic Species Account for the Seemingly Idiosyncratic Secondary Metabolism of Sarcophyton glaucum Specimens Collected in Palau Sarcophyton glaucum is one of the most abundant and chemically studied soft corals with over 100 natural products reported in the literature, primarily cembrane diterpenoids. Yet, wide variation in the chemistry observed from S. glaucum over the past 50 years has led to its reputation as a capricious producer of bioactive metabolites. Recent molecular phylogenetic analysis revealed that S. glaucum is not a single species but a complex of at least seven genetically distinct species not distinguishable using traditional taxonomic criteria. We hypothesized that perceived intraspecific chemical variation observed in S. glaucum was actually due to differences between cryptic species (interspecific variation). To test this hypothesis, we collected Sarcophyton samples in Palau, performed molecular phylogenetic analysis, and prepared chemical profiles of sample extracts using gas chromatography-flame ionization detection. Both unsupervised (principal component analysis) and supervised (linear discriminant analysis) statistical analyses of these profiles revealed a strong relationship between cryptic species membership and chemical profiles. Liquid chromatography with tandem mass spectrometry-based analysis using feature-based molecular networking permitted identification of the chemical drivers of this difference between clades, including cembranoid diterpenes (2 R,11 R,12 R)-isosarcophytoxide (5), (2 S,11 R,12 R)-isosarcophytoxide (6), and isosarcophine (7). Our results suggest that early chemical studies of Sarcophyton may have unknowingly conflated different cryptic species of S. glaucum, leading to apparently idiosyncratic chemical variation. Katherine N. Maloney, Ryan T. Botts, Taylor S. Davis, Bethany K. Okada, Elizabeth M. Maloney, Christopher A. Leber, Oscar Alvarado, Charlie Brayton, Andrés Mauricio Caraballo-Rodríguez, Jason V. Chari, Brent Chicoine, J. Chance Crompton, Sydney R. Davis, Samantha M. Gromek, Viqqi Kurnianda, Kim QuachRobert M. Samples, Vincent Shieh, Camille M. Sultana, Junichi Tanaka, Pieter C. Dorrestein, Marcy J. Balunas, Catherine S. McFadden 2020 Biology
Beyond treaty implementation: Multilevel governance and the politics of institutional reform in London's transportation sector The implementation of international environmental law is often construed as a one-way process, beginning with international agenda-setting and followed by national, and eventually local reforms in laws and policies with the goal of inducing behavior change on the ground.
From a bottom-up perspective, however, the picture is considerably more complex: local governments are simultaneously implementing numerous national and international legal mandates ‒ from trade and immigration laws to public health standards, national security measures, energy and building codes, land use regulations, and more. Particularly in large cities, local governments often have independent environmental initiatives that predate international treaties. Local discretion in adjudicating trade-offs among competing policy goals, deciding how to apportion costs and benefits, and designing projects looks a lot like agenda-setting authority, rather than merely implementation.
As a result, to understand global responses to climate change requires an analytic framework that can take account of multilevel governance, combining top-down and bottom-up perspectives. This study explores how local legal reforms unfold in a context of multilevel governance, with a focus on the push for climate-friendly transportation policies in London, comparing this to my ongoing research on the political dynamics of reform in Los Angeles. Paul F. Steinberg 2020 Humanities, Social Sciences, and the Arts
Linear Algebra with Applications, 10th Edition "You may have noticed something new on the cover of the book. Another author! Yes, after nearly 40 years as a "solo act," Steve Leon has a partner. New co-author Lisette de Pillis is a professor at Harvey Mudd College and brings her passion for teaching and solving real-world problems to this revision. The focus of this revision was transforming it from a primarily print-based learning tool to a digital learning tool. The eText is therefore filled with content and tools that will help bring the entire course to life for students in new ways and help you improve instruction." Steven J. Leon and Lisette de Pillis 2020 Mathematics
Mesenchymal Stem Cells Used as Carrier Cells of Oncolytic Adenovirus Results in Enhanced Oncolytic Virotherapy In this work, we develop a mathematical model that explores aspects of a new kind of cancer treatment that harnesses the unique characteristics of stem cells loaded with a specialized virus to carry targeted therapy to a tumor site. We are very proud to have been able to publish in Nature, Scientific Reports, which has a 2 year impact factor of 4.011, and a 56% acceptance rate Lisette de Pillis, K. Mahasa, R. Ouifki, A. Eladdadi, P. Maini, A.-R. Yoon, C.-O. Yun 2020 Mathematics
Agent-based and continuous models of hopper bands for the Australian plague locust: How resource consumption mediates pulse formation and geometry Locusts are significant agricultural pests. Under favorable environmental conditions flightless juveniles may aggregate into coherent, aligned swarms referred to as hopper bands. These bands are often observed as a propagating wave having a dense front with rapidly decreasing density in the wake. A tantalizing and common observation is that these fronts slow and steepen in the presence of green vegetation. This suggests the collective motion of the band is mediated by resource consumption. Our goal is to model and quantify this effect. We focus on the Australian plague locust, for which excellent field and experimental data is available. Exploiting the alignment of locusts in hopper bands, we concentrate solely on the density variation perpendicular to the front. We develop two models in tandem; an agent-based model that tracks the position of individuals and a partial differential equation model that describes locust density. In both these models, locust are either stationary (and feeding) or moving. Resources decrease with feeding. The rate at which locusts transition between moving and stationary (and vice versa) is enhanced (diminished) by resource abundance. This effect proves essential to the formation, shape, and speed of locust hopper bands in our models. From the biological literature we estimate ranges for the ten input parameters of our models. Sobol sensitivity analysis yields insight into how the band's collective characteristics vary with changes in the input parameters. By examining 4.4 million parameter combinations, we identify biologically consistent parameters that reproduce field observations. We thus demonstrate that resource-dependent behavior can explain the density distribution observed in locust hopper bands. This work suggests that feeding behaviors should be an intrinsic part of future modeling efforts.
Andrew J. Bernoff, Michael Culshaw-Maurer, Rebecca A. Everett, Maryann E. Hohn, W. Christopher Strickland, Jasper Weinburd 2020 Mathematics
Latch-based control of energy output in spring actuated systems The inherent force–velocity trade-off of muscles and motors can be overcome by instead loading and releasing energy in springs to power extreme movements. A key component of this paradigm is the latch that mediates the release of spring energy to power the motion. Latches have traditionally been considered as switches; they maintain spring compression in one state and allow the spring to release energy without constraint in the other. Using a mathematical model of a simplified contact latch, we reproduce this instantaneous release behaviour and also demonstrate that changing latch parameters (latch release velocity and radius) can reduce and delay the energy released by the spring. We identify a critical threshold between instantaneous and delayed release that depends on the latch, spring, and mass of the system. Systems with stiff springs and small mass can attain a wide range of output performance, including instantaneous behaviour, by changing latch release velocity. We validate this model in both a physical experiment as well as with data from the Dracula ant, Mystrium camillae, and propose that latch release velocity can be used in both engineering and biological systems to control energy output. Sathvik Divi, Xiaotian Ma, Mark Ilton, Ryan St. Pierre, Babak Eslami, S. N. Patek and Sarah Bergbreiter 2020 Physics
Graphs Are Not Enough: Using Interactive Visual Analytics in Storage Research Storage researchers have always been interested in understanding the complex behavior of storage systems with the help of statistics, machine learning, and simple visualization techniques. However, when a system's behavior is affected by hundreds or even thousands of factors, existing approaches break down. Results are often difficult to interpret, and it can be challenging for humans to apply domain knowledge to a complex system. We propose to enhance storage system analysis by applying "interactive visual analytics," which can address the aforementioned limitations. We have devised a suitable Interactive Configuration Explorer (ICE), and conducted several case studies on a typical storage system, to demonstrate its benefits for storage system researchers and designers. We found that ICE makes it easy to explore a large parameter space, identify critical parameters, and quickly zero in on optimal parameter settings. Zhen Cao, Stony Brook University; Geoff Kuenning, Harvey Mudd College; Klaus Mueller, Anjul Tyagi, and Erez Zadok, Stony Brook University 2019 Computer Science
Automatically Solving Deduction Games via Symbolic Execution, Model Counting, and Entropy Maximization We present a technique for automatically solving deduction games in which a player makes repeated queries to a running implementation of the game and receives a game outcome, with the goal of discovering an unknown secret value. By making multiple queries, a player iteratively reduces the uncertainty about the secret until it is known. We show how to synthesize player queries using static program analysis, model-counting, and information theory. The system we describe automatically solves deduction games implemented in a Python-based game specification language. Mara Downing, Chris Thompson, Lucas Bang 2019 Computer Science
The Futility of Bias-Free Learning and Search Building on the view of machine learning as search, we demonstrate the necessity of bias in learning, quantifying the role of bias (measured relative to a collection of possible datasets, or more generally, information resources) in increasing the probability of success. For a given degree of bias towards a fixed target, we show that the proportion of favorable information resources is strictly bounded from above. Furthermore, we demonstrate that bias is a conserved quantity, such that no algorithm can be favorably biased towards many distinct targets simultaneously. Thus bias encodes trade-offs. The probability of success for a task can also be measured geometrically, as the angle of agreement between what holds for the actual task and what is assumed by the algorithm, represented in its bias. Lastly, finding a favorably biasing distribution over a fixed set of information resources is provably difficult, unless the set of resources itself is already favorable with respect to the given task and algorithm. George D. Montanez, Jonathan Hayase, Julius Lauw, Dominique Macias, Akshay Trikha, Julia Vendemiatti 2019 Computer Science
Nonadiabatic Investigation of the Electronic Spectroscopy of trans-1,3-Butadiene Low-lying UV spectroscopy of trans-1,3-butadiene has been extensively studied by experimentalists and theorists. Though a host of techniques has been applied to understand its lowest electronic states, there are still important open questions. Among these are the positions of the two lowest valence excited states and the factors responsible for the spectral shape of the lowest allowed transitions. We present results from EOM-CC calculations in extended basis sets that are used to parametrize a three-electronic-state Koppel, Domcke, and Cederbaum (KDC) model. We test the sensitivity of the KDC model to a variety of parameters and address several outstanding questions regarding the spectrum. We find that the overall shape of the spectrum is determined primarily by the Franck–Condon envelope of the 11Bu state and that the princple impact of the doubly excited 21Ag state is to broaden the 11Bu peaks. There is only modest sensitivity to the relative position of these two states. We find that the lowest Rydberg state, the 11Bg state, has an unexpected impact on the third peak in the spectrum, and its effect is considerably more energy-dependent than that of the 21Ag state. Scott M. Rabidoux, Robert J. Cave, John F. Stanton 2019 Chemistry
A Trypanosoma brucei ORFeome-based Gain-of-Function Library reveals novel genes associated with melarsoprol resistance Trypanosoma brucei is an early branching protozoan that causes Human and Animal African Trypanosomiasis. Forward genetics approaches are powerful tools for uncovering novel aspects of Trypanosomatid biology, pathogenesis, and therapeutic approaches against trypanosomiasis. Here we have generated a T. brucei ORFeome consisting of over 90% of the targeted genome and used it to make an inducible Gain-of-Function library for broadly applicable forward genetic screening. Using a critical drug of last resort, melarsoprol, we conducted a proof of principle genetic screen. Hits arising from this screen support the significance of trypanothione, a key player in redox metabolism, as a target of melarsoprol and implicate novel proteins of the flagellum and mitochondria in drug resistance. This study has produced two powerful new genetic tools for kinetoplastida research, which are expected to promote major advances in kinetoplastida biology and therapeutic development in the years to come. M. Carter, H.S. Kim, S. Gomez, S. Gritz, S. Larson, D. Schultz, G.A. Hovel-Miner 2019 Biology
Identification of clinically approved small molecules that inhibit growth and promote surface remodeling in the African trypanosome Trypanosoma brucei are unicellular parasites endemic to Sub-Saharan Africa that cause fatal disease in humans and animals. Infection with these parasites is caused by the bite of the tsetse fly vector, and parasites living extracellularly in the blood of infected animals evade the host immune system through antigenic variation. Existing drugs for Human and Animal African Trypanosomiasis are difficult to administer and can have serious side effects. Resistance to some drugs is also increasing, creating an urgent need for alternative trypanosomiasis therapeutics. In addition to identifying drugs that inhibit trypanosome growth, we wish to identify small molecules that can induce bloodstream form parasites to differentiate into forms adapted for the insect vector. These insect stage parasites do not vary proteins on their cell surface, making them vulnerable to the host immune system. To identify drugs that trigger differentiation of the parasite from bloodstream to insect stages, we engineered bloodstream reporter parasites that express Green Fluorescent Protein (GFP) following induction of the invariant insect-stage specific procyclin transcript. Using these bloodstream reporter strains in combination with high-throughput flow cytometry, we screened a library of 1,585 U.S. or foreign-approved drugs and identified eflornithine, spironolactone, and phenothiazine as small molecules that induce transcription of procylin. Both eflornithine and spironolactone also affect transcript levels for a subset of differentiation associated genes. We further identified 154 compounds that inhibit trypanosome growth. As all of these compounds have already undergone testing for human toxicity, they represent good candidates for repurposing as trypanosome therapeutics. Finally, this study is proof of principle that fluorescent reporters are a useful tool for small molecule or genetic screens aimed at identifying molecules or processes that initiate remodeling of the parasite surface during life cycle stage transitions. Madison Elle Walsh, Eleanor Mary Naudzius, Savanah Jessica Diaz, Theodore William Wismar, Mikhail Martchenko, Danae Schulz 2019 Biology
MAD-TN: A Tool for Measuring Fluency in Human-Robot Collaboration Fluency is an important metric in Human-Robot Interaction (HRI) that describes the coordination with which humans and robots collaborate on a task. Fluency is inherently linked to the timing of the task, making temporal constraint networks a promising way to model and measure fluency. We show that the Multi-Agent Daisy Temporal Network (MAD-TN) formulation, which expands on an existing concept of daisy-structured networks, is both an effective model of human-robot collaboration and a natural way to measure a number of existing fluency metrics. The MAD-TN model highlights new metrics that we hypothesize will strongly correlate with human teammates' perception of fluency. James C. Boerkoel Jr., Gretchen Rice, Seth Isaacson 2019 Computer Science
DREAM: An Algorithm for Mitigating the Overhead of Robust Rescheduling Generating and executing temporal plans is difficult in uncertain environments. The current state-of-the-art algorithm for probabilistic temporal networks maintains a high success rate by rescheduling frequently as uncertain events are resolved, but this approach involves substantial resource overhead due to computing and communicating new schedules between agents. Aggressive rescheduling could thus reduce overall mission duration or success in situations where agents have limited energy or computing power, and may not be feasible when communication is limited. In this paper, we propose new approaches for heuristically deciding when rescheduling is most efficacious. We propose two compatible approaches, Allowable Risk and Sufficient Change, that can be employed in combination to compromise between the computation rate, the communication rate, and success rate for new schedules. We show empirically that both approaches allow us to gracefully trade success rate for lower computation and/or communication as compared to the state-of-the-art dynamic scheduling algorithm. Jordan R. Abrahams, David A. Chu, Grace Diehl, Marina Knittel, Judy Lin, Liam Lloyd, James C. Boerkoel Jr., Jeremy Frank 2019 Computer Science
Measuring and Optimizing Durability against Scheduling Disturbances Flexibility is a useful and common metric for measuring the amount of slack in a Simple Temporal Network (STN) solution space. We extend this concept to specific schedules within an STN's solution space, developing a related notion of durability that captures an individual schedule's ability to withstand disturbances and still remain valid. We identify practical sources of scheduling disturbances that motivate the need for durable schedules, and create a geometrically-inspired empirical model that enables testing a given schedule's ability to withstand these disturbances. We develop a number of durability metrics and use these to characterize and compute specific schedules that we expect to have high durability. Using our model of disturbances, we show that our durability metrics strongly predict a schedule's resilience to practical scheduling disturbances. We also demonstrate that the schedules we identify as having high durability are up to three times more resilient to disturbances than an arbitrarily chosen schedule is. Joon Young Lee, Vivaswat Ojha, James C. Boerkoel Jr. 2019 Computer Science
'Make this adult mess make sense again': the psychic lives of gentrification's children This paper advocates for increased scholarly curiosity about the painful and hopeful psychic agency of children and youth in critiquing neoliberal urban gentrification and imagining alternative forms of city life. It performs a geographically and theoretically informed reading of American director Ira Sachs' 2016 film Little Men, a story about a brief but intense childhood friendship that is ended by an eviction. Drawing on the gentrification and psychoanalytic geography literatures, I turn to psychoanalyst D.W. Winnicott's key clinical observations regarding 'antisocial' children and youth. Bringing these tools into dialogue with Little Men, I consider the revealing differences between the film's shooting script and the final cut, as well as the film's reception. Little Men and its child protagonists, I argue, should inspire more fine-grained attention to gentrification's psychic dimensions, which both animate the process and open it to contestation. David K. Seitz 2019 Humanities, Social Sciences, and the Arts
The Bias-Expressivity Trade-off Learning algorithms need bias to generalize and perform better than random guessing. We examine the flexibility (expressivity) of biased algorithms. An expressive algorithm can adapt to changing training data, altering its outcome based on changes in its input. We measure expressivity by using an information-theoretic notion of entropy on algorithm outcome distributions, demonstrating a trade-off between bias and expressivity. To the degree an algorithm is biased is the degree to which it can outperform uniform random sampling, but is also the degree to which is becomes inflexible. We derive bounds relating bias to expressivity, proving the necessary trade-offs inherent in trying to create strongly performing yet flexible algorithms. George D. Montañez, Julius Lauw, Dominique Macias, Akshay Trikha, Julia Vendemiatti 2019 Computer Science
The Labeling Distribution Matrix (LDM): A Tool for Estimating Machine Learning Algorithm Capacity Algorithm performance in supervised learning is a combination of memorization, generalization, and luck. By estimating how much information an algorithm can memorize from a dataset, we can set a lower bound on the amount of performance due to other factors such as generalization and luck. With this goal in mind, we introduce the Labeling Distribution Matrix (LDM) as a tool for estimating the capacity of learning algorithms. The method attempts to characterize the diversity of possible outputs by an algorithm for different training datasets, using this to measure algorithm flexibility and responsiveness to data. We test the method on several supervised learning algorithms, and find that while the results are not conclusive, the LDM does allow us to gain potentially valuable insight into the prediction behavior of algorithms. We also introduce the Label Recorder as an additional tool for estimating algorithm capacity, with more promising initial results. George D. Montañez, Pedro Sandoval Segura, Julius Lauw, Daniel Bashir, Kinjal Shah, Sonia Sehra, Dominique Macias 2019 Computer Science
Synthesis of Tris-Heterocycles via a Cascade IMCR/Aza Diels-Alder + CuAAC Strategy 6-Triazolylmethyl-pyrrolo[3,4-b]pyridin-5-one tris-heterocycles were synthesized in 43–57% overall yields. The two-stage synthesis involved a cascade process (Ugi-3CR/aza Diels-Alder/N-acylation/aromatization) followed by a copper-assisted alkyne-azide [3+2] cycloaddition (CuAAC). This efficient and convergent strategy proceeded via complex terminal alkynes functionalized with a fused bis-heterocycle at the α-position. The final products are ideal candidates for SAR studies as they possess two privileged scaffolds in medicinal chemistry: 4-substituted or 1,4-substituted 1H-1,2,3-triazoles and pyrrolo[3,4-b]pyridin-5-ones. David A. Vosburg, Manuel A. Rentería-Gómez, Alejandro Islas-Jácome, Shrikant G. Pharande, Rocío Gámez-Montaño 2019 Chemistry
Aqueous Dearomatization/Diels−Alder Cascade to a Grandifloracin Precursor A green laboratory experiment has been developed in which students perform an aqueous oxidation/cycloaddition reaction to convert salicyl alcohol into a pentacyclic diepoxydione that is readily isolated by filtration. Drawing on their knowledge of periodate-mediated 1,2-diol cleavage, students propose a mechanism for the oxidation of salicyl alcohol (which is not a 1,2-diol) and the structure of the transient product (prior to a spontaneous Diels−Alder dimerization). Students then characterize salicyl alcohol and their diepoxide product by mass spectrometry, IR spectroscopy, and H, C, and twodimensional NMR spectroscopy. The only organic solvents used are small amounts for IR and NMR spectroscopy. David A. Vosburg, Emily A. Shimizu, Brett Cory, Johnson Hoang, Giovanni G. Castro, Michael E. Jung 2019 Chemistry
The effect of size-scale on the kinematics of elastic energy release Elastically-driven motion has been used as a strategy to achieve high speeds in small organisms and engineered micro-robotic devices. We examine the size-scaling relations determining the limit of elastic energy release from elastomer bands that efficiently cycle mechanical energy with minimal loss. The maximum center-of-mass velocity of the elastomer bands was found to be size-scale independent, while smaller bands demonstrated larger accelerations and shorter durations of elastic energy release. Scaling relationships determined from these measurements are consistent with the performance of small organisms and engineered devices which utilize elastic elements to power motion. Mark Ilton, S. M. Cox, Thijs Egelmeers, Gregory P. Sutton,d S. N. Patek, Alfred J. Crosby 2019 Physics
Beyond power amplification: latch-mediated spring actuation is an
emerging framework for the study of diverse elastic systems Rapid biological movements, such as the extraordinary strikes of
mantis shrimp and accelerations of jumping insects, have captivated
generations of scientists and engineers. These organisms store
energy in elastic structures (e.g. springs) and then rapidly release it
using latches, such that movement is driven by the rapid conversion
of stored elastic to kinetic energy using springs, with the dynamics of
this conversion mediated by latches. Initially drawn to these systems
by an interest in the muscle power limits of small jumping insects,
biologists established the idea of power amplification, which refers
both to a measurement technique and to a conceptual framework
defined by the mechanical power output of a system exceeding
muscle limits. However, the field of fast elastically driven movements
has expanded to encompass diverse biological and synthetic
systems that do not have muscles – such as the surface tension
catapults of fungal spores and launches of plant seeds. Furthermore,
while latches have been recognized as an essential part of many
elastic systems, their role in mediating the storage and release of
elastic energy from the spring is only now being elucidated. Here, we
critically examine the metrics and concepts of power amplification and encourage a framework centered on latch-mediated spring actuation
(LaMSA). We emphasize approaches and metrics of LaMSA systems
that will forge a pathway toward a principled, interdisciplinary field. M. Ilton, S. J. Longo, S. M. Cox, E. Azizi, J. P. Olberding, R. St Pierre, S. N. Patek 2019 Physics
Why do Large Animals Never Actuate Their Jumps with Latch-Mediated Springs? Because They can Jump Higher Without Them As animals get smaller, their ability to generate usable work from muscle contraction is decreased by the muscle's force–velocity properties, thereby reducing their effective jump height. Very small animals use a spring-actuated system, which prevents velocity effects from reducing available energy. Since force–velocity properties reduce the usable work in even larger animals, why don't larger animals use spring-actuated jumping systems as well? We will show that muscle length–tension properties limit spring-actuated systems to generating a maximum one-third of the possible work that a muscle could produce—greatly restricting the jumping height of spring-actuated jumpers. Thus a spring-actuated jumping animal has a jumping height that is one-third of the maximum possible jump height achievable were 100% of the possible muscle work available. Larger animals, which could theoretically use all of the available muscle energy, have a maximum jumping height that asymptotically approaches a value that is about three times higher than that of spring-actuated jumpers. Furthermore, a size related "crossover point" is evident for these two jumping mechanisms: animals smaller than this point can jump higher with a spring-actuated mechanism, while animals larger than this point can jump higher with a muscle-actuated mechanism. We demonstrate how this limit on energy storage is a consequence of the interaction between length–tension properties of muscles and spring stiffness. We indicate where this crossover point occurs based on modeling and then use jumping data from the literature to validate that larger jumping animals generate greater jump heights with muscle-actuated systems than spring-actuated systems. Gregory P Sutton, Elizabeth Mendoza, Emanuel Azizi, Sarah J Longo, Jeffrey P Olberding, Mark Ilton, Sheila N Patek 2019 Physics
The Long and Short of Benford's Law N/A Arthur. T Benjamin 2019 Mathematics
Unified Tiling Proofs of a Family of Fibonacci Identities In a recent work, Baxter and Pudwell mentioned the following identity for the Fibonacci numbers Fn and noted that it can be proven via induction: For all n ≥ 1, F2n = 1 · F2n−2 + 2 · F2n−4 + · · · + (n − 1) · F2 + n. We give a combinatorial proof of this identity and a companion identity. This leads to an infinite family of identities, which are also given combinatorial proofs. Arthur. T Benjamin, Joshua Crouch, James A. Sellers 2019 Mathematics
Hunting rabbits on the hypercube We explore the Hunters and Rabbits game on the hypercube. In the process, we find the solution for all classes of graphs with an isoperimetric nesting property and find the exact hunter number of 𝑄𝑛 to be 1+∑𝑛−2𝑖=0(𝑖⌊𝑖/2⌋). In addition, we extend results to the situation where we allow the rabbit to not move between shots. Jessalyn Bolkema, Corbin Groothuis 2019 Mathematics
Waring's problem in finite rings In this paper we obtain explicit results for Waring's problem over general finite rings, especially matrix rings over finite fields by building on analogous results over finite fields. Commutative algebra, in particular the Jacobson radical and nilpotent ideals, plays an important role in our proofs. Yeşim Demiroğlu Karabulut 2019 Mathematics
Expanding phenomena over matrix rings In this paper, we study expanding phenomena in the setting of matrix rings. More precisely, we will prove that • If A is a set of M2(Fq) and |A| ≫ q 7/2 , then we have |A(A + A)|, |A + AA| ≫ q 4 . • If A is a set of SL2(Fq) and |A| ≫ q 5/2 , then we have |A(A + A)|, |A + AA| ≫ q 4 . We also obtain similar results for the cases of A(B + C) and A + BC, where A, B, C are sets in M2(Fq). Yeşim Demiroğlu Karabulut, Doowon Koh, Thang Pham, Chun-Yen Shen, Le Anh Vinh 2019 Mathematics
Cayley Digraphs Associated to Arithmetic Groups We explore a paradigm which ties together seemingly disparate areas in number theory, additive combinatorics, and geometric combinatorics including the classical Waring problem, the Furstenberg–Sárközy theorem on squares in sets of integers with positive density, and the study of triangles (also called 2-simplices) in finite fields. Among other results we show that if 𝔽𝑞 is the finite field of odd order q, then every matrix in 𝑀𝑎𝑡𝑑(𝔽𝑞),𝑑≥2 is the sum of a certain (finite) number of orthogonal matrices, this number depending only on d, the size of the matrix, and on whether q is congruent to 1 or 3 (mod 4), but independent of q otherwise. Yeşim Demiroğlu Karabulut, David Covert, Jonathan Pakianathan 2019 Mathematics
Chow Rings of Heavy/Light Hassett Spaces via Tropical Geometry We compute the Chow ring of an arbitrary heavy/light Hassett space M¯0,w. These spaces are moduli spaces of weighted pointed stable rational curves, where the associated weight vector w consists of only heavy and light weights. Work of Cavalieri et al. exhibits these spaces as tropical compactifications of hyperplane arrangement complements. The computation of the Chow ring then reduces to intersection theory on the toric variety of the Bergman fan of a graphic matroid. Keel has calculated the Chow ring A∗(M¯0,n) of the moduli space M¯0,n of stable nodal n-marked rational curves; his presentation is in terms of divisor classes of stable trees of ℙ1's having one nodal singularity. Our presentation of the ideal of relations for the Chow ring A∗(M¯0,w) is analogous. We show that pulling back under Hassett's birational reduction morphism ρw:M¯0,n→M¯0,w identifies the Chow ring A∗(M¯0,w) with the subring of A∗(M¯0,n) generated by divisors of w-stable trees, which are those trees which remain stable in M¯0,w. Siddarth Kannan, Dagan Karp, Shiyue Li 2019 Mathematics
Advection and Autocatalysis as Organizing Principles for Banded Vegetation Patterns We motivate and analyze a simple model for the formation of banded vegetation patterns. The model incorporates a minimal number of ingredients for vegetation growth in semiarid landscapes. It allows for comprehensive analysis and sheds new light onto phenomena such as the migration of vegetation bands and the interplay between their upper and lower edges. The key ingredient is the formulation as a closed reaction–diffusion system, thus introducing a conservation law that both allows for analysis and provides ready intuition and understanding through analogies with characteristic speeds of propagation and shock waves. Jasper Weinburd, Richard Samuelson, Zachary Singer, Arnd Scheel 2019 Mathematics
A next generation approach to species delimitation reveals the role of hybridization in a cryptic species complex of corals Our ability to investigate processes shaping the evolutionary diversification of corals (Cnidaria: Anthozoa) is limited by a lack of understanding of species boundaries. Discerning species of corals has been challenging due to a multitude of factors, including homoplasious and plastic morphological characters and the use of molecular markers that are either not informative or have not completely sorted. Hybridization can also blur species boundaries by leading to incongruence between morphology and genetics. We used traditional DNA barcoding and restriction-site associated DNA sequencing combined with coalescence-based and allele-frequency methods to elucidate species boundaries and simultaneously examine the potential role of hybridization in a speciose genus of octocoral, Sinularia. Results: Species delimitations using two widely used DNA barcode markers, mtMutS and 28S rDNA, were incongruent with one another and with the morphospecies identifications. When mtMutS and 28S were concatenated, a 0.3% genetic distance threshold delimited the majority of morphospecies. In contrast, 12 of the 15 examined morphospecies formed well-supported monophyletic clades in both concatenated RAxML phylogenies and SNAPP species trees of > 6000 RADSeq loci. DAPC and Structure analyses also supported morphospecies assignments, but indicated the potential for two additional cryptic species. Three morphologically distinct species pairs could not, however, be distinguished genetically. ABBA-BABA tests demonstrated significant admixture between some of those species, suggesting that hybridization may confound species delimitation in Sinularia. Conclusions: A genomic approach can help to guide species delimitation while simultaneously elucidating the processes generating coral diversity. Results support the hypothesis that hybridization is an important mechanism in the evolution of Anthozoa, including octocorals, and future research should examine the contribution of this mechanism in generating diversity across the coral tree of life. Andrea M. Quattrini, Tiana Wu, Keryea Soong, Ming-Shiou Jeng, Yehuda Benayahu, Catherine S. McFadden 2019 Biology
Relating Level of Inquiry in Laboratory Instructions to Student Learning Outcomes This research paper will describe the results of an experiment in which the level of inquiry in a laboratory manual is varied from guided inquiry to open inquiry by reducing the specificity of the instructions in the lab manual. The hypothesis is that less specific instructions will cause students to reflect on their actions in lab and, as a result, circle further around Kolb's experiential learning cycle during each step of the lab. This should result in improved recall and better integration of laboratory and classroom understanding. Student learning outcomes are assessed using an in-lab, direct assessment which evaluates both students' laboratory skills and their ability to relate experiences in the laboratory to classroom learning. Student attitudes are also assessed with surveys. Spencer Rosen, Sabrine Griifith, Eli Byrnes, Steven Michael Santana, Dr. Laura Palucki Blake, Matthew Spencer 2019 Engineering
A mathematical model for DC vaccine treatment of type I diabetes Mathematical modeling of Type I Diabetes (T1D) is a new path in my research journey, and was initiated through a discussion with folks from a startup biotech company developing treatments for skin grafting and T1D. There is currently no cure for T1D. In this paper we develop a new mathematical model of onset and progression of Type I Diabetes (T1D), and explore the potential use of dendritic cell immune-modulating therapy to manage the disease. Our analysis and computational simulations indicate that there are immune-state related windows of opportunity in which treatment intervention is more likely to be beneficial in protecting an individual from entering a diabetic state. Lisette De Pillis, Blerta Shtylla, Marissa Gee, An Do, Shahrokh Shabahang, Leif Eldevik 2019 Mathematics
Canvass: A Crowd-Sourced, Natural-Product Screening Library for Exploring Biological Space
Natural products and their derivatives continue to be wellsprings of nascent therapeutic potential. However, many laboratories have limited resources for biological evaluation, leaving their previously isolated or synthesized compounds largely or completely untested. To address this issue, the Canvass library of natural products was assembled, in collaboration with academic and industry researchers, for quantitative high-throughput screening (qHTS) across a diverse set of cell-based and biochemical assays. Characterization of the library in terms of physicochemical properties, structural diversity, and similarity to compounds in publicly available libraries indicates that the Canvass library contains many structural elements in common with approved drugs. The assay data generated were analyzed using a variety of quality control metrics, and the resultant assay profiles were explored using statistical methods, such as clustering and compound promiscuity analyses. Individual compounds were then sorted by structural class and activity profiles. Differential behavior based on these classifications, as well as noteworthy activities, are outlined herein. One such highlight is the activity of (−)-2(S)-cathafoline, which was found to stabilize calcium levels in the endoplasmic reticulum. The workflow described here illustrates a pilot effort to broadly survey the biological potential of natural products by utilizing the power of automation and high-throughput screening. S. E. Kearney, G. Zahoránszky-Kőhalmi, K. R. Brimacombe, M. J. Henderson, C. Lynch, T. Zhao, K. K. Wan, Z. Itkin, C. Dillon, M. Shen, D. M. Cheff, T. D. Lee, D. Bougie, K. Cheng, N. P. Coussens, D. Dorjsuren, R. T. Eastman, R. Huang, M. J. Iannotti, S. Karavadhi, C. Klumpp-Thomas, J. S. Roth, S. Sakamuru, W. Sun, S. A. Titus, A. Yasgar, Y. Zhang, J. Zhao, R. B. Andrade, M. Kevin Brown, N. Z. Burns, J. K. Cha, E. E. Mevers, J. Clardy, J. A. Clement, P. A. Crooks, G. D. Cuny, J. Ganor, J. Moreno, L. A. Morrill, E. Picazo, R. B. Susick, N. K. Garg, B. C. Goess, R. B. Grossman, C. C. Hughes, J. N. Johnston, M. M. Joullie, A. Douglas Kinghorn, D. G.I. Kingston, M. J. Krische, O. Kwon, T. J. Maimone, S. Majumdar, K. N. Maloney, E. Mohamed, B. T. Murphy, P. Nagorny, D. E. Olson, L. E. Overman, L. E. Brown, J. K. Snyder, J. A. Porco Jr., F. Rivas, S. A. Ross, R. Sarpong, I. Sharma, J. T. Shaw, Z. Xu, B. Shen, W. Shi, C. R.J. Stephenson, A. L. Verano, D. S. Tan, Y. Tang, R. E. Taylor, R. J. Thompson, D. A. Vosburg, J. Wu, W. M. Wuest, A. Zakarian, Y. Zhang, T. Ren, Z. Zuo, J. Inglese, S. Michael, Anton Simeonov, W. Zheng, P. Shinn, A. Jadhav, M. B. Boxer, M. D. Hall, M. Xia, R. Guha, J. M. Rohde 2018 Chemistry
Divergent Diels–Alder Reactions in the Biosynthesis and Synthesis of Endiandric-Type Tetracycles: A Computational Study Endiandric acids and related polyketide natural products arise from polyene precursors and occur naturally as fused and bridged tetracycles. In some cases, the intramolecular Diels–Alder reactions that produce fused and bridged tetracycles result from a diene tether that may act as either a 4π or 2π component in the cycloaddition. To examine the preference for fused or bridged products, we applied density functional theory (using the M06-2X and B3LYP functionals) to reactants with various substituents for both fused and bridged transition states. Fused products were generally preferred except when disfavored by extreme steric hindrance (e.g., a tert-butyl group). These computational results are consistent with experimental data and suggest the existence of as-yet undiscovered natural products. David A. Vosburg, Kareesa J. Kron, Mikaela KosichRobert J. Cave 2018 Chemistry
An Information-Theoretic Perspective on Overfitting and Underfitting Daniel Bashir '20, Sonia Sehra '20, Julius Lauw '20, Pedro Sandoval Segura '19, Dominique Macias '19 2020 Computer Science
A Castro Consensus: Understanding the Role of Dependence in Consensus Formation Jarred Allen '22, Cindy Lay CMC '22, George D. Montañez 2020 Computer Science
Enhanced mechanical properties of epoxy‐matrix nanocomposites reinforced with graphene synthesized in atmospheric plasmas Graphene can be synthesized in the gas phase using atmospheric plasmas. Gas‐phase‐synthesized graphene (GSG) possesses features that make it a promising filler material for enhancing the properties of polymers. In this study, epoxy‐matrix nanocomposites reinforced with GSG were investigated. Mixing GSG with epoxy showed that the nanomaterial effectively disperses and resists aggregation in polymer resins. Significant increases in both strength and strain at break were revealed through the tensile testing of GSG‐filled nanocomposites. In contrast, nanocomposites containing graphene nanoplatelets exhibited enhanced strength but diminished strain at break. Imaging of nanocomposite fracture surfaces by scanning electron microscopy indicated considerable matrix reinforcement by GSG. These results show that unique strengthening mechanisms exist in polymers reinforced with graphene synthesized in atmospheric plasmas. Kevin Nakahara, Jacob Knego, Taylor Sloop, Chance Bisquera, Nicole Subler, Albert Dato 2020 Engineering
Determining the dielectric constant of injection-molded polymer-matrix nanocomposites filled with barium titanate Barium titanate (BTO) is a ferroelectric perovskite with potential in energy storage applications. Previous research suggests that BTO dielectric constant increases as nanoparticle diameter decreases. This report recounts an investigation of this relationship. Injection-molded nanocomposites of 5 vol% BTO nanoparticles incorporated in a low-density polyethylene matrix were fabricated and measured. Finite-element analysis was used to model nanocomposites of all BTO sizes and the results were compared with experimental data. Both indicated a negligible relationship between BTO diameter and dielectric constant at 5 vol%. However, a path for fabricating and testing composites of 30 vol% and higher is presented here. Daniel Brito, Guadalupe Quirarte, Joshua Morgan, Eleanor Rackoff, Michael Fernandez, Dithi Ganjam, Albert Dato, and Todd C. Monson 2020 Engineering
Enhanced lubricating properties of oils containing graphene synthesized in atmospheric plasmas The use of gas-phase-synthesized graphene (GSG) as a lubricant additive that is capable of significantly enhancing the tribological properties of widely used oils is reported herein. GSG is pure, highly ordered, and exhibits an inherently crumpled morphology that causes the nanomaterial to self-disperse and resist aggregation in base oils and fully formulated lubricants. Micro-tribometer tests revealed that the wear of sliding surfaces was significantly reduced by up to 53% when relatively minute amounts of GSG (≤ 0.1 wt%) was added to canola oil, polyalphaolefin (PAO), fully-formulated petroleum oil, and fully-formulated full synthetic oil. Additionally, the wear reduction of surfaces caused by GSG remained consistent as the concentration of the nanomaterial was reduced in PAO, which indicates that GSG concentrations below 0.025 wt% in base oil could achieve similar reductions in wear. A controllable GSG segregation phenomenon in PAO is reported, which has the potential to enable the controlled wear of sliding surfaces and the recycling of GSG additives. GSG is produced in a single step through an environmentally friendly atmospheric plasma process. Our results demonstrate that GSG holds promise as a sustainable and effective anti-wear additive for lubricants used in engines and other tribological applications. Gordon Krauss, Albert Dato, Matthew Siniawski 2020 Engineering
Quantifying controllability in temporal networks with uncertainty Controllability for Simple Temporal Networks with Uncertainty (STNUs) has thus far been limited to three levels: strong, dynamic, and weak. Because of this, there is currently no systematic way for an agent to assess just how far from being controllable an uncontrollable STNU is. We provide new insights inspired by a geometric interpretation of STNUs to introduce the degrees of strong and dynamic controllability — continuous metrics that measure how far a network is from being controllable. We utilize these metrics to approximate the probabilities that an STNU can be dispatched successfully offline and online respectively. We introduce new methods for predicting the degrees of strong and dynamic controllability for uncontrollable networks. We further generalize these metrics by defining likelihood of controllability, a controllability measure that applies to Probabilistic Simple Temporal Networks (PSTNs). Finally, we empirically demonstrate that these metrics are good predictors of actual dispatch success rate for STNUs and PSTNs. Shyan Akmal, Savana Ammons, Hemeng Li, Michael Gao, Lindsay Popowski, James C. Boerkoel Jr. 2020 CS
Dynamic Control of Probabilistic Simple Temporal Networks The controllability of a temporal network is defined as an agent's ability to navigate around the uncertainty in its schedule and is well-studied for certain networks of temporal constraints. However, many interesting real-world problems can be better represented as Probabilistic Simple Temporal Networks (PSTNs) in which the uncertain durations are represented using potentially-unbounded probability density functions. This can make it inherently impossible to control for all eventualities. In this paper, we propose two new dynamic controllability algorithms that attempt to maximize the likelihood of successfully executing a schedule within a PSTN. The first approach, which we call Min-Loss DC, finds a dynamic scheduling strategy that minimizes loss of control by using a conflict-directed search to decide where to sacrifice the control in a way that optimizes overall success. The second approach, which we call Max-Gain DC, works in the other direction: it finds a dynamically controllable schedule and then attempts to progressively strengthen it by capturing additional uncertainty. Our approaches are the first known that work by finding maximally dynamically controllable schedules. We empirically compare our approaches against two existing PSTN offline dispatch approaches and one online approach and show that our Min-Loss DC algorithm outperforms the others in terms of maximizing execution success while maintaining competitive runtimes. Michael Gao, Lindsay Popowski, James Boerkoel 2020 CS
Reconciliation Reconsidered: In Search of a Most Representative Reconciliation in the Duplication-Transfer-Loss Model Maximum parsimony reconciliation is a fundamental technique for studying the evolutionary histories of pairs of entities such as genes and species, parasites and hosts, and species and their biogeographical habitats. In these contexts, reconciliation is generally performed using the duplication-transfer-loss (DTL) model in a maximum parsimony framework. While efficient maximum parsimony reconciliation algorithms are known for the DTL model, the number of such reconciliations can grow exponentially with the sizes of the two phylogenetic trees. Choosing a maximum parsimony reconciliation arbitrarily may lead to conclusions that are not supported, and even contradicted, by other equally optimal reconciliations. This paper addresses the fundamental problem of how well a single reconciliation can represent the entire space of optimal reconciliations. M. Grueter, K. Duran, R. Ramalingam, R. Libeskind-Hadas 2019 CS
Hierarchical Clustering of Maximum Parsimony Reconciliations Maximum parsimony reconciliation in the duplication-transfer-loss model is a widely-used method for analyzing the evolutionary histories of pairs of entities such as hosts and parasites, symbiont species, and species and genes. While efficient algorithms are known for finding maximum parsimony reconciliations, the number of such reconciliations can be exponential in the size of the trees. Since these reconciliations can differ substantially from one another, making inferences from any one reconciliation may lead to conclusions that are not supported, or may even be contradicted, by other maximum parsimony reconciliations. Therefore, there is a need to find small sets of best representative reconciliations when the space of solutions is large and diverse. R. Mawhorther and R. Libeskind-Hadas 2019 CS
Multiple Optimal Reconciliations under the Duplication-Loss-Coalescence Model Gene trees can differ from species trees due to a variety of biological phenomena, the most prevalent being gene duplication, horizontal gene transfer, gene loss, and coalescence. To explain topological incongruence between the two trees, researchers apply reconciliation methods, often relying on a maximum parsimony framework. However, while several studies have investigated the space of maximum parsimony reconciliations (MPRs) under the duplication-loss and duplication-transfer-loss models, the space of MPRs under the duplication-loss-coalescence (DLC) model remains poorly understood. To address this problem, we present new algorithms for computing the size of MPR space under the DLC model and sampling from this space uniformly at random. Our algorithms are efficient in practice, with runtime polynomial in the size of the species and gene tree when the number of genes that map to any given species is fixed, thus proving that the MPR problem is fixed-parameter tractable. We have applied our methods to a biological data set of 16 fungal species to provide the first key insights in the space of MPRs under the DLC model. Our results show that a plurality reconciliation, and underlying events, are likely to be representative of MPR space. H. Du, Y. S. Ong, M. Knittel, R. Mawhorter, N. Liu, G. Gross, R. Tojo, R. Libeskind-Hadas; Y-C. Wu
Inferring Pareto-Optimal Reconciliations across Multiple Event Costs under the Duplication-Loss-Coalescence Model, Reconciliation methods are widely used to explain incongruence between a gene tree and species tree. However, the common approach of inferring maximum parsimony reconciliations (MPRs) relies on user-defined costs for each type of event, which can be difficult to estimate. Prior work has explored the relationship between event costs and maximum parsimony reconciliations in the duplication-loss and duplication-transfer-loss models, but no studies have addressed this relationship in the more complicated duplication-loss-coalescence model. R. Mawhorter, N. Liu, R. Libeskind-Hadas, Y-C. Wu 2019 CS
Efficient Exact Algorithm for Computing All Pairwise Distances between Reconciliations in the Duplication-Transfer-Loss Model, Maximum parsimony reconciliation in the duplication-transfer-loss model is widely used in studying the evolutionary histories of genes and species and in studying coevolution of parasites and their hosts and pairs of symbionts. While efficient algorithms are known for finding maximum parsimony reconciliations, the number of reconciliations can grow exponentially in the size of the trees. An understanding of the space of maximum parsimony reconciliations is necessary to determine whether a single reconciliation can adequately represent the space or whether multiple representative reconciliations are needed. S. Santichaivekin, R. Mawhorter, R. Libeskind-Hadas 2019 CS
eMPRess: A Systematic Cophylogeny Reconciliation Tool We describe eMPRess, a software program for phylogenetic tree reconciliation under the duplication-transfer-loss model that systematically addresses the problems of choosing event costs and selecting representative solutions, enabling users to make more robust inferences S. Santichaivekin, Q. Yang, J. Liu, R. Mawhorter, J.Jiang, T. Wesley, Y-C. Wu, R. Libeskind-Hadas 2020 CS
An Integer Linear Programming Solution for the Most Parsimonious Reconciliation Problem under the Duplication-Loss-Coalescence Model Given a gene tree, a species tree, and an association between their leaves, the maximum parsimony reconciliation (MPR) problem seeks to find a mapping of the gene tree to the species tree that explains their incongruity using a biological model of evolutionary events. Unfortunately, when simultaneously accounting for gene duplication, gene loss, and coalescence, the MPR problem is NP-hard. While an exact algorithm exists, it can be problematic to use in practice due to time and memory requirements. In this work, we present an integer linear programming (ILP) formulation for solving the MPR problem when considering duplications, losses, and coalescence. Our experimental results on a simulated data set of 12 Drosophila species shows that our new algorithm is both accurate and scalable. Furthermore, in contrast to the existing exact algorithm, our formulation allows users to limit the maximum runtime and thus trade-off accuracy and scalability, making it an attractive choice for phylogenetic pipelines. M. Carothers, J. Gardi, G. Gross, T. Kuze, N. Liu, F. Plunkett, J. Qian, Y-C. Wu 2020 CS
Catalytic intramolecular hydroamination of aminoallenes using titanium complexes of chiral, tridentate, dianionic imine-diol ligands Alkylation of d- or l-phenylalanine or valine alkyl esters was carried out using methyl or phenyl Grignard reagents. Subsequent condensation with salicylaldehyde, 3,5-di-tert-butylsalicylaldehyde, or 5-fluorosalicylaldehyde formed tridentate, X2L type, Schiff base ligands. Chiral shift NMR confirmed retention of stereochemistry during synthesis. X-ray crystal structures of four of the ligands show either inter- or intramolecular hydrogen bonding interactions. The ligands coordinate to the titanium reagents Ti(NMe2)4 or TiCl(NMe2)3 by protonolysis and displacement of two equivalents of HNMe2. The crystal structure of one example of Ti(X2L)Cl(NMe2) was determined and the complex has a distorted square pyramidal geometry with an axial NMe2 ligand. The bis-dimethylamide complexes are active catalysts for the ring closing hydroamination of di- and trisubstituted aminoallenes. The reaction of hepta-4,5-dienylamine at 135 °C with 5 mol% catalyst gives a mixture of 6-ethyl-2,3,4,5-tetrahydropyridine (40-72%) and both Z- and E-2-propenyl-pyrrolidine (25-52%). The ring closing reaction of 6-methyl-hepta-4,5-dienylamine at 135 °C with 5 mol% catalyst gives exclusively 2-(2-methyl-propenyl)-pyrrolidine. The pyrrolidine products are obtained with enantiomeric excesses up to 17%. Fanrui Sha, Benjamin S. Mitchell, Chris Z. Ye, Chase S. Abelson, Eric W. Reinheimer, Pierre LeMagueres, Joseph D. Ferrara, Michael K. Takase, Adam R. Johnson 2019 Chemistry
Emphasizing Learning: The Impact of Student Surveys in the Reform of an Introductory Chemistry Course. This article discusses how a chemistry department paired the redesign of a required introductory-level chemistry sequence with assessment that privileged the understanding of how the course was functioning for students. The authors describe the development of this assessment and how results have been used to monitor student experience throughout the semester, inform teaching and curricular reform, reinforce course content for students, and engage students actively in reflecting on their own learning. Results suggest the assessment pro- vided valuable insight into teaching strategies and techniques that improve student experience and engagement as well as future program and course cur- ricula. This redesign serves as a case study showing how just-in-time formative assessment data can be collected in a relatively facile way and how resulting evidence can be used to inform efforts that improve the student experience in a course. Keywords: just-in-time formative assessment, pedagogy, curricular reform, chemistry, STEM education Van Heuvelen, K. M.; Blake, L. P.; Daub, G. W.; Hawkins, L. N.; Johnson, A. R.; Van Ryswyk, H.; Vosburg, D. A. 2019 Chemistry
einvigorating general chemistry by emphasizing connections between chemistry and society Insights and methods from the chemical sciences are directly relevant to global challenges such as climate change, renewable energy generation and storage, water purification, and food production. However, these connections are often opaque to students in general chemistry courses, who may get lost in the weeds of stoichiometry, VSEPR, and gas laws, and fail to see the relevance of their studies to their lives and their communities. Herein we describe a redesigned first-year undergraduate chemistry course that grounds chemical content in relevant societal applications. Students engage in collaborative, inquiry-based learning through an adapted POGIL methodology, and the highly structured class activities help students learn soft skills that enable success in higher education. Significant course revisions sometimes face resistance from key stakeholders, including students, faculty, and administration. We offer a case study in framing broader disciplinary concerns through the lens of institutional values to increase buy-in among key stakeholders Van Heuvelen, K. M., Daub, G. W., Hawkins, L. N., Johnson, A. R., Van Ryswyk, H., Vosburg, D. A 2020 Chemistry
A Community Springs to Action to Enable Virtual Laboratory Instruction. The COVID-19 pandemic put an abrupt end to face-to-face teaching at many colleges and universities. While numerous methods for synchronous and asynchronous teaching in lecture courses were quickly deployed, laboratory instruction presented a unique set of challenges. To develop online labs quickly would be a daunting task for an individual. However, contributions of many individuals could ease and hasten the transition to using virtual labs. The IONiC-VIPEr community of practice is one such community that sprung to action to provide virtual alternatives for inorganic chemistry laboratory instruction. Nataro, C. and Johnson, A. R. 2020 Chemistry
Catalytic intramolecular hydroamination of aminoallenes using titanium and tantalum complexes of sterically encumbered chiral sulfonamides Sha, F.; Shimizu, E. A.; Slocumb, H. S.; Towell, S. E.; Zhen, Y.; Porter, H. Z.; Takase, M.; Johnson, A. R. 2020 Chemistry
Teaching Molecular Orbital Theory Better. This chapter begins by discussing the teaching of symmetry and molecular orbital (MO) theory, and describing how the ideas and materials developed by Adam R. Johnson (AJ) transformed the class of Chip Nataro (CN). The chapter continues by illustrating methods for teaching beginning students MO theory for polyatomic main group compounds and transition-metal complexes. The procedure we describe is aimed at inorganic chemistry educators who want to improve their teaching of MO theory in the foundation level inorganic chemistry curriculum. The authors are located on opposite coasts of the United States, and thus the shared materials on the Virtual Inorganic Pedagogical Electronic Resource played a critical role in this story. The Interactive Online Network of Inorganic Chemists develops teaching materials based on the primary literature and shares knowledge with other instructors through the Virtual Inorganic Pedagogical Electronic Resource. This website is built on a philosophy of visible teaching, which calls for instructors to not only develop materials for their classes, but also to share them for implementation in other classrooms. This exchange has not been unidirectional, and our methods for teaching MO theory have continued to evolve through our collaboration. Johnson, A. R. and Nataro, C. 2020 Chemistry
Investing in Cycling Infrastructure Can Promote Social Justice While Tackling Climate Change Over a third of US passenger vehicle trips are less than 3 miles, suggesting there is significant potential for increasing cycling's share of transportation. Beyond the benefits for the global climate, investment in bicycle transportation infrastructure benefits social groups whose mobility needs are inadequately served by car-dominated transportation systems. This includes people who cannot afford a car; those whose age or ability prevents them from driving, most notably children and the elderly; and communities that lack opportunities for physical recreation. Many of these constituencies are underrepresented in local planning processes, giving rise to the term "invisible cyclists." Investing in active transportation while strengthening local democracy may offer the robust response required by an issue affecting so many over such long-time horizons. Steinberg, Paul F. 2019 HSA
Redefining the H-NS Protein Family: A Diversity of Specialized Core and Accessory Forms Exhibit Hierarchical Transcriptional Network Integration. H-NS is a nucleoid structuring protein and global repressor of virulence and horizontally-acquired genes in bacteria. H-NS can interact with itself or with homologous proteins, but protein family diversity and regulatory network overlap remain poorly defined. Here, we present a comprehensive phylogenetic analysis that revealed deep-branching clades, dispelling the presumption that H-NS is the progenitor of varied molecular backups. Each clade is composed exclusively of either chromosome-encoded or plasmid-encoded proteins. On chromosomes, stpA and newly discovered hlpP are core genes in specific genera, whereas hfp and newly discovered hlpC are sporadically distributed. Six clades of H-NS plasmid proteins (Hpp) exhibit ancient and dedicated associations with plasmids, including three clades with fidelity for plasmid incompatibility groups H, F or X. A proliferation of H-NS homologs in Erwiniaceae includes the first observation of potentially co-dependent H-NS forms. Conversely, the observed diversification of oligomerization domains may facilitate stable co-existence of divergent homologs in a genome. Transcriptomic and proteomic analysis in Salmonella revealed regulatory crosstalk and hierarchical control of H-NS homologs. We also discovered that H-NS is both a repressor and activator of Salmonella Pathogenicity Island 1 gene expression, and both regulatory modes are restored by Sfh (HppH) in the absence of H-NS. Fitzgerald, Stephen, Stefani C. Kary, Ebtihal Y. Alshabib, Keith D. MacKenzie, Daniel M. Stoebel, Tzu-Chiao Chao, and Andrew D. S. Cameron. " 2020 Biology
History in the Education of Scientists: Encouraging Judgment and Social Action The authors of this essay reflect on the experience of co-teaching a course on the history of genetics and race. The collaboration has pushed them both—a historian of science and a biologist—to consider how to make space for moral and scientific judgment in a history classroom. Drawing on examples from the course, they argue that it is possible to encourage social action and thoughtful critiques of past and current science without succumbing to a whiggish narrative of progress. Viven Hamilton and Daniel Stoebel 2020 HSA & Biology
Interplay of structure and charge order revealed by quantum oscillations in thin films of Pr2CuO4±δ The discovery of quantum oscillations in hole- and electron-doped cuprate families has underscored the importance of the Fermi surface in cuprate superconductivity. While the observed quantum oscillations in both families have revealed the presence of reconstructed Fermi surfaces, there remains an important distinction between the two. In hole-doped cuprates the oscillations are thought to arise from the effects of a charge density wave, while in the electron-doped cuprates it is thought that these oscillations occur from an antiferromagnetically reconstructed Fermi surface, despite the fact that the oscillations are observed in overdoped compounds, far from the putative antiferromagnetic critical point. In this work we study thin films of Pr2CuO4±δ, whose apparent doping can be finely tuned by annealing, allowing studies of quantum oscillations in samples straddling the critical point. We show that even though there is a mass enhancement of the quasiparticles, there are only small changes to the Fermi surface itself, suggesting that charge order is a more likely origin, with electronic correlations that are strongly dependent on the structural parameters. Nicholas P. Breznay, Ian M. Hayes, Nityan L. Nair, Toni Helm, James G. Analytis, Ross D. McDonald, Zengwei Zhu, Yoshiharu Krockenberger, Hiroshi Irie, Hideki Yamamoto, K. A. Modic, Alex Frano, Padraic Shafer, and Elke Arenholz 2019 Physics
High-temperature magnetic anomaly in the Kitaev hyperhoneycomb compound β−Li2IrO3 We report the existence of a high-temperature magnetic anomaly in the three-dimensional Kitaev candidate material, β− Li 2 IrO 3. Signatures of the anomaly appear in magnetization, heat capacity, and muon spin relaxation measurements. The onset coincides with a reordering of the principal axes of magnetization, which is thought to be connected to the onset of Kitaev-like correlations in the system. The anomaly also shows magnetic hysteresis with a spatially anisotropic magnitude that follows the spin-anisotropic exchange anisotropy of the underlying Kitaev Hamiltonian. We discuss possible scenarios for a bulk and impurity origin. Alejandro Ruiz, Vikram Nagarajan, Mayia Vranas, Gilbert Lopez, Gregory T McCandless, Itamar Kimchi, Julia Y Chan, Nicholas P Breznay, Alex Frañó, Benjamin A Frandsen, James G Analytis 2020 Physics
Competition between magnetic order and charge localization in Na2IrO3 thin crystal devices Spin orbit assisted Mott insulators such as sodium iridate (Na2IrO3) have been an important subject of study in recent years. In these materials, the interplay of electronic correlations, spin-orbit coupling, crystal field effects, and a honeycomb arrangement of ions bring exciting ground states, predicted in the frame of the Kitaev model. The insulating character of Na2IrO3 has hampered its integration to an electronic device, desirable for applications, such as the manipulation of quasiparticles interesting for topological quantum computing. Here we show through electronic transport measurements supported by angle-resolved photoemission spectroscopy (ARPES) experiments, that electronic transport in Na2IrO3 is ruled by variable range hopping and it is strongly dependent on the magnetic ordering transition known for bulk Na2IrO3, as well as on external electric fields. Electronic transport measurements allow us to deduce a value for the localization length and the density of states in our Na2IrO3 thin crystal devices, and offer an alternative approach to study insulating 2D-materials. Josue Rodriguez, Gilbert Lopez, Francisco Ramirez, Nicholas P Breznay, Robert Kealhofer, Vikram Nagarajan, Drew Latzke, Samantha Wilson, Naomy Marrufo, Peter Santiago, Jared Lara, Amirari Diego, Everardo Molina, David Rosser, Hadi Tavassol, Alessandra Lanzara, James G Analytis, Claudia Ojeda-Aristizabal 2020 Physics
Persistence of spin memory in a crystalline, insulating phase-change material The description of disorder-induced electron localization by Anderson over 60 years ago began a quest for novel phenomena emerging from electronic interactions in the presence of disorder. Even today, the interplay of interactions and disorder remains incompletely understood. This holds in particular for strongly disordered materials where charge transport depends on 'hopping' between localized sites. Here we report an unexpected spin sensitivity of the electrical conductivity at the transition from diffusive to hopping conduction in a material that combines strong spin-orbit coupling and weak inter-electronic interactions. In thin films of the disordered crystalline phase change material SnSb2Te4, a distinct change in electrical conductance with applied magnetic field is observed at low temperatures. This magnetoconductance changes sign and becomes anisotropic at the disorder-driven crossover from strongly localized (hopping) to weakly localized (diffusive) electron motion. The positive and isotropic magnetoconductance arises from disruption of spin correlations that inhibit hopping transport. This experimental observation of a recently hypothesized 'spin memory' demonstrates the spin plays a previously overlooked role in the disorder-driven transition between weak and strong localization in materials with strong spin–orbit interactions. Johannes Reindl, Hanno Volker, Nicholas P. Breznay & Matthias Wuttig 2019 Physics
Profit: Detecting and Quantifying Side Channels in Networked Applications. We present a black-box, dynamic technique to detect and quantify side-channel information leaks in networked applications that communicate through a TLS-encrypted stream. Given a user-supplied profiling-input suite in which some aspect of the inputs is marked as secret, we run the application over the inputs and capture a collection of variable-length network packet traces. The captured traces give rise to a vast side-channel feature space, including the size and timestamp of each individual packet as well as their aggregations (such as total time, median size, etc.) over every possible subset of packets. Finding the features that leak the most information is a difficult problem.
Our approach addresses this problem in three steps: 1) Global analysis of traces for their alignment and identification of emph{phases} across traces; 2) Feature extraction using the identified phases; 3) Information leakage quantification and ranking of features via estimation of probability distribution.
We embody this approach in a tool called Profit and experimentally evaluate it on a benchmark of applications from the DARPA STAC program, which were developed to assess the effectiveness of side-channel analysis techniques. Our experimental results demonstrate that, given suitable profiling-input suites, Profit is successful in automatically detecting information-leaking features in applications, and correctly ordering the strength of the leakage for differently-leaking variants of the same application. Nicolás Rosner, Ismet Burak Kadron, Lucas Bang, Tevfik Bultan 2019 CS
Incremental Attack Synthesis Information leakage is a signi cant problem in modern software systems. Information leaks due to side channels are especially hard to detect and analyze. In recent years, techniques have been developed for automated synthesis of adaptive side-channel attacks that recover secret values by iteratively generating inputs to reveal partial information about the secret based on the sidechannel observations. Prominent approaches of attack synthesis use symbolic execution, model counting, and meta-heuristics to maximize information gain. These approaches could bene t by reusing results from prior steps in each step. In this paper, we present an incremental approach to attack synthesis that reuses model counting results from prior iterations in each attack step to improve efficiency. Experimental evaluation demonstrates that our approach drastically improves performance, reducing the attack synthesis time by an order of magnitude. Seemanta Saha, William Eiers, Ismet Burak Kadron, Lucas Bang, Tevfik Bultan 2019 CS
Symbolic Execution + Model Counting + Entropy Maximization = Automatic Search Synthesis We present a method of automatically synthesizing steps to solve search problems. Given a specification of a search problem, our approach uses symbolic execution to analyze the specification in order to extract a set of constraints which model the problem. These constraints are used in a process called model counting, which is leveraged to compute probability distributions relating search steps to predicates about an unknown target. The probability distribution functions determine an information gain objective function based on Shannon entropy, which, when maximized, yields the next optimal step of the search. We prove that our algorithm converges to a correct solution, and discuss computational complexity issues. We implemented a domain specific language in which to write search problem specifications, enabling our static analysis phase. Our experiments demonstrate the effectiveness of our approach on a set of search problem case studies inspired by the domains of software security, computational geometry, AI for games, and user preference ranking. Mara Downing, Abtin Molavi, Lucas Bang 2020 CS
MCBAT: a practical tool for model counting constraints on bounded integer arrays. Model counting procedures for data structures are crucial for advancing the field of automated quantitative program analysis. We present a tool for Model Counting for Bounded Array Theory (MCBAT). MCBAT works on quantified integer array constraints in which all arrays have a finite length. We employ reductions from the theory of arrays to uninterpreted functions and linear integer arithmetic (LIA). Once reduced to LIA, we leverage Barvinok's polynomial time integer lattice point enumeration algorithm. Finally, we present a case study demonstrating applicability to automated quantitative program analysis. MCBAT is available for immediate use as a Docker image and the source code is freely available in our Github repository. Abtin Molavi, Mara Downing, Tommy Schneider, Lucas Bang 2020 CS
Virtually Constrained Dancing: Encoding Language in Movement and Sound. This paper presents the development of the TED (Tap Encoding Decoding) program with results and reflections on its usage. TED is a program to be used in partnership with a tap dancer for decoding tap dancing audio. To perform with TED, a tap dancer must execute their dance with steps that encode Morse code. This paper will elaborate on the processes by which TED was developed, including methodologies such as audio signal peak detection for tap dancing and audio decoding analysis. We also explore the relationship developed between the dancer and TED during experimentation and live performance. We draw upon notions of extended and embodied cognition to explain observations regarding the dancer's feedback driven adaptations to TED's outputs during their performance. The programmatic constraints introduced during partnership with TED result in novel choreographic challenges and impose atypical structure in improvisation, leading to unusual performance characteristics. Devon Frost, Shannon Steele, Lucas Bang 2020 CS
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Attack Synthesis for Strings using Meta-Heuristics Information leaks are a significant problem in modern computer systems and string manipulation is prevalent in modern software. We present techniques for automated synthesis of side-channel attacks that recover secret string values based on timing observations on string manipulating code. Our attack synthesis techniques iteratively generate inputs which, when fed to code that accesses the secret, reveal partial information about the secret based on the timing observations, leading to recovery of the secret at the end of the attack sequence. We use symbolic execution to extract path constraints, automata-based model counting to estimate the probability of execution paths, and meta-heuristic methods to maximize information gain based on entropy for synthesizing adaptive attack steps. Seemanta Saha, Ismet Burak Kadron, William Eiers, Lucas Bang, Tevfik Bultan 2019 CS
Reclassification of Sphingomonas aeria as a later heterotypic synonym of Sphingomonas carotinifaciens based on whole-genome sequence analysis. The 16S rRNA gene sequences of Sphingomonas carotinifaciens L9-754T and Sphingomonas aeria B093034T possess 99.71 % sequence similarity. Further studies were undertaken to clarify the taxonomic assignments of these species. Whole-genome comparisons showed that S. aeria B093034Tand S. carotinifaciens L9-754T shared 96.9 % average nucleotide identity, 98.4 % average amino acid identity and 76.1 % digital DNA–DNA hybridization values. These values exceeded or approached the recommended species delineation threshold values. Furthermore, a phylogenetic tree based on 41 of the most conserved genes provided additional evidence that S. aeria B093034T and S. carotinifaciens L9-754T are very closely related. Based on this evidence we propose the reclassification of S. aeria Xue et al. 2018 as a later heterotypic synonym of S. carotinifaciens Madhaiyan et al. 2017. Madhaiyan M, Saravanan VS, Wirth JS, Whitman WB 2020 Biology
Chitinasiproducens palmae gen. nov., sp. nov., a new member of the family Burkholderiaceae isolated from leaf tissues of oil palm (Elaesis guineensis Jacq.) A Gram-stain-negative, aerobic, rod-shaped, leaf-associated bacterium, designated JS23T, was isolated from surface-sterilized leaf tissue of an oil palm grown in Singapore and was investigated by polyphasic taxonomy. Phylogenetic analyses based on 16S rRNA gene sequences and 180 conserved genes in the genome of several members of Burkholderiaceae revealed that strain JS23T formed a distinct evolutionary lineage independent of other taxa within the family Burkholderiaceae . The predominant ubiquinone was Q-8. The primary polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, and an unidentified aminophospholipid. The major fatty acids were C16 : 0, summed feature 3 (C16 : 1 ω7c /C16 : 1 ω6c) and summed feature 8 (C18 : 1 ω7c /C18 : 1 ω6c). The size of the genome is 5.36 Mbp with a DNA G+C content of 66.2 mol%. Genomic relatedness measurements such as average nucleotide identity, genome-to-genome distance and digital DNA–DNA hybridization clearly distinguished strain JS23T from the closely related genera Burkholderia , Caballeronia , Mycetohabitans , Mycoavidus , Pandoraea , Paraburkholderia , Robbsia and Trinickia . Furthermore, average amino acid identity values and the percentages of conserved proteins, 56.0–68.4 and 28.2–45.5, respectively, were well below threshold values for genus delineation and supported the assignment of JS23T to a novel genus. On the basis of the phylogenetic, biochemical, chemotaxonomic and phylogenomic evidence, strain JS23T is proposed to represent a novel species of a new genus within the family Burkholderiaceae , for which the name Chitinasiproducens palmae gen. nov., sp. nov., is proposed with the type strain of JS23T (= DSM 27307T=KACC 17592T). Madhaiyan M, See-Too WS, Ee R, Saravanan VS, Wirth JS, Alex THH, Lin C, Kim SJ, Weon HY, Whitman WB, Kwon SW, Ji L 2020 Biology
Dimethylsulfoniopropionate sulfur and methyl carbon assimilation in Ruegeria species Dimethylsulfoniopropionate (DMSP) is abundant in marine environments and an important source of reduced carbon and sulfur for marine bacteria. While both Ruegeria pomeroyi and Ruegeria lacuscaerulensis possessed genes encoding the DMSP demethylation and cleavage pathways, their responses to DMSP differed. A glucose-fed, chemostat culture of R. pomeroyi consumed 99% of the DMSP even when fed a high concentration of 5 mM. At the same time, cultures released 19% and 7.1% of the DMSP as dimethylsulfide (DMS) and methanethiol, respectively. Under the same conditions, R. lacuscaerulensis consumed only 28% of the DMSP and formed one-third of the amount of gases. To examine the pathways of sulfur and methyl C assimilation, glucose-fed chemostats of both species were fed 100 μM mixtures of unlabeled and doubly labeled [dimethyl-13C, 34S]DMSP. Both species derived nearly all of their sulfur from DMSP despite high sulfate availability. In addition, only 33% and 50% of the methionine was biosynthesized from the direct capture of methanethiol in R. pomeroyi and R. lacuscaerulensis, respectively. The remaining methionine was biosynthesized by the random assembly of free sulfide and methyl-tetrahydrofolate derived from DMSP. Thus, although the two species possessed similar genes encoding DMSP metabolism, their growth responses were very different.
IMPORTANCE Dimethylsulfoniopropionate (DMSP) is abundant in marine environments and an important source of reduced carbon and sulfur for marine bacteria. DMSP is the precursor for the majority of atmospheric dimethylsulfide (DMS), a climatically active gas that connects the marine and terrestrial sulfur cycles. Although research into the assimilation of DMSP has been conducted for over 20 years, the fate of DMSP in microbial biomass is not well understood. In particular, the biosynthesis of methionine from DMSP has been a focal point, and it has been widely believed that most methionine was synthesized via the direct capture of methanethiol. Using an isotopic labeling strategy, we have demonstrated that the direct capture of methanethiol is not the primary pathway used for methionine biosynthesis in two Ruegeria species, a genus comprised primarily of globally abundant marine bacteria. Furthermore, although the catabolism of DMSP by these species varied greatly, the anabolic pathways were highly conserved. Wirth JS, Wang T, Huang Q, White RH, Whitman WB. 2020 Biology
Sphingomonas palmae sp. nov. and Sphingomonas gellani sp. nov., endophytically associated phyllosphere bacteria isolated from economically important crop plants In this study, two endophytic bacterial strains designated JS21-1T and S6-262T isolated from leaves of Elaeis guineensis and stem tissues of Jatropha curcas respectively, were subjected for polyphasic taxonomic approach. On R2A medium, colonies of strains JS21-1T and S6-262T are orange and yellow, respectively. Phylogenetic analyses using 16S rRNA gene sequencing and whole-genome sequences placed the strains in distinct clades but within the genus Sphingomonas. The DNA G + C content of JS21-1T and S6-262T were 67.31 and 66.95%, respectively. Furthermore, the average nucleotide identity and digital DNA-DNA hybridization values of strains JS21-1T and S6-262T with phylogenetically related Sphingomonas species were lower than 95% and 70% respectively. The chemotaxonomic studies indicated that the major cellular fatty acids of the strain JS21-1T were summed feature 8 (C18:1 ω7c and/or C18:1 ω6c), C16:0, and C14:0 2OH; strain S6-262T possessed summed feature 3 (C16:1 ω7c and/or iso-C15:0 2-OH) and summed feature 8 (C18:1 ω6c and/or C18:1 ω7c). The major quinone was Q10, and the unique polyamine observed was homospermidine. The polar lipid profile comprised of mixture of sphingoglycolipid, phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and certain uncharacterised phospholipids and lipids. Based on this polyphasic evidence, strains JS21-1T and S6-262T represent two novel species of the genus Sphingomonas, for which the names Sphingomonas palmae sp. nov. and Sphingomonas gellani sp. nov. are proposed, respectively. The type strain of Sphingomonas palmae sp. nov. is JS21-1T (= DSM 27348T = KACC 17591T) and the type strain of Sphingomonas gellani sp. nov. is S6-262T (= DSM 27346T = KACC 17594T). Madhaiyan M, Saravanan VS, Wirth JS, Alex THH, Kim SJ, Weon HY, Kwon SW, Whitman WB, Ji L 2020 Biology
Phylogenomic analyses of the Staphylococcaceae family suggest the reclassification of five species within the genus Staphylococcus as heterotypic synonyms, the promotion of five subspecies to novel species, the taxonomic reassignment of five Staphylococcus species to Mammaliicoccus gen. nov., and the formal assignment of Nosocomiicoccus to the family Staphylococcaceae Phylogenetic analyses based on 16S rRNA gene sequences of members of the family Staphylococcaceae showed the presence of para- and polyphyletic genera. This finding prompted a thorough investigation into the taxonomy of the Staphylococcaceae family by analysing their core genome phylogeny complemented with genome-based indices such as digital DNA–DNA hybridization, average nucleotide identity and average amino acid identity. The resulting data suggested the following proposals: Auricoccus indicus was reduced in taxonomic rank as a later heterotypic synonym of Abyssicoccus albus ; Staphylococcus petrasii subsp. jettensis as a later heterotypic synonym of Staphylococcus petrasii subsp. petrasii ; the unification of Staphylococcus aureus subsp. anaerobius and Staphylococcus aureus subsp. aureus as Staphylococcus aureus ; the unification of Staphylococcus carnosus subsp. utilis and Staphylococcus carnosus subsp. carnosus as Staphylococcus carnosus ; the unification of Staphylococcus saprophyticus subsp. bovis and Staphylococcus saprophyticus subsp. saprophyticus as Staphylococcus saprophyticus ; Staphylococcus succinis subsp. casei as the novel species Staphylococcus casei; Staphylococcus schleiferi subsp. coagulans as the novel species Staphylococcus coagulans; Staphylococcus petrasii subsp. croceilyticus as the novel species Staphylococcus croceilyticus; Staphylococcus petrasii subsp. pragensis as the novel species Staphylococcus pragensis; Staphylococcus cohnii subsp. urealyticus as the novel species Staphylococcus urealyticus; the reassignment of Staphylococcus sciuri , Staphylococcus fleurettii , Staphylococcus lentus , Staphylococcus stepanovicii and Staphylococcus vitulinus to the novel genus Mammaliicoccus with Mammaliicoccus sciuri as the type species; and the formal assignment of Nosocomiicoccus as a member of the family Staphylococcaceae . Madhaiyan M, Wirth JS, Saravanan VS, Whitman WB. 2020 Biology
A mathematical model for DC vaccine treatment of type I diabetes Type I diabetes (T1D) is an autoimmune disease that can be managed, but for which there is currently no cure. Recent discoveries, particularly in mouse models, indicate that targeted modulation of the immune response has the potential to move an individual from a diabetic to a long-term, if not permanent, healthy state. In this paper we develop a single compartment mathematical model that captures the dynamics of dendritic cells (DC and tDC), T cells (effector and regulatory), and macrophages in the development of type I diabetes. The model supports the hypothesis that differences in macrophage clearance rates play a significant role in determining whether or not an individual is likely to become diabetic subsequent to a significant immune challenge. With this model we are able to explore the effects of strengthening the anti-inflammatory component of the immune system in a vulnerable individual. Simulations indicate that there are windows of opportunity in which treatment intervention is more likely to be beneficial in protecting an individual from entering a diabetic state. This model framework can be used as a foundation for modeling future T1D treatments as they are developed. Blerta Shtylla, Marissa Gee, Shahrokh Shabahang, Leif Eldevik, Lisette DePillis 2019 Mathematics
Mesenchymal stem cells used as carrier cells of oncolytic adenovirus results in enhanced oncolytic virotherapy Mesenchymal stem cells (MSCs) loaded with oncolytic viruses are presently being investigated as a new modality of advanced/metastatic tumors treatment and enhancement of virotherapy. MSCs can, however, either promote or suppress tumor growth. To address the critical question of how MSCs loaded with oncolytic viruses affect virotherapy outcomes and tumor growth patterns in a tumor microenvironment, we developed and analyzed an integrated mathematical-experimental model. We used the model to describe both the growth dynamics in our experiments of firefly luciferase-expressing Hep3B tumor xenografts and the effects of the immune response during the MSCs-based virotherapy. We further employed it to explore the conceptual clinical feasibility, particularly, in evaluating the relative significance of potential immune promotive/suppressive mechanisms induced by MSCs loaded with oncolytic viruses. We were able to delineate conditions which may significantly contribute to the success or failure of MSC-based virotherapy as well as generate new hypotheses. In fact, one of the most impactful outcomes shown by this investigation, not inferred from the experiments alone, was the initially counter-intuitive fact that using tumor-promoting MSCs as carriers is not only helpful but necessary in achieving tumor control. Considering the fact that it is still currently a controversial debate whether MSCs exert a pro- or anti-tumor action, mathematical models such as this one help to quantitatively predict the consequences of using MSCs for delivering virotherapeutic agents in vivo. Taken together, our results show that MSC-mediated systemic delivery of oncolytic viruses is a promising strategy for achieving synergistic anti-tumor efficacy with improved safety profiles. Khaphetsi Joseph Mahasa, Lisette De Pillis, Rachid Ouifki, Amina Eladdadi, Philip Maini, A-Rum Yoon, Chae-Ok Yun 2020 Mathematics
Jumping archer fish exhibit multiple modes of fin-fin interaction Aquatic organisms jumping for aerial prey require high-performance propulsion, accurate aim, and trajectory control to succeed. Archer fish, capable of jumping up to twice their body length out of the water, address these considerations through multifaceted fin and body kinematics. In this study, we utilized 3D synthetic aperture particle image velocimetry to visualize the wakes of archer fish throughout the jumping process. We found that multiple modes of interaction between the anal and caudal fins occur during jump behaviors. Time-resolved volumetric measurements presented herein illustrate the hydrodynamics of each interaction mode in detail. Additionally, regardless of which fin uses and interactions were exhibited during a jump, we found similar relationships between the cumulative impulse of multiple propulsive vortices in the wake and the instantaneous ballistic momentum of the fish. Our results suggests that fin use may compensate for variations in individual kinematic events and in the aiming posture assumed prior to jumping and highlight how interactions between tailbeats and other fins help the archer fish reach necessary prey heights in a spatially- and visually-constrained environment. In the broader context of bioinspired propulsion, the archer fish exemplifies that multiple beneficial hydrodynamic interactions can be generated in a high-performance scenario using a single set of actuators. Leah Mendelson, Alexandra H. Techet 2020 Engineering
Search for a Dark Leptophilic Scalar in e+e- Collisions Many scenarios of physics beyond the standard model predict the existence of new gauge singlets, which might be substantially lighter than the weak scale. The experimental constraints on additional scalars with masses in the MeV to GeV range could be significantly weakened if they interact predominantly with leptons rather than quarks. At an e+e- collider, such a leptophilic scalar would be produced predominantly through radiation from a tau lepton. We report herein a search for a leptophilic scalar using data from collected from the BaBar experiment at SLAC. No significant signal is observed, and we set limits on the leptophilic scalar coupling to leptons in the mass range 0.04-7 GeV. These bounds significantly improve upon the current constraints, excluding almost entirely the parameter space favored by the observed discrepancy in the muon anomalous magnetic moment below 4 GeV at 90% confidence level. J.P. Lees et al., (BaBar collaboration) 2020 Physics
Baryogenesis and dark matter from freeze-in We propose a simple model in which the baryon asymmetry and dark matter are created via the decays and inverse decays of QCD-triplet scalars, at least one of which must be in the TeV mass range. Singlet fermions produced in these decays constitute the dark matter. The singlets never reach equilibrium, and their coherent production, propagation, and annihilation generates a baryon asymmetry. We find that the out-of-equilibrium condition and the dark matter density constraint typically require the lightest scalar to be long-lived, giving good prospects for detection or exclusion in current and upcoming colliders. In generalizing the leptogenesis mechanism of Akhmedov, Rubakov and Smirnov, our model expands the phenomenological possibilities for low-scale baryogenesis. Brian Shuve, David Tucker-Smith 2020 Physics
Discovering true munoium at LHCb We study the potential of the LHCb experiment to discover, for the first time, the true muonium bound state. We propose a search for the vector 13S1 state (TM), which kinetically mixes with the photon and dominantly decays to e+e-. We demonstrate that a search for eta -> TM gamma, TM -> e+e- in a displaced vertex can exceed a significance of 5 standard deviations assuming statistical uncertainties. We present two possible searches: an inclusive search for the e+e- vertex, and an exclusive search which requires an additional photon and a reconstruction of the eta mass. Xabier Cid Vidal, Philip Ilten, Jonathan Plews, Brian Shuve, Yotam Soreq 2019 Physics
Searching for long-lived particles beyond the Standard Model at the Large Hadron Collider Particles beyond the Standard Model (SM) can generically have lifetimes that are long compared to SM particles at the weak scale. When produced at experiments such as the Large Hadron Collider (LHC) at CERN, these long-lived particles (LLPs) can decay far from the interaction vertex of the primary proton–proton collision. Such LLP signatures are distinct from those of promptly decaying particles that are targeted by the majority of searches for new physics at the LHC, often requiring customized techniques to identify, for example, significantly displaced decay vertices, tracks with atypical properties, and short track segments. Given their non-standard nature, a comprehensive overview of LLP signatures at the LHC is beneficial to ensure that possible avenues of the discovery of new physics are not overlooked. Here we report on the joint work of a community of theorists and experimentalists with the ATLAS, CMS, and LHCb experiments—as well as those working on dedicated experiments such as MoEDAL, milliQan, MATHUSLA, CODEX-b, and FASER—to survey the current state of LLP searches at the LHC, and to chart a path for the development of LLP searches into the future, both in the upcoming Run 3 and at the high-luminosity LHC. The work is organized around the current and future potential capabilities of LHC experiments to generally discover new LLPs, and takes a signature-based approach to surveying classes of models that give rise to LLPs rather than emphasizing any particular theory motivation. We develop a set of simplified models; assess the coverage of current searches; document known, often unexpected backgrounds; explore the capabilities of proposed detector upgrades; provide recommendations for the presentation of search results; and look towards the newest frontiers, namely high-multiplicity 'dark showers', highlighting opportunities for expanding the LHC reach for these signals. Juliette Alimena, James Beacham, Martino Borsato, Yangyang Cheng, Xabier Cid Vidal, Giovanna Cottin, David Curtin, Albert De Roeck, Nishita Desai, Jared A Evans, Simon Knapen, Sabine Kraml, Andre Lessa, Zhen Liu, Sascha Mehlhase, Michael J Ramsey-Musolf, Heather Russell, Jessie Shelton, Brian Shuve, Monica Verducci, Jose Zurita 2020 Physics
Long-lived particles at the energy frontier: the MATHUSLA physics case We examine the theoretical motivations for long-lived particle (LLP) signals at the LHC in a comprehensive survey of standard model (SM) extensions. LLPs are a common prediction of a wide range of theories that address unsolved fundamental mysteries such as naturalness, dark matter, baryogenesis and neutrino masses, and represent a natural and generic possibility for physics beyond the SM (BSM). In most cases the LLP lifetime can be treated as a free parameter from the m scale up to the Big Bang Nucleosynthesis limit of m. Neutral LLPs with lifetimes above 100 m are particularly difficult to probe, as the sensitivity of the LHC main detectors is limited by challenging backgrounds, triggers, and small acceptances. MATHUSLA is a proposal for a minimally instrumented, large-volume surface detector near ATLAS or CMS. It would search for neutral LLPs produced in HL-LHC collisions by reconstructing displaced vertices (DVs) in a low-background environment, extending the sensitivity of the main detectors by orders of magnitude in the long-lifetime regime. We study the LLP physics opportunities afforded by a MATHUSLA-like detector at the HL-LHC, assuming backgrounds can be rejected as expected. We develop a model-independent approach to describe the sensitivity of MATHUSLA to BSM LLP signals, and compare it to DV and missing energy searches at ATLAS or CMS. We then explore the BSM motivations for LLPs in considerable detail, presenting a large number of new sensitivity studies. While our discussion is especially oriented towards the long-lifetime regime at MATHUSLA, this survey underlines the importance of a varied LLP search program at the LHC in general. By synthesizing these results into a general discussion of the top–down and bottom-up motivations for LLP searches, it is our aim to demonstrate the exceptional strength and breadth of the physics case for the construction of the MATHUSLA detector. David Curtin, Marco Drewes, Matthew McCullough, Patrick Meade, Rabindra N Mohapatra, Jessie Shelton, Brian Shuve, Elena Accomando, Cristiano Alpigiani, Stefan Antusch, Juan Carlos Arteaga-Velázquez, Brian Batell, Martin Bauer, Nikita Blinov, Karen Salomé Caballero-Mora, Jae Hyeok Chang, Eung Jin Chun, Raymond T Co, Timothy Cohen, Peter Cox, Nathaniel Craig, Csaba Csáki, Yanou Cui, Francesco D'Eramo, Luigi Delle Rose, P S Bhupal Dev, Keith R Dienes, Jeff A Dror, Rouven Essig, Jared A Evans, Jason L Evans, Arturo Fernández Tellez, Oliver Fischer, Thomas Flacke, Anthony Fradette, Claudia Frugiuele, Elina Fuchs, Tony Gherghetta, Gian F Giudice, Dmitry Gorbunov, Rick S Gupta, Claudia Hagedorn, Lawrence J Hall, Philip Harris, Juan Carlos Helo, Martin Hirsch, Yonit Hochberg, Anson Hook, Alejandro Ibarra, Seyda Ipek, Sunghoon Jung, Simon Knapen, Eric Kuflik, Zhen Liu, Salvator Lombardo, H J Lubatti, David McKeen, Emiliano Molinaro, Stefano Moretti, Natsumi Nagata, Matthias Neubert, Jose Miguel No, Emmanuel Olaiya, Gilad Perez, Michael E Peskin, David Pinner, Maxim Pospelov, Matthew Reece, Dean J Robinson, Mario Rodríguez Cahuantzi, Rinaldo Santonico, Matthias Schlaffer, Claire H Shepherd-Themistocleous, Andrew Spray, Daniel Stolarski, Martin A Subieta Vasquez, Raman Sundrum, Andrea Thamm, Brooks Thomas, Yuhsin Tsai, Brock Tweedie, Stephen M West, Charles Young, Felix Yu5, Bryan Zaldivar, Yongchao Zhang, Kathryn Zurek, José Zurita 2020 Physics
"U.S. Colonial Education in Guam, 1899-1950" Following the Spanish-American War of 1898 and the illegal overthrow and annexation of Hawai'i, the US government transplanted its colonial education program to places in the Caribbean and the Pacific Islands. Specifically, American Samoa, Guam, Hawai'i, Puerto Rico, the Philippines, and the US Virgin Islands would all have some aspect of the native boarding school system implemented. In many ways, the colonial education system in Guam was emblematic and exceptional to native boarding schools in the continental United States. Utilizing Guam as a case study reveals how the US military used schools as a site to spread settle colonial policies in an attempt to transform Chamorus into colonial subjects who would support American occupation. 2019 Asian American Studies/HSA