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ASU Scholarship Showcase


This growing collection, which contains many open access articles, consists of scholarly works authored by ASU community members. ASU-affiliated authors, who wish to deposit scholarly works, please use the Deposit form to describe your work.


Date Range
2006 2018


Computer simulations of the Ising model exhibit white noise if thermal fluctuations are governed by Boltzmann's factor alone; whereas we find that the same model exhibits 1/f noise if Boltzmann's factor is extended to include local alignment entropy to all orders. We show that this nonlinear correction maintains maximum entropy during equilibrium fluctuations. Indeed, as with the usual way to resolve Gibbs' paradox that avoids entropy reduction during reversible processes, the correction yields the statistics of indistinguishable particles. The correction also ensures conservation of energy if an instantaneous contribution from local entropy is included. Thus, a common mechanism for 1/f ...

Contributors
Chamberlin, Ralph, Nasir, Derek, College of Liberal Arts and Sciences, et al.
Created Date
2014-07-30

Mexicans and Mexican Americans have resided in Arizona since the early 16th century. Their history, however, is severely under-documented in the state’s archival repositories. As of 2012, this community is represented in a mere 1-2% of the state’s known archival holdings, and 98% of such documentation is held at Arizona State University’s Chicano/a Research Collection (CRC). This article provides a historical review of the CRC’s establishment in 1970 and how its founding Curator, Dr. Christine Marín, transformed a small circulating book collection into Arizona’s largest repository for Mexican American history. It goes on to examine how the CRC’s sitting Archivist ...

Contributors
Godoy-Powell, Nancy L., Dunham, Elizabeth G.
Created Date
2017-01-27

Remote sensors like Doppler lidars can map the winds with high accuracy and spatial resolution. One shortcoming of lidars is that the radial velocity measured by the lidar does not give a complete picture of the windfield necessitating additional data processing to reconstruct the windfield. Most of the popular vector retrieval algorithms rely on the homogenous wind field assumption which plays a vital role in reducing the indeterminacy of the inverse problem of obtaining Cartesian velocity from radial velocity measurements. Consequently, these methods fail in situations where the flow is heterogeneous e.g., Turbine wakes. Alternate methods are based either on ...

Contributors
Cherukuru, Nihanth, Calhoun, Ronald, Krishnamurthy, Raghavendra, et al.
Created Date
2017-10

MicroRNAs (miRNAs) are short non-coding RNAs that regulate gene output at the post-transcriptional level by targeting degenerate elements primarily in 3′untranslated regions (3′UTRs) of mRNAs. Individual miRNAs can regulate networks of hundreds of genes, yet for the majority of miRNAs few, if any, targets are known. Misexpression of miRNAs is also a major contributor to cancer progression, thus there is a critical need to validate miRNA targets in high-throughput to understand miRNAs' contribution to tumorigenesis. Here we introduce a novel high-throughput assay to detect miRNA targets in 3′UTRs, called Luminescent Identification of Functional Elements in 3′UTRs (3′LIFE). We demonstrate the ...

Contributors
Wolter, Justin, Kotagama, Kasuen, Pierre-Bez, Alexandra C., et al.
Created Date
2014-09-29

We previously reported a recombinant protein production system based on a geminivirus replicon that yields high levels of vaccine antigens and monoclonal antibodies in plants. The bean yellow dwarf virus (BeYDV) replicon generates massive amounts of DNA copies, which engage the plant transcription machinery. However, we noticed a disparity between transcript level and protein production, suggesting that mRNAs could be more efficiently utilized. In this study, we systematically evaluated genetic elements from human, viral, and plant sources for their potential to improve the BeYDV system. The tobacco extensin terminator enhanced transcript accumulation and protein production compared to other commonly used ...

Contributors
Diamos, Andy, Rosenthal, Sun, Mason, Hugh, et al.
Created Date
2016-02-24

Methodologists have developed mediation analysis techniques for a broad range of substantive applications, yet methods for estimating mediating mechanisms with missing data have been understudied. This study outlined a general Bayesian missing data handling approach that can accommodate mediation analyses with any number of manifest variables. Computer simulation studies showed that the Bayesian approach produced frequentist coverage rates and power estimates that were comparable to those of maximum likelihood with the bias-corrected bootstrap. We share an SAS macro that implements Bayesian estimation and use 2 data analysis examples to demonstrate its use.

Contributors
Enders, Craig, Fairchild, Amanda J., MacKinnon, David, et al.
Created Date
2013

During the last 40 years evidence from systematic case study analysis and behavioral experiments have provided a comprehensive perspective on how communities can manage common resources in a sustainable way. The conventional theory based on selfish rational actors cannot explain empirical observations. A more comprehensive theoretical framework of human behavior is emerging that include concepts such as trust, conditional cooperation, other-regarding preferences, social norms, and reputation. The new behavioral perspective also demonstrates that behavioral responses depend on social and biophysical context.

Contributors
Janssen, Marco, Julie Ann Wrigley Global Institute of Sustainability, School of Sustainability, et al.
Created Date
2015-02-01

Presented in this paper is a bi-directional out-of-plane actuator which combines the merits of the electrostatic repulsive principle and the electrostatic attractive principle. By taking advantage of the electrostatic repulsive mode, the common “pull-in” instability can be lessened to enlarge the displacement, and by applying the electrostatic attractive mode, the out-of-plane displacement is further enlarged. The implications of changing the actuator’s physical dimensions are discussed, along with the two-layer polysilicon surface microfabrication process used to fabricate such an actuator. The static characteristics of the out-of-plane displacement versus the voltage of both modes are tested, and displacements of 1.4 μm and ...

Contributors
Ren, Hao, Wang, Weimin, Tao, Fenggang, et al.
Created Date
2013-12-05

Biophotovoltaic devices employ photosynthetic organisms at the anode of a microbial fuel cell to generate electrical power. Although a range of cyanobacteria and algae have been shown to generate photocurrent in devices of a multitude of architectures, mechanistic understanding of extracellular electron transfer by phototrophs remains minimal. Here we describe a mediatorless bioelectrochemical device to measure the electrogenic output of a planktonically grown cyanobacterium, Synechocystis sp. PCC6803. Light dependent production of current is measured, and its magnitude is shown to scale with microbial cell concentration and light intensity. Bioelectrochemical characterization of a Synechocystis mutant lacking Photosystem II demonstrates conclusively that ...

Contributors
Cereda, Angelo, Hitchcock, Andrew, Symes, Mark D., et al.
Created Date
2014-03-17

Background Glycosylated proteins and lipids are important regulatory factors whose functions can be altered by addition or removal of sugars to the glycan structure. The glycans are recognized by sugar-binding lectins that serve as receptors on the surface of many cells and facilitate initiation of an intracellular signal that changes the properties of the cells. We identified a peptide that mimics the ligand of an N-acetylgalactosamine (GalNAc)-specific lectin and asked whether the peptide would express specific biological activity. Findings A 12-mer phage display library was screened with a GalNAc-specific lectin to identify an amino acid sequence that binds to the ...

Contributors
Eggink, Laura, Hoober, Kenneth, College of Liberal Arts and Sciences, et al.
Created Date
2009-02-11

This chapter is not a guide to embodied thinking, but rather a critical call to action. It highlights the deep history of embodied practice within the fields of dance and somatics, and outlines the value of embodied thinking within human-computer interaction (HCI) design and, more specifically, wearable technology (WT) design. What this chapter does not do is provide a guide or framework for embodied practice. As a practitioner and scholar grounded in the fields of dance and somatics, I argue that a guide to embodiment cannot be written in a book. To fully understand embodied thinking, one must act, move, ...

Contributors
Rajko, Jessica
Created Date
2018

We present stellar evolution models for 0.5 - 1.2 M[subscript ⊙] at scaled metallicities of 0.1 - 1.5 Z[subscript ⊙] and O/Fe values of 0.44 - 2.28 O/Fe[subscript ⊙]. The time dependent evolution of habitable zone boundaries are calculated for each stellar evolution track based on stellar mass, effective temperature, and luminosity parameterizations. The rate of change of stellar surface quantities and the surrounding habitable zone position are strong functions of all three quantities explored. The range of orbits that remain continuously habitable, or habitable for at least 2 Gyr, are provided. The results show that the detailed chemical characterization ...

Contributors
Truitt, Amanda, Young, Patrick, Spacek, Alexander, et al.
Created Date
2015-05-10

Malignant cancers that lead to fatal outcomes for patients may remain dormant for very long periods of time. Although individual mechanisms such as cellular dormancy, angiogenic dormancy and immunosurveillance have been proposed, a comprehensive understanding of cancer dormancy and the “switch” from a dormant to a proliferative state still needs to be strengthened from both a basic and clinical point of view. Computational modeling enables one to explore a variety of scenarios for possible but realistic microscopic dormancy mechanisms and their predicted outcomes. The aim of this paper is to devise such a predictive computational model of dormancy with an ...

Contributors
Chen, Duyu, Jiao, Yang, Torquato, Salvatore, et al.
Created Date
2014-10-16

Due to the limitation of current pharmacological therapeutic strategies, stem cell therapies have emerged as a viable option for treating many incurable neurological disorders. Specifically, human pluripotent stem cell (hPSC)-derived neural progenitor cells (hNPCs), a multipotent cell population that is capable of near indefinite expansion and subsequent differentiation into the various cell types that comprise the central nervous system (CNS), could provide an unlimited source of cells for such cell-based therapies. However the clinical application of these cells will require (i) defined, xeno-free conditions for their expansion and neuronal differentiation and (ii) scalable culture systems that enable their expansion and ...

Contributors
Tsai, Yihuan, Cutts, Joshua, Kimura, Azuma, et al.
Created Date
2015-05-13

Synchronization of neuronal activity is associated with neurological disorders such as epilepsy. This process of neuronal synchronization is not fully understood. To further our understanding, we have experimentally studied the progression of this synchronization from normal neuronal firing to full synchronization. We implemented nine FitzHugh-Nagumo neurons (a simplified Hodgkin-Huxley model) via discrete electronics. For different coupling parameters (synaptic strengths), the neurons in the ring were either unsynchronized or completely synchronized when locally coupled in a ring. When a single long-range connection (nonlocal coupling) was introduced, an intermediate state known as a chimera appeared. The results indicate that (1) epilepsy is ...

Contributors
Arumugam, Easwara Moorthy Essaki, Spano, Mark, Ira A. Fulton Schools of Engineering, et al.
Created Date
2015-01-01

With the advent of high-dimensional stored big data and streaming data, suddenly machine learning on a very large scale has become a critical need. Such machine learning should be extremely fast, should scale up easily with volume and dimension, should be able to learn from streaming data, should automatically perform dimension reduction for high-dimensional data, and should be deployable on hardware. Neural networks are well positioned to address these challenges of large scale machine learning. In this paper, we present a method that can effectively handle large scale, high-dimensional data. It is an online method that can be used for ...

Contributors
Roy, Asim, W.P. Carey School of Business, Computer Information Systems
Created Date
2015-08-10

Potential climate change impacts on summer precipitation and subsequent hydrologic responses in the southwestern U.S. are poorly constrained at present due to a lack of studies accounting for high resolution processes. In this investigation, we apply a distributed hydrologic model to the Beaver Creek watershed of central Arizona to explore its utility for climate change assessments. Manual model calibration and model validation were performed using radar-based precipitation data during three summers and compared to two alternative meteorological products to illustrate the sensitivity of the streamflow response. Using the calibrated and validated model, we investigated the watershed response during historical (1990–2000) ...

Contributors
Hawkins, Gretchen, Vivoni, Enrique, Robles-Morua, Agustin, et al.
Created Date
2015-07-01

Breast cancer persists as the most common cause of cancer death in women worldwide. Ovarian cancer is also a significant source of morbidity and mortality, as the fifth leading cause of cancer death among women. This reflects the continued need for further understanding and innovation in cancer treatment. Though breast and ovarian cancer usually present as distinct clinical entities, the recent explosion of large-scale -omics research has uncovered many overlaps, particularly with respect to genetic and epigenetic alterations. We compared genetic, microenvironmental, stromal, and epigenetic changes common between breast and ovarian cancer cells, as well as the clinical relevance of ...

Contributors
Longacre, Mckenna, Snyder, Nicole A., Housman, Genevieve, et al.
Created Date
2016-05-18

This article identifies equity outcomes associated with three biofuel systems in Brazil, Ethiopia and Guatemala. Acknowledging that winners and losers are socially and politically generated, the article identifies some of the factors behind the distribution of winners and losers along different stages of three sugarcane-ethanol supply chains. Analysing the outcomes for equity within each case study reveals an uneven distribution that we argue is related to the procedure and structure of the given sugarcane-ethanol system, and the recognition of the impacts on different actors within those structures. Increasing equity in sugarcane-ethanol systems will require greater openness in decision making processes, ...

Contributors
Hodbod, Jennifer, Tomei, Julia, Blaber-Wegg, Tina, et al.
Created Date
2015-06-01

Ecological models are a fundamental tool that archaeologists use to clarify our thinking about the processes that generate the archaeological record. Typically, arguments reasoned from a single model are bolstered by observing the consistency of ethnographic data with the argument. This validation of a model establishes that an argument is reasonable. In this paper, we attempt to move beyond validation by comparing the consistency of two arguments reasoned from different models that might explain corporate territorial ownership in a large ethnographic data set. Our results suggest that social dilemmas are an under appreciated mechanism that can drive the evolution of ...

Contributors
Freeman, Jacob, Anderies, John, College of Liberal Arts and Sciences, et al.
Created Date
2015-02-01

Background The extracellular sunscreen scytonemin is the most common and widespread indole-alkaloid among cyanobacteria. Previous research using the cyanobacterium Nostoc punctiforme ATCC 29133 revealed a unique 18-gene cluster (NpR1276 to NpR1259 in the N. punctiforme genome) involved in the biosynthesis of scytonemin. We provide further genomic characterization of these genes in N. punctiforme and extend it to homologous regions in other cyanobacteria. Results Six putative genes in the scytonemin gene cluster (NpR1276 to NpR1271 in the N. punctiforme genome), with no previously known protein function and annotated in this study as scyA to scyF, are likely involved in the assembly ...

Contributors
Soule, Tanya, Palmer, Kendra, Gao, Qunjie, et al.
Created Date
2009-07-24

Background. The purpose of this study was to compare the peak electromyography (EMG) of the most commonly-used position in the literature, the prone bent-leg (90°) hip extension against manual resistance applied to the distal thigh (PRONE), to a novel position, the standing glute squeeze (SQUEEZE). Methods. Surface EMG electrodes were placed on the upper and lower gluteus maximus of thirteen recreationally active females (age = 28.9 years; height = 164 cm; body mass = 58.2 kg), before three maximum voluntary isometric contraction (MVIC) trials for each position were obtained in a randomized, counterbalanced fashion. Results. No statistically significant (p < ...

Contributors
Contreras, Bret, Vigotsky, Andrew, Schoenfeld, Brad J., et al.
Created Date
2015-09-22

The Rehai and Ruidian geothermal fields, located in Tengchong County, Yunnan Province, China, host a variety of geochemically distinct hot springs. In this study, we report a comprehensive, cultivation-independent census of microbial communities in 37 samples collected from these geothermal fields, encompassing sites ranging in temperature from 55.1 to 93.6°C, in pH from 2.5 to 9.4, and in mineralogy from silicates in Rehai to carbonates in Ruidian. Richness was low in all samples, with 21–123 species-level OTUs detected. The bacterial phylum Aquificae or archaeal phylum Crenarchaeota were dominant in Rehai samples, yet the dominant taxa within those phyla depended on ...

Contributors
Hou, Weiguo, Wang, Shang, Dong, Hailiang, et al.
Created Date
2013-01-09

The term adaptive intervention has been used in behavioral medicine to describe operationalized and individually tailored strategies for prevention and treatment of chronic, relapsing disorders. Control systems engineering offers an attractive means for designing and implementing adaptive behavioral interventions that feature intensive measurement and frequent decision-making over time. This is illustrated in this paper for the case of a low-dose naltrexone treatment intervention for fibromyalgia. System identification methods from engineering are used to estimate dynamical models from daily diary reports completed by participants. These dynamical models then form part of a model predictive control algorithm which systematically decides on treatment ...

Contributors
Deshpande, Sunil, Rivera, Daniel, Younger, Jarred W., et al.
Created Date
2014-09-01

Background Heterogeneity within cell populations is relevant to the onset and progression of disease, as well as development and maintenance of homeostasis. Analysis and understanding of the roles of heterogeneity in biological systems require methods and technologies that are capable of single cell resolution. Single cell gene expression analysis by RT-qPCR is an established technique for identifying transcriptomic heterogeneity in cellular populations, but it generally requires specialized equipment or tedious manipulations for cell isolation. Results We describe the optimization of a simple, inexpensive and rapid pipeline which includes isolation and culture of live single cells as well as fluorescence microscopy ...

Contributors
Yaron, Jordan, Ziegler, Colleen, Tran, Thai, et al.
Created Date
2014-05-08

Acute Myeloid Leukemia (AML) is a fatal hematological cancer. The genetic abnormalities underlying AML are extremely heterogeneous among patients, making prognosis and treatment selection very difficult. While clinical proteomics data has the potential to improve prognosis accuracy, thus far, the quantitative means to do so have yet to be developed. Here we report the results and insights gained from the DREAM 9 Acute Myeloid Prediction Outcome Prediction Challenge (AML-OPC), a crowdsourcing effort designed to promote the development of quantitative methods for AML prognosis prediction. We identify the most accurate and robust models in predicting patient response to therapy, remission duration, ...

Contributors
Noren, David P., Long, Byron L., Norel, Raquel, et al.
Created Date
2016-06-28

We advocate a low-cost strategy for long-duration research into the ‘milligravity’ environment of asteroids, comets and small moons, where surface gravity is a vector field typically less than 1/1000 the gravity of Earth. Unlike the microgravity environment of space, there is a directionality that gives rise, over time, to strangely familiar geologic textures and landforms. In addition to advancing planetary science, and furthering technologies for hazardous asteroid mitigation and in situ resource utilization, simplified access to long-duration milligravity offers significant potential for advancing human spaceflight, biomedicine and manufacturing. We show that a commodity 3U (10 × 10 × 34 cm[superscript ...

Contributors
Asphaug, Erik, Thangavelautham, Jekan, Klesh, Andrew, et al.
Created Date
2017-06-05

We describe an online database of number fields which accompanies this paper. The database centers on complete lists of number fields with prescribed invariants. Our description here focuses on summarizing tables and connections to theoretical issues of current interest.

Contributors
Jones, John, Roberts, David P., College of Liberal Arts and Sciences, et al.
Created Date
2013-11-30

Community associated methicillin-resistant Staphylococcus aureus (CA-MRSA) has become a major cause of skin and soft tissue infections (SSTIs) in the US. We developed an age-structured compartmental model to study the spread of CA-MRSA at the population level and assess the effect of control intervention strategies. We used Monte-Carlo Markov Chain (MCMC) techniques to parameterize our model using monthly time series data on SSTIs incidence in children (≤19 years) during January 2004 -December 2006 in Maricopa County, Arizona. Our model-based forecast for the period January 2007–December 2008 also provided a good fit to data. We also carried out an uncertainty and ...

Contributors
Wang, Xiaoxia, Panchanathan, Sarada, Chowell-Puente, Gerardo, et al.
Created Date
2013-11-21

Background It has been 10 years since Terje Sagvolden founded Behavioral and Brain Functions. Body After setting the context, this paper reviews some of the contributions of articles in the journal to the literature on ADHD over that decade. Those articles provide a cross section of some of the most important ongoing themes in ADHD research. Conclusion Terje’s faith in the new journal was well founded. It has survived the first threat of new journals, crib death, because of the continuing quality and relevance of the articles it carries. It has a diversified portfolio of similar research in many other ...

Contributors
Killeen, Peter, College of Liberal Arts and Sciences, Department of Psychology
Created Date
2016-04-06

MALDI-TOF MS has been shown capable of rapidly and accurately characterizing bacteria. Highly reproducible spectra are required to ensure reliable characterization. Prior work has shown that spectra acquired manually can have higher reproducibility than those acquired automatically. For this reason, the objective of this study was to optimize automated data acquisition to yield spectra with reproducibility comparable to those acquired manually. Fractional factorial design was used to design experiments for robust optimization of settings, in which values of five parameters (peak selection mass range, signal to noise ratio (S:N), base peak intensity, minimum resolution and number of shots summed) commonly ...

Contributors
Zhang, Lin, Borror, Connie, Sandrin, Todd, et al.
Created Date
2014-03-24

MALDI-TOF MS has been utilized as a reliable and rapid tool for microbial fingerprinting at the genus and species levels. Recently, there has been keen interest in using MALDI-TOF MS beyond the genus and species levels to rapidly identify antibiotic resistant strains of bacteria. The purpose of this study was to enhance strain level resolution for Campylobacter jejuni through the optimization of spectrum processing parameters using a series of designed experiments. A collection of 172 strains of C. jejuni were collected from Luxembourg, New Zealand, North America, and South Africa, consisting of four groups of antibiotic resistant isolates. The groups ...

Contributors
Penny, Christian, Grothendick, Beau, Zhang, Lin, et al.
Created Date
2016-05-31

Cyanovirin-N (CV-N) is an antiviral lectin with potent activity against enveloped viruses, including HIV. The mechanism of action involves high affinity binding to mannose-rich glycans that decorate the surface of enveloped viruses. In the case of HIV, antiviral activity of CV-N is postulated to require multivalent interactions with envelope protein gp120, achieved through a pseudo-repeat of sequence that adopts two near-identical glycan-binding sites, and possibly involves a 3D-domain-swapped dimeric form of CV-N. Here, we present a covalent dimer of CV-N that increases the number of active glycan-binding sites, and we characterize its ability to recognize four glycans in solution. A ...

Contributors
Woodrum, Brian, Maxwell, Jason, Allen, Denysia, et al.
Created Date
2016-06-06

A structurally and compositionally well-defined and spectrally tunable artificial light-harvesting system has been constructed in which multiple organic dyes attached to a three-arm-DNA nanostructure serve as an antenna conjugated to a photosynthetic reaction center isolated from Rhodobacter sphaeroides 2.4.1. The light energy absorbed by the dye molecules is transferred to the reaction center, where charge separation takes place. The average number of DNA three-arm junctions per reaction center was tuned from 0.75 to 2.35. This DNA-templated multichromophore system serves as a modular light-harvesting antenna that is capable of being optimized for its spectral properties, energy transfer efficiency, and photostability, allowing ...

Contributors
Dutta, Palash, Levenberg, Symon, Loskutov, Andrey, et al.
Created Date
2014-11-26

We propose a novel, efficient approach for obtaining high-quality experimental designs for event-related functional magnetic resonance imaging (ER-fMRI), a popular brain mapping technique. Our proposed approach combines a greedy hill-climbing algorithm and a cyclic permutation method. When searching for optimal ER-fMRI designs, the proposed approach focuses only on a promising restricted class of designs with equal frequency of occurrence across stimulus types. The computational time is significantly reduced. We demonstrate that our proposed approach is very efficient compared with a recently proposed genetic algorithm approach. We also apply our approach in obtaining designs that are robust against misspecification of error ...

Contributors
Kao, Ming-Hung, Mittelmann, Hans, College of Liberal Arts and Sciences, et al.
Created Date
2013-11-30

Transmission systems are under stress and need to be upgraded. Better utilization of the existing grid provides a fast and cheap alternative to building new transmission. One way to improve the utilization of the transmission network is power flow control via flexible AC transmission system (FACTS) devices. While FACTS devices are used today, the utilization of these devices is limited; traditional dispatch models (e.g., security con-strained economic dispatch) assume a fixed, static transmission grid even though it is rather flexible. The primary barrier is the complexity that is added to the power flow problem. The mathe-matical representation of the DC ...

Contributors
Sahraei-Ardakani, Mostafa, Hedman, Kory, Ira A. Fulton Schools of Engineering, et al.
Created Date
2015-07

Nonuniform Fourier data are routinely collected in applications such as magnetic resonance imaging, synthetic aperture radar, and synthetic imaging in radio astronomy. To acquire a fast reconstruction that does not require an online inverse process, the nonuniform fast Fourier transform (NFFT), also called convolutional gridding, is frequently employed. While various investigations have led to improvements in accuracy, efficiency, and robustness of the NFFT, not much attention has been paid to the fundamental analysis of the scheme, and in particular its convergence properties. This paper analyzes the convergence of the NFFT by casting it as a Fourier frame approximation. In so ...

Contributors
Gelb, Anne, Song, Guohui, College of Liberal Arts and Sciences, et al.
Created Date
2013-11-30

Decoding motor intent from recorded neural signals is essential for the development of effective neural-controlled prostheses. To facilitate the development of online decoding algorithms we have developed a software platform to simulate neural motor signals recorded with peripheral nerve electrodes, such as longitudinal intrafascicular electrodes (LIFEs). The simulator uses stored motor intent signals to drive a pool of simulated motoneurons with various spike shapes, recruitment characteristics, and firing frequencies. Each electrode records a weighted sum of a subset of simulated motoneuron activity patterns. As designed, the simulator facilitates development of a suite of test scenarios that would not be possible ...

Contributors
Abdelghani, Mohamed N., Abbas, James, Horch, Kenneth W., et al.
Created Date
2014-11-14

Laboratory investigations into the amphibian chytrid fungus, Batrachochytrium dendrobatidis (Bd), have accelerated recently, given the pathogen’s role in causing the global decline and extinction of amphibians. Studies in which host animals were exposed to Bd have largely assumed that lab-maintained pathogen cultures retained the infective and pathogenic properties of wild isolates. Attenuated pathogenicity is common in artificially maintained cultures of other pathogenic fungi, but to date, it is unknown whether, and to what degree, Bd might change in culture. We compared zoospore production over time in two samples of a single Bd isolate having different passage histories: one maintained in ...

Contributors
Langhammer, Penny, Lips, Karen R., Burrowes, Patricia A., et al.
Created Date
2013-10-10

Antigen-antibody complexes are central players in an effective immune response. However, finding those interactions relevant to a particular disease state can be arduous. Nonetheless many paths to discovery have been explored since deciphering these interactions can greatly facilitate the development of new diagnostics, therapeutics, and vaccines. In silico B cell epitope mapping approaches have been widely pursued, though success has not been consistent. Antibody mixtures in immune sera have been used as handles for biologically relevant antigens, but these and other experimental approaches have proven resource intensive and time consuming. In addition, these methods are often tailored to individual diseases ...

Contributors
Whittemore, Kurt, Johnston, Stephen, Sykes, Kathryn, et al.
Created Date
2016-06-14

Polymerases that synthesize artificial genetic polymers hold great promise for advancing future applications in synthetic biology. However, engineering natural polymerases to replicate unnatural genetic polymers is a challenging problem. Here we present droplet-based optical polymerase sorting (DrOPS) as a general strategy for expanding polymerase function that employs an optical sensor to monitor polymerase activity inside the microenvironment of a uniform synthetic compartment generated by microfluidics. We validated this approach by performing a complete cycle of encapsulation, sorting and recovery on a doped library and observed an enrichment of ∼1,200-fold for a model engineered polymerase. We then applied our method to ...

Contributors
Larsen, Andrew, Dunn, Matthew, Hatch, Andrew, et al.
Created Date
2016-04-05

There is mounting evidence to suggest that the urban built form plays a crucial role in household energy consumption, hence planning energy efficient cities requires thoughtful design at multiple scales - from buildings, to neighborhoods, to urban regions. While data on household energy use are essential for examining the energy implications of different built forms, few utilities providing power and gas offer such information at a granular scale. Therefore, researchers have used various estimation techniques to determine household and neighborhood scale energy use. In this study we develop a novel method for estimating household energy demand that can be applied ...

Contributors
Zhang, Wenwen, Guhathakurta, Subhrajit, Pendyala, Ram, et al.
Created Date
2018-01-05

The common formula used for converting a chi-square test into a correlation coefficient for use as an effect size in meta-analysis has a hidden assumption which may be violated in specific instances, leading to an overestimation of the effect size. A corrected formula is provided.

Contributors
Rosenberg, Michael, Biodesign Institute, Center for Evolution and Medicine, et al.
Created Date
2010-04-07

The termites evolved eusociality and complex societies before the ants, but have been studied much less. The recent publication of the first two termite genomes provides a unique comparative opportunity, particularly because the sequenced termites represent opposite ends of the social complexity spectrum. Zootermopsis nevadensis has simple colonies with totipotent workers that can develop into all castes (dispersing reproductives, nest-inheriting replacement reproductives, and soldiers). In contrast, the fungus-growing termite Macrotermes natalensis belongs to the higher termites and has very large and complex societies with morphologically distinct castes that are life-time sterile. Here we compare key characteristics of genomic architecture, focusing ...

Contributors
Korb, Judith, Poulsen, Michael, Hu, Haofu, et al.
Created Date
2015-03-04

In spite of the recent interest and advances in linear controllability of complex networks, controlling nonlinear network dynamics remains an outstanding problem. Here we develop an experimentally feasible control framework for nonlinear dynamical networks that exhibit multistability. The control objective is to apply parameter perturbation to drive the system from one attractor to another, assuming that the former is undesired and the latter is desired. To make our framework practically meaningful, we consider restricted parameter perturbation by imposing two constraints: it must be experimentally realizable and applied only temporarily. We introduce the concept of attractor network, which allows us to ...

Contributors
Wang, Le-Zhi, Su, Riqi, Huang, Zi-Gang, et al.
Created Date
2016-04-14

Maximally random jammed (MRJ) particle packings can be viewed as prototypical glasses in that they are maximally disordered while simultaneously being mechanically rigid. The prediction of the MRJ packing density ϕMRJ, among other packing properties of frictionless particles, still poses many theoretical challenges, even for congruent spheres or disks. Using the geometric-structure approach, we derive for the first time a highly accurate formula for MRJ densities for a very wide class of two-dimensional frictionless packings, namely, binary convex superdisks, with shapes that continuously interpolate between circles and squares. By incorporating specific attributes of MRJ states and a novel organizing principle, ...

Contributors
Tian, Jianxiang, Xu, Yaopengxiao, Jiao, Yang, et al.
Created Date
2015-11-16

Tree-like structures are ubiquitous in nature. In particular, neuronal axons and dendrites have tree-like geometries that mediate electrical signaling within and between cells. Electrical activity in neuronal trees is typically modeled using coupled cable equations on multi-compartment representations, where each compartment represents a small segment of the neuronal membrane. The geometry of each compartment is usually defined as a cylinder or, at best, a surface of revolution based on a linear approximation of the radial change in the neurite. The resulting geometry of the model neuron is coarse, with non-smooth or even discontinuous jumps at the boundaries between compartments. We ...

Contributors
Herrera-Valdez, Marco A., Suslov, Sergei, Vega-Guzman, Jose M., et al.
Created Date
2014-07-09

Essential or enduring understandings are often defined as the underlying core concepts or “big ideas” we’d like our students to remember when much of the course content has been forgotten. The central dogma of molecular biology and how cellular information is stored, used, and conveyed is one of the essential understandings students should retain after a course or unit in molecular biology or genetics. An additional enduring understanding is the relationships between DNA sequence, RNA sequence, mRNA production and processing, and the resulting polypeptide/protein product. A final big idea in molecular biology is the relationship between DNA mutation and polypeptide ...

Contributors
Marshall, Pamela, New College of Interdisciplinary Arts and Sciences, School of Mathematical and Natural Sciences
Created Date
2017-08-11

A high-sensitivity, fully passive neurosensing system is presented for wireless brain signal monitoring. The proposed system is able to detect very low-power brain-like signals, viz. as low as -82 dBm (50 μVpp) at fneuro > 1 kHz. It is also able to read emulated neural signals as low as -70 dBm (200 μVpp) at fneuro > 100 Hz. This is an improvement of up to 22 dB in sensitivity as compared with previously reported neural signals. The system is comprised of an implanted neurosensor and an exterior interrogator. The neurosensor receives an external carrier signal and mixes it with the ...

Contributors
Lee, Cedric W. L., Kiourti, Asimina, Chae, Junseok, et al.
Created Date
2015-06-01

In proteins, functional divergence involves mutations that modify structure and dynamics. Here we provide experimental evidence for an evolutionary mechanism driven solely by long-range dynamic motions without significant backbone adjustments, catalytic group rearrangements, or changes in subunit assembly. Crystallographic structures were determined for several reconstructed ancestral proteins belonging to a GFP class frequently employed in superresolution microscopy. Their chain flexibility was analyzed using molecular dynamics and perturbation response scanning. The green-to-red photoconvertible phenotype appears to have arisen from a common green ancestor by migration of a knob-like anchoring region away from the active site diagonally across the β barrel fold. ...

Contributors
Kim, Hanseong, Zou, Taisong, Modi, Chintan, et al.
Created Date
2015-01-06