Digital Commons Network^™

Detailed Requirements For Robots In Autism Therapy, Alan Atherton, Bonnie Brinton, Mark Colton, Nicole Giullian, Michael A. Goodrich, Daniel Ricks

Faculty Publications

Robot-based autism therapy is a rapidly developing area of research, with a wide variety of robots being developed for use in clinical settings. Specific, detailed requirements for robots and user interfaces are needed to provide guidelines for the creation of robots that more effectively assist therapists in autism therapy. This paper enumerates a set of requirements for a clinical humanoid robot and the associated human interface. The design of two humanoid robots and an intuitive and flexible user interface for use by therapists in the treatment of children with autism are described.

Immature Citizens And The State, Vivian E. Hamilton

Faculty Publications

Citizens are born, but they are also made. How its citizens come to be—whether the educations they receive will expand or constrain their future options, whether the values they assimilate will encourage or dissuade their civic engagement, etc.—fundamentally concerns the state. Through the power it wields over a vast range of policymaking contexts, the state can significantly influence (or designate those who will influence) many of the formative experiences of young citizens. Young citizens’ accumulated experiences in turn can significantly influence the future mature citizens they will become. The state insufficiently considers the cumulative nature of its citizens’ development, however. …

Predicting Stability Of Alpha-Helical, Orthogonal-Bundle Proteins On Surfaces, Shuai Wei, Thomas A. Knotts

Faculty Publications

The interaction of proteins with surfaces is a key phenomenon in many applications, but current understanding of the biophysics involved is lacking. At present, rational design of such emerging technologies is difficult as no methods or theories exist that correctly predict how surfaces influence protein behavior. Using molecular simulation and a coarse-grain model, this study illustrates for the first time that stability of proteins on surfaces can be correlated with tertiary structural elements for alpha-helical, orthogonal-bundle proteins. Results show that several factors contribute to stability on surfaces including the nature of the loop region where the tether is placed and …

Repression Of Wnt Signaling By A Fer-Type Nonreceptor Tyrosine Kinase, Aaron P. Putzke, Joel H. Rothman

Faculty Publications

The Wnt signaling pathway must be properly modulated to ensure an appropriate output: pathological conditions result from either insufficient or excessive levels of Wnt signal. For example, hyperactivation of the Wnt pathway is associated with various cancers and subnormal Wnt signaling can lead to increased invasiveness of tumor cells. We found that the Caenorhabditis elegans ortholog of the Fer nonreceptor tyrosine kinase, FRK-1, limits Wnt signaling by preventing the adhesion complex-associated beta-catenin, HMP-2, from participating in Wnt-dependent specification of the endoderm during embryogenesis. Removal of FRK-1 function results in relocalization of HMP-2 to the nucleus of epidermal cells, and allows …

Glutamine Synthetase Partitioning In Native And Introduced Salt Marsh Grasses, Eric L.G. Hazelton, Thomas J. Knight Phd, Theresa A. Theodose Phd

Faculty Publications

Plants with higher glutamine synthetase (GS) activity in photosynthetic tissues than below-ground structures (high leaf:root [L:R] GS activity) show growth advantages over plants with a low L:R GS activity ratio. The benefits of a high L:R GS activity ratio are well documented in agricultural systems, but little is known about the ecology of GS partitioning in natural systems. To determine the ecological significance of GS partitioning, we measured above- and below-ground GS activity in Spartina grasses field-collected from a Maine salt marsh and others raised in a growth chamber from seed. The more stress-tolerant, faster growing S. alterniflora had a …

Heads Or Tails: L1 Insertion-Associated 5' Homopolymeric Sequences, Thomas J. Meyer, Deepa Srikanta, Erin M. Conlin, Mark A. Batzer

Faculty Publications

Background. L1s are one of the most successful autonomous mobile elements in primate genomes. These elements comprise as much as 17% of primate genomes with the majority of insertions occurring via target primed reverse transcription (TPRT). Twin priming, a variant of TPRT, can result in unusual DNA sequence architecture. These insertions appear to be inverted, truncated L1s flanked by target site duplications. Results. We report on loci with sequence architecture consistent with variants of the twin priming mechanism and introduce dual priming, a mechanism that could generate similar sequence characteristics. These insertions take the form of truncated L1s with hallmarks …

Three-Dimensional Structure Of The Weakly Associated Protein Homodimer Ser13 Using Rdcs And Paramagnetic Surface Mapping, Hsiau Wei Lee, Greg Wylie, Sonal Bansal, Xu Wang, Adam W. Barb, Megan A. Macnaughtan, Asli Ertekin, Gaetano T. Montelione, James H. Prestegard

Faculty Publications

The traditional NMR-based method for determining oligomeric protein structure usually involves distinguishing and assigning intra- and intersubunit NOEs. This task becomes challenging when determining symmetric homo-dimer structures because NOE cross-peaks from a given pair of protons occur at the same position whether intra- or intersubunit in origin. While there are isotope-filtering strategies for distinguishing intra from intermolecular NOE interactions in these cases, they are laborious and often prove ineffectual in cases of weak dimers, where observation of intermolecular NOEs is rare. Here, we present an efficient procedure for weak dimer structure determination based on residual dipolar couplings (RDCs), chemical shift …

A Global Census Of Fission Yeast Deubiquitinating Enzyme Localization And Interaction Networks Reveals Distinct Compartmentalization Profiles And Overlapping Functions In Endocytosis And Polarity, Ilektra Kouranti, Janel R. Mclean, Anna Feoktistova, Ping Liang, Alyssa E. Johnson, Rachel H. Roberts-Galbraith, Kathleen L. Gould

Faculty Publications

Ubiquitination and deubiquitination are reciprocal processes that tune protein stability, function, and/or localization. The removal of ubiquitin and remodeling of ubiquitin chains is catalyzed by deubiquitinating enzymes (DUBs), which are cysteine proteases or metalloproteases. Although ubiquitination has been extensively studied for decades, the complexity of cellular roles for deubiquitinating enzymes has only recently been explored, and there are still several gaps in our understanding of when, where, and how these enzymes function to modulate the fate of polypeptides. To address these questions we performed a systematic analysis of the 20 Schizosaccharomyces pombe DUBs using confocal microscopy, proteomics, and enzymatic activity …

The Herpes Simplex Virus Type 1 Ul20 Protein And The Amino Terminus Of Glycoprotein K (Gk) Physically Interact With Gb, Vladimir N. Chouljenko, Arun V. Iyer, Sona Chowdhury, Joohyun Kim, Konstantin G. Kousoulas

Faculty Publications

Herpes simplex virus type 1 (HSV-1) glycoprotein K (gK) and the UL20 protein (UL20p) are strictly required for virus-induced cell fusion, and mutations within either the gK or UL20 gene cause extensive cell fusion (syncytium formation). We have shown that gK forms a functional protein complex with UL20p, which is required for all gK and UL20p-associated functions in the HSV-1 life cycle. Recently, we showed that the amino-terminal 82 amino acids (aa) of gK (gKa) were required for the expression of the syncytial phenotype of the mutant virus gBΔ28 lacking the carboxyl-terminal 28 amino acids of gB (V. N. Chouljenko, …

Expression Of A Low Co2-Inducible Protein, Lci1, Increases Inorganic Carbon Uptake In The Green Alga Chlamydomonas Reinhardtii, Norikazu Ohnishi, Hideya Fukuzawa, Bratati Mukherjee, Tomoki Tsujikawa, Mari Yanase, Hirobumi Nakano, James V. Moroney

Faculty Publications

Aquatic photosynthetic organisms can modulate their photosynthesis to acclimate to CO2-limiting stress by inducing a carbon-concentrating mechanism (CCM) that includes carbonic anhydrases and inorganic carbon (Ci) transporters. However, to date, Ci-specific transporters have not been well characterized in eukaryotic algae. Previously, a Chlamydomonas reinhardtii mutant (lcr1) was identified that was missing a Myb transcription factor. This mutant had reduced light-dependent CO2 gas exchange (LCE) activity when grown under CO2-limiting conditions and did not induce the CAH1 gene encoding a periplasmic carbonic anhydrase, as well as two as yet uncharacterized genes, LCI1 and LCI6. In this study, LCI1 was placed under …

Stabilization Of A Chemostat Model With Haldane Growth Functions And A Delay In The Measurements, Frédéric Mazenc, Michael Malisoff

Faculty Publications

The stabilization of equilibria in chemostats with measurement delays is a complex and challenging problem, and is of significant ongoing interest in bioengineering and population dynamics. In this paper, we solve an output feedback stabilization problem for chemostat models having two species, one limiting substrate, and either Haldane or Monod growth functions. Our feedback stabilizers depend on a given linear combination of the species concentrations, which are both measured with a constant time delay. The values of the delays are unknown. Instead, one only knows an upper bound on the delays, and we allow the upper bound to be arbitrarily …

Delineation Of Differential Temporal Relations Between Specific Eating And Anxiety Disorders, Julia D. Buckner, Jose Silgado, Peter M. Lewinsohn

Faculty Publications

This study examined the temporal sequencing of eating and anxiety disorders to delineate which anxiety disorders increase eating disorder risk and whether individuals with eating disorders are at greater risk for particular anxiety disorders. The sample was drawn from the Oregon Adolescent Depression Project. Temporal relations between specific eating and anxiety disorders were examined after controlling for relevant variables (e.g., mood disorders, other anxiety disorders) over 14. years. After excluding those with anorexia nervosa (AN) in adolescence (T1), OCD was the only T1 anxiety disorder to predict AN by age 30 (T4). No T1 anxiety disorder was associated with T4 …

The Impact Of Racial Metric Variation In The Os Coxae On The Morphological Assessment Of Sex, Ginesse A. Listi

Faculty Publications

This study examines whether sex determination based on morphological traits in the os coxae is impacted by racial quantitative variation. Nineteen traits were evaluated independently by two observers in 876 os coxae. Chi-square test was used on a random sample of 400 individuals to assess whether the distribution of correct sex assessment varied for white and black individuals based on each trait individually and all 19 traits collectively, as well as on inter-observer agreement in correct sex assessment. Results indicate that accuracy of sex assessment varied between white and black individuals in certain individual traits; however, accuracy was not impacted …

A Sense Of Disentitlement: Frame-Shifting And Metaphor In Ashcroft V. Iqbal, Lisa A. Eichhorn

Faculty Publications

No abstract provided.

Integrating Concepts And Technologies To Advance The Study Of Bird Migration, W. Douglas Robinson, Melissa Bowlin, Isabelle Bisson, Judy Shamoun-Barnes, Kasper Thorup, Robert H. Diehl, Thomas H. Kunz, Sarah Mabey, David W. Winkler

Faculty Publications

Recent technological innovation has opened new avenues in migration research - for instance, by allowing individual migratory animals to be followed over great distances and long periods of time, as well as by recording physiological information. Here, we focus on how technology - specifically applied to bird migration - has advanced our knowledge of migratory connectivity, and the behavior, demography, ecology, and physiology of migrants. Anticipating the invention of new and smaller tracking devices, in addition to the ways that technologies may be combined to measure and record the behavior of migratory animals, we also summarize major conceptual questions that …

Is Love A Flimsy Foundation? Soulmate Versus Institutional Models Of Marriage, W. Bradford Wilcox, Jeffrey P. Dew

Faculty Publications

Steven Nock argued that love—understood narrowly in terms of emotional and sexual intimacy—was a flimsy foundation for relationships and that the institution of marriage provided a firmer footing for stable, high-quality relationships than love alone. Relying on data from the Marriage Matters Survey of 1414 married men and women in Louisiana (1998–2004), we extended Nock’s insights to consider whether contemporary marriages organized along institutional lines enjoyed more stability, satisfaction, and less conflict than marriages organized around a soulmate model. Largely consistent with Nock’s perspective, we found that individuals who embraced norms of marital permanency and gender specialization and were embedded …

Hopelessness, Depression, And Early Markers Of Endothelial Dysfunction In U.S. Adults, D. Phuong Do, Jennifer B. Dowd, Nalini Ranjit, James S. House, George A. Kaplan

Faculty Publications

Objective - This study examines whether the psychological traits of hopelessness and depressive symptoms are related to endothelial dysfunction.

Methods - Data come from a subsample of 434 respondents in the 2001-2003 Chicago Community Adult Health Study (CCAHS), a population-based survey designed to study the impact of psychological attributes, neighborhood environment, and socio-economic circumstances on adults age 18 and over. Circulating biomarkers of endothelial dysfunction including e-selectin, p-selectin and s-ICAM1 were obtained from serum samples. Hopelessness was measured by responses to two questions and depressive symptoms were measured by an 11-item version of the CES-D. Multivariate regression models tested whether …

Neighborhood Effects On Health: Concentrated Advantage And Disadvantage, Brian K. Finch, D. Phuong Do, Melonie Heron, Chloe E. Bird, Teresa Seeman, Nicole Lurie

Faculty Publications

We investigate an alternative conceptualization of neighborhood context and its association with health. Using an index that measures a continuum of concentrated advantage and disadvantage, we examine whether the relationship between neighborhood conditions and health varies by socio-economic status. Using NHANES III data geo-coded to census tracts, we find that while largely uneducated neighborhoods are universally deleterious, individuals with more education benefit from living in highly educated neighborhoods to a greater degree than individuals with lower levels of education.

Memristive Adaptive Filters, T. Driscoll, J. Quinn, S. Klein, H. T. Kim, B. J. Kim, Yuriy V. Pershin Dr, M. Di Ventra, D. N. Basov

Faculty Publications

Using the memristive properties of vanadium dioxide, we experimentally demonstrate an adaptive filter by placing a memristor into an LC contour. This circuit reacts to the application of select frequency signals by sharpening the quality factor of its resonant response, and thus “learns” according to the input waveform. The proposed circuit employs only analog passive elements, and may find applications in biologically inspired processing and information storage. We also extend the learning-circuit framework mathematically to include memory-reactive elements, such as memcapacitors and meminductors, and show how this expands the functionality of adaptive memory filters.

Electrochemical Patterning Of Organic Monolayers On Silicon, Sri Sai S. Vegunta, Johnpeter N. Ngunjiri, John C. Flake

Faculty Publications

Organic monolayers may be grafted onto silicon surfaces using an in situ electrochemical patterning method. In this technique, dielectric templates such as polystyrene spheres (ε=2.5) or poly(dimethylsiloxane) stamps (ε=2.3-2.8) are placed in close proximity to, or in direct contact with, silicon electrodes while a potential is applied to drive electrografting reactions. In this work, the authors describe methyl monolayer patterns created in anodic processes and phenylacetylene monolayer patterns created in cathodic processes. Both anodic and cathodic processes show similar chronoamperometric behavior, suggesting silicon passivation associated with the formation of monolayers. Atomic force microscopy shows the sizes, geometries, and thickness of …

Targeted Interactomics Reveals A Complex Core Cell Cycle Machinery In Arabidopsis Thaliana, Jelle Van Leene, Jens Hollunder, Dominique Eeckhout, Geert Persiau, Eveline Van De Slijke, Hilde Stals, Gert Van Isterdael, Aurine Verkest, Sandy Neirynck, Yelle Buffel, Stefanie De Bodt, Steven Maere, Kris Laukens, Anne Pharazyn, Paulo C.G. Ferreira, Nubia Eloy, Charlotte Renne, Christian Meyer, Jean Denis Faure, Jens Steinbrenner, Jim Beynon, John C. Larkin, Yves Van De Peer, Pierre Hilson, Martin Kuiper, Lieven De Veylder, Harry Van Onckelen, Dirk Inzé, Erwin Witters, Geert De Jaeger

Faculty Publications

Cell proliferation is the main driving force for plant growth. Although genome sequence analysis revealed a high number of cell cycle genes in plants, little is known about the molecular complexes steering cell division. In a targeted proteomics approach, we mapped the core complex machinery at the heart of the Arabidopsis thaliana cell cycle control. Besides a central regulatory network of core complexes, we distinguished a peripheral network that links the core machinery to up- and downstream pathways. Over 100 new candidate cell cycle proteins were predicted and an in-depth biological interpretation demonstrated the hypothesis-generating power of the interaction data. …

In Appreciation Of The Kind Of Rhetoric We Learn In School: An Institutional Perspective On The Rhetorical Situation And On Education, Kathleen F. Mcconnell

Faculty Publications

Theoretical discussion of the rhetorical situation has been dedicated largely to questions of its ontology and of how it is constituted. Where this ontological orientation has inclined theorists to treat the concept as a theoretical premise, an institutional orientation would instead frame constructivist accounts of the rhetorical situation as a political-pedagogical commitment and treat the ethical obligations that arise from any given situation as bound to specific institutional forms. From an institutional perspective, the rhetorical situation is to conscience as the institution of school is to education. The distinction of both rhetorical situations and schools lies not in their contrivedness …

Insights Into Particle Formation And Remineralization Using The Short-Lived Radionuclide, Thorium-234, Kanchan Maiti, Claudia R. Benitez-Nelson, Ken O. Buesseler

Faculty Publications

[1] Simple mass balance models are applied to a high resolution 234Th profile from the northwest Pacific to examine the magnitude, rate, and depth distribution of particle remineralization processes below the euphotic zone (Ez). Here, excess 234Th (234Th > 238U) below the Ez is attributed to fragmentation processes that result in the conversion of sinking to non‐sinking particles. By considering particulate organic carbon (POC) to 234Th ratios on particles, we show that POC flux attenuation is larger than for 234Th, which we attribute to bacterial and zooplankton consumption of sinking POC. Three case studies are used to demonstrate how different combinations …

Location, Location, Location: Compartmentalization Of Early Events In Leukotriene Biosynthesis, Marcia E. Newcomer, Nathaniel C. Gilbert

Faculty Publications

Leukotrienes (LTs), derived from arachidonic acid (AA) released from the membrane by the action of phospholipase A2, are potent lipid mediators of the inflammatory response. In 1983, Dahlén et al. demonstrated that LTC4, LTD4, and LTE4 mediate antigen-induced constriction of bronchi in tissue obtained from subjects with asthma (Dahlén, S. E., Hansson, G., Hedqvist, P., Björck, T., Granström, E., and Dahlén, B. (1983) Proc. Natl. Acad. Sci. U.S.A. 80, 1712-1716). Over the last 25+ years, substantial progress has been made in understanding how LTs exert their effects, and a broader appreciation for the numerous biological processes they mediate has emerged. …

Kinetic And Spectroscopic Studies Of Hemin Acquisition In The Hemophore Hasap From Pseudomonas Aeruginosa, Erik T. Yukl, Grace Jepkorir, Aileen Y. Alontaga, Lawrence Pautsch, Juan C. Rodriguez, Mario Rivera, Pierre Moënne-Loccoz

Faculty Publications

The extreme limitation of free iron has driven various pathogens to acquire iron from the host in the form of heme. Specifically, several Gram-negative pathogens secrete a heme binding protein known as HasA to scavenge heme from the extracellular environment and to transfer it to the receptor protein HasR for import into the bacterial cell. Structures of heme-bound and apo-HasA homologues show that the heme iron(III) ligands, His32 and Tyr75, reside on loops extending from the core of the protein and that a significant conformational change must occur at the His32 loop upon heme binding. Here, we investigate the kinetics …

Incorporating Genomics And Bioinformatics Across The Life Sciences Curriculum, Jayna L. Ditty, Christopher A. Kvaal, Brad Goodner, Sharyn K. Freyermuth, Cheryl Bailey, Robert A. Britton, Stuart G. Gordon, Sabine Heinhorst, Kelyenne Reed, Zhaohui Xu, Erin R. Sanders-Lorenz, Seth Axen, Edwin Kim, Mitrick Johns, Kathleen Scott, Cheryl A. Kerfeld

Faculty Publications

No abstract provided.

Titer-Plate Formatted Continuous Flow Thermal Reactors: Design And Performance Of A Nanoliter Reactor, Pin Chuan Chen, Daniel S. Park, Byoung Hee You, Namwon Kim, Taehyun Park, Steven A. Soper, Dimitris E. Nikitopoulos, Michael C. Murphy

Faculty Publications

Arrays of continuous flow thermal reactors were designed, configured, and fabricated in a 96-device (12 × 8) titer-plate format with overall dimensions of 120 mm × 96 mm, with each reactor confined to a 8 mm × 8 mm footprint. To demonstrate the potential, individual 20-cycle (740 nl) and 25-cycle (990 nl) reactors were used to perform the continuous flow polymerase chain reaction (CFPCR) for amplification of DNA fragments of different lengths. Since thermal isolation of the required temperature zones was essential for optimal biochemical reactions, three finite element models, executed with ANSYS (v. 11.0, Canonsburg, PA), were used to …

Insights Into Particle Formation And Remineralization Using The Short-Lived Radionuclide, Thoruim-234, Kanchan Maiti, Claudia R. Benitez-Nelson, Ken O. Buesseler

Faculty Publications

Simple mass balance models are applied to a high resolution ²³⁴Th profile from the northwest Pacific to examine the magnitude, rate, and depth distribution of particle remineralization processes below the euphotic zone (Ez). Here, excess ²³⁴Th (²³⁴Th > ²³⁸U) below the Ez is attributed to fragmentation processes that result in the conversion of sinking to non-sinking particles. By considering particulate organic carbon (POC) to ²³⁴Th ratios on particles, we show that POC flux attenuation is larger than for ²³⁴Th, which we attribute to bacterial and zooplankton consumption of sinking POC. Three case studies are …

Phase-Response Curves And Synchronized Neural Networks., Smeal Rm, Ermentrout Gb, White Ja

Faculty Publications

No abstract provided.

Increased Lipid Accumulation In The Chlamydomonas Reinhardtii Sta7-10 Starchless Isoamylase Mutant And Increased Carbohydrate Synthesis In Complemented Strains, Victoria H. Work, Randor Radakovits, Robert E. Jinkerson, Jonathan E. Meuser, Lee G. Elliott, David J. Vinyard, Lieve M.L. Laurens, G. Charles Dismukes, Matthew C. Posewitz

Faculty Publications

The accumulation of bioenergy carriers was assessed in two starchless mutants of Chlamydomonas reinhardtii (the sta6 [ADP-glucose pyrophosphorylase] and sta7-10 [isoamylase] mutants), a control strain (CC124), and two complemented strains of the sta7-10 mutant. The results indicate that the genetic blockage of starch synthesis in the sta6 and sta7-10 mutants increases the accumulation of lipids on a cellular basis during nitrogen deprivation relative to that in the CC124 control as determined by conversion to fatty acid methyl esters. However, this increased level of lipid accumulation is energetically insufficient to completely offset the loss of cellular starch that is synthesized by …