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Item 3D-Printed, Modular, and Parallelized Microfluidic System with Customizable Scaffold Integration to Investigate the Roles of Basement Membrane Topography on Endothelial Cells(2021-02-05) Jones, Curtis G.; Huang, Tianjiao; Chung, Jay H.; Chen, ChengpengBecause dysfunctions of endothelial cells are involved in many pathologies, in vitro endothelial cell models for pathophysiological and pharmaceutical studies have been a valuable research tool. Although numerous microfluidic-based endothelial models have been reported, they had the cells cultured on a flat surface without considering the possible 3D structure of the native ECM. Endothelial cells rest on the basement membrane in vivo, which contains an aligned microfibrous topography. To better understand and model the cells, it is necessary to know if and how the fibrous topography can affect endothelial functions. With conventional fully integrated microfluidic apparatus, it is difficult to include additional topographies in a microchannel. Therefore, we developed a modular microfluidic system by 3D-printing and electrospinning, which enabled easy integration and switching of desired ECM topographies. Also, with standardized designs, the system allowed for high flow rates up to 4000 µL/min, which covered the full shear stress range for endothelial studies. We found that the aligned fibrous topography on the ECM altered arginine metabolism in endothelial cells, and thus increased nitric oxide production. To the best of our knowledge, this is the most versatile endothelial model that has been reported, and the new knowledge generated thereby lays a groundwork for future endothelial research and modeling.Item A 4‐year zonal climatology of lower tropospheric CO₂ derived from ocean‐only Atmospheric Infrared Sounder observations(American Geophysical Union, 2008-09-20) Strow, L. Larrabee; Hannon, Scott E.A 4‐year zonally averaged climatology of atmospheric CO₂, ocean only, between ±60° latitude has been derived from the Atmospheric Infrared Sounder (AIRS) radiances. Using only very clear fields of view, the CO₂ profile in the computed radiances is scaled until agreement is found with observations. ECMWF forecast and analysis fields are used for the temperature profile in the computed radiances. The AIRS channels used to derive CO₂ amounts are nominally sensitive to CO₂ variability in the ∼300–800 mbar region (2–9 km), significantly lower in the atmosphere than that in previous studies using AIRS. Validation using aircraft measurements of CO₂ at 650 mbar indicates that the AIRS CO₂ results presented here are accurate to the 0.5–1.0 ppm level. The AIRS‐derived climatology clearly exhibits the CO₂ rectifier effect, with mean CO₂ values several parts per million lower than in those in the boundary layer. The AIRS CO₂ seasonal cycle has a relatively constant amplitude of ∼3 ppm from +10° to +60° latitude, which matches the boundary layer seasonal cycle amplitude near +10° latitude but is about three times smaller than that in the boundary layer amplitude at +60° latitude. Phase comparisons between the AIRS and boundary layer CO₂ seasonal cycles show the boundary layer phase leading AIRS in the Northern Hemisphere until ∼+10° latitude, where the phases cross and the AIRS higher‐altitude CO₂ begins to lead the boundary layer phase down to ∼−10° latitude. These results may offer new insight into CO₂ interhemispherical transport. Growth rates derived from the AIRS CO₂ climatology are 2.21 ± 0.24 ppm/year, in good agreement with in situ measurements.Item Abstracting Evidence: Documentary Process in the Service of Fictional Gameworlds(Game Studies, 2017-07) Oldenburg, AaronDocumentary filmmaking and the design of videogames have often converged in the form of “docugames”, games that aspire to the form of documentary. This paper looks at a related strategy for creating content and gameplay: that of using documentary processes, such as interviews and on-location evidence collection, for games that involve varying levels of fictionalization. It will discuss abstract approaches to the idea of realism in docugames as well as traditional documentary film. It will also detail an original design project that begins with documentary evidence collection and ends with an impressionistic fictionalized narrative. It will discuss the benefits of this approach, and the seemingly paradoxical creation of a form of realism through fictionalization. Playtesting results of this experiment will be detailed and related paths will be suggested for continued exploration.Item Adam Smith’s Approach to Public Policy: Astounding Deviation or Artful Moderation?(SSRN, 2010-12-01) Clark, MichaelRecent academic work has attempted to change the interpretation of Adam Smith from the founder of free market economics to a proponent of something much more akin to the modern welfare state. In a well known article Jacob Viner even claims that Smith’s departures from liberty were so great that an index of them would have astounded Smith. I suggest that Smith’s polite rhetorical strategy – represented by his explicit praise of the moderate rule Solon – has been under-appreciated. This paper aims to examine the Wealth of Nations with Smith’s polite approach in mind. I show that Smith’s interventionism was more limited than some suggest, and that some of the interventions contravened the liberty principle only mildly. I also show that virtually all of the interventions entertained or endorsed by Smith were part of the status quo in Scotland at the time. The approach also provides potential explanations for some of Smith’s well known inconsistencies, such as his endorsement of restriction in banking and lending at interest.Item Allosteric Inhibitors Have Distinct Effects, but Also Common Modes of Action, in the HCV Polymerase(2016-11-15) Davis, Brittny C.; Brown, Jodian A.; Thorpe, Ian F.The RNA-dependent RNA polymerase from the Hepatitis C Virus (gene product NS5B) is a validated drug target because of its critical role in genome replication. There are at least four distinct allosteric sites on the polymerase to which several small molecule inhibitors bind. In addition, numerous crystal structures have been solved with different allosteric inhibitors bound to the polymerase. However, the molecular mechanisms by which these small molecules inhibit the enzyme have not been fully elucidated. There is evidence that allosteric inhibitors alter the intrinsic motions and distribution of conformations sampled by the enzyme. In this study we use molecular dynamics simulations to understand the structural and dynamic changes that result when inhibitors are bound at three different allosteric binding sites on the enzyme. We observe that ligand binding at each site alters the structure and dynamics of NS5B in a distinct manner. Nonetheless, our studies also highlight commonalities in the mechanisms of action of the different inhibitors. Each inhibitor alters the conformational states sampled by the enzyme, either by rigidifying the enzyme and preventing transitions between functional conformational states or by destabilizing the enzyme and preventing functionally relevant conformations from being adequately sampled. By illuminating the molecular mechanisms of allosteric inhibition, these studies delineate the intrinsic functional properties of the enzyme and pave the way for designing novel and more effective polymerase inhibitors. This information may also be important to understand how allosteric regulation occurs in related viral polymerases and other enzymes.Item Altered State Machines: Coding Salvia Space(Psychedelic Press, 2017-11) Oldenburg, AaronSeer (KOR), Thinning and Brief Excursion (2016) are three videogames that attempt to proceduralize characteristics of the experience of the hallucinogenic chemical Salvinorin A, the active component of the sage variety salvia divinorum. The purpose of these experiments is to explore the boundaries of representations of space and self in digital virtual worlds, as well as to attempt to convey the intangible emotional (as well as anti-emotional) and philosophical aspects of the experience. The goal is to evoke in the player sensations of discomfort, loss of direct control and a sense of being outside of assumed videogame space.Item An alternative view of ecological community thresholds and appropriate analyses for their detection: comment(Ecological Society of America, 2011-10-01) King, Ryan S.; Baker, MatthewItem An Analysis of NCEP Tropical Cyclone Vitals and Potential Effects on Forecasting Models(American Meteorological Society, 2012-06-15) Trahan, Sam; Sparling, LynnThis study analyzes the Tropical Cyclone Vitals Database (TCVitals), which contains cyclone location, intensity, and structure information, generated in real time by forecasters. These data are used to initialize cyclones in several NCEP operational forecasting models via bogusing and vortex relocation methods. In many situations, time is of the essence and the TCVitals database represents the best real-time estimate of the cyclone state possible in real time, given the limitations of available data and time constraints inherent in real-time forecasting. NCEP and other users of TCVitals have a responsibility to work around the inevitable limitations of what forecasters can do for TCVitals in real time. With ensemble systems becoming available, a way to do that will soon be available. However, the TCVitals’ limitations must first be quantitatively understood so that model developers can take them into account. That is the motivation for the present study, which compares the TCVitals storm location and intensity to postseason reanalysis values found in the best-track database and statistically compares the TCVitals storm depth to 946 Tropical Rainfall Measuring Mission (TRMM) overpasses. All storms of tropical depression strength or stronger in all basins are analyzed, with a special focus on National Hurricane Center TCVitals for the North Atlantic and eastern Pacific basins, the main areas of responsibility for NCEP. In addition, the sensitivity to TCVitals on the Hurricane Weather Research and Forecasting (HWRF) model is examined by rerunning the 2011 HWRF for the 2010 North Atlantic season twice: once with TCVitals input and once with best-track input.Item Analysis of subsurface storage and streamflow generation in urban watersheds(Wiley, 2015-01-21) Bhaskar, Aditi S.; Welty, ClaireSubsurface storage as a regulator of streamflow was investigated as an explanation for the large proportion of pre‐event water observed in urban streams during storm events. We used multiple lines of inquiry to explore the relationship between pre‐event water proportion, subsurface storage, and streamflow under storm conditions. First, we used a three‐dimensional model of integrated subsurface and surface flow and solute transport to simulate an idealized hillslope to perform model‐based chemical hydrograph separation of stormflow. Second, we employed simple dynamical systems analysis to derive the relationship between subsurface storage and streamflow for three Baltimore, Maryland watersheds (3.8–14 km2 in area) along an urban‐to‐rural gradient. Last, we applied chemical hydrograph separation to high‐frequency specific conductance data in nested urban watersheds (∼50% impervious surface cover) in Dead Run, Baltimore County, Maryland. Unlike the importance of antecedent subsurface storage observed in some systems, we found that rainfall depth and not subsurface storage was the primary control on pre‐event water proportion in both field observations and hillslope numerical experiments. Field observations showed that antecedent stream base flow did not affect pre‐event water proportion or streamflow values under storm conditions. Hillslope model results showed that the relationship between streamflow values under storm conditions and subsurface storage was clockwise hysteretic. The simple dynamical systems approach showed that stream base flow in the most urbanized of three watersheds exhibited the largest sensitivity to changes in storage. This work raises questions about the streamflow generation mechanisms by which pre‐event water dominates urban storm hydrographs, and the shifts between mechanisms in rural and urban watersheds.Item Calculation of the expected output spectrum for a mid-infrared supercontinuum source based on As₂S₃ chalcogenide photonic crystal fibers(Optical Society of America, 2014-09-08) Weiblen, R. J.; Docherty, A.; Menyuk, Curtis; Shaw, L. B.; Sanghera, J. S.; Aggarwal, I. D.We computationally investigate supercontinuum generation in an As₂S₃ solid core photonic crystal fiber (PCF) with a hexagonal cladding of air holes. With a goal of obtaining a supercontinuum output spectrum that can predict what might be seen in an experiment, we investigate the spectral and statistical behavior of a mid-infrared supercontinuum source using a large ensemble average of 10⁶ realizations, in which the input pulse duration and energy vary. The output spectrum is sensitive to small changes (0.1%) in these pulse parameters. We show that the spectrum can be divided into three regions with distinct characteristics: a short-wavelength region with high correlation, a middle-wavelength region with minimal correlation, and a long-wavelength region where the behavior is dominated by a few rare large-bandwidth events. We show that statistically significant fluctuations exist in the experimentally expected output spectrum and that we can reproduce an excellent match to that spectrum with a converged shape and bandwidth using 5000 realizations.Item A Case Study of the Implementation of Staff Training Aimed at Reducing Rearrest (STARR)(United States Courts, 2016-06) Clodfelter, Tammatha; Holcomb, Jefferson; Alexander, Melissa; Marcum, Catherine; Richards, Tara; United States CourtsResearch on evidence-based correctional practices notes the critical importance of program implementation in assessing program effectiveness. In this article, the authors describe the implementation of a training program to improve officer-offender interactions in the federal probation system. They use several sources of information to assess implementation strategies and the success of those efforts within a single federal district.Item Cell deformation cytometry using diode-bar optical stretchers(Society of Photo-Optical Instrumentation Engineers., 2010-08-04) Sraj, Ihab; Eggleton, Charles D.; Jimenez, Ralph; Hoover, Erich E.; Squier, Jeffrey A.; Chichester, Justin; Marr, David W.The measurement of cell elastic parameters using optical forces has great potential as a reagent-free method for cell classification, identification of phenotype, and detection of disease; however, the low throughput associated with the sequential isolation and probing of individual cells has significantly limited its utility and application. We demonstrate a single-beam, high-throughput method where optical forces are applied anisotropically to stretch swollen erythrocytes in microfluidic flow. We also present numerical simulations of model spherical elastic cells subjected to optical forces and show that dual, opposing optical traps are not required and that even a single linear trap can induce cell stretching, greatly simplifying experimental implementation. Last, we demonstrate how the elastic modulus of the cell can be determined from experimental measurements of the equilibrium deformation. This new optical approach has the potential to be readily integrated with other cytometric technologies and, with the capability of measuring cell populations, enabling true mechanical-property-based cell cytometry.Item Comparisons of bispectral and polarimetric retrievals of marine boundary layer cloud microphysics: case studies using a LES–satellite retrieval simulator(Copernicus Publications, 2018-06-26) Miller, Daniel J.; Zhang, Zhibo; Platnick, Steven; Ackerman, Andrew S.; Werner, Frank; Cornet, Celine; Knobelspiesse, KirkMany passive remote-sensing techniques have been developed to retrieve cloud microphysical properties from satellite-based sensors, with the most common approaches being the bispectral and polarimetric techniques. These two vastly different retrieval techniques have been implemented for a variety of polar-orbiting and geostationary satellite platforms, providing global climatological data sets. Prior instrument comparison studies have shown that there are systematic differences between the droplet size retrieval products (effective radius) of bispectral (e.g., MODIS, Moderate Resolution Imaging Spectroradiometer) and polarimetric (e.g., POLDER, Polarization and Directionality of Earth's Reflectances) instruments. However, intercomparisons of airborne bispectral and polarimetric instruments have yielded results that do not appear to be systematically biased relative to one another. Diagnosing this discrepancy is complicated, because it is often difficult for instrument intercomparison studies to isolate differences between retrieval technique sensitivities and specific instrumental differences such as calibration and atmospheric correction. In addition to these technical differences the polarimetric retrieval is also sensitive to the dispersion of the droplet size distribution (effective variance), which could influence the interpretation of the droplet size retrieval. To avoid these instrument-dependent complications, this study makes use of a cloud remote-sensing retrieval simulator. Created by coupling a large-eddy simulation (LES) cloud model with a 1-D radiative transfer model, the simulator serves as a test bed for understanding differences between bispectral and polarimetric retrievals. With the help of this simulator we can not only compare the two techniques to one another (retrieval intercomparison) but also validate retrievals directly against the LES cloud properties. Using the satellite retrieval simulator, we are able to verify that at high spatial resolution (50m) the bispectral and polarimetric retrievals are highly correlated with one another within expected observational uncertainties. The relatively small systematic biases at high spatial resolution can be attributed to different sensitivity limitations of the two retrievals. In contrast, a systematic difference between the two retrievals emerges at coarser resolution. This bias largely stems from differences related to sensitivity of the two retrievals to unresolved inhomogeneities in effective variance and optical thickness. The influence of coarse angular resolution is found to increase uncertainty in the polarimetric retrieval but generally maintains a constant mean value.Item Complete Genome Sequences of HonestAbe, Anthony, and Taffo16, Three Cluster C Bacillus cereus Group Bacteriophages(American society for Microbiology, 2018-06-21) Lee, Martin; Puglisi, Kayla M.; Erill, Ivan; Caruso, Steven M.; UMBC STEM-BUILD Cohort 1Three cluster C Myoviridae bacteriophages that infect Bacillus cereus group bacteria were isolated from soil collected in the mid-Atlantic region using B. thuringiensis subsp. kurstaki as a host. Bacillus phages HonestAbe, Anthony, and Taffo16 each shared 90% or higher average nucleotide identities within their subclusters.Item Development of chromatofocusing techniques employing mixed-mode column packings for protein separations.(Elsevier B.V, 2013-11-06) Frey, Douglas D.; Guo, Hui; Li, XiangRecent studies reported in the literature using mixed-mode chromatography (MMC) column packings have shown that multiple modes of interactions between the column packing and proteins can be usefully exploited to yield excellent resolution as well as salt-tolerant adsorption of the target protein. In this study, a mixed-mode separation method using commercially available column packings was explored which combines the techniques of hydrophobic-interaction chromatography and chromatofocusing. Two different column packings, one based on mercapto-ethyl-pyridine (MEP) and the other based on hexylamine (HEA) were investigated with regard to their ability to separate proteins when using internally generated, retained pH gradients. The effects of added salt and urea on the behavior of the retained pH gradient and the protein separation achieved when using MMC column packings for chromatofocusing were also investigated. Numerical simulations using methods developed in previous work were shown to agree with experimental results when using reasonable physical parameters. These numerical simulations were also shown to be a useful qualitative method to select the compositions of the starting and elution buffers in order to achieve desired shapes for the pH and ionic strength gradients. The use of the method to fractionate blood serum was explored as a prototype example application.Item A different view: sensory drive in the polarized-light realm(Oxord academic, 2018-05-31) Cronin, Thomas W.Sensory drive, the concept that sensory systems primarily evolve under the influence of environmental features and that animal signals are evolutionarily shaped and tuned by these previously existing sensory systems, has been thoroughly studied regarding visual signals across many animals. Much of this work has focused on spectral aspects of vision and signals. Here, I review work on polarized-light signals of animals and relate these to what is known of polarization visual systems, polarized-light aspects of visual scenes, and polarization-related behavior (e.g., orientation, habitat-finding, contrast enhancement). Other than the broad patterns of scattered polarized light in the sky, most polarization in both terrestrial and aquatic environments results from either reflection or scattering in the horizontal plane. With overhead illumination, horizontal features such as the surfaces of many leaves or of air: water interfaces reflect horizontal polarization, and water scatters horizontally polarized light under most conditions. Several animal species have been demonstrated to use horizontally polarized light fields or features in critical aspects of their biology. Significantly, most biological signals are also horizontally polarized. Here, I present relevant polarization-related behavior and discuss the hypothesis that sensory drive has evolutionarily influenced the structure of polarization signals. The paper also considers the evolutionary origin of circular polarization vision and circularly polarized signals. It appears that this class of signals did not evolve under the influence of sensory drive. The study of signals based on polarized light is becoming a mature field of research.Item Dynamic Linkages Among U.S. Real Estate SectorsBefore and After the Housing Crisis(Springer, 2019-02) Yunus, Nafeesa; Finance and Economics; Finance and EconomicsThis study explores the dynamic nature of linkages among seven key real estate sectors which include residential, health, lodging-resort, storage, office, retail, and industrial. Long-run results reveal evidence of increased integration and contagion across the real estate sectors in the wake of the housing crisis. Short-run analyses suggest bi-directional causality and indicate that shocks to one real estate sector have a much more severe and persistent impact on other real estate sectors during the post-crisis period in comparison to the pre-crisis period. Finally, ripple effects are observed across the real estate sectors with shocks emanating from the "dominant" residential sector and spilling over to other real estate sectorsItem Dynamic ray tracing for modeling optical cell manipulation(OSA, 2010-07-23) Sraj, Ihab; Szatmary, Alex C.; Marr, David W. M.; Eggleton, Charles D.Current methods for predicting stress distribution on a cell surface due to optical trapping forces are based on a traditional ray optics scheme for fixed geometries. Cells are typically modeled as solid spheres as this facilitates optical force calculation. Under such applied forces however, real and non-rigid cells can deform, so assumptions inherent in traditional ray optics methods begin to break down. In this work, we implement a dynamic ray tracing technique to calculate the stress distribution on a deformable cell induced by optical trapping. Here, cells are modeled as three-dimensional elastic capsules with a discretized surface with associated hydrodynamic forces calculated using the Immersed Boundary Method. We use this approach to simulate the transient deformation of spherical, ellipsoidal and biconcave capsules due to external optical forces induced by a single diode bar optical trap for a range of optical powers.Item Effect of collaborative depression treatment on risk for diabetes: A 9-year follow-up of the IMPACT randomized controlled trial(PLoS ONE, 2018-08-23) Khambaty, Tasneem; Callahan, Christopher M.; Stewart, Jesse C.Considerable epidemiologic evidence and plausible biobehavioral mechanisms suggest that depression is an independent risk factor for diabetes. Moreover, reducing the elevated diabetes risk of depressed individuals is imperative given that both conditions are leading causes of death and disability. However, because no prior study has examined clinical diabetes outcomes among depressed patients at risk for diabetes, the question of whether depression treatment prevents or delays diabetes onset remains unanswered. Accordingly, we examined the effect of a 12-month collaborative care program for late-life depression on 9-year diabetes incidence among depressed, older adults initially free of diabetes. Participants were 119 primary care patients [M (SD) age: 67.2 (6.9) years, 41% African American] with a depressive disorder but without diabetes enrolled at the Indiana sites of the Improving Mood-Promoting Access to Collaborative Treatment (IMPACT) trial. Incident diabetes cases were defined as diabetes diagnoses, positive laboratory values, or diabetes medication prescription, and were identified using electronic medical record and Medicare/Medicaid data. Surprisingly, the rate of incident diabetes in the collaborative care group was 37% (22/59) versus 28% (17/60) in the usual care group. Even though the collaborative care group exhibited greater reductions in depressive symptom severity (p = .024), unadjusted (HR = 1.29, 95% CI: 0.69–2.43, p = .428) and adjusted (HR = 1.18, 95% CI: 0.61–2.29, p = .616) Cox proportional hazards models indicated that the risk of incident diabetes did not differ between the treatment groups. Our novel preliminary findings raise the possibility that depression treatment alone may be insufficient to reduce the excess diabetes risk of depressed, older adults.Item Effect of Viscoelasticity on the Analysis of Single-Molecule Force Spectroscopy on Live Cells(Elsevier Inc, 2012-07-03) Gupta, V.K.; Neeves, K.B.; Eggleton, C.D.Single-molecule force spectroscopy is used to probe the kinetics of receptor-ligand bonds by applying mechanical forces to an intermediate media on which the molecules reside. When this intermediate media is a live cell, the viscoelastic properties can affect the calculation of rate constants. We theoretically investigate the effect of media viscoelasticity on the common assumption that the bond force is equal to the instantaneous applied force. Dynamic force spectroscopy is simulated between two cells of varying micromechanical properties adhered by a single bond with a constant kinetic off-rate. We show that cell and microvilli deformation, and hydrodynamic drag contribute to bond forces that can be 28–90% lower than the applied force for loading rates of 10³–10⁷ pN/s, resulting in longer bond lifetimes. These longer bond lifetimes are not caused by changes in bond kinetics; rather, they are due to the mechanical response of the intermediate media on which the bonds reside. Under the assumption that the instantaneous bond force is equal to the applied force—thereby ignoring viscoelasticity—leads to 14–39% error in the determination of off-rates. We present an approach that incorporates viscoelastic properties in calculating the instantaneous bond force and kinetic dissociation parameter of the intermolecular bond.