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West Lafayette, IN, United States

Purdue University, located in West Lafayette, Indiana, is the flagship university of the six-campus Purdue University system. Purdue was founded on May 6, 1869, as a land-grant university when the Indiana General Assembly, taking advantage of the Morrill Act, accepted a donation of land and money from Lafayette businessman John Purdue to establish a college of science, technology, and agriculture in his name. The first classes were held on September 16, 1874, with six instructors and 39 students.The university was founded with the gift of $150,000 from John Purdue, a Lafayette business leader and philanthropist, along with $50,000 from Tippecanoe County, and 100 acres of land from Lafayette residents in support of the project. In 1869, it was decided that the new school would be built near the city of Lafayette and established as Purdue University, in the name of the institution’s principal benefactor.The West Lafayette campus offers more than 200 majors for undergraduates, over 70 master’s and doctoral programs, and professional degrees in pharmacy and veterinary medicine. In addition, Purdue has 18 intercollegiate sports teams and more than 900 student organizations. Today, Purdue is a member of the Big Ten Conference. Purdue enrolls the second largest student body of any university in Indiana as well as the fourth largest international student population of any university in the United States. Wikipedia.


Sironi L.,Harvard - Smithsonian Center for Astrophysics | Giannios D.,Purdue University
Astrophysical Journal | Year: 2014

The interaction of TeV photons from blazars with the extragalactic background light produces a relativistic beam of electron-positron pairs streaming through the intergalactic medium (IGM). The fate of the beam energy is uncertain. By means of two- and three-dimensional particle-in-cell simulations, we study the nonlinear evolution of dilute ultra-relativistic pair beams propagating through the IGM. We explore a wide range of beam Lorentz factors γ b ≫ 1 and beam-to-plasma density ratios α ≪ 1, so that our results can be extrapolated to the extreme parameters of blazar-induced beams (γ b 106 and α10-15, for powerful blazars). For cold beams, we show that the oblique instability governs the early stages of evolution, but its exponential growth terminates - due to self-heating of the beam in the transverse direction - when only a negligible fraction (α/γ b )1/310-7 of the beam energy has been transferred to the IGM plasma. Further relaxation of the beam proceeds through quasi-longitudinal modes, until the momentum dispersion in the direction of propagation saturates at Δp b, /γ b mec0.2. This corresponds to a fraction 10% of the beam energy - irrespective of γ b or α - being ultimately transferred to the IGM plasma (as compared to the heating efficiency of 50% predicted by one-dimensional models, which cannot properly account for the transverse broadening of the beam). For the warm beams generated by TeV blazars, the development of the longitudinal relaxation is suppressed, since the initial dispersion in beam momentum is already Δp b0, /γ b mec ≳ 1. Here, the fraction of beam energy ultimately deposited into the IGM is only α γ b 10-9. It follows that most of the beam energy is still available to power the GeV emission produced by inverse Compton up-scattering of the cosmic microwave background by the beam pairs. © 2014. The American Astronomical Society. All rights reserved..


Hu J.,CAS Institute of Physics | Hu J.,Purdue University
Physical Review X | Year: 2014

Parity is a fundamental quantum number used to classify a state of matter. Materials rarely possess ground states with odd parity. We show that the superconducting state in iron-based superconductors is classified as an odd-parity s-wave spin-singlet pairing state in a single trilayer FeAs/Se, the building block of the materials. In a low-energy effective model constructed on the Fe square bipartite lattice, the superconducting order parameter in this state is a combination of an s-wave normal pairing between two sublattices and an s-wave η pairing within the sublattices. The state has a fingerprint with a real-space sign inversion between the top and bottom As/Se layers. The results suggest that iron-based superconductors are a new quantum state of matter, and the measurement of the odd parity can help to establish high-temperature superconducting mechanisms.


Kim C.H.,Purdue University
Frontiers in Immunology | Year: 2013

The intestine is divided into specialized tissue areas that provide distinct microenvironments for T cells. Regulation of T-cell responses in the gut has been a major focus of recent research activities in the field. T cells in the intestine are regulated by the interplay between host and microbial factors. In the small intestine, retinoic acid (RA) is a major tissue factor that plays important roles in regulation of immune responses. In the large intestine, the influence of RA diminishes, but that of commensal bacterial products increases. RA, gut microbiota, and inflammatory mediators co-regulate differentiation, distribution, and/or effector functions of T cells. Coordinated regulation of immune responses by these factors promotes well-balanced immunity and immune tolerance. Dysregulation of this process can increase infection and inflammatory diseases. © 2013 Kim.


Wadsworth S.M.,Purdue University
Clinical Child and Family Psychology Review | Year: 2013

Taking our nation to war has exposed a generation of military families and children to combat and its consequences. Every dollar spent on bullets, trucks, fuel, and food carried a future 'tax' in the form of consequences for psychological and physical health and family relationships. In this commentary, I focus on several themes that emerge from the special collection or articles. For example, I consider how best to define the ecological niche(s) occupied by military-connected children and families. Not surprisingly given significant gaps in our knowledge, evidence regarding the well-being of military-connected children is mixed. I also consider the multi-layered environments within which individuals and families function, recognizing both the challenges and opportunities they provide. The need to respond rapidly to the evolving needs of military families has highlighted the value of both prevention science and implementation science. Public health models emphasizing a full continuum of care that emphasizes not only treatment but also universal, selective, and indicated prevention also are appealing given the uneven density, uncertain locations, and unknown identities of military families in civilian communities (Beardslee 2013; Murphy and Fairbank 2013). Finally, it is important to recognize that we are at the beginning, not the end, of the post-war lifetimes for the new generation of veterans and their families. © 2013 Springer Science+Business Media New York.


Gautschi W.,Purdue University
BIT Numerical Mathematics | Year: 2011

Vandermonde matrices with real nodes are known to be severely ill-conditioned. We investigate numerically the extent to which the condition number of such matrices can be reduced, either by row-scaling or by optimal configurations of nodes. In the latter case we find empirically the condition of the optimally conditioned n×n Vandermonde matrix to grow exponentially at a rate slightly less than (1+√) n. Much slower growth-essentially linear-is observed for optimally conditioned Vandermonde-Jacobi matrices. We also comment on the computational challenges involved in determining condition numbers of highly ill-conditioned matrices. © 2010 Springer Science + Business Media B.V.


A detailed numerical study was conducted to understand the transient flame propagation process and the flame-speed oscillation phenomenon in a carbon dust cloud. The modeling included the solution of a set of time-dependent conservation equations developed for the gas phase and the particle phase in a spherical coordinate. The gas-phase reactions used detailed chemistry, variable thermodynamic properties, and multicomponent transport properties. The particle-phase equations include the two-phase force interactions in the momentum equation by considering Stoke drag force and thermophoretic force resulting from the gas-phase temperature gradient. Mass and species transfer between the two phases were modeled as a result of both gas-phase and particle surface reactions. Energy transfer between the two phases, including convective, conductive, and radiative heat transfer, were included. Radiation absorption and emission by particles were both especially considered. The results show that because of the different inertia between particles and gas, a velocity slip occurs between the two phases in the region ahead of the flame front. The slip is more significant in the early flame propagation stage than in the later stage. The radiation heat losses of the hot gases and particles to the cold ambient and the radiation gain as a result of the absorption of unburned particles are both important in the present dust flame, because the characteristic time scale of the chemical reactions is longer than that of gaseous flames. Lastly, an analysis of the detailed numerical simulations shows that a slip between the gas and particle velocities is the cause of flame-speed oscillation. The slip leads to a periodic change in local particle number density in the reaction zone, which in turn changes the local fuel equivalence ratio periodically, causing the oscillation. © 2011 The Combustion Institute.


Plotnitsky A.,Purdue University
Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences | Year: 2016

Taking as its point of departure the discovery of the Higgs boson, this article considers quantum theory, including quantum field theory, which predicted the Higgs boson, through the combined perspective of quantum information theory and the idea of technology, while also adopting a nonrealist interpretation, in 'the spirit of Copenhagen', of quantum theory and quantum phenomena themselves. The article argues that the 'events' in question in fundamental physics, such as the discovery of the Higgs boson (a particularly complex and dramatic, but not essentially different, case), are made possible by the joint workings of three technologies: experimental technology, mathematical technology and, more recently, digital computer technology. The article will consider the role of and the relationships among these technologies, focusing on experimental and mathematical technologies, in quantum mechanics (QM), quantum field theory (QFT) and finite-dimensional quantum theory, with which quantum information theory has been primarily concerned thus far. It will do so, in part, by reassessing the history of quantum theory, beginning with Heisenberg's discovery of QM, in quantuminformational and technological terms. This history, the article argues, is defined by the discoveries of increasingly complex configurations of observed phenomena and the emergence of the increasingly complex mathematical formalism accounting for these phenomena, culminating in the standard model of elementary-particle physics, defining the current state of QFT. © 2016 The Author(s) Published by the Royal Society.


Miller J.D.,University of Georgia | Lynam D.R.,Purdue University
Personality Disorders: Theory, Research, and Treatment | Year: 2012

Since its publication, the Psychopathic Personality Inventory and its revision (Lilienfeld & Andrews, 1996; Lilienfeld & Widows, 2005) have become increasingly popular such that it is now among the most frequently used self-report inventories for the assessment of psychopathy. The current meta-analysis examined the relations between the two PPI factors (factor 1: Fearless Dominance; factor 2: Self-Centered Impulsivity), as well as their relations with other validated measures of psychopathy, internalizing and externalizing forms of psychopathology, general personality traits, and antisocial personality disorder symptoms. Across 61 samples reported in 49 publications, we found support for the convergent and criterion validity of both PPI factor 2 and the PPI total score. Much weaker validation was found for PPI factor 1, which manifested limited convergent validity and a pattern of correlations with central criterion variables that was inconsistent with many conceptualizations of psychopathy. © 2012 American Psychological Association.


Petropoulou M.,Purdue University
Monthly Notices of the Royal Astronomical Society | Year: 2014

We investigate the effects of hadronic cascades on the gamma-ray burst (GRB) prompt emission spectra in scenarios of efficient neutrino production. By assuming a fiducial GRB spectrum and a power-law proton distribution extending to ultrahigh energies, we calculate the proton cooling rate and the neutrino emission produced through photopion processes. For this, we employ a numerical code that follows the formation of the hadronic cascade by taking into account non-linear feedback effects, such as the evolution of the target photon field itself due to the contribution of secondary particles. We show that in cases of efficient proton cooling and subsequently efficient high-energy neutrino production, the emission from the hadronic cascade distorts and may even dominate the GRB spectrum. Taking this into account, we constrain the allowable values of the ratio ?p = Lp/L? , where Lp and L? are the isotropic equivalent proton and prompt gamma-ray luminosities. For the highest value of ?p that does not lead to the dominance of the cascading emission, we then calculate the maximum neutrino luminosity from a single burst and show that it ranges between (0.01-0.6)Lp and (0.5-1.4)L? for various parameter sets. We discuss possible implications of other parameters, such as the magnetic field strength and the shape of the initial gamma-ray spectrum, on our results. Finally, we compare the upper limit on ?p derived here with various studies in the field, and we point out the necessity of a self-consistent treatment of the hadronic emission in order to avoid erroneously high neutrino fluxes from GRB models. © 2014 The Authors Published by Oxford University Press on behalf of the Royal Astronomical Society.


For acceptable magnetic fusion reactor performance it is critical that net erosion of high-Z plasma facing material be much less than gross erosion. A detailed simulation of outer divertor-sputtered tungsten migration in the C-MOD tokamak, over an extended plasma campaign, shows a high ratio, ∼×10, of gross/net erosion, no core plasma contamination, and moderate transport of tungsten to lower divertor regions. These code predictions agree well with the available data. This is encouraging for high-Z material use in ITER and future fusion devices. © 2013 IAEA, Vienna.


Hao N.,CAS Institute of Physics | Hu J.,Purdue University
Physical Review B - Condensed Matter and Materials Physics | Year: 2014

We discuss the sign change of superconducting order parameters in both real and reciprocal spaces when the odd parity spin singlet pairing proposed recently by Hu [Phys. Rev. X 3, 031004 (2013)10.1103/PhysRevX.3.031004] is allowed. We show that in this case an nodeless antiphase s± can be generated. In a 2-Fe Brilliouin zone (BZ), sign change exists between two hole pockets and between two electron pockets. In a 1-Fe BZ, which includes two 2-Fe BZs, the sign change is between two 2-Fe BZs, which leads to a d-wave type sign distribution on the electron pockets, namely, an antiphase s± state with no symmetry protected gapless node on the electron pockets. This sign change character consistently explains experimental results related to sign change properties measured on both iron-pnictides and iron-chalcogenides. © 2014 American Physical Society.


Lyutikov M.,Purdue University
Monthly Notices of the Royal Astronomical Society | Year: 2010

Pulsars and central engines of long gamma-ray bursts - collapsars - may produce highly magnetized (Poynting-flux-dominated) outflows expanding in dense surroundings (interstellar medium or stellar material). For certain injection conditions, the magnetic flux of the wind cannot be accommodated within the cavity. In this case, ideal (non-dissipative) magnetohydrodynamics models, similar to the Kennel & Coroniti model of the Crab nebula, break down (the so-called 'sigma problem'). This is typically taken to imply that the wind should become particle-dominated on scales much smaller than the size of the cavity. The wind is then slowed down by a fluid-type (low magnetization) reverse shock. Recent Fermi results, indicating that the synchrotron spectrum of the Crab nebula extends well beyond the upper limit of the most efficient radiation-reaction-limited acceleration, contradict the presence of a low-sigma reverse shock. We propose an alternative possibility, that in nearly aligned pulsars the excessive magnetic flux is destroyed in a reconnection-like process in two regions: near the rotational axis and near the equator. We construct an example of such a highly magnetized wind having two distinct reconnection regions and suggest that these reconnection sites are observed as tori and jets in pulsar wind nebulae. The model reproduces, qualitatively, the observed morphology of the Crab nebula. In parts of the nebula dissipation occurs in a relativistically moving wind, alleviating requirements on the acceleration rate. © 2010 The Author. Journal compilation © 2010 RAS.


Lyutikov M.,Purdue University
Monthly Notices of the Royal Astronomical Society | Year: 2010

We develop a theoretical framework to construct axisymmetric magnetic equilibria in stars, consisting of both poloidal and toroidal magnetic field components. In a stationary axisymmetric configuration, the poloidal current is a function of the poloidal magnetic flux only, and thus should vanish on field lines extending outside of the star. Non-zero poloidal current (and the corresponding non-zero toroidal magnetic field) is limited to a set of toroid-shape flux surfaces fully enclosed inside the star. If we demand that there are no current sheets then on the separatrix delineating the regions of zero and finite toroidal magnetic field both the poloidal flux function (related to the toroidal component of the magnetic field) and its derivative (related to the poloidal component) should match. Thus, for a given magnetic field in the bulk of the star, the elliptical Grad-Shafranov equation that describes magnetic field structure inside the toroid is an ill-posed problem, with both Dirichlet and Newman boundary conditions and a priori unknown distribution of toroidal and poloidal electric currents. We discuss a procedure which allows to solve this ill-posed problem by adjusting the unknown current functions. We illustrate the method by constructing a number of semi-analytical equilibria connecting to outside dipole and having various poloidal current distribution on the flux surfaces closing inside the star. In particular, we find a poloidal current-carrying solution that leaves the shape of the flux function and, correspondingly, the toroidal component of the electric current, the same as in the case of no poloidal current. The equilibria discussed in this paper may have arbitrary large toroidal magnetic field, and may include a set of stable equilibria. The method developed here can also be applied to magnetic structure of differentially rotating stars, as well as to calculate velocity field in incompressible isolated fluid vortex with a swirl. © 2009 The Author. Journal compilation © 2009 RAS.


Bowen G.J.,Purdue University
Annual Review of Earth and Planetary Sciences | Year: 2010

Isotope ratios of actively cycled elements vary as a function of the biogeochemical processes in which they participate and the conditions under which those processes occur. The resultant spatiotemporal distribution of isotopes in environmental materials can be predicted using models of isotope-fractionating processes and data describing environmental conditions across space and time, and it has been termed an isoscape, or isotopic landscape. Analysis of isoscapes and comparison of isoscape predictions with observational data have been used to test biogeochemical models, calculate aerially integrated biogeochemical fluxes based on isotope mass balance, and determine spatial connectivity in biogeochemical, ecological, and anthropological systems. Isoscape models of varying quality are available for stable H, C, N, and O isotopes in a range of Earth surface systems, but significant opportunities exist to refine our understanding of biogeochemical cycles and our ability to predict isoscapes through the development of more mechanistic and more comprehensive isoscape models. Copyright © 2010 by Annual Reviews. All rights reserved.


Steinbuks J.,Purdue University
Energy Journal | Year: 2012

This paper investigates interfuel substitution, separately accounting for different types of energy use in the U.K. manufacturing sector. Econometric models of interfuel substitution are applied to aggregate energy use, as well as to a specific energy use process-thermal heating-where interfuel substitution is technologically feasible. Compared to the aggregate data, the estimated ownprice elasticities for all fuels and the cross-price elasticities for fossil fuels are considerably higher for thermal heating processes. Nonetheless, electricity is found to be a poor substitute for other fuels based on both aggregate data and, separately, for the heating process. An increase in real fuel prices from the Climate Change Levy in 2001 resulted in higher substitution elasticities based on aggregate data, and lower substitution elasticities for the thermal heating process. The results of a counterfactual decomposition of change in the estimated elasticities indicate that technological change was the major determinant of the differences in observed elasticities before and after the energy price increase. Copyright © 2012 by the IAEE. All rights reserved.


Ivanov B.A.,Russian Academy of Sciences | Melosh H.J.,Purdue University
Journal of Geophysical Research E: Planets | Year: 2013

We numerically modeled the formation of Rheasilvia crater, an enormous impact basin centered on asteroid 4 Vesta's south pole. Using a trial and error method, our models were adjusted to produce the best possible fit to Rheasilvia's size and shape, as observed during the Vesta orbital stage of the Dawn mission. The final model yields estimates of the shock wave decay, escaped material volume, depth of excavation, and other relevant characteristics, to the extent allowed by the two-dimensional (axially symmetric) approximation of the Simplified Arbitrary Lagrangian Eulerian hydrocode. Our model results permit interpretation of the Dawn data on Vesta's shape, topographic crater profiles, and the origin of the Vestoid asteroid family as escaped ejecta from the Rheasilvia crater. Key Points The numerical model is fitted to reproduce Rheasilvia crater size and shape We estimate shock decay, escaped mass, and excavation depth We analyze the Rheasilvia crater formation over the older Veneneia basin ©2013. American Geophysical Union. All Rights Reserved.


Huber M.,Purdue University | Caballero R.,University of Stockholm
Climate of the Past | Year: 2011

The early Eocene "equable climate problem", i.e. warm extratropical annual mean and above-freezing winter temperatures evidenced by proxy records, has remained as one of the great unsolved problems in paleoclimate. Recent progress in modeling and in paleoclimate proxy development provides an opportunity to revisit this problem to ascertain if the current generation of models can reproduce the past climate features without extensive modification. Here we have compiled early Eocene terrestrial temperature data and compared with climate model results using a consistent and rigorous methodology. We test the hypothesis that equable climates can be explained simply as a response to increased greenhouse gas forcing within the framework of the atmospheric component of the Community Climate System Model (version 3), a climate model in common use for predicting future climate change. We find that, with suitably large radiative forcing, the model and data are in general agreement for annual mean and cold month mean temperatures, and that the pattern of high latitude amplification recorded by proxies can be largely, but not perfectly, reproduced. © 2010 Author(s).


Bobet A.,Purdue University
Tunnelling and Underground Space Technology | Year: 2010

An analytical solution for a rectangular opening in an infinite elastic medium subjected to far-field shear stresses has been derived for drained and undrained loading conditions. A number of numerical simulations has been conducted to determine the distortion of a rectangular structure in an infinite elastic medium under far-field shear stresses also for drained and undrained conditions and when there is full slip or no slip at the ground-structure interface. The results show that the shape of the opening has a minor influence on the structure's deformations and that full-slip conditions result in lower deformations. Undrained conditions tend to reduce distortions when the structure is more flexible than the ground, but tend to increase them for stiffer structures. A comparison between results obtained for a rectangular lined opening and for a circular lined opening are presented, and show that deformations of a rectangular structure with no-slip can be estimated from equations derived for a circular opening with an incompressible liner and also with no-slip. The effects of flexibility, slip condition at the interface, and drained or undrained loading are different for circular tunnels than for rectangular tunnels. © 2009 Elsevier Ltd. All rights reserved.


Green J.A.M.,Bangor University | Huber M.,Purdue University
Geophysical Research Letters | Year: 2013

The tidally driven vertical diffusivity in the abyssal ocean during the early Eocene (55 Ma) is investigated using an established tidal model. A weak tide is predicted in the Eocene ocean, except in the Pacific. Consequently, the integrated global tidal dissipation rate is a mere 1.44TW, of which 40% dissipate in the Pacific. However, due to a stronger abyssal vertical stratification the predicted Eocene vertical diffusivities are consistently larger than at present. The results support the hypothesis that altered tidal dissipation may play a role in explaining the maintenance of past climate regimes, especially the anomalously warm temperatures in the southwest Pacific in the Eocene, and the low dissipation rates may be important for lunar evolution history. © 2013 American Geophysical Union. All Rights Reserved.


Cayon L.,Purdue University
Monthly Notices of the Royal Astronomical Society | Year: 2010

The standard inflationary model predicts an isotropic distribution of the cosmic microwave background temperature fluctuations. Detection of deviations from statistical isotropy would call for a revision of the physics of the early Universe. This paper introduces the variogram as a powerful tool for detecting and characterizing deviations from statistical isotropy in cosmic microwave background maps. Application to the Wilkinson Microwave Anisotropy Probe data clearly shows differences between the Northern and the Southern hemispheres. The sill and range of the Northern hemisphere's variogram are lower than those of the Southern hemisphere. Moreover, the variogram for the Northern hemisphere lies outside the 99 per cent confidence limit for scales of above 10°. Differences between the Northern and Southern hemispheres in the functional dependence of the variogram with the scale can be used as a validation benchmark for proposed anisotropic cosmological models. © 2010 The Author. Journal compilation © 2010 RAS.


Yazyev O.V.,Ecole Polytechnique Federale de Lausanne | Chen Y.P.,Purdue University
Nature Nanotechnology | Year: 2014

Graphene, a single atomic layer of graphitic carbon, has attracted intense attention because of its extraordinary properties that make it a suitable material for a wide range of technological applications. Large-area graphene films, which are necessary for industrial applications, are typically polycrystalline-that is, composed of single-crystalline grains of varying orientation joined by grain boundaries. Here, we present a review of the large body of research reported in the past few years on polycrystalline graphene. We discuss its growth and formation, the microscopic structure of grain boundaries and their relations to other types of topological defect such as dislocations. The Review further covers electronic transport, optical and mechanical properties pertaining to the characterizations of grain boundaries, and applications of polycrystalline graphene. We also discuss research, still in its infancy, performed on other two-dimensional materials such as transition metal dichalcogenides, and offer perspectives for future directions of research. © 2014 Macmillan Publishers Limited.


Torres-Company V.,Chalmers University of Technology | Weiner A.M.,Purdue University
Laser and Photonics Reviews | Year: 2014

The outstanding phase-noise performance of optical frequency combs has led to a revolution in optical synthesis and metrology, covering a myriad of applications, from molecular spectroscopy to laser ranging and optical communications. However, the ideal characteristics of an optical frequency comb are application dependent. In this review, the different techniques for the generation and processing of high-repetition-rate (>10 GHz) optical frequency combs with technologies compatible with optical communication equipment are covered. Particular emphasis is put on the benefits and prospects of this technology in the general field of radio-frequency photonics, including applications in high-performance microwave photonic filtering, ultra-broadband coherent communications, and radio-frequency arbitrary waveform generation. The outstanding phase-noise performance of optical frequency combs has led to a revolution in optical synthesis and metrology. In this review, the techniques for the generation and processing of high-repetition-rate (>10 GHz) optical frequency combs with technologies compatible with optical communication equipment are covered. Particular emphasis is put on the benefits and prospects of this technology in the general field of radio-frequency photonics, including applications in high-performance microwave photonic filtering, ultra-broadband coherent communications, and radio-frequency arbitrary waveform generation. © 2013 by WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.


Weaver C.M.,Purdue University
Physiology and Behavior | Year: 2010

The U.S. Dietary Guidelines for Americans recommends 3 cups of low fat milk or equivalent daily for most calorie levels [1]. Milk provides over 10% of the requirement for calcium, vitamin D, magnesium, phosphorus, potassium, riboflavin, protein, and carbohydrates for most people. Obtaining adequate intakes of calcium, potassium, and magnesium without milk in the diet requires effort. Milk has bioactive ingredients that may play unique roles in health. Benefits of dairy consumption are associated with reduced risk of low bone mass, stroke, metabolic syndrome, and some cancers. Concerns over milk consumption have focused on saturated fats historically. More research is needed to resolve potential concerns of milk consumption and risk of several disorders including ovarian cancer and soft tissue calcification. © 2010 Elsevier Inc.


This review focuses on the significance of deregulation of epigenetic mechanisms by the hepatitis B virus (HBV) X protein in hepatocarcinogenesis and HBV replication. Epigenetic mechanisms, DNA methylation, and specific histone modifications, e.g., trimethylation of H3 on lysine-27 or lysine-4, maintain 'cellular memory' by silencing expression of lineage-inducing factors in stem cells and conversely, of pluripotency factors in differentiated cells. The X protein has been reported to induce expression of DNA methyltransferases (DNMTs), likely promoting epigenetic changes during hepatocarcinogenesis. Furthermore, in cellular and animal models of X-mediated oncogenic transformation, protein levels of chromatin modifying proteins Suz12 and Znf198 are down-regulated. Suz12 is essential for the Polycomb Repressive Complex 2 (PRC2) mediating the repressive trimethylation of H3 on lysine-27 (H3K27me3). Znf198, stabilizes the LSD1-CoREST-HDAC complex that removes, via lysine demethylase1 (LSD1), the activating trimethylation of H3 on lysine-4 (H3K4me3). Down-regulation of Suz12 also occurs in liver tumors of woodchucks chronically infected by woodchuck hepatitis virus, an animal model recapitulating HBV-mediated hepatocarcinogenesis in humans. Significantly, subgroups of HBV-induced liver cancer re-express hepatoblast and fetal markers, and imprinted genes, suggesting hepatocyte reprogramming during oncogenic transformation. Lastly, down-regulation of Suz12 and Znf198 enhances HBV replication. Collectively, these observations suggest deregulation of epigenetic mechanisms by HBV X protein influences both the viral cycle and the host cell. © 2013 by the authors.


Running C.A.,Purdue University
Attention, Perception, and Psychophysics | Year: 2015

Large variability in thresholds to sensory stimuli is observed frequently even in healthy populations. Much of this variability is attributed to genetics and day-to-day fluctuation in sensitivity. However, false positives are also contributing to the variability seen in these tests. In this study, random number generation was used to simulate responses in threshold methods using different “stopping rules”: ascending 2-alternative forced choice (AFC) with 5 correct responses; ascending 3-AFC with 3 or 4 correct responses; staircase 2-AFC with 1 incorrect up and 2 incorrect down, as well as 1 up 4 down and 5 or 7 reversals; staircase 3-AFC with 1 up 2 down and 5 or 7 reversals. Formulas are presented for rates of false positives in the ascending methods, and curves were generated for the staircase methods. Overall, the staircase methods generally had lower false positive rates, but these methods were influenced even more by number of presentations than ascending methods. Generally, the high rates of error in all these methods should encourage researchers to conduct multiple tests per individual and/or select a method that can correct for false positives, such as fitting a logistic curve to a range of responses. © 2014, The Psychonomic Society, Inc.


Choi Y.,J. Craig Venter Institute | Szpankowski W.,Purdue University
IEEE Transactions on Information Theory | Year: 2012

Information theory traditionally deals with "conventional data," be it textual data, image, or video data. However, databases of various sorts have come into existence in recent years for storing "unconventional data" including biological data, social data, web data, topographical maps, and medical data. In compressing such data, one must consider two types of information: the information conveyed by the structure itself, and the information conveyed by the data labels implanted in the structure. In this paper, we attempt to address the former problem by studying information of graphical structures (i.e., unlabeled graphs). As the first step, we consider the Erdös-Rényi graphs G(n,p) over n vertices in which edges are added independently and randomly with probability p.We prove that the structural entropy of G(n,p) is (n/2)h(p) - log n! + o(1) = (n/2)h(p) - n log n + O(n) where h(p) = -p log p - (1 - p) log(1 - p) is the entropy rate of a conventional memoryless binary source. Then, we propose a two-stage compression algorithm that asymptotically achieves the structural entropy up to the n log n term (i.e., the first two leading terms) of the structural entropy. Our algorithm runs either in time O(n 2) in the worst case for any graph or in time O(n + e) on average for graphs generated by G(n,p), where e is the average number of edges. To the best of our knowledge, this is the first provable (asymptotically) optimal graph compressor for Erdös-Rényi graph models.We use combinatorial and analytic techniques such as generating functions, Mellin transform, and poissonization to establish these findings. Our experiments confirm the theoretical results and also show the usefulness of our algorithm for some real-world graphs such as the Internet, biological networks, and social networks. © 2011 IEEE.


The use of heterogeneous catalysts in liquid water, even at the moderate temperatures (<523 K) typical of most condensed-phase biomass conversion processes, is often fraught with issues related to structural instability and to active site inhibition caused by deactivation mechanisms that differ from those prevalent in the gas phase at higher temperatures. For porous silica-based oxides, one strategy to address these issues is to design or functionalize oxide surfaces with hydrophobic moieties or domains. Hydrophobic moieties can be present either at external crystallite surfaces or within the internal porous voids where most active sites typically reside. Both extracrystalline and intracrystalline hydrophobic environments can prevent the condensation of bulk water within internal void spaces and thus alleviate any transport restrictions its presence may cause, while only intracrystalline environments can influence the kinetic effects of molecular water at active sites. As a result, hydrophobic environments at both external and internal crystallite surfaces can have fundamentally different consequences for reactivity, in spite of the phenomenological similarities of their effects on observed reaction rates. The conceptual distinction between these two forms of hydrophobicity, together with accurate assessments of transport and kinetic contributions to measured reaction rates, can inform the placement of hydrophobic domains at appropriate locations in porous solids to cause predictable changes in reactivity. This mini-review discusses these concepts within the context of recent studies that have used hydrophobic Brønsted and Lewis acidic microporous and mesoporous oxides in catalytic reactions of biomass-derived molecules in liquid water and biphasic water-organic mixtures. © the Partner Organisations 2014.


Gelvin S.B.,Purdue University
Frontiers in Plant Science | Year: 2012

The genus Agrobacterium is unique in its ability to conduct interkingdom genetic exchange. Virulent Agrobacterium strains transfer single-strand forms ofT-DNA (T-strands) and several Virulence effector proteins through a bacterial type IV secretion system into plant host cells. T-strands must traverse the plant wall and plasma membrane, traffic through the cytoplasm, enter the nucleus, and ultimately target host chromatin for stable integration. Because any DNA sequence placed betweenT-DNA "borders" can be transferred to plants and integrated into the plant genome, the transfer and intracellular trafficking processes must be mediated by bacterial and host proteins that form complexes with T-strands. This review summarizes current knowledge of proteins that interact with T-strands in the plant cell, and discusses several models of T-complex (T-strand and associated proteins) trafficking. A detailed understanding of how these macromolecular complexes enter the host cell and traverse the plant cytoplasm will require development of novel technologies to follow molecules from their bacterial site of synthesis into the plant cell, and how these transferred molecules interact with host proteins and sub-cellular structures within the host cytoplasm and nucleus. © 2012 Gelvin.


Sozzani R.,North Carolina State University | Iyer-Pascuzzi A.,Purdue University
Current Opinion in Plant Biology | Year: 2014

Organ development in multicellular organisms is dependent on the proper balance between cell proliferation and differentiation. In the Arabidopsis root apical meristem, meristem growth is the result of cell divisions in the proximal meristem and cell differentiation in the elongation and differentiation zones. Hormones, transcription factors and small peptides underpin the molecular mechanisms governing these processes. Computer modeling has aided our understanding of the dynamic interactions involved in stem cell maintenance and meristem activity. Here we review recent advances in our understanding of postembryonic root stem cell maintenance and control of meristem size. © 2013 Elsevier Ltd.


Boltasseva A.,Purdue University
MRS Bulletin | Year: 2014

In recent years, the emerging areas of nanophotonics and, in particular, plasmonics and metamaterials, have seen an explosion of novel ideas. However, transforming revolutionary designs into practical devices requires a significant amount of effort. The constituent materials in plasmonic structures and metamaterials play a crucial role in realizing useful and efficient devices. Similar to the way silicon shaped the nanoelectronics field, finding the best set of materials for plasmonic and metamaterial devices could revolutionize the field of nanophotonics. As a potential solution, alternative plasmonic materials have recently gained significant attention. Metals, despite being essential components of plasmonic and metamaterial devices, pose many technological challenges toward the realization of practical devices - primarily due to their high optical loss, integration, and fabrication limitations. Hence, searching for an alternative is vital to the success of future nanophotonic devices. Several classes of materials, including doped semiconductor oxides and ceramics, are discussed as potential alternatives to metals that could lead to devices with drastically improved performance and new functionalities by providing low intrinsic loss, tunability, and compatibility with standard semiconductor fabrication processes. © 2014 Materials Research Society.


Amasyali M.F.,Yildiz Technical University | Ersoy O.K.,Purdue University
IEEE Transactions on Knowledge and Data Engineering | Year: 2014

The extended space forest is a new method for decision tree construction in which training is done with input vectors including all the original features and their random combinations. The combinations are generated with a difference operator applied to random pairs of original features. The experimental results show that extended space versions of ensemble algorithms have better performance than the original ensemble algorithms. To investigate the success dynamics of the extended space forest, the individual accuracy and diversity creation powers of ensemble algorithms are compared. The Extended Space Forest creates more diversity when it uses all the input features than Bagging and Rotation Forest. It also results in more individual accuracy when it uses random selection of the features than Random Subspace and Random Forest methods. It needs more training time because of using more features than the original algorithms. But its testing time is lower than the others because it generates less complex base learners. © 2014 IEEE.


Spence L.A.,Purdue University | Weaver C.M.,Tate and Lyle
Nutrition Reviews | Year: 2013

Recent research has reported a possible link between calcium supplementation and increased risk of cardiovascular disease and its endpoints in healthy, older adults. To evaluate the current evidence regarding the impact of calcium supplementation on cardiovascular disease risk and to address research gaps, the present review was conducted. Systematic reviews and meta-analyses were included, when available, along with original articles. The articles included in the review were obtained from PubMed using the following search terms: calcium intake, calcium supplementation, cardiovascular disease, myocardial infarction, mortality, and vascular calcification. The majority of the studies reviewed demonstrated no statistically significant adverse or beneficial effect of calcium supplementation on cardiovascular disease or its endpoints. While some studies indicate a possible increased risk, there is a lack of consensus on these findings and a need exists to further elucidate a mechanism. More experimental data are necessary to understand the impact of calcium intake, both levels and sources, on vascular calcification and vascular disease. The use of 41C kinetic modeling in the Ossabaw swine provides an approach for assessing soft tissue calcification in an atherosclerotic and normal state to address research gaps. © 2013 International Life Sciences Institute.


Jewett S.A.,Purdue University | Ivanisevic A.,North Carolina State University
Accounts of Chemical Research | Year: 2012

In a variety of applications where the electronic and optical characteristics of traditional, siliconbased materials are inadequate, recently researchers have employed semiconductors made from combinations of group III and V elements such as InAs. InAs has a narrow band gap and very high electron mobility in the near-surface region, which makes it an attractive material for high performance transistors, optical applications, and chemical sensing. However, silicon-based materials remain the top semiconductors of choice for biological applications, in part because of their relatively low toxicity. In contrast to silicon, InAs forms an unstable oxide layer under ambient conditions, which can corrode over time and leach toxic indium and arsenic components. To make InAs more attractive for biological applications, researchers have investigated passivation, chemical and electronic stabilization, of the surface by adlayer adsorption. Because of the simplicity, low cost, and flexibility in the type of passivating molecule used, many researchers are currently exploring wet-chemical methods of passivation.This Account summarizes much of the recent work on the chemical passivation of InAs with a particular focus on the chemical stability of the surface and prevention of oxide regrowth. We review the various methods of surface preparation and discuss how crystal orientation affects the chemical properties of the surface. The correct etching of InAs is critical as researchers prepare the surface for subsequent adlayer adsorption. HCl etchants combined with a postetch annealing step allow the tuning of the chemical properties in the near-surface region to either arsenic- or indium-rich environments. Bromine etchants create indium-rich surfaces and do not require annealing after etching; however, bromine etchants are harsh and potentially destructive to the surface. The simultaneous use of NH4OH etchants with passivating molecules prevents contact with ambient air that can occur during sample transfer between solutions. The passivation of InAs is dominated by sulfur-based molecules, which form stable In-S bonds on the InAs surface. Both sulfides and alkanethiols form well-defined monolayers on InAs and are dominated by In-S interactions. Sulfur-passivated InAs surfaces prevent regrowth of the surface oxide layer and are more stable in air than unpassivated surfaces.Although functionalization of InAs with sulfur-based molecules effectively passivates the surface, future sensing applications may require the adsorption of functional biomolecules onto the InAs surface. Current research in this area focuses on the passivation abilities of biomolecules such as collagen binding peptides and amino acids. These biomolecules can physically adsorb onto InAs, and they demonstrate some passivation ability but not to the extent of sulfur-based molecules. Because these adsorbents do not form covalent bonds with the InAs surface, they do not effectively block oxide regrowth. A mixed adlayer containing a biomolecule and a thiol on the InAs surface provides one possible solution: these hybrid surfaces enhance passivation but also maintain the presence of a biomolecule on the surface. Such surface functionalization strategies on InAs could provide long-term stability and make these surfaces suitable for biological applications. © 2012 American Chemical Society.


Chang C.Y.,Purdue University
Molecular & cellular proteomics : MCP | Year: 2012

Selected reaction monitoring (SRM) is a targeted mass spectrometry technique that provides sensitive and accurate protein detection and quantification in complex biological mixtures. Statistical and computational tools are essential for the design and analysis of SRM experiments, particularly in studies with large sample throughput. Currently, most such tools focus on the selection of optimized transitions and on processing signals from SRM assays. Little attention is devoted to protein significance analysis, which combines the quantitative measurements for a protein across isotopic labels, peptides, charge states, transitions, samples, and conditions, and detects proteins that change in abundance between conditions while controlling the false discovery rate. We propose a statistical modeling framework for protein significance analysis. It is based on linear mixed-effects models and is applicable to most experimental designs for both isotope label-based and label-free SRM workflows. We illustrate the utility of the framework in two studies: one with a group comparison experimental design and the other with a time course experimental design. We further verify the accuracy of the framework in two controlled data sets, one from the NCI-CPTAC reproducibility investigation and the other from an in-house spike-in study. The proposed framework is sensitive and specific, produces accurate results in broad experimental circumstances, and helps to optimally design future SRM experiments. The statistical framework is implemented in an open-source R-based software package SRMstats, and can be used by researchers with a limited statistics background as a stand-alone tool or in integration with the existing computational pipelines.


Wang F.,Purdue University
Physical Review C - Nuclear Physics | Year: 2010

We investigate effects of cluster particle correlations on two- and three-particle azimuth correlator observables sensitive to local strong parity violation. We use two-particle angular correlation measurements as inputs and estimate the magnitudes of the effects with straightforward assumptions. We found that the measurements of the azimuth correlator observables in the STAR experiment can be entirely accounted for by cluster particle correlations together with a reasonable range of cluster anisotropy in nonperipheral collisions. Our result suggests that new physics, such as local strong parity violation, may not be required to explain the correlator data. © 2010 The American Physical Society.


Liu X.,Purdue University
Translational Oncology | Year: 2015

Polo-like kinases (Plks) are a family of serine-threonine kinases that regulate multiple intracellular processes including DNA replication, mitosis, and stress response. Plk1, the most well understood family member, regulates numerous stages of mitosis and is overexpressed in many cancers. Plk inhibitors are currently under clinical investigation, including phase III trials of volasertib, a Plk inhibitor, in acute myeloid leukemia and rigosertib, a dual inhibitor of Plk1/phosphoinositide 3-kinase signaling pathways, in myelodysplastic syndrome. Other Plk inhibitors, including the Plk1 inhibitors GSK461364A, TKM-080301, GW843682, purpurogallin, and poloxin and the Plk4 inhibitor CFI-400945 fumarate, are in earlier clinical development. This review discusses the biologic roles of Plks in cell cycle progression and cancer, and the mechanisms of action of Plk inhibitors currently in development as cancer therapies. © 2015 The Authors. Published by Elsevier Inc.


Sawada T.,Purdue University
Journal of Vision | Year: 2010

This study tested perception of symmetry of 3D shapes from single 2D images. In Experiment 1, performance in discrimination between symmetric and asymmetric 3D shapes from single 2D line drawings was tested. In Experiment 2, performance in discrimination between different degrees of asymmetry of 3D shapes from single 2D line drawings was tested. The results showed that human performance in the discrimination was reliable. Based on these results, a computational model that performs the discrimination from single 2D images is presented. The model first recovers the 3D shape using a priori constraints: 3D symmetry, maximal 3D compactness, minimum surface area, and maximal planarity of contours. Then the model evaluates the degree of symmetry of the 3D shape. The model provided good fit to the subjects' data. © ARVO.


Smolyaninov I.I.,University of Maryland University College | Narimanov E.E.,Purdue University
Physical Review Letters | Year: 2010

We demonstrate that the extraordinary waves in indefinite metamaterials experience an ( - ++) effective metric signature. During a metric signature change transition in such a metamaterial, a Minkowski space-time is created together with a large number of particles populating the space-time. Such metamaterial models provide a tabletop realization of metric signature change events suggested to occur in Bose-Einstein condensates and quantum gravity theories. © 2010 The American Physical Society.


Jakes K.S.,Yeshiva University | Cramer W.A.,Purdue University
Annual Review of Genetics | Year: 2012

Colicins are protein toxins produced by Escherichia coli to kill related bacteria. They must cross the target cell outer membrane (OM), and some must also cross the inner membrane (IM). To accomplish cellular import, colicins have parasitized E. coli nutrient transporters as well as IM and periplasmic proteins normally used to maintain cell wall integrity or provide energy for nutrient uptake through transporters. Colicins have evolved to use both transporters and other membrane proteins through mechanisms different from those employed in physiological substrate uptake. Extended receptor-binding domains allow some colicins to search by lateral diffusion for binding sites on their OM translocators while bound to their primary OM receptor. Transport across the OM is initiated by entry of the unstructured N-terminal translocation domain into the translocator. Periplasmic and IM networks subsequently accomplish insertion of the colicin cytotoxic domain into or across the IM. © 2012 by Annual Reviews.


Schneider D.W.,Purdue University
Journal of Experimental Psychology: Learning Memory and Cognition | Year: 2015

Response congruency effects in task switching reflect worse performance for incongruent targets associated with different responses across tasks than for congruent targets associated with the same response. In the present study, the author investigated whether the effects can be produced solely by a mediated route for response selection, whereby targets are categorized with respect to both tasks, as opposed to a nonmediated route, whereby target-response instances from past experience are retrieved directly from long-term memory. The mediated route was isolated in 3 experiments by having subjects perform semantic categorization tasks on targets that were never repeated, thereby making the nonmediated route nonfunctional. Robust response congruency effects were observed for both response time and error rate in all experiments, indicating that the mediated route is sufficient to produce such effects by itself. The results imply that subjects engaged in dual-task processing despite no requirement to do so, raising questions about the modeling of response selection in task-switching situations. © 2014 American Psychological Association.


Leonard L.B.,Purdue University
Child Development Perspectives | Year: 2014

Children with specific language impairment (SLI) have a significant and longstanding deficit in spoken language ability that adversely affects their social and academic well-being. Studies of children with SLI in a wide variety of languages reveal diverse symptoms, most of which seem to reflect weaknesses in grammatical computation and phonological short-term memory. The symptoms of the disorder are sensitive to the type of language being acquired, with extraordinary weaknesses seen in those areas of language that are relatively challenging for younger typically developing children. Although these children's deficits warrant clinical and educational attention, their weaknesses might reflect the extreme end of a language aptitude continuum rather than a distinct, separable condition. © 2014 The Author. Child Development Perspectives © 2014 The Society for Research in Child Development.


Anthropogenic nitrogen deposition and projected increases in rainfall variability (the frequency of drought and heavy rainfall events) are expected to strongly influence ecosystem processes such as litter decomposition. However, how these two global change factors interact to influence litter decomposition is largely unknown. I examined how increased rainfall variability and nitrogen addition affected mass and nitrogen loss of litter from two tallgrass prairie species, Schizachyrium scoparium and Solidago canadensis, and isolated the effects of each during plant growth and during litter decomposition. I increased rainfall variability by consolidating ambient rainfall into larger events and simulated chronic nitrogen deposition using a slow-release urea fertilizer. S. scoparium litter decay was more strongly regulated by the treatments applied during plant growth than by those applied during decomposition. During plant growth, increased rainfall variability resulted in S. scoparium litter that subsequently decomposed more slowly and immobilized more nitrogen than litter grown under ambient conditions, whereas nitrogen addition during plant growth accelerated subsequent mass loss of S. scoparium litter. In contrast, S. canadensis litter mass and N losses were enhanced under either N addition or increased rainfall variability both during plant growth and during decomposition. These results suggest that ongoing changes in rainfall variability and nitrogen availability are accelerating nutrient cycling in tallgrass prairies through their combined effects on litter quality, environmental conditions, and plant community composition. © 2015, Springer-Verlag Berlin Heidelberg.


Schrader S.A.,Purdue University
American Journal of Physical Anthropology | Year: 2012

The effects of Egyptian imperial expansion into Nubia during the New Kingdom Period (1,550-1,069 BC) have been debated. Here, the impacts of the Egyptian Empire are investigated through an examination of osteological indicators of activity at the archaeological site of Tombos. Entheseal changes to fibrocartilaginous attachment sites and osteoarthritis are examined to infer what types of physical activities this colonial town was engaging in. Many of the skeletal remains at Tombos were comingled due to looting in antiquity; undisturbed burials are presented as a subsample of the population (n = 28) in which age, sex, and body size can be considered. The total sample (n = 85) is then analyzed to better understand overall levels of activity. A number of Nile River Valley bioarchaeological samples are used as points of comparison to the Tombos population. Results indicate that the inhabitants of Tombos had relatively low entheseal remodeling scores; this is highlighted when Tombos is juxtaposed with comparative samples, particularly in men. Furthermore, osteoarthritis, as assessed by eburnation, was also markedly infrequent at Tombos. Collectively, these results indicate a relatively low level of activity and support the hypothesis that Tombos may have served as an administrative center. © 2012 Wiley Periodicals, Inc.


Swithers S.E.,Purdue University
Appetite | Year: 2015

While no single factor is responsible for the recent, dramatic increases in overweight and obesity, a scientific consensus has emerged suggesting that consumption of sugar-sweetened products, especially beverages, is casually linked to increases in risk of chronic, debilitating diseases including type 2 diabetes, cardiovascular disease, hypertension and stroke. One approach that might be beneficial would be to replace sugar-sweetened items with products manufactured with artificial sweeteners that provide sweet tastes but with fewer calories. Unfortunately, evidence now indicates that artificial sweeteners are also associated with increased risk of the same chronic diseases linked to sugar consumption. Several biologically plausible mechanisms may explain these counterintuitive negative associations. For example, artificial sweeteners can interfere with basic learning processes that serve to anticipate the normal consequences of consuming sugars, leading to overeating, diminished release of hormones such as GLP-1, and impaired blood glucose regulation. In addition, artificial sweeteners can alter gut microbiota in rodent models and humans, which can also contribute to impaired glucose regulation. Use of artificial sweeteners may also be particularly problematic in children since exposure to hyper-sweetened foods and beverages at young ages may have effects on sweet preferences that persist into adulthood. Taken as a whole, current evidence suggests that a focus on reducing sweetener intake, whether the sweeteners are caloric or non-caloric, remains a better strategy for combating overweight and obesity than use of artificial sweeteners. © 2015 Elsevier Ltd.


Geng T.,Purdue University
Nature protocols | Year: 2011

Electroporation is a high-efficiency and low-toxicity physical gene transfer method. Classical electroporation protocols are limited by the small volume of cell samples processed (less than 10(7) cells per reaction) and low DNA uptake due to partial permeabilization of the cell membrane. Here we describe a flow-through electroporation protocol for continuous transfection of cells, using disposable devices, a syringe pump and a low-cost power supply that provides a constant voltage. We show transfection of cell samples with rates ranging from 40 μl min(-1) to 20 ml min(-1) with high efficiency. By inducing complex migrations of cells during the flow, we also show permeabilization of the entire cell membrane and markedly increased DNA uptake. The fabrication of the devices takes 1 d and the flow-through electroporation typically takes 1-2 h.


Raftery L.A.,University of Nevada, Las Vegas | Umulis D.M.,Purdue University
Current Opinion in Cell Biology | Year: 2012

Bone morphogenetic protein (BMP) signaling controls development and maintenance of many tissues. Genetic and quantitative approaches in Drosophila reveal that ligand isoforms show distinct function in wing development. Spatiotemporal control of BMP patterning depends on a network of extracellular proteins Pent, Ltl and Dally that regulate BMP signaling strength and morphogen range. BMP-mediated feedback regulation of Pent, Ltl, and Dally expression provides a system where cells actively respond to, and modify, the extracellular morphogen landscape to form a gradient that exhibits remarkable properties, including proportional scaling of BMP patterning with tissue size and the modulation of uniform tissue growth. This system provides valuable insights into mechanisms that mitigate the influence of variability to regulate cell-cell interactions and maintain organ function. © 2011 Elsevier Ltd.


Pierson T.C.,U.S. National Institutes of Health | Kuhn R.J.,Purdue University
Structure | Year: 2012

The four serotypes of dengue virus present a formidable challenge for the development of efficacious human vaccines. Cockburn and colleagues, in this issue of Structure, describe the structural basis of a cross-reactive neutralizing antibody, providing greater insight into immune protection and pathogenesis. © 2012 Elsevier Ltd. All rights reserved.


Although migration plays a critical role in the evolution and diversification of species, relatively little is known of the genetic architecture underlying this life history in any species. Rainbow and steelhead trout (Oncorhynchus mykiss) naturally segregate for both resident and migratory life-history types, respectively, as do other members of the salmonid family of fishes. Using an experimental cross derived from wild resident rainbow and wild migratory steelhead trout from Southeast Alaska and high throughput restriction-site associated DNA (RAD) tag sequencing, we perform a quantitative trait locus (QTL) analysis to identify the number, position, and relative contribution of genetic effects on a suite of 27 physiological and morphological traits associated with the migratory life history in this species. In total, 37 QTL are localized to 19 unique QTL positions, explaining 4-13.63% of the variation for 19 of the 27 migration-related traits measured. Two chromosomal positions, one on chromosome Omy12 and the other on Omy14 each harbor 7 QTL for migration-related traits, suggesting that these regions could harbor master genetic controls for the migratory life-history tactic in this species. Another QTL region on Omy5 has been implicated in several studies of adaptive life histories within this species and could represent another important locus underlying the migratory life history. We also evaluate whether loci identified in this out-crossed QTL study colocalize to genomic positions previously identified for associations with migration-related traits in a doubled haploid mapping family.


Savaiano D.A.,Purdue University
American Journal of Clinical Nutrition | Year: 2014

Yogurt is traditionally consumed throughout the world among populations who are seemingly unable to digest lactose. This review provides a historical overview of the studies that show lactose digestion and tolerance from yogurt by lactose-intolerant people. The lactose in yogurt is digested more efficiently than other dairy sources of lactose because the bacteria inherent in yogurt assist with its digestion. The bacterial lactase survives the acidic conditions of the stomach, apparently being physically protected within the bacterial cells and facilitated by the buffering capacity of yogurt. The increasing pH as the yogurt enters the small intestine and a slower gastrointestinal transit time allow the bacterial lactase to be active, digesting lactose from yogurt sufficiently to prevent symptoms in lactose-intolerant people. There is little difference in the lactase capability of different commercial yogurts, because they apparently contain Lactobacillus bulgaricus and Streptococcus thermophilus in sufficient quantities (108 bacteria/mL). However, Lactobacillus acidophilus appears to require cell membrane disruption to physically release the lactase. Compared with unflavored yogurts, flavored yogurts appear to exhibit somewhat reduced lactase activity but are still well tolerated. © 2014 American Society for Nutrition.


Stojnic M.,Purdue University
IEEE Journal on Selected Topics in Signal Processing | Year: 2010

It has been known for a while that ℓ 1-norm relaxation can in certain cases solve an under-determined system of linear equations. Recently, E. Candes (Robust uncertainty principles: Exact signal reconstruction from highly incomplete frequency information, IEEE Trans. Information Theory, vol. 52, no. 12, pp. 489509, Dec. 2006) and D. Donoho (High-dimensional centrally symmetric polytopes with neighborlines proportional to dimension, Disc. Comput. Geometry, vol. 35, no. 4, pp. 617652, 2006) proved (in a large dimensional and statistical context) that if the number of equations (measurements in the compressed sensing terminology) in the system is proportional to the length of the unknown vector then there is a sparsity (number of nonzero elements of the unknown vector) also proportional to the length of the unknown vector such that ℓ 1 -norm relaxation succeeds in solving the system. In this paper, in a large dimensional and statistical context, we determine sharp lower bounds on the values of allowable sparsity for any given number (proportional to the length of the unknown vector) of equations for the case of the so-called block-sparse unknown vectors considered in On the reconstruction of block-sparse signals with an optimal number of measurements, (M. Stojnic , IEEE Trans, Signal Processing, submitted for publication. © IEEE.


Conflicting accounts have been published in the veterinary literature regarding transmission of feline immunodeficiency virus (FIV) between cohabiting cats in mixed households, and the mechanics of possible casual transmission, if it occurs, are poorly understood. Similarly, there are conflicting reports of vertical transmission of FIV. The aim of the present study was to document the FIV serological status of cats taken into two rescue shelters. At rescue shelter 1 (Rescue 1), cats cohabited in a multi-cat household of FIV-negative and naturally-infected, FIV-positive cats. A study was performed that combined a retrospective review of records of FIV serological status at intake (Test 1) and prospective FIV serological testing (Tests 2 and 3). Retrospective records were analyzed at rescue shelter 2 (Rescue 2), where FIV-positive queens with litters of nursing kittens were taken into the shelter, before being rehomed. FIV serology was performed on all kittens after weaning.Initial test results (Test 1) for 138 cohabiting cats from Rescue 1 showed that there were 130 FIV-negative cats and eight FIV-positive cats (six male neutered and two female spayed). A second test (Test 2), performed in 45 of the FIV-negative and five of the FIV-positive cats at median 28 months after Test 1 (range, 1 month to 8.8 years) showed that results were unchanged. Similarly, a third test (Test 3), performed in four of the original FeLV-negative cats and one remaining FIV-positive cat at median 38 months after Test 1 (range, 4 months to 4 years), also showed that results were unchanged. These results show a lack of evidence of FIV transmission, despite years of exposure to naturally-infected, FIV-positive cats in a mixed household. At Rescue 2, records were available from five FIV-positive queens with 19 kittens. All 19 kittens tested FIV-negative, suggesting that vertical transmission had not occurred. © 2014 Elsevier Ltd.


Bowen G.J.,Purdue University | Zachos J.C.,University of California at Santa Cruz
Nature Geoscience | Year: 2010

The Palaeocene-Eocene Thermal Maximum (PETM), an approximately 170,000-year-long period of global warming about 56 million years ago, has been attributed to the release of thousands of petagrams of reduced carbon into the ocean, atmosphere and biosphere1,2. However, the fate of this excess carbon at the end of the event is poorly constrained: drawdown of atmospheric carbon dioxide has been attributed to an increase in the weathering of silicates or to increased rates of organic carbon burial1,3-5. Here we develop constraints on the rate of carbon drawdown based on rates of carbon isotope change in well-dated marine and terrestrial sediments spanning the event. We find that the rate of recovery is an order of magnitude more rapid than that expected for carbon drawdown by silicate weathering alone. Unless existing estimates of carbon stocks and cycling during this time are widely inaccurate, our results imply that more than 2,000 Pg of carbon were sequestered as organic carbon over 30,000 years at the end of the PETM. We suggest that the accelerated sequestration of organic carbon could reflect the regrowth of carbon stocks in the biosphere or shallow lithosphere that were released at the onset of the event. © 2010 Macmillan Publishers Limited. All rights reserved.


Pomeranz I.,Purdue University
IEEE Transactions on Very Large Scale Integration (VLSI) Systems | Year: 2012

Test sets that contain both broadside and skewed-load tests are important for achieving the highest possible delay fault coverage for standard-scan circuits. Both types of tests can be represented as s 1 v 1,s 2 v 2 where s 1 and s 2 are states, and v 1 and v 2 are primary input vectors. To facilitate the generation of a mixed test set that contains both broadside and skewed-load tests, this paper associates with s 2 a property that can be used for estimating whether a skewed-load or a broadside test is more likely to exist with s 2 in its second pattern. This paper uses this property for guiding a test generation procedure to consider only one of the two test types for most of the target faults. © 2011 IEEE.


Forbush K.T.,Purdue University | Watson D.,University of Notre Dame
Psychological Medicine | Year: 2013

Background Co-morbidity patterns in epidemiological studies of mental illness consistently demonstrate that a latent internalizing factor accounts for co-morbidity patterns among unipolar mood and anxiety disorders, whereas a latent externalizing factor underlies the covariation of substance-use disorders and antisocial behaviors. However, this structure needs to be extended to include a broader range of disorders. Method Exploratory and confirmatory factor analyses were used to examine the structure of co-morbidity using data from the Collaborative Psychiatric Epidemiological Surveys (n = 16 233). Results In the best-fitting model, eating and bipolar disorders formed subfactors within internalizing, impulse control disorders were indicators of externalizing, and factor-analytically derived personality disorder scales split between internalizing and externalizing. Conclusions This was the first large-scale nationally representative study that has included uncommon mental disorders with sufficient power to examine their fit within a structural model of psychopathology. The results of this study have important implications for conceptualizing myriad mental disorders. © 2012 Cambridge University Press.


Basu S.,Purdue University
Foundations of Computational Mathematics | Year: 2012

Toda (SIAM J. Comput. 20(5):865-877, 1991) proved in 1989 that the (discrete) polynomial time hierarchy, PH, is contained in the class P#P, namely the class of languages that can be decided by a Turing machine in polynomial time given access to an oracle with the power to compute a function in the counting complexity class #P. This result, which illustrates the power of counting, is considered to be a seminal result in computational complexity theory. An analogous result (with a compactness hypothesis) in the complexity theory over the reals (in the sense of Blum-Shub-Smale real machines (Blum et al. in Bull. Am. Math. Soc. 21(1):1-46, 1989) was proved in Basu and Zell (Found. Comput. Math. 10(4):429-454, 2010). Unlike Toda's proof in the discrete case, which relied on sophisticated combinatorial arguments, the proof in Basu and Zell (Found. Comput. Math. 10(4):429-454, 2010) is topological in nature; the properties of the topological join are used in a fundamental way. However, the constructions used in Basu and Zell (Found. Comput. Math. 10(4):429-454, 2010) were semi-algebraic-they used real inequalities in an essential way and as such do not extend to the complex case. In this paper, we extend the techniques developed in Basu and Zell (Found. Comput. Math. 10(4):429-454, 2010) to the complex projective case. A key role is played by the complex join of quasi-projective complex varieties. As a consequence, we obtain a complex analogue of Toda's theorem. The results of this paper, combined with those in Basu and Zell (Found. Comput. Math. 10(4):429-454, 2010), illustrate the central role of the Poincaré polynomial in algorithmic algebraic geometry, as well as in computational complexity theory over the complex and real numbers: the ability to compute it efficiently enables one to decide in polynomial time all languages in the (compact) polynomial hierarchy over the appropriate field. © 2011 SFoCM.


Elmqvist N.,Purdue University | Fekete J.-D.,University Paris - Sud
IEEE Transactions on Visualization and Computer Graphics | Year: 2010

We present a model for building, visualizing, and interacting with multiscale representations of information visualization techniques using hierarchical aggregation. The motivation for this work is to make visual representations more visually scalable and less cluttered. The model allows for augmenting existing techniques with multiscale functionality, as well as for designing new visualization and interaction techniques that conform to this new class of visual representations. We give some examples of how to use the model for standard information visualization techniques such as scatterplots, parallel coordinates, and node-link diagrams, and discuss existing techniques that are based on hierarchical aggregation. This yields a set of design guidelines for aggregated visualizations. We also present a basic vocabulary of interaction techniques suitable for navigating these multiscale visualizations. © 2010 IEEE.


Tyner W.E.,Purdue University
Global Food Security | Year: 2013

Biofuels are produced from agricultural commodities, so they represent a competing demand for those commodities. Therefore, it is clear that biofuels have some impact on agricultural commodity prices, so the food-fuel debate surrounds the relative contribution of biofuels to agricultural commodity price increases compared with other drivers. In this paper we have argued that there are many causes for the increase in food commodity prices-not biofuels alone. These include global supply and demand trends, regional or commodity specific supply disruptions, changes in the value of the US$, macroeconomic issues such as recession or financial crisis, trade policy changes, and biofuels. As for biofuels, we have argued that one must distinguish between biofuels driven by market forces and biofuels driven by government policy. Clearly the biofuel industries in the US, Brazil, and Europe were created with government support. However, at least in the US, the market is the major driver today for corn based ethanol. We have also argued that higher commodity prices adversely affect the poor, particularly the urban poor. However, there is another side to this picture, which is the supply increases that can be induced all over the world via the higher commodity prices. If governments establish policies that are conducive to supply growth, the higher commodity prices offer an opportunity to at least partially close the yield gap between developing and developed countries, thereby helping poor farmers in developing countries. Developing country farmers have already shown that markets work with the huge expansion in cropped area in many regions due to higher commodity prices. © 2013 Elsevier B.V.


Webb K.J.,Purdue University
Physical Review Letters | Year: 2013

The 1978 experiments by Jones and Leslie showing that the radiation pressure on a mirror depends on the background medium refractive index have yet to be adequately explained using a force model and have provided a leading challenge to the Abraham form of the electromagnetic momentum. Those experimental results are predicted for the first time using a force representation that incorporates the Abraham momentum by utilizing the power calibration method employed in the Jones and Leslie experiments. With an extension of the same procedure, the polarization and angle independence of the experimental data are also explained by this model. Prospects are good for this general form of the electromagnetic force density to be effective in predicting other experiments with macroscopic materials. Furthermore, the rigorous representation of material dispersion makes the representation important for metamaterials that operate in the vicinity of homogenized material resonances. © 2013 American Physical Society.


Yan B.,Purdue University
Physical Review Letters | Year: 2013

It is a fundamental problem in physics of what principle limits the correlations as predicted by our current description of nature, based on quantum mechanics. One possible explanation is the "global exclusivity" principle recently discussed in Phys. Rev. Lett. 110, 060402 (2013). In this work we show that this principle actually has a much stronger restriction on the probability distribution. We provide a tight constraint inequality imposed by this principle and prove that this principle singles out quantum correlations in scenarios represented by any graph. Our result implies that the exclusivity principle might be one of the fundamental principles of nature. © 2013 American Physical Society.


Bridgham S.D.,University of Oregon | Cadillo-Quiroz H.,Arizona State University | Keller J.K.,Chapman University | Zhuang Q.,Purdue University
Global Change Biology | Year: 2013

Understanding the dynamics of methane (CH4) emissions is of paramount importance because CH4 has 25 times the global warming potential of carbon dioxide (CO2) and is currently the second most important anthropogenic greenhouse gas. Wetlands are the single largest natural CH4 source with median emissions from published studies of 164 Tg yr-1, which is about a third of total global emissions. We provide a perspective on important new frontiers in obtaining a better understanding of CH4 dynamics in natural systems, with a focus on wetlands. One of the most exciting recent developments in this field is the attempt to integrate the different methodologies and spatial scales of biogeochemistry, molecular microbiology, and modeling, and thus this is a major focus of this review. Our specific objectives are to provide an up-to-date synthesis of estimates of global CH4 emissions from wetlands and other freshwater aquatic ecosystems, briefly summarize major biogeophysical controls over CH4 emissions from wetlands, suggest new frontiers in CH4 biogeochemistry, examine relationships between methanogen community structure and CH4 dynamics in situ, and to review the current generation of CH4 models. We highlight throughout some of the most pressing issues concerning global change and feedbacks on CH4 emissions from natural ecosystems. Major uncertainties in estimating current and future CH4 emissions from natural ecosystems include the following: (i) A number of important controls over CH4 production, consumption, and transport have not been, or are inadequately, incorporated into existing CH4 biogeochemistry models. (ii) Significant errors in regional and global emission estimates are derived from large spatial-scale extrapolations from highly heterogeneous and often poorly mapped wetland complexes. (iii) The limited number of observations of CH4 fluxes and their associated environmental variables loosely constrains the parameterization of process-based biogeochemistry models. © 2012 Blackwell Publishing Ltd.


Caballero R.,University College Dublin | Huber M.,Purdue University
Geophysical Research Letters | Year: 2010

Recent paleoclimate proxy reconstructions show that tropical surface temperatures may have been as high as 35-40C in the Early Cenozoic. Here, we study the tropical atmospheric circulation's response to temperatures in this range using a full-complexity atmospheric general circulation model (AGCM). We find that when equatorial surface temperatures exceed ∼33C, the model undergoes a transition to equatorial superrotation, a state with strong annual-and zonal-mean westerlies on the equator. The transition is driven by zonal momentum convergence due to large-amplitude transient eddies on the equator. These eddies have a structure similar to the observed Madden-Julian Oscillation (MJO). The model's MJO variability is weaker than observed when simulating the modern climate but increases sharply with temperature, coming to dominate the tropical variability and mean state of the warmest climates. Copyright © 2010 by the American Geophysical Union.


Kao S.-C.,Oak Ridge National Laboratory | Govindaraju R.S.,Purdue University
Journal of Hydrology | Year: 2010

Current drought information is based on indices that do not capture the joint behaviors of hydrologic variables. To address this limitation, the potential of copulas in characterizing droughts from multiple variables is explored in this study. Starting from the standardized index (SI) algorithm, a modified index accounting for seasonality is proposed for precipitation and streamflow marginals. Utilizing Indiana stations with long-term observations (a minimum of 80 years for precipitation and 50 years for streamflow), the dependence structures of precipitation and streamflow marginals with various window sizes from 1- to 12-months are constructed from empirical copulas. A joint deficit index (JDI) is defined by using the distribution function of copulas. This index provides a probability-based description of the overall drought status. Not only is the proposed JDI able to reflect both emerging and prolonged droughts in a timely manner, it also allows a month-by-month drought assessment such that the required amount of precipitation for achieving normal conditions in future can be computed. The use of JDI is generalizable to other hydrologic variables as evidenced by similar drought severities gleaned from JDIs constructed separately from precipitation and streamflow data. JDI further allows the construction of an inter-variable drought index, where the entire dependence structure of precipitation and streamflow marginals is preserved. © 2009 Elsevier B.V. All rights reserved.


Fassett C.I.,Mount Holyoke College | Minton D.A.,Purdue University
Nature Geoscience | Year: 2013

During the first billion years of Solar System evolution, following planetary accretion, the rate of impact cratering was substantially higher than over the past 3.5 Gyr. However, the causes, magnitude and evolution of the early impact flux remain unknown. In particular, uncertainty persists about whether the largest impact basins on the Moon and the other terrestrial planets formed from a cataclysmic bombardment in a narrow window of time about 3.9 Gyr ago, as initially suggested by the lunar sample collection, or over a more extended period. Recent observations relating to this so-called Late Heavy Bombardment imply that the window of bombardment was not as narrow and intense as originally envisaged. Nevertheless, numerical simulations suggest that the rocky bodies left behind after planetary accretion are insufficient in number to form the youngest large impact basins 4.0 to 3.7 Gyr ago. One viable hypothesis for the formation of these basins is the delivery of impactors to the inner Solar System following the migration of the giant planets, but this scenario also faces challenges. Clarifying the magnitude and length of the Late Heavy Bombardment has implications across the full range of planetary geosciences, from understanding the dynamical evolution of the Solar System to surface conditions on the terrestrial planets early in their history. © 2013 Macmillan Publishers Limited. All rights reserved.


Kruczenski M.,Purdue University
Journal of High Energy Physics | Year: 2014

The AdS/CFT correspondence relates Wilson loops in N=4 SYM theory to minimal area surfaces in AdS space. If the loop is a plane curve the minimal surface lives in hyperbolic space ℍ3 (or equivalently Euclidean AdS 3 space). We argue that finding the area of such extremal surface can be easily done if we solve the following problem: given two real periodic functions V 0,1(s), V 0,1(s +2π) = V 0,1(s) a third periodic function V 2(s) is to be found such that all solutions to the equation are (Formula presented.) anti-periodic in s ∈ [0, 2π] for any value of λ. This problem is equivalent to the statement that the monodromy matrix is trivial. It can be restated as that of finding a one complex parameter family of curves X(λ, s) where X(λ = 1, s) is the given shape of the Wilson loop and such that the Schwarzian derivative {X(λ, s), s} is meromorphic in λ with only two simple poles. We present a formula for the area in terms of the functions V 0,1,2 and discuss solutions to these equivalent problems in terms of theta functions. Finally, we also consider the near circular Wilson loop clarifying its integrability properties and rederiving its area using the methods described in this paper. © The Authors.


Bobet A.,Purdue University
Rock Mechanics and Rock Engineering | Year: 2011

Closed-form solutions for displacements and stresses of both the liner and the rock are presented for a deep circular tunnel excavated in transversely anisotropic rock above or below the water table subjected to static or seismic loading. The solutions are obtained with the assumption of elastic response of rock and liner, tied contact between rock and liner, impermeable liner, plane strain conditions along the tunnel axis and simultaneous excavation, and liner installation. The liner of a tunnel placed below the water table must support, in addition to the rock stresses, the full water pressure, while a tunnel located above the water table must support only the rock pressures. The solutions presented for static loading show, however, that displacements and stresses of the liner and rock are the same when the tunnel is placed above or below the water table as long as the total far-field stresses are the same. With rapid loading, e.g. seismic loading, excess pore pressures may be generated in saturated rock, which induce a different response than that of a tunnel excavated in dry rock. The analyses indicate that stresses and displacements are more uniform when excess pore pressures are produced, which seems to indicate that pore pressure generation tends to reduce non-uniform response in anisotropic rock. © 2010 Springer-Verlag.


Khraiwesh B.,King Abdullah University of Science and Technology | Zhu J.-K.,King Abdullah University of Science and Technology | Zhu J.-K.,Purdue University | Zhu J.,University of Maryland University College
Biochimica et Biophysica Acta - Gene Regulatory Mechanisms | Year: 2012

Small, non-coding RNAs are a distinct class of regulatory RNAs in plants and animals that control a variety of biological processes. In plants, several classes of small RNAs with specific sizes and dedicated functions have evolved through a series of pathways. The major classes of small RNAs include microRNAs (miRNAs) and small interfering RNAs (siRNAs), which differ in their biogenesis. miRNAs control the expression of cognate target genes by binding to reverse complementary sequences, resulting in cleavage or translational inhibition of the target RNAs. siRNAs have a similar structure, function, and biogenesis as miRNAs but are derived from long double-stranded RNAs and can often direct DNA methylation at target sequences. Besides their roles in growth and development and maintenance of genome integrity, small RNAs are also important components in plant stress responses. One way in which plants respond to environmental stress is by modifying their gene expression through the activity of small RNAs. Thus, understanding how small RNAs regulate gene expression will enable researchers to explore the role of small RNAs in biotic and abiotic stress responses. This review focuses on the regulatory roles of plant small RNAs in the adaptive response to stresses. This article is part of a Special Issue entitled: Plant gene regulation in response to abiotic stress. © 2011 Elsevier B.V.


Borgens R.B.,Purdue University | Liu-Snyder P.,Brown University
Quarterly Review of Biology | Year: 2012

Secondary injury is a term applied to the destructive and self-propagating biological changes in cells and tissues that lead to their dysfunction or death over hours to weeks after the initial insult (the "primary injury"). In most contexts, the initial injury is usually mechanical. The more destructive phase of secondary injury is, however, more responsible for cell death and functional deficits. This subject is described and reviewed differently in the literature. To biomedical researchers, systemic and tissue-level changes such as hemorrhage, edema, and ischemia usually define this subject. To cell and molecular biologists, "secondary injury" refers to a series of predominately molecular events and an increasingly restricted set of aberrant biochemical pathways and products. These biochemical and ionic changes are seen to lead to death of the initially compromised cells and "healthy" cells nearby through necrosis or apoptosis. This latter process is called "bystander damage." These viewpoints have largely dominated the recent literature, especially in studies of the central nervous system (CNS), often without attempts to place the molecular events in the context of progressive systemic and tissue-level changes. Here we provide a more comprehensive and inclusive discussion of this topic. © 2012 by The University of Chicago Press. All rights reserved.


Stuart J.,Purdue University
Current Opinion in Insect Science | Year: 2015

Within the context of the four-phase model of plant immunity, gene-for-gene interactions have gained new relevance. Genes conferring resistance to the Asian rice gall midge (Orseolia oryzae) and the small brown planthopper (Nilaparvata lugens) have been cloned in rice (Oryza sativa). Mutations in insect avirulence genes that defeat plant resistance have been identified and cloned. Results are consistent with both the gene-for-gene hypothesis and the new model of plant immunity. Insect resistance genes encode proteins with nucleotide binding sites and leucine-rich repeats. Insects use effectors that elicit effector-triggered immunity. At least seven-percent of Hessian fly genes are effector encoding. © 2015 Elsevier Inc. All rights reserved.


Lyutikov M.,Purdue University
Astrophysical Journal | Year: 2012

We reanalyze the Fermi spectra of the Geminga and Vela pulsars. We find that the spectrum of Geminga above the break is well approximated by a simple power law without the exponential cutoff, making Geminga's spectrum similar to that of Crab. Vela's broadband γ-ray spectrum is equally well fit with both the exponential cutoff and the double power-law shapes. In the broadband double power-law fits, for a typical Fermi spectrum of a bright γ-ray pulsar, most of the errors accumulate due to the arbitrary parameterization of the spectral roll-off. In addition, a power law with an exponential cutoff gives an acceptable fit for the underlying double power-law spectrum for a very broad range of parameters, making such fitting procedures insensitive to the underlying Fermi photon spectrum. Our results have important implications for the mechanism of pulsar high-energy emission. A number of observed properties of γ-ray pulsars - i.e., the broken power-law spectra without exponential cutoffs and stretching in the case of Crab beyond the maximal curvature limit, spectral breaks close to or exceeding the maximal breaks due to curvature emission, patterns of the relative intensities of the leading and trailing pulses in the Crab repeated in the X-ray and γ-ray regions, presence of profile peaks at lower energies aligned with γ-ray peaks - all point to the inverse Compton origin of the high-energy emission from majority of pulsars. © 2012. The American Astronomical Society. All rights reserved.


Nichols D.E.,Purdue University
Wiley Interdisciplinary Reviews: Membrane Transport and Signaling | Year: 2012

Of the 14 known types of serotonin receptors one of the most extensively studied is the 5-HT2A (5-hydroxytryptamine) receptor. In the brain, this receptor plays a key role in regulation of cortical function and cognition, appears to be the principal target for the hallucinogenic/psychedelic drugs such as lysergic acid diethylamide (LSD), and also is a target for the newest atypical antipsychotic agents, which are antagonists or inverse agonists at this site. Among the structure-activity relationships that are known for this receptor type, there are three chemical classes of agonists: tryptamines, ergolines, and phenethylamines. Important structural features are identified for agonist activity and some of these agonists have features in common. In addition to effects at the receptor will be the focus, these drugs are also hallucinogenic (psychedelic) agents, and much of the SAR was developed on the basis of effects in humans, before modern pharmacological techniques were available. A certain amount of our knowledge therefore relies on those human studies. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.


Gunasekera D.S.,Purdue University
Synlett | Year: 2012

A short, enantiomeric, synthesis of Shibasakis 3rd generation intermediate to form (-)-oseltamivir phosphate (Tamiflu®) has been achieved in eight steps with the use of inexpensive starting materials. A formal synthetic route to convert tamiflu into tamiphosphor via Fangs tamiphosphor intermediate has been accomplished. © Georg Thieme Verlag Stuttgart · New York.


Aure M.H.,University of Rochester | Konieczny S.F.,Purdue University | Ovitt C.E.,University of Rochester
Developmental Cell | Year: 2015

Current dogma suggests that salivary gland homeostasis is stem cell dependent. However, the extent ofstem cell contribution to salivary gland maintenance has not been determined. We investigated acinar cell replacement during homeostasis, growth, and regeneration, using an inducible CreERT2 expressed under the control of the Mist1 gene locus. Genetic labeling, followed by a chase period, showed that acinar cell replacement is not driven by the differentiation of unlabeled stem cells. Analysis using R26Brainbow2.1 reporter revealed continued proliferation and clonal expansion of terminally differentiated acinar cells in all major salivary glands. Induced injury also demonstrated the regenerative potential of pre-labeled acinar cells. Our results support a revised model for salivary gland homeostasis based predominantly on self-duplication of acinar cells, rather than on differentiation of stem cells. The proliferative capacity of differentiated acinar cells may prove critical in the implementation of cell-based strategies to restore the salivary glands. © 2015 Elsevier Inc.


Johnston C.T.,Purdue University
Clay Minerals | Year: 2010

In recent years, experimental and theoretical methods have provided new insights into the size, shape, reactivity, and stability of clay minerals. Although diverse and complex, the surface chemistry of all clay minerals is defined spatially on a common scale of nanometres. This review is organized around the nanoscale architecture of clay minerals examined at several different length scales. The first, and perhaps most important, is the length scale associated with H bonding in clay minerals. H bonding interactions define the size and shape of 1:1 phyllosilicates and dominate the surface chemistry of many clay minerals. Structural and surface OH groups contained within and on the surface of clay minerals provide a type of 'molecular reporter group' and are sensitive to subtle changes in their local environment. Examples of OH-reporter group studies in clay minerals, and the spatial scales at which they provide diagnostic information, are examined. The second length scale considered here is that associated with clay-water and clay-organic interactions. Inorganic and organic solutes can be used to explore the surface chemistry of clay minerals. Similar to the use of reporter groups, molecular probes have diagnostic properties that are sensitive to changes in their molecular environment. Clay-water interactions occur at a length scale that extends from the size of the H2O molecule (∼0.3 nm) to the larger scales associated with clay-swelling (>10 nm). Similarly, clay-organic interactions are also defined, in part, on the basis of their molecular size, in addition to the type of chemical bonding interactions that take place between the organic solute and the clay surface. Examples illustrating the use of clay-water and clay-organic solute interactions as molecular probes are presented. The largest scale to be considered is that of the particles themselves, with scales that approach micrometres. Recent developments in the synthesis and characterization of ultrathin hybrid films of clay minerals provide complementary information about the nature and distribution of active sites on clay minerals, as well as providing new opportunities to exploit the surface chemistry of clay minerals in the design of functional materials. © 2010 Mineralogical Society.


Bowling L.C.,Purdue University | Lettenmaier D.P.,University of Washington
Journal of Hydrometeorology | Year: 2010

Lakes, ponds, and wetlands are common features in many low-gradient arctic watersheds. Storage of snowmelt runoff in lakes and wetlands exerts a strong influence on both the interannual and interseasonal variability of northern rivers. This influence is often not well represented in hydrology models and the land surface schemes used in climate models. In this paper, an algorithm to represent the evaporation and storage effects of lakes and wetlands within the Variable Infiltration Capacity (VIC) macroscale hydrology model is described. The model is evaluated with respect to its ability to represent water temperatures, net radiation, ice freeze-thaw, and runoff production for a variety of high-latitude locations. It is then used to investigate the influence of surface storage on the spatial and temporal distribution of water and energy fluxes for the Kuparuk and Putuligayuk Rivers, on the Alaskan arctic coastal plain. Inclusion of the lake and wetland algorithm results in a substantial improvement of the simulated streamflow hydrographs, as measured using the monthly Nash-Sutcliffe efficiency. Simulations of runoff from the Putuligayuk watershed indicate that up to 80% of snow meltwater goes into storage each year and does not contribute to streamflow. Approximately 46% of the variance in the volume of snowmelt entering storage can be explained by the year-to-year variation in maximum snow water equivalent and the lake storage deficit from the previous summer. The simulated summer lake storage deficit is much lower than the cumulative precipitation minus lake evaporation (-47 mm, on average) as a result of simulated recharge from the surrounding uplands. © 2010 American Meteorological Society.


Olia A.S.,Purdue University | Prevelige Jr P.E.,University of Alabama at Birmingham | Johnson J.E.,Scripps Research Institute | Cingolani G.,Thomas Jefferson University
Nature Structural and Molecular Biology | Year: 2011

DNA viruses such as bacteriophages and herpesviruses deliver their genome into and out of the capsid through large proteinaceous assemblies, known as portal proteins. Here, we report two snapshots of the dodecameric portal protein of bacteriophage P22. The 3.25-Å-resolution structure of the portal-protein core bound to 12 copies of gene product 4 (gp4) reveals a ~1.1-MDa assembly formed by 24 proteins. Unexpectedly, a lower-resolution structure of the full-length portal protein unveils the unique topology of the C-terminal domain, which forms a ~200-Å-long α-helical barrel. This domain inserts deeply into the virion and is highly conserved in the Podoviridae family. We propose that the barrel domain facilitates genome spooling onto the interior surface of the capsid during genome packaging and, in analogy to a rifle barrel, increases the accuracy of genome ejection into the host cell.


Foli K.J.,Purdue University
Western Journal of Nursing Research | Year: 2010

A limited number of studies have explored parental depression in the postadoption time periods and these studies frequently lack a social context of the adoptive parent experience. The objective of this study is to form a midrange theoretical interpretation of parental postadoption depression as shared by adoptive parents and experts through a grounded theory approach. Semistructured interviews of adoptive parents, who acknowledge being depressed after the child is placed in the home, and adoption experts are audiotaped, transcribed, and coded to reveal themes. In total, 30 interviews are conducted. Researchers are also participant-observers during an adoptive parent support group meeting. Data reveal recurrent themes in relation to postadoption depression. These themes take into account the various contexts of adoption (international and domestic, public and private, etc.). Parents express unfulfilled and unrealistic expectations in the domains of self, child, family or friends, and society or others. A theoretical model is presented to facilitate the understanding of depression reported by adoptive parents. © The Author(s) 2010.


Swithers S.E.,Purdue University
Trends in Endocrinology and Metabolism | Year: 2013

The negative impact of consuming sugar-sweetened beverages on weight and other health outcomes has been increasingly recognized; therefore, many people have turned to high-intensity sweeteners like aspartame, sucralose, and saccharin as a way to reduce the risk of these consequences. However, accumulating evidence suggests that frequent consumers of these sugar substitutes may also be at increased risk of excessive weight gain, metabolic syndrome, type 2 diabetes, and cardiovascular disease. This paper discusses these findings and considers the hypothesis that consuming sweet-tasting but noncaloric or reduced-calorie food and beverages interferes with learned responses that normally contribute to glucose and energy homeostasis. Because of this interference, frequent consumption of high-intensity sweeteners may have the counterintuitive effect of inducing metabolic derangements. © 2013 Elsevier Ltd.


Martinez J.C.,Purdue University
Journal of Construction Engineering and Management | Year: 2010

This paper suggests the methodology to follow when conducting discrete-event simulation (DES) studies in construction engineering and management research. Emphasis is made on the steps that, due to the uniqueness of the construction environment, are particularly important yet are not discussed extensively in the general DES literature. Guidelines are provided to determine what aspects of a DES study demand a rigorous application of the theory depending on the purpose of the study. The paper concludes with the importance of properly understanding the probabilistic concepts upon which DES relies and on coupling this understanding with engineering judgment as a key for successful use of DES in construction research. © 2010 ASCE.


Dickson B.M.,Purdue University
Physical Review E - Statistical, Nonlinear, and Soft Matter Physics | Year: 2011

We present a unique derivation of metadynamics. This work leads to a more robust understanding of the error in the computed free energy than what has been obtained previously. Moreover, a formula for the exact free energy is introduced. The formula can be used to post-process any existing well-tempered metadynamics data, allowing one, in principle, to obtain an exact free energy regardless of the metadynamics parameters. © 2011 American Physical Society.


Leonard L.B.,Purdue University
Journal of Speech, Language, and Hearing Research | Year: 2011

Purpose: The author presents a tutorial on structural priming and its relevance to the study of grammatical development and language intervention. Method: The findings from structural priming studies are examined from the standpoint of the types of changes that occur in participants' language use, the contexts in which these changes occur, and the effects of these changes on participants' language knowledge. Details of children's grammatical development and language intervention are then considered in light of these findings. Results: Evidence from the structural priming literature provides insight into the transition from early conservative grammatical use to broader abstract grammatical use in young children, and suggests ways in which language intervention activities can be modified to promote greater grammatical change in children with language impairments. Conclusions: Structural priming is not divorced from everyday language use. Evidence from priming research can be put to use in the study of children's grammatical development and in shaping the methods that are used to facilitate children's grammatical abilities. © American Speech-Language-Hearing Association.


Francis G.,Purdue University | Francis G.,Ecole Polytechnique Federale de Lausanne
Genetics | Year: 2014

An article reporting statistical evidence for epigenetic transfer of learned behavior has important implications, if true. With random sampling, real effects do not always result in rejection of the null hypothesis, but the reported experiments were uniformly successful. Such an outcome is expected to occur with a probability of 0.004. © 2014 by the Genetics Society of America.


Agarwal A.,Bentley Systems Inc. | Varma A.H.,Purdue University
Engineering Structures | Year: 2014

This paper presents a qualitative assessment of the importance of gravity columns on the stability behavior of a typical mid-rise (10 story) steel building subjected to corner compartment fires. Two ten-story steel buildings with composite floor systems were designed following the design practices in the US. One of these buildings had perimeter moment resisting frames (MRFs) to resist lateral loads while the other building had an interior core of RC shear walls. Effects of gravity loads and fire conditions were simulated using the finite element method and numerical analysis techniques.The results from the numerical investigations indicated that gravity columns govern the overall stability of building structures under fire conditions. Gravity columns have the highest utilization ratio, and they are most likely to reach their critical temperatures first. If gravity column failure occurs, the load shed or dropped by the failed column has to be redistributed to the neighboring columns to maintain overall structural stability. This axial load redistribution can occur through the development of alternate load paths including catenary action. Simulation results indicate that the presence of steel reinforcement in the concrete slabs (in addition to the minimum shrinkage reinforcement) facilitates uniform redistribution of the axial load dropped by the failed gravity column to the neighboring columns. The additional steel reinforcement improves the flexural and tensile strengths of the composite floor system, which enhances its ability to develop alternate load paths including catenary action in the slab, and thus maintain structural stability after gravity column failure. © 2013.


Abdolrahim N.,Washington State University | Zbib H.M.,Washington State University | Bahr D.F.,Purdue University
International Journal of Plasticity | Year: 2014

Nanoscale metallic multilayers (NMM) have very high strength approaching a fraction of the theoretical limit. Their increased strength is attributed to the high interface density and is limited by the interfacial strength. As the density of interfaces increases (due to smaller layer thicknesses) the strength of NMM structures becomes increasingly determined by the specific nature and properties of the interfaces and is most likely controlled by the nucleation of dislocations from the interfaces. With focus on material systems with incoherent interfaces, we performed MD simulations to determine the controlling deformation mechanisms at different length scales for Cu-Nb multilayers under biaxial tensile deformation conditions. The results of the simulations show that there is a transition in the operative deformation mechanism in NMMs from Hall-Petch strengthening for the length scales of sub microns to microns, to individual dislocations confined to glide in individual layers for few nm to few tens of nm, and dislocation-nucleation-controlled models for less than few nanometers. Based on these results, we develop a Molecular dynamics-based rate-sensitive model for viscoplastic flow which describes the anisotropic deformation behavior of NMMs at different length scales. © 2013 Elsevier Ltd. All rights reserved.


Hasegawa P.M.,Purdue University
Environmental and Experimental Botany | Year: 2013

Soil and water salinity substantially constrain crop and biomass production. Research over the last two plus decades, facilitated by advances in molecular genetics and biotechnology, and with genetic model systems, has identified genes involved in salt acclimation or adaptation and linked these to critical mechanisms and processes. A case in point is present understanding of critical transport determinants that facilitate intra- and intercellular Na+ homeostasis of plants in saline environments predominated by NaCl. Pumps in the plasma membrane (H+-ATPase), and the tonoplast (H+-ATPase) and H+ pyrophosphatases (AVP1) generate proton electrochemical gradients necessary to energize Na+ efflux to the apoplast and influx into vacuoles, respectively. The plasma membrane Na+/H+ antiporter SOS1 is responsible for apoplastic efflux, and NHX type Na+/H+ antiporters for vacuolar and endosomal compartmentalization. Ca2+ ext reduces passive intracellular Na+ influx cells by decreasing Na+ transport through high affinity K+ uptake systems and what are presumed to be nonselective cation channels, and activating, through the SOS signal pathway, the SOS1 plasma membrane Na+/H+ antiporter. Moreover, there is greater understanding about how cellular transport systems functionally integrate to facilitate tissue and organismal Na+ homeostasis. Notable in this process are HKT1 Na+ transporters, which regulate Na+ loading into the root xylem, limiting flux to and accumulation in the shoot. This review will summarize ion transport systems that facilitate plant Na+ homeostasis. Halophyte and glycophyte salinity responses and transport determinant function are compared and contrasted. The potential of halophytes as genetic resources for unique alleles or loci of transport protein genes and transcriptional and post-transcriptional regulation of transport protein function are discussed in the context of crop salt tolerance. © 2013 Elsevier B.V.


Saxton W.M.,University of California at Santa Cruz | Hollenbeck P.J.,Purdue University
Journal of Cell Science | Year: 2012

Vigorous transport of cytoplasmic components along axons over substantial distances is crucial for the maintenance of neuron structure and function. The transport of mitochondria, which serves to distribute mitochondrial functions in a dynamic and non-uniform fashion, has attracted special interest in recent years following the discovery of functional connections among microtubules, motor proteins and mitochondria, and their influences on neurodegenerative diseases. Although the motor proteins that drive mitochondrial movement are now well characterized, the mechanisms by which anterograde and retrograde movement are coordinated with one another and with stationary axonal mitochondria are not yet understood. In this Commentary, we review why mitochondria move and how they move, focusing particularly on recent studies of transport regulation, which implicate control of motor activity by specific cell-signaling pathways, regulation of motor access to transport tracks and static microtubule-mitochondrion linkers. A detailed mechanism for modulating anterograde mitochondrial transport has been identified that involves Miro, a mitochondrial Ca2+-binding GTPase, which with associated proteins, can bind and control kinesin-1. Elements of the Miro complex also have important roles in mitochondrial fission-fusion dynamics, highlighting questions about the interdependence of biogenesis, transport, dynamics, maintenance and degradation. © 2012.


Lill M.,Purdue University
Methods in Molecular Biology | Year: 2013

Virtual screening has become a standard tool in drug discovery to identify novel lead compounds that target a biomolecule of interest. I present several concepts in ligand-based and structure-based virtual screening and discuss some of the current shortcomings and new developments. I also highlight approaches that combine concepts from structure- and ligand-based design. © Springer Science+Business Media, LLC 2013.


Beddoes K.D.,Purdue University
Engineering Studies | Year: 2012

This article examines the current state of feminism in the emerging field of engineering education and identifies barriers, challenges, and tensions experienced by scholars and educators who have been involved with feminist engineering education initiatives. Using data from fifteen in-depth interviews, I identified seven categories of barriers, challenges, and tensions. The categories were: engineering knowledge, culture, and training; engineering education as an emerging research field; publishing; institutional constraints; productive, non-alienating critique and the feminist label; legitimacy and risk; and sustainability. The findings reveal similarities with other academic fields and provide support for prior findings on factors that inhibit the growth of feminism within a field. The article offers a base of knowledge for those interested in further developing feminist projects, those interested in the history of engineering education, and those interested in the history of feminism in academic fields. © 2012 Copyright Taylor and Francis Group, LLC.


Miura K.,University of Tsukuba | Hasegawa P.M.,Purdue University
Trends in Cell Biology | Year: 2010

Post-translational modifications diversify proteome activity to mediate complex hierarchical regulatory processes that are crucial to eukaryotic cell function. Protein modification by Ub (ubiquitin) and Ubls (ubiquitin-like proteins) in plants, as in yeast and metazoans, is necessary for numerous cellular and developmental processes and for the genetic reprogramming that occurs in response to hormonal stimuli, host-pathogen interaction-related stimuli and environmental stimuli. Ub and Ubl modifications, such as sumoylation, facilitate molecular interaction with specific substrates. Recent evidence has permitted inference of the mechanisms by which Ubl modifications regulate physiological processes such as cell-cycle progression, abscisic acid signaling, development, and biotic and abiotic stress responses. This review presents our current understanding of sumoylation and other Ubl conjugation processes in plant biology. © 2010 Elsevier Ltd.


Nolte D.D.,Purdue University
Journal of biomedical optics | Year: 2011

Tissue dynamics spectroscopy uses digital holography as a coherence gate to extract depth-resolved quasi-elastic dynamic light scattering from inside multicellular tumor spheroids. The temporal speckle contrast provides endogenous dynamical images of proliferating and hypoxic or necrotic tissues. Fluctuation spectroscopy similar to diffusing wave spectroscopy is performed on the dynamic speckle to generate tissue-response spectrograms that track time-resolved changes in intracellular motility in response to environmental perturbations. The spectrograms consist of several frequency bands that range from 0.005 to 5 Hz. The fluctuation spectral density and temporal autocorrelations show the signature of constrained anomalous diffusion, but with large fluctuation amplitudes caused by active processes far from equilibrium. Differences in the tissue-response spectrograms between the proliferating outer shell and the hypoxic inner core differentiate normal from starved conditions. The differential spectrograms provide an initial library of tissue-response signatures to environmental conditions of temperature, osmolarity, pH, and serum growth factors.


Key N.L.,Purdue University
Journal of Propulsion and Power | Year: 2014

Vane clocking is the circumferential indexing of adjacent vane rows with similar vane counts. The clocking configuration can be arranged so that either all downstream vanes are positioned in the wakes shed from the upstream vanes, or the upstream vane wakes pass through every passage of the downstream vane row without any interaction with the vane surface. Experiments were performed in a compressor featuring geometry representative of the rear stages of a high-pressure compressor, with engine representative Mach numbers and Reynolds numbers. A miniature cross-film sensor was used to acquire instantaneous flow-angle and velocity information in the axial-tangential plane. For adiabatic flow of a perfect gas, the total temperature rise through a compressor stage will provide a measure of the amount of work done on the flow, directly impacting the stage isentropic efficiency. Total temperature profiles measured at the stator exit can be used to accurately measure the work done on the flow by the rotor immediately upstream of the vane row for adiabatic conditions.


Pomeranz I.,Purdue University
IEEE Transactions on Very Large Scale Integration (VLSI) Systems | Year: 2013

Functional broadside tests are two-pattern scan-based tests that avoid overtesting by ensuring that a circuit traverses only reachable states during the functional clock cycles of a test. In addition, the power dissipation during the fast functional clock cycles of functional broadside tests does not exceed that possible during functional operation. On-chip test generation has the added advantage that it reduces test data volume and facilitates at-speed test application. This paper shows that on-chip generation of functional broadside tests can be done using a simple and fixed hardware structure, with a small number of parameters that need to be tailored to a given circuit, and can achieve high transition fault coverage for testable circuits. With the proposed on-chip test generation method, the circuit is used for generating reachable states during test application. This alleviates the need to compute reachable states offline. © 2012 IEEE.


Adams B.D.,Yale University | Kasinski A.L.,Purdue University | Slack F.J.,Yale University
Current Biology | Year: 2014

Malignant neoplasms are consistently among the top four leading causes of death in all age groups in the United States, despite a concerted effort toward developing novel therapeutic approaches [1]. Our understanding of and therapeutic strategy for treating each of these neoplastic diseases have been improved through decades of research on the genetics, signaling pathways, and cellular biology that govern tumor cell initiation, progression and maintenance. Much of this work has concentrated on post-translational modifications and abnormalities at the DNA level, including point mutations, amplifications/ deletions, and chromosomal translocations, and how these aberrant events affect the expression and function of protein-coding genes. Only recently has a novel class of conserved gene regulatory molecules been identified as a major contributor to malignant neoplastic disease. This review focuses on how these small non-coding RNA molecules, termed microRNAs (miRNAs), can function as oncogenes or tumor suppressors, and how the misexpression of miRNAs and dysregulation of factors that regulate miRNAs contribute to the tumorigenic process. Specific focus is given to more recently discovered regulatory mechanisms that go awry in cancer, and how these changes alter miRNA expression, processing, and function. © 2014 Elsevier Ltd.


Salehinia I.,Washington State University | Bahr D.F.,Purdue University
International Journal of Plasticity | Year: 2014

Molecular dynamics simulations are applied to study the effects of orientation and the presence of structural defects on the compression/tension (C/T) asymmetry of copper single crystals. In addition to the perfect crystal, crystals with stacking fault tetrahedra, as a representative internal defect, are considered to investigate both homogeneous and heterogeneous deformation mechanisms. Both the normal stresses to the slip plane and the relative values of Schmid factor in compression and tension impact the C/T asymmetry. The presence of an SFT lowers the applied stress required for plastic deformation, but this effect is highly dependent on the crystal orientation and loading direction. The reduction in yield stress is larger in compression than in tension for almost all orientations. Results show that in general a structural defect would decrease the C/T asymmetry in copper, corresponding closely to previous experiments. The reduction in yield stress in tension is less sensitive to defects than that in compression, suggesting that compression test is a more reliable experimental tool for future size dependence studies, since structural defects are the main reason behind the observed size effects in materials. On the other hand, since the reduction in yield stress is almost constant in tension for all orientations, testing in this geometry is more efficient to determine the orientation dependence of the yield stress. © 2013 Elsevier Ltd. All rights reserved.


The integrity of the neuronal membrane is crucial for its function and cellular survival; thus, ineffective repair of damaged membranes may be one of the key elements underlying the neuronal degeneration and overall functional loss that occurs after spinal cord injury (SCI). it has been shown that polyethylene glycol (PEG) can reseal axonal membranes following various injuries in multiple in vitro and in vivo injury models. in addition, PEG may also directly prevent the effects of mitochondria-derived oxidative stress on intracellular components. Thus, PEG repairs mechanically injured cells by at least two distinct pathways: resealing of the disrupted plasma membrane and direct protection of mitochondria. Besides repairing primary membrane damage, PEG treatment also results in significant attenuation of oxidative stress, likely due to its capacity to reseal the membrane, thereby breaking the cycle of cellular damage and free-radical production. Based on this, in addition to the practicality of its application, we expect that PEG may be established as an effective treatment for SCI where membrane disruption and mitochondrial damage are implicated. © 2013 Shanghai Institutes for Biological Sciences, CAS and Springer-Verlag Berlin Heidelberg.


Bickham J.W.,Purdue University
Ecotoxicology | Year: 2011

Evolutionary Toxicology is the study of the effects of chemical pollutants on the genetics of natural populations. Research in Evolutionary Toxicology uses experimental designs familiar to the ecotoxicologist with matched reference and contaminated sites and the selection of sentinel species. It uses the methods of molecular genetics and population genetics, and is based on the theories and concepts of evolutionary biology and conservation genetics. Although it is a relatively young field, interest is rapidly growing among ecotoxicologists and more and more field studies and even controlled laboratory experiments are appearing in the literature. A number of population genetic impacts have been observed in organisms exposed to pollutants which I refer to here as the four cornerstones of Evolutionary Toxicology. These include (1) genome-wide changes in genetic diversity, (2) changes in allelic or genotypic frequencies caused by contaminant-induced selection acting at survivorship loci, (3) changes in dispersal patterns or gene flow which alter the genetic relationships among populations, and (4) changes in allelic or genotypic frequencies caused by increased mutation rates. It is concluded that population genetic impacts of pollution exposure are emergent effects that are not necessarily predictable from the mode of toxicity of the pollutant. Thus, to attribute an effect to a particular contaminant requires a careful experimental design which includes selection of appropriate reference sites, detailed chemistry analyses of environmental samples and tissues, and the use of appropriate biomarkers to establish exposure and effect. This paper describes the field of Evolutionary Toxicology and discusses relevant field studies and their findings. © 2011 Springer Science+Business Media, LLC.


Rowe H.I.,Purdue University
Restoration Ecology | Year: 2010

Tallgrass prairie has been severely compromised by conversion to agriculture, making it among the most endangered ecosystems in North America. Expanding remnant tracts with restoration is key to conserving self-sustaining prairie. Although restoration managers rarely have the opportunity to perform large-scale replicated studies, experienced practitioners gain important insights into the effectiveness of management practices over time. By synthesizing expert knowledge, we can identify techniques with a proven record of on-the-ground success. Using two surveys, 38 tallgrass prairie managers responsible for a total of 12,659 ha in 11 states were asked to describe the effectiveness of site preparation, seeding techniques, and management (fire, grazing, mowing) and to list top threats and impediments to seeded restoration techniques. The most effective technique identified for restoring previously tilled land is to initiate soybean-corn rotations so that weeds can be controlled prior to native planting. Managers prefer to end on a soybean crop, and plant native species without tilling. In cases with native remnant vegetation, remnant restoration techniques are employed, but results indicate improvements are needed. Most managers prefer high diversity, forb-rich, local ecotype seed mixtures. Managers use fire, mowing, and grazing primarily to increase native plant diversity. Invasive plants are a major threat to restorations and a majority of managers (68%) devote at least 25% of their total restoration effort on this issue. Economic (land acquisition and labor) and seed availability limitations constrain restoration management most. Increased efficiency of seeding and invasive plant control could help alleviate barriers to restoration. © 2010 Society for Ecological Restoration International.


Hepatitis C virus (HCV), like many other flaviviruses, is widely distributed worldwide with estimated chronically infected victims between 170 and 200 million. HCV inherent error-prone RNA-dependent RNA polymerase (RdRp) is an attractive target for medicinal chemists because of the conservative nature of NS5B nucleotide-binding site. In addition, the availability of several crystal structures for HCV RdRp paved the road for conducting rational-based drug design. At the same time, RdRp is responsible for high mutation rate and rapid development of resistance to the clinically-used therapeutics. To improve the viral response, combination therapy is regularly used. The success of co-therapy disciplines depends on targeting two different active sites. This review provides an overview about different scaffolds that target HCV RdPp with insights about their binding modes and possible induced mutant strains. © 2012 Elsevier Ltd. All rights reserved.


Liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) is widely used for quantitative proteomic investigations. The typical output of such studies is a list of identified and quantified peptides. The biological and clinical interest is, however, usually focused on quantitative conclusions at the protein level. Furthermore, many investigations ask complex biological questions by studying multiple interrelated experimental conditions. Therefore, there is a need in the field for generic statistical models to quantify protein levels even in complex study designs. We propose a general statistical modeling approach for protein quantification in arbitrary complex experimental designs, such as time course studies, or those involving multiple experimental factors. The approach summarizes the quantitative experimental information from all the features and all the conditions that pertain to a protein. It enables both protein significance analysis between conditions, and protein quantification in individual samples or conditions. We implement the approach in an open-source R-based software package MSstats suitable for researchers with a limited statistics and programming background. We demonstrate, using as examples two experimental investigations with complex designs, that a simultaneous statistical modeling of all the relevant features and conditions yields a higher sensitivity of protein significance analysis and a higher accuracy of protein quantification as compared to commonly employed alternatives. The software is available at http://www.stat.purdue.edu/~ovitek/Software.html.


Many of solved tertiary structures of unknown functions do not have global sequence and structural similarities to proteins of known function. Often functional clues of unknown proteins can be obtained by predicting small ligand molecules that bind to the proteins. In our previous work, we have developed an alignment free local surface-based pocket comparison method, named Patch-Surfer, which predicts ligand molecules that are likely to bind to a protein of interest. Given a query pocket in a protein, Patch-Surfer searches a database of known pockets and finds similar ones to the query. Here, we have extended the database of ligand binding pockets for Patch-Surfer to cover diverse types of binding ligands. We selected 9393 representative pockets with 2707 different ligand types from the Protein Data Bank. We tested Patch-Surfer on the extended pocket database to predict binding ligand of 75 non-homologous proteins that bind one of seven different ligands. Patch-Surfer achieved the average enrichment factor at 0.1 percent of over 20.0. The results did not depend on the sequence similarity of the query protein to proteins in the database, indicating that Patch-Surfer can identify correct pockets even in the absence of known homologous structures in the database.


Fujii H.,University of Turku | Zhu J.-K.,Purdue University
Cellular and Molecular Life Sciences | Year: 2012

Plants face various kinds of environmental stresses, including drought, salinity, and low temperature, which cause osmotic stress. An understanding of the plant signaling pathways that respond to osmotic stress is important for both basic biology and agriculture. In this review, we summarize recent investigations concerning the SNF1-related protein kinase (SnRK) 2 kinase family, which play central roles in osmotic stress responses. SnRK2s are activated by osmotic stress, and a mutant lacking SnRK2s is hypersensitive to osmotic stress. Many questions remain about the signaling pathway upstream and downstream of SnRK2s. Because some SnRK2s also functions in the abscisic acid (ABA) signaling pathway, which has recently been well clarified, study of SnRK2s in ABA signaling can provide clues regarding their roles in osmotic stress gnaling. © Springer Basel AG 2012.


Giordano N.,Purdue University
Journal of the Acoustical Society of America | Year: 2013

The aeroacoustics of a recorder are studied using a direct numerical simulation based on the Navier-Stokes equations in two dimensions. Spatial maps for the air pressure and velocity give a detailed picture of vortex shedding near the labium. Changes in the spectrum as a result of variations in the blowing speed are also investigated. The results are in good semi-quantitative agreement with general results for these phenomena from experiments. © 2013 Acoustical Society of America.


Thaler J.S.,Cornell University | McArta S.H.,Cornell University | Kaplan I.,Purdue University
Proceedings of the National Academy of Sciences of the United States of America | Year: 2012

Most organisms face the problem of foraging and maintaining growth while avoiding predators. Typical animal responses to predator exposure include reduced feeding, elevated metabolism, and altered development rate, all of which can be beneficial in the presence of predators but detrimental in their absence. How then do animals balance growth and predator avoidance? In a series of field and greenhouse experiments, we document that the tobacco hornworm caterpillar, Manduca sexta, reduced feeding by 30-40% owing to the risk of predation by stink bugs, but developed more rapidly and gained the same mass as unthreatened caterpillars. Assimilation efficiency, extraction of nitrogen from food, and percent body lipid content all increased during the initial phase (1-3 d) of predation risk, indicating that enhanced nutritional physiology allows caterpillars to compensate when threatened. However, we report physiological costs of predation risk, including altered body composition (decreased glycogen) and reductions in assimilation efficiency later in development. Our findings indicate that hornworm caterpillars use temporally dynamic compensatory mechanisms that ameliorate the trade-off between predator avoidance and growth in the short term, deferring costs to a period when they are less vulnerable to predation.


Kaplan I.,Purdue University
PLoS Biology | Year: 2012

Indirect plant defenses are those facilitating the action of carnivores in ridding plants of their herbivorous consumers, as opposed to directly poisoning or repelling them. Of the numerous and diverse indirect defensive strategies employed by plants, inducible volatile production has garnered the most fascination among plant-insect ecologists. These volatile chemicals are emitted in response to feeding by herbivorous arthropods and serve to guide predators and parasitic wasps to their prey. Implicit in virtually all discussions of plant volatile-carnivore interactions is the premise that plants "call for help" to bodyguards that serve to boost plant fitness by limiting herbivore damage. This, by necessity, assumes a three-trophic level food chain where carnivores benefit plants, a theoretical framework that is conceptually tractable and convenient, but poorly depicts the complexity of food-web dynamics occurring in real communities. Recent work suggests that hyperparasitoids, top consumers acting from the fourth trophic level, exploit the same plant volatile cues used by third trophic level carnivores. Further, hyperparasitoids shift their foraging preferences, specifically cueing in to the odor profile of a plant being damaged by a parasitized herbivore that contains their host compared with damage from an unparasitized herbivore. If this outcome is broadly representative of plant-insect food webs at large, it suggests that damage-induced volatiles may not always be beneficial to plants with major implications for the evolution of anti-herbivore defense and manipulating plant traits to improve biological control in agricultural crops. © 2012 Ian Kaplan.


Plotnitsky A.,Purdue University
Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences | Year: 2016

The project of this article is twofold. First, it aims to offer a new perspective on, and a new argument concerning, realist and non-realist mathematical models, and differences and affinities between them, using physics as a paradigmatic field of mathematical modelling in science. Most of the article is devoted to this topic. Second, the article aims to explore the implications of this argument for mathematical modelling in other fields, in particular in cognitive psychology and economics. © 2015 The Author(s) Published by the Royal Society. All rights reserved.


Adams S.B.,Purdue University
Veterinary surgery : VS : the official journal of the American College of Veterinary Surgeons | Year: 2010

To assess joint contamination with tissue and hair after arthrocentesis of equine fetlock joints. Experimental. Limb specimens from 8 equine cadavers. Soft tissues including the joint capsule were harvested from the dorsal aspect of the fetlock joints and mounted on a wooden frame. Needles inserted through the joint tissue preparation were flushed into tissue culture plates that were examined for tissue and hair debris. Variables evaluated were gauge and type of needle (16, 18, 20, and 22 G sharp disposable needles and 20 G disposable spinal needles with stylet), number of times each needle was used (1, 2, 3, 4), length of hair (unclipped, clipped, shaved with razor), and needle insertion speed (fast, slow). Descriptive and statistical evaluations were performed. Tissue contamination was identified in 1145 of 1260 wells and hair contamination was identified in 384 of 1260 wells. Twenty gauge needles inserted through unclipped hair resulted in the least amount of hair contamination. Compared with 20 G needles with fast insertion 1 time through unclipped hair the odds ratios for contamination with hair were significantly greater for 16 G sharp disposable needles, 20 G spinal needles, clipped hair, shaved hair, and reuse of the needles. Spinal needles inserted through unclipped hair transferred many long hairs into the joint space. Reuse of needles for arthrocentesis should be avoided. Removal of hair is not indicated for arthrocentesis with sharp injection needles but is recommended when using spinal needles with stylets. Joint contamination with hair and tissue debris will be decreased by specific needle insertion techniques. Decreased contamination of joints may reduce the frequency of joint infections after arthrocentesis.


Magana A.J.,Purdue University
Computers and Education | Year: 2014

Size and scale cognition is a critical aptitude associated with reasoning with concepts and systems in science, technology, engineering, and mathematics (STEM). However, the teaching and learning of concepts related to size and scale present major challenges because objects at certain scales are unable to be perceived by humans with the naked eye. A potential way to overcome this challenge could be by means of learning strategies coupled with multimedia learning. In this study we propose learning strategies, instantiated by multimedia are for learning tools that may result in improved learning of size and scale cognition based on the FS2C framework. This framework consists of five levels to characterize size and scale cognition and the cognitive processes supporting them. Participants of this quasi-experimental design included 224 undergraduate students who experienced one of three different multimedia for learning tools, and then were assessed through five tasks whose design was based on the FS2C framework. Results suggest that learning strategies prompting students to compare objects of different sizes, may increase their abilities in ordering and classifying objects. Having students to interact with a logarithmic scale may also have increased participant posttest performance scores in the numerical proportional and absolute measurement tasks. Finally, we propose that the use of multimedia for learning affordances like 3D interaction, zoom in and zoom out, and direct interaction with a scale metaphor may help students make explicit connections and become familiar with objects of different sizes and scales. © 2013 Elsevier Ltd. All rights reserved.


Hill J.C.,Purdue University | Choi K.-S.,University of Wisconsin - Madison
Journal of Materials Chemistry A | Year: 2013

Two n-type W-containing ternary oxides, CuWO4 and Bi 2WO6, were prepared as high surface area electrodes and characterized for use as photoanodes in a water-splitting photoelectrochemical cell. The synthesis involved electrochemical preparation of porous WO 3 electrodes and annealing them with Cu2+- or Bi 3+-containing solutions on their surfaces to form the respective electrodes. The resulting CuWO4 electrode had a bandgap of 2.3 eV, and showed excellent photostability and photocurrent-to-O2 conversion efficiency (ca. 100%) in 0.1 M borate buffer solution (pH 9). Bi 2WO6 had a bandgap of 2.8 eV but, regardless of its higher bandgap energy, Bi2WO6 showed an earlier photocurrent onset and much higher photocurrent than CuWO4 due to its more favorable CB edge and flatband potential position for water splitting. Bi 2WO6 also showed chemical stability over a wide pH range (-0.26 ≤ pH ≤ 9.0). The photocurrent-to-O2 conversion efficiency of Bi2WO6 was in the range of 50-75% and its photocurrent decayed over time, indicating photocorrosion. However, stable photocurrent was obtained when H2O2, which has faster oxidation kinetics than water, was introduced into the electrolyte as a hole scavenger. This suggests that the photocorrosion of Bi2WO6 can be suppressed when an oxygen evolution catalyst is placed on its surface to improve interfacial hole transfer kinetics. With proper oxygen evolution catalysts and improved charge transport properties, both CuWO4 and Bi2WO6 have the possibility of achieving better photoelectrochemical performances than WO3. © The Royal Society of Chemistry 2013.


Mengiste T.,Purdue University
Annual Review of Phytopathology | Year: 2012

Plants inhabit environments crowded with infectious microbes that pose constant threats to their survival. Necrotrophic pathogens are notorious for their aggressive and wide-ranging virulence strategies that promote host cell death and acquire nutrients for growth and reproduction from dead cells. This lifestyle constitutes the axis of their pathogenesis and virulence strategies and marks contrasting immune responses to biotrophic pathogens. The diversity of virulence strategies in necrotrophic species corresponds to multifaceted host immune response mechanisms. When effective, the plant immune system disarms the infectious necrotroph of its pathogenic arsenal or attenuates its effect, restricting further ingress and disease symptom development. Simply inherited resistance traits confer protection against host-specific necrotrophs (HSNs), whereas resistance to broad host-range necrotrophs (BHNs) is complex. Components of host genetic networks, as well as the molecular and cellular processes that mediate host immune responses to necrotrophs, are being identified. In this review, recent advances in our understanding of plant immune responses to necrotrophs and comparison with responses to biotrophic pathogens are summarized, highlighting common and contrasting mechanisms. © 2012 by Annual Reviews. All rights reserved.


When flow cytometric data on mixtures of cell populations are collected from samples under different experimental conditions, computational methods are needed (a) to classify the samples into similar groups, and (b) to characterize the changes within the corresponding populations due to the different conditions. Manual inspection has been used in the past to study such changes, but high-dimensional experiments necessitate developing new computational approaches to this problem. A robust solution to this problem is to construct distinct templates to summarize all samples from a class, and then to compare these templates to study the changes across classes or conditions. We designed a hierarchical algorithm, flowMatch, to first match the corresponding clusters across samples for producing robust meta-clusters, and to then construct a high-dimensional template as a collection of meta-clusters for each class of samples. We applied the algorithm on flow cytometry data obtained from human blood cells before and after stimulation with anti-CD3 monoclonal antibody, which is reported to change phosphorylation responses of memory and naive T cells. The flowMatch algorithm is able to construct representative templates from the samples before and after stimulation, and to match corresponding meta-clusters across templates. The templates of the pre-stimulation and post-stimulation data corresponding to memory and naive T cell populations clearly show, at the level of the meta-clusters, the overall phosphorylation shift due to the stimulation. We concisely represent each class of samples by a template consisting of a collection of meta-clusters (representative abstract populations). Using flowMatch, the meta-clusters across samples can be matched to assess overall differences among the samples of various phenotypes or time-points.


Esquivel-Rodriguez J.,Purdue University
BMC bioinformatics | Year: 2012

Many functionally important proteins in a cell form complexes with multiple chains. Therefore, computational prediction of multiple protein complexes is an important task in bioinformatics. In the development of multiple protein docking methods, it is important to establish a metric for evaluating prediction results in a reasonable and practical fashion. However, since there are only few works done in developing methods for multiple protein docking, there is no study that investigates how accurate structural models of multiple protein complexes should be to allow scientists to gain biological insights. We generated a series of predicted models (decoys) of various accuracies by our multiple protein docking pipeline, Multi-LZerD, for three multi-chain complexes with 3, 4, and 6 chains. We analyzed the decoys in terms of the number of correctly predicted pair conformations in the decoys. We found that pairs of chains with the correct mutual orientation exist even in the decoys with a large overall root mean square deviation (RMSD) to the native. Therefore, in addition to a global structure similarity measure, such as the global RMSD, the quality of models for multiple chain complexes can be better evaluated by using the local measurement, the number of chain pairs with correct mutual orientation. We termed the fraction of correctly predicted pairs (RMSD at the interface of less than 4.0Å) as fpair and propose to use it for evaluation of the accuracy of multiple protein docking.


PeptideProphet is a post-processing algorithm designed to evaluate the confidence in identifications of MS/MS spectra returned by a database search. In this manuscript we describe the "what and how" of PeptideProphet in a manner aimed at statisticians and life scientists who would like to gain a more in-depth understanding of the underlying statistical modeling. The theory and rationale behind the mixture-modeling approach taken by PeptideProphet is discussed from a statistical model-building perspective followed by a description of how a model can be used to express confidence in the identification of individual peptides or sets of peptides. We also demonstrate how to evaluate the quality of model fit and select an appropriate model from several available alternatives. We illustrate the use of PeptideProphet in association with the Trans-Proteomic Pipeline, a free suite of software used for protein identification.


Helie S.,Purdue University | Ell S.W.,University of Maine, United States | Ashby F.G.,University of California at Santa Barbara
Cortex | Year: 2015

This article focuses on the interaction between the basal ganglia (BG) and prefrontal cortex (PFC). The BG are a group of nuclei at the base of the forebrain that are highly connected with cortex. A century of research suggests that the role of the BG is not exclusively motor, and that the BG also play an important role in learning and memory. In this review article, we argue that one important role of the BG is to train connections between posterior cortical areas and frontal cortical regions that are responsible for automatic behavior after extensive training. According to this view, one effect of BG trial-and-error learning is to activate the correct frontal areas shortly after posterior associative cortex activation, thus allowing for Hebbian learning of robust, fast, and efficient cortico-cortical processing. This hypothesized process is general, and the content of the learned associations depends on the specific areas involved (e.g., associations involving premotor areas would be more closely related to behavior than associations involving the PFC). We review experiments aimed at pinpointing the function of the BG and the frontal cortex and show that these results are consistent with the view that the BG is a general purpose trainer for cortico-cortical connections. We conclude with a discussion of some implications of the integrative framework and how this can help better understand the role of the BG in many different tasks. © 2014 Elsevier Ltd.


Lyutikov M.,Purdue University
Monthly Notices of the Royal Astronomical Society | Year: 2012

Expansion of non-spherical relativistic blast waves is considered in the Kompaneets (the thin-shell) approximation. We find that relativistic motion effectively 'freezes out' the lateral dynamics of the shock front: only extremely strongly collimated shocks, with opening angles Δθ≤ 1/Γ 2, show appreciable modification of profiles due to sideways expansion. For less collimated profiles, the propagation is nearly ballistic; the sideways expansion of relativistic shocks becomes important only when they become mildly relativistic. Even though the post-shock pressure is equilibrated downstream on the sound crossing time-scale, this does not mean that the shape of the shock changes on the post-shock sound crossing time-scale. © 2012 The Authors Monthly Notices of the Royal Astronomical Society © 2012 RAS.


Grant R.W.,Purdue University | Dixit V.D.,Yale University
Obesity | Year: 2015

Objective This review will focus on the immunological aspects of adipose tissue and its potential role in development of chronic inflammation that instigates obesity-associated comorbidities. Methods The review used PubMed searches of current literature to examine adipose tissue leukocytosis. Results and Conclusions The adipose tissue of obese subjects becomes inflamed and contributes to the development of insulin resistance, type 2 diabetes, and metabolic syndrome. Numerous immune cells including B cells, T cells, macrophages, and neutrophils have been identified in adipose tissue, and obesity influences both the quantity and the nature of immune cell subtypes, which emerges as an active immunological organ capable of modifying whole-body metabolism through paracrine and endocrine mechanisms. Adipose tissue is a large immunologically active organ during obesity and displays hallmarks of both and innate and adaptive immune response. Despite the presence of hematopoietic lineage cells in adipose tissue, it is unclear whether the adipose compartment has a direct role in immune surveillance or host defense. Understanding the interactions between leukocytes and adipocytes may reveal the clinically relevant pathways that control adipose tissue inflammation and is likely to reveal mechanisms by which obesity contributes to increased susceptibility to both metabolic and certain infectious diseases. © 2014 The Obesity Society.


Overholser B.R.,Purdue University
The American journal of managed care | Year: 2011

Pharmacokinetic drug-drug interactions (DDIs) involving opioid analgesics can be problematic. Opioids are widely used, have a narrow therapeutic index, and can be associated with severe toxicity. The purpose of this review is to describe pharmacokinetic DDIs associated with opioids frequently encountered in managed care settings (morphine, codeine, oxycodone, oxymorphone, hydrocodone, hydromorphone, fentanyl, tramadol, and methadone). An introduction to the pharmacokinetic basis of DDIs is provided, and potential DDIs associated with opioids are reviewed. Opioids metabolized by the drug metabolizing enzymes of the cytochrome P450 (CYP450) system (codeine, oxycodone, hydrocodone, fentanyl, tramadol, and methadone) are associated with numerous DDIs that can result in either a reduction in opioid effect or excess opioid effects. Conversely, opioids that are not metabolized by that system (morphine, oxymorphone, and hydromorphone) tend to be involved in fewer CYP450-associated pharmacokinetic DDIs.


Introduction: Recent research has called upon investigators to exploit cross-national differences to uncover the cultural and structural factors influencing drug use. While the individual-level correlates are well-established, little is known about the association between cross-national variation in drug policies and young people's substance use. This study examines, net of individual-level predictors, the association between national-level drug policy and use of an illicit drug other than cannabis. Methods: The study uses Eurobarometer repeated cross-sectional surveys in 2002 and 2004 of adolescents aged 15-24 drawn in multistage, random probability samples proportional to population size and density within regions of their country (. N=. 15,191). Participants completed self-reported measures of last month drug use, attitudes toward drugs, school and work participation, and demographics. Gathered from several international bodies, national-level policy measures include drug offense levels, possession decriminalization, and presence and usage of harm reduction strategies. Results: Hierarchical logistic regression models demonstrate that, while controlling for important individual-level predictors, in countries where there is no restriction on possession of drugs for personal use, the odds of drug use in the last month are 79% lower (. p<. 0.05). On the other hand, higher usage of treatment and drug substitution are associated with higher levels of drug use. These results are robust to several alternate specifications. Conclusions: Among the strongest and most consistent findings, eliminating punishments for possession for personal use is not associated with higher drug use. The results indicate that researchers should take national-level context into account in individual-level studies of drug use. © 2012 Elsevier Ireland Ltd.


Bhosale J.S.,Purdue University
Review of Scientific Instruments | Year: 2011

A temperature tuned light emitting diode (LED) has several advantages over conventional sources for Fourier transform spectroscopy. The large radiation density of LEDs, concentrated in a small spectral region, is ideal for high resolution Fourier transform spectroscopy where a high signal-to-noise (S/N) ratio is desired. A simple, inexpensive LED source leads to a superior performance at high resolutions exceeding that of a tungsten halogen lamp, in the visible region of spectrum. © 2011 American Institute of Physics.


Snoeyink C.,Texas Tech University | Wereley S.,Purdue University
Optics Letters | Year: 2013

This Letter presents a technique for subdiffraction limit imaging termed Bessel beam microscopy (BBM). By placing a lens in series with an axicon in the optical path of a microscope, the diffraction-limited resolution of the base microscope is improved by one third. This improvement is demonstrated experimentally by resolving individual subdiffraction limit fluorescent beads in a close-pack arrangement. The behavior of the BBM system is explored using angular diffraction simulations, demonstrating the possibility of resolving features spaced as little as 110 nm apart when viewed with a 100 × 1.4 NA objective. Unique among super-resolution techniques, BBM acquires subdiffraction limit information in a single image with broadband unstructured illumination using only static geometric optics placed between the microscope and camera. © 2013 Optical Society of America.


Lyutikov M.,Purdue University
Physical Review D - Particles, Fields, Gravitation and Cosmology | Year: 2011

Understanding possible electromagnetic signatures of merging and collapsing compact objects is important for identifying possible sources of the LIGO signal. Electromagnetic emission can be produced as a precursor to the merger, as a prompt emission during the collapse of a neutron star and at the spin-down stage of the resulting Kerr-Newman black hole. For the neutron star-neutron star mergers, the precursor power scales as L BNS2GMNSRNS8/(Rorb7c), while for the neutron star-black hole mergers, it is (GM/(c2R NS))2 times smaller. We demonstrate that the time evolution of the axisymmetric force-free magnetic fields can be expressed in terms of the hyperbolic Grad-Shafranov equation, and we formulate the generalization of Ferraro's law of isorotation to time-dependent angular velocity. We find an exact nonlinear time-dependent Michel-type (split-monopole) structure of magnetospheres driven by spinning and collapsing neutron stars in Schwarzschild geometry. Based on this solution, we argue that the collapse of a neutron star into a black hole happens smoothly, without the natural formation of current sheets or other dissipative structures on the open field lines; thus, it does not allow the magnetic field to become disconnected from the star and escape to infinity. Therefore, as long as an isolated Kerr black hole can produce plasma and currents, it does not lose its open magnetic field lines. Its magnetospheric structure evolves towards a split monopole, and the black hole spins down electromagnetically (the closed field lines get absorbed by the hole). The "no-hair theorem," which assumes that the outside medium is a vacuum, is not applicable in this case: highly conducting plasma introduces a topological constraint forbidding the disconnection of the magnetic field lines from the black hole. Eventually, a single random large scale spontaneous reconnection event will lead to magnetic field release, shutting down the electromagnetic black hole engine forever. Overall, the electromagnetic power in all the above cases is expected to be relatively small. We also discuss the nature of short gamma-ray bursts and suggest that if the magnetic field is amplified to ∼1014G during the merger or the core collapse, the similarity of the early afterglow properties of long and short gamma-ray bursts can be related to the fact that in both cases a spinning black hole can retain a magnetic field for a sufficiently long time to extract a large fraction of its rotational energy and produce high energy emission via the internal dissipation in the wind. © 2011 American Physical Society.


Lyutikov M.,Purdue University
Physical Review D - Particles, Fields, Gravitation and Cosmology | Year: 2011

The motion of a Schwarzschild black hole with velocity v 0=β0c through a constant magnetic field B0 in vacuum induces a component of the electric field along the magnetic field, generating a nonzero second Poincaré electromagnetic invariant F*•F≠0. This will produce (e.g., via radiative effects and vacuum breakdown) an electric charge density of the order of ρind=B 0β0/(2πeRG), where RG=2GM/c2 is the Schwarzschild radius and M is the mass of the black hole; the charge density ρind is similar to the Goldreich-Julian density. The magnetospheres of moving black holes resemble in many respects the magnetospheres of rotationally-powered pulsars, with pair formation fronts and outer gaps, where the sign of the induced charge changes. As a result, the black hole will generate bipolar electromagnetic jets each consisting of two counter-aligned current flows (four current flows total), each carrying an electric current of the order I≈eB0RGβ 0. The electromagnetic power of the jets is L≈(GM) 2B02β02/c3; for a particular case of merging black holes the resulting Poynting power is L≈(GM) 3B02/(c5R), where R is the radius of the orbit. In addition, in limited regions near the horizon the first electromagnetic invariant changes sign, so that the induced electric field becomes larger than the magnetic field, E>B. As a result, there will be local dissipation of the magnetic field close to the horizon, within a region with the radial extent ΔR≈RGβ0. The total energy loss from a system of merging black holes is a sum of two components with similar powers, one due to the rotation of space-time within the orbit, driven by the nonzero angular momentum in the system, and the other due to the linear motion of the black holes through the magnetic field. Since the resulting electrodynamics is in many respects similar to pulsars, merging black holes may generate coherent radio and high energy emission beamed approximately along the orbital normal. In addition, merging black holes may produce observable wind-driven cavities. © 2011 American Physical Society.


Gregory J.W.,Ohio State University | Sakaue H.,Japan Aerospace Exploration Agency | Liu T.,Western Michigan University | Sullivan J.P.,Purdue University
Annual Review of Fluid Mechanics | Year: 2014

The development and capabilities of fast-responding pressure-sensitive paint (fast PSP) are reviewed within the context of recent applications to aerodynamic and acoustic investigations. PSP is an optical technique for determining surface pressure distributions by measuring changes in the intensity of emitted light, whereas fast PSP is an extension applicable to unsteady flows and acoustics. Most fast PSP formulations are based on the development of porous binders that allow for rapid oxygen diffusion and interaction with the chemical sensor. This article reviews the development of porous binders, the selection of luminophore molecules suitable for unsteady testing, dynamic calibrations of PSP, data-acquisition methods, and noteworthy applications for flow and acoustic diagnostics. Calibrations of the dynamic response of fast PSP show a flat frequency response to at least 6 kHz, with some paint formulations exceeding a response of 1 MHz. Various applications of fast PSP are discussed that highlight the capabilities of the technique, and concluding remarks highlight the need for the future development of fast PSP. Copyright © 2014 by Annual Reviews. All rights reserved.


Buczkowski G.,Purdue University
Biological Invasions | Year: 2010

Disturbance resulting from urbanization is a leading cause of biotic homogenization worldwide. Native species are replaced with widespread non-native species and ants are among the world's most notorious invaders. To date, all documented cases of ant invasions involve exotic introduced species that are spread around the world by human-mediated dispersal. I investigated the effect of urbanization on the evolution of invasive characteristics in a native ant species, the odorous house ant, Tapinoma sessile (Say). Colony social structure, life history traits, and the spatial pattern of nest distribution were compared by sampling T. sessile across a gradient of three distinct habitats: Natural, semi-natural, and urban. Results demonstrate a remarkable transition in colony social and spatial structure and life history traits between natural and urban environments. In natural habitats, T. sessile colonies are comprised of small, monogyne (single queen), and monodomous (single nest) colonies. In urban areas, T. sessile often exhibit extreme polygyny and polydomy, form large supercolonies, and become a dominant pest. Results also suggest that urban T. sessile colonies may have a negative impact on native ant abundance and diversity. In the natural environment T. sessile coexisted with a wide array of other ant species, while very few ant species were present in the urban environment invaded by T. sessile. Habitat degradation and urbanization can lead to extreme changes in social and spatial colony structure and life history traits in a native ant species and can promote the evolution of invasive characteristics such as polygyny, polydomy, and supercolonial colony structure. © 2010 Springer Science+Business Media B.V.


Leidy H.J.,University of Missouri | Campbell W.W.,Purdue University
Journal of Nutrition | Year: 2011

Increased eating frequency is postulated to increase metabolism, reduce hunger, improve glucose and insulin control, and reduce body weight, making it an enticing dietary strategy for weight loss and/or the maintenance of a healthy body weight. Because past research has primarily focused on the effects of eating frequency on changes in energy expenditure and body weight, limited data exist surrounding the impact of eating frequency on appetite control and energy intake. We provide a brief review of the controlled-feeding studies that primarily targeted the appetitive, hormonal, and food intake responses potentially altered with eating frequency. The 3 meal/d pattern served as the reference for defining increased or reduced eating frequency. In general, increased eating frequency led to lower peaks (P < 0.05) in perceived appetite, satiety, glucose, insulin, ghrelin, and PYY responses compared with reduced eating frequency. However, when examining these responses over the course of the day (i.e. using area under the curve assessments), no differences in any of these outcomes were observed. The rate of gastric emptying also appears to be unaltered with increased eating frequency. Subsequent food intake was examined in several studies with conflicting results. Regarding the effect of reduced eating frequency, several studies indicate significant increases in perceived appetite and reductions in perceived satiety when 1 or 2 meals were eliminated from the daily diet. Taken together, these findings suggest that increased eating frequency (>3 eating occasions/d) has minimal, if any, impact on appetite control and food intake, whereas reduced eating frequency (>3 eating occasions/d) negatively effects appetite control. © 2011 American Society for Nutrition. © 2011 American Society for Nutrition.


Engle S.E.,Purdue University
Journal of visualized experiments : JoVE | Year: 2012

Tobacco use leads to numerous health problems, including cancer, heart disease, emphysema, and stroke. Addiction to cigarette smoking is a prevalent neuropsychiatric disorder that stems from the biophysical and cellular actions of nicotine on nicotinic acetylcholine receptors (nAChRs) throughout the central nervous system. Understanding the various nAChR subtypes that exist in brain areas relevant to nicotine addiction is a major priority. Experiments that employ electrophysiology techniques such as whole-cell patch clamp or two-electrode voltage clamp recordings are useful for pharmacological characterization of nAChRs of interest. Cells expressing nAChRs, such as mammalian tissue culture cells or Xenopus laevis oocytes, are physically isolated and are therefore easily studied using the tools of modern pharmacology. Much progress has been made using these techniques, particularly when the target receptor was already known and ectopic expression was easily achieved. Often, however, it is necessary to study nAChRs in their native environment: in neurons within brain slices acutely harvested from laboratory mice or rats. For example, mice expressing "hypersensitive" nAChR subunits such as α4 L9'A mice (1) and α6 L9'S mice (2), allow for unambiguous identification of neurons based on their functional expression of a specific nAChR subunit. Although whole-cell patch clamp recordings from neurons in brain slices is routinely done by the skilled electrophysiologist, it is challenging to locally apply drugs such as acetylcholine or nicotine to the recorded cell within a brain slice. Dilution of drugs into the superfusate (bath application) is not rapidly reversible, and U-tube systems are not easily adapted to work with brain slices. In this paper, we describe a method for rapidly applying nAChR-activating drugs to neurons recorded in adult mouse brain slices. Standard whole-cell recordings are made from neurons in slices, and a second micropipette filled with a drug of interest is maneuvered into position near the recorded cell. An injection of pressurized air or inert nitrogen into the drug-filled pipette causes a small amount of drug solution to be ejected from the pipette onto the recorded cell. Using this method, nAChR-mediated currents are able to be resolved with millisecond accuracy. Drug application times can easily be varied, and the drug-filled pipette can be retracted and replaced with a new pipette, allowing for concentration-response curves to be created for a single neuron. Although described in the context of nAChR neurobiology, this technique should be useful for studying many types of ligand-gated ion channels or receptors in neurons from brain slices.


HogenEsch H.,Purdue University
Frontiers in Immunology | Year: 2012

Aluminum-containing adjuvants are widely used in preventive vaccines against infectious diseases and in preparations for allergy immunotherapy. The mechanism by which they enhance the immune response remains poorly understood. Aluminum adjuvants selectively stimulate a Th2 immune response upon injection of mice and a mixed response in human beings. They support activation of CD8 T cells, but these cells do not undergo terminal differentiation to cytotoxicT cells. Adsorption of antigens to aluminum adjuvants enhances the immune response by facilitating phagocytosis and slowing the diffusion of antigens from the injection site which allows time for inflammatory cells to accumulate. The adsorptive strength is important as high affinity interactions interfere with the immune response. Adsorption can also affect the physical and chemical stability of antigens. Aluminum adjuvants activate dendritic cells via direct and indirect mechanisms. Phagocytosis of aluminum adjuvants followed by disruption of the phagolysosome activates NLRP3-inflammasomes resulting in the release of active Im-1β and IL18. Aluminum adjuvants also activate dendritic cells by binding to membrane lipid rafts. Injection of aluminum-adjuvanted vaccines causes the release of uric acid, DNA, and ATP from damaged cells which in turn activate dendritic cells. The use of aluminum adjuvant is limited by weak stimulation of cell-mediated immunity. This can be enhanced by addition of other immunomodulatory molecules. Adsorption of these molecules is determined by the same mechanisms that control adsorption of antigens and can affect the efficacy of such combination adjuvants. The widespread use of aluminum adjuvants can be attributed in part to the excellent safety record based on a 70-year history of use. They cause local inflammation at the injection site, but also reduce the severity of systemic and local reactions by binding biologically active molecules in vaccines. © 2013 Hogen Esch.


Ghosh S.,Intel Corporation | Roy K.,Purdue University
Proceedings of the IEEE | Year: 2010

Variations in process parameters affect the operation of integrated circuits (ICs) and pose a significant threat to the continued scaling of transistor dimensions. Such parameter variations, however, tend to affect logic and memory circuits in different ways. In logic, this fluctuation in device geometries might prevent them from meeting timing and power constraints and degrade the parametric yield. Memories, on the other hand, experience stability failures on account of such variations. Process limitations are not exhibited as physical disparities only; transistors experience temporal device degradation as well. Such issues are expected to further worsen with technology scaling. Resolving the problems of traditional Si-based technologies by employing non-Si alternatives may not present a viable solution; the non-Si miniature devices are expected to suffer the ill-effects of process/temporal variations as well. To circumvent these nonidealities, there is a need to design ICs that can adapt themselves to operate correctly under the presence of such inconsistencies. In this paper, we first provide an overview of the process variations and time-dependent degradation mechanisms. Next, we discuss the emerging paradigm of variation-tolerant adaptive design for both logic and memories. Interestingly, these resiliency techniques transcend several design abstraction levelswe present circuit and microarchitectural techniques to perform reliable computations in an unreliable environment. © 2006 IEEE.


Tyner W.E.,Purdue University
Agricultural Economics | Year: 2010

This article addresses the evolving links between energy and agricultural markets. Prior to 2005, there was little correlation between energy and agricultural commodity prices. In 2006-2008, with the ethanol boom in the United States, there emerged a strong link between crude oil, gasoline, and corn prices. There was little link between ethanol and corn. However, in late 2008 and 2009, the markets changed as ethanol production came under severe economic pressure and 2 billion out of 12 billion gallons of capacity shut down. During this period ethanol became priced more on corn, as the breakeven corn price helped drive the ethanol market. This article explores the drivers in these markets as well as other major issues facing the corn ethanol industry in the United States such as the blend wall. The article concludes with a review of prospects of a future cellulosic biofuels industry. © 2010 International Association of Agricultural Economists.


Kularatne S.A.,Purdue University
Methods in molecular biology (Clifton, N.J.) | Year: 2010

Nanoparticulate medicines offer the advantage of allowing delivery of large quantities of unmodified drug within the same particle. Nanoparticle uptake by cancer cells can, however, be compromised due to the large size and hydrophilicity of the particle. To circumvent cell penetration problems and simultaneously improve tumor specificity, nanoparticulate medicines have been linked to targeting ligands that bind to malignant cell surfaces and enter cells by receptor-mediated endocytosis. In this chapter, we summarize multiple methods for delivering nanoparticles into cancer cells by folate receptor-mediated endocytosis, devoting special emphasis to folate-targeted liposomes. Folate receptor-mediated endocytosis has emerged as an attractive strategy for nanoparticle delivery due to both overexpression of the folate receptor on cancer cells and the rapid internalization of the receptor by receptor-mediated endocytosis.


Mosquera M.A.,Purdue University
Physical Review A - Atomic, Molecular, and Optical Physics | Year: 2013

The Runge-Gross action functional of time-dependent density-functional theory leads to a well-known causality paradox; that is, a perturbation of the electronic density in the future affects the response of the system in the present. This paradox is known to be caused by an inconsistent application of the Dirac-Frenkel variational principle. In view of the recent solutions to this problem, the action functional employed by Runge and Gross in their formulation of time-dependent density-functional theory is analyzed in the context of the Keldysh contour technique. The time-dependent electronic density and the concept of causality are extended to the contour. We derive a variational equation that obeys causality and relates the exchange-correlation potential with its kernel and the functional derivative of the exchange-correlation action functional with respect to the density. It is shown that the adiabatic local-density approximation is a consistent solution of this equation and that the time-dependent optimized potential method can also be derived from it. The formalism presented here can be used to find new approximation methods for the exchange-correlation potential and to avoid the causality dilemma. © 2013 American Physical Society.


White D.W.,Gundersen Lutheran Medical Center | Suzanne Beard R.,Purdue University | Suzanne Beard R.,Wake forest University | Barton E.S.,Wake forest University
Immunological Reviews | Year: 2012

Nearly all human beings, by the time they reach adolescence, are infected with multiple herpesviruses. At any given time, this family of viruses accounts for 35-40 billion human infections worldwide, making herpesviruses among the most prevalent pathogens known to exist. Compared to most other viruses, herpesviruses are also unique in that infection lasts the life of the host. Remarkably, despite their prevalence and persistence, little is known about how these viruses interact with their hosts, especially during the clinically asymptomatic phase of infection referred to as latency. This review explores data in human and animal systems that reveal the ability of latent herpesviruses to modulate the immune response to self and environmental antigens. From the perspective of the host, there are both potentially detrimental and surprisingly beneficial effects of this lifelong interaction. The realization that latent herpesvirus infection modulates immune responses in asymptomatic hosts forces us to reconsider what constitutes a 'normal' immune system in a healthy individual. © 2011 John Wiley & Sons A/S.


Noinaj N.,Purdue University | Rollauer S.E.,U.S. National Institute of Diabetes and Digestive and Kidney Diseases | Buchanan S.K.,U.S. National Institute of Diabetes and Digestive and Kidney Diseases
Current Opinion in Structural Biology | Year: 2015

The outer membranes (OM) of Gram-negative bacteria contain a host of β-barrel outer membrane proteins (OMPs) which serve many functions for cell survival and virulence. The biogenesis of these OMPs is mediated by the β-barrel assembly machinery (BAM) complex which is composed of five components including the essential core component called BamA that mediates the insertase function within the OM. The crystal structure of BamA has recently been reported from three different species, including a full-length structure from Neisseria gonorrhoeae. Mutagenesis and functional studies identified several conformational changes within BamA that are required for function, providing a significant advancement towards unraveling exactly how BamA and the BAM complex are able to fold and insert new OMPs in the OM. © 2015.


Specialized trafficking systems in eukaryotic cells serve a critical role in partitioning intracellular proteins between the nucleus and cytoplasm. Cytoplasmic proteins (including chromatin remodeling enzymes and transcription factors) must gain access to the nucleus to exert their functions to properly program fundamental cellular events ranging from cell cycle progression to gene transcription. Knowing that nuclear import mediated by members of the karyopherin α family of transport receptors plays a critical role in regulating development and differentiation, we wanted to determine the identity of proteins that are trafficked by this karyopherin α pathway. To this end, we performed a GST pull-down assay using porcine orthologs of karyopherin α1 (KPNA1) and karyopherin α7 (KPNA7) and prey protein derived from porcine fibroblast cells and used a liquid chromatography and tandem mass spectrometry (LC-MS/MS) approach to determine the identity of KPNA1 and KPNA7 interacting proteins. Our screen revealed that the proteins that interact with KPNA1 and KPNA7 are generally nuclear proteins that possess nuclear localization signals. We further validated two candidate proteins from this screen and showed that they are able to be imported into the nucleus in vivo and also interact with members of the karyopherin α family of proteins in vitro. Our results also reveal the utility of using a GST pull-down approach coupled with LC-MS/MS to screen for protein interaction partners in a non-traditional model system.


Lumineau F.,Purdue University | Henderson J.E.,IMD International
Journal of Operations Management | Year: 2012

This paper theoretically refines and empirically extends the debate on the type of interplay between relational experience and contractual governance in an under-researched area: supply chain disputes. We define relational experience as either cooperative or competitive; distinguish between control and coordination functions of contractual governance; and assess their interplay on the negotiation strategy used in disputes. Using a unique data set of buyer-supplier disputes, we find, in particular that increasing contractual control governance weakens the positive effect of cooperative relational experience on cooperative negotiation strategy. However, increasing contractual control governance for a buyer-supplier dyad with competitive relational experience will increase cooperative negotiation strategy. Contractual coordination governance reinforces the positive effect of cooperative relational experience. Through this study, we reach a better understanding of how and when contractual and relational governance dimensions interact; rather than whether they act as substitutes or complements as has been studied in prior research. We discuss the implications of these findings for the field of supply chain management. © 2012 Elsevier B.V. All rights reserved.


Machaty Z.,Purdue University
Cell and Tissue Research | Year: 2016

Mammalian embryo development begins when the fertilizing sperm triggers a series of elevations in the oocyte’s intracellular free Ca2+ concentration. The elevations are the result of repeated release and re-uptake of Ca2+ stored in the smooth endoplasmic reticulum. Ca2+ release is primarily mediated by the phosphoinositide signaling system of the oocyte. The system is stimulated when the sperm causes the hydrolysis of phosphatidylinositol 4,5-bisphosphate (PIP2) into inositol 1,4,5-trisphosphate (IP3) and diacylglycerol (DAG); IP3 then binds its receptor on the surface of the endoplasmic reticulum that induces Ca2+ release. The manner in which the sperm generates IP3, the Ca2+ mobilizing second messenger, has been the subject of extensive research for a long time. The sperm factor hypothesis has eventually gained general acceptance, according to which it is a molecule from the sperm that diffuses into the ooplasm and stimulates the phosphoinositide cascade. Much evidence now indicates that the sperm-derived factor is phospholipase C-zeta (PLCζ) that cleaves PIP2 and generates IP3, eventually leading to oocyte activation. A recent addition to the candidate sperm factor list is the post-acrosomal sheath WW domain-binding protein (PAWP), whose role at fertilization is currently under debate. Ca2+ influx across the plasma membrane is also important as, in the absence of extracellular Ca2+, the oscillations run down prematurely. In pig oocytes, the influx that sustains the oscillations seems to be regulated by the filling status of the stores, whereas in the mouse other mechanisms might be involved. This work summarizes the current understanding of Ca2+ signaling in mammalian oocytes. © 2015, The Author(s).


Neu C.P.,Purdue University
Osteoarthritis and Cartilage | Year: 2014

Functional imaging refers broadly to the visualization of organ or tissue physiology using medical image modalities. In load-bearing tissues of the body, including articular cartilage lining the bony ends of joints, changes in strain, stress, and material properties occur in osteoarthritis (OA), providing an opportunity to probe tissue function through the progression of the disease. Here, biomechanical measures in cartilage and related joint tissues are discussed as key imaging biomarkers in the evaluation of OA. Emphasis will be placed on the (1) potential of radiography, ultrasound, and magnetic resonance imaging to assess early tissue pathomechanics in OA, (2) relative utility of kinematic, structural, morphological, and biomechanical measures as functional imaging biomarkers, and (3) improved diagnostic specificity through the combination of multiple imaging biomarkers with unique contrasts, including elastography and quantitative assessments of tissue biochemistry. In comparison to other modalities, magnetic resonance imaging provides an extensive range of functional measures at the tissue level, with conventional and emerging techniques available to potentially to assess the spectrum of preclinical to advance OA. © 2014 Osteoarthritis Research Society International.


Janick J.,Purdue University
HortScience | Year: 2015

Nikolai Ivanovich Vavilov (1887–1943), one of the pioneers of 20th century plant breeding, is best known for seminal work in identifying centers of origins and diversity for cultivated plants. Vavilov studied genetics with William Bateson from 1913 to 1914 at the John Innis Horticultural Institute. In 1921, he was chosen by Vladimir Lenin to head the Branch of Applied Botany in Petrograd (St. Petersburg) and rose to be the Director of the All-Union Institute of Agriculture in Leningrad, where he oversaw agricultural research for the entire country. By 1934, Vavilov established more than 400 research institutes and experiment stations with a staff of 20,000. His efforts established the Soviet Union as a world leader in genetics and plant breeding in the 1920s and early 1930s. Vavilov carried out an extensive series of expeditions worldwide, including the United States, to collect germplasm; and he created the world’s largest repository, over 250,000 seed accessions. However, as a result of famine in the Soviet Union in the late 1920s, partly as a result of forced collectivization of peasants, Vavilov came in conflict with an ambitious agronomist, Trofim Lysenko, who came to prominence with an agricultural technique proposed in 1928, of exposing chilled, soaked seeds of wheat (dubbed vernalization) to extend production in northern areas of Russia. Lysenko’s rejection of Mendelian genetics won the support of Joseph Stalin, leading to the arrest and death sentence of Vavilov, although this was later commuted to 20 years imprisonment. Vavilov died of starvation in prison in 1943, thus entering the select group of martyrs of science along with Gordiano Bruno, Galileo Galilei, Antoine Lavoisier, and Georgii Karpechenko. © 2015, American Society for Horticultural Science. All Right reserved.


Leary J.F.,Purdue University
Canadian Journal of Ophthalmology | Year: 2010

SIZE matters... the size of the scalpel determines the precision of the surgery. Nanotechnology affords us the chance to construct nanotools that are on the size scale of molecules, allowing us to treat each cell of the human body as a patient. Nanomedicine will allow for eradication of disease at the single-cell level. Since nanotools are self-assembling, nanomedicine has the potential to perform parallel processing medicine on a massive scale. These nanotools can be made of biocompatible and biodegradable nanomaterials. They can be "smart" in that they can use sophisticated targeting strategies, which can perform error checking to prevent harm if even a very small fraction of them are mistargeted. Built-in molecular biosensors can provide controlled drug delivery with feedback control for individual cell dosing. If designed to repair existing cells rather than to just destroy diseased cells, these nanomedical devices can perform in-situ regenerative medicine, programming cells along less dangerous cell pathways to prevent tissues and organs from being destroyed by the treatments and thus providing an attractive alternative to allogeneic organ transplants. Nanomedical tools, while tiny in size, can have a huge impact on medicine and health care. Earlier and more sensitive diagnosis will lead to presymptomatic diagnosis and treatment of disease before permanent damage occurs to tissues and organs. This should result in the delivery of better medicine at lower costs with better outcomes. Lastly, and importantly, some of the first uses of nanotechnology and nanomedicine are occurring in the field of ophthalmology. Some of the potential benefits of nanotechnology for future treatment of retinopathies and optic nerve damage are discussed at the end of this paper.


Torrent-Sucarrat M.,CSIC - Institute of Advanced Chemistry of Catalonia | Francisco J.S.,Purdue University | Anglada J.M.,CSIC - Institute of Advanced Chemistry of Catalonia
Journal of the American Chemical Society | Year: 2012

Sulfuric acid can act as a catalyst of its own formation. We have carried out a computational investigation on the gas-phase formation of H 2SO4 by hydrolysis of SO3 involving one and two water molecules, and also in the presence of sulfuric acid and its complexes with one and two water molecules. The hydrolysis of SO3 requires the concurrence of two water molecules, one of them acting as a catalyzer, and our results predict an important catalytic effect, ranging between 3 and 11 kcal·mol-1 when the catalytic water molecule is substituted by a sulfuric acid molecule or one of its hydrates. In these cases, the reaction products are either bare sulfuric acid dimer or sulfuric acid dimer complexed with a water molecule. There are broad implications from these new findings. The results of the present investigation show that the catalytic effect of sulfuric acid in the SO3 hydrolysis can be important in the Earth's stratosphere, in the heterogeneous formation of sulfuric acid and in the formation of aerosols, in H2SO4 formation by aircraft engines, and also in understanding the formation of sulfuric acid in the atmosphere of Venus. © 2012 American Chemical Society.


Perception of speech in competing speech is facilitated by spatial separation of the target and distracting speech, but this benefit may arise at either a perceptual or a cognitive level of processing. Load theory predicts different effects of perceptual and cognitive (working memory) load on selective attention in flanker task contexts, suggesting that this paradigm may be used to distinguish levels of interference. Two experiments examined interference from competing speech during a word recognition task under different perceptual and working memory loads in a dual-task paradigm. Listeners identified words produced by a talker of one gender while ignoring a talker of the other gender. Perceptual load was manipulated using a nonspeech response cue, with response conditional upon either one or two acoustic features (pitch and modulation). Memory load was manipulated with a secondary task consisting of one or six visually presented digits. In the first experiment, the target and distractor were presented at different virtual locations (0° and 90° respectively), whereas in the second, all the stimuli were presented from the same apparent location. Results suggest that spatial cues improve resistance to distraction in part by reducing working memory demand. © 2010 The Psychonomic Society, Inc.


Despite the tremendous destruction wrought by catastrophes, social science holds few quantitative assessments of explanations for the rate of recovery. This article illuminates four factors-damage, population density, human capital, and economic capital-that are thought to explain the variation in the pace of population recovery following disaster; it also explores the popular but relatively untested factor of social capital. Using time-series, cross-sectional models and propensity score matching, it tests these approaches using new data from the rebuilding of 39 neighbourhoods in Tokyo after its 1923 earthquake. Social capital, more than earthquake damage, population density, human capital, or economic capital, best predicts population recovery in post-earthquake Tokyo. These findings suggest new approaches for research on social capital and disasters as well as public policy avenues for handling catastrophes. © Overseas Development Institute, 2012.


Bouck E.C.,Purdue University
Journal of Intellectual Disability Research | Year: 2014

Background: Although students with mild intellectual disability (MID) present unique educational needs and considerations, in research and in practice, they are sometimes aggregated with students with learning disabilities and emotional disorders and considered mild disabilities or aggregated with students with moderate/severe intellectual disability and labelled as intellectual disability. Method: This study is a secondary analysis of the NLTS2 data to understand the immediate (i.e. within 2 years) and longer-term outcomes (i.e. within 4 years, within 6 years and within 8 years) of secondary students with MID. Frequency distributions and a significant test were conducted to analyse data from the NLTS2. Results: Students with MID struggled with postschool success when considering employment, postsecondary education, and independent living. Across the span of time since graduation (i.e. within 2 years, within 4 years, within 6 years, and within 8 years), a lack of consistent pattern existed, in general, for these students with regards to outcomes. Students did not necessarily improve or decline in their outcomes the longer they were out of school. Conclusions: The postschool outcome data warrant critical examination of the factors contributing to the poor outcomes. The field needs to systematically understand what schools can control with regards to improved outcomes for students with MID - particularly employment regardless of the length of time out of school and independent living as the time since school exit increases - and then implement such practices. © 2013 MENCAP and International Association of the Scientific Study of Intellectual and Developmental Disabilities and John Wiley & Sons Ltd.


Posada G.,Purdue University
Attachment and Human Development | Year: 2013

Although Ainsworth and Bowlby's perspective on attachment relationships has instinctive underpinnings, they also recognized variability in the ways caregiving is implemented in different ecologies. Ainsworth's naturalistic observations in two different societies provided early evidence about the development of infant-mother attachment, differences in the quality of attachment relationships, and the role of maternal care in attachment development. Further, her research demonstrated the importance of an ethological approach for research within and across cultures. Employing similar concepts and methods, my collaborators and I have tested and expanded Bowlby's and Ainsworth's ideas about the generality of the sensitivity construct and sensitivity-security link. In our research, ethological observations have been key to elaborating the quality of care construct and studying child-mother attachment relationships in different cultures, social contexts, and ages. © 2013 © Taylor & Francis.


Straintronic logic is a promising platform for beyond Moores law computing. Using Bennett clocking mechanism, information can propagate through an array of strain-mediated multiferroic nanomagnets, exploiting the dipolar coupling between the magnets without having to physically interconnect them. Here, we perform a critical analysis of switching failures, i.e., error in information propagation due to thermal fluctuations through a chain of such straintronic devices. We solved stochastic Landau-Lifshitz-Gilbert equation considering room-temperature thermal perturbations and show that magnetization switching may fail due to inherent magnetization dynamics accompanied by thermally broadened switching delay distribution. Avenues available to circumvent such issue are proposed. © 2014 AIP Publishing LLC.


Acikmese B.,Jet Propulsion Laboratory | Corless M.,Purdue University
Automatica | Year: 2011

We consider the problem of designing observers to asymptotically estimate the state of a system whose nonlinear time-varying terms satisfy an incremental quadratic inequality that is parameterized by a set of multiplier matrices. Observer design is reduced to solving linear matrix inequalities for the observer gain matrices. The proposed observers guarantee exponential convergence of the state estimation error to zero. In addition to considering a larger class of nonlinearities than previously considered, this paper unifies earlier related results in the literature. The results are illustrated by application to several examples. © 2011 Elsevier Ltd. All rights reserved.


Buczkowski G.,Purdue University
Insectes Sociaux | Year: 2012

Eusocial insects often live in colonies comprised of an extensive network of interconnected nests and estimating colony spatial structure and colony boundaries may be difficult, especially in cryptic, subterranean species. A combination of aggression assays and protein marking was used to estimate nest spatial distribution in field populations of the highly polydomous cornfield ant, Lasius neoniger. The estimates were first obtained via 1-on-1 aggression tests for workers collected from different nests within the research plots. The aggression tests were followed by mark-recapture field studies which utilized rabbit IgG protein. The ants were allowed to self-mark by feeding on sucrose solution spiked with the IgG protein. Colony spatial structure was detected by sampling ants from different nests and analyzing them for the presence of the marker using an ELISA test. Estimates based on aggression tests were substantially higher relative to those based on protein marking. The average colony size based on aggression tests was 2.0 ± 0.2 m 2 and was significantly higher than the 1.1 ± 0.4 m 2 estimate based on protein marking. The estimate based on protein marking was even lower, 0.2 ± 0.1 m 2, when a Fluon-coated ring restricted ant feeding to the focal nest and prevented ants from other nests from feeding on the protein-marked sucrose. No significant correlation was detected between internest aggression and internest distance. Likewise, no correlation was detected between distance from the focal nest and the percentage of workers testing positive for the protein marker. The results show that both approaches have their own limitations, but their simultaneous use allows for a more accurate. © International Union for the Study of Social Insects (IUSSI) 2011.


Narimanov E.E.,Purdue University
Physical Review X | Year: 2014

We introduce a new 'universality class' of artificial optical media-photonic hypercrystals. These hyperbolic metamaterials, with periodic spatial variation of dielectric permittivity on subwavelength scale, combine the features of optical metamaterials and photonic crystals. In particular, surface waves supported by a hypercrystal possess the properties of both the optical Tamm states in photonic crystals and surface-plasmon polaritons at the metal-dielectric interface.


Treating differential molecular diffusion correctly and accurately remains as a great challenge to the modeling of turbulent non-premixed combustion. The aim of this paper is to develop consistent modeling strategies for differential molecular diffusion in flamelet models. Two types of differential molecular diffusion models are introduced, linear differential diffusion models and nonlinear differential diffusion models. A multi-component turbulent mixing layer problem is analyzed in detail to gain insights into differential molecular diffusion and its characteristics, particularly the dependence of differential molecular diffusion on the Reynolds number and the Lewis number. These characteristics are then used to validate the differential molecular diffusion models. Finally, the new models are applied to the modeling of a series of laboratory-scale turbulent non-premixed jet flames with different Reynolds number (Sandia Flames B, C, and D) to further assess the models' performance. © 2016 AIP Publishing LLC.


Cundiff S.T.,U.S. National Institute of Standards and Technology | Weiner A.M.,Purdue University
Nature Photonics | Year: 2010

Optical arbitrary waveform generation will allow waveforms to be synthesized at optical frequencies but with the flexibility currently available at radiofrequencies. This technique is enabled by combining frequency comb technology, which produces trains of optical pulses with a well-defined frequency spectrum, with pulse shaping methods, which are used to transform a train of ultrashort pulses into an arbitrary waveform. To produce a waveform that fills time, the resolution of the shaper must match the repetition rate of the original pulse train, which in turn must have a comb spectrum that is locked to the shaper. Here, we review the current efforts towards achieving optical arbitrary waveform generation and discuss the possible applications of this technology. © 2010 Macmillan Publishers Limited.


Manganese(v) imido complexes of 5,10,15-tris(pentafluorophenyl)corrole (H3tpfc) can be prepared by the reaction of MnIII(tpfc) and organic nitrene generated from either photolytic or thermal activation of organic azides. The terminal imido complexes of manganese(v) were among the first structurally characterized examples of MnV terminal imido complexes in the literature. They feature a short Mn≡N triple bond and a nearly linear M≡N-C angle. The ground state of (tpfc)MnV(NAr) is singlet. Contrary to expectations, arylimido complexes of manganese(v) were stable to moisture and did not undergo [NR] group transfer to olefins. Manganese(v) imido corrole with an activated tosyl imido ligand was prepared from iodoimine (ArINTs) and manganese(iii) corrole. The resulting complex (tpfc)Mn(NTs) is paramagnetic (S = 1), hydrolyzes to (tpfc)Mn(O) in the presence of water, abstracts hydrogen atoms from benzylic C-H bonds, and catalyzes aziridination of alkenes. Mechanistic studies on the aziridination and hydrogen atom transfer reactions are reviewed. This perspective also describes the reaction chemistry of the heme enzyme chlorite dismutase, the mechanism by which dioxygen is formed on a single-metal site, and recent advances in functional modelling of this enzyme. We also compare the reactivity of water-soluble iron versus manganese porphyrins towards the chlorite anion. © The Royal Society of Chemistry 2011.


Gelvin S.B.,Purdue University
Current Opinion in Microbiology | Year: 2010

Agrobacterium species transfer single-strand DNA and virulence effector proteins to plants. To understand how Agrobacterium achieves interkingdom horizontal gene transfer, scientists have investigated how the interaction of bacterial effector proteins with host proteins directs T-DNA to the plant nucleus. VirE2, a single-strand DNA binding protein, likely plays a key role in T-DNA nuclear targeting. However, subcellular trafficking of VirE2 remains controversial, with reports of both cytoplasmic and nuclear localization. The recent discovery that phosphorylation of the VirE2 interacting protein VIP1 modulates both nuclear targeting and transformation may provide a solution to this conundrum. Novel experimental systems that allow tracking of VirE2 as it exits Agrobacterium and enters the plant cell will also aid in understanding virulence protein/T-DNA cytoplasmic trafficking. © 2009 Elsevier Ltd. All rights reserved.


Srivastava B.K.,Purdue University
Nuclear Physics A | Year: 2014

Possible phase transition of strongly interacting matter from hadron to a quark-gluon plasma state have in the past received considerable interest. The clustering of color sources provides a framework of the partonic interactions in the initial stage of the collisions. The onset of deconfinement transition is identified by the spanning percolation cluster in 2D percolation. In this talk results are presented both for the multiplicity and the elliptic flow at RHIC and LHC energies. The thermodynamic quantities temperature, equation of state and transport coefficient are obtained in the framework of clustering of color sources. It is shown that the results are in excellent agreement with the recent lattice QCD calculations (LQCD). © 2014 Elsevier B.V. All rights reserved.


Wang C.-C.,Purdue University
IEEE Transactions on Information Theory | Year: 2012

Motivated by practical wireless network protocols, this paper focuses on wireless intersession network coding (INC) over a 1-hop neighborhood, of which the exact capacity region remains an open problem. Towards better understanding of the capacity, this work first models the wireless overhearing events by broadcast packet erasure channels that are memoryless and stationary. Since most INC gain is resulted from destinations overhearing packets transmitted by other sources, this work then focuses exclusively on the 2-staged INC schemes, which fully capture the throughput benefits of overheard message side information (MSI) through the use of one-time feedback but refrain from exploiting the broadcast spatial diversity gain of channel output feedback. Under this setting, a capacity outer bound is provided for any number of coexisting unicast sessions. For the special cases of, it is shown that the outer bound can be achieved and is indeed the capacity. To quantify the tightness of the outer bound for, a capacity inner bound for general is provided. Both the outer and inner bounds can be evaluated by any linear programming solver. Numeric results show that for with randomly chosen channel parameters, the difference between the outer and inner bounds is within 1% for 96.7% of the times. Focusing exclusively on the benefits of MSI, the results in this paper can also be viewed as the generalization of index-coding capacity from wireline broadcast with binary alphabets to wireless broadcast with high-order alphabets. © 2011 IEEE.


Mudawar I.,Purdue University
Journal of Electronic Packaging, Transactions of the ASME | Year: 2011

Boiling water in small channels that are formed along turbine blades has been examined since the 1970s as a means to dissipating large amounts of heat. Later, similar geometries could be found in cooling systems for computers, fusion reactors, rocket nozzles, avionics, hybrid vehicle power electronics, and space systems. This paper addresses (a) the implementation of two-phase microchannel heat sinks in these applications, (b) the fluid physics and limitations of boiling in small passages, and effective tools for predicting the thermal performance of heat sinks, and (c) means to enhance this performance. It is shown that despite many hundreds of publications attempting to predict the performance of two-phase microchannel heat sinks, there are only a handful of predictive tools that can tackle broad ranges of geometrical and operating parameters or different fluids. Development of these tools is complicated by a lack of reliable databases and the drastic differences in boiling behavior of different fluids in small passages. For example, flow boiling of certain fluids in very small diameter channels may be no different than in macrochannels. Conversely, other fluids may exhibit considerable confinement even in seemingly large diameter channels. It is shown that cutting-edge heat transfer enhancement techniques, such as the use of nanofluids and carbon nanotube coatings, with proven merits to single-phase macrosystems, may not offer similar advantages to microchannel heat sinks. Better performance may be achieved by careful optimization of the heat sink's geometrical parameters and by adapting a new class of hybrid cooling schemes that combine the benefits of microchannel flow with those of jet impingement. © 2011 American Society of Mechanical Engineers.


Background A conversation currently exists regarding secondary curriculum (e.g. academics, functional) for students with moderate/severe intellectual disability (ID) without a large research base connecting curriculum to outcomes. Method This study represented a secondary analysis of the National Longitudinal Transition Study-2 (NLTS2) data to understand in-school curriculum and educational programming for secondary students with moderate/severe ID as well as the relationship between curriculum and students' post-school outcomes. Statistical procedures such as frequency distributions, a significance test and logistic regression were utilised to analyse secondary data from the NLTS2. Results The results suggest the majority of students with moderate/severe ID received a functional curriculum as well as instruction in core content areas; however, their instruction primarily occurred in pull-out educational settings. The students also reported low rates for the post-school outcomes examined (i.e. independent living, employment and post-secondary attendance). Finally, curriculum (functional vs. academics) was not related to any post-school outcome examined (e.g. independent living, employment). Conclusions The data suggest additional research is needed to understand what factors impact post-school outcomes for students with moderate/severe ID. Yet - and regardless of the lack of impact - additional work is needed to help students achieve better post-school outcomes, including further examination of curriculum and instructional environments. © 2012 Blackwell Publishing Ltd.


Chaturvedi A.R.,Purdue University | Dolk D.R.,Naval Postgraduate School, Monterey | Drnevich P.L.,University of Alabama
MIS Quarterly: Management Information Systems | Year: 2011

In this research note, we examine the design, development, validation, and use of virtual worlds. Our purpose in doing so is to extend the design science paradigm by developing a set of design principles applicable to the context of virtual environments, particularly those using agent-based simulation as their underlying technology. Our central argument is that virtual worlds comprise a new class of information system, one that combines the structural aspects of traditional modeling and simulation systems in concert with emergent user dynamics of systems supporting emergent knowledge processes. Our approach involves two components. First, we review the characteristics of agent-based virtual worlds (ABVWs) to discern design requirements that may challenge current design theory. From this review, we derive a set of design principles based on deep versus emergent structures where deep structures reflect conventional modeling and simulation system architectures and emergent structures capture the unpredictable user-system dynamics inherent in emergent knowledge processes, which increasingly characterize virtual worlds. We illustrate how these design challenges are addressed with an exemplar of a complex mirror world, a large-scale ABVW we developed called Sentient World. Our contribution is the insight of partitioning ABVW architectures into deep and emergent structures that mirror modeling systems and emergent knowledge processes respectively, while developing extended design principles to facilitate their integration. We conclude with a discussion of the implications of our design principles for informing and guiding future research and practice.


Waser P.M.,Purdue University | Hadfield J.D.,University of Edinburgh
Molecular Ecology | Year: 2011

Estimating rates of movement among populations is never simple, and where young animals cannot all be captured at their birth sites, traditional field methods potentially underestimate dispersal rates. Genetic assignment tests appear to hold promise for detecting 'precapture' dispersal, and recent evidence suggests that even on the scale of dispersal between populations, genetic parentage analyses can also be informative. Herein, we examine the performance of both types of analysis with data from a 17-year study of dispersal in banner-tailed kangaroo rats Dipodomys spectabilis. We compare estimates of precapture dispersal from (i) the commonly used parentage analysis program cervus (ii) a pedigree-reconstruction program, MasterBayes, that combines genetic with spatial and other nongenetic information and (iii) genetic assignment procedures implemented by the program geneclass2, with (iv) rates of dispersal observed through recapture of a subset of animals initially marked shortly after weaning. geneclass2 estimates a larger proportion of precapture dispersers than MasterBayes, but both approaches as well as those based on field data alone, suggest that approximately 10% of adults in local populations are immigrants and that interpopulation dispersal is slightly female-biassed. All genetic procedures detect precapture dispersal between populations, but dispersers identified by MasterBayes are particularly compatible with what is independently known about body mass at dispersal, dispersal distance and distance between parents. Parentage analyses have considerable potential to infer the value of this otherwise elusive demographic parameter when most candidate parents can be genotyped and when nongenetic information, especially the distance separating candidate mothers and fathers, can be incorporated into the procedure. © 2011 Blackwell Publishing Ltd.


Wang C.-C.,Purdue University
IEEE Transactions on Information Theory | Year: 2012

This paper focuses on the 1-to-K broadcast packet erasure channel (PEC), a generalization of the broadcast binary erasure channel from the binary symbol to a finite field GF(q) with sufficiently large . We consider the setting in which the source node has instant feedback of the channel outputs of the receivers after each transmission. The main results of this paper are: (i) The capacity region for general 1-to-3 broadcast PECs and (ii) The capacity region for two types of 1-to-K broadcast PECs: the symmetric PECs, and the spatially independent PECs with onesided fairness constraints. This paper also develops (iii) A pair of outer and inner bounds of the capacity region for arbitrary-K-tobroadcast PECs, which can be easily evaluated by any linear programming solver. The proposed inner bound is proven by a new class of intersession network coding schemes, termed the packet evolution schemes, which is based on the concept of code alignment in GF(q)that is in parallel with the interference alignment techniques for the Euclidean space. Extensive numerical experiments show that the outer and inner bounds meet for almost all broadcast PECs encountered in practical scenarios and thus effectively bracket the capacity of general 1-to-K broadcast PECs with COF. © 2011 IEEE.


Pomeranz I.,Purdue University
IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems | Year: 2011

The use of multi-cycle (or multi-pattern) tests for delay faults can reduce the number of clock cycles required for test application, and enhance the ability of a test set to detect delay defects. This is achieved by exercising the circuit in functional mode for several clock cycles as part of each test. This advantage is especially important for multi-pattern functional broadside tests, which guarantee normal functional operation conditions during the functional clock cycles of the test. This paper describes a procedure for generating multi-pattern broadside tests. The procedure extends a two-pattern test set gradually to increase the number of patterns included in each test while reducing the number of tests. Experimental results demonstrate that significant reductions in the numbers of clock cycles are possible with the proposed procedure for both functional and arbitrary broadside test sets. © 2011 IEEE.


During the RHIC 2010 run, STAR has collected a large amount of minimum-bias, central and high pT trigger data in Au + Au collisions at √sNN=39,62.4and200GeV with the detector configured to minimize photon conversion background. In this article we report on a new high precision measurement of non-photonic electron mid-rapidity invariant yield, improved nuclear modification factor and v2 in Au + Au collisions at √sNN=200GeV. We also present measurements of mid-rapidity invariant yield at √sNN=62.4 and v2 at √sNN=39and62.4GeV. © 2013 Elsevier B.V.


Crane C.A.,Purdue University | Eckhardt C.I.,State University of New York at Buffalo
Journal of Counseling Psychology | Year: 2013

The current study evaluated the efficacy of a single-session brief motivational enhancement (BME) interview to increase treatment compliance and reduce recidivism rates in a sample of 82 recently adjudicated male perpetrators of intimate partner violence (IPV). Batterer intervention program attendance and completion as well as re-arrest records served as the primary outcome measures and were collected 6 months post-adjudication. Results indicated that BME was associated with increases in session attendance and treatment compliance. BME was not directly associated with reductions in recidivism. The relationship between BME and treatment compliance was moderated by readiness to change such that BME participants with low readiness to change attended more sessions and were more likely to be in compliance with the terms of a treatment than control participants with low readiness, while participants with high readiness attended sessions equally, regardless of study condition. Results indicate that outcomes may be improved through treatment efforts that consider individual differences, such as one's readiness to change, in planning interventions for IPV perpetrators © 2013 American Psychological Association.


Szpankowski W.,Purdue University | Verdu S.,Princeton University
IEEE Transactions on Information Theory | Year: 2011

The minimum expected length for fixed-to-variable length encoding of an n -block memoryless source with entropy H grows as n H + O(1), where the term O(1) lies between 0 and 1. However, this well-known performance is obtained under the implicit constraint that the code assigned to the whole n-block is a prefix code. Dropping the prefix constraint, which is rarely necessary at the block level, we show that the minimum expected length for a finite-alphabet memoryless source with known distribution grows as n H - 1\2 log n +O(1) unless the source is equiprobable. We also refine this result up to o(1) for those memoryless sources whose log probabilities do not reside on a lattice. © 2011 IEEE.


Wereley S.T.,Purdue University | Meinhart C.D.,University of California at Santa Barbara
Annual Review of Fluid Mechanics | Year: 2010

Microfluidic devices are becoming increasingly common and are seen in applications ranging from biology to nanotechnology and manufacturing. Flow behavior in these small domains can often be counterintuitive because of the low Reynolds number or the relative importance of surface forces. Micro-particle image velocimetry (μPIV) is a quantitative method that can be used to characterize the performance of such microfluidic systems with spatial resolutions better than one micron. Illustrating the impact of this measurement technique, more than 100 journal articles are published per year that feature μPIV velocity measurements. This article discusses the fundamentals of the technique, its theoretical background, and several applications. Copyright © 2010 by Annual Reviews. All rights reserved.


Mattes R.D.,Purdue University
Physiology and Behavior | Year: 2012

The sensory properties of foods and beverages are primary determinants of food choice. Some flavor components have an inherent hedonic valence that influences ingestive behavior. However, these hedonic impressions may be modified and others newly formed through their association with the post-ingestive consequences of food and beverage consumption. Flavor-active compounds, including spices, also modify digestive, absorptive and metabolic processes through direct activation of signaling pathways or via neurally-mediated cephalic phase responses. These may modify energy balance through effects on food digestion, energy absorption and metabolism. Thus, collectively, flavor has the potential to modify energy balance. Attempts to purposefully augment energy and nutrient intake have largely focused on the aging population where flavor fortification is posited to correct for diminishing sensory function. Evidence of efficacy is not strong, possibly due to methodological issues such as low statistical power and failure to match documented sensory limitations with the nature of the intervention. More rigorous testing should determine the viability of this therapeutic application of food flavors. The use of flavor compounds for weight reduction has yielded mixed results. Most trials have delivered the compounds via capsule precluding assessment of flavor to outcomes. Work with red pepper suggests there is an independent, albeit subtle, sensory effect on substrate oxidation coupled with a more general reduction of appetite and enhancement of energy expenditure. Flavor active compounds hold some promise for being more a part of the solution than the problem of disordered eating and unhealthy weight. © 2011 Elsevier Inc.


Many short gamma-ray bursts (GRBs) show prompt tails lasting up to hundreds of seconds that can be energetically dominant over the initial sub-second spike. In this paper we develop an electromagnetic model of short GRBs that explains the two stages of the energy release, the prompt spike and the prompt tail. The key ingredient of the model is the recent discovery that an isolated black hole can keep its open magnetic flux for times much longer than the collapse time and thus can spin down electromagnetically, driving the relativistic wind. First, the merger is preceded by an electromagnetic precursor wind with total power , reaching 3 × 1044 erg s-1 for typical neutron star masses of 1.4 M ⊙ and magnetic fields B ∼ 1012 G. If a fraction of this power is converted into pulsar-like coherent radio emission, this may produce an observable radio burst of a few milliseconds (like the Lorimer burst). At the active stage of the merger, two neutron stars produce a black hole surrounded by an accretion torus in which the magnetic field is amplified to ∼1015 G. This magnetic field extracts the rotational energy of the black hole and drives an axially collimated electromagnetic wind that may carry of the order of 10 50 erg, limited by the accretion time of the torus, a few hundred milliseconds. For observers nearly aligned with the orbital normal this is seen as a classical short GRB. After the accretion of the torus, the isolated black hole keeps the open magnetic flux and drives the equatorially (not axially) collimated outflow, which is seen by an observer at intermediate polar angles as a prompt tail. The tail carries more energy than the prompt spike, but its emission is de-boosted for observers along the orbital normal. Observers in the equatorial plane miss the prompt spike and interpret the prompt tail as an energetic long GRB (the supernova-less long burst GRB060505 and GRB060614 may belong to this category). We also demonstrate that episodic accretion onto the black hole of magnetized clouds that carry non-zero magnetic flux can be highly efficient in extracting the spin energy of the black hole, producing the electromagnetic outflows with power exceeding the average accretion power and total energy exceeding the rest mass energy of the accreted mass. We identify the late time flares with such accretion events. © 2013. The American Astronomical Society. All rights reserved.


Despite numerous and widespread calls for more ''useful'' climate-science information to inform policy, most climate science is still produced in a way that is consistent with the ''linear model'' of research that favors pure basic research over other approaches, resulting in missed opportunities to link useful climate science with decision makers. To improve the ability to adapt to a changing climate, it is necessary to improve the linkages between the production and supply of climate-science information with users' needs to ensure that the climate science is contextual, credible, trusted, and understood by the users. This paper reports on research that evaluated how three Regional Integrated Sciences and Assessments (RISA) programs produced useful climate information for improved decision support in a variety of sectors. Research indicates that these organizations utilized several processes and approaches to produce useful climate information, including identifying users' information needs; translating, communicating, and sharing knowledge; producing and situating social capital; building capacity in the user community to understand and utilize the climate-science information; and maintaining a flexible and nimble organization guided by strong leadership. The process of linking the production and supply of climate-science information with users' demands is a complex, highly contextual social process that requires ample resources and time management, research agendas that are ''end to end'' and can respond to changing contexts, and organizational commitment to support ''use-inspired'' research. Additional research is needed to improve evaluation methods and metrics used to assess climateservice organizations. © 2013 American Meteorological Society.


Rossmann M.G.,Purdue University
Quarterly Reviews of Biophysics | Year: 2013

This review is a partially personal account of the discovery of virus structure and its implication for virus function. Although I have endeavored to cover all aspects of structural virology and to acknowledge relevant individuals, I know that I have favored taking examples from my own experience in telling this story. I am anxious to apologize to all those who I might have unintentionally offended by omitting their work. The first knowledge of virus structure was a result of Stanley's studies of tobacco mosaic virus (TMV) and the subsequent X-ray fiber diffraction analysis by Bernal and Fankuchen in the 1930s. At about the same time it became apparent that crystals of small RNA plant and animal viruses could diffract X-rays, demonstrating that viruses must have distinct and unique structures. More advances were made in the 1950s with the realization by Watson and Crick that viruses might have icosahedral symmetry. With the improvement of experimental and computational techniques in the 1970s, it became possible to determine the three-dimensional, near-atomic resolution structures of some small icosahedral plant and animal RNA viruses. It was a great surprise that the protecting capsids of the first virus structures to be determined had the same architecture. The capsid proteins of these viruses all had a 'jelly-roll' fold and, furthermore, the organization of the capsid protein in the virus were similar, suggesting a common ancestral virus from which many of today's viruses have evolved. By this time a more detailed structure of TMV had also been established, but both the architecture and capsid protein fold were quite different to that of the icosahedral viruses. The small icosahedral RNA virus structures were also informative of how and where cellular receptors, anti-viral compounds, and neutralizing antibodies bound to these viruses. However, larger lipid membrane enveloped viruses did not form sufficiently ordered crystals to obtain good X-ray diffraction. Starting in the 1990s, these enveloped viruses were studied by combining cryo-electron microscopy of the whole virus with X-ray crystallography of their protein components. These structures gave information on virus assembly, virus neutralization by antibodies, and virus fusion with and entry into the host cell. The same techniques were also employed in the study of complex bacteriophages that were too large to crystallize. Nevertheless, there still remained many pleomorphic, highly pathogenic viruses that lacked the icosahedral symmetry and homogeneity that had made the earlier structural investigations possible. Currently some of these viruses are starting to be studied by combining X-ray crystallography with cryo-electron tomography. © Cambridge University Press 2013.


Cholewa B.D.,University of Wisconsin - Milwaukee | Liu X.,Purdue University | Ahmad N.,University of Wisconsin - Milwaukee
Cancer Research | Year: 2013

Polo-like kinase 1 (Plk1) is a well-established mitotic regulator with a diverse range of biologic functions continually being identified throughout the cell cycle. Preclinical evidence suggests that the molecular targeting of Plk1 could be an effective therapeutic strategy in a wide range of cancers; however, that success has yet to be translated to the clinical level. The lack of clinical success has raised the question of whether there is a true oncogenic addiction to Plk1 or if its overexpression in tumors is solely an artifact of increased cellular proliferation. In this review, we address the role of Plk1 in carcinogenesis by discussing the cell cycle and DNA damage response with respect to their associations with classic oncogenic and tumor suppressor pathways that contribute to the transcriptional regulation of Plk1. A thorough examination of the available literature suggests that Plk1 activity can be dysregulated through key transformative pathways, including both p53 and pRb. On the basis of the available literature, it may be somewhat premature to draw a definitive conclusion on the role of Plk1 in carcinogenesis. However, evidence supports the notion that oncogene dependence on Plk1 is not a late occurrence in carcinogenesis and it is likely that Plk1 plays an active role in carcinogenic transformation. ©2013 AACR.


The cornea is a central component of the camera eye of vertebrates and even slight corneal disturbances severely affect vision. The transcription factor PAX6 is required for normal eye development, namely the proper separation of the lens from the developing cornea and the formation of the iris and anterior chamber. Human PAX6 mutations are associated with severe ocular disorders such as aniridia, Peters anomaly and chronic limbal stem cell insufficiency. To develop the zebrafish as a model for corneal disease, we first performed transcriptome and in situ expression analysis to identify marker genes to characterise the cornea in normal and pathological conditions. We show that, at 7 days post fertilisation (dpf), the zebrafish cornea expresses the majority of marker genes (67/84 tested genes) found also expressed in the cornea of juvenile and adult stages. We also characterised homozygous pax6b mutants. Mutant embryos have a thick cornea, iris hypoplasia, a shallow anterior chamber and a small lens. Ultrastructure analysis revealed a disrupted corneal endothelium. pax6b mutants show loss of corneal epithelial gene expression including regulatory genes (sox3, tfap2a, foxc1a and pitx2). In contrast, several genes (pitx2, ctnnb2, dcn and fabp7a) were ectopically expressed in the malformed corneal endothelium. Lack of pax6b function leads to severe disturbance of the corneal gene regulatory programme.


Wang Y.,Purdue University
Philosophical transactions of the Royal Society of London. Series B, Biological sciences | Year: 2013

Single-molecule (SM) spectroscopy has been an exciting area of research offering significant promise and hope in the field of sensor development to detect targets at ultra-low levels down to SM resolution. To the experts and developers in the field of surface-enhanced Raman spectroscopy (SERS), this has often been a challenge and a significant opportunity for exploration. Needless to say, the opportunities and excitement of this multidisciplinary area impacts span the fields of physics, chemistry and engineering, along with a significant thrust in applications constituting areas in medicine, biology, environment and agriculture among others. In this review, we will attempt to provide a quick snapshot of the basics of SM-SERS, nanostructures and devices that can enable SM Raman measurement. We will conclude with a discussion on SERS implications in biomedical sciences.


Ritchie K.,Purdue University
Philosophical transactions of the Royal Society of London. Series B, Biological sciences | Year: 2013

Bacteria, such as Escherichia coli and Caulobacter crescentus, are the most studied and perhaps best-understood organisms in biology. The advances in understanding of living systems gained from these organisms are immense. Application of single-molecule techniques in bacteria have presented unique difficulties owing to their small size and highly curved form. The aim of this review is to show advances made in single-molecule imaging in bacteria over the past 10 years, and to look to the future where the combination of implementing such high-precision techniques in well-characterized and controllable model systems such as E. coli could lead to a greater understanding of fundamental biological questions inaccessible through classic ensemble methods.


Gelvin S.B.,Purdue University
Annual Review of Phytopathology | Year: 2010

Agrobacterium species genetically transform plants by transferring a region of plasmid DNA, T-DNA, into host plant cells. The bacteria also transfer several virulence effector proteins. T-DNA and virulence proteins presumably form T-complexes within the plant cell. er-T-complexes likely also form by interaction of plant-encoded proteins with T-complexes. These protein-nucleic acid complexes traffic through the plant cytoplasm, enter the nucleus, and eventually deliver T-DNA to plant chromatin. Integration of T-DNA into the plant genome establishes a permanent transformation event, permitting stable expression of T-DNA-encoded transgenes. The transformation process is complex and requires participation of numerous plant proteins. This review discusses our current knowledge of plant proteins that contribute to Agrobacterium-mediated transformation, the roles these proteins play in the transformation process, and the modern technologies that have been employed to elucidate the cell biology of transformation. © 2010 by Annual Reviews. All rights reserved.


Robicheaux F.,Purdue University
Physical Review A - Atomic, Molecular, and Optical Physics | Year: 2014

We describe calculations of elastic and inelastic scattering of neutral molecules and cold ions in a magnetic field. The molecule is assumed to have a magnetic and electric dipole moment. The external magnetic field splits the ground rovibrational energy levels of the molecule. The highest energy state within the ground rovibrational manifold increases in energy as the distance to the ion decreases leading to a repelling potential. At low energy, inelastic collisions are strongly suppressed due to the large distance of closest approach. Thus, a collision between a neutral molecule and a cold ion will lead to a decrease in the molecule's kinetic energy with no change in internal energy. We present results for the specific case of OH molecules cooled by Be+, Mg+, or Ca+ ions. Also, we perform molecular dynamics simulations of ions and molecules in a combined Paul trap and time-averaged orbiting potential trap. Our results suggest that sympathetic cooling of neutral molecules by ions would be possible if cold ions and molecules could be simultaneously trapped. © 2014 American Physical Society.


Peer W.A.,Purdue University
Annals of Botany | Year: 2011

BackgroundMetallopeptidases of the M1 family are found in all phyla (except viruses) and are important in the cell cycle and normal growth and development. M1s often have spatiotemporal expression patterns which allow for strict regulation of activity. Mutations in the genes encoding M1s result in disease and are often lethal. This family of zinc metallopeptidases all share the catalytic region containing a signature amino acid exopeptidase (GXMXN) and a zinc binding (HEXXH[18X]E) motif. In addition, M1 aminopeptidases often also contain additional membrane association and/or protein interaction motifs. These protein interaction domains may function independently of M1 enzymatic activity and can contribute to multifunctionality of the proteins.ScopeA brief review of M1 metalloproteases in plants and animals and their roles in the cell cycle is presented. In animals, human puromycin-sensitive aminopeptidase (PSA) acts during mitosis and perhaps meiosis, while the insect homologue puromycin-sensitive aminopeptidase (PAM-1) is required for meiotic and mitotic exit; the remaining human M1 family members appear to play a direct or indirect role in mitosis/cell proliferation. In plants, meiotic prophase aminopeptidase 1 (MPA1) is essential for the first steps in meiosis, and aminopeptidase M1 (APM1) appears to be important in mitosis and cell division.ConclusionsM1 metalloprotease activity in the cell cycle is conserved across phyla. The activities of the multifunctional M1s, processing small peptides and peptide hormones and contributing to protein trafficking and signal transduction processes, either directly or indirectly impact on the cell cycle. Identification of peptide substrates and interacting protein partners is required to understand M1 function in fertility and normal growth and development in plants. © 2011 The Author.


Kim K.H.,Purdue University
Annual review of food science and technology | Year: 2011

Although many food components are reportedly beneficial to body-weight management, lack of understanding of molecular mechanisms and their function in overall adiposity under physiological conditions hinders successful and safe development of antiobesity functional foods. A positive energy balance resulting from an increase in food intake, a reduced energy expenditure, and/or dysfunction of adipose biology is associated with the development of obesity. This article provides an overview of the components involved in energy balance and adipose development and function. There is evidence that numerous ingredients found in foods can modulate energy balance and adipose biology, thereby potentially lowering adiposity.


Purpura D.J.,Purdue University | Ganley C.M.,Florida State University
Journal of Experimental Child Psychology | Year: 2014

Children's early mathematics skills develop in a cumulative fashion; foundational skills form a basis for the acquisition of later skills. However, non-mathematical factors such as working memory and language skills have also been linked to mathematical development at a broad level. Unfortunately, little research has been conducted to evaluate the specific relations of these two non-mathematical factors to individual aspects of early mathematics. Thus, the focus of this study was to determine whether working memory and language were related to only individual aspects of early mathematics or related to many components of early mathematics skills. A total of 199 4- to 6-year-old preschool and kindergarten children were assessed on a battery of early mathematics tasks as well as measures of working memory and language. Results indicated that working memory has a specific relation to only a few-but critically important-early mathematics skills and language has a broad relation to nearly all early mathematics skills. © 2014 Elsevier Inc.


Makowski M.S.,Purdue University | Ivanisevic A.,North Carolina State University
Small | Year: 2011

Rapid and accurate molecular blood analysis is essential for disease diagnosis and management. Field-effect transistor (FET) biosensors are a type of device that promise to advance blood point-of-care testing by offering desirable characteristics such as portability, high sensitivity, brief detection time, low manufacturing cost, multiplexing, and label-free detection. By controlling device parameters, desired FET biosensor performance is obtained. This review focuses on the effects of sensing environment, micro-/nanoscale device structure, operation mode, and surface functionalization on device performance and long-term stability. © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.


Kelly B.C.,Purdue University
Journal of Psychoactive Drugs | Year: 2011

During recent years, there has been increasing interest in "legal highs" among youth and young adults. Salvia divinorum is a legally available hallucinogenic plant, primarily utilized in smokable form, that produces a brief but intense hallucinogenic experience for the user. Data are presented from an ethnographic project to provide a qualitative profile of salvia use among young adults. Most users report primarily using in home settings such as apartments and houses, although a significant minority report use in environments such as parks, bars, and parties. The intense nature of the substance creates a differential subjective experience. Some describe the intensity of the hallucinogenic experience in positive ways. Others find the experience so intense that they would not continue to use the substance. With regard to the health effects of salvia, most young adults report no significant negative health effects from salvia use, although some report a mental cloudiness. Beyond their own experiences, users did not report any negative health events among peers. The lack of reports of negative effects may reinforce social norms favorable towards salvia use. Overall, young adults report a relatively low risk profile for salvia divinorum, which may be influenced, in part, by its legal status. © Taylor & Francis Group, LLC.


Wenthold P.G.,Purdue University
Australian Journal of Chemistry | Year: 2010

The thermochemical properties of the benzynes have been the subject of investigation for nearly 50 years. This work provides an overview and assessment of all the experimental thermochemical properties that have been reported for the benzynes, or can be derived from reported thermochemical data. These properties include enthalpies of formation and thermochemical values that correspond to formation and dissociation of the benzynes by neutral and ionic processes. Thermochemical values are provided for both the ground-state singlet and the excited-state triplet states of the benzynes. The starting point for all the thermochemical consideration of the benzynes are the enthalpies of formation, which, in this work, are recommend to be 107.3 ± 3.5, 121.9 ± 3.1, and 138.0 ± 1.0 kcal mol-1 for ortho-, meta-, and para-benzyne, respectively (1 kcal mol-1 = 4.184 kJ mol -1). Whereas the paper predominantly focuses on the experimentally determined values, it also provides a comparison with theoretical studies that have examined the absolute thermochemical properties of the benzynes. © 2010 CSIRO.


Jones O.G.,Purdue University | Mezzenga R.,ETH Zurich
Soft Matter | Year: 2012

Protein fibrils are relevant not only in medicine and amyloid-related neurodegenerative diseases, but also as functional structures in material science or biology. The assembly of protein into fibrils can be promoted or inhibited based on the chosen environmental conditions and interaction with suitable components. We review here the key strategies for promotion and inhibition of protein fibrillation in both physiological and non-physiological conditions in order to create functional designs. The major variables discussed are solvent conditions, metals/ions, biopolymers, aromatic compounds, and surface active components. Due to bias in research directions, deeper investigation has traditionally been carried out for inhibition of fibrillation, but focus has recently shifted. Thus, while various strategies are presented on the breakdown of mature protein fibrils, emphasis is given to the approaches leading to increased rigidity and length of resultant fibrils. We highlight important areas in this field that require further development and promising lines of future experiments. © 2012 The Royal Society of Chemistry.


Scharf M.E.,Purdue University
Frontiers in Genetics | Year: 2015

Many recent breakthroughs in our understanding of termite biology have been facilitated by "omics" research. Omic science seeks to collectively catalog, quantify, and characterize pools of biological molecules that translate into structure, function, and life processes of an organism. Biological molecules in this context include genomic DNA, messenger RNA, proteins, and other biochemicals. Other permutations of omics that apply to termites include sociogenomics, which seeks to define social life in molecular terms (e.g., behavior, sociality, physiology, symbiosis, etc.) and digestomics, which seeks to define the collective pool of host and symbiont genes that collaborate to achieve high-efficiency lignocellulose digestion in the termite gut. This review covers a wide spectrum of termite omic studies from the past 15 years. Topics covered include a summary of terminology, the various kinds of omic efforts that have been undertaken, what has been revealed, and to a degree, what the results mean. Although recent omic efforts have contributed to a better understanding of many facets of termite and symbiont biology, and have created important new resources for many species, significant knowledge gaps still remain. Crossing these gaps can best be done by applying new omic resources within multi-dimensional (i.e., functional, translational, and applied) research programs. © 2015 Scharf.


Khlebnikov S.,Purdue University
Physics Letters, Section B: Nuclear, Elementary Particle and High-Energy Physics | Year: 2012

We describe application of the gauge/gravity to study of depairing current in thin superconducting wires. The large number N of colors of the gauge theory is identified with the number of filled transverse channels in the wire. On the gravity side, the physics is described by a system of D3 and D5 branes intersecting over a line. We consider the ground state of the system at fixed electric current and find that there is a continuous phase transition at a critical current, in the universality class of the dissipative XY model. We discuss relation of our results to recent experiments on statistics of the switching current in nanowires. © 2012.


Slipchenko L.V.,Purdue University
Journal of Physical Chemistry A | Year: 2010

A hybrid quantum mechanics/molecular mechanics (QM/MM) method for the electronic excited states has been developed. The equation-of-motion coupled cluster with single and double excitations method (EOM-CCSD) is used for the QM region, while the effective fragment potential (EFP) method describes a MM part. The EFP method overcomes the most significant limitation of QM/MM by replacing empirical MM interactions and QM/MM coupling by parameter-free first-principles-based ones, while retaining the computational efficiency of QM/MM. The developed QM/MM scheme involves quantum-mechanical coupling of the electrostatic and polarization terms in the QM/MM Hamiltonian and allows accurate calculation of the electronic excited states of chromophores in various environments. Applications to the water complexes of formaldehyde and p-nitroaniline show that the orbital relaxation of the solute in the electric field of the solvent provides the majority of the solvatochromic effect, and the response of the polarizable environment to the density of the specific electronic state is much smaller in magnitude. © 2010 American Chemical Society.


Francisco J.S.,Purdue University | Muckerman J.T.,Brookhaven National Laboratory | Yu H.-G.,Brookhaven National Laboratory
Accounts of Chemical Research | Year: 2010

Free radicals are important species in atmospheric chemistry, combustion, plasma environments, interstellar clouds, and biochemistry. Therefore, researchers would like to understand the formation mechanism, structure, stability, reactivity, spectroscopy, and dynamics of these chemical species. However, due to the presence of one or more unpaired electrons, radicals are often very reactive and have short lifetimes, which makes it difficult to conduct experiments. The HOCO radical appears in the atmosphere as well as in combustion environments and plays an important role in the conversion of CO to CO2. Through the interplay between theoretical and experimental investigations, researchers have only recently understood the chemical role of the HOCO radical. In this Account, we systematically describe the current state of knowledge of the HOCO radical based on recent theoretical and experimental studies. This radical's two stable conformers, trans- and cis-HOCO, have been identified by high-level ab initio calculations and experimental spectroscopy. trans-HOCO is more stable by approximately 1.8 kcal/mol. The heat of formation of HOCO (298 K) was determined to be -43.0 ± 0.5 kcal/mol, giving a potential well depth of 30.1 ± 0.5 kcal/mol relative to the asymptote of the reactants OH + CO. The HOCO radical is very reactive. In most reactions between the HOCO radical and atoms, the HOCO radical acts as a hydrogen donor to reaction partners. Generally, the hydrogen is transferred through the formation of an association intermediate, which then proceeds through a molecular elimination step to produce the reaction products. The reaction rates of HOCO with some small radicals fall in the range of 10-11-10-10 cm3 molecule-1 s-1. These results clearly illustrate important features in the reactivity of the HOCO radical with other molecules. © 2010 American Chemical Society.


Waters D.J.,Purdue University
ILAR Journal | Year: 2011

Researchers are counting on comparative biologists to fi nd alternative animal models of human aging that will foster experimental approaches to study disability-free longevity, not just the addition of years. This article presents one such alternative: the use of pet dogs living in the same environment as people to study the determinants of healthy longevity. There are both theoretical and practical reasons for this research model beyond the well-documented physiologic similarities between dogs and humans. First, a wealth of medical data-based on clinical and biochemical evaluation, medical imaging, and pathology-is available for pet dogs. Second, a vast array of phenotypic domains can be accurately assessed in dogs, ranging from cardiac contractility and glomerular integrity to the ability to climb stairs and interact with people. Moreover, studying pet dogs obviates the purchase and per diem costs typically associated with large animal research. Pet dogs may be particularly well suited for exploring (1) mechanisms of sex differences in longevity; (2) interventions to compress morbidity and enhance healthspan; (3) genomic correlates of successful aging phenotypes and endophenotypes; (4) heterogeneity in resistance to aging-related diseases, such as cancer; and (5) noninvasive biomarkers of particular target organs. Finally, between-breed differences in senescence trajectories and longevity may expand hypotheses of key genetic factors that contribute to sustained organ function and the postponement of disease. Yet the pet dog paradigm in aging research is nascent; tapping into the potential of this model will add to the existing strengths of conventional model systems.


Rault J.-L.,Purdue University
Applied Animal Behaviour Science | Year: 2012

Despite growing interest in promoting positive welfare, rather than just alleviating poor welfare, potential measures of good welfare, and means to provide it, have remained elusive. In humans social support improves stress-coping abilities, health, and promotes positive psychological welfare. Therefore, social support may be a key approach to promote positive physical and psychological welfare in farm animals. However, the roles of positive social behaviors and social support have been overlooked in comparison to negative social behaviors such as agonistic interactions. The benefits of social partners on an animal's stress coping abilities and welfare are yet poorly understood. The purpose of this paper is to review the protective or buffering effects of social support against stressful challenges and its potential implications for farm animal welfare. The biology of social support is first presented with its behavior, endocrine, autonomic and immune components. The major factors modulating the social support process are then synthesized. Research and implications for animal welfare in different farm species are discussed. Lastly, this review identifies research areas that especially deserve further attention in our effort to understand and implement social support in farm animal welfare. Social support could constitute one of the foundations for welfare researchers to leap from the absence of negative welfare to the provision of positive welfare and emotional experiences. © 2011 Elsevier B.V.


Elander D.,Purdue University
Physical Review D - Particles, Fields, Gravitation and Cosmology | Year: 2015

We study deformations of the Klebanov-Strassler background parametrized by the size of a dim-6 VEV. In the UV, these solutions describe the usual duality cascade of Klebanov-Strassler; however, below the scale ρ∗ set by the dim-6 VEV they exhibit hyperscaling violation over a range of the radial coordinate. Focusing on the spectrum of scalar glueballs, we find a parametrically light state, the mass of which is suppressed by ρ∗, becoming massless in the limit of ρ∗→∞. Along the way, we clarify the choice of IR and UV boundary conditions for the fluctuations in the bulk, and find agreement with previous calculations for the spectrum of Klebanov-Strassler. © 2015 American Physical Society.


South S.C.,Purdue University | Krueger R.F.,University of Minnesota
Developmental Psychology | Year: 2014

Conscientiousness is an important trait for understanding healthy aging. The present article addresses how behavioral and molecular genetics methodologies can aid in furthering explicating the link between conscientiousness and aspects of health and well-being in later life. We review the etiology of conscientiousness documented by both quantitative and molecular genetics methods. We also discuss the ways behavior genetics can be used to continue to help refine the concept of conscientiousness and to help identify points of etiological overlap between conscientiousness and healthy aging outcomes. Phenotypic research has established nontrivial associations between conscientiousness and important outcomes, but behavior genetic methods can determine what the causal (genetic and environmental) mechanisms are behind these relationships. An empirical example of one of these techniques is provided using twin data from the Midlife in the United States (MIDUS) study. We demonstrate that conscientiousness moderates genetic and environmental influences on problem alcohol use, such that greater levels of conscientiousness buffer against the random effects of the environment. Finally, suggestions for future work in this area are discussed. © 2012 American Psychological Association.


The hepatitis delta virus (HDV) ribozyme and related RNAs are widely dispersed in nature. This RNA is a small nucleolytic ribozyme that self-cleaves to generate products with a 2′,3′-cyclic phosphate and a free 5′-hydroxyl. Although small ribozymes are dependent on divalent metal ions under biologically relevant buffer conditions, they function in the absence of divalent metal ions at high ionic strengths. This characteristic suggests that a functional group within the covalent structure of small ribozymes is facilitating catalysis. Structural and mechanistic analyses have demonstrated that the HDV ribozyme active site contains a cytosine with a perturbed pK a that serves as a general acid to protonate the leaving group. The reaction of the HDV ribozyme in monovalent cations alone never approaches the velocity of the Mg 2+-dependent reaction, and there is significant biochemical evidence that a Mg 2+ ion participates directly in catalysis. A recent crystal structure of the HDV ribozyme revealed that there is a metal binding pocket in the HDV ribozyme active site. Modeling of the cleavage site into the structure suggested that this metal ion can interact directly with the scissile phosphate and the nucleophile. In this manner, the Mg 2+ ion can serve as a Lewis acid, facilitating deprotonation of the nucleophile and stabilizing the conformation of the cleavage site for in-line attack of the nucleophile at the scissile phosphate. This catalytic strategy had previously been observed only in much larger ribozymes. Thus, in contrast to most large and small ribozymes, the HDV ribozyme uses two distinct catalytic strategies in its cleavage reaction. © 2011 American Chemical Society.


Schneider S.P.,Purdue University
Journal of Spacecraft and Rockets | Year: 2010

The effects of surface ablation and blowing in hypersonic boundary layer transition are studied. Ground experiments that blow cold gases through a porous wall simulate only some of the surface mass-transfer effects induced by ablation on a high-enthalpy reentry vehicle, they do not simulate any of the reacting-flow effects. Simple algebraic parameters are not sufficient to capture the complex physics of the instability and transition process. Laganelli and co-researchers measured both transition and the boundary-layer profiles. Kaattari's measurements do provide a public-release dataset for comparing e N methods to transition for a hemisphere, although he measured only transition and not the boundary-layer profiles. Transition on bodies at AOA (angle of attack) is much more complex, because the flow is now three-dimensional, introducing crossflow and the crossflow instability. New experiments, computations, and theory are needed to develop physics-based models for prediction and control.


Kanoski S.E.,University of Pennsylvania | Davidson T.L.,Purdue University
Physiology and Behavior | Year: 2011

Intake of saturated fats and simple carbohydrates, two of the primary components of a modern Western diet, is linked with the development of obesity and Alzheimer's Disease. The present paper summarizes research showing that Western diet intake is associated with cognitive impairment, with a specific emphasis on learning and memory functions that are dependent on the integrity of the hippocampus. The paper then considers evidence that saturated fat and simple carbohydrate intake is correlated with neurobiological changes in the hippocampus that may be related to the ability of these dietary components to impair cognitive function. Finally, a model is described proposing that Western diet consumption contributes to the development of excessive food intake and obesity, in part, by interfering with a type of hippocampal-dependent memory inhibition that is critical in the ability of animals to refrain from responding to environmental cues associated with food, and ultimately from consuming energy intake in excess of that driven solely by caloric need. © 2011 Elsevier Inc.


Mattes R.D.,Purdue University
Physiology and Behavior | Year: 2011

There is increasing recognition that specialized processes once thought to be relatively isolated to the oral cavity (e.g., taste) and intestine (e.g., nutrient absorption) are better characterized as common and continuous. This is exemplified by accumulating evidence linking oral detection of dietary fats to their intestinal processing. This review first summarizes this literature focusing on purported gustatory signaling by free fatty acid stimulation and enterocyte lipid storage and mobilization in humans. It then willfully speculates on the possible functions of this integrated system. It is proposed that it may aid absorption of fat soluble nutrients, enhance acute energy intake, sustain intestinal function during long inter-meal intervals, modulate appetite and/or detoxify ingested compounds including free fatty acids. © 2011 Elsevier Inc.


Ferruzzi M.G.,Purdue University
Physiology and Behavior | Year: 2010

Epidemiological data suggest that consumption of coffee and tea is associated with a reduced risk of several chronic and degenerative diseases including cardiovascular disorders, diabetes, obesity and neurodegenerative disorders. Both coffee and tea are a rich source of phenolic compounds including chlorogenic acids in coffee; and flavan-3-ols as well as complex theaflavins and thearubigens in tea. Coffee and tea are two of the most commonly consumed beverages in the world and thus represent a significant opportunity to positively affect disease risk and outcomes globally. Central to this opportunity is a need to better understand factors that may affect the bioavailability of specific phenolic components from coffee and tea based beverages. An overview of the phenolic composition of coffee and tea is discussed in the context of how processing and composition might influence phenolic profiles and bioavailability of individual phenolic components. Specifically, the impact of beverage formulation, the extent and type of processing and the influence of digestion on stability, bioavailability and metabolism of bioactive phenolics from tea and coffee are discussed. The impact of co-formulation with ascorbic acid and other phytochemicals are discussed as strategies to improve absorption of these health promoting phytochemicals. A better understanding of how the beverage composition impacts phenolic profiles and their bioavailability is critical to development of beverage products designed to deliver specific health benefits. © 2010 Elsevier Inc.


Mattes R.D.,Purdue University
Physiology and Behavior | Year: 2010

Associations between hunger and eating and between thirst and drinking are generally weak. This stems, in part, from limitations in the measurement of these sensations which generally rely on temporal, motivational, metabolic and/or self-reported descriptive indices. Each is critically reviewed. Also problematic is the fact that the deterministic depletion-repletion concept of ingestive behavior fails to account for influences of a multitude of contravening cognitive, social, sensory and logistical factors. Although hunger and thirst serve some parallel purposes, sharp distinctions are also present with health implications. Of particular note are the observations that thirst ratings are higher and more stable over the day compared to hunger and thirst may be more motivating to drink than hunger is to eat. Coupling these observations with evidence that beverages have limited satiety value, they pose particular challenges and opportunities. Beverages can facilitate the delivery of nutrients to those desiring or requiring them, but also to those where they are not desired or required. The benefits and risks are a function of their use rather than their inherent properties. © 2010 Elsevier Inc.


Schneider D.W.,Purdue University
Acta Psychologica | Year: 2014

Compound cue retrieval is a computational model of a mediated route for response selection in task-switching situations. In previous studies, the model has been shown to account for response congruency effects when switching between two tasks, where response congruency reflects the degree of match between relevant and irrelevant task responses associated with a target stimulus. In the present study, the author derived a model prediction of graded response congruency effects in situations involving three tasks. The predicted pattern was observed for both response time and error rate in an experiment in which numerical categorization tasks were performed on single-digit targets. Implications for understanding response congruency effects and for developing models of task-switching performance are discussed. © 2014 Elsevier B.V.


Weaver C.M.,Purdue University
Current Osteoporosis Reports | Year: 2015

Interactions between the environment, the gut microbiome, and host characteristics that influence bone health are beginning to be explored. This is the first area where functional benefits from diet-induced changes in the gut microbiome have been reported for healthy people. Several prebiotics that reach the lower intestine have resulted in an altered gut microbiome that is thought to enhance fermentation of the fibers to produce short-chain fatty acids. These changes are positively correlated with increases in fractional calcium absorption in adolescents and with increases in measures of bone density and strength in animal models. New methodologies are available to explore mechanisms and to refine intervention strategies. © 2015, Springer Science+Business Media New York.


Tan S.Y.,University of South Australia | Mattes R.D.,Purdue University
European Journal of Clinical Nutrition | Year: 2013

Background/Objectives: Snacks contribute toward a significant proportion of human total daily energy intake. This study investigated the effects of almonds, a satiating and nutrient-rich, common snack, on postprandial glycemia, appetite, short-term body weight and fasting blood parameters when consumed with meals or alone as a snack. Methods: This was a 4-week randomized, parallel-arm study that entailed consuming almonds (43 g/day) with breakfast (BF) or lunch (LN), alone as a morning (MS) or afternoon (AS) snack or no almonds (CL). Participants (N=137) with increased risk for type 2 diabetes completed an oral glucose tolerance test (OGTT) and acute-feeding session at baseline, followed by almond consumption for 4 weeks before repeating the OGTT and acute-feeding trials. Anthropometric, biochemical and appetite responses were assessed. Results: Almonds lowered serum glucose responses postprandially. Effects were most prominent in the snack groups. Almonds, consumed as snacks, also reduced hunger and desire to eat during the acute-feeding session. After 4 weeks, anthropometric measurements and fasting blood biochemistries did not differ from the control group or across intervention groups. Without specific guidance, daily energy intake was reduced to compensate for energy from the provided almonds. Dietary monounsaturated fat and α-tocopherol intakes were significantly increased in all almond groups. Conclusion: Almonds provide post-ingestive metabolic and appetitive benefits and did not increase the risk for weight gain. This suggests that almonds may be a healthful snack option. Copyright © 2013 Macmillan Publishers Limited.


Xie W.,Purdue University
Nuclear Physics A | Year: 2013

Heavy quarks are unique probes to study the strongly-coupled Quark-Gluon Plasma created in relativistic heavy-ion collisions. Measuring the productions and correlations of both open heavy flavor and heavy quarkonia provides essential information to advance our understanding of the QCD medium's properties. With the excellent particle identification capabilities and large acceptance detectors, the STAR experiment at RHIC has measured the productions and correlations of heavy flavor hadrons of a wide variety of species in broad p T range. We present highlights of recent STAR heavy flavor measurements and also provide a brief overview of STAR future heavy flavor physics program. © 2013 Elsevier B.V.


We apply a data-driven method to STAR Au + Au collisions at sNN=200 GeV to isolate δ. η-dependent and δ. η-independent correlations by using two- and four-particle Q-cumulant vn measurements. The δ. η-independent part, dominated by flow, is found to be η-independent within the STAR TPC of ±1 unit of pseudo-rapidity. The δ. η-dependent part may be associated to nonflow, and is responsible for the δ. η drop in the measured two-particle v2 cumulant. We combine our result to four- and six-particle cumulants to gain further insights on the nature of flow fluctuations. © 2013 Elsevier B.V.


Calcium is the dominant mineral in bone and is a shortfall nutrient in the diet. For those consuming inadequate dietary calcium, calcium supplements have been a standard strategy for prevention of osteoporosis. Recently, calcium supplementation has been linked to both increased and decreased cardiovascular disease risk creating considerable uncertainty. Moreover, recent reports have shed uncertainty over the effectiveness of calcium supplements to reduce risk of fracture. The evidence for calcium supplementation effects to both reduce risk of fracture and increase coronary heart disease and mortality are reviewed. Although the importance of good calcium nutrition is well known, determining the advantage of calcium supplementation to either bone or heart health has been hampered by poor subject compliance and study design flaws. At present, the current Recommended Dietary Allowances for calciumstill appear to be a good target with potential risks for chronic disease if intakes fall too short or greatly exceed these recommendations. © Springer Science+Business Media 2014.


Wankat P.C.,Purdue University
Annual Review of Chemical and Biomolecular Engineering | Year: 2013

Three successful historical reforms of chemical engineering education were the triumph of chemical engineering over industrial chemistry, the engineering science revolution, and Engineering Criteria 2000. Current attempts to change teaching methods have relied heavily on dissemination of the results of engineering-education research that show superior student learning with active learning methods. Although slow dissemination of education research results is probably a contributing cause to the slowness of reform, two other causes are likely much more significant. First, teaching is the primary interest of only approximately one-half of engineering faculty. Second, the vast majority of engineering faculty have no training in teaching, but trained professors are on average better teachers. Significant progress in reform will occur if organizations with leverage - National Science Foundation, through CAREER grants, and the Engineering Accreditation Commission of ABET - use that leverage to require faculty to be trained in pedagogy. Copyright © 2013 by Annual Reviews. All rights reserved.


Flesch L.,Purdue University | Bendick R.,University of Montana
Geology | Year: 2012

The variation of mechanical properties with depth in the lithosphere determines the relationship between surface deformation and whole-lithosphere deformation, hence between surface deformation and whole-lithosphere dynamics. Where viscosity (or elastic strength) is a continuous function with depth, surface deformation can be used to constrain both force balance and rheological parameters. Where viscosity is discontinuous, but the upper crust and mantle lithosphere have comparable maximum values, surface deformation can be used to approximate force balance and rheological parameters, but tradeoffs mean that estimates of stress and viscosity are effective equivalent values rather than actual values. Where viscosity is both discontinuous and differs by much more than an order of magnitude between the upper crust and mantle lithosphere, information about both force balance and rheology are absent from the surface deformation, so surface observations alone are insufficient to estimate either the dynamic or mechanical state of the lithosphere. © 2012 Geological Society of America.


Knoch J.,TU Dortmund | Appenzeller J.,Purdue University
IEEE Electron Device Letters | Year: 2010

The impact of band lineup and source doping concentration on the performance of heterojunction tunnel FETs (H-TFETs) with type-II heterointerface is investigated by simulations. Exemplarily, H-TFETs based on InAs/Al xGa1-xSb heterostructures are studied. Varying the Al content x, the band lineup can be adjusted from staggered to broken. We find that a staggered band lineup and a medium source doping concentration yield the best on/off-state performance in terms of an inverse subthreshold slope that is smaller than 60 mV/dec and fT values in the terahertz range. © 2010 IEEE.


Park K.,Purdue University
ACS Nano | Year: 2013

Nanotechnology in drug delivery has been manifested into nanoparticles that can have unique properties both in vitro and in vivo, especially in targeted drug delivery to tumors. Numerous nanoparticle formulations have been designed and tested to great effect in small animal models, but the translation of the small animal results to clinical success has been limited. Successful translation requires revisiting the meaning of nanotechnology in drug delivery, understanding the limitations of nanoparticles, identifying the misconceptions pervasive in the field, and facing inconvenient truths. Nanoparticle approaches can have real impact in improving drug delivery by focusing on the problems at hand, such as enhancing their drug loading capacity, affinity to target cells, and spatiotemporal control of drug release. © 2013 American Chemical Society.


Fernandez-Juricic E.,Purdue University
Behavioural Processes | Year: 2012

Birds gather visual information through scanning behavior to make decisions relevant for survival (e.g., detecting predators and finding food). The goal of this study was (a) to review some visual properties involved in scanning behavior (retinal specialization for visual resolution and motion detection, visual acuity, and size of the blind area), and (b) hypothesize how the inter-specific variability in these properties may lead to different scanning strategies. The avian visual system has a high degree of heterogeneity in visual performance across the visual field, with some sectors providing higher levels of visual resolution and motion detection (e.g., retinal specializations) than others (e.g., peripheral retina and blind area). Thus, information quality will vary in different parts of the visual field, which contradicts some theoretical assumptions on information gathering. Birds need to move their eyes and heads to align the retinal specializations to different sectors of visual space. The rates of eye and head movements can then be used as proxies for scanning strategies. I propose specific predictions as to how each of the visual properties studied can affect scanning strategies in the context of predator detection in different habitat types and with different levels of predation risk. Establishing the degree of association between sensory specializations and scanning strategies can enhance our understanding of the evolution of anti-predator behavior. © 2011 Elsevier B.V.


Hertel T.W.,Purdue University
American Journal of Agricultural Economics | Year: 2011

The number of people which the world must feed is expected to increase by another 50% during the first half of this century. Finally, agriculture and forestry are likely to be the economic sectors whose productivity is most sharply affected by climate change. They begin by plotting population against hectares of cropland in 1900 and observe that areas with high population also had larger cropland areas, with the global average cropland area equaling 0.76 ha/capita. The model has one global production function which combines agricultural land with variable inputs to produce agricultural output. Recently there has been a surge of interest in Payments for Environmental Services (PES) by those seeking to preserve biodiversity and terrestrial carbon stocks. There is little doubt that the demand for such environmental services will grow over time, and this is likely to prove contentious in particular regions.


Mansfield S.D.,University of British Columbia | Kang K.-Y.,University of British Columbia | Chapple C.,Purdue University
New Phytologist | Year: 2012

• There is a pressing global need to reduce the increasing societal reliance on petroleum and to develop a bio-based economy. At the forefront is the need to establish a sustainable, renewable, alternative energy sector. This includes liquid transportation fuel derived from lignocellulosic plant materials. However, one of the current limiting factors restricting the effective and efficient conversion of lignocellulosic residues is the recalcitrance of the substrate to enzymatic conversion. • In an attempt to assess the impact of cell wall lignin on recalcitrance, we subjected poplar trees engineered with altered lignin content and composition to two potential industrial pretreatment regimes, and evaluated the overall efficacy of the bioconversion to ethanol process. • It was apparent that total lignin content has a greater impact than monomer ratio (syringyl: guaiacyl) on both pretreatments. More importantly, low lignin plants showed as much as a 15% improvement in the efficiency of conversion, with near complete hydrolysis of the cellulosic polymer. • Using genomic tools to breed or select for modifications in key cell wall chemical and/or ultrastructural traits can have a profound effect on bioenergy processing. These techniques may therefore offer means to overcome the current obstacles that underpin the recalcitrance of lignocellulosic substrates to bioconversion. © 2012 The Authors. New Phytologist © 2012 New Phytologist Trust.


Gordon M.S.,Iowa State University | Fedorov D.G.,Japan National Institute of Advanced Industrial Science and Technology | Pruitt S.R.,Iowa State University | Slipchenko L.V.,Purdue University
Chemical Reviews | Year: 2012

Research work conducted in the field of fragmentation methods, a route to accurate calculations on large systems, is presented. The restricted variational space (RVS) analysis and the constrained space orbital variations (CSOV) method improve on the KM scheme by employing fully antisymmetrized intermediate wave functions. Wu et al. developed a density-based energy decomposition (EDA), in which the energies of the intermediate states are calculated using the densities of the fragments, rather than their wave functions. In 2008, Xie et al. modified the formulation of X-Pol to obtain rigorously analytic gradients. In 2002, Inadomi et al. proposed the FMO-MO method, which according to the classification of fragment methods as discussed above, belongs to a different category from the rest of the FMO methods. Bettens et al., have developed an energy based fragmentation method based on the idea of isodesmic reactions.


Carberry A.R.,Tufts University | Lee H.-S.,Tufts University | Ohland M.W.,Purdue University
Journal of Engineering Education | Year: 2010

BACKGROUND: Self-concept can influence how an individual learns, but is often overlooked when assessing student learning in engineering. PURPOSE (HYPOTHESIS): To validate an instrument designed to measure individuals' self-concepts toward engineering design tasks, three research questions were investigated: (a) how well the items in the instrument represent the engineering design process in eliciting the task-specific self-concepts of self-efficacy, motivation, outcome expectancy and anxiety, (b) how well the instrument predicts differences in the self-efficacy held by individuals with a range of engineering experiences, and (c) how well the responses to the instrument align with the relationships conceptualized in self-efficacy theory. DESIGN/METHOD: A 36-item online instrument was developed and administered to 202 respondents. Three types of validity evidence were obtained for (a) representativeness of multi-step engineering design processes in eliciting self-efficacy, (b) the instrument's ability to differentiate groups of individuals with different levels of engineering experience and (c) relationships between self-efficacy, motivation, outcome expectancy, and anxiety as predicted by self-efficacy theory. RESULTS: Results indicate that the instrument can reliably identify individuals' engineering design self-efficacy (α = 0.967), motivation (α = 0.955), outcome expectancy (α = 0.967) and anxiety (α = 0.940). One-way ANOVA identified statistical differences in self-efficacy between high, intermediate and low experience groups at the ρ < 0.05 level. Self-efficacy was also shown to be correlated to motivation (0.779), outcome expectancy (0.919) and anxiety (-0.593) at the ρ < 0.01 level. CONCLUSIONS: The study showed that the instrument was capable of identifying individuals' self-concepts specific to the engineering design tasks.


Matusovich H.M.,Virginia Polytechnic Institute and State University | Streveler R.A.,Purdue University | Miller R.L.,Colorado School of Mines
Journal of Engineering Education | Year: 2010

BACKGROUND Recently published reports call for an increase in the number of engineering graduates and suggest appropriate characteristics that these graduates should embody. Accomplishing such change first requires understanding why students choose to pursue engineering degrees. PURPOSE (HYPOTHESIS) Framed in motivation theory, our purpose was to better understand how students choose engineering by answering the question: How do engineering students' engineering-related value beliefs contribute to their choices to engage and persist in earning engineering degrees? DESIGN/METHOD This research uses Eccles' expectancy-value theory in a qualitative, longitudinal examination of undergraduate students' choices to enroll and persist in engineering majors. In particular, the focus of this work is Eccles' subjective task value (STV) construct, which incorporates the personal importance an individual assigns to engaging in an activity. Using a multiple case study method approach, participants included eleven students (five men and six women) at a U.S. technical school. RESULTS Results demonstrate that different patterns exist in the types of value or personal importance that participants assign to earning an engineering degree. Moreover, a primary differentiating feature of these patterns is whether or not participants choose engineering because it is consistent with their personal identity or sense of self. CONCLUSIONS We conclude that values are very important in students' choices to become engineers. To increase persistence rates we must focus on values, especially by helping students connect their personal identities to engineering identities.


Wang F.,Purdue University
Progress in Particle and Nuclear Physics | Year: 2014

The novel phenomena observed in particle angular correlations are reviewed. They include the double-peak away-side azimuthal correlations in relativistic heavy-ion collisions and the long-range pseudorapidity near-side (ridge) correlations in heavy-ion as well as in proton-induced collisions. The collision system and energy dependence of these phenomena are examined, wherever possible and most abundantly for the ridge correlations. Their possible theoretical interpretations and what might be learned about the properties of the collision systems from theoretical comparisons are discussed. Prospective future measurements and theoretical undertakings are outlined that might help further the understanding of the physics mechanisms underlying these phenomena. © 2013 Elsevier B.V. All rights reserved.


Francis G.,Purdue University
Attention, Perception, and Psychophysics | Year: 2010

Van Lier, Vergeer, and Anstis (2009) reported that color information in a visual afterimage could spread across regions that were not colored in the inducing stimulus. The perceived color and shape of the afterimage could be manipulated by drawn contours that apparently trap the spread of afterimage color signals. They further hypothesized that the observed effects indicated a common mechanism for afterimage color filling-in and real-color filling-in phenomena. New simulations of the existing boundary contour system/feature contour system model of visual perception (Grossberg & Mingolla, 1985a, 198Sb) demonstrate the connection between these phenomena. © 2010 The Psychonomic Society, Inc.


Plotnitsky A.,Purdue University
Foundations of Physics | Year: 2015

This article is concerned with the role of fundamental principles in theoretical physics, especially quantum theory. The fundamental principles of relativity will be addressed as well, in view of their role in quantum electrodynamics and quantum field theory, specifically Dirac’s work, which, in particular Dirac’s derivation of his relativistic equation of the electron from the principles of relativity and quantum theory, is the main focus of this article. I shall also consider Heisenberg’s earlier work leading him to the discovery of quantum mechanics, which inspired Dirac’s work. I argue that Heisenberg’s and Dirac’s work was guided by their adherence to and their confidence in the fundamental principles of quantum theory. The final section of the article discusses the recent work by D’Ariano and coworkers on the principles of quantum information theory, which extend quantum theory and its principles in a new direction. This extension enabled them to offer a new derivation of Dirac’s equations from these principles alone, without using the principles of relativity. © 2015, Springer Science+Business Media New York.


Namkung Y.,Kyung Hee University | Jang S.S.,Purdue University
International Journal of Hospitality Management | Year: 2013

This study examines the effects of green practices at restaurants on customer-based brand equity formation. A survey of 512 American diners showed that implementing two aspects of green practices, food focused and environmentally focused, influenced customer perceptions of green brand image and behavioral intentions, whereas the effects of green practices on perceived quality were not significant. The relative impact of the two aspects of green practices differs by restaurant type. In upscale casual dining restaurants, green practices focused on foods were more effective in enhancing a green brand image and behavioral intentions as compared to those with an environmental focus. On the other hand, for casual dining customers the effects of green practices with an environmental focus were more convincing in terms of improving a restaurant's green brand image and behavioral intentions as compared to food focused initiatives. In relation to self-perception, the results indicated that diners with high health and environmental-consciousness responded more positively to restaurant green practices than those with a low self-perception of health and environmental-consciousness. © 2012 Elsevier Ltd.


Lee S.,Purdue University
Decision Support Systems | Year: 2012

An ambulance dispatching policy, Centrality policy, is proposed in an effort to reduce the response time in demanding emergency situations such as in natural disasters, based on the notion of centrality from the study on complex networks. The nearest neighbor (NN) policy prioritizes the emergency calls by closeness and it has been known effective in the literature. The NN policy is evolved into the Centrality policy by prioritizing the calls based on the centrality in addition to the closeness. The centrality enables to capture the efficiency of a call site in reaching out other current and future calls thus secure the long-term performance beyond the immediate performance pursued by the NN policy. Two parameters are associated with the Centrality policy: weight on centrality and choice of centrality measure. An extensive simulation-based sensitivity analysis is conducted on the algorithmic parameters to examine the role of centrality in ambulance dispatching. The analysis evidences the potential of centrality consideration in reducing the response time beyond the NN policy, given that these parameters are appropriately chosen. © 2012 Elsevier B.V. All rights reserved.


Khurgin J.B.,Johns Hopkins University | Boltasseva A.,Purdue University
MRS Bulletin | Year: 2012

Plasmonics aims at combining features of photonics and electronics by coupling photons with a free-electron gas, whose subwavelength oscillations (surface plasmons) enable manipulation of light at the nanoscale and engender the exciting properties of optical metamaterials. Plasmonics is facing a grand challenge of overcoming metal losses impeding its progress. We reflect on the reasons why subwavelength confinement and loss are intimately intertwined and investigate the physics of loss in conductors beyond the conventional Drude model. We suggest that commonly used noble metals may not be the best materials for plasmonics and describe alternate materials such as transparent conducting oxides and transition metal nitrides. We consider the prospects of compensating the loss with gain materials and conclude that the so-far elusive solution to the loss obstacle lies in finding better materials with lower losses. © 2012 Materials Research Society.


Graziano W.G.,Purdue University | Habashi M.M.,Iowa Wesleyan College
Personality and Social Psychology Review | Year: 2010

Examined at the behavioral level, prejudice and helping appear as qualitatively different and perhaps mutually incompatible social behaviors. As a result, the literatures on prejudice and helping evolved largely independent of each other. When they are examined at the process level, however, underlying similarities appear. Furthermore, when anomalies are examined within each of these two separate literatures, similarities become more apparent. Finally, the personality dimension of agreeableness is systematically related to both prejudice and helping. The authors propose that many forms of prejudice and helping are expressions of underlying processes of self-regulation and social accommodation. After discussing several other social-cognitive approaches to self-correction, the authors offer a novel opponent process model of motivation that integrates the apparently exclusive processes of prejudice and helping into a single system. © 2010 by the Society for Personality and Social Psychology, Inc.


As a successful technique for identifying residential mobility in other areas, this study investigates the feasibility of using 87Sr/ 86Sr analysis to track the movements of the ancient peoples of Egypt and Nubia in the Nile Valley, who interacted via trade, warfare, and political occupations over millennia. Dental enamel from faunal remains is used to examine variability in strontium sources in seven regional sites; human enamel samples are analyzed from eight Nile Valley sites in order to trace human movements. The faunal samples show a wide range of 87Sr/86Sr values demonstrating that some animals were raised in a variety of locales. The results of the human samples reveal overlap in 87Sr/86Sr values between Egyptian and Nubian sites; however, Egyptian 87Sr/ 86Sr values (mean/median [0.70777], sd [0.00027]) are statistically higher than the Nubian 87Sr/86Sr values (mean [0.70762], median [0.70757], sd [0.00036], suggesting that it is possible to identify if immigrant Egyptians were present at Nubian sites. Samples examined from the site of Tombos provide important information regarding the sociopolitical activities during the New Kingdom and Napatan periods. Based on a newly established local 87Sr/86Sr range, human values, and bioarchaeological evidence, this study confirms the preliminary idea that immigrants, likely from Egypt, were present during the Egyptian New Kingdom occupation of Nubia. In the subsequent Napatan period when Nubia ruled Egypt as the 25th Dynasty, 87Sr/86Sr values are statistically different from the New Kingdom component and indicate that only locals were present at Tombos during this developmental time. © 2013 Wiley Periodicals, Inc.


Phenylalanine is a vital component of proteins in all living organisms, and in plants is a precursor for thousands of additional metabolites. Animals are incapable of synthesizing phenylalanine and must primarily obtain it directly or indirectly from plants. Although plants can synthesize phenylalanine in plastids through arogenate, the contribution of an alternative pathway via phenylpyruvate, as occurs in most microbes, has not been demonstrated. Here we show that plants also utilize a microbial-like phenylpyruvate pathway to produce phenylalanine, and flux through this route is increased when the entry point to the arogenate pathway is limiting. Unexpectedly, we find the plant phenylpyruvate pathway utilizes a cytosolic aminotransferase that links the coordinated catabolism of tyrosine to serve as the amino donor, thus interconnecting the extra-plastidial metabolism of these amino acids. This discovery uncovers another level of complexity in the plant aromatic amino acid regulatory network, unveiling new targets for metabolic engineering.


Jeong E.,Samsung | Jang S.S.,Purdue University
International Journal of Hospitality Management | Year: 2011

This study empirically examined which restaurant experiences trigger customers to engage in positive electronic word-of-mouth (eWOM), where the quality of restaurant service (food quality, service quality, atmosphere, and price fairness) is the antecedent of eWOM communication. The results of this study suggest that (1) restaurants' food quality positively influences customers to spread positive eWOM, motivated by their desire to help the restaurant; (2) satisfactory restaurant experiences with service employees triggered positive eWOM, motivated by the need to help the restaurant or to express positive feelings; (3) a superior atmosphere in restaurants elicited positive eWOM motivated by a concern for others; and (4) price fairness in restaurants did not drive restaurant customers toward eWOM. Additionally, this study investigated sources of positive eWOM and types of eWOM media used among opinion leaders in the restaurant industry to enhance the practical implications of the study regarding online marketing. Because of the small number of opinion leaders in the study sample, specifying who the opinion leaders were (the source of eWOM) and the type of eWOM media the opinion leaders used had no effect. Further discussion and implications are provided in the text. © 2010 Elsevier Ltd.


Negishi E.-I.,Purdue University
Angewandte Chemie - International Edition | Year: 2011

Tools for chemists: The Nobel Prize in Chemistry 2010 was awarded for research on palladium-catalyzed cross-coupling in organic synthesis. Two of the Laureates, A. Suzuki and E. Negishi, report here first hand on the historical development and the current status of this research. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.


Wilker J.J.,Purdue University
Current Opinion in Chemical Biology | Year: 2010

The oceans are filled with an amazing variety of biological materials including the glues and cements of mussels, barnacles, tube worms, algae, and starfish. Recent studies on mussel adhesive are providing increasing evidence for a unique mechanism of material generation involving iron-induced protein oxidation and cross-linking chemistry. Insights are also being gathered on many of the other marine creatures producing adhesives. Beyond understanding biology, this growing knowledge is inspiring application development. New classes of biomimetic polymers are poised to provide the next generation of surgical adhesives and orthopedic cements. © 2009 Elsevier Ltd. All rights reserved.


Jackson S.,Purdue University | Chen Z.J.,Cellular One
Current Opinion in Plant Biology | Year: 2010

Polyploidy or whole genome duplication (WGD) occurs throughout the evolutionary history of many plants and some animals, including crops such as wheat, cotton, and sugarcane. Recent studies have documented rapid and dynamic changes in genomic structure and gene expression in plant polyploids, which reflects genomic and functional plasticity of duplicate genes and genomes in plants. Common features of uniparental gene regulation and nonadditive gene expression in regulatory pathways responsive to growth, development, and stresses in many polyploids have led to the conclusion that epigenetic mechanisms including chromatin modifications and small RNAs play central roles in shaping molecular and phenotypic novelty that may be selected and domesticated in many polyploid plants and crops. © 2009 Elsevier Ltd. All rights reserved.


Kirchmaier A.L.,Purdue University
FEBS Letters | Year: 2011

A vast array of proteins is recruited to the replication fork in a dynamic and coordinated manner through physical interactions with Proliferating Cell Nuclear Antigen, PCNA. How this complex exchange of PCNA binding partners is choreographed to ensure proper replication origin licensing, DNA synthesis during normal replication or repair of DNA damage, chromatin assembly, DNA methylation, histone modification, and sister chromatid cohesion is only beginning to be appreciated. In this review, several roles of ubiquitin-related modifications in the recruitment and turnover of PCNA-interacting proteins at the replication fork are considered. © 2011 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.


Blanchoin L.,CEA Grenoble | Staiger C.J.,Purdue University
Biochimica et Biophysica Acta - Molecular Cell Research | Year: 2010

The completed genome from the model plant Arabidopsis thaliana reveals the presence of a diverse multigene family of formin-like sequences, comprising more than 20 isoforms. This review highlights recent findings from biochemical, cell biological and reverse-genetic analyses of this family of actin nucleation factors. Important advances in understanding cellular function suggest major roles for plant formins during cytokinesis and cell expansion. Biochemical studies on a subset of plant formins emphasize the need to examine molecular mechanisms outside of mammalian and yeast systems. Notably, a combination of solution-based assays for actin dynamics and timelapse, single-filament imaging with TIRFM provide evidence for the first non-processive formin (AtFH1) in eukaryotes. Despite these advances it remains difficult to generate a consensus view of plant formin activities and cellular functions. One limitation to summarizing formin properties relates to the enormous variability in domain organization among the plant formins. Generating homology-based predictions that depend on conserved domains outside of the FH1 and FH2 will be virtually impossible for plant formins. A second major drawback is the lack of facile techniques for examining dynamics of individual actin filaments within live plant cells. This constraint makes it extremely difficult to bridge the gap between biochemical characterization of particular formin and its specific cellular function. There is promise, however, that recent technical advances in engineering appropriate fluorescent markers and new fluoresence imaging techniques will soon allow the direct visualization of cortical actin filament dynamics. The emergence of other model systems for studying actin cytoskeleton in vivo, such as the moss Physcomitrella patens, may also enhance our knowledge of plant formins. © 2008 Elsevier B.V.


Saeedifard M.,Purdue University | Iravani R.,University of Toronto
IEEE Transactions on Power Delivery | Year: 2010

The modular multilevel converter (MMC) is a newly introduced switch-mode converter topology with the potential for high-voltage direct current (HVDC) transmission applications. This paper focuses on the dynamic performance of an MMC-based, back-to-back HVDC system. A phase-disposition (PD) sinusoidal pulsewidth modulation (SPWM) strategy, including a voltage balancing method, for the operation of an MMC is presented in this paper. Based on the proposed PD-SPWM switching strategy, a mathematical model for the MMC-HVDC system, under both balanced and unbalanced grid operation modes, is developed. Dynamic performance of the MMC-based back-to-back HVDC converter system, based on time-domain simulation studies in the PSCAD/EMTDC environment, is then evaluated. The reported time-domain simulation results show that based on the adopted PD-SPWM switching strategy, the MMC-HVDC station can respond satisfactorily to the system dynamics and control commands under balanced and unbalanced conditions while maintaining voltage balance of the dc capacitors. © 2010 IEEE.


Netrakanti P.K.,Purdue University
Nuclear Physics A | Year: 2011

We present new results from 3-particle pseudorapidity (Δη) correlation at mid-rapidity in Au+Au collisions at sNN=200 GeV, measured by the STAR experiment. The charge ordering properties between associated and trigger particles are exploited to separate jet-like and ridge contributions in 3-particle δη-δη correlations. We found that like-sign triplets are dominated by ridge. The separated ridge, while narrow in δη is extremely broad in Δη The results indicate that the correlation of ridge particles are uniform not only with respect to the trigger particle but also between themselves event-by-event in our measured Δη In addition, the production of the ridge appears to be uncorrelated to the presence of the narrow jet-like component. © 2011 Elsevier B.V.


Molnar D.,Purdue University
Journal of Physics G: Nuclear and Particle Physics | Year: 2011

Identified particle observables from viscous hydrodynamics are sensitive to the fluid-to-particle conversion. Instead of the commonly assumed 'democratic' Grad ansatz for phase space corrections δf, we utilize corrections calculated from linearized covariant transport theory. Estimates based on a π-p system with binary collisions indicate that protons are much closer to equilibrium than pions, significantly affecting the dissipative reduction of differential elliptic flow in Au+Au at the RHIC. In addition, we test the linear response against fully nonlinear transport for a two-component massless system in a Bjorken scenario. Strikingly, we find that, while linear response accounts well for the dynamical sharing of shear stress, the momentum dependence of phase space corrections is best described by Grad's quadratic ansatz, and not the linear response solution. © 2011 IOP Publishing Ltd.


Skoby M.,Purdue University
Nuclear Physics A | Year: 2011

Forward-backward multiplicity correlations measured at STAR are discussed. A strong long-range correlation for inclusive charged hadrons was measured as a function of pseudorapidity separation (Δη) in Au+Au collisions at sNN=200 GeV, and were shown to decrease with decreasing centrality. STAR preliminary results show the correlation strength for pions, kaons, (anti)protons as a function of rapidity separation (Δ y) in 0-10% and 10-20% Au+Au collisions at sNN=200 GeV. The Color Glass Condensate picture, which describes particle sources as longitudinal flux tubes, predicts that the correlation will grow with centrality. Fluctuations in the number of gluons at early times will produce a long-range correlation strength larger for pions than for baryons. A strong, long-range correlation is measured for pions in central collisions, which decreases for 10-20% collisions. © 2011 Elsevier B.V.


Mattes R.,Purdue University
Physiology & behavior | Year: 2014

Energy intake is a function of the quantity of energy consumed per ingestive event and the number of these events. The marked increase of energy intake and body weight over the past 35 years indicates that there has been poor precision in the reciprocity of these two facets of intake. With recent study of the associations between gut "satiation" peptides and energy intake, there has been an emphasis on the contribution of portion size to positive energy balance. However, this orientation may not appropriately weight the contribution of ingestive frequency. Gut peptides are not purely satiation factors and metabolic and environmental cues may more strongly guide the onset and number of ingestive events. Evidence is presented that while both portion size and ingestive frequency have increased in the population, the latter may be more problematic for weight gain. The magnitude and time course of increments in ingestive frequency map better onto energy intake and BMI trends than changes of portion size. This may occur, in part, because dietary compensation and thermogenic effects are weaker for increases in ingestive frequency than portion size. Though not to the exclusion of consideration of portion size effects, improved weight management may be achieved with greater attention to the drivers of eating and drinking frequency. Copyright © 2013 Elsevier Inc. All rights reserved.


Byeon J.H.,Purdue University | Kim Y.-W.,Hoseo University
ACS Applied Materials and Interfaces | Year: 2013

The gas-phase self-assembly of reduced graphene oxide (rGO) nanoflakes with highly ordered ultrafine titania (TiO2) particles was performed and the resultant hybrid material displayed an enhanced photocatalytic performance, both in producing hydrogen and in degrading dyes. Freshly synthesized TiO 2 nanoparticles (∼35 nm in equivalent mobility diameter) were quantitatively incorporated with nanoscale rGO (∼36 nm in equivalent mobility diameter) in the form of TiO2/rGO hybrid nanoflakes (∼31 nm in equivalent mobility diameter). The TiO2/rGO hybrid flakes were finally employed to evaluate its photocatalytic activity, and it was found that the ability to achieve hydrogen production and dye degradation was greater than that of a hybridized material from commercial p25-TiO2 and large rGO. This gas-phase self-assembly also enhanced the photocatalytic activity by applying different spark configurations to prepare ZnO, Au, or Ag particles incorporated with rGO nanoflakes. © 2013 American Chemical Society.


Francis G.,Purdue University
i-Perception | Year: 2012

A recent study reported evidence of "wishful seeing," where observers reported seeing a desired object as being closer than other objects. A statistical analysis of the experimental findings reveals evidence of publication bias in the study, so the existence of wishful seeing remains unproven. © 2012 G Francis.


Francis G.,Purdue University
Journal of Experimental Psychology: General | Year: 2013

Elliot et al. (2010) reported multiple experimental findings that the color red modified women's ratings of attractiveness, sexual desirability, and status of a photographed man. An analysis of the reported statistics of these studies indicates that the experiments lack sufficient power to support these claims. Given the power of the experiments, the probability that the observed 12 findings would all reject the null hypothesis is only .005. Thus, the proper interpretation of the findings is that the studies are contaminated with publication bias. Either some experiments with null findings were not reported or the reported experiments were run improperly in a way that inflated the likelihood of rejecting the null hypothesis. Because of the presence of publication bias, the findings in Elliot et al. (2010) should be considered nonscientific or anecdotal. It remains an open question whether the color red influences women's ratings of men's attributes. © 2013 American Psychological Association.


Among immigrant Asian and Latino groups, the contrast between collectivism in traditional heritage and individualism in the mainstream American cultures presents unique challenges for their family relationships. This systematic review was designed to answer 3 fundamental questions: to what extent do(es) (a) acculturation mismatch (AM) correlate with intergenerational cultural conflict (ICC); (b) ICC correlate with offspring's mental health and educational outcomes; and (c) demographic and study characteristics moderate these relationships. Sixty-one research reports were reviewed, with 68 independent study samples (N = 14,453; 41 and 27 Asian and Latino/a samples, respectively) subjected to 3 meta-analyses. AM positively correlated with ICC (r = .23), which in turn negatively correlated with offspring mental health (r = -.20) and educational outcomes (r = -.09). Findings provided support for acculturation gap-distress theory. While these effect size estimates were small, participant and methodological variables affected their magnitude. Contrary to findings on intergenerational conflict within mainstream nonimmigrant families, the relationships among AM, ICC, and mental health were larger in young adult than adolescent groups within immigrant families. ICC significantly correlated with internalizing problems and adaptive functioning, but not externalizing problems. AM was more closely related to ICC among women and second-generation immigrant offspring. AM and ICC were more problematic among offspring who were low-risk and lived in less ethnically disperse regions, particularly when studied in cross-sectional studies. Effect sizes also differed significantly across measurement tools for the key constructs. Limitations to generalizability (few studies on educational outcomes, relative underrepresentation of Latino/a to Asian American samples), and implications for intervention and future research are discussed. © 2014 American Psychological Association.


Soler R.,Wageningen University | Erb M.,Max Planck Institute for Chemical Ecology | Kaplan I.,Purdue University
Trends in Plant Science | Year: 2013

Plants mediate interactions between insects, including leaf- and root-feeders; yet the underlying mechanisms and connection with ecological theory remain unresolved. In this review, based on novel insights into long-distance (i.e., leaf-leaf, root-shoot) defence signalling, we explore the role of phytohormones in driving broad-scale patterns of aboveground-belowground interactions that can be extrapolated to general plant-insect relationships. We propose that the outcome of intra-feeding guild interactions is generally negative due to induction of similar phytohormonal pathways, whereas between-guild interactions are often positive due to negative signal crosstalk. However, not all outcomes could be explained by feeding guild; we argue that future studies should target ecologically representative plant-insect systems, distinguish subguilds, and include plant growth hormones to improve our understanding of plant-mediated interactions. © 2012 Elsevier Ltd.


Staiger C.J.,Purdue University
Cell Host and Microbe | Year: 2016

Pseudomonas syringae secretes effectors from its type III secretion system to infect plants. In this issue of Cell Host & Microbe, Guo et al. (2016) determine that the T3SS effector, HopE1, targets calmodulin and the microtubule-associated protein MAP65-1 to subvert plant immunity. © 2016 Elsevier Inc.


Marais K.B.,Purdue University
Reliability Engineering and System Safety | Year: 2013

One class of maintenance optimization problems considers the notion of general repair maintenance policies where systems are repaired or replaced on failure. In each case the optimality is based on minimizing the total maintenance cost of the system. These cost-centric optimizations ignore the value dimension of maintenance and can lead to maintenance strategies that do not maximize system value. This paper applies these ideas to the general repair optimization problem using a semi-Markov decision process, discounted cash flow techniques, and dynamic programming to identify the value-optimal actions for any given time and system condition. The impact of several parameters on maintenance strategy, such as operating cost and revenue, system failure characteristics, repair and replacement costs, and the planning time horizon, is explored. This approach provides a quantitative basis on which to base maintenance strategy decisions that contribute to system value. These decisions are different from those suggested by traditional cost-based approaches. The results show (1) how the optimal action for a given time and condition changes as replacement and repair costs change, and identifies the point at which these costs become too high for profitable system operation; (2) that for shorter planning horizons it is better to repair, since there is no time to reap the benefits of increased operating profit and reliability; (3) how the value-optimal maintenance policy is affected by the system's failure characteristics, and hence whether it is worthwhile to invest in higher reliability; and (4) the impact of the repair level on the optimal maintenance policy. © 2013 Elsevier Ltd.


Adler P.B.,Utah State University | Dalgleish H.J.,Purdue University | Ellner S.P.,Cornell University
Journal of Ecology | Year: 2012

A change in a climate variable may alter a species' abundance not only through a direct effect on that species' vital rates, but also through 'indirect' effects mediated by species interactions. While recent work has highlighted cases in which indirect effects overwhelm the direct effects of climate, we lack robust generalizations to predict the strength of indirect effects. For communities dominated by non-trophic interactions, we propose that the potential for indirect effects of climate change declines with the strength of stabilizing niche differences. We tested this hypothesis by analysing an empirically parameterized four species population model. We quantified negative frequency dependence in population growth rates as a measure of stabilizing niche differences and projected the sensitivity of each species to direct and indirect effects of climate perturbations. Consistent with our hypothesis, species' sensitivities to indirect effects decreased rapidly with increasing stabilization by niche differences. Synthesis. Information about niche differences can identify species sensitive to indirect effects of climate change and determine when multispecies forecasting approaches are necessary. However, practical application of this generalization will require methods to predict niche differences from easily collected data. © 2011 The Authors. Journal of Ecology © 2011 British Ecological Society.


Low T.,Purdue University | Guinea F.,CSIC - Institute of Materials Science
Nano Letters | Year: 2010

Particular strain geometry in graphene could lead to a uniform pseudomagnetic field of order 10T and might open up interesting applications in graphene nanoelectronics. Through quantum transport calculations of realistic strained graphene flakes of sizes of 100 nm, we examine possible means of exploiting this effect for practical electronics and valleytronics devices. First, we found that elastic backscattering at rough edges leads to the formation of well-defined transport gaps of order 100 meV under moderate maximum strain of 10%. Second, the application of a real magnetic field induced a separation, in space and energy, of the states arising from different valleys, leading to a way of inducing bulk valley polarization which is insensitive to short-range scattering. © 2010 American Chemical Society.


Kujala J.V.,University of Jyvaskyla | Dzhafarov E.N.,Purdue University | Larsson J.-A.,Linkoping University
Physical Review Letters | Year: 2015

The notion of (non)contextuality pertains to sets of properties measured one subset (context) at a time. We extend this notion to include so-called inconsistently connected systems, in which the measurements of a given property in different contexts may have different distributions, due to contextual biases in experimental design or physical interactions (signaling): a system of measurements has a maximally noncontextual description if they can be imposed a joint distribution on in which the measurements of any one property in different contexts are equal to each other with the maximal probability allowed by their different distributions. We derive necessary and sufficient conditions for the existence of such a description in a broad class of systems including Klyachko-Can-Binicioʇlu-Shumvosky-type (KCBS), EPR-Bell-type, and Leggett-Garg-type systems. Because these conditions allow for inconsistent connectedness, they are applicable to real experiments. We illustrate this by analyzing an experiment by Lapkiewicz and colleagues aimed at testing contextuality in a KCBS-type system. © 2015 American Physical Society.


Richardson J.E.,Purdue University
Journal of Geophysical Research E: Planets | Year: 2011

This study demonstrates the efficacy of a recently developed, impact crater "excavation flow properties model" (EFPM) that accomplishes the following goals: (1) uses hydrodynamic streamline theory to develop the expressions that extend the classic impact ejecta scaling relationships into regions near the crater rim, where target strength and/or gravity bring crater excavation flow to a halt; (2) links this new, general ejecta position/velocity scaling relationship to the existing general crater size/volume scaling relationship, including the transition region between gravity-and strength-dominated cratering; (3) provides a means for estimating impact ejecta plume mass-density and ejecta blanket thickness, as a function of azimuth and distance from the impact site, in conditions ranging from low to high target strength; and (4) brings in our experimentally derived knowledge of impact ejection angles and the effects of oblique impact to develop a useful 2-D and 3-D model of both leading-edge and trailing-edge ejecta plume behavior. In this work, this excavation flow properties model is used to simulate the images and data produced by three laboratory impact studies which utilized modern, laser-based, non-intrusive means to investigate ejecta plume formation, expansion, and fallout from three different perspectives. Copyright 2011 by the American Geophysical Union.


Weisshaar T.A.,Purdue University
Journal of Aircraft | Year: 2013

The term 'morphing aircraft' describes a broad range of air vehicles and vehicle components that adapt to planned and unplanned multipoint mission requirements. Adaptation or morphing requires changing system features including vehicle 'states,' such as vehicle shape, during in-flight operation. The term morphing can be applied to almost any activity in which in-flight vehicle features are changed. As such, morphing has become a buzzword loosely applied to a wide variety of activities, some of which are disconnected from air vehicle morphing development. This has led to three myths: 1) morphing shape change is too expensive, 2) morphing aircraft must weigh more than nonmorphing aircraft, and 3) morphing requires exotic materials and complex systems. This paper attempts to dispel these myths by reviewing early morphing aircraft history to identify inventions and innovations that led to both successes and failures. The review also discusses recent government-sponsored activities in the United States: in particular, morphing systems development sponsored by the Defense Advanced Research Projects Agency viewed from the author's perspective as a former Defense Advanced Research Projects Agency Program Manager. The review concludes with identification of possible avenues for future morphing aircraft evolution and morphing device development.


Hall M.C.,Purdue University
Science Signaling | Year: 2010

Walther Flemming and his contemporaries first described the process of mitotic cell division on the basis of microscopic observations over a century ago. In the ensuing 100-plus years, the disciplines of cell biology, genetics, biochemistry, and molecular biology have provided a detailed, yet incomplete, molecular view of the mechanics and regulation of eukaryotic cell division and its relationship to diseases such as cancer. Now, genomic and proteomic technologies offer new and powerful tools to enhance our understanding of this amazingly intricate and fundamental life process. Proteomic studies shed new light on cell division through the large-scale mapping of cell cycle-dependent protein modifications. These studies alter our perception of the complexity of the cell cycle and will serve as a framework for future research efforts to completely characterize the molecular mechanisms of its regulation. Copyright 2008 the American Association for the Advancement of Science; all rights reserved.