Showing papers by "Worcester Polytechnic Institute published in 2003"

Comparison of calibration methods for atomic-force microscopy cantilevers

Abstract: Th es cientific community needs a rapid and reliable way of accurately determining the stiffness of atomic-force microscopy cantilevers. We have compared the experimentally determined values of stiffness for ten cantilever probes using four different methods. For rectangular silicon cantilever beams of well defined geometry, the approaches all yield values within 17% of the manufacturer’s nominal stiffness. One of the methods is new, based on the acquisition and analysis of thermal distribution functions of the oscillator’s amplitude fluctuations. We evaluate this method in comparison to the three others and recommend it for its ease of use and broad applicability.

Tight–loose coupling with customers: the enactment of customer orientation

Abstract: This article argues that tight linkages with customers present a paradox for the firm. The research question of this study is: What is the behavioral and cognitive process by which a firm establishes close links with its customers, and how can this process be both beneficial and detrimental? Existing theory and data from apparel retailers suggest that firms forge these tight links by enacting their customer environment. In the process of enactment, cognitions and actions reinforce each other and become increasingly focused. The tight coupling generated through enactment comes at the price of increased commitment and restricted vision. The author argues that firms should balance the natural process of tight coupling with a deliberate effort at loose coupling, and draws implications for further research on the organization-environment interface. Copyright © 2003 John Wiley & Sons, Ltd.

Identification of Ion-Selectivity Determinants in Heavy-Metal Transport P1B-type ATPases

Abstract: P1B-type ATPases transport a variety of metals (Cd2+, Zn2+, Pb2+, Co2+, Cu2+, Ag+, Cu+) across biomembranes. Characteristic sequences CP[C/H/S] in transmembrane fragment H6 were observed in the putative transporting metal site of the founding members of this subfamily (initially named CPx-ATPases). In spite of their importance for metal homeostasis and biotolerance, their mechanisms of ion selectivity are not understood. Studies of better-characterized P(II)-type ATPases (Ca-ATPase and Na,K-ATPase) have identified three transmembrane segments that participate in ion binding and transport. Testing the hypothesis that metal specificity is determined by conserved amino acids located in the equivalent transmembrane segments of P1B-type ATPases (H6, H7, and H8), 234 P1B-ATPase protein sequences were analyzed. This showed that although H6 contains characteristic CPX or XPC sequences, conserved amino acids in H7 and H8 provide signature sequences that predict the metal selectivity in each of five P1B-ATPase subgroups identified. These invariant amino acids contain diverse side chains (thiol, hydroxyl, carbonyl, amide, imidazolium) that can participate in transient metal coordination during transport and consequently determine the particular metal selectivity of each enzyme. Each subgroup shares additional structural characteristics such as the presence (or absence) of particular amino-terminal metal-binding domains and the number of putative transmembrane segments. These differences suggest unique functional characteristics for each subgroup in addition to their particular metal specificity.

Context-dependent data envelopment analysis—Measuring attractiveness and progress

Abstract: Data envelopment analysis (DEA) is a methodology for identifying the efficient frontier of decision making units (DMUs). Context-dependent DEA refers to a DEA approach where a set of DMUs are evaluated against a particular evaluation context. Each evaluation context represents an efficient frontier composed by DMUs in a specific performance level. The context-dependent DEA measures (i) the attractiveness when DMUs exhibiting poorer performance are chosen as the evaluation context, and (ii) the progress when DMUs exhibiting better performance are chosen as the evaluation context. The current paper extends the context-dependent DEA by incorporating value judgment into the attractiveness and progress measures. The method is applied to measuring the attractiveness of 32 computer printers. It is shown that the attractive measure helps (i) customers to select the best option, and (ii) printer manufacturers to identify the potential competitors.

Existence and convergence for quasi-static evolution in brittle fracture

Abstract: This paper investigates the mathematical well-posedness of the variational model of quasi-static growth for a brittle crack proposed by Francfort and Marigo in [15]. The starting point is a time discretized version of that evolution which results in a sequence of minimization problems of Mumford and Shah type functionals. The natural weak setting is that of special functions of bounded variation, and the main difficulty in showing existence of the time-continuous quasi-static growth is to pass to the limit as the time-discretization step tends to 0. This is performed with the help of a jump transfer theorem which permits, under weak convergence assumptions for a sequence {un} of SBV-functions to its BV-limit u, to transfer the part of the jump set of any test field that lies in the jump set of u onto that of the converging sequence {un}. In particular, it is shown that the notion of minimizer of a Mumford and Shah type functional for its own jump set is stable under weak convergence assumptions. Furthermore, our analysis justifies numerical methods used for computing the time-continuous quasi-static evolution. © 2003 Wiley Periodicals, Inc.

Knowing-Why About Data Processes and Data Quality

Abstract: Knowledge about work processes is a prerequisite for performing work. We investigate whether a certain mode of knowledge, knowing-why, affects work performance and whether the knowledge held by different work roles matters for work performance. We operationalize these questions in the specific domain of data production processes and data quality. We analyze responses from three roles within data production processes, data collectors, data custodians, and data consumers, to investigate the effects of different knowledge modes held by different work roles on data quality. We find that work roles and the mode of knowledge do matter. Specifically, data collectors with why-knowledge about the data production process contribute to producing better quality data. Overall, knowledge of data collectors is more critical than that of data custodians.

The effect of latency on user performance in Warcraft III

Abstract: Latency on the Internet is a well-known problem for interactive applications. With the increase in interactive network games comes the increased importance of understanding the effects of latency on user performance. Classes of network games such as First Person Shooters (FPS) and Real Time Strategy (RTS) differ in their user interaction model and hence susceptibility to latency. While previous work has measured the effects of latency on FPS games, there has been no systematic investigation of the effects of latency on RTS games. In this work, we design and conduct user studies that measure the impact of latency on user performance in Warcraft III, a popular RTS game. As a foundation for the research, we separated typical Warcraft III user interactions into the basic components of explore, build and combat, and analyzed each individually. We find modest statistical correlations between user performance and latency for exploration, but very weak correlations for building and combat. Overall, the effect of even very high latency, while noticeable to users, has a negligible effect on the outcome of the game. We attribute this somewhat surprising result to the nature of RTS game-play that clearly favors strategy over the real-time aspects.

Role of lipopolysaccharides in the adhesion, retention, and transport of Escherichia coli JM109.

Abstract: The role of lipopolysaccharides (LPS) in bacterial adhesion was investigated via atomic force microscopy (AFM). Adhesion between a silicon nitride tip and Escherichia coli JM109 was measured in water and 0.01 M phosphate-buffered saline (PBS) on untreated cells and on a sample of E. coli treated with 100 mM ethylenediaminetetraacetic acid (EDTA), which removes approximately 80% of the LPS molecules. LPS removal decreased the adhesion affinity between the bacterial cells and the AFM tip from -2.1 +/- 1.8 to -0.40 +/- 0.36 nN in water and from -0.74 +/- 0.44 to -0.46 +/- 0.23 nN in 0.01 M PBS (statistically different, Mann-Whitney rank sum test, P < 0.01). The distributions of adhesion affinities between E. coli LPS macromolecules and the AFM tip could be described by gamma distribution functions. Direct measurements of the adhesive force between E. coil and a surface were compared with adhesion in batch and column experiments, and agreement was observed between the influences of LPS on adhesion in each system. Bacterial batch retention to glass or in packed beds to quartz sand decreased after LPS removal. When interaction forces were measured during the approach of the AFM tip to a bacterium, steric repulsive forces were seen for both treated and untreated cells, but the repulsion was greater when the LPS was intact A model for steric repulsion predicted a reduction of the equilibrium length of the surface polymers from 242 to 64 nm in water and from 175 to 81 nm in buffer, after removal of a portion of the LPS. DLVO calculations based on conventional and soft-particle DLVO theories predicted higher energy barriers to adhesion for all surfaces after LPS removal, consistent with experimental findings. Adhesion forces between the AFM tip and bacterial polymers were correlated with bacterial attachment and retention, while measurements of interaction forces during the approach of the AFM tip to the bacterium did not correlate with subsequent adhesion behavior to glass or quartz sand.

Effect of bubble deformation on the properties of bubbly flows

Abstract: Direct numerical simulations of the motion of 27 three-dimensional deformable buoyant bubbles in periodic domains are presented The full Navier–Stokes equations are solved by a parallelized finite-difference/front-tracking method that allows a deformable interface between the bubbles and the suspending fluid and the inclusion of surface tension The Eotvos number is taken as equal to 5, so that the bubbles are ellipsoidal, and the Galileo number is 900, so that the rise Reynolds number of a single bubble in an unbounded flow is about 26 Three values of the void fraction have been investigated: 2%, 6% and 12% At 6%, a change in the behaviour of the bubbles is observed The bubbles are initially dispersed homogeneously throughout the flow field and their average rise Reynolds number is 23 After the bubbles have risen by about 90 bubble diameters, they form a vertical stream and accelerate The microstructure of the bubble suspension is analysed and an explanation is proposed for the formation of these streams The results for the ellipsoidal bubbles are compared to the results for nearly spherical bubbles, for which the Eotvos number is 1 and the Galileo number is 900 The dispersion of the bubbles and the velocity fluctuations in the liquid phase are analysed

Developing a framework for evaluating the logistics costs in global sourcing processes

Abstract: Global sourcing is becoming a prerequisite for companies competing in today's market. The logistics costs often comprise a large portion of the total global sourcing cost, thereby determining the effectiveness of this procurement strategy. However, evaluating the logistics cost in a global context is frequently difficult. This paper presents a five‐step evaluation framework and illustrates how this framework can be implemented using a case study at a leading firm in the US aviation industry and its part supplier in Chengdu, China. The framework not only identifies the key logistics cost items, but also suggests a way of quantifying each of the cost elements. The computational part of the framework can be easily implemented on spreadsheets and offers substantial flexibility to accommodate assessment of various transportation alternatives and sensitivity analysis.

Sorption in Proton-Exchange Membranes An Explanation of Schroeder’s Paradox

Abstract: A physicochemical model is proposed to describe sorption in proton-exchange membranes (PEMs), which can predict the complete isotherm as well as provide a plausible explanation for the long-unresolved phenomenon termed Schroeder's paradox, namely, the difference between the amounts sorbed from a liquid solvent vs. from its saturated vapor. The solvent uptake is governed by the swelling pressure caused within the membrane as a result of stretching of the polymer chains upon solvent uptake, Π M , as well as a surface pressure, Π σ , due to the curved vapor-liquid interface of pore liquid. Further, the solvent molecules in the membrane are divided into those that are chemically, or strongly, bound to the acid sites, λ C i, and others that are free to physically equilibrate between the fluid and the membrane phases, λ F i. The model predicts the isotherm over the whole range of humidities satisfactorily and also provides a rational explanation for the Schroeder's paradox.

Multiple material marching cubes algorithm

Abstract: The accurate reconstruction of three-dimensional (3D) boundary surfaces from two-dimensional (2D) medical images is a crucial procedure in most applications of computational biomedical engineering. This paper addresses an innovative system that efficiently reconstructs accurate, multiple-material, 3D surface meshes from 2D medical images. It is based on an enhanced marching cubes algorithm, the multi-material marching cubes algorithm (M3C), which extracts boundary surfaces between different materials within one sweep of the image stack in an integrated manner. The continuity and integrity of the surfaces are ensured with this robust algorithm. Surface adjustment algorithms were also revised to adapt to the multiple-material nature of the system. Copyright © 2003 John Wiley & Sons, Ltd.

Visual hierarchical dimension reduction for exploration of high dimensional datasets

Abstract: Traditional visualization techniques for multidimensional data sets, such as parallel coordinates, glyphs, and scatterplot matrices, do not scale well to high numbers of dimensions. A common approach to solving this problem is dimensionality reduction. Existing dimensionality reduction techniques usually generate lower dimensional spaces that have little intuitive meaning to users and allow little user interaction. In this paper we propose a new approach to handling high dimensional data, named Visual Hierarchical Dimension Reduction (VHDR), that addresses these drawbacks. VHDR not only generates lower dimensional spaces that are meaningful to users, but also allows user interactions in most steps of the process. In VHDR, dimensions are grouped into a hierarchy, and lower dimensional spaces are constructed using clusters of the hierarchy. We have implemented the VHDR approach into XmdvTool, and extended several traditional multidimensional visualization methods to convey dimension cluster characteristics when visualizing the data set in lower dimensional spaces. Our case study of applying VHDR to a real data set supports our belief that this approach is effective in supporting the exploration of high dimensional data sets.

Polysaccharide properties probed with atomic force microscopy

Abstract: In recent years, polysaccharides have been extensively studied using atomic force microscopy (AFM). Owing to its high lateral and vertical resolutions and ability to measure interaction forces in liquids at pico- or nano-Newton level, the AFM is an excellent tool for characterizing biopolymers. The first imaging studies showed the morphology of polysaccharides, but gradually more quantitative image analysis techniques were developed as the AFM grew easier to use in aqueous liquids and in non-contact modes. Recently, AFM has been used to stretch polysaccharides and characterize their physicochemical properties by application of appropriate polymer stretching models, using a technique called single-molecule force spectroscopy. From application of such models as the wormlike chain, freely jointed chain, extensible-freely jointed chain, etc., properties such as the contour length, persistence length and segment elasticity or spring constant can be calculated for polysaccharides. The adhesion between polysaccharides and surfaces has been quantified with AFM, and this application is particularly useful for studying polysaccharides on microbial and other types of cells, because their adhesion is controlled by biopolymer characteristics. This review presents a synthesis of the theory and techniques currently in use to probe the physicochemical properties of polysaccharides with AFM.

Effect of Stenosis Asymmetry on Blood Flow and Artery Compression: A Three-Dimensional Fluid-Structure Interaction Model

Abstract: A nonlinear three-dimensional thick-wall model with fluid-structure interactions is introduced to simulate blood flow in carotid arteries with an asymmetric stenosis to quantify the effects of stenosis severity, eccentricity, and pressure conditions on blood flow and artery compression (compressive stress in the wall). Mechanical properties of the tube wall are measured using a thick-wall stenosis model made of polyvinyl alcohal hydrogel whose mechanical properties are close to that of carotid arteries. A hyperelastic Mooney–Rivlin model is used to implement the experimentally measured nonlinear elastic properties of the tube wall. A 36.5% pre-axial stretch is applied to make the simulation physiological. The Navier–Stokes equations in curvilinear form are used for the fluid model. Our results indicate that severe stenosis causes critical flow conditions, high tensile stress, and considerable compressive stress in the stenosis plaque which may be related to artery compression and plaque cap rupture. Stenosis asymmetry leads to higher artery compression, higher shear stress and a larger flow separation region. Computational results are verified by available experimental data. © 2003 Biomedical Engineering Society. PAC2003: 8719Uv, 8710+e

Pixel-by-Pixel Spatiotemporal Progression of Focal Ischemia Derived Using Quantitative Perfusion and Diffusion Imaging

Abstract: Pixel-by-pixel spatiotemporal progression of focal ischemia (permanent occlusion) in rats was investigated using quantitative perfusion and diffusion magnetic resonance imaging every 30 minutes for 3 hours. The normal left-hemisphere apparent diffusion coefficient (ADC) was 0.76 +/- 0.03 x 10(-3) mm(2)/s and CBF was 0.7 +/- 0.3 mL x g(-1) x min(-1) (mean +/- SD, n=5). The ADC and CBF viability thresholds yielding the lesion volumes (LV) at 3 hours that best approximated the 2,3,5-triphenyltetrazolium chloride (TTC) infarct volumes (200 +/- 30 mm(3)) at 24 hours were 0.53 +/- 0.02 x 10(-3) mm(2)/s (30% +/- 2% reduction) and 0.30 +/- 0.09 mL x g(-1) x min(-1) (57% +/- 11% reduction), respectively. Temporal evolution of the ADC- and CBF-defined LV showed a significant "perfusion-diffusion mismatch" up to 2 hours (P < 0.05, n = 11), a potential therapeutic window. Based on the viability thresholds, three pixel clusters were identified on the CBF-ADC scatterplots: (1) a "normal" cluster with normal CBF and ADC, (2) an "ischemic core" cluster with markedly reduced CBF and ADC, and (3) a "mismatch" cluster with reduced CBF but slightly reduced ADC. These clusters were color-coded and mapped onto the image and CBF-ADC spaces. Lesions grew peripheral and medial to the initial ADC abnormality. In contrast to the CBF distribution, the ADC distribution in the ischemic hemisphere was bimodal; the relatively time-invariant bimodal-ADC minima were 0.57 +/- 0.02 x 10(-3) mm(2)/s (corresponding CBF 0.35 +/- 0.04 mL x g(-1) x min(-1)), surprisingly similar to the TTC-derived thresholds. Together, these results illustrate an analysis approach to systemically track the pixel-by-pixel spatiotemporal progression of acute ischemic brain injury.

Tetraploid Artemisia annua hairy roots produce more artemisinin than diploids

Abstract: Hairy root cultures of diploid Artemisia annua L. (clone YUT16) grow rapidly and produce the antimalarial sesquiterpene artemisinin. Little is known about how polyploidy affects the growth of transformed hairy roots and the production of secondary metabolites. Using colchicine, we produced four stable tetraploid clones of A. annua L. from the YUT16 hairy root clone. Analysis showed major differences in growth and artemisinin production compared to the diploid clone. Tetraploid clones produced up to six times more artemisinin than the diploid parent. This study provides an initial step in increasing our understanding of the role of polyploidy in secondary metabolite production, especially in hairy roots.

Oxygen tension imaging in the mouse retina.

Abstract: A newly developed microscope-based imaging system was used to measure the oxygen tension (PO2) inside the retinal and choroidal vessels of mice and to generate in vivo maps of retinal PO2. These maps were generated from the phosphorescence lifetimes of an injected palladium–porphyrin compound using a frequency-domain measurement. The system was fully calibrated and used to produce retinal PO2 maps at different inspiratory oxygen fractions. PO2 rose accordingly and predictably as inspiratory O2 was stepped from hypoxic to hyperoxic conditions. Important experimental and acquisition parameters necessary for applying phosphorescence lifetime imaging to the mouse eye were investigated, including camera exposure and intensifier gain settings. Because of a need to limit light exposure to the retina, PO2 map quality as measured by the coefficient of determination was investigated as a function of signal-to-noise and accumulated excitation energy deposition. With the development of this technology for use in mice, the potential for investigating the oxygen dynamics in genetically engineered mouse models of retinal disease, including diabetic retinopathy, glaucoma, and age-related macular degeneration, is advanced. © 2003 Biomedical Engineering Society. PAC2003: 4266Ew, 8763Lk, 8719Dd

Functional roles of metal binding domains of the Archaeoglobus fulgidus Cu(+)-ATPase CopA.

Abstract: CopA, a thermophilic membrane ATPase from Archaeoglobus fulgidus, drives the outward movement of Cu+ or Ag+ [Mandal et al. (2002) J. Biol. Chem. 277, 7201−7208]. This, as other PIB-ATPases, is characterized by a putative metal binding sequence (C380PC382) in its sixth transmembrane fragment and cytoplasmic metal binding sequences in its NH2- and COOH-terminal ends (C27AMC30 and C751HHC754). Using isolated CopA, we have studied the functional role of these three putative metal binding domains. Replacement of transmembrane Cys residues by Ala results in nonfunctional enzymes that are unable to hydrolyze ATP. However, the CPC → APA substituted enzyme binds ATP, indicating its correct folding and suggesting that enzyme turnover is prevented by the lack of metal binding to the transmembrane site. Replacement of C-terminal Cys by Ala (C751,754A) has no significant effect on ATPase activity, enzyme phosphorylation, apparent binding affinities of ligands, or E1−E2 equilibrium. In contrast, replacement of Cys in t...

Planar Minimally Rigid Graphs and Pseudo-Triangulations

Abstract: Pointed pseudo-triangulations are planar minimally rigid graphs embedded in the plane with pointed vertices (adjacent to an angle larger than 180 degrees. In this paper we prove that the opposite statement is also true, namely that planar minimally rigid graphs always admit pointed embeddings, even under certain natural topological and combinatorial constraints. We provide two proofs, which both yield efficient embedding algorithms. One based on Henneberg inductive constructions from combinatorial rigidity theory, the other on a generalization of Tutte's barycentric embeddings to directed graphs.

Synthesis of Zeolitic Mesoporous Materials by Dry Gel Conversion under Controlled Humidity

Abstract: A new variation to the dry gel conversion method for the preparation of zeolite is introduced, where the conversion to zeolite was accomplished under water vapor below the saturation condition. The dry gel was made either by vacuum concentration or by surfactant flocculation from a silica precursor sol after the preliminary hydrothermal step. Depending of the humidity under which the conversion took place, mesoporous structures with varying MFI crystallinity, BET, and crystalline external surface areas were produced. The effects of precursor preparation and surfactant flocculation conditions on mesoporosity and crystallinity of the final product, as well as the steam stability of the product, were also investigated. The approach could find general application in the synthesis of other zeolites as well as metal oxides.

Formation of Silicalite-1 Hollow Spheres by the Self-assembly of Nanocrystals

Abstract: A simple approach is reported for the preparation of hollow spheres with a 10−20-nm-thick shell of silicalite-1 nanocrystals. The nanocrystals were produced by the steaming of silicalite-1 nanoprecursors (NPs), collected with the help of surfactant from a clear synthesis solution immediately following the induction period. The nanocrystals produced were ≈10−20 nm with a BET surface area of 440−470 m2/g and an external surface area >112 m2/g. A water adsorption isotherm confirmed that the nanocrystals were hydrophobic in nature. These nanocrystals self-assembled into hollow spheres of 100−300-nm diameter when ultrasonicated in ammoniac ethanol.

Corticothalamic modulation during absence seizures in rats: a functional MRI assessment.

Abstract: Summary: Purpose: Functional magnetic resonance imaging (fMRI) was used to identify areas of brain activation during absence seizures in an awake animal model. Methods: Blood-oxygenation-level–dependent (BOLD) fMRI in the brain was measured by using T2*-weighted echo planar imaging at 4.7 Tesla. BOLD imaging was performed before, during, and after absence seizure induction by using γ-butyrolactone (GBL; 200 mg/kg, intraperitoneal). Results: The corticothalamic circuitry, critical for spike–wave discharge (SWD) formation in absence seizure, showed robust BOLD signal changes after GBL administration, consistent with EEG recordings in the same animals. Predominantly positive BOLD changes occurred in the thalamus. Sensory and parietal cortices showed mixed positive and negative BOLD changes, whereas temporal and motor cortices showed only negative BOLD changes. Conclusions: With the BOLD fMRI technique, we demonstrated signal changes in brain areas that have been shown, with electrophysiology experiments, to be important for generating and maintaining the SWDs that characterize absence seizures. These results corroborate previous findings from lesion and electrophysiological experiments and show the technical feasibility of noninvasively imaging absence seizures in fully conscious rodents.

Global sourcing: process and design for efficient management

Abstract: Although the literature on the strategic aspect of global sourcing is large, detailed studies on this procurement strategy from a process perspective are limited. This paper adopts the process viewpoint and examines the design and management issues associated with the global sourcing process based on a case study at a leading firm in the US aviation industry. The effectiveness of the company’s global sourcing process is evaluated, the design alternatives of the supply chain structure are compared, and the critical issues of efficient management of the process are summarized. Specifically, three logistics‐based criteria are developed to indicate the effectiveness of the transportation and distribution network. The paper also demonstrates that the process design can be assessed based on the dimensions of supply chain integration. Finally, a flow‐level matrix is developed to identify the critical issues of managing the global sourcing process.