Physical Sciences and Mathematics Commons^™

Centrifugal Compression Of Soft Particle Packings: Theory And Experiment, Kerstin Nordstrom, Emilie Verneuil, Wouter Ellenbroek, Tom Lubensky, Jerry Gollub, Douglas Durian

Douglas J. Durian

An exact method is developed for computing the height of an elastic medium subjected to centrifugal compression, for arbitrary constitutive relation between stress and strain. Example solutions are obtained for power-law media and for cases where the stress diverges at a critical strain—for example as required by packings composed of deformable but incompressible particles. Experimental data are presented for the centrifugal compression of thermo-responsive N-isopropylacrylamide (NIPA) microgel beads in water. For small radial acceleration, the results are consistent with Hertzian elasticity, and are analyzed in terms of the Young elastic modulus of the bead material. For large radial acceleration, the …

Striving For Cultural Competence In An Hiv Program: The Transformative Impact Of A Microsystem In A Larger Health Network, Judith N Sabino, Timothy Friel, Lynn Deitrick, Debbie Salas-Lopez

Debbie Salas-Lopez MD, MPH

No abstract provided.

Long-Term Survival For Patients With Acute Decompensated Heart Failure According To Ejection Fraction Findings, Andrew Coles, Kimberly Fisher, Chad Darling, Jorge Yarzebski, David Mcmanus, Joel Gore, Darleen Lessard, Robert Goldberg

Jorge L. Yarzebski

Limited data exist about the long-term prognosis of patients with acute decompensated heart failure (ADHF) further stratified according to ejection fraction (EF) findings. The primary objective of this population-based observational study was to characterize and compare trends in long-term prognosis after an episode of ADHF across 3 EF strata. Hospital medical records were reviewed for 3,604 residents of the Worcester, Massachusetts, metropolitan area who were discharged after ADHF from all 11 medical centers in central Massachusetts during 1995, 2000, 2002, and 2004 and had EF measurements during their index hospitalizations. The average age of this population was 75 years, most …

Effectiveness Of A Novel Spontaneous Carvacrol Nanoemulsion Against Salmonella Enterica Enteritidis And Escherichia Coli O157:H7 On Contaminated Mung Bean And Alfalfa Seeds, Kyle Landry, Yuhua Chang, David Julian Mcclements, Lynne Mclandsborough

Kyle S Landry

Diagnostic Performance Of Cardiac Troponin I For Early Rule-In And Rule-Out Of Acute Myocardial Infarction: Results Of A Prospective Multicenter Trial, Alan Storrow, Robert Christenson, Richard Nowak, Deborah Diercks, Adam Singer, Alan Wu, Erik Kulstad, Frank Lovecchio, Christian Fromm, Gary Headden, Tracie Potis, Christopher Hogan, Jon Schrock, Daniel Zelinski, Marna Greenberg, James Ritchie, Janna Chamberlin, Kurtis Bray, Daniel Rhodes, Deirdre Trainor, Dawn Holmes, Paula Southwick

Marna R Greenberg DO, MPH, FACEP

OBJECTIVES: To compare emergency department TnI serial sampling intervals, determine optimal diagnostic thresholds, and report representative diagnostic performance characteristics for early rule-in and rule-out of MI. METHODS: We prospectively measured TnI (AccuTnI+3™, Beckman Coulter) at serial time intervals in 1929 subjects with chest pain or equivalent ischemic symptoms suggestive of acute coronary syndromes at 14 medical centers. Diagnosis was adjudicated by an independent central committee. RESULTS: TnI ≥0.03ng/mL provided 96.0% sensitivity and 89.4% specificity at 1-3h after admission, and 94.9% sensitivity and 86.7% specificity at 3-6h. NPV (rule-out, non-MI) was 99.5% at 1-3h, and 99.0% at 3-6h when TnI is …

Pubertal And Adult Leydig Cell Function In Mullerian Inhibiting Substance-Deficient Mice, Xiufeng Wu, Ramamani Arumugam, Stephen Baker, Mary Lee

Mary M. Lee

Mullerian inhibiting substance (MIS) causes Mullerian duct regression during sexual differentiation and regulates postnatal Leydig cell development. MIS knockout (MIS-KO) mice with targeted deletions of MIS develop Leydig cell hyperplasia, but their circulating androgen concentrations are reportedly unaltered. We compared reproductive hormone profiles, androgen biosynthesis, and the expression of key steroidogenic and metabolic enzymes in MIS-KO and wild-type (WT) mice at puberty (36 d) and sexual maturity (60 d). In pubertal animals, basal testosterone and LH concentrations in plasma were lower in MIS-KO than WT mice, whereas human chorionic gonadotropin-stimulated testosterone concentrations were similar. In adults, basal LH, and both …

Functionalizing Carbon Nanotube Forests With 1,5-Diaminoaphthalene, Ben Pound, T. Shen

Ben Pound

Carbon Nanotube (CNT) Forests are vertically grown carbon nanotubes. They can be as tall as millimeters, with radii from less than one nanometer (single-walled) to tens of nanometers (multi-walled). Their high surface area to volume ratio provides a unique material system for biosensor applications. However, the CNT surface does not provide covalent bonding sites to many antibodies of interest. One approach is to attach linker molecules with aromatic rings via π-stacking to the CNT surface and activating the linker molecules to bind covalently to specific antibody molecules. Unfortunately, the conventional solution-based functionalization approach often leads to collapse of the CNT …

Functionalizing Carbon Nanotube Forests, Ben Pound, F. Shen

Ben Pound

A carbon nanotube forest is an array of carbon nanotubes vertically aligned and entangled. Because the aspect ratio of each tube can be more than 1000, the forest will greatly increase the number of potential binding sites on the surface for chemical and biological detector applications, if each bundle of tubes can be functionalized with specific molecules. The 1,5-diaminoaphthalene can be a versatile linker molecule for proteins. In this study, we characterize the concentration of 1,5-diaminoaphthalene in solvent by fluorescence spectroscopy. It appears, however, that the solvent collapses the carbon nanotube forest, resulting in no detectable fluorescence emission. Lithographically defined …

A Sophisticated Library Search Strategy Using Folksonomies And Similarity Matching, William Lund, Yiu-Kai Ng, Maria Pera

William Lund

Libraries, private and public, offer valuable resources to library patrons. As of today the only way to locate information archived exclusively in libraries is through their catalogs. Library patrons, however, often find it difficult to formulate a proper query, which requires using specific keywords assigned to different fields of desired library catalog records, to obtain relevant results. These improperly formulated queries often yield irrelevant results or no results at all. This negative experience in dealing with existing library systems turn library patrons away from library catalogs; instead, they rely on Web search engines to perform their searches first and upon …

Ensemble Methods For Historical Machine-Printed Document Recognition, William Lund

William Lund

The usefulness of digitized documents is directly related to the quality of the extracted text. Optical Character Recognition (OCR) has reached a point where well-formatted and clean machine- printed documents are easily recognizable by current commercial OCR products; however, older or degraded machine-printed documents present problems to OCR engines resulting in word error rates (WER) that severely limit either automated or manual use of the extracted text. Major archives of historical machine-printed documents are being assembled around the globe, requiring an accurate transcription of the text for the automated creation of descriptive metadata, full-text searching, and information extraction. Given document …

Effects Of Selective Grazing By Microzooplankton On Phytoplankton Composition In A Subtropical Estuary, Amanda Mcgehee

Amanda McGehee

Rates of phytoplankton growth and microzooplankton grazing were measured at two locations within the Bay of St. Louis, MS, over the course of three months to explore the dynamics of the phytoplankton community. Community growth rates were estimated based on the changes in chlorophyll a (chl a) concentration using the dilution technique, (Landry and Hassett, 1982) and a C-specific rate was obtained using chl a labeling (Redalje and Laws, 1981). Concentrations of chl a were determined using high performance liquid chromatography (HPLC) and fluorometry. HPLC was also employed to obtain class specific growth and grazing rates, using either marker pigments …

The Role Of Anharmonicity In Hydrogen-Bonded Systems: The Case Of Water Clusters, Berhane Temelso, George Shields

Berhane Temelso

The nature of vibrational anharmonicity has been examined for the case of small water clusters using second-order vibrational perturbation theory (VPT2) applied on second-order Møller–Plesset perturbation theory (MP2) potential energy surfaces. Using a training set of 16 water clusters (H2O)n=2–6,8,9 with a total of 723 vibrational modes, we determined scaling factors that map the harmonic frequencies onto anharmonic ones. The intermolecular modes were found to be substantially more anharmonic than intramolecular bending and stretching modes. Due to the varying levels of anharmonicity of the intermolecular and intramolecular modes, different frequency scaling factors for each region were necessary to achieve the …

Comparative Analysis Of A Transition Region Bright Point With A Blinker And Coronal Bright Point Using Multiple Eis Emission Lines, N Orange, H Oluseyi, D Chesny, M Patel, K Hesterly, L Preuss, C Neira, Niescja Turner

Niescja E. Turner

Since their discovery 20 year ago, transition region bright points have never been observed spectroscopically. Bright point properties have not been compared with similar transition region and coronal structures. In this work we have investigated three transient quiet Sun brightenings including a transition region bright point (TR BP), a coronal bright point (CBP) and a blinker. We use time-series observations of the extreme-ultraviolet emission lines of a wide range of temperature T(logT=5.3 – 6.4) from the EUV Imaging Spectrometer (EIS) onboard the Hinode satellite. We present the EIS temperature maps and Doppler maps, which are compared with magnetograms from theMichelson …

A Chebyshev Pseudo-Spectral Method To Solve The Space-Time Tempered Fractional Diffusion Equation

Cecile M Piret

Partial Molecular Volumes Of Lipids And Cholesterol., Alexander Greenwood, Stephanie Tristram-Nagle, John Nagle

Prof. Stephanie Tristram-Nagle Ph.D.

Volumetric measurements are reported for fully hydrated lipid/cholesterol bilayer mixtures using the neutral flotation method. Apparent specific volume data were obtained with the lipids DOPC, POPC and DMPC at T=30 degrees Celsius, DPPC at 50 degrees Celsius, and brain sphingomyelin (BSM) at 45 and 24 degrees Celsius for mole fractions of cholesterol x from 0 to 0.5. Unlike previous cholesterol mixture studies, we converted our raw data to partial molecular volume V(L) of the lipid and V(C) of the cholesterol. The partial molecular volumes were constant for POPC and DOPC as x was varied, but had sharp breaks for the …

Structure And Elasticity Of Lipid Membranes With Genistein And Daidzein Bioflavinoids Using X-Ray Scattering And Md Simulations., Mohit Raghunathan, Yuriy Zubovski, Richard Venable, Richard Pastor, John Nagle, Stephanie Tristram-Nagle

Prof. Stephanie Tristram-Nagle Ph.D.

This work reports the effects of the bioflavinoids genistein and daidzein on lipid bilayers as determined by volume measurements, X-ray scattering, and molecular dynamics simulations. The experimental and simulated total molecular volumes were found to be in outstanding agreement with each other before the addition of genistein and daidzein and also after their addition. Both bioflavinoids inserted into the hydrocarbon region of both DOPC and diphytanoylPC near the carbonyls of the lipids and both decreased the bilayer thicknesses. The long axes of both bioflavinoids were oriented nearly parallel to the plane of the bilayer with their carbonyl groups preferentially pointed …

Preparation Of Oriented, Fully Hydrated Lipid Samples For Structure Determination Using X-Ray Scattering., Stephanie Tristram-Nagle

Prof. Stephanie Tristram-Nagle Ph.D.

This chapter describes a method of sample preparation called "the rock and roll method," which is basically a solvent evaporation technique with controlled manual sample movement during evaporation of solvent from lipid/solvent mixtures that produces well-oriented thick stacks of about 2000 lipid bilayers. Many lipid types have been oriented using different solvent mixtures that balance solubilization of the lipid with uniform deposition of the lipid solution onto solid substrates. These well-oriented thick stacks are then ideal samples for collection of both X-ray diffraction data in the gel phase and X-ray diffuse scattering data in the fluid phase of lipids. The …

Effects Of Ether Vs. Ester Linkage On Lipid Bilayer Structure And Water Permeability., S. Deren Guler, D. Dipon Ghosh, Jianjun Pan, John Mathai, Mark Zeidel, John Nagle, Stephanie Tristram-Nagle

Prof. Stephanie Tristram-Nagle Ph.D.

The structure and water permeability of bilayers composed of the ether-linked lipid, dihexadecylphosphatidylcholine (DHPC), were studied and compared with the ester-linked lipid, dipalmitoylphosphaditdylcholine (DPPC). Wide angle X-ray scattering on oriented bilayers in the fluid phase indicate that the area per lipid A is slightly larger for DHPC than for DPPC. Low angle X-ray scattering yields A=65.1A(2) for DHPC at 48 degrees C. LAXS data provide the bending modulus, K(C)=4.2x10(-13)erg, and the Hamaker parameter H=7.2x10(-14)erg for the van der Waals attractive interaction between neighboring bilayers. For the low temperature phases with ordered hydrocarbon chains, we confirm the transition from a tilted …

Structure And Water Permeability Of Fully Hydrated Diphytanoylpc., Stephanie Tristram-Nagle, Dong Joo Kim, Nadia Akhunzada, Norbert Kucerka, John Mathai, John Katsaras, Mark Zeidel, John Nagle

Prof. Stephanie Tristram-Nagle Ph.D.

Diphytanoylphosphatidylcholine (DPhyPC) is a branched chain lipid often used for model membrane studies, including peptide/lipid interactions, ion channels and lipid rafts. This work reports results of volume measurements, water permeability measurements P(f), X-ray scattering from oriented samples, and X-ray and neutron scattering from unilamellar vesicles at T=30 degrees C. We measured the volume/lipid V(L)=1426+/-1A(3). The area/lipid was found to be 80.5+/-1.5A(2) when both X-ray and neutron data were combined with the SDP model analysis (Kucerka, N., Nagle, J.F., Sachs, J.N., Feller, S.E., Pencer, J., Jackson, A., Katsaras, J., 2008. Lipid bilayer structure determined by the simultaneous analysis of neutron and …

Structure Of Lipid Bilayers, John Nagle, Stephanie Tristram-Nagle

Prof. Stephanie Tristram-Nagle Ph.D.

The quantitative experimental uncertainty in the structure of fully hydrated, biologically relevant, fluid (L(alpha)) phase lipid bilayers has been too large to provide a firm base for applications or for comparison with simulations. Many structural methods are reviewed including modern liquid crystallography of lipid bilayers that deals with the fully developed undulation fluctuations that occur in the L(alpha) phase. These fluctuations degrade the higher order diffraction data in a way that, if unrecognized, leads to erroneous conclusions regarding bilayer structure. Diffraction measurements at high instrumental resolution provide a measure of these fluctuations. In addition to providing better structural determination, this …

Molecular Structures Of Fluid Phase Phosphatidylglycerol Bilayers As Determined By Small Angle Neutron And X-Ray Scattering., Jianjun Pan, Frederick Heberle, Stephanie Tristram-Nagle, Michelle Szymanski, Mary Koepfinger, John Katsaras, Norbert Kucerka

Prof. Stephanie Tristram-Nagle Ph.D.

We have determined the molecular structures of commonly used phosphatidylglycerols (PGs) in the commonly accepted biologically relevant fluid phase. This was done by simultaneously analyzing small angle neutron and X-ray scattering data, with the constraint of measured lipid volumes. We report the temperature dependence of bilayer parameters obtained using the one-dimensional scattering density profile model - which was derived from molecular dynamics simulations - including the area per lipid, the overall bilayer thickness, as well as other intrabilayer parameters (e.g., hydrocarbon thickness). Lipid areas are found to be larger than their phosphatidylcholine (PC) counterparts, a result likely due to repulsive …

Lipid Bilayer Structure., John Nagle, Stephanie Tristram-Nagle

Prof. Stephanie Tristram-Nagle Ph.D.

Fluctuations, inherent in flexible and biologically relevant lipid bilayers, make quantitative structure determination challenging. Shortcomings in older methods of structure determination have been realized and new methodologies have been introduced that take fluctuations into account. The large uncertainty in literature values of lipid bilayer structural parameters is being reduced.

Thermodynamic And Structural Characterization Of Amino Acid-Linked Dialkyl Lipids., Stephanie Tristram-Nagle, Ruthven Lewis, Joseph Blickenstaff, Michael Diprima, Bruno Marques, Ronald Mcelhaney, John Nagle, James Schneider

Prof. Stephanie Tristram-Nagle Ph.D.

Using differential scanning calorimetry (DSC), X-ray diffraction (XRD) and Fourier transform infrared spectroscopy (FTIR), we determined some thermodynamic and structural parameters for a series of amino acid-linked dialkyl lipids containing a glutamic acid-succinate headgroup and di-alkyl chains: C12, C14, C16 and C18 in CHES buffer, pH 10. Upon heating, DSC shows that the C12, C14 and annealed C16 lipids undergo a single transition which XRD shows is from a lamellar, chain ordered subgel phase to a fluid phase. This single transition splits into two transitions for C18, and FTIR shows that the upper main transition is predominantly the melting of …

Hiv Fusion Peptide Penetrates, Disorders, And Softens T-Cell Membrane Mimics., Stephanie Tristram-Nagle, Rob Chan, Edgar Kooijman, Pradeep Uppamoochikkal, Wei Qiang, David Weliky, Pradeep Uppamoochikkal

Prof. Stephanie Tristram-Nagle Ph.D.

This work investigates the interaction of N-terminal gp41 fusion peptide (FP) of human immunodeficiency virus type 1 (HIV-1) with model membranes in order to elucidate how FP leads to fusion of HIV and T-cell membranes. FP constructs were (i) wild-type FP23 (23 N-terminal amino acids of gp41), (ii) water-soluble monomeric FP that adds six lysines on the C-terminus of FP23 (FPwsm), and (iii) the C-terminus covalently linked trimeric version (FPtri) of FPwsm. Model membranes were (i) LM3 (a T-cell mimic), (ii) 1,2-dioleoyl-sn-glycero-3-phosphocholine, (iii) 1,2-dioleoyl-sn-glycero-3-phosphocholine/30 mol% cholesterol, (iv) 1,2-dierucoyl-sn-glycero-3-phosphocholine, and (v) 1,2-dierucoyl-sn-glycero-3-phosphocholine/30 mol% cholesterol. Diffuse synchrotron low-angle x-ray scattering from fully …

Orientation Of Tie-Lines In The Phase Diagram Of Dopc/Dppc/Cholesterol Model Biomembranes., Pradeep Uppamoochikkal, Stephanie Tristram-Nagle, John Nagle

Prof. Stephanie Tristram-Nagle Ph.D.

We report the direction of tie-lines of coexisting phases in a ternary diagram of DOPC/DPPC/cholesterol lipid bilayers, which has been a system of interest in the discussion of biological rafts. For coexisting Ld and Lo phases, we find that the orientation angle α of the tie-lines increases as the cholesterol concentration increases and it also increases as temperature increases from T = 15 °C to T = 30 °C. Results at lower cholesterol concentrations support the existence of a different two-phase coexistence region of Ld and So phases and the existence of a three-phase region separating the two two-phase regions. …

Alamethicin Aggregation In Lipid Membranes., Jianjun Pan, Stephanie Tristram-Nagle, John Nagle

Prof. Stephanie Tristram-Nagle Ph.D.

X-ray scattering features induced by aggregates of alamethicin (Alm) were obtained in oriented stacks of model membranes of DOPC(diC18:1PC) and diC22:1PC. The first feature obtained near full hydration was Bragg rod in-plane scattering near 0.11 A(-1) in DOPC and near 0.08 A(-1) in diC22:1PC at a 1:10 Alm:lipid ratio. This feature is interpreted as bundles consisting of n Alm monomers in a barrel-stave configuration surrounding a water pore. Fitting the scattering data to previously published molecular dynamics simulations indicates that the number of peptides per bundle is n = 6 in DOPC and n >or= 9 in diC22:1PC. The larger …

Lipid Bilayers: Thermodynamics, Structure, Fluctuations, And Interactions., Stephanie Tristram-Nagle, John Nagle

Prof. Stephanie Tristram-Nagle Ph.D.

This article, adapted from our acceptance speech of the Avanti Award in Lipids at the 47th Biophysical Society meeting in San Antonio, 2003, summarizes over 30 years of research in the area of lipid bilayers. Beginning with a theoretical model of the phase transition (J.F.N.), we have proceeded experimentally using dilatometry and density centrifugation to study volume, differential scanning calorimetry to study heat capacity, and X-ray scattering techniques to study structure of lipid bilayers as a function of temperature. Electron density profiles of the gel and ripple phases have been obtained as well as profiles from several fluid phase lipids, …

Crac Motif Peptide Of The Hiv-1 Gp41 Protein Thins Sopc Membranes And Interacts With Cholesterol., Alexander Greenwood, Jianjun Pan, Thalia Mills, John Nagle, Richard Epand, Stephanie Tristram-Nagle

Prof. Stephanie Tristram-Nagle Ph.D.

This study uses low-angle (LAXS) and wide-angle (WAXS) X-ray synchrotron scattering, volume measurements and thin layer chromatography to determine the structure and interactions of SOPC, SOPC/cholesterol mixtures, SOPC/peptide and SOPC/cholesterol/peptide mixtures. N-acetyl-LWYIK-amide (LWYIK) represents the naturally-occurring CRAC motif segment in the pretransmembrane region of the gp41 protein of HIV-1, and N-acetyl-IWYIK-amide (IWYIK), an unnatural isomer, is used as a control. Both peptides thin the SOPC bilayer by approximately 3 A, and cause the area/unit cell (peptide+SOPC) to increase by approximately 9 A2 from the area/lipid of SOPC at 30 degrees C (67.0+/-0.9 A2). Model fitting suggests that LWYIK's average position …

Volumetric Stability Of Lipid Bilayers., Kelsey Hallinen, Stephanie Tristram-Nagle, John Nagle

Prof. Stephanie Tristram-Nagle Ph.D.

In agreement with recent reports, a commercial densimeter has yielded a gradual decrease in lipid molecular volume of DPPC multilamellar vesicle dispersions in the gel phase upon repeated thermal cycling between 10 °C and 50 °C. The considerable size of this decrease would have significant implications for the physical chemistry of biomembranes. In contrast, neutral buoyancy measurements performed with similar thermal cycling indicate no gradual change in lipid volume in the gel phase at 20 °C. Remixing the lipid in the densimeter shows that the apparent volume decrease is an artifact. We conclude that gel phase DPPC bilayers exist in …

Α-Synuclein Induces Both Positive Mean Curvature And Negative Gaussian Curvature In Membranes., Anthony Braun, Eva Sevcsik, Pamela Chin, Elizabeth Rhoades, Stephanie Tristram-Nagle, Jonathan Sachs

Prof. Stephanie Tristram-Nagle Ph.D.

Using a combination of X-ray scattering, fluorescence correlation spectroscopy, coarse-grained molecular dynamics (MD) simulations and potential of mean force calculations, we have explored the membrane remodeling effects of monomeric α-synuclein (αS). Our initial findings from multiple approaches are that αS (1) causes a significant thinning of the bilayer and (2) stabilizes positive mean curvature, such that the maximum principle curvature matches that of synaptic vesicles, αS-induced tubules, and the synthetic lipid vesicles to which the protein binds most tightly. This suggests that αS binding to synaptic vesicles likely stabilizes their intrinsic curvature. We then show that αS induces local negative …