bluuebunny/crossref_metadata_2025 huggingface dataset:
Basic building units and properties of a fluorescence single plane illumination microscope
Authors: Greger K. , Swoger J. , Stelzer E. H. K.
Published: March 2007

The critical issue of all fluorescence microscopes is the efficient use of the fluorophores, i.e., to detect as many photons from the excited fluorophores as possible, as well as to excite only the fluorophores that are in focus. This issue is addressed in EMBL’s implementation of a light sheet based microscope [single plane illumination microscope (SPIM)], which illuminates only the fluorophores in the focal plane of the detection objective lens. The light sheet is a beam that is collimated in one and focused in the other direction. Since no fluorophores are excited outside the detectors’ focal plane, the method also provides intrinsic optical sectioning. The total number of observable time points can be improved by several orders of magnitude when compared to a confocal fluorescence microscope. The actual improvement factor depends on the number of planes acquired and required to achieve a certain signal to noise ratio. A SPIM consists of five basic units, which address (1) light detection, (2) illumination of the specimen, (3) generation of an appropriate beam of light, (4) translation and rotation of the specimen, and finally (5) control of different mechanical and electronic parts, data collection, and postprocessing of the data. We first describe the basic building units of EMBL’s SPIM and its most relevant properties. We then cover the basic principles underlying this instrument and its unique properties such as the efficient usage of the fluorophores, the reduced photo toxic effects, the true optical sectioning capability, and the excellent axial resolution. We also discuss how an isotropic resolution can be achieved. The optical setup, the control hardware, and the control scheme are explained in detail. We also describe some less obvious refinements of the basic setup that result in an improved performance. The properties of the instrument are demonstrated by images of biological samples that were imaged with one of EMBL’s SPIMs.
Gaussian-4 theory
Authors: Curtiss Larry A. , Redfern Paul C. , Raghavachari Krishnan
Published: March 2007

The Gaussian-4 theory (G4 theory) for the calculation of energies of compounds containing first- (Li–F), second- (Na–Cl), and third-row main group (K, Ca, and Ga–Kr) atoms is presented. This theoretical procedure is the fourth in the Gaussian-n series of quantum chemical methods based on a sequence of single point energy calculations. The G4 theory modifies the Gaussian-3 (G3) theory in five ways. First, an extrapolation procedure is used to obtain the Hartree-Fock limit for inclusion in the total energy calculation. Second, the d-polarization sets are increased to 3d on the first-row atoms and to 4d on the second-row atoms, with reoptimization of the exponents for the latter. Third, the QCISD(T) method is replaced by the CCSD(T) method for the highest level of correlation treatment. Fourth, optimized geometries and zero-point energies are obtained with the B3LYP density functional. Fifth, two new higher level corrections are added to account for deficiencies in the energy calculations. The new method is assessed on the 454 experimental energies in the G3∕05 test set [L. A. Curtiss, P. C. Redfern, and K. Raghavachari, J. Chem. Phys. 123, 124107 (2005)], and the average absolute deviation from experiment shows significant improvement from 1.13kcal∕mol (G3 theory) to 0.83kcal∕mol (G4 theory). The largest improvement is found for 79 nonhydrogen systems (2.10kcal∕mol for G3 versus 1.13kcal∕mol for G4). The contributions of the new features to this improvement are analyzed and the performance on different types of energies is discussed.
Electro-osmotic equilibria for a semipermeable shell filled with a solution of polyions
Authors: Tsekov Roumen , Vinogradova Olga I.
Published: March 2007

The authors study theoretically the electrostatic equilibria for a shell filled with a suspension of polyions (e.g., colloids, polyelectrolytes, etc.) and immersed in an infinite salt-free reservoir. The shell is treated as impermeable for polyions, but allowing free diffusion of counterions. From the solution of the linearized Poisson-Boltzmann equation we obtain the distribution of the potential and concentration profiles for polyions. The authors then derive explicit formulas for the excess electro-osmotic pressure of a polyion solution exerted by the shell. This is shown to be due to a concentration of polyions at the inner shell boundary and can be very different from the pressure of a corresponding bulk polyion solution.
Fluctuation-dissipation theorems in an expanding universe
Authors: Chevalier C. , Debbasch F.
Published: March 2007

The recently constructed minimal extension of the special relativistic Ornstein-Uhlenbeck process to curved space-time cannot be used to model realistically diffusions on cosmological scales because it does not take into account the evolution of the thermodynamical state of the matter with cosmological time. We therefore introduce a new class of non-minimal extensions characterized by time-dependent friction and noise coefficients. These new processes admit time-dependent Jüttner distributions as possible measures in momentum space; associated fluctuation-dissipation theorems are also proved and discussed.
Theoretical prediction of multiple fluid-fluid transitions in monocomponent fluids
Authors: Cervantes L. A. , Benavides A. L. , del Río F.
Published: March 2007

The authors use the analytical equation of state obtained by the discrete perturbation theory [A. L. Benavides and A. Gil-Villegas, Mol. Phys. 97, 1225 (1999)] to study the phase diagram of fluids with discrete spherical potentials formed by a repulsive square-shoulder plus an attractive square-well interaction (SS+SW). This interaction is characterized by the usual energy and size parameters plus three dimensionless parameters: two of them measuring the widths of the SS and the SW and the third the relative height of the SS. The matter of interest is that, for certain values of the interaction parameters, the SS+SW systems exhibit more than one first-order fluid-fluid transition. The evidence that several real substances (such as water, phosphorus, carbon, and silica, among others) exhibit an extra liquid-liquid transition has drawn interest into the study of interactions responsible for this behavior. The simple SS+SW fluid is one of the systems that, in spite of being spherically symmetric, shows multiple fluid-fluid transitions. In this work the authors investigate systematically the effect on the phase diagram of varying the interaction parameters. The use of an analytical free-energy equation gives a clear thermodynamic picture of the emergence of different types of critical points, throwing new light on the phase behavior of these fluids and thus clarifying previous results obtained by other techniques. The interplay of attractive and repulsive forces with several scale lengths produces very rich phase diagrams, including cases with three critical points. The region of the interaction-parameter space where multiple critical points appear is mapped for various families of interactions.
Stability of separation-shifted Lennard-Jones fluids
Authors: Heyes D. M. , Cass M. J. , Rickayzen G.
Published: March 2007

Ruelle’s thermodynamic stability criteria are applied to the separation-shifted Lennard-Jones (SSLJ) fluid, and the domain of its parameters giving “normal” thermodynamic stability in the thermodynamic limit is established. Fluids interacting with the SSLJ both conforming to and breaking these stability criteria were modeled using molecular dynamics computer simulation. For system sizes typical of most simulations, the transition between the two patterns of behavior was found to be smeared out over a range of parameter values. Thermodynamic instability is marked by a collapse of the system into a small “ball” or volume. The collapsed state nevertheless has some statistical mechanical properties typical of systems exhibiting normal thermodynamics (e.g., the kinetic and configurational temperatures were found to be the same in the collapsed state within statistics).
Modeling the selective partitioning of cations into negatively charged nanopores in water
Authors: Yang Lu , Garde Shekhar
Published: March 2007

Partitioning and transport of water and small solutes into and through nanopores are important to a variety of chemical and biological processes and applications. Here we study water structure in negatively charged model cylindrical [carbon nanotube (CNT)-like] nanopores, as well as the partitioning of positive ions of increasing size (Na+, K+, and Cs+) into the pore interior using extensive molecular dynamics simulations. Despite the simplicity of the simulation system—containing a short CNT-like nanopore in water carrying a uniformly distributed charge of qpore=−ne surrounded by n (=0,…,8) cations, making the overall system charge neutral—the results provide new and useful insights on both the pore hydration and ion partitioning. For n=0, that is, for a neutral nanopore, water molecules partition into the pore and form single-file hydrogen-bonded wire spanning the pore length. With increasing n, water molecules enter the pore from both ends with preferred orientations, resulting in a mutual repulsion between oriented water molecules at the pore center and creating a cavity-like low density region at the center. For low negative charge densities on the pore, the driving force for partitioning of positive ions into the pore is weak, and no partitioning is observed. Increasing the pore charge gradually leads to partitioning of positive ions into the pore. Interestingly, over a range of intermediate negative charge densities, nanopores display both thermodynamic as well as kinetic selectivity toward partitioning of the larger K+ and Cs+ ions into their interior over the smaller Na+ ions. Specifically, the driving force is in the order K+>Cs+>Na+, and K+ and Cs+ ions enter the pore much more rapidly than Na+ ions. At higher charge densities, the driving force for partitioning increases for all cations—it is highest for K+ ions—and becomes similar for Na+ and Cs+ ions. The variation of thermodynamic driving force and the average partitioning time with the pore charge density together suggest the presence of free energy barriers in the partitioning process. We discuss the role of ion hydration in the bulk and in the pore interior as well as of the pore hydration in determining the barrier heights for ion partitioning and the observed thermodynamic and kinetic selectivities.
Probing of a surface plasma wave by an obliquely incident laser on the metal surface
Authors: Singh D. B. , Kumar Gagan , Tripathi V. K.
Published: March 2007

A surface plasma wave (SPW) of frequency ω1 and wave number k1 propagating along a metal-free space boundary exerts a ponderomotive force on the free electrons, creating an electron density perturbation at frequency 2ω1. When a laser of frequency ω2 and wave number k2 is incident at a suitable angle on the metal surface, it gives rise to the oscillatory velocity of electrons at frequency ω2. This oscillatory velocity couples with the density perturbation to generate a nonlinear current at frequency 2ω1+ω2. The nonlinear current derives a radiating wave under suitable conditions. By measuring the amplitude of the radiating wave, the SPW field can be probed.
Room-temperature observation of a Coulomb blockade phenomenon in aluminum nanodots fabricated by an electrochemical process
Authors: Kimura Yasuo , Itoh Kazumasa , Yamaguchi Ryo-taro , Ishibashi Ken-ichi , Itaya Kingo , Niwano Michio
Published: March 2007

An aluminum nanodot was self-organized between two electrodes using the anodization process of an aluminum microelectrode of 3μm in width. The authors observed a clear Coulomb staircase with a very large Coulomb energy of about 2eV at room temperature. This very large Coulomb energy is attributed to the device structure which depends strongly on the aluminum nanodot formation mechanism. The authors’ results indicate that a single electron transistor operating at room temperature can be fabricated at an appropriate position using both bottom-up and top-down processes.
Mesoscopic restructuring and mass transport of metal atoms during reduction of the Ag(111)-p(4×4)-O surface with CO
Authors: Klust Andreas , Madix Robert J.
Published: March 2007

The reduction of the Ag(111)-p(4×4)-O surface oxide with CO was used to study the restructuring of the surface during reaction. Scanning tunneling microscopy images taken during the reaction show the formation of Ag islands and pits within the reacted areas surrounded by unreacted p(4×4)-O. The number of Ag adatoms incorporated in the Ag(111)-p(4×4)-O structure was determined to be 12 from the areas of these islands and pits. The evolution of the reacted area with exposure to CO indicates that direct reaction with the Ag(111)-p(4×4)-O is not preferred, but that the boundary between the p(4×4) and the freshly created Ag(111) surface is the source of the reactive oxygen.
Development of a wavelength-stabilized distributed Bragg reflector laser diode to the Cs-D2 line for field use in accurate geophysical measurements
Authors: Hori Teruhito , Araya Akito , Moriwaki Shigenori , Mio Norikatsu
Published: March 2007

We have developed a wavelength-stabilized laser diode (LD) for geophysical measurement devices, which benefit from the uniformity of laser light. Regarding this purpose, a system that has such characteristics as low power consumption, sturdiness against mechanical disturbances, and a long life with long-term frequency stability is especially required. Therefore, we adopt as the light source a distributed Bragg reflector (DBR) LD because it has various advantages concerning such properties. This paper describes the durable and compact wavelength-stabilized laser system. Since our DBR-LD oscillates at 852 nm, we selected the Cs-D2 line (6 S21∕2−6 P23∕2 transition) as a frequency reference to obtain a long-term stability in wavelength. Stabilization is performed by a feedback system using a modulation transfer (MT) method, which is a kind of Doppler-free saturated absorption spectroscopy, to acquire a saturated absorption signal with a high signal-to-noise ratio. Using this system, we could continuously lock the laser frequency to the hyperfine component of the Cs-D2 line for more than one week. By an Allan standard deviation measurement, the uncertainty of the stabilized laser frequency was found to be better than 1×10−10 (<40 kHz) in a Gatetime region longer than 100 s.
Inertial range scaling of scalar flux spectra in uniformly sheared turbulence
Authors: Bos W. J. T. , Bertoglio J.-P.
Published: March 2007

A model based on two-point closure theory of turbulence is proposed and applied to study the Reynolds number dependency of the scalar flux spectra in homogeneous shear flow with a cross-stream uniform scalar gradient. For the cross-stream scalar flux, in the inertial range the spectral behavior agrees with classical predictions and measurements. The streamwise scalar flux is found to be in good agreement with the results of atmospheric measurements. However, both the model results and the atmospheric measurements disagree with classical predictions. A detailed analysis of the different terms in the evolution equation for the streamwise scalar flux spectrum shows that nonlinear contributions are governing the inertial subrange of this spectrum and that these contributions are relatively more important than for the cross-stream flux. A new expression for the scalar flux spectra is proposed. It allows us to unify the description of the components in one single expression, leading to a classical K−7∕3 inertial range for the cross-stream component and to a new K−23∕9 scaling for the streamwise component that agrees better with atmospheric measurements than the K−3 prediction of J. C. Wyngaard and O. R. Coté [Quart. J. R. Met. Soc. 98, 590 (1972)].
Ionization front in a high-current gas discharge
Authors: Choueiri Edgar Y. , Randolph Thomas M.
Published: March 2007

Spectroscopic measurements of ion/neutral density ratio profiles are made inside the high-current, low-pressure discharge of a coaxial magnetoplasmadynamic thruster and show the existence of a thin ionization front, upstream in the discharge, that effectively ionizes the incoming gas to ionization levels above 50%. The measurements allow an estimate of the width of this ionization front to be on the order of a few millimeters. Due to the known existence of microturbulence in the plasma, which can produce suprathermal electrons, an explanation of the measurements based on the existence of a suprathermal tail in the electron energy distribution function is sought. A theoretical model for the width of the ionization front is combined with a multilevel excitation model for argon and shows that a Maxwellian electron distribution function cannot account for the small length scale of the ionization front, and that the latter is more consistent with an electron distribution function having a suprathermal population, the magnitude of which is estimated by comparing the model to the experiments.
Calculation of highly excited vibrational states using a Richardson-Leja-Davidson scheme
Authors: Karlsson Hans O.
Published: March 2007

An efficient computational scheme for calculating highly excited vibrational eigenstates is proposed, combining a Richardson-Leja spectral filter with a novel version of the Davidson method [J. Comput. Phys. 17, 87 (1975)]. Highly excited eigenstates of the Rb2 and H2O molecules are computed to test and verify the method. On the average less than 2.5 outer recursions per eigenstate are needed. For each outer Davidson recursion, less than 20 inner filter recursions per eigenstate are needed on the average.
A methodology for measuring in situ lattice strain of bulk polycrystalline material under cyclic load
Authors: Park Jun-Sang , Revesz Peter , Kazimirov Alexander , Miller Matthew P.
Published: March 2007

The material response of polycrystalline materials under cyclic loading is not fully understood. Even during uniaxial loading, individual grains embedded within the polycrystalline material can experience complicated strain histories. By quantifying the deformation state at the crystal level, we can begin to understand the conditions that lead to fatigue failure. An in situ powder diffraction method was developed and employed at the Cornell High Energy Synchrotron Source to measure the aggregate crystal response at various points in a material’s life using synchrotron x ray. A set of experiments was conducted using a load frame capable of exerting cyclic uniaxial loads on a specimen. A high speed x-ray shutter was developed to synchronize the x-ray beam and the loading cycle. Using the high speed shutter, the evolution of the lattice strains for the families of crystallographic planes was measured while the aggregate was under cyclic uniaxial loading, thus monitoring a live evolution of lattice strain in a cyclically loaded specimen. The methodology is demonstrated using uniaxial cyclic specimens machined from oxygen free conductivity (OFHC) copper sheet.
Ultrafast pulse radiolysis using a terawatt laser wakefield accelerator
Authors: Oulianov Dmitri A. , Crowell Robert A. , Gosztola David J. , Shkrob Ilya A. , Korovyanko Oleg J. , Rey-de-Castro Roberto C.
Published: March 2007

We report ultrafast pulse radiolysis transient absorption (TA) spectroscopy measurements from the Terawatt Ultrafast High Field Facility (TUHFF) at Argonne National Laboratory. TUHFF houses a 20 TW Ti:sapphire laser system that generates 2.5 nC subpicosecond pulses of multi-mega-electron-volt electrons at 10 Hz using laser wakefield acceleration. The system has been specifically optimized for kinetic TA measurements in a pump-probe fashion. This requires averaging over many shots which necessitates stable, reliable generation of electron pulses. The latter were used to generate excess electrons in pulse radiolysis of liquid water and concentrated solutions of perchloric acid. The hydronium ions in the acidic solutions react with the hydrated electrons resulting in the rapid decay of the transient absorbance at 800 nm on the picosecond time scale. Normalization of the TA signal leads to an improvement in the signal to noise ratio by a factor of 5 to 6. Due the pointing instability of the laser this improvement was limited to a 5 to 10 min acquisition period, requiring periodic recalibration and realignment. Time resolution, defined by the rise time of TA signal from hydrated electron in pulse radiolysis of liquid water, of a few picoseconds, has been demonstrated. The current time resolution is determined primarily by the physical dimensions of the sample and the detection sensitivity. Subpicosecond time resolution can be achieved by using thinner samples, more sensitive detection techniques, and improved electron beam quality.
Complex photonic band diagrams for finite-size photonic crystals with arbitrary defects
Authors: Wu Jiu Hui , Liu A. Q. , Ang L. K. , Cheng T. H. , Xu K. , Wu J. , Lin J. T.
Published: March 2007

Based on an effective propagation constant and a frequency-dependent dielectric constant, the plane wave method is extended to calculate the complex photonic band diagram and the density of states for electromagnetic waves propagating in a two-dimensional finite structure with nonoverlapping dielectric cylinders of arbitrary radii, which may be randomly embedded in a dielectric matrix. The effective propagation constant is obtained by using the Twersky formula [J. Math. Phys. 3, 700 (1962)] and the scattering matrix method. A case study shows that an embedded defect with optimal radius in a finite photonic crystal can increase the first photonic band gap as compared to the similar structure without the defect. This work is expected to provide a useful tool in determining the photonic properties of a disorder dielectric medium with arbitrary embedded nanoparticles and nanowires.
Chirp in a transistor laser: Franz-Keldysh reduction of the linewidth enhancement
Authors: Walter G. , James A. , Holonyak N. , Feng M.
Published: March 2007

A quantum well (QW) transistor laser with the capability of high current density, a collector current ensuring minimal operational change (beyond laser threshold) in base QW carrier population, a favorable long narrow emitter laser geometry, and built-in base-collector Franz-Keldysh absorption (with IE+IB+IC=0), is measured for chirp-related behavior. A relatively low transistor laser linewidth enhancement factor αe∼0.7 is obtained despite the resolution limitations of the measurement apparatus.
Thin strained layers inserted in compositionally graded SiGe buffers and their effects on strain relaxation and dislocation
Authors: Park J.-S. , Curtin M. , Bai J. , Bengtson S. , Carroll M. , Lochtefeld A.
Published: March 2007

The effect of inserting compressively or tensely strained layers into compositionally graded SiGe buffers on strain relaxation and threading dislocation density (TDD) was investigated. The samples having compressively strained layers showed lower TDD and more enhanced relaxation than those having tensely strained layers. In addition, dislocations were accumulated at the top part of the tensely strained layers within the graded buffers, while no accumulation was found at the compressively strained layers. These results might be due to the effect of strain from the thin inserted layers on the dislocation interactions in the compressively strained graded buffers.
Deep level transient spectroscopy of SnO2-based varistors
Authors: Fan Jiwei , Freer Robert
Published: March 2007

Deep level transient spectroscopy measurements were performed to investigate the effect of Nb2O5 and Cr2O3 on the electronic states of SnO2-based varistors. Two electron traps, Ec−0.30(±0.01)eV and Ec−0.69(±0.03)eV, were identified in both SnO2–CoO–Nb2O5 and SnO2–CoO–Nb2O5–Cr2O3 varistors. These two traps could be associated with the second ionization energy of oxygen vacancies VO∙∙ or impurities on host lattice site CoSn′ or NbSn∙. The two trap levels are not associated with chromium doping, since Cr2O3 doping only changes the donor density and trap densities.
Incorporation and drift of hydrogen at low temperatures in ZnO
Authors: Wang Y. L. , Ren F. , Kim H. S. , Pearton S. J. , Norton D. P.
Published: March 2007

Hydrogen is found to diffuse rapidly into ZnO from either a molecular (D2) gas source or from a D2 plasma at temperatures in the range of 100–200°C. In samples deuterated from a plasma excited at 13.56MHz, the incorporated deuterium concentration is saturated at 6×1018cm−3 throughout the entire 1.2μm epi-ZnO thickness at 250°C. This deuterium is stable against reverse bias application at 25°C for 24h. By sharp contrast, deuterium incorporated from exposure to D2 gas at 100°C can be entirely removed by reverse (negative) bias application in a diode structure using a Pt contact on the n-type ZnO. These results are consistent with the state of the deuterium in the ZnO being a function of both the concentration and the flux during incorporation. At low concentrations, the deuterium is likely to be in a positively charged atomic form or bound in defects that are readily dissociated by an electric field, while at higher concentrations the deuterium may be in neutral states such as D2 or OH complexes.
Scaling of number, size, and metabolic rate of cells with body size in mammals
Authors: Savage Van M. , Allen Andrew P. , Brown James H. , Gillooly James F. , Herman Alexander B. , Woodruff William H. , West Geoffrey B.
Published: March 2007

The size and metabolic rate of cells affect processes from the molecular to the organismal level. We present a quantitative, theoretical framework for studying relationships among cell volume, cellular metabolic rate, body size, and whole-organism metabolic rate that helps reveal the feedback between these levels of organization. We use this framework to show that average cell volume and average cellular metabolic rate cannot both remain constant with changes in body size because of the well known body-size dependence of whole-organism metabolic rate. Based on empirical data compiled for 18 cell types in mammals, we find that many cell types, including erythrocytes, hepatocytes, fibroblasts, and epithelial cells, follow a strategy in which cellular metabolic rate is body size dependent and cell volume is body size invariant. We suggest that this scaling holds for all quickly dividing cells, and conversely, that slowly dividing cells are expected to follow a strategy in which cell volume is body size dependent and cellular metabolic rate is roughly invariant with body size. Data for slowly dividing neurons and adipocytes show that cell volume does indeed scale with body size. From these results, we argue that the particular strategy followed depends on the structural and functional properties of the cell type. We also discuss consequences of these two strategies for cell number and capillary densities. Our results and conceptual framework emphasize fundamental constraints that link the structure and function of cells to that of whole organisms.
A Bipartite Signal Regulates the Faithful Delivery of Apical Domain Marker Podocalyxin/Gp135
Authors: Yu Chun-Ying , Chen Jen-Yau , Lin Yu-Yu , Shen Kuo-Fang , Lin Wei-Ling , Chien Chung-Liang , ter Beest Martin B.A. , Jou Tzuu-Shuh
Published: March 2007

Podocalyxin/Gp135 was recently demonstrated to participate in the formation of a preapical complex to set up initial polarity in MDCK cells, a function presumably depending on the apical targeting of Gp135. We show that correct apical sorting of Gp135 depends on a bipartite signal composed of an extracellular O-glycosylation–rich region and the intracellular PDZ domain–binding motif. The function of this PDZ-binding motif could be substituted with a fusion construct of Gp135 with Ezrin-binding phosphoprotein 50 (EBP50). In accordance with this observation, EBP50 binds to newly synthesized Gp135 at the Golgi apparatus and facilitates oligomerization and sorting of Gp135 into a clustering complex. A defective connection between Gp135 and EBP50 or EBP50 knockdown results in a delayed exit from the detergent-resistant microdomain, failure of oligomerization, and basolateral missorting of Gp135. Furthermore, the basolaterally missorted EBP50-binding defective mutant of Gp135 was rapidly retrieved via a PKC-dependent mechanism. According to these findings, we propose a model by which a highly negative charged transmembrane protein could be packed into an apical sorting platform with the aid of its cytoplasmic partner EBP50.
Troyer Syndrome Protein Spartin Is Mono-Ubiquitinated and Functions in EGF Receptor Trafficking
Authors: Bakowska Joanna C. , Jupille Henri , Fatheddin Parvin , Puertollano Rosa , Blackstone Craig
Published: March 2007

Troyer syndrome is an autosomal recessive hereditary spastic paraplegia caused by mutation in the spartin (SPG20) gene, which encodes a widely expressed protein of unknown function. This mutation results in premature protein truncation and thus might signify a loss-of-function disease mechanism. In this study, we have found that spartin is mono-ubiquitinated and functions in degradation of the epidermal growth factor receptor (EGFR). Upon EGF stimulation, spartin translocates from the cytoplasm to the plasma membrane and colocalizes with internalized EGF-Alexa. Knockdown of spartin by small interfering RNA decreases the rate of EGFR degradation and also affects EGFR internalization, recycling, or both. Furthermore, overexpression of spartin results in a prominent decrease in EGFR degradation. Taken together, our data suggest that spartin is involved in the intracellular trafficking of EGFR and that impaired endocytosis may underlie the pathogenesis of Troyer syndrome.
Direct Binding to Rsp5p Regulates Ubiquitination-independent Vacuolar Transport of Sna3p
Authors: Watson Hadiya , Bonifacino Juan S.
Published: March 2007

The sorting of integral membrane proteins such as carboxypeptidase S (Cps1p) into the luminal vesicles of multivesicular bodies (MVBs) in Saccharomyces cerevisiae requires ubiquitination of their cytosolic domains by the ubiquitin ligases Rsp5p and/or Tul1p. An exception is Sna3p, which does not require ubiquitination for entry into MVBs. The mechanism underlying this ubiquitination-independent MVB sorting pathway has not yet been characterized. Here, we show that Sna3p sorting into the MVB pathway depends on a direct interaction between a PPAY motif within its C-terminal cytosolic tail and the WW domains of Rsp5p. Disruption of this interaction inhibits vacuolar targeting of Sna3p and causes its accumulation in a compartment that overlaps only partially with MVBs. Surprisingly, Sna3p does require a functional ubiquitin-ligase HECT domain within Rsp5p; however, the dependence of Sna3p on HECT domain activity is distinct from that of Cps1p. Last, we show that Sna3p requires neither Tul1p nor the transmembrane adaptor protein Bsd2p for its MVB sorting. Our data demonstrate that Sna3p follows a novel ubiquitination-independent, but Rsp5p-mediated, sorting pathway to the vacuole.
The MAGUK Protein MPP7 Binds to the Polarity Protein hDlg1 and Facilitates Epithelial Tight Junction Formation
Authors: Stucke Volker M. , Timmerman Evy , Vandekerckhove Joel , Gevaert Kris , Hall Alan
Published: March 2007

Three groups of evolutionarily conserved proteins have been implicated in the establishment of epithelial cell polarity: the apically-localized proteins of the Par (Par3-Par6-aPKC-Cdc42) and Crumbs groups (Crb3-PALS1-PATJ) and the basolaterally localized proteins of the Dlg group (Dlg1-Scribble-Lgl). During epithelial morphogenesis, these proteins participate in a complex network of interdependent interactions that define the position and functional organization of adherens junctions and tight junctions. However, the biochemical pathways through which they control polarity are poorly understood. In this study, we identify an interaction between endogenous hDlg1 and MPP7, a previously uncharacterized MAGUK-p55 subfamily member. We find that MPP7 targets to the lateral surface of epithelial cells via its L27N domain, through an interaction with hDlg1. Loss of either hDlg1 or MPP7 from epithelial Caco-2 cells results in a significant defect in the assembly and maintenance of functional tight junctions. We conclude that the formation of a complex between hDlg1 and MPP7 promotes epithelial cell polarity and tight junction formation.
The Bacterial Two-Hybrid System as a Reporter System for Analyzing Protein-Protein Interactions
Authors: Giesecke Astrid V. , Joung J. Keith
Published: March 2007

INTRODUCTION

The bacterial two-hybrid system provides a convenient method for rapidly and quantitatively assessing the effect of specific mutations on protein-protein interactions. It is well suited to analyzing series of mutants (e.g., those generated from alanine scanning experiments or comprehensive mutagenesis of DNA-binding sites). The Escherichia coli lacZ gene (encoding β-galactosidase) serves as a reporter gene because its expression is easily measured using a quantitative assay. This protocol describes methods for assessing the interaction of hypothetical proteins X and Y in the bacterial two-hybrid system. Plasmids expressing the hybrid proteins DBD-X and RNAP-Y are constructed. Protein X can be fused either to a monomeric DBD (the zinc finger domain from the Zif268 protein) or to the dimeric bacteriophage λcI repressor protein. Protein Y can be fused either to the monomeric E. coli RNAP ω-subunit or to the dimeric E. coli RNAP α. Plasmids encoding these hybrid proteins are used to transform an appropriate lacZ reporter strain. Quantitative β-galactosidase assays are performed to measure the effect of the two-hybrid proteins on reporter gene expression. Following successful demonstration of X-Y interaction in this system, these protocols can be used to assess the effects of mutations on the interaction of X and Y.
Treatment of cryptosporidiosis in immunocompromised individuals: systematic review and meta‐analysis
Authors: Abubakar I. , Aliyu S. H. , Arumugam C. , Usman N. K. , Hunter P. R.
Published: March 2007

Cryptosporidium is a common cause of gastroenteritis and is associated with severe life‐threatening illness among immunocompromised individuals. This review aimed to assess the efficacy of interventions for the treatment and prevention of cryptosporidiosis among immunocompromised patients. A search of Medline, Embase and other electronic databases was carried out up to August 2005. Two reviewers independently extracted data and assessed study quality. The relative risk for each intervention was calculated. Seven trials involving 169 participants were included. Nitazoxanide and paramomycin were associated with a relative risk (RR) of reduction in the duration and frequency of diarrhoea of 0.83 [95% confidence interval (CI) 0.36, 1.94] and 0.74 (95% CI 0.42, 1.31), respectively, showing no evidence of effectiveness. Nitazoxanide led to significant evidence of oocyst clearance compared with placebo with a RR of 0.52 (95% CI 0.30, 0.91). The effect was not significant for HIV‐seropositive participants (RR 0.71, 95% CI 0.36, 1.37). HIV‐seronegative participants on nitazoxanide had a significantly higher relative risk of achieving parasitological clearance of 0.26 (95% CI 0.09, 0.80) based on a single study. No other intervention was associated with either a reduction in diarrhoea, mortality or a significant parasitological response. This review confirms the absence of evidence for effective agents in the management of cryptosporidiosis. The results indicate that nitaxozanide reduces load of parasites and may be useful in immunocompetent individuals. The absence of effective therapy highlights the importance of preventive interventions in this group of patients.
Factors for graft‐versus‐host disease after donor lymphocyte infusions with an escalating dose regimen: lack of association with cell dose
Authors: Fozza C. , Szydlo R.M. , Abdel‐Rehim M.M. , Nadal E. , Goldman J.M. , Apperley J.F. , Dazzi F.
Published: March 2007

We investigated the risk factors for graft‐versus‐host disease (GVHD) in 82 patients treated with donor lymphocyte infusions (DLI) using an escalating dose regimen for chronic myeloid leukaemia in relapse following conventional allografting. Two factors emerged as predictors of both acute and chronic GVHD: the infusion of male recipients with lymphocytes from a female donor and the interval between transplant and last DLI, but only the first remained significant at multivariate analysis. Surprisingly, lymphocyte dose did not influence the incidence of GVHD. Our results suggest that DLI can be given in large cell doses without increasing the risk of GVHD.
Factor VIIa analogue (V158D/E296V/M298Q‐FVIIa) normalises clot formation in whole blood from patients with severe haemophilia A
Authors: Sørensen Benny , Persson Egon , Ingerslev Jørgen
Published: March 2007

This study evaluated and compared the haemostatic potential of a recombinant factor VIIa (rFVIIa) analogue (V158D/E296V/M298Q‐FVIIa, NN1731, Novo Nordisk, Denmark) with rFVIIa (NovoSeven®, Novo Nordisk). In vitro studies were performed using freshly drawn whole blood (WB) from 14 patients with severe haemophilia A and two patients with inhibitory antibodies to FVIII, comparing NN1731 and rFVIIa against a buffer control. Fourteen healthy males served as controls. Dynamic WB coagulation profiles were recorded, quantitatively illustrating the initiation [clotting time = CT (s)], propagation [maximum velocity = MaxVel (mm*100/s)] and termination [maximum clot firmness = MCF (mm*100)] as determined by thromboelastography with minute amounts of tissue factor (TF, Innovin®– final dilution 1:50 000, c. 0·12 pM) serving as activator. WB clot stability was assessed using a separate set‐up including TF plus tissue plasminogen activator (final concentration 2 nmol/l), evaluating the MCF as well as the area under the elasticity curve (AUEC) after 60 min (mm*100*s). NN1731 shortened the CT more markedly than rFVIIa. At the dose tested, NN1731 even shortened CT in haemophilia below the value of healthy males. NN1731 accelerated MaxVel giving a value indistinguishable from that in healthy males. Furthermore, NN1731 increased clot stability more markedly than rFVIIa. Altogether, these in vitro studies on WB revealed a favourable haemostatic potential of NN1731 compared with rFVIIa in severe haemophilia A, both in the absence and presence of enhanced fibrinolytic activity.
Linking ecological theory with stream restoration
Authors: LAKE P. S. , BOND N. , REICH P.
Published: March 2007

1. Faced with widespread degradation of riverine ecosystems, stream restoration has greatly increased. Such restoration is rarely planned and executed with inputs from ecological theory. In this paper, we seek to identify principles from ecological theory that have been, or could be, used to guide stream restoration.

2. In attempts to re‐establish populations, knowledge of the species’ life history, habitat template and spatio‐temporal scope is critical. In many cases dispersal will be a critical process in maintaining viable populations at the landscape scale, and special attention should be given to the unique geometry of stream systems

3. One way by which organisms survive natural disturbances is by the use of refugia, many forms of which may have been lost with degradation. Restoring refugia may therefore be critical to survival of target populations, particularly in facilitating resilience to ongoing anthropogenic disturbance regimes.

4. Restoring connectivity, especially longitudinal connectivity, has been a major restoration goal. In restoring lateral connectivity there has been an increasing awareness of the riparian zone as a critical transition zone between streams and their catchments.

5. Increased knowledge of food web structure – bottom‐up versus top‐down control, trophic cascades and subsidies – are yet to be applied to stream restoration efforts.

6. In restoration, species are drawn from the regional species pool. Having overcome dispersal and environmental constraints (filters), species persistence may be governed by local internal dynamics, which are referred to as assembly rules.

7. While restoration projects often define goals and endpoints, the succession pathways and mechanisms (e.g. facilitation) by which these may be achieved are rarely considered. This occurs in spite of a large of body of general theory on which to draw.

8. Stream restoration has neglected ecosystem processes. The concept that increasing biodiversity increases ecosystem functioning is very relevant to stream restoration. Whether biodiversity affects ecosystem processes, such as decomposition, in streams is equivocal.

9. Considering the spatial scale of restoration projects is critical to success. Success is more likely with large‐scale projects, but they will often be infeasible in terms of the available resources and conflicts of interest. Small‐scale restoration may remedy specific problems. In general, restoration should occur at the appropriate spatial scale such that restoration is not reversed by the prevailing disturbance regime.

10. The effectiveness and predictability of stream ecosystem restoration will improve with an increased understanding of the processes by which ecosystems develop and are maintained. Ideas from general ecological theory can clearly be better incorporated into stream restoration projects. This will provide a twofold benefit in providing an opportunity both to improve restoration outcomes and to test ecological theory.
Restoring freshwater ecosystems in riverine landscapes: the roles of connectivity and recovery processes
Authors: JANSSON ROLAND , NILSSON CHRISTER , MALMQVIST BJÖRN
Published: March 2007

1. This paper introduces key messages from a number of papers emanating from the Second International Symposium on Riverine Landscapes held in August 2004 in Sweden, focusing on river restoration. Together these papers provide an overview of the science of river restoration, and point out future research needs.

2. Restoration tests the feasibility of recreating complex ecosystems from more simple and degraded states, thereby presenting a major challenge to ecological science. Therefore, close cooperation between practitioners and scientists would be beneficial, but most river restoration projects are currently performed with little or no scientific involvement.

3. Key messages emanating from this series of papers are: The scope, i.e. the maximum and minimum spatial extent and temporal duration of habitat use, of species targeted for restoration should be acknowledged, so that all relevant stages in their life cycles are considered. Species that have been lost from a stream cannot be assumed to recolonise spontaneously, calling for strategies to ensure the return of target species to be integrated into projects. Possible effects of invasive exotic species also need to be incorporated into project plans, either to minimise the impact of exotics, or to modify the expected outcome of restoration in cases where extirpation of exotics is impractical.

4. Restoration of important ecological processes often implies improving connectivity of the stream. For example, longitudinal and lateral connectivity can be enhanced by restoring fluvial dynamics on flood‐suppressed rivers and by increasing water availability in rivers subject to water diversion or withdrawal, thereby increasing habitat and species diversity. Restoring links between surface and ground water flow enhances vertical connectivity and communities associated with the hyporheic zone.

5. Future restoration schemes should consider where in the catchment to locate projects to make restoration most effective, consider the cumulative effects of many small projects, and evaluate the potential to restore ecosystem processes under highly constrained conditions such as in urban areas. Moreover, restoration projects should be properly monitored to assess whether restoration has been successful, thus enabling adaptive management and learning for the future from both successful and unsuccessful restorations.
The meaning of living with malodorous exuding ulcers
Authors: Lindahl Elisabeth , Norberg Astrid , Söderberg Anna
Published: March 2007

Aim.  This study illuminates the meaning of living with malodorous, exuding ulcers.

Background.  Difficulties for patients with chronic ulcers and the ulcers’ impact on patients’ daily life are described in the literature. Suffering and consolation are also addressed in the literature as important issues in nursing care.

Design.  The first author interviewed seven women and two men, aged 41–95, with various diagnoses.

Method.  We interpreted the transcribed interviews using a phenomenological hermeneutic method.

Results.  Two processes were identified: ‘being struck down’– themes: feeling dirty, being trapped, losing confidence, losing hope, becoming frustrated and protecting oneself; and ‘finding consolation’– themes: experiencing kinship, encountering genuineness and gaining control. The meaning of living with malodorous and exuding ulcers can be understood as being trapped in a debilitating process that slowly strikes one down. There is a longing for purity and wholeness and for one's life to improve. When people with malodorous, exuding ulcers encounter genuineness and feel loved, regarded and respected as fully human despite their ulcers, they feel purified. The contaminated body no longer contaminates their self‐image and self‐esteem and they feel restored and fully human again. Only when they feel fully human can they regain control and see life beyond their ulcers.

Conclusion.  Although nurses cannot make ulcers or smell disappear, they can contribute significantly to improve the patients’ life. Finding consolation makes patients feel purified despite their contaminated body.

Relevance to Clinical Practice.  This study points to the importance of seeing the human being beyond the ulcer and considering not only the body but the whole person.
Experiences of loss and chronic sorrow in persons with severe chronic illness
Authors: Ahlström Gerd
Published: March 2007

Aims and objectives. The aims of the present study were to describe losses narrated by persons afflicted with severe chronic physical illness and to identify the concomitant occurrence of chronic sorrow.

Background. Reactions connected with repeated losses are referred to in the literature as chronic sorrow, which has recently been described in conjunction with chronic illness.

Design. A qualitative study with an abductive approach of analysis, including both inductive and deductive interpretations.

Method. The study is based on 30 persons of working age with average disease duration of 18 years. The average age was 51 years. All of the persons had personal assistance for at least three months because of considerable need for help in daily life due to physical disability. Each person was interviewed twice. There was also an independent assessment of the deductive results concerning chronic sorrow.

Results. The inductive findings show that all persons had experienced repeated physical, emotional and social losses. Most common were ‘Loss of bodily function’, ‘Loss of relationship’, ‘Loss of autonomous life’ and ‘Loss of the life imagined’. ‘Loss of identity’ included the loss of human worth, dignity and a changed self‐image. In addition, the deductive findings suggest that chronic sorrow exists in the study population. Sixteen of 30 participating subjects were assessed by both assessors to be in a state of chronic sorrow and there was an especially high agreement with respect to one criterion of chronic sorrow ‘Loss experience, ongoing or single event’ (28 of 30 subjects).

Conclusions. This study shows that persons with severe chronic illness often experience recurring losses. These experiences are consistent with the phenomenon of chronic sorrow.

Relevance to clinical practice. Knowledge of the existence of chronic sorrow in persons with chronic illness will enable nurses to support these persons in a more sensitive and appropriate way.