bluuebunny/crossref_metadata_2025 huggingface dataset:
Drop size distributions and kinetic energy rates in variable intensity rainfall
Authors: Assouline S.
Published: November 2009

Rainfall kinetic energy is a key factor in soil erosion processes. It is determined by rainfall intensity, related drop size distribution (DSD), and the drops' terminal velocity. Temporal variability in rainfall intensity is reflected in the DSD and affects the rainfall kinetic energy during the event. Smith et al. (2009) reported on 1‐min interval rainfall intensity and corresponding DSD variability during a storm on 22 July 2006 at Princeton, New Jersey. They reported also on DSD characteristics of heavy convective rainfall events during the whole summer. It is shown that (1) a similar relationship between the mean drop size and the rainfall intensity characterized the local rainfall at both the seasonal and the single‐storm scale, and (2) using the mean drop size as a scaling factor of the DSD removes the rainfall intensity dependence also at the intrastorm scale, providing a powerful tool to deal with temporal variability of rainfall rates during rainfall events. For a given storm characterized by a specific temporal variability of rates, three different ways of evaluating kinetic energy per unit mass or time were applied. By comparison to estimates accounting for rainfall temporal variability and related full DSDs, representing the storm by mean intensity and drop diameter tends to overestimate kinetic energy for low intensities and underestimate it for the higher ones. The relative error for the kinetic energy per unit of mass is ±45% and shifts from negative to positive sign for I > 25 mm/h. For the kinetic energy per unit of time, the relative error ranges from −100% to +210% and changes sign from negative to positive for I > 45 mm/h. When temporal variation of intensity is accounted for but drops are characterized by their mean values instead of the full DSD, kinetic energy is underestimated by 20% on average. Consequently, accounting for temporal variability in rainfall intensity during a storm has a notable impact on the erosive power of the rainfall.
Effects of facultative symbionts and heat stress on the metabolome of pea aphids
Authors: Burke Gaelen , Fiehn Oliver , Moran Nancy
Published: November 2009

We examined metabolite pools of pea aphids with different facultative symbiont infections, and characterized their effects on aphid metabolism in baseline and heat stress conditions. The bacterial symbiont Serratia symbiotica protects aphid hosts from the detrimental results of heat stress and shields the obligate symbiont Buchnera from effects of heat. We investigated whether broad effects on metabolism might correlate with this protection. Both facultative symbiont infection and heat treatment had large effects on the aphid metabolome. All three pea aphid facultative symbionts had similar effects on aphid metabolism despite their evolutionary diversity. Paradoxically, heat triggers lysis of many S. symbiotica cells and a correlated rapid reduction in S. symbiotica titres within aphid hosts. We conclude that facultative symbionts can have substantial effects on host metabolic pools, and we hypothesize that the protective effects of S. symbiotica may reflect the delivery of protective metabolites to aphid or Buchnera cells, after heat exposure.
Pioglitazone Increases the Proportion of Small Cells in Human Abdominal Subcutaneous Adipose Tissue
Authors: McLaughlin Tracey M. , Liu T. , Yee Gail , Abbasi F. , Lamendola C. , Reaven G.M. , Tsao P. , Cushman S.W. , Sherman A.
Published: November 2009

Rodent and in vitro studies suggest that thiazolidinediones promote adipogenesis but there are few studies in humans to corroborate these findings. The purpose of this study was to determine whether pioglitazone stimulates adipogenesis in vivo and whether this process relates to improved insulin sensitivity. To test this hypothesis, 12 overweight/obese nondiabetic, insulin‐resistant individuals underwent biopsy of abdominal subcutaneous adipose tissue at baseline and after 12 weeks of pioglitazone treatment. Cell size distribution was determined via the Multisizer technique. Insulin sensitivity was quantified at baseline and postpioglitazone by the modified insulin suppression test. Regional fat depots were quantified by computed tomography (CT). Insulin resistance (steady‐state plasma insulin and glucose (SSPG)) decreased following pioglitazone (P < 0.001). There was an increase in the ratio of small‐to‐large cells (1.16 ± 0.44 vs. 1.52 ± 0.66, P = 0.03), as well as a 25% increase in the absolute number of small cells (P = 0.03). The distribution of large cell diameters widened (P = 0.009), but diameter did not increase in the case of small cells. The increase in proportion of small cells was associated with the degree to which insulin resistance improved (r = −0.72, P = 0.012). Visceral abdominal fat decreased (P = 0.04), and subcutaneous abdominal (P = 0.03) and femoral fat (P = 0.004) increased significantly. Changes in fat volume were not associated with SSPG change. These findings demonstrate a clear effect of pioglitazone on human subcutaneous adipose cells, suggestive of adipogenesis in abdominal subcutaneous adipose tissue, as well as redistribution of fat from visceral to subcutaneous depots, highlighting a potential mechanism of action for thiazolidinediones. These findings support the hypothesis that defects in subcutaneous fat storage may underlie obesity‐associated insulin resistance.
Primary Care Providers' Knowledge, Practices, and Perceived Barriers to the Treatment and Prevention of Childhood Obesity
Authors: Spivack Jordan G. , Swietlik Maggie , Alessandrini Evaline , Faith Myles S.
Published: November 2009

This study evaluated primary care providers' (PCPs, pediatricians, and nurse practitioners) knowledge, current practices, and perceived barriers to childhood obesity prevention and treatment, with an emphasis on first‐year well‐child care visits. A questionnaire was distributed to 192 PCPs in the primary care network at The Children's Hospital of Philadelphia (CHOP) addressing (i) knowledge of obesity and American Academy of Pediatrics (AAP) guidelines, (ii) anticipatory guidance practices at well visits regarding nutrition and exercise, and (iii) perceived barriers to childhood obesity treatment and prevention. Eighty pediatricians and seven nurse practitioners responded, and a minority correctly identified the definition (26%) and prevalence (9%) of childhood overweight and AAP guidelines for exercise (39%) and juice consumption (44%). Most PCPs (81%) spent 11–20 min per well visit during the first 2 years, and 79% discussed diet, nutrition, and exercise for ≥3 min. Although >95% of PCPs discussed juice, fruits and vegetables, sippy cups, and finger foods during the first year, over 35% never discussed fast food, TV, or candy, and 55% never discussed exercise. Few rated current resources as adequate to treat or prevent childhood obesity. Over 90% rated the following barriers for obesity prevention and treatment as important or very important: parent is not motivated, child is not motivated, parents are overweight, families often have fast food, watch too much TV, and do not get enough exercise. In conclusion, there is much room to improve PCPs' knowledge of obesity and AAP guidelines. Although PCPs rate fast‐food consumption, TV viewing, and lack of exercise as important treatment barriers, many never discussed these topics during the first year.
Body Perception and Satisfaction in Obese, Severely Obese, and Normal Weight Female Patients
Authors: Docteur Aurélie , Urdapilleta Isabel , Defrance Cécile , Raison Jocelyne
Published: November 2009

The objective of this study was to investigate body perception and the associated level of dissatisfaction among obese patients. Twenty patients from each category of obese, severely obese, and normal weight individuals had their pictures enlarged or thinned using a computer program to manipulate photographs taken from the front, profile angle, and back. The pictures were shown to patients to represent both the way they thought they appeared and the way they would like to appear. Our results show that severely obese patients correctly perceived themselves as being more corpulent than obese patients, who in turn correctly perceived themselves as being more corpulent than normal weight females. These results remained stable regardless of whether the pictures were taken from the front, profile angle, or back. These results are discussed in terms of clinical and therapeutic interventions.
Creep and its effect on Sn whisker growth
Authors: Osenbach John W.
Published: November 2009

A comprehensive quantitative whisker growth theory has been developed. In this theory whisker growth is controlled by the ratio of the long range grain boundary diffusion creep relaxation rate to the short range creep relaxation rate. The theory relies solely on solid state diffusion effects and does not require additional constraints or assumptions to explain whisker growth. It explains a number of heretofore relatively poorly explained and puzzling observations reported over the past 6 decades, including: (i) Sn films that are 1–10 μm thick are more susceptible to whisker growth than thinner or thicker films; (ii) Sn film contamination in the form of hydrocarbons, Cu, hydrogen, etc., tend to increase the whisker propensity; (iii) as-deposited Sn films tend to be more susceptible to whisker growth than fused films; (iv) postplate annealing tends to improve the whisker resistance; (v) whisker growth rate tends toward zero as the temperature exceeds 100 °C; (vi) whisker growth propensity depends upon the crystallographic orientation of the Sn film; and (vii) the large statistical variations reported in whisker density and incubation time. The theory predicts: (i) the magnitude of the as deposited film stress state is not fundamental to whisker growth; (ii) at high stresses where power law creep relaxation dominates, whiskers do not form.; (iii) whiskers occur in those regions of the film that are exposed to stresses lower than that required for power law creep; (iv) whiskers form when a quasiequilibrium stress state is achieved as the stress in the film tends toward zero; (v) anything that affects (limits or restrains) power law creep and its associated stress dissipation, such as grain boundary pinning, increases the propensity for whisker growth; (vi) pinning tends to increase the whisker propensity and increase the whisker growth rate; and (vii) films with certain crystallographic orientations and grain sizes are less prone to whisker growth, independent of the anisotropic thermomechanical properties, as a result of the anisotropic diffusion behavior of Sn.
An efficient tool for modeling and predicting fluid flow in nanochannels
Authors: Ahadian Samad , Mizuseki Hiroshi , Kawazoe Yoshiyuki
Published: November 2009

Molecular dynamics simulations were performed to evaluate the penetration of two different fluids (i.e., a Lennard-Jones fluid and a polymer) through a designed nanochannel. For both fluids, the length of permeation as a function of time was recorded for various wall-fluid interactions. A novel methodology, namely, the artificial neural network (ANN) approach was then employed for modeling and prediction of the length of imbibition as a function of influencing parameters (i.e., time, the surface tension and the viscosity of fluids, and the wall-fluid interaction). It was demonstrated that the designed ANN is capable of modeling and predicting the length of penetration with superior accuracy. Moreover, the importance of variables in the designed ANN, i.e., time, the surface tension and the viscosity of fluids, and the wall-fluid interaction, was demonstrated with the aid of the so-called connection weight approach, by which all parameters are simultaneously considered. It was revealed that the wall-fluid interaction plays a significant role in such transport phenomena, namely, fluid flow in nanochannels.
Periodic solutions on the Sturm–Liouville boundary value problem for two-dimensional wave equation
Authors: Ji Shuguan
Published: November 2009

In this paper, we study the periodic solutions to two-dimensional wave equation ytt−Δy+ay+g(y)=f(x,t) on (0,π)×(0,π)×R under the periodic conditions y(x,t+T)=y(x,t), yt(x,t+T)=yt(x,t), and the Sturm–Liouville boundary conditions a11y(0,x2,t)−b11yx1(0,x2,t)=0, a12y(π,x2,t)+b12yx1(π,x2,t)=0, a21y(x1,0,t)−b21yx2(x1,0,t)=0, and a22y(x1,π,t)+b22yx2(x1,π,t)=0 (aij2+bij2≠0 for i,j=1,2). Our main concept is that of the “weak solution,” which will be given in Sec. II. Then, by means of spectral analysis, we investigate some important properties of the wave operator with Sturm–Liouville boundary conditions. Finally, by using the properties we established and the duality principles in the work of Brézis [Bull. Am. Math. Soc. 8, 409 (1983)], the existence of periodic solutions is obtained.
Energy and density analysis of the H2 molecule from the united atom to dissociation: The Σ3g+ and Σ3u+ states
Authors: Corongiu Giorgina , Clementi Enrico
Published: November 2009

The first 14 Σ3g+ and the first 15 Σ3u+ states of the H2 molecule are computed with full configuration interaction both from Hartree–Fock molecular orbitals and Heitler–London atomic orbitals within the Born–Oppenheimer approximation, following recent studies for the Σ1g+ and Σ1u+ manifolds [Corongiu and Clementi, J. Chem. Phys. 131, 034301 (2009) and J. Phys. Chem. (in press)]. The basis sets utilized are extended and optimized Slater-type functions and spherical Gaussian functions. The states considered correspond to the configurations (1s1nl1) with n from 1 to 5; the internuclear separations sample the distances from 0.01 to 10 000 bohrs. For the first three Σ3g+ and Σ3u+ states and for the fourth and fifth Σ3g+ states, our computed energies at the equilibrium internuclear separation, when compared to the accurate values by Staszewska and Wolniewicz and by Kołos and Rychlewski, show deviations of about 0.006 kcal/mol, a test on the quality of our computations. Motivation for this work comes not only from obtaining potential energy curves for the high excited states of H2 but also from characterizing the electronic density evolution from the united atom to dissociation to provide a detailed analysis of the energy contributions from selected basis subsets and to quantitatively decompose the state energies into covalent and ionic components. Furthermore, we discuss the origin of the seemingly irregular patterns in potential energy curves in the two manifolds, between 4 and 6–9 bohrs—there are two systems of states: the first, from the united atom to about 4 bohrs, is represented by functions with principal quantum number higher than the one needed at dissociation; this system interacts at around 4 bohrs with the second system, which is represented by functions with principal quantum number corresponding to one of the dissociation products.
Grand canonical steady-state simulation of nucleation
Authors: Horsch Martin , Vrabec Jadran
Published: November 2009

Grand canonical molecular dynamics (GCMD) is applied to the nucleation process in a metastable phase near the spinodal, where nucleation occurs almost instantaneously and is limited to a very short time interval. With a variant of Maxwell’s demon, proposed by McDonald [Am. J. Phys. 31, 31 (1963)], all nuclei exceeding a specified size are removed. In such a steady-state simulation, the nucleation process is sampled over an arbitrary time span and all properties of the metastable state, including the nucleation rate, can be obtained with an increased precision. As an example, a series of GCMD simulations with McDonald’s demon is carried out for homogeneous vapor to liquid nucleation of the truncated-shifted Lennard-Jones (tsLJ) fluid, covering the entire relevant temperature range. The results are in agreement with direct nonequilibrium MD simulation in the canonical ensemble. It is confirmed for supersaturated vapors of the tsLJ fluid that the classical nucleation theory underpredicts the nucleation rate by two orders of magnitude.
A novel capacitance sensor for fireside corrosion measurement
Authors: Ban Heng , Li Zuoping
Published: November 2009

Fireside corrosion in coal-fired power plants is a leading mechanism for boiler tube failures. Online monitoring of fireside corrosion can provide timely data to plant operators for mitigation implementation. This paper presents a novel sensor concept for measuring metal loss based on electrical capacitance. Laboratory-scale experiments demonstrated the feasibility of design, fabrication, and operation of the sensor. The fabrication of the prototype sensor involved sputtering deposition of a thin metal coating with varying thickness on a ceramic substrate. Corrosion metal loss resulted in a proportional decrease in electrical capacitance of the sensor. Laboratory experiments using a muffle furnace with an oxidation environment demonstrated that low carbon steel coatings on ceramic substrate survived cyclic temperatures over 500 °C. Measured corrosion rates of sputtered coating in air had an Arrhenius exponential dependence on temperature, with metal thickness loss ranging from 2.0 nm/h at 200 °C to 2.0 μm/h at 400 °C. Uncertainty analysis indicated that the overall measurement uncertainty was within 4%. The experimental system showed high signal-to-noise ratio, and the sensor could measure submicrometer metal thickness changes. The laboratory experiments demonstrated that the sensor concept and measurement system are capable of short term, online monitoring of metal loss, indicating the potential for the sensor to be used for fireside corrosion monitoring and other metal loss measurement.
Capacitance tuning of nanoscale split-ring resonators
Authors: Jeppesen Claus , Mortensen Niels Asger , Kristensen Anders
Published: November 2009

We investigate the capacitance tuning of nanoscale split-ring resonators. Based on a simple inductor-capacitor circuit model, we derive an expression, where the inductance is proportional to the area while the capacitance reflects the aspect ratio of the slit. The resonance frequency may thus be tuned by the slit aspect ratio leaving the area, the lattice constant Λ, and nearest-neighbor coupling in periodic structures invariant. Experimental data follow the predictions of the simple LC-model.
Study on the characteristics of turbulent drag-reducing channel flow by particle image velocimetry combining with proper orthogonal decomposition analysis
Authors: Cai W.-H. , Li F.-C. , Zhang H.-N. , Li X.-B. , Yu B. , Wei J.-J. , Kawaguchi Y. , Hishida K.
Published: November 2009

Turbulent drag reduction of 30 ppm cetyltrimethyl ammonium chloride (CTAC) solution flow in a channel was investigated with particle image velocimetry (PIV) combining with proper orthogonal decomposition (POD). Measurements were made at inlet fluid temperature of 304 K and at Reynolds number 2.5×104 (based on the channel height, bulk velocity, and solvent viscosity) for both water and CTAC solution flows with 70.0% drag reduction rate. The two-component velocity fields in the streamwise-wall normal plane were recorded by PIV. In order to study the characteristics of turbulent drag-reducing channel flow, POD was performed to identify the near-wall coherent structures based on PIV-measured data. POD is a powerful low-dimensional analysis tool that can be used to identify coherent structures embedded in the turbulent shear flow. We mainly studied a comparison between the first dominant POD eigenmodes of water and drag-reducing CTAC solution flows. Coherent structures were seen as the sum of several eigenmodes that possess a dominant energy of the flow, say 90%. It was obtained that the amount of eigenmodes required for capturing the coherent structures was 233 and 195 for water and CTAC solution flows, respectively, which means the decrease in the complexity in CTAC solution flow. Based on the analysis of POD eigenmodes of water and CTAC solution flows, we captured the processes that can reflect the ejection motion of low-speed fluid from the wall and sweep motion of high-speed fluid toward the wall associating with turbulent bursting events. The results showed that CTAC additives can inhibit the turbulent bursting processes (both strength and occurrence frequency), resulting in a great decrease in turbulent contribution to frictional drag and drag reduction, which is sufficient to understand deeply the mechanism of turbulent drag reduction.
Dramatic excitation dependence of strong and stable blue luminescence of ZnO hollow nanoparticles
Authors: Zeng Haibo , Yang Shikuan , Xu Xiaoxia , Cai Weiping
Published: November 2009

Strong and stable blue luminescence was obtained from ZnO hollow nanoparticles. Significantly, dramatic excitation dependence was observed for blue emissions of ZnO: (1) band-gap energy (Eg) is the optimal excitation energy but smaller energies are still effective; (2) there exist several fixed emitting wavelengths in blue wave band, such as 412, 439, and 458 nm. These phenomena, combined with previously reported defect levels and formation thermodynamics, point out that the initial states of corresponding transitions to blue emissions could be zinc interstitials-related defect states, which were further verified by subsequent electron paramagnetic resonance examinations.
Superconducting nanowire single-photon detector in an optical cavity for front-side illumination
Authors: Baek Burm , Stern Jeffrey A. , Nam Sae Woo
Published: November 2009

We have integrated superconducting nanowire single-photon detectors (SNSPDs) with an optical cavity design for front-side illumination. Our optical cavity design increases the coupling efficiency of light to the nanowire detector and enables straightforward proximity fiber-coupling for a multichannel detector system. Using a confocal optical scanning technique, we measured a significantly enhanced optical absorptance of 73% in comparison with 20% in a typical bare nanowire device at 1550 nm and 3 K. Our method of fabrication of these devices on a silicon wafer and the local optical absorptance measurement are important steps toward developing next-generation SNSPD technology.
Particle transport in porous media: The role of inertial effects and path tortuosity in the velocity of the particles
Authors: Kampel Guido , Goldsztein Guillermo H. , Santamarina Juan C.
Published: November 2009

Fluid in porous media flows through tortuous paths. If the size of the solid particles suspended in the fluid and the fluid velocities are large enough, Brownian motion effects may not be dominant. In this parameter regime, the average velocity of the particles is different than that of the fluid. We obtain the relation between the average velocity of the particles and the average velocity of the fluid in the context of a simple mathematical model and we apply our results to flows near wells.
Subwavelength focusing behavior of high numerical-aperture phase Fresnel zone plates under various polarization states
Authors: Mote Rakesh G. , Yu S. F. , Zhou W. , Li X. F.
Published: November 2009

An analytical model is developed to study the subwavelength focusing characteristics of a binary phase Fresnel zone plate (FZP). The model shows that high numerical-aperture phase FZP under the illumination of linear polarized light produces rotationally asymmetric focal spot with beamwidth varying from 0.36λ to 0.79λ, where λ is the wavelength. On the other hand, rotationally symmetric focal spot with minimum beamwidth of 0.39λ can be obtained from the illumination of radial polarized light.
Simultaneous determination of intergranular interactions and intrinsic switching field distributions in magnetic materials
Authors: Hovorka O. , Liu Y. , Dahmen K. A. , Berger A.
Published: November 2009

We develop a generally applicable method for the accurate measurement of intrinsic switching field distributions and the determination of exchange and dipolar interactions in granular magnetic materials. The method is based on the simultaneous analysis of hysteresis loop and recoil curve data. Its validity and practical implementation are demonstrated by means of computational modeling using a reference function identification scheme. We find the methodology to be numerically accurate in a wide parameter range, far exceeding the previously utilized mean-field interaction regime used in other methodologies.
Photoreflectance and Fourier transform infrared spectroscopy study of intersubband transitions of a ZnxCd1−xSe/Znx′Cdy′Mg1−x′−y′Se asymmetric coupled quantum well structure for quantum cascade laser application
Authors: Wu J. D. , Huang C. T. , Huang Y. S. , Charles W. O. , Shen A. , Tamargo M. C.
Published: November 2009

Photoreflectance (PR) and Fourier transform infrared (FTIR) spectroscopy were used to study the intersubband (ISB) transitions of a ZnxCd1−xSe/Znx′Cdy′Mg1−x′−y′Se asymmetric coupled quantum well (ACQW) structure for quantum cascade laser (QCL) application. The PR spectrum revealed a wide range of possible optical transitions in the ACQW structure. A comprehensive analysis of the PR spectrum led to the identification of various interband transitions. The ISB transitions were estimated and confirmed by FTIR absorption measurements. The results demonstrated the use of PR as a complimentary technique to FTIR for the contactless and nondestructive characterization of ACQW structures for QCL application.
Memory effect of Mn5Ge3 nanomagnets embedded inside a Mn-diluted Ge matrix
Authors: Zhou Shengqiang , Shalimov Artem , Potzger Kay , Jeutter Nicole M. , Baehtz Carsten , Helm Manfred , Fassbender Jürgen , Schmidt Heidemarie
Published: November 2009

Crystalline Mn5Ge3 nanomagnets are formed inside a Mn-diluted Ge matrix using Mn ion implantation. A temperature-dependent memory effect and slow magnetic relaxation are observed below the superparamagnetic blocking temperature of Mn5Ge3. Our findings corroborate that the observed spin-glass-like features are caused by the size distribution of Mn5Ge3 nanomagnets, rather than by the interparticle interaction through the Mn-diluted Ge matrix.
Radio frequency operation of clocked quantum-dot cellular automata latch
Authors: Tang Yong , Orlov Alexei O. , Snider Gregory L. , Fay Patrick J.
Published: November 2009

The radio frequency operation of a single-electron latch based on Al–AlOx–Al tunnel junctions is presented. By capacitively coupling the latch to a radio frequency single electron transistor, charge switching on the microsecond timescale is demonstrated. The fast switching and high repeatability of the latch response indicates that high speed operation of pipelines, signal fan-outs, and more complex logic devices are possible with this technology. The experimental technique developed is also promising for enabling the investigation of the intrinsic switching speed in electronic quantum-dot cellular automata-based circuits.
Regioselective Deacetylation of Fully Acetylated Mono- and Di-Saccharides With Hydrazine Hydrate
Authors: Khan R , Konowicz PA , Gardossi L , Matulova M , Degennaro S
Published: November 2009

Selective deacetylation reactions of the peracetylated reducing disaccharides (1), (5), (9), (15), β-D- glucopyranose (17) and 2-acetamido-2-deoxy-β-D-glucopyranose (19), with 1.2 equiv. Of hydrazine hydrate in acetonitrile, gave predominantly the corresponding heptaacetates (2), (6), (10), (16), the tetraacetate (18) and the triacetate (20), with the free hydroxy group at C1. Reaction of (1) with 1.2 equiv. of hydrazine hydrate in N,N- dimethylformamide also afforded the heptaacetate (2), but in lower yield. When reactions of (1), (5) and (9) were performed with 2.5 equiv. of hydrazine hydrate, deacetylation also occurred at other positions to afford the corresponding hexaacetates (3), (7), (11) and (12), with hydroxy groups at C 1,2 or C 1,3, and the pentaacetates (4), (8) and (13), with hydroxy groups at C 1,2,3. Maltose octaacetate (9), in addition, yielded the tetraacetate (14) in which the free hydroxy groups were located at C1,2,2',3. Compound (15) on treatment with 2.5 equiv. of hydrazine hydrate afforded an intractable mixture. The reaction of methyl 2,3,4,6-tetra-O-acetyl-α-D-glucopyranoside (21) with 2.5 equiv. of hydrazine hydrate gave the 3,4,6-triacetate (22), a mixture of the 2,6- and the 3,6-diacetates (23) and (24), respectively, the 4,6-diacetate (25), and the 6-acetate (26).
Synthesis of Modified Aldonic Acids and Studies of Their Substrate Efficiency for Dihydroxy Acid Dehydratase (DHAD)
Authors: Limberg G , Limberg G , Thiem J , Thiem J
Published: November 2009

Modified aldopentonic and aldohexonic acids were synthesized in order to study the electronic requirements for a successful enzymatic conversion into their corresponding 2-keto 3-deoxy analogues by dihydroxy acid dehydratase (DHAD), an enzyme from the biosynthetic pathway of branched chain amino acids. Analytical tests with the novel artificial substrates (18)-(21) and (27) provided evidence that the amount of conversion could be enhanced by replacement of the hydroxy group at C4 of L-arabinonic acid (21) with less electron-withdrawing, ambivalent or electron-donating substituents. Modified aldohexonic acids were no substrates for DHAD, perhaps due to less perfect binding to the active site presumably for steric reasons. For 4-deoxy-L-threo-pentonic acid (18) the enzymatic conversion into 3,4-dideoxy-2-ketopentonic acid (29) by DHAD could be achieved on a preparative scale.
Synthesis of 2,3-Anhydro Glycosyl Phosphonates
Authors: Doanxuanlie m , Jenkins ID , Skelton BW , White AH
Published: November 2009

The synthesis of dimethyl 6-O-acetyl-2,3-anhydro-α-D- mannopyranosylphosphonates and the corresponding α- and β- allo derivatives is described. Dimethyl 4,6-di-O-acetyl-2,3-dideoxy-D-erythro-hex-2-enopyranosylphosphonates, although unreactive towards normal epoxidizing agents (3-chloroperoxybenzoic acid, trifluoroperoxyacetic acid, etc), underwent smooth epoxidation with hydrogen peroxide in the presence of sodium tungstate or dodecatungstophosphoric acid. An interesting regiospecific deacetylation of the 4-acetate occurred under these conditions. The structures of these anhydro glycosyl phosphonates were determined by 1H and 13C n.m.r. spectroscopy, and confirmed by X ray structural analysis in the case of dimethyl 6-O-acetyl-2,3-anhydro-α-D-mannopyranosylphosphonate , and of dimethyl 6-O-acetyl-2,3-anhydro-β-D-allopyranosylphosphonate.
Crystal and Molecular Structures of Penta-O-acetyl-aldehydo-D-glucose Dimethyl Acetal and of Hepta-O-acetyl-aldehydo-D-glucose Hydrate
Authors: Koll P , Kopf J
Published: November 2009

The solid-state structures of the title compounds were determined by conventional single-crystal X-ray crystallography. In both cases a planar zigzag conformation of the carbon skeleton is observed with a resulting 1,3-parallel orientation of O(2) and O(4). In the case of the heptaacetate even a second such arrangement is established between O(3) and one of the oxygens at C(1). These findings substantiate the claim that such conformations are not as unfavourable as previously was assumed by many authors.
Quaternary structure of the human Cdt1-Geminin complex regulates DNA replication licensing
Authors: De Marco V. , Gillespie P. J. , Li A. , Karantzelis N. , Christodoulou E. , Klompmaker R. , van Gerwen S. , Fish A. , Petoukhov M. V. , Iliou M. S. , Lygerou Z. , Medema R. H. , Blow J. J. , Svergun D. I. , Taraviras S. , Perrakis A.
Published: November 2009

All organisms need to ensure that no DNA segments are rereplicated in a single cell cycle. Eukaryotes achieve this through a process called origin licensing, which involves tight spatiotemporal control of the assembly of prereplicative complexes (pre-RCs) onto chromatin. Cdt1 is a key component and crucial regulator of pre-RC assembly. In higher eukaryotes, timely inhibition of Cdt1 by Geminin is essential to prevent DNA rereplication. Here, we address the mechanism of DNA licensing inhibition by Geminin, by combining X-ray crystallography, small-angle X-ray scattering, and functional studies in
Xenopus
and mammalian cells. Our findings show that the Cdt1:Geminin complex can exist in two distinct forms, a “permissive” heterotrimer and an “inhibitory” heterohexamer. Specific Cdt1 residues, buried in the heterohexamer, are important for licensing. We postulate that the transition between the heterotrimer and the heterohexamer represents a molecular switch between licensing-competent and licensing-defective states.
Ras is an indispensable coregulator of the class I
B
phosphoinositide 3-kinase p87/p110γ
Authors: Kurig Barbara , Shymanets Aliaksei , Bohnacker Thomas , Prajwal  , Brock Carsten , Ahmadian Mohammad Reza , Schaefer Michael , Gohla Antje , Harteneck Christian , Wymann Matthias P. , Jeanclos Elisabeth , Nürnberg Bernd
Published: November 2009

Class I
B
phosphoinositide 3-kinase γ (PI3Kγ) elicits various immunologic and cardiovascular responses; however, the molecular basis for this signal heterogeneity is unclear. PI3Kγ consists of a catalytic p110γ and a regulatory p87
PIKAP
(p87, also p84) or p101 subunit. Hitherto p87 and p101 are generally assumed to exhibit redundant functions in receptor-induced and G protein βγ (Gβγ)-mediated PI3Kγ regulation. Here we investigated the molecular mechanism for receptor-dependent p87/p110γ activation. By analyzing GFP-tagged proteins expressed in HEK293 cells, PI3Kγ-complemented bone marrow–derived mast cells (BMMCs) from p110γ
-/-
mice, and purified recombinant proteins reconstituted to lipid vesicles, we elucidated a novel pathway of p87-dependent, G protein–coupled receptor (GPCR)-induced PI3Kγ activation. Although p101 strongly interacted with Gβγ, thereby mediating PI3Kγ membrane recruitment and stimulation, p87 exhibited only a weak interaction, resulting in modest kinase activation and lack of membrane recruitment. Surprisingly, Ras-GTP substituted the missing Gβγ-dependent membrane recruitment of p87/p110γ by direct interaction with p110γ, suggesting the indispensability of Ras for activation of p87/p110γ. Consequently, interference with Ras signaling indeed selectively blocked p87/p110γ, but not p101/p110γ, kinase activity in HEK293 and BMMC cells, revealing an important crosstalk between monomeric and trimeric G proteins for p87/p110γ activation. Our data display distinct signaling requirements of p87 and p101, conferring signaling specificity to PI3Kγ that could open up new possibilities for therapeutic intervention.
Neural correlates of behavior in the mothManduca sextain response to complex odors
Authors: Riffell Jeffrey A. , Lei H. , Hildebrand John G.
Published: November 2009

WithManduca sextaas a model system, we analyzed how natural odor mixtures that are most effective in eliciting flight and foraging behaviors are encoded in the primary olfactory center in the brain, the antennal lobe. We used gas chromatography coupled with multiunit neural-ensemble recording to identify key odorants from flowers of two important nectar resources, the desert plantsDatura wrightiiandAgave palmeri, that elicited responses from individual antennal-lobe neurons. Neural-ensemble responses to theA. palmerifloral scent, comprising >60 odorants, could be reproduced by stimulation with a mixture of six of its constituents that had behavioral effectiveness equivalent to that of the complete scent. Likewise, a mixture of three floral volatiles fromD. wrightiielicited normal flight and feeding behaviors. By recording responses of neural ensembles to mixtures of varying behavioral effectiveness, we analyzed the coding of behaviorally “meaningful” odors. We considered four possible ensemble-coding mechanisms—mean firing rate, mean instantaneous firing rate, pattern of synchronous ensemble firing, and total net synchrony of firing—and found that mean firing rate and the pattern of ensemble synchrony were best correlated with behavior (R= 41% and 43%, respectively). Stepwise regression analysis showed that net synchrony and mean instantaneous firing rate contributed little to the variation in the behavioral results. We conclude that a combination of mean-rate coding and synchrony of firing of antennal-lobe neurons underlies generalization among related, behaviorally effective floral mixtures while maintaining sufficient contrast for discrimination of distinct scents.
Modulation of γ-secretase specificity using small molecule allosteric inhibitors
Authors: Shelton Christopher C. , Zhu Lei , Chau Deming , Yang Li , Wang Rong , Djaballah Hakim , Zheng Hui , Li Yue-Ming
Published: November 2009

γ-Secretase cleaves multiple substrates within the transmembrane domain that include the amyloid precursor protein as well as the Notch family of receptors. These substrates are associated with Alzheimer disease and cancer. Despite extensive investigation of this protease, little is known regarding the regulation of γ-secretase specificity. To discover selective inhibitors for drug development and for probing the mechanisms of γ-secretase specificity, we screened chemical libraries and consequently developed a di-coumarin family of inhibitors that preferentially inhibit γ-secretase-mediated production of Aβ42 over other cleavage activities. These coumarin dimer-based compounds interact with γ-secretase by binding to an allosteric site. By developing a multiple photo-affinity probe approach, we demonstrate that this allosteric binding causes a conformational change within the active site of γ-secretase at the S2 and S1 sub-sites that leads to selective inhibition of Aβ42. In conclusion, by using these di-coumarin compounds, we reveal a mechanism by which γ-secretase specificity is regulated and provide insights into the molecular basis by which familial presenilin mutations may affect the active site and specificity of γ-secretase. Furthermore, this class of selective inhibitors provides the basis for development of Alzheimer disease therapeutic agents.
Acute in vivo exposure to interferon-γ enables resident brain dendritic cells to become effective antigen presenting cells
Authors: Gottfried-Blackmore Andres , Kaunzner Ulrike W. , Idoyaga Juliana , Felger Jennifer C. , McEwen Bruce S. , Bulloch Karen
Published: November 2009

Dendritic cells (DC) are the professional antigen presenting cells (APC) that bridge the innate and adaptive immune system. Previously, in a CD11c/EYFP transgenic mouse developed to study DC functions, we anatomically mapped and phenotypically characterized a discrete population of EYFP+cells within the microglia that we termed brain dendritic cells (bDC). In this study, we advanced our knowledge of the function of these cells in the CD11c/EYFP transgenic mouse and its chimeras, using acute stimuli of stereotaxically inoculated IFNγ or IL-4 into the CNS. The administration of IFNγ increased the number of EYFP+bDC but did not recruit peripheral DC into the CNS. IFNγ, but not IL-4, upregulated the expression levels of major histocompatibility class II (MHC-II). In addition, IFNγ-activated EYFP+bDC induced antigen-specific naïve CD4 T cells to proliferate and secrete Th1/Th17 cytokines. Activated bDC were also able to stimulate naïve CD8 T cells. Collectively, these data reveal the Th1 cytokine IFNγ, but not the Th2 cytokine IL4, induces bDC to up-regulate MHC-II and become competent APC.
Quantifying uncertainty in genotype calls
Authors: Carvalho Benilton S. , Louis Thomas A. , Irizarry Rafael A.
Published: November 2009

Motivation: Genome-wide association studies (GWAS) are used to discover genes underlying complex, heritable disorders for which less powerful study designs have failed in the past. The number of GWAS has skyrocketed recently with findings reported in top journals and the mainstream media. Microarrays are the genotype calling technology of choice in GWAS as they permit exploration of more than a million single nucleotide polymorphisms (SNPs) simultaneously. The starting point for the statistical analyses used by GWAS to determine association between loci and disease is making genotype calls (AA, AB or BB). However, the raw data, microarray probe intensities, are heavily processed before arriving at these calls. Various sophisticated statistical procedures have been proposed for transforming raw data into genotype calls. We find that variability in microarray output quality across different SNPs, different arrays and different sample batches have substantial influence on the accuracy of genotype calls made by existing algorithms. Failure to account for these sources of variability can adversely affect the quality of findings reported by the GWAS.

Results: We developed a method based on an enhanced version of the multi-level model used by CRLMM version 1. Two key differences are that we now account for variability across batches and improve the call-specific assessment of each call. The new model permits the development of quality metrics for SNPs, samples and batches of samples. Using three independent datasets, we demonstrate that the CRLMM version 2 outperforms CRLMM version 1 and the algorithm provided by Affymetrix, Birdseed. The main advantage of the new approach is that it enables the identification of low-quality SNPs, samples and batches.

Availability: Software implementing of the method described in this article is available as free and open source code in the crlmm R/BioConductor package.

Contact:  rafa@jhu.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Folic Acid, Iron, and Zinc Contents in Chosen Food Products Prepared with Fortified Flours
Authors: Boen Thaís Rezende , Lima Pallone Juliana A.
Published: November 2009

In 2002, Brazil issued a regulation requiring that corn and wheat flours be fortified by the addition of folic acid and iron. The aim of the present work was to evaluate the levels of folic acid, iron, and zinc in macaroni, pizza, and bread prepared with fortified flour. The methodologies used for the mineral (FAAS) and vitamin (HPLC) determinations were validated and considered adequate. For macaroni, the folic acid content range was 50.0–182.4 μg/100 g. The iron and zinc levels were 1.6–5.4 mg/100 g and 0.7–1.0 mg/100 g, respectively. The pizza and bread samples contained 14.8–271.3 μg/100 g and 47.4–481.4 μg/100 g of folic acid, respectively. The iron and zinc levels were 2.6–7.3 mg/100 g and 0.4–0.9 mg/100 g, respectively, for pizza, and 3.0–12.4 mg/100 g and 0.4–0.8 mg/100 g for bread. The results indicated that the distribution of folic acid and iron in the majority of the samples tested was heterogeneous. This study could be of use to governmental authorities in their food fortification evaluation programs. Moreover, the average iron contents observed in the products could result in problems with zinc absorption, and it is important to consider that iron can induce oxidative stress in cells.
Personality predicts spatial responses to food manipulations in free-ranging great tits (
Parus major
)
Authors: van Overveld Thijs , Matthysen Erik
Published: November 2009

Personality differences measured under standardized lab-conditions are assumed to reflect differences in the way individuals cope with spatio-temporal changes in their natural environment, but few studies have examined how these are expressed in the field. We tested whether exploratory behaviour in a novel environment predicts how free-living individual great tits (
Parus major
) react to a change in food supply. We temporarily removed food at feeding stations during two summers and recorded the behavioural response of juvenile birds to these food manipulations using radio-tracking. When challenged by an abrupt change in food supply, fast-exploring individuals more rapidly switched to different foraging areas at longer distances from the feeder. This study is the first to show that personality traits predict the spatial response to experimentally induced changes in their natural environment.
Organisms on the move: ecology and evolution of dispersal
Authors: Gibbs Melanie , Saastamoinen Marjo , Coulon Aurélie , Stevens Virginie M.
Published: November 2009

The symposium and workshop ‘Organisms on the move:ecology and evolution of dispersal’, held in Ghent (Belgium), 14–18 September 2009, brought together a wide range of researchers using empirical and modelling approaches to examine the dispersal process. This meeting provided an opportunity to assess how much cross-fertilization there has been between empiricists and theoreticians, to present novel insights on dispersal patterns in plants, animals and micro-organisms and to measure the progress made in examining the causes and consequences of dispersal.
Cryptochromes—a potential magnetoreceptor: what do we know and what do we want to know?
Authors: Liedvogel Miriam , Mouritsen Henrik
Published: November 2009

Cryptochromes have been suggested to be the primary magnetoreceptor molecules underlying light-dependent magnetic compass detection in migratory birds. Here we review and evaluate (i) what is known about these candidate magnetoreceptor molecules, (ii) what characteristics cryptochrome molecules must fulfil to possibly underlie light-dependent, radical pair based magnetoreception, (iii) what evidence supports the involvement of cryptochromes in magnetoreception, and (iv) what needs to be addressed in future research. The review focuses primarily on our knowledge of cryptochromes in the context of magnetoreception.
Measurement of the mechanical properties of granular packs by wavelength-scanning interferometry
Authors: Zhou Yanzhou , Wildman Ricky D. , Huntley Jonathan M.
Published: November 2009

A wavelength-scanning interferometer has been constructed to observe both the normal and in-plane displacements particle by particle at the base of a model granular pack. The pack comprised 25 000 steel beads supported by a thick glass substrate and was subjected to local disturbing forces on its upper surface. The system allows measurement of normal displacements of the beads to a precision of
ca
0.1 nm, thereby providing highly accurate determination of contact forces while minimizing artefacts due to substrate and grain compliance. The probability distribution of the normalized contact force was found to be approximately independent of the applied load on the upper surface of the granular pack and has an exponential tail. The probability distributions of the normalized response force and lateral displacement have similar power-law tails. The interactions between contact forces and lateral displacements suggest that significant internal rearrangement occurs in the granular pack as the load is increased, and particle displacement plays an important role in the mechanics of the granular material.
A constrained eigenvalue problem and nodal and modal control of vibrating systems
Authors: Ram Y. M.
Published: November 2009

A constrained non-homogeneous linear eigenvalue problem is introduced. The application given to the problem is of finding the frequency and amplitudes of exciting forces that impose constraints on the configurations of vibratory modes. The scope of the problem is wider. It is shown that the problem may be transformed to a singular unsymmetric generalized eigenvalue problem. Depending on the given data the problem may have finite, infinite or empty spectrum. The solvability of the problem is analysed. Examples demonstrate the application and the various results.