bluuebunny/crossref_metadata_2025 huggingface dataset:
Spatial orientation and position distribution effect on the effective permeability of composites consisting of aligned flakes
Authors: Liu T. , Zhou P. H. , Deng L. J. , Tang W.
Published: December 2009

In this work, the effective permeability of two-phase composite materials is studied based on a three-dimensional model. In this model, the magnetic inclusions embedded in a dielectric matrix are set with aligned orientation and calculated by finite-difference time-domain method in both lossless and lossy cases. First, the sensitivity of the effective permeability of composites to the spatial orientation and position distribution of inclusions is analyzed. Second, since it is difficult to give an accurate effective permeability with classic effective medium theories, we have modified the well-known Maxwell–Garnett mixing rule by introducing the equivalent demagnetization factors and two fitting parameters α and β, indicating the extent of position distribution chaos. An excellent agreement is obtained between the theoretical and simulation results in the quasistatic limit. Finally, in the case of inclusions oriented at several directions in the matrix, an “averaging method” is proposed to calculate the effective permeability.
The thermal stability of Pt/epitaxial Gd2O3/Si stacks and its dependence on heat-treatment ambient
Authors: Lipp E. , Osten H. J. , Eizenberg M.
Published: December 2009

The stability of Pt/epitaxial Gd2O3/Si stacks is studied by monitoring the chemical and electrical properties following heat treatments in forming gas and in vacuum at temperatures between 400 and 650 °C. Our results show that stack instability is realized via diffusion of Gd through the Pt grain boundaries, which was observed after forming-gas annealing at 550 °C for 30 min. The Gd diffusion kinetics in forming gas is studied by secondary ion mass spectrometry analysis, showing that the diffusion process occurs according to C-type kinetics with an activation energy of 0.73±0.04 eV. Following vacuum heat treatments at 600 °C for 30 min, Si outdiffusion is observed, in addition to Gd outdiffusion. Si outdiffusion results in the formation of PtSi clusters on the metal surface following vacuum annealing at 650 °C. In contrast, in the case of forming-gas treatments, Si diffusion and silicide formation were detected only after annealing at 700 °C. The better stability of Pt/Gd2O3/Si stacks in forming gas is correlated with the content of oxygen in the Pt layer during the treatment.
Energy level alignments and photocurrents in crystalline Si/organic semiconductor heterojunction diodes
Authors: Campbell I. H. , Crone B. K.
Published: December 2009

We investigate electronic energy level alignment and photocurrent in crystalline silicon/organic/semitransparent metal heterojunction diodes. Optically thin films of poly[2-methoxy,5-(2′-ethyl-hexyloxy)-1,4-phenylene vinylene] (MEH-PPV), poly(9,9-dioctylfluorene) [PFO], pentacene (Pc), and C60 were deposited on n and p type Si wafers and diode structures were formed by depositing either a Au anode or Al cathode onto the organic film. The energy level alignment was assessed using built-in potential and capacitance-voltage measurements. In all cases, the results are consistent with near ideal vacuum energy level alignment between the organic and inorganic semiconductor. The diode current-voltage (I-V) characteristics are consistent with the electronic structure of the heterojunction interface. For n-Si/MEH-PPV/Au, the I-V curves are quantitatively described by an organic device model. For photocurrent measurements the diodes were illuminated through the semitransparent metal contact with optical wavelengths from 350–1100 nm. The photocurrent in the diode structure can be due to absorption either in the organic layer or Si substrate. For n-Si diodes, the 0 bias photocurrent is small with external quantum efficiencies (EQEs) less than 5×10−3 in all cases. The photocurrent is dominated by absorption in the organic layer for MEH-PPV, PFO, and C60 and by absorption in Si for Pc. For p-Si diodes, the 0 bias photocurrent is large with EQEs of ∼0.2 and is dominated by absorption in silicon for all organic layers. Both MEH-PPV and PFO form type I heterostructures with Si and photocurrent due to organic exciton dissociation is less efficient than in commonly used type II organic/organic heterostructures. Silicon/Pc and C60 heterojunctions are most likely type II with small valence (Pc) or conduction (C60) energy level differences. Surprisingly, no photocurrent was observed due to optical absorption in Pc most likely due to a chemical reaction between Pc and Si that prevented exciton dissociation at the heterojunction interface. In n-type/C60 structures photoconductive gain with EQE >3 was obtained and in p-type structures, the EQE was >0.15 and the spectral response of the photocurrent could be changed significantly from broad band absorption in Si to relatively narrow band absorption in C60.
Diblock copolymers in a cylindrical pore
Authors: Pinna Marco , Guo Xiaohu , Zvelindovsky Andrei V.
Published: December 2009

We show that a simple Ginzburg–Landau type theory can predict a tremendous rich “zoo” of diblock copolymer morphologies in cylindrical nanopores. Using the cell dynamics simulation we study in detail lamellar-, cylinder-, and eventually sphere-forming diblock copolymers melts in cylindrical nanopores. A very fast simulation method is proposed to be used as a research precursor for more elaborate computational techniques.
Structure and effects of vacancies in Σ3 (112) grain boundaries in Si
Authors: Feng C. B. , Nie J. L. , Zu X. T. , Al-Jassim M. M. , Yan Yanfa
Published: December 2009

Using the first-principle density-functional theory, we study the structure and effects of vacancies in Σ3 (112) grain boundary with the coincident-site lattice structure in Si. We find that the formation energy for a Si vacancy in the grain boundary is significantly lower than that in Si perfect region, indicating strong segregation of Si vacancy in grain boundary regions. The formation of Si vacancies in grain boundaries either cleans up the deep levels or facilitates complete passivation by H atoms. Our results suggest that vacancies in grain boundaries may play important role in determining grain boundary physics and passivation behavior.
Electronic properties of Ge dangling bond centers at Si1−xGex/SiO2 interfaces
Authors: Afanas’ev V. V. , Houssa M. , Stesmans A. , Souriau L. , Loo R. , Meuris M.
Published: December 2009

Comparison between densities of paramagnetic Ge dangling bond defects and shallow acceptor traps at interfaces of the condensation-grown Si1−xGex layers (0.28≤x≤0.93) with thermal SiO2 as a function of Ge fraction, x, reveals quantitative agreement. Moreover, defect densities detected in both magnetic resonance and electrical experiments exhibit reversible passivation-depassivation behavior with respect to hydrogen indicating observation of the same defect (Ge Pb1 center). The corresponding energy level is estimated to lie at 0.35±0.10 eV above the valence band in bulk Si, which makes these defects behave as shallow acceptors in Ge-rich Si1−xGex.
Maskless optical microscope lithography system
Authors: Park Eung Seok , Jang Doyoung , Lee Jaewoo , Kim Yun Jeong , Na Junhong , Ji Hyunjin , Choi Jae Wan , Kim Gyu-Tae
Published: December 2009

A simple maskless photolithography system employing an optical microscope, a motorized stage and a beam blanker is proposed. Based on a pattern design, the motorized stage shifts a resist-coated substrate exposed by a focused beam under a microscope. Microscale patterns are easily defined on a single nanowire without using a mask validating the application applying to the research requiring frequent changes or free-style designs in microscale test patterns.
Introducing sampling entropy in repository based adaptive umbrella sampling
Authors: Zheng Han , Zhang Yingkai
Published: December 2009

Determining free energy surfaces along chosen reaction coordinates is a common and important task in simulating complex systems. Due to the complexity of energy landscapes and the existence of high barriers, one widely pursued objective to develop efficient simulation methods is to achieve uniform sampling among thermodynamic states of interest. In this work, we have demonstrated sampling entropy (SE) as an excellent indicator for uniform sampling as well as for the convergence of free energy simulations. By introducing SE and the concentration theorem into the biasing-potential-updating scheme, we have further improved the adaptivity, robustness, and applicability of our recently developed repository based adaptive umbrella sampling (RBAUS) approach [H. Zheng and Y. Zhang, J. Chem. Phys. 128, 204106 (2008)]. Besides simulations of one dimensional free energy profiles for various systems, the generality and efficiency of this new RBAUS-SE approach have been further demonstrated by determining two dimensional free energy surfaces for the alanine dipeptide in gas phase as well as in water.
Optical waveguide and cavity effects on whispering-gallery mode resonances in a ZnO nanonail
Authors: Liu Jinzhang , Ngo Quang Minh , Park Kyung Ho , Kim Sangin , Ahn Yeong Hwan , Park Ji-Yong , Koh Ken Ha , Lee Soonil
Published: December 2009

Spatially resolved cathodoluminescence (CL) study of a ZnO nanonail, having thin shank, tapered neck, and hexagonal head sections, is reported. Monochromatic imaging and line-scan profiling indicate that the wave guiding and leaking from growth imperfections in addition to the oxygen-deficiency variation determine the spatial contrast of CL emissions. Occurrence of resonance peaks at identical wavelengths regardless of CL-excitation spots is inconsistent with the whispering-gallery mode (WGM) resonances of a two-dimensional cavity in the finite-difference time domain simulation. However, three-dimensioanl cavity simulation produced WGM peaks that are consistent with the experimental spectra, including transverse-electric resonances that are comparable to transverse-magnetic ones.
Low-voltage solution-processed n-channel organic field-effect transistors with high-k HfO2 gate dielectrics grown by atomic layer deposition
Authors: Tiwari Shree Prakash , Zhang Xiao-Hong , Potscavage William J. , Kippelen Bernard
Published: December 2009

High performance solution-processed n-channel organic field-effect transistors based on [6,6]-phenyl C61 butyric acid methyl ester with low operating voltages (3 V) are demonstrated using a high-k hafnium dioxide gate dielectric grown by atomic layer deposition. Devices exhibit excellent n-channel performance with electron mobility values up to 0.14 cm2/V s, threshold voltages of ∼0.3 V, current on/off ratios >105, and very low values of subthreshold slope (∼140 mV/decade).
The interlayer screening effect of graphene sheets investigated by Kelvin probe force microscopy
Authors: Lee N. J. , Yoo J. W. , Choi Y. J. , Kang C. J. , Jeon D. Y. , Kim D. C. , Seo S. , Chung H. J.
Published: December 2009

We report on the interlayer screening effect of graphene using Kelvin probe force microscopy (KPFM). By using a gate device configuration that enables the supply of electronic carriers in graphene sheets, the vertical screening properties were studied from measuring the surface potential gradient. The results show layer-dependence of graphene sheets, as the number of graphene layers increases, the surface potential decreases exponentially. In addition, we calculate the work function-related information of the graphene layers using KPFM.
Engineering the band gap of carbon nanotube for infrared sensors
Authors: Lai King Wai Chiu , Xi Ning , Fung Carmen Kar Man , Chen Hongzhi , Tarn Tzyh-Jong
Published: December 2009

Carbon nanotube (CNT) has been found to be one of the promising semiconducting materials for nanoelectronic sensors due to its unique electrical properties. Our group has developed a spectrum sensor using a single CNT and demonstrated its performance. In this paper, a steady and high-yield CNT band gap engineering will be developed and used to manufacture an appropriate CNT for infrared (IR) detection. The fabrication and experimental result of the CNT-based spectrum sensor will be presented. The results indicate that the CNT-based spectrum sensor is capable to sense near IR and middle-wave IR signals at room temperature.
Evaporation induced two-dimensional buckling within liquid droplet
Authors: Chen Ziguang , Liu Maozi , Liu Gang-yu , Tan Li
Published: December 2009

Evaporation of a liquid droplet containing a thin layer of surfactants atop could generate two-dimensional buckling on surfaces. Herringbone features were produced via embedded nanoparticle beds. We assign transient surface tension as the driving force for such a phenomenon. Considering the surfactant layer as a thin elastic film, a continuum model is employed to calculate the mechanical properties of the layer. Particularly, we estimated an elastic modulus of 4 GPa for the surfactant layer, indicating rather strong mechanical properties of these small molecules when they are close packed to form supramolecules via noncovalent binding.
What (Else) Matters? Policy Contexts, Emotional Geographies
Authors: Horton John , Kraftl Peter
Published: December 2009

In this paper we reflect upon a particular, policy-oriented evaluation of a Sure Start Centre: a small element of a UK government programme addressing children's well-being in ‘deprived’ neighbourhoods. Specifically, and contra some chief social-scientific accounts, we seek to acknowledge how ‘policy’ and ‘emotion’ were inseparable in this project. We suggest that policy and media discourses, and much extant research, regarding Sure Start have been characterised by a particular apprehension of what matters, which constitutes a particular assumption about how policy interventions, in ‘deprived’ neighbourhoods and elsewhere, should be evaluated. In marked contrast we propound qualitative data wherein users of the Sure Start Centre articulated how this facility mattered to them. Our aim is not simply to reiterate a twofold truism: policy is always emotional; emotions are latently political. Rather, we consider how, in the wake of this truism, more combinative, open-minded encounters between bodies of social-scientific endeavours conventionally labelled ‘policy relevant’ vis-à-vis ‘theoretical’ might yield more careful apprehensions of the emotion and affect in policy, and the politics of emotions and affects.
Ionic relations and osmotic adjustment in durum and bread wheat under saline conditions
Authors: Cuin Tracey Ann , Tian Yu , Betts Stewart A. , Chalmandrier Rémi , Shabala Sergey
Published: December 2009

Wheat breeding for salinity tolerance has traditionally focussed on Na+ exclusion from the shoot, but its association with salinity tolerance remains tenuous. Accordingly, the physiological significance of shoot Na+ exclusion and maintenance of an optimal K+ : Na+ ratio was re-evaluated by studying NaCl-induced responses in 50 genotypes of bread wheat (Triticum aestivum L.) and durum wheat (Triticum turgidum L. ssp. durum) treated with 150 mM NaCl. Overall, Na+ exclusion from the shoot correlated with salinity tolerance in both species and this exclusion was more efficient in bread compared with durum wheat. Interestingly, shoot sap K+ increased significantly in nearly all durum and bread wheat genotypes. Conversely, the total shoot K+ content declined. We argue that this increase in shoot sap K+ is needed to provide efficient osmotic adjustment under saline conditions. Durum wheat was able to completely adjust shoot sap osmolality using K+, Na+ and Cl–; it had intrinsically higher levels of these solutes. In bread wheat, organic osmolytes must contribute ~13% of the total shoot osmolality. In contrast to barley (Hordeum vulgare L.), NaCl-induced K+ efflux from seedling roots did not predict salinity tolerance in wheat, implying that shoot, not root K+ retention is important in this species.
Maintaining the yield of edible rice in a warming world
Authors: Fitzgerald Melissa A. , Resurreccion Adoracion P.
Published: December 2009

High temperature increases the amount of chalk in rice (Oryza sativa L.) grains, which causes grains to break during polishing, lowering the amount of rice for consumption. Here, we examined the effect of elevated temperature on substrate supply to the panicle, the capacity of the panicle to produce edible grains, and underlying factors affecting yield of edible grain in two varieties. During grain-filling, substrate supply followed a bell shaped curve, and high temperature significantly shortened supply time. The rate of grain-filling did not change and paddy yield fell in both varieties. In high temperature, yield loss in IR8 was due to lighter grains relative to those grown in cool temperature, but in IR60, it was due to the early sacrifice of 30% of the spikelets. The yield of edible rice was zero for IR8 and ~60% for IR60 for the high temperature treatments, and 100% for IR60 and 70% for IR8 in the cool temperature. IR60 differs from IR8 in regulation of substrate supply, architecture of the panicles and the capacity of the panicles to alter sink size in response to the stress and these factors may be responsible for the difference in edible rice in the two varieties.
Housekeeping gene selection in poplar plants under Cd-stress: comparative study for real-time PCR normalisation
Authors: Basa Brigitta , Solti Ádám , Sárvári Éva , Tamás László
Published: December 2009

Real-time RT–PCR is currently the most sensitive, specific and precise approach to analyse gene expression changes in plant stress studies. The determination of biologically meaningful transcript quantities requires accurate normalisation of the raw data. During relative quantification the reliability of the results depends on the stable expression of the endogenous control genes across the experimental samples. Four widely used internal control genes (cyclophilin, elongation factor 1α, polyubiquitin, tubulin β-chain) and two potential candidates (serine/threonine-protein phosphatase 2A and ubiquitin-conjugating enzyme) genes were assessed under Cd-stress and at different developmental stages in leaves of Populus jacquemontiana D. var. glauca H. Complementary DNA (RiboGreen) based quantification method revealed variations in the expression level of reference genes. The variability was more pronounced under severe stress conditions. Less variation was observed in the case of ef-1α, pp2a and ubc10. Transcript level changes of a target gene, psa-h, was also evaluated by two independent normalisation strategies, by the RiboGreen method or by using multiple references. The impact of variability of reference gene on the target gene evaluation was demonstrated. It was proved that in the absence of suitable housekeeping genes, for example under severe stress, RiboGreen method is convenient tool for transcript normalisation.
Impacts of UV radiation on growth and photosynthetic carbon acquisition in Gracilaria lemaneiformis (Rhodophyta) under phosphorus-limited and replete conditions
Authors: Xu Zhiguang , Gao Kunshan
Published: December 2009

Solar ultraviolet radiation (UVR, 280–400 nm) is known to negatively affect macroalgal growth and photosynthesis, while phosphorus availability may affect their sensitivity to UVR. Here, we show that UV-A enhanced the growth rate of the red macroalga, Gracilaria lemaneiformis Bory de Saint-Vincent under inorganic phosphorus (Pi)-replete but reduced it under Pi-limited conditions. Maximal net photosynthetic rates were significantly reduced by both UV-A and UV-B, but the apparent photosynthetic efficiency was enhanced in the presence of UV-A. The UV-induced inhibition was exacerbated under Pi-limited conditions. The activity of total carbonic anhydrase was enhanced and the photosynthetic affinity for exogenous inorganic carbon (Ci) was raised for thalli grown in the presence of UVR under both Pi-replete and Pi-limited conditions. The relative growth rate was closely related to Ci acquisition capability (Vmax/KDIC), which was enhanced by UVR exposure under Pi-replete but not significantly affected under Pi-limited conditions.
Interactive effects of high irradiance and moderate heat on photosynthesis, pigments, and tocopherol in the tree-fern Dicksonia antarctica
Authors: Volkova Liubov , Tausz Michael , Bennett Lauren T. , Dreyer Erwin
Published: December 2009

Effects of high irradiance and moderate heat on photosynthesis of the tree-fern Dicksonia antarctica (Labill., Dicksoniaceae) were examined in a climate chamber under two contrasting irradiance regimes (900 and 170 µmol photons m–2 s–1) and three sequential temperature treatments (15°C; 35°C; back to 15°C). High irradiance led to decline in predawn quantum yield of photochemistry, Fv/Fm (0.73), maximal Rubisco activity (Vcmax; from 37 to 29 µmol m–2s–1), and electron transport capacity (Jmax; from 115 to 67 µmol m–2 s–1). Temperature increase to 35°C resulted in further decreases in Fv/Fm (0.45) and in chlorophyll bleaching of high irradiance plants, while Vcmax and Jmax were not affected. Critical temperature for thylakoid stability (Tc) of D. antarctica was comparable with other higher plants (c. 47°C), and increases of Tc with air temperature were greater in high irradiance plants. Increased Tc was not associated with accumulation of osmotica or zeaxanthin formation. High irradiance increased the xanthophyll cycle pigment pool (V+A+Z, 91 v. 48 mmol mol–1 chlorophyll–1), de-epoxidation state (56% v. 4%), and α-tocopherol. Temperature increase to 35°C had no effect on V+A+Z and de-epoxidation state in both light regimes, while lutein, β-carotene and α-tocopherols increased, potentially contributing to increased membrane stability under high irradiance.
Human medial temporal lobe neurons respond preferentially to personally relevant images
Authors: Viskontas Indre V. , Quiroga Rodrigo Quian , Fried Itzhak
Published: December 2009

People with whom one is personally acquainted tend to elicit richer and more vivid memories than people with whom one does not have a personal connection. Recent findings from neurons in the human medial temporal lobe (MTL) have shown that individual cells respond selectively and invariantly to representations of famous people [Quian Quiroga R, Reddy L, Kreiman G, Koch C, Fried I (2005)
Nature
435(7045):1102–1107]. Observing these cells, we wondered whether photographs of personally relevant individuals, such as family members, might be more likely to generate such responses. To address this issue, we recorded the activity of 2,330 neurons in the human MTL while patients viewed photographs of varying personal relevance: previously unknown faces and landscapes, familiar but not necessarily personally relevant faces and landscapes, and finally, photographs of the patients themselves, their families, and the experimenters. Our findings indicate that personally relevant photographs are indeed more likely to elicit selective responses in MTL neurons than photographs of individuals with whom the patients have had no personal contact. These findings further suggest that relevant stimuli are encoded by a larger proportion of neurons than less relevant stimuli, given that familiar or personally relevant items are linked to a larger variety of experiences and memories of these experiences.
Comparative genomics of autism and schizophrenia
Authors: Crespi Bernard , Stead Philip , Elliot Michael
Published: December 2009

We used data from studies of copy-number variants (CNVs), single-gene associations, growth-signaling pathways, and intermediate phenotypes associated with brain growth to evaluate four alternative hypotheses for the genomic and developmental relationships between autism and schizophrenia: (
i
) autism subsumed in schizophrenia, (
ii
) independence, (
iii
) diametric, and (
iv
) partial overlap. Data from CNVs provides statistical support for the hypothesis that autism and schizophrenia are associated with reciprocal variants, such that at four loci, deletions predispose to one disorder, whereas duplications predispose to the other. Data from single-gene studies are inconsistent with a hypothesis based on independence, in that autism and schizophrenia share associated genes more often than expected by chance. However, differentiation between the partial overlap and diametric hypotheses using these data is precluded by limited overlap in the specific genetic markers analyzed in both autism and schizophrenia. Evidence from the effects of risk variants on growth-signaling pathways shows that autism-spectrum conditions tend to be associated with up-regulation of pathways due to loss of function mutations in negative regulators, whereas schizophrenia is associated with reduced pathway activation. Finally, data from studies of head and brain size phenotypes indicate that autism is commonly associated with developmentally-enhanced brain growth, whereas schizophrenia is characterized, on average, by reduced brain growth. These convergent lines of evidence appear most compatible with the hypothesis that autism and schizophrenia represent diametric conditions with regard to their genomic underpinnings, neurodevelopmental bases, and phenotypic manifestations as reflecting under-development versus dysregulated over-development of the human social brain.
A circadian clock in macrophages controls inflammatory immune responses
Authors: Keller Maren , Mazuch Jeannine , Abraham Ute , Eom Gina D. , Herzog Erik D. , Volk Hans-Dieter , Kramer Achim , Maier Bert
Published: December 2009

Time of day-dependent variations of immune system parameters are ubiquitous phenomena in immunology. The circadian clock has been attributed with coordinating these variations on multiple levels; however, their molecular basis is little understood. Here, we systematically investigated the link between the circadian clock and rhythmic immune functions. We show that spleen, lymph nodes, and peritoneal macrophages of mice contain intrinsic circadian clockworks that operate autonomously even ex vivo. These clocks regulate circadian rhythms in inflammatory innate immune functions: Isolated spleen cells stimulated with bacterial endotoxin at different circadian times display circadian rhythms in TNF-α and IL-6 secretion. Interestingly, we found that these rhythms are not driven by systemic glucocorticoid variations nor are they due to the detected circadian fluctuation in the cellular constitution of the spleen. Rather, a local circadian clock operative in splenic macrophages likely governs these oscillations as indicated by endotoxin stimulation experiments in rhythmic primary cell cultures. On the molecular level, we show that >8% of the macrophage transcriptome oscillates in a circadian fashion, including many important regulators for pathogen recognition and cytokine secretion. As such, understanding the cross-talk between the circadian clock and the immune system provides insights into the timing mechanism of physiological and pathophysiological immune functions.
Carboxylated molecules regulate magnesium content of amorphous calcium carbonates during calcification
Authors: Wang Dongbo , Wallace Adam F. , De Yoreo James J. , Dove Patricia M.
Published: December 2009

With the realization that many calcified skeletons form by processes involving a precursor phase of amorphous calcium carbonate (ACC), a new paradigm for mineralization is emerging. There is evidence the Mg content in biogenic ACC is regulated by carboxylated (acidic) proteins and other macromolecules, but the physical basis for such a process is unknown. We test the hypothesis that ACC compositions express a systematic relationship to the chemistry of carboxyl-rich biomolecules. A series of inorganic control experiments were conducted to establish the dependence of Mg/Ca ratios in ACC on solution composition. We then determined the influence of a suite of simple carboxylated organic acids on Mg content. Molecules with a strong affinity for binding Ca compared with Mg promote the formation of Mg-enriched ACC that is compositionally equivalent to high-magnesium calcites and dolomite. Measurements show Mg/Ca ratios are controlled by a predictable dependence upon the binding properties of the organic molecules. The trend appears rooted in the conformation and electrostatic potential topology of each molecule, but dynamic factors also may be involved. The dependence suggests a physical basis for reports that specific sequences of calcifying proteins are critical to modulating mineralization. Insights from this study may provide a plausible explanation for why some biogenic carbonates and carbonaceous cements often contain higher Mg signatures than those that are possible by classical crystal growth processes. The findings reiterate the controls of microenvironment on mineralization and suggest an origin of compositional offsets, or vital effects, long recognized by the paleoclimate community.
Identifying the missing steps of the autotrophic 3-hydroxypropionate CO
2
fixation cycle in
Chloroflexus aurantiacus
Authors: Zarzycki Jan , Brecht Volker , Müller Michael , Fuchs Georg
Published: December 2009

The phototrophic bacterium
Chloroflexus aurantiacus
uses a yet unsolved 3-hydroxypropionate cycle for autotrophic CO
2
fixation. It starts from acetyl-CoA, with acetyl-CoA and propionyl-CoA carboxylases acting as carboxylating enzymes. In a first cycle, (
S
)-malyl-CoA is formed from acetyl-CoA and 2 molecules of bicarbonate. (
S
)-Malyl-CoA cleavage releases the CO
2
fixation product glyoxylate and regenerates the starting molecule acetyl-CoA. Here we complete the missing steps devoted to glyoxylate assimilation. In a second cycle, glyoxylate is combined with propionyl-CoA, an intermediate of the first cycle, to form β-methylmalyl-CoA. This condensation is followed by dehydration to mesaconyl-C1-CoA. An unprecedented CoA transferase catalyzes the intramolecular transfer of the CoA moiety to the C4 carboxyl group of mesaconate. Mesaconyl-C4-CoA then is hydrated by an enoyl-CoA hydratase to (
S
)-citramalyl-CoA. (
S
)-Citramalyl-CoA is cleaved into acetyl-CoA and pyruvate by a tri-functional lyase, which previously cleaved (
S
)-malyl-CoA and formed β-methylmalyl-CoA. Thus, the enigmatic disproportionation of glyoxylate and propionyl-CoA into acetyl-CoA and pyruvate is solved in an elegant and economic way requiring only 3 additional enzymes. The whole bicyclic pathway results in pyruvate formation from 3 molecules of bicarbonate and involves 19 steps but only 13 enzymes. Elements of the 3-hydroxypropionate cycle may be used for the assimilation of small organic molecules. The 3-hydroxypropionate cycle is compared with the Calvin–Benson–Bassham cycle and other autotrophic pathways.
Impact of spatial clustering on disease transmission and optimal control
Authors: Tildesley Michael J. , House Thomas A. , Bruhn Mark C. , Curry Ross J. , O’Neil Maggie , Allpress Justine L. E. , Smith Gary , Keeling Matt J.
Published: December 2009

Spatial heterogeneities and spatial separation of hosts are often seen as key factors when developing accurate predictive models of the spread of pathogens. The question we address in this paper is how coarse the resolution of the spatial data can be for a model to be a useful tool for informing control policies. We examine this problem using the specific case of foot-and-mouth disease spreading between farms using the formulation developed during the 2001 epidemic in the United Kingdom. We show that, if our model is carefully parameterized to match epidemic behavior, then using aggregate county-scale data from the United States is sufficient to closely determine optimal control measures (specifically ring culling). This result also holds when the approach is extended to theoretical distributions of farms where the spatial clustering can be manipulated to extremes. We have therefore shown that, although spatial structure can be critically important in allowing us to predict the emergent population-scale behavior from a knowledge of the individual-level dynamics, for this specific applied question, such structure is mostly subsumed in the parameterization allowing us to make policy predictions in the absence of high-quality spatial information. We believe that this approach will be of considerable benefit across a range of disciplines where data are only available at intermediate spatial scales.
Coxibs interfere with the action of aspirin by binding tightly to one monomer of cyclooxygenase-1
Authors: Rimon Gilad , Sidhu Ranjinder S. , Lauver D. Adam , Lee Jullia Y. , Sharma Narayan P. , Yuan Chong , Frieler Ryan A. , Trievel Raymond C. , Lucchesi Benedict R. , Smith William L.
Published: December 2009

Pain associated with inflammation involves prostaglandins synthesized from arachidonic acid (AA) through cyclooxygenase-2 (COX-2) pathways while thromboxane A2formed by platelets from AA via cyclooxygenase-1 (COX-1) mediates thrombosis. COX-1 and COX-2 are both targets of nonselective nonsteroidal antiinflammatory drugs (nsNSAIDs) including aspirin whereas COX-2 activity is preferentially blocked by COX-2 inhibitors called coxibs. COXs are homodimers composed of identical subunits, but we have shown that only one subunit is active at a time during catalysis; moreover, many nsNSAIDS bind to a single subunit of a COX dimer to inhibit the COX activity of the entire dimer. Here, we report the surprising observation that celecoxib and other coxibs bind tightly to a subunit of COX-1. Although celecoxib binding to one monomer of COX-1 does not affect the normal catalytic processing of AA by the second, partner subunit, celecoxib does interfere with the inhibition of COX-1 by aspirin in vitro. X-ray crystallographic results obtained with a celecoxib/COX-1 complex show how celecoxib can bind to one of the two available COX sites of the COX-1 dimer. Finally, we find that administration of celecoxib to dogs interferes with the ability of a low dose of aspirin to inhibit AA-induced ex vivo platelet aggregation. COX-2 inhibitors such as celecoxib are widely used for pain relief. Because coxibs exhibit cardiovascular side effects, they are often prescribed in combination with low-dose aspirin to prevent thrombosis. Our studies predict that the cardioprotective effect of low-dose aspirin on COX-1 may be blunted when taken with coxibs.
Dysbindin regulates hippocampal LTP by controlling NMDA receptor surface expression
Authors: Tang Tina Tze-Tsang , Yang Feng , Chen Bo-Shiun , Lu Yuan , Ji Yuanyuan , Roche Katherine W. , Lu Bai
Published: December 2009

Abnormalities in NMDA receptor (NMDAR) function have been implicated in schizophrenia. Here, we show that
dysbindin
, a schizophrenia-susceptibility gene widely expressed in the forebrain, controls the surface expression of NMDARs in a subunit-specific manner. Imaging analyses revealed a marked increase in surface NR2A, but not NR2B, in hippocampal neurons derived from
dysbindin
-null mutant mice (Dys−/−). Exogenous expression of
dysbindin
reduced NR2A surface expression in both wild-type and Dys−/− neurons. Biotinylation experiments also revealed an increase in surface expression of endogenous NR2A in Dys−/− neurons. Disruption of the
dysbindin
gene dramatically increased NR2A-mediated synaptic currents, without affecting AMPA receptor currents, in hippocampal CA1 neurons. The Dys−/− hippocampal slices exhibited an enhanced LTP, whereas basal synaptic transmission, presynaptic properties, and LTD were normal. Thus, dysbindin controls hippocampal LTP by selective regulation of the surface expression of NR2A. These results reveal subunit-specific regulation of NMDARs by dysbindin, providing an unexpected link between these two proteins implicated in schizophrenia.
Epistatic interactions between genetic disorders of hemoglobin can explain why the sickle-cell gene is uncommon in the Mediterranean
Authors: Penman Bridget S. , Pybus Oliver G. , Weatherall David J. , Gupta Sunetra
Published: December 2009

Several human genetic disorders of hemoglobin have risen in frequency because of the protection they offer against death from malaria, sickle-cell anemia being a canonical example. Here we address the issue of why this highly protective mutant, present at high frequencies in subSaharan Africa, is uncommon in Mediterranean populations that instead harbor a diverse range of thalassemic hemoglobin disorders. We demonstrate that these contrasting profiles of malaria-protective alleles can arise and be stably maintained by two well-documented phenomena: an alleviation of the clinical severity of α- and β-thalassemia in compound thalassemic genotypes and a cancellation of malaria protection when α-thalassemia and the sickle-cell trait are coinherited. The complex distribution of globin mutants across Africa and the Mediterranean can therefore be explained by their specific intracellular interactions.
Itk tyrosine kinase substrate docking is mediated by a nonclassical SH2 domain surface of PLCγ1
Authors: Min Lie , Joseph Raji E. , Fulton D. Bruce , Andreotti Amy H.
Published: December 2009

Interleukin-2 tyrosine kinase (Itk) is a Tec family tyrosine kinase that mediates signaling processes after T cell receptor engagement. Activation of Itk requires recruitment to the membrane via its pleckstrin homology domain, phosphorylation of Itk by the Src kinase, Lck, and binding of Itk to the SLP-76/LAT adapter complex. After activation, Itk phosphorylates and activates phospholipase C-γ1 (PLC-γ1), leading to production of two second messengers, DAG and IP3. We have previously shown that phosphorylation of PLC-γ1 by Itk requires a direct, phosphotyrosine-independent interaction between the Src homology 2 (SH2) domain of PLC-γ1 and the kinase domain of Itk. We now define this docking interface using a combination of mutagenesis and NMR spectroscopy and show that disruption of the Itk/PLCγ1 docking interaction attenuates T cell signaling. The binding surface on PLCγ1 that mediates recognition by Itk highlights a nonclassical binding activity of the well-studied SH2 domain providing further evidence that SH2 domains participate in important signaling interactions beyond recognition of phosphotyrosine.
An arithmetic rule for spatial summation of excitatory and inhibitory inputs in pyramidal neurons
Authors: Hao Jiang , Wang Xu-dong , Dan Yang , Poo Mu-ming , Zhang Xiao-hui
Published: December 2009

Dendritic integration of excitatory and inhibitory inputs is critical for neuronal computation, but the underlying rules remain to be elucidated. Based on realistic modeling and experiments in rat hippocampal slices, we derived a simple arithmetic rule for spatial summation of concurrent excitatory glutamatergic inputs (
E
) and inhibitory GABAergic inputs (
I
). The somatic response can be well approximated as the sum of the excitatory postsynaptic potential (EPSP), the inhibitory postsynaptic potential (IPSP), and a nonlinear term proportional to their product (
k
*EPSP*IPSP), where the coefficient
k
reflects the strength of shunting effect. The
k
value shows a pronounced asymmetry in its dependence on
E
and
I
locations. For
I
on the dendritic trunk,
k
decays rapidly with
E–I
distance for proximal
E
s, but remains largely constant for distal
E
s, indicating a uniformly high shunting efficacy for all distal
E
s. For
I
on an oblique branch, the shunting effect is restricted mainly within the branch, with the same proximal/distal asymmetry. This asymmetry can be largely attributed to cable properties of the dendrite. Further modeling studies showed that this rule also applies to the integration of multiple coincident
E
s and
I
s. Thus, this arithmetic rule offers a simple analytical tool for studying
E–I
integration in pyramidal neurons that incorporates the location specificity of GABAergic shunting inhibition.
Substance Abuse Screening in Student Health Services
Authors: Rickman Kathleen J. , Mackey Thomas A.
Published: December 2009

Alcohol and drug abuse among college students in the United States concerns both educators and health care providers. Morbidity and mortality from binge drinking, automobile accidents, sexually transmitted diseases, and suicides continue to impact students between 18 and 25 years of age. Those providing health care services to this population have a responsibility to screen for substance abuse. The purpose of this study was to identify college and university student health services currently screening for AODA in students. A survey questionnaire was mailed to 873 student health clinics listed in the directory of the American College Health Association to determine frequency, methods, and outcomes of screening for AODA. Among the 277 respondents, 37% routinely screened for AODA; of those, only 40% had received training in AODA screening. Additional training is needed by student health care personnel; 76% stated that they would attend such training if it were available.
Perinatal Substance Use Patterns in Obstetrics-Gynecology
Authors: Veach Tracy L. , Sheld Harrison , Pistorello Jacqueline , Arkowitz Laura , Chappel John N.
Published: December 2009

Alcohol, tobacco, and other drug abuse (ATODA) prevalence and use patterns were examined in a university-based ambulatory clinic. Anonymous and confidential questionnaires, interviews, and medical record reviews were conducted with a sample of 139 women. Participants tended to be young (average age was 23 years old), unemployed (93%), and never married (55%). The average participant was 20 weeks pregnant and had sought care at 14.9 weeks. Thirty-eight percent were smokers, with 21.3 and 8.8% reporting use of alcohol or other drugs during pregnancy, respectively. Less than a quarter recalled being asked by their physicians or the clinic staff about alcohol and other drug use. Slightly more recalled being asked about tobacco (25.7%) and nutritional habits (31.6%). Assessment of ATODA issues is difficult with this population, where fear of prosecution may augment the standard barriers of denial and stigmatization. Nevertheless, it is clear that perinatal substance abuse requires more effective education and training in brief assessment and intervention strategies for ambulatory clinic staff as well as community treatment linkages.
Peer Counselor Training: One Component of a Medical Student Health and Effectiveness Program
Authors: McKinney Martha , McGann K. Patricia , Hunt J. Cashin , Edwards K. Suzanne
Published: December 2009

This paper describes a peer counselor training program designed to train student volunteers to help their fellow students with a wide range of difficulties caused or exacerbated by medical training. The training program is described in detail, demographic characteristics of the participants are compared to those of the rest of the student body, and the activities of the peer counselors are reported. The students did not differ significantly from the rest of the student body by age, race, gender, or academic standing. Eight percent of the student body used the services of the peer counselors, and two students were directed into treatment for alcoholism. Development of similar programs at other medical schools is recommended.
Models of Medical Care for HIV-infected Drug Users
Authors: Samet Jeffrey H. , Stein Michael D. , O'Connor Patrick G.
Published: December 2009

HIV-infected substance users present a variety of challenges to successful health care delivery. Difficulties in care arise from several issues including provider-patient mistrust, lack of education on the part of providers regarding issues related to addiction, and personal disorganization on the part of active users. Each of these issues affects patient adherence to medical regimens and access to care. Standard ambulatory medical settings may not effectively engage addicts in longitudinal comprehensive care. We present an overview and critique of models specifically designed to treat this population.
The Use of Contingency Contracting to Improve Outcome in Methadone Maintenance
Authors: Leal Jorge , Galanter Marc
Published: December 2009

Methadone programs today are faced with high rates of illicit drug use and patient attrition. Attempts to reduce illicit drug use and improve compliance have included the use of contingency contracting systems. Contingency contracting relies on the use of rewarding or aversive incentives to alter noncompliant behaviors. Their use has led to improvements in retention and compliance for a subgroup of otherwise noncompliant methadone maintenance program patients. Practical considerations in the implementation of contingency contracts, observations of their time-limited effects, and the need for more potent and efficacious incentives have become issues needing further research.
Interrater Reliability of the Alcoholism Denial Rating Scale
Authors: Breuer Hans H. , Goldsmith R. Jeffrey
Published: December 2009

The Denial Rating Scale (DRS) was developed to measure alcoholic denial. A previous study examined the interrater reliability of the DRS using only written treatment summaries. Estimates ranged from 0.67 to 0.77 (P < 0.001). In the current study, the investigators hypothesized that the reliability of the ratings would be enhanced with minimal training if they used a semistructured interview with a decision tree as well as videotaped interviews. Twenty interviews of voluntary alcoholic subjects were videotaped. Both investigators and five therapists from an alcoholism clinic participated in the study by rating the denial level of the subjects on the tapes. Through the use of the semistructured interview and the decision tree model, the interrater reliability was improved. Current estimates ranged from 0.827 to 0.966 (P < 0.001).
Childhood Experiences of Alcoholic African-American and Caucasian Women
Authors: Michels Philip J. , Johnson N. Peter , Sheridan David P.
Published: December 2009

Three hundred nine African-American and Caucasian alcoholic and nonalcoholic females ranging in age from 20 to 49 years old were individually administered a 77-page questionnaire. Results of a series of multivariate odds-ratio analyses based on self-report from memories of childhood indicate that alcoholic women reported significantly more nightmares, bedwetting, temper tantrums, phobias, bruxism, and nervous problems than nonalcoholic women. They reported significantly more school-related problems including expulsion/suspension, skipping school, trouble with school authorities, and dropping out of high school compared to nonalcoholic women. Feelings of nervousness, loneliness, and embarrassment around peers were reported significantly more often by alcoholic women. The prediction of alcoholism by childhood behavioral dysfunction differed as a function of race or age on only 4 of the 20 variables examined.
Abuse of Psychoactive Pharmaceuticals in Greece: Relevance of Disseminating Epidemiological and Clinical Research Findings to Postgraduate Medical Students
Authors: Kokkevi A. , Stefanis C. N.
Published: December 2009

In Greece, due to overconsumption of psychoactive pharmaceuticals either under medical supervision or illicitly, there is a growing need to reform the medical curricula, at both the undergraduate and the postgraduate level, and include as a priority subject the proper prescribing of psychoactive substances in order to limit negative consequences, particularly among the young, resulting from their improper and prolonged use. Further support of this need is provided by cross-sectional data presented in this paper deriving from two nationwide surveys, one on a student population ages 14-18 and the other on dependent individuals seeking treatment. Strong correlations were found between prescribed use of pharmaceuticals and both unprescribed and illicit drug use. The findings support the assumption that abuse of psychoactive drugs represents a masked phenomenon of dependency, sharing with illicit drug use common underlying factors such as psychological/behavioral problems and psychiatric comorbidity. All medical specialists, pediatricians and psychiatrists in particular need to be informed of the high risk of abuse of psychoactive pharmaceuticals and of the psychological factors underlying their use in order to modify their treatment approaches and prescribing practices.