bluuebunny/crossref_metadata_2025 huggingface dataset:
Critical assessment of methods of protein structure prediction (CASP)—round IX
Authors: Moult John , Fidelis Krzysztof , Kryshtafovych Andriy , Tramontano Anna
Published: September 2011

This article is an introduction to the special issue of the journal PROTEINS, dedicated to the ninth Critical Assessment of Structure Prediction (CASP) experiment to assess the state of the art in protein structure modeling. The article describes the conduct of the experiment, the categories of prediction included, and outlines the evaluation and assessment procedures. Methods for modeling protein structure continue to advance, although at a more modest pace than in the early CASP experiments. CASP developments of note are indications of improvement in model accuracy for some classes of target, an improved ability to choose the most accurate of a set of generated models, and evidence of improvement in accuracy for short “new fold” models. In addition, a new analysis of regions of models not derivable from the most obvious template structure has revealed better performance than expected. Proteins 2011; © 2011 Wiley‐Liss, Inc.
A structural and functional dissection of the cardiac stress response factor MS1
Authors: Fogl Claudia , Puckey Loretto , Hinssen Ulrike , Zaleska Mariola , El‐Mezgueldi Mohammed , Croasdale Rebecca , Bowman Andrew , Matsukawa Akira , Samani Nilesh J. , Savva Renos , Pfuhl Mark
Published: September 2011

MS1 is a protein predominantly expressed in cardiac and skeletal muscle that is upregulated in response to stress and contributes to development of hypertrophy. In the aortic banding model of left ventricular hypertrophy, its cardiac expression was significantly upregulated within 1 h. Its function is postulated to depend on its F‐actin binding ability, located to the C‐terminal half of the protein, which promotes stabilization of F‐actin in the cell thus releasing myocardin‐related transcription factors to the nucleus where they stimulate transcription in cooperation with serum response factor. Initial attempts to purify the protein only resulted in heavily degraded samples that showed distinct bands on SDS gels, suggesting the presence of stable domains. Using a combination of combinatorial domain hunting and sequence analysis, a set of potential domains was identified. The C‐terminal half of the protein actually contains two independent F‐actin binding domains. The most C‐terminal fragment (294–375), named actin binding domain 2 (ABD2), is independently folded while a proximal fragment called ABD1 (193–296) binds to F‐actin with higher affinity than ABD2 (KD 2.21 ± 0.47 μM vs. 10.61 ± 0.7 μM), but is not structured by itself in solution. NMR interaction experiments show that it binds and folds in a cooperative manner to F‐actin, justifying the label of domain. The architecture of the MS1 C‐terminus suggests that ABD1 alone could completely fulfill the F‐actin binding function opening up the intriguing possibility that ABD2, despite its high level of conservation, could have developed other functions. Proteins 2012. © 2011 Wiley Periodicals, Inc.
Structural insight into mechanism and diverse substrate selection strategy of L‐ribulokinase
Authors: Agarwal Rakhi , Burley Stephen K. , Swaminathan Subramanyam
Published: September 2011

The araBAD operon encodes three different enzymes required for catabolism of
L‐arabinose, which is one of the most abundant monosaccharides in nature.
L‐ribulokinase, encoded by the araB gene, catalyzes conversion of
L‐ribulose to
L‐ribulose‐5‐phosphate, the second step in the catabolic pathway. Unlike other kinases, ribulokinase exhibits diversity in substrate selectivity and catalyzes phosphorylation of all four 2‐ketopentose sugars with comparable kcat values. To understand ribulokinase recognition and phosphorylation of a diverse set of substrates, we have determined the X‐ray structure of ribulokinase from Bacillus halodurans bound to
L‐ribulose and investigated its substrate and ATP co‐factor binding properties. The polypeptide chain is folded into two domains, one small and the other large, with a deep cleft in between. By analogy with related sugar kinases, we identified 447GGLPQK452 as the ATP‐binding motif within the smaller domain.
L‐ribulose binds in the cleft between the two domains via hydrogen bonds with the side chains of highly conserved Trp126, Lys208, Asp274, and Glu329 and the main chain nitrogen of Ala96. The interaction of
L‐ribulokinase with
L‐ribulose reveals versatile structural features that help explain recognition of various 2‐ketopentose substrates and competitive inhibition by
L‐erythrulose. Comparison of our structure to that of the structures of other sugar kinases revealed conformational variations that suggest domain–domain closure movements are responsible for establishing the observed active site environment. Proteins 2012; © 2011 Wiley Periodicals, Inc.
Teachers learning from professional development in elementary science: Reciprocal relations between formative assessment and pedagogical content knowledge
Authors: Falk Andrew
Published: September 2011

Formative assessment, assessment used to inform subsequent learning, can have a powerful positive impact on student achievement, but little empirical work has been conducted to investigate the role of teachers' knowledge in its practice. This study investigated reciprocal relations between elementary science teachers' formative assessment practices and their pedagogical content knowledge (PCK). Data sources included video records and artifacts from a professional development (PD) program that engaged 11 teachers in collaborative analysis of their students' work. Analysis of the data showed that teachers' PCK was a resource in all aspects of their formative assessment practice, and teachers most frequently made use of their existing knowledge of instructional strategies and curriculum. It also showed that teachers constructed PCK through formative assessment by building and refining knowledge of curricular goals and student understanding over multiple PD sessions. Findings suggest that formative assessment can be a powerful opportunity for teachers to use, integrate, and generate PCK but that teachers require additional resources to build knowledge of instructional strategies. © 2011 Wiley Periodicals, Inc. Sci Ed 96:265–290, 2012
Film formation of yogurt under confined condition
Authors: Ma Liran , Luo Jianbin , Zhang Chenhui , Ma Zhizuo , Wang Yan , Dai Yuanjing
Published: September 2011

The yogurt film confined within a nanogap was investigated by the thin film interferometry between two solid surfaces. Significantly thick film was found even under a low speed, which indicated yogurt might have excellent lubrication performance. The film thickness was much higher than the prediction of elastohydrodynamic lubrication theory. Experiment results indicated that the thick confined film of yogurt can be induced by the adhesion of organic material, which can sustain high pressure without being extruded under low speed. The effect of the rolling speed on film thickness shows that the lubrication under a high rolling speed tends to be the elastohydrodynamic lubrication. Copyright © 2011 John Wiley & Sons, Ltd.
George of Laodicea: A Historical Reassessment
Authors: DelCOGLIANO MARK
Published: September 2011

For nearly forty years George of Laodicea (c. 290–359) played a significant role in the fourth-century Trinitarian controversy. Yet among scholars of the period his contribution has been understudied, underappreciated and misunderstood. This article aims to reconstruct George's career in a way that eliminates earlier distortions, corrects certain oft-repeated mistakes and includes frequently omitted evidence. It argues that George was one of the principal leaders of the Eusebian alliance in its last two decades. It also suggests that his leadership role in the Homoiousian alliance was more significant than is usually thought: he was the catalyst for its formation and emerged as its champion in the aftermath of the failed leadership of Basil of Ancyra.
How Coifi Pierced Christ's Side: A Re-Examination of Bede'sEcclesiastical History, II, Chapter 13
Authors: BARROW JULIA
Published: September 2011

This paper adopts an exegetical approach to Bede's narrative of the conversion of King Edwin of Northumbria in theHistoria ecclesiasticaii. 9–14. HE ii. 12–13, which is loosely based on passages in the WhitbyLifeof Gregory the Great, diverge significantly from the latter in order to explore biblical parallels. Bede's description of Coifi's ride to the pagan shrine at Goodmanham in order to throw a lance into it is an inversion of the account of the piercing of Christ's side inJohn xix.34:just as water flowed from Christ's side so the piercing of the shrine led to the baptism of the Northumbrians.
GEL CRITERIA FOR MOMENT CONDITION MODELS
Authors: Smith Richard J.
Published: September 2011

GEL methods that generalize and extend previous contributions are defined and analyzed for moment condition models specified in terms of weakly dependent data. These procedures offer alternative one-step estimators and tests that are asymptotically equivalent to their efficient two-step GMM counterparts. The basis for GEL estimation is via a smoothed version of the moment indicators using kernel function weights that incorporate a bandwidth parameter. Examples for the choice of bandwidth parameter and kernel function are provided. Efficient moment estimators based on implied probabilities derived from the GEL method are proposed, a special case of which is estimation of the stationary distribution of the data. The paper also presents a unified set of test statistics for overidentifying moment restrictions and combinations of parametric and moment restriction hypotheses.
Incidence of self-reported acute gastrointestinal infections in the community in Poland: a population-based study
Authors: BAUMANN-POPCZYK A. , SADKOWSKA-TODYS M. , ROGALSKA J. , STEFANOFF P.
Published: September 2011

A retrospective cross-sectional survey of self-reported acute gastrointestinal infection (AGI) incidence in the community was performed in Poland, from December 2008 to November 2009. The aim of the study was to estimate the magnitude and distribution of self-reported AGI, in order to calibrate the routine AGI surveillance system in Poland. The study population were randomly selected residents of all Polish regions, having a fixed telephone line. An equal number of telephone interviews were collected each month, requesting the interviewee to identify gastrointestinal symptoms that had occurred in the previous 4 weeks. The international AGI case definition was used. In total 3583 complete interviews were obtained. The compliance ratio was 26%. Of 3583 respondents, 240 (6·7%) individuals fulfilled the AGI case definition. The annualized incidence of acute gastroenteritis was 0·9/person-year (95% confidence interval 0·8–1·0). Comparison of the obtained annual AGI estimate (33·3 million infections) with the number of cases reported to national surveillance during the corresponding period (73 512), yielded an underreporting factor of 453 cases occurring in the community for each reported case. Of the 240 AGI cases, 30·4% consulted a general practitioner, and 4·6% were admitted to hospital. Samples for microbiological confirmation were collected from four (1·6%) cases. This first population-based study in eastern Europe has confirmed that AGI places a high burden on Polish society, which is underestimated by national surveillance data. Efforts are necessary to improve AGI reporting and diagnostic practices in order to increase the effectiveness of the Polish surveillance system in detecting threats related to new AGI pathogens, new routes of transmission or the potential for international spread.
Education Does Not Slow Cognitive Decline with Aging: 12-Year Evidence from the Victoria Longitudinal Study
Authors: Zahodne Laura B. , Glymour M. Maria , Sparks Catharine , Bontempo Daniel , Dixon Roger A. , MacDonald Stuart W.S. , Manly Jennifer J.
Published: September 2011

Although the relationship between education and cognitive status is well-known, evidence regarding whether education moderates the trajectory of cognitive change in late life is conflicting. Early studies suggested that higher levels of education attenuate cognitive decline. More recent studies using improved longitudinal methods have not found that education moderates decline. Fewer studies have explored whether education exerts different effects on longitudinal changes within different cognitive domains. In the present study, we analyzed data from 1014 participants in the Victoria Longitudinal Study to examine the effects of education on composite scores reflecting verbal processing speed, working memory, verbal fluency, and verbal episodic memory. Using linear growth models adjusted for age at enrollment (range, 54–95 years) and gender, we found that years of education (range, 6–20 years) was strongly related to cognitive level in all domains, particularly verbal fluency. However, education was not related to rates of change over time for any cognitive domain. Results were similar in individuals older or younger than 70 at baseline, and when education was dichotomized to reflect high or low attainment. In this large longitudinal cohort, education was related to cognitive performance but unrelated to cognitive decline, supporting the hypothesis of passive cognitive reserve with aging. (JINS, 2011, 17, 1039–1046)
Cognitive Outcomes for Extremely Preterm/Extremely Low Birth Weight Children in Kindergarten
Authors: Orchinik Leah J. , Taylor H. Gerry , Espy Kimberly Andrews , Minich Nori , Klein Nancy , Sheffield Tiffany , Hack Maureen
Published: September 2011

Our objectives were to examine cognitive outcomes for extremely preterm/extremely low birth weight (EPT/ELBW, gestational age <28 weeks and/or birth weight <1000 g) children in kindergarten and the associations of these outcomes with neonatal factors, early childhood neurodevelopmental impairment, and socioeconomic status (SES). The sample comprised a hospital-based 2001–2003 birth cohort of 148 EPT/ELBW children (mean birth weight 818 g; mean gestational age 26 weeks) and a comparison group of 111 term-born normal birth weight (NBW) classmate controls. Controlling for background factors, the EPT/ELBW group had pervasive deficits relative to the NBW group on a comprehensive test battery, with rates of cognitive deficits that were 3 to 6 times higher in the EPT/ELBW group. Deficits on a measure of response inhibition were found in 48% versus 10%, odds ratio (95% confidence interval) = 7.32 (3.32, 16.16),p< .001. Deficits on measures of executive function and motor and perceptual-motor abilities were found even when controlling for acquired verbal knowledge. Neonatal risk factors, early neurodevelopmental impairment, and lower SES were associated with higher rates of deficits within the EPT/ELBW group. The findings document both global and selective cognitive deficits in EPT/ELBW children at school entry and justify efforts at early identification and intervention. (JINS, 2011,17, 1067–1079)
Emotion Labeling and Socio-Emotional Outcomes 18 Months after Early Childhood Traumatic Brain Injury
Authors: Tlustos Sarah J. , Chiu C.-Y. Peter , Walz Nicolay Chertkoff , Taylor H. Gerry , Yeates Keith Owen , Wade Shari L.
Published: September 2011

A growing body of literature has documented evidence for emotion labeling (EL) deficits after traumatic brain injury (TBI); however, long-term effects of TBI on EL abilities, particularly among young children, are unclear. We investigated EL abilities and socio-emotional outcomes in 32 children with moderate–severe TBI, 23 with complicated-mild TBI, and 82 children with orthopedic injuries (OI), shortly after injury and at 18 months post-injury. All children were between 3:0 and 6:11 years of age at the time of injury. Repeated measures analyses indicated that all groups showed improved EL performance between acute and 18-month assessments, but that the moderate–severe TBI group improved at a slower rate than the OI group, so that the two groups showed significantly different performance at 18 months. Emotion labeling ability did not significantly contribute to the prediction of socio-emotional outcomes after controlling for pre-injury functioning. These results provide preliminary evidence of emerging EL deficits after early childhood TBI that are related to injury severity but that do not predict social and behavioral outcomes. (JINS, 2011, 17, 1132–1142)
Use of voluntarily fortified foods among adults in Finland
Authors: Hirvonen Tero , Kara Anna , Korkalo Liisa , Sinkko Harri , Ovaskainen Marja-Leena , Mikkilä Vera
Published: September 2011

Objective

To investigate the purchase and use of fortified foods, and to explore and compare background characteristics, food consumption and nutrient intakes among users and non-users of voluntarily fortified foods in Finland.

Design

A study based on the National FINDIET Survey 2007 (48 h recall), which included also a barcode-based product diary developed to assess the type, amount and users of voluntarily fortified foods. Logistic regression analysis was employed to investigate associations between background characteristics and the use of fortified foods.

Setting

Randomly chosen subgroup of 918 adult participants in the National FINDIET 2007 Survey.

Subjects

Men and women aged 25–64 years from five regions.

Results

The product group of voluntarily fortified foods purchased in the highest volume was yoghurts (44 % of the weight of all fortified food), followed by fruit drinks (36 %). The only characteristics independently associated with the use of voluntarily fortified foods were age (older people used them less commonly) and the consumption of fruit and vegetables (participants with the highest consumption used them more commonly). Users of fortified foods had higher consumption of yoghurt, juice drinks and ready-to-eat breakfast cereals (women only) than non-users, and lower consumption of boiled potatoes (men only).

Conclusions

Use of voluntarily fortified foods is associated with high consumption of fruit and vegetables but not with other health-related behaviours. The use of voluntarily fortified foods does not seem to even out the differences in nutrient intake among Finnish adults.
Explaining the cause of asymmetry in the electron foreshock
Authors: Balcerak Ernie
Published: September 2011

As the solar wind nears the edge of Earth's magnetosphere, it creates a bow shock, a region in which the solar wind speed drops abruptly. Some solar wind electrons bounce off the bow shock; these reflected electrons interact with oncoming solar wind in a region known as the electron foreshock. In the electron foreshock the reflected electrons generate plasma wave activity that results in radio wave emission. A new study shows that the sunward and antisunward wings of this electron foreshock differ. Analyzing wave and electron measurements from the Wind spacecraft, Pulupa et al. show that the asymmetry is due to the strahl, a beam of high‐velocity electrons that is a component of the solar wind. Strahl electrons bounce off the bow shock only into the sunward wing of the foreshock, and this asymmetry leads to enhanced plasma wave activity in the sunward wing. (Geophysical Research Letters, doi:10.1029/ 2011GL048029, 2011)
Martian soil oxidation‐reduction potential not too extreme for life
Authors: Balcerak Ernie
Published: September 2011

Ever since the NASA Viking mission, which reached Mars in 1976, there has been considerable interest in the composition of Martian soils. Some Viking measurements indirectly suggested that the soils contained highly oxidizing compounds, which could present extremely harsh conditions for life. Recent observations from the Phoenix Mars Mission pointed to evidence of perchlorate, a potentially highly oxidizing compound, in the Martian soils. However, some studies have noted that because perchlorate is highly stable, its presence in Martian soils cannot explain the Viking measurements.
Extravesicular intraneuronal migration of internalized botulinum neurotoxins without detectable inhibition of distal neurotransmission
Authors: Lawrence Gary W. , Ovsepian Saak V. , Wang Jiafu , Aoki K. Roger , Dolly J. Oliver
Published: September 2011

Intracellular protein transport routes can be studied using toxins that exploit these to enter cells. BoNTA (botulinum neurotoxin type A) is a protease that binds to peripheral nerve terminals, becomes endocytosed and causes prolonged blockade of transmitter release by cleaving SNAP-25 (synaptosome-associated protein of 25 kDa). Retrograde transport of the toxin has been suggested, but not of the transient muscle relaxant, BoNTE (botulinum neurotoxin type E). In the present study, dispersal of these proteases in compartmented cultures of rat sympathetic neurons was examined after focal application of BoNTA or BoNTE to neurites. A majority of cleaved SNAP-25 was seen locally, but some appeared along neurites and accumulated in the soma over several weeks. BoNTE yielded less cleaved SNAP-25 at distal sites due to shorter-lived enzymic activity. Neurite transection prevented movement of BoNTA. The BoNTA protease could be detected only in the supernatants of neurites or cell body lysates, hence these proteases must move along neuronal processes in the axoplasm or are reversibly associated with membranes. Substitution into BoNTE of the BoNTA acceptor-binding domain did not alter its potency or mobility. Spontaneous or evoked transmission to cell bodies were not inhibited by retrogradely migrated BoNTA except with high doses, concurring with the lack of evidence for a direct central action when used clinically.
Secretion of rat tracheal epithelial cells induces mesenchymal stem cells to differentiate into epithelial cells
Authors: Sun Zhaorui , Wang Yajing , Gong Xuemin , Su Hang , Han Xiaodong
Published: September 2011

Bone marrow MSCs (mesenchymal stem cells) can differentiate into various tissue cells, including epithelial cells. This presents interesting possibilities for cellular therapy, but the differentiation efficiency of MSCs is very low. We have explored specific inducing factors to improve the epithelial differentiation efficiency of MSCs. Under inducing conditions, MSCs differentiated into epithelial cells and expressed several airway epithelial markers using RTE (rat tracheal epithelial) cell secretions. Rat cytokine antibody array was used to detect cytokines of the RTE secretion components, in which 32 kinds of protein were found. Seven proteins [TRAIL (tumour necrosis factor‐related apoptosis‐inducing ligand), VEGF (vascular endothelial growth factor), BDNF (brain‐derived neurotrophic factor), TGFβ1 (transforming growth factor β1), MMP‐2 (metalloproteinases‐2), OPN (osteopontin) and activin A in RTE secretions] were assayed using ELISA kits. The four growth factors (VEGF, BDNF, TGFβ1 and activin A) were involved in regulating stem cell growth and differentiation. We speculated that these four play a vital role in the differentiation of MSCs into epithelial cells by triggering appropriate signalling pathways. To induce epithelial differentiation, MSCs were cultured using VEGF, BDNF, TGFβ1 and activin A. Differentiated MSCs were characterized both morphologically and functionally by their capacity to express specific markers for epithelial cells. The data demonstrated that MSCs can differentiate into epithelial cells induced by these growth factors.
Identification and localization of S100A6 in human umbilical cord
Authors: Jurewicz Ewelina , Kasacka Irena , Bańkowski Edward , Filipek Anna
Published: September 2011

S100A6, a calcium‐binding protein also known as calcyclin, was detected in human umbilical cord by immunoblotting. Immunohistochemical studies showed an intensive reaction for S100A6 in the walls of vessels and Wharton's jelly. In the latter, S100A6 was found not only in the myofibroblasts but also in the ECM (extracellular matrix) surrounding these cells. Affinity chromatography of S100A6 resin indicated that Wharton's jelly contains some proteins that could bind to S100A6. Thus these novel results show the presence of S100A6 in umbilical cord and suggest the involvement of this protein in intra‐ and extra‐cellular signalling pathways in this tissue.
Influence of crystallization-induced amorphous phase confinement onα- andβ-relaxation molecular mobility in parylene F
Authors: Diaham S. , Bechara M. , Locatelli M.-L. , Lebey T.
Published: September 2011

The molecular mobility of cooperative segmental (α-process) and local (β-process) motions in semicrystalline fluorinated parylene (PA-F) films has been studied using broadband dielectric spectroscopy in a wide temperature range. Particularly, the α-relaxation is, for the first time in a semicrystalline polymer, probed well above the glass transition temperature (∼10Tg) based on the PA-F strong difference between Tg and the crystallization temperature (Tc ∼ 16Tg). The influence of the amorphous phase confinement on the chain dynamics, induced by increasing crystallinity, is also explored. Thus, in the range of Tg, the α-relaxation is described by two crossover Vogel-Fulcher-Tamman characteristics, and the high temperature one presents an exacerbated low fragility. The space confinement of the amorphous regions, as characterized by x-ray diffraction, shows an important mobility restriction of both the α- and β-relaxations. The β-process, which has been related to CF2 group local motions, does not present a modification of its activation energy (Ea ∼ 30.8 kJ mol−1) with confinement, showing that it happens in the pure amorphous regions. The dielectric strength analysis of each process, through the Onsager-Kirkwood-Fröhlich (OKF) theory, has demonstrated that a rigid amorphous phase is strongly involved in the very high temperature range well above Tg. In the range around Tg, a peculiar behavior of the low temperature α-relaxation dielectric strength is reported, in agreement with the OKF temperature decreasing dependency that has been related to cooperative rearranging regions in the pure amorphous phase. The disappearance of the α-relaxation with the amorphous phase confinement leads to a transformation from 2D to 3D crystallite arrangements of the PA-F chains in correlation with the formation of spherulitic structures.
Interface shear microrheometer with an optically driven oscillating probe particle
Authors: Park Chang Young , Ou-Yang H. Daniel , Kim Mahn Won
Published: September 2011

We report the first experimental demonstration of an active interfacial shear microrheometer (ISMR) that uses a particle trapped by oscillating optical tweezers (OT) to probe the shear modulus \documentclass[12pt]{minimal}\begin{document}$G_s^*(\omega )$\end{document}Gs*(ω) of a gas/liquid interface. The most significant advantages of the oscillating OT in a rheology study are: (1) very high sensitivity compared to other active microrheology methods and (2) the ability to measure both the real and imaginary components of the complex shear modulus without relying on the use of Kramers-Kronig relation, which can be problematic at low frequencies for most of the passive methods. We demonstrate the utilities of our ISMR in two case studies: (1) a 1,2-dipalmitoyl-sn-glycero-3-phosphocholine monolayer and (2) a composite of poly(styrene sulfonate) and dioctadecyldimethylammonium at the air/water interface in regimes where no other active instruments can explore.
A robotics platform for automated batch fabrication of high density, microfluidics-based DNA microarrays, with applications to single cell, multiplex assays of secreted proteins
Authors: Ahmad Habib , Sutherland Alex , Shin Young Shik , Hwang Kiwook , Qin Lidong , Krom Russell-John , Heath James R.
Published: September 2011

Microfluidics flow-patterning has been utilized for the construction of chip-scale miniaturized DNA and protein barcode arrays. Such arrays have been used for specific clinical and fundamental investigations in which many proteins are assayed from single cells or other small sample sizes. However, flow-patterned arrays are hand-prepared, and so are impractical for broad applications. We describe an integrated robotics/microfluidics platform for the automated preparation of such arrays, and we apply it to the batch fabrication of up to eighteen chips of flow-patterned DNA barcodes. The resulting substrates are comparable in quality with hand-made arrays and exhibit excellent substrate-to-substrate consistency. We demonstrate the utility and reproducibility of robotics-patterned barcodes by utilizing two flow-patterned chips for highly parallel assays of a panel of secreted proteins from single macrophage cells.
Inversion of the direction of photo-induced mass transport in As20Se80 films: Experiment and theory
Authors: Kaganovskii Yu. , Beke D. L. , Charnovych S. , Kökényesi S. , Trunov M. L.
Published: September 2011

Diffusion mass transfer in thin chalcogenide films under illumination by a focused Gaussian beam have been studied both experimentally and theoretically. It is demonstrated that depending on the light intensity, waist of the beam, and the film thickness, one can obtain formation of either hillocks or dips in the illuminated regions. By comparison of the kinetics of hillock or dip formation on a surface of As20Se80 glass films with the results of our theoretical analysis, we have estimated the photo-induced diffusion coefficients, D, at various light intensities, I, and found D to be proportional to I (D = βI), with β ≈ 1.5 × 10−18 m4/J.
Switching-probability distribution of spin-torque switching in MgO-based magnetic tunnel junctions
Authors: Seki Takayuki , Fukushima Akio , Kubota Hitoshi , Yakushiji Kay , Yuasa Shinji , Ando Koji
Published: September 2011

The time-evolution of the switching characteristics of spin-torque switching in MgO-based magnetic tunnel junctions (MTJs) during more than 109 write/read cycles was measured experimentally. In the measurements, the magnetic field and current conditions were chosen to give a switching probability (Psw) of about 0.5, where Psw is most sensitive to changes in the magnetic properties of an MTJ cell. Interestingly, some MTJ cells showed small jumps of Psw, which can be attributed to random transitions between states with slightly different magnetic configurations. Such time-evolution measurement can be used to evaluate the stability of the switching characteristics of memory cells.
Linear and nonlinear convection in porous media between coaxial cylinders
Authors: Bringedal Carina , Berre Inga , Nordbotten Jan M. , Rees D. Andrew S.
Published: September 2011

We uncover novel features of three-dimensional natural convection in porous media by investigating convection in an annular porous cavity contained between two vertical coaxial cylinders. The investigations are made using a linear stability analysis, together with high-order numerical simulations using pseudospectral methods to model the nonlinear regime. The onset of convection cells and their preferred planform are studied, and the stability of the modes with respect to different types of perturbation is investigated. We also examine how variations in the Rayleigh number affect the convection modes and their stability regimes. Compared with previously published data, we show how the problem inherits an increased complexity regarding which modes will be obtained. Some stable secondary modes or mixed modes have been identified and some overlapping stability regions for different convective modes are determined.
Quantized space-charge waves in quasi-2D
Authors: Ridley B. K.
Published: September 2011

Hot-electron transport theory of standard semiconductor layered structures predicts the occurrence of negative differential resistance (NDR) associated with inter-valley electron transfer, negative effective mass, and real-space transfer. An analysis of the growth of quantized space-charge waves in single and double heterostructures in which no real-space transfer occurs is presented. It is shown that, in contrast to the situation in bulk material, growth is a complicated function of wave-vector because of quantization effects. As a consequence, growth is limited by quantization effects and diffusion to small wave-vectors. To illustrate the effect of quantization clearly, the analysis is limited to growth within the lowest sub-band. In spite of quantization differences, a quantitative comparison can be made by a simple rescaling. Growth is shown to be severely limited to small wave-vectors and its rate turns out to be independent of the details of quantization, being that for extreme confinement. The rate maximizes for a wave-vector of about 4 × 105 cm−1 corresponding to a frequency of 700 GHz. The criterion for domain formation in GaN systems becomes n02L≥1020cm-3, where n0 is the areal density of electrons and L is the sample length. As far as growth rate is concerned, the restriction to the lowest sub-band represents a worst-case scenario.
Architecture of source-drain cavity of a p-channel field effect transistor for embedding with epitaxial SiGe for enhanced performance
Authors: Parikh A. , Cai Z.
Published: September 2011

Increase in power consumption in field effect transistors has been curtailed in recent years by introduction of mechanical stress to achieve device speed gain over and above the traditional speed vs. power tradeoffs achieved only by scaling gate lengths. Increasingly, the source-drain region of p-channel field effect transistors are etched and epitaxial SiGe re-grown in the cavity to enhance hole mobility. However, the addition of stress as a method to improve performance would add to the process variability beyond the traditional source of lithography, now related to structure and dimension of the cavity and composition of SiGe. In this paper, compressive stress induced in the channel was directly measured using synchrotron x-ray diffraction. The samples were a set of gratings designed to map the transistor performance with varying design space. The x-ray beam was systematically stepped across the gratings at an interval of 200 nm and diffraction data collected to assess the extent of stress field. Diffraction space maps were created around the symmetric (004) and asymmetric (115) planes. Strain was deduced from Si peak shift and stress calculated from the Si elastic constants. Diffraction space maps around the asymmetric plane were used to deduce the mechanism and subsequent relaxation of strain. Diffraction data collected with x-ray beam placement close to the Si-SiGe vertical interface provided information from lateral SiGe epitaxy on the (110) plane. The presence of strained SiGe peak exhibiting tilt as well as “relaxed” SiGe peak surrounded by diffuse scattering due to dislocations were observed. The use of non-selective etch process resulted in cavity formation with multiple crystallographic planes. The subsequent relaxation mechanism that was dependent on the formation of misfit dislocations was perturbed, possibly due to pinning of the dislocations at the intersection of two crystallographic planes and served as the source of variability. Measured stress variation from 90 to 220 MPa was seen that resulted in estimated drive current enhancement variability from 5% to 15%. The maximum strain was seen where the SiGe film saw no relaxation and the energy formed due to hetero-epitaxy was transferred elastically as channel stress. The elastic relaxation was also accompanied by formation of tilted boundary. Based on these findings, the design of an ideal cavity that would maximize strain and minimize variability with layout was proposed.
Composition dependence of the viscosity and other physical properties in the arsenic selenide glass system
Authors: Musgraves J. David , Wachtel Peter , Novak Spencer , Wilkinson Jacklyn , Richardson Kathleen
Published: September 2011

The viscosity of the AsxSe100−x family of glasses has been measured for 10 ≤ x ≤ 40 using beam bending and parallel plate viscometry, and fit with the Vogel-Fulcher-Tamann (VFT) viscosity model. Measurement of other physical properties of the glasses, including the density, glass transition temperature, and coefficient of thermal expansion has been conducted in order to accurately calculate the viscosity as a function of temperature and glass composition. The variation in fragility of the glasses is explained in the context of frozen-in configurational entropy in the glasses. This configurational entropy has minima at the endpoints of the one-dimensional network of amorphous selenium and the fully three-dimensional network of As40Se60, and an apparent maximum at the composition As30Se70. The frozen-in configurational entropy can be well described by a modified entropy of mixing of two solid solutions model, implying that the topological contribution to configurational entropy is nearly constant across the composition space studied.
Efficient long-range collisional energy transfer between the E
g+(3P2) and D
u+(3P2) ion-pair states of I2, induced by H2O, observed using high-resolution Fourier transform emission spectroscopy
Authors: Ridley Trevor , Lawley Kenneth P. , Donovan Robert J. , Ross Amanda J.
Published: September 2011

Using high-resolution Fourier transform emission techniques, we have resolved rotational structure in the D0u+(3P2) → X0g+ emission following collisional transfer from the E0g+(3P2) state in I2. The P:R branch ratios in the E0g+(3P2) → D0u+(3P2) transfer are found to vary enormously with vE and vD. We show that the observed intensities are all consistent with the transfer being dominated by long-range, near-resonant collisions with residual H2O. Unequal P:R branch ratios in the E0g+(3P2) → A1u emission have been shown to result from mixing of the E0g+(3P2) and β1g(3P2) states via Ω-uncoupling.
Complex orientational ordering of C60 molecules on Au(111)
Authors: Tang Lin , Xie Yangchun , Guo Quanmin
Published: September 2011

The orientation and adsorption site for C60 molecules on Au(111) has been studied using low temperature scanning tunneling microscopy. A complex orientational ordering has been observed for molecules inside the “in-phase” (R0°) domain. A 7-molecule cluster consisting a central molecule sitting atop of a gold atom and 6 tilted surrounding molecules is identified as the structural motif. The 2√3 × 2√3-R30° phase consists of molecules bonding to a gold atomic vacancies with a preferred azimuthal orientation. The quasi-periodic R14° phase is composed of groups of similarly oriented molecules with the groups organized into a 4√3 × 4√3-R30° like super-lattice unit cell.
Better than Bragg: Optimizing the quality factor of resonators with aperiodic dielectric reflectors
Authors: Breeze Jonathan , Oxborrow Mark , McN Alford Neil
Published: September 2011

Periodic dielectric structures, such as Bragg reflectors and photonic band-gap crystals, are used to localize electromagnetic modes. A key parameter for electromagnetic resonators is the quality factor, Q. For conventional Bragg reflectors, losses occur predominantly in the first few reflectors and one of the materials usually has a low dielectric loss tangent. By varying the individual dimensions of the reflecting elements, a significant improvement in the Q-factor can be obtained. We verify this by constructing and measuring proof-of-principle microwave resonators.
Solution processed reduced graphene oxide ultraviolet detector
Authors: Chitara Basant , Krupanidhi S. B. , Rao C. N. R.
Published: September 2011

Electronic properties of graphene have been studied more extensively than its photonic applications, in spite of its exciting optical properties. Recent results on solar cells, light emitting diodes and photodetectors show its true potential in photonics and optoelectronics. Here, we have explored the use of reduced graphene oxide as a candidate for solution processed ultraviolet photodetectors. UV detection is demonstrated by reduced graphene oxide in terms of time resolved photocurrent as well as photoresponse. The responsivity of the detectors is found to be 0.12 A/W with an external quantum efficiency of 40%.
The continuing medical education activities and attitudes of Australian doctors working in different clinical specialties and practice locations
Authors: Stewart Grant D , Khadra Mohamed H
Published: September 2011

Background: Currently, it is not clear which
continuing medical education (CME) methods are
being used by senior doctors and what their
attitudes towards them are. The aims of this study
were to investigate which modes of CME delivery
senior Australian doctors utilise, to assess doctors?
attitudes towards CME and to determine any
differences in modes used and attitudes between
clinical specialties and practice locations.
Methods: A 52-statement questionnaire enquiring
about doctors? current CME activities and their
attitudes towards CME was distributed to 1336
senior Australian doctors.
Results: 494 doctors responded to the questionnaire.
Traditional forms of CME (eg, meetings,
conferences, journals and lectures) were most
commonly used. Doctors thought CME involving
face-to-face interaction was superior to electronic
forms of CME. All doctors, especially those in
hospital practice, had a positive attitude towards
CME but found lack of time a barrier to learning.
Rural doctors found CME sessions more difficult
to attend than did their metropolitan colleagues.
Conclusions: Traditional forms of CME were
more popular than modern CME approaches,
such as e-learning. Australian doctors had a
positive attitude towards undertaking CME
despite struggling to find time to perform CME.
The differences in attitudes towards CME demonstrated
between specialties and different practice
location will aid future CME planning.
It's not that bad: the views of consumers and carers about routine outcome measurement in mental health
Authors: Black Jennifer , Lewis Tania , McIntosh Pamela , Callaly Tom , Coombs Tim , Hunter Angie , Moore Louise
Published: September 2011

The mandatory use of routine outcome measurement
(ROM) has been introduced into all public
sector mental health services in Australia over the
past 6 years. Qualitative processes were used to
engage consumers and carers in suggesting how
the measures can be used in clinical practice. The
project involved an audit by survey, followed by a
range of interactive workshops designed to elicit
the views of consumers, carers and clinicians, as
well as to involve all parties in dialogue about
ROM. In addition, there was engagement of consumers
and carers in the training of clinicians in
the clinical use of ROM, and in the production of
promotional materials aimed at informing consumers
and carers about ROM. When consumers and
carers have had an opportunity to be involved in
ROM they have found it a useful experience, and
those who had not been involved can see the
potential. Consumers and carers indicated that
they believe the greatest opportunity arising from
the suite of measures is the use of the consumer
self-assessment measure the Behaviour and
Symptom Identification Scale (BASIS-32).
Medicare-related service use and costs among people with diagnosed and undiagnosed diabetes and respiratory conditions
Authors: Chittleborough Catherine R , Burke Michael J , Taylor Anne W , Wilson David H , Phillips Patrick J , Adams Robert J , Ruffin Richard E , North West Adelaide Health Study Team the
Published: September 2011

Objective: To compare Medicare-related costs
and service utilisation of people with diagnosed
diabetes, asthma or chronic obstructive pulmonary
disease (COPD) to those who were previously
undiagnosed, and those without these
conditions.
Design, setting and participants: Representative
cross-sectional study of people (18+ years)
living in the north-west area of Adelaide. Participants
were recruited by telephone interviews.
Biomedical and self-report data for 2352 participants
were linked to Medicare Australia Medicare
Benefits Schedule (MBS) data from 1997 to 2002.
Main outcome measures: Mean number and
cost (benefit paid) of MBS services for people with
diagnosed and previously undiagnosed diabetes,
asthma, and COPD, and those without these
conditions.
Results: Mean (�SD) MBS costs were significantly
greater for people diagnosed with diabetes
($4205 �2596), asthma ($3307 �2542), or COPD
($3779 �2529) than for those without these conditions.
MBS costs for people with asthma or COPD
that had not yet been diagnosed were also significantly
higher than for those without these conditions,
although this was inconsistent across
financial years.
Conclusions: Diabetes, asthma, and COPD are
costly conditions in terms of health service use.
Costs associated with undiagnosed asthma and
COPD are similar to their diagnosed states. Prevention
of progression along each chronic disease
continuum is likely to reduce costs.
The Indian Merchant Diaspora in Early Modern Central Asia and Iran
Authors: Levi Scott
Published: September 2011

Long before European merchants working for the Dutch and the English East India Companies sailed around the Cape of Good Hope, there were caste-based Indian family firms operating heavily-capitalized commercial institutions throughout north India. The directors of these firms enlisted many thousands of agents and placed them in markets strategic to their engagement in a variety of commercial activities, including large-scale transregional trade, brokering, money changing, and the financing of complex systems of rural credit and industrial production. Rather than triggering the decline of such indigenous commercial institutions, it is during the very period of European expansion into the Indian Ocean that the Indian family firms began to geographically diversify their portfolios by sending their agents to distant markets in port cities, villages, and major and minor urban centers as far away as Moscow.

In a recent work, Stephen Dale has uncovered the existence of an early modern Indian merchant diaspora with communities dispersed throughout Central Asia, Iran, the Caucasus and much of Russia.
Monitoring A level standards: tests, grades and other approximations
Authors: Murphy Roger , Wilmut John , Wood Roger
Published: September 2011

Many different approaches have been used to research the comparability of examination grades, such as those generated by A level examinations in different subjects and years, and by different examination boards. This paper reviews various definitions of comparability which have been used, and argues that all definitions of comparability incorporate specific values. The paper explores studies that have used general ability reference tests as an independent measure against which to compare examination grades. This methodology is shown to be seriously flawed. The paper goes on to discuss other approaches to researching the comparability of A level grades, including the use of previous GCSE grades of A level candidates.
Teaching the curriculum: policy and practice in Portugal and Belgium
Authors: DA COSTA FRANCISCO CARREIRO , PIÉRON MAURICE
Published: September 2011

Since 1989, the Portuguese education system has undergone curricular reform which has introduced deep structural changes to the subject of physical education (PE). PE has become a compulsory and examinable subject within the ‘core curriculum’ of all school years (1 st to 12th grade). National curricular plans for basic and secondary education have also been introduced. This paper provides a view of the political options which have underpinned the present curricular project of PE in Portugal and compares practices in that country with those in Belgium. The analysis first describes the ‘curriculum as text’ before focusing attention on the ‘curriculum as action’. The analysis explores the nature of teachers’, pupils’ and parents’ beliefs, values and attitudes that together mediate the curriculum as text, help define contexts of PE, and influence public and political attitudes towards the subject. The paper points to the importance of both researchers and teachers for the development of effective teaching and learning in PE.