bluuebunny/crossref_metadata_2025 huggingface dataset:
Fatty Acid Composition of the Brain, Retina, Liver and Adipose Tissue of the Grey Mouse Lemur (Microcebus murinus, Primate)
Authors: Pifferi Fabien , Perret Martine , Guesnet Philippe , Aujard Fabienne , Alessandri Jean‐Marc
Published: June 2012

The particular interest in supplementing human foods with n‐3 fatty acids has arisen from the findings that this series of polyunsaturated fatty acids (PUFA) have an impact on neuronal functions. Indeed vertebrates, including humans, preferentially use docosahexaenoic acid (DHA, 22:6n‐3) over other long‐chain n‐3 PUFA for the genesis of their neuronal and retinal membranes. The grey mouse lemur is a nocturnal prosimian primate originating from Madagascar. The increased use of this omnivorous primate in nutritional studies (chronic caloric restriction, n‐3 fatty acids supplementation), justifies the interest of determining their fatty acids body composition. In the present study, we report the fatty acid composition in lipid classes from the main target tissues (brain, retina, liver and adipose tissue) of six adult mouse lemurs raised under laboratory nutritional conditions. Among the main findings, n‐6‐docosapentaenoic acid (n‐6‐DPA; 22:5n‐6) is very low in the brain cortex and retina, whereas there is a very high accumulation of docosahexaenoic acid (DHA, 22:6n‐3) in the neural tissues compared to liver and plasma. In particular, DHA accounts for about one half of the total fatty acids in the retina ethanolamine glycerophospholipids. This high concentration clearly indicates that DHA is efficiently transferred from blood lipids to the outer segment of the mouse lemur retina. We conclude that the mouse lemur n‐3 PUFA metabolism efficiently drives DHA to neural tissues, through the blood–brain barrier and the blood–retina barrier.
Societal Aspects of Vulnerability to Natural Hazards
Authors: Zehetmair Swen
Published: June 2012

To date, social vulnerability research has focused primarily on the individual and household levels, and on social institutions relevant to these two benchmarks. In this paper, a widening of the perspective of social vulnerability to natural hazards is proposed to include socio-structural aspects. For a number of reasons, the sociological system theory, which is inextricably linked with the name of Niklas Luhmann, is an obvious choice for this undertaking. Firstly, Luhmann developed a consistent social theoretical definition of risk, which has significantly influenced risk and hazard research in social science. Furthermore, the system theory provides a theory of society that claims to be able to cover all social levels and to describe all social phenomena. The system theory assumes that in modern society social systems are formed of communications. Therefore, in this paper the view is taken that a system-theoretical inspired concept of social vulnerability must also assess communication. First, this paper describes empirical observations about the vulnerability of social systems. This is achieved on the one hand through a categorisation of four forms of social vulnerability. On the other hand, it is based on examples of vulnerability to flood risks in selected social systems. Finally, consideration is given to a system-theoretical concept of social vulnerability that sees the sensitivity of a social system in each of the respective system structures. Vulnerabilities can only be observed for a particular social system, because the configuration of system structures differs from system to system. These fundamental considerations have to be further explored in future work on a consistent social theoretical concept of vulnerability.
Elucidation of the binding preferences of peptide recognition modules: SH3 and PDZ domains
Authors: Teyra Joan , Sidhu Sachdev S. , Kim Philip M.
Published: June 2012

Peptide‐binding domains play a critical role in regulation of cellular processes by mediating protein interactions involved in signalling. In recent years, the development of large‐scale technologies has enabled exhaustive studies on the peptide recognition preferences for a number of peptide‐binding domain families. These efforts have provided significant insights into the binding specificities of these modular domains. Many research groups have taken advantage of this unprecedented volume of specificity data and have developed a variety of new algorithms for the prediction of binding specificities of peptide‐binding domains and for the prediction of their natural binding targets. This knowledge has also been applied to the design of synthetic peptide‐binding domains in order to rewire protein–protein interaction networks. Here, we describe how these experimental technologies have impacted on our understanding of peptide‐binding domain specificities and on the elucidation of their natural ligands. We discuss SH3 and PDZ domains as well characterized examples, and we explore the feasibility of expanding high‐throughput experiments to other peptide‐binding domains.
Minimally Invasive Distal Metatarsal Osteotomy in the Treatment of Primary Metatarsalgia
Authors: Tsz-Cheung Wong , Siu-Wah Kong
Published: June 2012

Introduction

Metatarsalgia is a common presentation to orthopaedic surgeons. Primary metatarsalgia is caused by chronic imbalance in weight-bearing distribution across the forefoot or between the forefoot and midfoot. Management of primary matatarsalgia is mainly conservative. Metatarsal osteotomy can be considered if conservative treatment has failed. Minimally Invasive Distal Metatarsal Osteotomy technique can achieve satisfactory outcomes.

Method and material

From April 2009 to May 2010, we performed distal metatarsal osteotomies using minimally invasive technique in four patients (3 females and 1 male). Stab incision was made, and metatarsal neck osteotomy was achieved with a burr. No internal fixation was performed. Full weight bearing walking was allowed on the first day after operation. Radiographs were taken before and after operations, and forefoot scores were documented by using the American College of Foot and Ankle Surgeons score.

Result

The average age of the four patients was 55.8 years (range 46–62). The average operation time was 40 minutes (range 24–65). Blood loss was minimal in all patients. The length of hospital stay was 4 days in all patients. All osteotomies healed uneventfully in 4 months. There was no major complication. The average metatarsal index decreased from 3.125 to 2.8 mm, and the average first/second intermetatarsal angle on lateral X-ray decreased from 6° to 2°. The average American College of Foot and Ankle Surgeons score improved from 66.25 (range 56–74) preoperatively to 96.25 (range 93–99) postoperatively.

Conclusion

Minimally Invasive Distal Metatarsal Osteotomy without internal fixation is a viable alternative to open procedure in the management of recalcitrant metatarsalgia.
PROTO-UTO-AZTECAN AS A MESOAMERICAN LANGUAGE
Authors: Hill Jane H.
Published: June 2012

New evidence is presented in support of the hypothesis that Proto-Uto-Aztecan (PUA) was spoken by a community of cultivators in the northwest quadrant of Mesoamerica. New cognates are presented in support of reconstructions of meanings of PUA words within the maize-cultivation domain. It is argued that some of this vocabulary was borrowed from an Otomanguean language, perhaps Proto-Oto-Chinantecan. In addition, it is argued that PUA included a vocabulary in the domain of pottery. New reconstructions of a pottery lexicon are proposed, and arguments that this vocabulary was borrowed from an Otomanguean language are presented. If PUA speakers were familiar with pottery, then PUA was spoken as late as 4400–4100b.p.and did not begin to break up into its daughter languages until after knowledge of pottery reached its speakers.
DESIGNING MONETARY AND FISCAL POLICY RULES IN A NEW KEYNESIAN MODEL WITH RULE-OF-THUMB CONSUMERS
Authors: Rossi Raffaele
Published: June 2012

This paper studies the determinacy properties of monetary and fiscal policy rules in a small-scale New Keynesian model. We modify the standard model in two ways. First, we allow positive public debt in the steady state as in Leeper [Journal of Monetary Economics 27, 129–147 (1991)]. Second, we add rule-of-thumb consumers as in Bilbiie [Journal of Economic Theory 140, 162–196 (2008)]. Leeper studied a model in which Ricardian equivalence holds, and he showed that monetary and fiscal policy can be studied independently. In Bilbiie's analysis, rule-of-thumb consumers break the Ricardian equivalence and generate important consequences for the design of monetary policy. In his model, steady-state public debt was equal to zero. We study a model with both rule-of-thumb consumers and positive steady-state public debt. We find that the mix of fiscal and monetary policies that guarantees equilibrium determinacy is sensitive to the exact values of the parameters of the model.
Plural Freedom
Authors: Krause Sharon R.
Published: June 2012

Some of the most interesting and important work on freedom in recent
years has been produced by feminist theorists (e.g., Friedman 2003;
Hirschmann 2003; Nedelsky 2011; Zerilli 2005; and see Anker, forthcoming).
Feminist theory has also generated important insights about the character
and conditions of human agency, the intersectional nature of human
identities, and the dynamics of political action that richly enhance our
understanding of freedom (Ackerly and Attanasi 2009; Alcoff 2006; Anzaldua
2007; Bartky 1990; Beltrán 2010; Benhabib 1992; Brown 1995; Butler 2004,
2006; Crenshaw 1989; Hill-Collins 2005; Love 2007; Mohanty 2003; Young
2005). Yet feminist perspectives on freedom—like others in political theory
today (e.g., Berlin 1990; Pettit 2000; Villa 2008)—are limited by their
tendency to conceive freedom in a monistic way. Whether freedom means the
exercise of personal choice (Hirschmann 2003), or inaugural acts of world
making (Arendt 1958; Zerilli 2005), or noninterference (Berlin 1990), or
nondomination (Pettit 2000), or something else, theorists generally describe
freedom as being just one thing. Yet the experiences that we have of freedom
come in different forms, and sometimes the different kinds of freedom that
we have, or that we seek, conflict with one another. Nor is it obvious that
these conflicts could ever be fully reconciled, even under ideal conditions.
Our freedom today is complex: We are at once free and unfree, in ways that
are multiple and often conflicting.
The Strategic Use of Gender and Race in Peru's 2011 Presidential
Campaign
Authors: Ewig Christina
Published: June 2012

The final round of Peru's 2011 presidential campaign featured two
dramatically different candidates. Ollanta Humala was a leftist nationalist
who sought to increase redistribution to the poorest and most marginalized.
Keiko Fujmori was a right-wing proponent of the free market and the
torchbearer of her father's presidential legacy of overcoming economic
crisis and terrorism in the 1990s. According to the extant scholarship on
the relationship between left parties and gender equality, we should have
expected the leftist candidate to support gender equality policies more
strongly.
Snow Metamorphism and Albedo Process (SMAP) model for climate studies: Model validation using meteorological and snow impurity data measured at Sapporo, Japan
Authors: Niwano Masashi , Aoki Teruo , Kuchiki Katsuyuki , Hosaka Masahiro , Kodama Yuji
Published: June 2012

We developed a multilayered physical snowpack model named Snow Metamorphism and Albedo Process (SMAP), which is intended to be incorporated into general circulation models for climate simulations. To simulate realistic physical states of snowpack, SMAP incorporates a state‐of‐the‐art physically based snow albedo model, which calculates snow albedo and solar heating profile in snowpack considering effects of snow grain size and snow impurities explicitly. We evaluated the performance of SMAP with meteorological and snow impurities (black carbon and dust) input data measured at Sapporo, Japan during two winters: 2007–2008 and 2008–2009, and found SMAP successfully reproduced all observed variations of physical properties of snowpack for both winters. We have thus confirmed that SMAP is suitable for climate simulations. With SMAP, we also investigated the effects of snow impurities on snowmelt at Sapporo during the two winters. We found that snowpack durations at Sapporo were shortened by 19 days during the 2007–2008 winter and by 16 days during the 2008–2009 winter due to radiative forcings caused by snow impurities. The estimated radiative forcings due to snow impurities during the accumulation periods were 3.7 W/m2 (it corresponds to albedo reduction in 0.05) and 3.2 W/m2 (albedo reduction in 0.05) for the 2007–2008 and 2008–2009 winters, respectively. While during the ablation periods they were 25.9 W/m2 (albedo reduction in 0.18) and 21.0 W/m2 (albedo reduction in 0.17) for each winter, respectively.
Evolutionary aspects of lithosphere discontinuity structure in the western U.S.
Authors: Levander Alan , Miller Meghan S.
Published: June 2012

We have produced common conversion point (CCP) stacked Ps and Sp receiver function image volumes of the Moho and lithosphere‐asthenosphere boundary (LAB) beneath the western United States using Transportable Array data. The large image volumes and the diversity of tectonic environments they encompass allow us to investigate evolution of these structural discontinuities. The Moho is a nearly continuous topographic surface, whereas the LAB is not and the seismic images show a more complex expression. The first order change in LAB depth in the western U.S. occurs along the Cordilleran hingeline, the former Laurasian passive margin along the southwestern Precambrian North American terranes. The LAB is about 50% deeper to the east of the hingeline than to the west, with most of the increase in LAB thickness being in the mantle lithosphere. We infer that the Moho and the LAB are Late Mesozoic or Cenozoic everywhere west of the hingeline, modified during Farallon subduction and its aftermath. Between the hingeline and the Rocky Mountain Front, the LAB, and to a lesser extent the Moho, have been partially reset during the Cenozoic by processes that continue today. Seismicity and recent volcanism in the interior of the western U.S. are concentrated along gradients in crustal and/or lithospheric thickness, for example the hingeline, and the eastern edge of the coastal volcanic‐magmatic terranes. To us this suggests that lateral gradients in integrated lithospheric strength focus deformation. Similarly, areas conjectured to be the sites of convective downwellings and associated volcanism are located along gradients in regional lithosphere thickness.
Parameterization of instantaneous global horizontal irradiance: Cloudy‐sky component
Authors: Sun Z. , Liu J. , Zeng X. , Liang H.
Published: June 2012

Radiation calculations in global numerical weather prediction (NWP) and climate models are usually conducted in 3‐hourly time interval in order to reduce the computational cost. This treatment can lead to an incorrect solar radiation at the Earth's surface which could be one of the error sources in modeled convection and precipitation. In order to improve the simulation of the diurnal cycle of solar radiation a fast scheme has been developed based on detailed radiative transfer calculations for a wide range of atmospheric conditions and can be used to determine the surface solar radiation at each model integration time step with affordable costs. This scheme is divided into components for clear‐sky and cloudy‐sky conditions. The clear‐sky component has been described in a companion paper. The cloudy‐sky component is introduced in this paper. The input variables required by this scheme are all available in NWP and climate models or can be obtained from satellite observations. Therefore, the scheme can be used in a global model to determine the surface GHI. It can also be used as an offline scheme to calculate the surface GHI using data from satellite measurements. SUNFLUX scheme has been tested using observations obtained from three Atmospheric Radiation Measurements (ARM) stations established by the U. S. Department of Energy. The results show that a half hourly mean relative error of GHI under all‐sky conditions is less than 7%. An important application of the scheme is in global climate models. The radiation sampling error due to infrequent radiation calculations is investigated using the SUNFLUX and ARM observations. It is found that errors in the surface net solar irradiance are very large, exceeding 800 W m−2at many non‐radiation time steps due to ignoring the effects of clouds. Use of the SUNFLUX scheme can reduce these errors to less than 50 W m−2.
Dust radiative forcing in snow of the Upper Colorado River Basin: 2. Interannual variability in radiative forcing and snowmelt rates
Authors: Skiles S. McKenzie , Painter Thomas H. , Deems Jeffrey S. , Bryant Ann C. , Landry Christopher C.
Published: June 2012

Here we present the radiative and snowmelt impacts of dust deposition to snow cover using a 6‐year energy balance record (2005–2010) at alpine and subalpine micrometeorological towers in the Senator Beck Basin Study Area (SBBSA) in southwestern Colorado, USA. These results follow from the measurements described in part I. We simulate the evolution of snow water equivalent at each station under scenarios of observed and dust‐free conditions, and +2°C and +4°C melt‐season temperature perturbations to these scenarios. Over the 6 years of record, daily mean dust radiative forcing ranged from 0 to 214 W m−2, with hourly peaks up to 409 W m−2. Mean springtime dust radiative forcings across the period ranged from 31 to 49 W m−2 at the alpine site and 45 to 75 W m−2 at the subalpine site, in turn shortening snow cover duration by 21 to 51 days. The dust‐advanced loss of snow cover (days) is linearly related to total dust concentration at the end of snow cover, despite temporal variability in dust exposure and solar irradiance. Under clean snow conditions, the temperature increases shorten snow cover by 5–18 days, whereas in the presence of dust they only shorten snow duration by 0–6 days. Dust radiative forcing also causes faster and earlier peak snowmelt outflow with daily mean snowpack outflow doubling under the heaviest dust conditions. On average, snow cover at the towers is lost 2.5 days after peak outflow in dusty conditions, and 1–2 weeks after peak outflow in clean conditions.
Absolutely continuous spectrum implies ballistic transport for quantum particles in a random potential on tree graphs
Authors: Aizenman Michael , Warzel Simone
Published: June 2012

We discuss the dynamical implications of the recent proof that for a quantum particle in a random potential on a regular tree graph absolutely continuous (ac) spectrum occurs non-perturbatively through rare fluctuation-enabled resonances. The main result is spelled in the title.
Theoretical investigation of rotationally inelastic collisions of CH2(${\tilde{X}}$X̃) with helium
Authors: Ma Lifang , Dagdigian Paul J. , Alexander Millard H.
Published: June 2012

Following our earlier work on collisions of He with the methylene radical in its excited \documentclass[12pt]{minimal}\begin{document}$\tilde{a}\,^1A_1$\end{document}ãA11 state [L. Ma, M. H. Alexander, and P. J. Dagdigian, J. Chem. Phys. 134, 154307 (2011)]10.1063/1.3575200, we investigate here the analogous relaxation of \documentclass[12pt]{minimal}\begin{document}$\textnormal {CH}_2$\end{document}CH2 in its ground \documentclass[12pt]{minimal}\begin{document}$\tilde{X}\,^3B_1$\end{document}X̃B13 electronic state. The molecule is treated as semi-rigid, with fixed bond lengths but a varying bond angle. We use an ab initio potential energy surface (PES) which is averaged over the CH2 bending angle weighted by the square of the bending wave function. The PES for the interaction of He with CH2 in the \documentclass[12pt]{minimal}\begin{document}$\tilde{X}$\end{document}X̃ state is considerably less anisotropic than for interaction with the \documentclass[12pt]{minimal}\begin{document}$\tilde{a}$\end{document}ã state since the two 2p electrons on the C atom are evenly distributed among the bonding and non-bonding molecular orbitals. We report quantum scattering calculations of state-to-state and total removal cross sections as well as total removal rate constants at room temperature. Because of the less pronounced anisotropy, these cross sections and rate constants are considerably smaller than for collisions of \documentclass[12pt]{minimal}\begin{document}${\rm CH}_2(\tilde{a})$\end{document} CH 2(ã) with He. Finally, we investigate the dependence of rotational inelasticity on the bending vibrational quantum number.
Designing of epoxy composites reinforced with carbon nanotubes grown carbon fiber fabric for improved electromagnetic interference shielding
Authors: Singh B. P. , Choudhary Veena , Saini Parveen , Mathur R. B.
Published: June 2012

In this letter, we report preparation of strongly anchored multiwall carbon nanotubes (MWCNTs) carbon fiber (CF) fabric preforms. These preforms were reinforced in epoxy resin to make multi scale composites for microwave absorption in the X-band (8.2-12.4GHz). The incorporation of MWCNTs on the carbon fabric produced a significant enhancement in the electromagnetic interference shielding effectiveness (EMI-SE) from −29.4 dB for CF/epoxy-composite to −51.1 dB for CF-MWCNT/epoxy multiscale composites of 2 mm thickness. In addition to enhanced EMI-SE, interlaminar shear strength improved from 23 MPa for CF/epoxy-composites to 50 MPa for multiscale composites indicating their usefulness for making structurally strong microwave shields.
Ozone Disinfection of Eggs from Gilthead Seabream Sparus aurata, Sea Bass Dicentrarchus labrax, Red Porgy, and Common Dentex Dentex dentex
Authors: Can Erkan , Karacalar Ulviye , Saka Sahin , Firat Kursat
Published: June 2012

The risk of fish pathogen transmission via eggs can be reduced by disinfection in ozonated seawater. The aim of this study was to determine the suitable conditions for ozone disinfection of the eggs of gilthead seabream Sparus aurata, sea bass Dicentrarchus labrax, red porgy Pagrus pagrus, and common dentex Dentex dentex. The eggs were disinfected with a concentration (C) of 0.5 mg of ozone/L of water at four different exposure times (T = 2, 4, 8, and 16 min). The hatching rate was determined in triplicate for each treatment. Bacterial colonies were counted on tryptic soy agar and thiosulfate–citrate–bile salts–sucrose agar. At the end of the experiment, bacterial load and hatching rate were assessed together to determine the optimal ozone treatment values, which were estimated in CT units (i.e., C [= 0.5 mg/L] × T [min]). Optimal values were CT 2–4 (T = 4–8 min; 18°C) for gilthead seabream and red porgy, CT 2 (T = 4 min; 18°C) for common dentex, and CT 4 (T = 8 min; 15°C) for sea bass.

Received April 12, 2011; accepted February 2, 2012
Role of Ti/Al relative thickness in the formation mechanism of Ti/Al/Ni/Au Ohmic contacts to AlGaN/GaN heterostructures
Authors: Kong Xin , Wei Ke , Liu Guoguo , Liu Xinyu
Published: June 2012

In this work, Ti/Al/Ni/Au Ohmic contacts to AlGaN/GaN heterostructures with different Ti/Al relative thicknesses were fabricated and characterized. A contact with Ti/Al relative thickness of 20/180 nm presented non-linear current–voltage response and bumpy surface morphology, while a contact with Ti/Al relative thickness of 20/120 nm demonstrated low contact resistance and flat surface morphology. We verify the existence of two electron transport mechanisms, namely carrier tunnelling and direct link through a TiN conductive pathway, by scanning transmission electron microscopy and corresponding electron dispersive x-ray spectra. Ti/Al relative thickness exerts a decisive influence on the alloy reaction processing. Superfluous Al consumes Ti, thus impeding the formation of low-resistance TiN and N vacancies. As a result, electron transport is restricted by the low-efficiency tunnelling mechanism. At the same time, the consumption of Ni causes damage to its blocking effect and arouses the free diffusion of metal alloys, which should be responsible for the rough surface.
Numerical simulation for production of O and N radicals in an atmospheric-pressure streamer discharge
Authors: Komuro Atsushi , Ono Ryo , Oda Tetsuji
Published: June 2012

A streamer discharge model is developed to analyse the characteristics of a pulsed positive streamer discharge in point-to-plane electrodes filled with oxygen–nitrogen mixed gas at room temperature and atmospheric pressure. In this paper we study the mechanisms of O and N radical production in an atmospheric-pressure streamer discharge. To confirm the validity of the simulation model, the discharge emission of light and the discharge current are compared with experimental data at several voltages in gas mixtures with 2–20% oxygen concentrations. The calculated streak picture and the axial distribution of streamer luminous intensity are in good agreement with our previous experimental results. After demonstrating the reliability of the model, we performed a numerical study on radical production by the streamer discharge. The experimentally obtained axial distributions of oxygen radical production in O2(20%)/N2 and nitrogen radical production in O2(2%)/N2 are successfully reproduced in our simulation. For the production of nitrogen radicals, two-step dissociation through the vibrationally excited states is predominant.
Guiding microwave radiation using laser-induced filaments: the hollow conducting waveguide concept
Authors: Alshershby Mostafa , Hao Zuoqiang , Lin Jingquan
Published: June 2012

A microwave waveguide that consists of a set of laser plasma filaments produced in air by the propagation of femtosecond laser pulses is investigated according to the hollow conducting waveguide concept. The conductivity, skin depth of the electromagnetic waves in this plasma waveguide and the energy required to excite such a waveguide are calculated for different possible configurations. A hollow conducting plasma waveguide is shown to support guided modes of electromagnetic radiation from millimetre to centimetre wavelength range. Our calculations show that, under the concept of conducting waveguide, it is more suitable to use the TE01 mode rather than TE11 to achieve an extended attenuation length. The attenuation length of the low-loss mode TE01 is shown to be dependent on the geometry of the plasma waveguides, the operating frequency and the plasma effective electron density. The effect of the plasma wall density spread on TE01 propagation is evaluated. Using the hollow conducting plasma waveguide operating in TE01 mode, an enhancement of microwave transmission over both free space propagation and dielectric plasma waveguide is obtained.
The effect of progressively increasing lithium coatings on plasma discharge characteristics, transport, edge profiles and ELM stability in the National Spherical Torus Experiment
Authors: Maingi R. , Boyle D.P. , Canik J.M. , Kaye S.M. , Skinner C.H. , Allain J.P. , Bell M.G. , Bell R.E. , Gerhardt S.P. , Gray T.K. , Jaworski M.A. , Kaita R. , Kugel H.W. , LeBlanc B.P. , Manickam J. , Mansfield D.K. , Menard J.E. , Osborne T.H. , Raman R. , Roquemore A.L. , Sabbagh S.A. , Snyder P.B. , Soukhanovskii V.A.
Published: June 2012

Lithium wall coatings have been shown to reduce recycling, suppress edge-localized modes (ELMs), and improve energy confinement in the National Spherical Torus Experiment (NSTX). Here we document the effect of gradually increasing lithium wall coatings on the discharge characteristics, with the reference ELMy discharges obtained in boronized, i.e. non-lithiated conditions. We observed a continuous but not quite monotonic reduction in recycling and improvement in energy confinement, a gradual alteration of edge plasma profiles, and slowly increasing periods of ELM quiescence. The measured edge plasma profiles during the lithium-coating scan were simulated with the SOLPS code, which quantified the reduction in divertor recycling coefficient from ∼98% to ∼90%. The reduction in recycling and fuelling, coupled with a drop in the edge particle transport rate, reduced the average edge density profile gradient, and shifted it radially inwards from the separatrix location. In contrast, the edge electron temperature (T
e) profile was unaffected in the H-mode pedestal steep gradient region within the last 5% of normalized poloidal flux, ψ
N ; however, the T
e gradient became steeper at the top of the H-mode pedestal for 0.8 < ψ
N < 0.94 with lithium coatings. The peak pressure gradients were comparable during ELMy and ELM-free phases, but were shifted away from the separatrix in the ELM-free discharges, which is stabilizing to the current-driven instabilities thought to be responsible for ELMs in NSTX.
Specification and maintenance of oligodendrocyte precursor cells from neural progenitor cells: involvement of microRNA-7a
Authors: Zhao Xianghui , Wu Jiang , Zheng Minhua , Gao Fang , Ju Gong
Published: June 2012

The generation of myelinating cells from multipotential neural stem cells in the CNS requires the initiation of specific gene expression programs in oligodendrocytes (OLs). We reasoned that microRNAs (miRNAs) could play an important role in this process by regulating genes crucial for OL development. Here we identified miR-7a as one of the highly enriched miRNAs in oligodendrocyte precursor cells (OPCs), overexpression of which in either neural progenitor cells (NPCs) or embryonic mouse cortex promoted the generation of OL lineage cells. Blocking the function of miR-7a in differentiating NPCs led to a reduction in OL number and an expansion of neuronal populations simultaneously. We also found that overexpression of this miRNA in purified OPC cultures promoted cell proliferation and inhibited further maturation. In addition, miR-7a might exert the effects just mentioned partially by directly repressing proneuronal differentiation factors including Pax6 and NeuroD4, or proOL genes involved in oligodendrocyte maturation. These results suggest that miRNA pathway is essential in determining cell fate commitment for OLs and thus providing a new strategy for modulating this process in OL loss diseases.
Empirical Bayes conditional independence graphs for regulatory network recovery
Authors: Mahdi Rami , Madduri Abishek S. , Wang Guoqing , Strulovici-Barel Yael , Salit Jacqueline , Hackett Neil R. , Crystal Ronald G. , Mezey Jason G.
Published: June 2012

Motivation: Computational inference methods that make use of graphical models to extract regulatory networks from gene expression data can have difficulty reconstructing dense regions of a network, a consequence of both computational complexity and unreliable parameter estimation when sample size is small. As a result, identification of hub genes is of special difficulty for these methods.

Methods: We present a new algorithm, Empirical Light Mutual Min (ELMM), for large network reconstruction that has properties well suited for recovery of graphs with high-degree nodes. ELMM reconstructs the undirected graph of a regulatory network using empirical Bayes conditional independence testing with a heuristic relaxation of independence constraints in dense areas of the graph. This relaxation allows only one gene of a pair with a putative relation to be aware of the network connection, an approach that is aimed at easing multiple testing problems associated with recovering densely connected structures.

Results: Using in silico data, we show that ELMM has better performance than commonly used network inference algorithms including GeneNet, ARACNE, FOCI, GENIE3 and GLASSO. We also apply ELMM to reconstruct a network among 5492 genes expressed in human lung airway epithelium of healthy non-smokers, healthy smokers and individuals with chronic obstructive pulmonary disease assayed using microarrays. The analysis identifies dense sub-networks that are consistent with known regulatory relationships in the lung airway and also suggests novel hub regulatory relationships among a number of genes that play roles in oxidative stress and secretion.

Availability and implementation: Software for running ELMM is made available at http://mezeylab.cb.bscb.cornell.edu/Software.aspx.

Contact: ramimahdi@yahoo.com or jgm45@cornell.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Performance of computational tools in evaluating the functional impact of laboratory-induced amino acid mutations
Authors: Gray Vanessa E. , Kukurba Kimberly R. , Kumar Sudhir
Published: June 2012

Summary: Site-directed mutagenesis is frequently used by scientists to investigate the functional impact of amino acid mutations in the laboratory. Over 10 000 such laboratory-induced mutations have been reported in the UniProt database along with the outcomes of functional assays. Here, we explore the performance of state-of-the-art computational tools (Condel, PolyPhen-2 and SIFT) in correctly annotating the function-altering potential of 10 913 laboratory-induced mutations from 2372 proteins. We find that computational tools are very successful in diagnosing laboratory-induced mutations that elicit significant functional change in the laboratory (up to 92% accuracy). But, these tools consistently fail in correctly annotating laboratory-induced mutations that show no functional impact in the laboratory assays. Therefore, the overall accuracy of computational tools for laboratory-induced mutations is much lower than that observed for the naturally occurring human variants. We tested and rejected the possibilities that the preponderance of changes to alanine and the presence of multiple base-pair mutations in the laboratory were the reasons for the observed discordance between the performance of computational tools for natural and laboratory mutations. Instead, we discover that the laboratory-induced mutations occur predominately at the highly conserved positions in proteins, where the computational tools have the lowest accuracy of correct prediction for variants that do not impact function (neutral). Therefore, the comparisons of experimental-profiling results with those from computational predictions need to be sensitive to the evolutionary conservation of the positions harboring the amino acid change.

Contact:  s.kumar@asu.edu
Towards the rational design of synthetic cells with prescribed population dynamics
Authors: Dalchau Neil , Smith Matthew J. , Martin Samuel , Brown James R. , Emmott Stephen , Phillips Andrew
Published: June 2012

The rational design of synthetic cell populations with prescribed behaviours is a long-standing goal of synthetic biology, with the potential to greatly accelerate the development of biotechnological applications in areas ranging from medical research to energy production. Achieving this goal requires well-characterized components, modular implementation strategies, simulation across temporal and spatial scales and automatic compilation of high-level designs to low-level genetic parts that function reliably inside cells. Many of these steps are incomplete or only partially understood, and methods for integrating them within a common design framework have yet to be developed. Here, we address these challenges by developing a prototype framework for designing synthetic cells with prescribed population dynamics. We extend the genetic engineering of cells (GEC) language, originally developed for programming intracellular dynamics, with cell population factors such as cell growth, division and dormancy, together with spatio-temporal simulation methods. As a case study, we use our framework to design synthetic cells with predator–prey interactions that, when simulated, produce complex spatio-temporal behaviours such as travelling waves and spatio-temporal chaos. An analysis of our design reveals that environmental factors such as density-dependent dormancy and reduced extracellular space destabilize the population dynamics and increase the range of genetic variants for which complex spatio-temporal behaviours are possible. Our findings highlight the importance of considering such factors during the design process. We then use our analysis of population dynamics to inform the selection of genetic parts, which could be used to obtain the desired spatio-temporal behaviours. By identifying, integrating and automating key stages of the design process, we provide a computational framework for designing synthetic systems, which could be tested in future laboratory studies.
Pseudoelastic behaviour of a natural material is achieved via reversible changes in protein backbone conformation
Authors: Harrington Matthew J. , Wasko S. Scott , Masic Admir , Fischer F. Dieter , Gupta Himadri S. , Fratzl Peter
Published: June 2012

The egg capsules of marine prosobranch gastropods, commonly know as whelks, function as a protective encapsulant for whelk embryos in wave-swept marine environments. The proteinaceous sheets comprising the wall of whelk egg capsules (WEC) exhibit long-range reversible extensibility with a hysteresis of up to 50 per cent, previously suggested to result from reversible changes in the structure of the constituent protein building blocks. Here, we further investigate the structural changes of the WEC biopolymer at various hierarchical levels using several different time-resolvedin situapproaches. We find strong evidence in these biological polymers for a strain-induced reversible transition from an ordered conformational phase to a largely disordered one that leads to the characteristic reversible hysteretic behaviour, which is reminiscent of the pseudoelastic behaviour in some metallic alloys. On the basis of these results, we generate a simple numerical model incorporating a worm-like chain equation to explain the phase transition behaviour of the WEC at the molecular level.
Integrative Comparative Analyses of Transcript and Metabolite Profiles from Pepper and Tomato Ripening and Development Stages Uncovers Species-Specific Patterns of Network Regulatory Behavior
Authors: Osorio Sonia , Alba Rob , Nikoloski Zoran , Kochevenko Andrej , Fernie Alisdair R. , Giovannoni James J.
Published: June 2012

Integrative comparative analyses of transcript and metabolite levels from climacteric and nonclimacteric fruits can be employed to unravel the similarities and differences of the underlying regulatory processes. To this end, we conducted combined gas chromatography-mass spectrometry and heterologous microarray hybridization assays in tomato (Solanum lycopersicum; climacteric) and pepper (Capsicum chilense; nonclimacteric) fruits across development and ripening. Computational methods from multivariate and network-based analyses successfully revealed the difference between the covariance structures of the integrated data sets. Moreover, our results suggest that both fruits have similar ethylene-mediated signaling components; however, their regulation is different and may reflect altered ethylene sensitivity or regulators other than ethylene in pepper. Genes involved in ethylene biosynthesis were not induced in pepper fruits. Nevertheless, genes downstream of ethylene perception such as cell wall metabolism genes, carotenoid biosynthesis genes, and the never-ripe receptor were clearly induced in pepper as in tomato fruit. While signaling sensitivity or actual signals may differ between climacteric and nonclimacteric fruit, the evidence described here suggests that activation of a common set of ripening genes influences metabolic traits. Also, a coordinate regulation of transcripts and the accumulation of key organic acids, including malate, citrate, dehydroascorbate, and threonate, in pepper fruit were observed. Therefore, the integrated analysis allows us to uncover additional information for the comprehensive understanding of biological events relevant to metabolic regulation during climacteric and nonclimacteric fruit development.
High-Resolution Mapping of a Fruit Firmness-Related Quantitative Trait Locus in Tomato Reveals Epistatic Interactions Associated with a Complex Combinatorial Locus
Authors: Chapman Natalie H. , Bonnet Julien , Grivet Laurent , Lynn James , Graham Neil , Smith Rebecca , Sun Guiping , Walley Peter G. , Poole Mervin , Causse Mathilde , King Graham J. , Baxter Charles , Seymour Graham B.
Published: June 2012

Fruit firmness in tomato (Solanum lycopersicum) is determined by a number of factors including cell wall structure, turgor, and cuticle properties. Firmness is a complex polygenic trait involving the coregulation of many genes and has proved especially challenging to unravel. In this study, a quantitative trait locus (QTL) for fruit firmness was mapped to tomato chromosome 2 using the Zamir Solanum pennellii interspecific introgression lines (ILs) and fine-mapped in a population consisting of 7,500 F2 and F3 lines from IL 2-3 and IL 2-4. This firmness QTL contained five distinct subpeaks, Firs.p.QTL2.1 to Firs.p.QTL2.5, and an effect on a distal region of IL 2-4 that was nonoverlapping with IL 2-3. All these effects were located within an 8.6-Mb region. Using genetic markers, each subpeak within this combinatorial locus was mapped to a physical location within the genome, and an ethylene response factor (ERF) underlying Firs.p.QTL2.2 and a region containing three pectin methylesterase (PME) genes underlying Firs.p.QTL2.5 were nominated as QTL candidate genes. Statistical models used to explain the observed variability between lines indicated that these candidates and the nonoverlapping portion of IL 2-4 were sufficient to account for the majority of the fruit firmness effects. Quantitative reverse transcription-polymerase chain reaction was used to quantify the expression of each candidate gene. ERF showed increased expression associated with soft fruit texture in the mapping population. In contrast, PME expression was tightly linked with firm fruit texture. Analysis of a range of recombinant lines revealed evidence for an epistatic interaction that was associated with this combinatorial locus.
How to hold on to your key information‐technology specialists
Authors: Ezulike Gozie
Published: June 2012

Purpose

Discusses what motivates people who work in information technology and looks at ways that companies can retain their key personnel.

Design/methodology/approach

Describes a retention and reward strategy for information‐technology specialists.

Findings

Details the importance of having a clear job specification, proper business planning, the possibility of flexible working, an effective training and development policy, staff surveys and exit interviews.

Practical implications

Emphasizes that IT specialists need to feel that they do a job well and that their input is recognized, valued and rewarded.

Social implications

Reveals that the market for IT specialists remains buoyant, despite the economic downturn.

Originality/value

Stresses the importance of organizations looking after their valued IT staff if they want to retain them.
The importance of balance in leadership development
Authors: Short Tom
Published: June 2012

Purpose

Describes research on the development of leaders in Australian rail organizations.

Design/methodology/approach

Details five areas where the “complementarity” contained in the Chinese yin and yang philosophy could help to restore balance in modern leadership.

Findings

Highlights the importance of balancing: principles and practices; technical and people skills; hard and soft skills; formal and informal learning; and self and others.

Practical implications

Advances the view that these five balances are relevant the world over; one aspect of leadership and management cannot live without the other, yet each aspect lives within the other.

Social implications

Demonstrates a way forward for management development at a time when the need for leadership development, capability building and talent management have reached dangerously low levels across the world and the position will deteriorate as baby‐boomers retire and leave behind a leadership “black hole”.

Originality/value

Postulates that one aspect of leadership and management cannot live without the other, yet each aspect lives within the other.
A new spirit for fostering organizational success
Authors: Little Bob
Published: June 2012

Purpose

Outlines and reports on a radical new approach to developing both an organization and its people to enable those people to be themselves in body, mind and spirit while at work and so feel fulfilled – and, in the process, enable the organization to be more successful.

Design/methodology/approach

Outlines the philosophy of Ecumenical Partnership Initiatives Compassion in Change (EPICC), a part of Workplace Matters; summarizes key industry trends identified in relevant research, and sets out EPICC's question‐based approach to achieving its clients' goals.

Findings

Reports research findings that only 20 percent of employees in large organizations feel their strengths are used every day and eight out of ten employees feel miscast in their job. Outlines a new way of business thinking with regard to human resources and development. Reports that, when dealing with business issues within the social paradigm, it is important to be open to things of the spirit.

Practical implications

Describes how people can “take their whole selves to work” and how organizations can reap the full benefits of encouraging this policy.

Social implications

Contends that financial results will be better, customers will be delighted and staff will thrive where the business can find the right balance between two management paradigms: the dominant economic – finance based, short term, zero‐sum, process, rational, controlling – and the emerging social paradigm based around relationships, ethics and inspiration.

Originality/value

Contains important insights into how this balance can be achieved.
Outcomes and well‐being part 2: a comparative longitudinal study of two models of homecare delivery and their impact upon the older person self‐reported subjective well‐being. A qualitative follow up study paper
Authors: Gethin‐Jones Stephen
Published: June 2012

Purpose

This paper aims to follow up on a previous quantitative research project which established that outcome‐focussed care appeared to be associated with an increase in the individuals' subjective well‐being. The purpose of this paper is to establish why the intervention enabled this.

Design/methodology/approach

The study utilised a qualitative approach to gather the subjective experience of the individual service users. The sample consisted of 20 service users, who were subject of two semi‐structured interviews; one interview at the start of the intervention and one at the six month stage. The data were then analysed under core themes raised by the service user in these interviews. The sample was divided into two, with one group receiving the outcome‐focussed model of care and the other group receiving the traditional time focussed care.

Findings

The research established that service users' subjective well‐being improved due to the ability of outcome‐focussed care to provide consistency, flexibility and most importantly the ability of the service user to form a relationship with the homecare workers providing their care.

Practical implications

This paper will assist professionals to understand why outcome‐focus care has a profound impact upon service users' subjective well‐being as opposed to the existing task focussed care.

Originality/value

This and the previous paper provide an insight into how different processes and models of intervention impact upon the subjective well‐being of socially isolated older people.