bluuebunny/crossref_metadata_2025_split huggingface dataset:
Classification of transporters using efficient radial basis function networks with position‐specific scoring matrices and biochemical properties
Authors: Ou Yu‐Yen , Chen Shu‐An , Gromiha M. Michael 
Published: January 2010

AbstractTransporters are proteins that are involved in the movement of ions or molecules across biological membranes. Transporters are generally classified into channels/pores, electrochemical transporters, and active transporters. Discriminating the specific class of transporters and their subfamilies are essential tasks in computational biology for the advancement of structural and functional genomics. We have systematically analyzed the amino acid composition, residue pair preference and amino acid properties in six different families of transporters. Utilizing the information, we have developed a radial basis function (RBF) network method based on profiles obtained with position specific scoring matrices for discriminating transporters belonging to three different classes and six families. Our method showed a fivefold cross validation accuracy of 76%, 73%, and 69% for discriminating transporters and nontransporters, three different classes and six different families of transporters, respectively. Further, the method was tested with independent datasets, which showed similar level of accuracy. A web server has been developed for discriminating transporters based on three classes and six families, and it is available at http://rbf.bioinfo.tw/∼sachen/tcrbf.html. We suggest that our method could be effectively used to identify transporters and discriminating them into different classes and families. Proteins 2010;. © 2010 Wiley‐Liss, Inc.
Near‐field study of light scattering at rough interfaces of a‐Si:H/µc‐Si:H tandem solar cells
Authors: Bittkau K. , Beckers T. 
Published: January 2010

AbstractLight scattering at randomly textured interfaces in tandem solar cells consisting of hydrogenated amorphous silicon (a‐Si:H) and hydrogenated microcrystalline silicon (µc‐Si:H) is studied in the optical near‐field experimentally by near‐field scanning optical microscopy (NSOM) and theoretically by a rigorous solution of Maxwell's equations using a Fourier ansatz. The work concentrates on the influence of evanescent light modes on the absorption in the a‐Si:H top cell. It is found that the improvement of solar cell efficiency due to the surface texturing is borne by evanescent light modes. For both, the theoretical and the experimental study, techniques are developed to extract the evanescent part of the light from the obtained data. From the theoretical results, the principal mechanism of light scattering in the optical near‐field regime is studied and, in particular, light which is trapped in the a‐Si:H top cell by total internal reflection is visualized. From the experimental results, a map of the local light trapping efficiency is generated and the correlation to morphological properties is studied.
Three hydrogenated amorphous silicon photodiodes stacked for an above integrated circuit colour sensor
Authors: Gidon Pierre , Giffard Benoit , Moussy Norbert , Parrein Pascale , Poupinet Ludovic 
Published: January 2010

AbstractWe present theoretical simulation and experimental results of a new colour pixel structure. This pixel catches the light in three stacked amorphous silicon photodiodes encompassed between transparent electrodes. The optical structure has been simulated for signal optimisation. The thickness of each stacked layer is chosen in order to absorb the maximum of light and the three signals allow to linearly calculate the CIE colour coordinates1with minimum error and noise. The whole process is compatible with an above integrated circuit (IC) approach. Each photodiode is an n‐i‐p structure. For optical reason, the upper diode must be controlled down to 25 nm thickness. The first test pixel structure allows a good recovering of colour coordinates. The measured absorption spectrum of each photodiode is in good agreement with our simulations. This specific stack with three photodiodes per pixel totalises two times more signal than an above IC pixel under a standard Bayer pattern2,3.In each square of this GretagMacbeth chart is the reference colour on the right and the experimentally measured colour on the left with three amorphous silicon photodiodes per pixel.magnified image
Optical demultiplexer based on an a‐SiC:H voltage controlled device
Authors: Louro P. , Vieira M. , Fernandes M. , Costa J. , Vieira M. A. , Caeiro J. , Neves N. , Barata M. 
Published: January 2010

AbstractIn this paper we present results on the use of a semiconductor heterostructure based on a‐SiC:H as a wavelength‐division demultiplexer for the visible light spectrum. The proposed device is composed of two stacked p‐i‐n photodiodes with intrinsic absorber regions adjusted to short and long wavelength absorption and carrier collection. An optoelectronic characterisation of the device was performed in the visible spectrum. Demonstration of the device functionality for WDM applications was done with three different input channels covering the long, the medium and the short wavelengths in the visible range. The recovery of the input channels is explained using the photocurrent spectral dependence on the applied voltage.An electrical model of the WDM device is proposed and supported by the solution of the respective circuit equations. Short range optical communications constitute the major application field however other applications are foreseen (© 2010 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
The effect of artichoke (Cynara scolymus L.) extract on respiratory chain system activity in rat liver mitochondria
Authors: Juzyszyn Z. , Czerny B. , Myśliwiec Z. , Pawlik A. , Droździk M. 
Published: January 2010

AbstractThe effect of artichoke extract on mitochondrial respiratory chain (MRC) activity in isolated rat liver mitochondria (including reaction kinetics) was studied. The effect of the extract on the activity of isolated cytochrome oxidase was also studied. Extract in the range of 0.68–2.72 μg/ml demonstrated potent and concentration‐dependent inhibitory activity. Concentrations ≥5.4 μg/ml entirely inhibited MRC activity. The succinate oxidase system (MRC complexes II–IV) was the most potently inhibited, its activity at an extract concentration of 1.36 μg/ml being reduced by 63.3% compared with the control (p < 0.05). The results suggest a complex inhibitory mechanism of the extract. Inhibition of the succinate oxidase system was competitive (Ki= 0.23 μg/ml), whereas isolated cytochrome oxidase was inhibited noncompetitively (Ki= 126 μg/ml). The results of this study suggest that the salubrious effects of artichoke extracts may rely in part on the effects of their active compounds on the activity of the mitochondrial respiratory chain system. Copyright © 2010 John Wiley & Sons, Ltd.
A quest for the algorithm for evaluating the molecular hardness
Authors: Ghosh Dulal C. , Islam Nazmul 
Published: January 2010

AbstractIn this work, we have basically launched a search whether the molecular hardness, an important conceptual descriptor of chemistry and physics, can be evaluated in terms of the atomic hardness values invoking various mathematical algorithms for averaging or not. Starting from the semi‐empirical radial dependent formula of computing global hardness of atoms suggested by us, we have derived an ansatz of the molecular hardness assuming that the hardness equalization principle is operative and justifiably valid. In this work, we have attempted a validity test of our ansatz for computing molecular hardness by application to real world. We have also computed the hardness of considerable number of molecules through various mathematical averaging techniques. We have also computed the hardness data of such molecules by invoking ab initio quantum chemical method through the formula of Parr and Pearson, (I − A)/2. Results demonstrate that the set of hardness data evaluated through our suggested ansatz have very close agreement with the ab initio hardness data compared to the sets of data obtained through the various averaging techniques. In our next effort, by exploiting the suggestion of Gazquez, we have evaluated the reaction energy of a number of hard–soft acid–base exchange reactions. On a comparative study, it is found that (i) the arithmetic formula does not predict the reaction path at all, (ii) other methods fail to explain all the reactions efficiently, and (iii) the molecular hardness evaluated by the method suggested by us represent the reaction surface quite reasonably. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011
Cross‐layer optimization for CDMA/TDD wireless mesh networks
Authors: Liao Deng , Elhakeem Ahmed 
Published: January 2010

AbstractThis paper proposes a new cross‐layer optimization algorithm for wireless mesh networks (WMNs). CDMA/TDD (code division multiple access/time division duplex) is utilized and a couple of TDD timeslot scheduling schemes are proposed for the mesh network backbone. Cross‐layer optimization involves simultaneous consideration of the signal to interference‐plus‐noise ratio (SINR) at the physical layer, traffic load estimation and allocation at medium access control (MAC) layer, and routing decision at the network layer. Adaptive antennas are utilized by the wireless mesh routers to take advantage of directional beamforming. The optimization formulation is subject to routing constraints and can be solved by general nonlinear optimization techniques. Comparisons are made with respect to the classic shortest‐path routing algorithm in the network layer. The results reveal that the average end‐to‐end successful packet rate (SPR) can be significantly improved by the cross‐layer approach. The corresponding optimized routing decisions are able to reduce the traffic congestion. Copyright © 2010 John Wiley & Sons, Ltd.
Low‐cost mounting arrangements for building‐integrated wind turbines
Authors: Udell David , Infield David , Watson Simon 
Published: January 2010

AbstractMicro‐generation is being widely promoted as a way for householders in the UK and elsewhere to take part in ‘the Green Revolution’. Building‐integrated wind turbines (BIWTs) provide a way to do this, enabling people to reduce their contribution to the problems of both climate change and decreasing fossil fuel availability. Although energy yields from BIWTs for many householders have been shown to be low, there are still situations where such turbines can make a useful contribution to electricity generation, e.g. in windier areas and for isolated detached buildings. The standards for the installation of BIWTs are still being developed including those for the safe mounting of turbines on domestic buildings. This paper investigates the current trend for mounting small wind turbines on the walls of domestic premises and compares this with an approach which uses roof timbers. It identifies the main characteristics of building construction which affect the integrity of such installations. European and British standards have been used to calculate wind and gravitational loads. Finite element models are used to derive working stresses and, hence, some basic principles of good design. The likely costs of wall and roof mounting are then compared. Installation and health and safety issues are also examined briefly. Copyright © 2010 John Wiley & Sons, Ltd.
Free convective flow between vertical porous plates with periodic heat input
Authors: Jha B.K. , Ajibade A.O. 
Published: January 2010

AbstractA suction/injection controlled free convective motion of a viscous incompressible fluid between two periodically heated infinite vertical parallel plates is presented. The temperature and velocity fields are separated into steady and periodic parts and the resulting second order ordinary differential equations solved to obtain the solution to the problem. The influence of each governing parameter is discussed with the aid of contour maps. The significant result from this study is that temperature is higher near the plate with injection while velocity is more enhanced near the plate with suction. It is also interesting to note that for large values of suction, the nature of the flow is that of constant heating of the plates, while for large values of Strouhal number, the flow behaves as if there was no suction/injection at the plates [11].
Modelling of thermo‐viscoelastic material behaviour of polyurethane close to the glass transition temperature
Authors: Johlitz M. , Scharding D. , Diebels S. , Retka J. , Lion A. 
Published: January 2010

AbstractIn this contribution a viscoelastic elastomer is examined with respect to its thermo‐mechanical behaviour. Therefore uniaxial tension tests and relaxation tests are performed at different constant temperatures up to the glass transition region. Hence an experimental data pool is provided. On the theoretical side a finite viscoelastic and incompressible material model is used and enhanced by temperature dependency in order to model the experimentally observed effects. The material parameters are strategically identified by means of biologic evolution strategies. Thereby it turned out that the investigated material cannot be modelled as a thermo‐rheologically simple material. Quite the contrary, a new ansatz is chosen.
Use of intrauterine devices in women with uterine anatomic abnormalities
Authors: Tepper Naomi K. , Zapata Lauren B. , Jamieson Denise J. , Curtis Kathryn M. 
Published: January 2010

AbstractObjectiveTo examine the evidence regarding the safety and effectiveness of intrauterine devices (IUDs) in women with uterine abnormalities.MethodsWe searched PubMed for all peer‐reviewed articles in any language that had been published on the topic from database inception to September 2009. Primary research articles were included if they addressed the safety or effectiveness of any type of IUD among women with Müllerian anomalies or uterine synechiae.ResultsIn total, 19 case reports or case series met the inclusion criteria. Reported complications included expulsion, pregnancy, bleeding, perforation, and pain. In several case reports, no complications were reported.ConclusionEvidence concerning the safety and effectiveness of IUD use among women with uterine abnormalities is very limited.
How Opportunity Costs Decrease the Probability of War in an Incomplete Information Game
Authors: Polachek Solomon , Xiang Jun 
Published: January 2010

AbstractThis article shows that the opportunity costs resulting from economic interdependence decrease the probability of war in an incomplete information game. This result is strongly consistent with existing empirical analyses of the inverse trade-conflict relationship but is the opposite of the conclusion reached by Gartzke, Li, and Boehmer, who reject the opportunity cost argument in a game-theoretic framework. As a result of our findings, one cannot dismiss the opportunity cost argument as the explanation why trading nations fight less. Instead our study reaffirms the central position of opportunity costs as the basis for the inverse trade-conflict relationship, thus implying that one need not rely on signaling.
Constraining Coercion? Legitimacy and Its Role in U.S. Trade Policy, 1975–2000
Authors: Pelc Krzysztof J. 
Published: January 2010

AbstractThe role of legitimacy in international relations is a topic of much debate, yet there is little understanding of the mechanism behind it. Here I address this discrepancy by asking: are state threats perceived as (il)legitimate more or less likely to be successful? By operationalizing illegitimacy as unilateral action in the presence of a multilateral option, I consider the variation in the success of U.S. trade measures from 1975 to 2000. As I show, the (il)legitimacy of threats modifies the nature of the signal sent by concessions to those threats, and this effect can be measured and predicted. I find that, controlling for material pressure, perceived illegitimacy of U.S. trade threats decreases the likelihood of a target conceding by over 34 percent. Moreover, it pays to resist: targets that resist illegitimate unilateral measures from the United States are 25 percent less likely to encounter similar unilateral measures over the following five years.
God, compatibilism, and the authorship of sin
Authors: HELM PAUL 
Published: January 2010

AbstractPeter Byrne has presented arguments against the effectiveness of two ‘defensive strategies’ deployed in my books Eternal God and The Providence of God respectively. These strategies were originally presented to support the cogency of ‘theological compatibilism’ by arguing against the claims that it is inconsistent with human responsibility, and that it entails that God is the author of sin. In this present article the author offers a number of clarifications to his original thesis and argues that Byrne's arguments do not succeed in their aim of undermining the two strategies.
TWO (OR THREE) NOTIONS OF FINITISM
Authors: GANEA MIHAI 
Published: January 2010

Finitism is given an interpretation based on two ideas about strings (sequences of symbols): a replacement principle extracted from Hilbert’s work and a counting principle inspired by Tait. These principles are used to justify an equational arithmetic${\cal T}_{{\cal L}^2 } $based on the algebra of lower elementary functions. The extension of this algebra to Grzegorczyk’s classɛ2can be justified by means of an additional finitistic choice principle, thus obtaining a second equational theory${\cal T}_{{\cal E}^2 } $. It is unknown whether${\cal T}_{{\cal E}^2 } $is strictly stronger than${\cal T}_{{\cal L}^2 } $sinceɛ2may coincide with the class of lower elementary functions.If the objects of arithmetic are taken to be binary numerals instead of tally numerals, then it becomes possible to provide a finitistic justification for a theory${\cal T}_B $that may be incomparable to${\cal T}_{{\cal E}^2 } $(neither of the two includes the other). I conclude by suggesting that the equational theory of Kalmar elementary functions is a strict upper bound for finitistic arithmetic.
Artificial Photosynthesis Would Unify the Electricity-Carbohydrate-Hydrogen Cycle for Sustainability
Authors: Zhang Yi-Heng Percival 
Published: January 2010

AbstractSustainable development requires balanced integration of four basic human needs – air (O2/CO2), water, food, and energy. To solve key challenges, such as CO2 fixation, electricity storage, food production, transportation fuel production, water conservation or maintaining an ecosystem for space travel, we wish to suggest the electricity-carbohydrate-hydrogen (ECHo) cycle, where electricity is a universal energy carrier, hydrogen is a clean electricity carrier, and carbohydrate is a high-energy density hydrogen (14.8 H2 mass% or 11-14 MJ electricity output/kg)carrier plus a food and feed source. Each element of this cycle can be converted to the other reversibly & efficiently depending on resource availability, needs, and costs. In order to implement such cycle, here we propose to fix carbon dioxide by electricity or hydrogen to carbohydrate (starch) plus ethanol by cell-free synthetic biology approaches. According to knowledge in the literature, the proposed artificial photosynthesis must be operative. Therefore, collaborations are urgently needed to solve several technological bottlenecks before large-scale implementation.
Fifteen years of APC/cyclosome: a short and impressive biography
Authors: Simpson-Lavy Kobi J. , Oren Yifat S. , Feine Oren , Sajman Julia , Listovsky Tammy , Brandeis Michael 
Published: January 2010

The APC/C (anaphase-promoting complex/cyclosome) discovered exactly 15 years ago by Avram Heshko and Marc Kirschner is by far the most complex ubiquitin ligase discovered so far. The APC/C is composed of roughly a dozen subunits and measures a massive 1.5 MDa. This huge complex, as well as its multiple modes of regulation, boasts impressive evolutionary conservation. One of its most puzzling features is its split personality: regulation of mitotic exit events on the one hand, and its ongoing activity during G1-phase, G0-phase and in terminally differentiated cells. The present short review is intended to provide a basic description of our current understanding of the APC/C, focusing on recent findings concerning its role in G1-phase and in differentiated cells.
Cell-wide analysis of secretory granule dynamics in three dimensions in living pancreatic β-cells: evidence against a role for AMPK-dependent phosphorylation of KLC1 at Ser517/Ser520 in glucose-stimulated insulin granule movement
Authors: McDonald Angela , Fogarty Sarah , Leclerc Isabelle , Hill Elaine V. , Hardie D. Grahame , Rutter Guy A. 
Published: January 2010

Glucose-stimulated insulin secretion from pancreatic β-cells requires the kinesin-1/Kif5B-mediated transport of insulin granules along microtubules. 5′-AMPK (5′-AMP-activated protein kinase) is a heterotrimeric serine/threonine kinase which is activated in β-cells at low glucose concentrations, but inhibited as glucose levels increase. Active AMPK blocks glucose-stimulated insulin secretion and the recruitment of insulin granules to the cell surface, suggesting motor proteins may be targets for this kinase. While both kinesin-1/Kif5B and KLC1 (kinesin light chain-1) contain consensus AMPK phosphorylation sites (Thr693 and Ser520, respectively) only recombinant GST (glutathione transferase)–KLC1 was phosphorylated by purified AMPK in vitro. To test the hypothesis that phosphorylation at this site may modulate kinesin-1-mediated granule movement, we developed an approach to study the dynamics of all the resolvable granules within a cell in three dimensions. This cell-wide approach revealed that the number of longer excursions (&gt;10 μm) increased significantly in response to elevated glucose concentration (30 versus 3 mM) in control MIN6 β-cells. However, similar changes were seen in cells overexpressing wild-type KLC1, phosphomimetic (S517D/S520D) or non-phosphorylatable (S517A/S520A) mutants of KLC1. Thus, changes in the phosphorylation state of KLC1 at Ser517/Ser520 seem unlikely to affect motor function.
Direct assignment of EPR spectra to structurally defined iron-sulfur clusters in complex I by double electron–electron resonance
Authors: Roessler Maxie M. , King Martin S. , Robinson Alan J. , Armstrong Fraser A. , Harmer Jeffrey , Hirst Judy 
Published: January 2010

In oxidative phosphorylation, complex I (NADH:quinone oxidoreductase) couples electron transfer to proton translocation across an energy-transducing membrane. Complex I contains a flavin mononucleotide to oxidize NADH, and an unusually long series of iron-sulfur (FeS) clusters, in several subunits, to transfer the electrons to quinone. Understanding coupled electron transfer in complex I requires a detailed knowledge of the properties of individual clusters and of the cluster ensemble, and so it requires the correlation of spectroscopic and structural data: This has proved a challenging task. EPR studies on complex I from
Bos taurus
have established that EPR signals N1b, N2 and N3 arise, respectively, from the 2Fe cluster in the 75 kDa subunit, and from 4Fe clusters in the PSST and 51 kDa subunits (positions 2, 7, and 1 along the seven-cluster chain extending from the flavin). The other clusters have either evaded detection or definitive signal assignments have not been established. Here, we combine double electron-electron resonance (DEER) spectroscopy on
B. taurus
complex I with the structure of the hydrophilic domain of
Thermus thermophilus
complex I. By considering the magnetic moments of the clusters and the orientation selectivity of the DEER experiment explicitly, signal N4 is assigned to the first 4Fe cluster in the TYKY subunit (position 5), and N5 to the all-cysteine ligated 4Fe cluster in the 75 kDa subunit (position 3). The implications of our assignment for the mechanisms of electron transfer and energy transduction by complex I are discussed.