bluuebunny/crossref_metadata_2025 huggingface dataset:
Nonperturbative time-convolutionless quantum master equation from the path integral approach
Authors: Nan Guangjun , Shi Qiang , Shuai Zhigang
Published: April 2009

The time-convolutionless quantum master equation is widely used to simulate reduced dynamics of a quantum system coupled to a bath. However, except for several special cases, applications of this equation are based on perturbative calculation of the dissipative tensor, and are limited to the weak system-bath coupling regime. In this paper, we derive an exact time-convolutionless quantum master equation from the path integral approach, which provides a new way to calculate the dissipative tensor nonperturbatively. Application of the new method is demonstrated in the case of an asymmetrical two-level system linearly coupled to a harmonic bath.
High-resolution electron spectroscopy and σ/π structures of M(pyridine) and M+(pyridine) (M=Li, Ca, and Sc) complexes
Authors: Krasnokutski Serge A. , Yang Dong-Sheng
Published: April 2009

Metal-pyridine (metal=Li, Ca, and Sc) complexes are produced in laser-vaporization molecular beams and studied by pulsed-field-ionization zero-electron-kinetic-energy (ZEKE) spectroscopy and theoretical calculations. Both σ and π structures are considered for the three complexes by theory, and preferred structures are determined by the combination of the ZEKE spectra and calculations. The Li and Ca complexes prefer a σ bonding mode, whereas the Sc complex favors a π mode. Adiabatic ionization energies and metal-ligand vibrational frequencies are determined from the ZEKE spectra. Metal-ligand bond dissociation energies of the neutral complexes are obtained from a thermodynamic cycle. The ionization energies follow the trend of Li-pyridine (32 460 cm−1)<Ca-pyridine(39 043 cm−1)<Sc-pyridine(42 816 cm−1), whereas the bond energies are in the order of Ca-pyridine (27.0 kJ mol−1)<Li-pyridine(49.1 kJ mol−1)<Sc-pyridine(110.6 kJ mol−1). The different bonding modes between the main group metals and transition element are discussed in terms of Sc 3d orbital involvement. The bond energy differences between the Li and Ca metals are explained by the number of valence s electrons and the size of the metal atoms.
Optical properties of rolled-up tubular microcavities from shaped nanomembranes
Authors: Huang G. S. , Kiravittaya S. , Bolaños Quiñones V. A. , Ding F. , Benyoucef M. , Rastelli A. , Mei Y. F. , Schmidt O. G.
Published: April 2009

Tubular optical microcavities have been fabricated by releasing prestressed SiO/SiO2 bilayer nanomembranes from polymer sacrificial layers, and their geometrical structure is well controlled by defining the shape of nanomembranes via photolithography. Optical measurements at room temperature demonstrate that resonant modes of microtubular cavities rolled up from circular shapes can be tuned in peak energy and relative intensity along the tube axes compared to those from square patterns. The resonant modes shift to higher energy with decreasing number of tube wall rotations and thickness, which fits well to finite-difference time-domain simulations. Polarization resolved measurements of the resonant modes indicate that their polarization axes are parallel to the tube axis, independent of the polarization of the excitation laser.
Magnetism and band gap narrowing in Cu-doped ZnO
Authors: Ferhat M. , Zaoui A. , Ahuja R.
Published: April 2009

First-principles calculations based on density functional theory are performed to study the magnetic, electronic, and optical properties of ZnO doped with 6.25%, 12.5%, and 18.75% of Cu. The Cu dopants are found spin polarized, and a net magnetic moment of 0.57μB is found for Cu at a composition of 6.25%. The calculations confirm an appreciable band gap reduction in ZnO in agreement with recent experimental results. The analysis of the partial density of states reveals that ferromagnetism and narrowing of ZnO band gap are due principally to the strong p-d mixing of O and Cu.
Cascade-energy-level alignment based organic photovoltaic cells by utilizing copper phthalocyanine as bipolar carrier transporting layer
Authors: Zhang Guang , Li Wenlian , Chu Bei , Chen Lili , Yan Fei , Zhu Jianzhuo , Chen Yiren , Lee C. S.
Published: April 2009

We demonstrate a cascade-energy-level alignment based organic photovoltaic cell by using stacking three materials with appropriate energy levels. A cell with a structure of ITO/4,4′,4″-tris[N,(3-methylphenyl)-N-phenylamino]-triphenylamine (m-MTDATA)/copper phthalocyanine (CuPc)/fullerene (C60)/4,4′-N,N′-dicarubreneazolebiphenyl (BCP)/LiF/Al was shown to have a power efficiency enhancement in more than 30% over that of a standard reference cell (ITO/CuPc/C60/BCP/LiF/Al), which has only one exciton-dissociation interface. The efficiency improvement was mainly ascribed to the ingenious cascade-energy-level alignment and the application of the bipolar carrier transporting property.
Room temperature photoluminescence of tensile-strained Ge/Si0.13Ge0.87 quantum wells grown on silicon-based germanium virtual substrate
Authors: Chen Yanghua , Li Cheng , Zhou Zhiwen , Lai Hongkai , Chen Songyan , Ding Wuchang , Cheng Buwen , Yu Yude
Published: April 2009

We report a room temperature study of the direct band gap photoluminescence of tensile-strained Ge/Si0.13Ge0.87 multiple quantum wells grown on Si-based germanium virtual substrates by ultrahigh vacuum chemical vapor deposition. Blueshifts of the luminescence peak energy from the Ge quantum wells in comparison with the Ge virtual substrate are in good agreement with the theoretical prediction when we attribute the luminescence from the quantum well to the cΓ1-HH1 direct band transition. The reduction in direct band gap in the tensile strained Ge epilayer and the quantum confinement effect in the Ge/Si0.13Ge0.87 quantum wells are directly demonstrated by room temperature photoluminescence.
Performance comparison between planar and tubular-shaped ambient air-breathing polymer electrolyte membrane fuel cells using three-dimensional computational fluid dynamics models
Authors: Al-Baghdadi Maher A. R. Sadiq
Published: April 2009

The development of physically representative models that allow reliable simulation of the processes under realistic conditions is essential to the development and optimization of fuel cells, the introduction of cheaper materials and fabrication techniques, and the design and development of novel architectures. Full three-dimensional, multiphase, nonisothermal computational fluid dynamics models of planar and novel tubular-shaped air-breathing polymer electrolyte membrane (PEM) fuel cell have been developed. These comprehensive models account for the major transport phenomena in planar and tubular-shaped air-breathing PEM fuel cell: convective and diffusive heat and mass transfer, electrode kinetics, transport and phase-change mechanism of water, and potential fields. The models are shown to understand the many interacting, complex electrochemical, and transport phenomena that cannot be studied experimentally. Fully three-dimensional results of the species profiles, temperature distribution, potential distribution, and local current density distribution are presented and analyzed with a focus on the physical insight and fundamental understanding for the planar and the novel tubular geometry of air-breathing PEM fuel cells.
Effect of conductivity of filler on the percolation threshold of composites
Authors: Deepa K. S. , Kumari Nisha S. , Parameswaran P. , Sebastian M. T. , James J.
Published: April 2009

Polytetrafluoroethylene (PTFE)-silver composites were prepared and the influence of conductivity, particle size, and interfacial area of Ag particle on the percolative behavior were investigated. Silver particles of two different grain sizes (3.5 and 5 μm) were individually mixed with PTFE and the corresponding variations in the dielectric properties were studied. The composite containing Ag particles of size 3.5 μm showed the percolation at 7 vol %, while for Ag particles of size 5 μm, the percolation is at 10 vol %. In both cases near the percolation, the interparticle distances were in the range of ∼3.3–3.8 μm.
Characterizing piezoscanner hysteresis and creep using optical levers and a reference nanopositioning stage
Authors: Xie H. , Rakotondrabe M. , Régnier S.
Published: April 2009

A method using atomic force microscope (AFM) optical levers and a reference nanopositioning stage has been developed to characterize piezoscanner hysteresis and creep. The piezoscanner is fixed on a closed-loop nanopositioning stage, both of which have the same arrangement on each axis of the three spatial directions inside the AFM-based nanomanipulation system. In order to achieve characterization, the optical lever is used as a displacement sensor to measure the relative movement between the nanopositioning stage and the piezoscanner by lateral tracking a well-defined slope with the tapping mode of the AFM cantilever. This setup can be used to estimate a piezoscanner’s voltage input with a reference displacement from the nanopositioning stage. The hysteresis and creep were accurately calibrated by the method presented, which use the current setup of the AFM-based nanomanipulation system without any modification or additional devices.
Size-dependent impurity activation energy in GaN nanowires
Authors: Yoon J. , Girgis A. M. , Shalish I. , Ram-Mohan L. R. , Narayanamurti V.
Published: April 2009

The effect of the surrounding dielectric on the conductivity of GaN nanowires is measured experimentally. The two following configurations are considered: bare suspended and SiO2-coated nanowires. The measured conductivity is consistently fitted by two exponential terms with different activation energies, indicating multichannel conduction. The larger energy, attributed to activation of impurities into the conduction subband, shows essentially inverse dependence on nanowire radius, consistent with the dielectric confinement effect. This agrees with calculated values from finite element analysis. The smaller energy is independent of the nanowire radius, suggesting a surface conduction channel.
Field dependent and high light sensitive organic phototransistors based on linear asymmetric organic semiconductor
Authors: Guo Yunlong , Du Chunyan , Di Chong-an , Zheng Jian , Sun Xiangnan , Wen Yugeng , Zhang Lei , Wu Weiping , Yu Gui , Liu Yunqi
Published: April 2009

The authors reported organic phototransistors (PTs) with octadecyltrichlorosilane treated SiO2/Si substrate based on anthra[2,3-b]benzo[d]thiophene. The organic PTs show a high mobility of 0.4 cm2 V−1 s−1, a maximum photoresponsivity of about 1000 A/W, and photocurrent/dark-current ratio of around 800 under white light irradiation with 30 μW/cm2. The data are comparable with those of PTs based on amorphous silicon. Meanwhile, it is interesting to see that the devices show a high air-stable property and high photosensitivity via electric-field enhanced process. All these phenomena were attributed to the intrinsic optic-electronic property of the organic semiconductor and optic-electric field effect.
Anisotropy of In incorporation in GaN/InGaN multiquantum wells prepared by epitaxial lateral overgrowth
Authors: Polyakov A. Y. , Govorkov A. V. , Smirnov N. B. , Markov A. V. , Lee In-Hwan , Ju Jin-Woo , Pearton S. J.
Published: April 2009

Microcathodoluminescence (MCL) spectra and monochromatic MCL images were measured for GaN/InGaN multiquantum well (MQW) structures prepared by epitaxial lateral overgrowth (ELOG). The MQW related peak is redshifted from 462 nm in the normally grown ELOG window region to 482 nm in the laterally overgrown ELOG wing region. Correspondingly, the former appears as dark contrast stripes for long wavelength MCL images and as bright stripes for the short wavelength MCL images. The redshift is consistent with a higher indium incorporation efficiency for growth in the [112¯0] direction compared to the [0001] direction.
Effects of N2–CO polarization beating on femtosecond coherent anti-Stokes Raman scattering spectroscopy of N2
Authors: Roy Sukesh , Richardson Daniel , Kinnius Paul J. , Lucht Robert P. , Gord James R.
Published: April 2009

The effects of broadband excitation employing femtosecond laser pulses on the coherent anti-Stokes Raman scattering (CARS) spectroscopy of N2 are investigated. We have previously demonstrated that the dephasing rate of the coherence, established by the impulsive excitation of N2 using femtosecond pump and Stokes beams, can be used for measuring gas-phase temperature in chemically reacting flows. The objective of the current work is to investigate the effects of polarization beating between N2 and CO on the measured gas-phase temperature using time-resolved femtosecond CARS spectroscopy of N2.
Pimping Climate Change: Richard Branson, Global Warming, and the Performance of Green Capitalism
Authors: Prudham Scott
Published: April 2009

On 21 September 2006 UK über-entrepreneur and Virgin Group Chairman Richard Branson pledged approximately £1.6 billion, the equivalent of all the profits from Virgin Atlantic and Virgin Trains for the next ten years, to fighting climate change. Since then, Branson has restated his commitment to action on global warming, including investment in technologies for sequestering carbon dioxide from the atmosphere. In this paper, I critically examine and engage with Branson's announcements as a specific entrée into a dialog about so-called ‘green capitalism’. I am particularly interested in the role of the entrepreneurial subject in environmental policy and environmental action. There are glaring problems associated with green capitalism as a mash-up of environmentalism with capitalism. One of these is the tethering of environmentalism to a political economy whose mantra is growth for growth's sake, or, in Marx's terms, accumulation for accumulation's sake. This has been discussed by some as the problem of capitalism's ecological metabolism or ‘metabolic rift’. Yet, while accumulation for accumulation's sake may well be anathema to progressive environmentalism and sustainability, I argue that this is not only an objective, quantitative problem but also one of the qualitative dimensions of produced nature and the cultural politics of environmentalism. Appreciation of this can be gleaned by reexamining Marx's discussion of the role of the bourgeois subject in the relentless drive to reproduce and expand capital accumulation via anarchic, entrepreneurial investment. Green capitalist orthodoxy relies on this source of innovative dynamism, but in the process obscures or overlooks the fact that accumulation for accumulation's sake is by definition guided by the anarchic and amoral search for profitable realization of surplus value. Moreover, in order for green capitalism to succeed, its legitimacy must be secured. I argue that this legitimacy derives in part from specific performances of green capitalism by entrepreneurial elites, also made evident by Branson and his commitments to climate action. All of this raises questions about the political, cultural, and ecological character of green capitalism, issues brought to the fore by Branson's brand of climate activism.
The Software-Simulated Airworld: Anticipatory Code and Affective Aeromobilities
Authors: Budd Lucy , Adey Peter
Published: April 2009

This paper is concerned with the way in which airspaces are organised, managed, and understood by virtual representations—software simulations that are tested and used both preemptively and in real time. We suggest that, while airspaces are often understood as simulations themselves—models and blueprints for real-world futures—they are among the most mediated of all contemporary social environments, produced not only through code, but based on scenarios which predict and plan for future events—real vitalities that might come true. Drawing on historical and contemporary examples of aeronautical software simulation employed by civilian and military aviation, we explore how code has become increasingly sophisticated and ubiquitous in response to the challenges set by the mobilities the simulations model and the affective susceptibility of the corporeal body that uses them. The paper explores how software simulations work to structure and mediate behaviour by producing specific emotional and affective experiences in order to prepare the body for future encounters.
Software, Objects, and Home Space
Authors: Dodge Martin , Kitchin Rob
Published: April 2009

Through a series of interrelated developments, software is imbuing everyday objects with capacities that allow them to do additional and new types of work. On the one hand, objects are remade and recast through interconnecting circuits of software that make them machine readable. On the other, objects are gaining calculative capacities and awareness of their environment that allow them to conduct their own work, with only intermittent human oversight, as part of diverse actant networks. In the first part of the paper we examine the relationship between objects and software in detail, constructing a taxonomy of new types of coded objects. In the second part we explore how the technicity of different kinds of coded objects is mobilised to transduce space by considering the various ways in which coded objects are reshaping home life in different domestic spaces.
Rethinking Time Geography in the Information Age
Authors: Couclelis Helen
Published: April 2009

As everyday activities are increasingly carried out at least in part through digitally mediated remote interaction, researchers interested in the complex relationships between urban activities, spaces, and travel are running up against the limits of familiar forms of time geography. This paper argues that because information and communication technologies (ICTs) are loosening the traditionally close links between activity, place, and time, physicalist models such as the space–time path and prism of time geography may need to be reexamined in light of the new realities. An important part of these new realities is the fact that virtual communications depend on specific kinds of material means (computers and mobile phones, in particular). These now compete with and complement a fundamentally different kind of material means (of physical transportation) which have traditionally been at the basis of time-geographic analyses. The paper proposes a novel conceptual framework for time geography, whereby people's space–time behavior is modeled not just in a three-dimensional space but in a multidimensional space. The framework amounts to a primitive domain ontology for conceptualizing human activity in an ICT-rich world, and can naturally accommodate activity in cyberspace as well as in physical space. The objectives are: (1) to expand our ability to understand activities in space and time in the age of ICT by explicitly representing choices of means (here, transportation-related and communication-related means) to serve specific ends: to be most useful, this should be done within the same model that also tracks people's spatiotemporal trajectories; (2) more specifically, to improve our ability to represent and analyze the increasing variety of activities carried out with the help of ICT as these relate to time and place, and (3) to do so in a way that conserves the power of traditional time geography and is practical enough to be implemented. A few simple examples are discussed and illustrated with the help of parallel coordinates plots.
Evolution of the Second-Story City: The Minneapolis Skyway System
Authors: Corbett Michael J , Xie Feng , Levinson David
Published: April 2009

This research describes the growth of the Minneapolis Skyway network and aims to determine if the growth of the system has followed a predictable path. We hypothesize that the system expanded to the places in which it was valued the most. The point accessibility of each block lying within and adjacent to the connected system for each expansion year is calculated and used to predict the expansion of the Skyway System. In order to determine how often the expansion connected the blocks with higher accessibility, a connection-choice logit model relating the probability of joining the network (in a given year) to accessibility measures and network size was employed. The results disclose that accessibility is a significant explanatory factor of network growth. In accordance with the findings from the logit model, a network-growth simulation model was then developed on the basis of the strongest-link assumption (ie for a link to be constructed, it must be ranked the highest in terms of increasing accessibility between the two blocks it connects). The results show that the simulation model performs well in predicting the sequence of skyway additions on the basis of the myopic strongest-link assumption. This suggests that—although various physical, economic, regulatory, and legal factors may have played a role—accessibility remains an important factor in predicting which links are connected during the growth of the Minneapolis Skyway network.
Fujita and Ogawa Revisited: An Agent-Based Modeling Approach
Authors: Heikkila Eric J , Wang Yiming
Published: April 2009

This paper builds on and extends a classic paper (hereafter referred to as F–O) published by Masahisa Fujita and Hideaki Ogawa in 1982. Their paper models the emergence of urban centers brought about by household and firm location decisions in the context of spatially differentiated labor and land market interactions. Their approach is an analytical one that seeks to characterize the equilibrium values of the system. In contrast, we employ an agent-based modeling (ABM) approach that seeks to replicate the individual household and firm behaviors that lead to equilibrium or nonequilibrium outcomes. The F–O model has little to say about what happens outside of equilibrium, while the ABM approach is preoccupied with this question and is particularly well suited to address questions of path dependency and bounded rationality that lie well beyond the scope of the F–O original. We demonstrate that the urban outcomes that emerge depend critically upon the bidding behavior of agents and the institutional context within which their decisions are made.
Inefficient Search of Large-Scale Space in Williams Syndrome: Further Insights on the Role of LIMK1 Deletion in Deficits of Spatial Cognition
Authors: Smith Alastair D , Gilchrist Iain D , Hood Bruce , Tassabehji May , Karmiloff-Smith Annette
Published: April 2009

Williams syndrome (WS) is a genetic disorder associated with impairments of spatial cognition. This has primarily been studied in small-scale space, and rarely in large-scale environments. In order to fully characterise the spatial deficits in WS, and also to address claims that the deletion of LIM-kinase 1 (LIMK1) on chromosome 7 is responsible for those deficits, we report an automated large-scale search task for humans that places the participant egocentrically within the search space. Search locations were defined as lights and switches embedded in the floor, and participants attempted to locate a hidden target by pressing the switch at potential locations. We compared individuals with WS to patients with smaller deletions (including LIMK1) in the critical region on chromosome 7. Whilst partial-deletion participants performed efficiently on the task, participants with WS demonstrated inefficient search profiles: their search slopes were steeper and they made significantly more erroneous revisits to previously inspected locations. Our findings indicate that spatial deficits associated with WS also affect large-scale spatial processing and suggest that hemizygous deletion of LIMK1 is not sufficient to account for any of the spatial deficits associated with WS.
Trace mineral nutrition for broiler chickens and prospects of application of organically complexed trace minerals: a review
Authors: Bao Y. M. , Choct M.
Published: April 2009

This review critically examines the literature on the current status of trace mineral nutrition and the effect of organically complexed trace minerals, focusing on copper (Cu), iron (Fe), manganese (Mn) and zinc (Zn), on broiler chicken production. The requirements of Cu, Fe, Mn and Zn by broiler chickens need to be redefined due to today’s fast growing birds and the availability of organic trace minerals. Zn is one of the key trace minerals for chickens and although it maintains a relatively stable tissue concentration, dietary deficiency of Zn strongly depresses the feed intake, and hence the growth, of broiler chickens. Based on studies using a semiconventional diet, it is reasonable to conclude that the total Zn requirement for broiler chickens is around 60 mg/kg up until day 14 and 70 mg/kg from 14 day onwards, including the Zn content in the basal diet. However, it is difficult to determine the requirements of other organic trace minerals such as Cu, Fe and Mn because under a Zn adequate condition, it is impossible to produce deficient symptoms of these minerals on the basis of growth response. It also identifies gaps in knowledge of inorganic and organic trace mineral nutrition for the modern broiler chicken.
Feed consumption, growth performance and carcass evaluation of Korean Holstein bulls fed either conventional or organic diets
Authors: Lee W. S. , Khan M. A. , Kim H. S. , Kim J. H. , Yang S. H. , Ki K. S. , Lee H. J. , Kim S. B. , Baek K. S. , Ha J. K.
Published: April 2009

Feed consumption, bodyweight gain and carcass evaluation of Holstein bulls fed either conventional (CON) or organic (ORG) diets were compared. Animals were randomly assigned to either CON (n = 15) or ORG (n = 15) treatments when 6 months old. Inclusion rates of the ingredients were similar in CON and ORG diets formulated for growing (6–12 months of age) and fattening (13–18 months of age) periods. Ingredients of organic origin were used to formulate ORG growing and fattening diets. The bulls on the CON diet were vaccinated, de-wormed and treated conventionally (with antibiotics) against any sign of illness. No dietary or implant growth promotant was used. The bulls on the ORG diet were vaccinated although they were not de-wormed or treated against illness using conventional methods. Instead they were allowed to recover naturally from illness for 3 days. However, if the illness persisted beyond 3 days, they were treated using conventional methods. Consumption of concentrate and rice straw during growing, fattening and overall periods (6–18 months of age) was the same in bulls fed the CON or ORG diets. Bodyweight gain, total dry matter (concentrate and straw) intake and feed to gain ratio during growing and fattening were not affected by the treatments. Daily feed cost and feed cost for unit gain were greater in bulls fed the ORG diet than those fed the CON diet. Weight of cold carcass and different carcass cuts of the bulls were not affected by the treatment. According to the Korean beef grading system, the carcasses from bulls fed either CON or ORG diets were graded similarly but were of lower quality. The Korean beef quality grade is primarily determined by marbling score. The bulls in this study were slaughtered earlier (at 18 months of age) than the conventional slaughtering age of beef cattle (~30 months) in Korea to produce highly marbled beef. It is concluded that the bulls fed ORG diets performed equally, and produced carcasses of similar quality, to those fed CON diets. However, feed costs for a unit bodyweight gain were significantly greater in the ORG diet compared with the CON diet.
Minimum levels of inclusion of copper and zinc proteinate amino acid chelates in growing and finishing pig diets
Authors: Hernández A. , Pluske J. R. , Souza D. N. D' , Mullan B. P.
Published: April 2009

The influence of increasing dietary concentrations of copper (Cu), together with low or high inclusion levels of zinc (Zn), on performance, faecal mineral concentrations and the mineral status of the body was examined in 216 Large White × Landrace pigs (initial weight 27 kg, final weight 107 kg). The base diets were supplemented with combinations of 0, 10, 30 or 50 mg/kg Cu and 40 or 80 mg/kg Zn in the proteinate amino acid chelate form (organic), according to a factorial arrangement of treatments. A control treatment containing levels of Cu and Zn similar to the high organic treatment in the form of sulfate (inorganic) was also included. Blood and faecal samples were collected on Days 21 and 49 of the experiment and tissue samples immediately after slaughter.
Across the entire growing and finishing phases, no significant treatment differences (P > 0.05) occurred in pig daily gain or feed intake, although feed conversion ratio was improved (P < 0.05) by the inclusion of proteinate amino acid chelate. Copper and Zn concentrations in faeces were in direct proportion to their inclusion level in the diet. Blood and tissue mineral concentrations were within normal physiological ranges in all treatments. Results showed that reducing Cu and Zn in grower–finisher diets from 50 to 0 mg/kg Cu and from 80 to 40 mg/kg Zn reduced faecal Cu and Zn concentrations by 90 and 40%, respectively, without compromising pig growth. However, when Cu was supplemented at 0 mg/kg, storage of Cu in the liver approached marginal levels, suggesting that some added dietary Cu is needed in grower–finisher diets, especially for pigs reared in commercial conditions.
Feeding time and sequence of forage rape and maize silage does not affect digestibility and rumen parameters in sheep
Authors: Kaur R. , Garcia S. C. , Fulkerson W. J.
Published: April 2009

The objective of this study was to evaluate the effect of time and sequence of feeding forage rape in relation to maize silage on whole tract digestibility and rumen parameters. Three rumen-fistulated castrated male sheep (45 ± 1.2 kg) were individually housed in metabolic crates and fed a diet comprising 25% forage rape, 25% maize silage, 10% concentrate and 40% short rotation ryegrass. The experimental design was a 3 × 3 Latin-square design and treatments were: forage rape fed after maize silage in the morning; forage rape fed before maize silage in the morning; and forage rape fed after maize silage in the afternoon. As the three treatments were identical in composition, the first experimental period comprised a 15-day adaptation period whereas the other two periods had a 7-day adaptation, each followed by 6-day sampling periods for measurement of feed intake and faeces and urine output (day 1–5). Rumen fluid was collected at day 6 of each sampling period and analysed for pH and ammonia concentration. In a subsequent experiment in sacco rumen degradation characteristics of all feeds were measured by incubating nylon bags in the rumen of each sheep. Neither dry matter (DM) intake (mean = 21.2 g/kg liveweight.day) nor whole tract in vivo DM (mean = 0.74) and neutral detergent fibre digestibility coefficients (mean = 0.69) were different (P > 0.05) among treatments. Similarly, neither rumen pH (6.19 ± 0.2) nor ammonia levels (27.2 ± 4.5 mg/100 mL) were affected (P > 0.05) by time of feeding forage rape in relation to maize silage. The calculated efficiency of microbial protein synthesis was similar (P = 0.73) for all treatments [mean = 17 g/day of microbial nitrogen (N) per kg of apparently digested organic matter in the rumen], although the excretion of urinary N was relatively high for all treatments due to high N intake and high degradation of N in forage rape. In conclusion, this study has revealed no effects of time and sequence of feeding forage rape with maize silage on rumen parameters and efficiency of feed utilisation. These results suggest that farmers using these forages can allocate these to animals based on practical convenience.
Forced periodic expression of G
1
cyclins phase-locks the budding yeast cell cycle
Authors: Charvin G. , Cross F. R. , Siggia E. D.
Published: April 2009

Phase-locking (frequency entrainment) of an oscillator, in which a periodic extrinsic signal drives oscillations at a frequency different from the unperturbed frequency, is a useful property for study of oscillator stability and structure. The cell cycle is frequently described as a biochemical oscillator; however, because this oscillator is tied to key biological events such as DNA replication and segregation, and to cell growth (cell mass increase), it is unclear whether phase locking is possible for the cell cycle oscillator. We found that forced periodic expression of the G
1
cyclin
CLN2
phase locks the cell cycle of budding yeast over a range of extrinsic periods in an exponentially growing monolayer culture. We characterize the behavior of cells in a pedigree using a return map to determine the efficiency of entrainment to the externally controlled pulse. We quantify differences between mothers and daughters and how synchronization of an expanding population differs from synchronization of a single oscillator. Mothers only lock intermittently whereas daughters lock completely and in a different period range than mothers. We can explain quantitative features of phase locking in both cell types with an analytically solvable model based on cell size control and how mass is partitioned between mother and daughter cells. A key prediction of this model is that size control can occur not only in G
1
, but also later in the cell cycle under the appropriate conditions; this prediction is confirmed in our experimental data. Our results provide quantitative insight into how cell size is integrated with the cell cycle oscillator.
Internal coarse-graining of molecular systems
Authors: Feret Jérôme , Danos Vincent , Krivine Jean , Harmer Russ , Fontana Walter
Published: April 2009

Modelers of molecular signaling networks must cope with the combinatorial explosion of protein states generated by posttranslational modifications and complex formation. Rule-based models provide a powerful alternative to approaches that require explicit enumeration of all possible molecular species of a system. Such models consist of formal rules stipulating the (partial) contexts wherein specific protein–protein interactions occur. These contexts specify molecular patterns that are usually less detailed than molecular species. Yet, the execution of rule-based dynamics requires stochastic simulation, which can be very costly. It thus appears desirable to convert a rule-based model into a reduced system of differential equations by exploiting the granularity at which rules specify interactions. We present a formal (and automated) method for constructing a coarse-grained and self-consistent dynamical system aimed at molecular patterns that are distinguishable by the dynamics of the original system as posited by the rules. The method is formally sound and never requires the execution of the rule-based model. The coarse-grained variables do not depend on the values of the rate constants appearing in the rules, and typically form a system of greatly reduced dimension that can be amenable to numerical integration and further model reduction techniques.
Switching direction in electric-signal-induced cell migration by cyclic guanosine monophosphate and phosphatidylinositol signaling
Authors: Sato Masayuki J. , Kuwayama Hidekazu , van Egmond Wouter N. , Takayama Airi L. K. , Takagi Hiroaki , van Haastert Peter J. M. , Yanagida Toshio , Ueda Masahiro
Published: April 2009

Switching between attractive and repulsive migration in cell movement in response to extracellular guidance cues has been found in various cell types and is an important cellular function for translocation during cellular and developmental processes. Here we show that the preferential direction of migration during electrotaxis in
Dictyostelium
cells can be reversed by genetically modulating both guanylyl cyclases (GCases) and the cyclic guanosine monophosphate (cGMP)-binding protein C (GbpC) in combination with the inhibition of phosphatidylinositol-3-OH kinases (PI3Ks). The PI3K-dependent pathway is involved in cathode-directed migration under a direct-current electric field. The catalytic domains of soluble GCase (sGC) and GbpC also mediate cathode-directed signaling via cGMP, whereas the N-terminal domain of sGC mediates anode-directed signaling in conjunction with both the inhibition of PI3Ks and cGMP production. These observations provide an identification of the genes required for directional switching in electrotaxis and suggest that a parallel processing of electric signals, in which multiple-signaling pathways act to bias cell movement toward the cathode or anode, is used to determine the direction of migration.
Identification of a fluorescent general anesthetic, 1-aminoanthracene
Authors: Butts Christopher A. , Xi Jin , Brannigan Grace , Saad Abdalla A. , Venkatachalan Srinivasan P. , Pearce Robert A. , Klein Michael L. , Eckenhoff Roderic G. , Dmochowski Ivan J.
Published: April 2009

We identified a fluorophore, 1-aminoanthracene (1-AMA), that is anesthetic, potentiates GABAergic transmission, and gives an appropriate dissociation constant,Kd≈ 0.1 mM, for binding to the general anesthetic site in horse spleen apoferritin (HSAF). 1-AMA fluorescence is enhanced when bound to HSAF. Thus, displacement of 1-AMA from HSAF by other anesthetics attenuates the fluorescence signal and allows determination ofKd, as validated by isothermal titration calorimetry. This provides a unique fluorescence assay for compound screening and anesthetic discovery. Additional electrophysiology experiments in isolated cells indicate that 1-AMA potentiates chloride currents elicited by GABA, similar to many general anesthetics. Furthermore, 1-AMA reversibly immobilizes stage 45–50Xenopus laevistadpoles (EC50= 16 μM) and fluorescence micrographs show 1-AMA localized to brain and olfactory regions. Thus, 1-AMA provides an unprecedented opportunity for studying general anesthetic distribution in vivo at the cellular and subcellular levels.
Single amino acid substitution in
Plasmodium yoelii
erythrocyte ligand determines its localization and controls parasite virulence
Authors: Otsuki Hitoshi , Kaneko Osamu , Thongkukiatkul Amporn , Tachibana Mayumi , Iriko Hideyuki , Takeo Satoru , Tsuboi Takafumi , Torii Motomi
Published: April 2009

The major virulence determinant of the rodent malaria parasite,
Plasmodium yoelii
, has remained unresolved since the discovery of the lethal line in the 1970s. Because virulence in this parasite correlates with the ability to invade different types of erythrocytes, we evaluated the potential role of the parasite erythrocyte binding ligand,
Py
EBL. We found 1 amino acid substitution in a domain responsible for intracellular trafficking between the lethal and nonlethal parasite lines and, furthermore, that the intracellular localization of
Py
EBL was distinct between these lines. Genetic modification showed that this substitution was responsible not only for
Py
EBL localization but also the erythrocyte-type invasion preference of the parasite and subsequently its virulence in mice. This previously unrecognized mechanism for altering an invasion phenotype indicates that subtle alterations of a malaria parasite ligand can dramatically affect host–pathogen interactions and malaria virulence.
A shortcut to identifying small molecule signals that regulate behavior and development in
Caenorhabditis elegans
Authors: Pungaliya Chirag , Srinivasan Jagan , Fox Bennett W. , Malik Rabia U. , Ludewig Andreas H. , Sternberg Paul W. , Schroeder Frank C.
Published: April 2009

Small molecule metabolites play important roles in
Caenorhabditis elegans
biology, but effective approaches for identifying their chemical structures are lacking. Recent studies revealed that a family of glycosides, the ascarosides, differentially regulate
C. elegans
development and behavior. Low concentrations of ascarosides attract males and thus appear to be part of the
C. elegans
sex pheromone, whereas higher concentrations induce developmental arrest at the dauer stage, an alternative, nonaging larval stage. The ascarosides act synergistically, which presented challenges for their identification via traditional activity-guided fractionation. As a result the chemical characterization of the dauer and male attracting pheromones remained incomplete. Here, we describe the identification of several additional pheromone components by using a recently developed NMR-spectroscopic approach, differential analysis by 2D NMR spectroscopy (DANS), which simplifies linking small molecule metabolites with their biological function. DANS-based comparison of wild-type
C. elegans
and a signaling-deficient mutant,
daf-22
, enabled identification of 3 known and 4 previously undescribed ascarosides, including a compound that features a
p
-aminobenzoic acid subunit. Biological testing of synthetic samples of these compounds revealed additional evidence for synergy and provided insights into structure–activity relationships. Using a combination of the three most active ascarosides allowed full reconstitution of the male-attracting activity of wild-type pheromone extract. Our results highlight the efficacy of DANS as a method for identifying small-molecule metabolites and placing them within a specific genetic context. This study further supports the hypothesis that ascarosides represent a structurally diverse set of nematode signaling molecules regulating major life history traits.
Structural and mechanistic insights into the association of PKCα-C2 domain to PtdIns(4,5)P
2
Authors: Guerrero-Valero Marta , Ferrer-Orta Cristina , Querol-Audí Jordi , Marin-Vicente Consuelo , Fita Ignacio , Gómez-Fernández Juan C. , Verdaguer Nuria , Corbalán-García Senena
Published: April 2009

C2 domains are widely-spread protein signaling motifs that in classical PKCs act as Ca
2+
-binding modules. However, the molecular mechanisms of their targeting process at the plasma membrane remain poorly understood. Here, the crystal structure of PKCα-C2 domain in complex with Ca
2+
, 1,2-dihexanoyl-
sn
-glycero-3-[phospho-
l
-serine] (PtdSer), and 1,2-diayl-
sn
-glycero-3-[phosphoinositol-4,5-bisphosphate] [PtdIns(
4
,
5
)P
2
] shows that PtdSer binds specifically to the calcium-binding region, whereas PtdIns(
4
,
5
)P
2
occupies the concave surface of strands β3 and β4. Strikingly, the structure reveals a PtdIns(
4
,
5
)P
2
-C2 domain-binding mode in which the aromatic residues Tyr-195 and Trp-245 establish direct interactions with the phosphate moieties of the inositol ring. Mutations that abrogate Tyr-195 and Trp-245 recognition of PtdIns(
4
,
5
)P
2
severely impaired the ability of PKCα to localize to the plasma membrane. Notably, these residues are highly conserved among C2 domains of topology I, and a general mechanism of C2 domain-membrane docking mediated by PtdIns(
4
,
5
)P
2
is presented.
Fibrillar amyloid-β burden in cognitively normal people at 3 levels of genetic risk for Alzheimer's disease
Authors: Reiman Eric M. , Chen Kewei , Liu Xiaofen , Bandy Daniel , Yu Meixiang , Lee Wendy , Ayutyanont Napatkamon , Keppler Jennifer , Reeder Stephanie A. , Langbaum Jessica B. S. , Alexander Gene E. , Klunk William E. , Mathis Chester A. , Price Julie C. , Aizenstein Howard J. , DeKosky Steven T. , Caselli Richard J.
Published: April 2009

Fibrillar amyloid-beta (Aβ) is found in the brains of many cognitively normal older people. Whether or not this reflects a predisposition to Alzheimer's disease (AD) is unknown. We used Pittsburgh Compound B (PiB) PET to characterize the relationship between fibrillar Aβ burden and this predisposition in cognitively normal older people at 3 mean levels of genetic risk for AD. Dynamic PiB PET scans, the Logan method, statistical parametric mapping, and automatically labeled regions of interest (ROIs) were used to characterize and compare cerebral-to-cerebellar PIB distribution volume ratios, reflecting fibrillar Aβ burden, in 28 cognitively normal persons (mean age, 64 years) with a reported family history of AD and 2 copies, 1 copy, and no copies of the apolipoprotein E (APOE) ε4 allele. The 8 ε4 homozygotes, 8 heterozygotes, and 12 noncarriers did not differ significantly in terms of age, sex, or cognitive scores. Fibrillar Aβ was significantly associated with
APOE
ε4 carrier status and ε4 gene dose in AD-affected mean cortical, frontal, temporal, posterior cingulate-precuneus, parietal, and basal ganglia ROIs, and was highest in an additional homozygote who had recently developed mild cognitive impairment. These findings suggest that fibrillar Aβ burden in cognitively normal older people is associated with
APOE
ε4 gene dose, the major genetic risk factor for AD. Additional studies are needed to track fibrillar Aβ accumulation in persons with different kinds and levels of AD risk; to determine the extent to which fibrillar Aβ, alone or in combination with other biomarkers and risk factors, predicts rates of cognitive decline and conversion to clinical AD; and to establish the role of fibrillar Aβ imaging in primary prevention trials.
Cells previously identified as retinal stem cells are pigmented ciliary epithelial cells
Authors: Cicero Samantha A. , Johnson Dianna , Reyntjens Steve , Frase Sharon , Connell Samuel , Chow Lionel M. L. , Baker Suzanne J. , Sorrentino Brian P. , Dyer Michael A.
Published: April 2009

It was previously reported that the ciliary epithelium (CE) of the mammalian eye contains a rare population of cells that could produce clonogenic self-renewing pigmented spheres in culture. Based on their ability to up-regulate genes found in retinal neurons, it was concluded that these sphere-forming cells were retinal stem cells. This conclusion raised the possibility that CE-derived retinal stem cells could help to restore vision in the millions of people worldwide who suffer from blindness associated with retinal degeneration. We report here that human and mouse CE-derived spheres are made up of proliferating pigmented ciliary epithelial cells rather than retinal stem cells. All of the cells in the CE-derived spheres, including the proliferating cells, had molecular, cellular, and morphological features of differentiated pigmented CE cells. These differentiated cells ectopically expressed nestin when exposed to growth factors and low levels of pan-neuronal markers such as beta-III-tubulin. Although the cells aberrantly expressed neuronal markers, they retained their pigmented CE cell morphology and failed to differentiate into retinal neurons in vitro or in vivo. Our results provide an example of a differentiated cell type that can form clonogenic spheres in culture, self-renew, express progenitor cell markers, and initiate neuronal differentiation that is not a stem or progenitor cell. More importantly, our findings highlight the importance of shifting the focus away from studies on CE-derived spheres for cell-based therapies to restore vision in the degenerating retina and improving techniques for using ES cells or retinal precursor cells.
Learning reward timing in cortex through reward dependent expression of synaptic plasticity
Authors: Gavornik Jeffrey P. , Shuler Marshall G. Hussain , Loewenstein Yonatan , Bear Mark F. , Shouval Harel Z.
Published: April 2009

The ability to represent time is an essential component of cognition but its neural basis is unknown. Although extensively studied both behaviorally and electrophysiologically, a general theoretical framework describing the elementary neural mechanisms used by the brain to learn temporal representations is lacking. It is commonly believed that the underlying cellular mechanisms reside in high order cortical regions but recent studies show sustained neural activity in primary sensory cortices that can represent the timing of expected reward. Here, we show that local cortical networks can learn temporal representations through a simple framework predicated on reward dependent expression of synaptic plasticity. We assert that temporal representations are stored in the lateral synaptic connections between neurons and demonstrate that reward-modulated plasticity is sufficient to learn these representations. We implement our model numerically to explain reward-time learning in the primary visual cortex (V1), demonstrate experimental support, and suggest additional experimentally verifiable predictions.