bluuebunny/crossref_metadata_2025 huggingface dataset:
General framework for nonholonomic mechanics: Nonholonomic systems on Lie affgebroids
Authors: Iglesias D. , Marrero Juan C. , Martín de Diego D. , Sosa Diana
Published: August 2007

This paper presents a geometric description of Lagrangian and Hamiltonian systems on Lie affgebroids subject to affine nonholonomic constraints. We define the notion of nonholonomically constrained system and characterize regularity conditions that guarantee that the dynamics of the system can be obtained as a suitable projection of the unconstrained dynamics. It is shown that one can define an almost aff-Poisson bracket on the constraint AV-bundle, which plays a prominent role in the description of nonholonomic dynamics. Moreover, these developments give a general description of nonholonomic systems and the unified treatment permits to study nonholonomic systems after or before reduction in the same framework. Also, it is not necessary to distinguish between linear or affine constraints and the methods are valid for explicitly time-dependent systems.
Er-doped silicon nanowires with 1.54μm light-emitting and enhanced electrical and field emission properties
Authors: Huang C. T. , Hsin C. L. , Huang K. W. , Lee C. Y. , Yeh P. H. , Chen U. S. , Chen L. J.
Published: August 2007

Erbium-doped silicon nanowires have been grown via a vapor transport and condensation method with ErCl3∙6H2O powder as part of the source in one step. The Er-doped silicon nanowires exhibit the room temperature photoluminescence at a wavelength of 1.54μm, ideal for optical communication. From I-V measurements, the resistivity of 4.2at.% Er-doped Si nanowires was determined to be 1.5×10−2Ωcm. The Er-doped silicon nanowires were found to possess excellent field emission properties with a field enhancement factor as high as 1260. The rich variety of enhanced physical properties exhibited by the Er-doped silicon nanowires points to versatile applications for advanced devices.
System for in situ studies of atmospheric corrosion of metal films using soft x-ray spectroscopy and quartz crystal microbalance
Authors: Forsberg J. , Duda L.-C. , Olsson A. , Schmitt T. , Andersson J. , Nordgren J. , Hedberg J. , Leygraf C. , Aastrup T. , Wallinder D. , Guo J.-H.
Published: August 2007

We present a versatile chamber (“atmospheric corrosion cell”) for soft x-ray absorption/emission spectroscopy of metal surfaces in a corrosive atmosphere allowing novel in situ electronic structure studies. Synchrotron x rays passing through a thin window separating the corrosion cell interior from a beamline vacuum chamber probe a metal film deposited on a quartz crystal microbalance (QCM) or on the inside of the window. We present some initial results on chloride induced corrosion of iron surfaces in humidified synthetic air. By simultaneous recording of QCM signal and soft x-ray emission from the corroding sample, correlation between mass changes and variations in spectral features is facilitated.
Signal conditioning for differential temperature measurement with thermistors using a generalized impedance converter
Authors: Castro Montero Enrique , Ramírez Muñoz Diego , Sánchez Moreno Jaime , Fong Barrio Julio , Salazar Mustelier Arquimides
Published: August 2007

In this article a differential temperature-to-time converter is presented using two thermistors in a generalized impedance converter, polarized in direct current. The voltage drop in one of the thermistors depends on the differential temperature at which both thermistors are exposed. Such voltage drop is compared to a signal which changes exponentially by obtaining a time interval which depends on the differential temperature. The results of the experimental tests support the theorethical analysis performed and at the same time offer a new possibility of application of the generalized impedance converter as a signal conditioning circuit.
Evaluation of the mechanical spectrum of the deposited materials in a composite system in torsion pendulum
Authors: Xu Z. C. , Ying X. N.
Published: August 2007

Previously, an approximate way to subtract the mechanical spectra (complex Young’s modulus) of deposited materials from a composite reed vibration was proposed [X. N. Ying, Physica B 387, 376 (2007)]. In this article, the way of subtraction of mechanical spectra of deposited materials was extended to the complex shear modulus by a composite torsion pendulum method. Previous approximate formulas to calculate the mechanical spectra of deposited materials were found still to be valid except that new parameters were used. This deduction shows that previous approximate formulas are very applicable in the mechanical spectrum measurement. At last, the experimental result of glycerol was shown in approximate formulas.
Enhanced In(Ga)As∕GaAs quantum dot based electro-optic modulation at 1.55μm
Authors: Moreau G. , Martinez A. , Cong D.-Y. , Merghem K. , Miard A. , Lemaître A. , Voisin P. , Ramdane A. , Krestnikov I. , Kovsh A. R. , Fischer M. , Koeth J.
Published: August 2007

The authors report a study of the linear electro-optic coefficient in waveguides containing InGaAs∕GaAs quantum dots with a band gap at 1.3μm. The Pockels effect is investigated in the 1.55μm telecommunication window. The measured linear electro-optic coefficient for InGaAs∕GaAs is ∼3.4×10−11m∕V, much higher than that of the bulk or quantum well material. An ∼35% enhancement of the phase variation is achieved compared to that obtained in bulk GaAs waveguides. Finally, a spectral bandwidth of ∼100nm is demonstrated in the 1.5–1.6μm window.
Luminescence properties of blue La1−xCexAl(Si6−zAlz)(N10−zOz) (z∼1) oxynitride phosphors and their application in white light-emitting diode
Authors: Takahashi Kohsei , Hirosaki Naoto , Xie Rong-Jun , Harada Masamichi , Yoshimura Ken-ichi , Tomomura Yoshitaka
Published: August 2007

This letter reports blue oxynitride phosphors of La1−xCexAl(Si6−zAlz)(N10−zOz) (z∼1) (termed JEM crystal phase) and their application for the white light-emitting diodes (LEDs). The JEM phosphor can be excited by 405nm light efficiently, and its spectrum can be tuned widely by changing the Ce concentration. The emission spectrum of this phosphor is as wide as 110nm in full width at half maximum, which is convenient to solid state lighting. The preparation of white LED was attempted by using a 405nm InGaN chip and oxynitride phosphors in this work. High color rendering index >95 was achieved in white LED with various correlated color temperatures, indicating the suitability of the JEM phosphor in solid-state lightings.
Dielectric relaxations of yttrium iron garnet ceramics over a broad temperature range
Authors: Wu Y. J. , Gao Y. , Chen X. M.
Published: August 2007

Dielectric response of Y3Fe5O12 ceramics was investigated over broad temperature and frequency ranges. Three dielectric relaxations were identified in the temperature range from 125to620K. A Debye-type dielectric relaxation at low temperatures (125–320K) with an activation energy of 0.29eV is shown to originate from the carrier hopping process between Fe2+ and Fe3+. In a higher temperature range (320–620K), a low frequency (f≦10kHz) dielectric relaxation with an activation energy of 0.84eV most likely arises from the inhomogeneous structure, such as grain boundaries. Another dielectric relaxation in a wider frequency range has a similar activation energy with conduction (Ea=1.00eV) suggests that it can be attributed to the conduction.
Critique of early models of the demographic impact of HIV/AIDS in sub-Saharan Africa based on contemporary empirical data from Zimbabwe
Authors: Gregson Simon , Nyamukapa Constance , Lopman Ben , Mushati Phyllis , Garnett Geoffrey P. , Chandiwana Stephen K. , Anderson Roy M.
Published: August 2007

Early mathematical models varied in their predictions of the impact of HIV/AIDS on population growth from minimal impact to reductions in growth, in pessimistic scenarios, from positive to negative values over a period of 25 years. Models predicting negative rates of natural increase forecast little effect on the dependency ratio. Twenty years later, HIV prevalence in small towns, estates, and rural villages in eastern Zimbabwe, has peaked within the intermediate range predicted by the early models, but the demographic impact has been more acute than was predicted. Despite concurrent declines in fertility, fueled in part by HIV infections (total fertility is now 8% lower than expected without an epidemic), and a doubling of the crude death rate because of HIV/AIDS, the rate of natural population increase between 1998 and 2005 remained positive in each socioeconomic stratum. In the worst-affected areas (towns with HIV prevalence of 33%), HIV/AIDS reduced growth by two-thirds from 2.9% to 1.0%. The dependency ratio fell from 1.21 at the onset of the HIV epidemic to 0.78, the impact of HIV-associated adult mortality being outweighed by fertility decline. With the benefit of hindsight, the more pessimistic early models overestimated the demographic impact of HIV epidemics by overextrapolating initial HIV growth rates or not allowing for heterogeneity in key parameters such as transmissibility and sexual risk behavior. Data collected since the late 1980s show that there was a mismatch between the observed growth in the HIV epidemic and assumptions made about viral transmission.
A honey bee odorant receptor for the queen substance 9-oxo-2-decenoic acid
Authors: Wanner Kevin W. , Nichols Andrew S. , Walden Kimberly K. O. , Brockmann Axel , Luetje Charles W. , Robertson Hugh M.
Published: August 2007

By using a functional genomics approach, we have identified a honey bee [
Apis mellifera
(Am)] odorant receptor (Or) for the queen substance 9-oxo-2-decenoic acid (9-ODA). Honey bees live in large eusocial colonies in which a single queen is responsible for reproduction, several thousand sterile female worker bees complete a myriad of tasks to maintain the colony, and several hundred male drones exist only to mate. The “queen substance” [also termed the queen retinue pheromone (QRP)] is an eight-component pheromone that maintains the queen's dominance in the colony. The main component, 9-ODA, acts as a releaser pheromone by attracting workers to the queen and as a primer pheromone by physiologically inhibiting worker ovary development; it also acts as a sex pheromone, attracting drones during mating flights. However, the extent to which social and sexual chemical messages are shared remains unresolved. By using a custom chemosensory-specific microarray and qPCR, we identified four candidate sex pheromone Ors (AmOr10, -11, -18, and -170) from the honey bee genome based on their biased expression in drone antennae. We assayed the pheromone responsiveness of these receptors by using
Xenopus
oocytes and electrophysiology. AmOr11 responded specifically to 9-ODA (EC
50
= 280 ± 31 nM) and not to any of the other seven QRP components, other social pheromones, or floral odors. We did not observe any responses of the other three Ors to any of the eight QRP pheromone components, suggesting 9-ODA is the only QRP component that also acts as a long-distance sex pheromone.
Current profile control and optimization under dominant electron heating in HL-2A
Authors: Gao Q.D. , Budny R.V. , Jiao Y.M. , Indireshkumar K.
Published: August 2007

The establishment of the current profile as in the hybrid scenario is studied under the condition of dominant electron heating in HL-2A. The scenarios with injecting lower hybrid (LH) and electron cyclotron (EC) waves are under numerical study. Carefully adjusting the position of non-inductive current driven by two groups of gyrotron, an optimizedq-profile was obtained withqa= 3.78 and a weak shear region extending to ρ ∼ 0.45 (where ρ is the square-root of toroidal flux normalized to its value at the plasma boundary) in low-density discharges of. When 0.5 MW LH power in the current drive mode and 0.95 MW EC power mainly for plasma heating are used to control the current profile, a hybrid discharge scenario with a weak magnetic shear region extended to ρ = 0.6 andqa= 3.21 is established by controlling the EC absorption position. The mechanism of the LH wave absorption in the HL-2A plasma causes interplay of the distribution of the LH driven current with the modification of the plasma configuration, which constitutes non-linearity in the LH wave deposition. Due to the non-linearity the LH wave deposition position changes spontaneously or oscillates. The oscillatory behaviour caused by the non-linear effect of the LH wave deposition is analysed.
Scaling of density peaking in H-mode plasmas based on a combined database of AUG and JET observations
Authors: Angioni C. , Weisen H. , Kardaun O.J.W.F. , Maslov M. , Zabolotsky A. , Fuchs C. , Garzotti L. , Giroud C. , Kurzan B. , Mantica P. , Peeters A.G. , Stober J.
Published: August 2007

For the first time, scalings for density peaking in tokamaks are obtained from a database consisting of observations from two devices, ASDEX Upgrade and JET. The investigation relies on an inversion method for the interferometer signals which grants consistent reconstructions despite differences in interferometer geometries. By combining observations from these devices, correlations between physics parameters investigated for their role in determining density peaking are reduced. Multiple regression analyses show that in the combined database collisionality is the most relevant parameter. The particle source provided by neutral beam injection provides a contribution to the peaking, which, although not negligible, is not large enough to explain the whole observed variation of density peaking. The device size, introduced as an alias for possible systematic differences between the devices not captured by the regression parameters, is found to play only a small role in regressions which include collisionality. Device size becomes relevant in scalings which exclude collisionality and include the ratio of the density to the Greenwald density limit. This indicates that density peaking is more likely to be a function of collisionality rather than of the fraction of the density limit. All the scalings which include collisionality in the regression variables predict a peaked density profile for the ITER standard scenario.
Locked mode thresholds on the MAST spherical tokamak
Authors: Howell D.F. , Hender T.C. , Cunningham G.
Published: August 2007

In a tokamak, misalignments of field coils and coil connections, introduced in the construction of the device, lead to small asymmetries in magnetic field known as error fields. Even at small levels these can stop the plasma rotating, driving resistive tearing modes that lead to plasma termination. Recently, a set of four error field correction coils has been installed on the MAST spherical tokamak. These coils have been used to correct for the error field, allowing MAST to operate in previously inaccessible regimes. With error field correction, MAST can operate at densities at least 30% lower than previously attained. The error field coils have also been used to apply large error fields to the plasma to explore the phenomenon of mode locking. It was found that the locked mode threshold scales with line averaged electron density, safety factor and toroidal field in a similar way to that found from conventional aspect ratio tokamaks. This scaling law has been used to estimate the locked mode threshold for a proposed power plant and a component test facility based on the spherical tokamak concept.
Recent improvements in confinement and beta in the MST reversed-field pinch
Authors: Den Hartog D.J. , Ahn J.-W. , Almagri A.F. , Anderson J.K. , Beklemishev A.D. , Blair A.P. , Bonomo F. , Borchardt M.T. , Brower D.L. , Burke D.R. , Cengher M. , Chapman B.E. , Choi S. , Clayton D.J. , Cox W.A. , Combs S.K. , Craig D. , Cummings H.D. , Davydenko V.I. , Demers D.R. , Deng B.H. , Ding W.X. , Ebrahimi F. , Ennis D.A. , Fiksel G. , Foust C. , Forest C.B. , Franz P. , Frassinetti L. , Gangadhara S. , Goetz J.A. , Harvey R.W. , Holly D.J. , Hudson B.F. , Ivanov A.A. , Kaufman M.C. , Kuritsyn A.V. , Lizunov A.A. , Lovell T.W. , Magee R.M. , Marrelli L. , Martin P. , McCollam K.J. , Miller M.C. , Mirnov V.V. , Nonn P.D. , O'Connell R. , Oliva S.P. , Piovesan P. , Prager S.C. , Predebon I. , Reusch J.A. , Sarff J.S. , Svidzinski V.A. , Tharp T.D. , Thomas M.A. , Tsidulko Yu.A. , Wyman M.D. , Yates T.
Published: August 2007

In the general area of confinement improvement and concept advancement, recent results in the Madison Symmetric Torus (MST) reversed-field pinch (RFP) include good confinement of both thermal and large-orbit ions and near doubling of total beta to 26% with deuterium pellet injection. Current profile control enables MST to reduce stochastic transport and achieve tokamak-like confinement. In standard RFP operation, substantial MHD tearing mode activity results in stochastic transport and an energy confinement time of about 1 ms in MST. Application of inductive current profile control reduces MHD activity and accompanying stochasticity, improving confinement by about a factor of ten. Previous work concentrated on electron confinement in improved-confinement RFP operation. Recent work confirms that ions are also well confined, and that high beta and improved confinement can be achieved simultaneously.
Carbon sequestration
Authors: Lal Rattan
Published: August 2007

Developing technologies to reduce the rate of increase of atmospheric concentration of carbon dioxide (CO2) from annual emissions of 8.6 Pg C yr–1from energy, process industry, land-use conversion and soil cultivation is an important issue of the twenty-first century. Of the three options of reducing the global energy use, developing low or no-carbon fuel and sequestering emissions, this manuscript describes processes for carbon (CO2) sequestration and discusses abiotic and biotic technologies. Carbon sequestration implies transfer of atmospheric CO2into other long-lived global pools including oceanic, pedologic, biotic and geological strata to reduce the net rate of increase in atmospheric CO2. Engineering techniques of CO2injection in deep ocean, geological strata, old coal mines and oil wells, and saline aquifers along with mineral carbonation of CO2constitute abiotic techniques. These techniques have a large potential of thousands of Pg, are expensive, have leakage risks and may be available for routine use by 2025 and beyond. In comparison, biotic techniques are natural and cost-effective processes, have numerous ancillary benefits, are immediately applicable but have finite sink capacity. Biotic and abiotic C sequestration options have specific nitches, are complementary, and have potential to mitigate the climate change risks.
Ecological restoration of farmland: progress and prospects
Authors: Wade Mark R , Gurr Geoff M , Wratten Steve D
Published: August 2007

Sustainable agricultural practices in conjunction with ecological restoration methods can reduce the detrimental effects of agriculture. The Society for Ecological Restoration International has produced generic guidelines for conceiving, organizing, conducting and assessing ecological restoration projects. Additionally, there are now good conceptual frameworks, guidelines and practical methods for developing ecological restoration programmes that are based on sound ecological principles and supported by empirical evidence and modelling approaches. Restoration methods must also be technically achievable and socially acceptable and spread over a range of locations. It is important to reconcile differences between methods that favour conservation and those that favour economic returns, to ensure that conservation efforts are beneficial for both landowners and biodiversity. One option for this type of mutual benefit is the use of agri-environmental schemes to provide financial incentives to landholders in exchange for providing conservation services and other benefits. However, further work is required to define and measure the effectiveness of agri-environmental schemes. The broader potential for ecological restoration to improve the sustainability of agricultural production while conserving biodiversity in farmscapes and reducing external costs is high, but there is still much to learn, particularly for the most efficient use of agri-environmental schemes to change land use practice.
Strategies and models for agricultural sustainability in developing Asian countries
Authors: Kesavan P.C , Swaminathan M.S
Published: August 2007

The green revolution of the 1960s and 1970s which resulted in dramatic yield increases in the developing Asian countries is now showing signs of fatigue in productivity gains. Intensive agriculture practiced without adherence to the scientific principles and ecological aspects has led to loss of soil health, and depletion of freshwater resources and agrobiodiversity. With progressive diversion of arable land for non-agricultural purposes, the challenge of feeding the growing populationwithout, at the same time, annexing more forestland and depleting the rest of life is indeed daunting. Further, even with food availability through production/procurement, millions of marginal farming, fishing and landless rural families have very low or no access to food due to lack of income-generating livelihoods. Approximately 200 million rural women, children and men in India alone fall in this category. Under these circumstances, the evergreen revolution (pro-nature, pro-poor, pro-women and pro-employment/livelihood oriented ecoagriculture) under varied terms are proposed for achieving productivity in perpetuity. In the proposed ‘biovillage paradigm’, eco-friendly agriculture is promoted along withon-andnon-farmeco-enterprises based on sustainable management of natural resources. Concurrently, the modern ICT-based village knowledge centres provide time- and locale-specific, demand-driven information needed for evergreen revolution and ecotechnologies. With a system of ‘farm and marine production by masses’, the twin goals of ecoagriculture and eco-livelihoods are addressed. The principles, strategies and models of these are briefly discussed in this paper.
Mcm10 and And-1/CTF4 recruit DNA polymerase α to chromatin for initiation of DNA replication
Authors: Zhu Wenge , Ukomadu Chinweike , Jha Sudhakar , Senga Takeshi , Dhar Suman K. , Wohlschlegel James A. , Nutt Leta K. , Kornbluth Sally , Dutta Anindya
Published: August 2007

The MCM2-7 helicase complex is loaded on DNA replication origins during the G1 phase of the cell cycle to license the origins for replication in S phase. How the initiator primase–polymerase complex, DNA polymerase α (pol α), is brought to the origins is still unclear. We show that And-1/Ctf4 (Chromosome transmission fidelity 4) interacts with Mcm10, which associates with MCM2-7, and with the p180 subunit of DNA pol α. And-1 is essential for DNA synthesis and the stability of p180 in mammalian cells. In Xenopus egg extracts And-1 is loaded on the chromatin after Mcm10, concurrently with DNA pol α, and is required for efficient DNA synthesis. Mcm10 is required for chromatin loading of And-1 and an antibody that disrupts the Mcm10–And-1 interaction interferes with the loading of And-1 and of pol α, inhibiting DNA synthesis. And-1/Ctf4 is therefore a new replication initiation factor that brings together the MCM2-7 helicase and the DNA pol α–primase complex, analogous to the linker between helicase and primase or helicase and polymerase that is seen in the bacterial replication machinery. The discovery also adds to the connection between replication initiation and sister chromatid cohesion.
Cytokine-dependent imatinib resistance in mouse BCR-ABL+, Arf-null lymphoblastic leukemia
Authors: Williams Richard T. , den Besten Willem , Sherr Charles J.
Published: August 2007

Retroviral transduction of the BCR-ABL kinase into primary mouse bone marrow cells lacking the Arf tumor suppressor rapidly generates polyclonal populations of continuously self-renewing pre-B cells, virtually all of which have leukemic potential. Intravenous infusion of 20 such cells into healthy syngeneic mice induces rapidly fatal, transplantable lymphoblastic leukemias that resist imatinib therapy. Introduction of BCR-ABL into Arf-null severe combined immunodeficient (SCID) bone marrow progenitors lacking the cytokine receptor common γ-chain yields leukemogenic pre-B cells that exhibit greater sensitivity to imatinib in vivo. Hence, salutary cytokines in the hematopoietic microenvironment can facilitate leukemic proliferation and confer resistance to targeted therapy.
microRNA miR-14 acts to modulate a positive autoregulatory loop controlling steroid hormone signaling in Drosophila
Authors: Varghese Jishy , Cohen Stephen M.
Published: August 2007

The insect steroid hormone Ecdysone and its receptor play important roles during development and metamorphosis and regulate adult physiology and life span. Ecdysone signaling, via the Ecdysone receptor (EcR), has been proposed to act in a positive autoregulatory loop to increase EcR levels and sensitize the animal to ecdysone pulses. Here we present evidence that this involves EcR-dependent transcription of the EcR gene, and that the microRNA miR-14 modulates this loop by limiting expression of its target EcR. Ecdysone signaling, via EcR, down-regulates miR-14. This alleviates miR-14-mediated repression of EcR and amplifies the response. Failure to limit EcR levels is responsible for the many of the defects observed in miR-14 mutants. miR-14 plays a key role in modulating the positive autoregulatory loop by which Ecdysone sensitizes its own signaling pathway.
Conductance and amantadine binding of a pore formed by a lysine‐flanked transmembrane domain of SARS coronavirus envelope protein
Authors: Torres Jaume , Maheswari Uma , Parthasarathy Krupakar , Ng Lifang , Liu Ding Xiang , Gong Xiandi
Published: August 2007

The coronavirus responsible for the severe acute respiratory syndrome (SARS‐CoV) contains a small envelope protein, E, with putative involvement in host cell apoptosis and virus morphogenesis. It has been suggested that E protein can form a membrane destabilizing transmembrane (TM) hairpin, or homooligomerize to form a regular TM α‐helical bundle. We have shown previously that the topology of the α‐helical putative TM domain of E protein (ETM), flanked by two lysine residues at C and N termini to improve solubility, is consistent with a regular TM α‐helix, with orientational parameters in lipid bilayers that are consistent with a homopentameric model. Herein, we show that this peptide, reconstituted in lipid bilayers, shows sodium conductance. Channel activity is inhibited by the anti‐influenza drug amantadine, which was found to bind our preparation with moderate affinity. Results obtained from single or double mutants indicate that the organization of the transmembrane pore is consistent with our previously reported pentameric α‐helical bundle model.
Modeling mutations in protein structures
Authors: Feyfant Eric , Sali Andrej , Fiser András
Published: August 2007

We describe an automated method for the modeling of point mutations in protein structures. The protein is represented by all non‐hydrogen atoms. The scoring function consists of several types of physical potential energy terms and homology‐derived restraints. The optimization method implements a combination of conjugate gradient minimization and molecular dynamics with simulated annealing. The testing set consists of 717 pairs of known protein structures differing by a single mutation. Twelve variations of the scoring function were tested in three different environments of the mutated residue. The best‐performing protocol optimizes all the atoms of the mutated residue, with respect to a scoring function that includes molecular mechanics energy terms for bond distances, angles, dihedral angles, peptide bond planarity, and non‐bonded atomic contacts represented by Lennard‐Jones potential, dihedral angle restraints derived from the aligned homologous structure, and a statistical potential for non‐bonded atomic interactions extracted from a large set of known protein structures. The current method compares favorably with other tested approaches, especially when predicting long and flexible side‐chains. In addition to the thoroughness of the conformational search, sampled degrees of freedom, and the scoring function type, the accuracy of the method was also evaluated as a function of the flexibility of the mutated side‐chain, the relative volume change of the mutated residue, and its residue type. The results suggest that further improvement is likely to be achieved by concentrating on the improvement of the scoring function, in addition to or instead of increasing the variety of sampled conformations.
Solution structure of recombinant somatomedin B domain from vitronectin produced in Pichia pastoris
Authors: Kjaergaard Magnus , Gårdsvoll Henrik , Hirschberg Daniel , Nielbo Steen , Mayasundari Anand , Peterson Cynthia B. , Jansson Anna , Jørgensen Thomas J.D. , Poulsen Flemming M. , Ploug Michael
Published: August 2007

The cysteine‐rich somatomedin B domain (SMB) of the matrix protein vitronectin is involved in several important biological processes. First, it stabilizes the active conformation of the plasminogen activator inhibitor (PAI‐1); second, it provides the recognition motif for cell adhesion via the cognate integrins (αvβ3, αvβ5, and αIIbβ3); and third, it binds the complex between urokinase‐type plasminogen activator (uPA) and its glycolipid‐anchored receptor (uPAR). Previous structural studies on SMB have used recombinant protein expressed in Escherichia coli or SMB released from plasma‐derived vitronectin by CNBr cleavage. However, different disulfide patterns and three‐dimensional structures for SMB were reported. In the present study, we have expressed recombinant human SMB by two different eukaryotic expression systems, Pichia pastoris and Drosophila melanogaster S2‐cells, both yielding structurally and functionally homogeneous protein preparations. Importantly, the entire population of our purified, recombinant SMB has a solvent exposure, both as a free domain and in complex with PAI‐1, which is indistinguishable from that of plasma‐derived SMB as assessed by amide hydrogen (1H/2H) exchange. This solvent exposure was only reproduced by one of three synthetic SMB products with predefined disulfide connectivities corresponding to those published previously. Furthermore, this connectivity was also the only one to yield a folded and functional domain. The NMR structure was determined for free SMB produced by Pichia and is largely consistent with that solved by X‐ray crystallography for SMB in complex with PAI‐1.
How similar are enzyme active site geometries derived from quantum mechanical theozymes to crystal structures of enzyme‐inhibitor complexes? Implications for enzyme design
Authors: DeChancie Jason , Clemente Fernando R. , Smith Adam J.T. , Gunaydin Hakan , Zhao Yi‐Lei , Zhang Xiyun , Houk K.N.
Published: August 2007

Quantum mechanical optimizations of theoretical enzymes (theozymes), which are predicted catalytic arrays of biological functionalities stabilizing a transition state, have been carried out for a set of nine diverse enzyme active sites. For each enzyme, the theozyme for the rate‐determining transition state plus the catalytic groups modeled by side‐chain mimics was optimized using B3LYP/6–31G(d) or, in one case, HF/3–21G(d) quantum mechanical calculations. To determine if the theozyme can reproduce the natural evolutionary catalytic geometry, the positions of optimized catalytic atoms, i.e., covalent, partial covalent, or stabilizing interactions with transition state atoms, are compared to the positions of the atoms in the X‐ray crystal structure with a bound inhibitor. These structure comparisons are contrasted to computed substrate–active site structures surrounded by the same theozyme residues. The theozyme/transition structure is shown to predict geometries of active sites with an average RMSD of 0.64 Å from the crystal structure, while the RMSD for the bound intermediate complexes are significantly higher at 1.42 Å. The implications for computational enzyme design are discussed.
Structure–activity study of the antibacterial peptide fallaxin
Authors: Nielsen Sandra L. , Frimodt‐Møller Niels , Kragelund Birthe B. , Hansen Paul R.
Published: August 2007

Fallaxin is a 25‐mer antibacterial peptide amide, which was recently isolated from the West Indian mountain chicken frog Leptodactylus fallax. Fallaxin has been shown to inhibit the growth of several Gram‐negative bacteria including Enterobacter cloacae, Escherichia coli, Klebsiella pneumoniae, and Pseudomonas aeruginosa. Here, we report a structure–activity study of fallaxin based on 65 analogs, including a complete alanine scan and a full set of N‐ and C‐terminal truncated analogs. The fallaxin analogs were tested for hemolytic activity and antibacterial activity against methicillin‐resistant Staphylococcus aureus (MRSA), vancomycin‐intermediate resistant S. aureus, (VISA), methicillin‐susceptible S. aureus (MSSA), E. coli, K. pneumoniae, and P. aeruginosa. We identified several analogs, which showed improved antibacterial activity compared to fallaxin. Our best candidate was FA12, which displayed MIC values of 3.12, 25, 25, and 50 μM against E. coli, K. pneumoniae, MSSA, and VISA, respectively. Furthermore, we correlated the antibacterial activity with various structural parameters such as charge, hydrophobicity 〈H〉, mean hydrophobic moment 〈μH〉, and α‐helicity. We were able to group the active and inactive analogs according to mean hydrophobicity 〈H〉 and mean hydrophobic moment 〈μH〉. Far‐UV CD‐spectroscopy experiments on fallaxin and several analogs in buffer, in TFE, and in membrane mimetic environments (small unilamellar vesicles) indicated that a coiled‐coil conformation could be an important structural trait for antibacterial activity. This study provides data that support fallaxin analogs as promising lead structures in the development of new antibacterial agents.
The structures of transcription factor CGL2947 from Corynebacterium glutamicum in two crystal forms: A novel homodimer assembling and the implication for effector‐binding mode
Authors: Gao Yong‐Gui , Yao Min , Itou Hiroshi , Zhou Yong , Tanaka Isao
Published: August 2007

Among the transcription factors, the helix‐turn‐helix (HTH) GntR family comprised of FadR, HutC, MocR, YtrA, AraR, and PlmA subfamilies regulates the most varied biological processes. Generally, proteins belonging to this family contain an N‐terminal DNA‐binding domain and a C‐terminal effector‐binding/oligomerization domain. The members of the YtrA subfamily are much shorter than other members of this family, with chain lengths of 120–130 residues with about 50 residues located in the C‐terminal domain. Because of this length, the mode of dimerization and the ability to bind effectors by the C‐terminal domain are puzzling. Here, we first report the structure of the transcription factor CGL2947 from Corynebacterium glutamicum, which belongs to the YtrA family. The monomer is composed of a DNA‐binding domain containing a winged HTH motif in the N terminus and two helices (α4 and α5) with a fishhook‐shaped arrangement in the C terminus. Helices α4 and α5 of two monomers intertwine together to form a novel homodimer assembly. The effector‐accommodating pocket with 2‐methyl‐2,4‐pentanediol (MPD) docked was located, and it was suggested to represent a novel mode of effector binding. The structures in two crystal forms (MPD‐free and ‐bound in the proposed effector‐binding pocket) were solved. The structural variations have implications regarding how the effector‐induced conformational change modulates DNA affinity for YtrA family members.
A metacommunity‐scale comparison of species‐abundance distribution models for plant communities of eastern Australia
Authors: Forster Michael A. , Warton David I.
Published: August 2007

Various models of the species‐abundance distribution (SAD) have been proposed to fit empirically derived data however there is no general consensus as to which model provides the best fit. Further, the zero‐sum multinomial SAD model (ZSM) was proposed as a metacommunity model, yet it has not previously been fitted at the metacommunity scale. We note that SAD models based on compound lognormal distributions (such as the Poisson‐lognormal, PLN, and the negative binomial‐lognormal models, NBLN) can also be thought of as metacommunity models, and we compare these with the ZSM when fitted as metacommunity models to SADs of related communities.

We collected five datasets in the Sydney Basin, eastern Australia, representing five different types of subtropical/temperate plant communities ranging from closed warm‐temperate rainforest to open wet sclerophyll forest to dry sclerophyll woodland. For each type of plant community, five local communities were identified across the Sydney Basin, and SAD data collected in five randomly placed 0.2‐ha quadrats at each local community. Analysis was performed at two levels: all abundance data from each local community were pooled across each metacommunity and analysed as a single pooled community; and a metacommunity model was fitted to all five local communities of a community type, simultaneously. For the pooled data, we considered the negative‐binomial (NB) and the log‐series (LS) models in addition to ZSM, PLN and NBLN. All five models performed similarly, however the LS had a better fit to three pooled communities and the ZSM and PLN to the remaining two communities. By contrast, the ZSM performed statistically better against the PLN and NBLN when considered as a metacommunity model. We conclude that the ZSM generally provides a more reliable null model for metacommunity abundance data than the lognormal model.
Bayesian clustering with AutoClass explicitly recognises uncertainties in landscape classification
Authors: Angus Webb J. , Bond Nicholas R. , Wealands Stephen R. , Mac Nally Ralph , Quinn Gerry P. , Vesk Peter A. , Grace Michael R.
Published: August 2007

Clustering of multivariate data is a commonly used technique in ecology, and many approaches to clustering are available. The results from a clustering algorithm are uncertain, but few clustering approaches explicitly acknowledge this uncertainty. One exception is Bayesian mixture modelling, which treats all results probabilistically, and allows comparison of multiple plausible classifications of the same data set. We used this method, implemented in the AutoClass program, to classify catchments (watersheds) in the Murray Darling Basin (MDB), Australia, based on their physiographic characteristics (e.g. slope, rainfall, lithology). The most likely classification found nine classes of catchments. Members of each class were aggregated geographically within the MDB. Rainfall and slope were the two most important variables that defined classes. The second‐most likely classification was very similar to the first, but had one fewer class. Increasing the nominal uncertainty of continuous data resulted in a most likely classification with five classes, which were again aggregated geographically. Membership probabilities suggested that a small number of cases could be members of either of two classes. Such cases were located on the edges of groups of catchments that belonged to one class, with a group belonging to the second‐most likely class adjacent. A comparison of the Bayesian approach to a distance‐based deterministic method showed that the Bayesian mixture model produced solutions that were more spatially cohesive and intuitively appealing. The probabilistic presentation of results from the Bayesian classification allows richer interpretation, including decisions on how to treat cases that are intermediate between two or more classes, and whether to consider more than one classification. The explicit consideration and presentation of uncertainty makes this approach useful for ecological investigations, where both data and expectations are often highly uncertain.
Estimating abundance from detection–nondetection data for randomly distributed or aggregated elusive populations
Authors: Zhou Shijie , Griffiths Shane P.
Published: August 2007

Estimating abundance is important in many ecological studies in order to understand the spatial and temporal dynamics of a population, which can assist in management and conservation. However, direct estimates of abundance can be difficult and expensive to obtain, particularly for wide‐ranging, rare or elusive species. An alternative – estimating from detection‐nondetection data – is a challenging but alluring concept to ecologists since the cost and effort of a study can be greatly reduced. This paper describes a method for estimating the abundance of randomly distributed or aggregated populations by using binary data where the probability of detection is less than one. The performances of the models were evaluated by computer simulations comprising 1620 cases. The results show that the accuracy of the abundance estimates increases as the sampling rate, efficiency of survey method, and the number of repeated surveys increase, whereas the accuracy declines as individuals become more aggregated. For a randomly distributed population, using a sampling rate of 0.05 in a survey method with a detection probability of 0.5, and repeating surveys three times provides sufficient accuracy of abundance. For an aggregated population, to achieve reasonably accurate abundance estimates the sampling rate should be doubled and each cell should be repeatedly surveyed on 4 to 6 occasions.
Does seed retention potential affect the distribution of plant species in highly fragmented calcareous grasslands?
Authors: Adriaens Dries , Honnay Olivier , Hermy Martin
Published: August 2007

Long‐distance dispersal is a crucial factor in the life‐cycle of plants, especially in our modern, highly fragmented landscapes. Because natural herds of large animals have disappeared and grazing practices have been abandoned, important potential vectors for seed dispersal over large distances may have been lost. In the context of the re‐establishment of grazing management for nature conservation purposes, it is therefore important to gain insight in the ability of grazing animals to act as seed dispersal vectors. Whereas local dispersal mainly occurs through standard vectors typically described based on morphological adaptations of the diaspore, large herbivores act as non‐standard seed dispersers. Therefore, traditional dispersal classes are loosing scientific relevance and continuous predictors of dispersal potential have been proposed. Here, we explored whether dispersal related plant traits, including the “seed retention potential”, could explain the distribution patterns of 180 plant species over 64 fragmented semi‐natural calcareous grasslands in Belgium. The distribution of habitat specialist plant species was strongly determined by the degree of isolation of the grasslands. Interestingly, species distribution patterns were clearly linked with a species’ potential to migrate through large grazers, as quantified by its retention potential: species producing seeds with high retention capacity were less affected by habitat isolation. Categorical dispersal classes based on seed morphology did not explain a species’ response to fragment isolation. Although seed retention potential outperformed simple seed dimensional traits, plant height, which is an indicator of epizoochorous attachment potential, was even more important. Therefore we suggest further extension of the epizoochorous retention potential model by incorporating basic ecological mechanisms that effectively contribute to successful dispersal events.
Congruence between floristic patterns of trees and lianas in a southwest Amazonian rain forest
Authors: J. Macía Manuel , Ruokolainen Kalle , Tuomisto Hanna , Quisbert Javier , Cala Victoria
Published: August 2007

The congruence in floristic patterns between different life‐forms of woody plants remains poorly understood in tropical rain forests. We explored whether the floristic patterns of woody plants, divided into small trees 2.5–10 cm dbh, large trees ≥10 cm dbh, and lianas ≥2.5 cm dbh were associated with each other or with patterns in soil properties, elevation, and geographical distances between sample plots. We also tested whether ecological amplitudes in relation to environmental variables differed among the plant groups. Trees and lianas were inventoried in 44 0.1‐ha plots, distributed among three lowland and two submontane sites in the Madidi National Park, Bolivia. Soil samples were analysed for physico‐chemical properties. Floristic differences between sites (as measured with each plant group separately) yielded significant Mantel correlations with each other, and with pH, Ca, Mg, elevation and geographical distance. Mantel correlations with edaphic distances were higher for large trees than small trees, but for Mantel correlations with geographical distance the situation was reversed. Environmental and geographical distances explained 31% of the variation in floristic differences for large trees, 22% for small trees, and 10% for lianas. The ecological amplitudes of lianas were wider than those of all trees for pH, Mg and elevation. The amplitudes of the two size classes of trees did not differ. In principal coordinates ordination, the three plant groups produced similar overall floristic patterns that were explainable by environmental factors.
Prospective cohort study of body mass index in adolescence and death from stomach cancer in Japan
Authors: Tanaka Tagayasu , Nagata Chisato , Oba Shino , Takatsuka Naoyoshi , Shimizu Hiroyuki
Published: August 2007

We investigated the association between body mass index (BMI) values and the risk of death from stomach cancer later in life. From 1992 to 2000, 28 443 participants (13 211 men and 15 232 women) were followed, and 129 deaths from stomach cancer (86 men and 43 women) occurred. BMI (BMI at the baseline) and BMI20y(BMI at age 20 years) were obtained by questionnaire at the beginning of the study. Men in the middle and highest tertiles of BMI20yhad a higher risk of death from stomach cancer than those in the lowest tertile (after controlling for covariates, hazard ratio [HR] = 2.73 with 95% confidence interval [CI] 1.26–5.89 for the middle tertile; HR = 2.15 with 95% CI 0.97–4.73 for the highest tertile), although there was no significant trend (P = 0.30). Likewise, women in the middle and highest tertiles of BMI20yhad an increased risk of death from stomach cancer (HR = 5.17 with 95% CI 1.50–17.87 for the middle tertile; HR = 4.22 with 95% CI 1.18–15.05 for the highest tertile;Pfor trend = 0.05). The analysis of BMI at the baseline did not show a significant relationship with the risk of death from stomach cancer. These results suggest that a high BMI20yis associated with an increased risk of death from stomach cancer. (Cancer Sci2007; 98: 1785–1789)