bluuebunny/crossref_metadata_2025 huggingface dataset:
Radiation reaction in 2+1 electrodynamics
Authors: Yaremko Yurij
Published: September 2007

A self-action problem for a pointlike charged particle arbitrarily moving in flat space-time of three dimensions is considered. Outgoing waves carry energy-momentum and angular momentum; the radiation removes energy, momentum, and angular momentum from the source which then undergoes a radiation reaction. We decompose Noether quantities carried by electromagnetic field into bound and radiative components. The bound terms are absorbed by individual particle’s characteristics within the renormalization procedure. Radiative terms together with already renormalized 3-momentum and angular momentum of pointlike charge constitute the total conserved quantities of our particle plus field system. Their differential consequences yield the effective equation of motion of radiating charge in an external electromagnetic field. In this integrodifferential equation the radiation reaction is determined by Lorentz force of pointlike charge acting upon itself plus nonlocal term which provides finiteness of the self-action.
Thermally compensated temperature sensor capable of highly accurate measurements on surfaces
Authors: Djeu N. , Kennedy J. L. , Djeu Derek
Published: September 2007

A thermally compensated temperature sensor capable of highly accurate determination of surface temperatures has been demonstrated. The probe consists of a single crystal Y3Al5O12 fiber terminating in a laser-heated Yb3Al5O12 phosphor. It has been shown to have a measurement accuracy of approximately 1 °C. In principle, this device should work in the proximity as well as the contact mode.
Site-controlled growth of Ge nanostructures on Si(100) via pulsed laser deposition nanostenciling
Authors: Cojocaru C. V. , Bernardi A. , Reparaz J. S. , Alonso M. I. , MacLeod J. M. , Harnagea C. , Rosei F.
Published: September 2007

The authors combine nanostenciling and pulsed laser deposition to pattern germanium (Ge) nanostructures into desired architectures. They have analyzed the evolution of the Ge morphology with coverage. Following the formation of a wetting layer within each area defined by the stencil’s apertures, Ge growth becomes three dimensional and the size and number of Ge nanocrystals evolve with coverage. Micro-Raman spectroscopy shows that the deposits are crystalline and epitaxial. This approach is promising for the parallel patterning of semiconductor nanostructures for optoelectronic applications.
In situ x-ray scattering study of self-organized nanodot pattern formation on GaSb(001) by ion beam sputtering
Authors: Plantevin O. , Gago R. , Vázquez L. , Biermanns A. , Metzger T. H.
Published: September 2007

The formation of self-organized nanodot patterns on GaSb(001) targets by ion beam sputtering has been studied in situ with grazing incidence small angle x-ray scattering. The temporal evolution of the patterns at different ion energies (300–1200eV) has been monitored. The authors evidence a rapid coarsening in the characteristic wavelength until reaching a saturation value that scales with ion energy. The pattern evolves slower toward saturation for the lower ion energy while attaining a higher correlation length (normalized to the wavelength). The pattern time dependence is correlated with the influence of the sputtering rate on the pattern formation.
On the electrical stress-induced oxide-trapped charges in thin HfO2∕SiO2 gate dielectric stack
Authors: Samanta Piyas , Zhu Chunxiang , Chan Mansun
Published: September 2007

Oxide charge buildup and its generation kinetics during constant voltage stress in TaN∕HfO2∕SiO2∕p-Si structures have been experimentally investigated. From the oxide charge relaxation experiments, nature and energy location of the as-fabricated intrinsic hole traps in the gate stack have also been determined. Our measurement results indicate that the dispersive proton transport through the interfacial SiO2 contributes larger than hole trapping in positive charge buildup in the stack. From the bias temperature stress measurement results in both control oxide and HfO2∕SiO2 stacks, we have identified overcoordinated [Si2=OH]+ centers as the proton-induced defects located in the interfacial SiO2 layer of the stack. Finally, an empirical equation is proposed to explain the stress-induced oxide positive charge buildup.
Controllable electromagnetic transmission based on dual-metallic grating structures composed of subwavelength slits
Authors: Cheng Chen , Chen Jing , Wu Qi-Yang , Ren Fang-Fang , Xu Ji , Fan Ya-Xian , Wang Hui-Tian
Published: September 2007

Electromagnetic (EM) transmission through dual-metallic grating (DMG) structures composed of slits arrays, with the longitudinal interval G and the lateral displacement L, is investigated by using the finite-difference time-domain method. The results show that the EM transmission property can be controlled by changing G or/and L, such as tunable wavelength of high transmission, changeable transmittance for a special wavelength, and suppressed EM transmission over a broad spectral range. The DMG structures have potential applications in the future photonics. In addition, some advantages of DMGs with respect to the single-metallic gratings are also discussed.
Low temperature LO-phonon dynamics of MgZnO nanoalloys
Authors: Huso Jesse , Morrison John L. , Hoeck Heather , Casey Erin , Bergman Leah , Pounds T. D. , Norton M. G.
Published: September 2007

In this paper, the authors present research on the low temperature resonant Raman scattering of the LO modes of Mg0.2Zn0.8O nanocrystals. They found that in the LO spectral range, two coupled modes appear: the main LO mode of the alloy and a low frequency mode redshifted by ∼27cm−1 relative to the main one. The low frequency mode was analyzed in terms of three mechanisms applicable to Raman scattering of an alloy system that might result in its activation: phase segregation due to the low solubility limit of the MgO–ZnO alloy system, a convolution of the A1(LO) with the E1(LO) mode, and an order-disorder state. Their analyses indicate that the principle mechanism that activates the low frequency mode is scattering due to the disordered state of the nanoalloys.
Slow electromagnetic propagation with low group velocity dispersion in an all-metamaterial-based waveguide
Authors: Dong J. W. , Wang H. Z.
Published: September 2007

The authors found that zero group velocity exists in a two-dimensional planar waveguide consisting of a left-handed metamaterial core and two identical claddings with negative permittivity. The mechanism is realized in a waveguide guiding a vortex mode, which results in the cancellation of the power flows between the core and the claddings. Moreover, by varying the waveguide thickness, the authors can manipulate the pulse velocity in the slow-light regime while simultaneously minimizing the pulse distortion. In addition, issues associated with energy loss are discussed.
Slip transfer through a general high angle grain boundary in nanocrystalline aluminum
Authors: Brandl C. , Bitzek E. , Derlet P. M. , Van Swygenhoven H.
Published: September 2007

The atomistic details of a slip transfer through a general high angle grain boundary in three dimensional nanocrystalline Al are reported and discussed in terms of possible implications for mesoscopic simulation models.
Ultrafast reconstruction of graphite by irradiating with highly charged ions
Authors: Miyamoto Yoshiyuki
Published: September 2007

Irradiating with highly charged Ar ions (Ar8+) causes an unanticipated structural reconstruction of graphite [T. Meguro et al., Appl. Phys. Lett. 79, 3866 (2001)] with a particular incidence energy of 400eV. To analyze this result, it is necessary to take into account charge transfer dynamics and ion dynamics simultaneously, which is not included in conventional first-principles scheme. An application of the time-dependent density functional theory coupled with molecular dynamics showed a variety of reconstructions (single vacancies, interlayer bridges, and sp3-like bonds) depending on Ar8+ incidence energies and should stimulate further research over a wide range of the incident energies.
An Approach to Metropolitan Governance and Finance
Authors: Bird Richard M , Slack Enid
Published: September 2007

In this paper we review several ‘models’ of governing structure found in metropolitan areas around the world from a fiscal perspective. We evaluate how different models achieve coordination of service delivery over the entire metropolitan area, the extent to which they allow for the equitable sharing of costs of services throughout the metropolitan area, and their ability to reduce negative or positive spillovers of service delivery across local boundaries. We then consider the advantages and disadvantages of different revenue-raising tools for metropolitan areas. We conclude by making a few suggestions with respect to metropolitan fiscal and governance developments in Latin America.
Cities and Regions Competing in the Global Economy: Knowledge and Local Development Policies
Authors: Malecki Edward J
Published: September 2007

Competitive places have developed diverse, multidimensional ways to attract mobile workers as well as mobile investment. Creative workers are the core of the knowledge economy and account for the varieties in its geography. Benchmarks, including knowledge metrics, innovation indices, and report cards, are increasingly common and increasingly critical to the monitoring of key features of economies and societies whose factors of production and of success are highly mobile. Consequently policies have become more sophisticated, but policy makers need to grasp the nature of place competition and the critical roles of knowledge in the strategies of the most competitive places.
Does it Matter Where IT Workers are Located?
Authors: Echeverri-Carroll Elsie , Ayala Sofia G , Kshetramade Mayuresh , Murthy Priyanka
Published: September 2007

The predominant view in the literature is that cities affect labor productivity because spatial proximity facilitates the transfer of ideas which make workers more productive. We also anticipate that information technology, or IT (both equipment and labor), by facilitating human communication and speeding up the flow of ideas and data, also contributes to enhancing the productivity of workers within cities. Thus, workers will be more productive in cities with a large endowment of these two factors of production. The objective of this paper is twofold. First, it describes the spatial characteristics of IT workers in the United States. Second, it tests the hypothesis that in cities with a higher endowment of IT workers wages (a proxy for productivity) would be higher after controlling for the characteristics of individual workers and city-specific characteristics that also affect wages. Using data from the 2000 US Census of Population (5% PUMS), we find evidence of a wage premium, especially for college-educated workers, associated with living in a city that has a large concentration of IT workers. On the basis of our findings, we propose to move the discussion on the future of cities from the effect of IT equipment on face-to-face communication to the impact on cities of losing IT workers.
Cities and Footlooseness: In Search of Place-Bound Companies and Effective Location Policies
Authors: van Geenhuizen Marina , Nijkamp Peter
Published: September 2007

The present study addresses the relevance of geographic proximity for companies in our age of advanced information and communication technology (ICT). Many visions of, and speculations on, an increased footlooseness of companies and a concomitant dispersal of urban economic activity have been published in recent years. To identify whether urban agglomeration economies (in particular, knowledge spillovers) are still a key force in preventing such dispersal, we investigate the degree of footlooseness of young, innovative companies. The exploratory analysis, based on interviews with twenty-one companies, employs an artificial intelligence method, called ‘rough-set analysis’, to increase our understanding of the crucial factors that influence needs for physical proximity. On the basis of these results, we argue that agglomeration economies still remain important for various categories of young, innovative, firms, even those providing ICT services, but that we need to make a distinction between agglomeration economies that work exclusively in the largest city (that is, Amsterdam) and agglomeration economies that cover a larger metropolitan area. The only fundamental change in proximity needs among these young, innovative companies originates from a small class of ‘network companies’, which are footloose even beyond the larger metropolitan area. The study also addresses urban policies to use opportunities better to attract companies with high proximity needs.
Face-to-Face, Buzz, and Knowledge Bases: Sociospatial Implications for Learning, Innovation, and Innovation Policy
Authors: Asheim Bjørn , Coenen Lars , Vang Jan
Published: September 2007

Whilst concurring with the new streams of literature in geography that highlight the importance of face-to-face and ‘buzz’ in the globalizing learning economy, we argue that this literature is misleading on three interrelated counts. Firstly, it conflates face-to-face and buzz; secondly, it fails to distinguish between the importance of face-to-face and buzz for industries drawing on different knowledge bases; and, thirdly, these conceptual inadequacies lead to an exaggeration of the importance of cities as sites for creativity and innovation, and hence regional competitiveness. By applying an industrial knowledge base approach, we seek to reconstruct an alternative framework that allows for a systematic differentiation between the importance of face-to-face and buzz for different industries. This provides a framework for developing a more nuanced understanding of the spatial implications of face-to-face communication and buzz for learning and innovation.
Firm Location in a Polycentric City: The Effects of Taxes and Agglomeration Economies on Location Decisions
Authors: Kohlhase Janet E , Ju Xiahong
Published: September 2007

The authors explore the determinants of firm location in a polycentric city with the aid of data for the Houston region. Firm location is modeled in a discrete-choice framework, with eight employment centers and outlying areas used as possible choices. Agglomerative and dispersive forces are explicitly treated, as are taxes and other characteristics that vary over space. The findings suggest that property taxes have large deterrent effects on firm locations for the four industrial groups analyzed here: oil and gas; manufacturing; finance, insurance and real estate (FIRE); and services. When agglomeration economies are present, they are weaker than the tax effects and are positive for only the FIRE and services industrial groups.
Simultaneous and Independent Acquisition of Multisensory and Unisensory Associations
Authors: Seitz Aaron R , Kim Robyn , van Wassenhove Virginie , Shams Ladan
Published: September 2007

Although humans are almost constantly exposed to stimuli from multiple sensory modalities during daily life, the processes by which we learn to integrate information from multiple senses to acquire knowledge of multisensory objects are not well understood. Here, we present results of a novel audio – visual statistical learning procedure where participants are passively exposed to a rapid serial presentation of arbitrary audio — visual pairings (comprised of artificial/synthetic audio and visual stimuli). Following this exposure, participants were tested with a two-interval forced-choice procedure in which their degree of familiarity with the experienced audio-visual pairings was evaluated against novel audio — visual combinations drawn from the same stimulus set. Our results show that subjects acquire knowledge of visual — visual, audio — audio, and audio — visual stimulus associations and that the learning of these types of associations occurs in an independent manner.
Hydrocarbon Surfactants for CO2: An Impossible Dream?
Authors: Eastoe Julian , Gold Sarah , Steytler David C.
Published: September 2007

It used to be thought that hydrocarbon ionic surfactants were incompatible with dense liquid or supercritical CO2, and fluorination of the chains was necessary to achieve any appreciable solubility. Here it is shown that branching of pendant hydrocarbon chains, especially methylation of the tips, can lead to substantial solubility enhancements in CO2 over normal linear chain hydrocarbon surfactants. In addition, increasing the number of these t-butyl-tipped groups from single-chained, through twin-tailed, to triple-chain surfactants has a profound effect on CO2 compatibility. High-pressure interfacial tension, small-angle neutron scattering, and near infrared spectroscopy have been applied to reveal the effects of surfactant structure on surface activity, aggregation, and solubility in CO2.
Determination of Contact Angles of Nanosized Silica Particles by Multi-Angle Single-Wavelength Ellipsometry
Authors: Hunter Timothy N. , Jameson Graeme J. , Wanless Erica J.
Published: September 2007

The determination of nanoparticle wettability is an area of great practical importance to materials science and engineering fields. There has been some recent interest in using spectroscopic analysis to indirectly categorize behaviour of monolayers, using the reflective and refractive properties of immersed particles. A method is developed here to calculate specific contact information for nanoparticles at an air–water interface, using single wavelength ellipsometry. A two-layer model is used that considers the refractive index of the immersed and non-immersed particle portions. Pressureâarea isotherms and Brewster angle images were used to confirm and categorize the nature of a packed monolayer, and ψ and Δ measurements taken of the interface. Immersion thickness was calculated and related to an equilibrium contact angle, and combined thickness data for the two layers was successfully related to the diameter of the particles.
Foams and Emulsions: the Importance of Structural Forces
Authors: Wasan Darsh T. , Nikolov Alex D.
Published: September 2007

We present a brief summary of the salient findings of our recent research delivered as a keynote lecture at the Australian Conference on Colloid and Interface Science held in Sydney in February 2007. We have developed a hybrid surface force apparatus (thin film capillary force balance) in conjunction with differential interference microscopy to show the phenomenon of microstructuring or stratification in thin films containing surfactant micelles, proteins, and nanoparticles separating two bubbles or droplets, as in foam and emulsion systems. The structural disjoining pressure, i.e. the structural force, arising because of the ordered microstructure formation inside thin liquid films between bubbles or drops, offers a new stabilization mechanism for foams, emulsions, and fluid-particle suspensions. In addition to the thin film approach, we also used both the Kossel diffraction and direct digitized optical imaging methods to directly observe the structure and stability of foam and emulsion systems. Our experiments were complemented by computations involving Monte Carlo simulations and the integral equation of statistical mechanics.
Aminimides as Potential CNS Acting Agents. I. Design, Synthesis, and Receptor Binding of 4′-Aryl Aminimide Analogues of Clozapine as Prospective Novel Antipsychotics
Authors: Capuano Ben , Crosby Ian T. , Lloyd Edward J. , Neve Juliette E. , Taylor David A.
Published: September 2007

A series of substituted 1-[4-(8-chloro-5H-dibenzo[b,e][1,4]diazepin-11-yl)-1-methylhexahydropyrazin-1-ium]-1-aminimide derivatives were designed on the basis of the physicochemical properties of the aminimide functional group and synthesized as potential antipsychotic agents for the treatment of schizophrenia. The target compounds were readily prepared in two steps from clozapine (8-chloro-11-(4-methylpiperazino)-5H-dibenzo[b,e][1,4]diazepine) and involved N-acylation of a common hydrazinium salt intermediate by an acyl chloride or activated ester in the presence of a strong base. The aminimides were tested for in vitro activity at the dopamine D4 and serotonin 5-HT2A receptors and were found to possess modest affinity for both receptor systems.
Physiological responses of the green alga Dunaliella parva (Volvocales, Chlorophyta) to controlled incremental changes in the N source
Authors: Giordano Mario , Norici Alessandra , Gilmour Daniel J. , Raven John A.
Published: September 2007

This work is aimed at obtaining information on the acclimation processes of the green flagellate Dunaliella parva Lerche to gradual changes in the N source from NO3– to NH4+, in continuous cultures. Photosynthesis, dark respiration, and light-independent carbon fixation (LICF) rates, chlorophyll a fluorescence, RUBISCO and phosphoenolpyruvate carboxylase (PEPc) activities, plasmalemma electrical potential difference, cell volume, and absolute or relative amounts of major cell constituents were measured. Two phases characterised the response to the transition from NO3– to NH4+: (1) an initial phase in which photosynthesis and anaplerosis were stimulated and protein increased; (2) a subsequent phase in which most parameters reached new values that were close to those at the beginning of the experiment (100% NO3–). The only exceptions were PEPc activity and LICF, whose rates remained at least 2-fold higher than at 100% NO3–, when NH4+ was the sole N source. The results are indicative of a tendency to re-establish homeostasis, after an initial perturbation of the intracellular composition. The roles of different metabolic processes during acclimation are discussed.
Identification and characterisation of acidic and novel basic forms of actinidin, the highly abundant cysteine protease from kiwifruit
Authors: Nieuwenhuizen Niels J. , Beuning Lesley L. , Sutherland Paul W. , Sharma Neelam N. , Cooney Janine M. , Bieleski Lara R. F. , Schröder Roswitha , MacRae Elspeth A. , Atkinson Ross G.
Published: September 2007

Actinidin is a cysteine protease found in Actinidia Lindl. (kiwifruit) species that affects the nutraceutical properties, processing characteristics and allergenicity of the fruit. Given the increased consumption of kiwifruit worldwide and the release of new varieties from different Actinidia species, the expression of actinidin mRNA and protein in a range of kiwifruit tissues was examined. Ten different actinidin mRNAs were identified encoding mature proteins of similar molecular weight (~24 kDa), but with predicted pIs ranging from acidic (pI 3.9) to basic (pI 9.3). In A. deliciosa ‘Hayward’ (green-fleshed kiwifruit) and A. chinensis ‘Hort16A’ and EM4 (gold-fleshed kiwifruit), actinidin mRNAs for acidic and basic proteins were expressed at comparable levels throughout ripening. Actinidin mRNA expression was highest in fruit at harvest, expression decreased as fruit ripened and was much lower in the core compared with outer pericarp tissue. Two-dimensional gel electrophoresis, combined with western analysis and liquid chromatography mass spectrometry (LC-MS) identified low levels of a novel basic actinidin protein in ripe A. deliciosa and A. chinensis fruit. Extremely high levels of an acidic actinidin protein were detected in A. deliciosa fruit and EM4, but this acidic protein appeared to be absent in ‘Hort16A’, the most important commercial cultivar of A. chinensis. Analyses on native gels indicated that both the basic and acidic actinidin isoforms in A. deliciosa were active cysteine proteases. Immunolocalisation showed that actinidin was present in small cells, but not large cells in the outer pericarp of mature A. deliciosa fruit at harvest. Within the small cells, actinidin was localised diffusely in the vacuole, associated with the plasma membrane, and in a layer in the plastids near starch granules. The presence of multiple forms of actinidin and varying protein levels in fruit will impact on the ability to breed new kiwifruit varieties with altered actinidin levels.
Incontinence in aging leaves: deteriorating water relations with leaf age in Agastachys odorata (Proteaceae), a shrub with very long-lived leaves
Authors: Jordan Gregory J. , Brodribb Timothy J.
Published: September 2007

This paper examines physiological characteristics of the leaves of Agastachys odorata R.Br., a wet-climate sclerophyllous shrub with very long-lived leaves. It addresses the hypothesis that cuticles become leakier to water vapour as leaves age. Astomatous cuticular conductance, whole-leaf minimum epidermal conductance, leaf damage and accumulation of epiphylls all increased several-fold with leaf age from first year growth to 10 years of age. Maximum carbon assimilation peaked 1 year after full leaf expansion, then declined. Intrinsic water use efficiency was highest in mid-aged leaves and declined markedly in the oldest leaves. Stomatal density, stomatal size and cuticle thickness did not vary significantly among ages. The older leaves were less effective at controlling water loss, resulting in decreases in water use efficiency. A differential increase in the conductance of the stomatal surface of the leaves relative to astomatous surface suggested that stomatal leakiness was significant in leaves over five years old. Although data for other species is ambiguous, the deterioration in A. odorata appears to be consistent with changes in the oldest leaves of other species. Thus, decreasing ability to use water efficiently appears to be a consequence of accumulated damage and may contribute to the need for leaf senescence in evergreen species with little self shading.
Correct dosage of
Fog2
and
Gata4
transcription factors is critical for fetal testis development in mice
Authors: Bouma Gerrit J. , Washburn Linda L. , Albrecht Kenneth H. , Eicher Eva M.
Published: September 2007

Previous reports suggested that humans and mice differ in their sensitivity to the genetic dosage of transcription factors that play a role in early testicular development. This difference implies that testis determination might be somewhat different in these two species. We report that the
Fog2
and
Gata4
transcription factors are haploinsufficient for testis determination in mice. Whether gonadal sex reversal occurs depends on genetic background (i.e., modifier genes). For example, C57BL/6J (B6) XY mice develop testes if they are heterozygous for a mutant
Fog2
(
Fog2
−) or
Gata4
(

Gata4
ki

) allele. However, if the B6 Y chromosome (Y
B6
) is replaced by the AKR Y chromosome (Y
AKR
), B6
Fog2
−/+ XY
AKR
mice develop ovaries, and B6

Gata4
ki

/+ XY
AKR
mice develop ovaries and ovotestes (gonads containing both ovarian and testicular tissue). Furthermore, DBA/2J (D2)
Fog2
−/+ XY
AKR
mice and (B6 × D2)F1 hybrid

Gata4
ki

/+ XY
AKR
mice develop testes.
Sry
is expressed in the mutant XY gonads, indicating that the lack of
Sry
expression is not the cause of ovarian tissue development in B6
Fog2
−/+ or

Gata4
ki

/+ XY
AKR
mice. However, up-regulation of
Sox9
expression, which is critical for normal testicular development, does not occur in mutant XY gonads that develop as ovaries. We conclude that under certain genetic conditions,
Sox9
up-regulation depends on the proper dosage of
Fog2
and
Gata4
. We propose that in humans the
FOG2
and/or
GATA4
genes might be haploinsufficient for normal testis determination and thus could be the cause of some previously unassigned cases of XY gonadal sex reversal.
Ribonucleoprotein-masked nicks at 50-kbp intervals in the eukaryotic genomic DNA
Authors: Székvölgyi Lóránt , Rákosy Zsuzsa , Bálint Bálint L. , Kókai Endre , Imre László , Vereb György , Bacsó Zsolt , Goda Katalin , Varga Sándor , Balázs Margit , Dombrádi Viktor , Nagy László , Szabó Gábor
Published: September 2007

By using a microscopic approach, field inversion single-cell gel electrophoresis, we show that preformed single-strand discontinuities are present in the chromatin of resting and proliferating mammalian and yeast cells. These single-strand breaks are primarily nicks positioned at ≈50-kbp intervals throughout the entire genome that could be efficiently labeled
in situ
by DNA polymerase I holoenzyme but not by Klenow fragment and terminal transferase unless after ribonucleolytic treatments. The RNA molecules involved appear to comprise R-loops, recognized by the S9.6 RNA/DNA hybrid-specific antibody. By using the breakpoint cluster region of the
Mixed Lineage Leukemia
(
MLL
) gene as a model, we have found that the number of manifest nicks detected by FISH performed after field inversion single-cell gel electrophoresis depends on epigenetic context, but the difference between germ-line and translocated MLL alleles is abolished by protease treatment. Our data imply that the double-stranded genomic DNA is composed of contiguous rather than continuous single strands and reveal an aspect of higher-order chromatin organization with ribonucleoprotein-associated persistent nicks defining ≈50-kbp domains.
Robust protein–protein interactions in crowded cellular environments
Authors: Deeds Eric J. , Ashenberg Orr , Gerardin Jaline , Shakhnovich Eugene I.
Published: September 2007

The capacity of proteins to interact specifically with one another underlies our conceptual understanding of how living systems function. Systems-level study of specificity in protein–protein interactions is complicated by the fact that the cellular environment is crowded and heterogeneous; interaction pairs may exist at low relative concentrations and thus be presented with many more opportunities for promiscuous interactions compared with specific interaction possibilities. Here we address these questions by using a simple computational model that includes specifically designed interacting model proteins immersed in a mixture containing hundreds of different unrelated ones; all of them undergo simulated diffusion and interaction. We find that specific complexes are quite robust to interference from promiscuous interaction partners only in the range of temperatures
T
design
>
T
>
T
rand
. At
T
>
T
design
, specific complexes become unstable, whereas at
T
<
T
rand
, formation of specific complexes is suppressed by promiscuous interactions. Specific interactions can form only if
T
design
>
T
rand
. This condition requires an energy gap between binding energy in a specific complex and set of binding energies between randomly associating proteins, providing a general physical constraint on evolutionary selection or design of specific interacting protein interfaces. This work has implications for our understanding of how the protein repertoire functions and evolves within the context of cellular systems.
Ancient DNA, pig domestication, and the spread of the Neolithic into Europe
Authors: Larson Greger , Albarella Umberto , Dobney Keith , Rowley-Conwy Peter , Schibler Jörg , Tresset Anne , Vigne Jean-Denis , Edwards Ceiridwen J. , Schlumbaum Angela , Dinu Alexandru , Bălăçsescu Adrian , Dolman Gaynor , Tagliacozzo Antonio , Manaseryan Ninna , Miracle Preston , Van Wijngaarden-Bakker Louise , Masseti Marco , Bradley Daniel G. , Cooper Alan
Published: September 2007

The Neolithic Revolution began 11,000 years ago in the Near East and preceded a westward migration into Europe of distinctive cultural groups and their agricultural economies, including domesticated animals and plants. Despite decades of research, no consensus has emerged about the extent of admixture between the indigenous and exotic populations or the degree to which the appearance of specific components of the “Neolithic cultural package” in Europe reflects truly independent development. Here, through the use of mitochondrial DNA from 323 modern and 221 ancient pig specimens sampled across western Eurasia, we demonstrate that domestic pigs of Near Eastern ancestry were definitely introduced into Europe during the Neolithic (potentially along two separate routes), reaching the Paris Basin by at least the early 4th millennium B.C. Local European wild boar were also domesticated by this time, possibly as a direct consequence of the introduction of Near Eastern domestic pigs. Once domesticated, European pigs rapidly replaced the introduced domestic pigs of Near Eastern origin throughout Europe. Domestic pigs formed a key component of the Neolithic Revolution, and this detailed genetic record of their origins reveals a complex set of interactions and processes during the spread of early farmers into Europe.
Nonhuman primate event-related potentials indexing covert shifts of attention
Authors: Woodman Geoffrey F. , Kang Min-Suk , Rossi Andrew F. , Schall Jeffrey D.
Published: September 2007

A half-century's worth of research has established the existence of numerous event-related potential components measuring different cognitive operations in humans including the selection of stimuli by covert attention mechanisms. Surprisingly, it is unknown whether nonhuman primates exhibit homologous electrophysiological signatures of selective visual processing while viewing complex scenes. We used an electrophysiological technique with macaque monkeys analogous to procedures for recording scalp event-related potentials from humans and found that monkeys exhibit short-latency visual components sensitive to sensory processing demands and lateralizations related to shifting of covert attention similar to the human N2pc component. These findings begin to bridge the gap between the disparate literatures by using electrophysiological measurements to study the deployment of visual attention in the brains of humans and nonhuman primates.
Oxidative stress causes bone loss in estrogen-deficient mice through enhanced bone marrow dendritic cell activation
Authors: Grassi Francesco , Tell Gianluca , Robbie-Ryan Michaela , Gao Yuhao , Terauchi Masakazu , Yang Xiaoying , Romanello Milena , Jones Dean P. , Weitzmann M. Neale , Pacifici Roberto
Published: September 2007

Increased production of tumor necrosis factor α (TNF) in the bone marrow (BM) in response to both oxidative stress and T cell activation contributes to the bone loss induced by estrogen deficiency, but it is presently unknown whether oxidative stress causes bone loss through T cells. Here we show that ovariectomy causes an accumulation in the BM of reactive oxygen species, which leads to increased production of TNF by activated T cells through up-regulation of the costimulatory molecule CD80 on dendritic cells. Accordingly, bone loss is prevented by treatment of ovariectomized mice with either antioxidants or CTLA4-Ig, an inhibitor of the CD80/CD28 pathway. In summary, reactive oxygen species accumulation in the BM is an upstream consequence of ovariectomy that leads to bone loss by activating T cells through enhanced activity of BM dendritic cells, and these findings suggest that the CD80/CD28 pathway may represent a therapeutic target for postmenopausal bone loss.
Structural insights into the Slit-Robo complex
Authors: Morlot Cecile , Thielens Nicole M. , Ravelli Raimond B. G. , Hemrika Wieger , Romijn Roland A. , Gros Piet , Cusack Stephen , McCarthy Andrew A.
Published: September 2007

Slits are large multidomain leucine-rich repeat (LRR)-containing proteins that provide crucial guidance cues in neuronal and vascular development. More recently, Slits have been implicated in heart morphogenesis, angiogenesis, and tumor metastasis. Slits are ligands for the Robo (Roundabout) receptors, which belong to the Ig superfamily of transmembrane signaling molecules. The Slit-Robo interaction is mediated by the second LRR domain of Slit and the two N-terminal Ig domains of Robo, but the molecular details of this interaction and how it induces signaling remain unclear. Here we describe the crystal structures of the second LRR domain of human Slit2 (Slit2 D2), the first two Ig domains of its receptor Robo1 (Ig1–2), and the minimal complex between these proteins (Slit2 D2-Robo1 Ig1). Slit2 D2 binds with its concave surface to the side of Ig1 with electrostatic and hydrophobic contact regions mediated by residues that are conserved in other family members. Surface plasmon resonance experiments and a mutational analysis of the interface confirm that Ig1 is the primary domain for binding Slit2. These structures provide molecular insight into Slit-Robo complex formation and will be important for the development of novel cancer therapeutics.
Human cone photoreceptor dependence on RPE65 isomerase
Authors: Jacobson Samuel G. , Aleman Tomas S. , Cideciyan Artur V. , Heon Elise , Golczak Marcin , Beltran William A. , Sumaroka Alexander , Schwartz Sharon B. , Roman Alejandro J. , Windsor Elizabeth A. M. , Wilson James M. , Aguirre Gustavo D. , Stone Edwin M. , Palczewski Krzysztof
Published: September 2007

The visual (retinoid) cycle, the enzymatic pathway that regenerates chromophore after light absorption, is located primarily in the retinal pigment epithelium (RPE) and is essential for rod photoreceptor survival. Whether this pathway also is essential for cone photoreceptor survival is unknown, and there are no data from man or monkey to address this question. The visual cycle is naturally disrupted in humans with Leber congenital amaurosis (LCA), which is caused by mutations in
RPE65
, the gene that encodes the retinoid isomerase. We investigated such patients over a wide age range (3–52 years) for effects on the cone-rich human fovea.
In vivo
microscopy of the fovea showed that, even at the youngest ages, patients with
RPE65
-LCA exhibited cone photoreceptor loss. This loss was incomplete, however, and residual cone photoreceptor structure and function persisted for decades. Basic questions about localization of RPE65 and isomerase activity in the primate eye were addressed by examining normal macaque. RPE65 was definitively localized by immunocytochemistry to the central RPE and, by immunoblotting, appeared to concentrate in the central retina. The central retinal RPE layer also showed a 4-fold higher retinoid isomerase activity than more peripheral RPE. Early cone photoreceptor losses in
RPE65
-LCA suggest that robust RPE65-based visual chromophore production is important for cones; the residual retained cone structure and function support the speculation that alternative pathways are critical for cone photoreceptor survival.
The hypothesis of reproductive compensation and its assumptions about mate preferences and offspring viability
Authors: Gowaty Patricia Adair , Anderson Wyatt W. , Bluhm Cynthia K. , Drickamer Lee C. , Kim Yong-Kyu , Moore Allen J.
Published: September 2007

The Compensation Hypothesis says that parents and prospective parents attempt to make up for lowered offspring viability by increasing reproductive effort to produce healthy, competitive offspring and by increasing investment in less viable, but still-living progeny (parental effects). The hypothesis assumes that offspring viability is lower when individuals are constrained (often through sexual conflict) to breed with individuals they do not prefer. We review results of experimental tests of the offspring-viability assumption in Tanzanian cockroaches, fruit flies, pipefish, wild mallards, and feral house mice. Experimental constraints on mating preferences lowered offspring viability in each of the studies. Females breeding under constraints laid more eggs or gave birth to more young than females breeding without or with fewer constraints on their mating preferences, and males mating under constraints on their mate preferences ejaculated more sperm than males mating without constraints. The number of eggs laid or offspring born was higher when female choosers were experimentally constrained to reproduce with males they did not prefer. Constrained females may increase fecundity to enhance the probability that they produce adult offspring with rarer phenotypes with survival benefits against offspring generation pathogens. Similarly, ejaculation of more sperm when males are paired with females they do not prefer may be a mechanism that provides more variable sperm haplotypes for prospective mothers or that may provide nutritional benefits to mothers and zygotes.
Getting specificity from simplicity in putative proteins from the prebiotic Earth
Authors: López de la Osa Jaime , Bateman David A. , Ho Sylvia , González Carlos , Chakrabartty Avijit , Laurents Douglas V.
Published: September 2007

Can unique protein structures arise from a limited set of amino acids present on the prebiotic Earth? To address this question, we have determined the stability and structure of KIA7, a 20-residue polypeptide containing chiefly Lys, Ile, and Ala. NMR methods reveal that KIA7 tetramerizes and folds on the millisecond time scale to adopt a four-helix X-bundle structure with a tightly and specifically packed core. Denaturation studies and hydrogen exchange measurements of KIA7 and several variants demonstrate that ridges-into-grooves packing of Ala and Ile side chains and the packing of a C-terminal aromatic group into the hydrophobic core are sufficient to give rise to a rather stable, well folded protein structure, with no favorable electrostatic interactions or tertiary or quaternary hydrogen bonds. Both modern proteins and RNAs can adopt specific structures, but RNAs do so with a limited “alphabet” of residues and types of stabilizing interactions. The results reported here show that specific, well folded protein structures can also arise from a highly reduced set of stabilizing interactions and amino acids that are thought to have been present on the prebiotic Earth.
Caenorhabditis elegans
neuronal regeneration is influenced by life stage, ephrin signaling, and synaptic branching
Authors: Wu Zilu , Ghosh-Roy Anindya , Yanik Mehmet Fatih , Zhang Jin Z. , Jin Yishi , Chisholm Andrew D.
Published: September 2007

We previously reported functional regeneration of
Caenorhabditis elegans
motor neurons after femtosecond laser axotomy. We report here that multiple neuronal types can regrow after laser axotomy using a variety of lasers. The precise pattern of regrowth varies with cell type, stage of animal, and position of axotomy. Mechanosensory axons cut in late larval or adult stages displayed extensive regrowth, yet failed to reach their target area because of guidance errors in the anteroposterior axis. By contrast, mechanosensory axons cut in early larval stages regrew at the same rate but with fewer anteroposterior guidance errors, and were more likely to reach their target area. In adult animals lacking the VAB-1 Eph receptor tyrosine kinase, mechanosensory axon regrowth was more accurate than in the wild type, suggesting that guidance errors of regrowing touch neuron axons are the result of Eph signaling. Kinase-dependent and kinase-independent Eph signaling influenced outgrowth and guidance of regrowing touch neurons, respectively. Mechanosensory neurons regrew when severed proximal to their collateral synaptic branch but did not regrow when severed distal to the branch point. However, the distal axon could regrow if the branch is removed surgically at the same time as distal axotomy, or at a later time. The touch neuron synaptic branch point may act as a sorting area to regulate growth. These findings reveal that multiple influences affect regenerative growth in
C. elegans
neurons.
Is Income Inequality Harmful for Regional Growth? Evidence from the European Union
Authors: Ezcurra Roberto
Published: September 2007

This article examines the relationship between income inequality and economic growth in the regions of several European Union countries over the period 1993—2002, using the information provided by the European Community Household Panel. Taking into consideration the relevance of spatial effects in this context, different versions of a spatial econometric model are estimated. The results indicate that the degree of income dispersion is negatively associated with regional growth. This finding is in fact robust to various alternative specifications including a number of additional explanatory variables, such as initial per capita GDP, the sectoral composition of economic activity, human capital stock, population density and market potential. Furthermore, the observed negative correlation between income inequality and economic performance does not depend on the specific measure used to quantify the degree of income dispersion.
The Demise of the Rent-controlled Public Housing Programmes of Ghana: The Story of the Tema Development Corporation
Authors: Asabere Paul
Published: September 2007

In 1952, a new town called Tema was created in Ghana. The master plan for Tema made provision for 19 planned communities, each having roughly 1500—2000 homes. About 6355 housing units are government-owned rental housing. The rental housing stock is the subject of this study. This paper reports an empirical study that shows that rent controls coupled with public management have caused investment values in the rental housing stock to disappear. For example, this study finds that the nominal rate of return on total investment for these rentals based on replacement value has a mean value of only 3 per cent. With inflation rates around 15 per cent during the study period, this implies a negative real rate of return. The findings provide empirical support and justification for recent attempts to privatise all rental public housing in Ghana. The study concludes with public policy recommendations.
The Redistributive Effect of Public Housing in Hong Kong
Authors: Lui Hon-Kwong
Published: September 2007

Public housing programmes in Hong Kong affect half of the population directly and the other half indirectly. This paper assesses the redistributive effect of public rental housing on income distribution. It uses a subsidised-to-market rent ratio method and an imputed rent method to convert transfer-in-kind of public rental housing into equivalent monetary value. Empirical results show that the provision of public housing alleviates the income inequality problem. However, the amount of public expenditure required achieving the same improvements in Gini coefficient and other inequality measures is small relative to the actual public expenditure on housing. Policy-makers should thoroughly review the existing public housing programmes.
Departures from Gibrat's Law, Discontinuities and City Size Distributions
Authors: Garmestani Ahjond S. , Allen Craig R. , Gallagher Colin M. , Mittelstaedt John D.
Published: September 2007

Cities are complex, self-organising, evolving systems and the emergent patterns they manifest provide insight into the dynamic processes in urban systems. This article analyses city size distributions, by decade, from the south-eastern region of the US for the years 1860—1990. It determines if the distributions are clustered into size classes and documents changes in the pattern of size classes over time. A statistical hypothesis test was also performed to detect dependence between city size and growth using discrete probability calculations under the assumption of Gibrat's law. The city size distributions for the south-eastern region of the US were discontinuous, with cities clustering into distinct size classes. The analysis also identified departures from Gibrat's law, indicating variable growth rates at different scales.
Spatial Distribution of High-rise Buildings within Urban Areas: The Case of the Tel-Aviv Metropolitan Region
Authors: Frenkel Amnon
Published: September 2007

The spatial aspects of high-rise buildings in the Tel-Aviv metropolitan region are examined, using empirical data gathered through a field survey. A multinomial logit model is employed to test hypotheses concerning the cyclic model of metropolitan region development. The results support empirical evidence of the spatial dispersal of high-rise buildings, indicating an initial process of reconcentration in the Tel-Aviv metropolitan pattern. The study concludes that intensive high-rise building is expected to develop extensively in the future, particularly in the core and inner-ring areas. The dispersal of this construction indicates a classic negative gradient pattern, moving from the core area towards the outskirts of the metropolitan region. In contrast, the classic pattern between centre and fringes does not hold within the built-up area of the metropolitan region.