bluuebunny/crossref_metadata_2025 huggingface dataset:
ABC Transporter Function and Regulation at the Blood–Spinal Cord Barrier
Authors: Campos Christopher R , Schröter Christian , Wang Xueqian , Miller David S
Published: April 2012

We present here an initial characterization of ATP binding cassette (ABC) transporter function and regulation at the blood–spinal cord barrier. We isolated capillaries from rat spinal cords and studied transport function using a confocal microscopy-based assay and protein expression using western blots. These capillaries exhibited transport function and protein expression of P-glycoprotein (Abcb1), multidrug resistance protein 2 (Mrp2, Abcc2), and breast cancer-related protein (Bcrp, Abcg2). Exposing isolated capillaries to dioxin (activates aryl hydrocarbon receptor) increased transport mediated by all three transporters. Brain and spinal cord capillaries from dioxin-dosed rats exhibited increased P-glycoprotein-mediated transport and increased protein expression for all three ABC transporters. These findings indicate similar ABC transporter expression, function, and regulation at the blood–spinal cord and blood–brain barriers.
Detecting differential usage of exons from RNA-Seq data
Authors: Anders Simon , Reyes Alejandro , Huber Wolfgang
Published: April 2012

RNA-Seq is a powerful tool for the study of alternative splicing and other forms of alternative isoform expression. Understanding the regulation of these processes requires sensitive and specific detection of differential isoform abundance in comparisons between conditions, cell types or tissues. We present DEXSeq, a statistical method to test for differential exon usage in RNA-Seq data. DEXSeq employs generalized linear models and offers reliable control of false discoveries by taking biological variation into account. DEXSeq detects genes, and in many cases specific exons, that are subject to differential exon usage with high sensitivity. We demonstrate the versatility of DEXSeq by applying it to several data sets. The method facilitates the study of regulation and function of alternative exon usage on a genome-wide scale. An implementation of DEXSeq is available as an R/Bioconductor package.This preprint has subsequently been published in Genome Research (doi:10.1101/gr.133744.111)
Genome Replikin Count Predicts Increased Lethality of Resistant Tuberculosis
Authors: Bogoch Samuel , Bogoch Elenore
Published: April 2012

The genomic Replikin Count of all the sequences on Pubmed of different strains of tuberculosis were analyzed. The lowest Counts occurred with species within the lowest drug resistance, the highest Counts with sequences of the highest drug resistance and lethality.
A novel apparatus/protocol designed for optogenetic manipulation and recording of individual neurons during a motivation and working memory task in the rodent
Authors: Dolzani Samuel , Cooper Donald
Published: April 2012

Innovative molecular tools allow neuroscientists to study neural circuitry associated with specific behaviors. Consequently, behavioral methods must be developed to interface with these new molecular tools in order for neuroscientists to identify the causal elements underlying behavior and decision-making processes. Here we present an apparatus and protocol for a novel Go/No-Go behavioral paradigm to study the brain attention and motivation/reward circuitry in awake, head-restrained rodents. This experimental setup allows: (1) Painless and stable restraint of the head and body; (2) Rapid acquisition to simple or complex operant tasks; (3) Repeated electrophysiological single and multiple unit recordings during ongoing behavior; (4) Pharmacological and viral manipulation of various brain regions via targeted guide cannula, and; (5) Optogenetic cell-type specific activation and silencing with simultaneous electrophysiological recording. In addition to the experimental advantages, the head-restraint system is relatively inexpensive and training parameters can be easily modulated to the specifications of the experimenter. The system runs on custom LabView software. In summary, our novel apparatus and protocol allows researchers to study and manipulate components of behavior, such as motivation, impulsivity, and reward-related working memory during an ongoing operant behavioral task without interference from non task-related behaviors. For more information on the custom apparatus, software or to collaborate please visit www.neuro-cloud.net/nature-precedings/dolzani.
Is There a Cognate Advantage for Typically Developing Spanish-Speaking English-Language Learners?
Authors: Kelley Alaina , Kohnert Kathryn
Published: April 2012

Purpose

Cross-linguistic cognates are words that share form and meaning in two languages (e.g.,
helicopter
–
helicóptero
); translation equivalents are words that share meaning but not form (e.g.,
house
–
casa
). Research consistently demonstrates a performance speed and/or accuracy advantage for processing cognates versus noncognates in bilingual adults; studies with children are limited, with equivocal results. We investigated the potential for a cognate advantage for processing expressive and receptive vocabulary in the spoken (vs. written) modality in typically developing Spanish-speaking English-language learners (ELLs).

Method

Thirty 8- to 13-year-old native Spanish-speaking children learning English as their second language completed standardized vocabulary tests in spoken English. Each test item was classified as a cognate or noncognate based on phonological overlap with its Spanish translation. Group and individual analyses were used to examine the effects of cognates.

Results

At the group level, children’s test scores were higher for items that were classified as cognates as compared to noncognates of comparable difficulty. However, not all children demonstrated this cognate advantage. Age predicted significant amounts of variance in cognate performance on the receptive test.

Conclusion

Overall, typically developing Spanish-speaking school-age ELL students demonstrated a cognate advantage. There was also considerable within-group variation in performance. Clinical implications are discussed, and directions for future study are provided.
Dialect-Neutral Indices of Narrative Cohesion and Evaluation
Authors: Burns Frances A. , de Villiers Peter A. , Pearson Barbara Z. , Champion Tempii B.
Published: April 2012

Purpose

This study compared the development of essential elements of narrative skill in children from African American English (AAE)- and general American English (GAE)-speaking communities using an innovative elicitation and evaluation protocol consisting of four key indices of narrative language: (a) reference contrasting, (b) temporal expressions, (c) mental state descriptions, and (d) understanding of behavior based on false belief.

Method

Participants were 291 AAE speakers and 238 GAE speakers, 4 to 9 years of age. Approximately one-third of both dialect groups were identified as having language impairments. Children generated 2 stories based on short picture sequences. Their stories were coded for the 4 key indices of narrative language. Analyses of variance were performed with subsets of the measures and a composite index with all measures combined as outcomes; and with age, dialect group, and clinical status as predictors.

Results

Age and clinical status had statistically significant effects on the subset measures and the composite score. Variation between AAE and GAE dialect was not a significant factor.

Conclusion

By focusing on dialect-neutral elements of narratives—creating links across sentences and providing mental state interpretations—this study adds to our knowledge of development and impairment in narrative production among both AAE- and GAE-background children.
Developmental Trajectory for Production of Prosody: Lexical Stress Contrastivity in Children Ages 3 to 7 Years and in Adults
Authors: Ballard Kirrie J. , Djaja Danica , Arciuli Joanne , James Deborah G. H. , van Doorn Jan
Published: April 2012

Purpose

Accurate production of lexical stress within English polysyllabic words is critical for intelligibility and is affected in many speech-language disorders. However, models of speech production remain underspecified with regard to lexical stress. In this study, the authors report a large-scale acoustic investigation of lexical stress production in typically developing Australian English–speaking children ages 3–7 years (
n
= 73) compared with young adults (
n
= 24).

Method

Participants named pictures of highly familiar strong–weak and weak–strong polysyllabic words. Of 388 productions, 325 met criteria for acoustic measurement. Relative vowel duration, peak intensity, and peak
f
0
over the first two syllables were measured.

Result

Lexical stress was marked consistently by duration and intensity but not
f
0
. Lexical stress on strong–weak words was adultlike by 3 years. All 3 measures showed significant differences between adults and children for weak–strong words still present at 7 years.

Conclusion

Our findings suggest that protracted development of weak–strong stress production reflects physiological constraints on producing short articulatory durations and rising intensity contours. Findings validate treatment that is centered on strong–weak stress production for children ≥ 3 years with dysprosody. Although intervention for the production of weak–strong words may be initiated before age 7 years, reference to normative acoustic data is preferable to relying on perceptual judgments of accuracy.
Components in time-varying graphs
Authors: Nicosia Vincenzo , Tang John , Musolesi Mirco , Russo Giovanni , Mascolo Cecilia , Latora Vito
Published: April 2012

Real complex systems are inherently time-varying. Thanks to new communication systems and novel technologies, today it is possible to produce and analyze social and biological networks with detailed information on the time of occurrence and duration of each link. However, standard graph metrics introduced so far in complex network theory are mainly suited for static graphs, i.e., graphs in which the links do not change over time, or graphs built from time-varying systems by aggregating all the links as if they were concurrent in time. In this paper, we extend the notion of connectedness, and the definitions of node and graph components, to the case of time-varying graphs, which are represented as time-ordered sequences of graphs defined over a fixed set of nodes. We show that the problem of finding strongly connected components in a time-varying graph can be mapped into the problem of discovering the maximal-cliques in an opportunely constructed static graph, which we name the affine graph. It is, therefore, an NP-complete problem. As a practical example, we have performed a temporal component analysis of time-varying graphs constructed from three data sets of human interactions. The results show that taking time into account in the definition of graph components allows to capture important features of real systems. In particular, we observe a large variability in the size of node temporal in- and out-components. This is due to intrinsic fluctuations in the activity patterns of individuals, which cannot be detected by static graph analysis.
A second degree Newton method in inverse scattering problem for a crack
Authors: Lee Kuo-Ming
Published: April 2012

For the inverse scattering problem from a sound-soft crack a second degree Newton method is proposed in this paper. Based on integral equations method, our scheme splits the inverse problem into a well-posed problem and a nonlinear ill-posed problem which will be linearized using a second degree method. Some reconstructions will be given to demonstrate the feasibility of the proposed method.
Low-cost caesium phosphate as n-dopant for organic light-emitting diodes
Authors: Wemken Jan Hauke , Krause Ralf , Mikolajick Thomas , Schmid Günter
Published: April 2012

We demonstrate the usage of caesium phosphate (Cs3PO4) as a low-cost n-dopant for conductivity enhancements of the electron transport layer in organic light-emitting diodes (OLEDs). Up to 9 orders of magnitude, reaching 2.3 × 10−5 S/cm with only 10% dopant concentration in 2,9-dimethyl-4,7-diphenyl-1,10-phenanthroline single-carrier devices, were achieved. Luminance current voltage and impedance spectroscopy measurements confirmed the increased conductivities of the single carrier devices in green light-emitting diodes. Constant operation voltages of below 4 V were realized independently of the electron transport layer (ETL) thickness, which was varied from 50–150 nm. Dielectric constants were modeled by usage of the least squares method. Measured and calculated capacitances based on the geometric properties and modeled dielectric constants varied by less than 1.3% for doped OLEDs, confirming the highly conductive nature of Cs3PO4-doped ETLs and demonstrating that a highly conductive electron transport layer can be understood as an extended cathode.
Variation and sign change of magnetostrictive strain as a function of Ni concentration in Ni-substituted ZnFe2O4 sintered nanoparticles
Authors: Adhikari R. , Sarkar A. , Limaye Mukta V. , Kulkarni S. K. , Das A. K.
Published: April 2012

Zn1-xNixFe2O4 nanoparticles were prepared with varying Ni concentration via sol-gel method. The magnetostrictive strains of sintered nanoparticles were measured using an indigenous optical cantilever beam magnetometer. The four regimes in variation of the magnetostrictive strains have been observed: (i) zero strain in the range, 0% to 25% Ni; (ii) positive (tensile) strain with a slow gradient in the range, 25% to 50% Ni; (iii) negative (compressive) strain with a fast gradient between 50% and 75% Ni; and (iv) maximum negative strain with a zero gradient between 75% and 100% Ni concentrations. The observed variation in magnetostriction is correlated with the structure of sintered nanoparticles characterized by x-ray diffraction and Mössbauer spectroscopy. The sign and magnitude of the measured magnetostrictive strain as a function of Ni concentration in the Zn1-xNixFe2O4 matrix are found to be related with the degree of inversion of the spinel structure.
Photonic band structures of two-dimensional magnetized plasma photonic crystals
Authors: Qi L.
Published: April 2012

By using modified plane wave method, photonic band structures of the transverse electric polarization for two types of two-dimensional magnetized plasma photonic crystals are obtained, and influences of the external magnetic field, plasma density, and dielectric materials on the dispersion curves are studied, respectively. Results show that two areas of flat bands appear in the dispersion curves due to the role of external magnetic field, and the higher frequencies of the up and down flat bands are corresponding to the right-circled and left-circled cutoff frequencies, respectively. Adjusting external magnetic field and plasma density can not only control positions of the flat bands, but also can control the location and width of the local gap; increasing relative dielectric constant of the dielectric materials makes omni-direction gaps appear.
Variational calculation of quantum mechanical/molecular mechanical free energy with electronic polarization of solvent
Authors: Nakano Hiroshi , Yamamoto Takeshi
Published: April 2012

Quantum mechanical/molecular mechanical (QM/MM) free energy calculation presents a significant challenge due to an excessive number of QM calculations. A useful approach for reducing the computational cost is that based on the mean field approximation to the QM subsystem. Here, we describe such a mean-field QM/MM theory for electronically polarizable systems by starting from the Hartree product ansatz for the total system and invoking a variational principle of free energy. The MM part is then recast to a classical polarizable model by introducing the charge response kernel. Numerical test shows that the potential of mean force (PMF) thus obtained agrees quantitatively with that obtained from a direct QM/MM calculation, indicating the utility of self-consistent mean-field approximation. Next, we apply the obtained method to prototypical reactions in several qualitatively different solvents and make a systematic comparison of polarization effects. The results show that in aqueous solution the PMF does not depend very much on the water models employed, while in nonaqueous solutions the PMF is significantly affected by explicit polarization. For example, the free energy barrier for a phosphoryl dissociation reaction in acetone and cyclohexane is found to increase by more than 10 kcal/mol when switching the solvent model from an empirical to explicitly polarizable one. The reason for this is discussed based on the parametrization of empirical nonpolarizable models.
Role of plasma activation in kinetics of carbon nanotube growth in plasma-enhanced chemical vapor deposition
Authors: Lebedeva Irina V. , Knizhnik Andrey A. , Gavrikov Alexey V. , Baranov Alexey E. , Potapkin Boris V. , Smith David J. , Sommerer Timothy J.
Published: April 2012

The effect of the acceleration of carbon nanotube (CNT) growth from methane via modification of the gas composition with plasma discharge is studied by means of kinetic modeling. A model of CNT growth describing the detailed gas-phase and surface kinetics of hydrocarbons in catalytic chemical vapor deposition is used. It is shown that the effect of plasma is related to the formation of active species in the gas phase that can easily adsorb and dissociate on the catalyst surface. It is also demonstrated that in addition to the adsorption of carbon precursors, the CNT growth rate can be limited by the gas-phase diffusion of carbon species to the catalyst surface. The critical energy input above which the dominant contribution to CNT growth is provided by non-radical neutral species is calculated and confirmed by analytic estimates.
Positron annihilation studies of fluorine-vacancy complexes in Si and SiGe
Authors: Edwardson C. J. , Coleman P. G. , El Mubarek H. A. W. , Gandy A. S.
Published: April 2012

The formation of fluorine-vacancy (FV) complexes in strained Si-SiGe-Si multilayer structures and relaxed SiGe layers of varying Ge content has been investigated using variable-energy positron annihilation spectroscopy, including Doppler-broadened spectra ratio curves. It has been found that in all sample types there are two distinct regions defined only by the damage created by the implanted F ions. The first, shallower region (from the surface to a depth of ∼200 nm) was found to contain a mixture of undecorated vacancies and FV complexes; there is no correlation between the vacancy or F concentration in this region and the Ge content. The multi-layer samples may also have O contamination that is not present in the relaxed samples. The second region (at depths ∼200–440 nm) contains primarily FV complexes in all samples. In the multi-layer samples secondary ion mass spectrometry (SIMS) results show peaks of F accumulating in, or at the interfaces of, each SiGe multi-layer; the FV complexes, however, are distributed over depths similar to those in the relaxed samples, with some localization at the SiGe layer located within the second region. The positron response is primarily to FV complexes formed by the F implant in all samples. The F: FV ratios are approximately 3–7: 1 in the relaxed samples. Positrons appear to be relatively insensitive to the largest of the F SIMS peaks which lies beyond the second region. This is probably because the F has filled all the open volume at the SiGe layer, leaving no positron trapping sites.
High non-inductive fraction H-mode discharges generated by high-harmonic fast wave heating and current drive in the National Spherical Torus Experiment
Authors: Taylor G. , Hosea J. C. , Kessel C. E. , LeBlanc B. P. , Mueller D. , Phillips C. K. , Valeo E. J. , Wilson J. R. , Ryan P. M. , Bonoli P. T. , Wright J. C. , Harvey R. W.
Published: April 2012

A deuterium H-mode discharge with a plasma current of 300 kA, an axial toroidal magnetic field of 0.55 T, and a calculated non-inductive plasma current fraction of 0.7–1 has been generated in the National Spherical Torus Experiment by 1.4 MW of 30 MHz high-harmonic fast wave (HHFW) heating and current drive. Seventy-five percent of the non-inductive current was generated inside an internal transport barrier that formed at a normalized minor radius ∼0.4. Three quarters of the non-inductive current was bootstrap current, and the remaining non-inductive current was generated directly by HHFW power inside a normalized minor radius ∼0.2.
Nonlinear excitations in strongly coupled Fermi-Dirac plasmas
Authors: Akbari-Moghanjoughi M.
Published: April 2012

In this paper, we use the conventional quantum hydrodynamics (QHD) model in combination with the Sagdeev pseudopotential method to explore the effects of Thomas-Fermi nonuniform electron distribution, Coulomb interactions, electron exchange, and ion correlation on the large-amplitude nonlinear soliton dynamics in Fermi-Dirac plasmas. It is found that in the presence of strong interactions, significant differences in nonlinear wave dynamics of Fermi-Dirac plasmas in the two distinct regimes of nonrelativistic and relativistic degeneracies exist. Furthermore, it is remarked that first-order corrections due to such interactions (which are proportional to the fine-structure constant) are more significant on soliton characteristics (particularly the amplitude) in the nonrelativistic plasma degeneracy regime rather than the relativistic one. In the relativistic degeneracy regime, however, these effects become less important and the electron quantum-tunneling and Pauli-exclusion dominate the nonlinear wave dynamics. Hence, application of non-interacting Fermi-Dirac QHD model to study the nonlinear wave dynamics in quantum plasmas, such as in compact stars is most appropriate for the relativistic degeneracy regime rather than nonrelativistic one.
Experimental analysis and computer simulation of a methodology for laser focusing in the solar cell characterization by laser beam induced current
Authors: Navas J. , Alcántara R. , Fernández-Lorenzo C. , Martín-Calleja J.
Published: April 2012

This paper presents a quick methodology for focusing a laser beam on a photoactive surface based on performing a single line scan while simultaneously modifying the laser's position over the surface and the distance between the focusing lens and the active surface. The methodology was tested using the computer simulation technique. Several configurations were computer simulated by programming different experimental situations to discover the situations in which this focusing methodology would provide optimum results. The conclusions obtained from computer simulation methodology were checked by means of experimental tests using several solar cells, such as a thin-film amorphous silicon solar cell, a monocrystalline silicon solar cell, and a polycrystalline silicon solar cell. From the tests performed, we concluded that optimum focusing is achieved in systems in which the laser beam induced current signal generated by the photoactive surface has no large heterogeneities (e.g., fingers or grain boundaries), artefacts, or defects. Thus, the best results are achieved in systems where the surface of the photovoltaic device has a certain degree of homogeneity.
Restricted forms of quantum supergroups
Authors: Chen Jialei , Yang Shilin
Published: April 2012

Assume that q is a root of unity. In the present paper, finite dimensional quantum supergroups \documentclass[12pt]{minimal}\begin{document}$\mathcal {O}_q \left( {GL(m|n)} \right)^\prime$\end{document}OqGL(m|n)′ and \documentclass[12pt]{minimal}\begin{document}$\mathcal {O}_q \left( {SL(m|n)} \right)^\prime$\end{document}OqSL(m|n)′ are constructed. They can be viewed as restricted forms of quantum supergroups \documentclass[12pt]{minimal}\begin{document}$\mathcal {O}_q \left( {GL(m|n)} \right)$\end{document}OqGL(m|n) and \documentclass[12pt]{minimal}\begin{document}$\mathcal {O}_q \left( {SL(m|n)} \right)$\end{document}OqSL(m|n), which are Hopf superalgebras. The PBW (Poincaré-Birkhoff-Witt) bases for these supergroups are also established.
Interfacial oxide re-growth in thin film metal oxide III-V semiconductor systems
Authors: McDonnell S. , Dong H. , Hawkins J. M. , Brennan B. , Milojevic M. , Aguirre-Tostado F. S. , Zhernokletov D. M. , Hinkle C. L. , Kim J. , Wallace R. M.
Published: April 2012

The Al2O3/GaAs and HfO2/GaAs interfaces after atomic layer deposition are studied using in situ monochromatic x-ray photoelectron spectroscopy. Samples are deliberately exposed to atmospheric conditions and interfacial oxide re-growth is observed. The extent of this re-growth is found to depend on the dielectric material and the exposure temperature. Comparisons with previous studies show that ex situ characterization can result in misleading conclusions about the interface reactions occurring during the metal oxide deposition process.
Microstructure and magnetization reversal of L1-FePt/[Co/Pt]N exchange coupled composite films
Authors: Guo H. H. , Liao J. L. , Ma B. , Zhang Z. Z. , Jin Q. Y. , Wang H. , Wang J. P.
Published: April 2012

Two series of perpendicular exchange coupled composites (ECC) films are prepared by dc magnetron sputtering, FePt(5)/[Co(0.2)/Pt(0.3)]N (ECC-I-N) and FePt(5)/[Co(0.2)/Pt(0.6)]N (ECC-II-N), respectively. Structure analyses reveal the epitaxial growth on (001) oriented L10 FePt island-like grains of [Co/Pt]N with (200) orientation. Coercivity HC and remanent coercivity HCR of both series samples decrease sharply compared to FePt, with the increase of the thickness of [Co/Pt]N. The angular dependence of HCR shows excellent angular tolerance.
Physics of ultra-high bioproductivity in algal photobioreactors
Authors: Greenwald Efrat , Gordon Jeffrey M. , Zarmi Yair
Published: April 2012

Cultivating algae at high densities in thin photobioreactors engenders time scales for random cell motion that approach photosynthetic rate-limiting time scales. This synchronization allows bioproductivity above that achieved with conventional strategies. We show that a diffusion model for cell motion (1) accounts for high bioproductivity at irradiance values previously deemed restricted by photoinhibition, (2) predicts the existence of optimal culture densities and their dependence on irradiance, consistent with available data, (3) accounts for the observed degree to which mixing improves bioproductivity, and (4) provides an estimate of effective cell diffusion coefficients, in accord with independent hydrodynamic estimates.
Freestanding nanostructures for three-dimensional superconducting nanodevices
Authors: Cui Ajuan , Li Wuxia , Luo Qiang , Liu Zhe , Gu Changzhi
Published: April 2012

Free-space nanostructures are the fundamental building blocks of three-dimensional (3D) nanodevices with multi-functionality beyond that achievable by planar devices. Here we developed a reliable technique for the site-specific post-growth geometrical manipulation of freestanding superconducting nanowires using ion-beam irradiation with nanometer-scale resolution to fabricate uniformly shaped and sized clean-surface 3D nanostructures. Such structures could integrate with conventional superconducting quantum interference devices to detect magnetic fields both parallel and normal to the substrate. Property characterizations suggest that our focused-ion-beam technique allows tailoring of freestanding superconducting loops for size and geometry, potentially for lab-on-chip experiments.
A model for the bandgap energy of the N-rich GaNAs(0 ≤ x ≤ 0.07)
Authors: Zhao Chuan-Zhen , Li Na-Na , Wei Tong , Tang Chun-Xiao , Lu Ke-Qing
Published: April 2012

A model for the bandgap energy of the N-rich GaNAs is developed. We find that the evolution of the conduction band minimum and the valence band maximum in the N-rich GaNAs is due to two factors. One is intraband coupling within the conduction band and separately within the valence band. The other one is the As level. It can pin the valence band maximum near the As level when the As content is large enough. It is also found that the character of the As impurity band is similar to the P impurity band in the N-rich GaNP.
Simulating Demography and Housing Demand in an Urban Region under Scenarios of Growth and Shrinkage
Authors: Lauf Steffen , Haase Dagmar , Seppelt Ralf , Schwarz Nina
Published: April 2012

After the fall of the Berlin wall in 1989, demographic decline and urban shrinkage brought massive changes in the housing stock in East German cities. Urban planners and policy makers face complex problems caused by the resulting vacancies and demolitions and the handling of urban brownfields in the inner city. At the same time, cities are under ongoing pressure of suburbanisation. Because existing models focus mainly on demographic and urban growth and their impact on housing stocks, we present a simulation model that is able to compute both growth and shrinkage processes. We uncover nonlinear dynamics and feedbacks between demography, housing preference, and supply of housing space. The simulation results show that, despite population decline, the increasing number of single households leads to a growing total housing demand in the central parts of the study area. Beyond this area, residential vacancies in multistorey housing segments will remain regardless of population growth. At the same time, the simulations show that, despite population shrinkage and an overall oversupply of flats, there is a negative net demand for flats in affordable prefabricated housing estates as the percentage of low-income households increases. These findings will help planners modify or adapt their visions of the residential function in shrinking cities and to adjust current programmes of renewal and restructuring.
Attitudes to Urban Walking in Tehran
Authors: Moeini Seyed Mehdi
Published: April 2012

There is a growing interest in increasing walking in urban areas, partly to reduce pollution and other problems related to transportation by cars, and partly to improve public health (through reasonable exercise such as walking). In this study several factors that influence the amount of pedestrian movement in Tehran (Iran) are explored. Data were collected through questionnaires and interviews, and included sociodemographic indicators, people's perceptions of the neighborhoods where they live or work, and daily walking time in District 6 of the City of Tehran. The results of the study show that security, street connectivity, public health education, and sociodemographic indicators such as age and education influence pedestrian movement in residential areas. Local sociocultural behavior and indicators such as age and education were found to be the most influential in the commercial areas in the study. On the other hand, the respondents' behavior showed that there is a surprisingly low tendency in the City of Tehran to walk out of choice. Almost all pedestrian movement appears to be in response to a need or an obligation to walk, such as for business or essential shopping.
Slime Mold Cities
Authors: Barker David
Published: April 2012

Inspired by the behavior of slime mold cells, Paul Krugman developed a simple one-dimensional model in which moving firms self-organize into cities. In this paper I show that extending the model into two dimensions significantly improves its realism. Cities in the two-dimensional model are similar in several respects to real cities: they grow and decline, they cluster near rivers and coasts, and, given certain parameters, their distribution follows Zipf's law. A calibration exercise, however, suggests that observed levels of agglomeration must be due to factors beyond those included in the model.
GIS-Based Multicriteria Evaluation Approach for Corridor Siting
Authors: Aissi Hassène , Chakhar Salem , Mousseau Vincent
Published: April 2012

Siting a linear facility such as a highway or a pipeline often requires a preliminary study in which one or several corridors are identified. Here we construct corridors as a collection of adjacent polygons specifying a ‘path’ from origin s to destination t. Formally, we make use of a graph, called the connectivity graph, in which vertices correspond to polygons and edges to adjacent polygons. Within this formal representation, a corridor corresponds to an s to t path in the connectivity graph. The corridors are evaluated on two criteria: (1) a quantitative criterion measuring the length of the corridor, and (2) a qualitative criterion measuring the quality of the corridor with respect to the suitability of crossing its component polygons. We first introduce a three-phase approach based on a coupling between a geographical information system (GIS) and multicriteria evaluation and devoted to handling biobjective corridor siting problems. Then, the proposed approach is validated through an example of a real-world application.
From a Fossil-Fuel to a Biobased Economy: The Politics of Industrial Biotechnology
Authors: Richardson Ben
Published: April 2012

Industrial biotechnology involves the replacement of petrochemical processes and inputs with more energy-efficient and renewable biological ones. It is already being used in the production of biofuels and bioplastics and has been touted as a means by which modern economies can be shifted toward a more competitive, low-carbon growth model. This paper does two things. First, it outlines the policy framework established in the European Union and the narrative of a knowledge-based bioeconomy (KBBE) underpinning this. Second, it argues that the ‘win–win’ rhetoric contained within the KBBE narrative is misleading. Among the different groups commenting on the use of industrial biotechnology, the paper locates cleavages between farmers and agribusiness, between those convinced and those sceptical of environmental technofixes, and between procorporate and anti-corporate NGOs. Taken together, they show the purported transition from a fossil-fuel to a bio-based economy to be a resolutely political one.
The Impact of EU Structural Funds on Regional Disparities within Member States
Authors: Kyriacou Andreas P , Roca-Sagalés Oriol
Published: April 2012

We examine the impact of structural and cohesion funds on regional disparities within EU countries over the period 1995–2006. We find that structural funds have reduced regional disparities over this period. Our empirical estimates also suggest that the effect of structural funds on regional disparities is potentially reversed above some level of transfer intensity (approximately 1.6% of country gross domestic product). This has implications for the desirable allocation of the funds across countries especially since, in the current programming period (2007–13), all the new member states of the Union except for Cyprus and Malta have a transfer intensity which exceeds this threshold.
The Effect of the Notional Interest Deduction on the Capital Structure of Belgian SMEs
Authors: Kestens Katrien , Van Cauwenberge Philippe , Christiaens Johan
Published: April 2012

In 2005 the Belgian government introduced a radically new measure into the corporate tax system: the notional interest deduction. This feature allows Belgian companies to deduct a fictitious interest cost on equity from their tax base and tackles the classical tax discrimination between debt and equity financing. We investigate whether changes in the debt ratios of Belgian small and medium-sized enterprises reflect changes in tax incentives induced by the notional interest deduction, up to three years after its introduction. To measure the tax incentives of the notional interest deduction, we incorporate the notional interest deduction into a simulation procedure of marginal tax rates. We find that (1) the notional interest deduction caused a significant decline in the average simulated marginal tax rates and (2) the change in simulated marginal tax rates due to the introduction of the notional interest deduction is significant in explaining the change in debt ratios.
Fish Handling and Ultrasound Procedures for Viewing the Ovary of Submersed, Nonanesthetized, Unrestrained Channel Catfish
Authors: Guitreau Amy M , Eilts Bruce E , Novelo Noel D , Tiersch Terrence R
Published: April 2012

This study addressed the development of rapid, straightforward, and minimally stressful procedures for the ultrasound imaging of ovaries of channel catfish Ictalurus punctatus in a commercial hatchery setting. The objectives were to (1) describe the ultrasound imaging equipment and settings used, (2) describe the fish handling procedures during imaging, and (3) illustrate image orientation with respect to the physical positioning of the probe and the catfish. Ultrasound images of the ovaries of channel catfish were recorded as digital video recordings (audio video interleave format) and as still images (ultrasound image format files). This study integrated the use of nonanesthetized, submersed fish within a recirculating tank system or portable container and a submersed waterproof probe, which enabled us to use water as a transmission medium for ultrasound. This allowed us to image the fish in ventral recumbency (upright swimming position) without using a physical restraint in the tank system, or by positioning the fish in the portable container by adjusting the position of its caudal peduncle with one hand and that of the probe with the other hand. The ease of using this technique allows it to be employed as a systematic method for fish handling under laboratory and hatchery conditions. The detailed ultrasound imaging procedures and instrument control settings reported can be used in future testing, improvement, and standardization of procedures for viewing ovaries in channel catfish and potentially other species.
Impact of Isolation on Hospital Consumer Assessment of Healthcare Providers and Systems Scores: Is Isolation Isolating?
Authors: Vinski Joan , Bertin Mary , Sun Zhiyuan , Gordon Steven M. , Bokar Daniel , Merlino James , Fraser Thomas G.
Published: April 2012

The Hospital Consumer Assessment of Healthcare Providers and Systems (HCAHPS) survey was used to measure the effect of isolation on patient satisfaction. Isolated patients reported lower scores for questions regarding physician communication and staff responsiveness. Overall scores for these domains were lower in isolated than in nonisolated patients.
Bacterial Contamination of an Automated Pharmacy Robot Used for Intravenous Medication Preparation
Authors: Cluck David , Williamson John C. , Glasgo Marty , Diekema Daniel , Sherertz Robert
Published: April 2012

Multiple cultures were positive forBacillus cereusduring routine quality assurance testing of a pharmacy robot that prepares intravenous medications. An investigation confirmed bacterial contamination of the robot as well as drug product made by the robot. The process and outcomes of the investigation are described in this report.
Aeschynomene evenia, a Model Plant for Studying the Molecular Genetics of the Nod-Independent Rhizobium-Legume Symbiosis
Authors: Arrighi Jean-François , Cartieaux Fabienne , Brown Spencer C. , Rodier-Goud Marguerite , Boursot Marc , Fardoux Joel , Patrel Delphine , Gully Djamel , Fabre Sandrine , Chaintreuil Clémence , Giraud Eric
Published: April 2012

Research on the nitrogen-fixing symbiosis has been focused, thus far, on two model legumes, Medicago truncatula and Lotus japonicus, which use a sophisticated infection process involving infection thread formation. However, in 25% of the legumes, the bacterial entry occurs more simply in an intercellular fashion. Among them, some Aeschynomene spp. are nodulated by photosynthetic Bradyrhizobium spp. that do not produce Nod factors. This interaction is believed to represent a living testimony of the ancestral state of the rhizobium–legume symbiosis. To decipher the mechanisms of this Nod-independent process, we propose Aeschynomene evenia as a model legume because it presents all the characteristics required for genetic and molecular analysis. It is a short-perennial and autogamous species, with a diploid and relatively small genome (2n = 20; 460 Mb/1C). A. evenia ‘IRFL6945’ is nodulated by the well-characterized photosynthetic Bradyrhizobium sp. strain ORS278 and is efficiently transformed by Agrobacterium rhizogenes. Aeschynomene evenia is genetically homozygous but polymorphic accessions were found. A manual hybridization procedure has been set up, allowing directed crosses. Therefore, it should be relatively straightforward to unravel the molecular determinants of the Nod-independent process in A. evenia. This should shed new light on the evolution of rhizobium–legume symbiosis and could have important agronomic implications.
A photonic heterostructure produces diverse iridescent colours in duck wing patches
Authors: Eliason Chad M. , Shawkey Matthew D.
Published: April 2012

The colours of birds are diverse but limited relative to the colours they can perceive. This mismatch may be partially caused by the properties of their colour-production mechanisms. Aside from pigments, several classes of highly ordered nanostructures (thin films, amorphous three-dimensional arrays) can produce a range of colours. However, the variability of any single nanostructural class has rarely been explored. Dabbling ducks are a speciose clade with substantial interspecific variation in the iridescent coloration of their wing patches (specula). Here, we use electron microscopy, spectrophotometry, polarization and refractive index-matching experiments, and optical modelling to examine these colours. We show that, in all species examined, speculum colour is produced by a photonic heterostructure consisting of both a single thin-film of keratin and a two-dimensional hexagonal lattice of melanosomes in feather barbules. Although the range of possible variations of this heterostructure is theoretically broad, only relatively close-packed, energetically stable variants producing more saturated colours were observed, suggesting that ducks are either physically constrained to these configurations or are under selection for the colours that they produce. These data thus reveal a previously undescribed biophotonic structure and suggest that both physical variability and constraints within single nanostructural classes may help explain the broader patterns of colour across Aves.
Quantitative three-dimensional microtextural analyses of tooth wear as a tool for dietary discrimination in fishes
Authors: Purnell Mark , Seehausen Ole , Galis Frietson
Published: April 2012

Resource polymorphisms and competition for resources are significant factors in speciation. Many examples come from fishes, and cichlids are of particular importance because of their role as model organisms at the interface of ecology, development, genetics and evolution. However, analysis of trophic resource use in fishes can be difficult and time-consuming, and for fossil fish species it is particularly problematic. Here, we present evidence from cichlids that analysis of tooth microwear based on high-resolution (sub-micrometre scale) three-dimensional data and new ISO standards for quantification of surface textures provides a powerful tool for dietary discrimination and investigation of trophic resource exploitation. Our results suggest that three-dimensional approaches to analysis offer significant advantages over two-dimensional operator-scored methods of microwear analysis, including applicability to rough tooth surfaces that lack distinct scratches and pits. Tooth microwear textures develop over a longer period of time than is represented by stomach contents, and analyses based on textures are less prone to biases introduced by opportunistic feeding. They are more sensitive to subtle dietary differences than isotopic analysis. Quantitative textural analysis of tooth microwear has a useful role to play, complementing existing approaches, in trophic analysis of fishes—both extant and extinct.
Energetically optimal running requires torques about the centre of mass
Authors: Usherwood James R. , Hubel Tatjana Y.
Published: April 2012

Bipedal animals experience ground reaction forces (GRFs) that pass close to the centre of mass (CoM) throughout stance, first decelerating the body, then re-accelerating it during the second half of stance. This results in fluctuations in kinetic energy, requiring mechanical work from the muscles. However, here we show analytically that, in extreme cases (with a very large body pitch moment of inertia), continuous alignment of the GRF through the CoM requires greater mechanical work than a maintained vertical force; we show numerically that GRFs passing between CoM and vertical throughout stance are energetically favourable under realistic conditions; and demonstrate that the magnitude, if not the precise form, of actual CoM-torque profiles in running is broadly consistent with simple mechanical work minimization for humans with appropriate pitch moment of inertia. While the potential energetic savings of CoM-torque support strategies are small (a few per cent) over the range of human running, their importance increases dramatically at high speeds and stance angles. Fast, compliant runners or hoppers would benefit considerably from GRFs more vertical than the zero-CoM-torque strategy, especially with bodies of high pitch moment of inertia—suggesting a novel advantage to kangaroos of their peculiar long-head/long-tail structure.
Revisiting the rocking block: closed-form solutions and similarity laws
Authors: Dimitrakopoulos Elias G. , DeJong Matthew J.
Published: April 2012

In this paper, the dynamic response of the rocking block subjected to base excitation is revisited. The goal is to offer new closed-form solutions and original similarity laws that shed light on the fundamental aspects of the rocking block. The focus is on the transient dynamics of the rocking block under finite-duration excitations. An alternative way to describe the response of the rocking block, informative of the behaviour of rocking structures under excitations of different intensity, is offered. In the process, limitations of standard dimensional analysis, related to the orientations of the involved physical quantities, are revealed. The proposed dimensionless and orientationless groups condense the response and offer a lucid depiction of the rocking phenomenon. When expressed in the appropriate dimensionless–orientationless groups, the rocking response becomes perfectly self-similar for slender blocks (within the small rotations range) and practically self-similar for non-slender blocks (larger rotations). Using this formulation, the nonlinear and non-smooth rocking response to pulse-type ground motion can be directly determined, and need only be scaled by the intensity and frequency of the excitation.
Impaired immune evasion in HIV through intracellular delays and multiple infection of cells
Authors: Althaus Christian L. , De Boer Rob J.
Published: April 2012

With its high mutation rate, HIV is capable of escape from recognition, suppression and/or killing by CD8+cytotoxic T lymphocytes (CTLs). The rate at which escape variants replace each other can give insights into the selective pressure imposed by single CTL clones. We investigate the effects of specific characteristics of the HIV life cycle on the dynamics of immune escape. First, it has been found that cells in HIV-infected patients can carry multiple copies of proviruses. To investigate how this process affects the emergence of immune escape, we develop a mathematical model of HIV dynamics with multiple infections of cells. Increasing the frequency of multiple-infected cells delays the appearance of immune escape variants, slows down the rate at which they replace the wild-type variant and can even prevent escape variants from taking over the quasi-species. Second, we study the effect of the intracellular eclipse phase on the rate of escape and show that escape rates are expected to be slower than previously anticipated. In summary, slow escape rates do not necessarily imply inefficient CTL-mediated killing of HIV-infected cells, but are at least partly a result of the specific characteristics of the viral life cycle.