bluuebunny/crossref_metadata_2025 huggingface dataset:
Suspended sediment load, bed load, and dissolved load yields from a semiarid drainage basin: A 15‐year study
Authors: Alexandrov Yulia , Cohen Hai , Laronne Jonathan B. , Reid Ian
Published: August 2009

A 15‐year record for the semiarid upland Eshtemoa catchment provides a basis for estimating the efflux of water, sediment, and solutes in a type of environment for which there is a dearth of information. Average annual runoff was 5.4 mm, giving a runoff coefficient of 2.1%. Average annual yields were 275 Mg km−2 for suspended sediment, 15.3 Mg km−2 for bed load, and 0.6 Mg km−2 for dissolved load, though distinct seasonal differences are identified and related to the prevalence of cellular, convectively enhanced storms in autumn and spring and frontal storms in winter. The majority of the average annual total sediment and solute yield of 291 Mg km−2 is generated by as few as 8 of the 74 flow events of the 15‐year record. The relative importance of bed load and the consequent ranking of the load components as suspended load ≫ bed load ≫ dissolved load distinguishes this dryland environment from its humid counterparts.
Hyporheic flow and residence time distributions in heterogeneous cross‐bedded sediment
Authors: Sawyer Audrey Hucks , Cardenas M. Bayani
Published: August 2009

The permeability heterogeneity of cross‐bedded sediment increases path lengths of river‐groundwater mixing (hyporheic exchange) in riverbeds and modifies the distribution of residence times. For two case studies, we numerically simulated fluid flow and solute transport through immobile bed forms composed of heterogeneous sediment and equivalent homogeneous sediment in order to clarify how cross‐bedded permeability structures impact hyporheic exchange. The two permeability fields are from the cross‐bedded Massillon Sandstone and modern climbing ripple deposits of the Brazos River (Texas). In both cases, permeability heterogeneity creates long hyporheic exchange paths but only slightly increases the depth of exchange relative to equivalent homogeneous sediment. In the Massillon example, permeability heterogeneity increases the proportion of long hyporheic residence times (>3 days). In the Brazos example, permeability heterogeneity increases the proportion of short residence times (<17 h). We attribute the different responses in residence time distributions to differences in permeability patterns near the sediment‐water interface. The tails of residence time distributions extend for tens of years and conform to a power law in both heterogeneous and homogeneous sediment. Current–bed form interactions are responsible for the long tails, as opposed to permeability heterogeneity.
Geometry of the Trachyte Mesa intrusion, Henry Mountains, Utah: Implications for the emplacement of small melt volumes into the upper crust
Authors: Wetmore Paul H. , Connor Charles B. , Kruse Sarah E. , Callihan Sean , Pignotta Geoffrey , Stremtan Ciprian , Burke Andrea
Published: August 2009

The Trachyte Mesa intrusion is one of several small satellite bodies to the larger intrusions of the Henry Mountains, Utah. Most previous studies have worked under the assumptions that Trachyte Mesa is blister shaped and intruded into flat and gently NW dipping strata. In this study we combine structural and geophysical data sets to constrain the structural geology of the host lithologies and the unmodified geometry of the intrusion. Trachyte Mesa intrudes a series of northeast trending upright and open folds formed within the Jurassic Entrada Formation. Truncation of these folds at the contact with the overlying Curtis/Summerville formations indicates the folds are Middle Jurassic. Magnetic and 2‐D resistivity surveys focused on the southwestern portion of the intrusion where it is concealed by overlying strata. These data clearly delineate the outline of the buried intrusion. The intrusion is 2.2 km long and 0.7 km wide with an average thickness of ∼15 m (maximum ∼40 m). The majority of the intrusion (both exposed and buried portions) is confined within the axis of a syncline bound to the NW and SE by anticlines. The intrusion does, however, overtop the hinge of the bounding anticline to the northwest in a few places along its length. In cross section the intrusion is characterized by concave‐up top and bottom surfaces, except along portions where it overtops the bounding anticline. The geometry and structural position of the Trachyte Mesa intrusion suggest that preexisting structure and the density of the magma relative to that of host rocks fundamentally controlled the emplacement of this intrusion.
EMAG2: A 2–arc min resolution Earth Magnetic Anomaly Grid compiled from satellite, airborne, and marine magnetic measurements
Authors: Maus S. , Barckhausen U. , Berkenbosch H. , Bournas N. , Brozena J. , Childers V. , Dostaler F. , Fairhead J. D. , Finn C. , von Frese R. R. B. , Gaina C. , Golynsky S. , Kucks R. , Lühr H. , Milligan P. , Mogren S. , Müller R. D. , Olesen O. , Pilkington M. , Saltus R. , Schreckenberger B. , Thébault E. , Caratori Tontini F.
Published: August 2009

A global Earth Magnetic Anomaly Grid (EMAG2) has been compiled from satellite, ship, and airborne magnetic measurements. EMAG2 is a significant update of our previous candidate grid for the World Digital Magnetic Anomaly Map. The resolution has been improved from 3 arc min to 2 arc min, and the altitude has been reduced from 5 km to 4 km above the geoid. Additional grid and track line data have been included, both over land and the oceans. Wherever available, the original shipborne and airborne data were used instead of precompiled oceanic magnetic grids. Interpolation between sparse track lines in the oceans was improved by directional gridding and extrapolation, based on an oceanic crustal age model. The longest wavelengths (>330 km) were replaced with the latest CHAMP satellite magnetic field model MF6. EMAG2 is available at http://geomag.org/models/EMAG2 and for permanent archive at http://earthref.org/cgi-bin/er.cgi?s=erda.cgi?n=970.
Effects of planet curvature and crust on the shock pressure field around impact basins
Authors: Louzada Karin L. , Stewart Sarah T.
Published: August 2009

We investigate the effects of planetary curvature and the crust‐mantle boundary on the shock pressure field around impact basins on Mars using acoustic ray path calculations and hydrocode simulations. Planet curvature and, to a lesser extent, increasing sound speed with depth shallow the zone of wave interference, where shock pressures decay rapidly to the surface. The depth to the interference zone boundary diverges from the flat surface solution for projectile‐to‐Mars radius ratios greater than ∼1% (transient craters greater than ∼300 km); the difference increases with distance from the impact point and projectile size. In hydrocode simulations (but not the simple ray path model), the presence of the crust‐mantle boundary produces nearly vertical pressure contours in the crust. Around Hellas basin, demagnetization occurs at shock pressures between 1.1 (±0.2) and 3.4 (±0.7) GPa, where the range is due to the uncertainty in the transient crater diameter.
Isolation of the global MLT thermal response to recurrent geomagnetic activity
Authors: Chang Loren C. , Thayer Jeffrey P. , Lei Jiuhou , Palo Scott E.
Published: August 2009

Recurrent geomagnetic activity at multi‐day periodicities (near 5.5, 7 and 9 day subharmonics of solar rotation) have been associated with high speed solar wind stream variations and have recently been shown to induce congruent multi‐day periodic responses in the global upper atmosphere. The ability to relate these periodicities in geomagnetic activity to global temperature observations from the TIMED/SABER instrument enables isolation of the global thermal response in the lower thermosphere and mesosphere due to geomagnetic activity. Observations from the TIMED/SABER instrument at altitudes below 120 km clearly show a zonally symmetric (s = 0) modulation in the global temperature field at a 9‐day period known to result from recurrent geomagnetic activity forced by corotating interaction regions (CIRs). The temporal variation of this zonally symmetric 9‐day perturbation in temperature is strongly correlated to the 9‐day variations in the Kp geomagnetic activity index in 2005, with the most significant correlation occurring above 110 km and polewards of 40° latitude in both hemispheres. The temperature amplitude at the 9 day period is in excess of 10 K above 110 km and increasing in amplitude poleward of 40°. The phase of the temperature maximum associated with such disturbances is coherent with altitude and hemisphere, with the disturbance occurring first near 110 km and then peaking at altitudes above and below this region hours later.
High numbers of Trichodesmium and diazotrophic diatoms in the southwest Indian Ocean
Authors: Poulton Alex J. , Stinchcombe Mark C. , Quartly Graham D.
Published: August 2009

We observed high cell numbers of large (>50μm) nitrogen‐fixing phytoplankton to the south and east of Madagascar in February 2005. The distribution of the nitrogen‐fixing (diazotrophic) taxa found was markedly different: Trichodesmium was most abundant (500–1000 trichomes L−1) in the waters at the southern tip of Madagascar; while high numbers of diazotrophic diatoms (125–500 cells L−1) were limited to the southeast of Madagascar. Using literature values of nitrogen‐fixation per cell, we estimate potential rates of nitrogen‐fixation for Trichodesmium (south of Madagascar) of 1–5 mmol N m−2 d−1 and for diazotrophic diatoms (east of Madagascar) of 0.4–2.4 mmol N m−2 d−1. These cell‐based estimates highlight the potential for significant nitrogen‐fixation in the southwest Indian Ocean. High numbers of diazotrophic diatoms in subtropical waters to the east of Madagascar may have important implications for the biogeochemistry of the austral phytoplankton bloom in this region.
The Evolution Ontology
Authors: Goldstein Adam
Published: August 2009

Existing ontologies model components of evolution, but none synthesize them or describe the framework of ideas used to conceptualize evolution. The Evolution Ontology (EO) aims to do just this. EO models processes (e.g. natural selection); contexts (e.g. habitats); the entities that undergo evolution; and the theories, methods, and disciplines of evolutionary science. Uses include data curation, data mining, and literature curation, EO’s developers working on the latter two for works of Darwin and the Biodiversity Heritage Library.
Developing a Mammalian Behaviour Ontology
Authors: Beck Tim , Hancock John , Mallon Ann-Marie
Published: August 2009

The use of the Entity + Quality (EQ) model in phenotypic descriptions is dependent on the use of specialised domain ontologies to define the entity under observation. A domain currently lacking a specialised ontology is mammalian behaviour, and so the Mammalian Behaviour Ontology is being constructed to address this. Top-level class distinctions are made between behavioural activities and behavioural functions of individuals, and those between two or more individuals. The ontology is manually developed and encourages contributions from domain experts.
Annotation-based meta-analysis of microarray experiments
Authors: Zheng Jie , Liu Junmin , Manduchi Elisabetta , Stoeckert, Christian
Published: August 2009

We are developing software applications to perform meta-analysis of microarray experiments based on standardized experiment annotations aiming to identify similar experiments and cluster experiments. The applications were tested on files obtained from the ArrayExpress public repository. Annotation terms were used to compute experiment dissimilarities to find experiments related to a query experiment. These applications may motivate efforts of bench biologists to better annotate experiments.
Maternal Insulin Sensitivity During Pregnancy Predicts Infant Weight Gain and Adiposity at 1 Year of Age
Authors: Hamilton Jill K. , Odrobina Ewa , Yin Junlang , Hanley Anthony J. , Zinman Bernard , Retnakaran Ravi
Published: August 2009

Emerging evidence suggests that fetal environmental exposures impact on future development of obesity. The objectives of this study were to assess the relationships between (i) maternal insulin sensitivity and glucose tolerance status in pregnancy and (ii) early infant weight gain and adiposity in the first year of life. In this prospective cohort study, 301 women underwent oral glucose tolerance testing for assessment of glucose tolerance status and insulin sensitivity (ISOGTT) in pregnancy. Their infants underwent anthropometric assessment at 12 months of age, including determination of weight gain in the first year of life and sum of skinfold thickness (SFT), a measure of infant adiposity. Infant weight gain and sum of SFT at 12 months did not differ according to maternal glucose tolerance status. On univariate analyses, weight gain from 0 to 12 months and sum of SFT were negatively associated with maternal ISOGTT during pregnancy. On multiple linear regression analysis, negative independent predictors of weight gain from 0 to 12 months were maternal ISOGTT during pregnancy (t = −2.73; P = 0.007), infant female gender (t = −3.16; P = 0.002), and parental education (t = −1.98; P = 0.05), whereas white ethnicity was a positive independent predictor (t = 2.68; P = 0.008). Maternal ISOGTT (t = −2.7; P = 0.008) and parental education (t = −2.58; P = 0.01) were independent negative predictors of sum of SFT at 12 months. Independent of maternal glucose tolerance status, maternal insulin resistance during pregnancy is associated with increased infant weight gain and adiposity over the first year of life. Further longitudinal study to evaluate obesity in this group of children will increase our understanding of the contribution of the intrauterine environment to their long‐term health.
Effects of a School‐based Weight Maintenance Program for Mexican‐American Children: Results at 2 Years
Authors: Johnston Craig A. , Tyler Chermaine , McFarlin Brian K. , Poston Walker S.C. , Haddock C. Keith , Reeves Rebecca S. , Foreyt John P.
Published: August 2009

The prevalence of childhood overweight has increased significantly, with the highest rates noted among Mexican Americans. Many negative health outcomes are associated with overweight; thus, there is a need for effective weight‐loss interventions tailored to this group. This study evaluated 24‐month outcomes of a randomized, controlled trial involving an intensive lifestyle‐based weight maintenance program targeting overweight Mexican‐American children at a charter school in Houston, Texas. A total of 60 children (33 males, 55%) between the ages of 10 and 14 at or >85th percentile for BMI were recruited. Participants were randomized to an instructor‐led intervention (ILI) or a self‐help (SH) program, both aimed at modifying eating and physical activity behaviors using behavior modification strategies. Changes in participants' standardized BMI (zBMI) were assessed at baseline, 1, and 2 years. Tricep skinfold, total cholesterol, triglycerides, high‐density lipoprotein cholesterol, and calculated low‐density lipoprotein were assessed at baseline and 1 year. ILI participants showed significantly greater decreases in zBMI at 1 and 2 years (F = 26.8, P < 0.001, F = 4.1, P < 0.05, respectively) compared to SH controls. ILI participants showed greater improvements in body composition, as measured by tricep skinfold (F = 9.75, P < 0.01). Children in the ILI condition experienced benefits with respect to total cholesterol (F = 7.19, P < 0.05) and triglycerides (F = 4.35, P < 0.05) compared to children in the SH condition. Overall, the school‐based intervention resulted in improved weight and clinical outcomes in overweight Mexican‐American children, and zBMI was maintained over 2 years.
Characterization of β‐Cell Mass and Insulin Resistance in Diet‐induced Obese and Diet‐resistant Rats
Authors: Paulsen Sarah J. , Jelsing Jacob , Madsen Andreas N. , Hansen Gitte , Lykkegaard Kirsten , Larsen Leif K. , Larsen Philip J. , Levin Barry E. , Vrang Niels
Published: August 2009

The selectively bred diet‐induced obese (DIO) and diet‐resistant (DR) rats represent a polygenetic animal model mimicking most clinical variables characterizing the human metabolic syndrome. When fed a high‐energy (HE) diet DIO rats develop visceral obesity, dyslipidemia, hyperinsulinemia, and insulin resistance but never frank diabetes. To improve our understanding of the underlying cause for the deteriorating glucose and insulin parameters, we have investigated possible adaptive responses in DIO and DR rats at the level of the insulin‐producing β‐cells. At the time of weaning, DR rats were found to have a higher body weight and β‐cell mass compared to DIO rats, and elevated insulin and glucose responses to an oral glucose load. However, at 2.5 months of age, and for the remaining study period, the effect of genotype became evident: the chow‐fed DIO rats steadily increased their body weight and β‐cell mass, as well as insulin and glucose levels compared to the DR rats. HE feeding affected both DIO and DR rats leading to an increased body weight and an increased β‐cell mass. Interestingly, although the β‐cell mass in DR rats and chow‐fed DIO rats appeared to constantly increase with age, the β‐cell mass in the HE‐fed DIO rats did not continue to do so. This might constitute part of an explanation for their reduced glucose tolerance. Collectively, the data support the use of HE‐fed DIO rats as a model of human obesity and insulin resistance, and accentuate its relevance for studies examining the benefit of pharmaceutical compounds targeting this disease complex.
Interleukin‐1 β increases gap junctional communication among synovial fibroblasts via the extracellular‐signal‐regulated kinase pathway
Authors: Niger Corinne , Howell Floyd D. , Stains Joseph P.
Published: August 2009

Background information. The gap junction protein, Cx43 (connexin 43), has been implicated in the aetiology of osteoarthritis. Studies have revealed that the size and number of gap junctions increase in synovial biopsies from patients with osteoarthritis. Furthermore, pharmacological inhibition of Cx43 function has been shown to reduce IL‐1β (interleukin‐1β)‐induced metalloproteinase production by synovial fibroblasts in vitro.

Results. In the present study, we examined the link between IL‐1β and Cx43 function. We demonstrated that treatment of a rabbit synovial fibroblast cell line with IL‐1β markedly increased the level of the Cx43 protein in a concentration‐ and time‐dependent manner. The impact on Cx43 protein levels appeared to occur post‐transcriptionally, as mRNA levels are unaffected by IL‐1β administration. Additionally, we showed by fluorescence microscopy that IL‐1β alters the cellular distribution of Cx43 to cell–cell junctions and is concomitant with a striking increase in gap junction communication. Furthermore, we demonstrated that the increase in Cx43 protein, and the associated change in protein localization and gap junction communication following IL‐1β treatment, are dependent upon activation of the ERK (extracellular‐signal‐regulated kinase) signalling cascade.

Conclusion. These data show that IL‐1β acts through the ERK signalling cascade to alter the expression and function of Cx43 in synovial fibroblasts.
The C-terminal domain is sufficient for endonuclease activity of Neisseria gonorrhoeae MutL
Authors: Duppatla Viswanadham , Bodda Chiranjeevi , Urbanke Claus , Friedhoff Peter , Rao Desirazu N.
Published: August 2009

The mutL gene of Neisseria gonorrhoeae has been cloned and the gene product purified. We have found that the homodimeric N. gonorrhoeae MutL (NgoL) protein displays an endonuclease activity that incises covalently closed circular DNA in the presence of Mn2+, Mg2+ or Ca2+ ions, unlike human MutLα which shows endonuclease activity only in the presence of Mn2+. We report in the present paper that the C-terminal domain of N. gonorrhoeae MutL (NgoL-CTD) consisting of amino acids 460–658 exhibits Mn2+-dependent endonuclease activity. Sedimentation velocity, sedimentation equilibrium and dynamic light scattering experiments show NgoL-CTD to be a dimer. The probable endonucleolytic active site is localized to a metal-binding motif, DMHAX2EX4E, and the nicking endonuclease activity is dependent on the integrity of this motif. By in vitro comparison of wild-type and a mutant NgoL-CTD protein, we show that the latter protein exhibits highly reduced endonuclease activity. We therefore suggest that the mode of excision initiation in DNA mismatch repair may be different in organisms that lack MutH protein, but have MutL proteins that harbour the D[M/Q]HAX2EX4E motif.
A universal magnification theorem. II. Generic caustics up to codimension five
Authors: Aazami A. B. , Petters A. O.
Published: August 2009

We prove a theorem about magnification relations for all generic general caustic singularities up to codimension five: folds, cusps, swallowtail, elliptic umbilic, hyperbolic umbilic, butterfly, parabolic umbilic, wigwam, symbolic umbilic, second elliptic umbilic, and second hyperbolic umbilic. Specifically, we prove that for a generic family of general mappings between planes exhibiting any of these singularities, and for a point in the target lying anywhere in the region giving rise to the maximum number of real preimages (lensed images), the total signed magnification of the preimages will always sum to zero. The proof is algebraic in nature and makes repeated use of the Euler trace formula. We also prove a general algebraic result about polynomials, which we show yields an interesting corollary about Newton sums that in turn readily implies the Euler trace formula. The wide field imaging surveys slated to be conducted by the Large Synoptic Survey Telescope are expected to find observational evidence for many of these higher-order caustic singularities. Finally, since the results of the paper are for generic general mappings, not just generic lensing maps, the findings are expected to be applicable not only to gravitational lensing but also to any system in which these singularities appear.
Intracavity nonlinearities in quantum-cascade lasers
Authors: Bai Jing , Citrin D. S.
Published: August 2009

We discuss various intracavity optical nonlinearities up to the third order in quantum-cascade lasers. The discussions are based on two kinds of nonlinearities, each toward respective applications. The susceptibilities at the second-harmonic or third-harmonic frequencies lead to harmonic generation for multicolor emission; moreover, the third-order susceptibility at the fundamental frequency results in a nonlinear refractive index, i.e., the Kerr nonlinearity, which is associated with self-pulsations in quantum-cascade lasers. The review surveys the technology progression for the enhancement of nonlinear frequency generation as well as the investigation of the physics behind the multimode output of quantum-cascade lasers. In addition, a simulation model accounting for intracavity nonlinear interactions in quantum-cascade lasers is introduced, which can be used to evaluate and further optimize the nonlinear performance.
Alternative dust acoustic solitary waves in a plasma consisting of superthermal electrons and nonthermal ions having kappa-vortex-like velocity distribution function
Authors: Aoutou Kamel , Tribeche Mouloud , Zerguini Taha Houssine
Published: August 2009

The existence of arbitrary amplitude dust acoustic solitary waves is investigated in an unmagnetized dusty plasma comprising a negatively charged dust fluid, superthermal electrons, and nonthermal ions having a κ-vortex-like velocity distribution function. It is shown that due to electron and ion superthermality, the present dusty plasma model may support subsonic as well as supersonic electrostatic solitary waves involving cusped potential humps. The interplay between different concepts of nonisothermality is highlighted. Our results should help to understand the role that phase-space holes may play in reconnection by scattering and energizing particles and to provide an explanation of the intense solitary structures observed by the FAST mission.
Influence of N2 and NH3 annealing on the nitrogen incorporation and k-value of thin ZrO2 layers
Authors: Weinreich W. , Ignatova V. A. , Wilde L. , Teichert S. , Lemberger M. , Bauer A. J. , Reiche R. , Erben E. , Heitmann J. , Oberbeck L. , Schröder U.
Published: August 2009

The influence of the annealing atmosphere and temperature on the crystalline phase and composition of thin ZrO2 layers grown by atomic layer deposition on silicon is analyzed. These physical parameters are correlated with the electrical performance of ZrO2 in metal-insulator-semiconductor capacitor structures. For this study, 5.3 nm thick ZrO2 films were annealed at selected temperatures in the range of 400–900 °C in either nitrogen or ammonia atmospheres. As shown by grazing-incidence x-ray diffraction, the films start to crystallize at temperatures above 400 °C, resulting in a capacitance increase. An annealing in NH3 results in a higher capacitance increase than annealing in N2. Angular-resolved x-ray photoelectron spectroscopy and secondary ion mass spectrometry show no changes in the chemical composition of ZrO2 after annealing in N2. In contrast, a significant amount of nitrogen is incorporated into the ZrO2 film and at the ZrO2/Si interface during the temperature treatment in NH3, as also indicated by energy-filtered transmission electron microscopy.
High efficiency annular magnetically insulated line oscillator-transit time oscillator with three separate frequencies in three bands
Authors: Xiao Renzhen , Sun Jun , Chen Changhua , Zhang Yongpeng , Shao Hao
Published: August 2009

To increase the efficiency of the magnetically insulated line oscillator (MILO) and expand its frequency band, a coaxial transit time oscillator (TTO) is introduced to use the load currents of an annular MILO, called the annular MILO-TTO, which comprises an inward-emitting MILO, an outward-emitting MILO, and a coaxial TTO. In simulation, when the input power is 78 GW and the diode voltage is 520 kV, three microwaves with powers of 3.2, 9.6, and 7.0 GW are generated, with a total efficiency of 25.4%, in the inward-emitting MILO, the outward-emitting MILO, and the coaxial TTO, and the frequencies are 1.7, 3.3, and 4.2 GHz, corresponding to L, S, and C bands, respectively.
Cryogenic instrumentation for fast current measurement in a silicon single electron transistor
Authors: Ferrus T. , Hasko D. G. , Morrissey Q. R. , Burge S. R. , Freeman E. J. , French M. J. , Lam A. , Creswell L. , Collier R. J. , Williams D. A. , Briggs G. A. D.
Published: August 2009

We present a realization of high bandwidth instrumentation at cryogenic temperatures and for dilution refrigerator operation that possesses advantages over methods using radio frequency single electron transistor or transimpedance amplifiers. The ability for the low temperature electronics to carry out faster measurements than with room temperature electronics is investigated by the use of a phosphorous-doped single electron transistor. A single shot technique is successfully implemented and used to observe the real-time decay of a quantum state. A discussion on various measurement strategies is presented and the consequences on electron heating and noise are analyzed.
Designing the Fit City: Public Health, Active Lives, and the (re)Instrumentalization of Urban Space
Authors: Herrick Clare
Published: August 2009

The relationship between the built environment, physical activity, and well-being is currently attracting concerted government attention in the UK which has been formalized through new sets of urban planning and design guidelines. In light of this, the author argues that the domains of intersection between the physical environment and governmental health and social agendas need further exploration. Furthermore, she asserts that urban geographers are theoretically and empirically well placed to undertake valuable and much needed research agendas within these domains. To explore these assertions, the author first sets out the recent turn to physical activity as an explicit policy concern. She then critically interrogates two recent sets of design guidelines, Active Design (Sport England) and the 2008 NICE guidance within the context of current UK policy thinking, before exploring the problematic nature of the instrumental readings of space they present. It is argued that this instrumental rationale may sanction the neglect of the intrinsic value and importance of active lives themselves to urban spaces, which, it is asserted, can have marked impacts on well-being. An appreciation of this opens up new geographical research agendas with respect to the built form, public health, and governance.
A Sex Difference in Facial Contrast and its Exaggeration by Cosmetics
Authors: Russell Richard
Published: August 2009

This study demonstrates the existence of a sex difference in facial contrast. By measuring carefully controlled photographic images, female faces were shown to have greater luminance contrast between the eyes, lips, and the surrounding skin than did male faces. This sex difference in facial contrast was found to influence the perception of facial gender. An androgynous face can be made to appear female by increasing the facial contrast, or to appear male by decreasing the facial contrast. Application of cosmetics was found to consistently increase facial contrast. Female faces wearing cosmetics had greater facial contrast than the same faces not wearing cosmetics. Female facial beauty is known to be closely linked to sex differences, with femininity considered attractive. These results suggest that cosmetics may function in part by exaggerating a sexually dimorphic attribute—facial contrast—to make the face appear more feminine and hence attractive.
Origins of phase contrast in the atomic force microscope in liquids
Authors: Melcher John , Carrasco Carolina , Xu Xin , Carrascosa José L. , Gómez-Herrero Julio , José de Pablo Pedro , Raman Arvind
Published: August 2009

We study the physical origins of phase contrast in dynamic atomic force microscopy (dAFM) in liquids where low-stiffness microcantilever probes are often used for nanoscale imaging of soft biological samples with gentle forces. Under these conditions, we show that the phase contrast derives primarily from a unique energy flow channel that opens up in liquids due to the momentary excitation of higher eigenmodes. Contrary to the common assumption, phase-contrast images in liquids using soft microcantilevers are often maps of short-range conservative interactions, such as local elastic response, rather than tip-sample dissipation. The theory is used to demonstrate variations in local elasticity of purple membrane and bacteriophage ϕ29 virions in buffer solutions using the phase-contrast images.
Allogeneic mesenchymal stem cells restore cardiac function in chronic ischemic cardiomyopathy via trilineage differentiating capacity
Authors: Quevedo Henry C. , Hatzistergos Konstantinos E. , Oskouei Behzad N. , Feigenbaum Gary S. , Rodriguez Jose E. , Valdes David , Pattany Pradip M. , Zambrano Juan P. , Hu Qinghua , McNiece Ian , Heldman Alan W. , Hare Joshua M.
Published: August 2009

The mechanism(s) underlying cardiac reparative effects of bone marrow-derived mesenchymal stem cells (MSC) remain highly controversial. Here we tested the hypothesis that MSCs regenerate chronically infarcted myocardium through mechanisms comprising long-term engraftment and trilineage differentiation. Twelve weeks after myocardial infarction, female swine received catheter-based transendocardial injections of either placebo (
n
= 4) or male allogeneic MSCs (200 million;
n
= 6). Animals underwent serial cardiac magnetic resonance imaging, and in vivo cell fate was determined by co-localization of Y-chromosome (Y
pos
) cells with markers of cardiac, vascular muscle, and endothelial lineages. MSCs engrafted in infarct and border zones and differentiated into cardiomyocytes as ascertained by co-localization with GATA-4, Nkx2.5, and α-sarcomeric actin. In addition, Y
pos
MSCs exhibited vascular smooth muscle and endothelial cell differentiation, contributing to large and small vessel formation. Infarct size was reduced from 19.3 ± 1.7% to 13.9 ± 2.0% (
P
< 0.001), and ejection fraction (EF) increased from 35.0 ± 1.7% to 41.3 ± 2.7% (
P
< 0.05) in MSC but not placebo pigs over 12 weeks. This was accompanied by increases in regional contractility and myocardial blood flow (MBF), particularly in the infarct border zone. Importantly, MSC engraftment correlated with functional recovery in contractility (
R
= 0.85,
P
< 0.05) and MBF (
R
= 0.76,
P
< 0.01). Together these findings demonstrate long-term MSC survival, engraftment, and trilineage differentiation following transplantation into chronically scarred myocardium. MSCs are an adult stem cell with the capacity for cardiomyogenesis and vasculogenesis which contribute, at least in part, to their ability to repair chronically scarred myocardium.
Structural organization of box C/D RNA-guided RNA methyltransferase
Authors: Ye Keqiong , Jia Ru , Lin Jinzhong , Ju Minghua , Peng Jin , Xu Anbi , Zhang Liman
Published: August 2009

Box C/D guide RNAs are abundant noncoding RNAs that primarily function to direct the 2′-O-methylation of specific nucleotides by base-pairing with substrate RNAs. In archaea, a bipartite C/D RNA assembles with L7Ae, Nop5, and the methyltransferase fibrillarin into a modification enzyme with unique substrate specificity. Here, we determined the crystal structure of an archaeal C/D RNA–protein complex (RNP) composed of all 3 core proteins and an engineered half-guide RNA at 4 Å resolution, as well as 2 protein substructures at higher resolution. The RNP structure reveals that the C-terminal domains of Nop5 in the dimeric complex provide symmetric anchoring sites for 2 L7Ae-associated kink-turn motifs of the C/D RNA. A prominent protrusion in Nop5 seems to be important for guide RNA organization and function and for discriminating the structurally related U4 snRNA. Multiple conformations of the N-terminal domain of Nop5 and its associated fibrillarin in different structures indicate the inherent flexibility of the catalytic module, suggesting that a swinging motion of the catalytic module is part of the enzyme mechanism. We also built a model of a native C/D RNP with substrate and fibrillarin in an active conformation. Our results provide insight into the overall organization and mechanism of action of C/D RNA–guided RNA methyltransferases.
Peptides modulating conformational changes in secreted chaperones: From in silico design to preclinical proof of concept
Authors: Kliger Yossef , Levy Ofer , Oren Anat , Ashkenazy Haim , Tiran Zohar , Novik Amit , Rosenberg Avi , Amir Anat , Wool Assaf , Toporik Amir , Schreiber Ehud , Eshel Dani , Levine Zurit , Cohen Yossi , Nold-Petry Claudia , Dinarello Charles A. , Borukhov Itamar
Published: August 2009

Blocking conformational changes in biologically active proteins holds therapeutic promise. Inspired by the susceptibility of viral entry to inhibition by synthetic peptides that block the formation of helix–helix interactions in viral envelope proteins, we developed a computational approach for predicting interacting helices. Using this approach, which combines correlated mutations analysis and Fourier transform, we designed peptides that target gp96 and clusterin, 2 secreted chaperones known to shift between inactive and active conformations. In human blood mononuclear cells, the gp96-derived peptide inhibited the production of TNFα, IL-1β, IL-6, and IL-8 induced by endotoxin by >80%. When injected into mice, the peptide reduced circulating levels of endotoxin-induced TNFα, IL-6, and IFNγ by >50%. The clusterin-derived peptide arrested proliferation of several neoplastic cell lines, and significantly enhanced the cytostatic activity of taxol in vitro and in a xenograft model of lung cancer. Also, the predicted mode of action of the active peptides was experimentally verified. Both peptides bound to their parent proteins, and their biological activity was abolished in the presence of the peptides corresponding to the counterpart helices. These data demonstrate a previously uncharacterized method for rational design of protein antagonists.
Small-molecule inhibitors reveal multiple strategies for Hedgehog pathway blockade
Authors: Hyman Joel M. , Firestone Ari J. , Heine Vivi M. , Zhao Yun , Ocasio Cory A. , Han Kyuho , Sun Mark , Rack Paul G. , Sinha Surajit , Wu Jason J. , Solow-Cordero David E. , Jiang Jin , Rowitch David H. , Chen James K.
Published: August 2009

Inappropriate activation of the Hedgehog (Hh) signaling pathway has been implicated in a diverse spectrum of cancers, and its pharmacological blockade has emerged as an anti-tumor strategy. While nearly all known Hh pathway antagonists target the transmembrane protein Smoothened (Smo), small molecules that suppress downstream effectors could more comprehensively remediate Hh pathway-dependent tumors. We report here four Hh pathway antagonists that are epistatic to the nucleocytoplasmic regulator Suppressor of Fused [Su(fu)], including two that can inhibit Hh target gene expression induced by overexpression of the Gli transcription factors. Each inhibitor has a unique mechanism of action, and their phenotypes reveal that Gli processing, Gli activation, and primary cilia formation are pharmacologically targetable. We further establish the ability of certain compounds to block the proliferation of cerebellar granule neuron precursors expressing an oncogenic form of Smo, and we demonstrate that Hh pathway inhibitors can have tissue-specific activities. These antagonists therefore constitute a valuable set of chemical tools for interrogating downstream Hh signaling mechanisms and for developing chemotherapies against Hh pathway-related cancers.
Processing of grammatical gender in French as a first and second language: Evidence from ERPs
Authors: Frenck-Mestre Cheryl , Foucart Alice , Carrasco-Ortiz Haydee , Herschensohn Julia
Published: August 2009

The present study examined the processing of grammatical gender in second language (L2) French as a function of language background (Experiment 1) and as a function of overt phonetic properties of agreement (Experiment 2) by examining Event Related Potential (ERP) responses to gender discord in L2 French. In Experiment 1 we explored the role of the presence/absence of abstract grammatical gender in the L1 (gendered German, ungendered English): we compared German and English learners of French when processing post-nominal plural (no gender cues on determiner) attributive adjectives that either agreed in gender with the noun or presented a gender violation. We found grammaticalized responses (P600) by native and L1 English learners, but no response by German L1, a result we attribute to the possible influence of plurality, which is gender neutralized in German DP concord. In Experiment 2, we examined the role of overt phonetic cues to noun-adjective gender agreement in French, for both native speakers and Spanish L2 learners of French, finding that both natives and L2 learners showed a more robust P600 in the presence of phonetic cues. These data, in conjunction with those of other ERP studies can best be accounted for by a model that allows for native language influence, that is not, however constrained by age of acquisition, and that must also allow for clear cues in the input to influence acquisition and/or processing.
La lecture des mots translinguistiques en français L3
Authors: Nilsson Anna
Published: August 2009

Université, university, universitet, la lecture, a lecture « conférence », lektyr « lecture de détente », fromage de chèvre, citronfromage « mousse au citron »… Voici quelques mots qui paraissent translinguistiques aux yeux du lecteur trilingue suédois (L1), anglais (L2), français (L3). Le lecteur construit le sens à l’aide du contexte et de différentes connaissances linguistiques et encyclopédiques. Comprendre un texte ne va pas toujours de soi en langue première et le lecteur est souvent confronté à des mots ambigus comme les homographes. Selon l’hypothèse d’un accès lexical non sélectif, la lecture entraîne l’activation de plusieurs mots candidats, dans une, deux ou plusieurs langues selon les compétences du lecteur. Lire et comprendre dans une langue étrangère se présente alors comme un véritable tour de force.   Nous chercherons à déterminer dans quelle mesure des facteurs comme le milieu d’apprentissage ou la langue des consignes des tâches, sont décisifs pour l’activation des mots translinguistiques chez les lecteurs pour lesquels le français est une langue étrangère en cours d’acquisition (L3). Le traitement des similitudes interlexicales constitue une pratique récurrente qui est plus ou moins contrôlée par les lecteurs, apprenants du français L3.
Age effects on self-perceived communicative competence and language choice among adult multilinguals
Authors: Dewaele Jean-Marc
Published: August 2009

The present study focuses on the effects of age of acquisition (AoA) on dependent variables that have been traditionally overlooked in research on age effects: (1) self-perceived communicative competence in speaking, comprehending, reading and writing; (2) language choice for emotional speech in different situations; and (3) language choice for mental calculation and inner speech. We consider the effect of AoA on a large variety of L2s, L3s and L4s of 1,579 adult bi- and multilinguals. Data were collected through an on-line questionnaire (Dewaele and Pavlenko 2001–2003). Statistical analyses revealed very strong AoA effects on most of the dependent variables in the L2 and L3 of participants. However, these AoA effects were generally non-significant in their L4. The findings are discussed in relation to the current understanding of the research on age effects in Second Language Acquisition.
Immunization Programs for Infants, Children, Adolescents, and Adults: Clinical Practice Guidelines by the Infectious Diseases Society of America
Authors: Pickering Larry K. , Baker Carol J. , Freed Gary L. , Gall Stanley A. , Grogg Stanley E. , Poland Gregory A. , Rodewald Lance E. , Schaffner William , Stinchfield Patricia , Tan Litjen , Zimmerman Richard K. , Orenstein Walter A.
Published: August 2009

Evidence-based guidelines for immunization of infants, children, adolescents, and adults have been prepared by an Expert Panel of the Infectious Diseases Society of America (IDSA). These updated guidelines replace the previous immunization guidelines published in 2002. These guidelines are prepared for health care professionals who care for either immunocompetent or immunocompromised people of all ages. Since 2002, the capacity to prevent more infectious diseases has increased markedly for several reasons: new vaccines have been licensed (human papillomavirus vaccine; live, attenuated influenza vaccine; meningococcal conjugate vaccine; rotavirus vaccine; tetanus toxoid, reduced diphtheria toxoid, and acellular pertussis [Tdap] vaccine; and zoster vaccine), new combination vaccines have become available (measles, mumps, rubella and varicella vaccine; tetanus, diphtheria, and pertussis and inactivated polio vaccine; and tetanus, diphtheria, and pertussis and inactivated polio/Haemophilus influenzae type b vaccine), hepatitis A vaccines are now recommended universally for young children, influenza vaccines are recommended annually for all children aged 6 months through 18 years and for adults aged ⩾50 years, and a second dose of varicella vaccine has been added to the routine childhood and adolescent immunization schedule. Many of these changes have resulted in expansion of the adolescent and adult immunization schedules. In addition, increased emphasis has been placed on removing barriers to immunization, eliminating racial/ethnic disparities, addressing vaccine safety issues, financing recommended vaccines, and immunizing specific groups, including health care providers, immunocompromised people, pregnant women, international travelers, and internationally adopted children. This document includes 46 standards that, if followed, should lead to optimal disease prevention through vaccination in multiple population groups while maintaining high levels of safety.
Bacterial Sec Protein Transport Is Rate-limited by Precursor Length: A Single Turnover Study
Authors: Liang Fu-Cheng , Bageshwar Umesh K. , Musser Siegfried M.
Published: August 2009

An in vitro real-time single turnover assay for the Escherichia coli Sec transport system was developed based on fluorescence dequenching. This assay corrects for the fluorescence quenching that occurs when fluorescent precursor proteins are transported into the lumen of inverted membrane vesicles. We found that 1) the kinetics were well fit by a single exponential, even when the ATP concentration was rate-limiting; 2) ATP hydrolysis occurred during most of the observable reaction period; and 3) longer precursor proteins transported more slowly than shorter precursor proteins. If protein transport through the SecYEG pore is the rate-limiting step of transport, which seems likely, these conclusions argue against a model in which precursor movement through the SecYEG translocon is mechanically driven by a series of rate-limiting, discrete translocation steps that result from conformational cycling of the SecA ATPase. Instead, we propose that precursor movement results predominantly from Brownian motion and that the SecA ATPase regulates pore accessibility.
Udu Deficiency Activates DNA Damage Checkpoint
Authors: Lim Chiaw-Hwee , Chong Shang-Wei , Jiang Yun-Jin
Published: August 2009

Udu has been shown to play an essential role during blood cell development; however, its roles in other cellular processes remain largely unexplored. In addition, ugly duckling (udu) mutants exhibited somite and myotome boundary defects. Our fluorescence-activated cell sorting analysis also showed that the loss of udu function resulted in defective cell cycle progression and comet assay indicated the presence of increased DNA damage in udutu24mutants. We further showed that the extensive p53-dependent apoptosis in udutu24mutants is a consequence of activation in the Atm–Chk2 pathway. Udu seems not to be required for DNA repair, because both wild-type and udu embryos similarly respond to and recover from UV treatment. Yeast two-hybrid and coimmunoprecipitation data demonstrated that PAH-L repeats and SANT-L domain of Udu interacts with MCM3 and MCM4. Furthermore, Udu is colocalized with 5-bromo-2′-deoxyuridine and heterochromatin during DNA replication, suggesting a role in maintaining genome integrity.
Hierarchical Inactivation of a Synthetic Human Kinetochore by a Chromatin Modifier
Authors: Cardinale Stefano , Bergmann Jan H. , Kelly David , Nakano Megumi , Valdivia Manuel M. , Kimura Hiroshi , Masumoto Hiroshi , Larionov Vladimir , Earnshaw William C.
Published: August 2009

We previously used a human artificial chromosome (HAC) with a synthetic kinetochore that could be targeted with chromatin modifiers fused to tetracycline repressor to show that targeting of the transcriptional repressor tTS within kinetochore chromatin disrupts kinetochore structure and function. Here we show that the transcriptional corepressor KAP1, a downstream effector of the tTS, can also inactivate the kinetochore. The disruption of kinetochore structure by KAP1 subdomains does not simply result from loss of centromeric CENP-A nucleosomes. Instead it reflects a hierarchical disruption of the outer kinetochore, with CENP-C levels falling before CENP-A levels and, in certain instances, CENP-H being lost more readily than CENP-C. These results suggest that this novel approach to kinetochore dissection may reveal new patterns of protein interactions within the kinetochore.