bluuebunny/crossref_metadata_2025 huggingface dataset:
Small is beautiful: Upscaling from microscale laminar to natural turbulent rivers
Authors: Malverti L. , Lajeunesse E. , Métivier F.
Published: October 2008

The use of microscale experimental rivers (with flow depths of the order of a few millimeters) to investigate natural processes such as alluvial fans dynamics, knickpoints migration, and channel morphologies, such as meandering and braiding has become increasingly popular in recent years. This raises the need to address the issue of how to extrapolate results from the experimental microscale at which flow is laminar to the scale of natural turbulent rivers. We address this question by performing measurements of average flow velocity and sediment transport in an experimental laminar river. The average flow velocity is correctly predicted from the Navier‐Stokes equation solved for a steady uniform laminar flow. Laminar sediment transport is found to be consistent with the law of Meyer‐Peter and Müller (1948) commonly used to describe sediment transport in natural turbulent rivers. We also show that surface tension is important only if the microscale river width is on the order of or smaller than the capillary length. These results allow us to demonstrate that the evolution of longitudinal bed profiles of turbulent and laminar rivers are governed by identical dimensionless equations and therefore follow the same dynamics. Differences of time and length scales at work in experimental and natural rivers are mainly encoded in the expression of two parameters, a diffusion coefficient and a threshold slope. On the basis of this analysis, we derive a set of equations allowing us to rescale bed elevation, downstream distance, time, and uplift rate from an experimental microscale river to the field scale. Finally, we show how this set of equations can be used to rescale these same parameters in the case of a temporally varying discharge.
Quantitative phenological observations of a mixed beech forest in northern Switzerland with digital photography
Authors: Ahrends Hella Ellen , Brügger Robert , Stöckli Reto , Schenk Jürg , Michna Pavel , Jeanneret Francois , Wanner Heinz , Eugster Werner
Published: October 2008

Vegetation phenology has a strong influence on the timing and phase of global terrestrial carbon and water exchanges and is an important indicator of climate change and variability. In this study we tested the application of inexpensive digital visible‐light cameras in monitoring phenology. A standard digital camera was mounted on a 45 m tall flux tower at the Lägeren FLUXNET/CarboEuropeIP site (Switzerland), providing hourly images of a mixed beech forest. Image analysis was conducted separately on a set of regions of interest representing two different tree species during spring in 2005 and 2006. We estimated the date of leaf emergence based on the levels of the extracted red, green and blue colors. Comparisons with validation data were in accordance with the phenology of the observed trees. The mean error of observed leaf unfolding dates compared with validation data was 3 days in 2005 and 3.6 days in 2006. An uncertainty analysis was performed and demonstrated moderate impacts on color values of changing illumination conditions due to clouds and illumination angles. We conclude that digital visible‐light cameras could provide inexpensive, spatially representative and objective information with the required temporal resolution for phenological studies.
An efficient near‐optimal approach to incoherent scatter radar parameter estimation
Authors: Nikoukar Romina , Kamalabadi Farzad , Kudeki Erhan , Sulzer Michael
Published: October 2008

We present a computationally efficient, near‐optimal approach to the estimation of ionospheric parameters from incoherent scatter radar measurements. The method consists of removing the range smearing of ionospheric autocorrelation function via a set of 1‐D deconvolutions and performing nonlinear least squares fitting on the deconvolved autocorrelation functions. To stabilize the solution in the presence of noise, we incorporate regularization techniques. The computational cost is reduced significantly by estimating the ionospheric parameters at individual altitudes, in comparison to full‐profile‐type analysis, which attempts to estimate ionospheric parameters at all altitudes simultaneously. The performance of the new technique is evaluated in a numerical example and is shown to give estimates of almost equal quality as the full‐profile technique but at a 95% reduction in computation.
Strong along‐arc variations in attenuation in the mantle wedge beneath Costa Rica and Nicaragua
Authors: Rychert C. A. , Fischer K. M. , Abers G. A. , Plank T. , Syracuse E. , Protti J. M. , Gonzalez V. , Strauch W.
Published: October 2008

Attenuation structure in the Central American subduction zone was imaged using local events recorded by the Tomography Under Costa Rica and Nicaragua array, a 20‐month‐long deployment (July 2004 until March 2006) of 48 seismometers that spanned the fore‐arc, arc, and back‐arc regions of Nicaragua and Costa Rica. P and S waveforms were inverted separately for the corner frequency and moment of each event and for the path‐averaged attenuation operator (t*) of each event‐station pair, assuming attenuation is slightly frequency‐dependent (∝ = 0.27). Then, tomographic inversions were performed for S and P attenuation (QS−1 and QP−1). Since P wave amplitudes reflect both shear and the bulk moduli, tomographic inversions were also performed to determine shear and bulk attenuation (QS−1 and Qκ−1), the loss of energy per cycle owing to shearing and uniform compression, respectively. Damping and other inversion tomographic parameters were systematically varied. As is typical in subduction zone attenuation studies, a less attenuating slab, upper plate, and wedge corner and a more attenuating mantle wedge were imaged. In addition, first‐order differences between the mantles beneath Nicaragua and Costa Rica were observed. The slab in Nicaragua is more attenuating than the slab in Costa Rica. A larger zone of higher shear attenuation also characterizes the Nicaraguan mantle wedge. Within the wedge, maximum attenuation values at 1 Hz correspond to Qs = 38–73 beneath Nicaragua and Qs = 62–84 beneath Costa Rica, and average values are Qs = 76–78 and Qs = 84–88, respectively. Attenuation variations correlate with along‐arc trends in geochemical indicators that suggest that melting beneath Nicaragua occurs at more hydrated conditions, and possibly to greater extents and depths, relative to northern Costa Rica. Shear attenuation dominates over bulk attenuation in the well‐resolved regions of the wedge. The more extensive zones of greater shear attenuation observed in the Nicaraguan wedge could be explained by higher temperatures and/or greater hydration, but comparison with petrological data suggests that hydration variations play a larger role. Average wedge attenuation values are comparable to estimates for the Andes and Japan, greater than those for Alaska, and less than those for Tonga‐Lau.
Seismic imaging of a possible paleoarc in the Izu‐Bonin intraoceanic arc and its implications for arc evolution processes
Authors: Kodaira Shuichi , Sato Takeshi , Takahashi Narumi , Yamashita Mikiya , No Tetsuo , Kaneda Yoshiyuki
Published: October 2008

Crustal evolution processes in intraoceanic arcs, including crustal accretion and rifting, have been long discussed. To examine crustal evolution in the Izu‐Bonin intraoceanic island arc, we conducted an active‐source wide‐angle seismic study along a north‐south profile (500 km long) within a possible paleoarc in the rear arc (i.e., the Nishi‐shichito ridge) about 150 km west of the present‐day volcanic front. In this study, the seismic velocity and reflectivity images are obtained using the wide‐angle seismic data. For the seismic velocity imaging, we applied refraction tomography in which 93,535 picks were used. The overall root‐mean‐square (rms) misfit calculated from the initial model of the refraction tomography was 483.1 ms, and those calculated from the final model were reduced to 66.7 ms. The resultant seismic image shows marked variations of crustal thickness along the seismic profile: thin crust (10–15 km thick) in the northern part, three discrete thick crustal segments (20–25 km thick) in the central part, and a moderately thick crust (∼15 km thick) in the southern part. These variations are mainly attributed to thickness variations of the middle crust having seismic velocity of 6.0–6.8 km/s. This variation of crustal thickness does not correlate with seafloor topography, which is characterized by post‐Miocene across‐arc seamount chains. It does correlate well with crustal variations observed along the present‐day volcanic front of the Izu‐Bonin arc. These findings suggest that the magmatic activity that created the across‐arc seamount chains had little effect on the rear‐arc crust and that the main part of the rear‐arc crust was created before the rear arc separated from the volcanic front. By correlating the structural variations along the rear arc (i.e., the variation of the average seismic velocity as well as the thickness of the middle crust) and those along the present‐day volcanic front, we found that the direction of rifting to separate the rear arc (paleoarc) from the present‐day volcanic front was north‐northeast.
Impacts of the fall 2007 California wildfires on surface ozone: Integrating local observations with global model simulations
Authors: Pfister G. G. , Wiedinmyer C. , Emmons L. K.
Published: October 2008

This study quantifies the impact of the fires in California in fall 2007 on regional air quality and especially on surface ozone by analyzing surface observations of ozone concentrations together with global chemistry transport model simulations. The latter include a synthetic tracer providing information about the amount of ozone produced from the fires. It is shown that the global model is well suited for simulating the overall fire impact and a valuable tool for extracting information about the fire influence from the observations. A clear increase in observed ozone is found when the model predicts a strong impact of pollution from the fires, where measured afternoon 8‐hour concentrations increased, on average, by about 10 ppb. The findings demonstrate that intense wildfire periods can significantly increase the frequency of ozone concentrations exceeding current U.S. health standards, and might cause violations also during photochemically less active seasons. The study also demonstrates the far‐reaching impact of ozone production from the fires.
Properties of the termination shock observed by Voyager 2
Authors: Li H. , Wang C. , Richardson J. D.
Published: October 2008

In August 2007, Voyager 2 reached the termination shock and entered the heliosheath at a distance of about 83.6 AU. Due to the variations of the solar wind dynamic pressure or waves on the shock front, the termination shock moved back and forth, and Voyager 2 crossed the termination shock multiple times. We use the best fit solution of the Monte‐Carlo method to define the upstream and downstream conditions and determine the properties of termination shock, such as the shock normal, speed, and strength. For the crossings on DOY 243.819‐243.875(shock 1) and DOY 243.99‐244.012(shock 2), the termination shock moved almost in the radial direction. The shock is nearly perpendicular, and the angle between the shock normal and the solar wind magnetic field is about 70°. In the case of the first crossing, the termination shock moved away from the Sun with a speed of about 100 km s−1, whereas the termination shock moved toward Sun with a speed of about 30 km s−1 for the second crossing. The density ratios of the termination shock are 2.2 and 1.6, respectively. For both crossing events, the flow is found to be still supersonic with respect to the thermal ions downstream of the termination shock, probably due to the fact that most of the solar wind energy is transferred to the pickup ions.
What do deep sea pressure fluctuations tell about short surface waves?
Authors: Farrell W. E. , Munk Walter
Published: October 2008

Short waves centered at the gravity to capillary transition (13.5 Hz) dominate the slope statistics of the sea surface and are responsible for most of the air‐sea momentum transfer (wind stress). Little is known about short “gravities.” In contrast, long gravities, with their characteristic κ−4 spectrum, have extensive observational support. We propose a fundamental distinction between long gravities, with their saturated (wind‐independent) spectrum, and short gravities, with their wind‐dependent spectrum. Evidence comes (surprisingly) from sea‐floor pressure fluctuations associated with non‐linear interactions between oppositely traveling surface waves of half their frequency. The bottom pressure spectrum shows a transition at about 6 Hz (3 Hz surface wave frequency) from an f−7 to an f−3 dependence that we associate with the long to short surface gravity wave transition. Further, the requirement of oppositely traveling energy places an integral restraint on the directional spread of the surface waves.
Effects of hydrophobic layers on evaporation from porous media
Authors: Shokri N. , Lehmann P. , Or D.
Published: October 2008

Early stages of evaporation from initially‐saturated porous media are marked by relatively high and constant evaporation rate (“stage 1”) supplied by capillary flow from the receding drying front to evaporating surface. At a characteristic front depth defined by pore size distribution, gravity exceeds capillary‐drive and interrupts liquid flow. Subsequently, evaporation falls to rates supported by vapor diffusion (“stage 2”). We investigated the role of thin hydrophobic layers on liquid phase continuity and on evaporative losses. Results confirm interruption of capillary flow by hydrophobic layers and overall reduction in evaporation mass loss. Persistence of capillary flow to the bottom of hydrophobic layer was evident by accumulation of dye tracer indicating formation of vaporization plane. Dye was not deposited on hydrophobic surfaces due to contact line configuration that promote evaporation away from pore walls. Evaporation flux across the hydrophobic layer was purely diffusive and proportional to diffusion length to the surface.
Pre‐existing caverns in salt formations could be the major cause of sinkhole hazards along the coast of the Dead Sea
Authors: Legchenko A. , Ezersky M. , Boucher M. , Camerlynck C. , Al‐Zoubi A. , Chalikakis K.
Published: October 2008

Since 1990 hundreds of sinkholes have appeared along the coast of the Dead Sea. In the literature the rapid development of sinkholes is explained as a result of a drop in the level of the Dead Sea. This model assumes very fast dissolution of large volumes of salt and the creation of new caverns that cause sinkholes in 10 to 20 years. However, the results of our geophysical study do not confirm the fast dissolution assumption. To explain the available field observations, we propose the following model: (1) slow dissolution of salt (much longer than 20 years) with the creation of caverns without development of sinkholes; (2) sinkhole development is triggered by the lowering of the groundwater level because the rocks overlying the salt formation become unsaturated; (3) the time of sinkhole appearance is controlled by the mechanical properties of the rocks that overlie pre‐existing caverns.
Abnormal vertical drifts of equatorial plasma before dawn and after sunset during the storm of 29–30 October 2003
Authors: Kil Hyosub , Oh Seung‐Jun , Paxton Larry J.
Published: October 2008

The ROCSAT‐1 observations of vertical ion velocity in low latitudes during the main phase of the storm of 29–30 October 2003 show an occurrence of abnormally large downward plasma drift before dawn and pronounced upward drift after sunset. At the time of the occurrence of the abnormal vertical plasma drifts at the terminators the background ionosphere shows an upward drift during 0800‐2000 LT and downward drift during 2000‐0800 LT. The global‐scale change in the vertical plasma drifts and its coincidence with the onset of dawn‐to‐dusk interplanetary electric field indicate that the disturbance drifts are associated with the penetration electric field (PE). The nightward PE at the terminators induces an accumulation of positive charges at the terminators; polarization electric fields develop by the charge accumulation; and the addition of the PE and polarization electric field can produce pronounced downward drift before dawn and upward drift after sunset.
Fewer jumps, less memory: Homogenized temperature records and long memory
Authors: Rust H. W. , Mestre O. , Venema V. K. C.
Published: October 2008

Air temperature records are commonly subjected to inhomogeneities, e.g., sudden jumps caused by a relocation of the measurement station or by installing a new type of shelter. We study the effect of these inhomogeneities on the estimation of the Hurst exponent and show that they bias the estimates toward larger values. The Hurst exponent is a parameter to measure long‐range dependence (LRD), which is a characteristic frequently used to describe the natural variability of temperature records. Analyzing a set of temperature time series before and after homogenization with respect to LRD, we find that the average Hurst exponent is clearly reduced for the homogenized series. To test whether (1) jumps cause this positive bias and (2) the homogenization does not artificially reduce the Hurst exponent estimates, we perform a simulation study. This test shows that inhomogeneities in the form of jumps bias the Hurst exponent estimation and that the homogenization procedure is able to remove this bias, leaving the Hurst exponent unchanged. This result holds for fractional autoregressive integrated moving average (FARIMA)‐based as well as for detrended fluctuation analysis‐based estimation. We conclude that the use of homogenized series is necessary to prevent misleading conclusions about the dependence structure and thus about subsequent analysis such as trend tests.
Structural control on late Miocene to Quaternary volcanism in the NE Honshu arc, Japan
Authors: Acocella Valerio , Yoshida Takeyoshi , Yamada Ryoichi , Funiciello Francesca
Published: October 2008

Volcanological and structural field data are used to define the tectonic control on the N–S volcanic arc of NE Honshu (Japan) since late Miocene. During late Miocene‐Pliocene, bimodal products were mainly erupted from along‐arc and NE–SW‐aligned and elongated calderas. The deformation pattern mostly consisted of N–S dextral faults and subordinate NE–SW extensional structures produced by NE–SW compression. This pattern, because of the indentation of the Kuril sliver, is similar to that of oblique convergence settings. Magma rose and extruded along NE–SW areas of localized extension created by the dextral faults. These extensional areas were uncoupled with regard to those, ∼E–W trending, inferred to have focused the rise of melts from the subducting slab in the mantle. During Quaternary, a larger amount of andesite was mainly erupted from along‐arc and ∼E–W‐aligned and elongated stratovolcanoes. The deformation pattern mostly consisted of N–S thrust faults and subordinate ∼E–W extensional structures, produced by ∼E–W compression, resulting from orthogonal convergence due to the variation in the absolute motion of the Pacific Plate. The ∼E–W extensional structures are the shallowest expression of ∼E–W‐trending hot mantle fingers, suggesting mantle‐crust coupling for the rise of magma. Such a coupling ensures (1) higher extrusion and (2) mixing between a deeper mafic and a shallower felsic magma, generating the andesites. The significantly larger volumes (Ma−1 200 km−1 of length of the arc) of magma erupted during Quaternary show that pure convergence conditions do not necessarily hinder the rise and extrusion of magma.
Peroxynitrite decreases arrhythmias induced by ischaemia reperfusion in anaesthetized dogs, without involving mitochondrial KATP channels
Authors: Kiss A , Juhász L , Huliák I , Végh Á
Published: October 2008

Background and purpose:

Exogenous peroxynitrite from nanomolar to micromolar concentrations exerts cardioprotection. Here, we have assessed its effects on ischaemia‐ and reperfusion‐induced ventricular arrhythmias in vivo and a possible role for mitochondrial KATP channels in these effects, using the channel inhibitor 5‐hydroxydecanoate (5‐HD).

Experimental approach:

Chloralose‐urethane‐anaesthetized dogs were treated twice for 5 min with peroxynitrite (100 nM, by intracoronary infusions) in both the absence and presence of 5‐HD (150 μg kg−1 min−1), and then subjected to 25 min occlusion of the left anterior descending coronary artery. The severity of ischaemia and of arrhythmias, as well as the levels of nitrotyrosine were assessed and compared with a group of control dogs, subjected only to a 25 min occlusion and reperfusion insult.

Key results:

Compared with controls, infusion of peroxynitrite markedly suppressed the number of ventricular premature beats (388±88 vs 133±44), the incidence of ventricular fibrillation both during occlusion (50% vs 10%) and reperfusion (100% vs 44%), and increased survival (0% vs 50%; all P<0.05). The severity of ischaemia (epicardial ST‐segment changes, inhomogeneity of electrical activation) during occlusion and nitrotyrosine levels on reperfusion were significantly less in the peroxynitrite‐treated dogs than in the controls. 5‐HD did not modify the cardioprotective effects of peroxynitrite.

Conclusion and implications:

Exogenous peroxynitrite provided antiarrhythmic protection in vivo, which might have been on account of a reduction in endogenous peroxynitrite formation. This protection seemed not to be mediated through mitoKATP channels.

British Journal of Pharmacology (2008) 155, 1015–1024; doi:fn1; published online 1 September 2008
Obesity Upregulates Genes Involved in Oxidative Phosphorylation in Livers of Diabetic Patients
Authors: Takamura Toshinari , Misu Hirofumi , Matsuzawa‐Nagata Naoto , Sakurai Masaru , Ota Tsuguhito , Shimizu Akiko , Kurita Seiichiro , Takeshita Yumie , Ando Hitoshi , Honda Masao , Kaneko Shuichi
Published: October 2008

Obesity is a major cause of insulin resistance and contributes to the development of type 2 diabetes. The altered expression of genes involved in mitochondrial oxidative phosphorylation (OXPHOS) has been regarded as a key change in insulin‐sensitive organs of patients with type 2 diabetes. This study explores possible molecular signatures of obesity and examines the clinical significance of OXPHOS gene expression in the livers of patients with type 2 diabetes. We analyzed gene expression in the livers of 21 patients with type 2 diabetes (10 obese and 11 nonobese patients; age, 53.0 ± 2.1 years; BMI, 24.4 ± 0.9 kg/m2; fasting plasma glucose, 143.0 ± 10.6 mg/dl) using a DNA chip. We screened 535 human pathways and extracted those metabolic pathways significantly altered by obesity. Genes involved in the OXPHOS pathway, together with glucose and lipid metabolism pathways, were coordinately upregulated in the liver in association with obesity. The mean centroid of OXPHOS gene expression was significantly correlated with insulin resistance indices and the hepatic expression of genes involved in gluconeogenesis, reactive oxygen species (ROS) generation, and transcriptional factors and nuclear co‐activators associated with energy homeostasis. In conclusion, obesity may affect the pathophysiology of type 2 diabetes by upregulating genes involved in OXPHOS in association with insulin resistance markers and the expression of genes involved in hepatic gluconeogenesis and ROS generation.
No Association of PTPN1 Polymorphisms With Macronutrient Intake and Measures of Adiposity
Authors: Bauer Florianne , Onland‐Moret N. Charlotte , Niehoff Anne G. , Elbers Clara C. , Grobbee Diederick E. , Wijmenga Cisca , van der Schouw Yvonne T.
Published: October 2008

The protein tyrosine phosphatase nonreceptor type1 (PTPN1) gene encodes for the protein tyrosine phosphatase 1B, which suppresses the signaling pathway of leptin. Variations of the PTPN1 gene may lead to changes in leptin sensitivity and thereby influence eating behavior and measures of obesity. This study investigated the association between single‐nucleotide polymorphisms (SNPs) of the PTPN1 gene and eating behavior and different measures of obesity, including visceral fat. We used data from a population‐based, cross‐sectional study of 382 Dutch white men aged 40–80 years. Self‐reported macronutrient intake was collected with a food frequency questionnaire. Anthropometrical measurements included BMI, waist and hip circumference, total lean and fat mass measured with dual‐energy X‐ray absorptiometry, and visceral and subcutaneous fat measured with ultrasound. Associations were studied using linear regression analysis. There were no statistically significant associations of SNPs in the PTPN1 gene with dietary phenotypes or measures of obesity.
Confirming a Biological Pathway in the Metabolic Syndrome—Insight from the NHANES 1999–2002
Authors: Lin Lian‐Yu , Kuo Hsu‐Ko , Li Hung‐Yuan , Hwang Juey‐Jen , Lin Jou‐Wei
Published: October 2008

The objective of this study was to examine the role of obesity in the development of the metabolic syndrome (MS). A total of 3,596 whites aged 19 years and above, who participated in the National Health and Nutrition Examination Survey (NHANES) 1999–2002, were included for analysis. Anthropometric measurements, biochemical profiles, and high‐sensitivity C‐reactive protein (CRP) were measured. A structural equation model (SEM) was constructed to elucidate a pathway in which obesity initiated the cascade leading to full MS. The results of SEM demonstrated that obesity was positively associated with elevated CRP level (B = 0.05, P < 0.001). This higher inflammatory state directed to insulin resistance (B = 0.32, P < 0.001), which in turn was positively associated with dyslipidemia (B = 0.06, P < 0.001). Obesity could also directly and positively affect blood pressure (B = 0.51, P < 0.001), without the mediation of insulin resistance and/or inflammation. The results of the cross‐sectional analysis in the white subjects have shown that obesity has a strong influence on hypertension that obtains little additional influence from inflammation or insulin resistance. The metabolic profile in the NHANES group has been confirmatory with the statement that there is a sequential effect from obesity to inflammation, insulin resistance, and dyslipidemia. This approach has allowed to inferring important biological insights about the nature of the relationships among the components of MS.
Breastfeeding and Childhood Obesity: Shift of the Entire BMI Distribution or Only the Upper Parts?
Authors: Beyerlein Andreas , Toschke André M. , von Kries Rüdiger
Published: October 2008

A protective effect of breastfeeding on overweight (binary) has been reported by meta‐analyses using logistic regression, whereas studies using linear regression and BMI (continuous) detected no significant association. To assess the relationship of these differences with different outcome classification, we compared results for linear, logistic, and quantile regression models in a cross‐sectional data set of considerable size. Height, weight, and questionnaire data on 9,368 preschool children were collected during school‐entry examinations in 1999 and 2002 in Bavaria, Southern Germany. We calculated multivariable linear, logistic, and quantile regression models with outcomes BMI, overweight, obesity, and BMI quantiles (as appropriate). Models considered the covariates breastfeeding (breastfed vs. never breastfed), gender, age, smoking in pregnancy, TV watching, maternal BMI, parental education, and early infant weight gain. No significant association was found in the linear regression model. In the logistic model, a significant association was observed for obesity (odds ratio: 0.72 (95% confidence interval (CI) 0.55, 0.94)). In quantile regression no significant point estimates were observed for the percentiles of 0.4–0.8. However, breastfeeding reduced the BMI of children having values on the 90th and 97th percentiles by −0.23 (95% CI −0.39, −0.07) and −0.26 (95% CI −0.45, −0.07) kg/m2, respectively, on average. In contrast, breastfeeding was significantly associated with a low shift toward higher BMI values for BMI quantiles of 0.03 and from 0.1 to 0.3. The detection of associations between breastfeeding and childhood body composition might be related to the coding of the response variable (continuous or binary) and the statistical method used (linear, logistic, or quantile regression). Quantile regression should additionally be applied in such studies.
Increasing Heritability of BMI and Stronger Associations With the FTO Gene Over Childhood
Authors: Haworth Claire M.A. , Carnell Susan , Meaburn Emma L. , Davis Oliver S.P. , Plomin Robert , Wardle Jane
Published: October 2008

The growing evidence of health risks associated with the rise in childhood obesity adds to the urgency of understanding the determinants of BMI. Twin analyses on repeated assessments of BMI in a longitudinal sample of >7,000 children indicated that the genetic influence on BMI becomes progressively stronger, with heritability increasing from 0.48 at age 4 to 0.78 at age 11. In the same large twin sample, the association between a common variant in the FTO gene and BMI increased in parallel with the rise in heritability, going from R2 < 0.001 at age 4 to R2 = 0.01 at age 11. These findings suggest that expression of FTO may become stronger throughout childhood. Increases in heritability may also be due to children increasingly selecting environments correlated with their genetic propensities.
Preatherosclerosis and Adiponectin Subfractions in Obese Adolescents
Authors: Mangge Harald , Almer Gunter , Haj‐Yahya Samih , Pilz Stefan , Gasser Robert , Möller Reinhard , Horejsi Renate
Published: October 2008

We evaluated total adiponectin, high‐molecular weight (HMW), medium‐molecular weight (MMW), low‐molecular weight (LMW) adiponectin subfractions, clinical parameters, routine lab parameters, lipids, metabolic, inflammatory biomarkers, and intima‐media thickness (IMT) of common carotid arteries in 70 obese juveniles and adolescents with preatherosclerosis and 55 normal weight controls of similar age and gender distribution. Compared with the controls, the obese probands had a significantly increased IMT (P < 0.001) and elevated ultra‐sensitive C‐reactive protein (P < 0.001) indicating early vascular burden. Total and HMW adiponectin were significantly decreased in the obese cohort. The ratio between HMW and total adiponectin was significantly decreased in obese probands whereas the LMW/total adiponectin ratio was increased. Overall, total‐, HMW, and MMW adiponectin were significantly negatively correlated with carotid IMT. The HMW/total adiponectin ratio correlated significantly negatively, and the LMW/total adiponectin ratio significantly positively with the IMT. Furthermore, HMW adiponectin was significantly positively correlated with high‐density lipoprotein (HDL)‐cholesterol and serum apolipoprotein A1, and negatively with BMI, triglycerides, homeostatic model assessment (HOMA)‐index, leptin, liver transaminases, and uric acid. This remained stable after controlling for gender. Multiple regression analysis of body measures and all other lab parameters showed the strongest correlation between HMW adiponectin and carotid IMT (β = −0.35, P < 0.001). Taken together, our study provides the first evidence that preatherosclerosis in obese juveniles and adolescents is associated with altered subfractions of adiponectin, whereas after multiple testing the HMW subfraction showed a better correlation to IMT compared with total adiponectin.
Mentoring in All Directions: Influence and Focus Throughout the Department
Authors: Seymour Patricia J. , Jackson Catherine A. , Sinclair J. Stephen , Weber Elizabeth G. , Wilding Marissa Klein
Published: October 2008

Mentoring in higher education is most often conceptualized as the relationship between a more senior and less experienced faculty member or between faculty and student in the process of imparting knowledge and skills from the mentor (senior member) to mentee (junior member). The top-down approach to mentoring is well described in educational and clinical teaching literature. This article describes the development of a multi-directional mentoring model that is employed within one academic department in communication sciences and disorders. In the multidirectional model, all members of the mentoring group including senior faculty, junior faculty, and students benefit from the experience of each member. The application of a multidirectional mentoring model is applied to the reciprocal teaching and learning processes between senior and junior faculty, a process in which the roles of mentor and mentee change related to the specialized expertise of each member.
Student Anticipations and Reactions to Hybrid Format Education
Authors: Ginsberg Sarah M.
Published: October 2008

This qualitative study examined student perceptions regarding a hybrid classroom format in which part of their learning took place in a traditional classroom and part of their learning occurred in an online platform. Pre-course and post-course anonymous essays suggest that students may be open to learning in this context; however, they have specific concerns as well. Students raised issues regarding faculty communication patterns, learning styles, and the value of clear connections between online and traditional learning experiences. Student concerns and feedback need to be addressed through the course design and by the instructor in order for them to have a positive learning experience in a hybrid format course.
Microsaccades drive illusory motion in theEnigmaillusion
Authors: Troncoso Xoana G. , Macknik Stephen L. , Otero-Millan Jorge , Martinez-Conde Susana
Published: October 2008

Visual images consisting of repetitive patterns can elicit striking illusory motion percepts. For almost 200 years, artists, psychologists, and neuroscientists have debated whether this type of illusion originates in the eye or in the brain. For more than a decade, the controversy has centered on the powerful illusory motion perceived in the paintingEnigma, created by op-artist Isia Leviant. However, no previous study has directly correlated theEnigmaillusion to any specific physiological mechanism, and so the debate rages on. Here, we show that microsaccades, a type of miniature eye movement produced during visual fixation, can drive illusory motion inEnigma. We asked subjects to indicate when illusory motion sped up or slowed down during the observation ofEnigmawhile we simultaneously recorded their eye movements with high precision. Before “faster” motion periods, the rate of microsaccades increased. Before “slower/no” motion periods, the rate of microsaccades decreased. These results reveal a direct link between microsaccade production and the perception of illusory motion inEnigmaand rule out the hypothesis that the origin of the illusion is purely cortical.
Generation of a highly inducible
Gal4
→
Fluc
universal reporter mouse for
in vivo
bioluminescence imaging
Authors: Pichler Andrea , Prior Julie L. , Luker Gary D. , Piwnica-Worms David
Published: October 2008

Full understanding of the functional complexity of the protein interactome requires mapping of biomolecular complexes within the cellular environment over biologically relevant time scales. New approaches to imaging interacting protein partners
in vivo
will allow the study of functional proteomics of human biology and disease within the context of living animals. Herein, we describe a universal transgenic reporter mouse strain that expresses firefly luciferase (
Fluc
) under the regulatory control of a concatenated Gal4 promoter (Tg
G4F(+/−)
). Using an adenovirus to deliver a fused binding-domain-activator chimera (Gal4BD-VP16), induction of bioluminescence in Tg
G4F(+/−)
tissues of up to 4 orders of magnitude was observed in fibroblasts, liver, respiratory epithelia, muscle, and brain. The Tg
G4F(+/−)
reporter strain allowed noninvasive detection of viral infectivity, duration of the infection as well as viral clearance in various tissues
in vivo
. To demonstrate protein–protein interactions in live mice, the well characterized interaction between tumor suppressor p53 (fused to Gal4BD) and large T antigen (TAg) (fused to VP16) was visualized
in vivo
by using a two-hybrid strategy. Hepatocytes of Tg
G4F(+/−)
mice transfected with p53/TAg demonstrated 48-fold greater induction of
Fluc
expression
in vivo
than noninteracting pairs. Furthermore, to demonstrate the feasibility of monitoring experimental therapy with siRNA
in vivo
, targeted knockdown of p53 resulted in markedly reduced light output, whereas use of a control siRNA had no effect on protein interaction-dependent induction of
Fluc
. Thus, this highly inducible
Gal4
→
Fluc
conditional reporter strain should facilitate imaging studies of protein interactions, signaling cascades, viral dissemination, and therapy within the physiological context of the whole animal.
Genotype-dependent variation of mitochondrial transcriptional profiles in interpopulation hybrids
Authors: Ellison Christopher K. , Burton Ronald S.
Published: October 2008

Hybridization between populations can disrupt gene expression, frequently resulting in deleterious hybrid phenotypes. Reduced fitness in interpopulation hybrids of the marine copepod
Tigriopus californicus
has been traced to interactions between the nuclear and mitochondrial genomes. Here, we determine transcript levels of four to six genes involved in the mitochondrial oxidative phosphorylation pathway for a series of parental and inbred hybrid lines using RT-qPCR. Both nuclear and mitochondrial-encoded genes are included in the analysis. Although all genes studied are up-regulated under salinity stress, only expression of genes located on the mtDNA differed among lines. Because mitochondrial genes are transcribed by a dedicated RNA polymerase encoded in the nuclear genome, we compare transcript levels among hybrid lines with different combinations of mitochondrial RNA polymerase and mtDNA genotypes. Lines bearing certain mtDNA-mitochondrial RNA polymerase genotypic combinations show a diminished capacity to up-regulate mitochondrial genes in response to hypoosmotic stress. Effects on the transcriptional profile depend on the specific interpopulation cross and are correlated with viability effects. We hypothesize that disruption of the mitochondrial transcriptional system in F
2
hybrids may play a central role in hybrid breakdown.
Accuracy of direct gradient sensing by single cells
Authors: Endres Robert G. , Wingreen Ned S.
Published: October 2008

Many types of cells are able to accurately sense shallow gradients of chemicals across their diameters, allowing the cells to move toward or away from chemical sources. This chemotactic ability relies on the remarkable capacity of cells to infer gradients from particles randomly arriving at cell-surface receptors by diffusion. Whereas the physical limits of concentration sensing by cells have been explored, there is no theory for the physical limits of gradient sensing. Here, we derive such a theory, using as models a perfectly absorbing sphere and a perfectly monitoring sphere, which, respectively, infer gradients from the absorbed surface particle density or the positions of freely diffusing particles inside a spherical volume. We find that the perfectly absorbing sphere is superior to the perfectly monitoring sphere, both for concentration and gradient sensing, because previously observed particles are never remeasured. The superiority of the absorbing sphere helps explain the presence at the surfaces of cells of signal-degrading enzymes, such as PDE for cAMP inDictyostelium discoideum(Dicty) and BAR1 for mating factor α in Saccharomyces cerevisiae (budding yeast). Quantitatively, our theory compares favorably with recent measurements of Dicty moving up a cAMP gradient, suggesting these cells operate near the physical limits of gradient detection.
Remodeling of DNA replication structures by the branch point translocase FANCM
Authors: Gari Kerstin , Décaillet Chantal , Delannoy Mathieu , Wu Leonard , Constantinou Angelos
Published: October 2008

Fanconi anemia (FA) is a genetically heterogeneous chromosome instability syndrome associated with congenital abnormalities, bone marrow failure, and cancer predisposition. Eight FA proteins form a nuclear core complex, which promotes tolerance of DNA lesions in S phase, but the underlying mechanisms are still elusive. We reported recently that the FA core complex protein FANCM can translocate Holliday junctions. Here we show that FANCM promotes reversal of model replication forks via concerted displacement and annealing of the nascent and parental DNA strands. Fork reversal by FANCM also occurs when the lagging strand template is partially single-stranded and bound by RPA. The combined fork reversal and branch migration activities of FANCM lead to extensive regression of model replication forks. These observations provide evidence that FANCM can remodel replication fork structures and suggest a mechanism by which FANCM could promote DNA damage tolerance in S phase.
Integrin α2β1 plays a critical role in osteoblast response to micron-scale surface structure and surface energy of titanium substrates
Authors: Olivares-Navarrete R. , Raz P. , Zhao G. , Chen J. , Wieland M. , Cochran D. L. , Chaudhri R. A. , Ornoy A. , Boyan B. D. , Schwartz Z.
Published: October 2008

Efforts to improve bone response to biomaterials have focused on ligands that bind α5β1 integrins. However, antibodies to α5β1 reduce osteoblast proliferation but do not affect differentiation when cells are grown on titanium (Ti). β1-silencing blocks the differentiation stimulus of Ti microtopography, suggesting that other β1 partners are important. Stably α2-silenced MG63 human osteoblast-like cells were used to test whether α2β1 specifically mediates osteoblast response to Ti surface micron-scale structure and energy. WT and α2-silenced MG63 cells were cultured on tissue culture polystyrene (TCPS) and Ti disks with different surface microtopographies: machined pretreatment (PT) surfaces [mean peak to valley roughness (
R
a
) < 0.02 μm], PT surfaces that were grit-blasted and acid-etched (SLA;
R
a
= 4 μm), and SLA with high surface energy (modSLA). Alkaline phosphatase (ALP), α2 and β1 mRNA, but not α5, αv, β3, type-I collagen, or osteocalcin, increased on SLA and modSLA at 6 days. α2 increased at 8 days on TCPS and PT, but remained unchanged on SLA and modSLA. α2-protein was reduced 70% in α2-siRNA cells, whereas α5-mRNA and protein were unaffected. α2-knockdown blocked surface-dependent increases in β1 and osteocalcin and decreases in cell number and increases in ALP and local factors typical of MG63 cells grown on SLA and modSLA [e.g., prostaglandin E
2
, osteoprotegerin, latent and active TGF-β1, and stimulatory effects of 1α,25(OH)
2
D
3
on these parameters]. This finding indicates that α2β1 signaling is required for osteoblastic differentiation caused by Ti microstructure and surface energy, suggesting that conclusions based on cell behavior on TCPS are not predictive of behavior on other substrates or the mechanisms involved.
Electrophysiological correlates of the brain's intrinsic large-scale functional architecture
Authors: He Biyu J. , Snyder Abraham Z. , Zempel John M. , Smyth Matthew D. , Raichle Marcus E.
Published: October 2008

Spontaneous fluctuations in the blood-oxygen-level-dependent (BOLD) signals demonstrate consistent temporal correlations within large-scale brain networks associated with different functions. The neurophysiological correlates of this phenomenon remain elusive. Here, we show in humans that the slow cortical potentials recorded by electrocorticography demonstrate a correlation structure similar to that of spontaneous BOLD fluctuations across wakefulness, slow-wave sleep, and rapid-eye-movement sleep. Gamma frequency power also showed a similar correlation structure but only during wakefulness and rapid-eye-movement sleep. Our results provide an important bridge between the large-scale brain networks readily revealed by spontaneous BOLD signals and their underlying neurophysiology.
Individual disease risk and multimetric analysis of Crohn disease
Authors: Gibson Jane , Collins Andrew , Morton Newton
Published: October 2008

Rare dominant genes with high penetrance can be identified by linkage without inbreeding, whereas rare recessive genes with high penetrance are most efficiently recognized by autozygosity mapping of homozygotes in pedigrees with preferential inbreeding. On the contrary, complex inheritance is characterized by common genes with low penetrance, for which family studies and inbreeding are inefficient. Here, we develop the Fisherian theory for diallelic cases and controls, show that it compares favorably with Bayesian estimates, and evaluate their currently low power for discriminating cases and controls in Crohn disease (CD). Significance is enhanced by inclusion of composite likelihood, but identification of causal loci is delayed by low recognition of gene function. Clearly, association mapping is not yet optimal, and so strenuous effort is justified to develop a more inclusive gene map and association tests more powerful than single markers and the current use of composite likelihood. Because of its relatively high heritability and the correspondingly large number of detected causal loci, CD presents an ideal test system to determine the power and flaws of competing methods of whole-genome case/control association analysis in publicly available data. Until such a test is exploited by competing statisticians, their Herculean efforts will be inconclusive, and the costly advances from increased sample size will be suboptimal and disappointing.
Method for Estimating Ultraviolet Germicidal Fluence Rates in a Hospital Room
Authors: Schafer Millie P. , Kujundzic Elmira , Moss Clyde E. , Miller Shelly L.
Published: October 2008

Background.

Upper-room air UV germicidal irradiation (UVGI) is an effective environmental control measure for mitigating the transmission of airborne infections. Many factors influence the efficacy of an upper-room air UVGI system, including the levels and distribution of radiation. The radiation levels experienced by airborne microorganisms can be estimated by measuring the fluence rate, which is the irradiance from all angles that is incident on a small region of space.

Methods.

The fluence rate can be estimated by use of a radiometer coupled to a planar detector. Measurements in 4 directions at a single point are taken and summed to estimate the fluence rate at that point. This measurement process is repeated at different sites in the room at a single height.

Results.

In the upper air of a test room, the UV fluence rate varied at least 3-fold, with the maximum rate occurring in the immediate vicinity of the fixtures containing lamps emitting UV radiation. In the area that would be occupied by the patient and/or healthcare personnel, no significant variation occurred in the UV fluence rate for a designated height. There was no significant statistical difference between measurements obtained by different individuals, by using a different alignment, or during 5 observation periods. Lamp failures were detected on multiple occasions.

Conclusion.

This method is simple, requires no specialized training, and permits regular monitoring of the necessary UV fluence rates needed to sustain the targeted airborne microorganisms' inactivation level. Additionally, this method allowed for the detection of changes in UV fluence rates in the upper air of the simulated hospital room.