bluuebunny/crossref_metadata_2025 huggingface dataset:
A ROLE FOR CULTURAL TRANSMISSION IN FERTILITY TRANSITIONS
Authors: Baudin Thomas
Published: November 2009

Cultural variables in economic analysis have recently experienced a strong renewal. This evolution sheds a new light on the old debate between the “Beckerian model” of fertility and the “synthesis model” of fertility. In this paper, I propose a fertility model making the evolution of culture endogenous. The whole population is divided into two cultures corresponding to specific preferences for fertility. Parents decide their fertility rate and try to transmit their culture to their children. Differential fertility between cultures gives rise to an evolutionary process while differential effort to transmit the parental culture gives rise to a cultural process. The long-run distribution of preferences and the average total fertility rate both result from interactions between these processes. As a result, a fertility transition cannot appear without productivity shocks in favor of the culture that is not biased toward quantity of children. However, asymmetric productivity shocks are not always sufficient to cause a fertility transition.
Childhood overweight and obesity among Kenyan pre-school children: association with maternal and early child nutritional factors
Authors: Gewa Constance A
Published: November 2009

Objective

To report on the prevalence of overweight and obesity among pre-school children in Kenya and examine the associations between childhood overweight and selected maternal and child-related factors.

Design

Demographic Health Survey data, multistage stratified cluster sampling methodology.

Setting

Rural and urban areas of Kenya.

Subjects

A total of 1495 children between the ages of 3 and 5 years in Kenya.

Results

Over 30 % of the children were stunted, approximately 16 % were underweight, 4 % were wasted, approximately 18 % were overweight and 4 % were obese; 8 % were both overweight/obese and stunted. Maternal overweight and obesity, higher levels of maternal education, being a large or very large child at birth, and being stunted were each associated with higher odds of overweight and obesity among Kenyan children. Older children and large household size were each associated with lower odds of overweight and obesity among Kenyan children.

Conclusions

The analysis demonstrates the presence of under- and overnutrition among Kenyan pre-school children and the importance of focusing on expanding efforts to prevent and treat malnutrition within this population. It also identifies some of the modifiable factors that can be targeted in these efforts.
Third millennium changing times
Authors: Wright Rita P.
Published: November 2009

Shannon Dawdy has presented us with a provocative dialogue on the question ‘is archaeology useful?’ In it, she forecasts a rather bleak future for our field, raising doubts about whether archaeology should be useful and whether it is ‘threatened with its own end-time’. Woven throughout her paper are major concerns about the use of archaeology for nationalistic ends and heritage projects which she deems fulfil the needs of archaeologists rather than those of the public they serve. In the final section of her paper, when she asks, ‘can archaeology save the world?’, Dawdy recommends that we reorient our research ‘away from reconstructions of the past and towards problems of the present’ (p. 140). In my contribution to this dialogue, I introduce an issue that reflects on cultural heritage, antiquities and artefact preservation, which, though they may seem antithetical, are closely aligned with Dawdy's concerns. As a prehistorian with a focus on the third millennium B.C. in the Near East and South Asia, I consider these issues to be the ‘big stories’ that have emerged in the early years of this third millennium, and those that speak directly to the usefulness of archaeology. Of course, it is not the only thing we do, but it is ‘useful’.
The uses of archaeology. A plea for diversity
Authors: Funari Pedro Paulo A. , de Carvalho Aline Vieira
Published: November 2009

Professor Dawdy's keynote speech addresses some of the main challenges of the discipline in the 21st century. Archaeology should not be self-serving, and it can even become dangerous, a possible consequence of a quest for its usefulness. A possible solution would be to focus efforts on environmental archaeology. Looking for ancient sustainable agricultural practices, for example, in order to better inform contemporary human adaptations, would be a path to follow. According to Dawdy, this useful, futurist archaeology finds a public ready for such an endeavour.
Schlaganfall
Authors: Weller
Published: November 2009

Der Schlaganfall ist eine der häufigsten neurologischen Erkrankungen und nimmt bedingt durch die Alterung der Gesellschaft an Inzidenz zu. Wirksame Behandlungsstrategien sind verfügbar, senken die Mortalität und verbessern die Prognose für ein unabhängiges Leben. Die intravenöse oder intraarterielle Thrombolyse hat mit einer number needed to treat (NNT) von 6 eine hohe Wirksamkeit, wenn sie innerhalb von 4.5 Stunden nach Symptombeginn angewandt wird. Der sichere Einsatz der Thrombolyse erfordert eingespielte Arbeitsabläufe eines geschulten Teams bestehend aus Neurologen und Pflegekräften und eine vor allem räumlich optimierte Infrastruktur (Aufnahme, Computertomographie, Kernspintomographie, Stroke Unit). Nach der perakuten Behandlung muss der Patient auf einer Stroke Unit überwacht und behandelt werden. Die Stroke Unit ist eine räumlich getrennte Überwachungs- oder Intensivstation mit spezifisch geschultem Personal. Die Behandlung auf einer Stroke Unit ist nicht nur genauso effektiv wie die Thrombolyse (NNT 6), sondern kommt zudem jedem Schlaganfallpatienten zu Gute. Von der Thrombolyse hingegen profitieren nur diejenigen Patienten, die innerhalb des 4.5-Stunden-Zeitfensters behandelt werden können. Nach der Akutphase erfordern die Therapieansätze der Sekundärprävention und der Neurorehabilitation eine lebenslange Weiterbehandlung des Schlaganfallpatienten. Die medizinische Organisationsstruktur der meisten europäischen Länder wie auch der Schweiz, die Akutbehandlung, Rehabilitation und chronische Weiterbehandlung in verschiedene Hände legt, ist für den Patienten verwirrend, oft redundant und selten sogar schadend. Einheitliche Behandlungspfade mit Therapien, deren Wirksamkeit bewiesen ist, sind genauso notwendig, wie eine kontinuierliche Betreuung durch einen oder einige wenige gut kommunizierende Ärzte und Therapeuten.
Forward and adjoint quasi‐geostrophic models of the geomagnetic secular variation
Authors: Canet Elisabeth , Fournier Alexandre , Jault Dominique
Published: November 2009

We introduce a quasi‐geostrophic model of core dynamics, which aims at describing core processes on geomagnetic secular variation timescales. It extends the formalism of Alfvén torsional oscillations by incorporating nonzonal motions. Within this framework, the magnetohydrodynamics takes place in the equatorial plane; it involves quadratic magnetic quantities, which are averaged along the direction of rotation of the Earth. In addition, the equatorial flow is projected on the core‐mantle boundary. It interacts with the magnetic field at the core surface, through the radial component of the magnetic induction equation. That part of the model connects the dynamics and the observed secular variation, with the radial component of the magnetic field acting as a passive tracer. We resort to variational data assimilation to formally construct the relationship between model predictions and observations. Variational data assimilation seeks to minimize an objective function by computing its sensitivity to its control variables. The sensitivity is efficiently calculated after integration of the adjoint model. We illustrate that framework with twin experiments, performed first in the case of the kinematic core flow inverse problem and then in the case of Alfvén torsional oscillations. In both cases, using the adjoint model allows us to retrieve core state variables which, while taking part in the dynamics, are not directly sampled at the core surface. We study the effect of several factors on the solution (width of the assimilation time window, amount and quality of data), and we discuss the potential of the model to deal with real geomagnetic observations.
Cold and dry processes in the Martian Arctic: Geomorphic observations at the Phoenix landing site and comparisons with terrestrial cold desert landforms
Authors: Levy Joseph S. , Head James W. , Marchant David R.
Published: November 2009

We analyze Surface Stereo Imager observations of rocks, sediments, and permafrost‐related landforms in the vicinity of the Phoenix lander, comparing the imaged features to analogous examples of physical weathering and periglacial processes observed in the Antarctic Dry Valleys. Observations at the Phoenix landing site of pitted rocks, “puzzle rocks” undergoing in‐situ breakdown, perched clasts, and thermal contraction crack polygon morphologies strikingly similar to terrestrial sublimation polygons, all strongly suggest that stable (non‐churning) permafrost processes dominate the Phoenix landing site. Morphological evidence suggests that cold‐desert processes, in the absence of wet active‐layer cryoturbation, and largely driven by sublimation of buried ice (either pore ice, excess ice, or both) are shaping the landscape.
Emissions of NOx, SO2, CO, and HCHO from commercial marine shipping during Texas Air Quality Study (TexAQS) 2006
Authors: Williams E. J. , Lerner B. M. , Murphy P. C. , Herndon S. C. , Zahniser M. S.
Published: November 2009

We report measurements of NOx, SO2, CO, and HCHO mass‐based emission factors from more than 200 commercial vessel encounters in the Gulf of Mexico and the Houston‐Galveston region of Texas during August and September, 2006. For underway ships, bulk freight carriers have the highest average NOx emissions at ∼87 g NOx (kg fuel)−1, followed by tanker ships at ∼79 g NOx (kg fuel)−1, while container carriers, passenger ships, and tugs all emit an average of about ∼60 g NOx (kg fuel)−1. Emission of NOx from stationary vessels was lower, except for container ships and tugs, and likely reflects use of medium‐speed diesel engines. Overall, our mean NOx emission factors are 10–15% lower than published data. Average emission of SO2 was lower for passenger ships and tugs and tows (6–7 g SO2 (kg fuel)−1) than for larger cargo vessels (20–30 g SO2 (kg fuel)−1). Our data for large cargo ships in this region indicate an average residual fuel sulfur content of ∼1.4% which is a factor of two lower than the global average of 2.7%. Emission of CO was low for all categories (7–16 g CO (kg fuel)−1), although our mean overall CO emission factor is about 10% higher than published data. Emission of HCHO was less than 5% that of CO. Despite considerable variability, no functional relationships, such as emissions changes with engine speed or load, could be discerned. Comparison of emission factors from ships to those from other sources suggests ship emissions in this region cannot be ignored.
A global comparison of carbon monoxide profiles and column amounts from Tropospheric Emission Spectrometer (TES) and Measurements of Pollution in the Troposphere (MOPITT)
Authors: Ho Shu‐Peng , Edwards David P. , Gille John C. , Luo Ming , Osterman Gregory B. , Kulawik Susan S. , Worden Helen
Published: November 2009

In this study, we compare carbon monoxide (CO) products from the Measurements of Pollution in the Troposphere (MOPITT) and Tropospheric Emission Spectrometer (TES) and investigate the possible causes of the differences between retrievals for these two data sets. Direct comparisons of CO retrievals for July 2006 show that TES CO concentrations are consistently biased lower than those of MOPITT by 25 ppbv near the surface and by 20 ppbv at 150 hPa, primarily due to different a priori profiles and covariance matrices used in the TES and MOPITT CO retrievals. To reduce the effects of different a priori constraints, we apply TES a priori profiles and covariance matrices to a modified MOPITT retrieval algorithm. The mean TES‐MOPITT CO difference decreases from −25 to −10 ppbv near the surface. To further account for retrieval smoothing errors due to different TES and MOPITT averaging kernels, TES averaging kernels are used to smooth MOPITT CO profiles to derive TES‐equivalent CO profiles. Compared to these, TES CO profiles are biased 1 ppbv lower near the surface and 4–9 ppbv lower in the troposphere, and the mean absolute TES and TES‐equivalent CO column difference is less than 6.5%. The mean TES and MOPITT CO differences due to smoothing errors are close to zero, and the remaining bias is primarily due to the combined effects of radiance biases, forward model errors, and the spatial and temporal mismatches of TES and MOPITT pixels.
Association of RBP4 Gene Variants and Serum HDL Cholesterol Levels in the Newfoundland Population
Authors: Shea Jennifer L. , Loredo‐Osti J. Concepción , Sun Guang
Published: November 2009

Retinol‐binding protein 4 (RBP4) is a novel adipokine that likely contributes to systemic insulin resistance and dyslipidemia. The role of genetic variations in RBP4 on phenotypes of glucose and lipid metabolism is not clear in humans. The purpose of this study was to examine five single‐nucleotide polymorphisms (SNPs) in the RBP4 gene to determine their relationship with markers of insulin resistance and serum lipids in the CODING Study. The CODING Study consists of 1,836 subjects recruited from the genetically homogeneous population of Newfoundland and Labrador (NL), Canada. Serum glucose, insulin, homeostasis model assessment of insulin resistance (HOMAIR), HOMA for β cell function (HOMAβ), total cholesterol (Chol), high‐density lipoprotein cholesterol (HDL‐C), low‐density lipoprotein cholesterol (LDL‐C), and triglycerides were determined after a 12‐h fast. Five SNPs within RBP4 (rs3758539, G/A 5′ flanking region; rs61461737, A/G intron; rs10882280, C/A intron; rs11187545, A/G intron; and rs12265684, C/G intron) were genotyped using TaqMan validated or functionally tested SNP genotyping assays. After correcting for multiple testing, we observed a significant association between the minor allele of two noncoding SNPs (rs10882280 and rs11187545) and higher serum HDL‐C (P = 0.043 and 0.042, respectively). No significant associations were observed with any other parameter related to lipid metabolism. We also found no significant association between any variant sites and markers of insulin resistance. Our results suggest that genetic variations in RBP4 may play a role in the differences in serum HDL‐C levels in the NL population.
Obesity and Functional Impairment: Influence of Comorbidity, Joint Pain, and Mental Health
Authors: Heo Moonseong , Pietrobelli Angelo , Wang Dan , Heymsfield Steven B. , Faith Myles S.
Published: November 2009

To examine the relationship between obesity and functional impairment and the influence of comorbidity, joint pain, and mental health on this association, we used US adult respondents (N = 430,912) to the 2007 Behavioral Risk Factor Surveillance Survey (BRFSS‐07). Functional impairment was indicated if a respondent was either (i) limited in any way or in any activities because of physical, mental, or emotional problems, or (ii) had any health problem that required using special equipment such as a cane, wheelchair, special bed, or special telephone. Approximately 62.8% of respondents were overweight or obese and 20.3% were functionally impaired. The unadjusted relationship between obesity and functional impairment revealed a classical J‐shaped pattern with odds ratios (95% confidence interval) compared to the normal weight group: 1.63 (1.54–1.73), 1.22 (1.20–1.25), 1.77 (1.73–1.81), 2.43 (2.36–2.51), and 4.12 (3.97–4.27) for underweight, overweight, obesity class I, II, and III, respectively. Although inclusion of different combinations of sociodemographic and medical covariates substantially attenuated the unadjusted association, the collective inclusion of all covariates in a single model did not eliminate the significant J‐shaped association resulting in the following corresponding adjusted odds ratios: 1.19 (1.13–1.25), 1.01 (0.99–1.04), 1.23 (1.19–1.27), 1.38 (1.32–1.44), and 1.92 (1.82–2.02). The attenuation was mostly influenced by medical comorbidity. In conclusion, functional impairment is associated with obesity, primarily due to medical comorbidity conditions. The significant residual association highlights the importance of sustainable obesity prevention and treatment at both the individual and public level as functional impairment can create burdens at individual, familial, and societal levels.
Recent advances in nitro sugar chemistry
Authors: Soengas Raquel G. , Estévez Juan C. , Estevez Amalia M. , Fernández Fernando , Estévez Ramón J.
Published: November 2009

This chapter reports the most relevant recent contributions in nitro sugar chemistry. It includes the following aspects: preparation of nitro sugars, formation of carbon–carbon bonds and transformation of the nitro group into other functionalities.
Thionocarbamates on carbohydrate scaffolds—from synthesis to bioactivity
Authors: Simão Ana Catarina , Rousseau Jolanta , Silva Sandrina , Rauter Amelia Pilar , Tatibouët Arnaud , Rollin Patrick
Published: November 2009

2-Thioxotetrahydro-1,3-O,N-heterocycles are commonly named cyclic thiocarbamates or thionocarbamates. The structural association of five- and six-membered thionocarbamates with diverse carbohydrate scaffolds has shown a promising potential in modern organic synthesis and in the preparation of biomolecules mimics. The principal pathways for their synthesis, the recent and most important developments of their chemical transformations as well as some examples of their biological activities will be considered in the following discussion.
Recent strategies for the preparation of C-1 glycals
Authors: Gómez Ana M. , Cristóbal López J.
Published: November 2009

C-1 Glycals, a relevant type of unsaturated branched sugar, are currently used in synthetic approaches towards C-glycosyl compounds and natural products. In this chapter we present a brief overview of the synthetic strategies employed for their preparation, which have been classified according to the type of starting material employed. Further modifications carried out on the C-1 glycals fall beyond the scope of this review and will not be discussed.
Anomeric effects in pyranosides and related acetals
Authors: Gerber-Lemaire Sandrine , Vogel Pierre
Published: November 2009

The anomeric effect, originally defined as the preference of an electronegative substituent at the anomeric position of pyranosides to stand in an axial rather than an equatorial position, results from the combination of multiple steric, stereoelectronic and medium interactions. A more generalized definition of the enthalpic anomeric effect refers to the gem-dioxy stabilizing effect which makes acetals more stable than their 1,n-dialkoxyalkane isomers (n > 1). This effect is far more important than the difference in stability between conformers of acetals as those found in axial and equatorial pyranoses and pyranosides. This review gives an up-dated view of enthalpic, conformational and also kinetic anomeric effects in pyranosides. The latter manifest themselves during heterolytical processes occuring at the anomeric centers of pyranosides and analogous compounds.
Energy band-alignment of a multimetal-layer gated metal-oxide-semiconductor structure
Authors: Li Zilan , Houssa Michel , Schram Tom , De Gendt Stefan , De Meryer Kristin
Published: November 2009

The energy band-alignment of a multimetal-layer gated metal-oxide-semiconductor structure is investigated. An analytical expression for the Fermi level of the metal stack is derived. It is shown that the thin metal layer contacting the gate dielectric plays a critical role in determining the work function of the whole metal stack, in agreement with experimental results.
Spectroscopic determination of the doping and mobility of terahertz quantum cascade structures
Authors: Lloyd-Hughes J. , Delley Y. L. , Scalari G. , Fischer M. , Liverini V. , Beck M. , Faist J.
Published: November 2009

Terahertz time-domain spectroscopy is shown to provide a convenient and rapid means to measure the conductivity of individual layers in semiconductor heterostructures such as terahertz quantum cascade lasers. By modeling the complex transmission at terahertz frequencies, the electron density and the in-plane momentum scattering time of the active regions and doped contact layers were determined for both GaAs/AlGaAs and InGaAs/InAlAs epilayers. The measured temperature dependence of the electron scattering rate revealed the significance of impurity and LO phonon scattering. The implications for laser operation at room temperature are discussed by considering the changes in absorption and resonant tunneling current with temperature.
Lorentz symmetric quantum field theory for symplectic fermions
Authors: Robinson Dean J. , Kapit Eliot , LeClair André
Published: November 2009

A free quantum field theory with Lorentz symmetry is derived for spin-half symplectic fermions in 2+1 dimensions. In particular, we show that fermionic spin-half fields may be canonically quantized in a free theory with a Klein–Gordon Lagrangian. This theory is shown to have all the required properties of a consistent free quantum field theory, namely, causality, unitarity, adherence to the spin-statistics theorem, CPT symmetry, and the Hermiticity and positive definiteness of the Hamiltonian. The global symmetry of the free theory is Sp(4)≃SO(5). Possible interacting theories of both the pseudo-Hermitian and Hermitian variety are then examined briefly.
Degradation mechanisms of organic ferroelectric field-effect transistors used as nonvolatile memory
Authors: Ng Tse Nga , Russo Beverly , Arias Ana Claudia
Published: November 2009

Organic ferroelectric field-effect transistors were fabricated by inkjet printing for use as nonvolatile memory. Changes in device hysteresis were measured for 7 days to determine the limiting properties that restrict memory retention time. It was found that shifts in threshold voltage contributed to ∼55% of the reduction in transistor current, while decreased dielectric capacitance and reduced semiconductor mobility accounted for ∼30% and ∼15% of the current decay, respectively. The decrease in mobility and the shifts in threshold voltages are caused by remnant dipolar alignment in the ferroelectric insulator, and the reduction in gate capacitance is explained by injected charges in the ferroelectric dielectric. A method to calibrate and extract the input switching voltage is presented, and this calibration accounts for variations in device characteristics with time and allows the ferroelectric transistors to be used as analog memories.
Enhancement of electric force by ion-neutral collisions
Authors: Makrinich G. , Fruchtman A.
Published: November 2009

The measured force exerted on an ion flow by an electric field is found to be larger than the electric force that can be exerted if the ions are collisionless. In addition, the increase of the gas pressure is found to result in an increase of the electric force despite a simultaneous decrease of the deposited electric power. Employing a simple model, we argue that these experimental findings result from the electric force being felt by the ions for a longer time, their residence time in the acceleration region is increased due to their slowing-down collisions with neutrals.
Design of graphene electronic devices using nanoribbons of different widths
Authors: Naumis G. G. , Terrones M. , Terrones H. , Gaggero-Sager L. M.
Published: November 2009

We present a simple design of a field effect transistor based on graphene nanoribbons, taking advantage of the metallic and semiconductor nature of nanoribbons with different widths. Such device could be constructed by using lithography techniques. The conductance of the proposed device is obtained by using the Kubo formula, assuming a strong damping due to the substrate and imperfections of the lattice. By removing the control electrodes, the design could also be used as an electrical resistance.
Phase equilibria in DOPC/DPPC: Conversion from gel to subgel in two component mixtures
Authors: Schmidt Miranda L. , Ziani Latifa , Boudreau Michelle , Davis James H.
Published: November 2009

Biological membranes contain a mixture of phospholipids with varying degrees of hydrocarbon chain unsaturation. Mixtures of long chain saturated and unsaturated lipids with cholesterol have attracted a lot of attention because of the formation of two coexisting fluid bilayer phases in such systems over a broad range of temperature and composition. Interpretation of the phase behavior of such ternary mixtures must be based on a thorough understanding of the phase behavior of the binary mixtures formed with the same components. This article describes the phase behavior of mixtures of 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) with 1,2-di-d31-palmitoyl-sn-glycero-3-phosphocholine (DPPC) between −20 and 50 °C. Particular attention has been paid to the phase coexistence below about 16 °C where the subgel phase appears. The changes in the shape of the spectrum (and its spectral moments) during the slow transformation process leads to the conclusion that below 16 °C the gel phase is metastable and the gel component of the two-phase mixture slowly transforms to the subgel phase with a slightly different composition. This results in a line of three-phase coexistence near 16 °C. Analysis of the transformation of the metastable gel domains into the subgel phase using the nucleation and growth model shows that the subgel domain growth is a two dimensional process.
Hot and super-hot hydrogen atoms in microwave plasma
Authors: Tatarova E. , Felizardo E. , Dias F. M. , Lino da Silva M. , Ferreira C. M. , Gordiets B.
Published: November 2009

“Super-hot” (kinetic energy ∼4–8 eV) and “hot” (kinetic energy ∼0.3 eV) H atoms were detected in a surface wave (500 MHz) generated H2 plasma column, at pressure p=0.01 mbar, from the analysis of the Hβ, Hγ, Hδ, and Hε emission line profiles. These profiles were found to evolve from single Gaussian to bi-Gaussian toward the plasma column end. Population inversion between the levels 5→4 and 6→4 was detected. At pressure p=0.2 mbar, super-hot atoms were not detected and the temperature of the hot atoms was found to increase with the upper level principal quantum number.
Individual charge-trapping dislocations in an ionic insulator
Authors: Wang Zhongchang , Tsukimoto Susumu , Saito Mitsuhiro , Ikuhara Yuichi
Published: November 2009

Insulating oxide materials find widespread technological applications where how their inside dislocations behave are known to influence or control performance. Here we demonstrate, by first-principles calculations on MgO, that individual dislocations can trap charges within empty space around their cores in an unusual pipelike way, regardless of whether the charges are produced via external excitation or impurity doping. Such effect of dislocations is crucial for many applied physics issues as well as opens up an avenue for exploring functional devices based on the confined charges.
Low-temperature magnetotransport behaviors of heavily Mn-doped (Ga,Mn)As films with high ferromagnetic transition temperature
Authors: Chen L. , Yan S. , Xu P. F. , Lu J. , Wang W. Z. , Deng J. J. , Qian X. , Ji Y. , Zhao J. H.
Published: November 2009

We report the low-temperature magnetotransport behaviors of (Ga,Mn)As films with the nominal Mn concentration x larger than 10%. The ferromagnetic transition temperature TC can be enhanced to 191 K after postgrowth annealing (Ga,Mn)As with x=20%. The temperature Tm, corresponding to the resistivity minimum in the curve of resistivity versus temperature at temperature below TC, depends on Mn concentration, annealing condition, and magnetic field. Moreover, we find that the variable-range hopping may be the main conductive mechanism when temperature is lower than Tm.
Root phenomics of crops: opportunities and challenges
Authors: Gregory Peter J. , Bengough A. Glyn , Grinev Dmitri , Schmidt Sonja , Thomas W. (Bill) T. B. , Wojciechowski Tobias , Young Iain M.
Published: November 2009

Reliable techniques for screening large numbers of plants for root traits are still being developed, but include aeroponic, hydroponic and agar plate systems. Coupled with digital cameras and image analysis software, these systems permit the rapid measurement of root numbers, length and diameter in moderate (typically <1000) numbers of plants. Usually such systems are employed with relatively small seedlings, and information is recorded in 2D. Recent developments in X-ray microtomography have facilitated 3D non-invasive measurement of small root systems grown in solid media, allowing angular distributions to be obtained in addition to numbers and length. However, because of the time taken to scan samples, only a small number can be screened (typically <10 per day, not including analysis time of the large spatial datasets generated) and, depending on sample size, limited resolution may mean that fine roots remain unresolved. Although agar plates allow differences between lines and genotypes to be discerned in young seedlings, the rank order may not be the same when the same materials are grown in solid media. For example, root length of dwarfing wheat (Triticum aestivum L.) lines grown on agar plates was increased by ~40% relative to wild-type and semi-dwarfing lines, but in a sandy loam soil under well watered conditions it was decreased by 24–33%. Such differences in ranking suggest that significant soil environment–genotype interactions are occurring. Developments in instruments and software mean that a combination of high-throughput simple screens and more in-depth examination of root–soil interactions is becoming viable.
Aggregate stability of salt-affected kaolinitic soils on the North-east Plateau, Thailand
Authors: Kaewmano C. , Kheoruenromne I. , Suddhiprakarn A. , Gilkes R. J.
Published: November 2009

The aggregate stability of 56 salt-affected soil samples from the North-east Plateau, Thailand, was related to soil properties. The soils were Typic Natraqualfs and a Typic Endoaqualf, which are commonly used for paddy rice cultivation. The soil textures are mostly clays and clay loams with clay contents ranging from 313 to 849 g/kg. The dominant mineral in the clay fraction is kaolinite with minor smectite and traces of illite and a little quartz. Aggregate stability of these soils, measured by the wet sieving method, ranges from 3 to91%. Electrical conductivity measured by the saturation extract method ranges from 0.6 to 16.2 dS/m and exchangeable sodium percentage ranges from 5 to 31%, so that the soil samples can be variously classed as saline, sodic, saline–sodic, and normal.
The soil property that is most strongly correlated with aggregate stability is pH (r = –0.84) followed by exchangeable potassium (r = +0.75), cation exchange capacity (r = +0.73), clay content (r = +0.72), extractable acidity (r = +0.66), and organic matter (r = +0.66). However contrary to much published literature, no significant relationships exist between aggregate stability and exchangeable sodium percentage, sodium adsorption ratio, or electrical conductivity. Multivariate stepwise regression analyses indicated that aggregate stability of these mostly saline–sodic soils was well predicted by a combination of soil pH and clay content, which is convenient as they are properties determined in routine soil surveys. The presence of small amounts of smectite and illite may have reduced the stability of the dominantly kaolinitic soil aggregates.
A dominant, coordinated T regulatory cell-IgA response to the intestinal microbiota
Authors: Cong Yingzi , Feng Ting , Fujihashi Kohtaro , Schoeb Trenton R. , Elson Charles O.
Published: November 2009

A T cell receptor transgenic mouse line reactive to a microbiota flagellin, CBir1, was used to define mechanisms of host microbiota homeostasis. Intestinal IgA, but not serum IgA, was found to block mucosal flagellin uptake and systemic T cell activation in mice. Depletion of CD4
+
CD25
+
Tregs decreased IgA
+
B cells, total IgA, and CBir1-specific IgA in gut within days. Repletion of T cell-deficient mice with either CD4
+
CD25
+
or CD4
+
foxp3
+
Tregs restored intestinal IgA to a much greater extent than their reciprocal CD4
+
subsets, indicating that Tregs are the major helper cells for IgA responses to microbiota antigens such as flagellin. We propose that the major role of this coordinated Treg-IgA response is to maintain commensalism with the microbiota.
Rapid modulation of spine morphology by the 5-HT2Aserotonin receptor through kalirin-7 signaling
Authors: Jones Kelly A. , Srivastava Deepak P. , Allen John A. , Strachan Ryan T. , Roth Bryan L. , Penzes Peter
Published: November 2009

The 5-HT2Aserotonin receptor is the most abundant serotonin receptor subtype in the cortex and is predominantly expressed in pyramidal neurons. The 5-HT2Areceptor is a target of several hallucinogens, antipsychotics, anxiolytics, and antidepressants, and it has been associated with several psychiatric disorders, conditions that are also associated with aberrations in dendritic spine morphogenesis. However, the role of 5-HT2Areceptors in regulating dendritic spine morphogenesis in cortical neurons is unknown. Here we show that the 5-HT2Areceptor is present in a subset of spines, in addition to dendritic shafts. It colocalizes with PSD-95 and with multiple PDZ protein-1 (MUPP1) in a subset of dendritic spines of rat cortical pyramidal neurons. MUPP1 is enriched in postsynaptic density (PSD) fractions, is targeted to spines in pyramidal neurons, and enhances the localization of 5-HT2Areceptors to the cell periphery. 5-HT2Areceptor activation by the 5-HT2receptor agonist DOI induced a transient increase in dendritic spine size, as well as phosphorylation of p21-activated kinase (PAK) in cultured cortical neurons. PAK is a downstream target of the neuronal Rac guanine nucleotide exchange factor (RacGEF) kalirin-7 that is important for spine remodeling. Kalirin-7 regulates dendritic spine morphogenesis in neurons but its role in neuromodulator signaling has not been investigated. We show that peptide interference that prevents the localization of kalirin-7 to the postsynaptic density disrupts DOI-induced PAK phosphorylation and spine morphogenesis. These results suggest a potential role for serotonin signaling in modulating spine morphology and kalirin-7's function at cortical synapses.
Contagious yawning in gelada baboons as a possible expression of empathy
Authors: Palagi E. , Leone A. , Mancini G. , Ferrari P. F.
Published: November 2009

Yawn contagion in humans has been proposed to be related to our capacity for empathy. It is presently unclear whether this capacity is uniquely human or shared with other primates, especially monkeys. Here, we show that in gelada baboons (Theropithecus gelada) yawning is contagious between individuals, especially those that are socially close, i.e., the contagiousness of yawning correlated with the level of grooming contact between individuals. This correlation persisted after controlling for the effect of spatial association. Thus, emotional proximity rather than spatial proximity best predicts yawn contagion. Adult females showed precise matching of different yawning types, which suggests a mirroring mechanism that activates shared representations. The present study also suggests that females have an enhanced sensitivity and emotional tuning toward companions. These findings are consistent with the view that contagious yawning reveals an emotional connection between individuals. This phenomenon, here demonstrated in monkeys, could be a building block for full-blown empathy.
Factorization and Lie point symmetries of general Lienard-type equation in the complex plane
Authors: Yeşiltaş Özlem
Published: November 2009

We present a variational approach to a general Lienard-type equation in order to linearize it and, as an example, the Van der Pol oscillator is discussed. The new equation which is almost linear is factorized. The point symmetries of the deformed equation are also discussed and the two-dimensional Lie algebraic generators are obtained.
Boron spectral line ratios helpful to characterize wall conditioned tokamak plasmas
Authors: Agarwal Bishu , Prakash Ram , Jain Jalaj , Kumar Vinay , Vasu P
Published: November 2009

The intensity ratios of spectral lines of a single species are often used as diagnostics for inferring the electron temperature or density in plasmas. Helium is a well-known example. In this paper, the atomic data and analysis structure (ADAS) database has been used to identify line ratios in boron that might prove useful for plasmas created in tokamaks for the wall conditioning of plasma-facing-surfaces. Using the collisional radiative (CR) model-based photon emission rate coefficients, a few line intensity ratios selectively sensitive only to temperature and those that are sensitive to density are presented.
Analyzing the Effects of Delaying Aster Separation on Furrow Formation during Cytokinesis in the Caenorhabditis elegans Embryo
Authors: Lewellyn Lindsay , Dumont Julien , Desai Arshad , Oegema Karen
Published: November 2009

Signaling by the centrosomal asters and spindle midzone coordinately directs formation of the cytokinetic furrow. Here, we explore the contribution of the asters by analyzing the consequences of altering interaster distance during the first cytokinesis of the Caenorhabditis elegans embryo. Delaying aster separation, by using TPXL-1 depletion to shorten the metaphase spindle, leads to a corresponding delay in furrow formation, but results in a single furrow that ingresses at a normal rate. Preventing aster separation, by simultaneously inhibiting TPXL-1 and Gα signaling-based cortical forces pulling on the asters, delays furrow formation and leads to the formation of multiple furrows that ingress toward the midzone. Disrupting midzone-based signaling, by depleting conserved midzone complexes, results in a converse phenotype: neither the timing nor the number of furrows is affected, but the rate of furrow ingression is decreased threefold. Simultaneously delaying aster separation and disrupting midzone-based signaling leads to complete failure of furrow formation. Based on these results, we propose that signaling by the separated asters executes two critical functions: 1) it couples furrow formation to anaphase onset by concentrating contractile ring proteins on the equatorial cortex in a midzone-independent manner and 2) it subsequently refines spindle midzone-based signaling to restrict furrowing to a single site.
Na+/H+Exchanger Regulatory Factor 1 Overexpression-dependent Increase of Cytoskeleton Organization Is Fundamental in the Rescue of F508del Cystic Fibrosis Transmembrane Conductance Regulator in Human Airway CFBE41o- Cells
Authors: Favia Maria , Guerra Lorenzo , Fanelli Teresa , Cardone Rosa Angela , Monterisi Stefania , Di Sole Francesca , Castellani Stefano , Chen Mingmin , Seidler Ursula , Reshkin Stephan Joel , Conese Massimo , Casavola Valeria
Published: November 2009

We have demonstrated that Na+/H+exchanger regulatory factor 1 (NHERF1) overexpression in CFBE41o- cells induces a significant redistribution of F508del cystic fibrosis transmembrane conductance regulator (CFTR) from the cytoplasm to the apical membrane and rescues CFTR-dependent chloride secretion. Here, we observe that CFBE41o- monolayers displayed substantial disassembly of actin filaments and that overexpression of wild-type (wt) NHERF1 but not NHERF1-Δ Ezrin-Radixin-Moesin (ERM) increased F-actin assembly and organization. Furthermore, the dominant-negative band Four-point one, Ezrin, Radixin, Moesin homology (FERM) domain of ezrin reversed the wt NHERF1 overexpression-induced increase in both F-actin and CFTR-dependent chloride secretion. wt NHERF1 overexpression enhanced the interaction between NHERF1 and both CFTR and ezrin and between ezrin and actin and the overexpression of wt NHERF1, but not NHERF1-ΔERM, also increased the phosphorylation of ezrin in the apical region of the cell monolayers. Furthermore, wt NHERF1 increased RhoA activity and transfection of constitutively active RhoA in CFBE41o- cells was sufficient to redistribute phospho-ezrin to the membrane fraction and rescue both the F-actin content and the CFTR-dependent chloride efflux. Rho kinase (ROCK) inhibition, in contrast, reversed the wt NHERF1 overexpression-induced increase of membrane phospho-ezrin, F-actin content, and CFTR-dependent secretion. We conclude that NHERF1 overexpression in CFBE41o- rescues CFTR-dependent chloride secretion by forming the multiprotein complex RhoA-ROCK-ezrin-actin that, via actin cytoskeleton reorganization, tethers F508del CFTR to the cytoskeleton stabilizing it on the apical membrane.
ARH: predicting splice variants from genome-wide data with modified entropy
Authors: Rasche Axel , Herwig Ralf
Published: November 2009

Motivation: Exon arrays allow the quantitative study of alternative splicing (AS) on a genome-wide scale. A variety of splicing prediction methods has been proposed for Affymetrix exon arrays mainly focusing on geometric correlation measures or analysis of variance. In this article, we introduce an information theoretic concept that is based on modification of the well-known entropy function.

Results: We have developed an AS robust prediction method based on entropy (ARH). We can show that this measure copes with bias inherent in the analysis of AS such as the dependency of prediction performance on the number of exons or variable exon expression. In order to judge the performance of ARH, we have compared it with eight existing splicing prediction methods using experimental benchmark data and demonstrate that ARH is a well-performing new method for the prediction of splice variants.

Availability and Implementation: ARH is implemented in R and provided in the Supplementary Material.

Contact:  rasche@molgen.mpg.de

Supplementary information:  Supplementary data are available at Bioinformatics online.
Modeling the interplay of single-stranded binding proteins and nucleic acid secondary structure
Authors: Forties Robert A. , Bundschuh Ralf
Published: November 2009

Motivation: There are many important proteins which bind single-stranded nucleic acids, such as the nucleocapsid protein in HIV and the RecA DNA repair protein in bacteria. The presence of such proteins can strongly alter the secondary structure of the nucleic acid molecules. Therefore, accurate modeling of the interaction between single-stranded nucleic acids and such proteins is essential to fully understand many biological processes.

Results: We develop a model for predicting nucleic acid secondary structure in the presence of single-stranded binding proteins, and implement it as an extension of the Vienna RNA Package. All parameters needed to model nucleic acid secondary structures in the absence of proteins have been previously determined. This leaves the footprint and sequence-dependent binding affinity of the protein as adjustable parameters of our model. Using this model we are able to predict the probability of the protein binding at any position in the nucleic acid sequence, the impact of the protein on nucleic acid base pairing, the end-to-end distance distribution for the nucleic acid and FRET distributions for fluorophores attached to the nucleic acid.

Availability: Source code for our modified version of the Vienna RNA package is freely available at http://bioserv.mps.ohio-state.edu/Vienna+P, implemented in C and running on Linux.

Contact:  bundschuh@mps.ohio-state.edu
Preventive Control of Pythium Root Dysfunction in Creeping Bentgrass Putting Greens and Sensitivity of Pythium volutum to Fungicides
Authors: Kerns J. P. , Soika M. D. , Tredway L. P.
Published: November 2009

Pythium root dysfunction (PRD), caused by Pythium volutum, has been observed on golf course putting greens established with creeping bentgrass in the southeastern United States since 2002. To evaluate preventative strategies for management of this disease, a 3-year field experiment was conducted in Pinehurst, NC on a ‘G-2’ creeping bentgrass putting green. Fungicide treatments were applied twice in the fall (September and October) and three times in the spring (March, April, and May) in each of the 3 years. Applications of pyraclostrobin provided superior preventative control compared with the other fungicides tested. Azoxystrobin and cyazofamid provided moderate control of PRD in two of three seasons. Experiments were conducted to determine whether the disease suppression provided by pyraclostrobin was due to fungicidal activity or physiological effects on the host. In vitro sensitivity to pyraclostrobin, azoxystrobin, fluoxastrobin, cyazofamid, mefenoxam, propamocarb, and fluopicolide was determined for 11 P. volutum isolates and 1 P. aphanidermatum isolate. Isolates of P. volutum were most sensitive to pyraclostrobin (50% effective concentration [EC50] value = 0.005), cyazofamid (EC50 = 0.004), and fluoxastrobin (EC50= 0.010), followed by azoxystrobin (EC50 = 0.052), and mefenoxam (EC50 = 0.139). P. volutum isolates were not sensitive to fluopicolide or propamocarb. Applications of pyraclostrobin did not increase the foliar growth rate or visual quality of creeping bentgrass in growth-chamber experiments. This work demonstrates that fall and spring applications of pyraclostrobin, azoxystrobin, and cyazofamid suppress the expression of PRD symptoms during summer and that field efficacy is related to the sensitivity of P. volutum to these fungicides.
Greenhouse Evaluation of Seed and Drench Treatments for Organic Management of Soilborne Pathogens of Spinach
Authors: Cummings Jaime A. , Miles Carol A. , du Toit Lindsey J.
Published: November 2009

The efficacy of 14 seed and drench treatments for control of soilborne damping-off pathogens in organic production of spinach was evaluated in a greenhouse study. The efficacy of each treatment was compared with nontreated seed and seed treated with a conventional fungicide for control of Fusarium oxysporum f. sp. spinaciae, Pythium ultimum, and Rhizoctonia solani. Two experimental seed treatments, GTG I and GTG II (each comprised of a proprietary organic disinfectant and the latter also containing Trichoderma harzianum T22), provided equivalent control to the conventional fungicide, mefenoxam, against P. ultimum in one trial and significant reduction of damping-off in the second trial. Natural II and Natural X (Streptomycete products), and Subtilex (Bacillus subtilis) seed treatments each suppressed damping-off significantly in one of the two trials. For R. solani, GTG I and Natural II seed treatments reduced damping-off as effectively as a drench with the fungicide Terraclor (pentachloronitrobenzene). A soil drench with Prestop (Gliocladium catenulatum) suppressed postemergence wilt caused by F. oxysporum in both trials; a compost tea drench and seed treatment with Yield Shield (Bacillus pumilis) each suppressed postemergence wilt in only one of two trials. GTG I and GTG II significantly increased seed germination compared to nontreated seed. No treatment was effective against all three pathogens, and some treatments exacerbated damping-off.