bluuebunny/crossref_metadata_2025 huggingface dataset:
Molecular dynamics studies of the energetics of translocation in model T7 RNA polymerase elongation complexes
Authors: Woo Hyung‐June , Liu Yuemin , Sousa Rui
Published: June 2008

Translocation in the single subunit T7 RNA polymerase elongation complex was studied by molecular dynamics simulations using the posttranslocated crystal structure with the fingers domain open, an intermediate stable in the absence of pyrophosphate, magnesium ions, and nucleotide substrate. Unconstrained and umbrella sampling simulations were performed to examine the energetics of translocations. The extent of translocation was quantified using reaction coordinates representing the average and individual displacements of the RNA‐DNA hybrid base pairs with respect to a reference structure. In addition, an unconstrained simulation was also performed for the product complex with the fingers domain closed, but with the pyrophosphate and magnesium removed, in order to examine the local stability of the pretranslocated closed state after the pyrophosphate release. The average spatial movement of the entire hybrid was found to be energetically costly in the post‐ to pretranslocated direction in the open state, while the pretranslocated state was stable in the closed complex, supporting the notion that the conformational state dictates the global stability of translocation states. However, spatial fluctuations of the RNA 3′‐end in the open conformation were extensive, with the typical range reaching 3–4 Å. Our results suggest that thermal fluctuations play more important roles in the translocation of individual nucleotides than in the movement of large sections of nucleotide strands: RNA 3′‐end can move into and out of the active site within a single conformational state, while a global movement of the hybrid may be thermodynamically unfavorable without the conformational change. Proteins 2008. © 2008 Wiley‐Liss, Inc.
A study of the electric quadrupole Raman processes of the proton‐conducting KHSeO4 and KDSeO4 single crystals using 1H, 2H and 39K NMR
Authors: Lim Ae Ran , Yoon Choon Sup
Published: June 2008

The spin–lattice relaxation time, T1, and the spin–spin relaxation time, T2, of the 1H, 2H, and 39K nuclei in KHSeO4 and KDSeO4 crystals were determined in the temperature range 160–420 K. The T1 of the 39K nuclei in the two crystals were found to decrease with increasing temperature, and the spin–lattice relaxation rate, T1–1, for 39K is proportional to Tk. In the case of KHSeO4, T1–1 for the 39K nuclei was found to have a very strong temperature dependence, i.e. it is proportional to T7. The temperature dependence of the 39K relaxation rate in KDSeO4 is in accordance with a Raman process, as T1–1 ∝ T2. Thus, for the 39K nuclei in the two crystals, Raman processes with k = 2 and 7 is due to the coupling of electric quadrupole moments to the thermal fluctuations of the local electric field gradients. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Strategic resources and performance: a meta‐analysis
Authors: Crook T. Russell , Ketchen David J. , Combs James G. , Todd Samuel Y.
Published: June 2008

Resource‐based theory (RBT) has emerged as a key perspective guiding inquiry into the determinants of organizational performance. Since the early 1990s, numerous studies have examined RBT's assertion that the extent to which organizations possess strategic resources is positively related to performance. Although many studies appear to support this assertion, there is no consensus regarding how strongly strategic resources relate to performance. To help resolve this issue, we meta‐analyze 125 studies of RBT that collectively encompass over 29,000 organizations. Our conservative estimate is that the effect size of the strategic resources–performance relationship is r̄c = 0.22. Moderator tests suggest that the resources‐performance link is stronger (1) when resources meet the criteria laid out in RBT and (2) for those performance measures that are not affected by potential value appropriation. When resources meet RBT's criteria and when performance measures are not affected by potential appropriation, the strength of the relationship grows to r̄c = 0.29. This suggests that the identification, development, and distribution of value from strategic resources should be a primary consideration for scholars, managers, and shareholders. Copyright © 2008 John Wiley & Sons, Ltd.
Exploring the impact of parental involvement on student development
Authors: Taub Deborah J.
Published: June 2008

This chapter considers the impact that parental involvement may have on the psychosocial development of college students.
Capitalizing on parent and family partnerships through programming
Authors: Ward‐Roof Jeanine A. , Heaton Patrick M. , Coburn Mary B.
Published: June 2008

Interaction with parents and family members continues to increase on college campuses across the nation. This chapter reviews best practices for communicating with and programming for parents and family members of enrolled students.
Effects of thermally oxidized triglycerides on the oxidative stability of soybean oil
Authors: Yoon S. H. , Jung M. Y. , Min D. B.
Published: June 2008

Soybean oil purified by silicic acid column chromatography did not contain peroxides, free fatty acids, phospholipids or oxidized polar compounds. The purified soybean oil was thermally oxidized at 180°C for 96 hr in the presence of air. The thermally oxidized compounds (31.3%) were separated from the purified soybean oil by gradient elution silicic acid chromatography. Thermally oxidized compounds contained hydroxyl groups, carbonyl groups andtrans double bonds according to the infrared spectrum. Thermally oxidized compounds were added to soybean oil and purified soybean oil at 0, 0.5, 1.0, 1.5 and 2.0% to study the effects of these compounds on the oxidative stability of oil. The oxidative stabilities of oils were determined by gas chromatographic analysis of volatile compound formation and molecular oxygen disappearance in the headspace of oil bottles. The thermally oxidized compounds showed prooxidant effects on the oxidative stabilities of both refined, bleached and deodorized soybean oil and purified soybean oil. Duncan's Multiple Range Test showed that thermally oxidized compounds had a significant effect on the volatile compound formatiion and oxygen disappearance in the headspace of oil at α=0.05.
Securing Europe's Energy Future: The Ukrainian Perspective
Authors: Tymoshenko Yulia
Published: June 2008

Ukraine holds a pivotal position geographically, historically and politically alongside Europe and Russia. It is experiencing first-hand how the remnants of communist policies on energy use influence current practices, and how inefficient energy use at the residential and industrial levels threatens economic growth and financial security. This article aims to address the challenge of energy insecurity, encouraging a pan-European attitude to practical policy formation and implementation. In outlining the issues, the challenges posed by the Russian and Eastern European psyche and the will of Western Europe, a case is presented for a meaningful project with the potential for the emerging democracies to play an essential role in ensuring the future energy stability of Europe.
Malnutrition prevalence in The Netherlands: results of the Annual Dutch National Prevalence Measurement of Care Problems
Authors: Meijers Judith M. M. , Schols Jos M. G. A. , vanBokhorst-de van der Schueren Marian A. E. , Dassen Theo , Janssen Maaike A. P. , Halfens Ruud J. G.
Published: June 2008

The objective of this study was to provide data on malnutrition prevalence in hospitals, nursing homes and home-care organisations in The Netherlands in a nationally representative sample, and to assess the factors such as age, sex, time since admission, ward type and disease for identifying patients at high risk of malnutrition. A cross-sectional, multi-centre design with a standardised questionnaire was used to measure the prevalence of malnutrition. Nutritional status was assessed by BMI, undesired weight loss and nutritional intake. In this study, 12 883 patients were included. The prevalence of malnutrition was the highest in hospitals (23·8 %), followed by home-care organisations (21·7 %) and nursing homes (19·2 %). Logistic regression analysis revealed no association with age, time since admission and ward type. Being female was associated with malnutrition only in nursing homes. Blood diseases, gastrointestinal tract diseases, infection, chronic obstructive pulmonary disease, dementia and cancer were the factors associated with malnutrition in hospitals. Dementia was associated with malnutrition in nursing homes, while gastrointestinal tract diseases, diabetes mellitus and cancer were the associated factors in home care. This study shows that malnutrition is still a substantial problem in hospitals, nursing homes and home care in The Netherlands. Malnutrition is a problem for more than one in five patients. Despite growing attention to the problem, more continued alertness is required.
Disability and the Implications of the Wellbeing Agenda: Some Reflections from the United Kingdom
Authors: EDWARDS CLAIRE , IMRIE ROB
Published: June 2008

A wellbeing agenda has emerged in government that seeks to promote a ‘politics of happiness’, in which citizens are, as the New Economics Foundation put it, ‘happy, healthy, capable and engaged’ (2004: 2). This article explores the wellbeing agenda in the UK, and its implications for disabled people. We argue that it is unlikely, in its present form, to contribute to the development of social theoretical, or more politically progressive, analysis and understanding of disablement in society. This is because of the emphasis on biologism, personality and character traits, and a policy prognosis that revolves around self-help and therapy, or individuated actions and (self) responsibilities.
Judging a Book by its Cover: Did Perceptions of the 1996 US Welfare Reforms Affect Public Support for Spending on the Poor?
Authors: HETLING ANDREA , McDERMOTT MONIKA L.
Published: June 2008

Research into public policy and public opinion demonstrates ample evidence that opinion affects policy, but relatively limited empirical findings regarding how policy might affect opinion: a process dubbed policy feedback. Much of the literature examines aggregate reactions to policy, while related public opinion research emphasises individual findings driven primarily by party affiliation or political ideology. This article takes the research one step further, examining whether individuals' judgements of policy effectiveness contribute to their support for or opposition to government policy spending. Specifically, it examines the case of US welfare reform and public reactions to it using a national survey conducted in 2001. Findings based on multinomial logistic regression analysis demonstrate not only that people's judgements of welfare reform's effectiveness contribute to their support for government spending on the poor, but also that the reasons behind their judgements matter.
Approximating the maximum ergodic average via periodic orbits
Authors: COLLIER D. , MORRIS I. D.
Published: June 2008

Let σ:ΣA→ΣA be a subshift of finite type, let $\mathcal {M}_\sigma $ be the set of all σ-invariant Borel probability measures on ΣA, and let $f\colon \Sigma _A \to \mathbb {R}$ be a Hölder continuous observable. There exists at least one σ-invariant measure μ which maximizes $\int f \,d\mu $. The following question was asked by B. R. Hunt, E. Ott and G. Yuan: how quickly can the maximum of the integrals $\int f \,d\mu $ be approximated by averages along periodic orbits of period less than p? We give an example of a Hölder observable f for which this rate of approximation is slower than stretched-exponential in p.
FETAL NEUROIMAGING
Authors: POOH R.K. , POOH K.H.
Published: June 2008

Imaging technologies have been remarkably improved and contribute to prenatal evaluation of fetal central nervous system (CNS) development and assessment of CNS abnormalities in utero.
Spatial and temporal variability in aerosol properties over the Mediterranean basin based on 6‐year (2000–2006) MODIS data
Authors: Papadimas C. D. , Hatzianastassiou N. , Mihalopoulos N. , Querol X. , Vardavas I.
Published: June 2008

The temporal variability of aerosol optical properties is investigated over the broader Mediterranean basin, with emphasis on aerosol optical depth (AOD) that is an effective measure of aerosol load. The study is performed using Collection 005 Level‐3 mean daily spectral aerosol data from the Moderate Resolution Imaging Spectroradiometer (MODIS) instrument on board the Terra and Aqua satellites, which cover the 6‐year period from 2000 to 2006. The results of our analysis reveal a significant interannual variability of AOD in the study region. Specifically, the regional mean visible AOD over land and ocean has decreased over the period 2000–2006 by 20% in relative percentage terms (or by 0.04 in absolute terms). This tendency is statistically significant according to the Man‐Kendall test. However, the decreasing tendency of AOD is not uniform over the whole basin. It appears mainly in the western parts of Iberian, Italian, and Balkan peninsulas (and coastal areas), as well as in the southern Anatolian peninsula. The analysis for summer (June to September) and winter (November to March) seasons revealed different tendencies in both AOD and precipitation. The summer‐period AOD has decreased by 0.04 (or by 14%) probably due to decreased emission rates of anthropogenic pollution. In contrast, the winter AOD has increased by 0.03 (or 19%) mainly related to decreased precipitation (associated with an increasing tendency in the NAO index). The decreasing tendency in MODIS AOD is in good agreement with corresponding AOD tendencies based on data from Aerobot Robotic Network (AERONET) stations in the study region and ground based PM10 measurements at selected stations.
A new river flooding scheme for global climate applications: Off‐line evaluation over South America
Authors: Decharme B. , Douville H. , Prigent C. , Papa F. , Aires F.
Published: June 2008

Given their strong interaction with both climate and the carbon cycle, wetlands and surface waters need to be parameterized in global general circulation models. For this purpose, a new simple flooding river scheme is proposed and evaluated over South America. The flood dynamics is described through the coupling between the ISBA land surface model and the TRIP river routing model including a prognostic flood reservoir. This reservoir fills when the river height exceeds a critical value and vice versa. The reservoir interacts with the soil hydrology through infiltration and with the overlying atmosphere through precipitation interception and free water surface evaporation. The model is tested in off‐line mode using the 10‐year ISLSCP‐2 atmospheric forcing. The evaluation is made against satellite‐derived inundation estimates as well as in situ river discharge observations. Besides a basin‐scale increase in annual surface evaporation, the results show improved monthly discharges over the Amazon and Parana rivers, as well as a reasonable agreement between the simulated flooded areas and satellite‐derived inundation estimates.
A review on Hilbert‐Huang transform: Method and its applications to geophysical studies
Authors: Huang Norden E. , Wu Zhaohua
Published: June 2008

Data analysis has been one of the core activities in scientific research, but limited by the availability of analysis methods in the past, data analysis was often relegated to data processing. To accommodate the variety of data generated by nonlinear and nonstationary processes in nature, the analysis method would have to be adaptive. Hilbert‐Huang transform, consisting of empirical mode decomposition and Hilbert spectral analysis, is a newly developed adaptive data analysis method, which has been used extensively in geophysical research. In this review, we will briefly introduce the method, list some recent developments, demonstrate the usefulness of the method, summarize some applications in various geophysical research areas, and finally, discuss the outstanding open problems. We hope this review will serve as an introduction of the method for those new to the concepts, as well as a summary of the present frontiers of its applications for experienced research scientists.
Internal melting in Antarctic sea ice: Development of “gap layers”
Authors: Ackley S. F. , Lewis M. J. , Fritsen C. H. , Xie Hongjie
Published: June 2008

An internal “gap” layer of deteriorated sea ice is co‐located with a significant microbial biological community in late first year and second year Antarctic sea ice in summer. We modeled gap layer formation using a thermal flux model based on the summer reversal in thermal gradient and the thermal conductivity found in the upper ice column. The conductive model gives internal sea ice melt rates (gap layer formation rates) between 0.1 to 0.75cm/day. The cumulative melted layer thicknesses during summer computed from these rates agree with field observations. Since the processes for forming these structures act in the vertical direction only and over a significant range of expected conditions, they are commonly formed in the Antarctic sea ice zone during summer, supporting a significant contribution of gap layers to the ice mass balance and productivity on a circumpolar basis.
A criterion for delimiting active periods within turbulent flows
Authors: Keylock C. J.
Published: June 2008

Delimiting effectively the extent of the major motions in atmospheric, tidal and fluvial turbulent flows is an important task for studies of mixing and particle transport. The most common method for this (quadrant analysis) is closely linked to the turbulent stresses but subdivides active periods in the flow into separate events. A method based on the pointwise Hölder characteristics of the velocity data is introduced in this paper and applied to extract the whole duration of the active periods, within which turbulence intensities and stresses are high for some of the time. The cross‐correlation structure of the Hölder series permits a simple threshold to be adopted. The technique is tested on data from a turbulent wake in a wind tunnel and flow over a forest canopy.
Micron-scale mapping of sulfur cycling across the oxycline of a cyanobacterial mat: a paired nanoSIMS and CARD-FISH approach
Authors: Fike David Andrew , Gammon Crystal Lynn , Ziebis Wiebke , Orphan Victoria Jeanne
Published: June 2008

The metabolic activities of microbial mats have likely regulated biogeochemical cycling over most of Earth's history. However, the relationship between metabolic activity and the establishment of isotopic geochemical gradients in these mats remains poorly constrained. Here we present a parallel microgeochemical and microbiological study of micron-scale sulfur cycling within hypersaline microbial mats from Guerrero Negro, Baja California Sur, Mexico. Dissolved sulfide within the mats was captured on silver discs and analyzed for its abundance and δ34S isotopic composition using high-resolution secondary ion mass spectrometry (nanoSIMS). These results were compared to sulfide and oxygen microelectrode profiles. Two-dimensional microgeochemical mapping revealed well-defined laminations in sulfide concentration (on scales from 1 to 200 μm), trending toward increased sulfide concentrations at depth. Sulfide δ34S decreased from ∼+10‰ to −20‰ in the uppermost 3 mm and oscillated repeatedly between −10‰ and −30‰ down to a depth of 8 mm. These variations are attributed to spatially variable bacterial sulfate reduction within the mat. A parallel examination of the spatial distribution of known sulfate-reducing bacteria within the family Desulfobacteraceae was conducted using catalyzed reporter deposition fluorescence in situ hybridization. Significant concentrations of Desulfobacteraceae were observed in both oxic and anoxic zones of the mat and occurred in several distinct layers, in large aggregates and heterogeneously dispersed as single cells throughout. The spatial distribution of these microorganisms is consistent with the variation in sulfide concentration and isotopic composition we observed. The parallel application of the methodologies developed here can shed light on micron-scale sulfur cycling within microbially dominated sedimentary environments.
Long-term experimental warming alters nitrogen-cycling communities but site factors remain the primary drivers of community structure in high arctic tundra soils
Authors: Walker Jennifer K M , Egger Keith N , Henry Gregory H R
Published: June 2008

Arctic air temperatures are expected to rise significantly over the next century. Experimental warming of arctic tundra has been shown to increase plant productivity and cause community shifts and may also alter microbial community structure. Hence, the objective of this study was to determine whether experimental warming caused shifts in soil microbial communities by measuring changes in the frequency, relative abundance and/or richness of nosZ and nifH genotypes. Five sites at a high arctic coastal lowland were subjected to a 13-year warming experiment using open-top chambers (OTCs). Sites differed by dominant plant community, soil parent material and/or moisture regimen. Six soil cores were collected from each of four replicate OTC and ambient plots at each site and subdivided into upper and lower samples. Differences in frequency and relative abundance of terminal restriction fragments were assessed graphically by two-way cluster analysis and tested statistically with permutational multivariate analysis of variance (ANOVA). Genotypic richness was compared using factorial ANOVA. The genotype frequency, relative abundance and genotype richness of both nosZ and nifH communities differed significantly by site, and by OTC treatment and/or depth at some sites. The site that showed the most pronounced treatment effect was a wet sedge meadow, where community structure and genotype richness of both nosZ and nifH were significantly affected by warming. Although warming was an important factor affecting these communities at some sites at this high arctic lowland, overall, site factors were the main determinants of community structure.
Indole cell signaling occurs primarily at low temperatures in Escherichia coli
Authors: Lee Jintae , Zhang Xue-Song , Hegde Manjunath , Bentley William E , Jayaraman Arul , Wood Thomas K
Published: June 2008

We have shown that the quorum-sensing signals acylhomoserine lactones, autoinducer-2 (AI-2) and indole influence the biofilm formation of Escherichia coli. Here, we investigate how the environment, that is, temperature, affects indole and AI-2 signaling in E. coli. We show in biofilms that indole addition leads to more extensive differential gene expression at 30 °C (186 genes) than at 37 °C (59 genes), that indole reduces biofilm formation (without affecting growth) more significantly at 25 and 30 °C than at 37 °C and that the effect is associated with the quorum-sensing protein SdiA. The addition of indole at 30 °C compared to 37 °C most significantly repressed genes involved in uridine monophosphate (UMP) biosynthesis (carAB, pyrLBI, pyrC, pyrD, pyrF and upp) and uracil transport (uraA). These uracil-related genes are also repressed at 30 °C by SdiA, which confirms SdiA is involved in indole signaling. Also, compared to 37 °C, indole more significantly decreased flagella-related qseB, flhD and fliA promoter activity, enhanced antibiotic resistance and inhibited cell division at 30 °C. In contrast to indole and SdiA, the addition of (S)-4,5-dihydroxy-2,3-pentanedione (the AI-2 precursor) leads to more extensive differential gene expression at 37 °C (63 genes) than at 30 °C (11 genes), and, rather than repressing UMP synthesis genes, AI-2 induces them at 37 °C (but not at 30 °C). Also, the addition of AI-2 induces the transcription of virulence genes in enterohemorrhagic E. coli O157:H7 at 37 °C but not at 30 °C. Hence, cell signals cause diverse responses at different temperatures, and indole- and AI-2-based signaling are intertwined.
Adiposity and Eating Behaviors in Patients Under Second Generation Antipsychotics
Authors: Blouin Mélissa , Tremblay Angelo , Jalbert Marie‐Eve , Venables Hélène , Bouchard Roch‐Hugo , Roy Marc‐André , Alméras Natalie
Published: June 2008

Background: Second generation antipsychotics (SGA) induce substantial weight gain but the mechanisms responsible for this phenomenon remain speculative.

Objective: To explore eating behaviors among SGA‐treated patients and compare them with nonschizophrenic healthy sedentary individuals (controls).

Methods and Procedures: Appetite sensations were recorded before and after a standardized breakfast using visual analog scales. Three hours after breakfast, a buffet‐type meal was offered to participants to document spontaneous food intake and food preferences. Satiety quotients (SQs) were calculated to determine the satiation of both meals and the Three‐Factor Eating Questionnaire (TFEQ) was used to document eating behaviors. Body composition and abdominal fat distribution were assessed.

Results: Compared with controls (n = 20), SGA‐treated patients (n = 18) showed greater adiposity indices (P ≤ 0.04). Patients' degree of hunger was also higher following the standardized breakfast (P = 0.03). Moreover, patients had significantly higher cognitive dietary restraint, disinhibition, and susceptibility to hunger scores than the reference group (P ≤ 0.05). Disinhibition in the reference group was positively associated with hunger triggered by external cues (r = 0.48, P = 0.03) whereas internal cues seem to mainly regulate emotional susceptibility to disinhibition in patients (r = 0.56, P = 0.02). Higher strategic restraint behavior in patients was associated with decreased satiation right after the buffet‐type meal (r = −0.56, P = 0.02).

Discussion: These exploratory findings suggest that patients under SGA seem to develop disordered eating behaviors in response to altered appetite sensations and increased susceptibility to hunger, a factor which may influence the extent of body weight gain triggered by these drugs.
Beverage Consumption Patterns of Children Born at Different Risk of Obesity
Authors: Kral Tanja V.E. , Stunkard Albert J. , Berkowitz Robert I. , Stallings Virginia A. , Moore Reneé H. , Faith Myles S.
Published: June 2008

Background: Increased intake of sugar‐sweetened beverages and fruit juice has been associated with overweight in children.

Objective: This study prospectively assessed beverage consumption patterns and their relationship with weight status in a cohort of children born at different risk for obesity.

Methods and Procedures: Participants were children born at low risk (n = 27) or high risk (n = 22) for obesity based on maternal prepregnancy BMI (kg/m2). Daily beverage consumption was generated from 3‐day food records from children aged 3–6 years and coded into seven beverage categories (milk, fruit juice, fruit drinks, caloric and noncaloric soda, soft drinks including and excluding fruit juice). Child anthropometric measures were assessed yearly.

Results: High‐risk children consumed a greater percentage of daily calories from beverages at age 3, more fruit juice at ages 3 and 4, more soft drinks (including fruit juice) at ages 3–5, and more soda at age 6 compared to low‐risk children. Longitudinal analyses showed that a greater 3‐year increase in soda intake was associated with an increased change in waist circumference, whereas a greater increase in milk intake was associated with a reduced change in waist circumference. There was no significant association between change in intake from any of the beverage categories and change in BMI z‐score across analyses.

Discussion: Children's familial predisposition to obesity may differentially affect their beverage consumption patterns. Future research should examine the extent to which dietary factors may play a role in pediatric body fat deposition over time.
The Lifetime Medical Cost Burden of Overweight and Obesity: Implications for Obesity Prevention
Authors: Finkelstein Eric A. , Trogdon Justin G. , Brown Derek S. , Allaire Benjamin T. , Dellea Pam S. , Kamal‐Bahl Sachin J.
Published: June 2008

This study quantifies age‐specific and lifetime costs for overweight (BMI: 25–29.9), obese I (BMI: 30–34.9), and obese II/III (BMI: >35) adults separately by race/gender strata. We use these results to demonstrate why private sector firms are likely to underinvest in obesity prevention efforts. Not only does the existence of Medicare reduce the economic burden that obesity imposes on private payers, but, from the perspective of a 20‐year‐old obese adult, the short‐term costs of obesity are small. This suggests that legislation that subsidizes wellness programs and/or mandates coverage for obesity treatments might make all firms better off. Ironically, Medicare has a greater incentive to prevent obesity because when an obese 65 year old enters the program, his/her costs are immediate and higher than costs for normal weight individuals.
Lagrangian structure functions in turbulence: A quantitative comparison between experiment and direct numerical simulation
Authors: Biferale L. , Bodenschatz E. , Cencini M. , Lanotte A. S. , Ouellette N. T. , Toschi F. , Xu H.
Published: June 2008

A detailed comparison between data from experimental measurements and numerical simulations of Lagrangian velocity structure functions in turbulence is presented. Experimental data, at Reynolds number ranging from Rλ=350 to Rλ=815, are obtained in a swirling water flow between counter-rotating baffled disks. Direct numerical simulations (DNS) data, up to Rλ=284, are obtained from a statistically homogeneous and isotropic turbulent flow. By integrating information from experiments and numerics, a quantitative understanding of the velocity scaling properties over a wide range of time scales and Reynolds numbers is achieved. To this purpose, we discuss in detail the importance of statistical errors, anisotropy effects, and finite volume and filter effects, finite trajectory lengths. The local scaling properties of the Lagrangian velocity increments in the two data sets are in good quantitative agreement for all time lags, showing a degree of intermittency that changes if measured close to the Kolmogorov time scales or at larger time lags. This systematic study resolves apparent disagreement between observed experimental and numerical scaling properties.
Time-resolved momentum imaging system for molecular dynamics studies using a tabletop ultrafast extreme-ultraviolet light source
Authors: Gagnon Etienne , Sandhu Arvinder S. , Paul Ariel , Hagen Kim , Czasch Achim , Jahnke Till , Ranitovic Predrag , Lewis Cocke C. , Walker Barry , Murnane Margaret M. , Kapteyn Henry C.
Published: June 2008

We describe a momentum imaging setup for direct time-resolved studies of ionization-induced molecular dynamics. This system uses a tabletop ultrafast extreme-ultraviolet (EUV) light source based on high harmonic upconversion of a femtosecond laser. The high photon energy (around 42eV) allows access to inner-valence states of a variety of small molecules via single photon excitation, while the sub-–10-fs pulse duration makes it possible to follow the resulting dynamics in real time. To obtain a complete picture of molecular dynamics following EUV induced photofragmentation, we apply the versatile cold target recoil ion momentum spectroscopy reaction microscope technique, which makes use of coincident three-dimensional momentum imaging of fragments resulting from photoexcitation. This system is capable of pump-probe spectroscopy by using a combination of EUV and IR laser pulses with either beam as a pump or probe pulse. We report several experiments performed using this system.
Power balance in a high-density field reversed configuration plasma
Authors: Renneke R. M. , Intrator T. P. , Hsu S. C. , Wurden G. A. , Waganaar W. J. , Ruden E. L. , Grabowski T. C.
Published: June 2008

A global power balance analysis has been performed for the Field Reversed Experiment with Liner high density (>5×1022m−3) field reversed configuration (FRC) plasma. The analysis was based on a zero-dimensional power balance model [D. J. Rey and M. Tuszewski, Phys. Fluids 27, 1514 (1984)]. The key findings are as follows. First, the percentage of radiative losses relative to total loss is an order of magnitude lower than previous lower density FRC experiments. Second, Ohmic heating was found to correlate with the poloidal flux trapping at FRC formation, suggesting that poloidal flux dissipation is primarily responsible for plasma heating. Third, high density FRCs analyzed in this work reinforce the low-density adiabatic scaling, which shows that particle confinement time and flux confinement time are approximately equal.
Bandstructure effects in ultra-thin-body double-gate field effect transistor: A fullband analysis
Authors: Majumdar Kausik , Bhat Navakanta
Published: June 2008

The properties of an n-channel ultra-thin-body (UTB) double-gate field effect transistor (DGFET), resulting from the bandstructure of the thin film Si channel, are discussed in this paper. The bandstructure has been calculated using a ten-orbital sp3d5s∗ tight-binding method. A number of intrinsic properties including band gap, density of states, intrinsic carrier concentration, and parabolic effective mass have been derived from the calculated bandstructure. The spatial distributions of intrinsic carrier concentration and ⟨100⟩ effective mass, resulting from the wave functions of different contributing subbands, are analyzed. A self-consistent solution of coupled Poisson-Schrödinger equations is obtained taking the full bandstructure into account, which is then applied to analyze volume inversion. The spatial distribution of carriers over the channel of a DGFET has been calculated and its effect on effective mass and channel capacitance is discussed.
Production of pulsed, mass-selected beams of metal and semiconductor clusters
Authors: Kamalou Omar , Rangama Jimmy , Ramillon Jean-Marc , Guinement Patrick , Huber Bernd A.
Published: June 2008

We report on the development of a beam line for mass-selected metal and semiconductor clusters. The cluster source combines the principles of plasma sputtering and gas condensation. Both techniques together allow to produce clusters in a wide size range. With the aid of a time-of-flight system, small clusters (i.e., Cun+, n<100) are selected and pure beams containing only one cluster size are provided. For large clusters (containing several thousands of atoms), a beam with a narrow size distribution is obtained. A 90° quadrupole deviator is used to separate charged clusters from neutral ones.
In situ fabrication of Co90Nb10 soft magnetic thin films with adjustable resonance frequency from 1.3to4.9GHz
Authors: Fan Xiaolong , Xue Desheng , Lin Min , Zhang Zhengmei , Guo Dangwei , Jiang Changjun , Wei Jianqiang
Published: June 2008

In this work, we realized in situ fabricated Co90Nb10 soft magnetic thin films, with variable in-plane uniaxial magnetic anisotropy, without using the field induced method or postfabrication treatment. In situ control over the in-plane uniaxial magnetic anisotropy field, which varied from 1.6to22.7kAm−1, was achieved by adjusting the deposition oblique angle from 0° to 38°. As a consequence, the resonance frequencies of the films were continuously increased from 1.3to4.9GHz.
Ultraviolet nanoimprinted polymer nanostructure for organic light emitting diode application
Authors: Jeon Sohee , Kang Jae-Wook , Park Hyung-Dol , Kim Jang-Joo , Youn Jae R. , Shim Jongyoup , Jeong Jun-ho , Choi Dae-Geun , Kim Ki-Don , Altun Ali Ozhan , Kim Se-Heon , Lee Yong-Hee
Published: June 2008

Light extraction efficiency of a conventional organic light emitting diode (OLED) remains limited to approximately 20% as most of the emission is trapped in the waveguide and glass modes. An etchless simple method was developed to fabricate two-dimensional nanostructures on glass substrate directly by using ultraviolet (UV) curable polymer resin and UV nanoimprint lithography in order to improve output coupling efficiency of OLEDs. The enhancement of the light extraction was predicted by the three-dimensional finite difference time domain method. OLEDs integrated on nanoimprinted substrates enhanced electroluminance intensity by up to 50% compared to the conventional device.
High-brightness relaxed-bend state in a pi cell stabilized by synchronized polymerization
Authors: Yang Bo-Ru , Elston Steve J. , Raynes Peter , Shieh Han-Ping D.
Published: June 2008

The authors report a synchronized polymer-stabilization technique which can be used to stabilize the nonpermanent states in liquid crystal devices. In this paper, a relaxed-bend state in a pi cell which has a lifetime of only 80ms is observed and then stabilized by this proposed technique. After stabilizing, the pi cell is immune to undesirable recovery into the splay or twist states, and its optical contrast is much higher than that of the conventional polymer-stabilized pi cell.
The Aryl Hydrocarbon Receptor Binds to E2F1 and Inhibits E2F1-induced Apoptosis
Authors: Marlowe Jennifer L. , Fan Yunxia , Chang Xiaoqing , Peng Li , Knudsen Erik S. , Xia Ying , Puga Alvaro
Published: June 2008

Cellular stress by DNA damage induces checkpoint kinase-2 (CHK2)-mediated phosphorylation and stabilization of the E2F1 transcription factor, leading to induction of apoptosis by activation of a subset of proapoptotic E2F1 target genes, including Apaf1 and p73. This report characterizes an interaction between the aryl hydrocarbon (Ah) receptor (AHR), a ligand-activated transcription factor, and E2F1 that results in the attenuation of E2F1-mediated apoptosis. In Ahr−/−fibroblasts stably transfected with a doxycycline-regulated AHR expression vector, inhibition of AHR expression causes a significant elevation of oxidative stress, γH2A.X histone phosphorylation, and E2F1-dependent apoptosis, which can be blocked by small interfering RNA-mediated knockdown of E2F1 expression. In contrast, ligand-dependent AHR activation protects these cells from etoposide-induced cell death. In cells expressing both proteins, AHR and E2F1 interact independently of the retinoblastoma protein (RB), because AHR and E2F1 coimmunoprecipitate from extracts of RB-negative cells. Additionally, chromatin immunoprecipitation assays indicate that AHR and E2F1 bind to the Apaf1 promoter at a region containing a consensus E2F1 binding site but no AHR binding sites. AHR activation represses Apaf1 and TAp73 mRNA induction by a constitutively active CHK2 expression vector. Furthermore, AHR overexpression blocks the transcriptional induction of Apaf1 and p73 and the accumulation of sub-G0/G1cells resulting from ectopic overexpression of E2F1. These results point to a proproliferative, antiapoptotic function of the Ah receptor that likely plays a role in tumor progression.
ARCHIPELAGO: A Dedicated Resource for Exploiting Past, Present, and Future Genomic Data on Disease Resistance Regulation in Rice
Authors: Vergne E. , Ballini E. , Droc G. , Tharreau D. , Nottéghem J.-L. , Morel J.-B.
Published: June 2008

Large amounts of expression data dealing with biotic stresses in rice have been produced in the past 5 years. Here, we extensively review approximately 70 publications and gather together information on more than 2,500 genes of the rice defense arsenal. This information was integrated into the OryGenesDB database. Several genes (e.g., metallothioneins and PBZ1) appear to be hallmarks of rice–pathogen interactions. Cross-referencing this information with the rice kinome highlighted some defense genes and kinases as possible central nodes of regulation. Cross referencing defense gene expression and quantitative trait loci (QTL) information identified some candidate genes for QTL. Overall, pathogenesis-related genes and disease regulators were found to be statistically associated with disease QTL. At the genomic level, we observed that some regions are richer than others and that some chromosomes (e.g., 11 and 12), which contain a lot of resistance gene analogs, have a low content of defense genes. Finally, we show that classical defense genes and defense-related genes such as resistance genes are preferentially organized in clusters. These clusters are not always coregulated and individual paralogs can show specific expression patterns. Thus, the rice defense arsenal has an ARCHIPELAGO-like genome structure at the macro and micro level. This resource opens new possibilities for marker-assisted selection and QTL cloning.
A Versatile Assay for the Identification of RNA Silencing Suppressors Based on Complementation of Viral Movement
Authors: Powers Jason G. , Sit Tim L. , Qu Feng , Morris T. Jack , Kim Kook-Hyung , Lommel Steven A.
Published: June 2008

The cell-to-cell movement of Turnip crinkle virus (TCV) in Nicotiana benthamiana requires the presence of its coat protein (CP), a known suppressor of RNA silencing. RNA transcripts of a TCV construct containing a reporter gene (green fluorescent protein) (TCV-sGFP) in place of the CP open reading frame generated foci of three to five cells. TCV CP delivered in trans by Agrobacterium tumefaciens infiltration potentiated movement of TCV-sGFP and increased foci diameter, on average, by a factor of four. Deletion of the TCV movement proteins in TCV-sGFP (construct TCVΔ92-sGFP) abolished the movement complementation ability of TCV CP. Other known suppressors of RNA silencing from a wide spectrum of viruses also complemented the movement of TCV-sGFP when delivered in trans by Agrobacterium tumefaciens. These include suppressors from nonplant viruses with no known plant movement function, demonstrating that this assay is based solely on RNA silencing suppression. While the TCV-sGFP construct is primarily used as an infectious RNA transcript, it was also subcloned for direct expression from Agrobacterium tumefaciens for simple quantification of suppressor activity based on fluorescence levels in whole leaves. Thus, this system provides the flexibility to assay for suppressor activity in either the cytoplasm or nucleus, depending on the construct employed.
Differential Gene Expression Between the Biotrophic-Like and Saprotrophic Mycelia of the Witches' Broom Pathogen Moniliophthora perniciosa
Authors: Rincones Johana , Scarpari Leandra M. , Carazzolle Marcelo F. , Mondego Jorge M. C. , Formighieri Eduardo F. , Barau Joan G. , Costa Gustavo G. L. , Carraro Dirce M. , Brentani Helena P. , Vilas-Boas Laurival A. , de Oliveira Bruno V. , Sabha Maricene , Dias Robson , Cascardo Júlio M. , Azevedo Ricardo A. , Meinhardt Lyndel W. , Pereira Gonçalo A. G.
Published: June 2008

Moniliophthora perniciosa is a hemibiotrophic fungus that causes witches' broom disease (WBD) in cacao. Marked dimorphism characterizes this fungus, showing a monokaryotic or biotrophic phase that causes disease symptoms and a later dikaryotic or saprotrophic phase. A combined strategy of DNA microarray, expressed sequence tag, and real-time reverse-transcriptase polymerase chain reaction analyses was employed to analyze differences between these two fungal stages in vitro. In all, 1,131 putative genes were hybridized with cDNA from different phases, resulting in 189 differentially expressed genes, and 4,595 reads were clusterized, producing 1,534 unigenes. The analysis of these genes, which represent approximately 21% of the total genes, indicates that the biotrophic-like phase undergoes carbon and nitrogen catabolite repression that correlates to the expression of phytopathogenicity genes. Moreover, downregulation of mitochondrial oxidative phosphorylation and the presence of a putative ngr1 of Saccharomyces cerevisiae could help explain its lower growth rate. In contrast, the saprotrophic mycelium expresses genes related to the metabolism of hexoses, ammonia, and oxidative phosphorylation, which could explain its faster growth. Antifungal toxins were upregulated and could prevent the colonization by competing fungi. This work significantly contributes to our understanding of the molecular mechanisms of WBD and, to our knowledge, is the first to analyze differential gene expression of the different phases of a hemibiotrophic fungus.
The Outer Membrane Protein TolC from Sinorhizobium meliloti Affects Protein Secretion, Polysaccharide Biosynthesis, Antimicrobial Resistance, and Symbiosis
Authors: Cosme Ana M. , Becker Anke , Santos Mário R. , Sharypova Larissa A. , Santos Pedro M. , Moreira Leonilde M.
Published: June 2008

Sinorhizobium meliloti is capable of establishing a symbiotic nitrogen fixation relationship with Medicago sativa. During this process, it must cope with diverse environments and has evolved different types of transport systems that help its propagation in the plant roots. TolC protein family members are the outer-membrane components of several transport systems involved in the export of diverse molecules, playing an important role in bacterial survival. In this work, we have characterized the protein TolC from S. meliloti 2011. An insertional mutation in the tolC gene strongly affected the resistance phenotype to antimicrobial agents and induced higher susceptibility to osmotic and oxidative stresses. Immunodetection experiments and comparison of the extracellular proteins present in the supernatant of the wild-type versus tolC mutant strains showed that the calcium-binding protein ExpE1, the endoglycanase ExsH, and the product of open reading frame SMc04171, a putative hemolysin-type calcium-binding protein, are secreted by a TolC-dependent secretion system. In the absence of TolC, neither succinoglycan nor galactoglucan were detected in the culture supernatant. Moreover, S. meliloti tolC mutant induced a reduced number of nonfixing nitrogen nodules in M. sativa roots. Taken together, our results confirm the importance of TolC in protein secretion, exopolysaccharide biosynthesis, antimicrobials resistance, and symbiosis.
Mutational Analysis of the Sinorhizobium meliloti Short-Chain Dehydrogenase/Reductase Family Reveals Substantial Contribution to Symbiosis and Catabolic Diversity
Authors: Jacob Asha I. , Adham Sirin A. I. , Capstick David S. , Clark Scott R. D. , Spence Tara , Charles Trevor C.
Published: June 2008

The short-chain dehydrogenase/reductase (SDR) family is one of the largest and most ubiquitous protein families in bacterial genomes. Despite there being a few well-characterized examples, the substrate specificities or functions of most members of the family are unknown. In this study, we carried out a large-scale mutagenesis of the SDR gene family in the alfalfa root nodule symbiont Sinorhizobium meliloti. Subsequent phenotypic analysis revealed phenotypes for mutants of 21 of the SDR-encoding genes. This brings the total number of S. meliloti SDR-encoding genes with known function or associated phenotype to 25. Several of the mutants were deficient in the utilization of specific carbon sources, while others exhibited symbiotic deficiencies on alfalfa (Medicago sativa), ranging from partial ineffectiveness to complete inability to form root nodules. Five of the mutants had both symbiotic and carbon utilization phenotypes. These results clearly demonstrate the importance of the SDR family in both symbiosis and saprotrophy, and reinforce the complex nature of the interaction of S. meliloti with its plant hosts. Further analysis of the genes identified in this study will contribute to the overall understanding of the biology and metabolism of S. meliloti in relation to its interaction with alfalfa.