bluuebunny/crossref_metadata_2025 huggingface dataset:
Nonlocal continuum electrostatic theory predicts surprisingly small energetic penalties for charge burial in proteins
Authors: Bardhan Jaydeep P.
Published: September 2011

We study the energetics of burying charges, ion pairs, and ionizable groups in a simple protein model using nonlocal continuum electrostatics. Our primary finding is that the nonlocal response leads to markedly reduced solvent screening, comparable to the use of application-specific protein dielectric constants. Employing the same parameters as used in other nonlocal studies, we find that for a sphere of radius 13.4 Å containing a single +1e charge, the nonlocal solvation free energy varies less than 18 kcal/mol as the charge moves from the surface to the center, whereas the difference in the local Poisson model is ∼35 kcal/mol. Because an ion pair (salt bridge) generates a comparatively more rapidly varying Coulomb potential, energetics for salt bridges are even more significantly reduced in the nonlocal model. By varying the central parameter in nonlocal theory, which is an effective length scale associated with correlations between solvent molecules, nonlocal-model energetics can be varied from the standard local results to essentially zero; however, the existence of the reduction in charge-burial penalties is quite robust to variations in the protein dielectric constant and the correlation length. Finally, as a simple exploratory test of the implications of nonlocal response, we calculate glutamate pKa shifts and find that using standard protein parameters (εprotein = 2–4), nonlocal results match local-model predictions with much higher dielectric constants. Nonlocality may, therefore, be one factor in resolving discrepancies between measured protein dielectric constants and the model parameters often used to match titration experiments. Nonlocal models may hold significant promise to deepen our understanding of macromolecular electrostatics without substantially increasing computational complexity.
Study of Nb2Oy (y = 2–5) anion and neutral clusters using anion photoelectron spectroscopy and density functional theory calculations
Authors: Mann Jennifer E. , Waller Sarah E. , Rothgeb David W. , Chick Jarrold Caroline
Published: September 2011

A study combining anion photoelectron spectroscopy and density functional theory calculations on the transition metal suboxide series, Nb2Oy− (y = 2−5), is described. Photoelectron spectra of the clusters are obtained, and Franck-Condon simulations using calculated anion and neutral structures and frequencies are used to evaluate the calculations and assign transitions observed in the spectra. The spectra, several of which exhibit partially resolved vibrational structure, show an increase in electron affinity with increasing cluster oxidation state. Hole-burning experiments suggest that the photoelectron spectra of both Nb2O2− and Nb2O3− have contributions from more than one structural isomer. Reasonable agreement between experiment and computational results is found among all oxides.
Polycrystalline iron nitride films fabricated by reactive facing-target sputtering: Structure, magnetic and electrical transport properties
Authors: Feng X. P. , Mi W. B. , Bai H. L.
Published: September 2011

Structure, magnetic and electrical transport properties of the reactive sputtered iron nitride films fabricated at different substrate temperatures (Ts) and nitrogen flow rates (FN2) were investigated systematically. The single-phase polycrystalline γ′-Fe4N film was obtained at FN2 = 20 sccm and Ts = 450 °C. The films are soft ferromagnetic at room temperature. The electrical resistivity (ρ) of the films fabricated at different FN2 and Ts decreases with the decreasing temperature, showing a metallic behavior. Meanwhile, a variety of magnetoresistance (MR) behaviors were observed depending on the applied magnetic field and measuring temperature. It can be deduced that the complex MR behaviors are dominated by Lorentz force, spin-orbit interaction, and weak localization effect.
Ferroelectric Zr0.5Hf0.5O2 thin films for nonvolatile memory applications
Authors: Müller J. , Böscke T. S. , Bräuhaus D. , Schröder U. , Böttger U. , Sundqvist J. , Kücher P. , Mikolajick T. , Frey L.
Published: September 2011

We report the observation of ferroelectricity in capacitors based on hafnium-zirconium-oxide. Hf0.5Zr0.5O2 thin films of 7.5 to 9.5 nm thickness were found to exhibit ferroelectric polarization-voltage hysteresis loops when integrated into TiN-based metal-insulator-metal capacitors. A remnant polarization of 16 μC/cm2 and a high coercive field of 1 MV/cm were observed. Further proof for the ferroelectric nature was collected by quasi-static polarization-voltage hysteresis, small signal capacitance-voltage, and piezoelectric measurements. Data retention characteristics were evaluated by a Positive Up Negative Down pulse technique. No significant decay of the initial polarization state was observed within a measurement range of up to two days.
Controlled oxygen vacancy induced p-type conductivity in HfO2−x thin films
Authors: Hildebrandt Erwin , Kurian Jose , Müller Mathis M. , Schroeder Thomas , Kleebe Hans-Joachim , Alff Lambert
Published: September 2011

We have synthesized highly oxygen deficient HfO2−x thin films by controlled oxygen engineering using reactive molecular beam epitaxy. Above a threshold value of oxygen vacancies, p-type conductivity sets in with up to 6 times 1021 charge carriers per cm3. At the same time, the band-gap is reduced continuously by more than 1 eV. We suggest an oxygen vacancy induced p-type defect band as origin of the observed behavior.
Influence of the silicon carbide surface morphology on the epitaxial graphene formation
Authors: Oliveira M. H. , Schumann T. , Ramsteiner M. , Lopes J. M. J. , Riechert H.
Published: September 2011

Graphene grown on SiC(0001) by Si depletion has a stepped surface with terraces and step heights up to 10 times larger than those observed in the original SiC surface. This is due to an additional step bunching that usually occurs during graphene formation. In this work, we show that such process can be suppressed by controlling the initial step structure of the SiC surface. In this case, the graphene monolayer is formed on the SiC without modification of the original surface morphology. We observe that the absence of step bunching during growth has no influence on the graphene structural quality.
Graphitization of n-type polycrystalline silicon carbide for on-chip supercapacitor application
Authors: Liu Fang , Gutes Albert , Laboriante Ian , Carraro Carlo , Maboudian Roya
Published: September 2011

Synthesis of silicon carbide-derived carbon films with excellent supercapacitor characteristics is demonstrated by a process that is fully compatible with standard microfabrication technology. NiTi alloy deposited on nitrogen-doped polycrystalline SiC films is shown to result in the growth of a rough, porous, high conductivity, nanocrystalline graphitic carbon film upon rapid thermal annealing to 1050 °C. Electrodes fabricated in this manner exhibit high charge/discharge rates with a time constant of about 0.062 s. Analysis shows that the incorporated nitrogen in the carbon electrode may induce pseudo-capacitance, and the electrodes exhibit the capacitance/area values comparable to those reported on carbon nanotube-based supercapacitors.
Simple finite subgroups of the Cremona group of rank 3
Authors: Prokhorov Yuri
Published: September 2011

We classify all finite simple subgroups of the Cremona group

C
r

3

(

C

)

\mathrm {Cr}_3(\mathbb {C})

.
Spectral sensitivity of the green photoreceptor of winged pea aphids
Authors: DÖRING THOMAS F. , KIRCHNER SASCHA M. , SKORUPSKI PETER , HARDIE JIM
Published: September 2011

Intracellular recordings are obtained from photoreceptors in the retina of winged (alate) pea aphids Acyrthosiphon pisum (Harris). The responses to monochromatic light, applied in 10‐nm steps over the range 320–650 nm, reveal that all recordings are from green receptors and the spectral sensitivity function of these photoreceptors peaks at 518 nm. A comparison between the spectral sensitivity of the green receptors and extracellular electroretinogram recordings suggests that additional sensitivity to the short‐wavelength light (ultraviolet and/or blue) is also likely to be present in the compound eye of pea aphids. An analysis of the pea aphid genome, comparing its translated nucleotide sequences with the those of the opsin genes of other insect species, supports this electrophysiological finding, although it could not be established whether A. pisum, in addition to the green receptor, has both blue and ultraviolet receptors in the compound eye. The implications of these results for the visual ecology of herbivorous insects are discussed.
Dynamic behavior of clathrin in Arabidopsis thaliana unveiled by live imaging
Authors: Ito Emi , Fujimoto Masaru , Ebine Kazuo , Uemura Tomohiro , Ueda Takashi , Nakano Akihiko
Published: September 2011

Clathrin‐coated vesicles (CCV) are necessary for selective transport events, including receptor‐mediated endocytosis on the plasma membrane and cargo molecule sorting in the trans‐Golgi network (TGN). Components involved in CCV formation include clathrin heavy and light chains and several adaptor proteins that are conserved among plants. Clathrin‐dependent endocytosis has been shown to play an integral part in plant endocytosis. However, little information is known about clathrin dynamics in living plant cells. In this study, we have visualized clathrin in Arabidopsis thaliana by tagging clathrin light chain with green fluorescent protein (CLC–GFP). Quantitative evaluations of colocalization demonstrate that the majority of CLC–GFP is localized to the TGN, and a minor population is associated with multivesicular endosomes and the Golgi trans‐cisternae. Live imaging further demonstrated the presence of highly dynamic clathrin‐positive tubules and vesicles, which appeared to mediate interactions between the TGNs. CLC–GFP is also targeted to cell plates and the plasma membrane. Although CLC–GFP colocalizes with a dynamin isoform at the plasma membrane, these proteins exhibit distinct distributions at newly forming cell plates. This finding indicates independent functions of CLC (clathrin light chains) and dynamin during the formation of cell plates. We have also found that brefeldin A and wortmannin treatment causes distinctly different alterations in the dynamics and distribution of clathrin‐coated domains at the plasma membrane. This could account for the different effects of these drugs on plant endocytosis.
Effect of Shading from Jointing to Maturity on High Molecular Weight Glutenin Subunit Accumulation and Glutenin Macropolymer Concentration in Grain of Winter Wheat
Authors: Li X. , Cai J. , Li H. , Bo Y. , Liu F. , Jiang D. , Dai T. , Cao W.
Published: September 2011

Accumulations of high molecular weight glutenin subunits (HMW‐GS) and glutenin macropolymer (GMP) in wheat grains are important indicators of grain quality. Two wheat cultivars, Yangmai 158 (shading tolerant) and Yangmai 11 (shading intolerant) which contains the same subunit pairs of 7 + 8 and 2 + 12, were used to evaluate the impacts of shading on HMW‐GS accumulation and GMP concentration in the grain. Three shading levels were implemented from jointing to maturity, i.e. S1, S2 and S3, in which the plants received 8 %, 15 % and 23 % less radiation of the control (S0), respectively. The initial formation of HMW‐GS was pre‐dated by shading. The rapid HMW‐GS accumulation duration was shortened, and the accumulation rate during late grain filling period was lowered in the two relatively severe shaded treatments (S2 & S3). Thus, the total HMW‐GS accumulation in single grain at maturity was lower in S2 and S3 than in the control (S0). However, concentrations of HMW‐GS and GMP at maturity increased because of the reduced single grain weight in S2 and S3, as compared to S0. In contrast, the low density shading (S1) prolonged the rapid accumulation duration of HMW‐GS, hence increased the accumulation and concentration of HMW‐GS in the grains. Consequently, S1 reduced falling number and SDS‐sedimentation volume, while shortened dough development time (DDT) and dough stability time (DST). In contrast, S2 and S3 increased falling number, wet‐gluten concentration and SDS‐sedimentation volume, and lengthened the DDT and DST. In addition, the fluctuations in accumulations of HMW‐GS and GMP and most quality traits because of shading in Yangmai 158 were less than Yangmai 11. The interrelations between HMW‐GS accumulation, GMP concentration and quality of grain and dough were further discussed.
Photoautotrophic symbiont and geography are major factors affecting highly structured and diverse bacterial communities in the lichen microbiome
Authors: Hodkinson Brendan P. , Gottel Neil R. , Schadt Christopher W. , Lutzoni François
Published: September 2011

Although common knowledge dictates that the lichen thallus is formed solely by a fungus (mycobiont) that develops a symbiotic relationship with an alga and/or cyanobacterium (photobiont), the non‐photoautotrophic bacteria found in lichen microbiomes are increasingly regarded as integral components of lichen thalli. For this study, comparative analyses were conducted on lichen‐associated bacterial communities to test for effects of photobiont‐types (i.e. green algal vs. cyanobacterial), mycobiont‐types and large‐scale spatial distances (from tropical to arctic latitudes). Amplicons of the 16S (SSU) rRNA gene were examined using both Sanger sequencing of cloned fragments and barcoded pyrosequencing. Rhizobiales is typically the most abundant and taxonomically diverse order in lichen microbiomes; however, overall bacterial diversity in lichens is shown to be much higher than previously reported. Members of Acidobacteriaceae, Acetobacteraceae, Brucellaceae and sequence group LAR1 are the most commonly found groups across the phylogenetically and geographically broad array of lichens examined here. Major bacterial community trends are significantly correlated with differences in large‐scale geography, photobiont‐type and mycobiont‐type. The lichen as a microcosm represents a structured, unique microbial habitat with greater ecological complexity and bacterial diversity than previously appreciated and can serve as a model system for studying larger ecological and evolutionary principles.
Outcome predictors in acute surgical admissions for lower gastrointestinal bleeding
Authors: Newman J. , Fitzgerald J. E. F. , Gupta S. , von Roon A. C. , Sigurdsson H. H. , Allen‐Mersh T. G.
Published: September 2011

Aim  The BLEED criterion is a triaging model for lower gastrointestinal bleeding (LGIB), which was developed and validated in the USA. We assessed the BLEED criteria in a UK population and aimed to elucidate factors that can be implemented for early risk stratification.

Method  Patients were identified from a prospectively maintained surgical admission database at a central London teaching hospital. Data were collected on 26 clinical factors available on initial presentation. The primary‐outcome end‐points included severe bleeding (persistent bleeding within the first 24 h, blood transfusion, a decrease in haematocrit of ≥ 20% or recurrent bleeding after ≥ 24 hours of stability) and adverse outcome (emergency surgery to control bleeding, intensive care unit [ITU] admission or death).

Results  One hundred and eighty‐four clinical episodes were identified, representing 3% of all surgical referrals. Twelve patients with upper gastrointestinal bleeding were excluded. Severe bleeding occurred in 110 (64%) patients. An adverse outcome was recorded in 20 (11.6%) patients, and 10 (5.4%) patients died during admission. The commonest aetiologies were diverticular disease, haemorrhoids and malignancy. Four prognosticators of adverse outcome were identified, these being: creatinine > 150μm (P = 0.002); age > 60 years (P = 0.001); abnormal haemodynamic parameters on presentation (P = 0.05); persistent bleeding within the first 24 h (P = 0.05); and area under the receiver–operating characteristics curve (AUC) = 0.79. The BLEED criteria were shown to be nonpredictive (AUC = 0.60).

Conclusion  The BLEED criterion was not shown to have any predictive value in this patient cohort. Our study has determined an independent set of prognostic factors that could be incorporated into initial triaging of patients presenting with LGIB. This may facilitate the early identification of patients requiring more aggressive resuscitation, admission to a monitored bed and consideration for early radiological or surgical intervention.
Extreme Measures of Agricultural Financial Risk
Authors: Morgan Wyn , Cotter John , Dowd Kevin
Published: September 2011

The agricultural marketing environment is inherently risky. Having accurate measures of risk helps farmers, policy‐makers and financial institutions make better informed decisions about how to deal with this risk. This article examines three tail quantile‐based risk measures applied to the estimation of extreme agricultural financial risk for corn and soybean production in the US: Value at Risk, Expected Shortfall and Spectral Risk Measures. We use Extreme Value Theory to model the tail returns and present results for these three different risk measures using agricultural futures market returns data. We compare estimated risk measures in terms of size and precision, and find that they are all considerably higher than Gaussian estimates. The estimated risk measures are also quite imprecise, and become more so as the risks involved become more extreme.
The natural history of hepatitis C virus infection acquired during childhood
Authors: Robinson Joan L. , Doucette Karen
Published: September 2011

Background

The outcome of patients with hepatitis C virus (HCV) infection acquired during childhood in the absence of antiviral therapy is not clear.

Aims

The purpose of this study was to review the outcome of untreated HCV acquired in childhood. Only population‐based studies were included, as referred cases would be predicted to have more severe disease.

Methods

A systematic review of the literature was completed up to October 2010 to identify studies where a population was screened for HCV infection that was presumably acquired during childhood. Demographical and clinical data were collected on infected patients who had not been treated with an antiviral. Primary outcome was development of a severe adverse outcome (cirrhosis, hepatoma, need for a liver transplant or liver‐related death).

Results

There were 25 studies reporting a total of 733 infected patients. Liver biopsy results were provided for 180 patients (25%), revealing cirrhosis in eight (1.0% of the total and 4.0% of those who had a biopsy). None of the other patients developed a severe adverse outcome. As a result of the small number of patients with a severe adverse outcome, risk factors for HCV progression could not be identified.

Conclusion

Although HCV can lead to liver transplantation and death during childhood, the vast majority of patients with disease acquired during childhood have slowly progressive disease. There is no clear indication for antiviral therapy in the majority of children with HCV infection.
Deep brain stimulation induces rapidly reversible transcript changes in Parkinson's leucocytes
Authors: Soreq Lilach , Bergman Hagai , Goll Yael , Greenberg David S. , Israel Zvi , Soreq Hermona
Published: September 2011

Subthalamic deep brain stimulation (DBS) reversibly modulates Parkinson's disease (PD) motor symptoms, providing an unusual opportunity to compare leucocyte transcripts in the same individuals before and after neurosurgery and 1 hr after stimulus cessation (ON‐ and OFF‐stimulus). Here, we report DBS‐induced reversibility and OFF‐stimulus restoration in 12 of 16 molecular functions and 3 of 4 biological processes shown in exon microarrays to be differentially expressed between PD patients and controls, post‐DBS from pre‐DBS and OFF from ON states. Intriguingly, 6 of 18 inflammation and immune‐related functions exhibited reversibility, and the extent of stimulus‐induced changes correlated with the neurological DBS efficacy, suggesting mechanistic implications. A minimal list of 29 transcripts that changed in all three comparisons between states discriminated pre‐surgery and OFF states from post‐surgery and controls. Six of these transcripts were found to be able to distinguish between PD patients and both healthy controls and patients with other neurological diseases in a previously published whole blood 3’ array data study of early PD patients. Our findings support the future use of this approach for identifying targets for therapeutic intervention and assessing the efficacy of current and new treatments in this and other neurological diseases.
Racial disparities in preterm birth: an overview of the potential role of nutrient deficiencies
Authors: DUNLOP ANNE L. , KRAMER MICHAEL R. , HOGUE CAROL J.R. , MENON RAMKUMAR , RAMAKRISHAN USHA
Published: September 2011

Objective. To give an overview of the literature for evidence of nutrient deficiencies as contributors to the disparity in preterm birth (PTB) between African‐American and Caucasian women. Design. Structured literature survey. Methods. We searched MEDLINE to identify observational and experimental studies that evaluated the relation between nutrient intake and/or supplementation and PTB. For nutrients for which studies supported an association, we searched MEDLINE for studies of the prevalence of deficiency in the USA by race. Main Outcome Measures. Summarized findings on nutrients for which there is both evidence of a role in PTB and variability in the prevalence of deficiency by race. Results. Nutrient deficiencies for which there are varying levels of evidence for an association with PTB and a greater burden among African‐American compared with Caucasian women include deficiencies of iron, folic acid, zinc, vitamin D, calcium and magnesium, and imbalance of ω‐3 and ω‐6 polyunsaturated fatty acids. There are inadequate high‐quality studies that investigate the role of nutrient deficiencies in PTB, their potential interaction with other risks, the proportion of excess risk for which they account, and whether supplementation can reduce the risk of, and racial disparities in, PTB in US populations. Conclusion. Deficiencies of several nutrients have varying levels of evidence of association with PTB and are of greater burden among African‐American compared with Caucasian women. Although further research is needed, strategies that improve the nutritional status of African‐American women may be a means of addressing a portion of the racial disparity in PTB.
Association of the FcγRIIB‐nt645+25A/G polymorphism with the expression level of the FcγRIIb receptor, the antibody response to Porphyromonas gingivalis and the severity of periodontitis
Authors: Sugita N. , Iwanaga R. , Kobayashi T. , Yoshie H.
Published: September 2011

Sugita N, Iwanaga R, Kobayashi T, Yoshie H. Association of the FcγRIIB‐nt645+25A/G polymorphism with the expression level of the FcγRIIb receptor, the antibody response to Porphyromonas gingivalis and the severity of periodontitis. J Periodont Res 2012; 47: 105–113. © 2011 John Wiley & Sons A/S

Background and Objective:  Human FcγRIIb is an immunoglobulin G (IgG) receptor that inhibits the activation of B lymphocytes through cross‐linking with the B‐cell receptor via immune complexes. This function acts as a negative regulator of antibody production. Our previous studies have demonstrated the gene polymorphisms in FcγRIIb to be associated with periodontitis. In this study, we presented a polymorphism –FcγRIIB‐nt645+25A/G (rs2125685) – in intron 4 and analyzed its functional relevance to periodontitis. We examined whether the FcγRIIB‐nt645+25A/G polymorphism is associated with periodontal parameters, the IgG response to the periodontopathic bacterium Porphyromonas gingivalis and/or the expression level of FcγRIIb on peripheral B lymphocytes.

Material and Methods:  Thirty‐two patients with chronic periodontitis were genotyped with nested PCR and by direct sequencing of genome DNA. The levels of serum IgG and of specific IgG subclasses for P. gingivalis sonicate and for the recombinant 40‐kDa outer membrane protein (OMP) were determined. The expression levels of FcγRIIb on peripheral B lymphocytes from 19 healthy donors were measured by flow cytometry.

Results:  Patients with the FcγRIIB‐nt645+25AA genotype showed significantly higher mean clinical attachment levels compared to patients with the FcγRIIB‐nt645+25GG genotype (p = 0.003) and a significantly lower IgG response to P. gingivalis sonicate and to the 40‐kDa OMP. The expression levels of FcγRIIb protein on the cell surface in peripheral B lymphocytes were higher in healthy donors with the FcγRIIB‐nt645+25AA genotype than in those with the FcγRIIB‐nt645+25GG genotype (p = 0.03).

Conclusion:  The higher expression levels of FcγRIIb in subjects with the FcγRIIB‐nt645+25AA genotype may induce a lower level of production of IgG against P. gingivalis and therefore more severe periodontitis.
Endocytosis of the Neuronal Glycine Transporter GLYT2: Role of Membrane Rafts and Protein Kinase C‐Dependent Ubiquitination
Authors: de Juan‐Sanz Jaime , Zafra Francisco , López‐Corcuera Beatriz , Aragón Carmen
Published: September 2011

Glycinergic neurotransmission is terminated by sodium‐ and chloride‐dependent plasma membrane transporters. The neuronal glycine transporter 2 (GLYT2) supplies the terminal with substrate to refill synaptic vesicles containing glycine. This crucial process is defective in human hyperekplexia, a condition that can be caused by mutations in GLYT2. Inhibitory glycinergic neurotransmission is modulated by the GLYT2 exocytosis/endocytosis equilibrium, although the mechanisms underlying the turnover of this transporter remain elusive. We studied GLYT2 internalization pathways and the role of ubiquitination and membrane raft association of the transporter in its endocytosis. Using pharmacological tools, dominant‐negative mutants and small‐interfering RNAs, we show that the clathrin‐mediated pathway is the primary mechanism for constitutive and regulated GLYT2 endocytosis in heterologous cells and neurons. We show that GLYT2 is constitutively internalized from cell surface lipid rafts, remaining associated with rafts in subcellular recycling structures. Protein kinase C (PKC) negatively modulates GLYT2 via rapid and dynamic redistribution of GLYT2 from raft to non‐raft membrane subdomains and increasing ubiquitinated GLYT2 endocytosis. This biphasic mechanism is a versatile means to modulate GLYT2 behavior and hence, inhibitory glycinergic neurotransmission. These findings may reveal new therapeutic targets to address glycinergic pathologies associated with alterations in GLYT2 trafficking.
A compliant tendon increases fatigue resistance and net efficiency during fatiguing cyclic contractions of mouse soleus muscle
Authors: Lichtwark G. A. , Barclay C. J.
Published: September 2011

Aim:  As muscles fatigue, their ability to generate mechanical work decreases as a result of decreased force generation and in cyclic activity, slower the relaxation. The purpose of this study was to determine whether a compliant tendon, connected in series with a muscle, would increase sustained work output during cyclic contractions.

Methods:  Experiments were performed in vitro (37 °C) using fibre bundles from mouse soleus muscles (n = 7). Each muscle performed two series of 40 brief contractions at a contraction frequency of 2 Hz and with a sinusoidal length change. One series was performed using the fibre bundle only and one with the fibre bundle and a compliant strip of latex connected between the muscle and the force recording apparatus.

Results:  When contracting with the latex strip, muscle work output was better maintained during the second half of the protocol than when performed without the latex, overall energy cost was reduced and mechanical efficiency was increased.

Conclusion:  The provision of a compliant tendon analogue increased the level of work output that could be sustained during cyclic contractions and reduced energy expenditure. It is proposed that both metabolic and mechanical consequences of the compliant tendon contribute to the improved performance.
Oligopolistic markets with sequential search and production cost uncertainty
Authors: Janssen Maarten , Pichler Paul , Weidenholzer Simon
Published: September 2011

This article analyzes a sequential search model where firms face identical but stochastic production costs, the realizations of which are unknown to consumers. We characterize a perfect Bayesian equilibrium satisfying a reservation price property and provide a sufficient condition for such an equilibrium to exist. We show that (i) firms set on average higher prices and make larger profits compared to the scenario where consumers observe production costs, (ii) expected prices and consumer welfare can be non‐monotonic in the number of firms, and (iii) the impact of production cost uncertainty vanishes as the number of firms becomes very large.
The roles of reputation and transparency on the behavior of biased experts
Authors: Bourjade Sylvain , Jullien Bruno
Published: September 2011

We analyze situations in which an expert is biased toward some decision but cares also about his reputation in the market for experts. The information the expert reveals decreases as his bias moves toward stronger preferences for the status quo. Surprisingly, revealing the intensity of the expert’s bias does not always improve the information he reveals in equilibrium. The presence of a second expert raises the first expert’s incentives to report truthfully when the market can identify the contribution of each expert, but reduces them when only the collective contribution is identified by the market.
Energy balances and greenhouse gas emissions of palm oil biodiesel in Indonesia
Authors: Harsono Soni Sisbudi , Prochnow Annette , Grundmann Philipp , Hansen Anja , Hallmann Claudia
Published: September 2011

This study presents a cradle‐to‐gate assessment of the energy balances and greenhouse gas (GHG) emissions of Indonesian palm oil biodiesel production, including the stages of land‐use change (LUC), agricultural phase, transportation, milling, biodiesel processing, and comparing the results from different farming systems, including company plantations and smallholder plantations (either out growers or independent growers) in different locations in Kalimantan and Sumatra of Indonesia. The findings demonstrate that there are considerable differences between the farming systems and the locations in net energy yields (43.6–49.2 GJ t−1 biodiesel yr−1) as well as GHG emissions (1969.6–5626.4 kg CO2eq t−1 biodiesel yr−1). The output to input ratios are positive in all cases. The largest GHG emissions result from LUC effects, followed by the transesterification, fertilizer production, agricultural production processes, milling, and transportation. Ecosystem carbon payback times range from 11 to 42 years.
Direct shoot organogenesis from hypocotyl explants of Jatropha curcasL. an important bioenergy feedstock
Authors: Sahoo Nirmala , Thirunavoukkarasu Manikannan , Behera Priya Ranjan , Satpathy Gargi Bala , Panda Prasanna Kumar
Published: September 2011

Multiple shoots were induced on hypocotyl segments reared from in vitro germinated seedlings of Jatropha curcas L., using Murashige and Skoog (MS) medium supplemented with N6‐benzyl adenine (BA) and kinetin (kin) either alone or in combination with indole‐3‐acetic acid (IAA). The combined treatment of 7.05 μm kin and 1.425 μm IAA resulted in maximum shoot production with an average shoot bud initiation of 12.1 per explant. The regenerated microshoots were transferred to root induction medium containing half‐strength MS salts supplemented with either indole‐3‐butyric acid (IBA) or IAA. Rooting of microshoots was best achieved on half‐strength MS medium supplemented with IBA (9.8 μm). Rooted plantlets were subsequently acclimatized under green house condition and the plantlets showed 70% survival.
Ethanol from sugarcane in Brazil: a ‘midway’ strategy for increasing ethanol production while maximizing environmental benefits
Authors: Buckeridge Marcos S. , De Souza Amanda P. , Arundale Rebecca A. , Anderson‐Teixeira Kristina J. , DeLucia Evan
Published: September 2011

This article reviews the history and current state of ethanol production from sugarcane in Brazil and presents a strategy for improving ecosystem services and production. We propose that it is possible to produce ethanol from sugarcane while maintaining or even recovering some of Brazil's unique neotropical biodiversity and ecosystem climate services. This approach to the future of sustainable and responsible ethanol production is termed the ‘midway’ strategy. The ‘midway’ strategy involves producing the necessary biotechnology to increase productivity while synergistically protecting and regenerating rainforest. Three main areas of scientific and technological advance that are key to realizing the ‘midway’ strategy are: (i) improving the quality of scientific data on sugarcane biology as pertains to its use as a bioenergy crop; (ii) developing technologies for the use of bagasse for cellulosic ethanol; and (iii) developing policies to improve the ecosystem services associated with sugarcane landscapes. This article discusses these three issues in the general context of biofuels production and highlights examples of scientific achievements that are already leading towards the ‘midway’ strategy.
Effect of nanoscale ripples on the formation of ZnO quantum dots
Authors: Chao Liang-Chiun , Chen Wei-Ruei , Chen Jun-Wei , Lai Syuan-Miao , Keiser Gerd
Published: September 2011

Nano-scale ripples on Si (100) substrates were prepared by argon ion beam sputtering at 6, 8, and 10 keV with an ion fluence of 5 × 1017 ions/cm2. The spatial wavelength of the nano-scale ripple increases as the ion beam energy increases, regardless of ion beam incident angles, indicating that ion beam induced diffusion is the dominant diffusion mechanism. ZnO quantum dots (QDs) with diameters less than 20 nm and heights less than 4 nm can be prepared over the temperature range from 200 ∼ 300 °C by reactive ion beam sputter deposition. Compared with ZnO QDs deposited on Si substrates without nano-scale ripple, the ion-beam textured substrate provides a wider processing window, improved dot size, and increased QD density.
UNCONDITIONALLY SECURE CONFERENCE KEY DISTRIBUTION: SECURITY NOTIONS, BOUNDS AND CONSTRUCTIONS
Authors: SAFAVI-NAINI REIHANEH , JIANG SHAOQUAN
Published: September 2011

A conference key distribution is a protocol that allows designated subset of users to calculate a shared private key. We consider unconditionally secure conference key distribution systems where the adversary has unlimited computational power, and focuses on a stronger and more realistic adversary model, proposed by Safavi-Naini and Jiang, in which the adversary in addition to corrupting subsets of users and obtaining their private keys, can access the conference keys of a number of uncorrupted conferences. We consider alternative definitions of security with this adversary model and show the relationship between them. An important efficiency parameter for conference key distribution systems is the size of the users' private keys. We derive lower bounds on the size of this key and discuss the results in comparison with the known bounds. We also consider one-round Interactive Conference Key Distribution Systems (ICKDS) in the new adversarial model where the adversary in addition to learning the private keys of the corrupted users and a number of conference keys, has access to the transcripts of some conferences. We show that under this new adversary model, the previously proposed one round protocol of Blundo et. al. is no longer secure and we construct an ICKDS with provable security in the new adversarial model.
REDUNDANCIES IN EXPLICITLY CONSTRUCTED TEN-DIMENSIONAL HETEROTIC STRING MODELS
Authors: RENNER TIMOTHY , GREENWALD JARED , MOORE DOUGLAS , CLEAVER GERALD
Published: September 2011

Using Baylor University's C ++ software for construction of weakly coupled free fermionic heterotic string models, called the FF Framework, we explicitly construct the level-1 Kač–Moody ten-dimensional heterotic string models with the aim of understanding the redundancies endemic to this construction method. We show that for models in any even number of large space–time dimensions with a massless left-mover and an odd ordered right-mover, the maximal number of space–time supersymmetries are present. We show that in order to produce all of the models for a given order, different basis vectors must be built; one cannot vary only the GSO coefficients. We also show that all combinations of two order-2 basis vectors do not produce the same models as all possible single order-4 basis vectors, implying the product of the orders used in a search does not necessarily determine the models built. We also show that to build all of the D = 10 level-1 models the inputs must be: sets of single order-6 basis vectors, pairs of basis vectors with orders 3 and 2, or sets of three order-2 basis vectors.
MODELING AND ANALYTICAL/NUMERICAL ANALYSIS OF WEAR PROCESSES IN A MECHANICAL FRICTION CLUTCH
Authors: AWREJCEWICZ J. , GRZELCZYK D.
Published: September 2011

This work is devoted to modeling and the analytical/numerical analysis of tribological processes occurring on the contact surface of shields of a mechanical friction clutch. Although the considered problems have been already studied earlier, however, simplified mathematical models have been used and applied. Unlike previous works, our work takes into account elasticity and wear properties of material of shields rubbing themselves. A general nonlinear differential model of wear is considered, as well as a wear model in the integral form taking into account gradual decrease of speed of wear of shields as a result of abrasive adapting to each other in the process of the exploitation. Equations modeling contact pressure on the contact surface of shields are derived and they yield the contact pressure and the wear of the shields. An analytical/numerical analysis is carried out with the qualitative and quantitative theories of differential and integral equations, including Laplace transformation. Many interesting results are obtained, illustrated and discussed. The presented results can be widened and used in other disciplines of the science, for instance, in physics of solids or biomechanics of various human joints.
STABILITY LOBES ANALYSIS OF NICKEL SUPERALLOYS MILLING
Authors: KĘCIK KRZYSZTOF , RUSINEK RAFAŁ , WARMIŃSKI JERZY
Published: September 2011

In this paper, we study the stability of a high speed milling process of nickel superalloys Inconel 713C by methods used in nonlinear dynamics. Stability Lobe Diagram was a result of modal analysis and next verified by recurrence plots, recurrence quantification analysis and classical nonlinear methods. A stability lobes diagram shows the indistinct boundary between chatter-free stable machining and unstable processes. Nevertheless, some recurrence quantification analysis measures give interesting results.
ENERGIES OF THE DYNAMICS IN A DOUBLE CIRCULAR PLATE NONLINEAR SYSTEM
Authors: HEDRIH KATICA R. (STEVANOVIĆ) , SIMONOVIĆ JULIJANA D.
Published: September 2011

This paper presents an analytical and numerical analysis of the transfer energy between plates for free and forced transversal vibrations of a visco-nonlinear elastically connected double circular plate. The analysis showed that the connection of Voigt–Kelvin type with the nonlinearity of third order between plates caused the appearance of two-frequency-like regime of time function, which corresponds to one eigen amplitude function of one nonlinear mode. Furthermore, the time functions of different vibration nonlinear modes are coupled, as well as energy transfer between plates in one eigen mode appear. More than two resonant jumps in the amplitude-frequency as in phase-frequency curves appear and cause more than two resonant jumps of the energy modes and the corresponding influence between nonlinear modes, as nonlinear interactions phenomena. Using the analytical results for the first asymptotic approximation of the amplitudes and phases of multifrequency particular solutions of such dynamics, it is possible to analyze the transfer energy between nonlinear modes in stationary and nonstationary regimes. A few numerical results from the analysis are presented in this paper together with the conclusions on the influence of nonlinearity in coupling layer on the dynamics and transfer of energy in such systems.
PARAMETRIC AND EXTERNAL RESONANCES IN KINEMATICALLY AND EXTERNALLY EXCITED NONLINEAR SPRING PENDULUM
Authors: STAROSTA ROMAN , SYPNIEWSKA–KAMIŃSKA GRAŻYNA , AWREJCEWICZ JAN
Published: September 2011

A weakly nonlinear 2-DOF system, parametrically and externally excited, is studied. An intensive energy transfer between modes of vibrations is discovered. Multiple scales method is used for recognizing resonances occurring in the system. The amplitude response functions for some chosen cases of resonances are obtained and studied. Many of the engineering systems can be investigated in the presented way.
A STRONG LAW OF COMPUTATIONALLY WEAK SUBSETS
Authors: KJOS-HANSSEN BJØRN
Published: September 2011

We show that in the setting of fair-coin measure on the power set of the natural numbers, each sufficiently random set has an infinite subset that computes no random set. That is, there is an almost sure event [Formula: see text] such that if [Formula: see text] then X has an infinite subset Y such that no element of [Formula: see text] is Turing computable from Y.
Electronic Structure and Physical-Chemistry Property Relationship for Oxazole Derivatives by Ab Initio and DFT Methods
Authors: Belaidi Salah , Mellaoui Malika
Published: September 2011

The geometric, electronic structure, effect of the substitution, and structure physical-chemistry relationship for oxazoles derivatives have been studied by ab initio and DFT theory. In the present work, the calculated values, namely, net charges, bond lengths, dipole moments, electron affinities, heats of formation, and QSAR properties are reported and discussed in terms of the reactivity of oxazole derivatives.
Jak2-Independent Activation of Stat3 by Intracellular Angiotensin II in Human Mesangial Cells
Authors: Singh Rekha
Published: September 2011

Ang II is shown to mediate the stimulatory effect of high glucose on TGF-b1 and extracellular matrix proteins in glomerular mesangial cells. Also inhibition of Ang II formation in cell media (extracellular) and lysates (intracellular) blocks high-glucose effects on TGF-b1 and matrix more effectively compared to inhibition of extracellular Ang II alone. To investigate whether intracellular Ang II can stimulate TGF-b1 and matrix independent of extracellular Ang II, cultured human mesangial cells were transfected with Ang II to increase intracellular Ang II levels and its effects on TGF-b1 and matrix proteins were determined. Prior to transfection, cells were treated with candesartan to block extracellular Ang II-induced responses via cell membrane AT1 receptors. Transfection of cells with Ang II resulted in increased levels of intracellular Ang II which was accompanied by increased production of TGF-b1, collagen IV, fibronectin, and cell proliferation as well. On further examination, intracellular Ang II was found to activate Stat3 transcription factor including increased Stat3 protein expression, tyrosine 705 phosphorylation, and DNA-binding activity. Treatment with AG-490, an inhibitor of Jak2, did not block intracellular Ang II-induced Stat3 phosphorylation at tyrosine 705 residue indicating a Jak2-independent mechanism used by intracellular Ang II for Stat3 phosphorylation. In contrast, extracellular Ang II-induced tyrosine 705 phosphorylation of Stat3 was inhibited by AG-490 confirming the presence of a Jak2-dependent pathway. These findings suggest that intracellular Ang II increases TGF-b1 and matrix in human mesangial cells and also activates Stat3 transcription factor without involvement of the extracellular Ang II signaling pathway.
Multiobjective Design Optimization of Grillage Systems according to LRFD-AISC
Authors: Talaslioglu Tugrul
Published: September 2011

Both the entire weight and joint displacements of grid structures are minimized at the same time in this study. Four multiobjective optimization algorithms, NSGAII, SPEAII, PESAII, and AbYSS are employed to perform computational procedures related to optimization processes. The design constraints related to serviceability and ultimate strength of grid structure are implemented from Load and Resistance Factor Design-American Institute of Steel Constructions (LRFD-AISC Ver.13). Hence, while the computational performances of these four optimization algorithms are compared using different combinations of optimizer-related parameters, the various strengths of grid members are also evaluated. For this purpose, multiobjective optimization algorithms (MOAs) employed are applied to the design optimization of three application examples and achieved to generate various optimal designations using different combinations of optimizer-related parameters. According to assessment of these optimal designations considering various quality indicators, IGD, HV, and spread, AbYSSS shows a better performance comparatively to the other three proposed MOAs, NSGAII, SPEAII, and PESAII.
Robot-Assisted Partial Cystectomy of a Bladder Pheochromocytoma
Authors: Kang Sung Gu , Kang Seok Ho , Choi Hoon , Ko Young Hwii , Park Hong Seok , Cheon Jun
Published: September 2011

Pheochromocytoma of the urinary bladder is an unusual tumor that typically presents with hypertensive crises related to micturition. We report here an unusual case of bladder pheochromocytoma that was treated by robotic-assisted laparoscopic partial cystectomy. A 35-year-old male patient presented with headache and hypertension related to micturition. The patient, who had a 3.5 × 4 cm solitary bladder tumor in the bladder dome, underwent robot-assisted partial cystectomy. The whole procedure was successfully performed using the robot without conversion to open surgery. The total operative time was 120 min and the estimated blood loss was 30 ml.
Adrenal Tumors with Venous Thrombosis: A Single-Institution Experience
Authors: Osman Yasser , Haraz Ahmed , El-Mekresh Mohsen , Gomha Abdul-Monem , El-Ghar Mohamed Abou , Eraky Ibrahim
Published: September 2011

Objective: To assess the incidence, imaging, surgical approach and prognosis of adrenal tumors associated with venous thrombosis. Material and Methods: Charts of 206 patients who underwent adrenal surgery were reviewed. Data of patients with pathologically confirmed venous thrombosis, utilized diagnostic modalities, operative treatment and prognosis were reviewed and analyzed. Results: Venous thrombosis was confirmed pathologically in 6 patients (2.9%). All were of male gender with age ranging between 2 and 54 years. The mean size of the masses was 11.5 ± 5.2 cm. Venous thrombosis was diagnosed preoperatively in 2 patients, adrenal vein thrombosis in 1 patient, and renal vein thrombosis in the others. Masses were successfully excised via an open approach in association with nephrectomy in 3 cases. There was no operative mortality or gross morbidity. Pathologically, thrombosis was limited to the adrenal vein in 4 patients and extended to the renal vein in 2. Pathology of the masses revealed neuroblastoma in 2, pheochromocytoma in 2, adrenocortical carcinoma in 1, and pleomorphic sarcoma in 1 case. Metastasis developed within 6 months in 3 of these patients. Conclusion: Venous thrombosis with adrenal tumors is a rare pathological condition in which open surgery is the standard of care. Primary malignant adrenal masses with venous thrombosis have a poor prognostic outcome.