bluuebunny/crossref_metadata_2025 huggingface dataset:
Notch1‐Snail1‐E‐cadherin pathway in metastatic hepatocellular carcinoma
Authors: Wang Xiao Qi , Zhang Wu , Lui Eric L.H. , Zhu Yongqiang , Lu Ping , Yu Xiaoming , Sun Jisan , Yang Sitian , Poon Ronnie T.P. , Fan Sheung Tat
Published: November 2011

Notch signaling, a critical pathway for tissue development, also contributes to tumorigenesis in many cancers, but its pathological function in liver cancer is not well defined. In our study, Notch1 expression and its clinicopathological parameters were evaluated in 82 human hepatocellular carcinoma (HCC) patients. Plasmid‐based siNotch1 shRNA was transiently or stably transfected into metastatic HCC cells and subsequently evaluated for the effects on orthotopic liver tumor metastasis in a mouse model as well as the effects on downstream pathways. Aberrant high expression of Notch1 was significantly associated with metastatic disease parameters in HCC patients, such as tumor‐node‐metastasis Stages III–IV and tumor venous invasion. Knocking‐down Notch1 reduced cell motility in vitro and orthotopic tumor metastasis from the liver to the lung in vivo in a mouse model. In metastatic HCC cells, abnormal expression of Notch1 was associated with increased expression of Snail1 and repressed expression of E‐cadherin; the Notch1‐Snail1‐E‐cadherin association can also be found in HCC patient tumors. Inhibition of Notch1 by shRNA abolished Snail1 expression, which further resulted in the re‐establishment of repressed E‐cadherin in metastatic HCC cells. Thus, abnormal Notch1 expression was strongly associated with HCC metastatic disease, which might be mediated through the Notch1‐Snail1‐E‐cadherin pathway. Knock‐down of Notch1 reversed HCC tumor metastasis in a mouse model. Therefore, these data suggest that effective targeting of Notch signaling might also inhibit tumor metastasis.
Cigarette smoking and lung cancer—relative risk estimates for the major histological types from a pooled analysis of case–control studies
Authors: Pesch Beate , Kendzia Benjamin , Gustavsson Per , Jöckel Karl‐Heinz , Johnen Georg , Pohlabeln Hermann , Olsson Ann , Ahrens Wolfgang , Gross Isabelle Mercedes , Brüske Irene , Wichmann Heinz‐Erich , Merletti Franco , Richiardi Lorenzo , Simonato Lorenzo , Fortes Cristina , Siemiatycki Jack , Parent Marie‐Elise , Consonni Dario , Landi Maria Teresa , Caporaso Neil , Zaridze David , Cassidy Adrian , Szeszenia‐Dabrowska Neonila , Rudnai Peter , Lissowska Jolanta , Stücker Isabelle , Fabianova Eleonora , Dumitru Rodica Stanescu , Bencko Vladimir , Foretova Lenka , Janout Vladimir , Rudin Charles M. , Brennan Paul , Boffetta Paolo , Straif Kurt , Brüning Thomas
Published: November 2011

Lung cancer is mainly caused by smoking, but the quantitative relations between smoking and histologic subtypes of lung cancer remain inconclusive. By using one of the largest lung cancer datasets ever assembled, we explored the impact of smoking on risks of the major cell types of lung cancer. This pooled analysis included 13,169 cases and 16,010 controls from Europe and Canada. Studies with population controls comprised 66.5% of the subjects. Adenocarcinoma (AdCa) was the most prevalent subtype in never smokers and in women. Squamous cell carcinoma (SqCC) predominated in male smokers. Age‐adjusted odds ratios (ORs) were estimated with logistic regression. ORs were elevated for all metrics of exposure to cigarette smoke and were higher for SqCC and small cell lung cancer (SCLC) than for AdCa. Current male smokers with an average daily dose of >30 cigarettes had ORs of 103.5 (95% confidence interval (CI): 74.8–143.2) for SqCC, 111.3 (95% CI: 69.8–177.5) for SCLC and 21.9 (95% CI: 16.6–29.0) for AdCa. In women, the corresponding ORs were 62.7 (95% CI: 31.5–124.6), 108.6 (95% CI: 50.7–232.8) and 16.8 (95% CI: 9.2–30.6), respectively. Although ORs started to decline soon after quitting, they did not fully return to the baseline risk of never smokers even 35 years after cessation. The major result that smoking exerted a steeper risk gradient on SqCC and SCLC than on AdCa is in line with previous population data and biological understanding of lung cancer development.
Comparison between TEWL and laser scanning microscopy measurements for the in vivo characterization of the human epidermal barrier
Authors: Vergou Theognosia , Schanzer Sabine , Richter Heike , Pels Ragna , Thiede Gisela , Patzelt Alexa , Meinke Martina C. , Sterry Wolfram , Fluhr Joachim W. , Lademann Jürgen
Published: November 2011

The analysis of the skin barrier properties is important in various fields of medical treatment and cosmetology. The development and improvement of topically applied substances require an objective analysis of the skin barrier characteristics. Transepidermal water loss (TEWL) measurement is the standard method to characterize epidermal barrier function. The most important disadvantage of this method though, is that it can be affected by different exogenous and endogenous factors, e.g. water content of the applied formulation and room temperature. In the present study, TEWL measurements are compared to laser scanning microscopic (LSM) measurements, concerning the use of these two methods for the non‐invasive in vivo characterization of the epidermal barrier function. The investigations were performed prior and subsequent to treatment of dry skin with a gel mixture, developed for skin treatment after radiotherapy for cancer. The present results indicate that in vivo laser scanning microscopy is an appropriate method for the characterization of the skin barrier structure without interference by external factors. (© 2012 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Two‐photon excited fluorescence lifetime measurements through a double‐clad photonic crystal fiber for tissue micro‐endoscopy
Authors: Knorr Florian , Yankelevich Diego R. , Liu Jing , Wachsmann‐Hogiu Sebastian , Marcu Laura
Published: November 2011

This paper presents an endoscopic configuration for measurements of tissue autofluorescence using two–photon excitation and time‐correlated single photon counting detection through a double‐clad photonic crystal fiber (DC‐PCF) without pre‐chirping of laser pulses. The instrument performance was evaluated by measurements of fluorescent standard dyes, biological fluorophores (collagen and elastin), and tissue specimens (muscle, cartilage, tendon). Current results demonstrate the ability of this system to accurately retrieve the fluorescence decay profile and lifetime of these samples. This simple setup, which offers larger penetration depth than one‐photon‐based techniques, may be combined with morphology‐yielding techniques such as photoacoustic and ultrasound imaging. (© 2012 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Daily administration of eldecalcitol (ED-71), an active vitamin D analog, increases bone mineral density by suppressing RANKL expression in mouse trabecular bone
Authors: Harada Suguru , Mizoguchi Toshihide , Kobayashi Yasuhiro , Nakamichi Yuko , Takeda Satoshi , Sakai Sadaoki , Takahashi Fumiaki , Saito Hitoshi , Yasuda Hisataka , Udagawa Nobuyuki , Suda Tatsuo , Takahashi Naoyuki
Published: November 2011

Eldecalcitol (ED-71) is a new vitamin D3 derivative recently approved for the treatment of osteoporosis in Japan. Previous studies have shown that the daily administration of ED-71 increases bone mineral density (BMD) by suppressing bone resorption in various animal models. In this study, we examined how ED-71 suppresses bone resorption in vivo, by analyzing bone histomorphometry and ex vivo osteoclastogenesis assays. Daily administration of ED-71 (50 ng/kg body weight) to 8-week-old male mice for 2 and 4 weeks increased BMD in the femoral metaphysis without causing hypercalcemia. Bone and serum analyses revealed that ED-71 inhibited bone resorption and formation, indicating that the increase in BMD is the result of the suppression of bone resorption. This suppression was associated with a decrease in the number of osteoclasts in trabecular bone. We previously identified cell cycle-arrested receptor activator of NF-κB (RANK)-positive bone marrow cells as quiescent osteoclast precursors (QOPs) in vivo. Daily administration of ED-71 affected neither the number of RANK-positive cells in vivo nor the number of osteoclasts formed from QOPs in ex vivo cultures. In contrast, ED-71 suppressed the expression of RANK ligand (RANKL) mRNA in femurs. Immunohistochemical experiments also showed that the perimeter of the RANKL-positive cell surface around the trabecular bone was significantly reduced in ED-71-treated mice than in the control mice. ED-71 administration also increased BMD in 12-week-old ovariectomized mice, through the suppression of RANKL expression in the trabecular bone. These results suggest that the daily administration of ED-71 increases BMD by suppressing RANKL expression in trabecular bone in vivo. © 2012 American Society for Bone and Mineral Research
A new haplotype in BMP4 implicated in ossification of the posterior longitudinal ligament (OPLL) in a Chinese population
Authors: Ren Yuan , Feng Jie , Liu Zhi‐zhong , Wan Hong , Li Jun‐hua , Lin Xin
Published: November 2011

Previous genome‐wide microarray analysis of candidate genes involved in the ossification of the posterior longitudinal ligament (OPLL) of the spine resulted in the identification of a novel, clinically relevant gene encoding bone morphogenetic protein 4 (BMP4) but was defined only by its expression patterns. The complete genomic BMP4 coding DNA from 450 patients with OPLL and 550 matched controls were sequenced and compared. We identified 18 SNPs, among which the minor alleles of SNP8 (C>T; p < 0.001; OR: 1.58), SNP13 (rs17563C>T; p < 0.001; OR: 1.76), and SNP14 (rs76335800A>T; p < 0.001; OR: 1.68) were associated with OPLL. Logistic regression analysis showed that the additive model of SNP8 (p < 0.001; OR: 3.48), SNP13 (p < 0.001; OR: 2.22), and SNP14 (p < 0.001; OR: 1.99) retained statistical significance. Linkage disequilibrium (LD) analysis identified a 3‐kbp block of intense LD in BMP4 and 1 specific haplotype, TGGGCTT (p < 0.001, OR: 2.54), which was associated with OPLL‐associated risk alleles and increased severity of OPLL, as shown by the distribution of ossified vertebrae in patients with OPLL (p = 0.002). Novel mutations in the BMP4 gene and a specific haplotype TGGGCTT appear to contribute to the risk of developing OPLL. Also the severity of OPLL seems to be mediated predominantly by genetic variations in this specific BMP4 gene region, but might be associated with other certain clinical and demographic characteristics in the Chinese population studied. © 2011 Orthopaedic Research Society Published by Wiley Periodicals, Inc. J Orthop Res 30:748–756, 2012
An Algorithm for the Analytic Network Process (ANP) Structure Design
Authors: Khademi Navid , Mohaymany Afshin S. , Shahi Jalil , Zerguini Seghir
Published: November 2011

The present paper delineates a three‐step algorithm for the analytic network process (ANP) structure design. When defining the decision goal and the alternative set, one can use the three‐step algorithm proposed in this paper, first, to specify the decision criteria, and second, to outline the structure of the ANP problem. To ease the process of ANP structure design, we present two novel data structures: the multiple‐effect tree and the multiple‐criteria tree. The multiple‐effect tree helps explore the apparent consequences of a given event or state—known in this paper as the decision alternatives—whereas the multiple‐criteria tree is considered the missing link between the multiple‐effect tree and the ANP structure. Employing the approach presented in this paper will help detect any mistakes in the ANP structure design. A numerical example is provided in the final section of the paper to better articulate the ideas. Copyright © 2011 John Wiley & Sons, Ltd.
Initial testing (stage 1) of SGI‐1776, a PIM1 kinase inhibitor, by the pediatric preclinical testing program
Authors: Batra Vandana , Maris John M. , Kang Min H. , Reynolds C. Patrick , Houghton Peter J. , Alexander Denise , Kolb E. Anders , Gorlick Richard , Keir Stephen T. , Carol Hernan , Lock Richard , Billups Catherine A. , Smith Malcolm A.
Published: November 2011

The PIM kinase inhibitor, SGI‐1776, was tested against the PPTP in vitro (1.0 nM–10 µM) and in vivo panels (148 mg/kg daily × 5 days for 3 weeks). SGI‐1776 exhibited cytotoxic activity in vitro with a median relative IC50 of 3.1 µM. SGI‐1776 induced significant differences in EFS distribution in vivo in 9 of 31 solid tumor xenografts and in 1 of 8 of the evaluable ALL xenografts. SGI‐1776 induced tumor growth inhibition meeting criteria for intermediate EFS T/C activity in 1 of 39 evaluable models. In contrast, SGI‐1776 induced complete responses of subcutaneous MV4;11 (B myeloid leukemia). Pediatr Blood Cancer 2012;59:749–752. © 2011 Wiley Periodicals, Inc.
Sorafenib as treatment for relapsed or refractory pediatric acute myelogenous leukemia
Authors: Watt Tanya C. , Cooper Todd
Published: November 2011

The prognosis for children with acute myelogenous leukemia (AML) has improved with overall survival rates of up to 65% [Pui et al. J Clin Oncol 2011; 29: 551–565]. However, the cure rate for AML lags behind that of acute lymphoblastic leukemia. Advances in AML leukemogenesis are leading to refined risk stratification. FMS like tyrosine kinase 3 (FLT3) mutations are independently associated with a poor prognosis. Newer kinase inhibitors, including sorafenib, have shown promise in adult studies. We report three pediatric patients with relapsed AML who achieved a sustained remission with sorafenib. Further trials are necessary to understand the role of sorafenib in pediatric AML. Pediatr Blood Cancer 2012;59:756–757. © 2011 Wiley Periodicals, Inc.
Nonvisualization of fetal gallbladder increases the risk of cystic fibrosis
Authors: Duguépéroux Ingrid , Scotet Virginie , Audrézet Marie‐Pierre , Saliou Anne‐Hélène , Collet Michel , Blayau Martine , Schmitt Sébastien , Kitzis Alain , Fresquet Fleur , Müller Françoise , Férec Claude
Published: November 2011

Objective

The aim of our study is to evaluate the prevalence of cystic fibrosis (CF) in fetuses referred for genetic testing because of ultrasonographic sign (nonvisualized fetal gallbladder – NVFGB).

Method

We reviewed the results of CFTR gene analysis over the period 2002 to 2009 in all consecutive cases referred because of NVFGB in Western France. We correlated these data with the presence of a more classical ultrasonographic finding (fetal echogenic bowel – FEB).

Results

Cystic fibrosis was diagnosed in 5 of the 37 fetuses with NVFGB (13.5%, 95% confidence interval (CI): [2.5%; 24.5%]) and in only 9 of the 229 other cases referred because of FEB (3.9%, 95% CI: [3.2%; 14.7%]). In our series, all CF‐affected fetuses with NVFGB also had FEB. The risk of CF was 11.6‐fold higher in fetuses with both indications (NVFGB + FEB) than in fetuses with isolated FEB (45.5% vs 3.9%, RR = 11.6, 95% CI: [4.7%; 28.8%], p = 0.0001). We also estimated that the residual risk of CF was less than 1 in 68 (1.5%) when a single mutation was identified in the fetus by our molecular protocol.

Conclusion

Ultrasonographic evidence of NVFGB is an additional risk factor for CF in cases with FEB. © 2011 John Wiley & Sons, Ltd.
Relationships between social support sources and early adolescents' mental health: The moderating effect of student achievement level
Authors: Stewart Tiffany , Suldo Shannon
Published: November 2011

This study examined how perceived social support from parents, classmates, and teachers jointly and uniquely predicted psychopathology (i.e., internalizing and externalizing symptoms) and wellness (i.e., life satisfaction) in a sample of 390 middle‐school students. This study also explored the protective nature of high student academic achievement in the relationship between social support and mental health. Social support was a significant predictor of all mental health outcomes, particularly life satisfaction. Although classmate and teacher support were significant unique predictors of students' internalizing and externalizing symptoms, respectively, parent support emerged as the strongest predictor of all indicators of mental health. Academic achievement moderated the direction and strength of the relationships between externalizing behavior and (a) classmate support, and (b) parent support, respectively. Specifically, classmate support emerged as adaptive for average‐ and high‐achieving students only, whereas academic achievement functioned as a protective factor against the manifestation of externalizing psychopathology among students with low parental support. Implications for school psychologists and directions for future research are discussed. © 2011 Wiley Periodicals, Inc.
Rural Poverty Dynamics and Refugee Communities in South Africa: A Spatial–Temporal Model
Authors: Sartorius Kurt , Sartorius Benn , Tollman Stephen , Schatz Enid , Kirsten Johann , Collinson Mark
Published: November 2011

The assimilation of refugees into their host community economic structures is often problematic. The paper investigates the ability of refugees in rural South Africa to accumulate assets over time relative to their host community. Bayesian spatial–temporal modelling was employed to analyse a longitudinal database that indicated that the asset accumulation rate of former Mozambican refugee households was similar to their host community; however, they were unable to close the wealth gap. A series of geo‐statistical wealth maps illustrate that there is a spatial element to the higher levels of absolute poverty in the former refugee villages. The primary reason for this is their physical location in drier conditions that are established further away from facilities and infrastructure. Neighbouring South African villages in close proximity, however, display lower levels of absolute poverty, suggesting that the spatial location of the refugees only partially explains their disadvantaged situation. In this regard, the results indicate that the wealth of former refugee households continues to be more compromised by higher mortality levels, poorer education, and less access to high‐return employment opportunities. The long‐term impact of low initial asset status appears to be perpetuated in this instance by difficulties in obtaining legal status in order to access state pensions, facilities, and opportunities. The usefulness of the results is that they can be used to sharpen the targeting of differentiated policy in a given geographical area for refugee communities in rural Africa. Copyright © 2011 John Wiley & Sons, Ltd.
Technology and Corporate Scope: Firm and Rival Innovation as Antecedents of Corporate Transactions
Authors: Kaul Aseem
Published: November 2011

This paper studies the role of technological innovation as an antecedent of changes in corporate scope. It argues that technological innovations prompt the firm to reconfigure its corporate portfolio—to redeploy resources to areas of new opportunity while it divests out of marginal businesses. Results from a cross‐industry sample of U.S. manufacturing firms show successful innovation by a firm is followed by both expansion into new areas through complementary resource seeking acquisitions and divestment out of existing noncore businesses. This relationship is found to be moderated by the level of investible resources available to the firm, and supports the notion of scarce resources as a constraint on firm scope. In addition, firms are found to change their corporate scope in response to rival innovation. Copyright © 2011 John Wiley & Sons, Ltd.
Evolutionary algorithms for the multi‐objective test data generation problem
Authors: Ferrer Javier , Chicano Francisco , Alba Enrique
Published: November 2011

Automatic test data generation is a very popular domain in the field of search‐based software engineering. Traditionally, the main goal has been to maximize coverage. However, other objectives can be defined, such as the oracle cost, which is the cost of executing the entire test suite and the cost of checking the system behavior. Indeed, in very large software systems, the cost spent to test the system can be an issue, and then it makes sense by considering two conflicting objectives: maximizing the coverage and minimizing the oracle cost. This is what we did in this paper. We mainly compared two approaches to deal with the multi‐objective test data generation problem: a direct multi‐objective approach and a combination of a mono‐objective algorithm together with multi‐objective test case selection optimization. Concretely, in this work, we used four state‐of‐the‐art multi‐objective algorithms and two mono‐objective evolutionary algorithms followed by a multi‐objective test case selection based on Pareto efficiency. The experimental analysis compares these techniques on two different benchmarks. The first one is composed of 800 Java programs created through a program generator. The second benchmark is composed of 13 real programs extracted from the literature. In the direct multi‐objective approach, the results indicate that the oracle cost can be properly optimized; however, the full branch coverage of the system poses a great challenge. Regarding the mono‐objective algorithms, although they need a second phase of test case selection for reducing the oracle cost, they are very effective in maximizing the branch coverage. Copyright © 2011 John Wiley & Sons, Ltd.
Actuator volumes and hr‐adaptive methods for three‐dimensional simulation of wind turbine wakes and performance
Authors: Creech Angus C.W. , Früh Wolf‐Gerrit , Clive Peter
Published: November 2011

This paper presents a three‐dimensional numerical model for horizontal axis wind turbines, capable of simulating both the dynamic response of the turbine to changing flow conditions, and the full wake generated by the turbine. The turbine model is coupled to computational fluid dynamics software using Large Eddy Simulation to solve for unsteady flow conditions, with the Smagorinsky method handling sub‐grid turbulence. Wind tunnel simulations are compared with experimental data, and then a simulation of a real turbine in complex terrain is compared with LIDAR data from the same site, in both cases agreeing favourably. Copyright © 2011 John Wiley & Sons, Ltd.
Impact of Preoperative Thrombocytosis on the Survival of Patients with Primary Colorectal Cancer
Authors: Sasaki Kazuhito , Kawai Kazushige , Tsuno Nelson H. , Sunami Eiji , Kitayama Joji
Published: November 2011

Background

Although thrombocytosis has been reported in patients with various types of cancer, the association between thrombocytosis and the clinicopathological features of patients with colorectal cancer (CRC) has not been fully investigated. We evaluated the clinical features associated with thrombocytosis in CRC.

Materials and methods

The medical records of 636 consecutive CRC patients undergoing surgery in our department between January 2002 and July 2008 were retrospectively reviewed. The correlation between the clinicopathological variables and the preoperative platelet count was analyzed by univariate and multivariate analyses. The impact of thrombocytosis on the prognosis of these patients was assessed, in comparison with the other clinicopathological variables.

Results

Platelet count showed significant correlation with gender, age, venous involvement, tumor size, depth of invasion, regional lymph node metastasis, distant metastasis in univariate analysis, and tumor size and depth of invasion were independent factors in multivariate analysis. The cancer‐specific survival (CSS) of CRC patients with thrombocytosis was significantly shorter than that for those without thrombocytosis (P < 0.001), specifically in patients with stage III CRC (P < 0.001). Multivariate analysis indicated that thrombocytosis was an independent prognostic factor of CSS (hazard ratio = 2.96, 95% confidence interval [CI] = 1.72–5.00). Moreover, within stage II CRC, the univariate analysis revealed that disease‐free survival (DFS) was associated with preoperative thrombocytosis, but not the other clinicopathological variables.

Conclusions

Preoperative thrombocytosis is not only an independent indicator of poor CSS in CRC patients but also an independent predictor of poor DFS in patients with stage II CRC.
Oxidative Stability of Conjugated Linoleic Acid Rich Soy Oil
Authors: Yettella Ramesh R. , Castrodale Chelsey , Proctor Andrew
Published: November 2011

This study was conducted to determine the oxidative stability of conjugated linoleic acid rich soy oil (CLARSO) and the effects of conjugated linoleic acid (CLA) levels on volatile oxidation products formed during CLARSO oxidation. CLARSO oxidative stability was determined by gravimetric analysis, peroxide value, headspace oxygen analysis and p‐anisidine value. Volatile oxidation compounds were analyzed by solid phase microextraction–gas chromatography with a flame ionization detector and a mass spectrometer. CLA oxidation results were highly dependent on analytical methods used and oxidation parameters measured. The gravimetric study showed a CLA concentration effect on oxidation, which was not seen in the headspace oxygen depletion and peroxide value. Volatile oxidation data indicate that CLARSO had significantly higher (p < 0.05) levels of pentanal and trans‐2‐heptenal than the other oils, but there was no significant difference between the amounts of any volatiles present in 8 and 15% CLARSO. This suggests that oxidation was greater in CLARSO and that CLA concentration did not affect oxidation.
Differential Survival in Europe and the United States: Estimates Based on Subjective Probabilities of Survival
Authors: Delavande Adeline , Rohwedder Susann
Published: November 2011

Cross-country comparisons of differential survival by socioeconomic status (SES) are useful in many domains. Yet, to date, such studies have been rare. Reliably estimating differential survival in a single country has been challenging because it requires rich panel data with a large sample size. Cross-country estimates have proven even more difficult because the measures of SES need to be comparable internationally. We present an alternative method for acquiring information on differential survival by SES. Rather than using observations of actual survival, we relate individuals’ subjective probabilities of survival to SES variables in cross section. To show that subjective survival probabilities are informative proxies for actual survival when estimating differential survival, we compare estimates of differential survival based on actual survival with estimates based on subjective probabilities of survival for the same sample. The results are remarkably similar. We then use this approach to compare differential survival by SES for 10 European countries and the United States. Wealthier people have higher survival probabilities than those who are less wealthy, but the strength of the association differs across countries. Nations with a smaller gradient appear to be Belgium, France, and Italy, while the United States, England, and Sweden appear to have a larger gradient.
Fabrication of polymer-based electronic circuits using photolithography
Authors: Zakhidov Alexander A. , Fong Hon Hang , DeFranco John A. , Lee Jin-Kyun , Taylor Priscilla G. , Ober Christopher K. , Malliaras George G. , He Mingqian , Kane Michael G.
Published: November 2011

We exploited the concept of solvent orthogonality to enable photolithography for high-resolution, high-throughput fabrication of electronic circuits based on a polymeric semiconductor. An array of ring oscillators utilizing top contact polymer thin film transistors with 1 μm channel length has been fabricated on a 100 mm wafer scale. We used high performance, air stable poly(2,5-bis(thiophene-2-yl)-(3,7-ditri-decanyltetrathienoacene) as our active semiconducting material. Owing to the small channel length and small overlap length, these devices have a signal propagation delay as low as 7 μs/stage.
Identification of key residues for protein conformational transition using elastic network model
Authors: Su Ji Guo , Jin Xu Xian , Hua Li Chun , Chen Wei Zu , Wang Cun Xin
Published: November 2011

Proteins usually undergo conformational transitions between structurally disparate states to fulfill their functions. The large-scale allosteric conformational transitions are believed to involve some key residues that mediate the conformational movements between different regions of the protein. In the present work, a thermodynamic method based on the elastic network model is proposed to predict the key residues involved in protein conformational transitions. In our method, the key functional sites are identified as the residues whose perturbations largely influence the free energy difference between the protein states before and after transition. Two proteins, nucleotide binding domain of the heat shock protein 70 and human/rat DNA polymerase β, are used as case studies to identify the critical residues responsible for their open-closed conformational transitions. The results show that the functionally important residues mainly locate at the following regions for these two proteins: (1) the bridging point at the interface between the subdomains that control the opening and closure of the binding cleft; (2) the hinge region between different subdomains, which mediates the cooperative motions between the corresponding subdomains; and (3) the substrate binding sites. The similarity in the positions of the key residues for these two proteins may indicate a common mechanism in their conformational transitions.
Effect of the starting surfaces of GaN on defect formation in epitaxial Co thin films
Authors: Li H. D. , Wong T. L. , Wang N. , Wang J. , Li Q. , Xie M. H.
Published: November 2011

Growths of Co epifilms on GaN(0001)-“1 × 1” and (1 × 1) surfaces were studied, where the structural properties of the crystals and the interfaces are compared. Stacking faults are seen to be abundant in epitaxial Co films grown on excess Ga covered GaN(0001)-“1 × 1” surface. Such stacking defects are effectively suppressed in Co films grown on less excess Ga covered GaN(0001)-(1 × 1) surfaces. The hetero-interface between Co and GaN(0001) is characterized by a disordered or amorphous region, and diffusion of Ga and N from the substrate into Co is suggested.
Microstructure dependence of the c-axis critical current density in second-generation YBCO tapes
Authors: Jia Y. , Welp U. , Crabtree G. W. , Kwok W. K. , Malozemoff A. P. , Rupich M. W. , Fleshler S. , Clem J. R.
Published: November 2011

C-axis current flow in high temperature superconductor (HTS) tape-shaped wires arises in configurations where the local wire axis is not perpendicular to the local magnetic field, such as in power cables with helically wound HTS tapes. The c-axis critical current density Jcc has been recently found to be orders of magnitude lower than the ab-plane critical current density Jcab. Here we report on Jcc (77 K, sf) values of various YBa2Cu3O7-based (YBCO) tapes with different microstructures. Our results show that the value of Jcc (77 K, sf) decreases significantly with increasing concentration of ab-plane stacking faults in YBCO thin films and that the critical current anisotropy γ = Jcab/Jcc can reach values as high as 2070, implying that in the highest-anisotropy tape, ∼20% of the tape width carries c-axis current in a helically wound power cable.
Optimized hierarchical equations of motion theory for Drude dissipation and efficient implementation to nonlinear spectroscopies
Authors: Ding Jin-Jin , Xu Jian , Hu Jie , Xu Rui-Xue , Yan YiJing
Published: November 2011

Hierarchical equations of motion theory for Drude dissipation is optimized, with a convenient convergence criterion proposed in advance of numerical propagations. The theoretical construction is on the basis of a Padé spectrum decomposition that has been qualified to be the best sum-over-poles scheme for quantum distribution function. The resulting hierarchical dynamics under the a priori convergence criterion are exemplified with a benchmark spin-boson system, and also the transient absorption and related coherent two-dimensional spectroscopy of a model exciton dimer system. We combine the present theory with several advanced techniques such as the block hierarchical dynamics in mixed Heisenberg-Schrödinger picture and the on-the-fly filtering algorithm for the efficient evaluation of third-order optical response functions.
Spectroscopic properties of alkali atoms embedded in Ar matrix
Authors: Jacquet E. , Zanuttini D. , Douady J. , Giglio E. , Gervais B.
Published: November 2011

We present a theoretical investigation of visible absorption and related luminescence of alkali atoms (Li, Na, and K) embedded in Ar matrix. We used a model based on core polarization pseudopotentials, which allows us to determine accurately the gas-to-matrix shifts of various trapping sites. The remarkable agreement between our calculated results and the experimental spectra recorded by several authors allows us to establish a clear assignment of the observed spectra, which are made of contributions from crystalline sites on the one hand, and of grain boundary sites on the other hand. Our study reveals remarkably large Stokes shifts, up to 9000 cm−1, which could be observed experimentally to identify definitely the trapping sites.
Anomalous kinetics in diffusion limited reactions linked to non-Gaussian concentration probability distribution function
Authors: de Anna Pietro , Le Borgne Tanguy , Dentz Marco , Bolster Diogo , Davy Philippe
Published: November 2011

We investigate anomalous reaction kinetics related to segregation in the one-dimensional reaction-diffusion system A + B → C. It is well known that spatial fluctuations in the species concentrations cause a breakdown of the mean-field behavior at low concentration values. The scaling of the average concentration with time changes from the mean-field t−1 to the anomalous t−1/4 behavior. Using a stochastic modeling approach, the reaction-diffusion system can be fully characterized by the multi-point probability distribution function (PDF) of the species concentrations. Its evolution is governed by a Fokker-Planck equation with moving boundaries, which are determined by the positivity of the species concentrations. The concentration PDF is in general non-Gaussian. As long as the concentration fluctuations are small compared to the mean, the PDF can be approximated by a Gaussian distribution. This behavior breaks down in the fluctuation dominated regime, for which anomalous reaction kinetics are observed. We show that the transition from mean field to anomalous reaction kinetics is intimately linked to the evolution of the concentration PDF from a Gaussian to non-Gaussian shape. This establishes a direct relationship between anomalous reaction kinetics, incomplete mixing and the non-Gaussian nature of the concentration PDF.
Positive quantization in the presence of a variable magnetic field
Authors: Măntoiu Marius , Purice Radu , Richard Serge
Published: November 2011

Starting with a previously constructed family of coherent states, we introduce the Berezin quantization for a particle in a variable magnetic field and we show that it constitutes a strict quantization of a natural Poisson algebra. The phase-space reinterpretation involves a magnetic version of the Bargmann space and leads naturally to Berezin-Toeplitz operators.
Rapid calculation of partition functions and free energies of fluids
Authors: Do Hainam , Hirst Jonathan D. , Wheatley Richard J.
Published: November 2011

The partition function (Q) is a central quantity in statistical mechanics. All the thermodynamic properties can be derived from it. Here we show how the partition function of fluids can be calculated directly from simulations; this allows us to obtain the Helmholtz free energy (F) via F = −kBT ln Q. In our approach, we divide the density of states, assigning half of the configurations found in a simulation to a high-energy partition and half to a low-energy partition. By recursively dividing the low-energy partition into halves, we map out the complete density of states for a continuous system. The result allows free energy to be calculated directly as a function of temperature. We illustrate our method in the context of the free energy of water.
Measurements and ab initio molecular dynamics simulations of the high temperature ferroelectric transition in hexagonal RMnO3
Authors: Tyson T. A. , Wu T. , Chen H. Y. , Bai J. , Ahn K. H. , Pandya K. I. , Kim S. B. , Cheong S.-W.
Published: November 2011

Measurements of the structure of hexagonal RMnO3 [R = rare earths (Ho) and Y] for temperatures significantly above the ferroelectric transition temperature (TFE) were conducted to determine the nature of the transition. The local and long range structural measurements were complemented by ab initio molecular dynamics simulations. With respect to the Mn sites in YMnO3 and HoMnO3, we find no large atomic (bond distances or thermal factors), electronic structure changes, or rehybridization on crossing TFE from local structural methods. The local symmetry about the Mn sites is preserved. With respect to the local structure about the Ho sites, a reduction of the average Ho–O bond with increased temperature is found. Ab initio molecular dynamics calculations on HoMnO3 reveal the detailed motions of all ions. Above ∼900 K there are large displacements of the Ho, O3, and O4 ions along the z axis which reduce the buckling of the MnO3/O4 planes. The changes result in O3/O4 ions moving to toward central points between pairs of Ho ions on the z axis. These structural changes make the coordination of Ho sites more symmetric thus extinguishing the electric polarization. At significantly higher temperatures, rotation of the MnO5 polyhedra occurs without a significant change in electric polarization. The Born effective charge tensor is found to be highly anisotropic at the O sites but does not change appreciably at high temperatures.
Optical and electrical properties of gold nanowires synthesized by electrochemical deposition
Authors: Yao Huijun , Duan Jinglai , Mo Dan , Yusuf Günel Hacı , Chen Yonghui , Liu Jie , Schäpers Thomas
Published: November 2011

Gold nanowire arrays with different sizes were fabricated by electrochemical deposition in etched ion-track templates. The diameter of the gold nanowires between 30 and 130 nm could be well adjusted by pore sizes in the templates through etching time. Single-crystalline nanowires were achieved by changing the parameters of electrochemical deposition. The morphology and crystal structure of the fabricated gold nanowires were characterized by means of scanning electron microscopy and transmission electron microscopy. The optical properties of the gold nanowire arrays embodied in templates were systematically measured by absorption spectra with a UV/Vis/NIR spectrophotometer. Due to the surface plasmon resonance effect, the extinction peaks of gold nanowire arrays possessed a red-shift with increasing wires diameter and a blue-shift with decreasing angle between incident light and nanowire arrays. The failure current density of the single gold nanowire as a function of diameter was determined and the failure mechanism was also discussed.
Potential of mean force between identical charged nanoparticles immersed in a size-asymmetric monovalent electrolyte
Authors: Guerrero-García Guillermo Iván , González-Mozuelos Pedro , de la Cruz Mónica Olvera
Published: November 2011

In a previous theoretical and simulation study [G. I. Guerrero-García, E. González-Tovar, and M. Olvera de la Cruz, Soft Matter 6, 2056 (2010)], it has been shown that an asymmetric charge neutralization and electrostatic screening depending on the charge polarity of a single nanoparticle occurs in the presence of a size-asymmetric monovalent electrolyte. This effect should also impact the effective potential between two macroions suspended in such a solution. Thus, in this work we study the mean force and the potential of mean force between two identical charged nanoparticles immersed in a size-asymmetric monovalent electrolyte, showing that these results go beyond the standard description provided by the well-known Derjaguin-Landau-Verwey-Overbeek theory. To include consistently the ion-size effects, molecular dynamics (MD) simulations and liquid theory calculations are performed at the McMillan-Mayer level of description in which the solvent is taken into account implicitly as a background continuum with the suitable dielectric constant. Long-range electrostatic interactions are handled properly in the simulations via the well established Ewald sums method and the pre-averaged Ewald sums approach, originally proposed for homogeneous ionic fluids. An asymmetric behavior with respect to the colloidal charge polarity is found for the effective interactions between two identical nanoparticles. In particular, short-range attractions are observed between two equally charged nanoparticles, even though our model does not include specific interactions; these attractions are greatly enhanced for anionic nanoparticles immersed in standard electrolytes where cations are smaller than anions. Practical implications of some of the presented results are also briefly discussed. A good accord between the standard Ewald method and the pre-averaged Ewald approach is attained, despite the fact that the ionic system studied here is certainly inhomogeneous. In general, good agreement between the liquid theory approach and MD simulations is also found.
Geometry optimization of bimetallic clusters using an efficient heuristic method
Authors: Lai Xiangjing , Xu Ruchu , Huang Wenqi
Published: November 2011

In this paper, an efficient heuristic algorithm for geometry optimization of bimetallic clusters is proposed. The algorithm is mainly composed of three ingredients: the monotonic basin-hopping method with guided perturbation (MBH-GP), surface optimization method, and iterated local search (ILS) method, where MBH-GP and surface optimization method are used to optimize the geometric structure of a cluster, and the ILS method is used to search the optimal homotop for a fixed geometric structure. The proposed method is applied to Cu38-nAun (0 ≤ n ≤ 38), Ag55-nAun (0 ≤ n ≤ 55), and Cu55-nAun (0 ≤ n ≤ 55) clusters modeled by the many-body Gupta potential. Comparison with the results reported in the literature indicates that the present method is highly efficient and a number of new putative global minima missed in the previous papers are found. The present method should be a promising tool for the theoretical determination of ground-state structure of bimetallic clusters. Additionally, some key elements and properties of the present method are also analyzed.
Critical thickness for plastic relaxation of SiGe on Si(001) revisited
Authors: Hartmann J. M. , Abbadie A. , Favier S.
Published: November 2011

We have revisited the critical thickness for plastic relaxation hc of SiGe on Si(001). To that end, we have started from prime 200-mm Si(001) wafers and grown (at 20 Torr with SiH2Cl2 and GeH4) various thickness and Ge content SiGe layers in an Epi Centura reduced-pressure–chemical-vapor-deposition chamber. Growth temperature was reduced from 700 °C to 550 °C, as the Ge content increased from 12% to 52%, to minimize surface roughening. X-ray diffraction (XRD) was performed on all samples to determine hc for the various Ge contents probed. Fully strained layers were characterized by: (i) peaks at a constant incidence angle that became narrower and more intense as the thickness increased, and (ii) the presence of numerous thickness fringes on each side of the layers’ peaks. Meanwhile, broader, less intense peaks (without thickness fringes) closer to the Si substrate peak were associated with plastically relaxed SiGe layers. Plastic strain relaxation was more gradual and less complete in higher Ge content layers grown at lower temperatures. We then performed haze and atomic force microscopy (AFM) measurements to have wafer and local scale quantifications of the surface roughening, which occurs when exceeding hc. For 12%, 22%, and 32% Ge, the haze and the surface roughness drastically increased for thicknesses greater than hc. For 42% Ge, the haze and the surface roughness were low for layers that had barely begun to relax, and became much larger for layers that were more plastically relaxed. Finally, for 52% Ge, there was a continuous but less pronounced increase of the haze and surface roughness when getting close to or exceeding hc. The critical thickness for plastic relaxation inferred from XRD was, for Ge content 22% and above, approximately two times higher than predicted by the People and Bean theory [Appl. Phys. Lett. 49, 229 (1986)]. However, some of the thickest SiGe 32%–52%, layers, considered fully strained in XRD, were observed by AFM to have a few “plow” lines, which are the surface signatures of misfit dislocations.
Enhanced amorphous stability of carbon-doped Ge2Sb2Te5: Ab Initio investigation
Authors: Cho Eunae , Youn Yong , Han Seungwu
Published: November 2011

The effects of carbon doping on structural and electronic properties of amorphous Ge2Sb2Te5 are studied by using ab initio molecular dynamics simulations. In comparison with Si, N, and O dopants, C dopants are found to fundamentally alter the local order of amorphous network by increasing the population of tetrahedral Ge atoms significantly. In addition, the density of ABAB-type squared rings is much smaller than for the undoped case. The present results indicate that carbon dopants are very effective in extending covalent nature in amorphous Ge2Sb2Te5 and enhancing amorphous stability.
Dynamic mechanism of equivalent conductivity minimum of electrolyte solution
Authors: Yamaguchi T. , Matsuoka T. , Koda S.
Published: November 2011

The theory on electric conductivity of electrolyte solutions we have developed [T. Yamaguchi, T. Matsuoka, and S. Koda, J. Chem. Phys. 127, 064508 (2007)] is applied to a model electrolyte solution that shows a minimum of equivalent conductivity as the function of concentration [T. Yamaguchi, T. Akatsuka, and S. Koda, J. Chem. Phys. 134, 244506 (2011)]. The theory succeeds in reproducing the equivalent conductivity minimum, whereas the mode-coupling theory (MCT) underestimates the conductivity in the low-concentration regime. The theory can also reproduce the decrease in the relaxation time of conductivity with increasing the concentration we have demonstrated with a Brownian dynamics simulation. A detailed analysis shows that the relaxation of the conductivity occurs through two processes. The faster one corresponds to the collision between a cation and an anion, and the slower one does to the polarization of the ionic atmosphere. The increase in the equivalent conductivity with concentration is attributed to the decrease in the effect of the ionic atmosphere, which is in turn explained by the fact that the counter ion cannot penetrate into the repulsive core when the Debye screening length is compatible or smaller than the ionic diameter. The same mechanism is also observed in MCT calculation with static structure factor determined by mean-spherical approximation.