bluuebunny/crossref_metadata_2025_split huggingface dataset:
Folding thermodynamics of β‐hairpins studied by replica‐exchange molecular dynamics simulations
Authors: Zerze Gül H. , Uz Bilge , Mittal Jeetain 
Published: May 2015

ABSTRACTWe study the differences in folding stability of β‐hairpin peptides, including GB1 hairpin and a point mutant GB1 K10G, as well as tryptophan zippers (TrpZips): TrpZip1, TrpZip2, TrpZip3‐1, and TrpZip4. By performing replica‐exchange molecular dynamics simulations with Amber03* force field (a modified version of Amber ff03) in explicit solvent, we observe ab initio folding of all the peptides except TrpZip3‐1, which is experimentally known to be the least stable among the peptides studied here. By calculating the free energies of unfolding of the peptides at room temperature and folding midpoint temperatures for thermal unfolding of peptides, we find that TrpZip4 and GB1 K10G peptides are the most stable β‐hairpins followed by TrpZip1, GB1, and TrpZip2 in the given order. Hence, the proposed K10G mutation of GB1 peptide results in enhanced stability compared to wild‐type GB1. An important goal of our study is to test whether simulations with Amber 03* model can reproduce experimentally predicted folding stability differences between these peptides. While the stabilities of GB1 and TrpZip1 yield close agreement with experiment, TrpZip2 is found to be less stable than predicted by experiment. However, as heterogenous folding of TrpZip2 may yield divergent thermodynamic parameters by different spectroscopic methods, mismatching of results with previous experimental values are not conclusive of model shortcomings. For most of the cases, molecular simulations with Amber03* can successfully reproduce experimentally known differences between the mutated peptides, further highlighting the predictive capabilities of current state‐of‐the‐art all‐atom protein force fields. Proteins 2015; 83:1307–1315. © 2015 Wiley Periodicals, Inc.
Impact of dopants and silicon structure dimensions on {113}‐defect formation during 2 MeV electron irradiation in an UHVEM
Authors: Vanhellemont J. , Anada S. , Nagase T. , Yasuda H. , Schulze A. , Bender H. , Rooyackers R. , Vandooren A. 
Published: May 2015

AbstractWhen processing Si nanowire based Tunnel Field Effect Transistors (TFETS's), a significant reduction of B diffusion with decreasing nanowire diameter is observed and attributed to reduced transient enhanced diffusion close to the nanowire surface caused by the recombination and out‐diffusion of excess self‐interstitials. In this study, Ultra High Voltage Electron Microscopy (UHVEM) is used to study in situ the formation of self‐interstitial clusters in nanowire based TFET containing samples prepared by Focused Ion Beam (FIB) thinning.Si nanowires with diameters ranging from 40 to 500 nm are irradiated in an UHVEM using different fluxes of 2 MeV electrons at temperatures between room temperature and 375 °C. A strong dependence of defect formation on nanowire radius and on dopant concentration and type is observed. The UHVEM observations are compared with simulations based on quasi‐chemical reaction rate theory and with two dimensional dopant concentration distributions determined with high‐vacuum Scanning Spreading Resistance Microscopy (SSRM). (© 2015 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Investigation of the kinetics of the chemical vapor deposition of aluminum from dimethylethylamine alane: experiments and computations
Authors: Aviziotis Ioannis G. , Duguet Thomas , Soussi Khaled , Kokkoris George , Cheimarios Nikolaos , Vahlas Constantin , Boudouvis Andreas G. 
Published: May 2015

AbstractExperiments and computations are performed for the metalorganic chemical vapor deposition (MOCVD) of aluminum (Al) from dimethylethylamine alane (DMEAA). The deposition rate as a function of the substrate temperature and the evolution of the deposition rate along the radius of the susceptor are experimentally determined, in a vertical, warm wall MOCVD reactor operating at 10 Torr, in the temperature range 139 °C‐240 °C. Following previously published mechanism for the decomposition of DMEAA, a predictive 3D model of the process is built, based on the mass, momentum, energy and species transport equations with the aim to simulate the process. Taking into account experimental results it is demonstrated that a volumetric and a surface reaction are responsible for the deposition of Al from DMEAA. For both reactions, first order Arrhenius kinetics are implemented and the kinetic parameters are determined through fitting to the experimental data. The results show satisfactory agreement between experiments and computations for almost the whole temperature range examined. (© 2015 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Intermolecular interaction between rare earth and manganese precursors in metalorganic chemical vapor deposition of perovskite manganite films
Authors: Nakamura Toshihiro 
Published: May 2015

AbstractThe gas‐phase reaction mechanism was investigated in liquid delivery metalorganic chemical vapor deposition (MOCVD) of praseodymium and lanthanum manganite films. We studied the gas‐phase behavior of praseodymium, lanthanum, and manganese precursors under actual CVD conditions by in situ infrared absorption spectroscopy. The rate of the decrease of the infrared absorbance due to Pr(DPM)3 was almost constant even if Mn(DPM)3 was added, indicating that the intermolecular interaction between Pr and Mn precursors in the gas phase is relatively weak in MOCVD of praseodymium manganite films. On the other hand, the temperature dependence of the infrared absorption indicates that the thermal decomposition of La(DPM)3 was promoted in the presence of Mn(DPM)3. The significant intermolecular interaction occurs between La and Mn precursors in the gas phase in MOCVD of lanthanum manganite films. (© 2015 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Growth mechanism of planar or nanorod structured tungsten oxide thin films deposited via aerosol assisted chemical vapour deposition (AACVD)
Authors: Ling Min , Blackman Chris 
Published: May 2015

AbstractAerosol assisted chemical vapour deposition (AACVD) is used to deposit tungsten oxide thin films from tungsten hexacarbonyl (W(CO)6) at 339 to 358 °C on quartz substrate. The morphologies of as‐deposited thin films, which are comprised of two phases (W25O73 and W17O47), vary from planar to nanorod (NR) structures as the distance from the inlet towards the outlet of the reactor is traversed. This is related to variation of the actual temperature on the substrate surface (ΔT = 19 °C), which result in a change in growth mode due to competition between growth rate (perpendicular to substrate) and nucleation rate (parallel to substrate). When the ratio of perpendicular growth rate to growth rate contributed by nucleation is higher than 7.1, the as‐deposited tungsten oxide thin film forms as NR. (© 2015 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Effects of calcium complexation on heparin‐like disaccharides. A combined theoretical, tandem mass spectrometry and ultraviolet experiment
Authors: Ortiz Daniel , Enjalbert Quentin , MacAleese Luke , Dugourd Philippe , Salpin Jean‐Yves 
Published: May 2015

RationaleIn order to shed light on the influence of the Ca2+ metal cation on the structure of heparin‐like (Hp) disaccharides, we have explored the gas‐phase structures of both [Hp, −2H]2− and [Ca(Hp), −3H]− ions by coupling experimental and theoretical methods.MethodsThe goal of this work was to (i) provide new evidence of the metal influence on the Hp structure, which can have important biological consequences, and (ii) to study the usefulness of metal complexation for the analytical distinction of Hp isomers. Collision‐induced dissociation (CID) and ultraviolet photodissociation (UVPD) fragments, as well as optical spectra recorded in the gas phase for both [Hp, −2H]2− and [Ca(Hp), −3H]− complexes were compared for I‐H, II‐S and III‐S isomers of Hp.ResultsIn the case of CID fragmentation, a change in the fragmentation pattern was observed upon calcium complexation, with respect to deprotonated Hp.ConclusionsRemarkably, when optical spectra are compared in the UV range, the metal effect on the carboxylic group absorption can be detected by an unambiguous blue‐shift (~20 nm). Copyright © 2015 John Wiley & Sons, Ltd.
On invariant sets and closed‐loop boundedness of Lure‐type nonlinear systems by LPV‐embedding
Authors: Seron Maria M. , De Doná José A. 
Published: May 2015

SummaryWe address the problem of achieving trajectory boundedness and computing ultimate bounds and invariant sets for Lure‐type nonlinear systems with a sector‐bounded nonlinearity. Our first contribution is to compare two systematic methods to compute invariant sets for Lure systems. In the first method, a linear‐like bound is considered for the nonlinearity, and this bound is used to compute an invariant set by regarding the nonlinear system as a linear system with a nonlinear perturbation. In the second method, the sector‐bounded nonlinearity is treated as a time‐varying parameterised linear function with bounded parameter variations, and then invariant sets are computed by embedding the nonlinear system into a convex polytopic linear parameter varying (LPV) system. We show that under some conditions on the system matrices, these approaches give identical invariant sets, the LPV‐embedding method being less conservative in the general case. The second contribution of the paper is to characterise a class of Lure systems, for which an appropriately designed linear state feedback achieves bounded trajectories of the closed‐loop nonlinear system and allows for the computation of an invariant set via a simple, closed‐form expression. The third contribution is to show that, for disturbances that are ‘aligned’ with the control input, arbitrarily small ultimate bounds on the system states can be achieved by assigning the eigenvalues of the linear part of the system with ‘large enough’ negative real part. We illustrate the results via examples of a pendulum system, a Josephson junction circuit and the well‐known Chua circuit. Copyright © 2015 John Wiley & Sons, Ltd.
Downstream Swimming Behaviour of Catadromous and Potamodromous Fish Over Spillways
Authors: Silva A. T. , Katopodis C. , Tachie M. F. , Santos J. M. , Ferreira M. T. 
Published: May 2015

AbstractFlow characteristics associated with spillways are important to restore ecological connectivity because spillways can either constrain or offer safe routes for downstream passage of fish. We studied the hydrodynamics of flow and downstream movement behaviour of the catadromous European eel (Anguilla anguilla) and the potamodromous Iberian barbel (Luciobarbus bocagei) in spillways with upstream face inclinations of θ = 90° (standard) 45° and 30° (modified). The standard spillway was tested for two water depths (H = 32 and 42 cm). Modified spillways facilitated downstream passage and reduced delay times of passage of the European eel. Upstream of the 90° spillway, distinct recirculation areas were observed, and associated turbulence strongly hampered downstream passage of fish. Both species were found to avoid turbulence, but barbel displayed stronger avoidance for areas of rapid changes in flow velocity when comparing to eels. Overall, eels were faster in passing the spillway and had a higher downstream passage success (80%) than barbel (32%). Eels were predominantly thigmotactic in contrast to barbel, which showed limited contact with structures. The results suggest that modified spillways may enhance passage survival. Copyright © 2015 John Wiley & Sons, Ltd.
From the Source to the Outlet: understanding the Distribution of Invasive Knotweeds along a North American River
Authors: Duquette M.‐C. , Compérot A. , Hayes L. F. , Pagola C. , Belzile F. , Dubé J. , Lavoie C. 
Published: May 2015

AbstractUnderstanding the drivers of exotic plant invasions along waterways is crucial for helping environmental managers devise effective control strategies. We combined a field survey, molecular data and a logistic regression model to further our understanding of the spatial distribution of Japanese (Fallopia japonica) and Bohemian (Fallopia × bohemica) knotweeds along the entire course (185 km) of a river located in Québec (Canada). Both knotweeds were abundant along the river, but each had a distinct spatial distribution pattern. Only one genotype for each knotweed species or hybrid was found, suggesting that the individuals established along the Chaudière River resulted from the propagation of rhizome or stem fragments. The distance from the nearest town or village was the only explanatory variable significantly correlated to the spatial distribution of knotweeds. However, spatial autoregressive coefficients were significant, indicating that knotweeds were more likely to occur close to other knotweeds. In summary, the invasion was probably initiated by the introduction, in riverside towns and villages, of a few individuals of the same genotype. The clones then spread vegetatively, probably during spring floods. The rhizome and stem fragments spread over short distances, dispersing downstream from urban centres. The introduction of just two knotweed genotypes along the Chaudière River was sufficient to initiate a massive riverside colonization, as few riparian vegetation types were apparently able to resist knotweed invasion. Copyright © 2015 John Wiley & Sons, Ltd.
Knowledge problems in climate change and security research
Authors: Lewis Kirsty H. , Lenton Timothy M. 
Published: May 2015

The demand for policy‐relevant information on climate change has never been higher, but there remains a gap between the type of information climate projections provide and an understanding of the consequences for human well‐being. This review explores the knowledge available to support assessments of climate change and security for a wide range of policy stakeholders. Both the climate science and social science communities undertake valuable research toward understanding climate change and the interaction of environment and security, but address different aspects of the problem. Differences in the types of knowledge produced include analytical methods, language, and scale issues. This makes research conclusions difficult to reconcile and provides a barrier to knowledge sharing. It is largely left to policy and security analysts to bring these two very different types of information together in accessible, policy‐relevant assessments. Often this is done by considering the potential implications of existing climate change projections, with little or no input from social scientists on the complexities of the relationship between environment and security. An alternative approach to climate change and security assessments is to consider the problem from a systems perspective. This approach has the potential to offer new insight across disciplines and improve the utility of research outcomes to inform action on climate change and security. WIREs Clim Change 2015, 6:383–399. doi: 10.1002/wcc.346This article is categorized under:

Integrated Assessment of Climate Change > Methods of Integrated Assessment of Climate Change
ECDGP: extended cluster‐based data gathering protocol for vehicular networks
Authors: Brik Bouziane , Lagraa Nasreddine , Lakas Abderrahmane , Cherroun Hadda , Cheddad Abbas 
Published: May 2015

AbstractAn important application in wireless networks is data collection. It aims to gather and deliver specific data for concerned authorities. Many researchers invest in vehicular ad hoc networks for that purpose to acquire data from different sources on the roads as from its vicinity. A vehicle is considered as a mobile data collector, it gathers real‐time or delay‐tolerant data such as road traffic, environmental information, and event advertisements. In a previous work, we have proposed a novel clustered data gathering protocol (CDGP) for vehicular ad hoc network, which improves the collection performance by implementing a new space division multiple access technique called dynamic space division multiple access and a retransmission mechanism in case of errors. However, CDGP supports only delay‐tolerant data as it does not use any aggregation technique. In this paper, we propose an enhancement of this protocol by extending it to support: (i) both real‐time and delay‐tolerant applications; (ii) multiple types of data; and (iii) aggregation of collected data prior to sending them to the initiator. We present the plausible analytical complexity of the extended CDGP, as we illustrate the superiority of its performance throughout the results obtained from simulation experiments, using a Freeway mobility model. Copyright © 2015 John Wiley & Sons, Ltd.
Proposed Minimum Rates of Surgery to Support Desirable Health Outcomes: An Observational Study Based on Three Strategies
Authors: Esquivel Micaela M. , Molina George , Uribe‐Leitz Tarsicio , Lipsitz Stuart R. , Rose John , Bickler Stephen , Gawande Atul A. , Haynes Alex B. , Weiser Thomas G. 
Published: May 2015

AbstractBackgroundThe global volume of surgery is estimated at 312.9 million operations annually, but rates of surgery vary dramatically. Identifying surgical rates associated with improved health outcomes would be useful for benchmarking and targeted health system strengthening.MethodsWe identified rates of surgery associated with a life expectancy (LE) of 74–75 years, a maternal mortality ratio (MMR) of less than or equal to 100 per 100,000 live births, and the estimated need for surgery in the seven global burden of disease (GBD) super‐regions based on the prevalence of surgical conditions. We compared our findings to surgical rates from Chile, China, Costa Rica, and Cuba (“4C”), countries with moderate resources but high health outcomes.ResultsThe median surgical rates associated with LE of 74–75 years (N = 17) and MMR below 100 (N = 109) are 4392 (IQR 2897–4873) and 5028 (IQR 4139–6778) operations per 100,000 people annually, respectively. The mean surgical rate estimated for the seven super‐regions was 4723 (95 % CI 3967–5478) operations per 100,000 people annually. The “4C” countries had a mean surgical rate of 4344 (95 % CI 2620–6068) operations per 100,000 people annually. Thirteen of the twenty‐one GBD regions, accounting for 78 % of the world’s population, do not achieve rates of surgery at the lowest end of this range.ConclusionsWe identified a narrow range of surgical rates associated with important health indicators. This target range can be used for benchmarking of surgical services, and as part of a policy aimed at strengthening health care systems and surgical capacity.
Use of Cardiac Magnetic Resonance Imaging Based Measurements of Inferior Vena Cava Cross-Sectional Area in the Diagnosis of Pericardial Constriction
Authors: Hanneman Kate , Thavendiranathan Paaladinesh , Nguyen Elsie T. , Moshonov Hadas , Wald Rachel , Connelly Kim A. , Paul Narinder S. , Wintersperger Bernd J. , Crean Andrew M. 
Published: May 2015

Purpose To evaluate the value of cardiac magnetic resonance imaging (MRI)–based measurements of inferior vena cava (IVC) cross-sectional area in the diagnosis of pericardial constriction. Methods Patients who had undergone cardiac MRI for evaluation of clinically suspected pericardial constriction were identified retrospectively. The diagnosis of pericardial constriction was established by clinical history, echocardiography, cardiac catheterization, intraoperative findings, and/or histopathology. Cross-sectional areas of the suprahepatic IVC and descending aorta were measured on a single axial steady-state free-precession (SSFP) image at the level of the esophageal hiatus in end-systole. Logistic regression and receiver-operating curve (ROC) analyses were performed. Results Thirty-six patients were included; 50% (n = 18) had pericardial constriction. Mean age was 53.9 ± 15.3 years, and 72% (n = 26) were male. IVC area, ratio of IVC to aortic area, pericardial thickness, and presence of respirophasic septal shift were all significantly different between patients with constriction and those without ( P < .001 for all). IVC to aortic area ratio had the highest odds ratio for the prediction of constriction (1070, 95% confidence interval [8.0-143051], P = .005). ROC analysis illustrated that IVC to aortic area ratio discriminated between those with and without constriction with an area under the curve of 0.96 (95% confidence interval [0.91-1.00]). Conclusions In patients referred for cardiac MRI assessment of suspected pericardial constriction, measurement of suprahepatic IVC cross-sectional area may be useful in confirming the diagnosis of constriction when used in combination with other imaging findings, including pericardial thickness and respirophasic septal shift.
The sleeper framing effect: The influence of frame valence on immediate and retrospective judgments
Authors: Isaac Mathew S. , Poor Morgan 
Published: May 2015

AbstractPrior research on attribute framing has documented a robust valence‐consistent shift whereby positively valenced options (e.g., 75% lean beef) are preferred over equivalent negatively valenced options (e.g., 25% fat beef). However, this research has typically explored how labels influence judgments of prospective or hypothetical consumption. In contrast, we examine how frames interact with actual consumption experiences to influence both immediate and retrospective judgments. We find evidence of a sleeper framing effect wherein a valence‐consistent shift emerges for retrospective judgments even when absent immediately after consumption. We attribute this effect to differences in how consumers integrate the more cognitive information of the frame with the more affective information acquired during consumption. Specifically, three experiments show that consumers attend to and rely relatively more on affective information from experience when making immediate judgments, but relatively more on cognitive information from the frame when making retrospective judgments. In addition, we identify the valence of the experience as an important boundary condition, such that the sleeper framing effect is most pronounced when the experience is relatively neutral in valence.
Autophagy induction impairs migration and invasion by reversing EMT in glioblastoma cells
Authors: Catalano Myriam , D'Alessandro Giuseppina , Lepore Francesca , Corazzari Marco , Caldarola Sara , Valacca Cristina , Faienza Fiorella , Esposito Vincenzo , Limatola Cristina , Cecconi Francesco , Di Bartolomeo Sabrina 
Published: May 2015

Cell migration and invasion are highly regulated processes involved in both physiological and pathological conditions. Here we show that autophagy modulation regulates the migration and invasion capabilities of glioblastoma (GBM) cells. We observed that during autophagy occurrence, obtained by nutrient deprivation or by pharmacological inhibition of the mTOR complexes, GBM migration and chemokine‐mediated invasion were both impaired. We also observed that SNAIL and SLUG, two master regulators of the epithelial–mesenchymal transition (EMT process), were down‐regulated upon autophagy stimulation and, as a consequence, we found a transcriptional and translational up‐regulation of N‐ and R‐cadherins. Conversely, in BECLIN 1‐silenced GBM cells, an increased migration capability and an up‐regulation of SNAIL and SLUG was observed, with a resulting decrease in N‐ and R‐cadherin mRNAs. ATG5 and ATG7 down‐regulation also resulted in an increased migration and invasion of GBM cells combined to an up‐regulation of the two EMT regulators. Finally, experiments performed in primary GBM cells from patients largely confirmed the results obtained in established cell cultures.Overall, our results indicate that autophagy modulation triggers a molecular switch from a mesenchymal phenotype to an epithelial‐like one in GBM cellular models. Since the aggressiveness and lethality of GBM is defined by local invasion and resistance to chemotherapy, we believe that our evidence provides a further rationale for including autophagy/mTOR‐based targets in the current therapeutical regimen of GBM patients.