bluuebunny/crossref_metadata_2025 huggingface dataset:
Hop‐derived prenylflavonoids are substrates and inhibitors of the efflux transporter breast cancer resistance protein (BCRP/ABCG2)
Authors: Tan Kee W. , Cooney Janine , Jensen Dwayne , Li Yan , Paxton James W. , Birch Nigel P. , Scheepens Arjan
Published: July 2014

Scope

Hops (Humulus lupulus L.) produce unique prenylflavonoids that exhibit interesting bioactivities. This study investigates the interactions between selected prenylflavonoids and breast cancer resistance protein (BCRP/ABCG2), an efflux transporter important for xenobiotic bioavailability and multidrug resistance (MDR).

Methods and results

ABCG2‐inhibitory activity of xanthohumol (XN), isoxanthohumol (IX), 6‐prenylnaringenin (6‐PN), 8‐prenylnaringenin (8‐PN), and 6,8‐diprenylnarigenin (6,8‐diPN) was evaluated using mitoxantrone accumulation and vesicular transport assays. XN, IX, and 8‐PN were tested for a substrate‐type relationship with ABCG2 using ATPase and bidirectional transport assays. The prenylflavonoids exhibited significant ABCG2‐inhibitory activities in mitoxantrone accumulation and vesicular transport assays. In the ATPase assay, XN, IX, and 8‐PN inhibited baseline and sulfasalazine‐stimulated ATPase activities with IC50 of 2.16–27.0 μM. IX and 8‐PNalso displayed bell‐shaped activation curves in Ko143‐suppressed membranes, indicating a substrate‐type relationship. For IX, efflux ratios of 1.25 ± 0.21 and 9.18 ± 0.56 were observed in wild type and ABCG2‐overexpressing MDCKII cell monolayers, respectively. The latter was reduced to 1.25 ± 0.15 in the presence of the ABCG2‐specific inhibitor Ko143, demonstrating an ABCG2‐mediated efflux of IX. Additionally, evidence was shown for the involvement of ABCG2 in the efflux of 8‐PN and/or its sulfate conjugate.

Conclusion

Prenylflavonoids are potent inhibitors of ABCG2 and therefore implicated in ABCG2‐mediated food/herb‐drug interactions and MDR. ABCG2‐mediated efflux of prenylflavonoids may represent one mechanism that regulates prenylflavonoid bioavailability.
Selection and evaluation of optimal two‐dimensional CAIPIRINHA kernels applied to time‐resolved three‐dimensional CE‐MRA
Authors: Weavers Paul T. , Borisch Eric A. , Riederer Stephen J.
Published: July 2014

Purpose

To develop and validate a method for choosing the optimal two‐dimensional CAIPIRINHA kernel for subtraction contrast‐enhanced MR angiography (CE‐MRA) and estimate the degree of image quality improvement versus that of some reference acceleration parameter set at R ≥ 8.

Methods

A metric based on patient‐specific coil calibration information was defined for evaluating optimality of CAIPIRINHA kernels as applied to subtraction CE‐MRA. Evaluation in retrospective studies using archived coil calibration data from abdomen, calf, foot, and hand CE‐MRA exams was accomplished with an evaluation metric comparing the geometry factor (g‐factor) histograms. Prospective calf, foot, and hand CE‐MRA studies were evaluated with vessel signal‐to‐noise ratio (SNR).

Results

Retrospective studies show g‐factor improvement for the selected CAIPIRINHA kernels was significant in the feet, moderate in the abdomen, and modest in the calves and hands. Prospective CE‐MRA studies using optimal CAIPIRINHA show reduced noise amplification with identical acquisition time in studies of the feet, with minor improvements in the hands and calves.

Conclusion

A method for selection of the optimal CAIPIRINHA kernel for high (R ≥ 8) acceleration CE‐MRA exams given a specific patient and receiver array was demonstrated. CAIPIRINHA optimization appears valuable in accelerated CE‐MRA of the feet and to a lesser extent in the abdomen. Magn Reson Med 73:2234–2242, 2015. © 2014 Wiley Periodicals, Inc.
Deformable registration for quantifying longitudinal tumor changes during neoadjuvant chemotherapy
Authors: Ou Yangming , Weinstein Susan P. , Conant Emily F. , Englander Sarah , Da Xiao , Gaonkar Bilwaj , Hsieh Meng‐Kang , Rosen Mark , DeMichele Angela , Davatzikos Christos , Kontos Despina
Published: July 2014

Purpose

To evaluate DRAMMS, an attribute‐based deformable registration algorithm, compared to other intensity‐based algorithms, for longitudinal breast MRI registration, and to show its applicability in quantifying tumor changes over the course of neoadjuvant chemotherapy.

Methods

Breast magnetic resonance images from 14 women undergoing neoadjuvant chemotherapy were analyzed. The accuracy of DRAMMS versus five intensity‐based deformable registration methods was evaluated based on 2,380 landmarks independently annotated by two experts, for the entire image volume, different image subregions, and patient subgroups. The registration method with the smallest landmark error was used to quantify tumor changes, by calculating the Jacobian determinant maps of the registration deformation.

Results

DRAMMS had the smallest landmark errors (6.05 ± 4.86 mm), followed by the intensity‐based methods CC‐FFD (8.07 ± 3.86 mm), NMI‐FFD (8.21 ± 3.81 mm), SSD‐FFD (9.46 ± 4.55 mm), Demons (10.76 ± 6.01 mm), and Diffeomorphic Demons (10.82 ± 6.11 mm). Results show that registration accuracy also depends on tumor versus normal tissue regions and different patient subgroups.

Conclusions

The DRAMMS deformable registration method, driven by attribute‐matching and mutual‐saliency, can register longitudinal breast magnetic resonance images with a higher accuracy than several intensity‐matching methods included in this article. As such, it could be valuable for more accurately quantifying heterogeneous tumor changes as a marker of response to treatment. Magn Reson Med 73:2343–2356, 2015. © 2014 Wiley Periodicals, Inc.
Phase‐field modeling and simulation of fracture in brittle materials with strongly anisotropic surface energy
Authors: Li Bin , Peco Christian , Millán Daniel , Arias Irene , Arroyo Marino
Published: July 2014

Crack propagation in brittle materials with anisotropic surface energy is important in applications involving single crystals, extruded polymers, or geological and organic materials. Furthermore, when this anisotropy is strong, the phenomenology of crack propagation becomes very rich, with forbidden crack propagation directions or complex sawtooth crack patterns. This problem interrogates fundamental issues in fracture mechanics, including the principles behind the selection of crack direction. Here, we propose a variational phase‐field model for strongly anisotropic fracture, which resorts to the extended Cahn‐Hilliard framework proposed in the context of crystal growth. Previous phase‐field models for anisotropic fracture were formulated in a framework only allowing for weak anisotropy. We implement numerically our higher‐order phase‐field model with smooth local maximum entropy approximants in a direct Galerkin method. The numerical results exhibit all the features of strongly anisotropic fracture and reproduce strikingly well recent experimental observations. Copyright © 2014 John Wiley & Sons, Ltd.
The proper generalized decomposition for the simulation of delamination using cohesive zone model
Authors: Metoui S. , Pruliere E. , Ammar A. , Dau F. , Iordanoff I.
Published: July 2014

The use of cohesive zone models is an efficient way to treat the damage especially when the crack path is known a priori. It is the case in the modeling of delamination in composite laminates. However, the simulations using cohesive zone models are expensive in a computational point of view. When using implicit time integration or when solving static problems, the non‐linearity related to the cohesive model requires many iteration before reaching convergence. In explicit approaches, an important number of iterations are also needed because of the time step stability condition. In this article, a new approach based on a separated representation of the solution is proposed. The proper generalized decomposition is used to build the solution. This technique coupled with a cohesive zone model allows a significant reduction of the computational cost. The results approximated with the proper generalized decomposition are very close the ones obtained using the classical finite element approach. Copyright © 2014 John Wiley & Sons, Ltd.
Novel structural modeling and mesh moving techniques for advanced fluid–structure interaction simulation of wind turbines
Authors: Bazilevs Y. , Korobenko A. , Deng X. , Yan J.
Published: July 2014

In this paper, we target more advanced fluid–structure interaction (FSI) simulations of wind turbines than reported previously. For this, we illustrate how the recent advances in isogeometric analysis of thin structures may be used for efficient structural mechanics modeling of full wind turbine structures, including tower, nacelle, and blades. We consider both horizontal axis and vertical axis wind turbine designs. We enhance the sliding–interface formulation of aerodynamics, previously developed to handle flows about mechanical components in relative motion such as rotor–tower interaction to allow nonstationary sliding interfaces. To accommodate the nonstationary sliding interfaces, we propose a new mesh moving technique and present its mathematical formulation. The numerical examples include structural mechanics verification for the new offshore wind turbine blade design, FSI simulation of a horizontal axis wind turbine undergoing yawing motion as it turns into the wind and FSI simulation of a vertical axis wind turbine. The FSI simulations are performed at full scale and using realistic wind conditions and rotor speeds. Copyright © 2014 John Wiley & Sons, Ltd.
Equilibrium and kinetic isotherms and parameters for molecularly imprinted with sclareol poly(acrylonitrile‐co‐acrylic acid) matrix
Authors: Dima Ştefan‐Ovidiu
Published: July 2014

The present work continues the previous studies concerning the synthesis and characterization of molecularly imprinted polymers (MIPs) with sclareol as template and three poly(acrylonitrile‐co‐acrylic acid) (AN:AA) copolymers with different ratios between monomers as matrices. The previous studies of rheology, elemental analysis, infrared spectroscopy, size exclusion chromatography, thermogravimetry, differential scanning calorimetry, batch rebinding tests, and Scatchard analysis, which confirmed the molecular imprinting, are being completed with the current equilibrium and kinetic adsorption studies. For this purpose, eight adsorption isotherms and three kinetic adsorption models were applied to six sets of experimental data obtained after three sclareol‐imprinted adsorbents (MIPs) and three nonimprinted adsorbents (NIPs) were submitted to batch adsorption experiments. After ordering the adsorption models according to the “minimum sum of normalized errors (SNE)” criteria, it was concluded that the adsorption in sclareol imprinted AN:AA copolymers is characterized by low surface coverage, takes place on heterogeneous binding sites and is reversible, while for NIPs the results suggest a difficult adsorption and/or easiness of template extraction, and that NIPs have homogeneous, but nonimprinted micropores. For the kinetic experiments, the minimum SNE for MIPs points to the first order kinetic model, fact that suggests a physical adsorption of template molecules on the imprinted sites. POLYM. ENG. SCI., 55:1152–1162, 2015. © 2014 Society of Plastics Engineers
Protein interactomics based on direct molecular fishing on paramagnetic particles: Practical realization and further SPR validation
Authors: Ivanov Alexis S. , Medvedev Alexei , Ershov Pavel , Molnar Andrey , Mezentsev Yury , Yablokov Evgeny , Kaluzhsky Leonid , Gnedenko Oksana , Buneeva Olga , Haidukevich Irina , Sergeev Gennadiy , Lushchyk Aliaksandr , Yantsevich Alexey , Medvedeva Marina , Kozin Sergey , Popov Igor , Novikova Svetlana , Zgoda Victor , Gilep Andrey , Usanov Sergey , Lisitsa Andrey , Archakov Alexander
Published: July 2014

There is increasing evidence that proteins function in the cell as integrated stable or temporally formed protein complexes, interactomes. Previously, using model systems we demonstrated applicability of direct molecular fishing on paramagnetic particles for protein interactomics (Ershov et al. Proteomics, 2012, 12, 3295). In the present study, we have used a combination of affinity‐based molecular fishing and subsequent MS for investigation of human liver proteins involved in interactions with immobilized microsomal cytochrome b5 (CYB5A), and also transthyretin and BSA as alternative affinity ligands (baits). The LC−MS/MS identification of prey proteins fished on these baits revealed three sets of proteins: 98, 120, and 220, respectively. Comparison analysis of these sets revealed only three proteins common for all the baits. In the case of paired analysis, the number of common proteins varied from 2 to 9. The binding capacity of some identified proteins has been validated by a SPR‐based biosensor. All the investigated proteins effectively interacted with the immobilized CYB5A (Kd values ranged from 0.07 to 1.1 μM). Results of this study suggest that direct molecular fishing is applicable for analysis of protein–protein interactions (PPI) under normal and pathological conditions, in which altered PPIs are especially important.
Giving voice to cancer patients: assessing non‐specific effects of an integrative oncology therapeutic program via short patient narratives
Authors: Keshet Yael , Schiff Elad , Samuels Noah , Ben‐Arye Eran
Published: July 2014

Objective

The aim of this study was to assess patient perspectives regarding non‐specific effects of a complementary medicine (CM) consultation and intervention within an integrative oncology setting.

Methods

Patients undergoing chemotherapy in a community‐based oncology service were referred by oncology healthcare providers to an integrative oncology physician trained in CM‐oriented supportive care. Assessment of concerns and well‐being was made using the Measure Yourself Concerns and Wellbeing questionnaire, at baseline and after 3 months of CM treatments, which were designed to improve quality of life (QoL) outcomes. Patients were asked to describe the most important aspects of the integrative treatment process. Free‐text narratives were examined using content analysis with ATLAS.Ti software for systematic coding.

Results

Of 152 patients' narratives analyzed, 44% reported an experience of patient‐centered care, including CM practitioners' approach of togetherness, uniqueness, and the invoking of an internal process. CM practitioner approach was experienced within a context of an enhanced sense of confidence; gaining a different perspective; and acquiring emotional resilience and empowerment.

Conclusions

Short patient narratives should be considered for patient‐reported outcomes, expressing perspectives of both effects and experience of care. CM may promote patient QoL‐related outcomes through non‐specific effects, enhancing patient‐centered care. The benefits of CM dependent on general therapeutic incidental aspects (i.e., common factors) warrant attention regarding non‐specific components of treatment. Copyright © 2014 John Wiley & Sons, Ltd.
Metacognitive aspects influence subjective well‐being in parents of children with cancer
Authors: Toffalini Enrico , Veltri Alessia , Cornoldi Cesare
Published: July 2014

Objective

Research suggests that metacognitive beliefs may be involved in psychological distress and even in the pathogenesis of emotional disorders. The present research is a first attempt to investigate how certain metacognitive aspects operate as favorable or adverse factors influencing subjective well‐being (SWB) in the parents of children with cancer.

Method

Thirty parents of children being treated for cancer completed questionnaires on their metacognitive beliefs (Metacognition Questionnaire), sensitivity to autobiographical memory, and self‐reported measures of positive and negative affect (Positive and Negative Affect Schedule). Results in the study group were compared with those obtained from 36 control parents of children being treated for acute, not life‐threatening illnesses (hospitalized control group) and from 30 control parents of healthy children (healthy control group).

Results

Parents in both the study group and the hospitalized control group reported less SWB than the healthy control group. Most important, metacognitive aspects explained up to 77% of the variance in SWB in parents of children with cancer, as opposed to only 23% in hospitalized control group and 33% in the healthy control group.

Conclusion

Different metacognitive aspects have a crucial role—both negative and positive—in SWB of parents of children with cancer. It is suggested that the psychological support for parents coping with a child suffering from oncological disease should assess such aspects and try to address them in clinical practice. Copyright © 2014 John Wiley & Sons, Ltd.
Engineering deamidation‐susceptible asparagines leads to improved stability to thermal cycling in a lipase
Authors: Bhanuramanand K. , Ahmad Shoeb , Rao N. M.
Published: July 2014

At high temperatures, protein stability is influenced by chemical alterations; most important among them is deamidation of asparagines. Deamidation kinetics of asparagines depends on the local sequence, solvent, pH, temperature, and the tertiary structure. Suitable replacement of deamidated asparagines could be a viable strategy to improve deamidation‐mediated loss in protein properties, specifically protein thermostability. In this study, we have used nano RP‐HPLC coupled ESI MS/MS approach to identify residues susceptible to deamidation in a lipase (6B) on heat treatment. Out of 15 asparagines and six glutamines in 6B, only five asparagines were susceptible to deamidation at temperatures higher than 75°C. These five positions were subjected to site saturation mutagenesis followed by activity screen to identify the most suitable substitutions. Only three of the five asparagines were found to be tolerant to substitutions. Best substitutions at these positions were combined into a mutant. The resultant lipase (mutC) has near identical secondary structure and improved thermal tolerance as compared to its parent. The triple mutant has shown almost two‐fold higher residual activity compared to 6B after four cycles at 90°C. MutC has retained more than 50% activity even after incubation at 100°C. Engineering asparagines susceptible to deamidation would be a potential strategy to improve proteins to withstand very high temperatures.
Engineering of an isolated p110α subunit of PI3Kα permits crystallization and provides a platform for structure‐based drug design
Authors: Chen Ping , Deng Ya‐Li , Bergqvist Simon , Falk Matthew D. , Liu Wei , Timofeevski Sergei , Brooun Alexei
Published: July 2014

PI3Kα remains an attractive target for the development of anticancer targeted therapy. A number of p110α crystal structures in complex with the nSH2‐iSH2 fragment of p85 regulatory subunit have been reported, including a few small molecule co‐crystal structures, but the utilization of this crystal form is limited by low diffraction resolution and a crystal packing artifact that partially blocks the ATP binding site. Taking advantage of recent data on the functional characterization of the lipid binding properties of p110α, we designed a set of novel constructs allowing production of isolated stable p110α subunit missing the Adapter Binding Domain and lacking or featuring a modified C‐terminal lipid binding motif. While this protein is not catalytically competent to phosphorylate its substrate PIP2, it retains ligand binding properties as indicated by direct binding studies with a pan‐PI3Kα inhibitor. Additionally, we determined apo and PF‐04691502 bound crystal structures of the p110α (105‐1048) subunit at 2.65 and 2.85 Å, respectively. Comparison of isolated p110α(105‐1048) with the p110α/p85 complex reveals a high degree of structural similarity, which validates suitability of this catalytically inactive p110α for iterative SBDD. Importantly, this crystal form of p110α readily accommodates the binding of noncovalent inhibitor by means of a fully accessible ATP site. The strategy presented here can be also applied to structural studies of other members of PI3KIA family.
Interaction of double‐stranded DNA with polymerized PprA protein from Deinococcus radiodurans
Authors: Adachi Motoyasu , Hirayama Hiroshi , Shimizu Rumi , Satoh Katsuya , Narumi Issay , Kuroki Ryota
Published: July 2014

Pleiotropic protein promoting DNA repair A (PprA) is a key protein that facilitates the extreme radioresistance of Deinococcus radiodurans. To clarify the role of PprA in the radioresistance mechanism, the interaction between recombinant PprA expressed in Escherichia coli with several double‐stranded DNAs (i.e., super coiled, linear, or nicked circular dsDNA) was investigated. In a gel‐shift assay, the band shift of supercoiled pUC19 DNA caused by the binding of PprA showed a bimodal distribution, which was promoted by the addition of 1 mM Mg, Ca, or Sr ions. The dissociation constant of the PprA‐supercoiled pUC19 DNA complex, calculated from the relative portions of shifted bands, was 0.6 μM with Hill coefficient of 3.3 in the presence of 1 mM Mg acetate. This indicates that at least 281 PprA molecules are required to saturate a supercoiled pUC19 DNA, which is consistent with the number (280) of bound PprA molecules estimated by the UV absorption of the PprA–pUC19 complex purified by gel filtration. This saturation also suggests linear polymerization of PprA along the dsDNA. On the other hand, the bands of linear dsDNA and nicked circular dsDNA that eventually formed PprA complexes did not saturate, but created larger molecular complexes when the PprA concentration was >1.3 μM. This result implies that DNA‐bound PprA aids association of the termini of damaged DNAs, which is regulated by the concentration of PprA. These findings are important for the understanding of the mechanism underlying effective DNA repair involving PprA.
Does Yang‐Mills theory describe quantum gravity?
Authors: Hanada M.
Published: July 2014

The strongest version of the gauge/gravity duality conjecture relates the 1/N correction in super Yang‐Mills theory and the quantum correction in superstring theory. We perform a quantitative test of this conjecture at finite temperature, by studying the D0‐brane matrix quantum mechanics and the black zero‐brane in type IIA superstring theory. We find good agreement, which strongly suggests that the super Yang‐Mills theory does provide us with a nonperturbative formulation of quantum gravity through the gauge/gravity duality.
Peptides derived from the copper‐binding region of lysyl oxidase exhibit antiangiogeneic properties by inhibiting enzyme activity: an in vitro study
Authors: Mohankumar Arun , Renganathan Bhuvanasundar , Karunakaran Coral , Chidambaram Subbulakshmi , Konerirajapuram Natarajan Sulochana
Published: July 2014

Despite the rigorous research on abnormal angiogenesis, there is a persistent need for the development of new and efficient therapies against angiogenesis‐related diseases. The role of Lysyl oxidase (LOX) in angiogenesis and cancer has been established in prior studies. Copper is known to induce the synthesis of LOX, and hence regulates its activity. Hypoxia‐induced metastasis is dependent on LOX expression and activity. It has been believed that the inhibition of LOX would be a therapeutic strategy to inhibit angiogenesis. To explore this, we designed peptides (M peptides) from the copper‐binding region of LOX and hypothesized them to modulate LOX. The peptides were characterized, and their copper‐binding ability was confirmed by mass spectrometry. The M peptides were found to reduce the levels of intracellular copper when the cells were co‐treated with copper. The peptides showed promising effect on aortic LOX, recombinant human LOX and LOX produced by human umbilical vein endothelial cells (HUVECs). The study also explores the effect of these peptides on copper and hypoxia‐stimulated angiogenic response in HUVECs. It was found that the M peptides inhibited copper/hypoxia‐induced LOX activity and inhibited stimulated HUVEC tube formation and migration. This clearly indicated the potential of M peptides in inhibiting angiogenesis, highlighting their role in the formulation of drugs for the same. Copyright © 2014 European Peptide Society and John Wiley & Sons, Ltd.
Impacts of Service and Infrastructure Provision on Indigenous Temporary Mobility in the Northern Territory of Australia: Insights from the 2011 Census
Authors: Zander Kerstin K. , Taylor Andrew J. , Carson Dean B.
Published: July 2014

Indigenous people comprise a significant proportion of the population living in remote parts of Australia, particularly in the north. A growing body of literature has documented high mobility between remote Indigenous settlements, service towns and cities. The extent and nature of this mobility is thought to be driven, at least partly, by the types of services and infrastructure available in communities. Understanding to what extent these service and infrastructure provisions drive people's mobility and the type of people who move is essential for creating policy for remote communities and making investment decisions. We use 2011 census data to examine this issue for the Northern Territory, the Australian jurisdiction with the highest Indigenous composition in its remote population, by constructing generalised linear mixed models comparing Indigenous people's actual locations on census night with their stated usual place of residence. We found that individual characteristics (gender and age) had high impacts on individuals being at home or away on census night and that good health care provision, government subsidised community jobs and Internet access are associated with higher levels of absences from home. Meanwhile, those living in communities that had recently received new houses were less likely to be away on census night. The results can contribute to the efficiency of service provision and to understanding the dynamics of Indigenous mobility. Copyright © 2014 John Wiley & Sons, Ltd.
Assimilation of vertical motion from simulated cloudy satellite imagery in an idealized single column model
Authors: Wakeling Matthew , Eyre John , Hughes Sue , Roulstone Ian
Published: July 2014

Satellite infrared sounders are invaluable tools for making observations of the structure of the atmosphere. They provide much of the observational data used to initialize atmospheric models, especially in regions that do not have extensive surface‐based observing systems, such as oceans. However, information is lacking in the presence of cloud, as the cloud layer is opaque to infrared radiation. This means that where information is most desired (such as in a developing storm) it is often in the shortest supply.

In order to explore the mathematics of assimilating data from cloudy radiances, a study has been performed using an idealized single‐column atmospheric model. The model simulates cloud development in an atmosphere with vertical motion, allowing the characteristics of a 2D‐Var data assimilation system using a single simulated infrared satellite observation taken multiple times to be studied. The strongly nonlinear nature of cloud formation poses a challenge for variational methods. The adjoint method produces an accurate gradient for the cost function and minimization is achieved using preconditioned conjugate gradients. The conditioning is poor and varies strongly with the atmospheric variables and the cost function has multiple minima, but acceptable results are achieved.

The assimilation system is provided with a prior forecast simulated by adding random correlated Gaussian error to the truth. Assimilating observations comparable to those available from current geostationary satellites allows vertical motion to be retrieved with an error of less than a centimetre per second in most conditions. Moreover, evaluating the second derivative of the cost function at the minimum provides an estimate of the uncertainty in the retrieval. This allows atmospheric states that do not provide sufficient information for retrieval of vertical motion to be detected (such as a cloudless atmosphere or a non‐moving opaque cloud layer in the upper troposphere). Retrieval is most accurate with upwards motion.
Field emission from diameter‐defined single‐walled carbon nanotubes
Authors: Irita Masaru , Homma Yoshikazu
Published: July 2014

Field electron emission (FE) from a structure‐defined single‐walled carbon nanotube (SWNT) was observed experimentally. A series of observations of the same SWNT by scanning electron microscopy, field emission microscopy, and transmission electron microscopy were performed for the characterization of the SWNT emitter. This characterization work was very difficult because the observations affected the sample. Additionally, different sample setups were needed in each observation. We improved measurement conditions to minimize the influence to SWNT and developed techniques of sample setup for these observations. Combining these techniques, FE from an individual diameter‐defined SWNT could be observed. The diameter of SWNT was ∼1.73 nm, and the FE current of 2.2 × 10−7 A was obtained at a low applied voltage of 270 V. We observed behaviors of the SWNT emitter including field emission microscopy image twisting during FE. Copyright © 2014 John Wiley & Sons, Ltd.
Molecular dynamics out of equilibrium: mechanics and measurables
Authors: Hernandez Rigoberto , Popov Alexander V.
Published: July 2014

Molecular dynamics is fundamentally the integration of the equations of motion over a representation of an atomic and molecular system. The most rigorous choice for performing molecular dynamics entails the use of quantum‐mechanical equations of motion and a representation of the molecular system through all of its electrons and atoms. For most molecular problems involving at least hundreds of atoms, but generally many more, this is simply computationally prohibitive. Thus the art of molecular dynamics lies in choosing the representation and the appropriate equations of motion capable of addressing the requisite measurables. When used adroitly, it can provide both equilibrium (averaged) and time‐dependent properties of a molecular system. Many computational packages now exist that perform molecular dynamics simulations. They generally include force fields to represent the interactions between atoms and molecules (smoothing out electrons through the Born‐Oppenheimer approximation) and integrate the remaining particles classically. Despite these simplifications, all‐atom molecular dynamics remains computationally inaccessible if one includes the number of atoms required to simulate mesoscopic solvents. Here we use analytical models to demonstrate how molecular dynamics can be used to limit the solvent size in systems experiencing either equilibrium or nonequilibrium conditions. It is equally important to address the measurables (such as reaction rates) that are to be obtained prior to the generation of the data‐intensive trajectories.WIREs Comput Mol Sci2014, 4:541–561. doi: 10.1002/wcms.1190

This article is categorized under:

Molecular and Statistical Mechanics > Molecular Dynamics and Monte-Carlo Methods

Theoretical and Physical Chemistry > Reaction Dynamics and Kinetics
The dynamics of an offshore wind turbine in parked conditions: a comparison between simulations and measurements
Authors: Shirzadeh Rasoul , Weijtjens Wout , Guillaume Patrick , Devriendt Christof
Published: July 2014

Offshore wind turbines are complex structures, and their dynamics can vary significantly because of changes in operating conditions, e.g., rotor‐speed, pitch angle or changes in the ambient conditions, e.g., wind speed, wave height or wave period. Especially in parked conditions, with reduced aerodynamic damping forces, the response due to wave actions with wave frequencies close to the first structural resonance frequencies can be high. Therefore, this paper will present numerical simulations using the HAWC2 code to study an offshore wind turbine in parked conditions. The model has been created according to best practice and current standards based on the design of an existing Vestas V90 offshore wind turbine on a monopile foundation in the Belgian North Sea. The damping value of the model's first fore‐aft mode has been tuned on the basis of measurements obtained from a long‐term ambient monitoring campaign on the same wind turbine. Using the updated model of the offshore wind turbine, the paper will present some of the effects of the different design parameters and the different ambient conditions on the dynamics of an offshore wind turbine. The results from the simulations will be compared with the processed data obtained from the real measurements. The accuracy of the model will be discussed in terms of resonance frequencies, mode shapes, damping value and acceleration levels, and the limitations of the simulations in modeling of an offshore wind turbine will be addressed. Copyright © 2014 John Wiley & Sons, Ltd.
Boolean modeling: a logic‐based dynamic approach for understanding signaling and regulatory networks and for making useful predictions
Authors: Albert Réka , Thakar Juilee
Published: July 2014

The biomolecules inside or near cells form a complex interacting system. Cellular phenotypes and behaviors arise from the totality of interactions among the components of this system. A fruitful way of modeling interacting biomolecular systems is by network‐based dynamic models that characterize each component by a state variable, and describe the change in the state variables due to the interactions in the system. Dynamic models can capture the stable state patterns of this interacting system and can connect them to different cell fates or behaviors. A Boolean or logic model characterizes each biomolecule by a binary state variable that relates the abundance of that molecule to a threshold abundance necessary for downstream processes. The regulation of this state variable is described in a parameter free manner, making Boolean modeling a practical choice for systems whose kinetic parameters have not been determined. Boolean models integrate the body of knowledge regarding the components and interactions of biomolecular systems, and capture the system's dynamic repertoire, for example the existence of multiple cell fates. These models were used for a variety of systems and led to important insights and predictions. Boolean models serve as an efficient exploratory model, a guide for follow‐up experiments, and as a foundation for more quantitative models.WIREs Syst Biol Med2014, 6:353–369. doi: 10.1002/wsbm.1273

This article is categorized under:

Biological Mechanisms > Cell Signaling

Analytical and Computational Methods > Dynamical Methods

Models of Systems Properties and Processes > Mechanistic Models
Basic solution of two 3D rectangular cracks in an orthotropic elastic media
Authors: Liu H.‐T. , Zhou Z.‐G. , Wu L.‐Z.
Published: July 2014

By using the generalized Almansi's theorem and the Schmidt method, the solution of two 3D rectangular cracks in an orthotropic elastic media is investigated. The problems are solved through 2D Fourier transform as three pairs of dual integral equations, in which the unknown variables are the displacement jumps across the crack surfaces. To solve the dual integral equations, the displacement jumps across the crack surfaces are directly expanded as a series of Jacobi polynomials. The effects of the geometric shape of the rectangular crack and the distance between two rectangular cracks on the stress intensity factors (SIFs) in an orthotropic elastic media are concluded.
Genomic resources and genetic diversity of captive lesser kudu (Tragelaphus imberbis)
Authors: Bock Friederike , Gallus Susanne , Janke Axel , Hailer Frank , Steck Beatrice L. , Kumar Vikas , Nilsson Maria A.
Published: July 2014

The lesser kudu (Tragelaphus imberbis) is a spiral‐horned antelope native to northeastern Africa. Individuals kept in zoological gardens are suspected to be highly inbred due to few founder individuals and a small breeding stock. A morphological study suggested two distinct subspecies of the lesser kudu. However, subspecies designation and population structure in zoological gardens has not been analyzed using molecular markers. We analyzed one mitochondrial marker and two nuclear intron loci (total: 2,239 nucleotides) in 52 lesser kudu individuals. Of these, 48 individuals were bred in captivity and sampled from seven different zoos. The four remaining individuals were recently captured in Somalia and are currently held in the Maktoum zoo. Maternally inherited mitochondrial sequences indicate substantial amounts of genetic variation in the zoo populations, while the biparentally inherited intron sequences are, as expected, less variable. The analyzed individuals show 10 mitochondrial haplotypes with a maximal distance of 10 mutational steps. No prominent subspecies structure is detectable in this study. For further studies of the lesser kudu population genetics, we present microsatellite markers from a low‐coverage genome survey using 454 sequencing technology. Zoo Biol. 33:440–445, 2014. © 2014 Wiley Periodicals Inc.
Bone Tumor Imaging, Then and Now
Authors: Mintz Douglas N. , Hwang Sinchun
Published: July 2014

Background

Musculoskeletal tumor imaging is a focused subspecialty of musculoskeletal radiology. The goals of imaging and techniques employed are continually evolving and often slightly different from those used in other musculoskeletal diseases. As these techniques change, it is occasionally useful to review what is new.

Questions/Purposes

The question addressed in this manuscript is what are the most interesting/relevant changes in each modality of musculoskeletal tumor imaging over the past 38 years, the length of time the newly emeritus chair of the Radiology and Imaging Department of Hospital for Special Surgery has been at the hospital.

Methods

This review is primarily expert opinion based in examining techniques used at the institutions of the authors, with support from current literature.

Results

The techniques of computed tomography (CT) and magnetic resonance imaging (MRI) are new to the imaging armamentarium, and ultrasound and nuclear medicine techniques have advanced considerably with technology. Although radiographs have also evolved, the changes are less apparent, except in how they are currently processed, viewed, and stored.

Conclusions

Radiographic evaluation is still critical to evaluating bone tumors. Newer techniques also play an important role in diagnosing and treating these neoplasms.
Influences of peers, teachers, and climate on students' willingness to intervene when witnessing anti‐transgender harassment
Authors: Wernick Laura J. , Kulick Alex , Inglehart M.H.
Published: July 2014

Transgender young people are at increased risk for bullying, harassment, and negative mental health and academic outcomes compared to the general population as well as compared to other members of lesbian, gay, bisexual, transgender, queer, questioning, and similarly identified (LGBTQQ) communities. To inform interventions to support transgender students, the present study investigates students' willingness to intervene when witnessing anti‐transgender harassment, using data collected from a participatory action research project investigating school climate. Multi‐step linear regression was used to test the impacts of hearing transphobic language and witnessing teachers and others students intervene, while controlling for demographics and school. Hostile climate negatively predicted intervention intentions while witnessing peer intervention positively predicted likelihood to intervene. Witnessing teacher intervention did not significantly predict the outcome. These findings suggest that youth‐led interventions in peer networks might be effective in diminishing transphobic bullying and supporting the healthy development of transgender young people.
Altered RyR2 regulation by the calmodulin F90L mutation associated with idiopathic ventricular fibrillation and early sudden cardiac death
Authors: Nomikos Michail , Thanassoulas Angelos , Beck Konrad , Vassilakopoulou Vyronia , Hu Handan , Calver Brian L. , Theodoridou Maria , Kashir Junaid , Blayney Lynda , Livaniou Evangelia , Rizkallah Pierre , Nounesis George , Lai F. Anthony
Published: July 2014

Calmodulin (CaM) association with the cardiac muscle ryanodine receptor (RyR2) regulates excitation–contraction coupling. Defective CaM–RyR2 interaction is associated with heart failure. A novel CaM mutation (CaMF90L) was recently identified in a family with idiopathic ventricular fibrillation (IVF) and early onset sudden cardiac death. We report the first biochemical characterization of CaMF90L. F90L confers a deleterious effect on protein stability. Ca2+‐binding studies reveal reduced Ca2+‐binding affinity and a loss of co‐operativity. Moreover, CaMF90L displays reduced RyR2 interaction and defective modulation of [3H]ryanodine binding. Hence, dysregulation of RyR2‐mediated Ca2+ release via aberrant CaMF90L–RyR2 interaction is a potential mechanism that underlies familial IVF.
“I can almost taste it:” Why people with strong positive emotions experience higher levels of food craving, salivation and eating intentions
Authors: Moore David J. , Konrath Sara
Published: July 2014

The goal of this paper is to examine whether individual differences in affect intensity predict people's responses to food advertisements. In doing so, we aim to uncover individual differences and situational factors that are associated with higher food cravings and other consumption‐related responses. Studies 1 and 2 identified three mediators (emotional memories, weak impulse control, and the intensity of pleasure anticipation) which indirectly link affect intensity to food cravings and behavioral intentions. Studies 3 and 4 identified two moderators (vividness of advertisement, dieting status of participants) of the relationship between affect intensity and consumption‐related outcomes. In Study 3 high affect intensity individuals reported stronger food cravings only in response to vivid advertising appeals. In Study 4, respondents with high levels of positive affectivity, a sub‐dimension of affect intensity, experienced increased salivation, but especially when they were dieters exposed to vivid food images. Implications for theory development and for marketing and public policy strategists are discussed.
Optimal design of trials to demonstrate the utility of genomically‐guided therapy: Putting Precision Cancer Medicine to the test
Authors: Dienstmann Rodrigo , Rodon Jordi , Tabernero Josep
Published: July 2014

The new age of Precision Cancer Medicine, with specific biomarkers being used to direct targeted agents, generally concerns only a subset of patients within a certain histopathologically defined tumor type. This paradigm is challenged by the need to perform widespread molecular screening in certified laboratories, with results available to clinicians within reasonable timeframe. Tumor heterogeneity and clonal evolution must be considered in the decision making process. Adaptive and innovative clinical trial designs exploring predictive algorithms and reconsideration of traditional efficacy endpoints are required to rapidly translate scientific discoveries into patient care. Furthermore, international collaboration in cancer research and open discussions on the availability of investigational agents will likely redefine the drug development and approval process in the coming years.
Thinking About Legal Culture
Authors: NELKEN David
Published: July 2014

This paper addresses the controversial concept of legal culture. It first considers the different meanings of the term and the variety of debates in which it figures. It then goes on to consider difficulties in deciding the units to which the term “legal culture” is applied, and the problems in using the term in explanations. It concludes by examining the way assumptions about what gives legal culture its coherence have implications for explaining how and when it changes. In each section of the argument an attempt is also made to show the relevance of these questions for theAsian Journal of Law and Societyas seen in the papers published in its first issue.
The Open Corporation
Authors: Parker Christine
Published: July 2014

The Open Corporation, originally published in 2002, set out a blueprint for effective corporate self-regulation, offering practical strategies for managers, stakeholders and regulators to build successful self-regulation management systems. Christine Parker examined the conditions under which corporate self-regulation of social and legal responsibilities were likely to be effective, covering a wide range of areas - from consumer protection to sexual harassment to environmental compliance. Focusing on the features that make self-regulation or compliance management systems effective, Parker argued that law and regulators needed to focus much more on 'meta-regulating' corporate self-regulation if democratic control over corporate action was to be established.
Fourier Analysis and Partial Differential Equations
Authors: Iorio, Jr Rafael José , Iorio Valéria de Magalhães
Published: July 2014

This book was first published in 2001. It provides an introduction to Fourier analysis and partial differential equations and is intended to be used with courses for beginning graduate students. With minimal prerequisites the authors take the reader from fundamentals to research topics in the area of nonlinear evolution equations. The first part of the book consists of some very classical material, followed by a discussion of the theory of periodic distributions and the periodic Sobolev spaces. The authors then turn to the study of linear and nonlinear equations in the setting provided by periodic distributions. They assume only some familiarity with Banach and Hilbert spaces and the elementary properties of bounded linear operators. After presenting a fairly complete discussion of local and global well-posedness for the nonlinear Schrödinger and the Korteweg-de Vries equations, they turn their attention, in the two final chapters, to the non-periodic setting, concentrating on problems that do not occur in the periodic case.
Introduction to Statistical Field Theory
Authors: Brézin Edouard
Published: July 2014

Knowledge of the renormalization group and field theory is a key part of physics, and is essential in condensed matter and particle physics. Written for advanced undergraduate and beginning graduate students, this textbook provides a concise introduction to this subject. The textbook deals directly with the loop expansion of the free energy, also known as the background field method. This is a powerful method, especially when dealing with symmetries, and statistical mechanics. In focussing on free energy, the author avoids long developments on field theory techniques. The necessity of renormalization then follows.
Finitary Probabilistic Methods in Econophysics
Authors: Garibaldi Ubaldo , Scalas Enrico
Published: July 2014

Econophysics applies the methodology of physics to the study of economics. However, whilst physicists have good understanding of statistical physics, they may be unfamiliar with recent advances in statistical conjectures, including Bayesian and predictive methods. Equally, economists with knowledge of probabilities do not have a background in statistical physics and agent-based models. Proposing a unified view for a dynamic probabilistic approach, this book is useful for advanced undergraduate and graduate students as well as researchers in physics, economics and finance. The book takes a finitary approach to the subject, discussing the essentials of applied probability, and covering finite Markov chain theory and its applications to real systems. Each chapter ends with a summary, suggestions for further reading, and exercises with solutions at the end of the book.