bluuebunny/crossref_metadata_2025 huggingface dataset:
Protons and alpha particles in the expanding solar wind: Hybrid simulations
Authors: Hellinger Petr , Trávníček Pavel M.
Published: September 2013

We present results of a two‒dimensional hybrid expanding box simulation of a plasma system with three ion populations, beam and core protons, and alpha particles (and fluid electrons), drifting with respect to each other. The expansion with a strictly radial magnetic field leads to a decrease of the ion perpendicular to parallel temperature ratios as well as to an increase of the ratio between the ion relative velocities and the local Alfvén velocity creating a free energy for many different instabilities. The system is most of the time marginally stable with respect to kinetic instabilities mainly due to the ion relative velocities; these instabilities determine the system evolution counteracting some effects of the expansion. Nonlinear evolution of these instabilities leads to large modifications of the ion velocity distribution functions. The beam protons and alpha particles are decelerated with respect to the core protons and all the populations are cooled in the parallel direction and heated in the perpendicular one. On the macroscopic level, the kinetic instabilities cause large departures of the system evolution from the double adiabatic prediction and lead to perpendicular heating and parallel cooling rates which are comparable to the heating rates estimated from the Helios observations.
Ground penetrating radar geologic field studies of the ejecta of Barringer Meteorite Crater, Arizona, as a planetary analog
Authors: Russell Patrick S. , Grant John A. , Williams Kevin K. , Carter Lynn M. , Brent Garry W. , Daubar Ingrid J.
Published: September 2013

Ground penetrating radar (GPR) has been a useful geophysical tool in investigating a variety of shallow subsurface geological environments on Earth. Here we investigate the capabilities of GPR to provide useful geologic information in one of the most common geologic settings of planetary surfaces, impact crater ejecta. Three types of ejecta are surveyed with GPR at two wavelengths (400 MHz, 200 MHz) at Meteor Crater, Arizona, with the goal of capturing the GPR signature of the subsurface rock population. In order to “ground truth” the GPR characterization, subsurface rocks are visually counted and measured in preexisting subsurface exposures immediately adjacent to and below the GPR transect. The rock size‐frequency distribution from 10 to 50 cm based on visual counts is well described by both power law and exponential functions, the former slightly better, reflecting the control of fragmentation processes during the impact‐ejection event. GPR counts are found to overestimate the number of subsurface rocks in the upper meter (by a factor of 2–3x) and underestimate in the second meter of depth (0.6–1.0x), results attributable to the highly scattering nature of blocky ejecta. Overturned ejecta that is fractured yet in which fragments are minimally displaced from their complement fragments produces fewer GPR returns than well‐mixed ejecta. The use of two wavelengths and division of results into multiple depth zones provides multiple aspects by which to characterize the ejecta block population. Remote GPR measurement of subsurface ejecta in future planetary situations with no subsurface exposure can be used to characterize those rock populations relative to that of Meteor Crater.
Improved methods for fluorescence background subtraction from Raman spectra
Authors: Cadusch P. J. , Hlaing M. M. , Wade S. A. , McArthur S. L. , Stoddart P. R.
Published: September 2013

Raman spectroscopy has attracted interest as a non‐invasive optical technique to study the composition and structure of a wide range of materials at the microscopic level. The intrinsic fluorescence background can be orders of magnitude stronger than the Raman scattering, and so, background removal is one of the foremost challenges for quantitative analysis of Raman spectra in many samples. A range of methods anchored in instrumental and computational programming approaches have been proposed for removing fluorescence background signals. An enhanced adaptive weighting scheme for automated fluorescence removal is reported, applicable to both polynomial fitting and penalized least squares approaches. Analysis of the background fitting results for ensembles of simulated spectra suggests that the method is robust and reliable and can significantly improve the background fit over the range of signal, shot noise and background parameters tested, while reducing the subjective nature of the process. The method was also illustrated by application to experimental data generated from aqueous solutions of bulk protein fibrinogen mixed with dextran. Copyright © 2013 John Wiley & Sons, Ltd.
Viewing angle enhanced integral imaging display based on double‐micro‐lens array
Authors: Wang Ya‐Zhou , Li Da‐Hai , Luo Cheng‐Gao , Wang Qiong‐Hua
Published: September 2013

A viewing angle enhanced integral imaging display, which consists of a double microlens array, and a display panel is proposed. The double microlens array includes a convex microlens array and a concave microlens array. The display panel is used to display original elemental image array. The convex microlens array, located near the display panel, is used to provide a virtual elemental image array for the concave microlens array. The concave microlens array, located far away from the display panel, is used to display integral images with the virtual elemental image array. Compared with the original elemental image, the pitch for each virtual elemental image is magnified by the corresponding convex microlens. As a result, the viewing angle is expanded. Simulations based on ray‐tracing are performed and the results agree well with the theory.
J‐Like Supramolecular Assemblies of Polyaniline in Water
Authors: Omelchenko Olga , Tomšík Elena , Zhigunov Alexander , Guskova Olga , Gribkova Oxana , Gospodinova Natalia
Published: September 2013

The consideration of polyaniline (PANI) as a supramolecular assembly similar to J‐aggregates of dyes is proposed. Fibrils with a length of more than 100 nm and a diameter of about 4 nm are formed in water during aniline polymerization, as shown by small‐angle X‐ray scattering. Long‐wavelength absorption of the fibrils, red‐shifted with respect to highly crystalline PANI film supports the idea about the formation of J‐aggregates. Their formation, similar to dyes, is promoted by the addition of a sulfonated polyelectrolyte and becomes more pronounced with an increase of the molar mass of the polyelectrolyte. Self‐organization of aniline oligomers in a polar environment is confirmed by atomistic molecular dynamics simulations.

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Sharp bounds for the first eigenvalue and the torsional rigidity related to some anisotropic operators
Authors: Pietra Francesco Della , Gavitone Nunzia
Published: September 2013

In this paper we prove a sharp upper bound for the first Dirichlet eigenvalue of a class of nonlinear elliptic operators which includes the operator , that is the p‐Laplacian, and , namely the pseudo‐p‐Laplacian. Moreover we prove a stability result by means of a suitable isoperimetric deficit. Finally, we give a sharp lower bound for the anisotropic p‐torsional rigidity.
Protective effect of a pomace olive oil concentrated in triterpenic acids in alterations related to hypertension in rats: Mechanisms involved
Authors: Valero‐Muñoz María , Martín‐Fernández Beatriz , Ballesteros Sandra , de la Fuente Esther , Quintela José Carlos , Lahera Vicente , de las Heras Natalia
Published: September 2013

Scope

Despite the amount of information and research on the effects of virgin olive oil and its components in cardiovascular disease, little attention has been paid to the effects of pomace olive oil, an olive oil subproduct traditionally used in Spain. The aim of the present study was to evaluate the potential effects of a pomace olive oil concentrated in triterpenic acids (POCTA) on blood pressure, cardiac hemodynamics, and functional and molecular vascular alterations associated with hypertension in spontaneously hypertensive rats (SHR).

Methods and results

The study showed that POCTA attenuated the increase of blood pressure in SHR. This effect was associated with an improvement in endothelium‐dependent relaxation, enhancement of vascular expression of endothelial nitric oxide synthase, and reduction of tumor necrosis factor alpha, transforming growth factor beta, and collagen I. Furthermore, POCTA improved cardiac hemodynamics (left ventricular systolic pressure and left ventricular end‐diastolic pressure) and decreased relative kidney and lung weights.

Conclusion

POCTA exerts antihypertensive effects together with vascular and hypertension target organ protection in SHR. Since interest in pomace olive oil has been low, the results of this study contribute to increasing awareness of its biological and nutritional values.
Polymeric Bio‐Inspired Dry Adhesives: Van der Waals or Electrostatic Interactions?
Authors: Izadi Hadi , Penlidis Alexander
Published: September 2013

With respect to the dry adhesion mechanism that geckos employ for their locomotion, it is commonly accepted that the adhesive performance of synthetic bio‐inspired dry adhesives results from the formation of van der Waals interactions at the tip or side of the dry adhesive fibrils with the substrate they are brought into contact with. However, what has been usually neglected in this connection is that electrostatic interactions may also be developed at the contact between any two materials via the familiar contact electrification (CE) phenomenon. Although CE is common and can have a large influence on interfacial interaction forces, its impact on adhesive properties of synthetic dry adhesives has been overlooked. Even so, recent reports on fabrication of polymeric dry adhesives, which can generate strong adhesion forces relying on electrostatic interactions coming from CE, have brought to light again the idea that charging the surface of dry adhesives, specifically polymeric ones, can play a very crucial role in their adhesive behavior. From this perspective, the main reasons that have caused the lack of attention to this concept and the possible contributions of CE in interfacial interactions of polymeric dry adhesives are thoroughly discussed in this current critical review.
Human cardiac 31P magnetic resonance spectroscopy at 7 tesla
Authors: Rodgers Christopher T. , Clarke William T. , Snyder Carl , Vaughan J. Thomas , Neubauer Stefan , Robson Matthew D.
Published: September 2013

Purpose

Phosphorus magnetic resonance spectroscopy (31P‐MRS) affords unique insight into cardiac energetics but has a low intrinsic signal‐to‐noise ratio (SNR) in humans. Theory predicts an increased 31P‐MRS SNR at 7T, offering exciting possibilities to better investigate cardiac metabolism. We therefore compare the performance of human cardiac 31P‐MRS at 7T to 3T, and measure T1s for 31P metabolites at 7T.

Methods

Matched 31P‐MRS data were acquired at 3T and 7T, on nine normal volunteers. A novel Look‐Locker CSI acquisition and fitting approach was used to measure T1s on six normal volunteers.

Results

T1s in the heart at 7T were: phosphocreatine (PCr) 3.05 ± 0.41s, γ‐ATP 1.82 ± 0.09s, α‐ATP 1.39 ± 0.09s, β‐ATP 1.02 ± 0.17s and 2,3‐DPG (2,3‐diphosphoglycerate) 3.05 ± 0.41s (N = 6). In the field comparison (N = 9), PCr SNR increased 2.8× at 7T relative to 3T, the Cramer‐Ráo uncertainty (CRLB) in PCr concentration decreased 2.4×, the mean CRLB in PCr/ATP decreased 2.7× and the PCr/ATP SD decreased 2×.

Conclusion

Cardiac 31P‐MRS at 7T has higher SNR and the spectra can be quantified more precisely than at 3T. Cardiac 31P T1s are shorter at 7T than at 3T. We predict that 7T will become the field strength of choice for cardiac 31P‐MRS. Magn Reson Med 72:304–315, 2014. © 2013 The Authors. Magnetic Resonance in Medicine Published by Wiley Periodicals, Inc. on behalf of International Society of Medicine in Resonance. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution, and reproduction in any medium, provided the original work is properly cited.
Urodynamic results, clinical efficacy, and complication rates of sacral intradural deafferentation and sacral anterior root stimulation in patients with neurogenic lower urinary tract dysfunction resulting from complete spinal cord injury
Authors: Krasmik D. , Krebs Jörg , van Ophoven Arndt , Pannek Jürgen
Published: September 2013

Aims

To investigate the outcome and complications of sacral deafferentation (SDAF) and sacral anterior root stimulation (SARS) in patients with neurogenic lower urinary tract dysfunction (NLUTD) resulting from complete spinal cord injury (SCI).

Methods

Retrospective chart analysis of 137 patients who underwent SDAF/SARS at a single institution. Patients were categorized as being at risk of renal damage when the maximum detrusor pressure was >40 cmH2O or detrusor compliance was <20 ml/cmH2O.

Results

After a mean follow‐up time of 14.8 ± 5.3 years, SDAF/SARS treatment significantly (P < 0.001) reduced the number of patients suffering from elevated detrusor pressure from 65 to 2, and from low detrusor compliance from 62 to 13, respectively. Mean bladder capacity significantly (P < 0.001) improved from 272.4 ± 143.0 to 475.0 ± 82.7 ml. The mean number of symptomatic UTI also decreased significantly (P < 0.001) from 6.2 ± 4.5 to 2.5 ± 2.6 per year. The number of patients suffering from incontinence had significantly (P < 0.001) decreased from 70 to 44. At the last follow‐up visit, 107 (78.1%) patients were still using the stimulator. A total of 84 complications requiring surgical revision were observed. Defects of the stimulator cables or the receiver plate were the most common events (n = 38). The retrospective design pertains to the limitations of the study.

Conclusions

Sacral deafferentation and SARS are an effective treatment option for refractory NLUTD in patients with complete SCI, despite a substantial long‐term complication rate. Neurourol. Urodynam. 33:1202–1206, 2014. © 2013 Wiley Periodicals, Inc.
Diffusion‐weighted MRI monitoring of pancreatic cancer response to radiofrequency heat‐enhanced intratumor chemotherapy
Authors: Zhang Tong , Zhang Feng , Meng Yanfeng , Wang Han , Le Thomas , Wei Baojie , Lee Donghoon , Willis Patrick , Shen Baozhong , Yang Xiaoming
Published: September 2013

The aim of this study was to evaluate the feasibility of using diffusion‐weighted MRI to monitor the early response of pancreatic cancers to radiofrequency heat (RFH)‐enhanced chemotherapy. Human pancreatic carcinoma cells (PANC‐1) in different groups and 24 mice with pancreatic cancer xenografts in four groups were treated with phosphate‐buffered saline (PBS) as a control, RFH at 42 °C, gemcitabine and gemcitabine plus RFH at 42 °C. One day before and 1, 7 and 14 days after treatment, diffusion‐weighted MRI and T2‐weighted imaging were applied to monitor the apparent diffusion coefficients (ADCs) of tumors and tumor growth. MRI findings were correlated with the results of tumor apoptosis analysis. In the in vitro experiments, the quantitative viability assay showed lower relative cell viabilities for treatment with gemcitabine plus RFH at 42 °C relative to treatment with RFH only and gemcitabine only (37 ± 5% versus 65 ± 4% and 58 ± 8%, respectively, p < 0.05). In the in vivo experiments, the combination therapy resulted in smaller relative tumor volumes than RFH only and chemotherapy only (0.82 ± 0.17 versus 2.23 ± 0.90 and 1.64 ± 0.44, respectively, p = 0.003). In vivo, 14‐T MRI demonstrated a remarkable decrease in ADCs at day 1 and increased ADCs at days 7 and 14 in the combination therapy group. The apoptosis index in the combination therapy group was significantly higher than those in the chemotherapy‐only, RFH‐only and PBS treatment groups (37 ± 6% versus 20 ± 5%, 8 ± 2% and 3 ± 1%, respectively, p < 0.05). This study confirms that it is feasible to use MRI to monitor RFH‐enhanced chemotherapy in pancreatic cancers, which may present new options for the efficient treatment of pancreatic malignancies using MRI/RFH‐integrated local chemotherapy. Copyright © 2013 John Wiley & Sons, Ltd.
Noninvasive fetal RHD genotyping by microfluidics digital PCR using maternal plasma from two alloimmunized women with the variant RHD(IVS3+1G>A) allele
Authors: Tsui Nancy B. Y. , Hyland Catherine A. , Gardener Glenn J. , Danon David , Fisk Nicholas M. , Millard Glenda , Flower Robert L. , Lo Y. M. Dennis
Published: September 2013

What's already known about this topic?

Noninvasive prenatal RHD typing can be achieved by using cell‐free fetal DNA in the plasma of RhD‐negative mothers.

For RhD‐negative mothers carrying intact but dysfunctional RHD gene variants, the abundant maternal RHD sequences in maternal plasma could interfere with the fetal RHD allele detection.

What does this study add?

Digital PCR provides a high analytical specificity to noninvasively determine the fetal inheritance of RHD allele in alloimmunized pregnancies involving maternal RHD variants.
Narcissism and Empathy in Young Offenders and Non–Offenders
Authors: Hepper Erica G. , Hart Claire M. , Meek Rosie , Cisek Sylwia , Sedikides Constantine
Published: September 2013

Understanding the individual factors that predispose persons to criminal behaviour is vital to reducing offending and rehabilitating those who have been sentenced to prison. This study examined the roles of narcissism (at both clinical and subclinical trait levels) and empathy, by comparing levels in young adult males currently serving a prison sentence to those with no history of criminal convictions. Prison participants had significantly higher levels of narcissism—in particular entitlement—than control participants, and this link was sequentially mediated by lower perspective–taking and subsequently lack of empathic concern. Trait narcissism showed stronger effects than narcissistic personality disorder symptoms. Narcissistic young men's feelings of entitlement and ensuing lack of empathy for others may account for their greater likelihood of criminal behaviour. Copyright © 2013 John Wiley & Sons, Ltd.
Die Sache mit dem Dreh
Authors: Thaller Sigrid , Mathelitsch Leopold
Published: September 2013

Perfekte Drehungen sind beim Geräteturnen, Trampolin‐ und Turmspringen ein Muss. Besonders interessant sind Scheindrehungen, für die fallende Katzen ein gutes Vorbild sind. Dabei bewegen sich Sportler mit einem Gesamtdrehimpuls Null durch die Luft. Durch bestimmte Bewegungen können sie trotzdem ihren Körper drehen. Aus physikalischer Sicht interessant ist zudem, dass Sportler sich bei Drehungen nicht in Inertialsystemen befinden. Es treten Scheinkräfte auf, die sie gezielt nutzen können, um Muskelkraft zu sparen.
Smart und flexibel
Authors: Rost Henning , Krumm Jürgen , Riethus Katrin , Ludwig Klaus
Published: September 2013

Die gedruckte Elektronik ist eine noch junge Plattform‐Technologie, die eine Vielzahl an neuen Produkten ermöglicht. Dabei bringt man über moderne Rolle‐zu‐Rolle‐Druckverfahren “elektronische Tinten” auf großflächigen und flexiblen Substraten auf. Schicht für Schicht entstehen elektronische Bauelemente, wie organische Feldeffekttransistoren (OFETs). Deren Schaltfrequenz wächst quadratisch mit der Miniaturisierung des Abstands zwischen Source‐ und Drain‐Elektrode. Für anspruchsvollere Anwendungen müssen die Druckverfahren deshalb eine Auflösung und auch Präzision im Mikrometerbereich erreichen. Es gibt bereits funktionierende Funketiketten (RFID‐Tags). Weitere Anwendungen sind transparente leitfähige Folien für berührungsempfindliche Displays und sogenannte Smart Objects.
Wann ist Schrödingers Katze wirklich tot?
Authors: Nimmrichter Stefan , Hornberger Klaus
Published: September 2013

Moderne Experimente bestätigen die Gesetze der Quantenmechanik auf immer größeren Skalen. Dabei stellt sich die Frage, wo der Übergang vom quantenmechanischen zum klassischen Verhalten stattfindet und ob das quantenmechanische Superpositionsprinzip seine Gültigkeit verliert. Wir haben ein Maß vorgeschlagen, das es ermöglicht, unterschiedliche quantenmechanische Experimente danach zu bewerten, wie sehr sie unser alltägliches, klassisches Weltbild in Frage stellen.
Dreiwandige Kohlenstoff‐Nanoröhren atmen lassen
Authors: Hirschmann Thomas Ch. , Nielsch Kornelius , Reichegger Andreas
Published: September 2013

Moderne Verfahren können gezielt kombiniert werden, um interessante nanoskalige Materialien, wie dreiwandige Kohlenstoff‐Nanoröhren, herzustellen. Eine Forschungsgruppe am Massachusetts Institute of Technology (MIT), an der Wissenschaftler der Universität Hamburg beteiligt waren, hat solche Nanoröhren mit Lasern spektroskopisch charakterisiert. Ein spannender Aspekt dieser experimentellen Ergebnisse betrifft die Wechselwirkungen im Innern von mehrwandigen Kohlenstoff‐Nanoröhren.
Der Berg ruft
Authors: Bührke Thomas
Published: September 2013

Ein Jahr nach seiner Landung auf dem Mars am 6. August 2012, hat der Rover Curiosity nur etwas mehr als einen Kilometer zurückgelegt, dabei jedoch einige interessante Funde gemacht. Nun soll er die acht Kilometer lange Fahrt zum Zentralberg Mount Sharp antreten. Dort erwartet ihn die eigentlich Missionsaufgabe: die Analyse von Sedimentschichten.
Das Splittern nach dem Schuss
Authors: Vollmer Michael , Möllmann Klaus‐Peter
Published: September 2013

Rohe Eier sind, zwischen Daumen und Zeigefinger gehalten, sehr stabil. Das gilt auch für kugelförmige Christbaumkugeln. Mit solchen Feiertagsutensilien lassen sich interessante physikalische Experimente zur Inkompressibilität von Flüssigkeiten anstellen – und mit Hochgeschwindigkeitskameras studieren.
Does the use of the revised Psychosocial Assessment Tool (PATrev) result in improved quality of life and reduced psychosocial risk in Canadian families with a child newly diagnosed with cancer?
Authors: Barrera M. , Hancock K. , Rokeach A. , Atenafu E. , Cataudella D. , Punnett A. , Johnston D. , Cassidy M. , Zelcer S. , Silva M. , Jansen P. , Bartels U. , Nathan P. C. , Shama W. , Greenberg C.
Published: September 2013

Objectives

Early psychosocial screening may guide interventions and ameliorate the adverse psychosocial effects of childhood cancer. The revised psychosocial assessment tool provides risk information – Universal (typical distress), Targeted (additional specific distress), and Clinical (severe distress) – about the child with cancer and his or her family. This pilot study investigated the benefits of providing a summary of family psychosocial risk information to the medical team treating the newly diagnosed child (Experimental Group, EG).

Method

We conducted a pilot randomized control trial with a sample of 67 parents, comparing the EG to the control group (CG) on parental perception of family psychosocial difficulties (revised psychosocial assessment tool risk levels), child behavior (behavior assessment scale for children‐2), pediatric quality of life (PedsQL), and parental anxiety (state‐anxiety scale of the state‐trait anxiety inventory ), 2–4 weeks after diagnosis (Time 1) and 6 months later (Time 2).

Results

Compared to the CG, participants in the EG had significantly reduced targeted and clinical risk (p < 0.001), and improved pain related PedsQL at Time 2 (p < 0.05). Scores for PedsQL total and nearly all subscales improved over time in both groups (p < 0.05 to p < 0.001). No changes in behavior scores were noted.

Conclusion

Preliminary findings suggest that providing a summary of the Psychosocial Assessment Tool to the treating team shortly after diagnosis may help reduce family wide psychosocial risk 6 months later and improve quality of life related to pain for children who are undergoing treatment for cancer. Copyright © 2013 John Wiley & Sons, Ltd.
Epigenetic susceptibility factors for prostate cancer with aging
Authors: Damaschke N. A. , Yang B. , Bhusari S. , Svaren J. P. , Jarrard D.F.
Published: September 2013

BACKGROUND

Increasing age is a significant risk factor for prostate cancer. The prostate is exposed to environmental and endogenous stress that may underlie this remarkable incidence. DNA methylation, genomic imprinting, and histone modifications are examples of epigenetic factors known to undergo change in the aging and cancerous prostate. In this review we examine the data linking epigenetic alterations in the prostate with aging to cancer development.

METHODS

An online search of current and past peer reviewed literature on epigenetic changes with cancer and aging was performed. Relevant articles were analyzed.

RESULTS

Epigenetic changes are responsible for modifying expression of oncogenes and tumor suppressors. Several of these changes may represent a field defect that predisposes to cancer development. Focal hypermethylation occurs at CpG islands in the promoters of certain genes including GSTP1, RARβ2, and RASSF1A with both age and cancer, while global hypomethylation is seen in prostate cancer and known to occur in the colon and other organs. A loss of genomic imprinting is responsible for biallelic expression of the well‐known Insulin‐like Growth Factor 2 (IGF2) gene. Loss of imprinting (LOI) at IGF2 has been documented in cancer and is also known to occur in benign aging prostate tissue marking the presence of cancer. Histone modifications have the ability to dictate chromatin structure and direct gene expression.

CONCLUSIONS

Epigenetic changes with aging represent molecular mechanisms to explain the increased susceptibly of the prostate to develop cancer in older men. These changes may provide an opportunity for diagnostic and chemopreventive strategies given the epigenome can be modified. Prostate 73:1721–1730, 2013. © 2013 Wiley Periodicals, Inc.
Applying conformational selection theory to improve crossdocking efficiency in 3‐phosphoinositide dependent protein kinase‐1
Authors: Kotasthane Anuja , Mulakala Chandrika , Viswanadhan Vellarkad N.
Published: September 2013

The emerging picture of biomolecular recognition is that of conformational selection followed by induced‐fit. Conformational selection theory states that binding partners exist in various conformations in solution, with binding involving a “selection” between complementary conformers. In this study, we devise a docking protocol that mimics conformational selection in protein–ligand binding and demonstrate that it significantly enhances crossdocking accuracy over Glide's flexible docking protocol, which is widely used in the pharmaceutical industry. Our protocol uses a pregenerated conformational ensemble to simulate ligand flexibility. The ensemble was generated by thorough conformational sampling coupled with conformer minimization. The generated conformers were then rigidly docked in the active site of the protein along with a postdocking minimization step that allows limited induced fit effects to be modeled for the ligand. We illustrate the improved performance of our protocol through crossdocking of 31 ligands to cocomplexed proteins of the kinase 3‐phosphoinositide dependent protein kinase‐1 extracted from the crystal structures 1H1W (ATP bound), 1OKY (staurosporine bound) and 3QD0 (bound to a potent inhibitor). Consistent with conformational selection theory, the performance of our protocol was the best for crossdocking to the cognate protein bound to the natural ligand, ATP. Proteins 2014; 82:436–451. © 2013 Wiley Periodicals, Inc.
Global fold of human cannabinoid type 2 receptor probed by solid‐state 13C‐, 15N‐MAS NMR and molecular dynamics simulations
Authors: Kimura Tomohiro , Vukoti Krishna , Lynch Diane L. , Hurst Dow P. , Grossfield Alan , Pitman Michael C. , Reggio Patricia H. , Yeliseev Alexei A. , Gawrisch Klaus
Published: September 2013

The global fold of human cannabinoid type 2 (CB2) receptor in the agonist‐bound active state in lipid bilayers was investigated by solid‐state 13C‐ and 15N magic‐angle spinning (MAS) NMR, in combination with chemical‐shift prediction from a structural model of the receptor obtained by microsecond‐long molecular dynamics (MD) simulations. Uniformly 13C‐ and 15N‐labeled CB2 receptor was expressed in milligram quantities by bacterial fermentation, purified, and functionally reconstituted into liposomes. 13C MAS NMR spectra were recorded without sensitivity enhancement for direct comparison of Cα, Cβ, and CO bands of superimposed resonances with predictions from protein structures generated by MD. The experimental NMR spectra matched the calculated spectra reasonably well indicating agreement of the global fold of the protein between experiment and simulations. In particular, the 13C chemical shift distribution of Cα resonances was shown to be very sensitive to both the primary amino acid sequence and the secondary structure of CB2. Thus the shape of the Cα band can be used as an indicator of CB2 global fold. The prediction from MD simulations indicated that upon receptor activation a rather limited number of amino acid residues, mainly located in the extracellular Loop 2 and the second half of intracellular Loop 3, change their chemical shifts significantly (≥1.5 ppm for carbons and ≥5.0 ppm for nitrogens). Simulated two‐dimensional 13Cα(i)13CO(i) and 13CO(i)15NH(i + 1) dipolar‐interaction correlation spectra provide guidance for selective amino acid labeling and signal assignment schemes to study the molecular mechanism of activation of CB2 by solid‐state MAS NMR. Proteins 2014; 82:452–465. © 2013 Wiley Periodicals, Inc.
Stability of viscoelastic continuum with negative‐stiffness inclusions in the low‐frequency range
Authors: Wang Yun‐Che , Ko Chih‐Chin
Published: September 2013

The stability of viscoelastic composites with negative stiffness (NS) inclusions and their associated extreme mechanical properties are studied with time‐domain finite element analysis and composite theory. In the finite element analysis, the stability of the plane‐strain, two‐phase NS composite is evaluated by monitoring the stress divergence under uniaxial straining. In addition, 2D and 3D two‐phase NS composites are studied by using composite theories and the elastic–viscoelastic correspondence principle. Effective stiffness and damping anomalies are observed, and the stability of the composites is evaluated. In the low frequency regime, stability conditions for purely elastic systems are suitable to estimate the stability of the viscoelastic composites. This is verified with the finite element analysis. For the 2D problem, the finite element analysis and composite theory agree well with each other in terms of the overall properties and stability. For the 3D problem, only the results obtained from the composite theory are presented. Our analysis shows that the extreme mechanical properties for both of the 2D and 3D cases are located near the strong ellipticity boundary. When the matrix modulus is suitably chosen to satisfy all stability conditions, the effective stiffness softening anomaly (i.e., damping enhancement) may be in the stability range. The effective stiffness enhancement locates in the non‐elliptic range of the negative inclusion bulk modulus parameter space.
Influence of precursor gas ratio and firing on silicon surface passivation by APCVD aluminium oxide
Authors: Davis Kristopher O. , Jiang Kaiyun , Wilson Marshall , Demberger Carsten , Zunft Heiko , Haverkamp Helge , Habermann Dirk , Schoenfeld Winston V.
Published: September 2013

Using a high throughput, in‐line atmosphere chemical vapor deposition (APCVD) tool, we have synthesized amorphous aluminum oxide (AlOx) films from precursors of trimethyl‐aluminum (TMA) and O2, yielding a maximum deposition 150 nm min–1 per wafer. For p‐type crystalline silicon (c‐Si) wafers, excellent surface passivation was achieved with the APCVD AlOx films, with a best maximum effective surface recombination velocity (Seff,max) of 8 cm/s following a standard industrial firing step. The findings could be attributed to the existence of large negative charge (Qf ≈ –3 × 1012 cm–2) and low interface defect density (Dit ≈ 4 × 1011 eV–1 cm–2) achieved by the films. This data demonstrates a high potential for APCVD AlOx to be used in high efficiency, low cost industrial solar cells. (© 2013 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Na‐site energy of P2‐type NaxM O2 (M = Mn and Co)
Authors: Tanabe D. , Shimono T. , Kobayashi W. , Moritomo Y.
Published: September 2013

P2‐type NaxM O2 (M = Mn and Co) is a promising cathode material for low‐cost sodium ion secondary batteries. In this structure, there are two different crystallographic Nai (i = 1 and 2) sites with different Coulomb potential $ (\varphi _i)$ provided by M4–x and O2–. Here, we experimentally determine a difference ${(\rm \Delta }\varepsilon \equiv \varepsilon _1 - \varepsilon _2)$ of Na‐site energies ${(}\varepsilon _i \equiv e\varphi {\kern 1pt} _i)$ based on the temperature dependence of the site occupancies. We find that ${\rm \Delta }\varepsilon \;{=}\;56\;{K}$ for Na0.52MnO2 is significantly smaller than 190 K for Na0.59CoO2. We interpret the suppressed ${\rm \Delta }\varepsilon $ in Na0.52MnO2 in terms of the screening effect of the Na+ charge. (© 2013 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Modeling Skewness in Vulnerability Discovery
Authors: Joh HyunChul , Malaiya Yashwant K.
Published: September 2013

A vulnerability discovery model attempts to model the rate at which the vulnerabilities are discovered in a software product. Recent studies have shown that the S‐shaped Alhazmi–Malaiya Logistic (AML) vulnerability discovery model often fits better than other models and demonstrates superior prediction capabilities for several major software systems. However, the AML model is based on the logistic distribution, which assumes a symmetrical discovery process with a peak in the center. Hence, it can be expected that when the discovery process does not follow a symmetrical pattern, an asymmetrical distribution based discovery model might perform better. Here, the relationship between performance of S‐shaped vulnerability discovery models and the skewness in target vulnerability datasets is examined. To study the possible dependence on the skew, alternative S‐shaped models based on the Weibull, Beta, Gamma and Normal distributions are introduced and evaluated. The models are fitted to data from eight major software systems. The applicability of the models is examined using two separate approaches: goodness of fit test to see how well the models track the data, and prediction capability using average error and average bias measures. It is observed that an excellent goodness of fit does not necessarily result in a superior prediction capability. The results show that when the prediction capability is considered, all the right skewed datasets are represented better with the Gamma distribution‐based model. The symmetrical models tend to predict better for left skewed datasets; the AML model is found to be the best among them. Copyright © 2013 John Wiley & Sons, Ltd.
Identification and Assessment of Factors Influencing Human Reliability in Maintenance Using Fuzzy Cognitive Maps
Authors: Aju kumar V. N. , Gandhi M. S. , Gandhi O. P.
Published: September 2013

Human element forms an inevitable part of maintenance activity and gets affected by a variety of interacting factors, ranging from environmental, organizational, job factors, and so on to personal characteristics, which bring in inherent variability in its reliability. Assessment of impact of these factors is, therefore, critical for human reliability estimation in maintenance. In every probabilistic risk, safety or maintenance analysis, human reliability does act as an effective aspect to assess implications of various aspects of the human performance. But the main constraint with various human reliability analysis methods is in judging the important human performance influencing factors. Because of high degree of uncertainty and variability that characterizes the plant maintenance environment, it is proposed to use the soft computing technique of fuzzy cognitive maps in exploring the importance of performance shaping factors in maintenance scenario. For this purpose, the maintenance environment is modeled in terms of factors affecting human reliability using cognitive maps. The causal relationships among these factors are explored and simulations performed to quantify its effect on the human reliability. The applicability of the methodology is demonstrated through an example. Copyright © 2013 John Wiley & Sons, Ltd.
An Integrative Loss Function Approach to Multi‐Response Optimization
Authors: Ouyang Linhan , Ma Yizhong , Byun Jai‐Hyun
Published: September 2013

Loss function approach is effective for multi‐response optimization. However, previous loss function approaches ignore the dispersion performance of squared error loss and model uncertainty. In this paper, a weighted loss function is proposed to simultaneously consider the location and dispersion performances of squared error loss to optimize correlated multiple responses with model uncertainty. We propose an approach to minimize the weighted loss function under the constraint that the confidence intervals of future predictions for the multiple responses should be contained in specification limits of the responses. An example is illustrated to verify the effectiveness of the proposed method. The results show that the proposed method can achieve reliable optimal operating condition under model uncertainty. Copyright © 2013 John Wiley & Sons, Ltd.
Improved Exponentially Weighted Moving Average Control Charts for Monitoring Process Mean and Dispersion
Authors: Haq Abdul , Brown Jennifer , Moltchanova Elena , Al‐Omari Amer Ibrahim
Published: September 2013

Exponentially weighted moving average (EWMA) control charts are mostly used to monitor the manufacturing processes. In this paper, we propose some improved EWMA control charts for detecting the random shifts in the process mean and process dispersion. These EWMA control charts are based on the best linear unbiased estimators obtained under ordered ranked set sampling (ORSS) and ordered imperfect ranked set sampling (OIRSS), named EWMA‐ORSS and EWMA‐OIRSS charts, respectively. Monte Carlo simulations are used to estimate the average run length, median run length and standard deviation of run length of the proposed EWMA control charts. It is observed that the EWMA‐ORSS mean control chart is able to detect the random shifts in the process mean substantially quicker than the Shewhart‐cumulative sum and the Shewhart‐EWMA control charts based on the RSS scheme. Both EWMA‐ORSS and EWMA‐OIRSS location charts perform better than the classical EWMA, hybrid EWMA, Shewhart‐EWMA and fast initial response‐EWMA charts. The EWMA‐ORSS dispersion control chart performs better than the simple random sampling based CS‐EWMA and other EWMA control charts in efficient detection of the random shifts that occur in the process variability. An application to real data is also given to explain the implementation of the proposed EWMA control charts. Copyright © 2013 John Wiley & Sons, Ltd.
Probing uranyl(VI) speciation in the presence of amidoxime ligands using electrospray ionization mass spectrometry
Authors: Mustapha Adetayo M. , Pasilis Sofie P.
Published: September 2013

RATIONALE

Extraction processes using poly(acrylamidoxime) resins are being developed to extract uranium from seawater. The main complexing agents in these resins are thought to be 2,6‐dihydroxyiminopiperidine (DHIP) and N1,N5‐dihydroxypentanediimidamide (DHPD), which form strong complexes with uranyl(VI) at the pH of seawater. It is important to understand uranyl(VI) speciation in the presence of these and similar amidoxime ligands to understand factors affecting uranyl(VI) adsorption to the poly(acrylamidoxime) resins.

METHODS

Experiments were carried out in positive ion mode on a quadrupole ion trap mass spectrometer equipped with an electrospray ionization source. The ligands investigated were DHIP, DHPD, and N1,N2‐dihydroxyethanediimidamide (DHED). DHED and DHPD differ only in the number of carbons separating the oxime groups. The effects on the mass spectra of changes in uranyl(VI):ligand ratio, pH, and ligand type were examined.

RESULTS

DHIP binds uranyl(VI) more effectively than DHPD or DHED in the pH range investigated, forming ions derived from solution‐phase species with uranyl(VI):DHIP stoichiometries of 1:1, 1:2, and 2:3. The 2:3 uranyl(VI):DHIP complex appears to be a previously undescribed solution species. Ions related to uranyl(VI):DHPD complexes were detected in very low abundance. DHED is a more effective complexing agent for uranyl(VI) than DHPD, forming ions having uranyl(VI):DHED stoichiometries of 1:1, 1:2, 1:3, and 2:3.

CONCLUSIONS

This study presents a first look at the solution chemistry of uranyl(VI)–amidoxime complexes using electrospray ionization mass spectrometry. The appearance of previously undescribed solution species suggests that the uranyl–amidoxime system is a rich and relatively complex one, requiring a more in‐depth investigation. Copyright © 2013 John Wiley & Sons, Ltd.
Lysozyme‐encapsulated gold nanocluster‐based affinity mass spectrometry for pathogenic bacteria
Authors: Chan Po‐Han , Wong Song‐Yi , Lin Shu‐Hsuan , Chen Yu‐Chie
Published: September 2013

RATIONALE

Bacterial infections can be difficult to treat and can lead to irreversible damage to patients if proper treatment is not provided in time. Additionally, the emerging threat from antibiotic‐resistant bacterial strains makes medical treatment even more difficult. Thus, rapid identification of infected bacterial strains is essential to assist diagnostics and medical treatment.

METHODS

Lysozymes are glycoside hydrolases that can bind with peptidoglycans on bacterial cell walls. In this work, we demonstrated that lysozyme‐encapsulated gold nanoclusters (lysozyme‐AuNCs) with red photoluminescence can be used as affinity probes to concentrate pathogenic bacteria. After bacteria had been probed by the lysozyme‐AuNCs in a sample solution, the lysozyme‐AuNC‐bacteria conjugates were readily spun down at a low centrifugation speed. The red emission from the AuNCs on the conjugates could be visualized with the naked eye under illumination of ultraviolet light. The bacteria in the conjugates can be identified by matrix‐assisted laser desorption/ionization mass spectrometry (MALDI‐MS) combined with principal component analysis (PCA).

RESULTS

We demonstrated that pathogenic bacteria including Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, pandrug‐resistant Acinetobacter baumannii, Staphylococcus aureus, Enterococcus faecalis, and vancomycin‐resistant Enterococcus faecalis (VRE) can be readily concentrated by the lysozyme‐AuNCs and distinguished by the results combining MALDI‐MS and PCA. Additionally, the possibility of using the current approach to differentiate E. faecalis from VRE was also demonstrated. The lowest detection concentration for E. coli using the current approach is ~106 cells/mL.

CONCLUSIONS

The results indicated that the lysozyme‐AuNCs are effective affinity probes for Gram‐positive and Gram‐negative bacteria. By combining the results from MALDI‐MS and PCA, different bacteria can be easily distinguished. The current approach can be potentially used to assist the identification of bacteria from biological fluids. Copyright © 2013 John Wiley & Sons, Ltd.
Documenting utility of paddlefish otoliths for quantification of metals using inductively coupled plasma mass spectrometry
Authors: Long James M. , Schaffler Jason J.
Published: September 2013

RATIONALE

The otoliths of the inner ear of fishes record the environment of their surrounding water throughout their life. For paddlefish (Polyodon spathula), otoliths have not been routinely used by scientists since their detriments were outlined in the early 1940s. We sought to determine if paddlefish otoliths were useful for resolving elemental information contained within.

METHODS

Adult paddlefish were collected from two wild, self‐sustaining populations in Oklahoma reservoirs in the Arkansas River basin. Juveniles were obtained from a hatchery in the Red River basin of Oklahoma. Otoliths were removed and laser ablation, inductively coupled plasma mass spectrometry (ICP‐MS) was used to quantify eight elements (Li, Mg, Mn, Rb, Sr, Y, Ba, and Pb) along the core and edge portions, which were analyzed for differences between otolith regions and among paddlefish sources.

RESULTS

Differences were found among samples for six of the eight elements examined. Otoliths from Red River basin paddlefish born in a hatchery had significantly lower amounts of Mg and Mn, but higher levels of Rb than otoliths from wild paddlefish in the Arkansas River basin. Concentrations of Y, Sr, and Ba were reduced on the edges of adult paddlefish from both reservoirs compared with the cores.

CONCLUSIONS

This research shows the utility of using an ICP‐MS analysis of paddlefish otoliths. Future research that seeks to determine sources of paddlefish production, such as which reservoir tributaries are most important for reproduction or what proportion of the population is composed of wild versus hatchery‐produced individuals, appears promising. Published in 2013. This article is a U.S. Government work and is in the public domain in the USA.
Finite‐time attitude stabilization for rigid spacecraft
Authors: Lu Kunfeng , Xia Yuanqing
Published: September 2013

This paper investigates the finite‐time attitude stabilization problem for rigid spacecraft in the presence of inertia uncertainties and external disturbances. Three nonsingular terminal sliding mode (NTSM) controllers are designed to make the spacecraft system converge to its equilibrium point or a region around its equilibrium point in finite time. In addition, these novel controllers are singularity‐free, and the presented adaptive NTSM control (ANTSMC) laws are chattering‐free. A rigorous proof of finite‐time convergence is developed. The proposed ANTSMC algorithms combine NTSM, adaptation and a constant plus power rate reaching law. Because the algorithms require no information about inertia uncertainties and external disturbances, they can be used in practical systems, where such knowledge is typically unavailable. Simulation results support the theoretical analysis.Copyright © 2013 John Wiley & Sons, Ltd.
Effect of Ni on the Stability of Retained Austenite and Mechanical Properties for TRIP Steels Containing Vanadium
Authors: Zhu Naqiong , Wu Qihao , He Yanlin , Lu Xiaogang , Li Lin , Hu Pengfei
Published: September 2013

Two V–Ni microalloyed transformation‐induced plasticity (TRIP) steels with different Ni content were designed and investigated. Transformed volume fraction of retained austenite as a function of tensile strain was measured using an X‐ray stress apparatus aided by microelectronic universal testing machine and the evaluation of the stability of retained austenite was conducted. Precipitation of carbides during bainitic isothermal transformation was investigated using the technique of carbon extraction replica and transmission electron microscopy. X‐ray diffraction was used to determine the volume fraction of retained austenite and its carbon content. In the present work, the effect of Ni addition on the stability of retained austenite and mechanical properties for TRIP steels was detailed.