bluuebunny/crossref_metadata_2025 huggingface dataset:
An assessment of current bioinformatic solutions for analyzing LC‐MS data acquired by selected reaction monitoring technology
Authors: Brusniak Mi‐Youn K. , Chu Caroline S. , Kusebauch Ulrike , Sartain Mark J. , Watts Julian D. , Moritz Robert L.
Published: May 2012

Selected reaction monitoring (SRM) is an accurate quantitative technique, typically used for small‐molecule mass spectrometry (MS). SRM has emerged as an important technique for targeted and hypothesis‐driven proteomic research, and is becoming the reference method for protein quantification in complex biological samples. SRM offers high selectivity, a lower limit of detection and improved reproducibility, compared to conventional shot‐gun‐based tandem MS (LC‐MS/MS) methods. Unlike LC‐MS/MS, which requires computationally intensive informatic postanalysis, SRM requires preacquisition bioinformatic analysis to determine proteotypic peptides and optimal transitions to uniquely identify and to accurately quantitate proteins of interest. Extensive arrays of bioinformatics software tools, both web‐based and stand‐alone, have been published to assist researchers to determine optimal peptides and transition sets. The transitions are oftentimes selected based on preferred precursor charge state, peptide molecular weight, hydrophobicity, fragmentation pattern at a given collision energy (CE), and instrumentation chosen. Validation of the selected transitions for each peptide is critical since peptide performance varies depending on the mass spectrometer used. In this review, we provide an overview of open source and commercial bioinformatic tools for analyzing LC‐MS data acquired by SRM.
Targeted proteomics for quantification of histone acetylation in Alzheimer's disease
Authors: Zhang Kangling , Schrag Matthew , Crofton Andrew , Trivedi Rishi , Vinters Harry , Kirsch Wolff
Published: May 2012

The epigenetic remodeling of chromatin histone proteins by acetylation has been the subject of recent investigations searching for biomarkers indicative of late onset cognitive loss. Histone acetylations affect the regulation of gene transcription, and the loss of learning induced deacetylation at specific histone sites may represent biomarkers for memory loss and Alzheimer's disease (AD). Selected‐reaction‐monitoring (SRM) has recently been advanced to quantitate peptides and proteins in complex biological systems. In this paper, we provide evidence that SRM‐based targeted proteomics can reliably quantify specific histone acetylations in both AD and control brain by identifying the patterns of H3 K18/K23 acetylations Results of targeted proteomics assays have been validated by Western blot (WB) analysis. As compared with LC‐MS/MS‐TMT (tandem‐mass‐tagging) and WB methods, the targeted proteomics method has shown higher throughput, and therefore promised to be more suitable for clinical applications. With this methodology, we find that histone acetylation is significantly lower in AD temporal lobe than found in aged controls. Targeted proteomics warrants increased application for studying epigenetics of neurodegenerative diseases.
Depression and cancer survivorship: importance of coping self‐efficacy in post‐treatment survivors
Authors: Philip Errol J. , Merluzzi Thomas V. , Zhang Zhiyong , Heitzmann Carolyn A.
Published: May 2012

Background

An estimated 30% of cancer patients are expected to experience clinically significant psychological distress during the treatment phase of their disease. Despite significant attention being directed to the mental health needs of individuals undergoing and completing treatment, there is less known about the mental health needs of survivors and the role of potential protective factors in survivorship, such as coping self‐efficacy and social support.

Method

One hundred and twenty‐four post‐treatment cancer survivors (mean age = 62.23 years, women = 70%, average 9.3 years post‐treatment) were asked to complete measures of physical symptoms, coping self‐efficacy, social support, and depression as part of a national convenience sample of cancer patients and survivors.

Results

About 20% of participants possessed scores on the Center for Epidemiologic Studies‐Depressed Mood Scale indicative of clinically relevant depression. Coping self‐efficacy was not only a significant predictor of depression (43% Variance Accounted For); it also partially mediated the relationship between symptoms and depression. Social support accounted for limited variance and was not a significant predictor of depression in a model containing both social support and coping self‐efficacy as predictors.

Conclusion

A substantial minority of post‐treatment survivors reported depression symptomatology. Coping self‐efficacy may be an important component of patients' adjustment and possible target for intervention. These results highlight the ongoing mental health and support needs of cancer survivors. Copyright © 2012 John Wiley & Sons, Ltd.
Lay understanding of common medical terminology in oncology
Authors: Pieterse Arwen H. , Jager Nienke A. , Smets Ellen M.A. , Henselmans Inge
Published: May 2012

Objective

The purpose of this study was to replicate and extend an earlier study carried out in the UK of lay understanding of cancer‐related terms in a Dutch sample, by (i) examining understanding of common terms relating to diagnosis, prognosis, and treatment and (ii) experimentally exploring the effect of medical jargon versus plain language use on individuals' perceived efficacy in interacting with oncologists, participating in medical decision making, and interpersonal trust.

Methods

One hundred ninety‐four lay people completed a questionnaire assessing (i) understanding, confidence in understanding, and worry after reading 10 scenarios presenting cancer‐related terms and (ii) perceived communication efficacy, decision‐making efficacy, and trust following a vignette portraying an oncologist using either jargon or plain language.

Results

On average, participants understood a majority (6.8 ± 1.6) of cancer‐related terms, yet only 2.2% understood all 10 terms correctly. Compared with incorrect understanding, correct understanding was generally related to higher confidence in understanding and to worry levels that better matched the scenarios. Language complexity did not significantly affect measures of perceived efficacy or trust. Overall confidence in understanding was significantly related to measures of perceived efficacy (p < 0.01).

Conclusion

Similar to the earlier UK study these results suggest that lay people's understanding of commonly‐used terms in oncology is suboptimal. Moreover, confidence in understanding was related to perceived efficacy in participating in the consultation. Oncologists should attempt to correct patient misunderstanding to alleviate unnecessary worry and potentially facilitate patient participation. Copyright © 2012 John Wiley & Sons, Ltd.
Assessment of motor function in people with multiple sclerosis
Authors: De Souza LH , Ashburn A
Published: May 2012

Multiple sclerosis (MS) is a chronic progressive disease of the central nervous system (CNS) which predominantly affects young adults. In order to provide physiotherapy appropriate to the needs of individuals with MS, it is necessary to assess and evaluate the nature and degree of motor and functional deficits. The aim of this research was to develop a physiotherapy assessment which would consistently and objectively evaluate motor function in people with MS. The Motor Club Assessment (MCA), originally developed for use in stroke patients, was identified as exhibiting several features which were consonant with the required criteria. It was therefore modified for use in MS. The Amended MCA (AMCA) was tested for inter‐rater agreement, which was found to be good for the lower limb motor section (weighted kappa = 0.80), the upper limb motor section (weighted kappa = 0.90), and the functional activities section (weighted kappa = 0.92). The internal consistency was high for the lower limb section (alpha = 0.97) and the functional activities section (alpha = 0.92), but could not be determined for the upper limb section due to a clear ceiling effect. The study demonstrated that the AMCA is a valid tool for assessment use by physiotherapists in MS patients, and that it has an acceptable level of reliability when used in a clinic setting by physiotherapists suitably experienced in the treatment of neurological patients.
Temperature dependence of the Raman spectra of Bi2Te3 and Bi0.5Sb1.5Te3 thermoelectric films
Authors: Li Duanhui , Li Liangliang , Liu Da‐Wei , Li Jing‐Feng
Published: May 2012

The temperature dependence of the Raman spectra of Bi2Te3 and Bi0.5Sb1.5Te3 thermoelectric films was investigated. The temperature coefficients of the Eg(2) peak positions were determined as –0.0137 cm–1/°C and –0.0156 cm–1/°C, respectively. The thermal expansion of the crystal caused a linear shift of the Raman peak induced by the temperature change. Based on the linear relation, a reliable and noninvasive micro‐Raman scattering method was shown to measure the thermal conductivity of the thermoelectric films. (© 2012 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Adsorption of glycidoxypropyl‐trimethoxy‐silane on α and β phases of titanium alloy Ti–6.5Al–1Mo–1V–2Zr
Authors: Liu Jian‐hua , Zhan Zhong‐wei , Yu Mei , Li Song‐mei , Wang Qiang , Zhang Jun , Wang Miao
Published: May 2012

The adsorption of glycidoxypropyl‐trimethoxy‐silane (GTMS) on α and β phases of titanium alloy Ti–6.5Al–1Mo–1V–2Zr was studied. The morphology and composition of coated alloy were investigated by using field‐emission scanning electron microscopy, energy dispersive spectroscopy, and atomic force microscopy. The quantitative characterization of GTMS adsorption was carried out by using XPS. The results showed that the β phase particles exhibited better ability to adsorb GTMS molecules than the α phase, especially at lower concentrations of GTMS, which resulted in a relatively nonuniform silane coating. The differences in the adsorption ability between the α phase and β phase particles were attributed to the different alloying elements contained in them and different characteristics of the oxides formed on them. Uniform adsorption of GTMS on the overall metal surface was achieved by increasing the concentration of GTMS to 1 vol.%. Copyright © 2012 John Wiley & Sons, Ltd.
Nuclear safeguards applications using LG‐SIMS with automated screening capabilities
Authors: Peres P. , Hedberg P. M. L. , Walton S. , Montgomery N. , Cliff J. B. , Rabemananjara F. , Schuhmacher M.
Published: May 2012

A primary tool for detecting undeclared nuclear activities is the analysis of uranium‐bearing particles collected on cotton swipes. For many years, secondary ion mass spectrometry (SIMS) has been used as one of the mainstay techniques for particle analysis of nuclear safeguards samples. SIMS is unique in that it is the only technique that can both localize the particles of interest and also provide the isotopic composition of single particles. This paper presents data obtained on standard uranium particle samples using large geometry (LG)‐SIMS instruments equipped with the newly developed, automated particle measurement screening software. Both sample screening measurements and microbeam analyses on individual particles are presented. The enhanced performance of the SIMS method for nuclear safeguards applications using LG‐SIMS instruments equipped with automated screening capabilities is also discussed. Copyright © 2012 John Wiley & Sons, Ltd. and Crown copyright
b/t‐Interaktionsdiagramme zum vereinfachten Beulsicherheitsnachweis nach DIN EN 1993‐1‐5 für Platten aller Baustahlsorten
Authors: Hillebrecht Volker , Rubert Achim , Strutzke Matthias
Published: May 2012

Nach kurzer Darstellung der historischen Entwicklungen und wesentlichen Unterschiede der Nachweisformate von DIN 18800‐3 und DIN EN 1993‐1‐5 gegen Plattenbeulen werden die Nachweisschritte der Methode der reduzierten Spannungen (einschließlich alternativer Formeln) der DIN EN 1993‐1‐5 zusammengestellt. Die damit entwickelten b/t‐Interaktionsdiagramme zum vereinfachten Beulnachweis des Membranspannungsfeldes Ed (sx,Ed, tEd) für zweiseitig gelenkig gelagerte Platten ersetzten das komplette Nachweisformat und sind für alle Baustahlsorten geeignet. Es werden Anwendungsbeispiele gezeigt und ein Ausblick auf zu erwartende Änderungen der DIN EN 1993‐1‐5 gegeben.

b/t‐interaction diagrams for a simple buckling assessment procedure according to EN 1993‐1‐5 for plates of all construction steel grades. Following a short summary of the historical development and the main differences between the plate buckling assessments of the German code DIN 18800‐3 and the new DIN EN 1993‐1‐5 a detailed table of the method of reduced stresses (including alternative formulas) is presented. b/t‐interaction diagrams for simply supported plates of any construction steel grade with membrane stress fields Ed (sx,Ed, tEd) are provided. They fully replace the buckling assessment procedure. Finally some examples and hints of future developments are shown.
Dynamische Systemantwort des Timoshenko‐Balkens unter Impulseinwirkung aus Detonation
Authors: Mensinger Martin , Trometer Stefan , Reyer Dominic
Published: May 2012

Stützenkonstruktionen werden für die Abtragung von Vertikallasten dimensioniert, zusätzliche horizontale Belastungen durch außergewöhnliche Einwirkungen wie Detonationen stellen dabei eine große Herausforderung dar. Die Bestimmung der dynamischen Systemantwort bei variabler Normalkraftauslastung ist notwendig, um die dynamischen Effekte unter einer solchen Impulsbelastung mit ausreichender Präzision abzubilden, sie zu verstehen und daraus die Beanspruchungen genau zu ermitteln. Die Wahl einer passenden Balkentheorie in Kombination mit einer effizienten Lösungsstrategie ist dabei von zentraler Bedeutung. Als zielführend hat sich die Modalanalyse erwiesen, die auf den Timoshenko‐Balken angewandt wird. Das Lösungsverfahren wird vorgestellt, untersucht und mit anderen ausgewählten Lösungsverfahren verglichen und diskutiert.

Dynamic system response of the Timoshenko beam subjected to impulsive loading due to explosion. Column constructions are designed to safely transfer vertical loads into the ground. Hence additional horizontal loading caused by accidental loading due to explosion constitute a major challenge. The determination of the dynamic system response at variable axial loading is required to identify the dynamic effects with adequate accuracy, to understand the mechanisms and to derive the design state. It is of importance to choose a suitable beam theory in combination with an efficient solution strategy. Herein, the modal analysis with an extension for continuous systems is applied on basis of the Timoshenko beam theory. The complete solution strategy is presented, investigated, compared with other selected strategies and discussed herein.
Analysis and design of a ZVS converter for high voltage input–low voltage output application
Authors: Yan Zhou , Bo‐Lin Wang
Published: May 2012

This paper proposes a full‐bridge (d = 50%) cascaded buck topology which is a very suitable circuit for high voltage input–low voltage output applications with high output current. Benefiting from working under a large duty cycle, the proposed converter can easily achieve zero voltage switching turn‐on and turn‐off of active switches in a full bridge. Small‐signal model of this topology is analyzed through its corresponding peak current mode control. Its small‐signal transfer function is given, and the control loop design is discussed. Advantages of this topology and operation principles are analyzed. Design guidelines, drawn from this analysis, are applied on a low‐voltage (3.3 V) output voltage prototype to validate the proposed concept. © 2012 Institute of Electrical Engineers of Japan. Published by John Wiley & Sons, Inc.
Motor performance investigation of an indirect matrix converter with a reactor‐free boost converter
Authors: Teck Chiang Goh , Itoh Jun‐ichi
Published: May 2012

This paper describes a three‐phase power converter which utilizes the neutral point of an induction motor and demonstrates the performance of the motor using the proposed method under various operating conditions. Several motor test results, such as the speed–torque characteristic, the torque impact, and the acceleration–deceleration characteristic, are included to confirm the performance of the induction motor. The structure of the proposed circuit consists primarily of an AC/AC converter [indirect matrix converter (IMC)] and a boost converter connected to the neutral point of the induction motor. In addition, this paper also proposes a method to reduce the ripple found in the battery current. Several experimental results show that the motor works well, and even the leakage inductance is utilized in the boost converter. © 2012 Institute of Electrical Engineers of Japan. Published by John Wiley & Sons, Inc.
Estimation of blade structural properties from experimental data
Authors: Bottasso C.L. , Cacciola S. , Croce A.
Published: May 2012

Wind turbine blades often present complex distributions of their stiffness, mass and inertial properties along the span. We propose a method to estimate such physical parameters so as to match given experimental observations. The procedure can be used to understand the nature of possible discrepancies between designed and manufactured blades and to provide updated high fidelity mathematical beam models to be used in aero‐elastic simulations. The formulation is based on the constrained optimization of a maximum likelihood cost function and a noisy measurement fusion approach whereby the data of multiple experiments are used simultaneously in a single estimation process. The proposed method is demonstrated first using simulated data and then in the identification of two real small wind turbine blades. Copyright © 2012 John Wiley & Sons, Ltd.
The Comprehensive R Archive Network
Authors: Hornik Kurt
Published: May 2012

The Comprehensive R Archive Network (CRAN) is a network of sites acting as the primary web service distributing R sources and binaries, extension packages, and documentation. We discuss this functionality in more detail, with particular emphasis on the CRAN package repository, and its underlying design and operation principles. WIREs Comput Stat 2012 doi: 10.1002/wics.1212

This article is categorized under:

Applications of Computational Statistics > Organizations and Publications
Biophysical properties of the voltage‐gated proton channel HV1
Authors: Musset Boris , DeCoursey Thomas
Published: May 2012

The biophysical properties of the voltage‐gated proton channel (HV1) are the key elements of its physiological function. The voltage‐gated proton channel is a unique molecule that in contrast to all other ion channels is exclusively selective for protons. Alone among proton channels, it has voltage‐ and time‐dependent gating like other ‘classical’ ion channels. HV1 is furthermore a sensor for the pH in the cell and the surrounding media. Its voltage dependence is strictly coupled to the pH gradient across the membrane. This regulation restricts opening of the channel to specific voltages at any given pH gradient, therefore allowing HV1 to perform its physiological task in the tissue it is expressed in. For HV1 there is no known blocker. The most potent channel inhibitor is zinc (Zn2+) which prevents channel opening. An additional characteristic of HV1 is its strong temperature dependence of both gating and conductance. In contrast to single‐file water‐filled pores like the gramicidin channel, HV1 exhibits pronounced deuterium effects and temperature effects on conduction, consistent with a different conduction mechanism than other ion channels. These properties may be explained by the recent identification of an aspartate in the pore of HV1 that is essential to its proton selectivity. WIREs Membr Transp Signal 2012, 1:605–620. doi: 10.1002/wmts.55

For further resources related to this article, please visit the WIREs website.
Use of a thermal camera to aid in capturing northern bobwhite quail chicks
Authors: Andes Alicia K. , Buckley Byron R. , Warren Thomas L. , Woods Paul C. , Yancey Sean R. , Dabbert C. Brad
Published: May 2012

There is a paucity of information concerning northern bobwhite (Colinus virginianus) chick demography caused by a deficiency of efficient published capture techniques and permanent unique markers for identification. In order to facilitate chick research, we employed a thermal camera to detect and capture chicks during the preflight stage (≤14 days old) brooded by a radiomarked female. We released a known number of chicks into native vegetation within a flight pen to test this technique. Observers (unaware of the number) then used a thermal camera to successfully count (≥95% intra‐class correlation coeff.; complete counts for each age class) and capture the chicks. In separate field tests, we homed to within 10 m of the roost location of wild radiomarked females before sunrise, circled the area until the brood heat signature was observed, and flushed the female from the chicks. We located 116 chicks from 43 broods with the thermal camera throughout the 2011 nesting season with 81% complete, 12% partial, and 7% failed captures attempts. Detection of chicks by the thermal camera was not affected by age. Complete brood abandonment was not detected as a result of capture events. The employment of a thermal camera to capture chicks should advance the success and efficiency of capture and thus promote research concerning brood ecology. © 2012 The Wildlife Society.
Substrate metabolism during basal and hyperinsulinemic conditions in adolescents and young‐adults with Barth syndrome
Authors: Cade W. Todd , Spencer Carolyn T. , Reeds Dominic N. , Waggoner Alan D. , O'Connor Robert , Maisenbacher Melissa , Crowley Jan R. , Byrne Barry J. , Peterson Linda R.
Published: May 2012

Background

Barth syndrome (BTHS) is a rare X‐linked disorder that is characterized by mitochondrial abnormalities, infantile or childhood onset of cardioskeletal myopathy, and high mortality rates. It is currently unknown if BTHS related mitochondrial dysfunction results in substrate metabolism abnormalities and thereby contributes to cardioskeletal myopathy in patients with BTHS.

Methods

Adolescents and young adults with BTHS (n = 5, 20 ± 4 yrs) and age and activity matched healthy controls (n = 5, 18 ± 4 yrs) underwent an hyperinsulinemic‐euglycemic clamp procedure with stable isotopically labeled tracers for measurement of lipolysis, fatty acid oxidation, glucose disposal, and whole‐body proteolysis rates; dual energy x‐ray absorptiometry for measurement of body composition and 2‐D and strain echocardiography for measurement of left ventricular function.

Results

Participants with BTHS had lower fat‐free mass (FFM) (BTHS: 31.4 ± 6.9 vs. Control: 46.7 ± 5.3 kg, p < 0.005), lower systolic function (strain, BTHS: ‐15.2 ± 2.4 vs. Control: −19.0 ± 2.4 %, p < 0.05), greater insulin‐stimulated glucose disposal rate per kg FFM (BTHS: 96.5 ± 16.3 vs. Control: 67.4 ± 17.6 μmol/kgFFM/min, p < 0.05), lower basal (BTHS: 4.6 ± 2.7 vs. Control: 11.9 ± 4.4 μmol/kgFM/min, p < 0.05) and hyperinsulinemic (BTHS: 1.6 ± 0.4 vs. Control: 3.6 ± 1.6 μmol/kgFM/min, p < 0.05) lipolytic rate per kg fat mass (FM), and a trend towards higher basal leucine rate of appearance per kg FFM (BTHS: 271.4 ± 69.3 vs. Control: 193.1 ± 28.7 μmol/kgFFM/hr, p = 0.07) compared to controls. Higher basal leucine rate of appearance per kg FFM (i.e. whole‐body proteolytic rate) tended to be associated with lower left ventricular systolic strain (r = −0.57, p = 0.09).

Conclusion

Whole‐body fatty acid, glucose and amino acid metabolism kinetics when expressed per unit of body composition are altered and appear to be related to cardioskeletal myopathy in humans with BTHS. Further studies examining myocardial substrate metabolism and whole‐body substrate metabolism during increased energy demands (e.g., exercise) and their relationships to skeletal and cardiac function are recommended.
Clinical Results and Failure Mechanisms of a Nonmodular Constrained Knee without Stem Extensions
Authors: Nam Denis , Umunna Ben-Paul N. , Cross Michael B. , Reinhardt Keith R. , Duggal Shivi , Cornell Charles N.
Published: May 2012

Introduction

In the setting of persistent knee instability despite appropriate ligament balancing for primary total knee arthroplasty, most surgeons advocate the use of an implant with increased articular constraint. These implants are commonly supplemented with stem extensions to improve stress transfer and decrease the risk of aseptic loosening. However, disadvantages exist with the use of stem extensions, including increased cost, intramedullary invasion, and diaphyseal pain. The objectives of this study were to (1) compare the clinical results as assessed by the Knee Society, Hospital for Special Surgery, and SF-12 scores, (2) determine the incidence of failure as defined by the need for a revision procedure, and (3) to analyze the causes or modes of failure of a nonmodular constrained condylar knee without the use of stem extensions versus a conventional, posterior-stabilized design.

Materials and Methods

From 2002 to 2007, 190 TKAs were implanted using a primary, nonmodular constrained (NMC) prosthesis without stem extensions. During the same time period, clinical data were available for 140 TKAs implanted using a standard, posterior-stabilized (PS) design. Preoperative demographic data was reviewed, in addition to the rate and reason for revision in each cohort. Clinical data included HSS, Knee Society, and SF-12 scores at the latest follow-up, and the results of the NMC and PS cohorts were statistically compared using a Student's two-tailed t test.

Results

The mean age of patients in the NMC cohort was 72.3 ± 10.2 years, and the mean length of follow-up was 7.3 ± 2.1 years. The mean age of the PS cohort was 67.1 ± 8.7 years, with a mean follow-up of 6.1 ± 2.2 years. No statistically significant differences in the HSS, Knee Society, or SF-12 scores were appreciated between the two cohorts. The revision rate in the NMC cohort was 4.2 % compared to 4.3 % for the PS cohort. The most common cause of failure in the NMC cohort was femoral component loosening, all of which occurred when Palacos cement was used for fixation. NMC components (55.6 %) implanted with Palacos cement failed due to femoral component loosening. In contrast, all PS components requiring revision were revised for persistent instability.

Discussion

At mid-term follow-up, NMC prostheses without stem extensions have excellent clinical results and are a viable option for patients with ligamentous instability. The use of Palacos cement in this scenario was associated with a high rate of femoral component loosening, possibly due to the decreased intrusion depth of Palacos when compared to Simplex cement.
Accuracy of Right and Left Ventricular Functional Assessment by Short-Axis vs Axial Cine Steady-State Free-Precession Magnetic Resonance Imaging: Intrapatient Correlation with Main Pulmonary Artery and Ascending Aorta Phase-Contrast Flow Measurements
Authors: James Susan H. , Wald Rachel , Wintersperger Bernd J. , Jimenez-Juan Laura , Deva Djeven , Crean Andrew M. , Nguyen Elsie , Paul Narinder S. , Ley Sebastian
Published: May 2012

Objective

The left ventricle (LV) is routinely assessed with cardiac magnetic resonance imaging (MRI) by using short-axis orientation; it remains unclear whether the right ventricle (RV) can also be adequately assessed in this orientation or whether dedicated axial orientation is required. We used phase-contrast (PC) flow measurements in the main pulmonary artery (MPA) and the ascending aorta (Aorta) as nonvolumetric standard of reference and compared RV and LV volumes in short-axis and axial orientations.

Methods

A retrospective analysis identified 30 patients with cardiac MRI data sets. Patients underwent MRI (1.5 T or 3 T), with retrospectively gated cine steady-state free-precession in axial and short-axis orientations. PC flow analyses of MPA and Aorta were used as the reference measure of RV and LV output.

Results

There was a high linear correlation between MPA-PC flow and RV–stroke volume (SV) short axis ( r = 0.9) and RV-SV axial ( r = 0.9). Bland-Altman analysis revealed a mean offset of 1.4 mL for RV axial and −2.3 mL for RV–short-axis vs MPA-PC flow. There was a high linear correlation between Aorta-PC flow and LV-SV short-axis ( r = 0.9) and LV-SV axial ( r = 0.9). Bland-Altman analysis revealed a mean offset of 4.8 m for LV short axis and 7.0 mL for LV axial vs Aorta-PC flow. There was no significant difference ( P = .6) between short-axis–LV SV and short-axis–RV SV.

Conclusion

No significant impact of the slice acquisition orientation for determination of RV and LV stroke volumes was found. Therefore, cardiac magnetic resonance workflow does not need to be extended by an axial data set for patients without complex cardiac disease for assessment of biventricular function and volumes.
Interfacial water molecules in SH3 interactions: Getting the full picture on polyproline recognition by protein–protein interaction domains
Authors: Zafra-Ruano Ana , Luque Irene
Published: May 2012

The recognition of proline‐rich sequences by protein–protein interaction modules is essential for many cellular processes. Nonetheless, in spite of the wealth of structural and functional information collected over the last two decades, polyproline recognition is still not well understood. The patent inconsistency between the generally accepted description of SH3 interactions, based primarily on the stacking of hydrophobic surfaces, and their markedly exothermic character is a clear illustration of the higher complexity of these systems. Here we review the structural and thermodynamic evidence revealing the need for a revision of the current binding paradigm, incomplete and clearly insufficient for a full understanding of binding affinity and specificity, to include interfacial water molecules as universal and relevant elements in polyproline recognition.
Perspective: Dynamics of receptor tyrosine kinase signaling complexes
Authors: Mayer Bruce J.
Published: May 2012

Textbook descriptions of signal transduction complexes provide a static snapshot view of highly dynamic events. Despite enormous strides in identifying the key components of signaling complexes and the underlying mechanisms of signal transduction, our understanding of the dynamic behavior of these complexes has lagged behind. Using the example of receptor tyrosine kinases, this perspective takes a fresh look at the dynamics of the system and their potential impact on signal processing.
Local dissipation scales and energy dissipation-rate moments in channel flow
Authors: Hamlington P. E. , Krasnov D. , Boeck T. , Schumacher J.
Published: May 2012

Local dissipation-scale distributions and high-order statistics of the energy dissipation rate are examined in turbulent channel flow using very high-resolution direct numerical simulations at Reynolds numbers ${\mathit{Re}}_{\tau } = 180$, $381$ and $590$. For sufficiently large ${\mathit{Re}}_{\tau } $, the dissipation-scale distributions and energy dissipation moments in the channel bulk flow agree with those in homogeneous isotropic turbulence, including only a weak Reynolds-number dependence of both the finest and largest scales. Systematic, but ${\mathit{Re}}_{\tau } $-independent, variations in the distributions and moments arise as the wall is approached for ${y}^{+ } \lesssim 100$. In the range $100\lt {y}^{+ } \lt 200$, there are substantial differences in the moments between the lowest and the two larger values of ${\mathit{Re}}_{\tau } $. This is most likely caused by coherent vortices from the near-wall region, which fill the whole channel for low ${\mathit{Re}}_{\tau } $.
Why Do Citizens Discount the Future? Public Opinion and the Timing of Policy Consequences
Authors: Jacobs Alan M. , Matthews J. Scott
Published: May 2012

It is widely assumed that citizens are myopic, weighing policies’ short-term consequences more heavily than long-term outcomes. Yet no study of public opinion has directly examined whether or why the timing of future policy consequences shapes citizens’ policy attitudes. This article reports the results of an experiment designed to test for the presence and mechanisms of time-discounting in the mass public. The analysis yields evidence of significant discounting of delayed policy benefits and indicates that citizens’ policy bias towards the present derives in large part from uncertainty about the long term: uncertainty about both long-run processes of policy causation and long-term political commitments. There is, in contrast, little evidence that positive time-preferences (impatience) or consumption-smoothing are significant sources of myopic policy attitudes.
HENRY HALLAM REVISITED
Authors: BENTLEY MICHAEL
Published: May 2012

Although Henry Hallam (1777–1859) is best known for his Constitutional History of England (1827) and as a founder of ‘whig’ history, to situate him primarily as a mere critic of David Hume or as an apprentice to Thomas Babington Macaulay does him a disservice. He wrote four substantial books of which the first, his View of the state of Europe during the middle ages (1818), deserves to be seen as the most important; and his correspondence shows him to have been integrated into the contemporary intelligentsia in ways that imply more than the Whig acolyte customarily portrayed by commentators. This article re-situates Hallam by thinking across both time and space and depicts a significant historian whose filiations reached to Europe and North America. It proposes that Hallam did not originate the whig interpretation of history but rather that he created a sense of the past resting on law and science which would be reasserted in the age of Darwin.
Site fidelity and behaviour of spinner dolphins (Stenella longirostris) in Moon Reef, Fiji Islands: implications for conservation
Authors: Cribb Nardi , Miller Cara , Seuront Laurent
Published: May 2012

Spinner dolphins (Stenella longirostris) were observed to frequent a tropical reef complex off the coast of Fiji on a regular basis. Boats from surrounding tourist destinations visit this reef on a nearly daily basis to observe the dolphins and partake in various tourist activities, such as snorkelling. The aim of the study was to determine whether this reef is a resting habitat for this population. Specifically, we objectively and quantitatively investigated whether spinner dolphins were primarily resting whilst present within the reef and also assessed whether the same individuals revisited the reef over time. Photo-identification techniques and boat based observations were conducted over two study periods (September 2009 and May 2010). Fifty-six recognizable individuals were identified during this period, with 70% resighted on 2 or more occasions. Resting was identified as the most consistent behaviour dolphins engaged in whilst present inside the reef. These preliminary results provide vital information which can be used as a tool in the development and implementation of conservation initiatives as well as providing a basis for future studies investigating the habitat characteristics of this reef.
Magnetic fabric of stalagmites and its formation mechanism
Authors: Zhu Zongmin , Zhang Shihong , Tang Changyan , Li Haiyan , Xie Shucheng , Ji Junliang , Xiao Guoqiao
Published: May 2012

Speleothems have been regarded as ideal archives for recording variations of the Earth's magnetic field because they crystallize rapidly and are seldom modified by post‐depositional processes, and because they can be precisely dated. Magnetic fabric research on speleothems has potential to reveal details of their interior structure and the distribution of ferrimagnetic minerals, which would benefit investigations of geomagnetic field behavior. Two stalagmites (HS4 and WD1) from caves in the middle reaches of the Yangtze River were collected for magnetic fabric study. The anisotropy of magnetic susceptibility (AMS) of the stalagmites is mainly controlled by calcite crystals and the directions of the minimum axes of AMS ellipsoids indicate that their crystallographic orientations are roughly perpendicular to the growth laminae. Anisotropy of the isothermal remanent magnetization (AIRM) indicates that the distributions of ferrimagnetic minerals in the stalagmites are not correlated with stalagmite growth laminae. Mean directions of the maximum principal axes of AIRM (R1 axes) for WD1 are close to that of the natural remanent magnetization, which suggests that the orientation of ferrimagnetic minerals in this stalagmite are likely to have been controlled by the geomagnetic field.
Temporal variability of the standing internal tide in the Browse Basin, Western Australia
Authors: Rayson M. D. , Jones N. L. , Ivey G. N.
Published: May 2012

We have investigated the seasonal evolution of the internal tide using a yearlong mooring record in the Browse Basin on the Australian North‐West Shelf. Using a modal harmonic‐decomposition technique, we studied the modulation of the semi‐diurnal kinetic energy, potential energy, energy flux, group velocity and sea surface height anomaly for different internal wave modes. A very coherent and energetic, locally generated internal tide dominated the mooring record during spring‐tide periods. Relationships amongst the wave variables suggest that the interaction of multiple waves formed a standing wave pattern. To assist in explaining the seasonal variability of this standing wave pattern, we used an analytical model of internal wave generation and propagation in a double‐shelf system, representative of the area, to highlight the effects of changes in the stratification and barotropic forcing. A comparison of the low‐mode wave energy indicated that the analytical solution overestimated the observed wave energy by a factor of two and failed to detect an apparent seasonal shift in the conversion rate. We discuss potential mechanisms for this discrepancy.
Subarctic and Arctic sea surface temperature and its relation to ocean heat content 1982–2010
Authors: Chepurin Gennady A. , Carton James A.
Published: May 2012

This is an examination of SST variability in the Subarctic and Arctic during the 29 year period 1982–2010, based primarily on data from the Pathfinder AVHRR data set as well as operational SST products from NOAA and the UK Meteorological Office. A goal is to explore the connection between SST variations in the subpolar gyres and SST variations further north, with emphasis on the Nordic Seas because of their atmospheric exposure and connection to the overturning circulation. After identifying and correcting for biases in Pathfinder AVHRR (also present in the operational products) the seasonal cycle and 29‐year warming trend is described. The analysis shows that much of the warming of the North Atlantic subpolar gyre during the period occurred in 1990s and compensated for cooling during the decades of the early 1960s to mid‐1990s in this same region. Superimposed on this warming trend the analysis reveals a succession of residual SST anomalies with 0.5°C amplitudes that seem to move out of the North Atlantic subpolar gyre into the Nordic Seas following the North Atlantic and Norwegian Currents. Within the Nordic Seas these SST anomalies slowly advect in a counterclockwise direction. After approximately six years part of the anomalies exits the Nordic Seas through the East Greenland Current. The connection between these SST anomalies and underlying anomalies of 0/300 m heat content is discussed. The existence of these SST anomaliesand their origin at lower latitudes highlights the importance of ocean exchanges in influencing Arctic climate.
Aeolian dune field geomorphology modulates the stabilization rate imposed by climate
Authors: Barchyn Thomas E. , Hugenholtz Chris H.
Published: May 2012

The activity of inland aeolian dune fields is typically related to the external forcing imposed by climate: active (bare) dunes are associated with windy and/or arid settings, and inactive (vegetated) dunes are associated with humid and/or calm environments. When a climate shifts the dune field reacts; however, the behavior, rate, and potential impact of diverse dune geomorphologies on these transitions are poorly understood. Here, we use a numerical model to systematically investigate the influence of dune field geomorphology (dune height, organization and collisions) on the time a dune field takes to stabilize. To generate diverse initial un‐vegetated dune field geomorphologies under unidirectional winds, we varied pre‐stabilization growth time and initial sediment thickness (termed equivalent sediment thickness: EST). Following dune field development from a flat bed, we introduced vegetation (simulating a climate shift) and transport‐vegetation feedbacks slowly stabilized the dune fields. Qualitatively, very young and immature dune fields stabilized quickly, whereas older dune fields took longer. Dune fields with greater EST stabilized quicker than those with less EST. Larger dunes stabilized quicker because of low celerity, which facilitated higher vegetation growth rates. Extended stabilization times were associated with the extension of parabolic dunes. Dune‐dune collisions resulted in premature stabilization; the frequency of collisions was related to dune spacing. Quantitatively comparing the distribution of deposition rates in a dune field to the deposition tolerance of vegetation provides a promising predictor of relative stabilization time. Dune fields with deposition rates dominantly above the deposition tolerance of vegetation advanced unimpeded and prolonged stabilization as parabolic dunes. Paleoenvironmental reconstructions or predictions of dune field activity should not assume that dune activity directly translates to climate, considerable lags to stabilizing climate shifts may exist in unidirectional dune forms.
Monitoring and modeling water‐vegetation interactions in groundwater‐dependent ecosystems
Authors: Orellana Felipe , Verma Parikshit , Loheide Steven P. , Daly Edoardo
Published: May 2012

In many regions around the world, groundwater is the key source of water for some vegetation species, and its availability and dynamics can define vegetation composition and distribution. In recent years the interaction between groundwater and vegetation has seen a renewed attention because of the impact of groundwater extraction on natural ecosystems' health and increasing interest in the restoration of riparian zones and wetlands. The literature provides studies that approach this problem from very different angles. Information on the vegetation species that are likely to depend on groundwater and the physical characteristics of such species can be found in a large body of literature in ecology and plant physiology. Environmental engineers, hydrologists, and geoscientists are more focused on ecosystem restoration and the estimation of a catchment's water balance, for which the groundwater transpired by vegetation might be an important component. Here we join together these different bodies of literature with the aim of providing the state of knowledge on groundwater‐dependent vegetation. We describe the physiological features that characterize groundwater‐dependent vegetation, review different methods to study vegetation water use in the field, discuss recent advances in the understanding of how groundwater levels might determine vegetation composition, and present a summary of the available mathematical models that include the interaction between groundwater levels and vegetative water use. Several future research directions are identified, such as the quantification and modeling of the partitioning of transpiration between unsaturated and saturated zones and the development of integrated models able to link hydrology, ecology, and geomorphology.
Modeling thermal dynamics of active layer soils and near‐surface permafrost using a fully coupled water and heat transport model
Authors: Jiang Yueyang , Zhuang Qianlai , O'Donnell Jonathan A.
Published: May 2012

Thawing and freezing processes are key components in permafrost dynamics, and these processes play an important role in regulating the hydrological and carbon cycles in the northern high latitudes. In the present study, we apply a well‐developed soil thermal model that fully couples heat and water transport, to simulate the thawing and freezing processes at daily time steps across multiple sites that vary with vegetation cover, disturbance history, and climate. The model performance was evaluated by comparing modeled and measured soil temperatures at different depths. We use the model to explore the influence of climate, fire disturbance, and topography (north‐ and south‐facing slopes) on soil thermal dynamics. Modeled soil temperatures agree well with measured values for both boreal forest and tundra ecosystems at the site level. Combustion of organic‐soil horizons during wildfire alters the surface energy balance and increases the downward heat flux through the soil profile, resulting in the warming and thawing of near‐surface permafrost. A projection of 21st century permafrost dynamics indicates that as the climate warms, active layer thickness will likely increase to more than 3 meters in the boreal forest site and deeper than one meter in the tundra site. Results from this coupled heat‐water modeling approach represent faster thaw rates than previously simulated in other studies. We conclude that the discussed soil thermal model is able to well simulate the permafrost dynamics and could be used as a tool to analyze the influence of climate change and wildfire disturbance on permafrost thawing.
One‐year aerosol profiling with EUCAARI Raman lidar at Shangdianzi GAW station: Beijing plume and seasonal variations
Authors: Hänel A. , Baars H. , Althausen D. , Ansmann A. , Engelmann R. , Sun J. Y.
Published: May 2012

The study examines seasonal and air‐flow‐dependent variations of the vertical distribution of aerosols at the Global Atmospheric Watch (GAW) station of Shangdianzi in the North China Plain 100 km northeast of Beijing. One‐year Raman lidar observations of profiles of aerosol extinction and backscatter coefficients at 532 nm were performed from April 2009 to March 2010 in the framework of the European Aerosol Cloud Climate and Air Quality Interactions (EUCAARI) project. In the nighttime statistics a two‐layer structure with the main haze layer reaching to 1–1.5 km height asl and an elevated aerosol layer on top with a top height of 2.5–5 km height asl was generally observed. A case study of a Beijing haze plume is presented to document the drastic changes in the environmental conditions over the background monitoring station during the passage of a strong haze front. Aerosol optical depth (AOD) and extinction coefficients increased from 0.2 to 1.2 and from 200 Mm−1 to 1000 Mm−1, respectively, within less than two hours. The statistical analysis revealed layer mean extinction coefficients of the haze layer most frequently from 200–600 Mm−1 and typically from 50–100 Mm−1in the elevated layer. The AOD ranged from about 0.3 for northerly air flows to, on average, 0.95 during southerly air flows. The lidar ratio shows a narrow distribution peaking at 60 sr in the haze layer caused by anthropogenic fine‐mode aerosol and a broad distribution from 40–90 sr in the elevated layer caused by the complex mixture of aged desert dust, biomass burning smoke, and industrial pollution over eastern Asia.