bluuebunny/crossref_metadata_2025_split huggingface dataset:
Short‐term effects of temperature on the abundance and diversity of magnetotactic cocci
Authors: Lin Wei , Wang Yinzhao , Pan Yongxin 
Published: February 2012

AbstractTemperature is one of the most important climate factors that can regulate the activity and growth of organisms. However, it is so far unclear how temperature influences the abundance and community composition of magnetotactic bacteria (MTB) that mineralize intracellular magnetite and/or greigite magnetosomes and play significant roles in the global iron cycling and sediment magnetization. To address this specific problem, in this study we have assessed the impact of temperature on freshwater magnetotactic cocci through laboratory microcosm simulations. Microcosms containing MTB were exposed to four constant temperatures ranging from 9°C to 37°C. After 10 days and 28 days of incubation, no significant differences in abundance were detected in microcosms at 9°C, 15°C, and 26°C (Student's t‐test, P > 0.05); however, microcosms exposed to 37°C exhibited a significant decrease of magnetotactic cocci abundance (P < 0.05). Dendrogram analysis of community‐amplified ribosomal DNA restriction analysis (community ARDRA) banding patterns distinguished the 37°C samples from samples at lower temperatures regardless of incubation periods. Furthermore, clone library analysis revealed that most of the operational taxonomic units (OTUs) detected in samples from 9°C to 26°C were absent from the 37°C microcosms, whereas six OTUs were exclusively detected in the 37°C samples. Community compositions from four incubation temperatures were further compared using statistical phylogenetic methods (UniFrac and LIBSHUFF), which revealed that the 37°C samples harbored phylogenetically distinct MTB communities compared to those found in 9°C, 15°C, and 26°C samples. Taken together, our results indicate that elevated temperature can influence the abundance and diversity of dominant members of magnetotactic cocci. This linkage further infers that the abundance and diversity of MTB (e.g., based on the fossil magnetosomes) may be useful in reconstruction of paleotemperature.
Gastrointestinal stability and bioavailability of (poly)phenolic compounds following ingestion of Concord grape juice by humans
Authors: Stalmach Angelique , Edwards Christine A. , Wightman JoLynne D. , Crozier Alan 
Published: February 2012

AbstractThe in vitro gastrointestinal stability of (poly)phenolic compounds in Concord grape juice was compared with recoveries in ileal fluid after the ingestion of the juice by ileostomists. Recoveries in ileal fluid indicated that 67% of hydroxycinnamate tartarate esters, and smaller percentages of the intake of other (poly)phenolic compounds, pass from the small intestine to the colon. The juice was also ingested by healthy subjects with an intact functioning colon. Peak plasma concentrations (Cmax) ranged from 1.0 nmol/L for petunidin‐3‐O‐glucoside to 355 nmol/L for dihydrocoumaric acid. Urinary excretion, as an indicator of bioavailability, varied from 0.26% for total anthocyanins to 24% for metabolites of hydroxycinnamate tartarate esters. The Cmax times of the anthocyanins indicated that their low level absorption occurred in the small intestine in contrast to hydroxycinnamate metabolites which were absorbed in both the small and the large intestine where the colonic microflora appeared responsible for hydrogenation of the hydroxycinnamate side chain. The bioavailability of the complex mixture of (poly)phenolic compounds in Concord grape juice, was very similar to that observed in previous studies when compounds were either fed individually or as major components in products containing a restricted spectrum of (poly)phenolic compounds.
Metabolite kinetics in C6 rat glioma model using magnetic resonance spectroscopic imaging of hyperpolarized [1‐13C]pyruvate
Authors: Park Jae Mo , Josan Sonal , Jang Taichang , Merchant Milton , Yen Yi‐Fen , Hurd Ralph E. , Recht Lawrence , Spielman Daniel M. , Mayer Dirk 
Published: February 2012

AbstractIn addition to an increased lactate‐to‐pyruvate ratio, altered metabolism of a malignant glioma can be further characterized by its kinetics. Spatially resolved dynamic data of pyruvate and lactate from C6‐implanted female Sprague–Dawley rat brain were acquired using a spiral chemical shift imaging sequence after a bolus injection of a hyperpolarized [1‐13C]pyruvate. Apparent rate constants for the conversion of pyruvate to lactate in three different regions (glioma, normal appearing brain, and vasculature) were estimated based on a two‐site exchange model. The apparent conversion rate constant was 0.018 ± 0.004 s−1 (mean ± standard deviation, n = 6) for glioma, 0.009 ± 0.003 s−1 for normal brain, and 0.005 ± 0.001 s−1 for vasculature, whereas the lactate‐to‐pyruvate ratio, the metabolic marker used to date to identify tumor regions, was 0.36 ± 0.07 (mean ± SD), 0.24 ± 0.07, and 0.12 ± 0.02 for glioma, normal brain, and vasculature, respectively. The data suggest that the apparent conversion rate better differentiate glioma from normal brain (P = 0.001, n = 6) than the lactate‐to‐pyruvate ratio (P = 0.02). Magn Reson Med, 2012. © 2012 Wiley Periodicals, Inc.
Model‐based mapping of fat unsaturation and chain length by chemical shift imaging—phantom validation and in vivo feasibility
Authors: Berglund Johan , Ahlström Håkan , Kullberg Joel 
Published: February 2012

AbstractKnowledge about the triglyceride (fat) 1H spectrum enables quantitative determination of several triglyceride characteristics. This work describes a model‐based chemical shift imaging method that separates water and fat signal and provides maps of three triglyceride quantities: fatty acid carbon chain length, unsaturation degree, and polyunsaturation degree. The method was validated by imaging a phantom containing 10 different oils using 1.5 and 3.0 T clinical scanners, with gas–liquid chromatography as reference. Repeated acquisitions demonstrated high reproducibility of the method. Statistical tests of correlation and linear regression were performed to examine the accuracy of the method. Significant correlation was found at both field strengths for all three quantities, and high correlation (r2 > 0.95) was found for measuring unsaturation degree and polyunsaturation degree. Feasibility of the method for in vivo imaging of the thigh was demonstrated at both field strengths. The estimates of unsaturation degree and polyunsaturation degree in subcutaneous adipose tissue were in agreement with literature values, while chain length appeared over estimated. The method has potential use in large‐scale cross‐sectional and longitudinal studies of triglyceride composition, and its relation to diet and various diseases. Magn Reson Med, 2012. © 2012 Wiley Periodicals, Inc.
A method to determine the necessity for global signal regression in resting‐state fMRI studies
Authors: Chen Gang , Chen Guangyu , Xie Chunming , Ward B. Douglas , Li Wenjun , Antuono Piero , Li Shi‐Jiang 
Published: February 2012

AbstractIn resting‐state functional MRI studies, the global signal (operationally defined as the global average of resting‐state functional MRI time courses) is often considered a nuisance effect and commonly removed in preprocessing. This global signal regression method can introduce artifacts, such as false anticorrelated resting‐state networks in functional connectivity analyses. Therefore, the efficacy of this technique as a correction tool remains questionable. In this article, we establish that the accuracy of the estimated global signal is determined by the level of global noise (i.e., non‐neural noise that has a global effect on the resting‐state functional MRI signal). When the global noise level is low, the global signal resembles the resting‐state functional MRI time courses of the largest cluster, but not those of the global noise. Using real data, we demonstrate that the global signal is strongly correlated with the default mode network components and has biological significance. These results call into question whether or not global signal regression should be applied. We introduce a method to quantify global noise levels. We show that a criteria for global signal regression can be found based on the method. By using the criteria, one can determine whether to include or exclude the global signal regression in minimizing errors in functional connectivity measures. Magn Reson Med, 2012. © 2012 Wiley Periodicals, Inc.
The preconditioned inverse iteration for hierarchical matrices
Authors: Benner Peter , Mach Thomas 
Published: February 2012

SUMMARYThe preconditioned inverse iteration is an efficient method to compute the smallest eigenpair of a symmetric positive definite matrix M. Here we use this method to find the smallest eigenvalues of a hierarchical matrix. The storage complexity of the data‐sparse ‐matrices is almost linear. We use ‐arithmetic to precondition with an approximate inverse of M or an approximate Cholesky decomposition of M. In general, ‐arithmetic is of linear‐polylogarithmic complexity, so the computation of one eigenvalue is cheap. We extend the ideas to the computation of inner eigenvalues by computing an invariant subspace S of (M − μI)2 by subspace preconditioned inverse iteration. The eigenvalues of the generalized matrix Rayleigh quotient μM(S) are the desired inner eigenvalues of M. The idea of using (M − μI)2 instead of M is known as the folded spectrum method. As we rely on the positive definiteness of the shifted matrix, we cannot simply apply shifted inverse iteration therefor. Numerical results substantiate the convergence properties and show that the computation of the eigenvalues is superior to existing algorithms for non‐sparse matrices.Copyright © 2012 John Wiley & Sons, Ltd.
Numerical simulation of flapping wings using a panel method and a high‐order Navier–Stokes solver
Authors: Persson P.‐O. , Willis D.J. , Peraire J. 
Published: February 2012

SUMMARYThe design of efficient flapping wings for human engineered micro aerial vehicles (MAVs) has long been an elusive goal, in part because of the large size of the design space. One strategy for overcoming this difficulty is to use a multifidelity simulation strategy that appropriately balances computation time and accuracy. We compare two models with different geometric and physical fidelity. The low‐fidelity model is an inviscid doublet lattice method with infinitely thin lifting surfaces. The high‐fidelity model is a high‐order accurate discontinuous Galerkin Navier–Stokes solver, which uses an accurate representation of the flapping wing geometry. To compare the performance of the two methods, we consider a model flapping wing with an elliptical planform and an analytically prescribed spanwise wing twist, at size scales relevant to MAVs. Our results show that in many cases, including those with mild separation, low‐fidelity simulations can accurately predict integrated forces, provide insight into the flow structure, indicate regions of likely separation, and shed light on design–relevant quantities. But for problems with significant levels of separation, higher‐fidelity methods are required to capture the details of the flow field. Inevitably high‐fidelity simulations are needed to establish the limits of validity of the lower fidelity simulations.Copyright © 2012 John Wiley & Sons, Ltd.
Interest mobilization in public health and social insurance: Argentina, Colombia, and Mexico in comparative perspective
Authors: Brachet‐Márquez Viviane , Alonso Guillermo V. , Uribe Gómez Mónica 
Published: February 2012

One revealing test for gauging the extent to which pluralist democracy has advanced in the recently (re)democratized countries of Latin America is to determine the extent to which interest groups have come to participate in policy making in formal, open, extensive, and accepted ways as they mostly do in advanced liberal democracies. In other words, is this a new era or more of the same? To provide insights into this question, using six hypotheses, this article compares social insurance reform in Argentina and Mexico, and public health reform in Colombia.It appears that the political processes through which the reforms were adopted were fairly democratic, although aspects of the old regimes in all three countries, particularly corporatist relationships, were indispensable backups. The weaknesses that were apparent, however, stem less from the old ways of doing political business and more from the immaturity of the democratic process. Plus, pressures were felt by the executive branches and their allies to show to the international community that their country was a safe place in which to invest. Copyright © 2012 John Wiley & Sons, Ltd.
Religious/spiritual coping resources and their relationship with adjustment in patients newly diagnosed with breast cancer in the UK
Authors: Thuné‐Boyle Ingela C. V. , Stygall Jan , Keshtgar Mohammed R. S. , Davidson Tim I. , Newman Stanton P. 
Published: February 2012

AbstractBackgroundReligious/spiritual resources may serve multiple functions in adjustment to cancer. However, there is very little evidence of the importance of religious/spiritual variables outside the USA. This paper reports the cross‐sectional data of a longitudinal study examining the beneficial and harmful effects of religious/spiritual coping resources on adjustment in the first year after a breast cancer diagnosis.MethodOne hundred and fifty‐five patients newly diagnosed with breast cancer were assessed after surgery. Several aspects of religiousness/spirituality in relation to anxiety and depression were examined: religiosity/spirituality, strength of faith, belief in God, private and public practices, spiritual involvement, perceived spiritual support and positive and negative religious coping strategies. Non‐religious coping, social support and optimism were also assessed.Results‘Feeling punished and abandoned by God’ significantly explained 5% of the variance in increased levels of anxiety but was partially mediated by denial coping. It was also partially mediated by acceptance coping, lowering levels of anxiety. Feeling punished and abandoned by God was a significant independent predictor of depressed mood, explaining 4% of the variance.ConclusionUsing religious/spiritual resources in the coping process during the early stages of breast cancer may play an important role in the adjustment process in patients with breast cancer. Patients may benefit from having their spiritual needs addressed as experiencing some form of religious/spiritual struggle may serve as a barrier to illness adjustment. Implications for research and clinical practices are discussed. Copyright © 2012 John Wiley & Sons, Ltd.
Research Perspectives on Unstable High‐alpine Bedrock Permafrost: Measurement, Modelling and Process Understanding
Authors: Krautblatter Michael , Huggel Christian , Deline Philip , Hasler Andreas 
Published: February 2012

ABSTRACTRock instability is believed to be causally linked to permafrost degradation, but it is difficult to demonstrate this directly because of the short record of slope failures in high mountains. While abductive scientific reasoning of ‘increasing permafrost‐related instability’ based on the short time frame of recorded rockfall events in high mountains is still difficult, our deductive systemic understanding points toward a strong process linkage between permafrost degradation and rock instability. Enhanced technical understanding of coupled thermo‐hydro‐mechanical processes and systemic geomorphic understanding of rock slope adjustment in space and over (reaction/relaxation) time are required to accurately predict hazards associated with the impact of climate change on permafrost in bedrock. We identify research needs in four major areas and at the interfaces between them: rock temperature measurement and modelling; remote sensing of rock walls; process understanding of rock mass instability; and flow propagation models of rock‐ice avalanches. This short communication identifies key interfaces between research directions to gain a better understanding of trajectories of destabilisation in time and space. We propose coordinated systemic research with respect to scale dependent and transient thermal behaviour, coupled thermo‐hydro‐mechanical understanding, enhanced remote inventorying of rock wall instability and integrated approaches for a better understanding and modelling of mixed avalanches. Copyright © 2012 John Wiley & Sons, Ltd.
Crystal structure of vinculin in complex with vinculin binding site 50 (VBS50), the integrin binding site 2 (IBS2) of talin
Authors: Yogesha S. D. , Rangarajan Erumbi S. , Vonrhein Clemens , Bricogne Gerard , Izard Tina 
Published: February 2012

AbstractThe cytoskeletal protein talin activates integrin receptors by binding of its FERM domain to the cytoplasmic tail of β‐integrin. Talin also couples integrins to the actin cytoskeleton, largely by binding to and activating the cytoskeletal protein vinculin, which binds to F‐actin through the agency of its five‐helix bundle tail (Vt) domain. Talin activates vinculin by means of buried amphipathic α‐helices coined vinculin binding sites (VBSs) that reside within numerous four‐ and five‐helix bundle domains that comprise the central talin rod, which are released from their buried locales by means of mechanical tension on the integrin:talin complex. In turn, these VBSs bind to the N‐terminal seven‐helix bundle (Vh1) domain of vinculin, creating an entirely new helix bundle that severs its head‐tail interactions. Interestingly, talin harbors a second integrin binding site coined IBS2 that consists of two five‐helix bundle domains that also contain a VBS (VBS50). Here we report the crystal structure of VBS50 in complex with vinculin at 2.3 Å resolution and show that intramolecular interactions of VBS50 within IBS2 are much more extensive versus its interactions with vinculin. Indeed, the IBS2‐vinculin interaction only occurs at physiological temperature and the affinity of VBS50 for vinculin is about 30 times less than other VBSs. The data support a model where integrin binding destabilizes IBS2 to allow it to bind to vinculin.
Thermal coefficients of the methyl groups within ubiquitin
Authors: Sabo T. Michael , Bakhtiari Davood , Walter Korvin F. A. , McFeeters Robert L. , Giller Karin , Becker Stefan , Griesinger Christian , Lee Donghan 
Published: February 2012

AbstractPhysiological processes such as protein folding and molecular recognition are intricately linked to their dynamic signature, which is reflected in their thermal coefficient. In addition, the local conformational entropy is directly related to the degrees of freedom, which each residue possesses within its conformational space. Therefore, the temperature dependence of the local conformational entropy may provide insight into understanding how local dynamics may affect the stability of proteins. Here, we analyze the temperature dependence of internal methyl group dynamics derived from the cross‐correlated relaxation between dipolar couplings of two CH bonds within ubiquitin. Spanning a temperature range from 275 to 308 K, internal methyl group dynamics tend to increase with increasing temperature, which translates to a general increase in local conformational entropy. With this data measured over multiple temperatures, the thermal coefficient of the methyl group order parameter, the characteristic thermal coefficient, and the local heat capacity were obtained. By analyzing the distribution of methyl group thermal coefficients within ubiquitin, we found that the N‐terminal region has relatively high thermostability. These results indicate that methyl groups contribute quite appreciably to the total heat capacity of ubiquitin through the regulation of local conformational entropy.
Control of polarized emission from selectively etched GaN/AlN quantum dot ensembles on Si(111)
Authors: Rich Daniel H. , Moshe Ofer , Damilano Benjamin , Massies Jean 
Published: February 2012

AbstractMultiple layers of GaN/AlN quantum dot (QD) ensembles were grown by the Stranski‐Krastanov method on Si(111) using molecular beam epitaxy. During the subsequent cooling from growth temperature, the thermal expansion coefficient mismatch between the Si substrate and GaN/AlN film containing the vertically stacked QDs leads to an additional biaxial tensile stress of 20–30 kbar in the III‐nitride film. We have selectively modified the thermal stress in the QD layers by etching a cross‐hatched pattern into the as‐grown sample using inductively coupled Cl2/Ar plasma reactive ion etching. The results show that a suitable choice of stripe width from ∼2 to 10 μm and orientation along [11‐20] and [1‐100] can create regions of in‐plane uniaxial stress that enable a selective and local control of the polarized luminescence from ensembles of QDs which were probed with cathodoluminescence. A theoretical modelling of the effects of carrier filling on the polarization anisotropy and the excitonic transition energy was performed, as based on three dimensional self‐consistent solutions of the Schrödinger and Poisson equations using the 6 × 6 k·p method (© 2012 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Electrical properties of MBE grown Si3N4–cubic GaN MIS structures
Authors: Zado A. , Lischka K. , As D. J. 
Published: February 2012

AbstractIn this work we report on the electrical characterization of non‐polar cubic GaN metal‐insulator‐semiconductor (MIS) structures. Si3N4 layers were deposited in‐situ on top of cubic GaN grown on 3C‐SiC (001) substrates. The electric characteristics of the MIS structures are measured by capacitance and admittance spectroscopy techniques. From the hysteresis in the capacitance‐voltage curves and the peak height of the conductance Gp –ω frequency curves the interface state densities are calculated.We find interface traps about 0.3 eV below the conduction band. The density of these traps is Dit = 2.5x1011 cm‐2eV‐1. This is one order of magnitude lower than in MIS structures with a Si3N4 insulator produced by plasma enhanced vapour deposition and two orders of magnitude lower than in MIS structures on c‐GaN with SiO2 as insulator (© 2012 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Influence of substrate biasing on the growth of c‐axis oriented AlN thin films by RF reactive sputtering in pure nitrogen
Authors: Monteagudo‐Lerma L. , Naranjo F. B. , González‐Herráez M. , Fernández S. 
Published: February 2012

AbstractWe report on the investigation of the influence of deposition conditions on structural, morphological and optical properties of AlN thin films deposited on sapphire (Al2O3) substrates by radio‐frequency (RF) reactive sputtering. The deposition parameters studied are RF power, substrate temperature and substrate bias, while using pure nitrogen as reactive gas. The effect of such deposition parameters on AlN film properties are analyzed by different characterization methods as high resolution X‐ray diffraction (HRXRD), field emission scanning electron microscopy (FESEM) and linear optical transmission. AlN thin films with a full‐width at half‐maximum (FWHM) of the rocking curve obtained for the (0002) diffraction peak of 1.2º are achieved under optimized conditions. The time resolved evolution of the self and externally‐induced biasing of the substrate during deposition process is monitored and analyzed in terms of the rate of atomic species incorporation into the layer. The bias‐induced change of the atomic incorporation leads to an enhancement in the structural quality of the layer and an increase of the deposition rate. (© 2012 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)