bluuebunny/crossref_metadata_2025_split huggingface dataset:
Leukocyte integrin αLβ2 transmembrane association dynamics revealed by coarse‐grained molecular dynamics simulations
Authors: Chng Choon‐Peng , Tan Suet‐Mien 
Published: March 2011

AbstractIntegrins are transmembrane (TM) proteins that mediate bidirectional mechanical signaling between the extracellular matrix and the cellular cytoskeletal network. Each integrin molecule consists of non‐covalently associated α‐ and β‐subunits, with each subunit consisting of a large ectodomain, a single‐pass TM helix, and a short cytoplasmic tail. Previously we found evidence for a polar interaction (hydrogen bond) in the outer membrane clasp (OMC) of the leukocyte integrin αLβ2 TMs that is absent in the platelet integrin αIIβ3 OMC. Here, we compare the self‐assembly dynamics of αLβ2 and αIIβ3 TM helices in a model membrane using coarse‐grained molecular dynamics simulations. We found that although αIIβ3 TM helices associate more easily, packing is suboptimal. In contrast, αLβ2 TM helices achieve close‐to‐optimal packing. This suggests that αLβ2 TM packing is more specific, possibly due to the interhelix hydrogen bond. Theoretical association free energy profiles show a deeper minimum at a smaller helix‐helix separation for αLβ2 compared with αIIβ3. The αIIβ3 profile is also more rugged with energetic barriers whereas that of αLβ2 is almost without barriers. Disruption of the interhelix hydrogen bond in αLβ2 via the β2T686G mutation results in poorer association and a similar profile as αIIβ3. The OMC polar interaction in αLβ2 thus plays a significant role in the packing of the TM helices. Proteins 2011; © 2011 Wiley‐Liss, Inc.
Observing the osmophobic effect in action at the single molecule level
Authors: Aioanei Daniel , Tessari Isabella , Bubacco Luigi , Samorì Bruno , Brucale Marco 
Published: March 2011

AbstractProtecting osmolytes are widespread small organic molecules able to stabilize the folded state of most proteins against various denaturing stresses in vivo. The osmophobic model explains thermodynamically their action through a preferential exclusion of the osmolyte molecules from the protein surface, thus favoring the formation of intrapeptide hydrogen bonds. Few works addressed the influence of protecting osmolytes on the protein unfolding transition state and kinetics. Among those, previous single molecule force spectroscopy experiments evidenced a complexation of the protecting osmolyte molecules at the unfolding transition state of the protein, in apparent contradiction with the osmophobic nature of the protein backbone. We present single‐molecule evidence that glycerol, which is a ubiquitous protecting osmolyte, stabilizes a globular protein against mechanical unfolding without binding into its unfolding transition state structure. We show experimentally that glycerol does not change the position of the unfolding transition state as projected onto the mechanical reaction coordinate. Moreover, we compute theoretically the projection of the unfolding transition state onto two other common reaction coordinates, that is, the number of native peptide bonds and the weighted number of native contacts. To that end, we augment an analytic Ising‐like protein model with support for group‐transfer free energies. Using this model, we find again that the position of the unfolding transition state does not change in the presence of glycerol, giving further support to the conclusions based on the single‐molecule experiments. Proteins 2011; © 2011 Wiley‐Liss, Inc.
Anomalous temperature and interfacial‐coupling dependence of exchange bias in antiferromagnetic (core)/ferromagnetic (shell) nanoparticles
Authors: Hu Yong , Du An 
Published: March 2011

AbstractIn a single composite ferromagnetic/antiferromagnetic (AFM) nanoparticle with an unconventional core/shell morphology, the effects of temperature and interfacial coupling on the exchange bias (EB) are studied by performing a modified Monte Carlo method. With the decrease of temperature, three distinct behaviors of the EB are obtained as a result of the state transitions of the AFM spins from completely free via partially free and partially frozen, and, finally, to completely frozen. The behaviors of the coercivity are nonmonotonic due to the energy competitions and the thermal fluctuations. Moreover, the cooling field affects strongly the low‐temperature behaviors of the EB. The EB field obtained after field cooling is negative and almost constant, independent of the interfacial coupling. However, after zero‐field cooling, the EB field may exhibit a sign‐reversal behavior with increasing interfacial coupling at low temperature. On the basis of the theory of the surplus magnetization, it is revealed that the drastic temperature dependence and the energy competition mechanism at the interface in the cooling process are responsible for this unique property in such novel nanostructures.
A PRESUMPTIVE STANDARD FOR ENVIRONMENTAL FLOW PROTECTION
Authors: Richter B. D. , Davis M. M. , Apse C. , Konrad C. 
Published: March 2011

ABSTRACTThe vast majority of the world's rivers are now being tapped for their water supplies, yet only a tiny fraction of these rivers are protected by any sort of environmental flow standard. While important advances have been made in reducing the cost and time required to determine the environmental flow needs of both individual rivers and types of rivers in specific geographies, it is highly unlikely that such approaches will be applied to all, or even most, rivers within the forseeable future. As a result, the vast majority of the planet's rivers remain vulnerable to exploitation without limits. Clearly, there is great need for adoption of a “presumptive standard” that can fill this gap. In this paper we present such a presumptive standard, based on the Sustainability Boundary Approach of Richter (2009) which involves restricting hydrologic alterations to within a percentage‐based range around natural or historic flow variability. We also discuss water management implications in applying our standard. Our presumptive standard is intended for application only where detailed scientific assessments of environmental flow needs cannot be undertaken in the near term. Copyright © 2011 John Wiley & Sons, Ltd.
MACROINVERTEBRATES IN ABANDONED CHANNELS: ASSEMBLAGE CHARACTERISTICS AND THEIR INDICATIONS FOR CHANNEL MANAGEMENT
Authors: Pan B.‐Z. , Wang Z.‐Y. , Xu M.‐Z. 
Published: March 2011

ABSTRACTAlluvial floodplains contain four types of abandoned channels: old river courses, oxbow lakes, oxtail lakes and riparian wetlands. These result from avulsions, meander cutoffs, ice‐jam floods and stem‐channel shifts, respectively. With the exception of old river courses, which belong to terrestrial ecosystems, abandoned‐channel types are important components of freshwater ecosystems. During 2006–2009, we conducted systematic investigations of macroinvertebrates in three types of freshwater abandoned channels and identified 93 taxa of macroinvertebrates belonging to 51 families and 88 genera. In the assemblage composition, most taxa were similar to those found in river‐isolated lakes and river mainstreams. Moreover, abandoned channels supported many unique benthic taxa, which are important complementary resources for the entire river system. In the abandoned channels that were covered with a layer of silt, standing crops were higher than that found in the river mainstream where the bed sediment consisted mainly of sand. Conversely, in abandoned channels that were covered with fine sand, standing crops were lower than in the gravel streambed. Some abandoned channels, such as the riparian wetlands of the East River that are freely connected with the mainstream, were characterized by the highest biodiversity and the greatest biomass. In regions less affected by human activities, abandoned channels need to be connected with mainstreams by flooding at least once every 3 years to maintain at least half of the maximum amount of macroinvertebrate resources. In regions more affected by human activities, abandoned channels need to be connected with mainstreams at least once every year. Copyright © 2011 John Wiley & Sons, Ltd.
Response modeling methodology
Authors: Shore Haim 
Published: March 2011

AbstractResponse modeling methodology (RMM) is a general platform for modeling monotone convex relationships. Unique to RMM models is their ‘continuous convexity’ property, which allows the data to ‘select’ the final form of the model via the estimated parameters (analogously with the Box–Cox transformation). This renders RMM a versatile and effective platform for empirical modeling of random variation (‘distribution fitting’) and of systematic variation (‘relational modeling’). In this overview, we detail the motivation that led to the development of RMM, explain RMM core concepts, and introduce RMM basic model and variations. Allied maximum‐likelihood estimation procedures are detailed, separately for models of random variation and for models of systematic variation. Numerical examples demonstrate RMM effectiveness in comparison to other current approaches. Current literature on RMM (about 25 publications), available software, and ongoing research are also addressed. WIREs Comp Stat 2011 3 357–372 DOI: 10.1002/wics.151This article is categorized under:

Statistical and Graphical Methods of Data Analysis > Density Estimation
Statistical Learning and Exploratory Methods of the Data Sciences > Modeling Methods
Statistical and Graphical Methods of Data Analysis > Modeling Methods and Algorithms
Algorithms and Computational Methods > Maximum Likelihood Methods
PIXE simulation in Geant4
Authors: Mantero A. , Ben Abdelouahed H. , Champion C. , El Bitar Z. , Francis Z. , Guèye P. , Incerti S. , Ivanchenko V. , Maire M. 
Published: March 2011

AbstractGeant4 is a general purpose and open source C + + Monte Carlo simulation toolkit, widely used in the scientific community. It is able to simulate physical interactions of particles through matter. According to the user's needs, models for the simulation of electromagnetic (EM) interactions are provided in two Geant4 subpackages, the ‘standard’ EM subpackage, well suited for a wide range of applications and the ‘low‐energy’ EM subpackage, able to reach the electronVolt regime. Particle‐induced X‐ray emission (PIXE) is a well known and a very useful technique for quantitative elemental analysis in environmental, archaeological, biological, medical and space applications. An atomic de‐excitation module is part of the Geant4 ‘low‐energy’ EM subpackage since 1999 and has been validated in recent years. PIXE simulation has been included in this subpackage in 2001 and new ionisation cross‐sectional models following the ECPSSR theory have been added for the PIXE simulation in 2008. In 2010, these models have been further extended to higher energies. In this work, we present new results on the verification of these models and an overview of the new interface to PIXE modelling prepared for the recent public release of the Geant4 toolkit (December 2010) allowing a unified usage of the Geant4 de‐excitation module by both ‘standard’ and ‘low‐energy’ subpackages. Copyright © 2011 John Wiley & Sons, Ltd.
In vivo 3D imaging of Drosophila melanogaster using PIXE‐micron‐CT
Authors: Ohkura S. , Ishii K. , Matsuyama S. , Terakawa A. , Kikuchi Y. , Kawamura Y. , Catella G. , Hashimoto Y. , Fujikawa M. , Hamada N. , Fujiki K. , Hatori E. , Yamazaki H. 
Published: March 2011

AbstractCharacteristic X‐rays from a pure metal target bombarded with a few MeV proton micro‐beams can be used as a point source of quasi‐monochromatic X‐rays. On the basis of this idea, we have previously developed a microscopic computed tomography (CT) which we called particle induced X‐ray emission (PIXE)‐micron‐CT. We applied our CT to observe organs in a body of a living Drosophila, which is popularly used in various fundamental studies, such as gene research. We optimized the beam spot size of proton micro‐beam, redesigned the geometry of the PIXE‐micron‐CT and improved the sample preparation method. As a result of these efforts, the CT scan time could be reduced to less than a sixth of its previous value without degrading the spatial resolution. Three‐dimensional (3D) images of a living Drosophila in different growth stages were obtained. The forms of organs changed significantly depending on the growth stage. The CT images of living Drosophila were much different from those of dead or formalin fixed ones. The in vivo 3D imaging by PIXE‐micron‐CT is very useful and is one of the powerful tool in biological and medical studies. Copyright © 2011 John Wiley & Sons, Ltd.
Micro‐PIXE studies of Ni‐elimination strategies in representatives of two families of beetles feeding on Ni‐hyperaccumulating plant Berkheya coddii
Authors: Migula P. , Przybyłowicz W. J. , Nakonieczny M. , Augustyniak M. , Tarnawska M. , Mesjasz‐Przybyłowicz J. 
Published: March 2011

AbstractPlants may use the ability to hyperaccumulate toxic metals in their defence against herbivores. Insects can counteract and feed on toxic plants. Among grazers of Ni‐hyperaccumulating Berkheya coddii, some beetles tolerate Ni (Chrysolina clathrata, former name Chrysolina pardalina; Epilachna nylanderi). The adaptive mechanisms against Ni toxicity were studied in these species using micro‐PIXE quantitative elemental mapping and by microscopy techniques. Distinct differences were found in mechanisms used for Ni‐elimination in both species. Functional comparisons and quantification of data extracted from selected micro‐areas in target organs responsible for metal circulation (digestive tract and Malpighian tubules) were made. Similar detoxification mechanism is used against metals through spheric granules, which in E. nylanderi are formed mainly in the midgut, while in C. clathrata in Malpighian tubules and midgut. Elemental maps showed positive correlations of Ni and Zn in Malpighian tubules of E. nylanderi without such effect in C. clathrata. Quantitative relations of K+ and Cl− indicate higher osmotic pressure increasing reabsorption of water necessary for Ni transportation to the intestine lumen and further rejection outside the body. Copyright © 2011 John Wiley & Sons, Ltd.
Infinite-dimensional stochastic differential equations related to random matrices
Authors: Osada Hirofumi 
Published: March 2011

AbstractWe solve infinite-dimensional stochastic differential equations (ISDEs) describing an infinite number of Brownian particles interacting via two-dimensional Coulomb potentials. The equilibrium states of the associated unlabeled stochastic dynamics are the Ginibre random point field and Dyson’s measures, which appear in random matrix theory. To solve the ISDEs we establish an integration by parts formula for these measures. Because the long-range effect of two-dimensional Coulomb potentials is quite strong, the properties of Brownian particles interacting with two-dimensional Coulomb potentials are remarkably different from those of Brownian particles interacting with Ruelle’s class interaction potentials. As an example, we prove that the interacting Brownian particles associated with the Ginibre random point field satisfy plural ISDEs.
Effect of Stipa tenacissima L. on the structure of plant co‐occurrence networks in a semi‐arid community
Authors: Saiz Hugo , Alados Concepción L. 
Published: March 2011

AbstractNetwork approaches can increase our understanding of both changes in ecosystems and the role that individual species play in such changes. In ecology, networks have been applied mainly to the study of food webs and mutualistic interactions, with few studies on plant communities. This study used a network approach to examine a semi‐arid plant community along a Stipa tenacissima abundance gradient at two locations in SE Spain: (1) an open shrub land where S. tenacissima is a highly competitive species, and (2) an alpha steppe where S. tenacissima forms the end stable successional community. In alpha steppe, the influence of slope was also examined. We detected that S. tenacissima influenced the network structuring process, and that network organization changed along the gradient. In open shrub land, when S. tenacissima became abundant, it dominated the community and other species disappeared. This resulted in a reduction of the number of links that S. tenacissima established. At the alpha‐steppe, S. tenacissima coexists with other species, developing more links as it becomes more abundant. On gentle slope zones of alpha steppe, S. tenacissima is more competitive and becomes dominant for high abundance values, reducing its links with other species. The organization of networks varied similarly in both locations. When plant species reduce their abundance and number, links are more heterogeneously distributed in networks. This leads to a concentration of most of the links around a few species, particularly S. tenacissima, which is the most abundant in this case. We conclude that, in order to study plant communities, it is convenient to consider the properties of individual components together with the interaction between them.
Plasma Levels of trans‐Fatty Acids are Low in Exclusively Breastfed Infants of Adolescent Mothers
Authors: de Souza Santos da Costa Roseli , da Silva Santos Flavia , da Conceição Felipe Domingues , Saunders Claudia , de Carvalho Sardinha Fatima Lúcia , de Miranda Chaves Célia Regina Moutinho , da Graças Tavares do Carmo Maria 
Published: March 2011

AbstractThe purpose of this study was to determine the levels of trans‐octadecenoic acid (C18:1‐trans) and trans‐isomers of linoleic acid (18:2‐trans), as well as long‐chain polyunsaturated fatty acids (LC‐PUFA), in the plasma from infants of adolescent mothers at 3 months of age, exclusively breastfed, and the relationship with the levels of the same isomers in plasma and milk of the mothers. Samples of blood and mature milk were obtained from 49 healthy adolescent mothers and their exclusively breastfed infants treated at the Instituto Fernandes Figueira‐Fundação Oswaldo Cruz (IFF‐FIOCRUZ) in Rio de Janeiro, Brazil. trans‐Fatty acids (TFA) were analyzed by gas chromatography. The results of this study showed low levels of TFA in milk (1.53%), maternal plasma (0.50%), and plasma of infants (0.74%). The results show that, although TFA have been found in the plasma of the studied infants, the LC‐PUFA levels are kept within normal limits. No association between TFA presence and parameters of nutritional status of the infants was observed, probably due to the low levels of these fatty acids found in this study.
Determination of Polyunsaturated Fatty Esters (PUFA) in Biodiesel by GC/GC–MS and 1H‐NMR Techniques
Authors: Chopra Anju , Tewari A. K. , Vatsala S. , Kumar Ravindra , Sarpal A. S. , Basu B. 
Published: March 2011

AbstractIn the present work, methods based on Gas Chromatography (GC), Gas Chromatography–Mass Spectrometry (GC–MS) and 1H‐NMR techniques was developed for the characterization and estimation of Polyunsaturated Fatty Esters (PUFA) in biodiesel. The GC method enables the separation, identification and estimation of these polyunsaturated fatty acid methyl esters to be carried out using a highly polar capillary column (100% cyanopropyl silicon). GC–MS was utilized for unambiguous identification and estimation of esters and isomers present in biodiesel. The estimation of PUFA content is important because PUFA content is a part of the EN 14214 specifications of biodiesel. There is no existing standard method for the estimation of total PUFA content in biodiesel. The developed GC method also quantifies EPA and DHA (C20:5 and C22:6) fatty acid methyl esters which can be used as markers for the estimation of fish oil biodiesel. The presence of EPA and DHA indicates the contamination of fish oil in biodiesel. Further, the 1H‐NMR technique has also been employed to identify and estimate PUFA containing ≥3 double bonds. The PUFA content was estimated from the integral intensities of the chemical shift region corresponding to all type of double bonds in the 1H‐NMR spectra. Based on the developed method, GC fingerprinting of various biodiesel samples was carried out to estimate a PUFA content as low as 1,000 ppm.
New MR sequences in daily practice: susceptibility weighted imaging. A pictorial essay
Authors: Gasparotti Roberto , Pinelli Lorenzo , Liserre Roberto 
Published: March 2011

Abstract

Background
Susceptibility-weighted imaging (SWI) is a relatively new magnetic resonance (MR) technique that exploits the magnetic susceptibility differences of various tissues, such as blood, iron and calcification, as a new source of contrast enhancement. This pictorial review is aimed at illustrating and discussing its main clinical applications.

Methods
SWI is based on high-resolution, three-dimensional (3D), fully velocity-compensated gradient-echo sequences using both magnitude and phase images. A phase mask obtained from the MR phase images is multiplied with magnitude images in order to increase the visualisation of the smaller veins and other sources of susceptibility effects, which are displayed at best after post-processing of the 3D dataset with the minimal intensity projection (minIP) algorithm.

Results
SWI is very useful in detecting cerebral microbleeds in ageing and occult low-flow vascular malformations, in characterising brain tumours and degenerative diseases of the brain, and in recognizing calcifications in various pathological conditions. The phase images are especially useful in differentiating between paramagnetic susceptibility effects of blood and diamagnetic effects of calcium. SWI can also be used to evaluate changes in iron content in different neurodegenerative disorders.

Conclusion
SWI is useful in differentiating and characterising diverse brain disorders.
The cytoskeleton and nucleus: the role of actin as a modulator of neuronal gene expression
Authors: Knöll B. , Beck H. 
Published: March 2011

Abstract
Actin, arranged for example in stress fibres, provides a fundamental cytoskeletal frame­work function to all cell types. Notably, there is now mounting evidence that, in addition to cytoplasmic cytoskeletal regulation, ac­tin treadmilling provides a signal modulat­ing nuclear gene expression. In altering gene regulation, cytoplasmic and most likely also a nucleus-resident actin provides an addition­al (gene) regulatory twist to cell motility. So far, the transcription factor serum response factor (SRF) alongside its myocardin-relat­ed transcription factor (MRTF) cofactors has emerged as the main target of actin dynam­ics. In this review, we discuss the impact of actin signalling on nuclear gene expression in the nervous system, where the actin-MRTF-SRF module contributes to various processes including neuronal motility.