bluuebunny/crossref_metadata_2025_split huggingface dataset:
A study on the use of radar and lidar for characterizing ultragiant aerosol
Authors: Madonna F. , Amodeo A. , D'Amico G. , Pappalardo G. 
Published: August 2013

AbstractFrom 19 April to 19 May 2010, volcanic aerosol layers originating from the Eyjafjallajökull volcano were observed at the Institute of Methodologies for Environmental Analysis of the National Research Council of Italy Atmospheric Observatory, named CIAO (40.60°N, 15.72°E, 760 m above sea level), in Southern Italy with a multiwavelength Raman lidar. During this period, ultragiant aerosols were also observed at CIAO using a colocated 8.45 mm wavelength Doppler radar. The Ka‐band radar signatures observed in four separate days (19 April and 7, 10, and 13 May) are consistent with the observation of nonspherical ultragiant aerosols characterized by values of linear depolarization ratio (LDR) higher than –4 dB. Air mass back trajectory analysis suggests a volcanic origin of the ultragiant aerosols observed by the radar. The observed values of the radar reflectivity (Ze) are consistent with a particle effective radius (r) larger than 50–75 µm. Scattering simulations based on the T‐matrix approach show that the high LDR values can be explained if the observed particles have an absolute aspect ratio larger than 3.0 and consist of an internal aerosol core and external ice shell, with a variable radius ratio ranging between 0.2 and 0.7 depending on the shape and aspect ratio. Comparisons between daytime vertical profiles of aerosol backscatter coefficient (β) as measured by lidar and radar LDR reveal a decrease of β where ultragiant particles are observed. Scattering simulations based on Mie theory show how the lidar capability in typing ultragiant aerosols could be limited by low number concentrations or by the presence of an external ice shell covering the aerosol particles. Preferential vertical alignment of the particles is discussed as another possible reason for the decrease of β.
Controlled Microstructuring of Janus Particles Based on a Multifunctional Poly(ethylene glycol)
Authors: Sokolovskaya Ekaterina , Yoon Jaewon , Misra Asish C. , Bräse Stefan , Lahann Jörg 
Published: August 2013

A novel water insoluble, multifunctional poly(ethylene glycol), poly(hydrazide ethylene glycol‐co‐benzyl glycidyl ether) (P(HZ‐co‐BnGE)), is synthesized via thiol‐ene click reaction of poly(allyl glycidyl ether‐co‐benzyl glycidyl ether) (P(AGE‐co‐BnGE)). The base polymer P(AGE‐co‐BnGE) is previously prepared by anionic ring‐opening copolymerization of the corresponding monomers. To demonstrate utility, bicompartmental microspheres and microcylinders containing P(HZ‐co‐BnGE) in one of the compartments are prepared via electrohydrodynamic (EHD) co‐jetting. Next, spatially controlled surface reactivity toward sugars is demonstrated by selective binding of 2α‐mannobiose to the P(HZ‐co‐BnGE) compartment only, as confirmed by a carbohydrate‐lectin‐binding assay. These sugar‐reactive hydrazide‐presenting microparticles have potential applications for glyco‐targeted drug delivery.
image
A Rocket‐Like Encapsulation and Delivery System with Two‐Stage Booster Layers: pH‐Responsive Poly(methacrylic acid)/Poly(ethylene glycol) Complex‐Coated Hollow Silica Vesicles
Authors: Lay Chee Leng , Kumar Jatin N. , Liu Connie K. , Lu Xuehong , Liu Ye 
Published: August 2013

Rocket‐like vesicles formed are composed of poly(acrylic aicd) (PMAA )/poly(ethylene glycol) (PEG) complex coated hollow silica spheres, and the structure and composition of the vesicles are characterized using TGA, 1H NMR, FTIR, and TEM. Although only one‐third of EG units of PEG brushes grafted to hollow silica spheres form the complex with PMAA via hydrogen bonding, the first “booster” layer composed of PMAA/PEG complex can provide secure encapsulation of model compound calcein blue under an acidic condition. The second “booster” layer composed of PEG brushes can be formed by changing acidic pH to 7.4 through the disassociation of the PMAA/PEG complex. A higher molecular weight PMAA exhibits a faster disassembly due to the formation of a looser PMAA/PEG complex on the surfaces of hollow silica spheres.
image
Immunity protein release from a cell‐bound nuclease colicin complex requires global conformational rearrangement
Authors: Vankemmelbeke Mireille , Housden Nicholas G. , James Richard , Kleanthous Colin , Penfold Christopher N. 
Published: August 2013

AbstractNuclease colicins bind their target receptor BtuB in the outer membrane of sensitive Escherichia coli cells in the form of a high‐affinity complex with their cognate immunity proteins. The release of the immunity protein from the colicin complex is a prerequisite for cell entry of the colicin and occurs via a process that is still relatively poorly understood. We have previously shown that an energy input in the form of the cytoplasmic membrane proton motive force is required to promote immunity protein (Im9) release from the colicin E9/Im9 complex and colicin cell entry. We report here that engineering rigidity in the structured part of the colicin translocation domain via the introduction of disulfide bonds prevents immunity protein release from the colicin complex. Reduction of the disulfide bond by the addition of DTT leads to immunity protein release and resumption of activity. Similarly, the introduction of a disulfide bond in the DNase domain previously shown to abolish channel formation in planar bilayers also prevented immunity protein release. Importantly, all disulfide bonds, in the translocation as well as the DNase domain, also abolished the biological activity of the Im9‐free colicin E9, the reduction of which led to a resumption of activity. Our results show, for the first time, that conformational flexibility in the structured translocation and DNase domains of a nuclease colicin is essential for immunity protein release, providing further evidence for the hypothesis that global structural rearrangement of the colicin molecule is required for disassembly of this high‐affinity toxin‐immunity protein complex prior to outer membrane translocation.
Imaging EGFR and HER2 by PET and SPECT: A Review
Authors: Corcoran Emily B. , Hanson Robert N. 
Published: August 2013

AbstractIn an effort to discover a noninvasive method for predicting which cancer patients will benefit from therapy targeting the EGFR and HER2 proteins, a large body of the research has been conducted toward the development of PET and SPECT imaging agents, which selectively target these receptors. We provide a general overview of the advances made toward imaging EGFR and HER2, detailing the investigation of PET and SPECT imaging agents ranging in size from small molecules to monoclonal antibodies.
Interrelationships among genetic C677T polymorphism of 5,10‐methylenetetrahydrofolate reductase, biochemical folate status, and lymphocytic p53 oxidative damage in association with tumor malignancy and survivals of patients with hepatocellular carcinoma
Authors: Kuo Chang‐Sheng , Huang Chi‐Yun , Kuo Hsing‐Tao , Cheng Chin‐Pao , Chen Chien‐Hung , Lu Chin‐Li , Yang Feili‐Lo , Syu Huang Rwei‐Fen 
Published: August 2013

ScopeMetabolic genotypes of 5,10‐methylenetetrahydrofolate reductase (MTHFR) and folate status on oxidative DNA lesions in hepatocellular carcinoma (HCC) has not been elucidated. The aims of the study were to investigate the folate‐polymorphic interactions on genetic oxidative damage in association with advanced HCC malignancy and prognosis.Methods and resultsThe study included 232 HCC patients with folate nutrition, MTHFR C677T polymorphic, p53 genetic and tumour pathological data collected and analyzed for their survivals after a 7.8‐years following up. By adjustment for oxidative risk factors of HCC, the compound CT and TT genotypes in relative to the CC wild‐type were associated with 83% reduced lymphocytic p53 oxidative lesions of HCC patients with RBC folate lower than 688 ng/mL (OR: 0.17, 95%CI: 0.07–0.43). Such genetic protective effects by the CT/TT genotypes were 2‐fold enhanced among those with high RBC folate (OR: 0.08, 95% CI: 0.03–0.21, P for interaction < 0.001). For those with non‐folate‐deficient status, the compound CT and TT vs. CC genotypes were associated with 80% reduced risks of advanced HCC stages (III&IV) (OR: 0.2, 95%CI: 0.08–0.56). Such protection was negated either by adjustment of lymphocytic p53 oxidative lesions or by 3‐fold increased risks among those with high RBC status (OR: 0.6, 95%CI; 0.31–1.41, P for interaction = 0.009). Multivariate Cox proportional hazards analysis showed that the CT/TT genotypes vs. CC wild‐type were the independent predictable factor for better survival outcome of HCC patients (HR: 0.48, CI = 0.30–0.79). For CC homozygote, the second vs. the bottom tertile levels of RBC status were associated with 2‐fold increased mortality rate of HCC patients (HR: 2.05, CI = 1.0–4.1).ConclusionOur data demonstrated that reduced MTHFR activities associated with the MTHFR T allele may interact with RBC folate as the risk modifiers of lymphocytic p53 oxidative lesions of HCC patients. The CT/TT genotypes correlated with lower risks of late‐stage HCC and a favorable survival of HCC patients, depending on p53 oxidative lesions or RBC folate status.
Structure and stability of the C‐terminal helical bundle of the E. coli mechanosensitive channel of large conductance
Authors: Walton Troy A. , Rees Douglas C. 
Published: August 2013

AbstractThe crystal structure of the cytoplasmic domain (CTD) from the mechanosensitive channel of large conductance (MscL) in E. coli has been determined at 1.45 Å resolution. This domain forms a pentameric coiled coil similar to that observed in the structure of MscL from M. tuberculosis and also found in the cartilage oligomeric matrix protein (COMPcc). It contains canonical hydrophobic and atypical ionic interactions compared to previously characterized coiled coil structures. Thermodynamic analysis indicates that while the free EcMscL‐CTD is less stable than other coiled coils, it is likely to remain folded in context of the full‐length channel.
Wild type and mutants of the HET‐s(218–289) prion show different flexibility at fibrillar ends: A simulation study
Authors: Friedman Ran , Caflisch Amedeo 
Published: August 2013

ABSTRACTThe C‐terminal segment (residues 218–289) of the HET‐s protein of the filamentous fungus Podosporina anserina is a prion‐forming domain. The structural model of the HET‐s(218–289) amyloid fibril based on solid‐state nuclear magnetic resonance (NMR) restraints shows a β solenoid topology which is comprised of a β‐sheet core and interconnecting loops. For the single‐point mutants Phe286Ala and Trp287Ala, slower aggregation rates in vitro and loss of prionic infectivity have been reported recently. Here we have used molecular dynamics to compare the flexibility of the mutants and wild type. The simulations, initiated from a trimeric aggregate extracted from the NMR structural model, show structural stability on a 100‐ns time scale for wild type and mutants. Analysis of the fluctuations along the simulations reveals that the mutants are less flexible than the wild type in the C‐terminal segment at only one of the two external monomers. Analysis of interaction energy and buried accessible surface indicates that residue Phe286 in particular is stabilized in the Trp287Ala mutant. The simulation results provide an atomistic explanation of the suggestion (based on indirect experimental evidence) that flexibility at the protofibril end(s) is required for fibril elongation. Moreover, they provide further evidence that the growth of the HET‐s amyloid fibril is directional. Proteins 2014; 82:399–404. © 2013 Wiley Periodicals, Inc.
Improved flexible refinement of protein docking in CAPRI rounds 22–27
Authors: Shen Yang 
Published: August 2013

ABSTRACTSince the fourth evaluation for critical assessment of prediction of interactions (CAPRI), we have made improvements in three major areas in our refinement approach, namely the treatment of conformational flexibility, the binding free energy model, and the search algorithm. First, we incorporated backbone flexibility into our previous approach, which only optimized rigid backbone poses with limited side‐chain flexibility. Here, we formulated and solved the conformational search as a hierarchical optimization problem (involving rigid‐body poses, backbone flexibility, and side‐chain flexibility). Second, we used continuum electrostatic calculations to include solvation effects in the binding free energy model. Finally, we eliminated sloppy modes (directions in which the free energy is essentially constant) to improve the efficiency of the search. With these improvements, we produced correct predictions for 6 of the 10 latest CAPRI targets, including one high, three medium, and two acceptable accuracy predictions. Compared to our previous performance in CAPRI, substantial improvements have been made for targets requiring homology modeling. Proteins 2013; 81:2129–2136. © 2013 Wiley Periodicals, Inc.
A framework for evaluating model error using asymptotic convergence in the Eady model
Authors: Visram A. R. , Cotter C. J. , Cullen M. J. P. 
Published: August 2013

AbstractOperational weather forecasting requires the accurate simulation of atmospheric motions on scales ranging from the synoptic down to tens of kilometres. Weather fronts, characteristic of midlatitude weather systems, are generated through baroclinic instability on the large scale but are anisotropic features in which temperature and winds can vary rapidly on the short scale.We present a framework for evaluating model error in terms of asymptotic convergence using the Eady model. Through rescaling the problem, we are able to approach solutions of a balanced model, given by the semi‐geostrophic equations, using the non‐hydrostatic, incompressible Euler–Boussinesq Eady equations. Using this approach, we are able to validate the numerical implementation and assess the long‐term performance in terms of solution lifecycles.We present results using a finite‐difference method with semi‐implicit time‐stepping and semi‐Lagrangian transport, and show that we are able to proceed past the point of frontal collapse and recover the theoretical convergence rate. We propose that numerical diffusion of potential vorticity after collapse, as a result of insufficient Lagrangian conservation, is detrimental to the long‐term evolution of the solution.
A nested sampling particle filter for nonlinear data assimilation
Authors: Elsheikh Ahmed H. , Hoteit Ibrahim , Wheeler Mary F. 
Published: August 2013

AbstractWe present an efficient nonlinear data assimilation filter that combines particle filtering with the nested sampling algorithm. Particle filters (PF) utilize a set of weighted particles as a discrete representation of probability distribution functions (PDF). These particles are propagated through the system dynamics and their weights are sequentially updated based on the likelihood of the observed data. Nested sampling (NS) is an efficient sampling algorithm that iteratively builds a discrete representation of the posterior distributions by focusing a set of particles to high‐likelihood regions. This would allow the representation of the posterior PDF with a smaller number of particles and reduce the effects of the curse of dimensionality. The proposed nested sampling particle filter (NSPF) iteratively builds the posterior distribution by applying a constrained sampling from the prior distribution to obtain particles in high‐likelihood regions of the search space, resulting in a reduction of the number of particles required for an efficient behaviour of particle filters. Numerical experiments with the 3‐dimensional Lorenz63 and the 40‐dimensional Lorenz96 models show that NSPF outperforms PF in accuracy with a relatively smaller number of particles.
Energy efficient comparator for successive approximation register ADCs with application to encryption schemes in wireless communication
Authors: Yuan Shitong , Liang Jing 
Published: August 2013

AbstractSecurity is a very broad topic; particular attention has been paid in communications, networking on security issues. However, in practical applications, providing security services increases the computation and the occupation of system resources. This problem is particularly important when the energy is a limited resource for mobile communication devices operating on battery. Thus, energy efficient security devices are very necessary for the communication. This paper designed a new low voltage, low power consumption comparator for successive approximation register analog to digital converter to improve the energy efficiency in the problem of secure communication. Then, analyze the energy consumption of the new comparator security system compared with traditional design. We mainly focus on three communication protocols, which use the block cipher. The results show that the system's energy consumption is greatly reduced when the new comparator is used, Copyright © 2013 John Wiley & Sons, Ltd.
Three‐Dimensional Investigations of Inclusions in Ferroalloys
Authors: Bi Yanyan , Karasev Andrey , Jönsson Pär G. 
Published: August 2013

AbstractAs the requirements on material properties increase, there has been a demand on an additional knowledge on the effect of impurities in the ferroalloys on the properties. Thus, the number, morphology, size, and composition of inclusions in four different ferroalloys (FeTi, FeNb, FeSi, and SiMn) were investigated. This was done in three dimensions (3D) by using scanning electron microscopy in combination with energy dispersive spectroscopy after electrolytic extraction of the ferroalloy samples. The non‐metallic and metallic inclusions were successfully analyzed on the surface of film filter. Thereafter, the particle size distribution was plotted for most of the non‐metallic inclusions. The non‐metallic inclusions were found to be REM oxides in FeTi, FeSi, and SiMn, Al2O3, Ti–Nb–S–O oxides in FeNb and silicon oxides in SiMn. Moreover, the intermetallic inclusions were found to be a Ti–Fe phase in FeTi, Ca–Si, and Fe–Si–Ti phases in FeSi and a Mn–Si phase in SiMn. In addition, the almost pure single metallic phases were found to be Ti in FeTi, Nb in FeNb, and Si in FeSi.
Experimental investigation of steel structure with innovative H‐type steel unbuckling braces
Authors: Hao Xiao‐Yan , Li Hong‐Nan , Li Gang , Makino Toshio 
Published: August 2013

SUMMARYThe unbuckling brace, acting as a combination of a conventional brace and displacement‐dependent damper, can successfully avoid the bucking and consequent fracture compared with the conventional brace, which has been widely applied in concentrically braced frame structures. In this paper, the H‐type steel unbuckling brace (SUB), which is welded by steel flats and core made of low‐yield steel, is presented. The quasi‐static tests, the shaking table tests of a steel structure with SUBs and conventional central braces and the numerical analysis of a real steel building with and without SUBs are conducted in this study to evaluate the performance of SUBs. The results demonstrate that the SUBs have excellent plastic deformation capacity, stable energy dissipation capacity and no stiffness degradation, and can provide certain initial stiffness to the structure and dissipate earthquake input energy by yielding behaviour. Moreover, it is effective in reducing the structural response, and in particular, in controlling the structural displacement. In conclusion, the SUB proposed is a lateral resistant member with high stiffness and strength and an excellent energy dissipation device, which is much more competitive than the conventional brace in improving lateral resistance and seismic performance of the frame structure. Copyright © 2013 John Wiley & Sons, Ltd.
Pollen baiting facilitates the isolation of marine thraustochytrids with potential in omega-3 and biodiesel production
Authors: Gupta Adarsha , Wilkens Serena , Adcock Jacqui L , Puri Munish , Barrow Colin J 
Published: August 2013

Abstract
Marine heterotrophic microbes are capable of accumulating large amounts of lipids, omega-3 fatty acids, carotenoids, and have potential for biodiesel production. Pollen baiting using Pinus radiata pollen grain along with direct plating techniques were used in this study as techniques for the isolation of oil-producing marine thraustochytrid species from Queenscliff, Victoria, Australia. Thirteen isolates were obtained using either direct plating or using pine pollen, with pine pollen acting as a specific substrate for the surface attachment of thraustochytrids. The isolates obtained from the pollen baiting technique showed a wide range of docosahexaenoic acid (DHA) accumulation, from 11 to 41 % of total fatty acid content (TFA). Direct plating isolates showed a moderate range of DHA accumulation, from 19 to 25 % of TFA. Seven isolates were identified on the basis of 18S rRNA sequencing technique as Thraustochytrium species, Schizochytrium species, and Ulkenia species. Although both methods appear to result in the isolation of similar strains, pollen baiting proved to be a simpler method for the isolation of these relatively slow-growing organisms.
Efficient secretion of lipase r27RCL in Pichia pastoris by enhancing the disulfide bond formation pathway in the endoplasmic reticulum
Authors: Sha Chong , Yu Xiao-Wei , Zhang Meng , Xu Yan 
Published: August 2013

Abstract
The lipase r27RCL from Rhizopus chinensis CCTCC M201021 was heterologously expressed in Pichia pastoris GS115 by simultaneous co-expression with two secretion factors ERO1p and PDI involved in the endoplasmic reticulum (ER). Compared to the expression of the lipase alone (12,500 U/ml), co-expression with these two proteins resulted in the production of larger total quantities of enzymes. The largest increase was seen when the combined ERO1p/PDI system was co-expressed, resulting in approximately 30 % higher enzyme yields (16,200 U/ml) than in the absence of co-expressed secretion factors. The extracellular protein concentration of the recombinant strain Co XY RCL-5 reached 9.39 g/l in the 7-l fermentor. Simultaneously, the fermentation time was also shortened by about 8 h compared to that of the control. The substrate-specific consumption rate (Qs) and the product-specific production rate (Qp) were both investigated in this research. In conclusion, the space–time yield was improved by co-expression with ERO1p and PDI. This is a potential strategy for high level expression of other heterologous proteins in P. pastoris.
Genetic Counselor Perceptions of Genetic Counseling Session Goals: A Validation Study of the Reciprocal‐Engagement Model
Authors: Hartmann Julianne E. , Veach Patricia McCarthy , MacFarlane Ian M. , LeRoy Bonnie S. 
Published: August 2013

AbstractAlthough some researchers have attempted to define genetic counseling practice goals, no study has obtained consensus about the goals from a large sample of genetic counselors. The Reciprocal‐Engagement Model (REM; McCarthy Veach, Bartels & LeRoy, 2007) articulates 17 goals of genetic counseling practice. The present study investigated whether these goals could be generalized as a model of practice, as determined by a larger group of clinical genetic counselors. Accordingly, 194 genetic counselors were surveyed regarding their opinions about the importance of each goal and their perceptions of how frequently they achieve each goal. Mean importance ratings suggest they viewed every goal as important. Factor analysis of the 17 goals yielded four factors: Understanding and Appreciation, Support and Guidance, Facilitative Decision‐Making, and Patient‐Centered Education. Patient‐Centered Education and Facilitative Decision‐Making goals received the highest mean importance ratings. Mean frequency ratings were consistently lower than importance ratings, suggesting genetic counseling goals may be difficult to achieve and/or not applicable in all situations. A number of respondents provided comments about the REM goals that offer insight into factors related to implementing the goals in clinical practice. This study presents preliminary evidence concerning the validity of the goals component of the REM.