bluuebunny/crossref_metadata_2025_split huggingface dataset:
Plasmonic measurements of monoclonal antibody self‐association using self‐interaction nanoparticle spectroscopy
Authors: Jayaraman Jayapriya , Wu Jiemin , Brunelle Molly C. , Cruz Anna Marie M. , Goldberg Deborah S. , Lobo Brian , Shah Ambarish , Tessier Peter M. 
Published: February 2014

ABSTRACTOne of the most significant challenges in developing therapeutic monoclonal antibodies (mAbs) is their unpredictable solubilities and viscosities at the high concentrations required for subcutaneous delivery. This challenge has motivated the development of screening assays that rapidly identify mAb variants with minimal self‐association propensities and/or formulation conditions that suppress mAb self‐association. Here we report an improved version of self‐interaction nanoparticle spectroscopy (SINS) capable of characterizing both repulsive and attractive self‐interactions between diverse mAbs. The basis of SINS is that self‐interactions between mAbs immobilized on gold nanoparticles increase (repulsion) or decrease (attraction) interparticle distances, which shift the wavelength of maximum absorbance (plasmon wavelength) in opposite directions. We find that the robustness of SINS is improved by varying the amount of immobilized mAb by co‐adsorbing a polyclonal antibody. The slopes of the plasmon wavelength shifts as a function of the amount of immobilized mAb (0.01–0.1 mg/mL) are correlated with diffusion interaction parameters measured at two to three orders of magnitude higher antibody concentrations. The ability of SINS to rapidly screen mAb self‐association in a microplate format using dilute mAb solutions makes it well suited for use in diverse settings ranging from antibody discovery to formulation. Biotechnol. Bioeng. 2014;111: 1513–1520. © 2014 Wiley Periodicals, Inc.
Fluorescence‐based soft sensor for at situ monitoring of chinese hamster ovary cell cultures
Authors: Ohadi Kaveh , Aghamohseni Hengameh , Legge Raymond L. , Budman Hector M. 
Published: February 2014

ABSTRACTMulti‐wavelength fluorescence spectroscopy was investigated as a potential tool for use in monitoring key process variables that include: viable and dead cells, recombinant protein, glucose, and ammonia concentrations for Chinese hamster ovary (CHO) cells during cultivation. For the purpose of calibrating the fluorescence‐based empirical model, cells were grown in batch mode with different initial glucose and glutamine concentrations. Spectrofluorometer settings were optimized to ensure reproducibility and accuracy of the acquired spectra. With the purpose of gaining qualitative insight into the evolution of the spectra, the trajectories of individual fluorophore peaks were studied during the cultivation process. Spectral changes related to biomass and secreted proteins were investigated by comparing the spectra at various stages during the downstream processing. A partial least square regression (PLSR) was used to formulate empirical models that related the input data set, i.e., the fluorescence excitation–emission matrix, to the actual state of the system including viable cell and dead cells and recombinant protein, glucose, and ammonia concentrations. The models exhibited accurate prediction ability for the process variables of interest. Biotechnol. Bioeng. 2014;111: 1577–1586. © 2014 Wiley Periodicals, Inc.
Self‐Force in 1D Electrostatic Particle‐in‐Cell Codes for NonEquidistant Grids
Authors: Duras J. , Matyash K. , Tskhakaya D. , Kalentev O. , Schneider R. 
Published: February 2014

AbstractEffects of non‐equidistant grids on momentum conservation is studied for simple test cases of an electrostatic 1D PIC code. The aim is to reduce the errors in energy and momentum conservation. Assuming an exact Poisson solver only numerical errors for the particle mover are analysed. For the standard electric field calculation using a central‐difference scheme, artificial electric fields at the particle position are generated in the case when the particle is situated next to a cell size change. This is sufficient to destroy momentum conservation. A modified electric field calculation scheme is derived to reduce this error. Independent of the calculation scheme additional fake forces in a two‐particle system are found which result in an error in the total kinetic energy of the system. This contribution is shown to be negligible for many particle systems. To test the accuracy of the two electric field calculation schemes numerical tests are done to compare with an equidistant grid set‐up. All tests show an improved momentum conservation and total kinetic energy for the modified calculation scheme of the electric field. (© 2014 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Improved method to retain cytosolic reporter protein fluorescence while staining for nuclear proteins
Authors: Heinen André P. , Wanke Florian , Moos Sonja , Attig Sebastian , Luche Hervé , Pal Prajna Paramita , Budisa Nediljko , Fehling Hans Jörg , Waisman Ari , Kurschus Florian C. 
Published: February 2014

AbstractStaining of transcription factors (TFs) together with retention of fluorescent reporter proteins is hindered by loss of fluorescence using current available methods. In this study, it is shown that current TF staining protocols do not destroy fluorescent proteins (FPs) but rather that fixation is not sufficient to retain FPs in the cytosol of the permeabilized cells. In this article, a simple and reliable protocol is elaborated, which allows efficient TF and cytokine staining while retaining FPs inside fixed cells. © 2014 International Society for Advancement of Cytometry
Grassland invaders and their mycorrhizal symbionts: a study across climate and invasion gradients
Authors: Bunn Rebecca A. , Lekberg Ylva , Gallagher Christopher , Rosendahl Søren , Ramsey Philip W. 
Published: February 2014

AbstractControlled experiments show that arbuscular mycorrhizal fungi (AMF) can increase competitiveness of exotic plants, potentially increasing invasion success. We surveyed AMF abundance and community composition in Centaurea stoebe and Potentilla recta invasions in the western USA to assess whether patterns were consistent with mycorrhizal‐mediated invasions. We asked whether (1) AMF abundance and community composition differ between native and exotic forbs, (2) associations between native plants and AMF shift with invading exotic plants, and (3) AMF abundance and/or community composition differ in areas where exotic plants are highly invasive and in areas where they are not. We collected soil and roots from invaded and native forb communities along invasion gradients and in regions with different invasion densities. We used AMF root colonization as a measure of AMF abundance and characterized AMF communities in roots using 454‐sequencing of the LSU‐rDNA region. All plants were highly colonized (>60%), but exotic forbs tended to be more colonized than natives (P < 0.001). We identified 30 AMF operational taxonomic units (OTUs) across sites, and community composition was best predicted by abiotic factors (soil texture, pH). Two OTUs in the genera Glomus and Rhizophagus dominated in most communities, and their dominance increased with invasion density (r = 0.57, P = 0.010), while overall OTU richness decreased with invasion density (r = −0.61, P = 0.006). Samples along P. recta invasion gradients revealed small and reciprocal shifts in AMF communities with >45% fungal OTUs shared between neighboring native and P. recta plants. Overall, we observed significant, but modest, differences in AMF colonization and communities between co‐occurring exotic and native forbs and among exotic forbs across regions that differ in invasion pressure. While experimental manipulations are required to assess functional consequences, the observed patterns are not consistent with those expected from strong mycorrhizal‐mediated invasions.
An ecological cost associated with protective symbionts of aphids
Authors: Polin Sarah , Simon Jean‐Christophe , Outreman Yannick 
Published: February 2014

AbstractBeneficial symbioses are widespread and diverse in the functions they provide to the host ranging from nutrition to protection. However, these partnerships with symbionts can be costly for the host. Such costs, so called “direct costs”, arise from a trade‐off between allocating resources to symbiosis and other functions such as reproduction or growth. Ecological costs may also exist when symbiosis negatively affects the interactions between the host and other organisms in the environment. Although ecological costs can deeply impact the evolution of symbiosis, they have received little attention. The pea aphid Acyrthosiphon pisum benefits a strong protection against its main parasitoids from protective bacterial symbionts. The ecological cost of symbiont‐mediated resistance to parasitism in aphids was here investigated by analyzing aphid behavior in the presence of predatory ladybirds. We showed that aphids harboring protective symbionts expressed less defensive behaviors, thus suffering a higher predation than symbiont‐free aphids. Consequently, our study indicates that this underlined ecological cost may affect both the coevolutionary processes between symbiotic partners and the prevalence of such beneficial bacterial symbionts in host natural populations.
Fault tolerant, energy efficient and secure clustering scheme for mobile machine‐to‐machine communications
Authors: Karim Lutful , Anpalagan Alagan , Nasser Nidal , Almhana Jalal , Woungang Isaac 
Published: February 2014

ABSTRACTDesigning energy efficient, fault tolerant and secure clustering scheme is important for machine‐to‐machine (M2M) communications that comprise a large number of sensors. Existing works on M2M communications include designing M2M layered architecture, device model, Quality of Service (QoS) categorisation of M2M services and potential M2M applications. However, designing secure and fault tolerant clustering schemes has not received much attention in M2M research. Thus, this paper introduces a fault tolerant, energy efficient and secure clustering scheme for M2M (FESM) area networks that minimises the number of cluster heads (CHs) and active nodes to reduce network energy consumption. The machine type communication gateway and CHs transmit beacon messages to discover the failure of CHs and member nodes, respectively. The security mechanism is lightweight but efficient. It uses simple permutation‐based shared keys between (i) member nodes and CHs; (ii) gateway nodes and CHs; and (iii) CHs and machine type communication gateway. Experimental results demonstrate that the FESM clustering scheme reduces network energy consumption and increases network lifetime as compared with the existing Fault Tolerant and Energy Efficient Clustering Protocol (FTEEC), Dynamic Static Clustering Protocol (DSC) and Low Energy Adaptive Clustering Hierarchy (LEACH) protocols. We also analyse the security mechanism of the FESM protocol and find that it is very effective against well‐known attacks such as sybil, wormhole and black hole. Copyright © 2014 John Wiley & Sons, Ltd.
A Chimera method for the incompressible Navier–Stokes equations
Authors: Houzeaux G. , Eguzkitza B. , Aubry R. , Owen H. , Vázquez M. 
Published: February 2014

SUMMARYThe Chimera method was developed three decades ago as a meshing simplification tool. Different components are meshed independently and then glued together using a domain decomposition technique to couple the equations solved on each component. This coupling is achieved via transmission conditions (in the finite element context) or by imposing the continuity of fluxes (in the finite volume context). Historically, the method has then been used extensively to treat moving objects, as the independent meshes are free to move with respect to the others. At each time step, the main task consists in recomputing the interpolation of the transmission conditions or fluxes. This paper presents a Chimera method applied to the Navier–Stokes equations. After an introduction on the Chimera method, we describe in two different sections the two independent steps of the method: the hole cutting to create the interfaces of the subdomains and the coupling of the subdomains. Then, we present the Navier–Stokes solver considered in this work. Implementation aspects are then detailed in order to apply efficiently the method to this specific parallel Navier–Stokes solver. We conclude with some examples to demonstrate the reliability and application of the proposed method. Copyright © 2014 John Wiley & Sons, Ltd.
CO2 storage safety and leakage monitoring in the CCS demonstration project of Jilin oilfield, China
Authors: Zhang Liang , Huang Haidong , Wang Yanqing , Ren Bo , Ren Shaoran , Chen Guoli , Zhang Hua 
Published: February 2014

AbstractJilin oilfield is conducting the first large‐scale demonstration project on CO2 storage and enhanced oil recovery (EOR) in the northeast of China. A comprehensive monitoring program has been designed and deployed in the target reservoir of block H‐59 using a wide range of techniques to monitor the injection and production systems, the CO2 migration fronts, and potential CO2 leakage pathways. Tube fault detection, corrosion inhibitors, anti‐CO2 corrosion cement, and production dynamic analysis have been adopted to guarantee the safety at the well site. CO2 movement in the reservoir is detected mainly by gas tracer, electric spontaneous potential measurement, and fluid sampling. Near‐surface environmental monitoring is also conducted around the injection site. Field experience has shown that the monitoring targets should be focused on the reservoir, near‐surface, and injection and production systems. Applying monitoring techniques to ensure the integrity of wellbores can not only prevent the leakage of CO2, but also avoid the blind expansion of monitoring program scopes. It is reliable and economical to take full advantage of techniques based on wellbores to monitor CO2 movement in oil reservoirs with dense well patterns. Up to April 2013, nearly 21.7 × 104 tons of CO2 has been injected without obvious leakage caused by integrity failure of wells or the geological structure of reservoir. More than 96% of injected CO2 has been safely stored with the rest of injected CO2 normally breakthrough in the production wells. The preliminary monitoring experience obtained can provide valuable guidance for the future enlarged Jilin project and other CO2 EOR and storage operations.
Are power calculations useful? A multicentre neuroimaging study
Authors: Suckling John , Henty Julian , Ecker Christine , Deoni Sean C. , Lombardo Michael V. , Baron‐Cohen Simon , Jezzard Peter , Barnes Anna , Chakrabarti Bhismadev , Ooi Cinly , Lai Meng‐Chuan , Williams Steven C. , Murphy Declan G.M. , Bullmore Edward ,   for the MRC AIMS Consortium
Published: February 2014

AbstractThere are now many reports of imaging experiments with small cohorts of typical participants that precede large‐scale, often multicentre studies of psychiatric and neurological disorders. Data from these calibration experiments are sufficient to make estimates of statistical power and predictions of sample size and minimum observable effect sizes. In this technical note, we suggest how previously reported voxel‐based power calculations can support decision making in the design, execution and analysis of cross‐sectional multicentre imaging studies. The choice of MRI acquisition sequence, distribution of recruitment across acquisition centres, and changes to the registration method applied during data analysis are considered as examples. The consequences of modification are explored in quantitative terms by assessing the impact on sample size for a fixed effect size and detectable effect size for a fixed sample size. The calibration experiment dataset used for illustration was a precursor to the now complete Medical Research Council Autism Imaging Multicentre Study (MRC‐AIMS). Validation of the voxel‐based power calculations is made by comparing the predicted values from the calibration experiment with those observed in MRC‐AIMS. The effect of non‐linear mappings during image registration to a standard stereotactic space on the prediction is explored with reference to the amount of local deformation. In summary, power calculations offer a validated, quantitative means of making informed choices on important factors that influence the outcome of studies that consume significant resources. Hum Brain Mapp 35:3569–3577, 2014. © 2014 The Authors. Human Brain Mapping Published by Wiley Periodicals, Inc.
Functional lateralization of the anterior insula during feedback processing
Authors: Späti Jakub , Chumbley Justin , Brakowski Janis , Dörig Nadja , Grosse Holtforth Martin , Seifritz Erich , Spinelli Simona 
Published: February 2014

AbstractEffective adaptive behavior rests on an appropriate understanding of how much responsibility we have over outcomes in the environment. This attribution of agency to ourselves or to an external event influences our behavioral and affective response to the outcomes. Despite its special importance to understanding human motivation and affect, the neural mechanisms involved in self‐attributed rewards and punishments remain unclear. Previous evidence implicates the anterior insula (AI) in evaluating the consequences of our own actions. However, it is unclear if the AI has a general role in feedback evaluation (positive and negative) or plays a specific role during error processing. Using functional magnetic resonance imaging and a motion prediction task, we investigate neural responses to self‐ and externally attributed monetary gains and losses. We found that attribution effects vary according to the valence of feedback: significant valence × attribution interactions in the right AI, the anterior cingulate cortex (ACC), the midbrain, and the right ventral putamen. Self‐attributed losses were associated with increased activity in the midbrain, the ACC and the right AI, and negative BOLD response in the ventral putamen. However, higher BOLD activity to self‐attributed feedback (losses and gains) was observed in the left AI, the thalamus, and the cerebellar vermis. These results suggest a functional lateralization of the AI. The right AI, together with the midbrain and the ACC, is mainly involved in processing the salience of the outcome, whereas the left is part of a cerebello‐thalamic‐cortical pathway involved in cognitive control processes important for subsequent behavioral adaptations. Hum Brain Mapp 35:4428–4439, 2014. © 2014 Wiley Periodicals, Inc.
Algorithm to predict postoperative complications in oropharyngeal and oral cavity carcinoma
Authors: Santoro Luigi , Tagliabue Marta , Massaro Maria Angela , Ansarin Mohssen , Calabrese Luca , Giugliano Gioacchino , Alterio Daniela , Cossu Rocca Maria , Grosso Enrica , Plànicka Marek , Benazzo Marco , Chiesa Fausto 
Published: February 2014

AbstractBackgroundPreoperative data in patients with oral cavity/oropharyngeal cancer may predict postoperative complications that may modify therapeutic choices and improve patient care.MethodWe reviewed 320 consecutive patients with oral cavity/oropharyngeal cancer, operated on 2003 through 2006 at the European Institute of Oncology. By multivariate analysis of preoperative patient and tumor characteristics, we developed an algorithm to predict postoperative complications. We tested the algorithm on a new series of 307 patients operated on 2007 through 2010.ResultsThe final algorithm used to produce a nomogram was comprised of: alcohol consumption (p = .01), site of primary (p = .03), interaction of clinical T classification to sex (p = .007), and type of neck dissection (p < .0001). The algorithm had good ability to predict complications (concordance index [c‐index] 0.74) in the new series.ConclusionThe nomogram accurately predicts presurgical risk of postoperative local/systemic complications in patients with oral cavity/oropharyngeal cancer and can be used to adapt therapy to patient characteristics, optimize ward admissions, and improve care. © 2014 Wiley Periodicals, Inc. Head Neck 37: 548–556, 2015
A marriage of convenience: Hybridization of surface plasmon and dielectric waveguide modes
Authors: Alam Muhammad Z. , Aitchison J. Stewart , Mojahedi Mo 
Published: February 2014

AbstractPlasmonics has attracted a lot of interest in the past few years because of its unique features, especially for its ability to confine light in extremely small volumes. However, application of plasmonics is restricted by the large propagation loss associated with plasmonic waveguides. On the other hand, dielectric waveguides enjoy low loss, although the mode confinement is relatively weaker. Hybrid plasmonic waveguides (HPWGs), which combine these two guiding mechanisms, allow one to utilize the benefits of both technologies. Over the past few years there have been intense research activities around the world on this new guiding scheme. In this work the operating principle of HPWGs, various HPWG structures proposed by different research groups, and their potentail applications are reviewed.
Uniqueness and exponential stability of almost periodic positive solution for Lasota‐Wazewska model with impulse and infinite delay
Authors: Yao Zhijian 
Published: February 2014

AbstractIn this paper, impulsive Lasota‐Wazewska model with infinite delay is studied. By using fixed point theorem of decreasing operator, we obtain sufficient conditions for the existence of unique almost periodic positive solution. Particularly, we give iterative sequence, which converges to the almost periodic positive solution. Moreover, we investigate exponential stability of the almost periodic positive solution by Liapunov functional. Copyright © 2014 John Wiley & Sons, Ltd.
Derivation of human embryonic stem cell lines without any exogenous growth factors
Authors: Liu Cai Xia , Zhang Ren Li , Gao Jun , Li Tao , Ren Zi , Zhou Can Quan , Wen An Min 
Published: February 2014

SUMMARYHuman embryonic stem cell (hESC) lines are traditionally derived through immunosurgery. Their maintenance in culture requires the presence of mouse embryonic fibroblasts (MEFs) as feeder cells and media supplemented with basic fibroblast growth factor (bFGF) or other growth factors—both of which might introduce animal‐derived culture components. The drawbacks associated with immunosurgery, MEF co‐culture, and the cost of growth factors necessitate the exploration of a xeno‐free method to maintain the self‐renewal capacity of hESCs. Here, we describe an isolation method for the human inner cell mass (ICM), which was then cultured in the absence of exogenous growth factors and in the presence of human foreskin fibroblasts (HFFs) as feeder cells. Three hESC lines were obtained from poor‐quality embryos by this near‐xeno‐free protocol. After culturing for more than 10 months, the hESCs retained normal morphology, expressed all expected cell surface markers, could differentiate to embryoid bodies upon culture in vitro, and formed teratomas in vivo. Furthermore, secretion of bFGF by HFFs was observed. In conclusion, this is the first study to describe an inexpensive, xeno‐free culture system for the isolation and maintenance of hESCs that does not require bFGF supplementation. Mol. Reprod. Dev. 9999: XX–XX, 2014. © 2014 Wiley Periodicals, Inc.