bluuebunny/crossref_metadata_2025_split huggingface dataset:
High‐throughput measurement, correlation analysis, and machine‐learning predictions for pH and thermal stabilities of Pfizer‐generated antibodies
Authors: King Amy C. , Woods Matthew , Liu Wei , Lu Zhijian , Gill Davinder , Krebs Mark R. H. 
Published: June 2011

AbstractGenerating stable antibodies is an important goal in the development of antibody‐based drugs. Often, thermal stability is assumed predictive of overall stability. To test this, we used different internally created antibodies and first studied changes in antibody structure as a function of pH, using the dye ANS. Comparison of the pH50 values, the midpoint of the transition from the high‐pH to the low‐pH conformation, allowed us for the first time to rank antibodies based on their pH stability. Next, thermal stability was probed by heating the protein in the presence of the dye Sypro Orange. A new data analysis method allowed extraction of all three antibody unfolding transitions and showed close correspondence to values obtained by differential scanning calorimetry. T1%, the temperature at which 1% of the protein is unfolded, was also determined. Importantly, no correlations could be found between thermal stability and pH50, suggesting that to accurately quantify antibody stability, different measures of protein stability are necessary. The experimental data were further analyzed using a machine‐learning approach with a trained model that allowed the prediction of biophysical stability using primary sequence alone. The pH stability predictions proved most successful and were accurate to within pH ±0.2.
Serum prostate specific antigen changes in cynomolgus monkeys (Macaca fascicularis) on a high sugar high fat diet
Authors: Mubiru James N. , Garcia‐Forey Magdalena , Cavazos Nicole , Hemmat Peggah , Dick Edward J. , Owston Michael A. , Bauer Cassondra A. , Shade Robert E. , Rogers Jeffrey 
Published: June 2011

AbstractBACKGROUNDAn inverse relationship between serum prostate specific antigen (PSA) levels and body mass index (BMI) has been reported in men but not in any animal model.METHODSSerum PSA in a colony of cynomolgus monkeys was assayed and correlated to body weight, prostate weight, and age. In addition, 15 animals were selected and fed a high sugar high fat (HSHF) diet for 49 weeks to increase their BMI and correlate it to PSARESULTSSerum PSA levels were positively correlated to prostate weight (r = 0.515, P = 0.025) and age (r = 0.548, P = 0.00072) but was not significantly correlated to body weight (r = −0.032, P = 0.419). For the animals on the HSHF diet, body weight, lean mass, fat mass, and BMI were significantly higher at 49 weeks than at baseline (P < 0.01). PSA was not significantly correlated to body weight and insulin at both baseline and 49 weeks. PSA was negatively correlated to BMI and insulin resistance (HOMA‐IR) at 49 weeks but not at baseline. In addition, we observed hepatic steatosis and increases in serum liver enzymes.CONCLUSIONSIncreases in BMI in cynomolgus monkeys as a result of consuming a HSHF diet resulted in PSA changes similar to those in humans with increased BMI. Cynomolgus monkeys are a useful model for investigating the relationship between obesity, diabetes, and PSA changes resulting from prostate gland pathology. Prostate 72:469–475, 2012. © 2011 Wiley Periodicals, Inc.
How T cell receptors interact with peptide‐MHCs: A multiple steered molecular dynamics study
Authors: Cuendet Michel A. , Zoete Vincent , Michielin Olivier 
Published: June 2011

AbstractThe T‐cell receptor (TCR) interaction with antigenic peptides (p) presented by the major histocompatibility complex (MHC) molecule is a key determinant of immune response. In addition, TCR‐pMHC interactions offer examples of features more generally pertaining to protein‐protein recognition: subtle specificity and cross‐reactivity. Despite their importance, molecular details determining the TCR‐pMHC binding remain unsolved. However, molecular simulation provides the opportunity to investigate some of these aspects. In this study, we perform extensive equilibrium and steered molecular dynamics simulations to study the unbinding of three TCR‐pMHC complexes. As a function of the dissociation reaction coordinate, we are able to obtain converged H‐bond counts and energy decompositions at different levels of detail, ranging from the full proteins, to separate residues and water molecules, down to single atoms at the interface. Many observed features do not support a previously proposed two‐step model for TCR recognition. Our results also provide keys to interpret experimental point‐mutation results. We highlight the role of water both in terms of interface resolvation and of water molecules trapped in the bound complex. Importantly, we illustrate how two TCRs with similar reactivity and structures can have essentially different binding strategies. Proteins 2011; © 2011 Wiley‐Liss, Inc.
Predicting large‐scale conformational changes in proteins using energy‐weighted normal modes
Authors: Palmer David S. , Jensen Frank 
Published: June 2011

AbstractWe report the development of a method to improve the sampling of protein conformational space in molecular simulations. It is shown that a principal component analysis of energy‐weighted normal modes in Cartesian coordinates can be used to extract vectors suitable for describing the dynamics of protein substructures. The method can operate with either atomistic or user‐defined coarse‐grained models of protein structure. An implicit reverse coarse‐graining allows the dynamics of all‐atoms to be recovered when a coarse‐grained model is used. For an external test set of four proteins, it is shown that the new method is more successful than normal mode analysis in describing the large‐scale conformational changes observed on ligand binding. The method has potential applications in protein–ligand and protein–protein docking and in biasing molecular dynamics simulations. Proteins 2011; © 2011 Wiley‐Liss, Inc.
What to do when nothing has happened?
Authors: Freeman Raymond “Randy” 
Published: June 2011

AbstractOften, during a layer of protection analysis (LOPA) or a quantitative risk analysis (QRA) study, historical information indicates no occurrences of a particular undesired event in the plant or system. The simple reply that the frequency or rate is zero because the event has never happened is sometimes heard by the analyst during review meetings. The analyst must then decide on an appropriate measure of the frequency of the undesired event. This article presents methods based on statistical tools for developing a measure of the frequency or failure rate of an event when the historical information includes no occurrences of the event. The article compares the various available statistical tools. Guidance is presented on methods to incorporate historical information of no failures into a LOPA or QRA study. Examples on the application of the recommended methods to deal with the problem are presented. © 2011 American Institute of Chemical Engineers Process Saf Prog, 2011
Two safety reviews before formal PHAs
Authors: Wincek John C. 
Published: June 2011

AbstractMany companies do not formally begin to address process safety for new processes until a detailed design is available for study—this can lead to hazards being overlooked until the formal PHA is performed. At that stage it may be difficult to make fundamental process changes. Even when companies do conduct process safety reviews during the earlier phases of a project, they often lack formalized and documented methodologies. This article describes two safety reviews that should be conducted earlier in the design process: (a) conceptual stage hazard review and (b) preliminary hazard analysis. These reviews will identify and document important safety features such as (a) inherent safety concepts, (b) major accident hazards, and (c) safeguards. These efforts lighten the workload on the formal PHA team, because the major hazards have already been identified and protected against. © 2011 American Institute of Chemical Engineers Process Saf Prog, 2011
Bt maize and integrated pest management ‐ a European perspective
Authors: Meissle Michael , Romeis Jörg , Bigler Franz 
Published: June 2011

AbstractThe European corn borer (Ostrinia nubilalis), the Mediterranean corn borer (Sesamia nonagrioides) and the western corn rootworm (Diabrotica virgifera virgifera) are the main arthropod pests in European maize production. Practised pest control includes chemical control, biological control and cultural control such as ploughing and crop rotation. A pest control option that is available since 1996 is maize varieties that are genetically engineered (GE) to produce insecticidal compounds. GE maize varieties available today express one or several genes from Bacillus thuringiensis (Bt) that target corn borers or corn rootworms. Incentives to growing Bt maize are simplified farm operations, high pest control efficiency, improved grain quality and ecological benefits. Limitations include the risk of resistance evolution in target pest populations, risk of secondary pest outbreaks and increased administration to comply with licence agreements. Growers willing to plant Bt maize in the European Union (EU) often face the problem that authorisation is denied. Only one Bt maize transformation event (MON810) is currently authorised for commercial cultivation, and some national authorities have banned cultivation. Spain is the only EU member state where Bt maize adoption levels are currently delivering farm income gains near full potential levels. In an integrated pest management (IPM) context, Bt maize can be regarded as a preventive (host plant resistance) or a responsive pest control measure. In any case, Bt maize is a highly specific tool that efficiently controls the main pests and allows combination with other preventive or responsive measures to solve other agricultural problems including those with secondary pests. Copyright © 2011 Society of Chemical Industry
The susceptibility of small fruits and cherries to the spotted‐wing drosophila, Drosophila suzukii
Authors: Lee Jana C , Bruck Denny J , Curry Hannah , Edwards David , Haviland David R , Van Steenwyk Robert A , Yorgey Brian M 
Published: June 2011

AbstractBACKGROUND: The spotted‐wing drosophila, Drosophila suzukii Matsumura, is native to Asia and was first detected in the North American mainland and Europe in 2008–2010. Drosophila suzukii is a serious economic pest to stone and small fruits because the female lays eggs within ripening fruit on a plant before harvest, which can lead to crop loss. The aim of this study was to evaluate the susceptibility of blackberries, blueberries, cherries, grapes, raspberries and strawberries to D. suzukii among various ripeness stages and cultivars.RESULTS: In 26 no‐choice and choice replicated laboratory cage tests on ripeness stages, fruits were generally susceptible to D. suzukii once fruits started to color. Few D. suzukii developed on green fruit, wine grapes or overripe blueberries. In seven cultivar tests, D. suzukii preferences ranged from no differences to fourfold differences for specific cultivars of blackberries, blueberries, raspberries and wine grapes. As brix levels increased, more eggs were laid or more D. suzukii developed on blackberries, blueberries, cherries, raspberries and strawberries. In a choice test of various fruit types, strawberries, raspberries, blackberries, cherries and blueberries were more susceptible to D. suzukii than green table grapes ('Thompson').CONCLUSION: The results suggest that fruits may become susceptible to D. suzukii as they start to turn color, and that specific varieties of grapes and overripe blueberries have low susceptibility to D. suzukii. Copyright © 2011 Society of Chemical Industry
Droplet size and efficacy of an adulticide–larvicide ultralow‐volume formulation on Aedes aegypti using different solvents and spray application methods
Authors: Harburguer Laura , Seccacini Emilia , Licastro Susana , Zerba Eduardo , Masuh Héctor 
Published: June 2011

AbstractBACKGROUND: When cases of dengue are reported or the density of adult Aedes aegypti (L.) becomes too high, ultralow‐volume (ULV) application of insecticides is the recommended control method. The droplet size of an aerosol insecticide influences its efficiency in killing adult mosquitoes. Many studies have been carried out to determine the optimum droplet size that maximises vector control efforts, but only a few have determined droplet‐size spectra for specific equipment using different solvents and comparing thermal and non‐thermal aerosols.RESULTS: The present study showed that the droplet size for a water‐based adulticide–larvicide formulation was larger than for the same formulation diluted in gasoil or biodiesel. No significant differences in adult mortality were observed between sprayers and solvents, but efficacy decreased with distance from the sprayer nozzle. Adult emergence inhibition was more than 90% when using water as a solvent for both thermal and cold foggers, and the efficacy did not decrease with distance from the sprayer nozzle. On the other hand, oil‐based solvents became less effective with distance.CONCLUSION: The use of water as a solvent with both thermal and cold foggers improves the efficacy of the studied formulation containing permethrin as adulticide and pyriproxyfen as larvicide in scaled‐up assays. Moreover, it reduces the environmental impact and costs of spraying by comparison with formulations using oil solvents. Copyright © 2011 Society of Chemical Industry
Magneto‐elasticity in amorphous ferromagnets: Basic principles and applications
Authors: Barandiarán J. M. , Gutiérrez J. , García‐Arribas A. 
Published: June 2011

AbstractFerromagnetic metallic glasses (FMG) show a very special combination of magnetic, elastic, and magnetostrictive properties that have rocketed their most extended technological applications, mainly in the field of sensors and surveillance labels. The amorphous structure results in the cancellation of the magnetic anisotropy as a result of the averaging out of the atomic scale local anisotropy in a region of the order of the exchange correlation length. Magnetostriction, however, does not cancel out, and values similar to the corresponding crystalline alloys are displayed by the amorphous ones. The absolute values of magnetostriction are not very high, but the extremely magnetic softness of the alloys does balance the competition between stress and magnetic field. In particular, the magnetoelastic coupling coefficient can reach values as high as 0.98, the highest in any known material. Magnetoelasticity, defined as the magnetization change caused by stress, reaches outstanding values in FMGs and a number of applications do use such properties for sensing applications. We can briefly review some of them, either based on static or magnetoelastic wave resonance operation. The most widely extended application is their use as magnetoelastic resonant elements in electronic surveillance labels. New applications of FMGs are under development. Hybrid magnetoelectric (magnetostrictive/piezoelectric) materials have been devised, using highly magnetostrictive amorphous alloys working at resonance. Possible applications of such new materials are briefly discussed.
Structural and enthalpy relaxation processes in pure ethanol
Authors: Kabtoul B. , Ramos M. A. 
Published: June 2011

AbstractIn this work, we present new calorimetric and thermodynamic measurements conducted on pure ethanol for its two kinds of glass transition, namely the conventional or structural glass transition and also the dynamical freezing of the plastic crystal (PC) state into an orientationally‐disordered crystal (or glassy crystal), that are found to occur exactly at the same temperature (Tg ≈ 97 K) and with comparable discontinuities in the specific heat. We have studied the dependence of the corresponding fictive temperatures on the different cooling rates and/or thermal annealing processes followed. The apparent activation energy and the concomitant fragility index were thus calculated for each glassy phase of ethanol, finding that the PC is a stronger “glass former” than the supercooled liquid.
Lithium niobosilicate glass doped with samarium: Dielectric and optical analysis
Authors: Nico C. , Graça M. P. F. , Monteiro T. , Valente M. A. 
Published: June 2011

AbstractLithium niobate (LiNbO3 – LN) is a large bandgap [3.78 eV at room temperature (RT)] semiconductor mainly known by its ferroelectric behaviour and excellent non‐linear optical, electro‐optical and piezoelectric properties. In this study 91SiO2–4Li2O–4Nb2O5–1Sm2O3 (mol%) glasses were prepared by sol–gel. Glass–ceramics were obtained through heat‐treatments (HTs) of the dried gel. The samples structure was studied by X‐ray diffraction (XRD) and scanning electron microscopy (SEM). The HT above 600 °C promotes the crystallization of LiNbO3 and SmNbO4. For heat HT above 800 °C, SiO2 crystallites also precipitate. SEM micrographs indicate that the size of the particles and aggregation phenomena is promoted with the increase of the HT temperature. The electric characterization was performed as a function of the temperature and frequency. The main contribution for the electric conductivity behaviour is the number of network modifier ions, which decreases with the increase of the HT temperature. The dielectric constant and loss value decrease with the increase of the HT temperature. Dielectric relaxation mechanisms were observed in the samples HT below 800 °C. At RT, the photoluminescence (PL) spectra, revealed a red light emission, due to the 4G5/2 → 6HJ = 5/2,7/2,9/2 transitions of Sm3+ ion. The results suggest that the intraionic emission is promoted when the lanthanide ions are inserted in the amorphous matrix. Auto‐absorptions of the samarium ion and large emission bands were detected and assigned to the crystalline and amorphous phases of SiO2. The obtained results reflect the decisive effect of HT temperature in the structural, electric and optical properties of these glasses.
Enhanced coercivity of as‐prepared and chemically modified multiwalled carbon nanotubes
Authors: Kuryliszyn‐Kudelska I. , Małolepszy A. , Mazurkiewicz M. , Stobinski L. , Kurzydłowski K. J. , Dobrowolski W. 
Published: June 2011

AbstractThe systematic magnetic and structural properties of as‐prepared, “Fe” catalyst based multiwalled carbon nanotubes (MWCNTs), and chemically modified MWCNTs were studied. The structural characterization by means of transmission electron microscopy, X‐ray diffraction, and Raman spectroscopy was performed. DC magnetization up to 9 T was studied. We examined the influence of chemical treatment (purification procedure) on the magnetic properties of MWCNT's. The significant changes in the saturation magnetization after chemical treatment were observed. However, we noticed high magnetic coercivity values for as‐prepared as well as chemically modified samples.
Role of energy level alignment in solar cells sensitized with a metal‐free organic dye: A combined experimental and theoretical approach
Authors: Oprea Corneliu I. , Dumbravă Anca , Enache Irina , Lungu Jeanina , Georgescu Adrian , Moscalu Florin , Oprea Camelia , Gîrţu Mihai A. 
Published: June 2011

AbstractWe report results of combined experimental and theoretical studies of dye‐sensitized solar cells (DSSCs) using 5‐(4‐sulfophenylazo)salicylic acid disodium salt, known as Mordant Yellow 10 (MY‐10), as TiO2 sensitizer. We focus on a single dye but vary the solvent and the pH of the solution as well as the photoelectrode preparation conditions to determine the conditions for best photovoltaic conversion efficiency. We found experimentally that the efficiency, measured under standard air mass 1.5 global (AM 1.5G) conditions, was higher in solutions of ethanol than of water, but still small (up to 0.174%), although the fill factor (FF) was large (up to 0.73). Of the dyes in ethanol, MY‐10 in alkaline solution showed the best matching of the solar spectrum but displayed the lowest efficiency. Density functional theory (DFT) calculations provided the optimized geometry, electronic structure, and electronic spectrum of the dye in fully protonated as well as partially and totally deprotonated forms, in solution. The calculated optical spectra are consistent with the experimental data, with strong absorption in the visible range only for the alkaline dye solution. The low device efficiency is very likely related to the weak optical absorption in the visible range. The much higher photovoltaic conversion efficiency of the DSSCs fabricated using acid or roughly neutral pH solutions, corresponding to the protonated and partially deprotonated forms of MY‐10, respectively, is likely caused by the better alignment of the ground state of the dye with the redox level of the electrolyte. The decrease with pH of the dye solution of the short‐circuit current was linked to a weaker charge injection from the excited state of the dye to the conduction band of the oxide, which is correlated with the shifting of the excited state of the dye deeper into the CB edge of the semiconductor. The variation of the open‐circuit voltage with the pH of the solution was linked to the adjustment of the conduction band edge of TiO2, depending on the number of protons transferred from the dye to the oxide surface. Based on our results, we analyze the relative importance of the main criteria that should be met by a dye to be used in a DSSC.
Effect of annealing temperature on the magnetic properties of Zn0.97Al0.03O nanoparticles
Authors: Gao Hua , Gao Daqiang , Yang Guijin , Zhang Jing , Zhang Jinlin , Shi Zhenhua , Xue Desheng 
Published: June 2011

AbstractAl doped ZnO nanoparticles were synthesized by the sol‐gel technique. X‐ray diffraction, selected area electron diffraction, inductively coupled plasma‐atomic emission and X‐ray photoelectron spectroscopy results ruled out impurity and other phases in Zn0.97Al0.03O nanoparticles annealing at different temperatures. Magnetic measurements indicate that all the samples have the obvious room temperature ferromagnetism. With the increase of annealing temperatures from 500 to 900 °C, the saturation magnetization of nanoparticles decreases with the reduction of defect‐related emission. Together with the electron paramagnetic resonance results, the observed ferromagnetic ordering of Zn0.97Al0.03O nanoparticles annealing at different temperatures is consider to be related to the singly charged oxygen vacancies.
Polymer light‐emitting diodes with doped hole‐transport layers
Authors: Lu Mingtao , Nicolai Herman T. , Kuik Martijn , Wetzelaer Gert‐Jan A. H. , Wildeman Jurjen , Palmaerts Arne , Blom Paul W. M. 
Published: June 2011

AbstractWe demonstrate a solution processed bi‐layer PLED based on poly(p‐phenylene vinylene) derivatives using orthogonal solvents. To lower the voltage drop the hole transport layer (HTL) based on poly[2,5‐bis(2′‐ethylhexyloxy)‐co‐2,5‐bis(butoxy)‐1,4‐phenylenevinylene] (BEH/BB‐PPV (1:3)) is doped with tetracyano‐tetrafluoro‐quinodimethane (F4TCNQ). The conductivity of BEH/BB‐PPV (1:3) was observed to increase by two orders of magnitude upon doping with F4TCNQ. The doped HTL was observed to lower the operating voltage of a double layer PLED, but suffers from additional quenching by the dopant at higher voltages due to the lack of an electron blocking functionality.
Catalytic growth of hexagonally aligned ZnO nanorods
Authors: Madel Manfred , Xie Yong , Tischer Ingo , Neuschl Benjamin , Feneberg Martin , Frey Reinhard , Thonke Klaus 
Published: June 2011

AbstractAligned ZnO nanorods were prepared using colloid‐based self‐assembling techniques to structure the gold catalyst. Two different processes were used and are compared. The ZnO nanorods were grown with diameters between 200 and 500 nm and adjustable length by a chemical vapor deposition process in a horizontal tube furnace. They show high crystalline quality as confirmed by photoluminescence and spatially and spectrally resolved cathodoluminescence measurements. Hexagonal ordering of the nanorods has been achieved for areas of several square millimeters.