bluuebunny/crossref_metadata_2025_split huggingface dataset:
Re‐engineering specificity in 1,3‐1, 4‐β‐glucanase to accept branched xyloglucan substrates
Authors: Addington Trevor , Calisto Barbara , Alfonso‐Prieto Mercedes , Rovira Carme , Fita Ignasi , Planas Antoni 
Published: September 2010

AbstractFamily 16 carbohydrate active enzyme members Bacillus licheniformis 1,3‐1,4‐β‐glucanase and Populus tremula x tremuloides xyloglucan endotransglycosylase (XET16‐34) are highly structurally related but display different substrate specificities. Although the first binds linear gluco‐oligosaccharides, the second binds branched xylogluco‐oligosaccharides. Prior engineered nucleophile mutants of both enzymes are glycosynthases that catalyze the condensation between a glycosyl fluoride donor and a glycoside acceptor. With the aim of expanding the glycosynthase technology to produce designer oligosaccharides consisting of hybrids between branched xylogluco‐ and linear gluco‐oligosaccharides, enzyme engineering on the negative subsites of 1,3‐1,4‐β‐glucanase to accept branched substrates has been undertaken. Removal of the 1,3‐1,4‐β‐glucanase major loop and replacement with that of XET16‐34 to open the binding cleft resulted in a folded protein, which still maintained some β‐glucan hydrolase activity, but the corresponding nucleophile mutant did not display glycosynthase activity with either linear or branched glycosyl donors. Next, point mutations of the 1,3‐1,4‐β‐glucanase β‐sheets forming the binding site cleft were mutated to resemble XET16‐34 residues. The final chimeric protein acquired binding affinity for xyloglucan and did not bind β‐glucan. Therefore, binding specificity has been re‐engineered, but affinity was low and the nucleophile mutant of the chimeric enzyme did not show glycosynthase activity to produce the target hybrid oligosaccharides. Structural analysis by X‐ray crystallography explains these results in terms of changes in the protein structure and highlights further engineering approaches toward introducing the desired activity. Proteins 2011. © 2010 Wiley‐Liss, Inc.
Consumer complaints and accidents related to food packaging
Authors: Caner Cengiz , Pascall Melvin A. 
Published: September 2010

AbstractThis study investigated consumer complaints related to food packaging design and the occurrence of injuries associated with the opening of various types of containers. Each study participant (245) took a 15 min fact‐to‐face interview and was asked attitudinal questions about 10 different categories of packaging including cans, glass and plastic bottles and jars, and paper‐based composite packages. The subjects were also asked whether they had been injured while opening these packaging types. The survey showed that cans which needed a tool for opening were most difficult to enter. In some cases the tool was the source of injury. The respondents were also most concerned about deformation, spillage and product wastage associated with these types of containers. This included brick‐type composite packages without a peelable seal over the pour spout. A large percentage of the respondents felt that more information was needed on the various methods of opening packages in general. Glass bottles and jars were most likely to be used for storage of products after they were emptied of their original contents. The results of this study could be used by manufacturers to assist them in the design and development of packaging with a lower potential to cause accidents and injuries. Copyright © 2010 John Wiley & Sons, Ltd.
Optical properties of amorphous and crystalline silicon surfaces functionalized with Agn adsorbates
Authors: Lajoie Travis W. , Ramirez Jessica J. , Kilin Dmitri S. , Micha David A. 
Published: September 2010

AbstractLight absorption by nanostructured surfaces of silicon, relevant to the capture of solar radiation, has been modeled starting from their atomic structure and calculating electronically excited states. Thin, two‐layer silicon slabs were cut from a model optimized amorphous supercell and studied to elucidate the effect of adsorbate geometry and size for small silver clusters chemisorbed onto the hydrogen‐passivated semiconductor surface. Density functional (DFT) and time‐dependent DFT (TD‐DFT) methods were performed to calculate optical properties of the amorphous Agn/a‐Si surface. Optimized geometries, density of states, band gap and binding energies, and excited‐stated spectra and oscillator strengths have been calculated within the DFT and TD‐DFT approaches. The results demonstrate the correlation between these properties and the size of the systems, and are compared with those we previously obtained for the corresponding crystalline Agn/Si(111) surfaces. Similar trends are observed for the amorphous and crystalline silicon slabs as the number of silver atoms included in the clusters were increased. Our results demonstrate that Agn clusters adsorbed on amorphous slabs are significant contributors to increased light absorption of lower energy photons. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2010
Characterisation of alkylamine ethoxylates (ANEOs) in commercial herbicide formulations using liquid chromatography/electrospray ionisation mass spectrometry
Authors: Corbera M. , Simonet B. M. , Salvadó V. , Hidalgo M. 
Published: September 2010

AbstractA quantitative method is described for the characterization of alkylamine ethoxylate (ANEO) surfactants in commercial herbicide formulations using reversed‐phase high‐performance liquid chromatography with electrospray ionization mass spectrometric detection. The proposed protocol allows the simultaneous determination of a full range of oligomers which were monitored as [M–H]+ ions in positive ion mode. The instrumental detection limits (LODs) were 0.5 µg. The method developed was successfully applied to the determination of ANEOs in a number of glyphosate formulations. Both the total concentration of these surfactants and the oligomer distribution varied between the different commercial herbicides analysed. The precision of the determination of the oligomers in samples ranged from 0.5 to 15%. Copyright © 2010 John Wiley & Sons, Ltd.
Cracking study of pentakis(dimethylamino)tantalum vapors by Knudsen cell mass spectrometry
Authors: Violet Perrine , Nuta Ioana , Chatillon Christian , Blanquet Elisabeth 
Published: September 2010

AbstractOrganometallic molecules are commonly used as gaseous precursors in Atomic Layer Deposition/Chemical Vapor Deposition (ALD/CVD) processes. However, the use of these molecules, which are generally thermally unstable at temperatures close to the deposition temperature, requires an understanding of their gas‐phase chemical behavior. The thermal cracking of the gaseous precursor, pentakis(dimethylamino) tantalum (PDMAT), generally adopted in the ALD/CVD TaN deposition processes, has been studied in the temperature range from 343 to 723K using a specific reactor coupled with a high‐temperature mass spectrometer. This reactor – built as tandem Knudsen cells – consists of two superimposed cells. The first stage reactor – an evaporation cell – provides an input saturated vapor flow operating from room temperature to 333K. The second stage cell, named the cracking cell, operated from 333 to 723K in the present study. Experiments showed the appearance of many gaseous species when the cracking temperature increased and, in particular, dimethylamine, corresponding to the saturated organic branches of PDMAT. Decomposition products of the HNC2H6 branch were observed at relatively high temperature, namely above 633K. This gas‐phase study – as for the preceding saturated one – shows the presence of oxygen‐containing molecules in PDMAT cracked vapor. Thus, it explains the systematic presence of oxygen contamination in the deposited TaN films observed in ALD/CVD industrial processes. Copyright © 2010 John Wiley & Sons, Ltd.
Effect of acidification on elemental and isotopic compositions of sediment organic matter and macro‐invertebrate muscle tissues in food web research
Authors: Mazumder Debashish , Iles Jordan , Kelleway Jeff , Kobayashi Tsuyoshi , Knowles Lisa , Saintilan Neil , Hollins Suzanne 
Published: September 2010

AbstractStable isotope techniques in food web studies often focus on organic carbon in food sources which are subsequently assimilated in the tissue of consumer organisms through diet. The presence of non‐dietary carbonates in bulk samples can affect their δ13C values, altering how their results are interpreted. Acidification of samples is a common practice to eliminate any inorganic carbon present prior to analysis. We examined the effects of pre‐analysis acidification on two size fractions of sediment organic matter (SOM) from marine and freshwater wetlands and pure muscle tissue of a common freshwater invertebrate (Cherax destructor). The elemental content and isotopic ratios of carbon and nitrogen were compared between paired samples of acidified and control treatments. Our results showed that acidification does not affect the elemental or isotopic values of freshwater SOM. In the marine environment acidification depleted the δ13C and δ15N values of the fine fraction of saltmarsh and δ15N values of mangrove fine SOM. Whilst acidification did not change the elemental content of invertebrate muscle tissue, the δ13C and δ15N values were affected. We recommend to researchers considering using acidification techniques on material prepared for stable isotope analysis that a formal assessment of the effect of acidification on their particular sample type should be undertaken. Further detailed investigation to understand the impact of acidification on elemental and isotopic values of organic matter and muscular tissues is required. Copyright © 2010 John Wiley & Sons, Ltd.
Improved characterization of tomato polyphenols using liquid chromatography/electrospray ionization linear ion trap quadrupole Orbitrap mass spectrometry and liquid chromatography/electrospray ionization tandem mass spectrometry
Authors: Vallverdú‐Queralt Anna , Jáuregui Olga , Medina‐Remón Alexander , Andrés‐Lacueva Cristina , Lamuela‐Raventós Rosa M. 
Published: September 2010

AbstractTomato (Lycopersicon esculentum Mill.) is the second most important fruit crop worldwide. Tomatoes are a key component in the Mediterranean diet, which is strongly associated with a reduced risk of chronic degenerative diseases. In this work, we use a combination of mass spectrometry (MS) techniques with negative ion detection, liquid chromatography/electrospray ionization linear ion trap quadrupole‐Orbitrap‐mass spectrometry (LC/ESI‐LTQ‐Orbitrap‐MS) and liquid chromatography/electrospray ionization tandem mass spectrometry (LC/ESI‐MS/MS) on a triple quadrupole, for the identification of the constituents of tomato samples. First, we tested for the presence of polyphenolic compounds through generic MS/MS experiments such as neutral loss and precursor ion scans on the triple quadrupole system. Confirmation of the compounds previously identified was accomplished by injection into the high‐resolution system (LTQ‐Orbitrap) using accurate mass measurements in MS, MS2 and MS3 modes. In this way, 38 compounds were identified in tomato samples with very good mass accuracy (<2 mDa), three of them, as far as we know, not previously reported in tomato samples. Copyright © 2010 John Wiley & Sons, Ltd.
Measurements of nitrogen isotope composition of plants and surface soils along the altitudinal transect of the eastern slope of Mount Gongga in southwest China
Authors: Liu Xian‐zhao , Wang Guoan 
Published: September 2010

AbstractThe natural abundances of stable nitrogen isotopes in plants and soils have been viewed as recorders that can be used to reconstruct paleoclimate and ecological processes or to indicate the biogeochemical cycle of nitrogen in nature. This study systematically measured the nitrogen isotope composition (δ15N) in plants and surface soils along an altitudinal transect of elevation range of 1200 to 4500 m on the eastern slope of Mount Gongga in southwest China. The influences of photosynthetic pathways on plant δ15N as well as the effects of temperature and precipitation on δ15N altitudinal trends in plants and surface soils are discussed. Across this altitude transect, the δ15N values of C3 and C4 plants on Mount Gongga range between −9.87‰ and 7.58‰ with a mean value of −1.33‰, and between −3.98‰ and 4.38‰ with a mean value of −0.25‰, respectively. There is an evident δ15N difference between C3 plants and C4 plants. If, however, you only compare C4 plants with those C3 plants growing at the same altitudinal range, no significant difference in δ15N exists between them, suggesting that photosynthetic pathway does not have an influence on the plant δ15N values. In addition, we found that C3, C4 plants and surface soil (0–5 cm depth) all trend significantly towards more negative δ15N with increasing elevation. Furthermore, this study shows that the mean annual temperature and the mean annual precipitation positively and negatively correlate with δ15N in C3 and C4 plants, respectively. This indicates that precipitation and temperature are the main controlling factors of the δ15N variation in plants with altitude. We propose that lower δ15N values of plants and soils at higher altitude should be attributed to lower mineralization and lower net nitrification rates induced by low temperature and abundant rainfall. Copyright © 2010 John Wiley & Sons, Ltd.
Targeted serum metabolite profiling of nucleosides in esophageal adenocarcinoma
Authors: Djukovic Danijel , Baniasadi Hamid R. , Kc Ravi , Hammoud Zane , Raftery Daniel 
Published: September 2010

AbstractNucleosides are indicators of the whole‐body turnover of transfer RNA. Based on the activity of cancer cells these molecules could potentially be used as cancer biomarkers, and several studies have determined that the metabolic levels of nucleosides are significantly altered in cancer patients compared to control groups. Here we report a targeted metabolite investigation of serum nucleosides in esophageal adenocarcinoma specimens. We quantified eight nucleosides using high‐performance liquid chromatography/triple quadrupole mass spectrometry (HPLC/TQMS) and determined that the metabolic levels of 1‐methyladenosine (p <2.14 × 10−7), N2,N2‐dimethylguanosine (p <2.78 × 10−7), N2‐methylguanosine (p <2.48 × 10−6) and cytidine (p <6.98 × 10−4) were significantly elevated while the concentration of uridine (p <3.74 × 10−3) was significantly lowered in serum samples from cancer patients compared to those of control group. Our results suggest that nucleosides could potentially serve as useful biomarkers to identify esophageal adenocarcinoma. Copyright © 2010 John Wiley & Sons, Ltd.
An algorithm for the design of group sequential triangular tests for single‐arm clinical trials with a binary endpoint
Authors: McWilliams Thomas P. 
Published: September 2010

AbstractConsider the problem of testing H0:p⩽p0 vs H1:p>p0, where p could, for example, represent the response rate to a new drug. The group sequential TT is an efficient alternative to a single‐stage test as it can provide a substantial reduction in the expected number of test subjects. Whitehead provides formulas for determining stopping boundaries for this test. Existing research shows that test designs based on these formulas (WTTs) may not meet Type I error and/or power specifications, or may be over‐powered at the expense of requiring more test subjects than are necessary.We present a search algorithm, with program available from the author, which provides an alternative approach to triangular test design. The primary advantage of the algorithm is that it generates test designs that consistently meet error specifications. In tests on nearly 1000 example combinations of n (group size), p0, p1, α, and β the algorithm‐determined triangular test (ATT) design met specified Type I error and power constraints in every case considered, whereas WTT designs met constraints in only 10 cases. Actual Type I error and power values for the ATTs tend to be close to specified values, leading to test designs with favorable average sample number performance. For cases where the WTT designs did meet Type I error and power constraints, the corresponding ATT designs also had the advantage of providing, on average, a modest reduction in average sample numbers calculated at p0, p1, and (p0 + p1)/2. Copyright © 2010 John Wiley & Sons, Ltd.
A mixed‐effects model approach for estimating the distribution of usual intake of nutrients: The NCI method
Authors: Tooze Janet A. , Kipnis Victor , Buckman Dennis W. , Carroll Raymond J. , Freedman Laurence S. , Guenther Patricia M. , Krebs‐Smith Susan M. , Subar Amy F. , Dodd Kevin W. 
Published: September 2010

AbstractIt is of interest to estimate the distribution of usual nutrient intake for a population from repeat 24‐h dietary recall assessments. A mixed effects model and quantile estimation procedure, developed at the National Cancer Institute (NCI), may be used for this purpose. The model incorporates a Box–Cox parameter and covariates to estimate usual daily intake of nutrients; model parameters are estimated via quasi‐Newton optimization of a likelihood approximated by the adaptive Gaussian quadrature. The parameter estimates are used in a Monte Carlo approach to generate empirical quantiles; standard errors are estimated by bootstrap. The NCI method is illustrated and compared with current estimation methods, including the individual mean and the semi‐parametric method developed at the Iowa State University (ISU), using data from a random sample and computer simulations. Both the NCI and ISU methods for nutrients are superior to the distribution of individual means. For simple (no covariate) models, quantile estimates are similar between the NCI and ISU methods. The bootstrap approach used by the NCI method to estimate standard errors of quantiles appears preferable to Taylor linearization. One major advantage of the NCI method is its ability to provide estimates for subpopulations through the incorporation of covariates into the model. The NCI method may be used for estimating the distribution of usual nutrient intake for populations and subpopulations as part of a unified framework of estimation of usual intake of dietary constituents. Copyright © 2010 John Wiley & Sons, Ltd.
Empirical evidence about the UML: a systematic literature review
Authors: Budgen D. , Burn A. J. , Brereton O. P. , Kitchenham B. A. , Pretorius R. 
Published: September 2010

AbstractThe Unified Modeling Language (UML) was created on the basis of expert opinion and has now become accepted as the ‘standard’ object‐oriented modelling notation. Our objectives were to determine how widely the notations of the UML, and their usefulness, have been studied empirically, and to identify which aspects of it have been studied in most detail. We undertook a mapping study of the literature to identify relevant empirical studies and to classify them in terms of the aspects of the UML that they studied. We then conducted a systematic literature review, covering empirical studies published up to the end of 2008, based on the main categories identified. We identified 49 relevant publications, and report the aggregated results for those categories for which we had enough papers—metrics,comprehension,model quality,methods and toolsandadoption. Despite indications that a number of problems exist with UML models, researchers tend to use the UML as a ‘given’ and seem reluctant to ask questions that might help to make it more effective. Copyright © 2010 John Wiley & Sons, Ltd.
COIVA: context‐aware and ontology‐powered information visualization architecture
Authors: Hervás Ramón , Bravo José 
Published: September 2010

AbstractThis paper exploits semantics to apply context in run‐time adaptation, particularly for services in a user‐centered smart environment. Context‐sensitive services are usually focused on their own information without interoperation pretensions. It is necessary to enable common context models and systems in order to make context‐aware applications interoperable. Moreover, context management systems need to implement mechanisms to support the dynamic behavior of the users and their surroundings, including techniques to adapt the model to their future needs, to maintain the context information at run‐time and to be interoperable with external context models. By adapting web semantic technologies we can enable smarter and more proactive operation of context management systems. Copyright © 2010 John Wiley & Sons, Ltd.
Benzo(a)pyrene induces p73 mRNA expression and necrosis in human lung adenocarcinoma H1299 cells
Authors: Jiang Ying , Rao Kaimin , Yang Guangtao , Chen Xi , Wang Qian , Liu Ailin , Zheng Hongyan , Yuan Jing 
Published: September 2010

Abstractp53 can mediate DNA damage‐induced apoptosis in various cell lines treated with Benzo(a)pyrene (BaP). However, the potential role of p73, one of the p53 family members, in BaP‐induced apoptotic cell death remains to be determined. In this study, normal fetal lung fibroblasts (MRC‐5) and human lung adenocarcinoma cells (H1299, p53‐null) were treated with BaP at concentrations of 8, 16, 32, 64, and 128 μM for 4 and 12 h. The oxidative stress status, extent of DNA damage, expression of p53, p73, mdm2, bcl‐2, and bax at the mRNA and protein levels, and the percentages of apoptosis and/or necrosis were assessed. In the two BaP‐treated cell lines, we observed increased malondialdehyde (MDA) formation and decreased superoxide dismutase (SOD) and glutathione peroxidase (GSH‐Px) activity at 4 h after the treatment; furthermore, at the time points of 4 and 12 h, we observed extremely high levels of DNA damage. In addition, at 4 h after the treatment, BaP had induced necrosis in MRC‐5 and H1299 cells, but it had inhibited apoptosis in MRC‐5 cells (P < 0.01 for all). Furthermore, in BaP‐treated H1299 cells, only the p73 mRNA level was up‐regulated. The results suggested that BaP‐induced DNA damage could trigger a shift from apoptotic cell death toward necrotic cell death and that necrotic cell death is independent of p53 and p73 in these cell lines. Future studies are needed to investigate the time course of changes in the type of BaP‐induced cell death in more cell lines. © 2010 Wiley Periodicals, Inc. Environ Toxicol, 2012.
Pulmonary toxicity assessment of multiwalled carbon nanotubes in rats following intratracheal instillation
Authors: Reddy A. Rama Narsimha , Reddy Y. Narsimha , Krishna Devarakonda R. , Himabindu V. 
Published: September 2010

AbstractIn this study, we have evaluated the pulmonary toxicity of intratracheally (i.t.) instilled two multi walled carbon nanotubes (MWCNT) in rats. The lungs of rats were instilled with phosphate buffered saline + 1% of Tween 80 or MWCNT or carbonyl iron or quartz particles at a dose of 0.2, 1, and 5 mg/kg b.w. Following exposure, bronchoalveolar lavage (BAL) fluid was collected from the lungs to analyze lactate dehydrogenase (LDH), alkaline phosphatase (ALP), lipid peroxidation products (MDA; malondialdehyde), and total microprotein (MTP) levels at 24 h, one week, one month, and three months post instillation periods. The lungs of particle exposed rats were also collected at the same intervals to evaluate for histopathology. Exposures of MWCNT and quartz particles to rats produced transient dose dependant increase in BAL fluid LDH, ALP, MDA, and MTP values than control at all post exposure periods. Results of lung histopathology revealed that exposure of MWCNT produced a dose dependant focal peribronchiolar lymphoid aggregates, foamy alveolar macrophage accumulation, lymphoplasmocytic infiltration, fibrosis and diffuse alveolar damage. In conclusion, instillation of MWCNT produced a greater pulmonary toxicity in rats and was comparable with that of quartz. © 2010 Wiley Periodicals, Inc. Environ Toxicol, 2012.