bluuebunny/crossref_metadata_2025 huggingface dataset:
Principal component and normal mode analysis of proteins; a quantitative comparison using the GroEL subunit
Authors: Skjaerven Lars , Martinez Aurora , Reuter Nathalie
Published: September 2010

Principal component analysis (PCA) and normal mode analysis (NMA) have emerged as two invaluable tools for studying conformational changes in proteins. To compare these approaches for studying protein dynamics, we have used a subunit of the GroEL chaperone, whose dynamics is well characterized. We first show that both PCA on trajectories from molecular dynamics (MD) simulations and NMA reveal a general dynamical behavior in agreement with what has previously been described for GroEL. We thus compare the reproducibility of PCA on independent MD runs and subsequently investigate the influence of the length of the MD simulations. We show that there is a relatively poor one‐to‐one correspondence between eigenvectors obtained from two independent runs and conclude that caution should be taken when analyzing principal components individually. We also observe that increasing the simulation length does not improve the agreement with the experimental structural difference. In fact, relatively short MD simulations are sufficient for this purpose. We observe a rapid convergence of the eigenvectors (after ca. 6 ns). Although there is not always a clear one‐to‐one correspondence, there is a qualitatively good agreement between the movements described by the first five modes obtained with the three different approaches; PCA, all‐atoms NMA, and coarse‐grained NMA. It is particularly interesting to relate this to the computational cost of the three methods. The results we obtain on the GroEL subunit contribute to the generalization of robust and reproducible strategies for the study of protein dynamics, using either NMA or PCA of trajectories from MD simulations. Proteins 2010. © 2010 Wiley‐Liss, Inc.
Mapping mouse IL‐13 binding regions using structure modeling, molecular docking, and high‐density peptide microarray analysis
Authors: Madala Satish K. , Dolan Michael A. , Sharma Deepak , Ramalingam Thirumalai R. , Wilson Mark S. , Mentink‐Kane Margaret M. , Masison Daniel C. , Wynn Thomas A.
Published: September 2010

Interleukin‐13 is a Th2‐associated cytokine responsible for many pathological responses in allergic asthma including mucus production, inflammation, and extracellular matrix remodeling. In addition, IL‐13 is required for immunity to many helminth infections. IL‐13 signals via the type‐II IL‐4 receptor, a heterodimeric receptor of IL‐13Rα1 and IL‐4Rα, which is also used by IL‐4. IL‐13 also binds to IL‐13Rα2, but with much higher affinity than the type‐II IL‐4 receptor. Binding of IL‐13 to IL‐13Rα2 has been shown to attenuate IL‐13 signaling through the type‐II IL‐4 receptor. However, molecular determinants that dictate the specificity and affinity of mouse IL‐13 for the different receptors are largely unknown. Here, we used high‐density overlapping peptide arrays, structural modeling, and molecular docking methods to map IL‐13 binding sequences on its receptors. Predicted binding sequences on mouse IL‐13Rα1 and IL‐13Rα2 were in agreement with the reported human IL‐13 receptor complex structures and site‐directed mutational analysis. Novel structural differences were identified between IL‐13 receptors, particularly at the IL‐13 binding interface. Notably, additional binding sites were observed for IL‐13 on IL‐13Rα2. In addition, the identification of peptide sequences that are unique to IL‐13Rα1 allowed us to generate a monoclonal antibody that selectively binds IL‐13Rα1. Thus, high‐density peptide arrays combined with molecular docking studies provide a novel, rapid, and reliable method to map cytokine‐receptor interactions that may be used to generate signaling and decoy receptor‐specific antagonists. Proteins 2010. © 2010 Wiley‐Liss, Inc.
Improved identification of outer membrane beta barrel proteins using primary sequence, predicted secondary structure, and evolutionary information
Authors: Mizianty Marcin J. , Kurgan Lukasz
Published: September 2010

Membrane proteins (MPs) are difficult to identify in genomes and to crystallize, making it hard to determine their tertiary structures. MPs could be categorized into α‐helical (AMP) and outer membrane proteins which mostly include beta barrel folds (OMBBs). The AMPs are relatively easy to predict from a protein sequence because they usually include several long membrane‐spanning hydrophobic α‐helices. The OMBBs play important roles in cell biology, they are targeted by multiple drugs, and they are more challenging to identify as they have shorter membrane‐spanning regions which lack a folding patern, that is, as consistent as in the case of the AMPs. Hence, accurate in silico methods for prediction of OMBBs from their primary sequences are needed. We present an accurate sequence‐based predictor of OMBBs, called OMBBpred, which utilizes a Support Vector Machine classifier and a custom‐designed set of 34 novel numerical descriptors derived from predicted secondary structures, hydrophobicity, and evolutionary information. Our method outperforms modern existing OMBB predictors and achieves accuracy of above 98% when tested on two existing benchmark datasets and 96% on a new large dataset. OMBBpred reduces the error rates of the second best method, depending on the dataset used, by between 13 and 65%, and generates predictions with high specificity of above 96%. Our solution is a useful tool for high‐throughput discovery of the OMBBs on a genome scale and can be found at http://biomine.ece. ualberta.ca/OMBBpred/OMBBpred.htm. Proteins 2010. © 2010 Wiley‐Liss, Inc.
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

Family 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

This 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

Light 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

A 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

Organometallic 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

Stable 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

Tomato (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

The 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

Nucleosides 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

Consider 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

It 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

The 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

This 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

p53 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

In 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.
Statistical methods in language processing
Authors: Abney Steven
Published: September 2010

The termstatistical methodshere refers to a methodology that has been dominant in computational linguistics since about 1990. It is characterized by the use of stochastic models, substantial data sets, machine learning, and rigorous experimental evaluation. The shift to statistical methods in computational linguistics parallels a movement in artificial intelligence more broadly. Statistical methods have so thoroughly permeated computational linguistics that almost all work in the field draws on them in some way. There has, however, been little penetration of the methods into general linguistics. The methods themselves are largely borrowed from machine learning and information theory. We limit attention to that which has direct applicability to language processing, though the methods are quite general and have many nonlinguistic applications.

Not every use of statistics in language processing falls understatistical methodsas we use the term. Standard hypothesis testing and experimental design, for example, are not covered in this article.WIREs Cogni Sci2011 2 315–322 DOI: 10.1002/wcs.111

This article is categorized under:

Linguistics > Computational Models of Language
Genetic, genomic, and molecular tools for studying the protoploid yeast, L. waltii
Authors: Di Rienzi Sara C. , Lindstrom Kimberly C. , Lancaster Ragina , Rolczynski Lisa , Raghuraman M. K. , Brewer Bonita J.
Published: September 2010

Sequencing of the yeast Kluyveromyces waltii (recently renamed Lachancea waltii) provided evidence of a whole genome duplication event in the lineage leading to the well‐studied Saccharomyces cerevisiae. While comparative genomic analyses of these yeasts have proven to be extremely instructive in modeling the loss or maintenance of gene duplicates, experimental tests of the ramifications following such genome alterations remain difficult. To transform L. waltii from an organism of the computational comparative genomic literature into an organism of the functional comparative genomic literature, we have developed genetic, molecular and genomic tools for working with L. waltii. In particular, we have characterized basic properties of L. waltii (growth, ploidy, molecular karyotype, mating type and the sexual cycle), developed transformation, cell cycle arrest and synchronization protocols, and have created centromeric and non‐centromeric vectors as well as a genome browser for L. waltii. We hope that these tools will be used by the community to follow up on the ideas generated by sequence data and lead to a greater understanding of eukaryotic biology and genome evolution. Copyright © 2010 John Wiley & Sons, Ltd.
Endoscopic Lumbar Sympathectomy Following Thoracic Sympathectomy in Patients with Palmoplantar Hyperhidrosis
Authors: Rieger Roman , de Paula Loureiro Marcelo , Pedevilla Sonja , de Oliveira Ramon Antunes
Published: September 2010

Background

Palmoplantar hyperhidrosis is a common disease that leads to significant psychosocial strain for the affected person. Although the treatment of palmar symptoms with endoscopic thoracic sympathectomy (ETS) is clinically established, there are few data on the efficacy of an endoscopic lumbar sympathectomy (ELS) for the elimination of plantar symptoms. Especially the occurrence of unwanted side effects associated with sequential ETS and ELS has not been examined sufficiently.

Methods

The study includes 130 patients, 8 men and 122 women, with severe palmoplantar hyperhidrosis who were already previously treated with ETS. An average of 28 months after the ETS, bilateral ELS was performed on all patients due to persistent severe plantar hyperhidrosis. After ELS the perioperative morbidity, elimination rate of the plantar hyperhidrosis, the frequency of unwanted side effects, and satisfaction with the result were evaluated. Follow‐up examinations were carried out on 96 patients (74%) with a mean follow‐up of 37 months (3–90 months).

Results

A total of 260 lumbar sympathectomies were successfully carried out endoscopically. Mortality was zero, intraoperative complications occurred in three (2.3%) patients and postoperative complications in six (4.6%). Plantar hyperhidrosis was eliminated in 93 patients (97%), 3 (3%) patients developed a one‐sided recurrence. Seven patients (7%) developed minor compensatory sweating, and in 17 patients (18%) compensatory sweating that existed before the ELS was slightly increased. Transient postsympathectomy neuralgia was observed in 18 patients (19%), and none of the patients showed a sexual function disorder. Altogether, 77 patients (80%) were very satisfied with the postoperative result, and 16 (17%) were partially satisfied.

Conclusions

The sesequential performance of ELS after ETS appears to be a safe, effective therapy option for patients with severe palmoplantar hyperhidrosis. However, more experience with a larger number of patients and longer follow‐up investigations are necessary to confirm the safety of four‐limb sympathectomy.
Role of Temperature in the Growth of Silver Nanoparticles Through a Synergetic Reduction Approach
Authors: Jiang XC , Chen WM , Chen CY , Xiong SX , Yu AB
Published: September 2010

This study presents the role of reaction temperature in the formation and growth of silver nanoparticles through a synergetic reduction approach using two or three reducing agents simultaneously. By this approach, the shape-/size-controlled silver nanoparticles (plates and spheres) can be generated under mild conditions. It was found that the reaction temperature could play a key role in particle growth and shape/size control, especially for silver nanoplates. These nanoplates could exhibit an intensive surface plasmon resonance in the wavelength range of 700–1,400 nm in the UV–vis spectrum depending upon their shapes and sizes, which make them useful for optical applications, such as optical probes, ionic sensing, and biochemical sensors. A detailed analysis conducted in this study clearly shows that the reaction temperature can greatly influence reaction rate, and hence the particle characteristics. The findings would be useful for optimization of experimental parameters for shape-controlled synthesis of other metallic nanoparticles (e.g., Au, Cu, Pt, and Pd) with desirable functional properties.
Developmental malformation of the corpus callosum: a review of typical callosal development and examples of developmental disorders with callosal involvement
Authors: Paul Lynn K.
Published: September 2010

This review provides an overview of the involvement of the corpus callosum (CC) in a variety of developmental disorders that are currently defined exclusively by genetics, developmental insult, and/or behavior. I begin with a general review of CC development, connectivity, and function, followed by discussion of the research methods typically utilized to study the callosum. The bulk of the review concentrates on specific developmental disorders, beginning with agenesis of the corpus callosum (AgCC)—the only condition diagnosed exclusively by callosal anatomy. This is followed by a review of several genetic disorders that commonly result in social impairments and/or psychopathology similar to AgCC (neurofibromatosis-1, Turner syndrome, 22q11.2 deletion syndrome, Williams yndrome, and fragile X) and two forms of prenatal injury (premature birth, fetal alcohol syndrome) known to impact callosal development. Finally, I examine callosal involvement in several common developmental disorders defined exclusively by behavioral patterns (developmental language delay, dyslexia, attention-deficit hyperactive disorder, autism spectrum disorders, and Tourette syndrome).
Characterization of Total and Individual Sterols in Canola Sprouts
Authors: Hamama Anwar A. , Bhardwaj Harbans L.
Published: September 2010

In this study, the contents of total and individual phytosterols in sprouts made from seeds of seven canola (Brassicanapus L.) lines (Acropolis, Banjo, Jetton, KS‐7740, KSM3‐1‐124, Mussette and Virginia), grown at three locations in Virginia (Orange, Petersburg and Suffolk), were determined. Canola sprouts contained, on an average, 36.3 g sterols in 100 g of unsaponifiable matter (UNSAP), 10.7 mg sterols in 1 g of oil and 2.4 mg sterols in 1 g of dry sprouts. The contents of individual phytosterols (μg per g of oil) in canola sprouts were 1,162 brassicasterol, 3,799 campesterol, 34 stigmasterol, 5,359 β‐sitosterol, 201 Δ5‐avenasterol and 97 Δ7‐stigmastenol. Canola lines had significant effects on the contents of oil, brassicasterol and campesterol. Locations had significant effects on the oil, UNSAP, total sterols, brassicasterol, stigmasterol and β‐sitosterol. The oil content in canola sprouts was positively correlated with total sterols and Δ5‐avenasterol, whereas oil content was negatively correlated with brassicasterol content. In general, the contents of campesterol and β‐sitosterol increased with an increase in total sterol content. The concentrations of sterols were in the following decreasing order: β‐sitosterol > campesterol > brassicasterol > Δ5‐avenasterol > Δ7‐stigmastenol > stigmasterol. These results indicate that canola sprouts may have the potential as a natural source of dietary sterols and might be desirable for human nutrition.
Imaging with non-FDG PET tracers: outlook for current clinical applications
Authors: Lopci Egesta , Nanni Cristina , Castellucci Paolo , Montini Gian Carlo , Allegri Vincenzo , Rubello Domenico , Chierichetti Franca , Ambrosini Valentina , Fanti Stefano
Published: September 2010

Apart from the historical and clinical relevance of positron emission tomography (PET) with 18F-fluorodeoxyglucose (18F-FDG), various other new tracers are gaining a remarkable place in functional imaging. Their contribution to clinical decision-making is irreplaceable in several disciplines. In this brief review we aimed to describe the main non-FDG PET tracers based on their clinical relevance and application for patient care.
The surfactant lipid transporter ABCA3 is N‐terminally cleaved inside LAMP3‐positive vesicles
Authors: Engelbrecht Stefanie , Kaltenborn Eva , Griese Matthias , Kern Sunčana
Published: September 2010

MINT‐7996380, MINT‐7996593, MINT‐7996607: LAMP3
(uniprotkb:Q9UQV4) and
ABCA3
(uniprotkb:Q99758)
colocalize
(MI:0403) by
fluorescence microscopy
(MI:0416)
Older but not wiser—Predicting a partner's preferences gets worse with age
Authors: Scheibehenne Benjamin , Mata Jutta , Todd Peter M.
Published: September 2010

To test the influence of relationship length on ability to predict a partner's preferences, 58 younger (M = 24.1 years) and 20 older (M = 68.7 years) couples made predictions in three domains that varied in daily importance. While prediction accuracy was generally better than chance, longer relationship length correlated with lower prediction accuracy and greater overconfidence. The difference in accuracy between older and younger couples increased for strong preferences and when controlling for preference reliability over time. Independent of relationship length, prediction accuracy was higher for important domains, for strong, reliable, and stereotypical preferences, and when couples were more similar.
Fluid and magmatic processes in the formation of the Ary-Bulak ongonite massif (eastern Transbaikalia)
Authors: Peretyazhko I.S. , Savina E.A.
Published: September 2010

The paper discusses the formation conditions of the Ary-Bulak ongonite massif (eastern Transbaikalia). Studies of melt and fluid inclusions have shown that, along with crystalline phases and a silicate melt, ongonitic magma contained aqueous–saline fluids of different types, fluoride melts compositionally similar to fluorite, sellaite, cryolite, chiolite, and more complex aluminum fluorides as well as silicate melts with abnormal Cs and As contents. An ongonite melt crystallized with the participation of P–Q fluids as vapor solutions, presumably NaF-containing and slightly admixed with chlorides. We studied the properties and composition of brine inclusions from Ca- and F-rich rocks on the margin of the massif. Depending on the thermophysical properties of the host rocks and ongonite melt, the duration of its crystallization has been estimated for a magma chamber of the size and shape of the Ary-Bulak massif. Magma chamber cooling has been modeled, and the density, viscosity, and Rayleigh number of the ongonite melt have been estimated from the composition of silicate glasses in melt inclusions. These data strongly suggest intense convection in the residual magma chamber lasting for centuries. We have calculated possible fluid overpressure during the crystallization and degassing of the ongonite melt in a closed magma chamber.

Calcium- and fluorine-rich aphyric and porphyritic rocks on the southwestern margin of the massif might have formed by the following mechanism. Local decompression in the magma chamber quenched an oxygen-containing calcium fluoride melt accumulated at the crystallization front, and then these rocks altered during the interaction with fluids. When penetrating the marginal zone, a P–Q magmatic fluid which coexisted with the melt in the residual chamber cooled and changed its composition and properties. This caused the fluid to boil and segregate into immiscible phases: a vapor solution and a brine extremely rich in Cl, F, K, Cs, Mn, Fe, and Al. The fluoride and silicate liquids were immiscible; the silicate melts had abnormal Cs and As contents; changes in the composition and properties of the magmatic fluids caused them to boil and produce brines. All this is evidence for complex fluid–magma interaction and heterogeneous ongonitic magma during the crystallization of the Ary-Bulak rocks. These processes were favored by the low viscosity and high mobility of the F- and water-rich ongonite melt, intense melt convection in the residual chamber, and rising fluid pressure during its degassing.
Fifty years of seismic anisotropy studies in Russia
Authors: Obolentseva I.R. , Chichinina T.I.
Published: September 2010

This is a historic overview of seismic anisotropy studies in Russia run as part of seismic exploration work in the 1940s through the 1980s, with a focus on main research lines. At the early stage in the 1940s through 1950s, most important contributions belonged to A.G. Tarkhov, Yu.V. Risnichenko, and S.M. Rytov (averaging the parameters of stratified media), I.I. Gurvich (processing reflection and refraction traveltime curves in media with elliptical anisotropy), and N.I. Berdennikova (shear-wave velocity anisotropy). In the 1960s–1980s, there were two basic schools of thought: one of G.I. Petrashen’, with a more theoretical approach, and the other of N.N. Puzyrev dealing more with experimental work. Most of experiments addressed a newly discovered phenomenon of azimuthal anisotropy. This anisotropy appearing as “anomalous” polarization of shear and converted waves was found out to result from vertical fractures in rocks. The unusual polarization became understood owing to Klem-Musatov’s model of a subsurface with a system of aligned cracks. The problem was fully resolved after field data had been processed with an algorithm by I.R. Obolentseva and S.B. Gorshkalev, for separating the total field of interfering shear waves of two types into fast and slow phases polarized in crack-parallel and crack-orthogonal directions, respectively.
Restoration of seismic data using the two-dimensional DMO equation
Authors: Pozdnyakov V.A. , Mezentsev E.V.
Published: September 2010

This paper presents a method for restoring missing seismic traces by using the two-dimensional dip moveout (DMO) equation. A fundamentally new formulation of the initial-boundary-value problem based on the Goursat problem is proposed. A modified finite element method is used for numerical solution. The method is tested on model examples and actual seismic data.
Economic Performance and Elite Defection from Hegemonic Parties
Authors: Reuter Ora John , Gandhi Jennifer
Published: September 2010

Hegemonic party regimes are non-democratic regimes that (1) rule with the aid of a dominant political party and (2) hold multi-party elections. Elite coalitions organized under the aegis of a hegemonic party are most vulnerable in elections that coincide with poor economic performance. A declining economy provides elites with a platform around which they can mobilize support to challenge incumbents in elections. As a result, the likelihood of defections from hegemonic parties increases as income declines. This study’s original dataset, which includes 227 elections for the chief executive in hegemonic party dictatorships from 1946 to 2004, and its case studies of defections in Zimbabwe under ZANU-PF in 2008 and Turkey under the Democratic Party in 1955 provide evidence for this proposition.
La genèse de la méthode cartésienne : la mathesis universalis et la rédaction de la quatrième des Règles pour la direction de l’esprit
Authors: de Oliveira Érico Andrade M.
Published: September 2010

RÉSUMÉ : À bien des égards, la Règle IV paraît être formée de deux textes distincts, ce que devrait justifier la différence entre la mathesis universalis et la méthode cartésienne. Cette interprétation conventionnelle est remise en cause en montrant que la révision qui s’opère au sein de la mathématique fait de celle-ci une méthode qui contraint les sciences à instituer l’ordre et la mesure dans leurs recherches. Ainsi, la discussion sur la mathesis universalis ne vise pas une science mathématique d’un niveau supérieur, mais a eu pour but la mise en œuvre d’une universalisation des méthodes menant à la découverte de la vérité.
Attention, Perception, and Thought in Aristotle
Authors: Corkum Phil
Published: September 2010

ABSTRACT: In the first part of the paper, I’ll rehearse an argument that perceiving that we see and hear isn’t a special case of perception in Aristotle but is rather a necessary condition for any perception whatsoever: the turning of one’s attention to the affection of the sense organs. In the second part of the paper, I’ll consider the thesis that the activity of the active intellect is analogous to perceiving that we see and hear.