bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hybrid domain decomposition algorithms for compressible and almost incompressible elasticity
Authors: Dohrmann Clark R. , Widlund Olof B. 
Published: October 2009

AbstractOverlapping Schwarz methods are considered for mixed finite element approximations of linear elasticity, with discontinuous pressure spaces, as well as for compressible elasticity approximated by standard conforming finite elements. The coarse components of the preconditioners are based on spaces, with a number of degrees of freedom per subdomain which are uniformly bounded, which are similar to those previously developed for scalar elliptic problems and domain decomposition methods of iterative substructuring type, i.e. methods based on nonoverlapping decompositions of the domain. The local components of the new preconditioners are based on solvers on a set of overlapping subdomains.In the current study, the dimension of the coarse spaces is smaller than in recently developed algorithms; in the compressible case all independent face degrees of freedom have been eliminated while in the almost incompressible case five out of six are not needed. In many cases, this will result in a reduction of the dimension of the coarse space by about one half compared with that of the algorithm previously considered. In addition, in spite of using overlapping subdomains to define the local components of the preconditioner, values of the residual and the approximate solution need only to be retained on the interface between the subdomains in the iteration of the new hybrid Schwarz algorithm. The use of discontinuous pressures makes it possible to work exclusively with symmetric, positive‐definite problems and the standard preconditioned conjugate gradient method.Bounds are established for the condition number of the preconditioned operators. The bound for the almost incompressible case grows in proportion to the square of the logarithm of the number of degrees of freedom of individual subdomains and the third power of the relative overlap between the overlapping subdomains, and it is independent of the Poisson ratio as well as jumps in the Lamé parameters across the interface between the subdomains. Numerical results illustrate the findings. Copyright © 2009 John Wiley & Sons, Ltd.
A case of treponematosis from pre‐Columbian Chaco Canyon, New Mexico
Authors: Marden K. , Ortner D. J. 
Published: October 2009

AbstractAlthough numerous cases of treponemal infection have been identified in prehispanic New World skeletal remains, none has been reported from Chaco Canyon, New Mexico. Chaco Canyon was the epicentre of a broad culture system that spanned the Four Corners region of the pre‐Columbian Southwestern United States. A burial recovered from the central Great House of Chaco Canyon, Pueblo Bonito, exhibits lesions indicative of treponematosis. However, the pathological condition of this individual has heretofore been only tentatively diagnosed because the skeleton was collected from a commingled context and distributed across four separate catalogue numbers. Now reassociated, these remains exhibit a pattern of pathological changes strongly indicative of treponemal disease. This case not only adds to the growing body of literature on the clinical expression and geographic distribution of pre‐Columbian treponematosis, but also demonstrates the utility of painstaking reassociation of commingled human remains. Copyright © 2009 John Wiley & Sons, Ltd.
Synthesis, characterization and thermal properties of novel epoxy/expandable graphite composites
Authors: Chiang Chin‐Lung , Hsu Shu‐Wei 
Published: October 2009

AbstractEpoxy resins are widely used as coatings, adhesives and primers and in semiconductor encapsulation. A requirement that has recently gained importance is that of flame resistance, and imparting flame retardancy to epoxy resins has attracted much attention. Expandable graphite (EG) can improve flame‐retardant properties of polymers. Due to poor compatibility between polymer matrix and EG, flame‐retardant performance will be impaired. EG can be functionalized using a coupling agent. This gives rise to covalent bonding between organic and inorganic phases. This will improve the compatibility between filler and polymer to enhance the thermal stability of composites. X‐ray photoelectron spectroscopy was used to characterize the functionalizing reaction between coupling agent and EG. Thermogravimetric analysis (TGA) and integral procedural decomposition temperature (IPDT) were used to calculate the thermal stability of composites. The results show that functionalized EG can improve the thermal stability of the composites. TGA/mass spectroscopy (MS) shows that the amount of toxic gases liberated from the composites is less than that from pure epoxy. Novel epoxy/EG composites were prepared successfully via the sol–gel method. The results of TGA, IPDT and TGA/MS showed that functionalized EG can enhance the thermal stability of composites and can suppress the production of toxic gases. The composite materials could provide a safer choice. Copyright © 2009 Society of Chemical Industry
Histone post‐translational modifications by HPLC‐ESI‐MS after HT29 cell treatment with histone deacetylase inhibitors
Authors: Naldi Marina , Calonghi Natalia , Masotti Lanfranco , Parolin Carola , Valente Sergio , Mai Antonello , Andrisano Vincenza 
Published: October 2009

AbstractThe goal of the present work is to establish a correlation between the degree of histone post‐translational modifications and the effects caused by treatment of HT29 colon cancer cells with class I‐selective (MS‐275 and MC1855), class II‐selective (MC1568), and non‐selective (suberoylanilide hydroxamic acid (SAHA) histone deacetylase inhibitors (HDACi). This correlation could afford a mean to better understand the mechanism of action of new, more potent, and selective HDACi directly on the cells. To this end, LC coupled to MS was applied in studies of time and concentration‐dependent treatment with HDACi in HT29 cells. The results were correlated to their potency of histone deacetylase inhibition and to their effects on the cell cycle. The results indicate that the four tested inhibitors show a different pattern of time‐ and concentration‐dependent modification after treatment of HT29 cells. At the selected concentrations, they cause different histone hyperacetylation and different cell cycle effects. In particular, SAHA (non‐selective HDACi) affected hyperacetylation of all histones and caused massive cell death. MC1855 (class I‐selective HDACi, hydroxamate) proved to be more potent and less toxic (cell arrest in G2/M phase) than SAHA. MS‐275 (class I‐selective HDACi, benzamide) exhibited a higher degree of hyperacetylation of H4 and a lower degree of H2A, H2B, and H3 acetylation, causing a cell arrest in G0/G1 phase. On the contrary, MC1568 (class II‐selective HDACi) produced only a modest hyperacetylation of H4, was ineffective on the other histones, and showed no effect on cell cycle in HT29 cells.
PeptideDepot: Flexible relational database for visual analysis of quantitative proteomic data and integration of existing protein information
Authors: Yu Kebing , Salomon Arthur R. 
Published: October 2009

AbstractRecently, dramatic progress has been achieved in expanding the sensitivity, resolution, mass accuracy, and scan rate of mass spectrometers able to fragment and identify peptides through MS/MS. Unfortunately, this enhanced ability to acquire proteomic data has not been accompanied by a concomitant increase in the availability of flexible tools allowing users to rapidly assimilate, explore, and analyze this data and adapt to various experimental workflows with minimal user intervention. Here we fill this critical gap by providing a flexible relational database called PeptideDepot for organization of expansive proteomic data sets, collation of proteomic data with available protein information resources, and visual comparison of multiple quantitative proteomic experiments. Our software design, built upon the synergistic combination of a MySQL database for safe warehousing of proteomic data with a FileMaker‐driven graphical user interface for flexible adaptation to diverse workflows, enables proteomic end‐users to directly tailor the presentation of proteomic data to the unique analysis requirements of the individual proteomics lab. PeptideDepot may be deployed as an independent software tool or integrated directly with our high throughput autonomous proteomic pipeline used in the automated acquisition and post‐acquisition analysis of proteomic data.
A highly sensitive near‐infrared fluorescent detection method to analyze signalling pathways by reverse‐phase protein array
Authors: Dupuy Laurence , Gauthier Christophe , Durand Guillaume , Musnier Astrid , Heitzler Domitille , Herledan Adrien , Sakanyan Vehary , Crépieux Pascale , Reiter Eric 
Published: October 2009

AbstractThe comprehensive and quantitative analysis of the protein phosphorylation patterns in different cellular context is of considerable and general interest. The ability to quantify phosphorylation of discrete signalling proteins in large collections of biological samples would greatly favour the development of systems biology in the field of cell signalling. Reverse‐phase protein array (RPPA) potentially represents a very attractive approach to map signal transduction networks with high throughput. In the present report, we describe an improved detection method for RPPA combining near‐infrared with one or two rounds of tyramide‐based signal amplification. The LOQ was lowered from 6.84 attomoles with a direct detection protocol to 0.21 attomole with two amplification steps. We validated this method in the context of intracellular signal transduction triggered by follicle‐stimulating hormone in HEK293 cells. We consistently detected phosphorylated proteins in the sub‐attomole range from less than 1 ng of total cell extracts. Importantly, the method correlated with Western blot analysis of the same samples while displaying excellent intra‐ and inter‐slide reproducibility. We conclude that RPPA combined with amplified near‐infrared detection can be used to capture the subtle regulations intrinsic to signalling network dynamics at an unprecedented throughput, from minute amounts of biological samples.
Interactive learning: Lessons from two hybrids over two decades
Authors: Fields Stanley 
Published: October 2009

AbstractThe initial yeast two‐hybrid experiment – published in 1989 – described an approach to detecting protein–protein interactions that has flourished over the last two decades, leading to the assembly of large‐scale data sets of these interactions. Yet the yeast assay originated because of the laboratory's interests in technology development, not because of its need to identify partners of any protein then under study. In addition to such motivating forces, other features of the process of originating a technology can be revealed by considering the lessons of the two‐hybrid approach. These include the value of timeliness in a method's development, the willingness of an investigator to try experimental approaches that prove fruitless, the ability of biological macromolecules to display surprising attributes, the benefits of a community expending efforts to expand the uses of a technology platform, and the role of scientific training of those who work in technology.
The structural analysis of protein–protein interactions by NMR spectroscopy
Authors: O'Connell Mitchell R. , Gamsjaeger Roland , Mackay Joel P. 
Published: October 2009

AbstractA comprehensive understanding of protein–protein interactions is an important next step in our quest to understand how the information contained in a genome is put into action. Although a number of experimental techniques can report on the existence of a protein– protein interaction, very few can provide detailed structural information. NMR spectroscopy is one of these, and in recent years several complementary NMR approaches, including residual dipolar couplings and the use of paramagnetic effects, have been developed that can provide insight into the structure of protein–protein complexes. In this article, we review these approaches and comment on their strengths and weaknesses.
Protein composition of Trypanosoma brucei mitochondrial membranes
Authors: Acestor Nathalie , Panigrahi Aswini K. , Ogata Yuko , Anupama Atashi , Stuart Kenneth D. 
Published: October 2009

AbstractMitochondria consist of four compartments, outer membrane, intermembrane space, inner membrane, and matrix; each harboring specific functions and structures. In this study, we used LC‐MS/MS to characterize the protein composition of Trypanosoma brucei mitochondrial (mt) membranes, which were enriched by different biochemical fractionation techniques. The analyses identified 202 proteins that contain one or more transmembrane domain(s) and/or positive GRAVY scores. Of these, various criteria were used to assign 72 proteins to mt membranes with high confidence, and 106 with moderate‐to‐low confidence. The sub‐cellular localization of a selected subset of 13 membrane assigned proteins was confirmed by tagging and immunofluorescence analysis. While most proteins assigned to mt membrane have putative roles in metabolic, energy generating, and transport processes, ∼50% have no known function. These studies result in a comprehensive profile of the composition and sub‐organellar location of proteins in the T. brucei mitochondrion thus, providing useful information on mt functions.
Isatin‐binding proteins of rat and mouse brain: Proteomic identification and optical biosensor validation
Authors: Buneeva Olga , Gnedenko Oksana , Zgoda Victor , Kopylov Arthur , Glover Vivette , Ivanov Alexis , Medvedev Alexei , Archakov Alexander 
Published: October 2009

AbstractIsatin (indole‐2,3‐dione) is an endogenous indole that has a distinct and discontinuous distribution in the brain and in other mammalian tissues and body fluids. Its output is increased under conditions of stress and anxiety. Isatin itself and its analogues exhibit a wide range of pharmacological activities but its specific biological targets still are not well characterized. Affinity chromatography of Triton X‐100 lysates of soluble and particulate fractions of mouse and rat whole brain homogenates on 5‐aminocaproyl‐isatin‐Sepharose followed by subsequent proteomic analysis resulted in identification of 65 and 64 individual proteins, respectively. Isatin‐binding capacity of some of the identified proteins has been validated in an optical biosensor study using a Biacore 3000 optical biosensor, 5‐aminocarproyl‐isatin, and 5‐aminoisatin as the affinity ligands. The Kd values (of 0.1–20 μM) obtained during the optical biosensor experiments were consistent with the range of Kd values recently reported for [3H]isatin binding to brain sections. Although the number of isatin‐binding proteins identified in the mouse and rat brain was similar, only 21 proteins (about one‐third) were identical in the two species. This may be one reason for the differences in isatin effects in rats and mice reported in the literature.
Isolation and 2‐D‐DIGE proteomic analysis of intracellular and extracellular forms of Listeria monocytogenes
Authors: Van de Velde Sébastien , Delaive Edouard , Dieu Marc , Carryn Stéphane , Van Bambeke Françoise , Devreese Bart , Raes Martine , Tulkens Paul M. 
Published: October 2009

AbstractThe pathogenicity of Listeria monocytogenes is related to its ability of invading and multiplying in eukaryotic cells. Its main virulence factors are now well characterized, but limited proteomic data is available concerning its adaptation to the intracellular environment. In this study, L. monocytogenes EGD (serotype 1/2a) grown in human THP‐1 monocytes (24 h) were successfully separated from host organelles and cytosolic proteins by differential and isopycnic centrifugation. For control, we used cell homogenates spiked with bacteria grown in broth. Proteomes from both forms of bacteria were compared using a 2‐D‐DIGE approach followed by MALDI‐TOF analysis to identify proteins. From 1684 distinct spots, 448 were identified corresponding to 245 distinct proteins with no apparent contamination of host proteins. Amongst them, 61 show underexpression (stress defense; transport systems, carbon metabolism, pyrimidines synthesis, D‐Ala‐D‐Ala ligase) and 22 an overexpression (enzymes involved in the synthesis of cell envelope lipids, glyceraldehyde‐3‐phosphate, pyruvate and fatty acids). Our proteomic analysis of intracellular L. monocytogenes (i) suggests that bacteria thrive in a more favorable environment than extracellularly, (ii) supports the concept of metabolic adaptation of bacteria to intracellular environment and (iii) may be at the basis of improved anti‐Listeria therapy.
Improved reproducibility of reverse‐phase protein microarrays using array microenvironment normalization
Authors: Anderson Troy , Wulfkuhle Julia , Liotta Lance , Winslow Raimond L. , Petricoin Emanuel 
Published: October 2009

AbstractWe introduce a novel experimental methodology for the reverse‐phase protein microarray platform which reduces the typical measurement CV as much as 70%. The methodology, referred to as array microenvironment normalization, increases the statistical power of the platform. In the experiment, it enabled the detection of a 1.1‐fold shift in prostate specific antigen concentration using approximately six technical replicates rather than the 37 replicates previously required. The improved reproducibility and statistical power should facilitate clinical implementation of the platform.
Study of TATP: Spontaneous Transformation of TATP to DADP – Full Paper
Authors: Matyáš Robert , Pachman Jiri , Ang How‐Ghee 
Published: October 2009

AbstractThe TATP prepared in the presence of catalysts such as methanesulfonic, perchloric, or sulfuric acid, has been found to undergo spontaneous transformation to DADP. This transformation, however, does not occur if TATP is purified or prepared using hydrochloric acid. Using nitric acid or tin(IV) chloride for catalysis results in TATP that transforms to DADP only to a small extent (max. 1%). The rate of transformation depends on the storage temperature and on the molar ratio of catalyst to acetone (nc/na) used during the preparation of TATP. The faster rate of the transformation was observed at high temperatures and higher molar ratio nc/na.
The stability and degradation of a new biological pesticide, pyoluteorin
Authors: Zhang Jingfang , Wang Wei , Lu Xiaohui , Xu Yuquan , Zhang Xuehong 
Published: October 2009

AbstractBACKGROUND: Pyoluteorin (Plt) is a polyketide metabolite produced by fluorescent Pseudomonas. It controls a wide range of pests, including bacteria, epiphytes and weeds. It could become widely used as a new biological pesticide. However, ignorance of the stability of Plt is an obstacle to its use. This work studied the stability of Plt and its degradation under different conditions, including temperature, pH and UV–visible light irradiation.RESULTS: Degradation of Plt followed first‐order reaction kinetics. The degradation rate increased with increased temperature. The derived activation energy was 11.06 J mol−1 K−1. Plt was relatively stable in neutral solutions, in contrast to acid and alkaline solutions. Visible irradiation had no obvious effect on Plt stability, while UV irradiation greatly decreased its half‐life to 3–4 days, in contrast to its half‐life of 25 days in the dark.CONCLUSION: Plt is relatively stable in pure water solutions and at room temperature, with a half‐life of more than 20 days. However, UV irradiation and acidic or alkaline solutions will enhance its degradation, reducing its half‐life by a factor of 0.1–0.3. Before Plt is widely used as a pesticide, it might be necessary to modify the structure of Plt to make it more stable. Copyright © 2009 Society of Chemical Industry
Positron annihilation study in inorganic‐polymer nano‐composites
Authors: Chen H. M. , Jean Y.C. , Lee L. James , Yang Jintao , Huang James 
Published: October 2009

AbstractPositron annihilation lifetime experiments in a series of polystyrene (PS) nano‐composites of different wt% of SiO2 as a function of temperature have been performed and the glass transition temperatures are determined. Previously, in PS/CNF(carbon nanofiber), a system with strong interfacial bonding, we found single glass transition temperature (Tg), which increases with wt% of CNF. Currently, in PS/SiO2 nano‐composites, a weak interfacial interaction system, we found that there are two Tgs, one at 57 oC, which is lower than the PS bulk Tg (= 91 °C). The lower Tg is interpreted from the free volume in the weak bonding interface between PS and SiO2. This result is consistent with our previous slow positron beam results of PS on Si substrate, which shows a significant lower Tg in the interface than in the bulk PS. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Nano scale free volume study of 70 MeV carbon C5+ ion induced modification in Makrofol‐KL polycarbonate by positron annihilation
Authors: Kumar Rajesh , Prasad Rajendra 
Published: October 2009

AbstractLatent ion tracks produced in the polymers due to the damage produced by the passage of swift heavy ions (SHI) contain amorphous material with highest degree of disorder, resulting in to the change of free volume properties which have strong correlation with the macroscopic properties of the material. To study the modification induced by heavy ions through Positron annihilation lifetime spectroscopy (PALS) 30 μm thin Makrofol‐KL polycarbonate (PC) films were irradiated with C5+ ions of energy 70 MeV to the fluences of 106, 107 and 108 ions/cm2 from 15 UD Pelletron accelerator, N. Delhi. From the o‐Ps lifetime, mean free volume hole radius, micro‐void volume and fractional free volume have been computed which are found to increase with the fluence of the ions. Increase in free volume has been attributed to chain scission. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Li3+ ion irradiation effects on polyamide nylon6,6 studied by positron annihilation lifetime and Doppler broadening spectroscopy
Authors: Prasad Rajendra , Kumar Rajesh , Nambissan P. M. G. , Singh Fouran , Ali S. Asad 
Published: October 2009

AbstractSwift Heavy ion (SHI) irradiation of polymeric materials changes their free volume properties which are strongly correlated to their macroscopic structure. 250 μm thick Polyamide Nylon‐6,6(PN‐6,6) polymer films were irradiated with 50 MeV Li3+ ions from Pelletron accelerator to the fluences of 5 x 1010, 1011, 5 x 1011, 1 x 1012, 5 x 1012, 1013 and 3.5 x 1013 ions/cm2. The effect of heavy ion irradiation on the free volume was studied by Positron Annihilation Lifetime (PAL) and Doppler Broadening Spectroscopy (DBS). Mean free volume hole radius, free volume and fractional free volume of micro‐voids, obtained from o‐Ps lifetime decrease with fluence and is attributed to cross linking. S parameter which is supposed to change due to vacancies type defects created due to SHI irradiation also decreases. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)