bluuebunny/crossref_metadata_2025 huggingface dataset:
TRACE ELEMENTS IN CEPHALOPOD CALCIFIED TISSUE: CUTTLEBONE AS A POSSIBLE TRACER FOR LIFE HISTORICAL EVENTS OF CUTTLEFISH
Authors: IKEDA Y. , ARAI N. , SAKAMOTO W. , YOSHIDA K.
Published: May 2007

Trace elements in a cuttlebone, a buoyant calcified tissue developing simultaneously with the individual growth, of an adult giant cuttlefish originating from the water of Ishigaki Island were measured by PIXE to examine the ontogenetic change of the element concentration. Beside calcium (major element), iron, zinc, manganese, copper, bromine and relatively large amounts of strontium were detected in the cuttlebone. Strontium concentration varied with position along the cuttlebone: it was high near the spine (the portion that deposited at the paralarval stage), then showed some variations at the middle portion of the cuttlebone (the portion that deposited from young stage to sub-adult stage) and became the highest near the locus (the portion that deposited near the catch date, i.e., adult stage). This variation was compared to migration of this species between inshore and offshore waters.
MICRO-PIXE EVALUATION OF Fe DISTRIBUTION IN BARLEY ROOTS
Authors: SCHNEIDER THORSTEN , POVH BOGDAN , STRASSER OLIVER , GIERTH MARKUS , PRZYBYLOWICZ WOJCIECH , MESJASZ-PRZYBYLOWICZ JOLANTA , CHURMS CECIL , SCHÜßLER ARTHUR
Published: May 2007

High Fe concentrations were reported from roots of plants grown in soil. This has been discussed as a possible Fe source for plants, since the concentrations shown in the roots were much higher than in the shoots.

There are, however, also some indications that soil contamination at the root surface of soil grown plants could have led to an overestimation of the Fe concentration in roots.

Fe distribution in root cross sections of barley (Hordeum vulgare L. cv. Alexis) has been studied to investigate this hypothesis.

Micro-PIXE analyses in point and mapping mode were complemented by the STIM technique. Based on the correlation between Fe and soil-related elements ( Ti , Al and Si ), most of Fe located at the root surface could be attributed to soil contamination. It could also be shown that this soil contamination leads to an overestimation of Fe concentration in roots.
STUDY OF HEAVY METALS IN WHEAT AND PADDY GRAINS
Authors: VIJAYAN V. , BEHERA S. N. , TRIPATHY P. S. M. , SINGH GULAB
Published: May 2007

A large fraction of coal extracted from the earth is burnt in thermal power stations. In the combustion process most of the mineral matters in the coal are fused into an fly ash. Fly ash has a great potential for use in agriculture as a provider of major and micro nutrients to plants. Concentrations of some elements in the soil may increase when fly ash is applied to the soil. This paper presents the results on analysis of heavy metals in crops of wheat and paddy grown over last two years on coal ash-applied soils of Bakreswar and Farakka sites as a part of Fly Ash Mission projects on bulk scale utilization of coal ash in agricultural lands by Particle Induced X-ray Emission(PIXE) and Energy Dispersive X-ray Fluorescence(EDXRF) techniques.
INFLUENCE OF THE ANTHROPOGENIC SOURCES ON THE AIR QUALITY IN LJUBLJANA REGION
Authors: BUDNAR MILOŠ , PUC MIHA D.
Published: May 2007

The air quality sampling and analysis of airborne particulate matter (APM) in Ljubljana region has been started, recently. The sampler is positioned at around 10 km from the city limits in the direction of the prevailing winds. The aerosol samples were measured by a standard in-vacuum PIXE arrangement. The measured concentrations show the influences of the industry and traffic at the city.
PIXE ANALYSIS OF SUSPENDED PARTICULATE MATTER ORIGINALLY COLLECTED FOR BETA-RAY ABSORPTION MASS MONITORING
Authors: NAKAMURA MASARU , ISE HIROAKI
Published: May 2007

A method of transferring suspended particulate matter (SPM) from the used filter of a beta-absorption mass monitor to a polycarbonate filter for subsequent PIXE analysis has been developed. The method allows determination of the relative elemental composition of SPM. It was demonstrated that PIXE analysis can detect S , Cl , Fe and Zn in SPM sampled over a one-hour period.
ELEMENTAL ANALYSIS OF RIVER SEDIMENTS BY PIXE AND PIGE
Authors: KENNEDY V. JOHN , AUGUSTHY A. , VARIER K. M. , MAGUDAPATHY P. , PANCHAPAKESAN S. , NAIR K. G. M. , VIJAYAN V.
Published: May 2007

The Chaliyar river, located in Kerala, India has shown preoccupying pollution levels, that constitute a threat to public health and the ecological system. PIXE and PIGE techniques have been employed to measure the elemental concentrations in the river sediment samples. Thick targets were prepared out of the sediment samples collected from various sites along the course of the river. The measurements were carried out using 3 MeV proton beam obtained from 3 MV Tandem pelletron accelerator at Institute of Physics, Bhubaneswar. The elemental concentrations, especially that of heavy metals, at different sites are discussed in detail. Our results show that sediments from a site where the industrial activities are high are significantly high in concentrations of heavy metals ( Cr , Ni , Cu , Zn , Hg and Pb ) than those collected from non-industrial sites. The measured values are compared with the average composition of unpolluted river sediments and other national and international river sediments.
Trace Element Analysis of The Otani Collection's Dunhuang and Turfan Manuscripts by PIXE
Authors: KOHNO M. , YOSHIDA K. , MORITANI K. , NORIZAWA K. , ENAMI K. , KASAJIMA H. , UEYAMA D. , TAKADA J. , MATSUSHITA R.
Published: May 2007

In order to classify the Otani Collection's Dunhuang and Turfan manuscripts, their trace elements were analyzed by PIXE. The paper samples of these manuscripts were fallen off when they were photographed for a CD-ROM catalog. These samples were very small and their size was less than several millimeters. In addition, some paper fragments dating from the late Edo-era of Japan and the late Qing Dynasty of China, and modern Japanese handmade paper were analyzed using PIXE and NAA. Quite interesting results were obtained when analyzing the trace elements – Na , Mg , Al , Si , S , Cl , K , Ca , Sc , Mn , Fe , Cu , Zn , As , Br , Sr , Ba , Pb , La , Sm . It was found that Dunhuang and Turfan papers of the Otani Collection were characterized by its highest iron and bromine content. The reason of the highest iron content probably originates in their making process and/or depends on their preservative environment. On the other hand, it became clear as for the highest bromine content that the origin is from fumigation of methyl bromide.
EXTERNAL PIXE ANALYSIS OF OLD INKS AND PAPERS
Authors: HASSANZADEH A. , LAMEHI-RACHTI M. , OLIAIY P. , RAHIGHI J. , SHOKOUHI F.
Published: May 2007

Proton Induced X-ray Emission, PIXE is a very well established analytical method. This technique of analysis can equally be applied both in vacuum, internal PIXE, and in atmosphere, external PIXE. External PIXE has been applied to material analysis in Van de Graaff laboratory at AEOI using filters and funny filters. Advantages of using these filters have been studied when analysing ancient written documents such as envelopes, inks, and newspapers. This technique clearly demonstrated the differences between new and old inks and papers. More data is needed to show other features of this technique.
ON RELEVANT PIXE INFORMATION FOR DETERMINING THE COMPOSITIONAL ANALYSIS OF ANCIENT SILVER AND BRONZE COINS
Authors: CONSTANTINESCU B. , KENNEDY V. JOHN , DEMORTIER G.
Published: May 2007

In this work, external PIXE was applied for the analysis of ancient silver and bronze coins. Turkish and Romanian silver coins, Roman and Byzantine bronze coins were investigated using a 3 MeV proton beam. To evaluate the in-depth distribution of major and minor elements ( Cu , Ag , Au , Pb for silver matrix and Cu , Zn , Ag , Sn , Pb for copper matrix), the coins were polished using silicon carbide abrasives. In order to test the homogeneity of the coins, measurements were carried out at three different impact points. Each position of the samples was carefully controlled in order to avoid differences in geometrical factors from one analysis to another. All the analyses were performed on flat external and bright regions so as to exclude the irradiation of possible inclusions or deposits. The calculations of the elemental concentrations in the coins were made by relative to reference standard alloys ( Ag - Cu , Cu - Sn , Sn - Pb ).
APPLICATION OF PIXE TO STUDY ANCIENT IRANIAN SILVER COINS
Authors: OLIAIY P. , SHOKOUHI F. , LAMEHI-RACHTI M. , RAHIGHI J. , ANDAMI P. , DILMAGHANI J. , ETEZADI M.
Published: May 2007

Ancient Iranian silver coins minted in various parts of the ancient Iran from Transoxiana to Mesopotamia over a time span of 460 years (247BC-208AD) during Parthians dynasty were analysed by PIXE with a 2.2 MeV proton beam. Forty seven silver coins owned by Tamashagah-e-Pool (museum of money) in Tehran were examined in this study. The possible correlation between the composition of coins and the minting time or the minting location of coins has been the prime objective of the present study. Elemental analysis of ancient coins could also reveal the direct relation with the political and economical situation and also with the metallurgy of the minting time. Results on the contents of principal component elements ( Fe , Ni , Cu , As , Br , Ag , Sn , Sb , Ba , Au and Pb ) are presented and discussed.
CATEGORICITY FROM ONE SUCCESSOR CARDINAL IN TAME ABSTRACT ELEMENTARY CLASSES
Authors: GROSSBERG RAMI , VANDIEREN MONICA
Published: May 2007

We prove that from categoricity in λ+ we can get categoricity in all cardinals ≥ λ+ in a χ-tame abstract elementary classe [Formula: see text] which has arbitrarily large models and satisfies the amalgamation and joint embedding properties, provided [Formula: see text] and λ ≥ χ.

For the missing case when [Formula: see text], we prove that [Formula: see text] is totally categorical provided that [Formula: see text] is categorical in [Formula: see text] and [Formula: see text].
THE CLASSIFICATION PROBLEM FOR p-LOCAL TORSION-FREE ABELIAN GROUPS OF RANK TWO
Authors: HJORTH GREG , THOMAS SIMON
Published: May 2007

We prove that if p ≠ q are distinct primes, then the classification problems for p-local and q-local torsion-free abelian groups of rank two are incomparable with respect to Borel reducibility.
Unexpected evidence for active brown adipose tissue in adult humans
Authors: Nedergaard Jan , Bengtsson Tore , Cannon Barbara
Published: May 2007

The contention that brown adipose tissue is absent in adult man has meant that processes attributed to active brown adipose tissue in experimental animals (mainly rodents), i.e., classical nonshivering thermogenesis, adaptive adrenergic thermogenesis, diet-induced thermogenesis, and antiobesity, should be either absent or attributed to alternative (unknown) mechanisms in man. However, serendipidously, as a consequence of the use of fluorodeoxyglucose positron emission tomography (FDG PET) to trace tumor metastasis, observations that may change that notion have recently been made. These tomography scans have visualized symmetrical areas of increased tracer uptake in the upper parts of the human body; these areas of uptake correspond to brown adipose tissue. We examine here the published observations from a viewpoint of human physiology. The human depots are somewhat differently located from those in rodents, the main depots being found in the supraclavicular and the neck regions with some additional paravertebral, mediastinal, para-aortic, and suprarenal localizations (but no interscapular). Brown adipose tissue activity in man is acutely cold induced and is stimulated via the sympathetic nervous system. The prevalence of active brown adipose tissue in normal adult man can be only indirectly estimated, but it would seem that the prevalence of active brown adipose tissue in the population may be at least in the range of some tens of percent. We conclude that a substantial fraction of adult humans possess active brown adipose tissue that thus has the potential to be of metabolic significance for normal human physiology as well as to become pharmaceutically activated in efforts to combat obesity.
Evolution, atmospheric oxygen, and complex disease
Authors: Koch Lauren Gerard , Britton Steven L.
Published: May 2007

If evolution is an accurate statement of our biology, then disease must be tightly associated with its patterns. We considered selection for more optimal capacity for energy transfer as the most general pattern of evolution. From this, we propose that the etiology of complex disease is linked tightly to the evolutionary transition to cellular complexity that was afforded by the steep thermodynamic gradient of an oxygen atmosphere. In accord with this thesis, clinical studies reveal a strong statistical link between low aerobic capacity and all-cause mortality. In addition, large-scale unbiased network analyses demonstrate the pivotal role of oxygen metabolism in cellular function. The demonstration that multiple disease risks segregated during two-way artificial selection for low and high aerobic capacity in rats provides a remote test of these possible connections between evolution, oxygen metabolism, and complex disease. Even more broadly, an atmosphere with oxygen may be uniquely essential for development of complex life anywhere because oxygen is stable as a diatomic gas, is easily transported, and has a high electronegativity for participation in energy transfer via redox reactions.
Microarray analysis of the temporal response of skeletal muscle to methylprednisolone: comparative analysis of two dosing regimens
Authors: Almon Richard R. , DuBois Debra C. , Yao Zhenling , Hoffman Eric P. , Ghimbovschi Svetlana , Jusko William J.
Published: May 2007

The transcriptional response of skeletal muscle to chronic corticosteroid exposure was examined over 168 h and compared with the response profiles observed following a single dose of corticosteroid. Male adrenalectomized Wistar rats were given a constant-rate infusion of 0.3 mg·kg−1·h−1methylprednisolone for up to 7 days via subcutaneously implanted minipumps. Four control and forty drug-treated animals were killed at ten different time points during infusion. Liver total RNAs were hybridized to 44 individual Affymetrix REA230A gene chips. Previously, we described a filtration approach for identifying genes of interest in microarray data sets developed from tissues of rats treated with methylprednisolone (MPL) following acute dosing. Here, a similar approach involving a series of three filters was applied sequentially to identify genes of interest. These filters were designed to eliminate probe sets that were not expressed in the tissue, not regulated by the drug, or did not meet defined quality control standards. Filtering eliminated 86% of probe sets, leaving a remainder of 2,316 for further consideration. In a previous study, 653 probe sets were identified as MPL regulated following administration of a single (acute) dose of the drug. Comparison of the two data sets yielded 196 genes identified as regulated by MPL in both dosing regimens. Because of receptor downregulation, it was predicted that genes regulated by receptor-glucocorticoid response element interactions would exhibit tolerance in chronic profiles. However, many genes did not exhibit steroid tolerance, indicating that present perspectives on the mechanism of glucocorticoid action cannot entirely explain all temporal profiles.
Roles of the calcineurin and CaMK signaling pathways in fast-to-slow fiber type transformation of cultured adult mouse skeletal muscle fibers
Authors: Mu Xiaodong , Brown Lisa D. , Liu Yewei , Schneider Martin F.
Published: May 2007

Two Ca2+-dependent signaling pathways, mediated by the Ca2+-activated phosphatase calcineurin and by the Ca2+-activated kinase Ca2+/calmodulin-dependent kinase (CaMK), are both believed to function in fast-to-slow skeletal muscle fiber type transformation, but questions about the relative importance of the two pathways still remain. Here, the differential gene expression during fast-to-slow fiber type transformation was studied using cultured adult flexor digitorum brevis (FDB) fibers and a custom minimicroarray system containing 21 fiber type-specific marker genes. After 3 days of culture, unstimulated fibers showed a generally slower gene expression profile; 3 days of electric field stimulation of cultured FDB fibers with a slow fiber-type pattern transformed the fibers to an even slower gene expression profile. Unstimulated FDB fibers overexpressing constitutively active calcineurin featured a slower gene expression profile, except four genes, indicating that transformation occurred, but was incomplete with activation of the calcineurin pathway alone. In both unstimulated FDB fibers and slow-type electrically stimulated FDB fibers, blocking of CaMK pathway with KN93 generated a faster gene expression profile compared with the negative control KN92, indicating that CaMK pathway functions during the transformation induced by both unstimulated culturing and slow fiber-type electrical stimulation. Moreover, neither the calcineurin nor the CaMK pathway alone could maximally activate the transformation, and coordination of the two pathways is required to accomplish a complete fast-to-slow fiber type transformation.
A Better Cure Rate with 800 mg than with 400 mg Clarithromycin Regimens in One-Week Triple Therapy for Helicobacter pylori Infection in Cigarette-Smoking Peptic Ulcer Patients
Authors: Ishioka Hidehiko , Mizuno Motowo , Take Susumu , Ishiki Kuniharu , Nagahara Yasuhiro , Yoshida Tomowo , Okada Hiroyuki , Yokota Kenji , Oguma Keiji
Published: May 2007

Background/Aims: In Helicobacter pylori eradication therapy, using a proton pump inhibitor plus amoxicillin and clarithromycin (PPI/AC regimen), the impact of the clarithromycin dose and smoking on efficacy is conflicting. Here, we compared the efficacy of 400 and 800 mg of clarithromycin in the regimen in relation to smoking in patients with peptic ulcer disease. Methods: We studied 601 H. pylori-positive patients with peptic ulcer disease who had received amoxicillin 750 mg and clarithromycin 200 or 400 mg together with lansoprazole 30 mg b.i.d. Results: 305 patients were treated with a regimen containing 400 mg of clarithromycin (C400 group), and 296 patients with a regimen containing 800 mg (C800 group). Overall cure rates between the two groups were not significantly different, but the cure rate in the C800 group was significantly better than that in the C400 group among patients infected with clarithromycin-sensitive strains (p = 0.03). This difference could be attributed to differences among smokers versus non-smokers: the cure rate among smokers in the C800 group (91.0%) was better than that in the C400 group (80.0%, p = 0.003). Conclusions: 800 mg of clarithromycin is recommended in the PPI/AC regimen for patients who smoke and are infected with clarithromycin-sensitive H. pylori.
Transverse Cracking of M40J/PMR-II-50 Composites under Thermal—Mechanical Loading
Authors: Ju Jaehyung , Morgan Roger J. , Creasy Terry S. , Shin E. Eugene
Published: May 2007

In this study, the effects of thermal cycling combined with mechanical loading on the microcracking of M40J/PMR-II-50 are investigated. Characterization of the failure mechanisms are conducted based on the critical parameters which cause composite microcracking, as presented in Part I. Based on the test results in Part I, the tests with intermediate in-plane lamina strain (0.175—0.350%) and an increased number of thermal cycles are added. Elevated temperature thermal cycling (23—250°C) is also added to the original test plan to investigate the thermal cycling temperature amplitude effect on microcracking of the composites. Observations indicate that the elevated temperature exposure under mechanical loads causes an easy fiber/matrix debonding. Subsequent exposure to cryogenic temperatures results in fiber/matrix debonding due to the high thermal stresses associated with fiber/ matrix thermal expansion mismatch. Crack propagation under cryogenic exposures is shown to be dominant with an increasing number of thermal cycles, especially when combined with high temperature exposure associated with high amplitude of cyclic thermal stresses.
Deformation Micromechanics of a Thermoplastic—Thermoset Fiber—Matrix Interface using the Single Fiber Composite Test
Authors: Gonzalez-Chi P.I. , Young R.J.
Published: May 2007

The development of high performance fibers, based on polyethylene (PE) fiber opened the possibility of manufacturing composites with high strength and lightness and gave a modern application to an old fashioned material. In the present study, the interfacial micromechanics between gel-spun PE fibers and epoxy resin is studied using Raman spectroscopy. The poor adhesive properties between PE and any matrix material makes it ideal for studying the debonding process; the interfacial failure is relatively easy to promote. The study of the deformation micromechanics and failure of the thermoplastic—thermoset interface will eventually lead to the control of this type of hybrid composite, which represent a new kind of materials.

The single fiber composite geometry was used to study the interface and how it was affected by different chemical treatments on the fiber surface, which created an interface between the PE fiber and the epoxy matrix. Prior to treatment, the interaction between them was nonexistent. Stress profiles along the fiber were obtained using Raman spectroscopy and the interface performance was assessed using a partial debonding model. The results not only lead to calculation of the interfacial shear stress (ISS), but also aid in understanding the debonding process and levels of stress required for the composite interface to fail.
Manufacturing of Braided Thermoplastic Composites with Carbon/Nylon Commingled Fibers
Authors: Laberge-Lebel Louis , Suong Van Hoa
Published: May 2007

Commingled fibers, a blend of reinforcement and matrix filaments within the tow, provide a good material arrangement to overcome the high viscosity at melt of thermoplastic matrices. This study first characterizes the architecture of a carbon/nylon commingled yarn by microscopy. Then, braiding technology is used to manufacture the tubes at various braiding angles. Laminates are then made by compression molding with preforms extracted from the braids. The consolidation quality is examined using the constituent content method and microscopy. Tensile and flexural properties are obtained for a wide range of angles. Fracture analysis of tensile coupons is realized. Finally, the tensile modulus is predicted using classical lamination theory.
Prediction of Bearing Strength in Fiber Metal Laminates
Authors: Krimbalis P.P. , Poon C. , Fawaz Z. , Behdinan K.
Published: May 2007

Finite element (FE) analyses are carried out on bolt bearing testing scenarios based on data found in the literature. Both layer-by-layer and smeared property FE models are created to calculate the compressive characteristic dimension (CCD) for three GLARE variants. A novel re-definition of conventional CCD is proposed which is governed by the yield strength of aluminum. The new definition also incorporates the two-phase nature of GLARE, as well as the delamination/ buckling phenomenon for pin/bolt bearing, in a bearing failure mode. A previously unconsidered, orthotropic plate buckling analysis is also conducted in a conservative, worst case scenario sense on the laterally unsupported prepreg layers. Results of the buckling analysis suggest that the prepreg contribution to bearing strength, in a bearing failure mode, is at best negligible and joint collapse is governed by the yielding and delamination of the aluminum layers. Calculation of a CCD, based on the new yield strength definition, produced consistent values amongst all GLARE variants considered in the layer-by-layer analysis suggesting that the CCD is a property of the material alone.
Brand-new lifestyle: consumer-oriented programmes on Chinese television
Authors: Xu Janice Hua
Published: May 2007

This article studies the growth of the consumer-oriented genre in Chinese television and examines the role of television in the construction of new class identities. The author discusses three kinds of programmes of this genre — market trend guides, `scam warning' reports, and skill-focused lifestyle programmes, providing case studies for each type. These developments indicate that television is playing an important role in the dynamics of class stratification in China through the creation of new cultural capital and the segmentation of audiences along socioeconomic lines. Although television has always been a part of the effort in building a homogenized national culture in China's modernization process, it is now contributing to the formation of class subjectivities and reinforcing the increasingly visible class divisions in society.
`Motherhood, ambition and risk': mediating the sporting hero/ine in Conservative Britain
Authors: Gilchrist Paul
Published: May 2007

In May 1995, a 33 year-old woman named Alison Hargreaves made her name by becoming the first woman (and second person) to make an unaided solo ascent of the world's highest mountain, Everest. She was constructed as an exemplar of the highest order, a national heroine to be proud of, and in the vein of a series of British female heroes who punctuate the typically masculine narrative of national achievement. By August she was dead, the victim of a violent storm on the upper reaches of the peak they call the Savage Mountain, K2. The focus of vitriolic media attention, Hargreaves was stripped of her heroic status and condemned for the irresponsibility of leaving her two small children motherless, and so opened a national debate on `motherhood, ambition and risk'. This article explores that debate. In so doing it probes the meaning of heroism, as both a culturally mediated idea of extraordinary actions, and as part of a wider politics of recognition and representation that calls for a consideration of the role of public communication.
Synthesis and TGA Evaluation of Novel Triphosphate Esters
Authors: Kiran Y.B. , Devendranath Reddy C. , Gunasekar D. , Naga Raju C. , Barbosa L.C.A. , Marney D.C.O. , Russell L.J.
Published: May 2007

Several new substituted organo tri/thiotriphosphate esters were synthesized by condensing cyclic oxaza/dioxaphosphorochloridates/ thiochloridates with K2HPO4 in the presence of tetrabutylammonium iodide. The functionality on the phosphate was systematically changed by synthesis, thus allowing evaluation and comparison of a range of phosphate esters with highly varied structural features. They were subjected to thermogravimetric analysis, derivative thermogravimetric analysis, and differential thermal analysis to assess their thermal stability and potential use as flame retardants. It has been found that their thermal degradations, being highly complex and dependent upon a number of molecular structural features, are difficult to rationalize on simple rules.
Three-dimensional Elasticity Solution for Uniformly Loaded Cross-ply Laminates and Sandwich Plates
Authors: Zenkour Ashraf M.
Published: May 2007

This article establishes the bending problem of cross-ply laminated plates using the three-dimensional elasticity equations as well as the technique based on the state space concept. It presents a wide variety of results for the symmetric and antisymmetric analyses of rectangular multilayer plates subjected to a sinusoidally/uniformly distributed load (SDL/UDL). In addition, this study provides a strong mathematical tool allowing one to determine, in an exact and unified manner, the state of stress and displacement of cross-ply laminated composites and sandwich plates. The well-known results (given in Pagano ((1970), Exact Solutions for Rectangular Bidirectional Composites and Sandwich Plates, Journal of Composite Materials, 4(1): 20—24.) and Pagano and Hatfield ((1972), Elastic Behaviour of Multilayered Bidirectional Composites, AIAA Journal, 10(12): 931—933.) due to the exact three-dimensional elasticity solution are in fact special cases of the present technique.
Behavior of Sandwich Plates Reinforced with Polyurethane/Polyurea Interlayers under Blast Loads
Authors: Bahei-El-Din Yehia A. , Dvorak George J.
Published: May 2007

In this study, the behavior of conventional and modified sandwich plate designs subjected to blast loads is examined with the finite element method. The conventional sandwich design consists of thin outer (loaded side) and inner facesheets made of fibrous laminates, separated by a layer of structural foam core. In the modified designs, a thin ductile interlayer is inserted between the outer facesheet and the foam core. Two materials are selected for the interlayers; one is rate-independent, hyperelastic (polyurethane, PUR), and the other is rate and pressure-dependent, elastic—plastic (polyurea). A comparison is made between the two enhanced designs and the conventional design during an extended time period of 5.0 ms under an exponential pressure impulse lasting for 0.05 ms, and has a peak pressure of 100 MPa. Results show that utilizing PUR or polyurea to separate the outer facesheet and the foam core leads to a much reduced core compression, facesheet vibration, and overall deflection compared to the conventional design. Similar reductions are found in the kinetic energy and the stored and dissipated strain energy. This is attributed to the ability of the interlayers to store energy and shield the inner foam by exhibiting great stiffness under pressure. Although strain rates as high as 104 s—1 are produced by the blast pressure impulse in the sandwich plates, the strains in both the PUR and the polyurea interlayers are relatively small. This leads to generally similar responses for the two interlayer types, with the initially stiffer PUR providing a slightly better protection for the foam core.
Nanocomposite Fiber Based Web and Membrane Formation and Characterization
Authors: Adanur Sabit , Ascioglu Birgul
Published: May 2007

Electrospinning is used to produce polyvinyl alcohol (PVA) fibers. Electrospun nano and micro sized fibers are collected on nonwoven fabrics to form a web and membranes. Optimization is carried out by considering some of the parameters, such as voltage, spinning time, polymer solution, distance between the collector and the needle. Beading effect, effect of solution viscosity, and voltage are investigated. Mechanical and thermal properties are measured by differential scanning calorimetry (DSC) and thermogravimetric analysis (TGA). Surface tension properties are examined. Glass transition and melting temperature are increased with the addition of nanoclay to PVA. Nanoclay also increases the barrier properties and thermal stability of PVA fibers. Yarn samples are produced by twisting nano-micro fibers. Tensile strength of the yarn samples is measured.
Proteinase-activated receptor 4 stimulation-induced epithelial-mesenchymal transition in alveolar epithelial cells
Authors: Ando Seijitsu , Otani Hitomi , Yagi Yasuhiro , Kawai Kenzo , Araki Hiromasa , Fukuhara Shirou , Inagaki Chiyoko
Published: May 2007

Background

Proteinase-activated receptors (PARs; PAR1–4) that can be activated by serine proteinases such as thrombin and neutrophil catepsin G are known to contribute to the pathogenesis of various pulmonary diseases including fibrosis. Among these PARs, especially PAR4, a newly identified subtype, is highly expressed in the lung. Here, we examined whether PAR4 stimulation plays a role in the formation of fibrotic response in the lung, through alveolar epithelial-mesenchymal transition (EMT) which contributes to the increase in myofibroblast population.

Methods

EMT was assessed by measuring the changes in each specific cell markers, E-cadherin for epithelial cell, α-smooth muscle actin (α-SMA) for myofibroblast, using primary cultured mouse alveolar epithelial cells and human lung carcinoma-derived alveolar epithelial cell line (A549 cells).

Results

Stimulation of PAR with thrombin (1 U/ml) or a synthetic PAR4 agonist peptide (AYPGKF-NH2, 100 μM) for 72 h induced morphological changes from cobblestone-like structure to elongated shape in primary cultured alveolar epithelial cells and A549 cells. In immunocytochemical analyses of these cells, such PAR4 stimulation decreased E-cadherin-like immunoreactivity and increased α-SMA-like immunoreactivity, as observed with a typical EMT-inducer, tumor growth factor-β (TGF-β). Western blot analyses of PAR4-stimulated A549 cells also showed similar changes in expression of these EMT-related marker proteins. Such PAR4-mediated changes were attenuated by inhibitors of epidermal growth factor receptor (EGFR) kinase and Src. PAR4-mediated morphological changes in primary cultured alveolar epithelial cells were reduced in the presence of these inhibitors. PAR4 stimulation increased tyrosine phosphorylated EGFR or tyrosine phosphorylated Src level in A549 cells, and the former response being inhibited by Src inhibitor.

Conclusion

PAR4 stimulation of alveolar epithelial cells induced epithelial-mesenchymal transition (EMT) as monitored by cell shapes, and epithelial or myofibroblast marker at least partly through EGFR transactivation via receptor-linked Src activation.
HMM-ModE – Improved classification using profile hidden Markov models by optimising the discrimination threshold and modifying emission probabilities with negative training sequences
Authors: Srivastava Prashant K , Desai Dhwani K , Nandi Soumyadeep , Lynn Andrew M
Published: May 2007

Background

Profile Hidden Markov Models (HMM) are statistical representations of protein families derived from patterns of sequence conservation in multiple alignments and have been used in identifying remote homologues with considerable success. These conservation patterns arise from fold specific signals, shared across multiple families, and function specific signals unique to the families. The availability of sequences pre-classified according to their function permits the use of negative training sequences to improve the specificity of the HMM, both by optimizing the threshold cutoff and by modifying emission probabilities to minimize the influence of fold-specific signals. A protocol to generate family specific HMMs is described that first constructs a profile HMM from an alignment of the family's sequences and then uses this model to identify sequences belonging to other classes that score above the default threshold (false positives). Ten-fold cross validation is used to optimise the discrimination threshold score for the model. The advent of fast multiple alignment methods enables the use of the profile alignments to align the true and false positive sequences, and the resulting alignments are used to modify the emission probabilities in the original model.

Results

The protocol, called HMM-ModE, was validated on a set of sequences belonging to six sub-families of the AGC family of kinases. These sequences have an average sequence similarity of 63% among the group though each sub-group has a different substrate specificity. The optimisation of discrimination threshold, by using negative sequences scored against the model improves specificity in test cases from an average of 21% to 98%. Further discrimination by the HMM after modifying model probabilities using negative training sequences is provided in a few cases, the average specificity rising to 99%. Similar improvements were obtained with a sample of G-Protein coupled receptors sub-classified with respect to their substrate specificity, though the average sequence identity across the sub-families is just 20.6%. The protocol is applied in a high-throughput classification exercise on protein kinases.

Conclusion

The protocol has the potential to maximise the contributions of discriminating residues to classify proteins based on their molecular function, using pre-classified positive and negative sequence training data. The high specificity of the method, and increasing availability of pre-classified sequence data holds the potential for its application in sequence annotation.
A meta-data based method for DNA microarray imputation
Authors: Jörnsten Rebecka , Ouyang Ming , Wang Hui-Yu
Published: May 2007

Background

DNA microarray experiments are conducted in logical sets, such as time course profiling after a treatment is applied to the samples, or comparisons of the samples under two or more conditions. Due to cost and design constraints of spotted cDNA microarray experiments, each logical set commonly includes only a small number of replicates per condition. Despite the vast improvement of the microarray technology in recent years, missing values are prevalent. Intuitively, imputation of missing values is best done using many replicates within the same logical set. In practice, there are few replicates and thus reliable imputation within logical sets is difficult. However, it is in the case of few replicates that the presence of missing values, and how they are imputed, can have the most profound impact on the outcome of downstream analyses (e.g. significance analysis and clustering). This study explores the feasibility of imputation across logical sets, using the vast amount of publicly available microarray data to improve imputation reliability in the small sample size setting.

Results

We download all cDNA microarray data ofSaccharomyces cerevisiae, Arabidopsis thaliana, andCaenorhabditis elegansfrom the Stanford Microarray Database. Through cross-validation and simulation, we find that, for all three species, our proposed imputation using data from public databases is far superior to imputation within a logical set, sometimes to an astonishing degree. Furthermore, the imputation root mean square error for significant genes is generally a lot less than that of non-significant ones.

Conclusion

Since downstream analysis of significant genes, such as clustering and network analysis, can be very sensitive to small perturbations of estimated gene effects, it is highly recommended that researchers apply reliable data imputation prior to further analysis. Our method can also be applied to cDNA microarray experiments from other species, provided good reference data are available.
Evaluation of gene-expression clustering via mutual information distance measure
Authors: Priness Ido , Maimon Oded , Ben-Gal Irad
Published: May 2007

Background

The definition of a distance measure plays a key role in the evaluation of different clustering solutions of gene expression profiles. In this empirical study we compare different clustering solutions when using the Mutual Information (MI) measure versus the use of the well known Euclidean distance and Pearson correlation coefficient.

Results

Relying on several public gene expression datasets, we evaluate the homogeneity and separation scores of different clustering solutions. It was found that the use of the MI measure yields a more significant differentiation among erroneous clustering solutions. The proposed measure was also used to analyze the performance of several known clustering algorithms. A comparative study of these algorithms reveals that their "best solutions" are ranked almost oppositely when using different distance measures, despite the found correspondence between these measures when analysing the averaged scores of groups of solutions.

Conclusion

In view of the results, further attention should be paid to the selection of a proper distance measure for analyzing the clustering of gene expression data.
Locational distribution of gene functional classes in Arabidopsis thaliana
Authors: Riley Michael C , Clare Amanda , King Ross D
Published: May 2007

Background

We are interested in understanding the locational distribution of genes and their functions in genomes, as this distribution has both functional and evolutionary significance. Gene locational distribution is known to be affected by various evolutionary processes, with tandem duplication thought to be the main process producing clustering of homologous sequences. Recent research has found clustering of protein structural families in the human genome, even when genes identified as tandem duplicates have been removed from the data. However, this previous research was hindered as they were unable to analyse small sample sizes. This is a challenge for bioinformatics as more specific functional classes have fewer examples and conventional statistical analyses of these small data sets often produces unsatisfactory results.

Results

We have developed a novel bioinformatics method based on Monte Carlo methods and Greenwood's spacing statistic for the computational analysis of the distribution of individual functional classes of genes (from GO). We used this to make the first comprehensive statistical analysis of the relationship between gene functional class and location on a genome. Analysis of the distribution of all genes except tandem duplicates on the five chromosomes of A. thaliana reveals that the distribution on chromosomes I, II, IV and V is clustered at P = 0.001. Many functional classes are clustered, with the degree of clustering within an individual class generally consistent across all five chromosomes. A novel and surprising result was that the locational distribution of some functional classes were significantly more evenly spaced than would be expected by chance.

Conclusion

Analysis of the A. thaliana genome reveals evidence of unexplained order in the locational distribution of genes. The same general analysis method can be applied to any genome, and indeed any sequential data involving classes.
From genes to functional classes in the study of biological systems
Authors: Al-Shahrour Fátima , Arbiza Leonardo , Dopazo Hernán , Huerta-Cepas Jaime , Mínguez Pablo , Montaner David , Dopazo Joaquín
Published: May 2007

Background

With the popularisation of high-throughput techniques, the need for procedures that help in the biological interpretation of results has increased enormously. Recently, new procedures inspired in systems biology criteria have started to be developed.

Results

Here we present FatiScan, a web-based program which implements a threshold-independent test for the functional interpretation of large-scale experiments that does not depend on the pre-selection of genes based on the multiple application of independent tests to each gene. The test implemented aims to directly test the behaviour of blocks of functionally related genes, instead of focusing on single genes. In addition, the test does not depend on the type of the data used for obtaining significance values, and consequently different types of biologically informative terms (gene ontology, pathways, functional motifs, transcription factor binding sites or regulatory sites from CisRed) can be applied to different classes of genome-scale studies. We exemplify its application in microarray gene expression, evolution and interactomics.

Conclusion

Methods for gene set enrichment which, in addition, are independent from the original data and experimental design constitute a promising alternative for the functional profiling of genome-scale experiments. A web server that performs the test described and other similar ones can be found at:http://www.babelomics.org.
VSGdb: a database for trypanosome variant surface glycoproteins, a large and diverse family of coiled coil proteins
Authors: Marcello Lucio , Menon Suraj , Ward Pauline , Wilkes Jonathan M , Jones Nicola G , Carrington Mark , Barry J David
Published: May 2007

Background

Trypanosomes are coated with a variant surface glycoprotein (VSG) that is so densely packed that it physically protects underlying proteins from effectors of the host immune system. Periodically cells expressing a distinct VSG arise in a population and thereby evade immunity. The main structural feature of VSGs are two long α-helices that form a coiled coil, and sets of relatively unstructured loops that are distal to the plasma membrane and contain most or all of the protective epitopes. The primary structure of different VSGs is highly variable, typically displaying only ~20% identity with each other. The genome has nearly 2000VSGgenes, which are located in subtelomeres. Only one VSG gene is expressed at a time, and switching betweenVSGs primarily involves gene conversion events. The archive of silentVSGs undergoes diversifying evolution rapidly, also involving gene conversion. The VSG family is a paradigm for α helical coiled coil structures, epitope variation and GPI-anchor signals. At the DNA level, the genes are a paradigm for diversifying evolutionary processes and for the role of subtelomeres and recombination mechanisms in generation of diversity in multigene families. To enable ready availability ofVSGsequences for addressing these general questions, and trypanosome-specific questions, we have created VSGdb, a database of all known sequences.

Description

VSGdb contains fully annotatedVSGsequences from the genome sequencing project, with which it shares all identifiers and annotation, and other available sequences. The database can be queried in various ways. Sequence retrieval, in FASTA format, can deliver protein or nucleotide sequence filtered by chromosomes or contigs, gene type (functional, pseudogene, etc.), domain and domain sequence family. Retrieved sequences can be stored as a temporary database for BLAST querying, reports from which include hyperlinks to the genome project database (GeneDB) CDS Info and to individual VSGdb pages for each VSG, containing annotation and sequence data. Queries (text search) with specific annotation terms yield a list of relevant VSGs, displayed as identifiers leading again to individual VSG web pages.

Conclusion

VSGdbhttp://www.vsgdb.org/is a freely available, web-based platform enabling easy retrieval, via various filters, of sets of VSGs that will enable detailed analysis of a number of general and trypanosome-specific questions, regarding protein structure potential, epitope variability, sequence evolution and recombination events.
Normalization method for metabolomics data using optimal selection of multiple internal standards
Authors: Sysi-Aho Marko , Katajamaa Mikko , Yetukuri Laxman , Orešič Matej
Published: May 2007

Background

Success of metabolomics as the phenotyping platform largely depends on its ability to detect various sources of biological variability. Removal of platform-specific sources of variability such as systematic error is therefore one of the foremost priorities in data preprocessing. However, chemical diversity of molecular species included in typical metabolic profiling experiments leads to different responses to variations in experimental conditions, making normalization a very demanding task.

Results

With the aim to remove unwanted systematic variation, we present an approach that utilizes variability information from multiple internal standard compounds to find optimal normalization factor for each individual molecular species detected by metabolomics approach (NOMIS). We demonstrate the method on mouse liver lipidomic profiles using Ultra Performance Liquid Chromatography coupled to high resolution mass spectrometry, and compare its performance to two commonly utilized normalization methods: normalization byl2norm and by retention time region specific standard compound profiles. The NOMIS method proved superior in its ability to reduce the effect of systematic error across the full spectrum of metabolite peaks. We also demonstrate that the method can be used to select best combinations of standard compounds for normalization.

Conclusion

Depending on experiment design and biological matrix, the NOMIS method is applicable either as a one-step normalization method or as a two-step method where the normalization parameters, influenced by variabilities of internal standard compounds and their correlation to metabolites, are first calculated from a study conducted in repeatability conditions. The method can also be used in analytical development of metabolomics methods by helping to select best combinations of standard compounds for a particular biological matrix and analytical platform.