bluuebunny/crossref_metadata_2025 huggingface dataset:
Familiarity and the Inferential Theory of Perception
Authors: Richeimer Joel
Published: September 2006

Not all empirical work in the psychology of perception has operated explicitly within a theoretical framework. But when it has, that framework has usually been provided by the inferential theory of perception. I argue that in spite of its explanatory strengths, the inferential theory of perception conceals a well-established empirical phenomenon. That phenomenon is known in ordinary parlance as ‘familiarity’. I discuss why the inferential theory of perception cannot deal with familiarity and what it reveals about the limits of the inferential theory of perception.
Making Time
Authors: Jalas Mikko
Published: September 2006

This article adopts a point of view of practice theories and elucidates how temporal orientations commence in the interactions of humans and the material world. Empirically the article focuses on the contemporary practices of wooden boating. Such practices offer a variety of different temporal orientations, which include emancipatory uchronias, flow states, altruistic care of common heritage and craft identities of mastering traditional skills. These positions within wooden boating result out of a distinct historic development. The practices of wooden boating also frequently imply stress and heavy toll on time, and entail subtle negotiations between self-determination and duties as a practitioner.
Railway Time and Rubber Time
Authors: Tsuji Yohko
Published: September 2006

This article addresses the co-existence of rigid punctuality and a rubber-like flexibility in the Japanese conception of time. It examines how the clock and social norms shape the everyday use of time related to railways, work, and appointments in Japan. It demonstrates that multiple discourses of time and the complicated interactions among them create temporal complexity in which the seeming contradiction between rigidity and flexibility is compromised. The data derive from long-term participant-observation research among Japanese in Japan and abroad.
Life's on Hold
Authors: Hogben Susan
Published: September 2006

Intimate relationships are forged on and sustained by the appreciation of mutually significant events. When someone is missing, as a result of a reportedly unmotivated absence, expectations of the continuity of relationships are disrupted. Using data from publicly available texts I examine how people experience such an absence. Harvey Sacks’s notion of the ‘private calendar’ helps explicate how remaining family members experience literal and figurative desynchronization that suggests missing might be more potently understood as waiting. Finally, it seems that the duration of the absence helps family members account for the enduring lack of communication.
Modelling and Analysis of an Oscillatory Dynamic System Using the Hybrid State Approach: An Experimental Case
Authors: Adli Mehmet Arif , Dogruel Murat
Published: September 2006

Many existing dynamic systems contain mechanical effects like inertia, elasticity and friction, as well as hysteretic effects, relays, flip-flops and discrete decision makers, sensors and actuators. The effective modelling of such systems is essential for a thorough analysis and to improve our understanding. In general, both discrete and continuous dynamics are simultaneously in action and interact with each other. In this work, a non-linear oscillatory dynamic system, which has both continuous and discrete dynamics, is considered, and an experimental setup is constructed. For an efficient and effective analysis, the discrete and continuous dynamics are treated simultaneously using a hybrid state modelling approach. The simulations and experiments are performed for different conditions of the system to investigate their effect on its behaviour. The use of the hybrid state modelling approach for dynamic systems containing interacting discrete and continuous state dynamics is demonstratedbothnumericallyandexperimentally.
Numerical modelling of 3D plastic flow and heat transfer during friction stir welding of stainless steel
Authors: Nandan R. , Roy G. G. , Lienert T. J. , DebRoy T.
Published: September 2006

Three-dimensional (3D) viscoplastic flow and temperature field during friction stir welding (FSW) of 304 austenitic stainless steel were mathematically modelled. The equations of conservation of mass, momentum and energy were solved in three dimensions using spatially variable thermophysical properties using a methodology adapted from well established previous work in fusion welding. Non-Newtonian viscosity for the metal flow was calculated considering strain rate and temperature dependent flow stress. The computed profiles of strain rate and viscosity were examined in light of the existing literature on thermomechanical processing of alloys. The computed results showed significant viscoplastic flow near the tool surface, and convective transport of heat was found to be an important mechanism of heat transfer. The computed temperature and velocity fields demonstrated strongly 3D nature of the transport of heat and mass indicating the need for 3D calculations. The computed temperature profiles agreed well with the corresponding experimentally measured values. The non-Newtonian viscosity for FSW of stainless steel was found to be of the same order of magnitude as that for the FSW of aluminium. Like FSW of aluminium, the viscosity was found to be a strong function of both strain rate and temperature, while strain rate was found to be the most dominant factor. A small region of recirculating plasticised material was found to be present near the tool pin. The size of this region was larger near the shoulder and smaller further away from it. Streamlines around the pin were influenced by the presence of the rotating shoulder, especially at higher elevations. Stream lines indicated that material was transported mainly around the pin in the retreating side.
Evaluation of through thickness residual stress in multipass butt welded joint by using inherent strain
Authors: Mochizuki M.
Published: September 2006

The through thickness residual stress of an eight pass butt welded plate joint is evaluated using inherent strain analysis. The residual stress distribution is obtained in detail along the thickness direction from measurements using multiple strain gauges. The residual stresses agree with the results of the thermal elastic–plastic analysis as well as the values obtained by direct measurement of the specimen surface, which is not used in inherent strain analysis. These results indicate that both inherent strain analysis and thermal elastic–plastic analysis are effective in evaluating through thickness residual stress. Therefore, each analysis method should be chosen after considering the object to be evaluated and the characteristics to be analysed.
Changes in toughness at low oxygen concentrations in steel weld metals
Authors: Terashima S. , Bhadeshia H. K. D. H.
Published: September 2006

Oxides in steel weld metals can initiate fracture or can improve toughness by influencing the development of beneficial microstructures. In this work, the authors conducted experiments in which the oxygen concentration was varied from 20 to 560 ppmw (parts per million by weight) in weld metals with tensile strength in the range 580–780 MPa. It is demonstrated that low and medium strength weld metals benefit from oxides up to a concentration of ∼200 ppmw as consistent with previous research, because acicular ferrite is stimulated in the microstructure. By contrast, oxides are detrimental to the toughness of high strength weld deposits at low oxygen concentrations under 140 ppmw, because the microstructure remains a predominantly martensite and the oxides simply serve to nucleate fracture. In high strength weld metal, therefore, good toughness is achieved even at low oxygen concentration of 20 ppmw O.
Deformation and fracture behaviour of P91 steel weldments at high temperatures
Authors: Ceyhan U. , Dogan B.
Published: September 2006

Microtensile specimen tests are conducted across similar welds of a P91 steel at 873 K. Specimens of different surface conditions are tested at two different loading rates, 0·2 and 0·5 mm min−1, in order to study the effects of surface finish and loading rate on mechanical properties of P91 steel. Deformation behaviour is studied with an SEM on specimen side surfaces. Correlation between microstructural behaviour and mechanical properties is studied both in microtensile and standard tensile tests.
Wetting behaviour of Cu based active brazing alloys on siliconised graphite
Authors: Chen J. C. , Hao C. Y. , Zhang J. S.
Published: September 2006

The effects of Al and silicon additions to Cu based brazing alloy and the surface free silicon on siliconised graphite substrate on the wetting behaviour of the siliconised graphite by Cu–Al–Si–Ti alloys were investigated using the sessile drop technique at 1100°C. The contact angles were measured and the interfacial reactions were analysed. It was shown that surface free Si on siliconised graphite had a great positive effect on the contact angle. Furthermore, interfacial reactions could be controlled by adjusting the contents of Si and Al in brazing alloys.
Humping mechanisms present in high speed welding
Authors: Soderstrom E. , Mendez P.
Published: September 2006

As welding speeds continually increase owing to automation and newer processes, a common defect that occurs is humping. Humping is the periodic occurrence of beadlike protuberances. The objective of the present investigation is to review current and previous researches that were made on humping, including both experimental and theoretical studies. It is found that humping can be classified into two distinct categories of formation: gouging region morphology and beaded cylinder morphology. Various theories that explain the two types of humping formation are examined. Experimental data compiled from many sources are presented to verify the models and explain the fundamental mechanisms of humping morphology. Humping prevention measures that can be applied directly to industrial fabrication are also included. The direct benefit is increased travel speeds that reduce production costs.
Size distribution of oxides and toughness of steel weld metals
Authors: Terashima S. , Bhadeshia H. K. D. H.
Published: September 2006

Experiments have been conducted to modify the size distribution of oxide particles in steel weld metals which have predominantly martensitic microstructures. It is found that the toughness improves significantly when the particles are refined, even when the total concentration of oxygen is unchanged in the process.
Evaluation of cold metal transfer (CMT) process for welding aluminium alloy
Authors: Pickin C. G. , Young K.
Published: September 2006

Cold metal transfer (CMT) is an automated welding process based on dip transfer welding, characterised by controlled material deposition during the short circuit of the wire electrode to the workpiece. Preliminary results are presented examining the suitability of this process for welding aluminium alloy. Trials show that in comparison with pulsed metal inert gas (MIG) welding, CMT exhibits a higher electrode melting coefficient. By adjusting the short circuit duration penetration can be controlled with only a small change in electrode deposition. Furthermore, by mixing pulsed MIG welding with CMT welding the working envelope of the process is greatly extended allowing thicker material sections to be welded with improved weld bead aesthetics.
Experimental study on improving welding efficiency of twin electrode TIG welding method
Authors: Leng X.-S. , Zhang G.-J. , Wu L.
Published: September 2006

Twin electrode TIG (T-TIG) welding is a new method, which woks with two electrodes insulated from each other in a welding torch. In the present study, the T-TIG welding system was established. Then the force and heat effects of T-TIG coupling arc were analysed by measuring arc pressure and arc static voltage–ampere characteristic respectively. After that, high speed thin plate and high deposition grooved thick plate welding experiments were carried out with both T-TIG and conventional TIG welding methods. The results show that with similar arc heat input, the T-TIG coupling arc has much lower arc pressure than TIG single arc. The characteristic makes T-TIG welding suitable for high efficiency welding on the basis of maintaining the original advantages of TIG welding.
Study on TIG welding of dissimilar Mg alloy and Cu with Fe as interlayer
Authors: Liu L.-M. , Wang S.-X. , Zhu M.-L.
Published: September 2006

Dissimilar Mg alloy and Cu lap joints were prepared by tungsten inert gas (TIG) welding with Fe as an interlayer, without producing intermetallic compounds MgCu2 and Mg2Cu. Copper and Fe were joined together in the form of remelt deposit welding and Mg alloy and Fe plate were joined together in the form of brazing. During tensile testing, the joints between Fe plate and Mg alloy fractured, and Mg alloy and Fe plate were joined together by interatomic force. Metallic oxides produced in the interface between Mg and Fe resulted in reduction in the mechanical properties of the welded joints.
Pulsed laser welding of Steelite, a steel polypropylene laminate
Authors: Gower H. L. , Richardson I. M. , Pieters R. R. G. M.
Published: September 2006

Laminated products are gaining importance as structural materials and it is becoming increasingly important to join them quickly and effectively. The possibility of using pulsed laser welding to join Steelite, a steel polypropylene steel sandwich structure, has been examined, and in the present paper, the authors describe how various combinations of focal spot diameter, pulse duration and pulse power influence the weld. The most important factors contributing to the final weld dimensions are pulse energy, pulse duration and focal spot size. It is shown that although the polymer core affects the final weld dimensions, the development of the weld is comparable with that in monolithic materials. Furthermore, a smaller focal spot diameter was shown to result in more reliable results, a smaller heat affected zone, and reduced damage to the polypropylene core. The results for single spot welds demonstrate the feasibility of using overlapping spot welds to make butt joints in metal polymer laminates.
Dimensionless correlation to estimate peak temperature during friction stir welding
Authors: Roy G. G. , Nandan R. , DebRoy T.
Published: September 2006

A dimensionless correlation has been developed based on Buckingham's π-theorem to estimate the peak temperature during friction stir welding (FSW). A relationship is proposed between dimensionless peak temperature and dimensionless heat input. Apart from the estimation of peak temperature, it can also be used for the selection of welding conditions to prevent melting of the workpiece during FSW. The correlation includes thermal properties of the material and the tool, the area of the tool shoulder and the rotational and translation speeds of the tool. The peak temperatures reported in the literature during FSW of various materials and welding conditions were found to be in fair agreement with the proposed correlation.
Fatigue properties and failure characterisation of self-piercing riveted 6111 aluminium sheet joints
Authors: Khanna S. K. , Long X. , Krishnamoorthy S. , Agrawal H. N.
Published: September 2006

Aluminium has been long considered as an alternative material for steel in the automobile industry. However, welding of aluminium is more difficult and prone to defects compared with steel. Therefore other methods of joining aluminium sheets are being investigated. In the present investigation, the fatigue properties of self-piercing riveted joints in 6111 aluminium alloy sheets has been studied using tensile shear and coach peel type specimens. Different thickness combinations of aluminium sheet joints and different load ratio R were also investigated in the fatigue tests. Fatigue crack initiation and growth were observed and analysed. It has been found that the maximum fatigue load increases with increasing sheet thickness in both tensile shear and coach peel specimens, but this increase is smaller for high fatigue cycles. With the same maximum fatigue load, specimens under load ratio of R=0·3 have a longer fatigue life than that of specimens under R = 0·1. In most of the cases (>90%), specimens failed in the upper sheet (with the rivet head) during fatigue loading in the case of equal thickness combination and thick upper sheet combination, for both tensile shear and coach peel specimens. As for different thickness combination rivet joints, the thinner sheets are usually the places where failure occurs whichever it is the upper sheet or lower sheet in the combination.
Microstructure characteristics of resistance spot welds of AZ31 Mg alloy
Authors: Wang Y. R. , Feng J. C. , Zhang Z. D.
Published: September 2006

The experimental investigation was carried out to study the weld microstructure of resistance spot welding of AZ31 Mg alloy 1 mm thick. A fine and homogeneous non-equilibrium microstructure of globular α grains, surrounded by eutectic mixtures of α and β (Mg17Al12), was achieved. The thermal–electrical–mechanical analysis model was employed to simulate the thermal history and the temperature gradient. It was found that a combination of the welding conditions and the particular thermophysical properties of the AZ31Mg alloy established a uniform temperature distribution throughout the weld pool and this thermal condition is ideal for nucleation throughout the melt metal and equiaxed grain structure forming.
Numerical analysis of single sided spot welding process used in sheet to tube joining
Authors: Liang C.-P. , Lin Z.-Q. , Chen G.-L. , Li Y.-B.
Published: September 2006

As a new kind of lightweight structure, hydroformed tubes are now widely used in vehicle bodies. The single sided spot welding (SSSW) is a variation of resistance welding used in joining hydroformed closed tubular parts and vehicle structures. During the process of SSSW, large deformation and complex contact status of the workpieces occur because there is no inside support. The time variation of the contact region and pressure distribution changes the flow paths for electric current timely and brings a fierce shunting at the position far away from the axis line, which prevents the heat concentration at the faying surface of workpieces. The characteristics of SSSW different from those of classical resistance welding mentioned above make it difficult to determine rational welding processing parameters for SSSW. In the present paper, a comprehensive structural–thermoelectric model is established. Using the incrementally coupled analysis of finite element analysis, the electrical, thermal and mechanical aspects of sheet to tube process using SSSW are investigated. The mechanical characteristic of specimens during the squeeze and welding progress, the electric current density transient distribution, the nugget formation process, and the effects of welding parameters for SSSW are discussed. It is found that ring nugget is obtained by sheet to tube SSSW. Modifying electrode force during welding cycle is a valid method to obtain acceptable nugget with shorter welding time or less energy. The calculated results of nugget size and location are in good agreement with those of experimental observations.
Effects of welding parameters on melting energy of CO2 laser–GMA hybrid welding
Authors: Gao M. , Zeng X. Y. , Hu Q. W.
Published: September 2006

A series of CO2 laser–gas metal arc (GMA) hybrid welding experiments were carried out on the mild steel workpiece to investigate the effects of the welding parameters, such as laser power, arc current and the distance between laser and arc D LA, on the melting energy. A dimensionless parameter psi was introduced to indicate the change in the melting energy of hybrid welding. The results showed that with different welding parameters, the melting energy of hybrid welding was changed by the two heat sources (laser and arc) interaction. With an optimal combination welding parameters, psi can be increased up to 23%. Finally, the role of the two different mechanisms in the heat sources interaction was quantitatively discussed in terms of psi. It can be concluded that when D LA<4 mm, the interaction between the laser induced plasma and the arc plasma dominates the heat sources interaction, therefore the changes of melting energy, whereas the heat sources interaction is only dominated by the preheating mechanism when D LA≥4 mm.
Weldability of 17-4PH stainless steel in overaged heat treated condition
Authors: Das C. R. , Dey H. C. , Srinivasan G. , Albert S. K. , Bhaduri A. K. , Dasgupta A.
Published: September 2006

Studies on the weldability of 17-4PH stainless steel, in the 621°C overaged condition, showed that Creq/Nieq ratio higher than 1·5 resulted in primary ferritic mode of solidification in the weld metal. Post-weld aging treatment at 482°C enhanced the strength of the weld joint with corresponding reduction in impact toughness of the weld metal while post-weld aging at 621°C caused marginal reduction in strength of the weld joint with significant increase in impact toughness of the weld metal.
In situ observation of morphological development for acicular ferrite in weld metal
Authors: Terasaki H. , Komizo Y.
Published: September 2006

Acicular ferrite is regarded as the most desirable microstructural feature, in view of strength and toughness, in mild and low alloy steel weld metals. Recent evolution and diversity of mechanical property for base metal demand the same property as the weld. Therefore, understanding of the formation mechanism for acicular ferrite microstructure in weld is one of the essential problems for low alloy steel weld. In the present work, the morphological development of acicular ferrite in situ, was observed during weld cooling. The sample designed to form acicular ferrite microstructure was schematically heated and cooled by infrared imaging furnace and the morphological developments were directly observed using laser scanning conforcal microscopy. The nucleation and growing at inclusion, sympathetic nucleation and impingement event of acicular ferrite were directly shown in high time resolution.
Sensing and seam tracking of welding line in backingless V groove welding
Authors: Yamane S. , Yamamoto H. , Kaneko Y. , Oshima K.
Published: September 2006

The formation of stable back beads in the first layer weld during one side multilayer welding is important to achieve high quality welded metal joints. The authors tried to apply the switch back welding method to butt welding to join discs with flat metal plates without backing plates. During the welding, the gap was detected by processing the weld pool image taken with a CCD camera. Moreover, the tip of the electrode wire is changing owing to a curve of its wire extension in accordance with a rotation of the torch axis. Even though teaching is achieved before the welding, the weaving centre is shifted from the gap centre. The controller of the seam tracking was designed to prevent any steady state error.
Intravascular large B-cell lymphoma (IVLBCL): a clinicopathologic study of 96 cases with special reference to the immunophenotypic heterogeneity of CD5
Authors: Murase Takuhei , Yamaguchi Motoko , Suzuki Ritsuro , Okamoto Masataka , Sato Yumiko , Tamaru Jun-ichi , Kojima Masaru , Miura Ikuo , Mori Naoyoshi , Yoshino Tadashi , Nakamura Shigeo
Published: September 2006

Intravascular large B-cell lymphoma (IVLBCL) is pathologically distinct with a broad clinical spectrum and immunophenotypic heterogeneity. A series of 96 patients with IVLBCL (median age, 67 years; range, 41-85 years; 50 men) was reviewed. Anemia/thrombocytopenia (84%), hepatosplenomegaly (77%), B symptoms (76%), bone marrow involvement (75%), and hemophagocytosis (61%) were frequently observed. The International Prognostic Index score was high or high-intermediate in 92%. For 62 patients receiving anthracycline-based chemotherapies, median survival was 13 months. CD5, CD10, Bcl-6, MUM1, and Bcl-2 were positive in 38%, 13%, 26%, 95%, and 91% of tumors, respectively. All 59 CD10− IVLBCL cases examined were nongerminal center B-cell type because they lacked the Bcl-6+MUM1− immunophenotype. CD5 positivity was associated with a higher prevalence of marrow/blood involvement and thrombocytopenia and a lower frequency of neurologic abnormalities among patients with CD10−IVLBCL. Compared with 97 cases of de novo CD5+CD10−diffuse LBCL, 31 cases of CD5+CD10−IVLBCL exhibited higher frequencies of poor prognostic parameters, except age. Multivariate analysis in IVLBCL revealed that a lack of anthracycline-based chemotherapies (P < .001, hazard ratio [HR]: 9.256), age older than 60 years (P = .012, HR: 2.459), and thrombocytopenia less than 100 × 109/L (P = .012, HR: 2.427) were independently unfavorable prognostic factors; CD5 positivity was not. Beyond immunophenotypic diversity, IVLBCL constitutes a unique group with aggressive behavior.
Nitric oxide plays a critical role in suppression of T-cell proliferation by mesenchymal stem cells
Authors: Sato Kazuya , Ozaki Katsutoshi , Oh Iekuni , Meguro Akiko , Hatanaka Keiko , Nagai Tadashi , Muroi Kazuo , Ozawa Keiya
Published: September 2006

The molecular mechanisms by which mesenchymal stem cells (MSCs) suppress T-cell proliferation are poorly understood, and whether a soluble factor plays a major role remains controversial. Here we demonstrate that the T-cell–receptor complex is not a target for the suppression, suggesting that downstream signals mediate the suppression. We found that Stat5 phosphorylation in T cells is suppressed in the presence of MSCs and that nitric oxide (NO) is involved in the suppression of Stat5 phosphorylation and T-cell proliferation. The induction of inducible NO synthase (NOS) was readily detected in MSCs but not T cells, and a specific inhibitor of NOS reversed the suppression of Stat5 phosphorylation and T-cell proliferation. This production of NO in the presence of MSCs was mediated by CD4 or CD8 T cells but not by CD19 B cells. Furthermore, inhibitors of prostaglandin synthase or NOS restored the proliferation of T cells, whereas an inhibitor of indoleamine 2,3-dioxygenase and a transforming growth factor–β–neutralizing antibody had no effect. Finally, MSCs from inducible NOS−/− mice had a reduced ability to suppress T-cell proliferation. Taken together, these results suggest that NO produced by MSCs is one of the major mediators of T-cell suppression by MSCs.
Distinct memory CD4+ T-cell subsets mediate immune recognition of Epstein Barr virus nuclear antigen 1 in healthy virus carriers
Authors: Heller Kevin N. , Upshaw Jenica , Seyoum Beza , Zebroski Henry , Münz Christian
Published: September 2006

CD4+ T cells, specific for transforming latent infection with the Epstein Barr virus (EBV), consistently recognize the nuclear antigen 1 of EBV (EBNA1). EBNA1-specific effector CD4+ T cells are primarily T-helper 1 (TH1) polarized. Here we show that most healthy EBV carriers have such IFN-secreting EBNA1-specific CD4+ T cells at a frequency of 0.03% of circulating CD4+ T cells. In addition, healthy carriers have a large pool of CD4+ T cells that proliferated in response to EBNA1 and consisted of distinct memory-cell subsets. Despite continuous antigen presence due to persistent EBV infection, half of the proliferating EBNA1-specific CD4+ T cells belonged to the central-memory compartment (TCM). The remaining EBNA1-specific CD4+ T cells displayed an effector-memory phenotype (TEM), of which a minority rapidly secreted IFN upon stimulation with EBNA1. Based on chemokine receptor analysis, all EBNA1-specific TCM CD4+ T cells were TH1 committed. Our results suggest that protective immune control of chronic infections, like EBV, includes a substantial reservoir of TCM CD4+ TH1 precursors, which continuously fuels TH1-polarized effector cells.
Control of coronavirus infection through plasmacytoid dendritic-cell–derived type I interferon
Authors: Cervantes-Barragan Luisa , Züst Roland , Weber Friedemann , Spiegel Martin , Lang Karl S. , Akira Shizuo , Thiel Volker , Ludewig Burkhard
Published: September 2006

This study demonstrates a unique and crucial role of plasmacytoid dendritic cells (pDCs) and pDC-derived type I interferons (IFNs) in the pathogenesis of mouse coronavirus infection. pDCs controlled the fast replicating mouse hepatitis virus (MHV) through the immediate production of type I IFNs. Recognition of MHV by pDCs was mediated via TLR7 ensuring a swift IFN-α production following encounter with this cytopathic RNA virus. Furthermore, the particular type I IFN response pattern was not restricted to the murine coronavirus, but was also found in infection with the highly cytopathic human severe acute respiratory syndrome (SARS) coronavirus. Taken together, our results suggest that rapid production of type I IFNs by pDCs is essential for the control of potentially lethal coronavirus infections.
MicroArray Facility: a laboratory information management system with extended support for Nylon based technologies
Authors: Honoré Paul , Granjeaud Samuel , Tagett Rebecca , Deraco Stéphane , Beaudoing Emmanuel , Rougemont Jacques , Debono Stéphane , Hingamp Pascal
Published: September 2006

Background

High throughput gene expression profiling (GEP) is becoming a routine technique in life science laboratories. With experimental designs that repeatedly span thousands of genes and hundreds of samples, relying on a dedicated database infrastructure is no longer an option.

GEP technology is a fast moving target, with new approaches constantly broadening the field diversity. This technology heterogeneity, compounded by the informatics complexity of GEP databases, means that software developments have so far focused on mainstream techniques, leaving less typical yet established techniques such as Nylon microarrays at best partially supported.

Results

MAF (MicroArray Facility) is the laboratory database system we have developed for managing the design, production and hybridization of spotted microarrays. Although it can support the widely used glass microarrays and oligo-chips, MAF was designed with the specific idiosyncrasies of Nylon based microarrays in mind. Notably single channel radioactive probes, microarray stripping and reuse, vector control hybridizations and spike-in controls are all natively supported by the software suite. MicroArray Facility is MIAME supportive and dynamically provides feedback on missing annotations to help users estimate effective MIAME compliance. Genomic data such as clone identifiers and gene symbols are also directly annotated by MAF software using standard public resources. The MAGE-ML data format is implemented for full data export. Journalized database operations (audit tracking), data anonymization, material traceability and user/project level confidentiality policies are also managed by MAF.

Conclusion

MicroArray Facility is a complete data management system for microarray producers and end-users. Particular care has been devoted to adequately model Nylon based microarrays. The MAF system, developed and implemented in both private and academic environments, has proved a robust solution for shared facilities and industry service providers alike.
Detection of potentially valuable polymorphisms in four group I intron insertion sites at the 3'-end of the LSU rDNA genes in biocontrol isolates of Metarhizium anisopliae
Authors: Márquez Marcela , Iturriaga Enrique A , Quesada-Moraga Enrique , Santiago-Álvarez Cándido , Monte Enrique , Hermosa Rosa
Published: September 2006

Background

The entomopathogenic anamorphic fungus Metarhizum anisopliae is currently used as a biocontrol agent (BCA) of insects. In the present work, we analyzed the sequence data obtained from group I introns in the large subunit (LSU) of rDNA genes with a view to determining the genetic diversity present in an autochthonous collection of twenty-six M. anisopliae isolates selected as BCAs.

Results

DNA fragments corresponding to the 3'-end of the nuclear LSU rDNA genes of 26 M. anisopliae isolates were amplified by PCR. The amplicon sizes ranged from 0.8 to 3.4-kb. Four intron insertion sites, according to Escherichia coli J01695 numbering, were detected- Ec1921, Ec2066, Ec2449 and Ec2563- after sequencing and analysis of the PCR products. The presence/absence of introns allowed the 26 isolates to be distributed into seven genotypes. Nine of the isolates tested showed no introns, 4 had only one, 3 two, and 10 displayed three introns. The most frequent insertion sites were Ec1921 and Ec2449. Of the 26 isolates, 11 showed insertions at Ec2563 and a 1754-bp sequence was observed in ten of them. The most-parsimonious (MP) tree obtained from parsimony analysis of the introns revealed a main set containing four-groups that corresponded to the four insertion sites.

Conclusion

Four insertion sites of group I introns in the LSU rDNA genes allowed the establishment of seven genotypes among the twenty-six biocontrol isolates of M. anisopliae. Intron insertions at the Ec2563 site were observed for first time in this species.
Serum neuron-specific enolase as early predictor of outcome after in-hospital cardiac arrest: a cohort study
Authors: Rech Tatiana H , Vieira Silvia ReginaRios , Nagel Fabiano , Brauner Janete Salles , Scalco Rosana
Published: September 2006

Introduction

Outcome after cardiac arrest is mostly determined by the degree of hypoxic brain damage. Patients recovering from cardiopulmonary resuscitation are at great risk of subsequent death or severe neurological damage, including persistent vegetative state. The early definition of prognosis for these patients has ethical and economic implications. The main purpose of this study was to investigate the prognostic value of serum neuron-specific enolase (NSE) in predicting outcomes in patients early after in-hospital cardiac arrest.

Methods

Forty-five patients resuscitated from in-hospital cardiac arrest were prospectively studied from June 2003 to January 2005. Blood samples were collected, at any time between 12 and 36 hours after the arrest, for NSE measurement. Outcome was evaluated 6 months later with the Glasgow outcome scale (GOS). Patients were divided into two groups: group 1 (unfavorable outcome) included GOS 1 and 2 patients; group 2 (favorable outcome) included GOS 3, 4 and 5 patients. The Mann–Whitney U test, Student's t test and Fisher's exact test were used to compare the groups.

Results

The Glasgow coma scale scores were 6.1 ± 3 in group 1 and 12.1 ± 3 in group 2 (means ± SD; p < 0.001). The mean time to NSE sampling was 20.2 ± 8.3 hours in group 1 and 28.4 ± 8.7 hours in group 2 (p = 0.013). Two patients were excluded from the analysis because of sample hemolysis. At 6 months, favorable outcome was observed in nine patients (19.6%). Thirty patients (69.8%) died and four (9.3%) remained in a persistent vegetative state. The 34 patients (81.4%) in group 1 had significantly higher NSE levels (median 44.24 ng/ml, range 8.1 to 370) than those in group 2 (25.26 ng/ml, range 9.28 to 55.41; p = 0.034).

Conclusion

Early determination of serum NSE levels is a valuable ancillary method for assessing outcome after in-hospital cardiac arrest.
Analysis of proinflammatory activity of highly purified eukaryotic recombinant HMGB1 (amphoterin)
Authors: Rouhiainen Ari , Tumova Sarka , Valmu Leena , Kalkkinen Nisse , Rauvala Heikki
Published: September 2006

HMGB1 (amphoterin) is a 30-kDa heparin-binding protein that mediates transendothelial migration of monocytes and has proinflammatory cytokine-like activities. In this study, we have investigated proinflammatory activities of both highly purified eukaryotic HMGB1 and bacterially produced recombinant HMGB1 protens. Mass analyses revealed that recombinant eukaryotic HMGB1 has an intrachain disulphide bond. In mass analysis of tissue-derived HMGB1, two forms were detected: the carboxyl terminal glutamic acid residue lacking form and a full-length form. Cell culture studies indicated that both eukaryotic and bacterial HMGB1 proteins induce TNF-α secretion and nitric oxide release from mononuclear cells. Affinity chromatography analysis revealed that HMGB1 binds tightly to proinflammatory bacterial substances. A soluble proinflammatory substance was separated from the bacterial recombinant HMGB1 by chloroform-methanol treatment. HMGB1 interacted with phosphatidylserine in both solid-phase binding and cell culture assays, suggesting that HMGB1 may regulate phosphatidylserine-dependent immune reactions. In conclusion, HMGB1 polypeptide has a weak proinflammatory activity by itself, and it binds to bacterial substances, including lipids, that may strengthen its effects.
Targeted in vivo expression of IFN-γ-inducible protein 10 induces specific antitumor activity
Authors: Yang Xiuli , Chu Yiwei , Wang Ying , Zhang Ruihua , Xiong Sidong
Published: September 2006

Although it is known that the chemoattractant effect of IFN-γ inducible protein 10 (IP-10), a CXC chemokine (CXCL10), plays an important role in T cell-mediated antitumor immunity in vivo, whether IP-10 is involved in modulating the proliferation, survival and functional activation of tumor-specific T cells remains poorly investigated. Using an experimental mouse tumor model, we demonstrated that the in vivo growth of 4T1 tumor cells harboring IP-10 gene (4T1-IP-10) was inhibited. Mice inoculated with 4T1-IP-10 tumor cells expressing functional IP-10 survived over 90 days, whereas mice injected with control parental 4T1 cells and mice of control 4T1 cells transduced with control plasmid all succumbed to the tumor by day 38 after tumor inoculation. Mechanical analysis showed that targeted expression of IP-10 in 4T1 tumor cells markedly enhanced the infiltration of tumor-specific T cells into the 4T1-IP-10 tumor. These tumor infiltrating T lymphocytes (TILs) recruited by IP-10 were potent cytolytic killers against 4T1 tumor cells and were able to proliferate and produce high levels of IFN-γ in response to 4T1 cells. In vivo administration of IP-10-recruited TILs induced vigorous proliferation of these TILs in situ in the 4T1-IP-10 tumor but not in the 4T1-pcDNA3 and parental 4T1 tumors. Furthermore, culture of TILs together with recombinant IP-10 significantly enhanced the proliferation and expansion of IP-10-recruited TILs in response to 4T1 tumor antigens. These results suggest that IP-10 is not only able to chemoattract tumor-specific T cells into the local tissue, but also enhance the proliferation, survival, and functional activation of these TILs, leading to the tumor regression. Thus, targeted expression of IP-10 in vivo will allow for the development of a novel approach for immunotherapy of tumor.
CD4+ T cells stimulate memory CD8+ T cell expansion via acquired pMHC I complexes and costimulatory molecules, and IL-2 secretion
Authors: Shi Meiqing , Hao Siguo , Chan Tim , Xiang Jim
Published: September 2006

The rapid and efficient expansion of CD8+ memory T cells after the second encounter with a pathogen constitutes a hallmark trait of adaptive immunity. Yet, the contribution of CD4+ T cells to the expansion of memory CD8+ T cells remains the subject of controversy. Here, we show that, antigen-specific CD4+ T cells, once activated by dendritic cells (DC) in vitro, have the capacity to stimulate expansion of memory CD8+ T cells in vivo. The memory CD8+ T cell expansion triggered by active CD4+ T cells are mediated through DC-derived MHC I/peptide complexes and CD80 molecules displayed on the active CD4+ T cells, with the involvement of IL-2 secreted by the active CD4+ T cells. These results highlight a previously undescribed role of active CD4+ T cells in triggering expansion of memory CD8+ T cells.
HMGB1-secreting capacity of multiple cell lineages revealed by a novel HMGB1 ELISPOT assay
Authors: Wähämaa Heidi , Vallerskog Therese , Qin Shixin , Lunderius Carolina , LaRosa Gregory , Andersson Ulf , Harris Helena Erlandsson
Published: September 2006

High mobility group box protein 1 (HMGB1) exerts different biological functions dependent on its cellular localization. Nuclear HMGB1 maintains chromatin architecture and is required for undisturbed transcription activity, and extracellularly released HMGB1 mediates inflammation and tissue regeneration. A present paucity of readily accessible methods to quantify released HMGB1 represents a problem concerning the exploration of HMGB1 biology. We have now developed a HMGB1-specific ELISPOT assay enabling enumeration of individual HMGB1-releasing cells. The method also allows automated, semiquantitative assessment of released HMGB1 by evaluating areas of single HMGB1 spots. Actively secreted HMGB1 as well as cells passively releasing the protein following necrotic cell death are visualized distinctly using this ELISPOT assay. Kinetics of HMGB1 secretion after different stimuli was studied using cell lines of various lineages. IFN-γ already induced substantial HMGB1 secretion from the monocytic cell line RAW 264.7 within 24 h and even more so after 48 h. LPS only stimulated a modest HMGB1 release within 24 h, but this increased considerably by 48 h. TNF-induced HMGB1 release was unexpectedly low. Mast cells, which share the secretory, lysosomal pathway with macrophages/monocytes, did not secrete HMGB1 in response to any studied mode of activation. Most transformed cells overexpress HMGB1, but the ELISPOT assay revealed that all transformed cell lines will not actively secrete the protein. We believe the ELISPOT method provides a novel tool to study pathways promoting or inhibiting HMGB1 secretion.
Prestack scalar reverse-time depth migration of 3D elastic seismic data
Authors: Sun Robert , McMechan George A. , Lee Chen-Shao , Chow Jinder , Chen Chen-Hong
Published: September 2006

Using two independent, 3D scalar reverse-time depth migrations, we migrate the reflected P- and S-waves in a prestack 3D, three-component (3-C), elastic seismic data volume generated with a P-wave source in a 3D model and recorded at the top of the model. Reflected P- and S-waves are extracted by divergence (a scalar) and curl (a 3-C vector) calculations, respectively, during shallow downward extrapolation of the elastic seismic data. The imaging time for the migrations of both the reflected P- and P-S converted waves at each point is the one-way P-wave traveltime from the source to that point.The divergence (the extracted P-waves) is reverse-time extrapolated using a finite-difference solution of the 3D scalar wave equation in a 3D P-velocity modeland is imaged to obtain the migrated P-image. The curl (the extracted S-waves) is first converted into a scalar S-wavefield by taking the curl’s absolute value as the absolute value of the scalar S-wavefield and assigning a positive sign if the curl is counterclockwise relative to the source or a negative sign otherwise. This scalar S-wavefield is then reverse-time extrapolated using a finite-difference solution of the 3D scalar wave equation in a 3D S-velocity model, and it is imaged with the same one-way P-wave traveltime imaging condition as that used for the P-wave. This achieves S-wave polarity uniformity and ensures constructive S-wave interference between data from adjacent sources. The algorithm gives satisfactory results on synthetic examples for 3D laterally inhomogeneous models.
Wave-equation-based seismic illumination analysis
Authors: Xie Xiao-Bi , Jin Shengwen , Wu Ru-Shan
Published: September 2006

We present a wave-equation-based method for seismic illumination analysis. A one-way wave-equation-based, generalized screen propagator is used to extrapolate the wavefields from sources and receivers to the subsurface target. A local plane-wave analysis is used at the target to calculate localized, directional energy fluxes for both source and receiver wavefields. We construct an illumination matrix using these energy fluxes to quantify the target illumination conditions. The target geometry information is used to manipulate the illumination matrix and generate different types of illumination measures. The wave-equation-based approach can properly handle forward multiple-scattering phenomena, including focusing/defocusing, diffraction, and interference effects. It can be directly applied to complex velocity models. Velocity-model smoothing and Fresnel-zone smoothing are not required. Different illumination measurements derived from this method can be applied to target-oriented or volumetric illumination analyses. This new method is flexible and practical for illumination analysis in complex 2D and 3D velocity models with nontrivial acquisition and target geometries.
Stochastic inversion of pressure and saturation changes from time-lapse AVO data
Authors: Veire Helene Hafslund , Borgos Hilde Grude , Landrø Martin
Published: September 2006

Effects of pressure and fluid saturation can have the same degree of impact on seismic amplitudes and differential traveltimes in the reservoir interval; thus, they are often inseparable by analysis of a single stacked seismic data set. In such cases, time-lapse AVO analysis offers an opportunity to discriminate between the two effects. We quantify the uncertainty in estimations to utilize information about pressure- and saturation-related changes in reservoir modeling and simulation. One way of analyzing uncertainties is to formulate the problem in a Bayesian framework. Here, the solution of the problem will be represented by a probability density function (PDF), providing estimations of uncertainties as well as direct estimations of the properties.

A stochastic model for estimation of pressure and saturation changes from time-lapse seismic AVO data is investigated within a Bayesian framework. Well-known rock physical relationships are used to set up a prior stochastic model. PP reflection coefficient differences are used to establish a likelihood model for linking reservoir variables and time-lapse seismic data. The methodology incorporates correlation between different variables of the model as well as spatial dependencies for each of the variables. In addition, information about possible bottlenecks causing large uncertainties in the estimations can be identified through sensitivity analysis of the system. The method has been tested on 1D synthetic data and on field time-lapse seismic AVO data from the Gullfaks Field in the North Sea.