bluuebunny/crossref_metadata_2025 huggingface dataset:
WASP: a Web-based Allele-Specific PCR assay designing tool for detecting SNPs and mutations
Authors: Wangkumhang Pongsakorn , Chaichoompu Kridsadakorn , Ngamphiw Chumpol , Ruangrit Uttapong , Chanprasert Juntima , Assawamakin Anunchai , Tongsima Sissades
Published: August 2007

Background

Allele-specific (AS) Polymerase Chain Reaction is a convenient and inexpensive method for genotyping Single Nucleotide Polymorphisms (SNPs) and mutations. It is applied in many recent studies including population genetics, molecular genetics and pharmacogenomics. Using known AS primer design tools to create primers leads to cumbersome process to inexperience users since information about SNP/mutation must be acquired from public databases prior to the design. Furthermore, most of these tools do not offer the mismatch enhancement to designed primers. The available web applications do not provide user-friendly graphical input interface and intuitive visualization of their primer results.

Results

This work presents a web-based AS primer design application called WASP. This tool can efficiently design AS primers for human SNPs as well as mutations. To assist scientists with collecting necessary information about target polymorphisms, this tool provides a local SNP database containing over 10 million SNPs of various populations from public domain databases, namely NCBI dbSNP, HapMap and JSNP respectively. This database is tightly integrated with the tool so that users can perform the design for existing SNPs without going off the site. To guarantee specificity of AS primers, the proposed system incorporates a primer specificity enhancement technique widely used in experiment protocol. In particular, WASP makes use of different destabilizing effects by introducing one deliberate 'mismatch' at the penultimate (second to last of the 3'-end) base of AS primers to improve the resulting AS primers. Furthermore, WASP offers graphical user interface through scalable vector graphic (SVG) draw that allow users to select SNPs and graphically visualize designed primers and their conditions.

Conclusion

WASP offers a tool for designing AS primers for both SNPs and mutations. By integrating the database for known SNPs (using gene ID or rs number), this tool facilitates the awkward process of getting flanking sequences and other related information from public SNP databases. It takes into account the underlying destabilizing effect to ensure the effectiveness of designed primers. With user-friendly SVG interface, WASP intuitively presents resulting designed primers, which assist users to export or to make further adjustment to the design. This software can be freely accessed at http://bioinfo.biotec.or.th/WASP.
Quantitative multiplex detection of plant pathogens using a novel ligation probe-based system coupled with universal, high-throughput real-time PCR on OpenArrays™
Authors: van Doorn Ronald , Szemes Marianna , Bonants Peter , Kowalchuk George A , Salles Joana F , Ortenberg Elen , Schoen Cor D
Published: August 2007

Background

Diagnostics and disease-management strategies require technologies to enable the simultaneous detection and quantification of a wide range of pathogenic microorganisms. Most multiplex, quantitative detection methods available suffer from compromises between the level of multiplexing, throughput and accuracy of quantification. Here, we demonstrate the efficacy of a novel, high-throughput, ligation-based assay for simultaneous quantitative detection of multiple plant pathogens. The ligation probes, designated Plant Research International-lock probes (PRI-lock probes), are long oligonucleotides with target complementary regions at their 5' and 3' ends. Upon perfect target hybridization, the PRI-lock probes are circularized via enzymatic ligation, subsequently serving as template for individual, standardized amplification via unique probe-specific primers. Adaptation to OpenArrays™, which can accommodate up to 3072 33 nl PCR amplifications, allowed high-throughput real-time quantification. The assay combines the multiplex capabilities and specificity of ligation reactions with high-throughput real-time PCR in the OpenArray™, resulting in a flexible, quantitative multiplex diagnostic system.

Results

The performance of the PRI-lock detection system was demonstrated using 13 probes targeting several significant plant pathogens at different taxonomic levels. All probes specifically detected their corresponding targets and provided perfect discrimination against non-target organisms with very similar ligation target sites. The nucleic acid targets could be reliably quantified over 5 orders of magnitude with a dynamic detection range of more than 104. Pathogen quantification was equally robust in single target versus mixed target assays.

Conclusion

This novel assay enables very specific, high-throughput, quantitative detection of multiple pathogens over a wide range of target concentrations and should be easily adaptable for versatile diagnostic purposes.
An unusual presentation of adenoid cystic carcinoma of the minor salivary glands with cranial nerve palsy: a case study
Authors: Abdul-Hussein Amal , Morris Pierre A , Markova Tsveti
Published: August 2007

Background

Adenoid Cystic Carcinoma (ACC) is a rare tumor entity and comprises about 1% of all malignant tumor of the oral and maxillofacial region. It is slow growing but a highly invasive cancer with a high recurrence rate. Intracranial ACC is even more infrequent and could be primary or secondary occurring either by direct invasion, hematogenous spread, or perineural spread. We report the first case of the 5th and 6th nerve palsy due to cavernous sinus invasion by adenoid cystic carcinoma.

Case presentation

A 49-year-old African American female presented to the emergency room complaining of severe right-sided headache, photophobia, dizziness and nausea, with diplopia. The patient had a 14 year history migraine headaches, hypertension, and mild intermittent asthma. Physical examination revealed right lateral rectus muscle palsy with esotropia. There was numbness in all three divisions of the right trigeminal nerve. Motor and sensory examination of extremities was normal. An MRI of the brain/brain stem was obtained which showed a large mass in the clivus extending to involve the nasopharynx, pterygoid plate, sphenoid and right cavernous sinuses.

Biopsy showed an ACC tumor with a cribriform pattern of the minor salivary glands. The patient underwent total gross surgical resection and radiation therapy.

Conclusion

This is a case of ACC of the minor salivary glands with intracranial invasion. The patient had long history of headaches which changed in character during the past year, and symptoms of acute 5th and 6th cranial nerve involvement. Our unique case demonstrates direct invasion of cavernous sinus and could explain the 5th and 6th cranial nerve involvement as histopathology revealed no perineural invasion.
Influence of IFN-gamma and its receptors in human breast cancer
Authors: García-Tuñón Ignacio , Ricote Mónica , Ruiz A Antonio , Fraile Benito , Paniagua Ricardo , Royuela Mar
Published: August 2007

Background

Interferons are a group of proteins that trigger multiple responses including prevention of viral replication, inhibition of cell growth, and modulation of cell differentiation. In different mammary carcinoma cell lines IFNγ induces growth arrest at mid-G1. At the present there are noin vivostudies in human breast. The aim of this study was to investigate the expression patterns of IFNγ and its two receptors (IFNγ-Rα and IFNγ-Rβ) by Western blot and immunohistochemistry, in order to elucidate its role in the different types of human breast cancer (in situand infiltrative).

Methods

Immunohistochemical and semiquantitative study of IFNγ, its receptors types (IFNγ-Rα and IFNγ-Rβ), cell proliferation (proliferating cell nuclear antigen, also named PCNA), and apoptosis (TUNEL method) was carried between the three breast groups (fibrocystic lesions,in situtumors and infiltrating tumors).

Results

In the three groups of patients, IFNγ and IFNγ-Rα immunoreactions appeared in the cytoplasm while IFNγ-Rβ also was found in the nucleus. The optical density to IFNγ was higher inin situcarcinoma than in benign and infiltrating tumors. When we observed IFNγ-Rα, the optical density was lower in infiltrating carcinoma than in benign andin situtumors (the higher density). To IFNγ-Rβ, the optical density was similar in the three group samples. In tumor samples PCNA and TUNEL index was significantly higher; than in benign diseases. PCNA index increased with the malignance. No significant differences were found between cancer types to TUNEL. IFNγ could be a potential therapeutic tool in breast cancer. However, tumor cells are able to escape from the control of this cytokine in the early tumor stages; this is probably due to a decreased expression of IFNγ, or also to an alteration of either its receptors or some transduction elements.

Conclusion

We conclude that the decrease in the % positive samples that expressed IFNγ and IFNγ-Rα together with the nuclear localization of IFNγ-Rβ, could be a tumoral cell response, although perhaps insufficient to inhibit the uncontrolled cell proliferation. Perhaps, IFNγ might be unable to activate p21 to stop the cell cycle, suggesting a possible participation in breast cancer development.
Corticosterone mediates electroacupuncture-produced anti-edema in a rat model of inflammation
Authors: Li Aihui , Zhang Rui-Xin , Wang Yi , Zhang Haiqing , Ren Ke , Berman Brian M , Tan Ming , Lao Lixing
Published: August 2007

Background

Electroacupuncture (EA) has been reported to produce anti-edema and anti-hyperalgesia effects on inflammatory disease. However, the mechanisms are not clear. The present study investigated the biochemical mechanisms of EA anti-inflammation in a rat model.

Methods

Three experiments were conducted on male Sprague-Dawley rats (n = 7–8/per group). Inflammation was induced by injecting complete Freund's adjuvant (CFA) subcutaneously into the plantar surface of one hind paw. Experiment 1 measured plasma corticosterone (CORT) levels to see if EA regulates CORT secretion. Experiment 2 studied the effects of the adrenal gland on the therapeutic actions of EA using adrenalectomy (ADX) rats. Experiment 3 determined whether a prototypical glucocorticoid receptor antagonist, RU486, affects EA anti-edema. EA treatment, 10 Hz at 3 mA and 0.1 ms pulse width, was given twice, for 20 min each, once immediately after CFA administration and again 2 h post-CFA. Plasma CORT levels, paw thickness, indicative of the intensity of inflammation, and paw withdrawal latency (PWL) were measured 2 h and 5 h after the CFA injection.

Results

EA significantly increased plasma corticosterone levels 2 h (5 folds) and 5 h (10 folds) after CFA administration compared to sham EA control, but EA alone in naive rats and CFA alone did not induce significant increases in corticosterone. Adrenalectomy blocked EA-produced anti-edema, but not EA anti-hyperalgesia. RU486 (15 μl, 15 μg/μl), a prototypical glucocorticoid receptor antagonist, also prevented EA anti-edema.

Conclusion

The data demonstrate that EA activates the adrenals to increase plasma corticosterone levels and suppress edema and suggest that EA effects differ in healthy subjects and in those with pathologies.
Differential cytokine gene expression profiles in the three pathological forms of sheep paratuberculosis
Authors: Smeed Jennifer A , Watkins Craig A , Rhind Susan M , Hopkins John
Published: August 2007

Background

Johne's disease is a chronic inflammatory disease of the gut caused by infection withMycobacterium aviumsubspeciesparatuberculosis(MAP). Symptoms include wasting, diarrhoea, loss of condition and eventual death. Three forms of Johne's disease have been described in sheep – paucibacillary, multibacillary and asymptomatic. The paucibacillary form is characterized by an inflammatory, Th1-type immune response. The multibacillary form of the disease, which disseminates the infection, is characterized by macrophage infiltration mediated by a Th2-type immune response, and asymptomatic animals have no clinical symptoms or pathology but are infected with MAP. What determines these three forms of the disease is unknown. To further understand these differences, we used real-time RT-PCR to compare the expression of thirteen cytokine and cytokine-related genes in ileal tissue from sheep with the three forms of the disease.

Results

Three pathological forms of sheep paratuberculosis were defined on the basis of histopathology, cytochemistry (Zeihl-Neelsen) and IS900 PCR. Paucibacillary lesions have largely T cell and eosinophil infiltration and are ZN negative; multibacillary lesions have macrophage infiltration and large numbers of acid-fast bacteria. The pauci- and multibacillary forms are linked to the differential expression of IFNγ and IL-10 respectively. In addition the increased levels of the proinflammatory cytokines (IL-1β and TNFα), IL-8, IL-18 and TRAF-1 in both diseased forms is indicative of persistent inflammatory lesions. No changes were seen in IL-1α in any sheep ileum tissues. Asymptomatic animals are IS900+ with normal histology but have significantly decreased levels of IL-18 and increased levels TNFα.

Conclusion

We have quantified the expression levels of thirteen cytokine and cytokine related genes in three forms of ovine paratuberculosis using real-time PCR analyses and confirm that sheep pauci- and multibacillary disease are linked to type 1 and type 2 T cell responses respectively. The expression patterns of other cytokines shows that both disease forms have an inflammatory aetiology but that the central role for IL-1α in bovine paratuberculosis is not seen in the sheep infection. Asymptomatic animals are infected and show no pathology but can be distinguished, in terms of cytokine expression pattern, from uninfected controls.
A physical map of the bovine genome
Authors: Snelling Warren M , Chiu Readman , Schein Jacqueline E , Hobbs Matthew , Abbey Colette A , Adelson David L , Aerts Jan , Bennett Gary L , Bosdet Ian E , Boussaha Mekki , Brauning Rudiger , Caetano Alexandre R , Costa Marcos M , Crawford Allan M , Dalrymple Brian P , Eggen André , Everts-van der Wind Annelie , Floriot Sandrine , Gautier Mathieu , Gill Clare A , Green Ronnie D , Holt Robert , Jann Oliver , Jones Steven JM , Kappes Steven M , Keele John W , de Jong Pieter J , Larkin Denis M , Lewin Harris A , McEwan John C , McKay Stephanie , Marra Marco A , Mathewson Carrie A , Matukumalli Lakshmi K , Moore Stephen S , Murdoch Brenda , Nicholas Frank W , Osoegawa Kazutoyo , Roy Alice , Salih Hanni , Schibler Laurent , Schnabel Robert D , Silveri Licia , Skow Loren C , Smith Timothy PL , Sonstegard Tad S , Taylor Jeremy F , Tellam Ross , Van Tassell Curtis P , Williams John L , Womack James E , Wye Natasja H , Yang George , Zhao Shaying ,   the International Bovine BAC Mapping Consortium
Published: August 2007

Background

Cattle are important agriculturally and relevant as a model organism. Previously described genetic and radiation hybrid (RH) maps of the bovine genome have been used to identify genomic regions and genes affecting specific traits. Application of these maps to identify influential genetic polymorphisms will be enhanced by integration with each other and with bacterial artificial chromosome (BAC) libraries. The BAC libraries and clone maps are essential for the hybrid clone-by-clone/whole-genome shotgun sequencing approach taken by the bovine genome sequencing project.

Results

A bovine BAC map was constructed with HindIII restriction digest fragments of 290,797 BAC clones from animals of three different breeds. Comparative mapping of 422,522 BAC end sequences assisted with BAC map ordering and assembly. Genotypes and pedigree from two genetic maps and marker scores from three whole-genome RH panels were consolidated on a 17,254-marker composite map. Sequence similarity allowed integrating the BAC and composite maps with the bovine draft assembly (Btau3.1), establishing a comprehensive resource describing the bovine genome. Agreement between the marker and BAC maps and the draft assembly is high, although discrepancies exist. The composite and BAC maps are more similar than either is to the draft assembly.

Conclusion

Further refinement of the maps and greater integration into the genome assembly process may contribute to a high quality assembly. The maps provide resources to associate phenotypic variation with underlying genomic variation, and are crucial resources for understanding the biology underpinning this important ruminant species so closely associated with humans.
The roles of binding site arrangement and combinatorial targeting in microRNA repression of gene expression
Authors: Hon Lawrence S , Zhang Zemin
Published: August 2007

Background

MicroRNAs (miRNAs) are small noncoding RNAs that bind mRNA target transcripts and repress gene expression. They have been implicated in multiple diseases, such as cancer, but the mechanisms of this involvement are not well understood. Given the complexity and degree of interactions between miRNAs and target genes, understanding how miRNAs achieve their specificity is important to understanding miRNA function and identifying their role in disease.

Results

Here we report factors that influence miRNA regulation by considering the effects of both single and multiple miRNAs targeting human genes. In the case of single miRNA targeting, we developed a metric that integrates miRNA and mRNA expression data to calculate how changes in miRNA expression affect target mRNA expression. Using the metric, our global analysis shows that the repression of a given miRNA on a target mRNA is modulated by 3' untranslated region length, the number of target sites, and the distance between a pair of binding sites. Additionally, we show that some miRNAs preferentially repress transcripts with longer CTG repeats, suggesting a possible role for miRNAs in repeat expansion disorders such as myotonic dystrophy. We also examine the large class of genes targeted by multiple miRNAs and show that specific types of genes are progressively more enriched as the number of targeting miRNAs increases. Expression microarray data further show that these highly targeted genes are downregulated relative to genes targeted by few miRNAs, which suggests that highly targeted genes are tightly regulated and that their dysregulation may lead to disease. In support of this idea, cancer genes are strongly enriched among highly targeted genes.

Conclusion

Our data show that the rules governing miRNA targeting are complex, but that understanding the mechanisms that drive such control can uncover miRNAs' role in disease. Our study suggests that the number and arrangement of miRNA recognition sites can influence the degree and specificity of miRNA-mediated gene repression.
A simple projection moiré system to measure displacements of aircraft structures
Authors: Galietti U , Genovese K , Lamberti L , Posa D
Published: August 2007

This work presents a simple projection moiré system (PMS) to measure displacements of large-scale aeronautical components. The system includes standard optics, uses a standard fringe-processing method, and relies on a simple analytical model to recover topographic information. An extensive calibration campaign, based on design of experiments, is conducted in order to find the best analytical model for retrieving the out-of-plane displacement field from the moiré pattern and to find the optimal combination of parameters involved in the measurement system.

In order to check the suitability of the present PMS device for practical industrial applications, distortions induced by aerodynamic loads on a landing-light glazing of an Airbus A340 are measured. Experimental results are in good agreement with other measurements carried out independently.
Influence of the wheel-rail contact instationary process on contact parameters
Authors: Baeza L , Fuenmayor F J , Carballeira J , Roda A
Published: August 2007

The rapid convergence of the tangential rolling contact parameters to their stationary values, combined with the high computational cost associated with calculations using instationary models, has meant that stationary models are usually employed in railway dynamics. However, the validity of stationary models when the applied contact conditions are subjected to rapid changes has not been sufficiently investigated. With the objective of deducing the effects of the evolution of the instationary process on the contact parameters, the tangential contact problem is solved for a set of reference conditions. For this purpose a calculation model is adapted, from which it is possible to analyse the evolution of the contact parameters when the forces exerted between rail and wheel are subjected to rapid changes. From the calculations made, situations impossible to simulate by means of stationary theories are obtained according to the frequency of variation in the forces, such as slip zones in the leading edge of the contact area and reverse contact (locally, the traction field is opposite to the direction of the external force transmitted to the contact).
The influence function for self-equilibrating forces on a semi-infinite wedge
Authors: Qiu H , Hills D A , Dini D
Published: August 2007

A solution is derived for the surface displacements arising on the faces of a semi-infinite sharp notch subjected to loading by two equal normal forces, one on each wedge face, applied an equal distance from the notch root. This is achieved by a novel, but robust, procedure using a line of strain nuclei applied along an inclined line within a half-plane and permits good convergence of the solution both in the neighbourhood of the points of application of the forces and at the notch root.
Sensitivity analysis of cooling methods and geometric parameters in the assembly procedure of bascule bridge fulcra
Authors: Nguyen C , Kaw A K , Paul J
Published: August 2007

To assemble the fulcrum of a bascule bridge, a trunnion is shrink fitted into a hub, followed by shrink fitting of the trunnion-hub (TH) assembly into the girder of the bridge. To shrink the TH assembly, it is cooled in a medium such as liquid nitrogen; however, during this process in some cases, the hub cracks. To reduce the possibility of such failures, a formal design-of-experiments study is conducted to find the influence of geometrical parameters such as the hub outer diameter and the radial interference (at the TH interface), and different cooling methods on design parameters such as the critical crack lengths and stress ratios. Cooling methods include immersion in, first, liquid nitrogen; second, a dry-ice-alcohol bath followed by liquid nitrogen; third, a refrigerated air chamber followed by liquid nitrogen; and, fourth, a refrigerated air chamber followed by a dry-ice-alcohol bath and then liquid nitrogen. The cooling method contributes the most to increasing the critical crack length (between 58 and 79 per cent) and increasing the stress ratio (between 48 and 84 per cent) when considering the TH assembly procedures in representative fulcrum geometries. Moreover, the second cooling method, which is immersion of the TH assembly in a dry-ice-alcohol bath followed by immersion in liquid nitrogen, gives larger critical crack lengths (between 262 and 406 per cent) and larger stress ratios (between 17 and 87 per cent) compared with the current cooling method that uses only liquid nitrogen.
Stresses in the vicinity of an unreinforced mitre intersection: An experimental and finite element comparison
Authors: Wood J
Published: August 2007

The experimental investigation reported provides elastic stresses in the vicinity of the unreinforced intersection of a single 90° mitred bend, subjected to an in-plane bending moment. The specimen was extensively strain gauged on the outer surface. A small number of rosettes were also laid on the inside surface close to the welded intersection. The procedures used for the successful installation of the inside surface gauges are discussed. In the experiment, consideration was also given to deflections and rotations. Satisfactory comparisons with adaptive- p thin-shell finite element results were obtained in general and differences are explained in terms of the known experimental variables and finite element approximations. The nature of the stresses at such intersections is discussed and various methods of obtaining fatigue ‘hot-spot’ stresses are considered.
Study of tube flaring forming limit in the tube flaring process
Authors: Yeh Fung-Huei
Published: August 2007

The aim of the current paper is to develop analytical theories for industry to predict the relations between the punch stroke, flaring ratio, tube thickness, and flaring forming limit in the tube flaring process. The volume incompressible condition, Levy-Mises equation, and explicit die profile description are combined to derive the analytical expressions relating the flaring ratio to the punch stroke and velocity in the tube flaring process. Then, according to the stress equilibrium state of a small tube element, the relation of the tube-end thickness ratio to the flaring ratio is developed on the basis of Tresca's criterion. Combining these two analytical theories and the fractured thickness at the tube end, the flaring forming limit can be determined. An elastoplastic finite element method based on the updated Lagrangian formulation is also developed to verify the analytical theories. A flaring experiment, using a 30° semi-cone angle to describe the conical die, is conducted to validate the analytical theories and simulated results. It is found that relations such as tube thickness ratio to flaring ratio, and punch stroke ratio to flaring ratio, show good agreement between analytical theories, finite element prediction, and experiment.
Fretting contact with finite friction of a functionally graded coating with arbitrarily varying elastic modulus Part 1: Normal loading
Authors: Ke L-L , Wang Y-S
Published: August 2007

The two-dimensional normal contact of a functionally graded coated half-space by a rigid cylindrical punch under the action of a monotonically increasing normal load is considered. Friction with a finite coefficient is assumed between the contact surfaces. The whole contact region is composed of an inner stick region and two outer slip regions. The linear multilayered model is used to model functionally graded materials (FGMs) with arbitrarily varying shear modulus and constant Poisson's ratio under plane strain deformation, i.e. the FGM is divided into several sublayers and in each sublayer the shear modulus is assumed to be a linear function while Poisson's ratio is a constant. With the use of the transfer matrix method and Fourier integral transform technique, the problem is reduced to a set of Cauchy singular integral equations. An iterative method is developed to determine the stick-slip region. Normal and tangential tractions in the whole contact region are calculated. It is found that the stick region depends on the gradient of the functionally graded coating as well as on Poisson's ratio and the friction coefficient. The results also show that appropriate gradual variation in the shear modulus can significantly alter the contact traction. This may lead to suppression of Hertzian cracking at the edges of the contact region and thus modify the contact damage. Therefore, it is believed that FGM coatings would have potential applications in improving the resistance to contact damage at the contact surfaces.
Fretting contact with finite friction of a functionally graded coating with arbitrarily varying elastic modulus Part 2: Tangential loading
Authors: Ke L-L , Wang Y-S
Published: August 2007

Fretting is a major cause of surface damage, with fretting fatigue crack initiation at the contact surface subjected to a small-scale oscillatory tangential motion. In the present paper, which is part 2 of the series, the fretting contact between a functionally graded coated half-space and a rigid cylindrical punch is considered for the case where, first, a constant normal load is applied, and then a cyclically varying tangential load, which is less than that necessary to cause complete sliding, is applied. The functionally graded coated half-space is under conditions of plane strain deformation. The whole contact region is composed of an inner stick region and two outer slip regions in which Coulomb's friction law is assumed to apply. Owing to the mismatch in material constants of the punch and half-space, the problem is fully coupled and can be reduced to two coupled Cauchy singular integral equations. Based on the analyses of normal loading in part 1, contact tractions and in-plane stresses associated with tangential loading are calculated in the whole contact region. The results show that appropriate gradual variation in the shear modulus can significantly alter the contact tractions and in-plane stresses. This may lead to suppression of crack initiation at the edges of the contact region and thus modify the fretting contact damage. Therefore, it is believed that functionally graded material coatings would have potential applications in improving the resistance to fretting contact damage at the contact surfaces.
Finite element method analysis of a spur gear with a corrected profile
Authors: Pasta A , Mariotti G Virzí
Published: August 2007

The difference between the stress value calculated by a two-dimensional finite element model of spur gears and those obtained by the rules in ISO 6336 was evaluated. Hertz theory, which provides information on the extension of the contact area and the maximum value of the contact pressure, was used to choose the dimensions of the elements. The mesh was created using the stress analytical solution relative to a model consisting of two cylinders in contact.

Analogous optimization was executed for the mesh of the teeth feet; a mesh of 15 elements was considered optimum, because it minimized the difference to 0.5 per cent in the bending stress calculation. Stress values, obtained using the finite element method (FEM), are generally lower than those obtained with the ISO rules. Hence, this approach yields a conservative determination of the effective material strength. In all the examined cases, the difference was less than 2.5 per cent.

The set FEM technique gives a result accuracy of better than 1 per cent; the difference between the stress obtained by FEM and those obtained by ISO 6336 is less than 2.5 per cent, so that the FEM confirmed, consistent with the ISO rules, that correction of the profile results in significant benefits with respect to determination of the mechanical resistance of spur gears.
A study on an anti-lock braking system controller and rear-wheel controller to enhance vehicle lateral stability
Authors: Song Jeonghoon , Kim Heungseob , Boo Kwangsuck
Published: August 2007

This paper presents a mathematical vehicle model that is designed to analyse and improve the dynamic performance of a vehicle. A wheel slip controller for anti-lock braking system (ABS) brakes is formulated using a sliding mode controller and a proportional-integral-derivative (PID) controller for rear wheel steering is also designed to enhance the stability, steerability, and driveability of the vehicle during transient manoeuvres. The braking and steering performances of controllers are evaluated for various driving conditions, such as straight and J-turn manoeuvres. The simulation results show that the proposed full car model is sufficient to predict vehicle responses accurately. The developed ABS reduces the stopping distance and increases the longitudinal and lateral stability of both two-and four-wheel steering vehicles. The results also demonstrate that the use of a rear wheel controller as a yaw motion controller can increase its lateral stability and reduce the slip angle at high speeds.
Optimization of stratification combustion in a spark ignition engine by double-pulse port fuel injection
Authors: Wang T , Peng Z , Liu S-L , Xiao H-D , Zhao H
Published: August 2007

The potential of lean burn in a spark-ignition (SI) engine with optimized fuel injection was experimentally investigated and numerically simulated. The experiments were carried out on a production SI engine which has a port fuel injection (PFI) system. The previous port electronic fuel injection system was modified and the technique of double-pulse fuel injection (DFI) was employed. By regulating injection timings and proportions of DFI, the air-fuel mixture stratification was significantly improved and the expected lean burn was implemented. The experimental results showed that the reduction of fuel consumption with DFI could be above 10 per cent over quite a wide load range, compared to single fuel injection. With optimized fuel injection timings and double-pulse proportions, the ideal engine performance and emissions can be achieved with a two to three times higher air-fuel ratio (AFR) than single fuel injection.

With numerical simulation, the effects of mixture stratification formed by different fuel injection amounts and timings were analysed using a phenomenological model. The mixture in the cylinder was divided into different regions that distribute spherically around the spark plug and consist of a central region of stoichiometric air-fuel mixture and a gradually leaner outside region. Simulation results demonstrated that the improvements in fuel economy and emissions with DFI were mainly attributed to increased stratification zones and a reduced AFR gradient in the stratification zones.
The performance and emission characteristics of emulsified fuel in a direct injection diesel engine
Authors: Ashok M P , Saravanan C G
Published: August 2007

Diesel engines are employed as the major propulsion power sources because of their simple, robust structure and high fuel economy. It is expected that diesel engines will be widely used in the foreseeable future. However, an increase in the use of diesel engines causes a shortage of fossil fuel and results in a greater degree of pollution. To regulate the above, identifying an alternative fuel to the diesel engine with less pollution is essential. Ethanol–diesel emulsion is one such method, used for the preparation of an alternative fuel for the diesel engine. Experimental investigations were carried out to compare the performance of diesel fuel with different ratios 50D: 50E (50 per cent diesel No: 2: 50 per cent ethanol –100 per cent proof) and 60D: 40E emulsified fuels. In the next phase, experiments were conducted for the selected emulsified fuel ratio 50D: 50E for different high injection pressures and the results are compared. The results show that for the emulsified fuel ratios, there is a marginal increase in torque, power, NO x, emissions, and decreasing values of carbon monoxide (CO), sulphur dioxide (SO2) emissions at the maximum speed conditions, compared with diesel fuel. Also, it is found that an increase in injection pressure of the engine running with emulsified fuel decreases CO and smoke emissions especially between 1500 to 2000 r/min with respect to the diesel fuel.
Experimental study on the cycle-by-cycle variations of homogeneous charge compression ignition combustion using primary reference fuels and their mixtures
Authors: Xingcai Lu , Libin Ji , Junjun Ma , Zhen Huang
Published: August 2007

In this paper, the combustion stabilities and cycle-by-cycle variations of homogeneous charge compression ignition (HCCI) combustion using neat n-heptane, PRF20, PRF40, PRF50, and PRF60 were investigated. In-cylinder pressures of 100 combustion cycles for each test fuel on a single-cylinder engine were recorded. Consequently, cycle-to-cycle variations of the main combustion parameters and performance parameters were analysed, and the interdependency between the combustion parameter and performance parameters were also evaluated. The results reveal that the cycle-by-cycle variations deteriorate with the increase of the research octane number (RON). Especially, the coefficient of variations (COVs) of all parameters increase substantially when the RON of test fuels exceeds 40. For a certain test fuel, the COVs of combustion parameters that were used to depict the combustion characteristics during the early stage of combustion are very small, the COVs of combustion parameters that were used to describe the combustion characteristics of the post stage of the combustion are the largest, and the COVs of the i.m.e.p. and Pmax maintain at a middle level. Furthermore, a better interdependency also exists between the ignition timing of the low temperature reaction (LTR) and high temperature reaction (HTR), between the maximum pressure rise rate and its corresponding crank angle, between the peak values of the heat release and its corresponding crank angle.
Design characteristics for temporomandibular joint disc tissue engineering: Learning from tendon and articular cartilage
Authors: Johns D E , Athanasiou K A
Published: August 2007

Tissue engineering of chondrocytic or fibroblastic musculoskeletal tissues has been relatively well studied compared with that of the temporomandibular joint (TMJ) disc. Early attempts at tissue engineering the disc have been misguided owing to a lack of understanding of the composition and function of the TMJ disc. The objective of this review is to compare the TMJ disc with a chondrocytic tissue (hyaline articular cartilage) and a fibroblastic tissue (tendon) to understand better the properties of this fibrocartilaginous tissue. The TMJ disc has 25 times more glycosaminoglycan (GAG) per dry weight than tendon but half that of articular cartilage. The disc's tensile modulus is six times more than cartilage but orders less than tendon. The GAG content and tensile modulus suggest that the TMJ disc is characterized as a tissue between hyaline cartilage and tendon, but the disc appears more tendon like when considering its collagen make-up and cell content. Like tendon, the TMJ disc contains primarily collagen type I at 85 per cent per dry weight, while articular cartilage has 30 per cent less collagen, which is type II. Knowledge of quantitative comparisons between joint tissues can give extensive insight into how to improve tissue engineering of the TMJ disc.
Light and low-frequency pulsatile hydrostatic pressure enhances extracellular matrix formation by bone marrow mesenchymal cells: An in-vitro study with special reference to cartilage repair
Authors: Luo Z-J , Seedhom B B
Published: August 2007

Ovine bone marrow mesenchymal cells (BMMCs) were seeded on to non-woven filamentous plasma-treated polyester scaffolds and cultured in a chondrogenic medium for 4 weeks. Thereafter a pulsatile hydrostatic pressure (PHP) was applied to these cell-scaffolds constructs at an amplitude of 0.1 MPa and frequency of 0.25 Hz, for 30 min a day, over a period of 10 days. Samples ( n=6) were removed 24 h after PHP stimulation at days 1, 4, 7, and 10 for biochemical analysis. Similar analyses were conducted, at the same time points, on control samples that were not subjected to a PHP. The results showed that the glycosaminoglycan (GAG) content did not significantly increase until after the application of a PHP for 7 days. The GAG content was 1.5 and 2.7 times higher in the PHP group than in the control group at days 7 and 10 respectively ( p < 0.01). The deoxyribonucleic acid (DNA) content was 1.5 times greater in the PHP group than in the control group at day 10 ( p < 0.01). GAG synthesis amounts, expressed as the total GAG contents per microgram of DNA, were 1.6 and 1.8 times higher in the PHP group than in the control group at days 7 and 10 respectively ( p < 0.01). The total collagen content in the medium did not change until after PHP application for 10 days, when it was 1.9 times higher than the control ( p < 0.05). The results suggest that a light PHP applied at a low frequency has a cumulative stimulatory effect on the BMMCs' metabolic activities including cell proliferation and synthesis of the extracellular matrix.
Mechanotransduction pathways of low-intensity ultrasound in C-28/I2 human chondrocyte cell line
Authors: Choi B H , Choi M H , Kwak M-G , Min B-H , Woo Z H , Park S R
Published: August 2007

Low-intensity ultrasound (LIUS) has recently been considered to be an effective method to induce cartilage repair and/or regeneration after injury. Nevertheless, there is no study to provide a cellular mechanism or signal pathways of LIUS stimulation. The current study is designed to investigate the effects of LIUS on the mechanotransduction pathways in C-28/I2, an immortalized human chondrocyte cell line. C-28/I2 cells were treated with LIUS at an intensity of 200 mW/cm2 using Noblelife™ from Duplogen. The role of stretch-activated channels (SAC) and integrins that are most well-known mechanoreceptors on the chondrocyte cell surface was first examined in mediating the LIUS effects on the expression of type II collagen and aggrecan. When analysed by reverse transcriptase polymerase chain reaction (RT-PCR) and immunohistochemistry, gadolinium (a specific inhibitor of SACs) or GRGDSP (a peptide inhibitor of integrins) specifically reduced the LIUS-induced elevation of type II collagen and aggrecan expressions depending on the incubation time. In addition, the LIUS treatment of C-28/I2 cells induced the phosphorylation of c-Jun N-terminal kinase (JNK) and extracellular signal-regulated kinase (ERK) but not p38 kinase among the members of the mitogen-activated protein kinases (MAPKs). The phosphorylation of ERK by LIUS was repressed by a specific inhibitor of the ERK pathway and integrin function. These results suggest that the LIUS signal might be mediated via canonical mechanoreceptors of SACs and integrins and subsequently through JNK and ERK pathways. The present study provides the first evidence for the activation of the mechanotransduction pathways by LIUS in human chondrocytes.
Chitosan-based hyaluronan hybrid polymer fibre scaffold for ligament and tendon tissue engineering
Authors: Majima T , Irie T , Sawaguchi N , Funakoshi T , Iwasaki N , Harada K , Minami A , Nishimura S-I
Published: August 2007

To establish medical use of tissue engineering technology for ligament and tendon injuries, a scaffold was developed which has sufficient ability for cell growth, cell differentiation, and mechanical properties. The scaffold made from chitosan and 0.1 per cent hyaluronic acid has adequate biodegradability and biocompatibility. An animal experiment showed that the scaffold has less toxicity and less inflammation induction. Furthermore, in-vivo animal experiments showed that the mechanical properties of the engineered ligament or tendon had the possibility to stabilize the joint. It was shown that newly developed hybrid-polymer fibre scaffold has feasibility for joint tissue engineering.
Tissue engineering of the synovial joint: The role of cell density
Authors: Troken A , Marion N , Hollister S , Mao J
Published: August 2007

The ultimate goal in the tissue engineering of the synovial joint is to fabricate biologically derived analogues that can replace severely degenerated or traumatized synovial joint components. A number of challenges must be addressed before reaching this ultimate goal. In this report, the relevance of cell seeding density in the synthesis of chondrogenic and osteogenic matrices from human mesenchymal stem cells is explored. Human mesenchymal stem cells (hMSCs) were differentiated into chondrogenic cells and osteogenic cells ex vivo and encapsulated in poly(ethylene glycol) diacrylate (PEGDA) hydrogel at densities of 5 × 106 cells/ml, 40 × 106 cells/ml, and 80 × 106 cells/ml, in addition to a cell-free poly(ethylene glycol) (PEG) control group (0 × 106 cells/ml). Cell-seeded or cell-free PEG constructs were separately incubated in vitro for 4 weeks or implanted in vivo in the dorsum of immunodeficient rats for 4 weeks. In-vitro data demonstrated that hMSC-derived chondrocytes or hMSC-derived osteoblasts maintained their lineages per Safranin O and von Kossa staining after incubation for 4 weeks. The general pattern of initial cell seeding densities of 5 × 106 cells/ml, 40 × 106 cells/ml, and 80 × 106 cells/ml were preserved following in-vitro cultivation. Similarly, in-vivo data revealed that hMSC-derived chondrocytes and hMSC-derived osteoblasts maintained their respective lineages and the pattern of cell-seeding densities. An attempt was made to fabricate a composite construct with PEGDA hydrogel and polycaprolactone (PCL) with designed internal porosity for an osteochondral graft. Various cell-seeding densities as delineated in this report can be realized in the composite PEG-PCL graft. The findings demonstrate that cell-seeding density is likely a key parameter to consider in tissue-engineering design. The source of cells can either be transplanted cells or internally recruited cells.
Residual gas fraction measurement and computation
Authors: Giansetti P , Colin G , Higelin P , Chamaillard Y
Published: August 2007

To meet future pollutant emissions standards, it is crucial to be able to estimate not only the cycle-by-cycle mass but also the cycle-by-cycle composition of the combustion chamber charge. This charge consists of fresh air, fuel, and residual gas from the previous cycle. Unfortunately, the residual gas fraction cannot be directly measured. Two experimental methods have been designed to determine the residual gas fraction. The reference method is based on an in-cylinder sampling method. The second one is based on a hydrocarbon (HC) analysis of the exhaust gases.

Two models have been compared to the experimental results. A one-dimensional computational fluid dynamics (CFD) code (WAVE) and a zero-dimensional model (AMESIM), which takes into account gas compressibility. The aim of the study was to compare the results of CFD codes (one- and zero-dimensional) to experimental results. If the code is validated by the experiments, it should be possible to determine residual gas fractions without needing a large experimental set-up.
A model for simulating the instantaneous crank kinematics and total mechanical losses in a multicylinder in-line engine
Authors: Potenza R , Dunne J. F. , Vulli S , Richardson D
Published: August 2007

A two-degree-of-freedom dynamic model is constructed to simulate the instantaneous crank kinematics and total mechanical losses arising in a multicylinder gasoline engine coupled to a dynamometer. The simulation model is driven using specified cylinder gas pressures, and loaded by nominal brake torque and total friction losses. Existing semi-empirical torque loss models (based on calibrated single-cylinder diesel engine data) are used to account for the instantaneous friction losses in the piston-ring assembly, in bearings, and in auxiliaries. The model is specialized to the simulation of crank kinematics and matched brake torque for a three-cylinder in-line direct injection spark ignition (DISI) engine, without a gearbox. This allows the total friction loss to be separated from the brake torque for an engine not fitted with the very large number of sensors otherwise needed to calibrate analytical friction models. An equivalent simulation model is also constructed using GT-Crank, which excludes explicit reference to friction. In using both models to simulate steady state operation at a specified mean engine speed, the output torque is matched by iteration. The GT-Crank model necessarily compensates for internal losses by exaggerating the total output torque. Both simulation models are compared with measured crank kinematics and brake torque obtained from a dynamometer-loaded I3 DISI engine. The paper shows that by comparing the matched output torque from simulation with the measured output torque from the engine, the proposed model gives a very good high-speed prediction of the total mechanical losses. At low speed, the instantaneous model is still not accurate. It is also shown, however, that apart from the no-load condition, use of an average torque to compensate for friction (as in GT-Crank) is wholly acceptable for simulating instantaneous crank kinematics. This is the first reported instance of a simulation model (which includes the particular form of semi-empirical friction loading) being comprehensively compared and verified using multicylinder DISI engine data.