bluuebunny/crossref_metadata_2025 huggingface dataset:
Three-Dimensional Micromechanical Model for Quasi-Brittle Solids with Residual Strains under Tension
Authors: Feng Xi-Qiao , Gross Dietmar
Published: July 2008

Presented in this paper is a three-dimensional micromechanical model that enables the simulation of microcrack-weakened quasi-brittle materials with permanent residual strains subjected to tension. The microcracking damage of such a material is described by the concept of domain of microcrack growth. It is thought that the occurrence of residual strains is attributable to two reasons, namely, the release of microscopic residual stresses due to microcracking and the microscopic plastic deformation along microcrack front edges. By introducing the analytical results of the two physical mechanisms into the constitutive relation, a micromechanical damage model is established to describe the effective response of microcrack-weakened quasi-brittle materials such as ceramics and concrete under complex loading/unloading paths. The response of such a material is divided into four stages, namely, the stages of linear elasticity, pre-peak nonlinearity, post-peak stress drop, and strain softening before macroscopic fracture.
Modeling Very Low Cycle Fatigue
Authors: Dufailly J. , Lemaitre J.
Published: July 2008

The damage mechanics allows the formulation of a three-dimensional kinetic law of damage evolution adapted to very low cycle fatigue where the number of cycles are as low as one to twenty. Its applicability is shown by an identification on an Inconel 718 alloy at 630°C and by an application as a post processor after a finite element analysis of an axisymmetric structure to determine the number of cycles to crack initiation. The corresponding experiments are also reported.
Fracture in Structured Continua
Authors: Mariano Paolo Maria
Published: July 2008

The expression of the energy release rate for the growth of a macrocrack in an elastic-plastic matrix, weakened by a distribution of flat microcracks, is deduced in this paper. The two-dimensional and the three-dimensional case are considered.
On Micromechanical Evolutionary Damage Models for Polycrystalline Ceramics
Authors: Ju J. W.
Published: July 2008

Evolutionary micromechanical constitutive models for polycrystalline MgO ceramics with distributed dislocations and integranular microcracks are presented. Based on the description of dominant modes of microstructural changes in polycrystals, the kinetics of microcrack evolution in a typical grain is studied. Four basic deformation modes are considered within the micromechanics framework—the elastic deformation, slip band, microcrack nucleation, and microcrack kinking mechanisms. In particular, a slip band is assumed to be caused by the Frank-Read dislocation source, and a microcrack is assumed to be nucleated by the Zener-Stroh mechanism.

At the onset, the stress-strain relation of the polycrystalline MgO ceramics is taken as linearly elastic. As the loading stress increases, slips will occur first in those crystals having the "easiest" slip planes at an angle of 45 degree. At some point, the stress in front of a dislocation pileup will exceed the cohesive strength of an intergranular plane. Therefore, a microcrack will nucleate on the grain boundary ("Cleavage 2" process). By computing the strain and compliance contributions due to many probabilistically distributed and evolutionary dislocations, microcracks and kinked microcracks, effective moduli and stress-strain relations can be derived based on micromechanics and approximate effective medium methods. Effects of different grain size distributions are investigated in detail by considering five cases (the fixed grain size, uniform distribution, normal distribution, square-root normal distribution, and linear decreasing distribution functions). The proposed models are subsequently applied to uniaxial tensile loadings, biaxial loadings, and residual stresses. Several interesting evolutionary examples are also presented to illustrate the capability and behavior of the proposed micromechanical damage models.
Three-Dimensional Inelastic Stress Analysis of Center Notched Composite Laminates with Damage
Authors: Chow C. L. , Yang Fan
Published: July 2008

In this paper, a constitutive model for characterization of mechanical response in inelastic composite materials due to damage developed recently by the authors is first outlined. The formulation is based on the concept of damage surface and on the assumption that the change of material behavior is independent of loading path over which the damage state of material develops, but is dependent on the current stress state and the energy dissipated. The method is applied to describe the behaviors of graphite fiber reinforced composite laminates containing a small hole. The elastic-damaged response of interlaminar stresses in the composite laminates due to uniaxial tension is investigated with the aid of displacement-based finite element method. The initiation and development of damage zones in the laminates are examined using a three-dimensional analysis. The results of interlaminar stress distributions of the composite laminates analyzed with and without taking material stiffness degradation into account under the same external loading condition are presented and discussed.
Crack Opening Geometry in Cracked Composite Laminates
Authors: Varna J. , Berglund L. A. , Krasnikovs A. , Chihalenko A.
Published: July 2008

Talreja and coworkers have reported brittle and tough polymer matrix composites to show different cross-ply laminate stiffness reductions due to transverse cracks, despite very similar elastic properties. Studies of crack opening displacement (COD) in [0,,,90,] laminates may help in solution of this problem. Approximate analytical models based on the variational approach pioneered by Hashin were therefore applied in addition to FEM-calculations. Approximate models were concluded not to be reliable for future analyses of this problem. Experimental COD for brittle GF/EP laminates at low crack densities was fairly well predicted by FEM-calculations. None of the models were able to predict experimental data at high crack densities. Residual plastic strains are suggested as an explanation and may also be responsible for reported matrix-related differences in stiffness reduction.
Effective Moduli of Microcracked Rocks: Theories and Experiments
Authors: Chau K. T. , Wong Robina H. C.
Published: July 2008

This paper compares and contrasts the predicted effective moduli by the self-consistent and noninteracting methods and examines the range of validity for both models; predictions by these two models are compared to experimental observations on natural rocks containing microcracks and artificial rocks containing inserted microcracks. Crack density (e) in real rocks is obtained by counting cracks under microscope and those in replicated rocks is, of course, predetermined; these crack densities are then compared to the crack densities interpreted from the changes in ultrasonic wave speeds, using either self-consistent model or noninteracting crack model. For natural rocks, the noninteracting prediction seems to agree better with experiments than the self-consistent method for E c 0.2, but both theoretical predictions deviate from experimental observation for e > 0.2. For replicated rocks, both theories give prediction comparable to experiments for E c 0.2, but underestimate the actual value for e > 0.2. Therefore, a better damage model is needed for solids with crack density larger than 0.2.
Effect of Some Parameters on the Plastic Fatigue Behavior with Micromechanical Approach
Authors: Abdul-Latif A. , Saanouni K.
Published: July 2008

The fatigue life and the micro-damage heterogeneity for FCC polycrystalline metals are qualitatively evaluated employing a coupled phenomenological micro-mechanical model of the early plastic fatigue damage initiation. This model is based on the slip theory and on the localization homogenization technique associated with the self-consistent scheme. For representing the micro-damage on each slip system, an internal damage variable dS is introduced. The influence of the main parameters of this model (aggregate composition, damage interaction matrix Drs, and loading path) on the related plastic fatigue phenomena as the fatigue lives and the micro-damage heterogeneity is studied. Hence, various fatigue simulations are performed using several types of aggregates and different loading paths (simple and complex). It is shown that such parameters have great influences on the fatigue behavior. Moreover, the distributions of the local damage heterogeneity are studied under the effect of each determined parameter.
Analysis of Shear Damage Evolution
Authors: Silberschmidt Vadim V.
Published: July 2008

Shear damage development under constant stress is studied on the basis of the analytical solution of kinetic equations of damage accumulation. The existence of two threshold stresses is linked with the presence of three various stress intervals and respective regimes of damage growth. Utilization of the limit value of damage level as the failure criterion allows the scaling of the time-to-failure to be analyzed. The effect of initial damage on failure development is investigated.
A Microcrack Description of Creep Damage in Crystalline Solids with Different Behaviour in Tension and Compression
Authors: Betten Josef , Sklepus Sergiy , Zolochevsky Alexander
Published: July 2008

A three-dimensional creep damage model for polycrystalline materials with parallel flat microcracks is presented, employing a damage vector. This model describes simultaneously damage induced anisotropy, different damage in tension and compression, and different creep properties in tension and compression. The equivalent stress in the creep potential contains joint invariants of the stress tensor and the damage vector. The proposed constitutive equation for creep together with the damage evolution equation take into account the primary, secondary, and tertiary creep. It is shown how three damage dependent functions in the proposed model can be determined from a series of basic experiments. The theoretical results have been compared with the experimental results for two- and three-dimensional stress states of various materials.
An Isotropic Damage Model Based on a Tensorial Representation of Damage
Authors: Eskandari H. , Nemes J. A.
Published: July 2008

A 3-D phenomenological model of isotropic damage is developed for brittle solids based on the effective stress concept. The shortcomings of the commonly used scalar variable, as representative of isotropic damage, are discussed. It is shown that isotropic damage is best represented by an isotopic tensor of rank four. The damage evolution law is postulated using strain tensor invariants, based on decomposition of strain energy. The model is tested with experimental results for two cases: uniaxial compression of quartzite rock and uniaxial tension of a quasi-isotropic graphite-epoxy laminated composite. Simulations and experimental results show that Poisson's ratio increases in both cases.
Unilateral Effect in Plastic Fatigue with Micromechanical Approach
Authors: Abdul-Latif A.
Published: July 2008

Based on the slip theory, a micromechanical model of damaged-inelastic behavior, which was recently proposed for metallic polycrystalline structures (FCC), is extended in order to describe the unilateral effect in low-cycle fatigue with a small strain assumption. In this micromechanical model, the micro-damage variables initiate and then evolve on the activated crystallographic slip systems. These variables are coupled with micro-macro constitutive equations. The formulation of the unilateral character of the damage (activation and deactivation) is limited only to the macroscopic level using the isotropic damaged concept. At this point, the unilateral effect is introduced with the help of a simple phenomenological constant. It allows to appropriately describe the macro-damage parameter evolution during the closure of defects (inactive phase) with the continuity of the stress-strain response.
Fatigue Life Prediction of Single Crystals for Turbine Blade Applications
Authors: Gallerneau Franck , Chaboche Jean-Louis
Published: July 2008

This paper describes a fatigue life prediction model accounting for high temperature applications of metallic materials. The formulation of the model is for general anisotropy and multiaxiality of loading. This phenomenological model distinguishes between an initiation phase and a propagation phase, and takes into account oxidation and creep effects on fatigue life. An application of the model is given for a coated single crystal superalloy for turbine blades. Model predictions are in good agreement with a large set of experimental data for mechanical loading including thermomechanical fatigue tests. A new experimental device, designed to produce a thermal gradient in the thickness of thin walled specimens, is also presented. This device has been used with polycrystalline and monocrystalline superalloys. Corresponding life predictions, performed by using recent anisotropic models, are presented for the single crystal superalloy.
Hierarchical Co-evolution of Cooperating Agents Acting in the Brain-Arena
Authors: Maniadakis Michail , Trahanias Panos
Published: July 2008

Recently, many brain-inspired models have been used in attempts to support the cognitive abilities of artificial organisms. In this article, we introduce a computational framework to facilitate these efforts, emphasizing the cooperative performance of brain substructures. Specifically, we introduce an agent-based representation of brain areas, together with a hierarchical cooperative co-evolutionary design mechanism. The proposed methodology is capable of designing biologically inspired cognitive systems, considering both the specialties of brain areas and their cooperative performance. The effectiveness of the proposed approach is demonstrated by designing a brain-inspired model of working memory usage. The co-evolutionary scheme enforces the cooperation of agents representing the involved brain areas, facilitating the accomplishment of two different tasks by the same model. Furthermore, we investigate the performance of the model in lesion conditions, highlighting the distinct roles of agents representing brain areas. The implemented model is embedded in a simulated robotic platform to support its cognitive and behavioral capabilities.
Sex Trafficking in Nepal
Authors: Crawford Mary , Kaufman Michelle R.
Published: July 2008

There has been little systematic research on therapy, rehabilitation, and social reintegration of women formerly trafficked into prostitution. This study examines characteristics and outcomes of Nepali sex trafficking survivors. Twenty case files of survivors rehabilitated in the shelter of an antitrafficking NGO were randomly selected. All individuals in the sample suffered somatic and behavioral sequelae. Three quarters of the survivors eventually returned to their villages to live. These results suggest that current rehabilitation and reintegration programs are producing positive results. However, there is need for more systematic diagnosis, record keeping, and outcome studies as well as education to reduce stigma and promote safe migration practices.
Maternal Blame
Authors: Terrance Cheryl , Plumm Karyn , Little Betsi
Published: July 2008

Participants ( N = 126) read one of four scenarios depicting an incident of child physical abuse inflicted by the father. Scenarios varied history of wife abuse (present vs. absent) and severity of child abuse (battering vs. death). Overall, the father was held highly responsible. Greater maternal culpability was assigned when a history of wife abuse was present. The degree to which the mother should have been able to predict the incident of child abuse and maternal responsibility were mitigated when the abuse resulted in the death of her child. Perceptions of maternal psychological stability were jeopardized as a function of the presence of wife abuse. Implications are discussed.
Angle Factors and Projected Area Factors for Comfort Analysis of Subjects in Complex Confined Enclosures: Analytical Relations and Experimental Results
Authors: La Gennusa Maria , Nucara Antonino , Pietrafesa Matilde , Rizzo Gianfranco , Scaccianoce Gianluca
Published: July 2008

This paper addresses an important problem in the evaluation of the thermal comfort of people living or working in the sort of confined spaces typical of current architecture. In the details, a new algorithm is proposed for the evaluation of the angle factors of people within rooms characterized by complex shapes, where the envelope components are not always mutually orthogonal. The algorithm is based on field data obtained by means of an experimental photographic apparatus which allows measurements of projected area factors of seated or standing people in such complex confined environments.
The Impact of Kitchen Activities on Indoor Pollutant Concentrations
Authors: Tian Liwei , Guoqiang Zhang  , Quan Zhang  , Moschandreas D.J. , Hao Junhong , Jianping Lin  , Yanhui Liu
Published: July 2008

A preliminary Indoor Air Quality study was performed in 26 residential homes in 6 cities in different climate zones in China. In Chinese urban environments, coal gas and natural gas are used as the main fuels for cooking. Analysis of the results employed the ratio of living room to kitchen (L/K) pollutant concentrations and the correlation of their levels to assess the transport of pollutants indoors. Sources in the kitchen affect living room concentrations of SO2, NO, NO2, and CO, less so that of CO2 levels and weakly of PM10. Among all the pollutants, SO2 has the minimum 0.88 L/K ratio value, and maximum correlation value, R2=0.89; on the other hand, PM10 has the maximum L/K ratio value, 1.20 and minimum R 2-value, 0.55, which means that PM10 is mostly influenced by activities and other factors that do not take place in the kitchen. Concentrations of SO2 differed significantly depending on the fuel type used for cooking with coal gas producing 87.6% higher SO2 concentrations than natural gas. Concentrations of CO2 and PM10 were the same regardless of gas type. The type of ventilation was found to influence polluant concentrations with a mechanical exhaust system showing higher efficiency than a natural ventilation system in exhausting pollutants. The period and style of cooking also affected concentrations of pollutants in the kitchen.
Effect of surface treatment of carbon fibre on impact and tribological properties of thermoplastic polyimide composite under oil lubricated condition
Authors: Li J. , Cheng X. H.
Published: July 2008

Rare earth solution (RES) surface modification and air oxidation methods were used to improve the interfacial adhesion of the carbon fibre reinforced polyimide (CF/PI) composite. The impact and tribological properties of the PI composites reinforced by the carbon fibres treated with different surface modification methods were comparatively investigated. Results showed that the impact strength of CF/PI composite was improved 28% after RES treatment. And PI composite filled with RES treated CF registered excellent friction and wear properties under oil lubricated condition. The improvement of impact and tribological properties of the CF/PI composite was mainly due to the improvement in interfacial adhesion after RES treatment.
Recrystallisation and dilatometric behaviour of low carbon and ultralow carbon steels
Authors: De Cock T. , Capdevila C. , Ferrer J. P. , Caballero F. G. , Jiménez J. A. , de Andrés C. García
Published: July 2008

During continuous heating of a cold rolled low carbon steel, a dilatometric anomaly has been detected before the well known ferrite to austenite transformation. The detailed study of the processes occurring during the heating and comparison with the case of an ultralow carbon steel showed that this anomaly is related to the change in dislocation density during recrystallisation.
Microstructure characterisation and mechanical properties of rapidly solidified Mg–Zn–Ca alloys with Ce addition
Authors: Chen Z. H. , Zhou T. , Chen D. , Yan H. G. , Chen J. H.
Published: July 2008

The rapidly solidified (RS) Mg–Zn–Ca based alloys with Ce addition were produced via atomising the alloy melt and subsequently splat quenching the atomised droplets on the water cooled copper twin rollers in the form of flakes. The alloys were characterised by XRD, SEM, HRTEM, DSC and microhardness. All the alloys are characteristic of fine grains in the size of 1–5 μm. The RS Mg–6Zn–5Ca ternary alloy is composed of α–Mg, Mg2Ca, Ca2Mg6Zn3 and a small quantity of Mg51Zn20, Mg2Zn3 and MgZn2. With the increment of Ce, the Mg12Ce phase in the alloy increases and the Mg51Zn20, Mg2Zn3 and Ca2Mg6Zn3 phases decrease, seemly indicating that the proper Ce content is beneficial to the suppression of the latter phases. Moreover, the addition of Ce to the Mg–Zn–Ca alloy contributes to the enhanced thermal stability of the phases in the alloys, especially for the Mg–6Zn–5Ca–3Ce alloy. The microhardness of the RS alloys increases with the increment of Ce, and the strengthening mechanism is discussed.
Graded Ni–YSZ anode coatings for solid oxide fuel cell prepared by EB-PVD
Authors: Meng B. , Sun Y. , He X. D. , Li M. W.
Published: July 2008

In order to reduce concentration polarisation from the solid oxide fuel cell (SOFC) anode and the internal stress originating from the thermal expansion mismatch between the anode and electrolyte, a NiO–YSZ coating with a graded composition distribution was prepared by electron beam physical vapour deposition (EB-PVD) through adjusting the electron beam currents. Then the graded Ni–YSZ coating was obtained after a reduction treatment from this NiO–YSZ coating. A graded distribution in contents of both nickel and zirconium was found in this Ni–YSZ coating from the electron probe microanalysis (EPMA) result. Scanning electron microscopy (SEM) observation exhibited a continuous variation in porosity and pore diameter along the direction across the coating thickness. In this coating, a high porosity of up to 43% and an average pore diameter of about 1 µm were obtained in the part close to the substrate, while a low porosity of 10% and mean pore diameters of about tens of nanometres were achieved in the part close to the coating surface. This pore structure not only could decrease the concentration polarisation, but also facilitate the following preparation of dense electrolyte films.
Quench hardening of 0·4%C steel using aqueous electrolyte plasma as heat source
Authors: Roy A. , Parihar S. J. , Singh A. , Sharma R. C. , Shekhar R.
Published: July 2008

Quench hardening of 0·4%C steel has been achieved using aqueous electrolyte plasma as heat source. Cylindrical specimens (8 mm diameter) of 0·4%C steel (cathode) were placed at the centre of a cylindrical stainless steel ring of 100 mm diameter (anode) in 15 wt-%Na2CO3 aqueous solution. Continuous electrolyte plasma was generated by electrical discharge at voltages higher than ∼90 V in a narrow layer at the specimen (cathode) surface. The aqueous electrolyte plasma caused rapid heating of the active electrode (cathode) to 900–1200°C in few seconds at applied voltages in the range of 95–140 V. On subsequent rapid cooling, the steel specimen transformed to martensite structure. The process can be adopted for surface modification techniques such as nitriding and carburising. Feasibility of anodising using this technique may also be explored.
Corrosion behaviour of 316L stainless steel coated by amorphous and semicrystalline polypyrrole
Authors: Ashrafi A. , Golozar M. A. , Mallakpour S.
Published: July 2008

Using galvanostatic technique, electrochemical polymerisation of pyrrole on 316L stainless steel substrates was achieved in aqueous solution of oxalic acid and pyrrole. Common amorphous structure was obtained at high current density (1 mA cm–2). Conversely, semicrystalline polypyrrole coating was achieved at very low current density (0⋅01 mA cm–2). Using grazing incidence small angle X-ray scattering method, the degree of crystallinity was estimated to be 68%. Corrosion resistance of polypyrrole coatings in 0⋅1M NaCl solution was investigated employing potentiodynamic polarisation and electrochemical impedance spectroscopy methods. Results obtained showed that crystallinity of polypyrrole coating would decrease the corrosion current density and increase the polarisation resistance as well as pore resistance.
Neuropilin-1 in regulation of VEGF-induced activation of p38MAPK and endothelial cell organization
Authors: Kawamura Harukiyo , Li Xiujuan , Goishi Katsutoshi , van Meeteren Laurens A. , Jakobsson Lars , Cébe-Suarez Stéphanie , Shimizu Akio , Edholm Dan , Ballmer-Hofer Kurt , Kjellén Lena , Klagsbrun Michael , Claesson-Welsh Lena
Published: July 2008

Vascular endothelial growth factor (VEGF)–A regulates vascular development and angiogenesis. VEGF isoforms differ in ability to bind coreceptors heparan sulfate (HS) and neuropilin-1 (NRP1). We used VEGF-A165 (which binds HS and NRP1), VEGF-A121 (binds neither HS nor NRP1), and parapoxvirus VEGF-E-NZ2 (binds NRP1 but not HS) to investigate the role of NRP1 in organization of endothelial cells into vascular structures. All 3 ligands induced similar level of VEGFR-2 tyrosine phosphorylation in the presence of NRP1. In contrast, sprouting angiogenesis in differentiating embryonic stem cells (embryoid bodies), formation of branching pericyte-embedded vessels in subcutaneous matrigel plugs, and sprouting of intersegmental vessels in developing zebrafish were induced by VEGF-A165 and VEGF-E-NZ2 but not by VEGF-A121. Analyses of recombinant factors with NRP1-binding gain- and loss-of-function properties supported the conclusion that NRP1 is critical for VEGF-induced sprouting and branching of endothelial cells. Signal transduction antibody arrays implicated NRP1 in VEGF-induced activation of p38MAPK. Inclusion of the p38MAPK inhibitor SB203580 in VEGF-A165–containing matrigel plugs led to attenuated angiogenesis and poor association with pericytes. Our data strongly indicate that the ability of VEGF ligands to bind NRP1 influences p38MAPK activation, and formation of functional, pericyte-associated vessels.
The impact of soluble tumor necrosis factor receptor etanercept on the treatment of idiopathic pneumonia syndrome after allogeneic hematopoietic stem cell transplantation
Authors: Yanik Gregory A. , Ho Vincent T. , Levine John E. , White Eric S. , Braun Thomas , Antin Joseph H. , Whitfield Joel , Custer Joseph , Jones Dawn , Ferrara James L. M. , Cooke Kenneth R.
Published: July 2008

Idiopathic pneumonia syndrome (IPS) refers to a diffuse, noninfectious, acute lung injury after hematopoietic stem cell transplantation. Historically, IPS is associated with respiratory failure and mortality rates exceeding 50%. Preclinical studies have implicated tumor necrosis factor-α as an important effector molecule in the development of disease. We studied the tumor necrosis factor-α inhibitor, etanercept, combined with corticosteroids in treating 15 patients (median age, 18 years; range, 1-60 years) with IPS. Eight of 15 patients required mechanical ventilation at therapy onset. Etanercept was administered subcutaneously at a dose of 0.4 mg/kg (maximum 25 mg) twice weekly, for a maximum of 8 doses. Therapy was well tolerated with no infectious pulmonary complications noted. Ten of 15 patients had a complete response, defined as the ability to discontinue supplemental oxygen support during study therapy. The median time to complete response was 7 days (range, 3-18 days), with a day 28 survival of 73%. IPS onset was associated with elevations of several inflammatory proteins in the bronchoalveolar lavage fluid and plasma, and response to therapy correlated with reductions in pulmonary and systemic inflammation. The combination of etanercept and corticosteroids is safe and is associated with high response rates and improved survival in patients with IPS.
Differential Th17 CD4 T-cell depletion in pathogenic and nonpathogenic lentiviral infections
Authors: Brenchley Jason M. , Paiardini Mirko , Knox Kenneth S. , Asher Ava I. , Cervasi Barbara , Asher Tedi E. , Scheinberg Phillip , Price David A. , Hage Chadi A. , Kholi Lisa M. , Khoruts Alexander , Frank Ian , Else James , Schacker Timothy , Silvestri Guido , Douek Daniel C.
Published: July 2008

Acute HIV infection is characterized by massive loss of CD4 T cells from the gastrointestinal (GI) tract. Th17 cells are critical in the defense against microbes, particularly at mucosal surfaces. Here we analyzed Th17 cells in the blood, GI tract, and broncheoalveolar lavage of HIV-infected and uninfected humans, and SIV-infected and uninfected sooty mangabeys. We found that (1) human Th17 cells are specific for extracellular bacterial and fungal antigens, but not common viral antigens; (2) Th17 cells are infected by HIV in vivo, but not preferentially so; (3) CD4 T cells in blood of HIV-infected patients are skewed away from a Th17 phenotype toward a Th1 phenotype with cellular maturation; (4) there is significant loss of Th17 cells in the GI tract of HIV-infected patients; (5) Th17 cells are not preferentially lost from the broncheoalveolar lavage of HIV-infected patients; and (6) SIV-infected sooty mangabeys maintain healthy frequencies of Th17 cells in the blood and GI tract. These observations further elucidate the immunodeficiency of HIV disease and may provide a mechanistic basis for the mucosal barrier breakdown that characterizes HIV infection. Finally, these data may help account for the nonprogressive nature of nonpathogenic SIV infection in sooty mangabeys.
Gene-based microsatellite development for mapping and phylogeny studies in eggplant
Authors: Stàgel Anikò , Portis Ezio , Toppino Laura , Rotino Giuseppe Leonardo , Lanteri Sergio
Published: July 2008

Background

Eggplant (Solanum melongena L.) is a member of the Solanaceae family. In spite of its widespread cultivation and nutritional and economic importance, its genome has not as yet been extensively investigated. Few analyses have been carried out to determine the genetic diversity of eggplant at the DNA level, and linkage relationships have not been well characterised. As for the other Solanaceae crop species (potato, tomato and pepper), the level of intra-specific polymorphism appears to be rather limited, and so it is important that an effort is made to develop more informative DNA markers to make progress in understanding the genetics of eggplant and to advance its breeding. The aim of the present work was to develop a set of functional microsatellite (SSR) markers, via an in silico analysis of publicly available DNA sequence.

Results

From >3,300 genic DNA sequences, 50 SSR-containing candidates suitable for primer design were recovered. Of these, 39 were functional, and were then applied to a panel of 44 accessions, of which 38 were cultivated eggplant varieties, and six were from related Solanum species. The usefulness of the SSR assays for diversity analysis and taxonomic discrimination was demonstrated by constructing a phylogeny based on SSR polymorphisms, and by the demonstration that most were also functional when tested with template from tomato, pepper and potato. As a results of BLASTN analyses, several eggplant SSRs were found to have homologous counterparts in the phylogenetically related species, which carry microsatellite motifs in the same position.

Conclusion

The set of eggplant EST-SSR markers was informative for phylogenetic analysis and genetic mapping. Since EST-SSRs lie within expressed sequence, they have the potential to serve as perfect markers for genes determining variation in phenotype. Their high level of transferability to other Solanaceae species can be used to provide anchoring points for the integration of genetic maps across species.
Genomic and expression analysis of glycosyl hydrolase family 35 genes from rice (Oryza sativa L.)
Authors: Tanthanuch Waraporn , Chantarangsee Mallika , Maneesan Janjira , Ketudat-Cairns James
Published: July 2008

Background

Many plant β-galactosidases (Bgals) have been well characterized and their deduced biological functions mainly involve degradation of structural pectins, xyloglucans or arabinogalactoproteins in plant cell walls. However, gene multiplicity in glycosyl hydrolase family 35 (GH35), to which these proteins belong, implies diverse functions. In this study, the gene multiplicity, apparent evolutionary relationships and transcript expression of rice Bgal genes were examined, in order to predict their biological functions.

Results

Fifteen rice Bgal genes were identified in the plant genome, one of which encodes a protein similar to animal Bgals (OsBgal9), and the remaining 14 fall in a nearly plant-specific subfamily of Bgals. The presence of both classes of Bgals in bryophytes, as well as vascular plants, suggests both gene lineages were present early in plant evolution. All 15 proteins were predicted to contain secretory signal sequences, suggesting they have secretory pathway or external roles. RT-PCR and database analysis found two distinct lineages to be expressed nearly exclusively in reproductive tissues and to be closely related toArabidopsisBgals expressed most highly in flower and pollen. On the other hand,OsBgal6is expressed primarily in young vegetative tissues, and alternative splicing in panicle prevents its production of full-length protein in this reproductive tissue.OsBgal11also showed alternative splicing to produce different length proteins. OsBgal13 produced by recombinant expression inEscherichia colihydrolyzed α-L-arabinoside in addition to β-D-galactoside and β-(1→3)-, β-(1→4)- and β-(1→6)- linked galacto-oligosaccharides.

Conclusion

RiceGH35contains fifteen genes with a diversity of protein sequences, predicted locations and expression and splicing patterns that suggest that OsBgals enzymes may play a variety of roles in metabolism of cell wall polysaccharides, glycoproteins and glycolipids.
Association between invasive cancer of the cervix and HIV-1 infection in Tanzania: the need for dual screening
Authors: Kahesa Crispin , Mwaiselage Julius , Wabinga Henry R , Ngoma Twalib , Kalyango Joan N , Karamagi Charles AS
Published: July 2008

Background

Cancer of the cervix is the second commonest malignancy in females worldwide and is the leading malignancy among women in Tanzania. Cancer of the cervix has been strongly associated with Human Papilloma Virus (HPV) which is a sexually transmitted disease. However, the role of HIV-1 in the aetiology of cancer of the cervix is less clear. Studies suggest that HPV and HIV-1 infection are synergistic and therefore their dual occurrence may fuel increased incidence of cancer of the cervix and AIDS. We therefore conducted a study to determine the association between cancer of the cervix and HIV-1.

Methods

The study was carried out in Ocean Road Cancer Institute, Dar-es-salaam, Tanzania between January and March 2007. A hospital-based case control design was used to study 138 cases and 138 controls. The cases were consenting women 18 years and above with histologically confirmed squamous cell carcinoma of the cervix, while the controls were consenting non-cancer adult women attendants or visitors. The participants were counselled and tested for HIV-1 and interviewed to assess risk factors for cancer of the cervix and HIV-1. Estimation of risk was done by computing odds ratios and confidence intervals. Confounding and interaction between the factors were assessed using logistic regression.

Results

HIV-1 prevalence was much higher among the cases (21.0%) than among the controls (11.6%). In logistic regression, HIV-1 was associated with cancer of the cervix (OR = 2.9, 95% CI = 1.4–5.9). Among the cases the mean age was lower for HIV-1 infected (44.3 years) than HIV-1 uninfected women (54 years, p = 0.0001).

Conclusion

HIV-1 infection is associated with invasive cancer of the cervix. Resource-constrained countries with a high burden of HIV-1 and cervical cancer should adopt a high-risk approach that targets HIV-1 positive women for screening of cervical cancer initially by utilizing HIV/AIDS resources.
Evaluation of the genetic polymorphism of Plasmodium falciparum P126 protein (SERA or SERP) and its influence on naturally acquired specific antibody responses in malaria-infected individuals living in the Brazilian Amazon
Authors: Pratt-Riccio Lilian Rose , Sallenave-Sales Selma , de Oliveira-Ferreira Joseli , da Silva Bruno T , Guimarães Monick Lindenmeyer , Santos Fátima , de Simone Thatiane S , Morgado Mariza G , de Simone Salvatore G , Ferreira-Da-Cruz Maria de Fátima , Daniel-Ribeiro Cláudio T , Zalis Mariano G , Camus Daniel , Banic Dalma M
Published: July 2008

Background

The Plasmodium falciparum P126 protein is an asexual blood-stage malaria vaccine candidate antigen. Antibodies against P126 are able to inhibit parasite growth in vitro, and a major parasite-inhibitory epitope has been recently mapped to its 47 kDa N-terminal extremity (octamer repeat domain – OR domain). The OR domain basically consists of six octamer units, but variation in the sequence and number of repeat units may appear in different alleles. The aim of the present study was to investigate the polymorphism of P126 N-terminal region OR domain in P. falciparum isolates from two Brazilian malaria endemic areas and its impact on anti-OR naturally acquired antibodies.

Methods

The study was carried out in two villages, Candeias do Jamari (Rondonia state) and Peixoto de Azevedo (Mato Grosso state), both located in the south-western part of the Amazon region. The repetitive region of the gene encoding the P126 antigen was PCR amplified and sequenced with the di-deoxy chain termination procedure. The antibody response was evaluated by ELISA with the Nt47 synthetic peptide corresponding to the P126 OR-II domain.

Results

Only two types of OR fragments were identified in the studied areas, one of 175 bp (OR-I) and other of 199 bp (OR-II). A predominance of the OR-II fragment was observed in Candeias do Jamari whereas in Peixoto de Azevedo both fragments OR-I and OR-II were frequent as well as mixed infection (both fragments simultaneously) reported here for the first time. Comparing the DNA sequencing of OR-I and OR-II fragments, there was a high conservation among predicted amino acid sequences of the P126 N-terminal extremity. Data of immune response demonstrated that the OR domain is highly immunogenic in natural conditions of exposure and that the polymorphism of the OR domain does not apparently influence the specific immune response.

Conclusion

These findings confirm a limited genetic polymorphism of the P126 OR domain in P. falciparum isolates and that this limited genetic polymorphism does not seem to influence the development of a specific humoral immune response to P126 and its immunogenicity in the studied population.
Heminested reverse-transcriptase polymerase chain reaction (hnRT-PCR) as a tool for rabies virus detection in stored and decomposed samples
Authors: Araújo Danielle B , Langoni Helio , Almeida Marilene F , Megid Jane
Published: August 2008

Background

The use of methods, both sensitive and specific, for rabies diagnosis are important tools for the control and prophylaxis of the disease. Reverse-Transcriptase Polymerase Chain Reaction (RT-PCR) has been used in rabies diagnosis with good results, even in decomposed materials. Additionally, molecular techniques have been used for epidemiological studies and to gain a better knowledge of viral epidemiology.

Findings

The aim of this work was to evaluate the RT-PCR and hnRT-PCR for rabies virus detection in original tissues stored at -20°C for different periods considering their use for rabies virus detection in stored and decomposed samples. RT-PCR and hnRT-PCR were evaluated in 151 brain samples from different animal species, thawed and left at room temperature for 72 hours for decomposition.

The RT-PCR and hnRT-PCR results were compared with previous results from Direct Fluorescent Antibody Test and Mouse Inoculation Test. From the 50 positive fresh samples, 26 (52%) were positive for RT-PCR and 45 (90%) for hnRT-PCR. From the 48 positive decomposed samples, 17 (34, 3%) were positive for RT-PCR and 36 (75%) for hnRT-PCR. No false-positives results were found in the negatives samples evaluated to the molecular techniques.

Conclusion

These results show that the hnRT-PCR was more sensitive than RT-PCR, and both techniques presented lower sensibility in decomposed samples. The hnRT-PCR demonstrated efficacy in rabies virus detection in stored and decomposed materials suggesting it's application for rabies virus retrospective epidemiological studies.
Fast comparison of DNA sequences by oligonucleotide profiling
Authors: Arnau Vicente , Gallach Miguel , Marín Ignacio
Published: August 2008

Background

The comparison of DNA sequences is a traditional problem in genomics and bioinformatics. Many new opportunities emerge due to the improvement of personal computers, allowing the implementation of novel strategies of analysis.

Findings

We describe a new program, called UVWORD, which determines the number of times that each DNA word present in a sequence (target) is found in a second sequence (source), a procedure that we have called oligonucleotide profiling. On a standard computer, the user may search for words of a size ranging from k = 1 to k = 14 nucleotides. Average counts for groups of contiguous words may also be established. The rate of analysis on standard computers is from 3.4 (k = 14) to 16 millions of words per second (1 ≤ k ≤ 8). This makes feasible the fast screening of even the longest known DNA molecules.

Discussion

We show that the combination of the ability of analyzing words of relatively long size, which occur very rarely by chance, and the fast speed of the program allows to perform novel types of screenings, complementary to those provided by standard programs such as BLAST. This method can be used to determine oligonucleotide content, to characterize the distribution of repetitive sequences in chromosomes, to determine the evolutionary conservation of sequences in different species, to establish regions of similar DNA among chromosomes or genomes, etc.
Prediction of protein secondary structures with a novel kernel density estimation based classifier
Authors: Chang Darby Tien-Hao , Ou Yu-Yen , Hung Hao-Geng , Yang Meng-Han , Chen Chien-Yu , Oyang Yen-Jen
Published: August 2008

Background

Though prediction of protein secondary structures has been an active research issue in bioinformatics for quite a few years and many approaches have been proposed, a new challenge emerges as the sizes of contemporary protein structure databases continue to grow rapidly. The new challenge concerns how we can effectively exploit all the information implicitly deposited in the protein structure databases and deliver ever-improving prediction accuracy as the databases expand rapidly.

Findings

The new challenge is addressed in this article by proposing a predictor designed with a novel kernel density estimation algorithm. One main distinctive feature of the kernel density estimation based approach is that the average execution time taken by the training process is in the order of O(nlogn), where n is the number of instances in the training dataset. In the experiments reported in this article, the proposed predictor delivered an average Q3 (three-state prediction accuracy) score of 80.3% and an average SOV (segment overlap) score of 76.9% for a set of 27 benchmark protein chains extracted from the EVA server that are longer than 100 residues.

Conclusion

The experimental results reported in this article reveal that we can continue to achieve higher prediction accuracy of protein secondary structures by effectively exploiting the structural information deposited in fast-growing protein structure databases. In this respect, the kernel density estimation based approach enjoys a distinctive advantage with its low time complexity for carrying out the training process.
Norepinephrine to increase blood pressure in endotoxaemic pigs is associated with improved hepatic mitochondrial respiration
Authors: Regueira Tomas , Bänziger Bertram , Djafarzadeh Siamak , Brandt Sebastian , Gorrasi Jose , Takala Jukka , Lepper Philipp M , Jakob Stephan M
Published: August 2008

Introduction

Low blood pressure, inadequate tissue oxygen delivery and mitochondrial dysfunction have all been implicated in the development of sepsis-induced organ failure. This study evaluated the effect on liver mitochondrial function of using norepinephrine to increase blood pressure in experimental sepsis.

Methods

Thirteen anaesthetized pigs received endotoxin (Escherichia coli lipopolysaccharide B0111:B4; 0.4 μg/kg per hour) and were subsequently randomly assigned to norepinephrine treatment or placebo for 10 hours. Norepinephrine dose was adjusted at 2-hour intervals to achieve 15 mmHg increases in mean arterial blood pressure up to 95 mmHg. Systemic (thermodilution) and hepatosplanchnic (ultrasound Doppler) blood flow were measured at each step. At the end of the experiment, hepatic mitochondrial oxygen consumption (high-resolution respirometry) and citrate synthase activity (spectrophotometry) were assessed.

Results

Mean arterial pressure (mmHg) increased only in norepinephrine-treated animals (from 73 [median; range 69 to 81] to 63 [60 to 68] in controls [P = 0.09] and from 83 [69 to 93] to 96 [86 to 108] in norepinephrine-treated animals [P = 0.019]). Cardiac index and systemic oxygen delivery (DO2) increased in both groups, but significantly more in the norepinephrine group (P < 0.03 for both). Cardiac index (ml/min per·kg) increased from 99 (range: 72 to 112) to 117 (110 to 232) in controls (P = 0.002), and from 107 (84 to 132) to 161 (147 to 340) in norepinephrine-treated animals (P = 0.001). DO2 (ml/min per·kg) increased from 13 (range: 11 to 15) to 16 (15 to 24) in controls (P = 0.028), and from 16 (12 to 19) to 29 (25 to 52) in norepinephrine-treated animals (P = 0.018). Systemic oxygen consumption (systemic VO2) increased in both groups (P < 0.05), whereas hepatosplanchnic flows, DO2 and VO2 remained stable. The hepatic lactate extraction ratio decreased in both groups (P = 0.05). Liver mitochondria complex I-dependent and II-dependent respiratory control ratios were increased in the norepinephrine group (complex I: 3.5 [range: 2.1 to 5.7] in controls versus 5.8 [4.8 to 6.4] in norepinephrine-treated animals [P = 0.015]; complex II: 3.1 [2.3 to 3.8] in controls versus 3.7 [3.3 to 4.6] in norepinephrine-treated animals [P = 0.09]). No differences were observed in citrate synthase activity.

Conclusion

Norepinephrine treatment during endotoxaemia does not increase hepatosplanchnic flow, oxygen delivery or consumption, and does not improve the hepatic lactate extraction ratio. However, norepinephrine increases the liver mitochondria complex I-dependent and II-dependent respiratory control ratios. This effect was probably mediated by a direct effect of norepinephrine on liver cells.