bluuebunny/crossref_metadata_2025 huggingface dataset:
Association of cartilage‐specific deletion of peroxisome proliferator–activated receptor γ with abnormal endochondral ossification and impaired cartilage growth and development in a murine model
Authors: Monemdjou Roxana , Vasheghani Faezeh , Fahmi Hassan , Perez Gemma , Blati Meryem , Taniguchi Noboru , Lotz Martin , St‐Arnaud René , Pelletier Jean‐Pierre , Martel‐Pelletier Johanne , Beier Frank , Kapoor Mohit
Published: December 2011

Objective

Long bones develop through the strictly regulated process of endochondral ossification within the growth plate, resulting in the replacement of cartilage by bone. Defects in this process can result in skeletal abnormalities and a predisposition to degenerative joint diseases such as osteoarthritis (OA). Studies suggest that activation of the transcription factor peroxisome proliferator–activated receptor γ (PPARγ) is an important therapeutic target in OA. To devise PPARγ‐related therapies in OA, it is critical to identify the role of this transcription factor in cartilage biology. Therefore, this study sought to determine the in vivo role of PPARγ in endochondral ossification and cartilage development, using cartilage‐specific PPARγ–knockout (KO) mice.

Methods

Cartilage‐specific PPARγ–KO mice were generated using the Cre/loxP system. Histomorphometric and immunohistochemical analyses were performed to assess the patterns of ossification, proliferation, differentiation, and hypertrophy of chondrocytes, skeletal organization, bone density, and calcium deposition in the KO mice.

Results

PPARγ‐KO mice exhibited reductions in body length, body weight, length of the long bones, skeletal growth, cellularity, bone density, calcium deposition, and trabecular bone thickness, abnormal organization of the growth plate, loss of columnar organization, shorter hypertrophic zones, and delayed primary and secondary ossification. Immunohistochemical analyses for Sox9, 5‐bromo‐2′‐deoxyuridine, p57, type X collagen, and platelet endothelial cell adhesion molecule 1 revealed reductions in the differentiation, proliferation, and hypertrophy of chondrocytes and in vascularization of the growth plate in mutant mice. Isolated chondrocytes and cartilage explants from mutant mice showed aberrant expression of Sox9 and extracellular matrix markers, including aggrecan, type II collagen, and matrix metalloproteinase 13. In addition, chondrocytes from mutant mice exhibited enhanced phosphorylation of p38 and decreased expression of Indian hedgehog.

Conclusion

The presence of PPARγ is required for normal endochondral ossification and cartilage development in vivo.
Epirubicin potentiates recombinant adeno‐associated virus type 2/5–mediated TRAIL expression in fibroblast‐like synoviocytes and augments the antiarthritic effects of rAAV2/5‐TRAIL
Authors: Shi Juan , Diao Zhijuan , Zhou Jiansuo , Zhu Jieqing , Yuan Haiqin , You Xin , Liu Yanxin , Zheng Dexian
Published: December 2011

Objective

Synovial cells in rheumatoid synovium display abnormal proliferation, which leads to joint destruction. TRAIL has been described as a proapoptotic factor in fibroblast‐like synoviocytes (FLS). This study was undertaken to investigate the functions of rAAV2/5‐TRAIL in human FLS and in arthritic mice.

Methods

Primary human FLS were infected with rAAV2/5‐TRAIL in the presence or absence of epirubicin. Transgene expression was monitored by both enzyme‐linked immunosorbent assay and flow cytometry. The disease‐modulating activity of epirubicin plus rAAV2/5‐TRAIL was investigated in mice with collagen‐induced arthritis (CIA).

Results

Subtoxic doses of epirubicin potentiated rAAV2/5‐mediated TRAIL expression in FLS and simultaneously enhanced the sensitivity of FLS to TRAIL. Epirubicin treatment up‐regulated death receptor 4 (DR‐4) and DR‐5 expression and down‐regulated FLIP expression, thereby enhancing the activation of procaspase 3, procaspase 8, and procaspase 9. An in vivo study showed that the combination of rAAV2/5‐TRAIL gene therapy and epirubicin chemotherapy provided augmented antiarthritic effects in a mouse model of CIA. The intraarticular injection of rAAV2/5‐TRAIL combined with epirubicin treatment significantly reduced the severity and incidence of CIA and joint swelling in the animals. Histologic evaluations revealed that inflammatory cell infiltration, cartilage destruction, and bone erosion were significantly reduced in the joints of the mice receiving the synthetic treatment. Results of a viral genome copy number assay indicated that epirubicin dramatically augmented the expression of rAAV2/5‐TRAIL without altering its tissue distribution.

Conclusion

These results suggest that epirubicin enhances the antiarthritic effect of rAAV2/5‐TRAIL and that combination treatment might be an important therapeutic alternative, with practical significance for rheumatoid arthritis.
Brewer's spent grain: Characterization and standardization procedure for the enzymatic hydrolysis by Bacillus cereus strain
Authors: Kotlar Catalina E. , Belagardi Mariela , Roura Sara I.
Published: December 2011

An important way to reuse agroindustrial by‐products and to produce added‐value products consists of the production of protein hydrolysates. In the current study, we used Brewer's spent grain (BSG), mainly because of its availability and cost, as a substrate for the enzymatic hydrolysis by Bacillus cereus. First, the physicochemical and microbiological characterization of BSG batches from three varieties was carried out. Furthermore, the optimal fermentation upstream processes for enzymatic hydrolysis by B. cereus were defined. Finally, the ability of B. cereus to hydrolyze different fractions of BSG was analyzed and possible synergistic effects of this bacterium along with other proteolytic bacteria were also investigated. Results showed that the naturally associated microflora was predominantly thermophilic aerobic bacteria and the drying process was the better alternative for BSG preservation. Water, lipids, and ash content differed significantly among the three varieties; however, no statistically significant differences were found in the protein content among them. After BSG characterization studies, the following protocol was set to obtain the fermentation substrate (FS): drying at 60°C for 24–48 H; sieving, grinding, and polyphenol extraction with an alcohol–water solution; and finally autoclaving. A synergistic effect was observed when B. cereus was inoculated with Pseudomonas strains in FS.
First Stereoselective Total Synthesis of Isoaspinonene through a Baylis–Hillman/Olefin Cross‐Metathesis Protocol
Authors: Radha Krishna Palakodety , Alivelu Munagala , Prabhakar Rao Tadikamalla
Published: December 2011

The first stereoselective and efficient total synthesis of isoaspinonene by using Baylis–Hillman reaction, chelation‐controlled vinyl Grignard reaction, Wittig olefination, and olefin cross‐metathesis reaction of a hitherto unreported substrate as the key steps is described.
CE of inorganic species – A review of methodological advancements over 2009–2010
Authors: Kubáň Petr , Timerbaev Andrei R.
Published: December 2011

This article is the seventh in a series examining biannually the methodological developments in the field of CE analysis of inorganic species and covers relevant documents published between January 2009 and December 2010. Following an analysis of the significant accomplishments that have impacted the field in two recent years, a survey of advances in general CE methodology is presented. Subsequently, several notable trends that can be perceived in this well‐established field are discussed: the continuing rise of ME and consequent development of suitable detection techniques, most notably contactless conductivity detection, the constant pace of advances in speciation analysis, and an increase in non‐analytical CE applications to study complexation and (bio)transformation reactions of metal analytes. A range of recently emerged multi‐detection designs, ICP‐MS interface devices, and separation systems, for which outpacing work has been conducted, are also brought into focus.
Recent advances in the analysis of antibiotics by CE and CEC
Authors: Pérez‐Fernández Virginia , Domínguez‐Vega Elena , Crego Antonio L. , García Maria Ángeles , Marina Maria Luisa
Published: December 2011

This article reviews the recent developments achieved in the analysis of antibiotics by CE and CEC. CZE has mainly been employed although other separation modes have also been used. Different detection systems coupled to CE have been reported for antibiotic determination. Enhancement on sensitivity through the use of diverse offline, inline, and online preconcentration approaches is also described. Special attention has been paid to sample treatment steps and to the applications developed in different research areas such as the pharmaceutical, biological, food, and environmental. This manuscript covers the period of time from the previous review published in June 2009 until May 2011.
Surface modification for PDMS‐based microfluidic devices
Authors: Zhou Jinwen , Khodakov Dmitriy A. , Ellis Amanda V. , Voelcker Nicolas H.
Published: December 2011

This review focuses on advances reported from April 2009 to May 2011 in PDMS surface modifications for the application in microfluidic devices. PDMS surface modification techniques presented here include improved plasma and graft polymer coating, dynamic surfactant treatment, hydrosilylation‐based surface modification and surface modification with nanomaterials such as carbon nanotubes and metal nanoparticles. Recent efforts to generate topographical and chemical patterns on PDMS are also discussed. The described surface modifications not only increase PDMS wettability, inhibit or reduce non‐specific adsorption of hydrophobic species onto the surfaces in the act, but also result in the display of desired functional groups useful for molecular separations, biomolecular detection via immunoassays, cell culture and emulsion formation.
Quality control issues and the identification of rare functional variants with next‐generation sequencing data
Authors: Hemmelmann Claudia , Daw E. Warwick , Wilson Alexander F.
Published: December 2011

Next‐generation sequencing of large numbers of individuals presents challenges in data preparation, quality control, and statistical analysis because of the rarity of the variants. The Genetic Analysis Workshop 17 (GAW17) data provide an opportunity to survey existing methods and compare these methods with novel ones. Specifically, the GAW17 Group 2 contributors investigate existing and newly proposed methods and study design strategies to identify rare variants, predict functional variants, and/or examine quality control. We introduce the eight Group 2 papers, summarize their approaches, and discuss their strengths and weaknesses. For these investigations, some groups used only the genotype data, whereas others also used the simulated phenotype data. Although the eight Group 2 contributions covered a wide variety of topics under the general idea of identifying rare variants, they can be grouped into three broad categories according to their common research interests: functionality of variants and quality control issues, family‐based analyses, and association analyses of unrelated individuals. The aims of the first subgroup were quite different. These were population structure analyses that used rare variants to predict functionality and examine the accuracy of genotype calls. The aims of the family‐based analyses were to select which families should be sequenced and to identify high‐risk pedigrees; the aim of the association analyses was to identify variants or genes with regression‐based methods. However, power to detect associations was low in all three association studies. Thus this work shows opportunities for incorporating rare variants into the genetic and statistical analyses of common diseases. Genet. Epidemiol. 35:S22–S28, 2011. © 2011 Wiley Periodicals, Inc.
Multiple testing in high‐throughput sequence data: experiences from Group 8 of Genetic Analysis Workshop 17
Authors: König Inke R. , Nsengimana Jeremie , Papachristou Charalampos , Simonson Matthew A. , Wang Kai , Weisburd Jason A.
Published: December 2011

The use of high‐throughput sequence data in genetic epidemiology allows the investigation of common and rare variants in the entire genome, thus increasing the amount of information and the potential number of statistical tests performed within one study. As a consequence, the problem of multiple testing may become even more pressing than in previous studies. As an important challenge, the exact number of statistical tests depends on the actual statistical method used. Furthermore, many statistical approaches for the analysis of sequence data require permutation. Thus it may be difficult to also use permutation to estimate correct type I error levels as in genome‐wide association studies. In view of this, a separate group at Genetic Analysis Workshop 17 was formed with a focus on multiple testing. Here, we present the approaches used for the workshop. Apart from tackling the multiple testing problem, the new group focused on different issues. Some contributors developed and investigated modifications of existing collapsing methods. Others aimed at improving the identification of functional variants through a reduction and analysis of the underlying data dimensions. Two research groups investigated the overall accumulation of rare variation across the genome and its value in predicting phenotypes. Finally, other investigators left the path of traditional statistical analyses by reversing null and alternative hypotheses and by proposing a novel resampling method. We describe and discuss all these approaches. Genet. Epidemiol. 35:S61–S66, 2011. © 2011 Wiley Periodicals, Inc.
Lessons learned from Genetic Analysis Workshop 17: transitioning from genome‐wide association studies to whole‐genome statistical genetic analysis
Authors: Wilson Alexander F. , Ziegler Andreas
Published: December 2011

Genetic Analysis Workshop 17 (GAW17) focused on the transition from genome‐wide association study designs and methods to the study designs and statistical genetic methods that will be required for the analysis of next‐generation sequence data including both common and rare sequence variants. In the 166 contributions to GAW17, a wide variety of statistical methods were applied to simulated traits in population‐ and family‐based samples, and results from these analyses were compared to the known generating model. In general, many of the statistical genetic methods used in the population‐based sample identified causal sequence variants (SVs) when the estimated locus‐specific heritability, as measured in the population‐based sample, was greater than about 0.08. However, SVs with locus‐specific heritabilities less than 0.03 were rarely identified consistently. In the family‐based samples, many of the methods detected SVs that were rarer than those detected in the population‐based sample, but the estimated locus‐specific heritabilities for these rare SVs, as measured in the family‐based samples, were substantially higher (>0.2) than their corresponding heritabilities in the population‐based samples. Substantial inflation of the type I error rate was observed across a wide variety of statistical methods. Although many of the contributions found little inflation in type I error for Q4, a trait with no causal SVs, type I error rates for Q1 and Q2 were well above their nominal levels with the inflation for Q1 being higher than that for Q2. It seems likely that this inflation in type I error is due to correlations among SVs. Genet. Epidemiol. 35:S107–S114, 2011. © 2011 Wiley Periodicals, Inc.
Steroid 5α‐reductase in adult rat brain after neonatal testosterone administration
Authors: Sánchez Pilar , Torres Jesús M. , del Moral Raimundo G. , de Dios Luna Juan , Ortega Esperanza
Published: December 2011

Testosterone (T) plays an important role in developing brain, dictating sex‐specific behavior and physiology. 3α,5α‐Reduced neurosteroids also regulate reproductive behavior. The key enzyme in the biosynthesis of these neurosteroids is 5α‐reductase (5α‐R), expressed as two isozymes, 5α‐R1 and 5α‐R2. In this study, T and sesame oil (vehicle) were administered during postnatal sexual differentiation of the central nervous system (CNS) and mRNA levels of 5α‐R isozymes, were measured using quantitative RT‐PCR in prefrontal cortex of male and female rats with different androgenic status at adulthood. Our results indicate that T concentrations during postnatal sexual differentiation of the rat CNS, among other sex‐dependent factors, influence brain levels of 5α‐R isozymes in adulthood and the pattern of their regulation by androgen hormones. © 2011 IUBMB Life, 2011
Role of oxidative stress in the pathogenesis of sickle cell disease
Authors: Chirico Erica N. , Pialoux Vincent
Published: December 2011

Sickle cell disease (SCD) is a class of hemoglobinopathy in humans, which causes a disruption of the normal activities in different systems. Although this disease begins with the polymerization of red blood cells during its deoxygenating phase, it can erupt into a cascade of debilitating conditions such as ischemia‐reperfusion injury, inflammation, and painful vaso‐occlusion crises. The purpose of this review is to discuss how these phenomena can result in the formation of oxidative stress as well as limit nitric oxide (NO) bioavailability and decrease antioxidant status. The cumulative effects of these traits cause an increase in other forms of reactive oxygen species (ROS), which in turn intensify the symptoms of SCD and generate a vicious circle. Finally, we will discuss antioxidant therapeutic strategies that limit ROS generation and subsequently increase NO bioavailability with respect to endothelial protection in SCD. © IUBMB, IUBMB Life, 2011.
Balanced steady‐state free precession fMRI with intravascular susceptibility contrast agent
Authors: Zhou Iris Y. , Cheung Matthew M. , Lau Condon , Chan Kevin C. , Wu Ed X.
Published: December 2011

One major challenge in echo planar imaging‐based functional MRI (fMRI) is the susceptibility‐induced image distortion. In this study, a new cerebral blood volume‐weighted fMRI technique using distortion‐free balanced steady‐state free precession (bSSFP) sequence was proposed and its feasibility was investigated in rat brain at 7 Tesla. After administration of intravascular susceptibility contrast agent (monocrystalline iron oxide nanoparticle [MION] at 15 mg/kg), unilateral visual stimulation was presented using a block‐design paradigm. With repetition time/echo time = 3.8/1.9 ms and α = 18°, bSSFP fMRI was performed and compared with the conventional cerebral blood volume‐weighted fMRI using post‐MION gradient echo and spin echo echo planar imaging. The results showed that post‐MION bSSFP fMRI provides comparable sensitivity but with no severe image distortion and signal dropout. Robust negative responses were observed during stimulation and activation patterns were in excellent agreement with known neuroanatomy. Furthermore, the post‐MION bSSFP signal was observed to decrease significantly during hypercapnia challenge, indicating its sensitivity to cerebral blood volume changes. These findings demonstrated that post‐MION bSSFP fMRI is a promising alternative to conventional cerebral blood volume‐weighted fMRI. This technique is particularly suited for fMRI investigation of animal models at high field. Magn Reson Med, 2012. © 2011 Wiley Periodicals, Inc.
In vivo detection of excitotoxicity by manganese‐enhanced MRI: Comparison with physiological stimulation
Authors: Gobbo Oliviero L. , Petit Fanny , Gurden Hirac , Dhenain Marc
Published: December 2011

Manganese‐enhanced MRI (MEMRI) is a powerful technique for the in vivo monitoring of brain function in animals. Manganese enters into cells through calcium channels, i.e., voltage‐gated calcium channels and activated glutamate receptors (e.g.,N‐methyl‐D‐aspartate receptors).N‐methyl‐D‐aspartate receptors are activated both in normal physiological and pathophysiological conditions. Consistent with these mechanisms, we showed that in the olfactory bulb, the MEMRI signal strongly increases when excitotoxic mechanisms are induced by an administration of aN‐methyl‐D‐aspartate receptor agonist, quinolinate. We found that the intensity of the MEMRI signal in excitotoxic conditions is similar to the odor‐evoked signal in normal physiological conditions. Finally, we showed that the dynamics of the MEMRI signal are determined by the early phase of manganese in the olfactory bulb. Overall, these data show that, in addition to physiological studies, MEMRI can be used as an in vivo method to follow‐up the dynamics of excitotoxic events. Magn Reson Med, 2012. © 2011 Wiley Periodicals, Inc.
CRABP‐II methylation: A critical determinant of retinoic acid resistance of medulloblastoma cells
Authors: Fu Yuan-Shan , Wang Qian , Ma Jing-Xin , Yang Xiang-Hong , Wu Mo-Li , Zhang Kai-Li , Kong Qing-You , Chen Xiao-Yan , Sun Yuan , Chen Nan-Nan , Shu Xiao-Hong , Li Hong , Liu Jia
Published: December 2011

Medulloblastoma cells exhibit varied responses to therapy by all‐trans retinoic acid (RA). The underlying mechanism for such diverse effects however remains largely unclear. In this study, we attempted to elucidate the molecular basis of RA resistance through the study of RA signaling components in both RA‐sensitive (Med‐3) and RA‐resistant (UW228‐2 and UW228‐3) medulloblastoma cells. The results revealed that RARα/β/γ and RXRα/β/γ were found in the three cell lines. Expression of CRABP‐I and CRABP‐II was seen in Med‐3 cells, up‐regulated when treated with RA, but was absent in UW228‐2 and UW228‐3 cells regardless of RA treatment. Bisulfite sequencing revealed 8 methylated CG sites at the promoter region of CRABP‐II in UW228‐2 and UW228‐3 but not in Med‐3 cells. Demethylation by 5‐aza‐2′‐deoxycytidine recovered CRABP‐II expression. Upon restoration of CRABP‐II expression, both UW228‐2 and UW228‐3 cells responded to RA treatment by forming neuronal‐like differentiation, synaptophysin expression, β‐III tubulin upregulation, and apoptosis. Furthermore, CRABP‐II specific siRNA reduced RA sensitivity in Med‐3 cells. Tissue microarray‐based immunohistochemical staining showed variable CRABP‐II expression patterns among 104 medulloblastoma cases, ranging from negative (42.3%), partly positive (14.4%) to positive (43.3%). CRABP‐II expression was positively correlated with synaptophysin (rs = 0.317; p = 0.001) but not with CRABP‐I expression (p > 0.05). In conclusion, aberrant methylation in CRABP‐II reduces the expression of CRABP‐II that in turn confers RA resistance in medulloblastoma cells. Determination of CRABP‐II expression or methylation status may enable a personalized RA therapy in patients with medulloblastomas and other types of cancers.
SUM–PRODUCT ESTIMATES AND MULTIPLICATIVE ORDERS OFγANDγ+γ−1IN FINITE FIELDS
Authors: SHPARLINSKI IGOR
Published: December 2011

Using a recent result on the sum–product problem, we estimate the number of elementsγin a prime finite field such that bothγandγ+γ−1are of small order.
Chemical interaction between the larva of a dipteran parasitoid and its coleopteran host: A case of exploitation of the communication system during the searching behaviour?
Authors: Groba H.F. , Castelo M.K.
Published: December 2011

The robber flyMallophora ruficaudais one of the principal apicultural pests in the Pampas region of Argentina. As adults, the flies prey on honey bees and other insects; while, as larvae, they parasitize scarab beetle larvae. Females ofM. ruficaudalay eggs away from the host in tall grasses. After being dispersed by the wind, larvae drop to the ground, where they dig in search of their hosts. It is known that second instar larvae ofM. ruficaudaexhibit active host searching behaviour towards its preferred host, third instar larva ofCyclocephala signaticollis, using host-related chemical cues. Furthermore, previous works show that these chemical cues are produced in the posterior body half of hosts. However, the precise anatomical origin of these cues and whether they mediate any behaviour ofC. signaticollislarvae remains yet unknown. In order to determine the precise origin of the chemical cue, we carried out olfactometer assays with different stimuli of extracts of the posteriorC. signaticollisbody half. Additionally, we tested whetherC. signaticollisis attracted to any of the same extracts as in the previous experiments. We found that both second instar ofM. ruficaudaand third instar ofC. signaticollisare attracted to extracts of the fermentation chamber (proctodeum). This is the first report of attraction of conspecific larvae in scarab beetles. We discuss a possible case of system communication exploitation in an immature parasitoid-host system.
Chrono- and lithostratigraphy of a Mesozoic–Tertiary fore- to intra-arc basin: Adelaide Island, Antarctic Peninsula
Authors: RILEY TEAL R. , FLOWERDEW MICHAEL J. , WHITEHOUSE MARTIN J.
Published: December 2011

The Mesozoic fore-arc of the Antarctic Peninsula is exposed along its west coast. On Adelaide Island, a 2–3 km succession of turbiditic coarse sandstones and volcanic rocks is exposed. Four U–Pb (zircon) ages are presented here that, in combination with a new stratigraphy, have permitted a robust chrono- and lithostratigraphy to be constructed, which in turn has allowed tentative correlations to be made with the Fossil Bluff Group of Alexander Island, where the ‘type’ fore-arc sequences are described. The lithostratigraphy of Adelaide Island includes the definition of five volcanic/sedimentary formations. The oldest formation is the Buchia Buttress Formation (149.5 ± 1.6 Ma) and is correlated with the Himalia Ridge Formation of Alexander Island. The sandstone–conglomerate dominated succession of the Milestone Bluff Formation (113.9 ± 1.2 Ma) is tentatively correlated with the Pluto Glacier Formation of Alexander Island. Three dominantly volcanic formations are recognized on Adelaide Island, akin to the volcanic rocks of the Alexander Island Volcanic Group; the Mount Liotard Formation is formed of 2 km of basaltic andesite lavas, whilst the Bond Nunatak Formation is also dominated by basaltic andesite lavas, but interbedded with volcaniclastic rocks. The Reptile Ridge Formation has been dated at 67.6 ± 0.7 Ma and is characterized by hydrothermally altered rhyolitic crystal-lithic tuffs. Tentative correlations between Adelaide Island and Alexander Island preclude the two areas forming part of distinct terranes as has been suggested previously, and a proximal source for volcaniclastic sediments also indicates an exotic terrane origin is unlikely.
Period functions for Hecke triangle groups, and the Selberg zeta function as a Fredholm determinant
Authors: MÖLLER M. , POHL A. D.
Published: December 2011

We characterize Maass cusp forms for any cofinite Hecke triangle group as 1-eigenfunctions of appropriate regularity of a transfer operator family. This transfer operator family is associated to a certain symbolic dynamics for the geodesic flow on the orbifold arising as the orbit space of the action of the Hecke triangle group on the hyperbolic plane. Moreover, we show that the Selberg zeta function is the Fredholm determinant of the transfer operator family associated to an acceleration of this symbolic dynamics.
Motion prediction and supervisory control of the macro–micro parallel manipulator system
Authors: Duan Xuechao , Qiu Yuanying , Mi Jianwei , Zhao Ze
Published: December 2011

This paper deals with the motion prediction and control of the macro–micro parallel manipulator system for a 500-m-aperture spherical radio telescope (FAST). Firstly, based on principles of parallel mechanism, a decoupled tracking and prediction algorithm to predict the position and orientation of the movable macro parallel manipulator is presented in this paper. Then, taken as the upper layer supervisory controller in the joint space of the micro parallel manipulator, the adaptive interaction PID controller utilizing the adaptive interaction algorithm to adjust the parameters of a canonical PID controller is discussed. In addition, the digital servo filters with feedforward are employed in the linear actuators as the lower layer controllers. Experimental results of a one-tenth scale FAST field model validate the effectiveness of the supervisory controller and the motion prediction algorithm.
Off‐fault tensile cracks: A link between geological fault observations, lab experiments, and dynamic rupture models
Authors: Ngo D. , Huang Y. , Rosakis A. , Griffith W. A. , Pollard D.
Published: December 2011

We examine the local nature of the dynamic stress field in the vicinity of the tip of a semi‐infinite sub‐Rayleigh (slower than the Rayleigh wave speed,cR) mode II crack with a velocity‐weakening cohesive zone. We constrain the model using results from dynamic photoelastic experiments, in which shear ruptures were nucleated spontaneously in Homalite‐100 plates along a bonded, precut, and inclined interface subject to a far‐field uniaxial prestress. During the experiments, tensile cracks grew periodically along one side of the shear rupture interface at a roughly constant angle relative to the shear rupture interface. The occurrence and inclination of the tensile cracks are explained by our analytical model. With slight modifications, the model can be scaled to natural faults, providing diagnostic criteria for interpreting velocity, directivity, and static prestress state associated with past earthquakes on exhumed faults. Indirectly, this method also allows one to constrain the velocity‐weakening nature of natural ruptures, providing an important link between field geology, laboratory experiments, and seismology.
Radial transport of energetic ions in the presence of trapped electron mode turbulence
Authors: Chowdhury J. , Wang W. , Ethier S. , Manickam J. , Ganesh R.
Published: December 2011

The nature of transport of hot ions is studied in the presence of microturbulence generated by the trapped electron mode in a Tokamak using massively parallel, first principle based global nonlinear gyrokinetic simulation, and with the help of a passive tracer method. Passing and trapped hot ions are observed to exhibit inverse and inverse square scaling with energy, while those with isotropic pitch distribution are found to exhibit inverse dependence on energy. For all types of hot ions, namely, isotropic, passing, and trapped, the radial transport appears to be subdiffusive for the parameters considered.
Dipolar vortices and collisional instability in rotating electron-positron-ion plasmas
Authors: Haque Q.
Published: December 2011

Linear dispersion relation of electrostatic waves is derived for rotating electron-positron-ion (e-p-i) plasmas. The role of the rotational plasma frequency on drift wave through Coriolis force in the pulsar magnetosphere is discussed. This wave can couple with acoustic mode. In the nonlinear regime, stationary solution in the form of dipolar vortices is obtained. At the end we have also found the collisional instability in the presence of neutral-ion collisions for this rotating e-p-i plasma. The importance of the study with respect to astrophysical plasmas is also pointed out.
Plasmon effects on the entanglement fidelity for elastic collisions in hot quantum plasmas
Authors: Jung Young-Dae
Published: December 2011

The plasmon and screening effects on the entanglement fidelity for the elastic electron-ion collision are investigated in hot quantum plasmas. The partial wave analysis and effective interaction including the plasmon couplings are employed to obtain the entanglement fidelity function in hot quantum plasmas. It is shown that the plasmon effect enhances the entanglement fidelity in quantum plasmas for 0<β(≡ℏωp/kBT)<0.8 and, however, suppresses the entanglement fidelity for 0.8<β<1, where ωp is the plasmon frequency, kB is the Boltzmann constant, and T is the plasma temperature. It is also found that the entanglement fidelity decreases with increasing Debye length and collision energy.
When beauty is only skin deep; optimizing the sensitivity of specular neutron reflectivity for probing structure beneath the surface of thin films
Authors: Majkrzak Charles F. , Carpenter Elisabeth , Heinrich Frank , Berk Norman F.
Published: December 2011

Specular neutron reflectometry has become an established probe of the nanometer scale structure of materials in thin film and multilayered form. It has contributed especially to our understanding of soft condensed matter of interest in polymer science, organic chemistry, and biology and of magnetic hard condensed matter systems. In this paper we examine a number of key factors which have emerged that can limit the sensitivity of neutron reflection as such a probe. Among these is loss of phase information, and we discuss how knowledge about material surrounding a film of interest can be applied to help resolve the problem. In this context we also consider what role the quantum phenomenon of interaction-free measurement might play in enhancing the statistical efficiency for obtaining reflectivity or transmission data.
Annealing temperature window for tunneling magnetoresistance and spin torque switching in CoFeB/MgO/CoFeB perpendicular magnetic tunnel junctions
Authors: Meng H. , Sbiaa R. , Wang C. C. , Lua S. Y. H. , Akhtar M. A. K.
Published: December 2011

Annealing temperature (Ta) and free layer thickness dependencies of magnetic properties and spin-transfer torque switching were investigated in CoFeB-MgO based magnetic tunnel junctions with perpendicular magnetic anisotropy (PMA). Annealing process was found to be critical to buildup PMA. As Ta increases, switching field of free layer and reference layer is enhanced first then drops, corresponding to the improvement and collapse of PMA in both layers. However, it should be noted that PMA of free layer and the tunneling magnetoresistive (TMR) are maximized at different Ta zones. Spin transfer torque study pointed out that switching current density (Jc) depends on the combined effects from PMA, spin polarization, and saturation magnetization, which all depend on Ta values. Thickness dependence study revealed that Jc relies on the competing results of the thickness and PMA. The lowest critical switching current density achieved is 2.1 MA/cm2, accompanied with a TMR around 52% at room temperature.
Nanopolaritonics with a continuum of molecules: Simulations of molecular-induced selectivity in plasmonics transport through a continuous Y-shape
Authors: Neuhauser Daniel
Published: December 2011

Using the recent NF (near-field) formulation for electrodynamics on the nanoscale, we simulate transport in a Y-shape gold nanostructure in the presence of 2-level molecules. NF is shown to be easily integrated with the Liouville equation, producing a simple and efficient nanopolaritons (plasmons-excitons) solver, with a large time step. Two cases are considered: coating of the gold structure with molecular layers thinner than the structure, and filling space with aligned molecules. In both cases significant effects on the radiation transport are obtained even for low molecular densities. At low densities the effects are primarily an overall reduction of the plasmonics peak, but at higher densities there is a significant selectivity control by the molecules. A redshift is predicted, especially for the space-filling case. The combined nanopolariton shows qualitative hybridization, and the spectral peaks separate with increasing coupling, i.e., with increasing molecular densities. The results open the way to “control of light by light,” i.e., controlling plasmonic light transport by inducing a change in the direction of the guiding molecular dipoles through radiation or other means.
How does spallation microdamage nucleate in bulk amorphous alloys under shock loading?
Authors: Huang X. , Ling Z. , Zhang H. S. , Ma J. , Dai L. H.
Published: December 2011

Specially designed plate-impact experiments have been conducted on a Zr-based amorphous alloy using a single-stage light gas gun. To understand the microdamage nucleation process in the material, the samples are subjected to dynamic tensile loadings of identical amplitude (∼ 3.18 GPa) but with different durations (83–201 ns). A cellular pattern with an equiaxed shape is observed on the spallation surface, which shows that spallation in the tested amorphous alloy is a typical ductile fracture and that microvoids have been nucleated during the process. Based on the observed fracture morphologies of the spallation surface and free-volume theory, we propose a microvoid nucleation model of bulk amorphous alloys. It is found that nucleation of microvoids at the early stage of spallation in amorphous alloys results from diffusion and coalescence of free volume, and that high mean tensile stress plays a dominant role in microvoid nucleation.
A universal gauge for thermal conductivity of silicon nanowires with different cross sectional geometries
Authors: Chen Jie , Zhang Gang , Li Baowen
Published: December 2011

By using molecular dynamics simulations, we study thermal conductivity of silicon nanowires (SiNWs) with different cross sectional geometries. It is found that thermal conductivity decreases monotonically with the increase of surface-to-volume ratio (SVR). More interestingly, a simple universal linear dependence of thermal conductivity on SVR is observed for SiNWs with modest cross sectional area (larger than 20 nm2), regardless of the cross sectional geometry. As a result, among different shaped SiNWs with the same cross sectional area, the one with triangular cross section has the lowest thermal conductivity. Our study provides not only a universal gauge for thermal conductivity among different cross sectional geometries, but also a designing guidance to tune thermal conductivity by geometry.
Ground state for nonlinear Schrödinger equation with sign-changing and vanishing potential
Authors: Wang Zhengping , Zhou Huan-Song
Published: December 2011

We are concerned with the least energy solution (i.e., ground state) for the following stationary nonlinear Schrödinger equation: \documentclass[12pt]{minimal}\begin{document}$-\Delta u(x)+ \lambda V(x) u(x)=K(x)f(u), \ x\break\in {\mathbb {R}^{N}}, \ N\ge 3,$\end{document}−Δu(x)+λV(x)u(x)=K(x)f(u),x∈RN,N≥3, where λ > 0, V(x) changes sign and may vanish at infinity, f(s) is superlinear or asymptotically linear at infinity. If V(x) > 0, it is shown by T. Weth [Calculus Var. Partial Differ. Equ. 27, 421 (2006)] that the energy of any sign-changing solution of the equation is larger than two times the least energy. But if V(x) changes sign, we find that the equation does have a sign-changing ground state for λ > 0 large. Moreover, our results show that it is impossible to get a solution of the equation by seeking a minimizer of the energy functional of the equation over the so called Nehari manifold when V(x) changes sign.
The excitation function for Li + HF → LiF + H at collision energies below 80 meV
Authors: Bobbenkamp Rolf , Loesch Hansjürgen , Mudrich Marcel , Stienkemeier Frank
Published: December 2011

We have measured the dependence of the relative integral cross section of the reaction Li + HF → LiF + H on the collision energy (excitation function) using crossed molecular beams. By varying the intersection angle of the beams from 37° to 90° we covered the energy range 25  meV ⩽ Etr ⩽ 131 meV. We observe a monotonous rise of the excitation function with decreasing energy over the entire energy range indicating that a possible translational energy threshold to the reaction is significantly smaller than 25 meV. The steep rise is quantitatively recovered by a Langevin-type excitation function based on a vanishing threshold and a mean interaction potential energy ∝R−2.5 where R is the distance between the reactants. To date all threshold energies deduced from ab initio potentials and zero-point vibrational energies are at variance with our results, however, our findings support recent quantum scattering calculations that predict significant product formation at collision energies far below these theoretical thresholds.
Electronic structure and symmetry of valence states of epitaxial NiTiSn and NiZr0.5Hf0.5Sn thin films by hard x-ray photoelectron spectroscopy
Authors: Kozina Xeniya , Jaeger Tino , Ouardi Siham , Gloskowskij Andrei , Stryganyuk Gregory , Jakob Gerhard , Sugiyama Takeharu , Ikenaga Eiji , Fecher Gerhard H. , Felser Claudia
Published: December 2011

The electronic band structure of thin films and superlattices made of Heusler compounds with NiTiSn and NiZr0.5Hf0.5Sn composition was studied by means of polarization dependent hard x-ray photoelectron spectroscopy. The linear dichroism allowed to distinguish the symmetry of the valence states of the different types of layered structures. The films exhibit a larger amount of "in-gap" states compared to bulk samples. It is shown that the films and superlattices grown with NiTiSn as starting layer exhibit an electronic structure close to bulk materials.
Synthesis and Structure of a Dimeric, Anionic Thioglycolate Derivative of Manganese Carbonyl
Authors: Dai Yuan , Nicholson Brian K.
Published: December 2011

The thioglycolate anion reacts with BrMn(CO)5 to form a dimeric complex with bridging sulfur atoms of formula [Mn2(thioglycolate)2(CO)6]2–. This was isolated as the Et3NH+ salt and fully characterized for comparison with the previously reported thiosalicylate analogue.
Effects of hydromulch on post-fire erosion and plant recovery in chaparral shrublands of southern California
Authors: Hubbert Ken R. , Wohlgemuth Pete M. , Beyers Jan L.
Published: December 2011

Following the Cedar Fire (one of seven large wildfires that burned in southern California during the autumn of 2003), aerial hydromulch was applied at 50 and 100% cover to reduce hillslope erosion in chaparral shrublands. Our objectives were to determine the effectiveness of hydromulch in preventing erosion, and to see if plant recovery was hindered by treatment. We installed 54 silt fences to measure sediment production. Five 1-m2 grids were placed behind each fence to measure plant recovery. Hydromulch was effective in reducing erosion immediately after the fire; however, its benefits appeared to be limited to the first 2–4 months following fire, raising doubts as to its overall cost-effectiveness. The rapid breakdown of the hydromulch during the first 6 months after the wildfire provided little hillslope protection during the above-average October 2004 storm events. During the October events, both rainfall amount and storm intensity played a role in the magnitude of sediment production. Hydromulch did not affect post-fire plant recovery, with plant cover measuring >60% at all sites less than 2 years following the wildfire. Accelerated growth of chamise and forbs was likely due to hydromulch prolonging soil moisture retention. Large accumulations of dead litter following die-off of the herbaceous species could increase dry fuels, thus promoting wildfire and therefore shortening the fire return interval.
NRPSsp: non-ribosomal peptide synthase substrate predictor
Authors: Prieto Carlos , García-Estrada Carlos , Lorenzana Diego , Martín Juan Francisco
Published: December 2011

Summary: Non-ribosomal peptide synthetases (NRPSs) are multi-modular enzymes, which biosynthesize many important peptide compounds produced by bacteria and fungi. Some studies have revealed that an individual domain within the NRPSs shows significant substrate selectivity. The discovery and characterization of non-ribosomal peptides are of great interest for the biotechnological industries. We have applied computational mining methods in order to build a database of NRPSs modules that bind to specific substrates. We have used this database to build a hidden Markov model predictor of substrates that bind to a given NRPS.

Availability: The database and the predictor are freely available on an easy-to-use website at www.nrpssp.com.

Contact:  carlos.prieto@unileon.es

Supplementary information:  Supplementary data is available at Bioinformatics online.
Lipids, lipoproteins, and atherogenesis
Authors: Gouni-Berthold Joanna , Krone Wilhelm
Published: December 2011

• Lipids and lipoproteins have a central role in the pathogenesis of atherosclerosis.

• The concentration of low-density lipoprotein (LDL) is strongly and directly related to risk of atherosclerosis whereas high-density lipoprotein (HDL) is inversly related, low HDL being an independent risk factor.

• The role of plasma triglycerides is less well defined.

• The ratio of apolipoprotein B (the major apolipoprotein of LDL) to apolipoprotein A-1 (the major apolipoprotein of HDL) is emerging as the best predictor of atherosclerotic risk.
Risk estimation systems in clinical use: SCORE, HeartScore, Framingham, PROCAM, ASSIGN, and QRISK
Authors: McGorrian Catherine , Leong Tora , D'Agostino Ralph , Coney Marie-Therese , Graham Ian M.
Published: December 2011

• Atherosclerosis underlying cardiovascular disease (CVD) is a multifactorial disease; hence, global risk estimation is necessary for making clinical decisions.

• Individuals with serious inherited lipid disorders, for example, those with familial hypercholesterolaemia are at high risk and need intensive lipid management and attention to other risk factors.

• Individuals with established CVD have declared themselves to be at high risk and need intensive management.

• For other persons, risk estimation systems described in this chapter help to identify those with unexpectedly high or low risk and hence help to avoid undertreatment or overtreatment.
Combination therapy for the management of hyperlipidaemia
Authors: Wierzbicki Anthony S.
Published: December 2011

• Low doses of multiple drugs can be combined to treat patients intolerant to statin therapy

• Combination therapy to reduce LDL-C is increasingly necessary to reduce LDL-C >; 50% as required in the highest risk patients

• Statins have little effect on risk driven by low HDL-C and increasingly niacin (nicotinic acid) and fibrates are used in combination with statins to optimize the total lipid profile

• Large-scale end point studies with statin-other drug combinations are underway.
Vascular imaging
Authors: Kalla Manish , Halcox Julian
Published: December 2011

• Atherosclerosis is a dynamic process that affects most medium and large calibre arteries, particularly the coronary and carotid arteries.

• Atherosclerotic changes in the arteries develop over many decades before clinical presentation.

• First cardiac events are often either myocardial infarction or death, with most acute coronary events triggered by destabilization and rupture of lipid, rich, thin capped, usually only mildly obstructive plaques.

• Early identification of subclinical atherosclerosis and high-risk plaque/preclinical disease is of value in assessing a patient's future risk of developing clinical disease.

• Angiography remains the gold standard investigation but visualizes only stenoses, which are a late manifestation of the atherosclerotic process.

• Newer modalities such as computed tomography (CT) angiography, B mode carotid ultrasound, and magnetic resonance imaging (MRI) can identify at-risk individuals without invasive investigations.

• Functional and anatomical imaging together holds great promise in for accurate identification of patients with high-risk plaque.
Common problems in lipid management
Authors: Reckless John
Published: December 2011

• Cholesterol and low-density lipoprotein (LDL)-cholesterol are causal factors for atheromatous cardiovascular disease (CVD), and moderate and higher levels are a near obligate for disease development.

• Statin drugs have overwhelming evidence of benefit at low side effect risk.

• Estimation of an individual's CVD risk is required from a number of factors, and CVD prevention requires attention to all abnormal modifiable factors in individuals at higher risk.

• Identifying, counselling, and appropriate treatment of individuals at high CVD risk is a current challenge for health care professionals.

• Guidelines have been produced to help, and Government has provided levers to encourage their application.