bluuebunny/crossref_metadata_2025_split huggingface dataset:
6‐Dehydrogingerdione, an active constituent of dietary ginger, induces cell cycle arrest and apoptosis through reactive oxygen species/c‐Jun N‐terminal kinase pathways in human breast cancer cells
Authors: Hsu Ya‐Ling , Chen Chung‐Yi , Hou Ming‐Feng , Tsai Eing‐Mei , Jong Yuh‐Jyh , Hung Chih‐Hsing , Kuo Po‐Lin 
Published: February 2010

AbstractThis study is the first to investigate the anticancer effect of 6‐dehydrogingerdione (DGE), an active constituent of dietary ginger, in human breast cancer MDA‐MB‐231 and MCF‐7 cells. DGE exhibited effective cell growth inhibition by inducing cancer cells to undergo G2/M phase arrest and apoptosis. Blockade of cell cycle was associated with increased levels of p21, and reduced amounts of cyclin B1, cyclin A, Cdc2 and Cdc25C. DGE also enhanced the levels of inactivated phosphorylated Cdc2 and Cdc25C. DGE triggered the mitochondrial apoptotic pathway indicated by a change in Bax/Bcl‐2 ratios, resulting in caspase‐9 activation. We also found the generation of reactive oxygen species is a critical mediator in DGE‐induced cell growth inhibition. DGE clearly increased the activation of apoptosis signal‐regulating kinase 1 and c‐Jun N‐terminal kinase (JNK), but not extracellular signal‐regulated kinase 1/2 (ERK1/2) and p38. In addition, antioxidants vitamin C and catalase significantly decreased DGE‐mediated JNK activation and apoptosis. Moreover, blocking JNK by specific inhibitors suppressed DGE‐triggered mitochondrial apoptotic pathway. Taken together, these findings suggest that a critical role for reactive oxygen species and JNK in DGE‐mediated apoptosis of human breast cancer.
Diffusion tensor imaging of renal ischemia reperfusion injury in an experimental model
Authors: Cheung Jerry S. , Fan Shu Juan , Chow April M. , Zhang Jingbo , Man Kwan , Wu Ed X. 
Published: February 2010

AbstractRenal ischemia reperfusion injury (IRI) is a major cause of acute renal failure. It occurs in various clinical settings such as renal transplantation, shock and vascular surgery. Serum creatinine level has been used as an index for estimating the degree of renal functional loss in renal IRI. However, it only evaluates the global renal function. In this study, diffusion tensor imaging (DTI) was used to characterize renal IRI in an experimental rat model. Spin‐echo echo‐planar DTI with b‐value of 300 s/mm2 and 6 diffusion gradient directions was performed at 7 T in 8 Sprague‐Dawley (SD) with 60‐min unilateral renal IRI and 8 normal SD rats. Apparent diffusion coefficient (ADC), directional diffusivities and fractional anisotropy (FA) were measured at the acute stage of IRI. The IR‐injured animals were also examined by diffusion‐weighted imaging with 7 b‐values up to 1000 s/mm2 to estimate true diffusion coefficient (Dtrue) and perfusion fraction (Pfraction) using a bi‐compartmental model. ADC of injured renal cortex (1.69 ± 0.24 × 10−3 mm2/s) was significantly lower (p < 0.01) than that of contralateral intact cortex (2.03 ± 0.35 × 10−3 mm2/s). Meanwhile, both ADC and FA of IR‐injured medulla (1.37 ± 0.27 × 10−3 mm2/s and 0.28 ± 0.04, respectively) were significantly less (p < 0.01) than those of contralateral intact medulla (2.01 ± 0.38 × 10−3 mm2/s and 0.36 ± 0.04, respectively). The bi‐compartmental model analysis revealed the decrease in Dtrue and Pfraction in the IR‐injured kidneys. Kidney histology showed widespread cell swelling and erythrocyte congestion in both cortex and medulla, and cell necrosis/apoptosis and cast formation in medulla. These experimental findings demonstrated that DTI can probe both structural and functional information of kidneys following renal IRI. Copyright © 2010 John Wiley & Sons, Ltd.
Monitoring of the effect of intervertebral disc nucleus pulposus ablation by MRI
Authors: Saar Galit , Zilberman Yoram , Shinar Hadassah , Keinan‐Adamsky Keren , Pelled Gadi , Gazit Dan , Navon Gil 
Published: February 2010

AbstractIn order to investigate intervertebral disc (IVD) degeneration and repair, a quantitative non‐invasive tool is needed. Various MRI methods including qCPMG, which yields dipolar echo relaxation time (TDE), magnetization transfer contrast (MTC), and 1H and 2H double quantum filtered (DQF) MRI were used in the present work to monitor changes in rat IVD after ablation of the nucleus pulposus (NP), serving as a model of severe IVD degeneration. In the intact IVD, a clear distinction between the annulus fibrosus (AF) and the NP is obtained on T2 and TDE weighted images as well as on MTC maps, reflecting the high concentration of ordered collagen fibers in the AF. After ablation of the NP, the distinction between the compartments is lost. T2 and TDE relaxation times are short throughout the disc and MTC is high. 1H and 2H DQF signal, which in intact discs is obtained only for the AF, is now observable throughout the tissue. These results indicate that after ablation, there is an ingression of collagen fibers from the AF into the area that was previously occupied by the NP, as was confirmed by histology. Copyright © 2010 John Wiley & Sons, Ltd.
Prediction of the human membrane proteome
Authors: Fagerberg Linn , Jonasson Kalle , von Heijne Gunnar , Uhlén Mathias , Berglund Lisa 
Published: February 2010

AbstractMembrane proteins are key molecules in the cell, and are important targets for pharmaceutical drugs. Few three‐dimensional structures of membrane proteins have been obtained, which makes computational prediction of membrane proteins crucial for studies of these key molecules. Here, seven membrane protein topology prediction methods based on different underlying algorithms, such as hidden Markov models, neural networks and support vector machines, have been used for analysis of the protein sequences from the 21 416 annotated genes in the human genome. The number of genes coding for a protein with predicted α‐helical transmembrane region(s) ranged from 5508 to 7651, depending on the method used. Based on a majority decision method, we estimate 5539 human genes to code for membrane proteins, corresponding to approximately 26% of the human protein‐coding genes. The largest fraction of these proteins has only one predicted transmembrane region, but there are also many proteins with seven predicted transmembrane regions, including the G‐protein coupled receptors. A visualization tool displaying the topologies suggested by the eight prediction methods, for all predicted membrane proteins, is available on the public Human Protein Atlas portal (www.proteinatlas.org).
Computational modeling of human paraoxonase 1: preparation of protein models, binding studies, and mechanistic insights
Authors: Sanan Toby T. , Muthukrishnan Sivaramakrishnan , Beck Jeremy M. , Tao Peng , Hayes Carrigan J. , Otto Tamara C. , Cerasoli Douglas M. , Lenz David E. , Hadad Christopher M. 
Published: February 2010

AbstractThe enzyme human paraoxonase 1 (huPON1) has demonstrated significant potential for use as a bioscavenger for treatment of exposure to organophosphorus (OP) nerve agents. Herein we report the development of protein models for the human isoform derived from a crystal structure of a chimeric version of the protein (pdb ID: 1V04) and a homology model derived from the related enzyme diisopropylfluorophosphatase (pdb ID: 1XHR). From these structural models, binding modes for OP substrates are predicted, and these poses are found to orient substrates in proximity to residues known to modulate specificity of the enzyme. Predictions are made with regard to the role that residues play in altering substrate binding and turnover, in particular with regard to the stereoselectivity of the enzyme, and the known differences in activity related to a natural polymorphism in the enzyme. Potential mechanisms of action of the protein for catalytic hydrolysis of OP substrates are also evaluated in light of the proposed binding modes. Copyright © 2010 John Wiley & Sons, Ltd.
Cluster modeling of quasi‐adaptive phases in vitreous germanium selenides
Authors: Shpotyuk Oleh , Golovchak Roman , Boyko Vitaliy , Kozyukhin Sergei 
Published: February 2010

AbstractThe developed cluster modeling approach based on ab‐initio calculations with RHF/6‐311G* basis set testifies absence of intermediate optimally‐constrained phase in binary Gex Se100‐x system within 20 ≤ x < 26 domain. It is shown, that character “outrigger raft” carcass is conserved for all glass compositions within expected reversibility window. Thus, the structure of binary Gex Se100‐x glasses can be described in terms of “chains crossing” model in case of x < 12, mixed “chains crossing” and “outrigger raft” models in case of 12 ≤ x < 20 and modified “outrigger raft” model in case of x ≥ 20. The expected reversibility window in binary Gex Se100‐x glasses is shown to be only quasi‐adaptive phase, based on “outrigger raft” structural motive with two edge‐ and four corner‐sharing tetrahedra interconnected by optimally‐constrained Ge‐Se‐Se‐Ge bridges with extra Se atoms in ring‐like configurations replaced Se‐Se dimers. The results of quantum mechanics modeling are confirmed well by high‐resolution X‐ray photoelectron spectroscopy measurements in this system. (© 2010 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Regulation of insulin action by an extract of Artemisia dracunculus L. in primary human skeletal muscle culture: A proteomics approach
Authors: Kheterpal Indu , Coleman Liana , Ku Ginger , Wang Zhong Q. , Ribnicky David , Cefalu William T. 
Published: February 2010

AbstractAn ethanolic extract of Artemisia dracunculus L. (PMI 5011) has been observed to decrease glucose and insulin levels in animal models and enhance cellular signaling in cultured cells. To determine the mechanism of action of PMI‐5011, we have measured changes in protein expression in human primary skeletal muscle culture (HSMC) from subjects with Type 2 diabetes. After obtaining skeletal muscle biopsies, HSMCs were initiated, grown to confluence, and exposed to 10 µg/mL PMI 5011 overnight. Two‐dimensional difference in‐gel electrophoresis was used to separate proteins, and liquid chromatography mass spectrometry was used to identify differentially regulated proteins. Additionally, real‐time polymerase chain reaction (PCR) was used to confirm candidate proteins identified. These data demonstrate that a well characterized botanical extract of Artemisia dracunculus L. significantly modulates proteins involved in regulating inflammatory pathways, particularly the NFκB complex system. Copyright © 2010 John Wiley & Sons, Ltd.
Cluster SIMS depth profiling of stereo‐specific PMMA thin films on Si
Authors: Mahoney Christine M. 
Published: February 2010

AbstractCluster SIMS, employing an SF5+ polyatomic primary ion sputter source, in conjunction with a Bi3+ analysis source, was utilized to depth profile through poly(methylmethacrylate) (PMMA) thin films (approximately 140 nm) of variable tacticity. The damage characteristics of the stereospecific PMMA films under SF5+ bombardment were measured as a function of temperature in the range of − 75 °C–150 °C. On average, the isotactic PMMA exhibited the least amount of damage accumulation as compared to syndiotactic and atactic PMMA, with increased signal constancy as a function of SF5+ dose and sharper PMMA/Si interface widths in the temperature range of 0 °C–80 °C. These improvements in sputter properties were attributed to steric hindrances along the side‐chain moieties in isotactic PMMA, causing increased strain along the main‐chain backbone, and consequently increasing the likelihood of main‐chain scission. Similar to previous studies, − 75 °C yielded the most ideal depth profiles for all tacticities, exhibiting the least amount of damage accumulation in the form of characteristic signal loss and interfacial broadening. There were also significant improvements in the damage characteristics at higher temperatures as compared to 25 °C. However, other interfacial artifacts started to appear at or near the glass transition temperature (Tg) of the various polymers, indicative of increased interfacial damage at these higher temperatures. Published in 2010 by John Wiley & Sons, Ltd.
Influence of current density on the distribution of tungsten tracer in porous anodic alumina films
Authors: Zhou F. , LeClere D. J. , Garcia‐Vergara S. J. , Skeldon P. , Thompson G. E. , Habazaki H. 
Published: February 2010

AbstractPorous anodic alumina films have been much studied recently due to interest in the application of the self‐ordered porosity in nanotechnological systems. Experimental investigations have identified anodising regimes that generate pores with a relatively high degree of long‐range order. However, the growth mechanism of the films, and its relation to the ordering of pores, is only partially understood. In the present work, the growth processes are studied over a range of current densities for films formed in oxalic acid. The films are formed on sputtering‐deposited substrates containing tungsten nanolayers that provide W6+ tracer species in the films. The distributions of tracer species are observed by scanning and transmission electron microscopes and the amounts of tracer species quantified by Rutherford backscattering spectroscopy. It is shown that the tungsten tracer remains within an inner region of the cells, with a tungsten‐free region being present next to the pore walls during the growth of the anodic films. Further, the thickness of the anodic film relative to that of oxidised metal increases with increasing current density, which is associated with an increase in the efficiency of film formation. This behaviour is consistent with the formation of pores by flow of film material in the barrier layer to the pore wall regions. Copyright © 2010 John Wiley & Sons, Ltd.
Ablative analysis of black and colored toners using LA‐ICP‐TOF‐MS for the forensic discrimination of photocopy and printer toners
Authors: Szynkowska M. I. , Czerski K. , Paryjczak T. , Parczewski A. 
Published: February 2010

AbstractPhotocopy and printer toners were analyzed using ICP‐TOF‐MS (inductively coupled plasma time‐of‐flight mass spectrometry) with laser ablation (LA). Isotopic analysis of black and colored toners allows identification and discrimination of covering materials from different producers. The results of 201 samples of black toners were analyzed according to the following chemometric methods: cluster analysis (CA) and principal component analysis (PCA). In addition, 23 samples of colored toners were tested. Chemometric manipulation of the elemental mass spectra obtained using the ‘Fingerprinting OptiMass 9500’ program showed an effective system for the rapid comparative analysis of unknown samples. Copyright © 2010 John Wiley & Sons, Ltd.
Electrograining of aluminium in HCl: effect of the alloy for high‐speed processing lines
Authors: Sánchez S. A. , González‐García J. , Esclapez M. D. , Díez‐García M. I. , Del Río J. F. , Gazapo J. L. 
Published: February 2010

AbstractElectrograining of aluminium in hydrochloric acid is one of the most commonly used processes for manufacturing printing lithographic plates. Two of the main features to be taken into account are the final morphology of the electrograined surface and the susceptibility of the alloy to be processed or, more specifically, the speed of the processing line. Both issues determine the efficiency of the production in terms of quality and time. In this work, a widely used commercial aluminium alloy (1050) is compared with a new experimental one (1050 modified with Zn) and with a higher strength alloy (namely 1020). In order to analyse their response to a.c. graining in HCl for high‐speed lines, some techniques such as image analysis or interferometry have been used. In general, the alloys doped with Zn and Mg present a better response to litho processing in terms of graining activity and reduction of streakiness when treatment of lower time periods is applied due to their influence as pitting initiators. Copyright © 2010 John Wiley & Sons, Ltd.
Automatic verification of Java programs with dynamic frames
Authors: Smans Jan , Jacobs Bart , Piessens Frank , Schulte Wolfram 
Published: February 2010

Abstract
Framing in the presence of data abstraction is a challenging and important problem in the verification of object-oriented programs Leavens et al. (Formal Aspects Comput (FACS) 19:159–189, 2007). The dynamic frames approach is a promising solution to this problem. However, the approach is formalized in the context of an idealized logical framework. In particular, it is not clear the solution is suitable for use within a program verifier for a Java-like language based on verification condition generation and automated, first-order theorem proving. In this paper, we demonstrate that the dynamic frames approach can be integrated into an automatic verifier based on verification condition generation and automated theorem proving. The approach has been proven sound and has been implemented in a verifier prototype. The prototype has been used to prove correctness of several programming patterns considered challenging in related work.
Assessment of social cognition in patients with multiple sclerosis
Authors: OUELLET JULIE , SCHERZER PETER B. , ROULEAU ISABELLE , MÉTRAS PHILIPPE , BERTRAND-GAUVIN CAROLINE , DJERROUD NADÉRA , BOISSEAU ÉMILIE , DUQUETTE PIERRE 
Published: February 2010

AbstractWe examined the capacity of patients with multiple sclerosis (MS) to attribute mental states to others and to identify cognitive abilities that subserve theory of mind (ToM). In this article, we report findings on 41 out-patients with diagnosed MS who underwent detailed neuropsychological and social-cognitive assessment. They were subdivided into a cognitively intact (n=15) and cognitively impaired (n=26) group according to their neuropsychological test results. Their results were compared with those of 20 age- and education-matched controls. MS patients with cognitive impairments were found to have more difficulties attributing mental states to others than did cognitively intact MS patients and normal controls on two ToM measures; short stories (Happé, Winner, & Brownell, 1998) and video clips (Ouellet, Bédirian, Charbonneau, & Scherzer, 2009). When attention, memory, and working memory were controlled, performance on the WAIS-III Picture Arrangement task accounted for 17.3% of the variance in performance on the video clips task. Performance on a WAIS-III index composed of Similarities and Comprehension subtests, accounted for 7.0% of the variance in performance on the short stories task. These results provide some preliminary information on the effect of MS-related cognitive deficits on the ability to attribute mental states to others. (JINS, 2010, 16, 287–296.)
Listening as Covert Performance
Authors: Cross Ian 
Published: February 2010

ABSTRACTThis paper presents a view of musical listening as an active, dynamic and interactive process. After briefly considering the historical valorization of listening as critical act within Western musical culture, the paper describes the cognitive processes of schematization that are involved in musical listening. The central role of active engagement with the auditory environment in eliciting emotional responses to music is then sketched out, and the scope and limits of the attentional and motoric processes involved in processes of entrainment – focal in the experience of musical time – are outlined. Neuroscientific evidence that suggests that music is best conceived in terms of a perception–action cycle is reviewed, and the paper concludes by proposing that music is best conceptualized – from a biological perspective – as a communicative medium that is optimal for the management of situations of social uncertainty.
Ketogenic diet slows down mitochondrial myopathy progression in mice
Authors: Ahola-Erkkilä Sofia , Carroll Christopher J. , Peltola-Mjösund Katja , Tulkki Valtteri , Mattila Ismo , Seppänen-Laakso Tuulikki , Orešič Matej , Tyynismaa Henna , Suomalainen Anu 
Published: February 2010

AbstractMitochondrial dysfunction is a major cause of neurodegenerative and neuromuscular diseases of adult age and of multisystem disorders of childhood. However, no effective treatment exists for these progressive disorders. Cell culture studies suggested that ketogenic diet (KD), with low glucose and high fat content, could select against cells or mitochondria with mutant mitochondrial DNA (mtDNA), but proper patient trials are still lacking. We studied here the transgenic Deletor mouse, a disease model for progressive late-onset mitochondrial myopathy, accumulating mtDNA deletions during aging and manifesting subtle progressive respiratory chain (RC) deficiency. We found that these mice have widespread lipidomic and metabolite changes, including abnormal plasma phospholipid and free amino acid levels and ketone body production. We treated these mice with pre-symptomatic long-term and post-symptomatic shorter term KD. The effects of the diet for disease progression were followed by morphological, metabolomic and lipidomic tools. We show here that the diet decreased the amount of cytochrome c oxidase negative muscle fibers, a key feature in mitochondrial RC deficiencies, and prevented completely the formation of the mitochondrial ultrastructural abnormalities in the muscle. Furthermore, most of the metabolic and lipidomic changes were cured by the diet to wild-type levels. The diet did not, however, significantly affect the mtDNA quality or quantity, but rather induced mitochondrial biogenesis and restored liver lipid levels. Our results show that mitochondrial myopathy induces widespread metabolic changes, and that KD can slow down progression of the disease in mice. These results suggest that KD may be useful for mitochondrial late-onset myopathies.
Longevity of seeds of Poa pratensis and Lolium perenne as affected by simulated soil tillage practices and its implications for contamination of herbage seed crops
Authors: Jensen P. K. 
Published: February 2010

AbstractIn grass‐seed production, the purity of the product is of major importance and high purity can only be obtained by preventing contamination with other species and cultivars during the whole crop rotation. In this context, seeds of previously grown grass species or varieties are particularly important. This study investigated the influence of different soil tillage practices on persistence of newly shed seeds of two grass species, Poa pratensis and Lolium perenne. Leaving the seeds at or close to the soil surface reduced seed survival of both species to low levels compared with strategies that involved a deep incorporation of the seeds shortly after seed‐shedding. Survival rate of seeds of P. pratensis after 1 year was reduced to a low level when seeds were left at the soil surface for 2–3 months before incorporation. Seeds of L. perenne were less persistent and survival rate after 1 year was generally very low if the seeds were left near the soil surface for approximately 1 month before deeper incorporation. Use of the stale seedbed technique to reduce the seedbank of the two species in the autumn ahead of a spring‐established grass‐seed crop was also found to be effective in reducing the potential risk of contamination.