bluuebunny/crossref_metadata_2025_split huggingface dataset:
Handedness correlates with the dominant Parkinson side: A systematic review and meta‐analysis
Authors: van der Hoorn Anouk , Burger Huibert , Leenders Klaus L. , de Jong Bauke M. 
Published: October 2011

AbstractParkinson's disease (PD) characteristically presents with asymmetrical symptoms, contralateral to the side of the most extensive cerebral affection. This intriguing asymmetry, even included in the definition for diagnosing PD, however, is still part of a mystery. The relation with handedness as a common indicator of cerebral asymmetry might provide a clue in the search for causal factors of asymmetrical symptom onset in PD. This possible relationship, however, is still under debate. The objective of this study was to establish whether a relation between handedness and dominant PD side exists. We searched for cross‐sectional or cohort studies that registered handedness and onset side in PD patients in PubMed, EMBASE, and Web of Science from their first record until 14 February 2011. Data about handedness and dominant PD side was extracted. Authors who registered both but not described their relation were contacted for further information. Odds ratios (ORs) were analyzed with a fixed effect Mantel‐Haenszel model. Heterogeneity and indications of publication bias were limited. Our electronic search identified 10 studies involving 4405 asymmetric PD patients. Of the right‐handed patients, 2413 (59.5%) had right‐dominant and 1644 (40.5%) had left‐dominant PD symptoms. For the left‐handed patients this relation was reversed, with 142 (40.8%) right‐dominant and 206 (59.2%) left‐dominant PD symptoms. Overall OR was 2.13 (95% confidence interval [CI], 1.71–2.66). Handedness and symptom dominance in PD are firmly related with each other in such a way that the PD symptoms emerge more often on the dominant hand‐side. Possible causal factors are discussed. © 2011 Movement Disorder Society
Adaptive self‐calibrating iterative GRAPPA reconstruction
Authors: Park Suhyung , Park Jaeseok 
Published: October 2011

AbstractParallel magnetic resonance imaging in k‐space such as generalized auto‐calibrating partially parallel acquisition exploits spatial correlation among neighboring signals over multiple coils in calibration to estimate missing signals in reconstruction. It is often challenging to achieve accurate calibration information due to data corruption with noises and spatially varying correlation. The purpose of this work is to address these problems simultaneously by developing a new, adaptive iterative generalized auto‐calibrating partially parallel acquisition with dynamic self‐calibration. With increasing iterations, under a framework of the Kalman filter spatial correlation is estimated dynamically updating calibration signals in a measurement model and using fixed‐point state transition in a process model while missing signals outside the step‐varying calibration region are reconstructed, leading to adaptive self‐calibration and reconstruction. Noise statistic is incorporated in the Kalman filter models, yielding coil‐weighted de‐noising in reconstruction. Numerical and in vivo studies are performed, demonstrating that the proposed method yields highly accurate calibration and thus reduces artifacts and noises even at high acceleration. Magn Reson Med, 2011. © 2011 Wiley Periodicals, Inc.
A novel augmented Lagrangian‐based formulation for upper‐bound limit analysis
Authors: Vicente da Silva M. , Antão A. N. 
Published: October 2011

SUMMARYThis paper describes a novel upper‐bound formulation of limit analysis. This formulation is an innovative variant of an existing two‐field mixed formulation based on the augmented Lagrangian method also developed by the authors. A natural approach is used to describe the deformation of each finite element. Furthermore, and in contrast to the previous formulation, two independent field approximations are now both used to define the velocity field, defined globally and at element level. It is shown that this feature allows a governing system of uncoupled linear equations to be obtained. Some numerical examples in plane strain conditions are presented in order to illustrate the current model performance. In conclusion, the potential and advantages of this new approach are discussed. Copyright © 2011 John Wiley & Sons, Ltd.
Application of spectral filtering to discontinuous Galerkin methods on triangulations
Authors: Meister A. , Ortleb S. , Sonar Th. 
Published: October 2011

AbstractWe adapt the spectral viscosity (SV) formulation implemented as a modal filter to a discontinuous Galerkin (DG) method solving hyperbolic conservation laws on triangular grids. The connection between SV and spectral filtering, which is undertaken for the first time in the context of DG methods on unstructured grids, allows to specify conditions on the filter strength regarding time step choice and mesh refinement. A crucial advantage of this novel damping strategy is its low computational cost. We furthermore obtain new error bounds for filtered Dubiner expansions of smooth functions. While high order accuracy with respect to the polynomial degree N is proven for the filtering procedure in this case, an adaptive application is proposed to retain the high spatial approximation order. Although spectral filtering stabilizes the scheme, it leaves weaker oscillations. Therefore, as a postprocessing step, we apply the image processing technique of digital total variation (DTV) filtering in the new context of DG solutions and prove conservativity in the limit for this filtering procedure. Numerical experiments for scalar conservation laws confirm the designed order of accuracy of the DG scheme with adaptive modal filtering for polynomial degrees up to 8 and the viability of spectral and DTV filtering in case of shocks. © 2011 Wiley Periodicals, Inc. Numer Methods Partial Differential Eq 2011
Cell–matrix interactions in muscle disease
Authors: Carmignac Virginie , Durbeej Madeleine 
Published: October 2011

AbstractThe extracellular matrix (ECM) provides a solid scaffold and signals to cells through ECM receptors. The cell–matrix interactions are crucial for normal biological processes and when disrupted they may lead to pathological processes. In particular, the biological importance of ECM–cell membrane–cytoskeleton interactions in skeletal muscle is accentuated by the number of inherited muscle diseases caused by mutations in proteins conferring these interactions. In this review we introduce laminins, collagens, dystroglycan, integrins, dystrophin and sarcoglycans. Mutations in corresponding genes cause various forms of muscular dystrophy. The muscle disorders are presented as well as advances toward the development of treatment. Copyright © 2011 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
The cellular pathology of lysosomal diseases
Authors: Cox Timothy M , Cachón‐González M Begoña 
Published: October 2011

AbstractWith a constitutive recycling function and the capacity to digest exogenous material as well as endogenous organelles in the process of autophagy, lysosomes are at the heart of the living cell. Dynamic interactions with other cellular components ensure that the lysosomal compartment is a central point of convergence in countless diverse diseases. Inborn lysosomal (storage) diseases represent about 70 genetically distinct conditions, with a combined birth frequency of about 1 in 7500. Many are associated with macromolecular storage, causing physical disruption of the organelle and cognate structures; in neurons, ectopic dendritogenesis and axonal swelling due to distension with membraneous tubules and autophagic vacuoles are observed. Disordered autophagy is almost universal in lysosomal diseases but biochemical injury due to toxic metabolites such as lysosphingolipid molecules, abnormal calcium homeostasis and endoplasmic reticulum stress responses and immune‐inflammatory processes occur. However, in no case have the mechanistic links between individual clinico‐pathological manifestations and the underlying molecular defect been precisely defined. With access to the external fluid‐phase and intracellular trafficking pathways, the lysosome and its diseases are a focus of pioneering investment in biotechnology; this has generated innovative orphan drugs and, in the case of Gaucher's disease, effective treatment for the haematological and visceral manifestations. Given that two‐thirds of lysosomal diseases have potentially devastating consequences in the nervous system, future therapeutic research will require an integrative understanding of the unitary steps in their neuro pathogenesis. Informative genetic variants illustrated by patients with primary defects in this organelle offer unique insights into the central role of lysosomes in human health and disease. We provide a conspectus of inborn lysosomal diseases and their pathobiology; the cryptic evolution of events leading to irreversible changes may be dissociated from the cellular storage phenotype, as revealed by the outcome of therapeutic gene transfer undertaken at different stages of disease. Copyright © 2011 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Microtubule‐binding protein CLIP‐170 is a mediator of paclitaxel sensitivity
Authors: Sun Xiaodong , Li Dengwen , Yang Yunfan , Ren Yuan , Li Jingyu , Wang Zaizhu , Dong Bin , Liu Min , Zhou Jun 
Published: October 2011

AbstractCLIP‐170 is a microtubule‐binding protein and participates in diverse microtubule‐associated cellular activities by regulating microtubule dynamics. Here we provide evidence that CLIP‐170 is a mediator of the sensitivity of the anti‐microtubule drug paclitaxel in breast cancer. In vitro cell proliferation assays reveal that CLIP‐170 expression in breast cancer cell lines correlates with their sensitivity to paclitaxel. In addition, CLIP‐170 expression in clinical samples of breast cancer correlates with the pathological response of tumours to paclitaxel‐containing chemotherapy. Mitotic index and caspase‐3 activity analyses reveal that CLIP‐170 increases the abilities of paclitaxel to block cell cycle progression at mitosis and to induce apoptosis in breast cancer cells. By microtubule sedimentation assay and binding affinity analysis, we further find that CLIP‐170 promotes paclitaxel binding to microtubules. In vitro tubulin polymerization assay shows that CLIP‐170 enhances the activity of paclitaxel to promote microtubule assembly. These results demonstrate that CLIP‐170 mediates paclitaxel sensitivity in breast cancer via a microtubule‐dependent mechanism. Copyright © 2012 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Activated growth signaling pathway expression in Ewing sarcoma and clinical outcome
Authors: Mora Jaume , Rodríguez Eva , de Torres Carmen , Cardesa Teresa , Ríos José , Hernández Teresa , Cardesa Antonio , de Alava Enrique 
Published: October 2011

AbstractBackgroundIn Ewing sarcoma (EWS) most of the research on signaling pathways has been performed on cell lines or animal models. The objective of the current study was to determine the relation between clinical outcome and the expression of proteins involved in active growth signaling pathways.MethodsA paraffin‐embedded microarray of 45 human primary EWS tissue specimens was stained with the antibodies against c‐KIT, AKT, p‐AKT, p‐mTOR, IGF‐1R, IGFBP‐3, MAPK, p27KIP1, and p70S6 kinase. Immunohistochemical staining was correlated with patient overall survival (OS).ResultsIn the univariate analysis 3 variables showed statistical significance to predict survival: presence of metastasis, p‐mTOR, and p27KIP1. A positive stain for p‐mTOR (hazard ratio of 4.74 [95% CI (57, 121)]) was significantly (log‐rank test with a P = 0.029) associated with better OS. Also, a positive stain for p27KIP1 (hazard ratio of 6.87 [95% CI (77, 136)] was significantly (log‐rank test with a P = 0.009) associated with better OS. Multivariate analysis showed metastasis (HR: 4.3; 95% CI: 0.99, 19; P = 0.05), p‐mTOR (HR: 4.8 with 95% CI: 0.6, 38; P = 0.13) and p27 (HR: 5.3; 95% CI: 1.37, 20; P = 0.01) as independent prognostic factors of outcome.ConclusionsIn our series, p‐mTOR and p27KIP1 protein overexpression were independently associated with better survival. Pediatr Blood Cancer 2012; 58: 532–538. © 2011 Wiley Periodicals, Inc.
Aggressive peripheral CD70‐positive t‐cell lymphoma associated with severe chronic active EBV infection
Authors: Shaffer Donald R. , Sheehan Andrea M. , Yi Zhongzhen , Rodgers Cheryl C. , Bollard Catherine M. , Brenner Malcolm K. , Rooney Cliona M. , Heslop Helen E. , Gottschalk Stephen 
Published: October 2011

AbstractSevere chronic active Epstein–Barr virus infection (CAEBV) in T or NK cells is a rare complication of latent EBV infection. CAEBV associated T‐cell lymphoproliferative disease (LPD) consists of polyclonal lesions as well as aggressive lymphomas. Here, we report such a patient. In addition, we show that this primary CAEBV associated T‐cell lymphoma expresses CD70 and is sensitive to killing by CD70‐specific T cells, identifying CD70 as a potential immunotherapeutic target for CAEBV‐associated T‐cell lymphoma. Pediatr Blood Cancer 2012;59:758–761. © 2011 Wiley Periodicals, Inc.
Correlation between processing conditions and fiber breakage during compounding of glass fiber‐reinforced polyamide
Authors: Inceoglu Funda , Ville Julien , Ghamri Nessim , Pradel Jean Laurent , Durin Audrey , Valette Rudy , Vergnes Bruno 
Published: October 2011

AbstractThe inter‐relationship between processing conditions and fiber breakage has been studied for glass fiber‐reinforcedpolyamide 12, prepared using (i) an internal batch mixer, (ii) a laboratory scale corotating twin screw extruder, and (iii) an industrial scale twin screw extruder. The average fiber lengths and fiber length distributions were measured for various compounding conditions (screw or rotor speed, mixing time, feed rate). Experimental results have shown that fiber breakage depends on both screw speed and mixing time, the later being controlled, in an extruder, by the feed rate. For a given compounding system (batch mixer or twin screw extruder), the energy input (specific mechanical energy, SME) during the compounding process is found to be a reliable parameter, which governs fiber length (average, minimal, and maximal) evolution. Experimental data are correctly described with a model defining change in fiber length as a function of SME. POLYM. COMPOS., 2011. © 2011 Society of Plastics Engineers
Amphiphilic poly(acrylonitrile‐co‐acrylic acid)/silver nanocomposite additives for the preparation of antibiofouling membranes with improved properties
Authors: Jewrajka Suresh K. , Haldar Soumya 
Published: October 2011

AbstractThis work focuses the preparation of polymer‐silver nanocomposite (Ag‐Nc) dense free standing films and nonwoven fabric supported porous ultrafiltration membranes with improved membrane performance and long‐term antibiofouling properties. New polyacrylonitrle‐based Ag‐Ncs, poly(acrylonitrle‐co‐acrylic acid)‐silver (PAN‐co‐PAA‐Ag) containing 35 wt% of PAA and 0.35–0.65 wt% of Ag‐nanoparticles (Nps) were synthesized and used as additives for the fabrication of PAN‐based (PAN/PAN‐co‐PAA‐Ag) Ag‐Nc porous membranes and dense‐free standing films. The Ag‐Nps were homogeneously dispersed into the PAN‐co‐PAA random copolymer matrix. The prepared membranes (PAN/PAN‐co‐PAA‐Ag) showed combination of properties such as excellent antimicrobial activity towards both Gram Negative and Gram Positive bacteria (prevent biofilm formation), improved protein antifouling properties, and enhanced water flux when compared to neat PAN‐based membrane. The antimicrobial properties, hydrophilicity, and the water flux of various membranes follow the following order for the membranes PAN < PAN/PAN‐co‐PAA < PAN/PAN‐co‐PAA‐Ag. Extraneous addition of small amount of polyethylene glycol (PEG) during preparation of additive i.e. [PEG + PAN‐co‐PAA]‐Ag further improved the protein antifouling properties of the PAN‐based membranes (PAN/[PEG+PAN‐co‐PAA‐Ag]). The dispersed Ag‐Nps were stable on the surface of phase inverted membranes for long period of time and PAN/PAN‐co‐PAA‐Ag membranes are therefore suitable for long‐term water treatment under bacterial environment. POLYM. COMPOS., 2011. © 2011 Society of Plastics Engineers
Are all quantitative postmarketing signal detection methods equal? Performance characteristics of logistic regression and Multi‐item Gamma Poisson Shrinker
Authors: Berlin Conny , Blanch Carles , Lewis David J. , Maladorno Dionigi D. , Michel Christiane , Petrin Michael , Sarp Severine , Close Philippe 
Published: October 2011

ABSTRACTPurposeThe detection of safety signals with medicines is an essential activity to protect public health. Despite widespread acceptance, it is unclear whether recently applied statistical algorithms provide enhanced performance characteristics when compared with traditional systems. Novartis has adopted a novel system for automated signal detection on the basis of disproportionality methods within a safety data mining application (Empirica™ Signal System [ESS]). ESS uses two algorithms for routine analyses: empirical Bayes Multi‐item Gamma Poisson Shrinker and logistic regression (LR).MethodsA model was developed comprising 14 medicines, categorized as “new” or “established.” A standard was prepared on the basis of safety findings selected from traditional sources. ESS results were compared with the standard to calculate the positive predictive value (PPV), specificity, and sensitivity. PPVs of the lower one‐sided 5% and 0.05% confidence limits of the Bayes geometric mean (EB05) and of the LR odds ratio (LR0005) almost coincided for all the drug‐event combinations studied.ResultsThere was no obvious difference comparing the PPV of the leading Medical Dictionary for Regulatory Activities (MedDRA) terms to the PPV for all terms. The PPV of narrow MedDRA query searches was higher than that for broad searches. The widely used threshold value of EB05 = 2.0 or LR0005 = 2.0 together with more than three spontaneous reports of the drug‐event combination produced balanced results for PPV, sensitivity, and specificity.ConclusionsConsequently, performance characteristics were best for leading terms with narrow MedDRA query searches irrespective of applying Multi‐item Gamma Poisson Shrinker or LR at a threshold value of 2.0. This research formed the basis for the configuration of ESS for signal detection at Novartis. Copyright © 2011 John Wiley & Sons, Ltd.
Turn‐on chemosensors for silver ions based on oligomers with diaza‐16‐crown 6‐ether receptors and aromatic fluorophore end groups
Authors: Yamaguchi Isao , Shingai Saki 
Published: October 2011

AbstractThe reaction of N‐(2,4‐dinitrophenyl)pyridinium chloride (1), diaza‐18‐crown 6‐ether (DA18C6) and 2,5‐bis(aminophenyl)‐1,3,4‐oxadiazole (2) caused the opening of the pyridinium ring and yielded an ionic oligomer (oligomer‐1) comprising a 5‐DA18C6‐penta‐2,4‐dienylideneammonium chloride main chain and 2‐(4‐aminophenyl)‐5‐phenyl‐1,3,4‐oxadiazole or 2‐(4‐N‐phenylpyridinium)‐5‐phenyl‐1,3,4‐oxadiazole end groups. Accordingly, the reaction of 1, DA18C6 and 2,7‐diaminofluorene (3) yielded oligomer‐2. The structures of oligomer‐1 and oligomer‐2 were determined by comparing their 1H NMR spectra with those of model compounds, which were synthesized by the 1:1 reaction of 1 with 2 or 3. Oligomer‐1 and oligomer‐2 exhibited weak bluish‐green photoluminescence (PL) before the inclusion of Ag+ in the DA18C6 receptor, after which they exhibited strong bluish‐green PL. These observations can be explained by the occurrence of photoinduced electron transfer in the oligomers. Copyright © 2011 Society of Chemical Industry
Predicting nucleic acid binding interfaces from structural models of proteins
Authors: Dror Iris , Shazman Shula , Mukherjee Srayanta , Zhang Yang , Glaser Fabian , Mandel‐Gutfreund Yael 
Published: October 2011

AbstractThe function of DNA‐ and RNA‐binding proteins can be inferred from the characterization and accurate prediction of their binding interfaces. However, the main pitfall of various structure‐based methods for predicting nucleic acid binding function is that they are all limited to a relatively small number of proteins for which high‐resolution three‐dimensional structures are available. In this study, we developed a pipeline for extracting functional electrostatic patches from surfaces of protein structural models, obtained using the I‐TASSER protein structure predictor. The largest positive patches are extracted from the protein surface using the patchfinder algorithm. We show that functional electrostatic patches extracted from an ensemble of structural models highly overlap the patches extracted from high‐resolution structures. Furthermore, by testing our pipeline on a set of 55 known nucleic acid binding proteins for which I‐TASSER produces high‐quality models, we show that the method accurately identifies the nucleic acids binding interface on structural models of proteins. Employing a combined patch approach we show that patches extracted from an ensemble of models better predicts the real nucleic acid binding interfaces compared with patches extracted from independent models. Overall, these results suggest that combining information from a collection of low‐resolution structural models could be a valuable approach for functional annotation. We suggest that our method will be further applicable for predicting other functional surfaces of proteins with unknown structure. Proteins 2012. © 2011 Wiley Periodicals, Inc.
Mathematical Simulation of Flow Field for Molten Steel in an 80–ton Single Snorkel Vacuum Refining Furnace
Authors: Yang Xue‐Min , Zhang Meng , Wang Fei , Duan Jian‐Ping , Zhang Jian 
Published: October 2011

AbstractThe three–dimensional flow field of molten steel in an 80–ton single snorkel vacuum refining furnace has been mathematically simulated to attain the optimal configuration and operation parameters, such as the bottom blowing Ar flow rate, the eccentric position of bottom blowing Ar port at ladle bottom, the single snorkel inner diameter, and the single snorkel immersion depth into molten steel. The mathematical simulation results show that a stable flow field of molten steel can be achieved in 70–second; meanwhile, the maximal circulation intensity of molten steel in the 80–ton single snorkel vacuum refining furnace can be found on a cross–section with y as 0 mm based on the middle of ladle bottom as circular point of the Cartesian space coordinate under the condition of injecting Ar gas on x coordinate considering the asymmetry of flow field for molten steel in the single snorkel vacuum refining furnace. The recommended parameters of the 80–ton single snorkel vacuum refining furnace with ideal circulation intensity as 970.1 kg/s are the bottom blowing Ar flow rate as 450–500 Nl/min, the eccentric position of bottom blowing Ar port as 250 mm, the single snorkel inner diameter as 1000 mm, and the single snorkel immersion depth as 500 mm.