bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dietary apigenin reduces LPS‐induced expression of miR‐155 restoring immune balance during inflammation
Authors: Arango Daniel , Diosa‐Toro Mayra , Rojas‐Hernandez Laura S. , Cooperstone Jessica L. , Schwartz Steven J. , Mo Xiaokui , Jiang Jinmai , Schmittgen Thomas D. , Doseff Andrea I. 
Published: January 2015

ScopeHigh incidence of inflammatory diseases afflicts the increasing aging‐population infringing a great health burden. Dietary flavonoids, including the flavone apigenin, are emerging as important anti‐inflammatory nutraceuticals due to their health benefits, lack of adverse effects and reduced costs. MicroRNAs (miRs) play a central role in inflammation by regulating gene expression, yet how dietary ingredients affect miRs is poorly understood. The aim of this study was to identify miRs involved in the anti‐inflammatory activity of apigenin and apigenin‐rich diets and determine their immune regulatory mechanisms in macrophages and in vivo.Methods and resultsA high‐throughput quantitative reverse transcriptase PCR screen of 312 miRs in macrophages revealed that apigenin reduced LPS‐induced miR‐155 expression. Analyses of miR‐155 precursor and primary transcript indicated that apigenin regulated miR‐155 transcriptionally. Apigenin‐reduced expression of miR‐155 led to the increase of anti‐inflammatory regulators forkhead box O3a and smooth‐muscle‐actin and MAD‐related protein 2 in LPS‐treated macrophages. In vivo, apigenin or a celery‐based apigenin‐rich diet reduced LPS‐induced expression of miR‐155 and decreased tumor necrosis factor α in lungs from LPS‐treated mice.ConclusionThese results demonstrate that apigenin and apigenin‐rich diets exert effective anti‐inflammatory activity in vivo by reducing LPS‐induced expression of miR‐155, thereby restoring immune balance.
PROMISE: Parallel‐imaging and compressed‐sensing reconstruction of multicontrast imaging using SharablE information
Authors: Gong Enhao , Huang Feng , Ying Kui , Wu Wenchuan , Wang Shi , Yuan Chun 
Published: January 2015

PurposeA typical clinical MR examination includes multiple scans to acquire images with different contrasts for complementary diagnostic information. The multicontrast scheme requires long scanning time. The combination of partially parallel imaging and compressed sensing (CS‐PPI) has been used to reconstruct accelerated scans. However, there are several unsolved problems in existing methods. The target of this work is to improve existing CS‐PPI methods for multicontrast imaging, especially for two‐dimensional imaging.Theory and MethodsIf the same field of view is scanned in multicontrast imaging, there is significant amount of sharable information. It is proposed in this study to use manifold sharable information among multicontrast images to enhance CS‐PPI in a sequential way. Coil sensitivity information and structure based adaptive regularization, which were extracted from previously reconstructed images, were applied to enhance the following reconstructions. The proposed method is called Parallel‐imaging and compressed‐sensing Reconstruction Of Multicontrast Imaging using SharablE information (PROMISE).ResultsUsing L1‐SPIRiT as a CS‐PPI example, results on multicontrast brain and carotid scans demonstrated that lower error level and better detail preservation can be achieved by exploiting manifold sharable information. Besides, the privilege of PROMISE still exists while there is interscan motion.ConclusionUsing the sharable information among multicontrast images can enhance CS‐PPI with tolerance to motions. Magn Reson Med 73:523–535, 2015. © 2014 Wiley Periodicals, Inc.
Whole‐body magnetic resonance imaging evaluation of facioscapulohumeral muscular dystrophy
Authors: Leung Doris G. , Carrino John A. , Wagner Kathryn R. , Jacobs Michael A. 
Published: January 2015

ABSTRACTIntroduction: Facioscapulohumeral muscular dystrophy (FSHD) is a hereditary disorder that causes progressive muscle wasting. Increasing knowledge of the pathophysiology of FSHD has stimulated interest in developing biomarkers of disease severity. Methods: Two groups of MRI scans were analyzed: whole‐body scans from 13 subjects with FSHD; and upper and lower extremity scans from 34 subjects with FSHD who participated in the MYO‐029 clinical trial. Muscles were scored for fat infiltration and edema‐like changes. Fat infiltration scores were compared with muscle strength and function. Results: The analysis revealed a distinctive pattern of both frequent muscle involvement and frequent sparing in FSHD. Averaged fat infiltration scores for muscle groups in the legs correlated with quantitative muscle strength and 10‐meter walk times. Conclusions: Advances in MRI technology allow for acquisition of rapid, high‐quality, whole‐body imaging in diffuse muscle disease. This technique offers a promising disease biomarker in FSHD and other muscle diseases. Muscle Nerve 52: 512–520, 2015
Effects of gender and hand dominance on size of the lower trapezius muscle
Authors: Uthaikhup Sureeporn , Wannaprom Nipaporn , Kummaung Panuwat 
Published: January 2015

ABSTRACTIntroduction: The influence of gender and hand dominance on the size of the lower trapezius muscle has not been studied. We aimed to identify the effects of gender and hand dominance on thickness of this muscle. Methods: Thirty healthy subjects (15 men and 15 women) were recruited for the study. The thickness of the lower trapezius muscles was measured bilaterally at the level of T8 at rest and with contraction at 130° of shoulder abduction using ultrasound imaging. Results: Men had significantly greater thickness of the lower trapezius muscle than women, both at rest and with contraction (P < 0.01). Greater lower trapezius muscle thickness was found on the dominant side compared with the non‐dominant side (P < 0.05). Conclusion: Gender and side dominance differences should be controlled for when investigating lower trapezius muscle thickness. Muscle Nerve 52: 576–579, 2015
Quantitative and qualitative adaptations of muscle fibers to glucocorticoids
Authors: Minetto Marco Alessandro , Qaisar Rizwan , Agoni Valentina , Motta Giovanna , Longa Emanuela , Miotti Danilo , Pellegrino Maria Antonietta , Bottinelli Roberto 
Published: January 2015

ABSTRACTIntroduction: The aim of this study was to understand the effects of short‐term glucocorticoid administration in healthy subjects. Methods: Five healthy men received dexamethasone (8 mg/day) for 7 days. Vastus lateralis muscle biopsy and knee extension torque measurement were performed before and after administration. A large number of individual muscle fibers were dissected from the biopsy samples (pre‐administration: n = 165, post‐administration: n = 177). Results: Maximal knee extension torque increased after administration (∼13%), whereas both type 1 and type 2A fibers had decreased cross‐sectional area (type 1: ∼11%, type 2A: ∼17%), myosin loss (type 1: ∼18%, type 2A: ∼32%), and loss of specific force (type 1: ∼24%, type 2A: ∼33%), which were preferential for fast fibers. Conclusion: Short‐term dexamethasone administration in healthy subjects elicits quantitative and qualitative adaptations of muscle fibers that precede (and may predict) the clinical appearance of myopathy in glucocorticoid‐treated subjects. Muscle Nerve 52: 631–639, 2015
Hybrid time integration and coupled solution methods for nonlinear finite element analysis of partially saturated deformable porous media at small strain
Authors: Kim Jaehong , Wang Wei , Regueiro Richard A. 
Published: January 2015

SummaryThe goal of the paper is to determine the most efficient, yet accurate and stable, finite element nonlinear solution method for analysis of partially saturated deformable porous media at small strain. This involves a comparison between fully implicit, semi‐implicit, and explicit time integration schemes, with monolithically coupled and staggered‐coupled nonlinear solution methods and the hybrid combination thereof. The pore air pressure pa is assumed atmospheric, that is, pa=0 at reference pressure. The solid skeleton is assumed to be pressure‐sensitive nonlinear isotropic elastic. Coupled partially saturated ‘consolidation’ in the presence of surface infiltration and traction is simulated for a simple one‐dimensional uniaxial strain example and a more complicated plane strain slope example with gravity loading. Three mixed plane strain quadrilateral elements are considered: (i) Q4P4; (ii) stabilized Q4P4S; and (iii) Q9P4; “Q” refers to the number of solid skeleton displacement nodes, and “P” refers to the number of pore fluid pressure nodes. The verification of the implementation against an analytical solution for partially saturated pore water flow (no solid skeleton deformation) and comparison between the three time integration schemes (fully implicit, semi‐implicit, and explicit) are presented. It is observed that one of the staggered‐coupled semi‐implicit schemes (SIS(b)), combined with the fully implicit monolithically coupled scheme to resolve sharp transients, is the most efficient computationally. Copyright © 2015 John Wiley & Sons, Ltd.
Maintenance and flight scheduling of low observable aircraft
Authors: Cho Philip , Farias Vivek , Kessler John , Levi Retsef , Magnanti Thomas , Zarybnisky Eric 
Published: January 2015

AbstractIn this article, we focus on relatively new maintenance and operational scheduling challenges that are faced by the United States Air Force concerning low‐observable (LO) or stealth aircraft. The LO capabilities of an aircraft degrade stochastically as it flies, making it difficult to make maintenance scheduling decisions. Maintainers can address these damages, but must decide, which aircraft should be put into maintenance, and for how long. Using data obtained from an active duty Air Force F‐22 wing and interviews with Air Force maintainers and program specialists, we model this problem as a generalization of the well‐known restless multiarmed bandit superprocess. Specifically, we use an extension of the traditional model to allow for actions that require varying lengths of time, and generate two separate index policies from a single model; one for maintenance actions and one for the flying action. These index policies allow maintenance schedulers to intuitively, quickly, and effectively rank a fleet of aircraft based on each aircraft's LO status and decide, which aircraft should enter into LO maintenance and for how long, and which aircraft should be used to satisfy daily sortie requirements. Finally, we present extensive data‐driven, detailed simulation results, where we compare the performance of the index policies against policies currently used by the Air Force, as well as some other possible more naive heuristics. The results indicate that the index policies significantly outperform existing policies in terms of fully mission capable (FMC) rates. In particular, the experiments highlight the importance of coordinated maintenance and flying decisions. © 2015 Wiley Periodicals, Inc. 62:60–80, 2015
Prospective cardiac MRI for the analysis of biventricular function in children undergoing cancer treatments
Authors: de Ville de Goyet Maëlle , Brichard Benedicte , Robert Annie , Renard Laurette , Veyckemans Francis , Vanhoutte Laetitia , Moniotte Stephane 
Published: January 2015

BackgroundCardiotoxicity is one of the most serious long‐term complications in childhood cancer survivors. Measurement of the left ventricular ejection and shortening fraction remains the most common screening tool for cardiac systolic dysfunction. However, M‐mode echocardiography can be viewed as a crude approach as refined strategies are now available. The aim of this prospective study was to determine the role of cardiac MRI in the detection of subclinical left or right ventricular dysfunction as well as the prevalence of myocardial scaring in patients undergoing cancer treatments.ProcedureEighty‐one children were enrolled in a pre‐chemotherapy and then in a yearly protocol including a: (i) clinical evaluation; (ii) laboratory evaluation; (iii) electrocardiogram; (iv) echocardiogram; and (v) a cardiac magnetic resonance imaging (cMRI).ResultsEarly left ventricular systolic dysfunction was only detected in two patients. The entire cohort presented a significant increase of the left atrial volume as measured by cMRI. This finding correlated with the total cumulative dose of anthracyclines (r = 0.34; P < 0.05) and the mean left ventricular radiation dose (r = 0.86; P < 0.05). We also observed a mild increase of myocardial scaring, similarly correlated to the radiation dose (r = 0.85; P < 0.05).ConclusionsScreening tools for late‐onset cardiomyopathy secondary to cancer treatment are lacking. Our findings support the use of cMRI for the evaluation of the left atrial volume, as an early marker of diastolic dysfunction, and myocardial delayed enhancement, as a marker of myocardial fibrosis and scaring. Longer follow‐up and larger studies are still needed to better define the role of cMRI in the evaluation of childhood cancer survivors. Pediatr Blood Cancer 2015;62:867–874. © 2015 Wiley Periodicals, Inc.
Expression profile analysis of microRNAs in prostate cancer by next‐generation sequencing
Authors: Song Chunjiao , Chen Huan , Wang Tingzhang , Zhang Weiguang , Ru Guomei , Lang Juan 
Published: January 2015

BACKGROUNDProstate cancer (PCa) is the second leading cause of tumor mortality among males in western societies. In China, the diagnostic and fatality rate of PCa is increasing yearly.METHODSTo characterize underlying molecular mechanisms, the microRNA (miRNA) profile of high‐grade PCa, low‐grade PCa, and benign prostate hyperplasia (BPH) were compared using high‐throughput Illumina sequencing and quantitative real‐time PCR (qRT‐PCR) methods. Moreover, a variety of biological information softwares and databases were applied to predict the target genes of miRNA, molecular functions, and signal pathways.RESULTSEighteen miRNAs were differentially expressed (fold change ≥2, P < 0.05), of which thirteen were upregulated and five were downregulated by sequencing. This was confirmed by qRT‐PCR in more clinical tissue samples. In the tumors, miRNAs (miR‐125b‐5p, miR‐126‐5p, miR‐151a‐5p, miR‐221‐3p, and miR‐222‐3p) were significantly upregulated with downregulation of miR‐486‐5p. In addition, 13 novel miRNAs were identified from three prostate tissue libraries, with 12 of them assayed in 21 human normal tissues by qRT‐PCR. Multiple databases indicated target genes for these differentially expressed miRNAs. Function annotation of target genes indicated that most of them tend to target genes involved in signal transduction and cell communication, especially cancer‐related PI3K‐Akt and p53 signaling pathway.CONCLUSIONSThe small RNA transcriptomes obtained in this study uncovers six differentially expressed miRNAs and 12 novel miRNAs, and provides a better understanding of the expression and function of miRNAs in the development of PCa and reveals several miRNAs in PCa that may have biomarker and therapeutic potentials. Prostate 75: 500–516, 2015. © 2015 Wiley Periodicals, Inc.
Reduced alphabet for protein folding prediction
Authors: Huang Jitao T. , Wang Titi , Huang Shanran R. , Li Xin 
Published: January 2015

ABSTRACTWhat are the key building blocks that would have been needed to construct complex protein folds? This is an important issue for understanding protein folding mechanism and guiding de novo protein design. Twenty naturally occurring amino acids and eight secondary structures consist of a 28‐letter alphabet to determine folding kinetics and mechanism. Here we predict folding kinetic rates of proteins from many reduced alphabets. We find that a reduced alphabet of 10 letters achieves good correlation with folding rates, close to the one achieved by full 28‐letter alphabet. Many other reduced alphabets are not significantly correlated to folding rates. The finding suggests that not all amino acids and secondary structures are equally important for protein folding. The foldable sequence of a protein could be designed using at least 10 folding units, which can either promote or inhibit protein folding. Reducing alphabet cardinality without losing key folding kinetic information opens the door to potentially faster machine learning and data mining applications in protein structure prediction, sequence alignment and protein design. Proteins 2015; 83:631–639. © 2015 Wiley Periodicals, Inc.
Hierarchical domain‐motion analysis of conformational changes in sarcoplasmic reticulum Ca2+‐ATPase
Authors: Kobayashi Chigusa , Koike Ryotaro , Ota Motonori , Sugita Yuji 
Published: January 2015

ABSTRACTSarco(endo)plasmic reticulum Ca2+‐ATPase transports two Ca2+ per ATP‐hydrolyzed across biological membranes against a large concentration gradient by undergoing large conformational changes. Structural studies with X‐ray crystallography revealed functional roles of coupled motions between the cytoplasmic domains and the transmembrane helices in individual reaction steps. Here, we employed “Motion Tree (MT),” a tree diagram that describes a conformational change between two structures, and applied it to representative Ca2+‐ATPase structures. MT provides information of coupled rigid‐body motions of the ATPase in individual reaction steps. Fourteen rigid structural units, “common rigid domains (CRDs)” are identified from seven MTs throughout the whole enzymatic reaction cycle. CRDs likely act as not only the structural units, but also the functional units. Some of the functional importance has been newly revealed by the analysis. Stability of each CRD is examined on the morphing trajectories that cover seven conformational transitions. We confirmed that the large conformational changes are realized by the motions only in the flexible regions that connect CRDs. The Ca2+‐ATPase efficiently utilizes its intrinsic flexibility and rigidity to response different switches like ligand binding/dissociation or ATP hydrolysis. The analysis detects functional motions without extensive biological knowledge of experts, suggesting its general applicability to domain movements in other membrane proteins to deepen the understanding of protein structure and function. Proteins 2015; 83:746–756. © 2015 Wiley Periodicals, Inc.
Process, Policy, and Implementation of Pool‐Wide Drawdowns on the Upper Mississippi River: A Promising Approach for Ecological Restoration of Large Impounded Rivers
Authors: Kenow K. P. , Benjamin G. L. , Schlagenhaft T. W. , Nissen R. A. , Stefanski M. , Wege G. J. , Jutila S. A. , Newton T. J. 
Published: January 2015

AbstractThe Upper Mississippi River (UMR) has been developed and subsequently managed for commercial navigation by the U.S. Army Corps of Engineers (USACE). The navigation pools created by a series of lock and dams initially provided a complex of aquatic habitats that supported a variety of fish and wildlife. However, biological productivity declined as the pools aged. The River Resources Forum, an advisory body to the St. Paul District of the USACE, established a multiagency Water Level Management Task Force (WLMTF) to evaluate the potential of water level management to improve ecological function and restore the distribution and abundance of fish and wildlife habitat. The WLMTF identified several water level management options and concluded that summer growing season drawdowns at the pool scale offered the greatest potential to provide habitat benefits over a large area. Here we summarize the process followed to plan and implement pool‐wide drawdowns on the UMR, including involvement of stakeholders in decision making, addressing requirements to modify reservoir operating plans, development and evaluation of drawdown alternatives, pool selection, establishment of a monitoring plan, interagency coordination, and a public information campaign. Three pool‐wide drawdowns were implemented within the St. Paul District and deemed successful in providing ecological benefits without adversely affecting commercial navigation and recreational use of the pools. Insights are provided based on more than 17 years of experience in planning and implementing drawdowns on the UMR. Copyright © 2015 John Wiley & Sons, Ltd.
Re‐operating the Three Gorges Reservoir for Environmental Flows: A Preliminary Assessment of Trade‐offs
Authors: Rheinheimer D. E. , Liu P. , Guo S. 
Published: January 2015

AbstractThe Three Gorges Reservoir (TGR), located on the Yangtze River in China, is operated for hydropower, flood control and navigation, with minimal environmental releases. This study explored the potential trade‐offs between better environmental releases from the TGR and hydropower generation using three performance indicators. Spearman's rank correlation coefficient between unimpaired flows and regulated flows was used as an indicator of environmental performance (eco rho). Energy generation as a fraction of capacity (energy fraction) and power reliability were used as hydropower performance indicators. We first assessed TGR performance without and with basic instream flow requirements (IFRs). We then imposed an IFR consisting of a minimum release of fraction k of inflow and maximum release of 1/k of inflow and assessed the sensitivity of reservoir performance to different fixed k values. Finally, we allowed k to vary within the year in a genetic algorithm to estimate the Pareto optimal trade‐offs between performance indicators. In all cases, flood and navigation rules were prioritized over environmental and hydropower. With a fixed k of 1.0, eco rho increased from 0.865 to nearly 1.0 (completely natural). Energy fraction reduced from 43.5 to 39.3%, or about 9.5%, and power reliability decreased from 97.0 to 59.2%. The Pareto optimal trade‐off surface not only showed similar results but also indicated that energy fraction and environmental performance can both be increased together, up to a point, but at a cost of reliability. This study helps understand the potential costs of re‐operating the TGR. Limitations and potential future directions are discussed. Copyright © 2015 John Wiley & Sons, Ltd.
An investigation of statistical software testing
Authors: Thévenod‐Fosse P , Waeselynck H 
Published: January 2015

AbstractSoftware validation embodies two notions: fault removal and fault forecasting. Statistical testing involves exercising a piece of software by supplying it with input values that are randomly selected according to a defined probability distribution on its input domain. It can be used as a practical tool for revealing faults in a fault removal phase, and for assessing software dependability in a fault forecasting phase. In both of these, its efficiency is linked to the adequacy of the input probability distribution with respect to the test experiment goal. In this paper a mixed validation strategy combining deterministic and random test data is defined, and the theoretical and experimental work performed to support the strategy is reported. The quoted results relate to the unit testing of four real programs from the nuclear field. They confirm the high fault revealing power of statistical structural testing. Two main directions for further investigation of statistical testing are indicated by the reported work. These are described and solutions to the associated problems are outlined.
Validating software measures
Authors: Fenton Norman , Kitchenham Barbara 
Published: January 2015

AbstractThere are two distinct notions of validation for software measures. On the one hand there is the informal notion that a measure is only valid if it is useful and practical. Although this view of validation is important, it is almost impossible to test. On the other hand there is a formal notion of validation of measures and it is this view which is addressed here. By considering software measures in the context of measurement theory, and by considering a classification of software entities into products, processes and resources the paper describes what the authors believe are the necessary (but not sufficient) activities required for validation, and show how far this deviates from the ‘accepted’ view of validation.