bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mechanisms of constitutive activation of Janus kinase 2‐V617F revealed at the atomic level through molecular dynamics simulations
Authors: Lee Tai‐Sung , Ma Wanlong , Zhang Xi , Giles Francis , Kantarjian Hagop , Albitar Maher 
Published: February 2009

AbstractBACKGROUND:The tyrosine kinase Janus kinase 2 (JAK2) is important in triggering nuclear translocation and regulation of target genes expression through signal transducer and activator of transcription pathways. The valine‐to‐phenylalanine mutation at amino acid 617 (V617F), which results in the deregulation of JAK2, has been implicated in the oncogenesis of chronic myeloproliferative disease. However, both the mechanism of JAK2 autoinhibition and the mechanism of V617F constitutive activation remain unclear.METHOD:In this work, the authors used molecular dynamics simulation techniques to establish plausible mechanisms of JAK2 autoinhibition and V617F constitutive activation at the atomic level.RESULTS:In wild‐type JAK2, the activation loop of JAK2‐homology domain 1 (JH1) is pulled toward the JH1/JH2 interface through interactions with key residues of JH2, especially S591, F595, and V617, and stabilizes the inactivated form of JH1. In the case of V617F, through the aromatic ring‐ring stacking interaction, F617 blocks the interaction of JH1 the activation loop, S591, and F595, thus causing the JH1 activation loop to move back to its activated form.CONCLUSIONS:The current results indicated that this simulation‐derived mechanism of JAK2 autoregulation is consistent with current available experimental evidence and may lead to a deeper understanding of JAK2 and other kinase systems that are regulated by pseudokinases. Cancer 2009. © 2009 American Cancer Society.
Efficiency of the German electricity wholesale market
Authors: Growitsch Christian , Nepal Rabindra 
Published: February 2009

AbstractOne of the major challenges of liberalising European electricity markets is to create competitive and efficient power trading markets. In this paper, we assess the overall efficiency of the German electricity wholesale market using cointegration analysis and error correction modelling. Applying these techniques allows us to evaluate the wholesale market efficiency in terms of price adjustments and the rapidity towards the adjustment in the price discovery and adjustment process. We show that the wholesale market seems to be inefficient and not well functioning. The inability of European Energy Exchange spot market in providing an efficient price reference to the power market suggest that the power exchange still lacks liquidity. Second, our results indicate that bilateral contracts keep the wholesale electricity prices intact with the EEX prices and also stabilise the volatility in the German wholesale market. Also, the econometric results suggest that the existence of the OTC market along with power exchange is creating a competitive effect in the wholesale market in Germany. Copyright © 2009 John Wiley & Sons, Ltd.
SNP selection and multidimensional scaling to quantify population structure
Authors: Miclaus Kelci , Wolfinger Russ , Czika Wendy 
Published: February 2009

AbstractIn the new era of large‐scale collaborative Genome Wide Association Studies (GWAS), population stratification has become a critical issue that must be addressed. In order to build upon the methods developed to control the confounding effect of a structured population, it is extremely important to visualize and quantify that effect. In this work, we develop methodology for single nucleotide polymorphism (SNP) selection and subsequent population stratification visualization based on deviation from Hardy‐Weinberg equilibrium in conjunction with non‐metric multidimensional scaling (MDS); a distance‐based multivariate technique. Through simulation, it is shown that SNP selection based on Hardy‐Weinberg disequilibrium (HWD) is robust against confounding linkage disequilibrium patterns that have been problematic in past studies and methods as well as producing a differentiated SNP set. Non‐metric MDS is shown to be a multivariate visualization tool preferable to principal components in conjunction with HWD SNP selection through theoretical and empirical study from HapMap samples. The proposed selection tool offers a simple and effective way to select appropriate substructure‐informative markers for use in exploring the effect that population stratification may have in association studies. Genet. Epidemiol. 33:488–496, 2009. © 2009 Wiley‐Liss, Inc.
Bayesian intervals for linkage locations
Authors: Sinha Ritwik , Igo Robert P. , Saini Shiv K. , Elston Robert C. , Luo Yuqun 
Published: February 2009

AbstractIntermediate fine mapping has received considerable attention recently, with the goal of providing statistically precise and valid chromosomal regions for fine mapping following initial identification of broad regions that are linked to a disease. The following classes of methods have been proposed and compared in the literature: (1) LOD‐support intervals, (2) generalized estimating equations, (3) bootstrap, and (4) confidence set inference framework. These methods provide confidence intervals either with coverage levels deviating from the nominal confidence levels or that are not fully efficient. Here, we propose a novel Bayesian method for constructing such intervals using affected sibling pair data. The susceptibility gene location is treated as a parameter in this method, with a uniform prior. A Metropolis‐Hastings algorithm is implemented to sample from the posterior distribution and highest posterior density intervals of the disease gene locations are constructed. Correct coverage levels are maintained by our method. Both simulation studies and an application to a rheumatoid arthritis dataset demonstrate the improved efficiency of the Bayesian intervals compared with existing methods. Genet. Epidemiol. 33:604–616, 2009. © 2009 Wiley‐Liss, Inc.
Syntheses of new quinoline‐containing heterocyclic scaffolds using inter‐ and intramolecular Pd‐catalyzed amination
Authors: Bogányi Borbála , Kámán Judit 
Published: February 2009

Abstractmagnified imageA tandem inter‐ and intramolecular Pd‐catalyzed amination protocol was studied on 4‐chloro‐3‐iodoquinoline and 3‐chloro‐4‐iodoquinoline with different aminohetarenes. Applying this method, ten novel quinoline derivatives and eight new heterocyclic ring systems were synthesized. J. Heterocyclic Chem., (2009).
New heterocycles from tetrazines and oxadiazoles
Authors: Chavez David E. , Parrish Damon A. 
Published: February 2009

Abstract
magnified imageThe reactivity of 3,4‐diamino‐1,2,5‐oxadiazole (2) toward nucleophilic substitution of 3,6‐bis(3,5‐dimethylpyrazol‐1yl)‐1,2,4,5‐tetrazine (1) was studied. A new class of high nitrogen heterocyclic systems was prepared. It was determined that 3,4‐diamino‐1,2,5‐oxadiazole did not display the required nucleophilicity to be reactive. However, the anion of 3,4‐diamino‐1,2,5‐oxadiazole, prepared by treatment with strong base, was sufficiently reactive to act as a nucleophile. J. Heterocyclic Chem., (2009).
Insulin‐like growth factor‐I improves chondrogenesis of predifferentiated human umbilical cord mesenchymal stromal cells
Authors: Wang Limin , Detamore Michael S. 
Published: February 2009

AbstractHuman umbilical cord mesenchymal stromal cells (hUCMSCs) are an attractive cell source for tissue engineering with numerous advantages over other adult stem cell sources, such as great expansion ability in vitro and extensive availability. The objective of this 6‐week study was to test the hypothesis that switching from chondrogenic transforming growth factor‐beta3 (TGF‐β3) to anabolic insulin‐like growth factor‐I (IGF‐I) at the 3‐week time point would produce more cartilage‐like matrix than TGF‐β3 alone. hUCMSCs were seeded into polyglycolic acid (PGA) scaffolds and then cultured in chondrogenic medium containing TGF‐β3 for 3 weeks. The TGF‐β3‐treated hUCMSCs were then exposed for 3 more weeks to one of four different conditions: (1) continued in chondrogenic medium, (2) control medium (no TGF‐β3), (3) control medium with 10 ng/ml IGF‐I, or (4) control medium with 100 ng/ml IGF‐I. Compared to continuing with TGF‐β3, switching to IGF‐I increased collagen production, and furthermore increased both collagen type II gene expression and immunostaining. In conclusion, the shift from TGF‐β3 to IGF‐I at week 3 resulted in a significant increase of cartilage‐like extracellular matrix, confirming our hypothesis. © 2009 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 27: 1109–1115, 2009
Cartilage abnormalities associated with defects of chondrocytic primary cilia in Bardet‐Biedl syndrome mutant mice
Authors: Kaushik Anjan P. , Martin James A. , Zhang Qihong , Sheffield Val C. , Morcuende Jose A. 
Published: February 2009

AbstractPrimary cilia are found on nearly every mammalian cell, including osteocytes, fibroblasts, and chondrocytes. However, the functions of primary cilia have not been extensively studied in these cells, particularly chondrocytes. Interestingly, defects in the primary cilium result in skeletal defects such as polydactyly in Bardet‐Biedl syndrome (BBS), a ciliary disorder that also results in obesity, retinopathy, and cognitive impairments. Wild‐type mice and mutant mice of the ciliary proteins Bbs1, Bbs2, and Bbs6 were evaluated with respect to histological and biochemical differences in chondrocytes from articular cartilage and xiphoid processes. Using immunofluorescence microscopy, chondrocytic cilia were visualized from the load‐bearing joints and non‐load‐bearing xiphoid processes. Significant differences in ciliary morphology were not identified between mutant and wild‐type mice. However, after expanding chondrocytes in cell culture and implanting them in solid agarose matrix, it was seen that the fraction of ciliated cells in cultures from mutant mice was significantly lower than in the wild‐type cultures (p < 0.05). In addition, in Safranin‐O‐stained whole joint sections, Bbs mutant mice had significantly lower articular joint thickness (p < 0.05) and lower proteoglycan content saturation (p < 0.05) than wild‐type mice. Moreover, there were statistically significant differences of cell distribution between Bbs mutant and wild‐type mice (p < 0.05), indicating that mutant articular cartilage had changes consistent with early signs of osteoarthritis. These data indicate that Bbs genes and their functions in the chondrocytic primary cilium are important for normal articular cartilage maintenance. © 2009 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 27: 1093–1099, 2009
Functional sensibility assessment. Part I: develop a reliable apparatus to assess momentary pinch force control
Authors: Chiu Haw‐Yen , Hsu Hsiu‐Yun , Kuo Li‐Chieh , Chang Jer‐Hao , Su Fong‐Chin 
Published: February 2009

AbstractA precise magnitude and timing control of pinch performance is based on accurate feed‐forward and feedback control mechanisms. Ratio of peak pinch force and maximum load force during a functional performance is a sensitive parameter to reflect the ability to scale pinch force output according to actual loads. A pinch apparatus was constructed to detect momentary pinch force modulation of 20 subjects with normal hand sensation. The results indicated high intra‐class correlation coefficient and small coefficient of variation of the detected force ratio among three repeated tests, which represented that the stability test of the measured response confirmed the feasibility of this apparatus. The force ratio for a 480 g object with a steel surface ranged between 1.77 and 1.98. Normal subjects were able to scale and contribute pinch force precisely to a pinch‐holding‐up test. This study may provide clinicians a reliable apparatus and method to analyze the recovery of functional sensibility in patients with nerve injuries. © 2009 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 27: 1116–1121, 2009
Edge‐fault‐tolerant pancyclicity of alternating group graphs
Authors: Tsai Ping‐Ying , Chen Gen‐Huey , Fu Jung‐Sheng 
Published: February 2009

AbstractThe alternating group graph, which belongs to the class of Cayley graphs, is one of the most versatile interconnection networks for parallel and distributed computing. Previously, the alternating group graph was shown to be pancyclic, i.e., containing cycles of all possible lengths. In this article, we further show that the alternating group graph remains pancyclic, even if there are up to 2n − 6 edge faults, where n ≥ 3 is the dimension of the alternating group graph. The result is optimal with respect to the number of edge faults tolerated. © 2009 Wiley Periodicals, Inc. NETWORKS, 2009
Simultaneous solution of Lagrangean dual problems interleaved with preprocessing for the weight constrained shortest path problem
Authors: Muhandiramge Ranga , Boland Natashia 
Published: February 2009

AbstractConventional Lagrangean preprocessing for the network Weight Constrained Shortest Path Problem (WCSPP), for example Beasley and Christofides (Beasley and Christofides, Networks 19 (1989), 379–394), calculates lower bounds on the cost of using each node and edge in a feasible path using a single optimal Lagrange multiplier for the relaxation of the WCSPP. These lower bounds are used in conjunction with an upper bound to eliminate nodes and edges. However, for each node and edge, a Lagrangean dual problem exists whose solution may differ from the relaxation of the full problem. Thus, using one Lagrange multiplier does not offer the best possible network reduction. Furthermore, eliminating nodes and edges from the network may change the Lagrangean dual solutions in the remaining reduced network, warranting an iterative solution and reduction procedure. We develop a method for solving the related Lagrangean dual problems for each edge simultaneously which is iterated with eliminating nodes and edges. We demonstrate the effectiveness of our method computationally: we test it against several others and show that it both reduces solve time and the number of intractable problems encountered. We use a modified version of Carlyle and Wood's (38th Annual ORSNZ Conference, Hamilton, New Zealand, November, 2003) enumeration algorithm in the gap closing stage. We also make improvements to this algorithm and test them computationally. © 2009 Wiley Periodicals, Inc. NETWORKS, 2009
Nanodisks protect amphotericin B from ultraviolet light and oxidation‐induced damage
Authors: Tufteland Megan L , Selitrennikoff Claude P , O Ryan Robert 
Published: February 2009

AbstractBACKGROUND: Macrolide polyene antibiotics possess potent broad‐spectrum antifungal properties. Use of these agents in the field or in controlled environments is impeded by their poor water solubility and susceptibility to oxidation‐ and/or light‐induced degradation. While typically used for human disease therapy, there is potential to expand the utility of polyene macrolide antibiotics, such as amphotericin B, for control of fungal disease infestation in agricultural settings. Thus, the susceptibility of this antibiotic to exposure‐induced activity loss was evaluated.RESULTS: Incubation of the prototype polyene amphotericin B (AMB) with phospholipid vesicles and apolipoprotein A‐I results in the formation of nanoscale complexes, termed nanodisks (NDs), capable of solubilizing significant quantities of AMB. To evaluate whether AMB incorporation into NDs conferred protection against light‐ or oxidation‐induced damage, yeast growth inhibition assays were conducted. Compared with AMB solubilized in detergent micelles, AMB incorporated into NDs was protected from damage caused by exposure to UV light as well as by KMnO4‐induced oxidation. Furthermore, AMB‐NDs inhibited growth of the turfgrass fungus Marasmius oreades Fr.CONCLUSION: Results suggest that this water‐soluble formulation of a natural, biodegradable, antifungal agent represents a potential cost‐effective, non‐toxic and environmentally friendly substitute for chemical agents currently employed to control a range of fungal infestations. Copyright © 2009 Society of Chemical Industry
Representation and prediction of the Indian Ocean dipole in the POAMA seasonal forecast model
Authors: Zhao Mei , Hendon Harry H. 
Published: February 2009

AbstractPredictive skill of the Indian Ocean Dipole (IOD) using the Bureau of Meteorology's POAMA seasonal forecast model is assessed in light of the model's ability to represent the coupled nature of the IOD. The analysis is based on a ten‐member ensemble of nine‐month forecasts that are initialized from observed ocean and atmosphere states once per month for the period 1982–2006. Some aspects of the IOD are well represented by the POAMA forecast model, including the seasonal phase locking of the development of the IOD but the IOD's horizontal structure is distorted and its amplitude weakens with increasing forecast lead time, while at the same time the IOD becomes spuriously overdependent on ENSO. These deficiencies in the representation of the IOD are attributed to model error (including horizontal resolution and development of biases in the mean state), which affects depiction of important coupled dynamics for the IOD as well as the role of remote forcing of the IOD by ENSO (which itself exhibits distortion of its spatial structure attributed to biases in the simulated mean state).In the light of these limitations of representing the IOD in the POAMA forecast model, skilful prediction of the peak phase of the IOD in September–November is limited to about a four‐month lead time, with a rapid drop in skill for forecasts initialized before June. Forecast skill for the IOD appears to be limited mainly by ability to predict development of SST anomalies in its eastern pole. Potential predictability estimates, assuming a perfect model, indicate great scope for improved prediction, although the IOD is much less predictable (potentially and in practice) than ENSO. The deficient depiction of the IOD at longer lead times means that estimates of potential predictability assuming a perfect model may be unreliable. Copyright © 2009 Royal Meteorological Society
Excellent Prognosis of Patients with Nonhereditary Medullary Thyroid Carcinoma with Ultrasonographic Findings of Follicular Tumor or Benign Nodule
Authors: Fukushima Mitsuhiro , Ito Yasuhiro , Hirokawa Mitsuyoshi , Miya Akihiro , Kobayashi Kaoru , Akasu Haruki , Shimizu Kazuo , Miyauchi Akira 
Published: February 2009

AbstractBackgroundMedullary thyroid carcinoma (MTC) accounts for only 1.4% of all thyroid malignancies in Japan. Generally, MTC shows ultrasonographic findings typical of thyroid carcinoma. However, in our experience, some MTC may be diagnosed as a follicular tumor or a benign nodule on ultrasonography because ultrasonographic findings of malignancy are lacking. In this study we investigated differences in biological behavior between these two types of MTC.MethodsSeventy‐seven patients with nonhereditary MTC who underwent surgery in our department between 1988 and 2007 were enrolled in this study. Of these patients, 54 were diagnosed as having thyroid carcinoma (malignant, or M‐type) but the remaining 23 were diagnosed as having follicular tumor or benign nodule (benign, or B‐type) on ultrasonography.ResultsClinically apparent lateral node metastasis, extrathyroid extension, and extranodal tumor extension were observed in 37%, 17%, and 11% of M‐type patients, respectively, but none of the B‐type patients showed any of these features. All B‐type patients but only 59% of M‐type patients were biochemically cured. Lymph node metastasis was pathologically confirmed in 38 and 65% of B‐type and M‐type patients, respectively. Eight patients showed recurrence and three have died of carcinoma to date; all of these patients were M‐type patients.ConclusionsB‐type MTC is highly indolent and shows an excellent prognosis. However, thyroidectomy and lymph node dissection for B‐type MTC should be the same as for M‐type MTC because 38% of B‐type MTC showed pathologic node metastasis.
Clinical Risk Assessment: Identifying Patients at High Risk for Heart Failure
Authors: Babb Marsha 
Published: February 2009

ABSTRACTCare requirements differ for individual patients in the heart failure continuum of care. Few tools exist that enable the bedside nurse to assess the cardiac surgical patient effectively.A quality improvement project was conducted at a level I trauma center in the mid‐Atlantic United States to identify perioperative heart failure patients who do poorly after cardiac surgery.The surgical patient who is at high risk for adverse events after coronary artery bypass graft surgery can be identified by clustering 11 characteristics. Of 1,971 patients studied, 294 had adverse outcomes. Data indicated that any cluster of the characteristics was intensified when emergency status was added. AORN J 89 (February 2009) 273–288. © AORN, Inc, 2009.
Too Old For School? Barriers Nurses Can Overcome When Returning to School
Authors: Morgenthaler Marcia 
Published: February 2009

ABSTRACTNurses may face a number of perceived barriers, such as geographical location, time, and cost, when deciding to return to school for additional education.Viable solutions to overcome these barriers include distance education, effective time management, and tuition assistance programs. AORN J 89 (February 2009) 335–345. © AORN, Inc, 2009.
Social Support During Anesthesia Induction in an Adult Surgical Population
Authors: Mayne Ian P. , Bagaoisan Cora 
Published: February 2009

ABSTRACTA surgical procedure is a stressful experience for the patient and his or her support persons. In addition, the unfamiliar OR environment may be overwhelming for the surgical patient.This project assessed whether there is a need for support‐person presence during anesthesia induction in the adult surgical population at an academic hospital. A survey was used to measure the respondents' opinions related to different aspects of social support during the induction process.The results of this project did not exhibit a significant need for a support person to be present during anesthesia induction. AORN J 89 (February 2009) 307–320. © AORN, Inc, 2009.
The Endovascular Approach to Abdominal Aortic Aneurysm Repair
Authors: Tinkham Michelle Rovena 
Published: February 2009

ABSTRACTEndovascular aneurysm repair (EVAR) affords patients the opportunity to undergo a less invasive method of repairing abdominal aortic aneurysms. The EVAR procedure results in a shorter hospital stay, less pain, and less chance of morbidity. This procedure can be performed in a variety of settings (eg, OR, interventional radiology suite, cardiac catheterization laboratory), each of which has its own benefits and challenges. Recently, hybrid ORs have been designed to perform both endovascular and open procedures.AORN has many applicable recommended practices to guide perioperative nurses in the safe provision of care during EVAR procedures. AORN J 89 (February 2009) 289–302. © AORN, Inc, 2009.