bluuebunny/crossref_metadata_2025_split huggingface dataset:
Improved gradient‐echo 3D magnetic resonance imaging using pseudo‐echoes created by frequency‐swept pulses
Authors: Park Jang‐Yeon , DelaBarre Lance , Garwood Michael 
Published: February 2006

AbstractFrequency‐swept pulses are not typically employed to excite spins in NMR. When used for selective excitation in MRI, such pulses do not produce a proper echo because the phase of the transverse magnetization varies in a quadratic manner across the slice or slab. Previously, frequency‐swept pulses such as the chirp pulse have been shown to offer an approach to reduce the peak radiofrequency power required for excitation. It has also been shown that chirp excitation produces a unique type of echo (dubbed “pseudo‐echo” here) and images can be generated from the resultant pseudo‐echoes using a quadratic reconstruction method (J.G. Pipe, Magn Reson Med 1995;33:24–33). The present work describes a general theory and methods for exciting spins with other types of frequency‐swept pulses (HSn pulses), which offer the advantage of delivering better excitation profiles than the chirp pulse. Here, pseudo‐echoes are produced with HSn pulses in conventional gradient‐echo 3D MRI, and high‐quality images are reconstructed using standard fast Fourier transformation. An optional apodization procedure using a sliding window function is also introduced. When the dynamic range of the analog‐to‐digital converter is limiting, signal‐to‐noise ratio of pseudo‐echo imaging is superior to that obtained with standard excitations. Magn Reson Med, 2006. © 2006 Wiley‐Liss, Inc.
Detection of myocardial capillary orientation with intravascular iron‐oxide nanoparticles in spin‐echo MRI
Authors: Vignaud Alexandre , Rodriguez Ignacio , Ennis Daniel B. , DeSilva Ranil , Kellman Peter , Taylor Joni , Bennett Eric , Wen Han 
Published: February 2006

AbstractIn mammalian hearts the capillaries are closely aligned with the muscle fibers. We report our observation of a main‐field direction‐dependent contrast in MR spin‐echo (SE) images of the heart in the presence of Ferumoxtran‐10, an intravascular iron‐oxide nanoparticle contrast agent (CA). We describe a novel MRI method for mapping the preferential orientation of capillaries in the myocardial wall. The eigenvector corresponding to the minimum eigen value of the R2 relaxation rate tensor is consistent with the expected orientation of the capillary network. Preliminary results also demonstrate the feasibility of this method for in vivo application to rodent imaging. Magn Reson Med, 2006. Published © 2006 Wiley‐Liss, Inc.
Eosinophilia, myositis, and myasthenia gravis associated with a thymoma
Authors: Avni Irit , Sharabi Yehonatan , Sadeh Menachem , Buchman Aron S. 
Published: February 2006

AbstractHypereosinophilia has been associated with a wide variety of systemic disorders, including myositis. Myositis develops in a minority of patients with myasthenia gravis associated with a thymoma. We present a patient who developed a life‐threatening myopathy in which testing demonstrated the concurrence of hypereosinophilia, myositis, and myasthenia gravis associated with thymoma. Thymoma‐associated T‐cell abnormalities may well have contributed to this rare association. This case underscores the need to reevaluate constantly the presumed cause of clinical complaints, as more than one cause may be present. Muscle Nerve, 2006
A mathematical programming approach for improving the robustness of least sum of absolute deviations regression
Authors: Giloni Avi , Sengupta Bhaskar , Simonoff Jeffrey S. 
Published: February 2006

AbstractThis paper discusses a novel application of mathematical programming techniques to a regression problem. While least squares regression techniques have been used for a long time, it is known that their robustness properties are not desirable. Specifically, the estimators are known to be too sensitive to data contamination. In this paper we examine regressions based on Least‐sum of Absolute Deviations (LAD) and show that the robustness of the estimator can be improved significantly through a judicious choice of weights. The problem of finding optimum weights is formulated as a nonlinear mixed integer program, which is too difficult to solve exactly in general. We demonstrate that our problem is equivalent to a mathematical program with a single functional constraint resembling the knapsack problem and then solve it for a special case. We then generalize this solution to general regression designs. Furthermore, we provide an efficient algorithm to solve the general nonlinear, mixed integer programming problem when the number of predictors is small. We show the efficacy of the weighted LAD estimator using numerical examples. © 2006 Wiley Periodicals, Inc. Naval Research Logistics, 2006
Proteomic identification of alterations in metabolic enzymes and signaling proteins in hypokalemic nephropathy
Authors: Thongboonkerd Visith , Chutipongtanate Somchai , Kanlaya Rattiyaporn , Songtawee Napat , Sinchaikul Supachok , Parichatikanond Paisal , Chen Shui‐Tein , Malasit Prida 
Published: February 2006

AbstractHypokalemic nephropathy caused by prolonged K+ deficiency is associated with metabolic alkalosis, polydipsia, polyuria, growth retardation, hypertension, and progressive tubulointerstitial injury. Its pathophysiology, however, remains unclear. We performed gel‐based, differential proteomics analysis of kidneys from BALB/c mice fed with high‐normal‐K+ (HNK), low‐normal‐K+ (LNK), or K+‐depleted diet for 8 wk (n = 6 in each group). Plasma K+ levels were 4.62 ± 0.35, 4.46 ± 0.23, and 1.51 ± 0.21 mmol/L for HNK, LNK, and KD mice, respectively (p < 0.0001; KD vs. others). With comparable amounts of food intake, the KD mice drank significantly more water than the other two groups and had polyuria. Additionally, the KD mice had growth retardation, metabolic alkalosis, markedly enlarged kidneys, renal tubular dilation, intratubular deposition of amorphous and laminated hyaline materials, and tubular atrophy. A total of 33 renal proteins were differentially expressed between the KD mice and others, whereas only eight proteins were differentially expressed between the HNK and LNK groups, as determined by quantitative intensity analysis and ANOVA with Tukey's post hoc multiple comparisons. Using MALDI‐MS and/or quadrupole‐TOF MS/MS, 30 altered proteins induced by K+‐depletion were identified as metabolic enzymes (e.g., carbonic anhydrase II, aldose reductase, glutathione S‐transferase GT41A, etc.), signaling proteins (14–3‐3 ε, 14–3‐3 ζ, and cofilin 1), and cytoskeletal proteins (γ‐actin and tropomyosin). Some of these altered proteins, particularly metabolic enzymes and signaling proteins, have been demonstrated to be involved in metabolic alkalosis, polyuria, and renal tubular injury. Our findings may lead to a new road map for research on hypokalemic nephropathy and to better understanding of the pathophysiology of this medical disease when the functional and physiological significances of these altered proteins are defined.
The early responses of Arabidopsis thaliana cells to cadmium exposure explored by protein and metabolite profiling analyses
Authors: Sarry Jean‐Emmanuel , Kuhn Lauriane , Ducruix Céline , Lafaye Alexandra , Junot Christophe , Hugouvieux Véronique , Jourdain Agnès , Bastien Olivier , Fievet Julie B. , Vailhen Dominique , Amekraz Badia , Moulin Christophe , Ezan Eric , Garin Jérôme , Bourguignon Jacques 
Published: February 2006

AbstractTo get more insight into plant cell response to cadmium (Cd) stress, both proteomic and metabolomic “differential display” analyses were performed on Arabidopsis thaliana cells exposed to different concentrations of the toxic chemical. After a 24 h treatment, soluble proteins extracted from untreated and treated cells were separated by 2‐D‐PAGE and image analyses were performed to quantify and compare protein levels. Proteins up‐ and down‐regulated in response to Cd were identified by MS and mapped into specific metabolic pathways and cellular processes, highlighting probable activation of the carbon, nitrogen, and sulfur metabolic pathways. For some of these proteins, Northern blot and RT‐PCR analyses were performed to test transcript accumulation in response to Cd. In parallel, metabolite profiling analyses by LC coupled to ESI MS were initiated to better characterize the metabolic adaptation to the chemical stress. This study revealed that the main variation at the metabolite level came from the presence of six different families of phytochelatins, in A. thaliana cells treated with Cd, whose accumulation increases with Cd concentrations. Taken together these data provide an overview of the molecular and cellular changes elicited by Cd exposure.
Human colostrum: Identification of minor proteins in the aqueous phase by proteomics
Authors: Palmer David J. , Kelly Van C. , Smit Anne‐Marie , Kuy Sulee , Knight Catriona G. , Cooper Garth J. 
Published: February 2006

AbstractHuman colostrum is an important source of protective, nutritional and developmental factors for the newborn. We have investigated the low abundance proteins in the aqueous phase of human colostrum, after depletion of the major proteins secretory IgA, lactoferrin, alpha‐lactalbumin and HSA by immunoabsorption, using 2‐D LC and gel‐based proteomic methods. One hundred and fifty‐one proteins were identified, 83 of which have not been previously reported in human colostrum, or milk. This is the first comprehensive proteomic analysis of human colostrum produced during the first 48 h of lactation.
A proteomics approach to survey the antigenicity of the influenza virus by mass spectrometry
Authors: Morrissey Bethny , Downard Kevin M. 
Published: February 2006

AbstractA proteomics‐based approach is described that combines gel electrophoresis and MS in order to identify protein interactions and the nature of the interaction interface with high‐sample throughput and sensitivity. Results for protein antigens of the influenza virus have demonstrated that the approach can be successfully employed to detect determinants within the hemagglutinin antigen of two divergent type A forms of the virus in present circulation. The determinants are localised to residues 206–224 following tryptic digestion of the hemagglutinin antigen. Specific peptide–antibody complexes formed after treatment of gel‐recovered antigen are shown to be able to be preserved on the MALDI target array as has been previously demonstrated in this laboratory for whole virus. The approach has broad applicability for the analysis of a wide array of protein complexes with identification of the interaction interface in a single step with high‐sample throughput and at low sample levels.
Interactions and prediction of phase diagrams in ternary blends comprising poly(vinyl acetate), poly(vinyl p‐phenol), and poly(methyl methacrylate)
Authors: Liu Hung‐Ling , Li Shu‐Hsien , Woo Eamor M. 
Published: February 2006

AbstractThis study investigated and discovered a new miscible ternary blend system comprising three amorphous polymers: poly(vinyl acetate) (PVAc), poly(vinyl p‐phenol) (PVPh), and poly(methyl methacrylate) (PMMA) using thermal analysis and optical and scanning electron microscopies. The ternary compositions are largely miscible except for a small region of borderline ternary miscibility near the side, where the binary blends of PVAc/PMMA are originally of a borderline miscibility with broad Tg. In addition to the discovering miscibility in a new ternary blend, another objective of this study was to investigate whether the introduction of a third polymer component (PVPh) with hydrogen bonding capacity might disrupt or enhance the metastable miscibility between PVAc and PMMA. The PVPh component does not seem to exert any “bridging effect” to bring the mixture of PVAc and PMMA to a better state of miscibility; neither does the Δχ effect seem to disrupt the borderline miscible PVAc/PMMA blend into a phase‐separated system by introducing PVPh. Apparently, the ternary is able to remain in as a miscible state as the binary systems owing to the fact that PVPh is capable of maintaining roughly equal H‐bonding interactions with either PVAc or PMMA in the ternary mixtures to maintain balanced interactions among the ternary mixtures. © 2006 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 44: 1147–1160, 2006
Scoring a diverse set of high‐quality docked conformations: A metascore based on electrostatic and desolvation interactions
Authors: Camacho Carlos J. , Ma Hui , Champ P. Christoph 
Published: February 2006

AbstractPredicting protein–protein interactions involves sampling and scoring docked conformations. Barring some large structural rearrangement, rapidly sampling the space of docked conformations is now a real possibility, and the limiting step for the successful prediction of protein interactions is the scoring function used to reduce the space of conformations from billions to a few, and eventually one high affinity complex. An atomic level free‐energy scoring function that estimates in units of kcal/mol both electrostatic and desolvation interactions (plus van der Waals if appropriate) of protein–protein docked conformations is used to rerank the blind predictions (860 in total) submitted for six targets to the community‐wide Critical Assessment of PRediction of Interactions (CAPRI; http://capri.ebi.ac.uk). We found that native‐like models often have varying intermolecular contacts and atom clashes, making unlikely that one can construct a universal function that would rank all these models as native‐like. Nevertheless, our scoring function is able to consistently identify the native‐like complexes as those with the lowest free energy for the individual models of 16 (out of 17) human predictors for five of the targets, while at the same time the modelers failed to do so in more than half of the cases. The scoring of high‐quality models developed by a wide variety of methods and force fields confirms that electrostatic and desolvation forces are the dominant interactions determining the bound structure. The CAPRI experiment has shown that modelers can predict valuable models of protein–protein complexes, and improvements in scoring functions should soon solve the docking problem for complexes whose backbones do not change much upon binding. A scoring server and programs are available at http://structure.pitt.edu. Proteins 2006. © 2006 Wiley‐Liss, Inc.
4‐Fluoroproline derivative peptides: effect on PPII conformation and SH3 affinity
Authors: Ruzza Paolo , Siligardi Giuliano , Donella‐Deana Arianna , Calderan Andrea , Hussain Rohanah , Rubini Chiara , Cesaro Luca , Osler Alessio , Guiotto Andrea , Pinna Lorenzo A. , Borin Gianfranco 
Published: February 2006

AbstractEukaryotic signal transduction involves the assembly of transient protein–protein complexes mediated by modular interaction domains. Specific Pro‐rich sequences with the consensus core motif PxxP adopt the PPII helix conformation upon binding to SH3 domains. For short Pro‐rich peptides, little or no ordered secondary structure is usually observed before binding interactions. The association of a Pro‐rich peptide with the SH3 domain involves unfavorable binding entropy due to the loss of rotational freedom on forming the PPII helix. With the aim of stabilizing the PPII helix conformation in the Pro‐rich HPK1 decapeptide PPPLPPKPKF (P2), a series of P2 analogues was prepared, in which specific Pro positions were alternatively occupied by 4(S)‐ or 4(R)‐4‐fluoro‐L‐proline. The interactions of these peptides with the SH3 domain of the HPK1‐binding partner HS1 were quantitatively analyzed by the NILIA‐CD approach. A CD thermal analysis of the P2 analogues was performed to assess their propensity to adopt the PPII helix conformation. Contrary to our expectations, the Kd values of the analogues were lower than that of the parent peptide P2. These results clearly show that the induction of a stable PPII helix conformation in short Pro‐rich peptides is not sufficient to increase their affinity toward the SH3 domain and that the effect of 4‐fluoroproline strongly depends on the position of this residue in the sequence and the chirality of the substituent in the pyrrolidine ring. Copyright © 2006 European Peptide Society and John Wiley & Sons, Ltd.
New peptide conjugates with 9‐aminoacridine: synthesis and binding to DNA
Authors: ŠebestíK Jaroslav , Stibor Ivan , HlavÁček Jan 
Published: February 2006

AbstractNew peptides—9‐aminoacridine conjugates with an ethylene diamine linker—have been synthesized (both solution and solid phase methods were used) and their interactions with DNA have been studied. The affinity of H‐Phe‐Gln‐Gly‐Ile2‐NHCH2CH2NH‐Acr conjugate and of its extended analogue containing 6‐aminohexanoic acid to DNA were lower than that of a standard H‐Gly‐NHCH2CH2NH‐Acr conjugate. The results fit well into our concept of peptide conjugates with lowered binding activity to DNA, which could be capable of unlimited extravascular distribution. Moreover, new structures could be potentially useful as the mild tuners of DNA interaction with strong bis‐acridine binders. Copyright © 2006 European Peptide Society and John Wiley & Sons, Ltd.
Vegetation development and restoration potential of drained reservoirs following dam removal in Wisconsin
Authors: Orr Cailin H. , Stanley Emily H. 
Published: February 2006

AbstractDam removal is potentially a powerful tool for river and riparian restoration. However, long‐term studies on the fate of former reservoirs do not exist, limiting assessment of the utility of dam removal as a means of riparian restoration. We took advantage of the decades‐long legacy of dam removals in Wisconsin to determine human uses of drained reservoirs and to evaluate vegetation establishment and species replacement at these sites. More than half of the 30 dam removal sites in southern Wisconsin over the past 47 years were used as commercial areas, parks and agricultural land, and active riparian restoration occurred on only two sites. For the 13 sites that were allowed to revegetate on their own, plants established in the first growing season and cover was very high at all sites in 2001. Species diversity and frequency (defined as percentage of sampled quadrats where a species is present) of trees were positively correlated with time since removal. No relationship existed between site age and frequencies of other growth forms, nor were there significant relationships between site age and the number or frequency of introduced species. However, mean frequency of introduced species was 75% per site and several sites were dominated by the introduced grass Phalaris arundinacea. Frequency of P. arundinacea was negatively correlated with number of native forbs, and lowest species diversity occurred on sites dominated by P. arundinacea. Ordination analyses revealed substantial site‐to‐site variation in vegetation that was weakly associated with gradients of site location, age, area, and soil phosphorus. Thus, temporal vegetation dynamics following dam removal were site‐specific. Rapid revegetation demonstrates the potential of these sites for riparian restoration. However, if dam removal is used as a means of restoring native riparian communities, then approaches must be tailored to individual sites and will need to focus on techniques to minimize establishment of aggressive invading species. Copyright © 2006 John Wiley & Sons, Ltd.
Public and private codes in living systems theory
Authors: Bailey Kenneth D. 
Published: February 2006

AbstractAn extremely important, but often unheralded, contribution in living systems theory is the explication of internal coding and data transformation within a system, particularly recoding from ‘public’ to ‘private’ information, and vice versa. The importance of such coding and recoding in systems has received increased visibility recently through the development of ‘public key infrastructure’ (PKI) technology for Internet security. The purpose of this paper is to analyze the role of the subsystems of LST in dealing with public and private codes. The relevance of public and private codes for social autopoiesis is also discussed. It is shown that public and private codes play a central role in providing both system security and system identity. Copyright © 2006 John Wiley & Sons, Ltd.
Working at the interface between systems and complexity thinking: insights from a market access design project for poor livestock producers
Authors: Woog Robert , Cavana Robert Y. , Roberts Roger , Packham Roger 
Published: February 2006

AbstractThis paper discusses the insights and reflections that lead to the development of a methodology informed by working at the interface between systems thinking and complexity theory. This arose from three workshops held at the University of Western Sydney to address barriers to market access for poor livestock producers, as part of a project for FAO's Pro‐Poor Livestock Policy Initiative. The first full‐day workshop was based around systems thinking methods using a group model‐building approach. By the end of the workshop the group concluded that the issues were far too complex to be addressed satisfactorily with this approach. Complexity theory was proposed as a suitable way forward. The next two half‐day workshops used complexity thinking methods to come up with a set of attractors and a shared mental model, which provided greater insights into the problem issues. The paper concludes with the reflections gained from the workshop activities Copyright © 2006 John Wiley & Sons, Ltd.
Treating socio‐technical systems as engineering systems: some conceptual problems
Authors: Kroes Peter , Franssen Maarten , Poel Ibo van de , Ottens Maarten 
Published: February 2006

AbstractSystems engineering has been plagued by the problem of how to separate a system from its environment or context, in particular from its social context. We propose to include anything in the system that is necessary for performing its intended function and that may be the object of design. For certain engineering systems, such as civil aviation systems, this implies that human agents and social institutions have to be taken as integral parts of these systems. These ‘socio‐technical’ systems are of a hybrid nature because they are constituted by different kinds of elements, intentional and non‐intentional: social institutions, human agents and technical artefacts. This paper analyses two different roles that human agents, as elements of socio‐technical systems, may play with regard to technical artefacts. Furthermore, it discusses some conceptual problems concerning the modelling of socio‐technical systems that are due to the hybrid nature of these systems. Copyright © 2006 John Wiley & Sons, Ltd.
A theoretical base for high‐level simulation of organizational information systems
Authors: Palmius Joel 
Published: February 2006

AbstractThe design of organizational information systems is a study of the complex. An organizational information system in the Human Activity System sense is the sum total of all that contributes to distributing information within an organization. This includes the human actors participating in the system. Managing information about such a system is a difficult task. Technical support for measuring organizational information systems and comparing different ideas about organizational information systems would thus be useful. A high‐level simulation of information systems could be such a technical support. There are a number of issues making such a simulation infeasible today. These mainly arise from the complexity of the simulation model, and in consequence of the data input problem. However, by introducing isomorphism and object templates, it is possible to solve some of these problems. In order to utilize these approaches, a framework for isomorphic simulations needs to be developed. Copyright © 2006 John Wiley & Sons, Ltd.