bluuebunny/crossref_metadata_2025 huggingface dataset:
Automated application component placement in data centers using mathematical programming
Authors: Zhu Xiaoyun , Santos Cipriano , Beyer Dirk , Ward Julie , Singhal Sharad
Published: August 2008

In this article we address the application component placement (ACP) problem for a data center. The problem is defined as follows: for a given topology of a network consisting of switches, servers and storage devices with varying capabilities, and for a given specification of a component‐based distributed application, decide which physical server should be assigned to each application component, such that the application's processing, communication and storage requirements are satisfied without creating bottlenecks in the infrastructure, and that scarce resources are used most efficiently. We explain how the ACP problem differs from traditional task assignment in distributed systems, or existing grid scheduling problems. We describe our approach of formalizing this problem using a mathematical optimization framework and further formulating it as a mixed integer program (MIP). We then present our ACP solver using GAMS and CPLEX to automate the decision‐making process. The solver was numerically tested on a number of examples, ranging from a 125‐server real data center to a set of hypothetical data centers with increasing size. In all cases the ACP solver found an optimal solution within a reasonably short time. In a numerical simulation comparing our solver to a random selection algorithm, our solver resulted in much more efficient use of scarce network resources and allowed more applications to be placed in the same infrastructure. Copyright © 2008 John Wiley & Sons, Ltd.
A game‐theoretic model for capacity‐constrained fair bandwidth allocation
Authors: Yan Yonghe , El‐Atawy Adel , Al‐Shaer Ehab
Published: August 2008

Data stream providers face a hard decision to satisfy the requirements of their subscribers. Each user has a minimum and a maximum required bandwidth. The server should be able to decide which requests can be satisfied and how much bandwidth will be allocated to each. We present a theoretical framework in a distributed mechanism for fair bandwidth allocation on a network with various bottleneck links. In our model, a user is guaranteed a minimum bandwidth and charged a price for the bandwidth allocated. A utility function is defined over the allocated bandwidth for a specific maximum requested bandwidth. We then present a non‐cooperative game with social welfare function to resolve users' conflicting bandwidth capacity requests at bottleneck links. We also show that our proposed game‐theoretic solution guarantees fair bandwidth allocation as defined in our residual capacity fairness. In order to guarantee the minimum bandwidth requirement, we integrate an admission control mechanism in our solution. However, global optimal admission conditions are not easy to implement for large networks. Therefore, we propose a distributed admission scheme. As a result, the paper presents fair and practical distributed algorithms for bandwidth allocation and admission control in enterprise networks. Our simulation and evaluation study shows that the distributed approach is sufficiently close to the global optimal solution. Copyright © 2008 John Wiley & Sons, Ltd.
Preconditioning iterative algorithm for the electromagnetic scattering from a large cavity
Authors: Wang Yingxi , Du Kui , Sun Weiwei
Published: September 2008

A preconditioning iterative algorithm is proposed for solving electromagnetic scattering from an open cavity embedded in an infinite ground plane. In this iterative algorithm, a physical model with a vertically layered medium is employed as a preconditioner of the model of general media. A fast algorithm developed in (SIAM J. Sci. Comput. 2005; 27:553–574) is applied for solving the model of layered media and classical Krylov subspace methods, restarted GMRES, COCG, and BiCGstab are employed for solving the preconditioned system. Our numerical experiments on cavity models with large numbers of mesh points and large wave numbers show that the algorithm is efficient and the number of iterations is independent of the number of mesh points and dependent upon the wave number. Copyright © 2008 John Wiley & Sons, Ltd.
The British are not coming!: UK higher education and the nonprofit sector
Authors: Palmer Paul , Bogdanova Mariana
Published: September 2008

The rationale for the growth of nonprofit management education in the United States has recently been charted by O'Neill (2005). Ten years previously, the United States and the United Kingdom were at similar levels of development. By 2006 the parallel lines had been broken. Why has nonprofit management education expanded in the United States while provision of graduate education for the voluntary sector in the United Kingdom has stood still? This article explores the factors that have prevented parallel growth in education provision. It argues that the university as an institution, both in terms of its nature and its power structures, is one of those factors. It presents the story of the closing of the world's first voluntary sector course at the London School of Economics and concludes with reflection on the likely future of voluntary sector management education provision in the United Kingdom.
Searching for critical issues in philanthropy
Authors: Til Jon Van
Published: September 2008

Who Really Cares: America's Charity Divide—Who Gives, Who Doesn't, and Why It Matters, by Arthur C. Brooks. New York: Basic Books, 2006. 256 pp., $26.00 cloth, $16.95 paper.

Foundations and Public Policy: The Mask of Pluralism, by Joan Roelofs. Albany: State University of New York Press, 2003. 270 pp., $29.95 paper.

The Foundation: A Great American Secret, by Joel Fleishman. New York: PublicAffairs, 2007. 384 pp., $27.95 cloth.

The Billionaire Who Wasn't: How Chuck Feeney Secretly Made and Gave Away a Fortune, by Conor O'Clery. New York: PublicAffairs, 2007. 352 pp., $26.95 cloth.
From social change organizations to social movements
Authors: Whitman John R.
Published: September 2008

From the Ground Up: Grassroots Organizations Making Social Change, by Carol Chetkovich and Frances Kunreuther. Ithaca, N.Y.: Cornell University Press, 2006. 216 pp., $49.95 cloth.
Recruiting African American smokers into intervention research: Relationships between recruitment strategies and participant characteristics
Authors: Webb Monica S. , Seigers Danielle , Wood Elizabeth A.
Published: September 2008

The purposes of this study were to (a) to describe an 8‐month recruitment campaign to enroll African American smokers (N = 249) into a randomized controlled trial and (b) examine characteristics of participants recruited through proactive (face‐to‐face), reactive (television, radio, or newspaper ads inviting participants), and combination (both reactive and proactive) approaches. Reactive recruitment was most successful (43%), followed by proactive (31%), and combination (26%) recruitment. Compared to proactive recruitment, reactive recruitment was associated with lower nicotine dependence, and greater readiness to quit, processes of change engagement, and acculturation. Combination recruitment was associated with lower nicotine dependence and greater readiness to quit. The differences according to recruitment strategy could be used to tailor recruitment strategies for African American smokers. © 2008 Wiley Periodicals, Inc. Res Nurs Health 32:86–95, 2009
Durable ultra‐hydrophobic surfaces for self‐cleaning applications
Authors: Rios P. F. , Dodiuk H. , Kenig S. , McCarthy S. , Dotan A.
Published: September 2008

Self‐cleaning surfaces have received a great deal of attention, both in research studies and commercial applications. Both transparent and non‐transparent self‐cleaning surfaces are highly desirable as they offer many advantages, and their potential applications are endless. The self‐cleaning mechanism can be seen in nature. The Lotus flower, a symbol of purity in Asian cultures, grows in muddy waters, but it stays clean and untouched by dirt, organisms, and pollutants. The Lotus leaf self‐cleaning surface is hydrophobic and rough, showing a multi‐layer morphology of nanoscaled roughness. While hydrophobicity produces a high contact angle, the surface morphology reduces the adhesion of water drops to the surface, which slides easily across the leaf surface carrying the dirt particles with them. Different ultra‐hydrophobic, non‐transparent, and transparent coatings, for potential self‐cleaning applications, were produced on polycarbonate (PC) substrates, using hydrophobic chemistry and different configurations of roughening micro‐ and nano‐particles. However, in most cases, these coatings present low adhesion and durability. The stability and durability of the ultra‐hydrophobic surfaces is of key importance for potential, commercially viable, self‐cleaning applications thus durability and stability enhancement of such coatings was attempted by different methods, evaluated, and eventually improved using a solvent‐bonding technique. Copyright © 2008 John Wiley & Sons, Ltd.
Preparation of silica/polymer hybrid microspheres and the corresponding hollow polymer microspheres with functional groups
Authors: Liu Guangyu , Li Longyu , Yang Xinlin , Dai Zhao
Published: September 2008

Monodisperse functional silica/polymer core–shell hybrid microspheres were prepared by a two‐stage reaction with silica grafting of 3‐(methacryloxy)propyl trimethoxysiliane (MPS) as core and polymer as shell having various functional groups such as chloromethyl, pyridyl, carboxylic acid, hydroxyl, and ester. MPS‐modified silica core was synthesized by the Stöber method and subsequently grafted with MPS as the first‐stage reaction. The functional polymer shell was then encapsulated over the MPS‐modified silica by distillation precipitation copolymerization of divinylbenzene (DVB) as a crosslinker and comonomers with different functional groups, including chloromethylstyrene (CMSt), vinyl pyridine (VPy), methacrylic acid (MAA), 2‐hydroxyethylmethacrylate (HEMA), ethyl methacrylate (EMA), ethyleneglycol dimethacrylate (EGDMA), and trimethylol propanetrimethacrylate (Trim), in neat acetonitrile with 2,2′‐azobisisobutyronitrile (AIBN) as an initiator. The encapsulation of the functional polymer shell onto the MPS‐modified silica core particles was driven by the capture of oligomer radicals the vinyl groups on the surface of the MPS‐modified silica cores during the second‐stage distillation precipitation copolymerization in the absence of any stabilizer or surfactant. The functionality and the shell thickness of the inorganic/polymer core–shell hybrid particles were controlled by the amount of DVB crosslinker and the functional comonomers during the copolymerization. The corresponding hollow polymer microspheres with various functional groups, including chloromethyl, pyridyl, carboxylic acid, and ester groups were further developed after the selective removal of silica core with hydrofluoric acid. The functional core–shell silica/polymer hybrid microspheres and the corresponding functional hollow polymer microspheres were characterized with transmission electron microscopy (TEM) and Fourier transform infrared spectra (FT‐IR). Copyright © 2008 John Wiley & Sons, Ltd.
Nanoindentation of dry and aged pultruded composites containing fillers and low profile additives
Authors: Ben Daly H. , Hfaied N. , Zidi M. , Guelorget B. , Boukhili R.
Published: August 2008

In this article, the distribution through the thickness of both the matrix's modulus and the interfacial shear strength (IFSS) in dry and aged pultruded polyester/glass fiber composites containing fillers and low profile additives are experimentally evaluated, using the nanoindentation test. The obtained results indicate that for the dry composite, both the matrix's modulus and the IFSS are constant across the thickness of that material. As a consequence of the immersion in distilled water at high temperature (65°C), the IFSS was found to exhibit a parabolic trend through the thickness of the aged specimen, with the lowest value at the external surfaces. Such minimum was reached after a short time of immersion. At the saturation time, the IFSS at all layers of the aged specimen reaches lowest value. This was not the case for the matrix's modulus, since the later was found to be not affected by the amount of the absorbed humidity. Similar results were obtained after immersion in sea water at the same temperature. However, the only difference noted was at the external surface of the aged specimen where additional degradation had taken place in the matrix and at the fiber/matrix interface. This was attributed to the accumulation of a large amount of salt molecules at the external surface of the aged specimen during the exposure process. Additional mechanical tests show that after 120 days immersion in hot water the interlaminar shear strength of the material as measured according to the ASTM standard D2344, is reduced by 35%. POLYM. COMPOS., 2008. © 2008 Society of Plastics Engineers
Inverse determination of elastic constants of composite materials
Authors: Hwang Shun‐Fa , Yeh Cyuan‐Kuan , Chung Sung‐Chin
Published: August 2008

Vibration testing, combined with a numerical method, is a potential alternative approach for determining elastic constants of materials because of its nondestructive characteristic, single test, and producing average properties. To simplify the modeling processes and to find better results, the numerical method of combining finite element analysis and a hybrid genetic algorithm is proposed to inversely determine the elastic constants from the vibration testing data in this work. As verified from the available data of literatures, the repeatability and accuracy of the proposed inverse determination method are confirmed. Four composite specimens with different stacking sequence and thickness are used to determine their elastic constants. As applied to obtain the four or five elastic constants of composite materials, the performance of the proposed method is excellent. To obtain the four elastic constant for thin composite plates, it is better to use unidirectional and thick enough laminates. To determine the five elastic constants for thick composite plates, it is suggested to use unidirectional laminates with the length‐to‐thickness ratio less than or equal to 50. To conquer the effect of measurement error or missing frequencies, it is necessary to carefully exclude these frequencies in the objective function, and reasonable results could be obtained by the proposed method. POLYM. COMPOS., 2009. © 2008 Society of Plastics Engineers
Verschränkte Spiegel. Ein realisierbares Gedankenexperiment
Authors: Schnabel Roman , Müller‐Ebhardt Helge , Rehbein Henning
Published: August 2008

Die Herstellung von verschränkten Quantenobjekten aus Photonen oder Ionen ist bereits Routine. Da die Quantenmechanik der Größe und Schwere solcher Objekte keine prinzipielle Obergrenze setzt, sollten sich auch makroskopische Gegenstände miteinander verschränken lassen. Allerdings stellt das hohe Ansprüche an die Experimentiertechnik, vor allem im Bereich der Laser‐ und Kältetechnik, sowie an die Methoden zur Entkopplung der Objekte von der Umgebung. Die hier vorgestellte Idee nutzt einen Laserstrahl, um zwei massive Spiegel miteinander zu verschränken. Das entsprechende Experiment soll in den nächsten Jahren realisiert werden. Es könnte sogar eine Demonstration des Einstein‐Podolsky‐Rosen‐Paradoxons mit makroskopischen Objekten ermöglichen.
Kurzzeitaufnahmen von Molekülen
Authors: Meckel Moritz , Dörner Reinhard , Staudte André
Published: August 2008

Eine neue Technik ermöglicht es, in einem einzigen Experiment Informationen über das höchste besetzte Molekülorbital sowie den Bindungsabstand eines Moleküls zu gewinnen. Damit sind Physiker der J.W. Goethe‐Universität Frankfurt in Zusammenarbeit mit Kollegen am National Research Council of Canada dem Ziel näher gekommen, in Echtzeit zu beobachten, wie sich sowohl das atomare Gerüst als auch die Elektronenwolke eines Moleküls während einer chemischen Reaktion verändern.
A Comparative Study of Poly(propylene) Surface Oxidation in DC Low‐Pressure Oxygen and Water Vapor Discharges and in Flowing Afterglow of Water Vapor Discharge
Authors: Rybkin Vladimir , Kuvaldina Elena , Grinevich Andrey , Choukourov Andrey , Iwai Hideo , Biederman Hynek
Published: September 2008

The influence of direct current (DC) discharges in oxygen and water vapor and in a flowing afterglow of water vapor discharge onto the surface of poly(propylene) (PP) films was studied. The surface properties of PP were characterized by Fourier transform infrared by attenuated total reflectance (FTIR/ATR), X‐ray photoelectron spectroscopy (XPS), Atomic force microscopy (AFM), and contact angle measurement. The action of oxygen and water vapor plasma was found to be similar in terms of the composition of functional groups formed. Unlike plasma action, the PP surface treatment in water vapor discharge afterglow provided a more uniform composition of oxygen‐containing groups and greater depth of the modified layer. The formation of alcohol, carbonyl, and carboxyl groups has been observed. The treatment of PP films led to the increase in surface‐free energy, the polymer surface becoming more smooth and homogeneous.

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Plasma Synthesis of Coated Metal Nanoparticles with Surface Properties Tailored for Dispersion
Authors: Tavares Jason , Swanson Edward J. , Coulombe Sylvain
Published: September 2008

A method to produce copper nanoparticles coated with an organic plasma polymer layer is presented. The reaction mechanism for plasma polymerization of ethylene glycol is elucidated, and hydroxyl, methanol and ethanol radicals are shown to be present in the RF discharge. UV radiation is shown to have a significant effect on radical formation. Empirical evidence suggests that nanoparticles exhibit enhanced reactivity. Contact angle measurements of coated particles deposited onto copper collection surfaces show hydrophilic or hydrophobic properties when ethylene glycol or ethane, respectively, is used as the precursor gas. Such properties facilitate dispersion into other media by improving the interaction between the solid and liquid phases.

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Dexamethasone did not suppress immune boosting by personalized peptide vaccination for advanced prostate cancer patients
Authors: Naito Masayasu , Itoh Kyogo , Komatsu Nobukazu , Yamashita Yuichi , Shirakusa Takafumi , Yamada Akira , Moriya Fukuko , Ayatuka Hitoshi , Mohamed Elnisr Rashed , Matsuoka Kei , Noguchi Masanori
Published: September 2008

BACKGROUND

To evaluate the immunological responses of personalized peptide vaccination combined with low‐dose glucocorticoids for advanced hormone refractory prostate cancer (HRPC) patients (pts).

METHODS

Eleven pts with advanced HRPC were treated with the vaccination and low‐dose glucocorticoids; 6 pts with 10 mg/day of prednisolone (PDL) followed by 1 mg/day of dexamethasone at the time of progression, 1 pt with PDL, and 4 pts with dexamethasone. Peptide‐specific cellular and humoral responses were employed to monitor pre‐ and post‐ (6th) vaccination samples.

RESULTS

The vaccination combined with glucocorticoids was well tolerated with no severe adverse effects. Increments of IgG responses were observed in 1 of 4 or 8 of 10 pts tested who received PDL or dexamethasone, respectively, increment of cytotoxic T lymphocyte activity was observed in 2 of 4 or 5 of 7 pts tested, respectively. Vaccination with PDL or dexamethasone resulted in a decline of PSA (at least 50%) in 1 of 7 or 6 of 10 pts with significantly longer median TTP in the dexamethasone group, respectively.

CONCLUSION

Vaccination combined with dexamethasone could be recommended for further clinical trials from both immunological and clinical points of view. Prostate © 2008 Wiley‐Liss, Inc.
Long‐Term assessment of prostate cancer progression free survival: Evaluation of pathological parameters, nuclear shape and molecular biomarkers of pathogenesis
Authors: Veltri Robert W. , Isharwal Sumit , Miller M. Craig , Epstein Jonathan I. , Mangold Leslie A. , Humphreys Elizabeth , Partin Alan W.
Published: September 2008

Background

Molecular pathways of proliferation, angiogenesis, neuroendocrine differentiation, apoptosis and alterations in nuclear structure of cancer epithelial cells are important in the pathogenesis of prostate cancer (PCa). Therefore, we evaluated the prognostic value of these parameters in 105 clinically localized PCa tumors with long‐term follow‐up after radical prostatectomy for progression‐free survival (PFS).

Method

Nuclear roundness variance (NRV) was calculated for tumor nuclei using the graphic tracing DynaCELL system. Immunohistochemistry assessed expression of Ki67, PCNA (proliferation), Chromogranin A (neuroendocrine differentiation), CD31 (angiogenesis), BCL2 (apoptosis), and Her‐2/neu (oncogene) in the tumors. Cox proportional hazards regression, Spearman's rank correlation, and Kaplan–Meier plots were employed to analyze the data.

Results

Gleason score, focal vs. non‐focal extra‐prostatic extension, organ confined status, NRV, Her‐2/neu, CD‐31 and Ki67 were univariately significant predictors of PFS. NRV was the most significant prognostic indicator with the highest concordance index (0.7) for PFS. Gleason score, NRV and Her‐2/neu were multivariately significant and yielded a concordance index of 0.77.

Conclusion

Her‐2/neu oncogene and NRV were shown to be significant in the prediction of PFS. The assessment of alterations in nuclear structure using NRV proved to be the most significant factor in the prediction of PFS. Integration of image analysis‐based NRV and molecular biomarkers with pathologic parameters should be considered for validation in the prediction of PFS. Prostate © 2008 Wiley‐Liss, Inc.
Structure‐based design of a T‐cell receptor leads to nearly 100‐fold improvement in binding affinity for pepMHC
Authors: Haidar Jaafar N. , Pierce Brian , Yu Yong , Tong Weiwei , Li Michael , Weng Zhiping
Published: September 2008

T‐cell receptors (TCRs) are proteins that recognize peptides from foreign proteins bound to the major histocompatibility complex (MHC) on the surface of an antigen‐presenting cell. This interaction enables the T cells to initiate a cell‐mediated immune response to terminate cells displaying the foreign peptide on their MHC. Naturally occurring TCRs have high specificity but low affinity toward the peptide‐MHC (pepMHC) complex. This prevents the usage of solubilized TCRs for diagnosis and treatment of viral infections or cancers. Efforts to enhance the binding affinity of several TCRs have been reported in recent years, through randomized libraries and in vitro selection. However, there have been no reported efforts to enhance the affinity via structure‐based design, which allows more control and understanding of the mechanism of improvement. Here, we have applied structure‐based design to a human TCR to improve its pepMHC binding. Our design method evolved based on iterative steps of prediction, testing, and generating more predictions based on the new data. The final design function, named ZAFFI, has a correlation of 0.77 and average error of 0.35 kcal/mol with the binding free energies of 26 point mutations for this system that we measured by surface plasmon resonance (SPR). Applying the filter that we developed to remove nonbinding predictions, this correlation increases to 0.85, and the average error decreases to 0.3 kcal/mol. Using this algorithm, we predicted and tested several point mutations that improved binding, with one giving over sixfold binding improvement. Four of the point mutations that improved binding were then combined to give a mutant TCR that binds the pepMHC 99 times more strongly than the wild‐type TCR. Proteins 2009. © 2008 Wiley‐Liss, Inc.
Zn2+‐linked dimerization of UreG from Helicobacter pylori, a chaperone involved in nickel trafficking and urease activation
Authors: Zambelli Barbara , Turano Paola , Musiani Francesco , Neyroz Paolo , Ciurli Stefano
Published: September 2008

The biosynthesis of the active metal‐bound form of the nickel‐dependent enzyme urease involves the formation of a lysine‐carbamate functional group concomitantly with the delivery of two Ni2+ ions into the precast active site of the apoenzyme and with GTP hydrolysis. In the urease system, this role is performed by UreG, an accessory protein belonging to the group of homologous P‐loop GTPases, often required to complete the biosynthesis of nickel‐enzymes. This study is focused on UreG from Helicobacter pylori (HpUreG), a bacterium responsible for gastric ulcers and cancer, infecting large part of the human population, and for which urease is a fundamental virulence factor. The soluble HpUreG was expressed in E. coli and purified to homogeneity. On‐line size exclusion chromatography and light scattering indicated that apo‐HpUreG exists as a monomer in solution. Circular dichroism, which demonstrated the presence of a well‐defined secondary structure, and NMR spectroscopy, which revealed a large number of residues that appear structured on the basis of their backbone amide proton chemical shift dispersion, indicated that, at variance with other UreG proteins so far characterized, this protein is significantly folded in solution. The amino acid sequence of HpUreG is 29% identical to that of HypB from Methanocaldococcus jannaschii, a dimeric zinc‐binding GTPase involved in the in vivo assembly of [Ni,Fe]‐hydrogenase. A homology‐based molecular model of HpUreG was calculated, which allowed us to identify structural and functional features of the protein. Isothermal titration microcalorimetry demonstrated that HpUreG specifically binds 0.5 equivalents of Zn2+ per monomer (Kd = 0.33 ± 0.03 μM), whereas it has 20‐fold lower affinity for Ni2+ (Kd = 10 ± 1 μM). Zinc ion binding (but not Ni2+ binding) causes protein dimerization, as confirmed using light scattering measurements. The structural rearrangement occurring upon Zn2+‐binding and consequent dimerization was evaluated using circular dichroism and fluorescence spectroscopy. Fully conserved histidine and cysteine residues were identified and their role in zinc binding was verified by site‐directed mutagenesis and microcalorimetry. The results are analyzed and discussed with respect to analogous examples of GTPases in nickel metabolism. Proteins 2009. © 2008 Wiley‐Liss, Inc.
Crystal structure of Ultralente—A microcrystalline insulin suspension
Authors: Wagner Armin , Diez Joachim , Schulze‐Briese Clemens , Schluckebier Gerd
Published: September 2008

Ultralente insulin has been one of the commercially most important insulin preparations in diabetes treatment over the last 50 years. It is a suspension of insulin microcrystals which dissolve slowly following subcutaneous injection. Because of the small crystal size of about 25 × 25 × 5 μm3 the atomic structure has been elusive until now. Here we present the crystal structures from Ultralente and their precursor microcrystals from the industrial manufacturing process. During this process insulin undergoes a conformational change within the microcrystals. Both structures show canonical folding of the insulin molecules but exhibit a number of new features when compared with other insulin structures. Surprisingly, we found that the Ultralente crystals bind the conservation agent methylparaben, which slows down dissolution of the crystals and thus contributes to the long duration of action. Proteins 2009. © 2008 Wiley‐Liss, Inc.
Solution structure of the Pseudomonas putida protein PpPutA45 and its DNA complex
Authors: Halouska Steven , Zhou Yuzhen , Becker Donald F. , Powers Robert
Published: September 2008

Proline utilization A (PutA) is a membrane‐associated multifunctional enzyme that catalyzes the oxidation of proline to glutamate in a two‐step process. In certain, gram‐negative bacteria such as Pseudomonas putida, PutA also acts as an auto repressor in the cytoplasm, when an insufficient concentration of proline is available. Here, the N‐terminal residues 1–45 of PutA from P. putida (PpPutA45) are shown to be responsible for DNA binding and dimerization. The solution structure of PpPutA45 was determined using NMR methods, where the protein is shown to be a symmetrical homodimer (12 kDa) consisting of two ribbon‐helix‐helix (RHH) structures. DNA sequence recognition by PpPutA45 was determined using DNA gel mobility shift assays and NMR chemical shift perturbations (CSPs). PpPutA45 was shown to bind a 14 base‐pair DNA oligomer (5′‐GCGGTTGCACCTTT‐3′). A model of the PpPutA45‐DNA oligomer complex was generated using Haddock 2.1. The antiparallel β‐sheet that results from PpPutA45 dimerization serves as the DNA recognition binding site by inserting into the DNA major groove. The dimeric core of four α‐helices provides a structural scaffold for the β‐sheet from which residues Thr5, Gly7, and Lys9 make sequence‐specific contacts with the DNA. The structural model implies flexibility of Lys9 which can make hydrogen bond contacts with either guanine or thymine. The high sequence and structure conservation of the PutA RHH domain suggest interdomain interactions play an important role in the evolution of the protein. Proteins 2009. © 2008 Wiley‐Liss, Inc.
Identifying polymer‐forming SAM domains
Authors: Meruelo Alejandro D. , Bowie James U.
Published: September 2008

Sterile alpha motif (SAM) domains are common protein modules in eukaryotic cells. It has not been possible to assign functions to uncharacterized SAM domains because they have been found to participate in diverse functions ranging from protein–protein interactions to RNA binding. Here we computationally identify likely members of the subclass of SAM domains that form polymers. Sequences were virtually threaded onto known polymer structures and then evaluated for compatibility with the polymer. We find that known SAM polymers score better than the vast majority of known nonpolymers: 100% (7 of 7) of known polymers and only 8% of known nonpolymers (1 of 12) score above a defined threshold value. Of 2901 SAM family members, we find 694 that score above the threshold and are likely polymers, including SAM domains from the proteins Lethal Malignant Brain Tumor, Bicaudal‐C, Liprin‐β, Adenylate Cyclase, and Atherin. Proteins 2009. © 2008 Wiley‐Liss, Inc.
COCO: A simple tool to enrich the representation of conformational variability in NMR structures
Authors: Laughton Charles A. , Orozco Modesto , Vranken Wim
Published: September 2008

NMR structures are typically deposited in databases such as the PDB in the form of an ensemble of structures. Generally, each of the models in such an ensemble satisfies the experimental data and is equally valid. No unique solution can be calculated because the experimental NMR data is insufficient, in part because it reflects the conformational variability and dynamical behavior of the molecule in solution. Even for relatively rigid molecules, the limited number of structures that are typically deposited cannot completely encompass the structural diversity allowed by the observed NMR data, but they can be chosen to try and maximize its representation. We describe here the adaptation and application of techniques more commonly used to examine large ensembles from molecular dynamics simulations, to the analysis of NMR ensembles. The approach, which is based on principal component analysis, we call COCO (“Complementary Coordinates”). The COCO approach analyses the distribution of an NMR ensemble in conformational space, and generates a new ensemble that fills “gaps” in the distribution. The method is very rapid, and analysis of a 25‐member ensemble and generation of a new 25 member ensemble typically takes 1–2 min on a conventional workstation. Applied to the 545 structures in the RECOORD database, we find that COCO generates new ensembles that are as structurally diverse—both from each other and from the original ensemble—as are the structures within the original ensemble. The COCO approach does not explicitly take into account the NMR restraint data, yet in tests on selected structures from the RECOORD database, the COCO ensembles are frequently good matches to this data, and certainly are structures that can be rapidly refined against the restraints to yield high‐quality, novel solutions. COCO should therefore be a useful aid in NMR structure refinement and in other situations where a richer representation of conformational variability is desired—for example in docking studies. COCO is freely accessible via the website www.ccpb.ac.uk/COCO. Proteins 2009. © 2008 Wiley‐Liss, Inc.
Coevolution in defining the functional specificity
Authors: Chakrabarti Saikat , Panchenko Anna R.
Published: September 2008

Covariation between sites can arise due to a common evolutionary history. At the same time, structure and function of proteins play significant role in evolvability of different sites that are not directly connected with the common ancestry. The nature of forces which cause residues to coevolve is still not thoroughly understood, it is especially not clear how coevolutionary processes are related to functional diversification within protein families. We analyzed both functional and structural factors that might cause covariation of specificity determinants and showed that they more often participate in coevolutionary relationships with each other and other sites compared with functional sites and those sites that are not under strong functional constraints. We also found that protein sites with higher number of coevolutionary connections with other sites have a tendency to evolve slower. Our results indicate that in some cases coevolutionary connections exist between specificity sites that are located far away in space but are under similar functional constraints. Such correlated changes and compensations can be realized through the stepwise coevolutionary processes which in turn can shed light on the mechanisms of functional diversification. Proteins 2009. Published 2008 Wiley‐Liss, Inc.
Solution structures and DNA binding properties of the N‐terminal SAP domains of SUMO E3 ligases from Saccharomyces cerevisiae and Oryza sativa
Authors: Suzuki Rintaro , Shindo Heisaburo , Tase Akira , Kikuchi Yoshiko , Shimizu Mitsuhiro , Yamazaki Toshimasa
Published: September 2008

SUMO E3 ligase of the Siz/PIAS family that promotes sumoylation of target proteins contains SAP motif in its N‐terminal region. The SAP motif with a consensus sequence of 35 residues was first proposed to be as a new DNA binding motif found in diverse nuclear proteins involved in chromosomal organization. We have determined solution structures of the SAP domains of SUMO ligases Siz1 from yeast and rice by NMR spectroscopy, showing that the structure of the SAP domain (residues 2–105) of rice Siz1 is a four‐helix bundle with an up‐down‐extended loop‐down‐up topology, whereas the SAP domain (residues 1–111) of yeast Siz1 is comprised of five helices where the fifth helix α5 causes a significant change in the alignment of the four‐helix bundle characteristic to the SAP domains of the Siz/PIAS family. We have also demonstrated that both SAP domains have binding ability to an A/T‐rich DNA, but that binding affinity of yeast Siz1 SAP is at least by an order of magnitude higher than that of rice Siz1 SAP. Our NMR titration experiments clearly showed that yeast Siz1 SAP uses α2‐helix for DNA binding more effectively than rice Siz1 SAP, which would result from the dislocation of this helix due to the existence of the extra helix α5. In addition, based on the structures of the SAP domains determined here and registered in Protein Data Bank, general features of structures of the SAP domains are discussed in conjunction with equivocal nature of their DNA binding. Proteins 2009. © 2008 Wiley‐Liss, Inc.
Satisfaction of hydrogen‐bonding potential influences the conservation of polar sidechains
Authors: Worth Catherine L. , Blundell Tom L.
Published: September 2008

Although polar amino acids tend to be found on the surface of proteins due to their hydrophilic nature, their important roles within the core of proteins are now becoming better recognized. It has long been understood that a significant number of mainchain functions will not achieve hydrogen bond satisfaction through the formation of secondary structures; in these circumstances, it is generally buried polar residues that provide hydrogen bond satisfaction. Here, we describe an analysis of the hydrogen‐bonding of polar amino acids in a set of structurally aligned protein families. This allows us not only to calculate the conservation of each polar residue but also to assess whether conservation is correlated with the hydrogen‐bonding potential of polar sidechains. We show that those polar sidechains whose hydrogen‐bonding potential is satisfied tend to be more conserved than their unsatisfied or nonhydrogen‐bonded counterparts, particularly when buried. Interestingly, these buried and satisfied polar residues are significantly more conserved than buried hydrophobic residues. Forming hydrogen bonds to mainchain amide atoms also influences conservation, with those satisfied buried polar residues that form two hydrogen bonds to mainchain amides being significantly more conserved than those that form only one or none. These results indicate that buried polar residues whose hydrogen‐bonding potential is satisfied are likely to have important roles in maintaining protein structure. Proteins 2009. © 2008 Wiley‐Liss, Inc.
Consensus scoring for enriching near‐native structures from protein–protein docking decoys
Authors: Liang Shide , Meroueh Samy O. , Wang Guangce , Qiu Chao , Zhou Yaoqi
Published: September 2008

The identification of near native protein–protein complexes among a set of decoys remains highly challenging. A strategy for improving the success rate of near native detection is to enrich near native docking decoys in a small number of top ranked decoys. Recently, we found that a combination of three scoring functions (energy, conservation, and interface propensity) can predict the location of binding interface regions with reasonable accuracy. Here, these three scoring functions are modified and combined into a consensus scoring function called ENDES for enriching near native docking decoys. We found that all individual scores result in enrichment for the majority of 28 targets in ZDOCK2.3 decoy set and the 22 targets in Benchmark 2.0. Among the three scores, the interface propensity score yields the highest enrichment in both sets of protein complexes. When these scores are combined into the ENDES consensus score, a significant increase in enrichment of near‐native structures is found. For example, when 2000 dock decoys are reduced to 200 decoys by ENDES, the fraction of near‐native structures in docking decoys increases by a factor of about six in average. ENDES was implemented into a computer program that is available for download at http://sparks.informatics.iupui.edu. Proteins 2009. © 2008 Wiley‐Liss, Inc.
An all‐atom structure‐based potential for proteins: Bridging minimal models with all‐atom empirical forcefields
Authors: Whitford Paul C. , Noel Jeffrey K. , Gosavi Shachi , Schug Alexander , Sanbonmatsu Kevin Y. , Onuchic José N.
Published: September 2008

Protein dynamics take place on many time and length scales. Coarse‐grained structure‐based$ {\bf (G{\overline o})} $models utilize the funneled energy landscape theory of protein folding to provide an understanding of both long time and long length scale dynamics. All‐atom empirical forcefields with explicit solvent can elucidate our understanding of short time dynamics with high energetic and structural resolution. Thus, structure‐based models with atomic details included can be used to bridge our understanding between these two approaches. We report on the robustness of folding mechanisms in one such all‐atom model. Results for the B domain of Protein A, the SH3 domain of C‐Src Kinase, and Chymotrypsin Inhibitor 2 are reported. The interplay between side chain packing and backbone folding is explored. We also compare this model to a Cαstructure‐based model and an all‐atom empirical forcefield. Key findings include: (1) backbone collapse is accompanied by partial side chain packing in a cooperative transition and residual side chain packing occurs gradually with decreasing temperature, (2) folding mechanisms are robust to variations of the energetic parameters, (3) protein folding free‐energy barriers can be manipulated through parametric modifications, (4) the global folding mechanisms in a Cαmodel and the all‐atom model agree, although differences can be attributed to energetic heterogeneity in the all‐atom model, and (5) proline residues have significant effects on folding mechanisms, independent of isomerization effects. Because this structure‐based model has atomic resolution, this work lays the foundation for future studies to probe the contributions of specific energetic factors on protein folding and function. Proteins 2009. © 2008 Wiley‐Liss, Inc.
Visualizing molecular wavefunctions using Monte Carlo methods
Authors: Alexander S. A. , Coldwell R. L.
Published: September 2008

Using explicitly correlated wavefunctions and variational Monte Carlo we calculate the electron density, the electron density difference, the intracule density, the extracule density, two forms of the kinetic energy density, the Laplacian of the electron density, the Laplacian of the intracule density, and the Laplacian of the extracule density on a dense grid of points for the ground state of the hydrogen molecule at three internuclear distances (0.6, 1.4, 8.0). With these values we construct a contour plot of each function and describe how it can be used to visualize the distribution of electrons in this molecule. We also examine the influence of electron correlation on each expectation value by calculating each function with a Hartree–Fock wavefunction and then comparing these values with our explicitly correlated values. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2009
The role of resonances in building cross sections: The Mittag‐Leffler expansion in a two‐channel scattering
Authors: Shilyaeva Ksenia , Elander Nils , Yarevsky Evgeny
Published: September 2008

The Mittag‐Leffler formalism for identifying resonance contributions to a two‐body scattering cross section is extended here from the one channel case to the two channel case. The reduced partial wave cross sections based on subtracting S‐matrix residues are compared with expressions which can be derived from the Breit‐Wigner approximation. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2009
Developing and assessing a force and motion learning progression
Authors: Alonzo Alicia C. , Steedle Jeffrey T.
Published: September 2008

Learning progressions are ordered descriptions of students' understanding of a given concept. In this paper, we describe the iterative process of developing a force and motion learning progression and associated assessment items. We report on a pair of studies designed to explore the diagnosis of students' learning progression levels. First, we compare the use of ordered multiple‐choice (OMC) and open‐ended (OE) items for assessing students relative to the learning progression. OMC items appear to provide more precise diagnoses of students' learning progression levels and to be more valid, eliciting students' conceptions more similarly to cognitive interviews. Second, we explore evidence bearing on two challenges concerning reliability and validity of level diagnoses: the consistency with which students respond to items set in different contexts and the ways in which students interpret and use language in responding to items. As predicted, students do not respond consistently to similar problems set in different contexts. Although the language used in OMC items generally seems to reflect student thinking, misinterpretation of the language in items may lead to inaccurate diagnoses for a subset of students. Both issues are less problematic for classroom applications than for use of learning progressions in large‐scale testing. © 2008 Wiley Periodicals, Inc. Sci Ed 93: 389–421, 2009
Adsorption of water on JSC‐1A (simulated moon dust samples)—a surface science study
Authors: Goering J. , Sah Shweta , Burghaus U. , Street K. W.
Published: September 2008

JSC‐1a (a simulated lunar dust sample) supported on a silica wafer (SiO2/Si(111)) has been characterized by scanning electron microscopy (SEM), energy dispersive x‐ray (EDX) spectroscopy, and Auger electron spectroscopy (AES). The adsorption kinetics of water has been studied primarily by thermal desorption spectroscopy (TDS) and in addition by collecting isothermal adsorption transients. Blind experiments on the silica support have been performed as well. JSC‐1a consists mostly of aluminosilicate glass and other minerals containing Fe, Na, Ca, and Mg, as characterized in detail in prior studies, for example, at NASA. The particle sizes span the range from a few micrometers up to 100 µm. At small exposures, H2O TDS is characterized by broad (100–450) K structures; at large exposures, distinct TDS peaks emerge, which are assigned to amorphous solid water (ASW) (145 K) and crystalline ice (CI) (165 K). Water dissociates on JSC‐1a at small exposures but not on the bare silica support. Coadsorption TDS data (alkane–water mixtures) indicate that rather porous condensed ice layers form at large exposures, with the mineral particles acting most likely as nucleation sites. At thermal impact energies, the initial adsorption probability amounts to 0.92 ± 0.05. It is evident that the drop‐and‐dry technique, developed in studies about nanoparticles/tubes, can be extended to obtain samples for surface science studies based on powders consisting of particles with rather large diameters. Copyright © 2008 John Wiley & Sons, Ltd.
Tragverhalten von Stahlgussbauteilen in Offshore‐Windenergie‐Anlagen unter vorwiegend ruhender und nicht ruhender Beanspruchung
Authors: Lüddecke Falk , Rücker Werner , Seidel Marc , Assheuer Jens
Published: September 2008

Für die Installation von Offshore‐Windenergie‐Anlagen der 5‐Megawattklasse vor der Küste Deutschlands in der Nordsee ist es erforderlich, Gründungsstrukturen in hoher Stückzahl wirtschaftlich herstellen zu können. Für den Wassertiefenbereich der Nordsee wird im Rahmen dieses Aufsatzes der Konstruktions‐typ Jacket hinsichtlich dynamischer Eigenschaften untersucht.

Darüber hinaus wird über Stahlgussbauteile berichtet, die in den hochbelasteten Knotenpunkten des Jackets verbaut werden. Derzeit ist es üblich, Jackets aus handelsüblichen Stahlhohlprofilen zu fertigen, die an den Enden zu einer Knotenverbindung miteinander verschweißt werden. Diese Lösung besitzt jedoch eine Vielzahl von Nachteilen, über die nachfolgend berichtet wird.

Bauteile aus Stahlguss hingegen weisen unter anderem die Vorteile auf, universell einsetzbar und in Form bzw. Gestaltung völlig frei wählbar zu sein. Um das komplexe Tragverhalten dieser Stahlgussbauteile bewerten zu können, wurden neben Simulationsrechnungen auch Laborversuche durchgeführt. Es wurde das Tragverhalten unter statischer Belastung am Stahlgussbauteil im 1:1‐Modell und das Ermüdungsverhalten an Stahlgussproben getestet.
Die Ingenieurbauwerke für die Verkehrserschließung der Neuen Landesmesse in Stuttgart
Authors: Angelmaier Volkhard , Andelfinger Joachim , Herrmann Jörg , Sandner Dieter
Published: September 2008

Das weithin sichtbare Parkhaus gilt mittlerweile als Erkennungszeichen der Neuen Landesmesse Stuttgart und bietet mit einer Gesamtfläche von 125000 m2 4100 Fahrzeugen eine Parkmöglichkeit. Das wesentliche Prinzip der Stahl‐Verbundkonstruktion besteht in einem weitgehend lager‐ und fugenlosen Bauwerk. Die fachwerkartigen Hauptträger mit Spannweiten von knapp 100 m sind dabei in ein räumliches Gesamtsystem ähnlich dem Chassis‐Prinzip im Fahrzeugbau integriert und annähernd biegesteif mit den Hauptstützen verbunden. Dieser Grundgedanke der semi‐integralen Bauweise war für die Stahlverbundbrücken der Messe‐erschließung ebenfalls entwurfsbestimmend. Wiederkehrende Gestaltungselemente vermitteln einen in sich geschlossenen Gesamteindruck der Ingenieurbauwerke für die Verkehrserschließung der neuen Landesmesse.