bluuebunny/crossref_metadata_2025_split huggingface dataset:
Clinical characteristics and outcome of children with Burkitt lymphoma in Uganda according to HIV infection
Authors: Orem Jackson , Maganda Albert , Mbidde Edward Katongole , Weiderpass Elisabete 
Published: September 2008

AbstractBackgroundCharacteristics of children with Burkitt lymphoma (BL) and HIV infection have not been described in Uganda before.ProcedureWe reviewed records at Uganda Cancer Institute (UCI) for years 1994–2004, to compare clinical features and outcome of BL in children who are HIV positive and negative (HIV+, HIV−). As statistical methods we used Student's t‐test, Chi‐square and Kaplan–Meier's to compare both groups.ResultsOf 1,462 records of children retrieved, 228 met the eligibility criteria and were reviewed (158 HIV−, 70 HIV+). There were 139 (61%) males and 89 (39%) females. The mean age was 6.9 years (HIV+ 6.7, HIV− 7.1). One hundred seventy‐one cases (75%) had facial tumor (HIV+ 71.4%, HIV− 76.6%). HIV positive children presented significantly with extrafacial disease (lymphadenopathy 67%, hepatic masses 51%, and thoracic masses 10%). Presentation with advanced stage disease occurred more frequently in HIV positive patients compared to HIV negative patients. Treatment response rates to chemotherapy were similar irrespective of HIV status. However, overall survival was poorer in HIV positive patients with a median survival of 11.79 months (P‐value < 0.000, 95% CI 8.65–14.92).ConclusionsBL in Uganda presents frequently with facial disease irrespective of HIV status. However HIV+ BL also presents commonly with extra facial sites, mainly lymphadenopathy. There is no difference in response to treatment with chemotherapy, but HIV+ BL patients have poorer survival. There is need for further characterization of BL in Uganda to understand the role of HIV in disease process and outcome. Pediatr. Blood Cancer © 2008 Wiley‐Liss, Inc.
Prevalence of and risk factors for prostatitis in African American men: The Flint Men's Health Study
Authors: Wallner Lauren P. , Clemens J. Quentin , Sarma Aruna V. 
Published: September 2008

AbstractINTRODUCTIONProstatitis is a common, yet ill‐defined condition without clear diagnostic criteria and treatment strategies. Previous studies examining the prevalence and correlates of prostatitis are limited in their inclusion of primarily white populations. The objective of the current study was to identify prevalence of and risk factors for prostatitis in a population‐based sample of African‐American men.METHODSIn 1996, a probability sample of 703 African‐American men, aged 40–79, residing in Genesee County, Michigan without a prior history of prostate cancer/surgery provided responses to a structured interview‐administered questionnaire which elicited information regarding sociodemographics, current stress and health ratings, and past medical history, including history of physician diagnosed prostatitis, BPH and sexually transmitted diseases. Logistic regression was used to identify predictors of prostatitis after adjustment for age.RESULTSForty‐seven (6.7%) of the 703 men reported a history of prostatitis. Increased frequency of sexual activity and physical activity were significantly associated with decreased odds of disease. Moderate to severe lower urinary tract symptoms (LUTS) and a history of BPH were significantly associated with prostatitis after adjustment for age.CONCLUSIONAfter adjustment for age, LUTS severity and history of BPH were associated with increased odds of prostatitis. BMI, physical activity and sexual frequency were associated with decreased odds of prostatitis. Finally, poor emotional and physical health, high perceived stress and low social support were associated with an increased risk of prostatitis history. Importantly, these findings suggest that the primary risk factors for this condition are largely modifiable and highlight potential targets for future prevention. Prostate 69: 24–32, 2009. © 2008 Wiley–Liss, Inc.
Selected‐fit versus induced‐fit protein binding: Kinetic differences and mutational analysis
Authors: Weikl Thomas R. , von Deuster Carola 
Published: September 2008

AbstractThe binding of a ligand molecule to a protein is often accompanied by conformational changes of the protein. A central question is whether the ligand induces the conformational change (induced‐fit), or rather selects and stabilizes a complementary conformation from a pre‐existing equilibrium of ground and excited states of the protein (selected‐fit). We consider here the binding kinetics in a simple four‐state model of ligand–protein binding. In this model, the protein has two conformations, which can both bind the ligand. The first conformation is the ground state of the protein when the ligand is off, and the second conformation is the ground state when the ligand is bound. The induced‐fit mechanism corresponds to ligand binding in the unbound ground state, and the selected‐fit mechanism to ligand binding in the excited state. We find a simple, characteristic difference between the on‐ and off‐rates in the two mechanisms if the conformational relaxation into the ground states is fast. In the case of selected‐fit binding, the on‐rate depends on the conformational equilibrium constant, whereas the off‐rate is independent. In the case of induced‐fit binding, in contrast, the off‐rate depends on the conformational equilibrium, while the on‐rate is independent. Whether a protein binds a ligand via selected‐fit or induced‐fit thus may be revealed by mutations far from the protein's binding pocket, or other “perturbations” that only affect the conformational equilibrium. In the case of selected‐fit, such mutations will only change the on‐rate, and in the case of induced‐fit, only the off‐rate. Proteins 2009. © 2008 Wiley‐Liss, Inc.
Molecular basis for dimer formation of TRβ variant D355R
Authors: Jouravel Natalia , Sablin Elena , Togashi Marie , Baxter John D. , Webb Paul , Fletterick Robert J. 
Published: September 2008

AbstractProtein quality and stability are critical during protein purification for X‐ray crystallography. A target protein that is easy to manipulate and crystallize becomes a valuable product useful for high‐throughput crystallography for drug design and discovery. In this work, a single surface mutation, D355R, was shown to be crucial for converting the modestly stable monomeric ligand binding domain of the human thyroid hormone receptor (TR LBD) into a stable dimer. The structure of D335R TR LBD mutant was solved using X‐ray crystallography and refined to 2.2 Å resolution with Rfree/R values of 24.5/21.7. The crystal asymmetric unit reveals the TR dimer with two molecules of the hormone‐bound LBD related by twofold symmetry. The ionic interface between the two LBDs comprises residues within loop H10‐H11 and loop H6‐H7 as well as the C‐terminal halves of helices 8 of both protomers. Direct intermolecular contacts formed between the introduced residue Arg 355 of one TR molecule and Glu 324 of the second molecule become a part of the extended dimerization interface of 1330 Å2 characteristic for a strong complex assembly that is additionally strengthened by buffer solutes. Proteins 2009. © 2008 Wiley‐Liss, Inc.
Structural characterization of the α‐hemolysin monomer from Staphylococcus aureus
Authors: Meesters Christian , Brack Antje , Hellmann Nadja , Decker Heinz 
Published: September 2008

Abstractα‐Hemolysin from Staphylococcus aureus is secreted as a water‐soluble monomer and assembles on membranes to oligomerize into a homo‐heptameric, water‐filled pore. These pores lead to lysis and cell death. Although the structure of the heptameric pore is solved by means of X‐ray crystallography, structures of intermediate states—from the soluble monomer to all potential “pre‐pore” structures—are yet unknown. Here, we propose a model of the monomeric α‐hemolysin in solution based on molecular modeling, verified by small angle X‐ray scattering data. This structure reveals details of the monomeric conformation of the α‐hemolysin, for example inherent flexibility, along with definite differences in comparison to the structures used as templates. Proteins 2009. © 2008 Wiley‐Liss, Inc.
Substrate induced structural and dynamics changes in human phosphomevalonate kinase and implications for mechanism
Authors: Olson Andrew L. , Yao Huili , Herdendorf Timothy J. , Miziorko Henry M. , Hannongbua Supa , Saparpakorn Patchareenart , Cai Sheng , Sem Daniel S. 
Published: September 2008

AbstractPhosphomevalonate kinase (PMK) catalyzes an essential step in the mevalonate pathway, which is the only pathway for synthesis of isoprenoids and steroids in humans. PMK catalyzes transfer of the γ‐phosphate of ATP to mevalonate 5‐phosphate (M5P) to form mevalonate 5‐diphosphate. Bringing these phosphate groups in proximity to react is especially challenging, given the high negative charge density on the four phosphate groups in the active site. As such, conformational and dynamics changes needed to form the Michaelis complex are of mechanistic interest. Herein, we report the characterization of substrate induced changes (Mg‐ADP, M5P, and the ternary complex) in PMK using NMR‐based dynamics and chemical shift perturbation measurements. Mg‐ADP and M5P Kd's were 6–60 μM in all complexes, consistent with there being little binding synergy. Binding of M5P causes the PMK structure to compress (τc = 13.5 nsec), whereas subsequent binding of Mg‐ADP opens the structure up (τc = 15.6 nsec). The overall complex seems to stay very rigid on the psec‐nsec timescale with an average NMR order parameter of S2 ∼0.88. Data are consistent with addition of M5P causing movement around a hinge region to permit domain closure, which would bring the M5P domain close to ATP to permit catalysis. Dynamics data identify potential hinge residues as H55 and R93, based on their low order parameters and their location in extended regions that connect the M5P and ATP domains in the PMK homology model. Likewise, D163 may be a hinge residue for the lid region that is homologous to the adenylate kinase lid, covering the “Walker‐A” catalytic loop. Binding of ATP or ADP appears to cause similar conformational changes; however, these observations do not indicate an obvious role for γ‐phosphate binding interactions. Indeed, the role of γ‐phosphate interactions may be more subtle than suggested by ATP/ADP comparisons, because the conservative O to NH substitution in the β‐γ bridge of ATP causes a dramatic decrease in affinity and induces few chemical shift perturbations. In terms of positioning of catalytic residues, binding of M5P induces a rigidification of Gly21 (adjacent to the catalytically important Lys22), although exchange broadening in the ternary complex suggests some motion on a slower timescale does still occur. Finally, the first nine residues of the N‐terminus are highly disordered, suggesting that they may be part of a cleavable signal or regulatory peptide sequence. Proteins 2009. © 2008 Wiley‐Liss, Inc.
Systematic classification of CDR‐L3 in antibodies: Implications of the light chain subtypes and the VL–VH interface
Authors: Kuroda Daisuke , Shirai Hiroki , Kobori Masato , Nakamura Haruki 
Published: September 2008

AbstractAntibody modeling is widely used for the analysis of antibody–antigen interactions and for the design of potent antibody drugs. The antibody combining site is composed of six complementarity determining regions (CDRs). The CDRs, except for CDR‐H3, which is the most diverse CDR, form limited numbers of canonical structures, which can be identified from the amino acid sequences. A method to classify the CDR‐H3 structure from its amino acid sequence was previously proposed. However, since those CDR structures were classified, many more antibody crystal structures have been determined. We performed systematic analyses of the CDR‐L3 structures and found novel canonical structures, and we also classified a previously identified canonical structure into two subtypes. In addition, two differently defined canonical structures in the κ and λ subtypes were classified into the same canonical structure. We also identified a key residue in CDR‐L3, which determines the conformation of CDR‐H3. Several analyses of CDR‐L3 loops longer than nine residues were performed. These new findings should be useful for structural modeling and are eventually expected to accelerate the design of antibody drugs. Proteins 2009. © 2008 Wiley‐Liss, Inc.
Modelling MOSFET gate length variability for future technology nodes
Authors: Patsis G. P. 
Published: September 2008

AbstractGate length variability due to intra or inter die variations can lead to considerable mismatch between devices even inside the same chip. This variability has to be considered in detail and new device models should be developed, aiming in modelling its effects on the electrical characteristics devices. In this work the Philips MM11 MOSFET model is extended to incorporate gate length variability. This is introduced by dividing the device width into sub‐units following a Gaussian gate length distribution, with appropriate line‐width roughness. The combined model is used to quantify the drain‐source current in terms of gate line‐width roughness. The model is coded in VHDL‐AMS in order to be used for simulation of circuit behaviour inside the framework of appropriate system simulation software such as Ansfoft's Simplorer. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
TEM investigations of (In,Ga)N/GaN quantum structures
Authors: Manolaki P. , Häusler I. , Kirmse H. , Neumann W. , Smałc‐Koziorowska J. , Skierbiszewski C. 
Published: September 2008

AbstractThe paper reports on the influence of the growth temperature on the structural and chemical properties of (In,Ga)N quantum wells (QWs) on GaN. Two different samples A and B were fabricated. The QWs of the sample A were grown at a constant temperature of 600 °C. For the QWs of the sample B the temperature was 530 °C, while for the GaN barrier it was raised to 600 °C. The chemical and structural properties were studied by electron diffraction contrast imaging using the 0001 and 0002 reflection, respectively. Sample A exhibits homogeneous (In,Ga)N QWs. For sample B some undulated strain contrast of the QWs is visible hinting to the formation of quantum dots (QDs). The self‐organisation of (In,Ga)N QDs in sample B is also evidenced by composition sensitive STEM‐HAADF imaging, where the individual (In,Ga)N layers exhibit inhomogeneous intensity as well as varied thickness. Moreover, energy dispersive X‐ray spectroscopy yielded enrichment of indium at QD sites. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Growth of III‐nitride quantum dots and their applications to blue‐green LEDs
Authors: Moustakas T. D. , Xu Tao , Thomidis C. , Nikiforov A. Yu , Zhou Lin , Smith David J. 
Published: September 2008

AbstractIn this paper we discuss the growth of InN, GaN and InGaN QDs by MBE on either GaN or AlN templates. InN QDs on GaN templates were found to occur without an InN wetting layer, a result consistent with the large lattice mismatch of 11% between InN and GaN. Self‐assembled GaN QDs were grown on AlN templates, using the modified Stranski‐Krastanov mode of growth. The microstructure and the size distribution of such QDs in a single layer or a superlattice structure were investigated by electron microscopy and atomic force microscopy. Finally, the self assembly of InGaN QDs on GaN templates using the Stranski‐Krastanov mode and the applications of such QDs to blue‐green LEDs are addressed. The results indicate that InGaN / GaN multiple quantum dots (MQDs) are highly strained and their emission at low injection is red shifted with respect to that of a single layer of QDs due to quantum confined Stark effect. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Connection between a few Jeziorski‐Monkhorst ansatz‐based methods
Authors: Kong Liguo 
Published: September 2008

AbstractDifferent Jeziorski‐Monkhorst ansatz‐based methods are unified according to how to group terms to eliminate the redundancy problem. It is found that some seemingly different methods used to do MRCC are equivalent. It is argued that the various defining equations are not entirely proper, in the sense that the proper residual condition is not satisfied. This may partially rationalize the unsatisfactory performance of the various methods for single reference systems. In contrast, the MRexpT method satisfies the proper residual condition and it is expected that it will outperform other JM ansatz‐based methods in single‐reference cases. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2009
Complexity analysis of ionization processes and isoelectronic series
Authors: Antolín J. , Angulo J. C. 
Published: September 2008

AbstractInformation‐theoretic magnitudes measuring randomness (Shannon entropy, exponential entropy, power entropy), spread (variance), localization (disequilibrium or self‐similarity) and intrinsic accuracy (Fisher information) are used to compute several measures of complexity consisting, each one, of two localization–delocalization factors. These proposals have been tested on known, simple, but strongly organized and hierarchical systems (atoms) and processes (ionization). A complete numerical analysis at the Hartree–Fock level is done in position, momentum, and product spaces, where similar trends are followed by all studied complexities. It is also found that the complexity planes clearly reveal shell‐filling patterns across the periodic table. Characteristic features accompanying the ionization process are identified, and the physical reasons for the observed patterns are described. We conclude that (i) the studied complexity measures detect not only randomness or localization, but also pattern and organization, and (ii) their study is not only sufficient in the usual position space, but also in the complementary momentum space, to have a complete description of the information–theoretic behavior of these systems. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2009
Stability, spectroscopic constants, and dissociation of CO2+: A theoretical study
Authors: Mondal Bhaskar , Bera Narayan C. , Das Abhijit K. 
Published: September 2008

AbstractStability, spectroscopic constants, and dissociation of CO2+ have been studied in detail using ab initio MP2, CCSD and CCSD(T) methods, and density functional B3LYP method. The stability and the ambiguity between the ground and metastable state of the molecular dication have been discussed. The spectroscopic constants of the molecular dication have been compared with the experimental and theoretical values wherever available. Various charge symmetric and charge asymmetric dissociation pathways of CO2+ have been investigated. After dissociation, the fragmented atoms and ions are considered to be either in their ground or in their metastable state. Interesting results have been obtained for the charge symmetric and charge asymmetric dissociation of the diatomic dication. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2009
Chiral discrimination in hydrogen‐bonded complexes of 2‐methylol oxirane with hydrogen peroxide
Authors: Zhang Guiqiu , Yin Aixia , Chen Dezhan 
Published: September 2008

AbstractA systematic quantum chemical study reveals the effects of chirality on the intermolecular interactions between two chiral molecules bound by hydrogen bonds. The methods used are second‐order Møller–Plesset perturbation theory (MP2) with the 6‐311++g(d,p) basis set. Complexes via the OH···O hydrogen bond formed between the chiral 2‐methylol oxirane (S) and chiral HOOH (P and M) molecules have been investigated, which lead to four diastereomeric complexes. The nomenclature of the complexes used in this article is enantiomeric configuration sign corresponding to English letters. Such as: sm, sp. The relative positions of the methylol group and the hydrogen peroxide are designated as syn (same side) and anti (opposite side). The largest chirodiastaltic energy was ΔEchir = −1.329 kcal mol−1 [9% of the counterpoise correct average binding energy De(corr)] between the sm‐syn and sp‐anti in favor of sm‐syn. The largest diastereofacial energy was −1.428 kcal mol−1 between sm‐syn and sm‐anti in favor of sm‐syn. To take into account solvents effect, the polarizable continuum model (PCM) method has been used to evaluate the chirodiastaltic energies, and diastereofacial energies of the 2‐methylol oxirane···HOOH complexes. The chiral 2,3‐dimethylol oxirane (S, S) is C2 symmetry which offers two identical faces. Hence, the chirodiastaltic energy is identical to the diastereomeric energy, and is ΔEchir = 0.563 kcal mol−1 or 5.3% of the De(corr) in favor of s,s‐p. The optimized structures, interaction energies, and chirodiastaltic energies for various isomers were estimated. The harmonic frequencies, IR intensities, rotational constants, and dipole moments were also reported. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2009
The communication of meaning in social systems
Authors: Leydesdorff Loet , Franse Sander 
Published: September 2008

AbstractThe sociological domain is different from the psychological one insofar as meaning can be communicated at the supra‐individual level. The computation of anticipatory systems enables us to distinguish between these domains in terms of weakly and strongly anticipatory systems with a structural coupling between them. Anticipatory systems have been defined as systems which entertain models of themselves. The model provides meaning to the modelled system from the perspective of hindsight, that is, by advancing along the time axis towards possible future states. Strongly anticipatory systems construct their own future states. The dynamics of weak and strong anticipations can be simulated as incursion and hyper‐incursion, respectively. Hyper‐incursion generates ‘horizons of meaning’ among which choices have to be made by incursive agency. Copyright © 2008 John Wiley & Sons, Ltd.
Modern management of renal cancer
Authors: Swallow Tom , Anderson Chris 
Published: September 2008

AbstractAlthough the prognosis for patients with metastatic kidney cancer is poor, those presenting with localised disease are potentially curable with nephrectomy alone. The authors explain how newer, targeted therapeutic agents show promise of extending survival, and outline recent advances in surgical options and the development of more precise prognostic indicators of disease progression and survival. Copyright © 2008 Wiley Interface Ltd
Modern management of postmenopausal bleeding
Authors: Munot Sarika , Lane Geoffrey 
Published: September 2008

AbstractPostmenopausal bleeding is any unscheduled vaginal bleeding that occurs after 12 months of amenorrhoea in a woman of postmenopausal age. Although a benign cause is likely, bleeding is the most common presenting symptom of endometrial cancer and should always be regarded with suspicion and investigated promptly. Copyright © 2008 Wiley Interface Ltd
Routing with hexagonal virtual coordinates in wireless sensor networks
Authors: Sheu Jang‐Ping , Hsieh Kun‐Ying , Ding Ming‐Lung 
Published: September 2008

AbstractUsing geographic routing, like GPSR, is efficient for ad hoc and wireless sensor networks, but it requires that nodes be aware of their physical positions. However, if there are holes in the network, routing across them using GPSR will lead to a lot of overloaded nodes on their boundaries. In this paper, we propose a distributed protocol, named hexagonal virtual coordinate (HVC), for constructing a virtual coordinate system. After the HVC is constructed, the nodes in the network will be aware of the relative coordinates among the landmarks through the HVC chart. Based on the HVC chart, a source node can find an auxiliary routing path (ARP) to indicate the direction of the journey from the source to the destination. Simulation results show that our protocol can support geographic routing efficiently, and the landmarks found by our protocol are uniformly located in the network even if some holes exist within it. In addition, our protocol is resilient to various network shapes and can find a load balancing routing path to the destination even if this path comes across holes in the network. Copyright © 2008 John Wiley & Sons, Ltd.