bluuebunny/crossref_metadata_2025 huggingface dataset:
Self‐Assembly in Water of Poly(acrylic acid)‐Based Diblock Copolymers Synthesized by Nitroxide‐Mediated Polymerization
Authors: Laruelle Gaël , François Jeanne , Billon Laurent
Published: November 2004

Summary: Amphiphilic diblock copolymers consisting of a hydrophilic block, poly(acrylic acid), and a hydrophobic block, polystyrene, were synthesized by direct nitroxide‐mediated polymerization using the PS block as a macro‐initiator for the first time. Several techniques were used to characterize the amphiphilic block copolymers (size exclusion chromatography, NMR spectroscopy). The proposed method can lead to samples with a broad range of composition and molar mass. Preliminary studies of their self‐assembly in aqueous medium using fluorescence spectroscopy and small‐angle neutron scattering are presented.

Schematic of the formation of the PS‐b‐PAA block copolymers and their micellization in aqueous media.

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Schematic of the formation of the PS‐b‐PAA block copolymers and their micellization in aqueous media.
Effect of Titanium on Fluxional Behavior of Unbridged Metallocene Catalysts
Authors: Polo Eleonora , Losio Simona , Zecchi Gaetano , Bertini Fabio , Sacchi Maria Carmela
Published: November 2004

Summary: Thanks to the use of a ligand consisting of a saturated ring fused to the cyclopentadienyl moiety, which sensibly increases the stability of titanocenes, it was possible to investigate the oscillating behavior of titanium catalysts in propylene polymerization for the first time. The titanium‐based catalysts yield poly(propylene)s with new and interesting microstructures. Indeed, in spite of the significantly lower isotactic pentad content [mmmm], the average lengths of the isotactic blocks (Niso) are similar or even higher than that obtained with the zirconium‐based homologues. Accordingly, differential scanning calorimetry (DSC) analysis shows melting peaks which are more evident than those obtained with the zirconium homologues. The study of the microstructure of the poly(propylene)s obtained with these catalysts allowed us to participate in the still open discussion on the oscillating mechanism of unbridged metallocenes.

The titanium‐based catalysts employed in this study.

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The titanium‐based catalysts employed in this study.
Polymer Nanocomposites Using Urchin‐Shaped Carbon Nanotube‐Silica Hybrids as Reinforcing Fillers
Authors: Zhang Wei‐De , Phang In Yee , Shen Lu , Chow Shue Yin , Liu Tianxi
Published: November 2004

Summary: Carbon nanotubes (CNTs) have been grown on MCM‐41 supported Fe nanoparticles and the as‐prepared (no further purification) CNT‐silica hybrid was directly incorporated into nylon‐6 (PA6) by simple melt‐compounding. The urchin‐shaped CNT‐silica hybrid filler was observed to be homogeneously dispersed throughout the matrix by scanning electron and transmission electron microscopy. Compared with neat PA6, the tensile modulus and strength of the composite are greatly improved by about 110%, with incorporation of only 1 wt.‐% CNT‐silica filler.

SEM image and schematic representation showing polymer chains wrapping around the urchin‐shaped CNT‐silica hybrid filler.

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SEM image and schematic representation showing polymer chains wrapping around the urchin‐shaped CNT‐silica hybrid filler.
Poly(pyrazinoquinoxaline)s: New n‐Type Conjugated Polymers That Exhibit Highly Reversible Reduction and High Electron Affinity
Authors: Zhu Yan , Yen Cheng‐Tyng , Jenekhe Samson A. , Chen Wen‐Chang
Published: November 2004

Summary: The pyrazinoquinoxaline‐based conjugated polymers poly(2,7‐diphenylpyrazino(2,3‐g)quinoxaline‐3,8‐diyl‐1,4‐phenylene) (PZQP) and poly(2,7‐diphenylpyrazino(2,3‐g)quinoxaline‐3,8‐diyl‐2,5‐thiophene) (PZQT) have been synthesized and characterized. PZQP and PZQT have optical band gaps of 2.44 and 1.76 eV, respectively. Both polymers showed highly reversible electrochemical reduction, with an electron affinity of 3.6 eV for PZQP and 3.8 eV for PZQT. The electronic structures of PZQP, PZQT, and related poly(pyrazinoquinoxaline)s, were calculated by density functional theory and compared with the experimental results.

Molecular structure and reduction cyclic voltammogram of PZQP.

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Molecular structure and reduction cyclic voltammogram of PZQP.
Cyclic nucleotide phosphodiesterases and their role in immunomodulatory responses: Advances in the development of specific phosphodiesterase inhibitors
Authors: Castro Ana , Jerez Maria Jose , Gil Carmen , Martinez Ana
Published: November 2004

The activity of phosphodiesterases (PDEs) is associated with a wide variety of diseases and an intense effort toward the development of specific PDEs inhibitors has been generated for the last years. They are the enzymes responsible for the hydrolysis of intracellular cyclic adenosine and guanosine monophosphate, and their complexity, as well as their different functional role, makes these enzymes a very attractive therapeutic target. This review is focused on the role of PDEs played on immunomodulatory processes and the advance on the development of specific inhibitors, covering PDEs mainly related to the regulation of autoimmune processes, PDE4 and PDE7. The review also highlights the novel structural classes of PDE4 and PDE7 inhibitors, and the therapeutic potential that combined PDE4/PDE7 inhibitors offer as immunomodulatory agents. © 2004 Wiley Periodicals, Inc. Med Res Rev
Asymptotic properties of the steady fall of a body in viscous fluids
Authors: Nečasová Š.
Published: November 2004

The paper deals with the properties of the steady fall of a body in linear fluids (Oseen and Stokes cases) and in nonlinear fluids (Navier–Stokes fluids) in Lq structure. Copyright © 2004 John Wiley & Sons, Ltd.
Mucoepidermoid carcinoma of the parotid gland in a child previously treated for acute lymphoblastic leukemia
Authors: Boccon‐Gibod Liliane , Boman Françoise , Josset Patrice , Landman‐Parker Judith
Published: November 2004

Occurrence of second cancers is a major concern for the care of children cured of cancer. Children treated for acute lymphoblastic leukemia (ALL) have an increased risk for developing mucoepidermoid carcinomas (MEC) of the parotid gland. The latent period ranges from 5 to 16 years. A 3‐year‐old boy presented with pre‐B ALL. Treatment included multidrug chemotherapy and prophylactic intrathecal injections of methotrexate and prednisolone. Low‐grade MEC of the left parotid gland was diagnosed at the age of 7 years, only 1 year after completing treatment. Local lymph nodes were not metastatic, and course was favorable 8 years after complete surgical excision. This case report is remarkable for the early diagnosis of second cancer, only 4 years after diagnosis of ALL, and its occurrence in parotid gland without previous head and neck irradiation. It highlights the need for concern about second cancers of the parotid gland in children treated for ALL. Pediatr Blood Cancer 2005;44:673–675. © 2004 Wiley‐Liss, Inc.
A comparison of self‐reported satisfaction between adolescents treated in a “teenage” unit with those treated in adult or paediatric units
Authors: Reynolds B.C. , Windebank K.P. , Leonard R.C.F. , Wallace W.H.B.
Published: November 2004

Background

Despite recommendations that adolescents should have in‐patient management amongst their peers, there is little literature to support this. The study aim was to evaluate and contrast patient satisfaction for teenage cancer patients treated in two settings. The first is a split site unit (a paediatric ward and adult cancer centre in different locations within one city) and the second, a dedicated adolescent unit for patients aged 13–20.

Procedure

Eligible patients aged 13–20 years received treatment from September 1997 to June 2000 and totalled sixty‐five adolescents. The patients were identified at both centres from departmental databases. Postal questionnaires (the Youth Satisfaction Questionnaire) were sent to those eligible.

Results

Patients receiving treatment in the teenage cancer unit (TCU) were not significantly more satisfied overall than those receiving treatment in adult or paediatric units. However, significant differences were noted in: recreational and relaxation facilities (P < 0.005, P < 0.0002), studying space (P < 0.004), ward noise (P < 0.02), and company of the same age (P < 0.0001). The Grade Point Average (a score of all specific items) was higher in favour of the TCU (P < 0.03). Patients at both centres were dissatisfied with hospital food and menus offered.

Conclusions

Adolescents with cancer are satisfied with the overall care they receive independent of whether it is a TCU or a split site unit. Teenagers are significantly more satisfied with environmental aspects of care in the TCU. More research is required to establish the correct provision for teenagers with cancer. This is the first study that contrasts satisfaction between different centres and thus adding to an understanding of the needs of teenagers with cancer. © 2004 Wiley‐Liss, Inc.
Osteonecrosis: A treatment related toxicity in childhood acute lymphoblastic leukemia (ALL)—experiences from trial ALL‐BFM 95
Authors: Bürger Britta , Beier Rita , Zimmermann Martin , Beck Jörn D. , Reiter Alfred , Schrappe Martin
Published: November 2004

Background

Osteonecrosis (ON) as a complication during treatment of acute lymphoblastic leukemia (ALL) has gained rising attention over the past decade. Corticosteroids, representing an essential element of antileukemic therapy, are known to induce ON, which in turn may cause significant morbidity. Due to spontaneous reporting of affected patients with ON, a group‐wide evaluation was performed to determine incidence, risk factors, and morbidity for ON.

Procedure

Patients were identified via spontaneous reporting to the study center and via questionnaire, addressing all 64 participating centers. We retrospectively analyzed 1,951 patients below 18 years of age who were treated according to trial ALL‐BFM 95 between 01.01.1996 and 30.06.2000.

Results

Thirty‐one patients (14 male, 17 female) affected by ON were identified. The overall 5‐year cumulative incidence for ON is 1.8%. The incidence for patients <10 years is 0.2%, whereas for patients ≥10 years it is 8.9% (P = 0.00) and 16.7% (P = 0.003) for patients ≥15 years. The majority (n = 20) showed ON in two or more joints, and the joints most commonly affected were knees (14 patients, 24 affected knees) and hips (11 patients, 20 affected joints). Thirteen out of 31 patients had to undergo surgery in the course of their disease.

Conclusions

Symptomatic ON is a rare event in patients treated with BFM‐type chemotherapy with an overall 5‐year cumulative incidence of 1.8%. The age group ≥10 years, and particularly adolescents ≥15 years have a significantly higher risk of developing ON. © 2004 Wiley‐Liss, Inc.
Early molecular detection of central nervous system relapse in a child with systemic anaplastic large cell lymphoma: Case report and review of the literature
Authors: Armstrong Gregory , Szallasi Arpad , Biegel Jaclyn A. , Shurtleff Sheila , Bilaniuk Larissa T. , Womer Richard B. , Choi John Kim
Published: November 2004

We report a case of anaplastic large cell lymphoma (ALCL) with central nervous system relapse in an 11‐year‐old boy. The relapse was suspected on morphologic examination of the cytospin preparations of the cerebrospinal fluid (CSF) with a WBC of 10 cells/μl. CSF relapse was confirmed using immunohistochemistry (IHC), fluorescence in situ hybridization (FISH), and reverse transcriptase‐polymerase chain reaction (RT‐PCR) for abnormal ALK expression or gene structure. The patient developed large intracranial metastases, despite systemic, and intrathecal chemotherapy. This case demonstrates the feasibility of detecting ALCL in paucicellular CSF specimens and suggests that even low CSF involvement can herald massive parenchymal disease. © 2004 Wiley‐Liss, Inc.
Theoretical exposure of chronically treated patients to lipid lowering agents
Authors: Kucera Zdenek , Vlcek Jiri , Hejdova Miroslava
Published: November 2004

Purpose

The objective was to analyse the exposure to lipid lowering agents (LLA) using the databases of health insurance companies and to appraise its concordance with the findings of evidence based medicine.

Methods

Three health insurance companies' prescription based databases were analysed in the years 1997–2000. All inhabitants in the Czech Republic (CR) have to be insured. The insured person with a recorded prescription for LLA in the year of interest was defined as a patient, the insured person with a recorded prescription for LLA in the years bordering the year of interest was defined as a chronically treated patient. In the year of interest the percentage of chronically treated patients without LLA medication, with ‘very low’ (<122 defined daily doses (DDD)/year), ‘low’ (122–243 DDD/year) and ‘adequate’ (>243 DDD/year) consumption was determined.

Results

During the observed period the total consumption of LLA increased among 450 000 inhabitants twice (by 109.6%) to 24.8 DDD/1000 inhabitants/day. In 2000 the rate of the consumption of statins and fibrates represented 34.2 and 65.6% respectively. In 1998 33.5% and in 1999 41.0% of the chronically treated patients occurred in the ‘adequate’ consumption group.

Conclusions

The signals of inappropriate drug treatment such as the preferred use of fibrates and low doses of LLA prescribed to the Czech population were identified. Conversely, the increasing proportion of the chronically treated patients belonging to the group with the ‘adequate’ consumption could be considered as a positive signal. Copyright © 2004 John Wiley & Sons, Ltd.
Selective prescribing of atypical antipsychotics
Authors: Breekveldt‐Postma Nancy S. , Schillevoort Igor , Nolen Willem A. , Veraart Christiaan P. W. M. , Herings Ron M. C.
Published: November 2004

Purpose

The aim of the study was to investigate whether the most recent introduced atypical antipsychotics olanzapine and risperidone were preferentially prescribed to patients susceptible to develop extrapyramidal side effects (EPS) and those not responding adequately to typical antipsychotics.

Methods

Data were obtained from the Dutch PHARMO system that includes complete medication and hospital admission records of 675 000 residents of 14 Dutch cities. A total number of 129 new users of olanzapine and 142 new users of risperidone as well as 507 new users of typical antipsychotic drugs were identified from our database in the period of 1996–1998. The prevalence of markers of EPS, therapy resistance and therapy non‐compliance were assessed in the period of 1 year prior to a new start of an antipsychotic.

Results

New use of olanzapine and risperidone was significantly associated with previous use of other antipsychotics (odds ratio 4.0, 95%CI: 2.5–6.7 and odds ratio 3.0, 95%CI: 2.0–4.7, respectively). New use of olanzapine and risperidone was also associated with previous use of anticholinergic drugs compared to users of typical antipsychotics (over three and two times more, respectively). This effect diminished when adjusted for previous use of antipsychotics.

Conclusions

In particular olanzapine and also risperidone were selectively prescribed to patients formerly treated with other antipsychotics and to those susceptible for EPS. If not recognised or controlled for, observational studies comparing different antipsychotic drugs may produce biased results on efficacy or frequency of side effects for the different types of antipsychotics. Copyright © 2004 John Wiley & Sons, Ltd.
Amine‐cured epoxy/clay nanocomposites. II. The effect of the nanoclay aspect ratio
Authors: Miyagawa Hiroaki , Rich Michael J. , Drzal Lawrence T.
Published: November 2004

The thermophysical and mechanical properties of a nanocomposite material composed of amine‐cured diglycidyl ether of bisphenol A (DGEBA) reinforced with organomontmorillonite clay are reported. The storage modulus at 100 °C, which was above the glass‐transition temperature (Tg), increased approximately 350% with the addition of 10 wt % (6.0 vol %) of clay. Below the Tg, the storage modulus at 30 °C increased 50% relative to the value of unfilled epoxy. It was determined that the Tg linearly increased as a function of clay volume percent. The tensile modulus of epoxy at room temperature increased approximately 50% with the addition of 10 wt % of clay. The reinforcing effect of the organoclay nanoplatelets is discussed with respect to the Tandon–Weng and Halpin–Tsai models. A pseudoinclusion model is proposed to describe the behavior of randomly oriented, uniformly dispersed platelets in nanocomposite materials. © 2004 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 42: 4391–4400, 2004
Glass‐transition temperature behavior of alumina/PMMA nanocomposites
Authors: Ash Benjamin J. , Siegel Richard W. , Schadler Linda S.
Published: November 2004

Alumina/poly(methyl methacrylate) (PMMA) nanocomposites were synthesized by an in situ free‐radical polymerization process with 38 and 17 nm diameter γ‐alumina nanoparticles. At extremely low filler weight fractions (<1.0 wt % of 38 nm fillers or < 0.5 wt % of 17 nm fillers) the glass‐transition temperature (Tg) of the nanocomposites drops by 25 °C when compared to the neat polymer. Further additions of filler (up to 10 wt %) do not lead to additional Tg reductions. The thermal behavior is shown to vary with particle size, but this dependence can be normalized with respect to a specific surface area. The nanocomposite Tg phenomenon is hypothesized to be because of nonadhering nanoparticles that serve as templates for a porous system with many internal interfaces that break up the percolating structure of dynamically heterogeneous domains recently suggested by Long, D.; and Lequeux, F. Eur Phys J E 2001, 4, 371 to be responsible for the Tg reductions in polymer ultrathin films. The results also point to a far field effect of the nanoparticle surface on the bulk matrix. © 2004 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 42: 4371–4383, 2004
Asphyxiating tracheal bronchogenic cyst
Authors: Baets F. De , Daele S. Van , Schelstraete P. , Haerynck F. , Vermassen F. , Broers C.
Published: November 2004

We report on a 7‐month old infant with severe respiratory distress secondary to a paratracheal bronchogenic cyst. Respiratory relief was achieved by transtracheal puncture of the cyst. Surgical removal of the cyst was performed 1 week later because of radiological evidence of reaccumulation of fluid. Pediatr Pulmonol. 2004; 38:488–490. © 2004 Wiley‐Liss, Inc.
Radiological and pulmonary function outcomes of children with SARS
Authors: Li A.M. , So H.K. , Chu W. , Ng P.C. , Hon K.L. , Chiu W.K. , Leung C.W. , Yau Y.S. , Mo W.K. , Fok T.F.
Published: November 2004

We examined the radiological and pulmonary function outcomes of children affected with severe acute respiratory syndrome (SARS) at 6 months from diagnosis. Twenty‐one female and 26 male Chinese patients (median age, 13.6 years; interquartile range, 9.9–16.0) were studied. In each subject, high‐resolution computed tomography (HRCT) of the thorax and pulmonary function were assessed. All children were asymptomatic and had a normal clinical examination. Mild pulmonary abnormalities were detected on HRCT in 16 (34.0%) subjects, including residual ground‐glass opacification (n = 5), air trapping (n = 8), and a combination of ground‐glass changes and air trapping (n = 3). The need for oxygen supplementation (P = 0.02) and lymphopenia during the course of illness (P = 0.012) were significant risk factors in predicting abnormal HRCT. There were no significant lung function differences between those with and without HRCT abnormalities. Despite complete clinical resolution, a considerable proportion of children affected with SARS had abnormal HRCT findings at 6 months. These abnormalities were more prevalent in those with severe disease. It is important that careful follow‐up be carried out to assess the clinical significance and persistence of such abnormalities. Pediatr Pulmonol. 2004; 38:427–433. © 2004 Wiley‐Liss, Inc.
Principal eigenvector of contact matrices and hydrophobicity profiles in proteins
Authors: Bastolla Ugo , Porto Markus , Roman H. Eduardo , Vendruscolo Michele
Published: November 2004

With the aim of studying the relationship between protein sequences and their native structures, we adopted vectorial representations for both sequence and structure. The structural representation was based on the principal eigenvector of the fold's contact matrix (PE). As has been recently shown, the latter encodes sufficient information for reconstructing the whole contact matrix. The sequence was represented through a hydrophobicity profile (HP), using a generalized hydrophobicity scale that we obtained from the principal eigenvector of a residue–residue interaction matrix, and denoted as interactivity scale. Using this novel scale, we defined the optimal HP of a protein fold, and, by means of stability arguments, predicted to be strongly correlated with the PE of the fold's contact matrix. This prediction was confirmed through an evolutionary analysis, which showed that the PE correlates with the HP of each individual sequence adopting the same fold and, even more strongly, with the average HP of this set of sequences. Thus, protein sequences evolve in such a way that their average HP is close to the optimal one, implying that neutral evolution can be viewed as a kind of motion in sequence space around the optimal HP. Our results indicate that the correlation coefficient between N‐dimensional vectors constitutes a natural metric in the vectorial space in which we represent both protein sequences and protein structures, which we call vectorial protein space. In this way, we define a unified framework for sequence‐to‐sequence, sequence‐to‐structure and structure‐to‐structure alignments. We show that the interactivity scale is nearly optimal both for the comparison of sequences to sequences and sequences to structures. Proteins 2005. © 2004 Wiley‐Liss, Inc.
The impact of protein flexibility on protein–protein docking
Authors: Ehrlich Lutz P. , Nilges Michael , Wade Rebecca C.
Published: November 2004

Accounting for protein flexibility in protein–protein docking algorithms is challenging, and most algorithms therefore treat proteins as rigid bodies or permit side‐chain motion only. While the consequences are obvious when there are large conformational changes upon binding, the situation is less clear for the modest conformational changes that occur upon formation of most protein–protein complexes. We have therefore studied the impact of local protein flexibility on protein–protein association by means of rigid body and torsion angle dynamics simulation. The binding of barnase and barstar was chosen as a model system for this study, because the complexation of these 2 proteins is well‐characterized experimentally, and the conformational changes accompanying binding are modest. On the side‐chain level, we show that the orientation of particular residues at the interface (so‐called hotspot residues) have a crucial influence on the way contacts are established during docking from short protein separations of approximately 5 Å. However, side‐chain torsion angle dynamics simulations did not result in satisfactory docking of the proteins when using the unbound protein structures. This can be explained by our observations that, on the backbone level, even small (2 Å) local loop deformations affect the dynamics of contact formation upon docking. Complementary shape‐based docking calculations confirm this result, which indicates that both side‐chain and backbone levels of flexibility influence short‐range protein–protein association and should be treated simultaneously for atomic–detail computational docking of proteins. Proteins 2005. © 2004 Wiley‐Liss, Inc.
A genomic perspective of protein kinases in Plasmodium falciparum
Authors: Anamika  , Srinivasan N. , Krupa A.
Published: November 2004

Protein kinases are central to regulation of cellular signaling in the eukaryotes. Well‐conserved and lineage‐specific protein kinases have previously been identified from various completely sequenced genomes of eukaryotes. The current work describes a genome‐wide analysis for protein kinases encoded in the Plasmodium falciparum genome. Using a few different profile matching methods, we have identified 99 protein kinases or related proteins in the parasite genome. We have classified these kinases into subfamilies and analyzed them in the context of noncatalytic domains that occur in these catalytic kinase domain–containing proteins. Compared to most eukaryotic protein kinases, these sequences vary significantly in terms of their lengths, inserts in catalytic domains, and co‐occurring domains. Catalytic and noncatalytic domains contain long stretches of repeats of positively charged and other polar amino acids. Various components of the cell cycle, including 4 cyclin‐dependent kinase (CDK) homologues, 2 cyclins, 1 CDK regulatory subunit, and 1 kinase‐associated phosphatase, are identified. Identification of putative mitogen‐activated protein (MAP) Kinase and MAP Kinase Kinase of P. falciparum suggests a new paradigm in the highly conserved signaling pathway of eukaryotes. The calcium‐dependent kinase family, well represented in P. falciparum, shows varying domain combinations with EF‐hands and pleckstrin homology domains. The analysis reveals a new subfamily of protein kinases having limited sequence similarity with previously known subfamilies. A new transmembrane kinase with 6 membrane‐spanning regions is identified. Putative apicoplast targeting sequences have been detected in some of these protein kinases, suggesting their export to the apicoplast. Proteins 2005. © 2004 Wiley‐Liss, Inc.
Both helical propensity and side‐chain hydrophobicity at a partially exposed site in α‐helix contribute to the thermodynamic stability of ubiquitin
Authors: Loladze Vakhtang V. , Makhatadze George I.
Published: November 2004

Improving helical propensity of residues was proposed as one of the approaches to increase protein stability. Here the contribution of the helix propensity and hydrophobicity of residues at partially buried positions of α‐helix to the stability of a model protein—ubiquitin— is explored. Thermodynamic stabilities of 13 ubiquitin variants with substitutions at a partially buried helical residue were measured by differential scanning calorimetry. It was found that the dynamic range of stabilities for different amino acid residues at this partially buried position is 3 times larger than that expected based on helical propensity alone. Correlation analysis shows that both helical propensity and hydrophobicity are important in defining the relative stabilities of the studied ubiquitin variants. These results provide experimental evidence that partially buried positions are potentially useful sites for engineering proteins with enhanced thermostability. Proteins 2005. © 2004 Wiley‐Liss, Inc.
Fold recognition by combining sequence profiles derived from evolution and from depth‐dependent structural alignment of fragments
Authors: Zhou Hongyi , Zhou Yaoqi
Published: November 2004

Recognizing structural similarity without significant sequence identity has proved to be a challenging task. Sequence‐based and structure‐based methods as well as their combinations have been developed. Here, we propose a fold‐recognition method that incorporates structural information without the need of sequence‐to‐structure threading. This is accomplished by generating sequence profiles from protein structural fragments. The structure‐derived sequence profiles allow a simple integration with evolution‐derived sequence profiles and secondary‐structural information for an optimized alignment by efficient dynamic programming. The resulting method (called SP3) is found to make a statistically significant improvement in both sensitivity of fold recognition and accuracy of alignment over the method based on evolution‐derived sequence profiles alone (SP) and the method based on evolution‐derived sequence profile and secondary structure profile (SP2). SP3 was tested in SALIGN benchmark for alignment accuracy and Lindahl, PROSPECTOR 3.0, and LiveBench 8.0 benchmarks for remote‐homology detection and model accuracy. SP3 is found to be the most sensitive and accurate single‐method server in all benchmarks tested where other methods are available for comparison (although its results are statistically indistinguishable from the next best in some cases and the comparison is subjected to the limitation of time‐dependent sequence and/or structural library used by different methods.). In LiveBench 8.0, its accuracy rivals some of the consensus methods such as ShotGun‐INBGU, Pmodeller3, Pcons4, and ROBETTA. SP3 fold‐recognition server is available on http://theory.med.buffalo.edu. Proteins 2005. © 2004 Wiley‐Liss, Inc.
Phase transitions and transport phenomena in Li0.25Cu1.75Se superionic compound
Authors: Balapanov M. Kh. , Bikkulova N. N. , Mukhamedyanov U. Kh. , Asilguschina G. N. , Musalimov R. Sh. , Zeleev M. Kh.
Published: November 2004

Phase transformation points in Li0.25Cu1.75Se mixed electronic–ionic conductor have been determined by calorimetric, conductometric and thermoelectric measurements. The phase transformation (PT) from triclinic to monoclinic occurs at 403–413 K. At 503–515 K the monoclinic phase is followed by a rhombohedral modification. Both of these PTs are accompanied by drops on the calorimetric curve. At about 653 K observed anomalies in the temperature dependencies of the ionic conductivity, of the chemical diffusion coefficient and the jump of the ionic Seebeck coefficient have been induced by the PT to hexagonal phase. Neutron diffraction studies reveal the cubic structure of Li0.25Cu1.75Se compound (with space group Fm3m) at 773 K. The corresponding PT causes anomalies in the electrical and diffusion properties at 703–713 K. Cu ions are statistically distributed over tetrahedral and trigonal voids in an Fm3m cage; lithium ions randomly occupy 32(f) positions. (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Dynamics of Ising spin chains with nearest‐neighbour and next‐nearest‐neighbour interactions in random fields
Authors: Ismail G. , Bannora K. , Hassan S.
Published: November 2004

A one‐dimensional system of six coupled random field Ising spins is studied by Glauber dynamics. The nearest‐neighbour and next‐nearest‐neighbour interactions are taken into consideration. Two distributions of random fields (RF) – binary and Gaussian distribution – are investigated. We consider four cases of exchange couplings: ferro–ferromagnetic (F–F), ferro–antiferromagnetic (F–AF), antiferro–ferromagnetic (AF–F) and antiferro–antiferromagnetic (AF–AF). The system is fully frustrated, undergoes a zero‐temperature phase transition and has multiple local energy minima in both distributions. The dynamics of the four systems are solved exactly in both distributions of RF. The effects of random fields are discussed. The number of diverging relaxation times is equal to the number of energy minima minus one. The longest relaxation times verify the Arrhenius law with energy barrier determined by the energy needed to invert the ground‐state spin configuration. At low temperatures, according to the Arrhenius law, the spectrum of relaxation times shows a double‐peak distribution on a logarithmic scale. In the Gaussian distribution of RF the energy‐barrier distribution is continuous while it is quasi‐discrete in the binary distribution. (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
The perturbative construction of the effective soft‐spin Hamiltonian of the system of magnetized nano‐loops
Authors: Horváth D. , Gmitra M. , Baláž P.
Published: November 2004

The effective large‐scale Hamiltonian of a planar system of nano‐loops in a weakly excited flux‐closed magnetized state has been constructed by means of a perturbative technique based on micromagnetic theory. The Hamiltonian is written by means of two classes of collective variables: the continuous soft spins and discrete vorticity charges. Analytical and numerical calculations of the inter‐loop magnetostatic energy are compared for a pair of magnetic nano‐loops. The transformation from small‐scale to collective variables is performed for intra‐loop exchange‐coupling, magnetostatic and Zeeman energy terms. Evidence of correlations of uniform vortex charges in low‐energy configurations is uncovered numerically. The generalization of the perturbative method that deals with more realistic out‐of‐plane excitations is also considered. (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Magnetic properties of a transverse spin‐$ {3 \over 2} $ Ising model with random longitudinal field
Authors: Liang Ya‐Qiu , Wei Guo‐Zhu , Song Guo‐Li
Published: November 2004

Within the framework of the effective‐field theory with correlations, a spin‐$ {3 \over 2} $ transverse Ising model in the longitudinal random‐field on a honeycomb lattice is studied. The phase diagrams and the behavior of the tricritical point are examined. The possible re‐entrance phenomena displayed by the system due to the competition effects that occur for the appropriate ranges of the random and transverse field are investigated. The longitudinal and transverse magnetizations, the longitudinal quadrupolar moments and internal energy are given numerically for a honeycomb lattice (z = 3). (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Improvement of photoluminescence efficiency in stacked Ge/Si/Ge quantum dots with a thin Si spacer
Authors: Chen P. S. , Lee S. W. , Peng Y. H. , Liu C. W. , Tsai M.‐J.
Published: November 2004

In this work, two successive layers of Ge quantum dots separated by a thin Si spacer grown by ultra‐high‐vacuum chemical vapor deposition were demonstrated. With an optimal thickness of the thin Si spacer, the sandwiched Ge (13.1 ML)/Si (28 ML)/Ge (13.1 ML) quantum dots suppress the coarsening of Ge quantum dots and efficiently increase the uniformity of the quantum dots. Cross‐sectional transmission electron microscopy shows that the Si/Ge underlayers provide preferred nucleation sites for the overlayer Ge deposition. Such a modification avoids the formation of Ge superdomes and prevents the occurrence of threading dislocations even at such a thin Si spacer thickness. A stronger photoluminescence intensity of these sandwich Ge/Si/Ge quantum dots was observed compared with that of 26.2 eq‐ML Ge quantum dots without using any intermediate Si layer. Furthermore, the narrower width of the photoluminescence spectra indicates that the Ge/Si/Ge dots are more uniform compared with the 13.1 and 26.1 eq‐ML Ge quantum dots. Five‐fold bilayers of Ge/Si/Ge/Si(150 ML) have been achieved to enhance the photo‐emission efficiency. (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Investigations on the local structures of the two trigonal Er3+ centers in KMgF3
Authors: Wu Shao‐Yi , Dong Hui‐Ning , Wei Wang‐He
Published: November 2004

The local structures of the two trigonal Er3+ (167Er) centers I and II in KMgF3 are theoretically studied using the perturbation formulas of the g factors for a 4f11 ion in trigonal symmetry. In these formulas the contributions to the g factors from the second‐order perturbation terms and admixtures of various states are taken into account. Based on the studies, the centers I and II are attributed to, respectively, the Er3+ impurity occupying the octahedral Mg2+ site with a K+ vacancy VK and the dodecahedral K+ site with a Mg2+ vacancy VMg along the C3 axis due to charge compensation. According to the calculations, the Er3+ ion in either center is found to undergo an axial displacement ΔZL (L = I or II) towards the compensator (VK or VMg) along the C3 axis because of electrostatic attraction. The calculated g factors for both the Er3+ centers based on the displacements ΔZL show reasonable agreement with the observed values. The local structures of the two centers are discussed. The theoretical studies in this paper may be useful for understanding the optical properties of Er3+‐doped KMgF3. (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Magnetoconductivity of planar crystalline systems and its semiclassical quantization
Authors: Olszewski S. , Pietrachowicz M. , Baszczak M.
Published: November 2004

The tensor of magnetoconductivity is examined for the tightly‐bounds‐electrons in the planar crystallographic lattices originating from three cubic lattice kinds (simple, body‐centered and face‐centered). The magnetic field is assumed to be directed perpendicularly to the crystallographic plane and the relaxation time entering the conductivity tensor is derived from the crystal band structure. The presence of the lattice potential is found to be essential for calculating a finite value of the Hall conductivity, which, in general, exhibits a rather feeble dependence on position of the Landau level within the energy band. A quasi‐constant behavior in the band of states is obtained also for a quantal increment of the Hall conductivity between two neighboring Landau levels. For different cubic lattices this increment is an approximately constant number being close toe2/h. On the other hand, the quanta of the diagonal components of the tensor of magnetoconductivity per one Landau level are much larger thane2/hfor an almost empty band, but they tend to decrease very rapidly to zero with an increase of the band filling. For a strong magnetic field – and not too low temperatures – the components of the tensor of magnetoresistance are found to increase linearly with the strength of the field. A remarkable quantitative agreement between the theory and experiment is demonstrated for the Hall resistance of the planar crystalline structures. (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Binding energy of relativistic hydrogenic impurities in cylindrical quantum well wires under an applied electric field
Authors: Meşe A. I. , Okan S. E.
Published: November 2004

The ground state binding energy of a hydrogenic impurity in infinite cylindrical GaAs quantum well wires subjected to an external electric field applied perpendicular to the symmetry axis of the wire is studied within the relativistic approach. A rapid decrease of the binding energy for different intensities of the electric field with increasing wire radius is predicted. Furthermore, the relativistic effects are emphasised by comparing them with the non‐relativistic results. (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Low‐field magnetic behavior of LaMn2–xNixSi2 silicides
Authors: Gencer A. , Kįlįç A. , Kervan S.
Published: November 2004

We have performed X‐ray diffraction (XRD) and AC magnetic susceptibility measurements on polycrystalline LaMn2–xNixSi2 (0.0 ≤ x ≤ 2.0) silicides for magnetic characterization in fields of about a few Oe at a temperature range 15–325 K. All compounds crystallize in the naturally layered ThCr2Si2‐type structure with the space group I4/mmm. Substitution of Ni for Mn leads to a linear decrease in the lattice constant c and the unit cell volume, while it gives rise to a change of magnetic properties from ferromagnetic to anti‐ferromagnetic behavior for small values of x < 1. The sample with x = 0.8 has a Néel temperature of about 35 K, associated with anti‐ferromagnetic behavior. However, for x = 1, anti‐ferromagnetic behavior is diminished and paramagnetic behavior becomes dominant. For x = 2, the sample becomes virtually non‐magnetic. The samples with x ≤ 0.5 exhibit mixed magnetic properties composed of ferromagnetic and anti‐ferromagnetic interactions, below the Curie temperature TC(Mn). The results are collected in the magnetic phase diagram. (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
How do electrons travel in unusual metallic fluorides of Ag2+?
Authors: Jaroń Tomasz , Grochala Wojciech , Hoffmann Roald
Published: November 2004

We investigate computationally two representative examples of higher fluorides of Ag(II), namely KAgF3 and AgFBF4. Both compounds formally contain linear (Ag–F)+ chains, in which divalent silver is coordinated additionally by four fluoride anions. For AgFBF4, the equatorial coordination is weak, and leads to metallic conductivity in 1D, as emerges from our band structure calculations. For KAgF3, however, the axial coordination is very strong, and the compound is virtually a 2D metal (i.e. it is mainly the x2–y2 orbitals of Ag that participate in electronic transport in this interesting material). (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Multi‐residue liquid chromatography/tandem mass spectrometry method for the detection of non‐steroidal anti‐inflammatory drugs in bovine muscle: optimisation of ion trap parameters
Authors: Van Hoof Nathalie , De Wasch Katia , Poelmans Sofie , Noppe Herlinde , De Brabander Hubert
Published: November 2004

A multi‐residue liquid chromatography/tandem mass spectrometry method (LC/MS2) was developed for the detection of the non‐steroidal anti‐inflammatory drugs acetylsalicylic acid (via the marker residue salicylic acid), flunixin, phenylbutazone, tolfenamic acid, meloxicam and ketoprofen, in bovine muscle. After extraction of the bovine muscle with acetonitrile, the cleanup was performed using a Oasis HLB column. The evaporated eluate was reconstituted and analysed by LC/MS2. To obtain optimal detection of salicylic acid and phenylbutazone, the ion trap mass spectrometric parameters activation q and maximum ion injection time, respectively, were optimised. The activation q for salicylic acid was increased to obtain reliable detection of both salicylic acid and its product ion. The maximum ion injection time for the time segment containing phenylbutazone was decreased since there were not enough scans across the chromatographic peak of this compound. The multi‐residue method was able to detect the different analytes below or at the maximum residue limit (MRL) or minimum required performance limit (MRPL) or, in the case of phenylbutazone and ketoprofen, at 100 and 20 μg kg−1, respectively. Copyright © 2004 John Wiley & Sons, Ltd.
Use of 18O3‐clodronate as an internal standard for the quantitative analysis of clodronate in human plasma by gas chromatography/electron ionisation mass spectrometry
Authors: Leis Hans Jörg , Fauler Günter , Windischhofer Werner
Published: November 2004

A sensitive and specific method for the quantitative determination of clodronate in human plasma is presented. The drug was extracted from plasma by anion‐exchange chromatography and derivatised to the tetra‐tert‐butyldimethylsilyl derivative. 18O3‐Clodronate was prepared from unlabeled clodronate and used as an internal standard. Gas chromatography/mass spectrometry (GC/MS) under electron ionisation conditions was used for quantitative measurement of the drug, using m/z 643.16 and 651.17 for target and internal standard, respectively. Calibration graphs were linear within the range of 10–1280 ng/mL plasma. Intra‐day precision was 1.8% (10 ng/mL), 0.5% (40 ng/mL), 1.0% (120 ng/mL), 0.5% (200 ng/mL), 0.5% (400 ng/mL) and 2.7% (800 ng/mL) and inter‐day variability was found to be 0.7% (10 ng/mL), 1.6% (40 ng/mL), 1.3% (120 ng/mL), 2.3% (200 ng/mL), 2.5% (400 ng/mL) and 1.2% (800 ng/mL). Intra‐day accuracy showed deviations of 0.8% (10 ng/mL), 0.8% (40 ng/mL), 0.9% (120 ng/mL), 0.9% (200 ng/mL), 1.9% (400 ng/mL) and 0.3% (800 ng/mL) and intra‐day accuracy was of −1.4% (10 ng/mL), 0.0% (40 ng/mL), −0.7% (120 ng/mL), −0.4% (200 ng/mL), −1.2% (400 ng/mL) and −3.3% (800 ng/mL). The stable isotope labeled standard was found to be stable under analysis conditions. Copyright © 2004 John Wiley & Sons, Ltd.
Assay of histamine by nano‐liquid chromatography/tandem mass spectrometry with a packed nanoelectrospray emitter
Authors: Song Yaru , Quan Zhe , Liu Yi‐Ming
Published: November 2004

A nano‐liquid chromatographic /tandem mass spectrometric (nanoHPLC/MS/MS) method has been developed for the sensitive determination of histamine, a vital neurotransmitter. The method involved pre‐column derivatization of histamine with 7‐fluoro‐4‐nitrobenzoxadiazole (NBD‐F), thus increasing the hydrophobicity of the analyte and allowing it to be retained and stacked on a nanoelectrospay emitter packed with C18 reversed‐phase particles. Sodium 1‐heptanesulfonate, added as an ion‐pairing reagent in the mobile phase for sample loading, was found to facilitate greatly the analyte retention. The packed nanoelectrospray emitter was easily prepared using fused‐silica capillary of 75 μm i.d., and included creating an electrospray emitter tip and then slurry‐packing a 5 cm long column with 5 μm silica‐based particles. After sample loading, the mobile phase was changed for separation and a characteristic precursor‐to‐product ion transition, m/z 275 → 258, was used for the quantification. A linear calibration curve in the range from 1.0–100 ng/mL histamine with an r2 value of 0.9995 was obtained. The detection limit was estimated to be 0.1 ng/mL histamine in water. In a preliminary validation, the method was applied to determine histamine in alcoholic beverages and rat brain tissues. Copyright © 2004 John Wiley & Sons, Ltd.
Automating proteome analysis: improvements in throughput, quality and accuracy of protein identification by peptide mass fingerprinting
Authors: Canelle Ludovic , Pionneau Cédric , Marie Arul , Bousquet Jordane , Bigeard Jean , Lutomski Didier , Kadri Tewfik , Caron Michel , Joubert‐Caron Raymonde
Published: November 2004

The use of robots has major effects on maximizing the proteomic workflow required in an increasing number of high‐throughput projects and on increasing the quality of the data. In peptide mass finger printing (PMF), automation of steps downstream of two‐dimensional gel electrophoresis is essential. To achieve this goal, the workflow must be fluid. We have developed tools using macros written in Microsoft Excel and Word to complete the automation of our platform. Additionally, because sample preparation is crucial for identification of proteins by matrix‐assisted laser desorption/ionization (MALDI) mass spectrometry, we optimized a sandwich method usable by any robot for spotting digests on a MALDI target. This procedure enables further efficient automated washing steps directly on the MALDI target. The success rate of PMF identification was evaluated for the automated sandwich method, and for the dried‐droplet method implemented on the robot as recommended by the manufacturer. Of the two methods, the sandwich method achieved the highest identification success rate and sequence coverage of proteins. Copyright © 2004 John Wiley & Sons, Ltd.
Use of high‐performance liquid chromatography/electrospray ionization collision‐induced dissociation mass spectrometry for structural identification of monohydroxylated progesterones
Authors: Kang Min‐Jung , Lisurek Michael , Bernhardt Rita , Hartmann Rolf W.
Published: November 2004

For the structural identification of monohydroxylated progesterones synthesized by microorganisms, a method was developed using a combination of high‐performance liquid chromatography and electrospray ionization collision‐induced dissociation mass spectrometry (HPLC/ESI‐CIDMS). The retention times and MS/MS spectra of 11 different standards at 30 eV were collected and compared. The identification of D‐ring‐hydroxylated progesterones (15β‐, 16α‐, 17α‐ and 21‐OH‐P) using ESI‐CIDMS was not possible. However, they were separated chromatographically using a 65:35 mixture of water and acetonitrile containing 0.5% acetic acid. The other hydroxylated progesterones (2α‐, 6β‐, 7β‐, 9α‐, 11α‐, 11β‐, and 19‐OH‐P) could be identified by comparison of eight fragments. The complete separation of 11 standards was achieved chromatographically. The developed assay was evaluated by the identification of monohydroxylated progesterones produced by CYP106A2 from Bacillus megaterium ATCC 13368. Copyright © 2004 John Wiley & Sons, Ltd.