bluuebunny/crossref_metadata_2025 huggingface dataset:
An efficient memory operations optimization technique for vector loops on Itanium 2 processors
Authors: Jalby William , Lemuet Christophe , Touati Sid‐Ahmed‐Ali
Published: January 2006

To keep up with a large degree of instruction level parallelism (ILP), the Itanium 2 cache systems use a complex organization scheme: load/store queues, banking and interleaving. In this paper, we study the impact of these cache systems on memory instructions scheduling. We demonstrate that, if no care is taken at compile time, the non‐precise memory disambiguation mechanism and the banking structure cause severe performance loss, even for very simple regular codes. We also show that grouping the memory operations in a pseudo‐vectorized way enables the compiler to generate more effective code for the Itanium 2 processor. The impact of this code optimization technique on register pressure is analyzed for various vectorization schemes. Copyright © 2006 John Wiley & Sons, Ltd.
Incentive‐based scheduling in Grid computing
Authors: Zhu Yanmin , Xiao Lijuan , Xu Zhiwei , Ni Lionel M.
Published: January 2006

With the rapid development of high‐speed wide‐area networks and powerful yet low‐cost computational resources, Grid computing has emerged as an attractive computing paradigm. In typical Grid environments, there are two distinct parties, resource consumers and resource providers. Enabling an effective interaction between the two parties (i.e. scheduling jobs of consumers across the resources of providers) is particularly challenging due to the distributed ownership of Grid resources. In this paper, we propose an incentive‐based peer‐to‐peer (P2P) scheduling for Grid computing, with the goal of building a practical and robust computational economy. The goal is realized by building a computational market supporting fair and healthy competition among consumers and providers. Each participant in the market competes actively and behaves independently for its own benefit. A market is said to be healthy if every player in the market gets sufficient incentive for joining the market. To build the healthy computational market, we propose the P2P scheduling infrastructure, which takes the advantages of P2P networks to efficiently support the scheduling. The proposed incentive‐based algorithms are designed for consumers and providers, respectively, to ensure every participant gets sufficient incentive. Simulation results show that our approach is successful in building a healthy and scalable computational economy. Copyright © 2006 John Wiley & Sons, Ltd.
G‐PASS: an instance‐oriented security infrastructure for Grid travelers
Authors: Ma Tianchi , Chen Lin , Wang Cho‐Li , Lau Francis C. M.
Published: January 2006

Grid computing unifies distributed resources via its support for the creation and use of virtual organizations (VOs), where a VO represents a collection of distributed resources to be accessed through predefined resource sharing and coordination policies. We consider a special type of mobile processes, named Grid travelers, which can travel across boundaries of VOs for the detection of resource availability, to negotiate for the approval of access privileges and to conduct remote execution. A new security infrastructure named G‐PASS is proposed to guarantee the validity and integrity of the travelers and the critical security knowledge they collect while traveling, especially while crossing some VOs. G‐PASS borrows the idea of passport and custom, as well as the procedures for people's travel in real life, to provide role‐based delegation mapping and access control. We demonstrate the power and feasibility of G‐PASS with a simulated mobile agent environment and a distributed ray‐tracing application running on multiple VOs. Various security overheads coming from migration decisions and actual agent or process migration are reported. G‐PASS can be installed with Grid Security Infrastructure (GSI) as the base, which makes it compatible with the existing Grid middleware. Copyright © 2006 John Wiley & Sons, Ltd.
Human and pig SRY 5′ flanking sequences can direct reporter transgene expression to the genital ridge and to migrating neural crest cells
Authors: Boyer Alexandre , Pilon Nicolas , Raiwet Diana L. , Lussier Jacques G. , Silversides David W.
Published: January 2006

Mechanisms for sex determination vary greatly between animal groups, and include chromosome dosage and haploid–diploid mechanisms as seen in insects, temperature and environmental cues as seen in fish and reptiles, and gene‐based mechanisms as seen in birds and mammals. In eutherian mammals, sex determination is genetic, and SRY is the Y chromosome located gene representing the dominant testes determining factor. How SRY took over this function from ancestral mechanisms is not known, nor is it known what those ancestral mechanisms were. What is known is that SRY is haploid and thus poorly protected from mutations, and consequently is poorly conserved between mammalian species. To functionally compare SRY promoter sequences, we have generated transgenic mice with fluorescent reporter genes under the control of various lengths of human and pig SRY 5′ flanking sequences. Human SRY 5′ flanking sequences (5 Kb) supported reporter transgene expression within the genital ridge of male embryos at the time of sex determination and also supported expression within migrating truncal neural crest cells of both male and female embryos. The 4.6 Kb of pig SRY 5′ flanking sequences supported reporter transgene expression within the male genital ridge but not within the neural crest; however, 2.6 Kb and 1.6 Kb of pig SRY 5′ flanking sequences retained male genital ridge expression and now supported extensive expression within cells of the neural crest in embryos of both sexes. When 2 Kb of mouse SRY 5′ flanking sequences (−3 to −1 Kb) were placed in front of the 1.6 Kb of pig SRY 5′ flanking sequences and this transgene was introduced into mice, reporter transgene expression within the male genital ridge was retained but neural crest expression was lost. These observations suggest that SRY 5′ flanking sequences from at least two mammalian species contain elements that can support transgene expression within cells of the migrating neural crest and that additional SRY 5′ flanking sequences can extinguish this expression. Developmental Dynamics 235:623–632, 2006. © 2006 Wiley‐Liss, Inc.
Reactivity of 4,4‐Dichloro‐1,1‐diphenyl‐2‐azabutadiene Towards Alkoxides and Thiolates: Synthesis of Functionalised π‐Conjugated 2‐Azabutadienes and Unexpected 1,4‐Thiazine Formation
Authors: Jacquot‐Rousseau Sandrine , Schmitt Gérard , Khatyr Abderrahim , Knorr Michael , Kubicki Marek M. , Vigier Estelle , Blacque Olivier
Published: January 2006

Treatment of 4,4‐dichloro‐1,1‐diphenyl‐2‐azabuta‐1,3‐diene [Cl2C=C(H)‐N=CPh2] (1) with excess sodium isopropylthiolate or sodium thiophenolate in DMF yielded the 2‐azabutadiene derivatives (RS)2C=C(H)–N=CPh2 (2) (2a R = iPr; 2b R = Ph). Nucleophilic attack of the sodium salt of ethyl thioglycolate on 1 afforded as the sole product the six‐membered heterocyclic compound ethyl 2‐ethoxycarbonylmethylthio‐5,5‐diphenyl‐5,6‐dihydro‐4H‐1,4‐thiazine‐6‐carboxylate (5). The reaction is initiated by substitution of the two vinyl‐bound chloro substituents to give {EtO(O=)CCH2S}2C=C(H)–N=CPh2 (2c) as intermediate. A mechanism that accounts for the subsequent cyclisation reaction is proposed. The 2‐azabutadiene derivative (PhO)2C=C(H)–N=CPh2 (7) was obtained by the reaction of 1 with sodium phenolate. The regioselectivity of the incoming nucleophile is roughly correlated with its hardness/softness in accord with Pearson’s HSAB principle. The molecular structures of 2a,b, 5 and 7 were determined by single‐crystal X‐ray diffraction. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2006)
Synthesis and Modulation of Bis(triazine) Hydrogen‐Bonding Receptors
Authors: Mason Pamela V. , Champness Neil R. , Collinson Simon R. , Fisher Matthew G. , Goretzki Gudrun
Published: January 2006

The synthesis of bis(triazine) molecules capable of acting as synthetic receptors for barbiturate guest molecules is described. The binding properties are also reported illustrating the modulation of the binding properties of these species by the modification of the hydrogen‐bonding patterns of the receptor molecule, namely 1,3‐N,N′‐bis[4‐(dibenzylamino)‐6‐(butylamino)‐1,3,5‐triazin‐2‐yl]xylylenediamine (1). Thus 1,3‐O,O′‐bis[4‐(dibenzylamino)‐6‐(butylamino)‐1,3,5‐triazin‐2‐yl]benzenedimethanol (3) and 1,3‐O,O′‐bis[4‐(dibenzylamino)‐6‐(diethylamino)‐1,3,5‐triazin‐2‐yl]benzenedimethanol (5) have been prepared, and their binding constants compared to those observed for 1. In the case of compounds 3 and 5 the hydrogen‐bonding secondary amines at the apex of the receptor 1 are substituted by non‐hydrogen‐bonding ether links. The hydrogen‐bonding ability is further modified in the case of 5 by the removal of all hydrogen‐bond donors from the receptor site, replacing secondary amines by tertiary amines. NMR binding studies illustrate how these simple modifications of the hydrogen‐bonding patterns of these receptors influences the overall strength of binding demonstrating a simple mechanism for controlling host‐guest complex formation. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2006)
First Total Synthesis of Longimicin D
Authors: Tominaga Hiroaki , Maezaki Naoyoshi , Yanai Minori , Kojima Naoto , Urabe Daisuke , Ueki Risa , Tanaka Tetsuaki
Published: January 2006

We have accomplished the first total synthesis of longimicin D (1), which displays potent cytotoxicity against human pancreatic carcinoma cells. The bis‐THF core bearing congested stereocenters was constructed by our methodology for synthesis of poly‐THF cores, which consists of asymmetric alkynylation with the C4 unit and stereodivergent THF ring formation. Although we had planned to join the C9–C34 bis‐THF core segment 2 and the C1–C8 γ‐lactone segment 3, a model study revealed that the coupling was difficult. We resolved the problem by applying asymmetric alkynylation of bis‐THF aldehyde 24 with functionalized alkyne 19 respresenting the polymethylene chain from the C3 to C12 position. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2006)
Studies of DNA Damage Inhibition by Dietary Antioxidants Using Metallopolyion/DNA Sensors
Authors: Mugweru Amos , Rusling James
Published: January 2006

Voltammetric sensors featuring thin‐films containing osmium and ruthenium metallopolymers were evaluated to monitor the influence of antioxidants on DNA damage reactions. In the first example, apigenin, chrysin, and ascorbic acid were shown to inhibit oxidation of DNA by hydroxyl radicals generated with Fenton's reagent. A second example involved films of DNA with myoglobin (Mb) as an enzyme mimic which was used to convert styrene to styrene oxide. Here, the Ru peak of the sensor served as a marker of DNA damage from adduct formation between nucleobases and styrene oxide. There was no influence of the antioxidants on the reaction of styrene oxide itself with DNA films, but significant damage protection was afforded by micromolar amounts of antioxidants when styrene oxide was generated by Mb in the sensor films. This suggests that protection ensued from action of the antioxidants at the enzyme conversion level, probably by reduction of the active ferryloxy intermediate of the protein. Results demonstrate the usefulness of the thin metallopolyion/DNA film sensors in investigations of DNA damage inhibition.
Bone morphogenetic protein 7 is widely overexpressed in primary breast cancer
Authors: Alarmo Emma‐Leena , Rauta Jenita , Kauraniemi Päivikki , Karhu Ritva , Kuukasjärvi Tuula , Kallioniemi Anne
Published: January 2006

Bone morphogenetic proteins (BMP) make up a family of extracellular signaling molecules that play a critical role in vertebrate development and both inhibit and stimulate growth in cancer cells. BMP7 was recently identified in our genomewide copy number and expression survey as being activated through amplification in breast cancer cell lines. In the present study, we further explored BMP7 gene copy number and expression changes in 22 breast cancer cell lines and 146 primary breast tumors. FISH analysis revealed that BMP7 copy number varied greatly from one cell line to another, with three cell lines showing extremely high‐level amplification. Among primary tumors, BMP7 copy number was increased in 16% of the cases. BMP7 mRNA expression was determined in the cell lines and in a subset of 44 tumor samples by RT‐PCR or quantitative real‐time RT‐PCR, respectively. Despite elevated mRNA levels in cancer cells, there was no significant association between copy number increase and mRNA expression, even though the highest expression was seen in cell lines and tumors with increased BMP7 copy number. Most interestingly, immunohistochemical analysis revealed BMP7 protein staining in all 11 breast cancer cell lines examined and strongly elevated BMP7 protein expression in 71.4% of the tumor samples as compared to normal mammary epithelium. Our results illustrate the frequent involvement of BMP7 alterations in breast cancer and especially highlight overexpression of the BMP7 protein in a very large fraction of primary breast tumors, thus suggesting a possible functional role for BMP7 in breast cancer development. © 2006 Wiley‐Liss, Inc.
Alpha‐tocopherol (vitamin E) induces rapid, nonsustained proliferation in cultured rat microglia
Authors: Flanary Barry E. , Streit Wolfgang J.
Published: January 2006

Microglial cells undergo cell division in vitro, as well as in vivo after brain injury. Mitotic activity of microglia suggests that they have limited life spans and rely on self‐renewal to replace senescent cells. In the current study we examined long‐term effects of antioxidants vitamin E and alpha‐lipoic acid on cultured rat microglia with respect to proliferative ability, telomere length, telomerase activity, and interleukin‐1β (IL‐1β) production. We report that vitamin E induces dramatic microglial proliferation, as measured by MTT assay and BrdU incorporation, surpassing that of the well‐known microglial mitogen granulocyte macrophage–colony stimulating factor, and therefore establishing vitamin E as the most potent, known mitogen for microglia in vitro. The high rate of microglial proliferation resulted in a concomitant decrease in telomere length and telomerase activity. Production of IL‐1β was significantly decreased in vitamin E–treated microglia in vitro. Our findings provide an impetus to investigate potential benefits of vitamin E supplementation on microglial renewal capacity in vivo during aging or after brain injury. © 2006 Wiley‐Liss, Inc.
Systematic Gaussian basis‐set limit using completeness‐optimized primitive sets. A case for magnetic properties
Authors: Manninen Pekka , Vaara Juha
Published: January 2006

We discuss the connection between the completeness of a basis set, measured by the completeness profiles introduced by Chong (Can J Chem 1995, 73, 79) at a certain exponent interval, and the possibility of reproducing molecular properties that arise either in the region close to the atomic nuclei or in the valence region. We present a scheme for generating completeness‐optimized Gaussian basis sets, in which a preselected range of exponents is covered to an arbitrary accuracy. This is done by requiring Gaussian functions, the exponents of which are selected without reference to the atomic structure, to span the range with completeness profile as close to unity as wanted with as few functions as possible. The initial exponent range can be chosen suitable for calculations of molecular energetics or other valence‐like properties. By extending the exponent range, properties requiring augmentation of the basis at a given angular momentum value and/or in a given distance range from the nucleus may be straightforwardly and systematically treated. In this scheme a universal, element‐independent exponent set is generated in an automated way. The relation of basis‐set completeness and performance in the calculation of magnetizability, nuclear magnetic shielding, and spin–spin coupling is tested with the completeness‐optimized primitive sets and literature basis sets. © 2006 Wiley Periodicals, Inc. J Comput Chem 27: 434–445, 2006
Development and progression of alopecia in the vitamin D receptor null mouse
Authors: Bikle Daniel D. , Elalieh Hashem , Chang Sandra , Xie Zhongjian , Sundberg John P.
Published: January 2006

Humans with selected mutations in the vitamin D receptor (VDR) and mouse models lacking VDR develop alopecia. Mice null for the Vdr gene are born with a normal coat of hair, but fail to initiate normal hair follicle cycling. In this study, we examined the morphology of the hair follicle of the Vdr null mouse during days 13–22 when the hair follicle normally initiates and completes the first catagen. We then explored the possibility that the abnormality in hair follicle cycling was associated with abnormal expression of hairless (Hr), a putative transcriptional regulator known to regulate hair follicle cycling and recently shown to regulate VDR transcriptional activity. Our results demonstrate the progressive deterioration of the hair follicle through catagen. Comparable to VDR, Hr was found in the basal cells of the epidermis and ORS of the hair follicle. However, Hr was also found in the IRS and matrix of the follicle, regions with little or no VDR. Hr levels increased during catagen, reaching a peak by day 19. Levels of Hr were greater in the Vdr null mice compared to wildtype controls, results confirmed by quantitative RT‐PCR. We conclude that lack of VDR causes disruption of hair follicle structure during the first catagen resulting in failure of subsequent hair follicle cycling. These changes are associated with increased expression of Hr, suggesting a role for VDR in regulating Hr expression. Both Hr and VDR are required for normal hair follicle cycling. J. Cell. Physiol. 207: 340–353, 2006. © 2006 Wiley‐Liss, Inc.
SOCS‐2 interferes with myotube formation and potentiates osteoblast differentiation through upregulation of JunB in C2C12 cells
Authors: Ouyang Xinshou , Fujimoto Minoru , Nakagawa Reiko , Serada Satoshi , Tanaka Toshio , Nomura Shintaro , Kawase Ichiro , Kishimoto Tadamitsu , Naka Tetsuji
Published: January 2006

Suppressor of cytokine signaling (SOCS)‐2 regulates normal postnatal growth and its deficiency in mice causes gigantism with increased bone length and proportional enlargement in skeletal muscles. Using C2C12 mesenchymal precursor cell line as a model, we investigated a possible role of SOCS‐2 in the differentiation process of mesenchymal precursors. Stable transfection of SOCS‐2 into C2C12 cells resulted in the acceleration of proliferation and survival, and inhibition of spontaneous myotube formation. In addition, SOCS‐2 potentiated bone morphogenic protein (BMP)‐induced transdifferentiation of C2C12 cells into osteoblast phenotypes. These effects of SOCS‐2 on C2C12 cells differed strikingly from that of SOCS‐1, another member of SOCS family, and its mechanisms were evaluated. SOCS‐2 did not alter BMP‐induced phosphorylation and nuclear accumulation of Smad1, nor the expression of inhibitory‐Smads mRNA. However, SOCS‐2 enhanced BMP‐induced transcriptional activation of the Smad‐responsive reporter gene, suggesting that the action of SOCS‐2 is exerted at the transcriptional level. Interestingly, SOCS‐2 overexpression in C2C12 cells increased the endogenous JunB protein, one of the key transcriptional factors in the control of BMP/Smad signaling responsiveness. In addition, the proteasome inhibitor enhanced JunB protein expression in C2C12 cells. Moreover, we found that SOCS‐2 reduced JunB ubiquitination in COS‐7 cells. Although SOCS‐2 is a modulator of growth hormone (GH) signaling, the upregulation of JunB by SOCS‐2 did not require GH signaling. Taken together, these results suggest that SOCS‐2 positively regulates endogenous JunB protein expression in C2C12 cells through inhibition of JunB destabilization by the ubiquitin–proteasome pathway, and thereby regulates the cell fate of mesenchymal precursors. J. Cell. Physiol. 207: 428–436, 2006. © 2006 Wiley‐Liss, Inc.
In vivo association of CReMM/CHD9 with promoters in osteogenic cells
Authors: Shur I. , Socher R. , Benayahu D.
Published: January 2006

Molecular mechanisms that control cell differentiation involve with chromatin remodeling activities. We recently identified Chromatin Related Mesenchymal Modulator (CReMM), a CHD protein expressed by mesenchymal cells. In this study, we analyzed CReMM expression on RNA and protein levels during embryonic development in mouse skeletal tissues. CReMM appears transiently during mesenchymal cell differentiation, being detected first in osteoprogenitors and declining in mature cells. A novel aspect of the study elaborates on in vivo association of CReMM with promoters in cells obtained by laser capture micro‐dissection (LCM) technique from periosteum and endochondreal ossification regions. Using chromatin immunoprecipitation (ChIP), we proved that CReMM binds to skeletal tissue‐specific promoters: CBFA1, biglycan, osteocalcin (OC), collagen‐II, and myosin in a differential manner. The results imply that CReMM selectively interacts with analyzed promoters activated in the tissue at the appropriate time of development. The identification of CReMM and its tissue distribution and function provides an attractive clue for the study of transcriptional regulation of osteogenic cells' maturation. J. Cell. Physiol. 207: 374–378, 2006. © 2006 Wiley‐Liss, Inc.
SERS and infrared reflection‐absorption spectroscopy of NO on cold‐deposited Cu
Authors: Lust M. , Pucci A. , Otto A.
Published: January 2006

Surface enhanced Raman spectroscopy (SERS) of NO on cold‐deposited Cu yields only bands of the dissociation products of NO, but not the stretching bands of NO. In contrast, infrared reflection‐absorption spectroscopy (IRRAS) on similarly prepared samples displays strong NO stretching bands and only a very weak band of N2O from multilayer NO. The differences can be explained neither by thermal or photo‐desorption nor by photochemical effects in the laser focus. Whereas the SERS results may be explained by the action of special sites, it is still unclear why the IRRAS signal from the dissociation products of NO at the ‘catalytically active sites’ is below the noise level. Copyright © 2006 John Wiley & Sons, Ltd.
North–South/South–North partnerships: closing the ‘mutuality gap’
Authors: Johnson Hazel , Wilson Gordon
Published: January 2006

This article examines mutuality and difference in partnerships. Partnership is a widely‐debated concept: it can represent collaboration based on equality and mutually‐beneficial processes and outcomes; it can also involve highly unequal power relations and determination of means and ends. The article examines the construction of mutuality based on difference in practitioner to practitioner partnerships between local governments in Uganda and the UK. It argues that some of the lessons from these partnerships can help to rethink partnerships in other contexts. First, practitioner to practitioner partnerships can pose an alternative to partnerships based simply on divisions of labour between organisations. Second, partnerships conceived as learning models that build on mutuality and difference offer the potential to challenge power relations. Rethinking how practitioner to practitioner partnerships can be made more effective in this respect can provide models for other types of partnership. Copyright © 2006 John Wiley & Sons, Ltd.
Conductivity enhancement in raw polypyrrole and polypyrrole nanoparticle dispersions
Authors: Pomposo José‐Adolfo , Ochoteco Estibalitz , Pozo Cristina , Carrasco Pedro‐Maria , Grande Hans‐Jürgen , Rodríguez Francisco‐Javier
Published: January 2006

For certain commercial applications of polypyrrole (PPy), an enhancement of the electrical conductivity of the material is the key to industrial success. In this paper it will be shown that raw PPy with high conductivity (>150 S/cm) can be obtained in very good yield (>90%) by appropriate selection of both bi‐functional additives and reaction conditions which increase the oxidative polymerization rate of pyrrole. The presence of new active centers for the polymerization is demonstrated by UV measurements. In addition, raw PPy synthesized according to the improved method of synthesis shows good stability of the conductivity upon aging at high temperature (150°C) in air. Finally, new PPy dispersions are reported with an average particle size of 67 nm obtained by sonochemical synthesis that can be incorporated into conventional plastic paints for direct metallization of plastics. The conductivity of the new metallization paint developed was 0.4 S/cm with a PPy content of 10 wt%. Copyright © 2006 John Wiley & Sons, Ltd.
Enhanced funding of pharmacoepidemiology through patenting the disclosure of adverse event information
Authors: Classen John B.
Published: January 2006

Purpose

Known drug adverse events have been estimated to be between the 4th and 6th leading cause of death in the US (1). There are currently insufficient funds to perform the quantity and quality of studies necessary to ensure all drug adverse events are discovered in a timely fashion.

Methods/Results

One approach to attract capital for pharmacoepidemiology studies is to patent the discoveries from the studies. Potential investors, whether executives of branded pharmaceutical companies or not, will consider funding pharmacoepidemiology studies if they can expect to receive competitive returns on their investments. Pharmacoepidemiolists who desire to patent their discoveries should seek novel drug‐drug and drug‐food interactions or negative interactions between drugs and certain phenotypes, genotypes or preexisting comorbidities.

Conclusion

These discoveries can lead to safer, and patentable, use of the drug by avoiding these interactions. Copyright © 2006 John Wiley & Sons, Ltd.
Profiling humoral autoimmune repertoire of dilated cardiomyopathy (DCM) patients and development of a disease‐associated protein chip
Authors: Horn Sabine , Lueking Angelika , Murphy Derek , Staudt Alexander , Gutjahr Claudia , Schulte Kirsten , König Andrea , Landsberger Martin , Lehrach Hans , Felix Stephan B. , Cahill Dolores J.
Published: January 2006

Dilated cardiomyopathy (DCM) is a myocardial disease characterized by progressive depression of myocardial contractile function and ventricular dilatation. Thirty percent of DCM patients belong to the inherited genetic form; the rest may be idiopathic, viral, autoimmune, or immune‐mediated associated with a viral infection. Disturbances in humoral and cellular immunity have been described in cases of myocarditis and DCM. A number of autoantibodies against cardiac cell proteins have been identified in DCM. In this study, we have profiled the autoantibody repertoire of plasma from DCM patients against a human protein array consisting of 37 200 redundant, recombinant human proteins and performed qualitative and quantitative validation of these putative autoantigens on protein microarrays to identify novel putative DCM specific autoantigens. In addition to analyzing the whole IgG autoantibody repertoire, we have also analyzed the IgG3 antibody repertoire in the plasma samples to study the characteristics of IgG3 subclass antibodies. By combining screening of a protein expression library with protein microarray technology, we have detected 26 proteins identified by the IgG antibody repertoire and 6 proteins bound by the IgG3 subclass. Several of these autoantibodies found in plasma of DCM patients, such as the autoantibody against the Kv channel‐interacting protein, are associated with heart failure.
Crystal structure and morphology of phenyl‐capped tetraaniline in the leucoemeraldine oxidation state
Authors: Zhou Yunchun , Geng Jianxin , Li Gao , Zhou Enle , Chen Liang , Zhang Wanjin
Published: January 2006

A series of crystals of phenyl‐capped tetraaniline in the leucoemeraldine oxidation state were obtained at different isothermal temperatures and were observed directly under transmission electron microscope. The crystals obtained at higher temperatures exhibit more perfect structures than those obtained at lower temperatures. Both the lamella thickness and the crystal size increase with crystallization temperature. The tetraaniline is apt to form larger scale crystals under lower degree of supercooling. However, their crystal structures keep steady with the crystallization temperature. The tetramer was found to adopt a monoclinic lattice with unit cell parameter of a = 13.93 Å, b = 8.82 Å, c = 23.20 Å, and β = 95.03°, as determined using electron diffraction tilting method combined with wide‐angle X‐ray diffraction experiment. © 2006 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 44: 764–769, 2006
Prediction of buried helices in multispan alpha helical membrane proteins
Authors: Adamian Larisa , Liang Jie
Published: January 2006

Analysis of a database of structures of membrane proteins shows that membrane proteins composed of 10 or more transmembrane (TM) helices often contain buried helices that are inaccessible to phospholipids. We introduce a method for identifying TM helices that are least phospholipid accessible and for prediction of fully buried TM helices in membrane proteins from sequence information alone. Our method is based on the calculation of residue lipophilicity and evolutionary conservation. Given that the number of buried helices in a membrane protein is known, our method achieves an accuracy of 78% and a Matthew's correlation coefficient of 0.68. A server for this tool (RANTS) is available online at http://gila.bioengr.uic.edu/lab/. Proteins 2006. © 2006 Wiley‐Liss, Inc.
Regeneration of sugarcane elite breeding lines and engineering of stem borer resistance
Authors: Weng Li‐Xing , Deng Haihua , Xu Jin‐Ling , Li Qi , Wang Lian‐Hui , Jiang Zide , Zhang Hai Bao , Li Qiwei , Zhang Lian‐Hui
Published: January 2006

Five elite sugarcane breeding lines were tested for efficiency in embryogenesis and plant regeneration. All of them produced regenerative embryogenic calli but with varied efficiencies. To engineer strongly insect‐resistant sugarcanes, the GC content of a truncated cry1Ac gene, which encodes the active region of Cry1Ac insecticidal δ‐endotoxin, was increased from the original 37.4 to 47.5% following the sugarcane codon usage pattern. The synthetic cry1Ac gene (s‐cry1Ac) was placed under the control of maize ubiquitin promoter and introduced by microprojectile bombardment into the embryogenic calli of sugarcane lines YT79‐177 and ROC16. Southern blotting analysis showed that multicopies of s‐cry1Ac were integrated into the genomes of transgenic sugarcane lines. Immunoblotting analysis identified 18 transgenic lines expressing detectable levels of s‐Cry1Ac, which were estimated in the range of 1.8–10.0 ng mg−1 total soluble proteins. Four transgenic and two parental lines were assayed for sugarcane stem borer resistance in leaf tissue feeding trials and greenhouse plant assays. The results showed that, while the untransformed control lines were severely damaged in both leaves and stems, the transgenic sugarcane lines expressing high levels of s‐Cry1Ac proteins were highly resistant to sugarcane stem borer attack, resulting in complete mortality of the inoculated insects within 1 week after inoculation. Copyright © 2006 Society of Chemical Industry
Effect of interface roughness on the magnetic anisotropy in epitaxial Fe films
Authors: Chemam F. , Boukhalfa R. , Bouabellou A.
Published: January 2006

We have grown by molecular beam epitaxy (MBE) 300 Å Fe films on single crystal MgO(001) substrates with Ag buffer layer with a thickness varying from 0 to 150 Å. The epitaxial growth and structure quality of the films were verified by reflection high‐energy electron diffraction (RHEED) and X‐ray diffraction. Small angle X‐ray diffraction revealed the dependence of interfacial roughness on the thickness of Ag buffer layer. In‐plane magnetic anisotropy was determined by means of magneto‐optic Kerr effect at room temperature. The analysis of hysteresis loops showed a dependence of uniaxial anisotropy field Hu and coercive fields on the Ag buffer layer. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Full electronic structure calculation of the biological activity in P173L enzyme
Authors: Xu L. N. , Zhang L. L. , Guo Z. , Zhou L. X.
Published: January 2006

The biological activity variation along with the temperature in the heat‐sensitive mutant P173L with 26316 electrons has been studied by full electronic structure calculation and parallel molecular dynamics from temperature 302–318 K. The change of the energy gap between the frontier orbital energy level occupied by each of the four residues and the lowest unoccupied molecular orbital energy level was worked out as an index to quantify the biological activity variation. We reproduced the experimental results suggested by Fomenkov et al.: Residues GLU77, ASP94, GLU111, and GLU113 were essential to the enzyme catalytic function and the enzyme cleavage activity is decreased in turn at temperatures 303, 310, and 315 K. Moreover, our calculations revealed more elaborate information that was not found by the experiment: There is a range of temperature (∼307–313 K) between the experimental temperatures 303–315 K in which the enzyme cleavage activity increases. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006
Implementation of the replica‐exchange molecular dynamics method for rigid bodies
Authors: Moskovsky A. A. , Vanovschi V. V. , Konyukhov S. S. , Nemukhin A. V.
Published: January 2006

We describe an implementation of the replica‐exchange molecular dynamics (REMD) algorithm for rigid‐body molecular dynamics targeting its application in the flexible effective fragment quantum mechanical–molecular mechanical (QM/MM) method. The main objective of the stage of the project is to obtain an efficient minimization tool for the MM subsystem. The computer program developed allows one to carry out calculations of molecular dynamics trajectories for atomic particles and for rigid bodies at constant temperature, using the chain Nose–Hoover thermostat. For REMD calculations, the OpenTS dynamic parallelization is used, which allows one to run simulations either on single computational clusters or on meta‐clusters. A two‐level parallelization scheme has been implemented, assuming that both REMD (upper level) and individual molecular dynamics trajectories (lower level) are parallelized. Structures of small and large water clusters as well as protein conformations are considered as first applications. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006
Simultaneous determination of ten antihistamine drugs in human plasma using pipette tip solid‐phase extraction and gas chromatography/mass spectrometry
Authors: Hasegawa Chika , Kumazawa Takeshi , Lee Xiao‐Pen , Fujishiro Masaya , Kuriki Ayako , Marumo Akemi , Seno Hiroshi , Sato Keizo
Published: January 2006

Ten antihistamine drugs, diphenhydramine, orphenadrine, chlorpheniramine, diphenylpyraline, triprolidine, promethazine, homochlorcyclizine, cyproheptadine, cloperastine and clemastine, have been found to be extractable from human plasma samples using MonoTip C18 tips, inside which C18‐bonded monolithic silica gel was fixed. Human plasma (0.1 mL) containing the ten antihistamines was mixed with 0.4 mL of distilled water and 25 µL of a 1 M potassium phosphate buffer (pH 8.0). After centrifugation of the mixture, the supernatant fraction was extracted to the C18 phase of the tip by 25 repeated aspirating/dispensing cycles using a manual micropipettor. The analytes retained on the C18 phase were then eluted with methanol by five repeated aspirating/dispensing cycles. The eluate was injected into a gas chromatography (GC) injector without evaporation and reconstitution steps, and was detected by a mass spectrometer with selected ion monitoring in the positive‐ion electron impact mode. The separation of the ten drugs from each other and from impurities was generally satisfactory using a DB‐1MS column (30 m × 0.32 mm i.d., film thickness 0.25 µm). The recoveries of the ten antihistamines spiked into plasma were 73.8–105%. The regression equations for the ten antihistamines showed excellent linearity with detection limits of 0.02–5.0 ng/0.1 mL. The within‐day and day‐to‐day coefficients of variation for plasma were not greater than 9.9%. The data obtained from determination of diphenhydramine and chlorpheniramine in human plasma after oral administration of the drugs are also presented. Copyright © 2006 John Wiley & Sons, Ltd.
High‐throughput quantification for a drug mixture in rat plasma – a comparison of Ultra Performance™ liquid chromatography/tandem mass spectrometry with high‐performance liquid chromatography/tandem mass spectrometry
Authors: Yu Kate , Little David , Plumb Rob , Smith Brian
Published: January 2006

A quantitative Ultra Performance™ liquid chromatography/tandem mass spectrometry (UPL/MS/MS) protocol was developed for a five‐compound mixture in rat plasma. A similar high‐performance liquid chromatography/tandem mass spectrometry (HPLC/MS/MS) quantification protocol was developed for comparison purposes. Among the five test compounds, three preferred positive electrospray ionization (ESI) and two preferred negative ESI. As a result, both UPLC/MS/MS and HPLC/MS/MS analyses were performed by having the mass spectrometer collecting ESI multiple reaction monitoring (MRM) data in both positive and negative ion modes during a single injection. Peak widths for most standards were 4.8 s for the HPLC analysis and 2.4 s for the UPLC analysis. There were 17 to 20 data points obtained for each of the LC peaks. Compared with the HPLC/MS/MS method, the UPLC/MS/MS method offered 3‐fold decrease in retention time, up to 10‐fold increase in detected peak height, with 2‐fold decrease in peak width. Limits of quantification (LOQs) for both HPLC and UPLC methods were evaluated. For UPLC/MS/MS analysis, a linear range up to four orders of magnitude was obtained with r2 values ranging from 0.991 to 0.998. The LOQs for the five analytes ranged from 0.08 to 9.85 ng/mL. Three levels of quality control (QC) samples were analyzed. For the UPLC/MS/MS protocol, the percent relative standard deviation (RSD%) for low QC (2 ng/mL) ranged from 3.42 to 8.67% (N = 18). The carryover of the UPLC/MS/MS protocol was negligible and the robustness of the UPLC/MS/MS system was evaluated with up to 963 QC injections. Copyright © 2006 John Wiley & Sons, Ltd.
Integration testing of object‐oriented components using finite state machines
Authors: Gallagher Leonard , Offutt Jeff , Cincotta Anthony
Published: January 2006

In object‐oriented terms, one of the goals of integration testing is to ensure that messages from objects in one class or component are sent and received in the proper order and have the intended effect on the state of the objects that receive the messages. This research extends an existing single‐class testing technique to integration testing of multiple classes. The single‐class technique models the behaviour of a single class as a finite state machine, transforms the representation into a data flow graph that explicitly identifies the definitions and uses of each state variable of the class, and then applies conventional data flow testing to produce test case specifications that can be used to test the class. This paper extends those ideas to inter‐class testing by developing flow graphs, finding paths between pairs of definitions and uses, detecting some infeasible paths and automatically generating tests for an arbitrary number of classes and components. It introduces flexible representations for message sending and receiving among objects and allows concurrency among any or all classes and components. Data flow graphs are stored in a relational database and database queries are used to gather def‐use information. This approach is conceptually simple, mathematically precise, quite powerful and general enough to be used for traditional data flow analysis. This testing approach relies on finite state machines, database modelling and processing techniques and algorithms for analysis and traversal of directed graphs. The paper presents empirical results of the approach applied to an automotive system. This work was prepared by U.S. Government employees as part of their official duties and is, therefore, a work of the U.S. Government and not subject to copyright. Published in 2006 by John Wiley & Sons, Ltd.
Assessment of unilateral spatial neglect in children using the Teddy Bear Cancellation Test
Authors: Laurent‐Vannier Anne , Chevignard Mathilde , Pradat‐Diehl Pascale , Abada Geneviève , De Agostini Maria
Published: January 2006

The purpose of the study was to provide normative data for the Teddy Bear Cancellation Test (TBCT) and to evaluate prospectively the frequency of unilateral spatial neglect (USN) in children with acquired brain injury (ABI). In the control group (n=419; 218 males, 201 females; mean age 5y 1mo [SD 1y 4mo]; range 3 to 8y) omissions were rare and decreased with age. A left displacement of the first three teddy bears cancelled was observed with increasing age. This preferential left‐to‐right cancelling strategy was interpreted as learned under the influence of reading habits. The same test was used prospectively in 41 children with ABI (24 males, 17 females; mean age 5y 5mo [SD 2y]; range 3 to 8y) admitted to a paediatric rehabilitation department specializing in acquired brain lesions. In patients and controls, children under 6 years of age omitted more items than older children. The localization of omissions was skewed significantly to the left in children with right‐sided lesions compared with children with left‐sided lesions. USN was observed in seven patients with ABI. Left USN was found in three of the 10 patients with right‐sided ABI. Right USN was present in two of the patients with 15 left‐sided ABI and two of the 16 patients with non‐lateralized ABI. Left USN is frequent in children after right‐sided brain injury. The relatively high incidence of right spatial neglect in children is discussed in relation to the development of hemispheric specialization.
Evidence from two genetic syndromes for the independence of spatial and visual working memory
Authors: Vicari Stefano , Carlesimo Giovanni Augusto
Published: January 2006

This study aimed at investigating the possible dissociation between visual‐object and visual‐spatial working memory (WM) in individuals with Williams syndrome (WS) and Down syndrome (DS). Four study groups were included: WS group (10 males, 5 females) with a mean chronological age (CA) of 19 years 8 months (SD 6y 1mo) and a mean mental age (MA)of 6 years 11 months (SD 1y 5mo); WS comparison group (7 males, 8 females) comprised of typically developing children with a mean CA of 6 years 10 months (SD 10mo) and a mean MA of 6 years 11 months (SD 8mo)matched as a group with the participants with WS on the basis of mental age; DS group (11 males, 7 females) with a mean CA of 15 years 10 months (SD 5y 8mo) and a mean MA of 5 years 2 months (SD 8mo); and DS comparison group (10 males, 8 females) with a mean CA of 5 years and 1 month (SD 7mo)and a mean MA of 5 years 2 months (SD 8mo) selected to match the DS group on the basis of mental age. They were all administered tests that explored visual perception (Visual Perception Test ‐ Subtest 4 and Line Orientation tests), visual imagery (imaging the colour of objects and the tail length of well‐known animals), spatial imagery (mental rotation of visually presented or verbally evoked objects), and WM for visual‐object and visual‐spatial information. Individuals with WS exhibited specific difficulties in the visual‐spatial, but not the visual‐object, WM task. Instead, people with DS showed reduced performance in both tests. However, whereas the observed deficit in individuals with DS persisted when perceptual abilities were taken into account, the deficit in individuals with DS was compensated when their scores were adjusted for performance on perceptual tasks. These results support the hypothesis of a dissociation within the sketch‐pad slave system in the WM model and reinforce the view of intellectual disability as a non‐unitary condition.
Predicting additional care in young children with neurodevelopmental disability: a systematic literature review
Authors: Meester‐Delver Anke , Beelen Anita , Hennekam Raoul , Hadders‐Algra Mijna , Nollet Frans
Published: January 2006

Children with developmental disabilities often show a variety of associated impairments that lead to a lifelong need for additional care. Careful assessment of these impairments is required not only for diagnostic purposes but also to inform the parents about the expected additional care needs in the future. We present a systematic review of the literature to identify instruments that classify the type and amount of this care for the individual child. A literature search was performed in the Medline database (January 1966‐ June 2005) on instruments that classify the type and amount of expected additional care needs in the future. Seven standardized measurement instruments describing current additional care needs were identified, but none of these instruments was developed to provide information about the expected need for additional care in the future. For parents of young children with non‐progressive developmental disorders it is essential to be informed on the expectations of required additional care in the future. However, comprehensive instruments providing such information are currently lacking and, thus, need to be developed.
An Edition of the Long Version of Peter the Chanter's Verbum AbbreviatumPetri Cantoris Parisiensis. Verbum adbreviatum. Textus conflatus. By Monique Boutry. (Corpus Christianorum. Continuatio Mediaeualis, 196.) Pp. lxxiv+994. Turnhout: Brepols, 2004. €395. 2 503 04961 3
Authors: BALDWIN JOHN W.
Published: January 2006

Peter the Chanter (d. 1197) was arguably the foremost theologian at the Paris of his day. Envisaging the house of theology as composed of lecturing, disputing and preaching, he himself was the first to compose lectiones on all the books of the Bible; his questiones were collected in a large Summa de sacramentis; and although few of his sermons have survived, he wrote a popular manual of moral theology for preachers, the Verbum abbreviatum (VA), that has survived in nearly a hundred manuscripts across western Europe. The VA was the first of the Chanter's works to be published, in 1639 by the Belgian monk Georges Galopin in a serviceable edition from three northern French manuscripts. It was given wide circulation when abbé Migne republished it in the Patrologia Latina in 1855. In 1905 Camille Miroux was the first to recognise that the VA had survived in two versions, a long one in six manuscripts and a short one in at least forty manuscripts that became the vulgate version and was that edited by Galopin. In a Handschrift Reise in 1959 I examined seventy-three of the eighty-five manuscripts known to me and published my findings, classifications and conclusions in Masters, princes and merchants. Galopin had also found a fragment of the long version which he published as an appendix to his own edition. Although it is futile to determine how many have consulted this fragment in Migne's reprint, to my knowledge I am the only one who has printed extracts from the complete long version.
Faith and History on the Eve of Enlightenment: Ernst Salomon Cyprian, Gottfried Arnold, and the History of Heretics
Authors: DIXON C. SCOTT
Published: January 2006

When it first appeared in Germany, Gottfried Arnold's History of heretics (1699) was a publishing sensation, immediately causing a stir due to its radical reinterpretation of the Christian past. Numerous scholars wrote against it, but the most determined was the Orthodox Lutheran Ernst Salomon Cyprian, who considered the central thesis of the work – that the history of the Christian Church was a history of decline – a deliberate attack on the principles of Lutheran belief. In Cyprian's view, Arnold's reading of the past was shaped by a cast of personal faith which not only rewrote the Protestant narrative of Christian history, but threatened the very fabric of Lutheran belief.