bluuebunny/crossref_metadata_2025_split huggingface dataset:
Backbone–backbone geometry of tertiary contacts between α‐helices
Authors: Källblad Per , Dean Philip M. 
Published: June 2004

AbstractKnowledge about how secondary‐structure elements combine together to form the tertiary structure is crucial for understanding protein folding. We have examined packing solutions for α‐helices by performing a crystal survey of the underlying backbone–backbone inter‐geometry of tertiary contacts. The information content is different from, and complementary to, the results of side‐chain to side‐chain crystal surveys and studies of helix–helix‐crossing angles. Six geometry descriptors were recorded from each tertiary contact in nonredundant data sets of globular and transmembrane proteins. The descriptors included distances, angles, and dihedral angles that together describe completely the underlying geometry of each contact. From the results it is possible to identify differences in the geometry requirements of tertiary contacts between α‐helices in general and transmembrane α‐helices. The differences become more apparent when the correlation between the different geometry descriptors is analyzed. The results are compared with those of other types of secondary structure. Finally, an investigation of how the geometry of tertiary contacts changes with the amino‐acid types involved in the contact is performed using multivariate techniques. The results of this study provide a well‐defined overview of the underlying structural framework of tertiary contacts between α‐helices, in both globular and TM environments, that will have valuable implications for predicting protein tertiary structure. Proteins 2004. © 2004 Wiley‐Liss, Inc.
Conventional and unconventional techniques in quantum chemistry
Authors: Quiney Harry M. , Grant Ian P. 
Published: June 2004

AbstractThe computational cost of ab initio molecular electronic structure calculations is dominated by the generation of electron–electron repulsion integrals, of which there are O(N4), where N is the dimension of the basis set. Even if allowance is made for integral economization schemes, the rapidity with which the computational cost grows as N increases is a problem for all ab initio calculations, particularly the intrinsically more laborious relativistic approaches. There is therefore a strong motive to search for accurate but inexpensive algorithms without having to simplify the equations. We report a preliminary assessment of a promising new scheme that scales much more slowly with N. The key idea is the equivalence of the conventional expression for the energy of an atom or molecule with the integral of the energy density of the related electromagnetic fields over all space. The electrostatic energy density can be constructed cheaply as the sum of scalar products of O(N2) pairs of electric fields Eij(r) generated by the overlap charge densities ρij(r). The integration of the total energy density over the whole molecule can be done by adapting a numerical integration scheme used in contemporary density functional (DFT) algorithms requiring only a relatively small number of cubature points. We explore the implications of this approach for calculations in quantum chemistry. In relativistic quantum theory the total energy can be expressed as the sum of scalar products of both electric Eij(r) fields and magnetic Bij(r) fields generated by the overlap charge and current densities. In the long‐wavelength approximation, in which retardation is neglected, this leads to a new interpretation of the Breit interaction energy as the energy of the associated magnetic fields. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2004
Closed formulae for (1s|1s), Slater two‐center integrals, using the three‐center nuclear attraction integral program in spherical coordinates
Authors: Jain J. L. , Jones H. W. , Weatherford C. A. , Hoggan P. E. 
Published: June 2004

AbstractThe strategy of using expansions in spherical harmonics of displaced Slater‐type (exp(−αx)) orbitals to evaluate multicenter molecular integrals is applied to three‐centered nuclear attraction integrals (potential due to the product of separated Slater‐type orbitals). Closed formulae are produced for nine terms of an infinite series for interior region, (inside − ipot) r2 < a, and 14 terms for Exterior Region, (outside − epot) r2 > a. The value a = 2 is chosen for the interior region and r = 14 for the exterior region. Our focus is to obtain a closed formula for the Slater formula. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2004
Produktmodelle zur Optimierung der Projektabwicklung
Authors: Haller Hans‐Walter , Hörenbaum Christoph , Osterrieder Peter , Saal Helmut 
Published: June 2004

AbstractEin Produktmodell ist ein ganzheitlicher EDV‐Standard, durch den sämtliche Anwendungssoftware in Bauprojekten verlustfrei gekoppelt werden kann. In diesem Beitrag werden die Entstehung und die Anwendung zweier verwandter Produktmodelle beschrieben: die “Produktschnittstelle Stahlbau”, die für die Projektabwicklung und die Fertigung im Stahlbau entwickelt wurde und vom Deutschen Stahlbau‐Verband zur Anwendung empfohlen wird, sowie deren Übertragung auf den Holzbau, das Produktmodell “Datentransfer im Holzbau (DtH)“.
A numerical method for choice of weighting matrices in active controlled structures
Authors: AGRANOVICH G. , RIBAKOV Y. , BLOSTOTSKY B. 
Published: June 2004

AbstractA feedback control system usually implements active and semi‐active control of seismically excited structures. The objective of the control system is described by a performance index, including weighting matrix norms. The choice of weighting matrices is usually based on engineering experience. A new procedure for weighting matrix components choice based on the parametric optimization method is developed in this study. It represents a two‐step optimization process. In the first step a discrete‐time control system is synthesized according to a quadratic performance index. In the second step the weighting coefficients are obtained using the results of the first step. Numerical simulation of a typical structure subjected to earthquakes is carried out in order to demonstrate the effectiveness of the proposed method. It shows that applying the proposed technique provides a choice of the weighting matrices and results in enhanced structural behaviour under different earthquakes. Copyright © 2003 John Wiley & Sons, Ltd.
Role of the 14–3–3 protein in carbon metabolism of the pathogenic yeast Candida albicans
Authors: Wang Ying‐Kai , Das Biswadip , Huber David H. , Wellington Melanie , Kabir M. Anaul , Sherman Fred , Rustchenko Elena 
Published: June 2004

AbstractWe previously demonstrated that the pathogenic yeast Candida albicans effectively adapts to utilize L‐sorbose (Sou+) by a novel mechanism based on the loss of one copy of chromosome 5, probably due to the reduction of copy number of a negative regulator located on this chromosome. We report here another negative regulator of L‐sorbose utilization, an orthologue of the Saccharomyces cerevisiae BMH1 gene, which encodes the evolutionarily conserved protein 14–3–3. This essential gene is located on chromosome 1, does not have paralogues, and is supposedly a component of the regulatory network. Experiments involving disruption of one allele of BMH1 and overexpression of BMH1 revealed that BMH1 represses the transcription of SOU1, which is responsible for the utilization of L‐sorbose. Although the exact mechanism of the interaction between BMH1 and SOU1 is not known, it is clear that the control is based on the ratio of gene copy number, and that BMH1 does not control the loss of chromosome 5, the major mechanism producing Sou+ mutants. We propose that function of BMH1 as a negative regulator of SOU1 contributes to a general cellular homeostasis. This is a first report on the role of the C. albicans essential gene BMH1 as a negative regulator of the utilization of secondary carbon source in yeast, which further substantiates the involvement of 14–3–3 proteins in diverse functions. Copyright © 2004 John Wiley & Sons, Ltd.
A simple and efficient procedure for transformation of Schizosaccharomyces pombe
Authors: Morita Tomotake , Takegawa Kaoru 
Published: June 2004

AbstractWe describe a simple and efficient procedure for transformation of Schizosaccharomyces pombe. Sz. pombe colonies grown on minimal (SD) plates were directly removed and suspended in a 100 µl reaction mixture containing 70 µl PLATE solution (50% polyethylene glycol‐4000, 100 mM lithium acetate, 10 mM Tris–HCl, pH 4.9, and 1 mM EDTA), 10 µl plasmid DNA (1 µg), 10 µl carrier DNA (100 µg) and 10 µl sterile distilled water. After incubation at 30 °C for 1 h followed by heat shock treatment at 42 °C for 15 min, the reaction mixture was spread on a selection plate. The transformation efficiency obtained using the procedure was approximately 8000 transformants/µg DNA. The method is simple and time‐saving, making it especially useful for a large number of samples and when a high transformation efficiency is not required. Copyright © 2004 John Wiley & Sons, Ltd.
Optimized cassettes for fluorescent protein tagging in Saccharomyces cerevisiae
Authors: Sheff Mark A. , Thorn Kurt S. 
Published: June 2004

AbstractGreen fluorescent protein (GFP) has become an increasingly popular protein tag for determining protein localization and abundance. With the availability of GFP variants with altered fluorescence spectra, as well as GFP homologues from other organisms, multi‐colour fluorescence with protein tags is now possible, as is measuring protein interactions using fluorescence resonance energy transfer (FRET). We have created a set of yeast tagging vectors containing codon‐optimized variants of GFP, CFP (cyan), YFP (yellow), and Sapphire (a UV‐excitable GFP). These codon‐optimized tags are twice as detectable as unoptimized tags. We have also created a tagging vector containing the monomeric DsRed construct tdimer2, which is up to 15‐fold more detectable than tags currently in use. These tags significantly improve the detection limits for live‐cell fluorescence imaging in yeast, and provide sufficient distinguishable fluorophores for four‐colour imaging. Copyright © 2004 John Wiley & Sons, Ltd.
To be suspended or to be cut off? Differences in the performance of two types of leaf‐rolls constructed by the attelabid beetle Cycnotrachelus roelofsi
Authors: Kobayashi Chisato , Kato Makoto 
Published: June 2004

AbstractThe attelabid beetle Cycnotrachelus roelofsi constructs two types of leaf‐rolls (cradles): one is suspended from leaves (suspended type), and the other is severed from the leaves (cut‐off type). To evaluate differences in performance between these two cradle types, we monitored densities, survival rates, and mortality factors throughout the active season, from April to June. The proportions of the two cradle types changed over time; the suspended type was dominant early in the season but was gradually replaced by the cut‐off type. Irrespective of differences in mortality factors between the two cradle types, the survival rate was always higher in the cut‐off type than in the suspended type. Beetle mortality tended to be highest at the egg stage, and the predominant cause of mortality was parasitism by two minute trichogrammatid wasp species, Poropoea morimotoi and P. sp.1. Parasitism by P. morimotoi was significantly higher in cut‐off cradles than in suspended cradles, when cut‐off cradles were abundant, whereas parasitism by P. sp.1 tended to be higher in suspended cradles when suspended cradles were abundant. These results suggest opposed frequency‐dependent attacks by P. morimotoi and P. sp.1. We discuss how these egg parasitoids maintain coexistence of these two cradle types.
The effect of clopidogrel on apoptosis—an in vivo study
Authors: Yalcin Ridvan , Erkan Aycan , Ergun Mehmet Ali , Yurtcu Erkan 
Published: June 2004

AbstractClopidogrel is widely used in cardiovascular medicine, and is believed to play an important role in the pathogenesis of many cardiovascular disease processes. In particular, patients undergoing coronary stenting, who are commonly treated with clopidogrel, are candidates for in‐stent restenosis. This is mainly caused by neointimal hyperplasia, so it is important to consider whether clopidogrel affects neointimal hyperplasia via apoptosis. Lymphocytes, especially T‐cells, are known to play a key role in the initiation and formation of atherosclerotic plaques. The aim of this study was to investigate the effect of clopidogrel on human lymphocyte apoptosis, using a DNA fragmentation assay.
Behavioral manifestations of autism in the first year of life
Authors: Zwaigenbaum Lonnie , Bryson Susan , Rogers Tracey , Roberts Wendy , Brian Jessica , Szatmari Peter 
Published: June 2004

AbstractIn the interest of more systematically documenting the early signs of autism, and of testing specific hypotheses regarding their underlying neurodevelopmental substrates, we have initiated a longitudinal study of high‐risk infants, all of whom have an older sibling diagnosed with an autistic spectrum disorder. Our sample currently includes 150 infant siblings, including 65 who have been followed to age 24 months, who are the focus of this paper. We have also followed a comparison group of low‐risk infants. Our measures include a novel observational scale (the first, to our knowledge, that is designed to assess autism‐specific behavior in infants), a computerized visual orienting task, and standardized measures of temperament, cognitive and language development. Our preliminary results indicate that by 12 months of age, siblings who are later diagnosed with autism may be distinguished from other siblings and low‐risk controls on the basis of: (1) several specific behavioral markers, including atypicalities in eye contact, visual tracking, disengagement of visual attention, orienting to name, imitation, social smiling, reactivity, social interest and affect, and sensory‐oriented behaviors; (2) prolonged latency to disengage visual attention; (3) a characteristic pattern of early temperament, with marked passivity and decreased activity level at 6 months, followed by extreme distress reactions, a tendency to fixate on particular objects in the environment, and decreased expression of positive affect by 12 months; and (4) delayed expressive and receptive language. We discuss these findings in the context of various neural networks thought to underlie neurodevelopmental abnormalities in autism, including poor visual orienting. Over time, as we are able to prospectively study larger numbers and to examine interrelationships among both early‐developing behaviors and biological indices of interest, we hope this work will advance current understanding of the neurodevelopmental origins of autism.
Intraoral Drainage: Recommended as the Initial Approach for the Treatment of ParapHaryngeal Abscesses
Authors: Amar Yannick G. , Manoukian John J. 
Published: June 2004

OBJECTIVEWe sought to compare the efficacy, safety, and cost of intraoral drainage (IOD) of parapharyngeal abscesses (PPAs) in the pediatric population with those of the more commonly used external neck drainage (END).PATIENTS AND STUDY DESIGN AND SETTINGAn 11‐year retrospective review was conducted of all patients admitted to a tertiary‐care, university‐affiliated, pediatric hospital with a diagnosis of PPA. Patients were divided into 2 groups according to the treatment received (IOD or END) and were followed to 1 month postoperatively. All children referred to our institution with a final diagnosis of PPA were included in the study.OUTCOMEOutcome measures were duration of anesthesia, duration of postoperative intravenous antibiotics (DPOIA), length of postoperative hospital stay (LPOHS), and occurrence of complications.RESULTSFifteen patients underwent IOD, and 10 patients, END. IOD shortened anesthesia time by 31.7 minutes compared with END (P = 0.0003). IOD was associated with a decrease in DPOIA and LPOHS by 1.1 days (P = 0.1931) and 1.6 days (P = 0.0649), respectively. The cost of treatment was thereby reduced. No complications were encountered in either group.CONCLUSIONSIOD is a safe and effective treatment for PPA in the pediatric population. It leads to decreased morbidity, shortened anesthesia time, and reduced economic burden. (Otolaryngol Head Neck Surg 2004;130:676‐80.)
Pediatric Total Tonsillectomy Using Coblation Compared to Conventional Electrosurgery: A Prospective, Controlled Single‐Blind Study
Authors: Stoker Kelly E. , Don Debra M. , Kang D. Richard , Haupert Michael S. , Magit Anthony , Madgy David N. 
Published: June 2004

OBJECTIVEPostoperative recovery after tonsillectomy using Coblation excision (CES) was compared with conventional electrosurgery (ES).STUDY DESIGN AND SETTINGPatients aged 3 to 12 years from 3 clinical sites were randomly assigned and blinded to receive tonsillectomy using CES (n = 44) or ES (n = 45).RESULTSOperative parameters did not differ between groups. Return to normal diet, activity, and pain‐free status were similar, although fewer CES patients contacted the physician regarding postoperative complications (33% vs 54%; p = 0.081), experienced nausea (35% vs 62%, p = 0.013), or had localized site‐specific swelling (p < 0.05) during the 2 weeks after surgery. In addition, CES children tended to discontinue prescription narcotics 1 day earlier than ES patients (7 vs 8 days, p = 0.071) and took one half as many daily doses. More CES than ES parents rated the postoperative experience as ‘better than expected’ (79% vs 60%, p = 0.055).CONCLUSION AND SIGNIFICANCE: Children who received CES tonsillectomy appeared to experience a better quality postoperative course, with no detriment to operative benefits of conventional electrosurgery. (Otolaryngol Head Neck Surg 2004;130: 666‐75.)
Practice Parameter: Laryngeal Electromyography (An Evidence‐Based Review)
Authors: Sataloff Robert T. , Mandel Steven , Mann Eric A. , Ludlow Christy L. 
Published: June 2004

This paper reports on an evidence‐based review of laryngeal electromyography (EMG) as a technique for use in the diagnosis, prognosis, and treatment of laryngeal movement disorders including the laryngeal dystonias, vocal fold paralysis, and other neurolaryngological disorders. The authors performed a systematic review of the medical literature from 1944 through 2001 on the clinical application of EMG to laryngeal disorders. The review yielded 584 articles of which 33 met the predefined inclusion criteria. The evidence demonstrated that in a double‐blind treatment trial of botulinum toxin versus saline, laryngeal EMG used to guide injections into the thyroarytenoid muscle in persons with adductor spasmodic dysphonia was beneficial. A cross‐over comparison between laryngeal EMG‐guided injection and endoscopic injection of botulinum toxin into the posterior cricoarytenoid muscle in abductor spasmodic dysphonia found no significant difference between the 2 techniques and no significant treatment benefit. Based on the evidence, laryngeal EMG is possibly useful for the injection of botulinum toxin into the thyroarytenoid muscle in the treatment of adductor spasmodic dysphonia. There were no evidence‐based data sufficient to support or refute the value of laryngeal EMG for the other uses investigated, although there is extensive anecdotal literature suggesting that it is useful for each of them. There is an urgent need for evidence‐based research addressing other applications in the use of laryngeal EMG for other applications. (Otolaryngol Head Neck Surg 2004;130: 770‐9.)
Geometry of the DNA strands within the RecA nucleofilament: role in homologous recombination
Authors: Prévost Chantal , Takahashi Masayuki 
Published: June 2004

1. Introduction 4302. Transformations of the RecA filament 4312.1 The different forms of the RecA filament 4312.2 Orientation and position of the RecA monomers in the active filament 4332.3 Transmission of structural information along the filament 4333. RecA-induced DNA deformations 4353.1 Characteristics of RecA-bound DNA 4353.2 Stretching properties of double-stranded DNA 4363.3 DNA bound to architectural proteins 4373.4 Implications for RecA-induced DNA deformations 4383.5 Axial distribution of the DNA stretching deformation 4384. Contacts between RecA and the DNA strands 4404.1 The DNA-binding sites 4404.2 Possible arrangement of loops L1 and L2 and the three bound strands of DNA 4425. Strand arrangement during pairing reorganization 4445.1 Hypotheses for DNA strand association 4445.2 Association via major or minor grooves 4465.3 Post-strand exchange geometries 4466. Conclusion 4477. Acknowledgments 4488. References 448Homologous recombination consists of exchanging DNA strands of identical or almost identical sequence. This process is important for both DNA repair and DNA segregation. In prokaryotes, it involves the formation of long helical filaments of the RecA protein on DNA. These filaments incorporate double-stranded DNA from the cell's genetic material, recognize sequence homology and promote strand exchange between the two DNA segments. DNA processing by these nucleofilaments is characterized by large amplitude deformations of the double helix, which is stretched by 50% and unwound by 40% with respect to B-DNA. In this article, information concerning the structure and interactions of the RecA, DNA and ATP molecules involved in DNA strand exchange is gathered and analyzed to present a view of their possible arrangement within the filament, their behavior during strand exchange and during ATP hydrolysis, the mechanism of RecA-promoted DNA deformation and the role of DNA deformation in the process of homologous recombination. In particular, the unusual characteristics of DNA within the RecA filament are compared to the DNA deformations locally induced by architectural proteins which bind in the DNA minor groove. The possible role and location of two flexible loops of RecA are discussed.
The ElectroAcoustic Resource Site (EARS): philosophy, foundation and aspirations
Authors: ATKINSON SIMON , LANDY LEIGH 
Published: June 2004

This paper introduces the ElectroAcoustic Resource Site project (EARS), taking a tripartite approach: first outlining the project's philosophy, then reporting on work-to-date and finishing with a discussion of the project's ambitions and aims.The project's aim is the development of a dynamic, multi-lingual, international, publicly available Internet-based bibliographical resource designed to enhance the scholarly infrastructure of electroacoustic music studies, in particular, the musicology of electroacoustic music. Through the use of hypertext structures and linking systems the site will help to contextualise specific research within the broad field of electroacoustic music studies, as well as making helpful links between related areas/items of scholarship. The project aspires to assist access to current, past and evolving areas of scholarship and will attempt to redress certain imbalances in the ease of access to areas of research within the field. The project will strive to conceive of electroacoustic music in its widest possible sense, acknowledge the interdisciplinary nature of the field, and aspire to the greatest possible breadth and inclusiveness. The EARS project is coordinated by an international consortium, is directed by the authors and can be found at http://www.mti.dmu.ac.uk/EARS