bluuebunny/crossref_metadata_2025_split huggingface dataset:
Site‐specific N‐glycosylation analysis: matrix‐assisted laser desorption/ionization quadrupole‐quadrupole time‐of‐flight tandem mass spectral signatures for recognition and identification of glycopeptides
Authors: Krokhin Oleg , Ens Werner , Standing Kenneth G. , Wilkins John , Perreault Hélène 
Published: August 2004

AbstractThe identification of glycosylation sites in proteins is often possible through a combination of proteolytic digestion, separation, mass spectrometry (MS) and tandem MS (MS/MS). Liquid chromatography (LC) in combination with MS/MS has been a reliable method for detecting glycopeptides in digestion mixtures, and for assigning glycosylation sites and glycopeptide sequences. Direct interfacing of LC with MS relies on electrospray ionization, which produces ions with two, three or four charges for most proteolytic peptides and glycopeptides. MS/MS spectra of such glycopeptide ions often lead to ambiguous interpretation if deconvolution to the singly charged level is not used. In contrast, the matrix‐assisted laser desorption/ionization (MALDI) technique usually produces singly charged peptide and glycopeptide ions. These ions require an extended m/z range, as provided by the quadrupole‐quadrupole time‐of‐flight (QqTOF) instrument used in these experiments, but the main advantages of studying singly charged ions are the simplicity and consistency of the MS/MS spectra. A first aim of the present study is to develop methods to recognize and use glycopeptide [M+H]+ ions as precursors for MS/MS, and thus for glycopeptide/glycoprotein identification as part of wider proteomics studies. Secondly, this article aims at demonstrating the usefulness of MALDI‐MS/MS spectra of N‐glycopeptides. Mixtures of diverse types of proteins, obtained commercially, were prepared and subjected to reduction, alkylation and tryptic digestion. Micro‐column reversed‐phase separation allowed deposition of several fractions on MALDI plates, followed by MS and MS/MS analysis of all peptides. Glycopeptide fractions were identified after MS by their specific m/z spacing patterns (162, 203, 291 u) between glycoforms, and then analyzed by MS/MS. In most cases, MS/MS spectra of [M+H]+ ions of glycopeptides featured peaks useful for determining sugar composition, peptide sequence, and thus probable glycosylation site. Peptide‐related product ions could be used in database search procedures and allowed the identification of the glycoproteins. Copyright © 2004 John Wiley & Sons, Ltd.
Channel estimation and interference suppression for uplink CDMA mobile communication systems
Authors: Zheng Zi‐Wei , Yang Zhi‐Xing , Zhu Yi‐Sheng , Pan Chang‐Yong 
Published: August 2004

AbstractWireless communications for mobile telephone and data transmission is currently undergoing very rapid development. Code division multiple‐access (CDMA) implemented with direct sequence spread spectrum signaling is among the most promising multiplexing technologies for cellular telecommunications services. In this paper, jointly period inserted pilot symbols assisted recursive (PIPSAR) channel estimation and interference suppression techniques are proposed for uplink CDMA mobile communication systems. The uplink CDMA mobile communication system model is described in the form of space‐time domain through antenna array and multipath expression. Interference suppression is achieved by using adaptive minimum mean squared error (MMSE) digital filters that span several successive received chip oversampling vectors of a symbol interval. PIPSAR techniques are used to estimate channel parameters. The correlation between the successive periods is considered to further improve the performance of the proposed scheme. Analysis and simulations are used to evaluate the performance of the proposed scheme. Copyright © 2004 John Wiley & Sons, Ltd.
Radio resource metric estimation for a TDD‐CDMA system supporting wireless internet traffic
Authors: Lee Yeonwoo , McLaughlin Steve 
Published: August 2004

AbstractIn this paper, the effect of wireless internet traffic on the functionality of a radio resource metric estimation (RME) applicable to a TDD‐CDMA system which incorporates a multirate transmission scheme (such as multicode and multislot) with simple call admission control algorithm is investigated. A solution for efficient inter‐working between the physical layer and the higher layers is proposed, a resource metric mapping function (RMMF) that can deliver information about the state of the current channel load condition by the monitoring of signal‐to‐interference ratio (SIR) bursts and also the availability of a code pool by estimating the mean and the standard deviation of SIR bursts. This function is defined and demonstrated by means of an average raw BER mapping diagram as a function of the mean and the standard deviation of SIR bursts according to the multirate transmission method. By using this kind of mapping function combined with throughput estimation, the radio resource allocation algorithm can successfully reflect the current interference and mobile radio channel characteristics. Copyright © 2004 John Wiley & Sons, Ltd.
A survey of QoS enhancements for IEEE 802.11 wireless LAN
Authors: Ni Qiang , Romdhani Lamia , Turletti Thierry 
Published: August 2004

AbstractQuality‐of‐service (QoS) is a key problem of today's IP networks. Many frameworks (IntServ, DiffServ, MPLS etc.) have been proposed to provide service differentiation in the Internet. At the same time, the Internet is becoming more and more heterogeneous due to the recent explosion of wireless networks. In wireless environments, bandwidth is scarce and channel conditions are time‐varying and sometimes highly lossy. Many previous research works show that what works well in a wired network cannot be directly applied in the wireless environment. Although IEEE 802.11 wireless LAN (WLAN) is the most widely used IEEE 802.11 wireless LAN (WLAN) standard today, it cannot provide QoS support for the increasing number of multimedia applications. Thus, a large number of 802.11 QoS enhancement schemes have been proposed, each one focusing on a particular mode. This paper summarizes all these schemes and presents a survey of current research activities. First, we analyze the QoS limitations of IEEE 802.11 wireless MAC layers. Then, different QoS enhancement techniques proposed for 802.11 WLAN are described and classified along with their advantages/drawbacks. Finally, the upcoming IEEE 802.11e QoS enhancement standard is introduced and studied in detail. Copyright © 2004 John Wiley & Sons, Ltd.
A versatile toolbox for PCR‐based tagging of yeast genes: new fluorescent proteins, more markers and promoter substitution cassettes
Authors: Janke Carsten , Magiera Maria M. , Rathfelder Nicole , Taxis Christof , Reber Simone , Maekawa Hiromi , Moreno‐Borchart Alexandra , Doenges Georg , Schwob Etienne , Schiebel Elmar , Knop Michael 
Published: August 2004

AbstractTagging of genes by chromosomal integration of PCR amplified cassettes is a widely used and fast method to label proteins in vivo in the yeast Saccharomyces cerevisiae. This strategy directs the amplified tags to the desired chromosomal loci due to flanking homologous sequences provided by the PCR‐primers, thus enabling the selective introduction of any sequence at any place of a gene, e.g. for the generation of C‐terminal tagged genes or for the exchange of the promoter and N‐terminal tagging of a gene. To make this method most powerful we constructed a series of 76 novel cassettes, containing a broad variety of C‐terminal epitope tags as well as nine different promoter substitutions in combination with N‐terminal tags. Furthermore, new selection markers have been introduced. The tags include the so far brightest and most yeast‐optimized version of the red fluorescent protein, called RedStar2, as well as all other commonly used fluorescent proteins and tags used for the detection and purification of proteins and protein complexes. Using the provided cassettes for N‐ and C‐terminal gene tagging or for deletion of any given gene, a set of only four primers is required, which makes this method very cost‐effective and reproducible. This new toolbox should help to speed up the analysis of gene function in yeast, on the level of single genes, as well as in systematic approaches. Copyright © 2004 John Wiley & Sons, Ltd.
Linkages among adolescent girls’ romantic relationships, best friendships, and peer networks
Authors: Kuttler Ami Flam , La Greca Annette M 
Published: August 2004

AbstractThis study examined the linkages among girls’ best friendships and romantic relationships and accounted for the level of dating involvement as a moderating variable. Social exchange and Sullivan's socioemotional theories served as guides in this process. Questionnaires were administered to 446 girls aged 15–19 years. Results showed that: (a) dating is associated with more positive and less negative interactions with best friends; (b) increasing age and dating involvement are linked with increased reliance on romantic partners; (c) romantic relationships have more negative interactions than best friendships; and (d) peer‐network size and structure is related to dating behaviour. Mid to late adolescence is a time when girls shift attention away from friends and towards romantic partners.
Time-on-task effect in trait anhedonia
Authors: Dubal Stéphanie , Jouvent Roland 
Published: August 2004

AbstractThe capacity to sustain attention was explored in a sample of anhedonic subjects according to the Chapman physical anhedonia scale. Sustained attention was determined by studying task-induced changes over the duration of the Eriksen response competition task [Percept. Psychophys. 16 (1974) 143]. Anhedonic subjects had longer reaction times (RTs), but missed no more targets than control subjects. Anhedonic subject RTs got longer with time-on-task (TOT) and displayed greater intra-subject variability. These results confirm those of a previous study indicating that anhedonic subjects may have developed a more conservative response strategy [Psychophysiology 37 (2000) 711] and suggest that this strategy may result in a more rapid decrease in energetical resources. Moreover, the greater intra-subject variability demonstrates the importance of assessing performance over time and its relationship to the variability of responses in the cognitive performance of anhedonic subjects.
Predictors of work disabilities in patients with panic disorder with agoraphobia
Authors: Latas Milan , Starcevic Vladan , Vucinic Dusanka 
Published: August 2004

AbstractObjectiveThe aim of this study was to ascertain predictors of work insufficiency in patients with panic disorder (PD) with agoraphobia (AG).MethodLinear regression was used to identify predictors of work insufficiency in a sample of 72 consecutive outpatients with PD with AG. Intensity of work insufficiency was ascertained from modified National Institute of Mental Health Panic Questionnaire (NIMH PQ). That represented dependent variable. Independent variables were demographic data, duration of illness, presence of comorbid current major depression episode, presence of any personality disorder and scores on the Panic and Agoraphobia Scale (PAS) subscales: panic attacks, AG (avoidance behavior), anticipatory anxiety and worries about health.ResultsPatients reported severe work insufficiency. The best predict variable for the work insufficiency in patients with PD with AG was high score on the PAS dimension of AG.ConclusionPatients generally reported severe effects of PD with AG on work efficacy and the results suggested that the impaired work efficacy was the most associated with avoidance behavior. These results recommend that the treatment of PD with AG patients should be related to decreasing avoidance behavior in order to establish adequate work performance in patients.
Arginine 60 in the ArsC arsenate reductase of E. coli plasmid R773 determines the chemical nature of the bound As(III) product
Authors: DeMel Srini , Shi Jin , Martin Philip , Rosen Barry P. , Edwards Brian F.P. 
Published: August 2004

AbstractArsenic is a ubiquitous environmental toxic metal. Consequently, organisms detoxify arsenate by reduction to arsenite, which is then excreted or sequestered. The ArsC arsenate reductase from Escherichia coli plasmid R773, the best characterized arsenic‐modifying enzyme, has a catalytic cysteine, Cys 12, in the active site, surrounded by an arginine triad composed of Arg 60, Arg 94, and Arg 107. During the reaction cycle, the native enzyme forms a unique monohydroxyl Cys 12‐thiol‐arsenite adduct that contains a positive charge on the arsenic. We hypothesized previously that this unstable intermediate allows for rapid dissociation of the product arsenite. In this study, the role of Arg 60 in product formation was evaluated by mutagenesis. A total of eight new structures of ArsC were determined at resolutions between 1.3 Å and 1.8 Å, with Rfree values between 0.18 and 0.25. The crystal structures of R60K and R60A ArsC equilibrated with the product arsenite revealed a covalently bound Cys 12‐thiol‐dihydroxyarsenite without a charge on the arsenic atom. We propose that this intermediate is more stable than the monohydroxyarsenite intermediate of the native enzyme, resulting in slow release of product and, consequently, loss of activity.
Lipid binding in rice nonspecific lipid transfer protein‐1 complexes from Oryza sativa
Authors: Cheng Hui‐Chun , Cheng Pei‐Tsung , Peng Peiyu , Lyu Ping‐Chiang , Sun Yuh‐Ju 
Published: August 2004

AbstractNonspecific lipid transfer proteins (nsLTPs) facilitate the transfer of phospholipids, glycolipids, fatty acids and steroids between membranes, with wide‐ranging binding affinities. Three crystal structures of rice nsLTP1 from Oryza sativa, complexed with myristic (MYR), palmitic (PAL) or stearic acid (STE) were determined. The overall structures of the rice nsLTP1 complexes belong to the four‐helix bundle folding with a long C‐terminal loop. The nsLTP1–MYR and the nsLTP1–STE complexes bind a single fatty acid while the nsLTP1–PAL complex binds two molecules of fatty acids. The C‐terminal loop region is elastic in order to accommodate a diverse range of lipid molecules. The lipid molecules interact with the nsLTP1‐binding cavity mainly with hydrophobic interactions. Significant conformational changes were observed in the binding cavity and the C‐terminal loop of the rice nsLTP1 upon lipid binding.
Delineation and analysis of the conceptual data model implied by the “IUPAC Recommendations for Biochemical Nomenclature”
Authors: Fox‐Erlich Susan , Martyn Timothy O. , Ellis Heidi J.C. , Gryk Michael R. 
Published: August 2004

AbstractComputational analysis of the bonding, geometric, and topological relationships within proteins typically takes on the order of hours, mainly devoted to the writing of scripts and code to correctly parse the data. The Structured Query Language (SQL) built into modern database management systems eliminates the need for data parsing, effectively reducing the analysis time to seconds. To this end, we have formulated a conceptual data model (CDM) for proteins based on the IUPAC recommendations for biochemical nomenclature. This conceptual data model makes explicit the inherent bonding relationships between the atoms of a protein, as well as the geometric (bond angle and torsion angle) and topological (chirality) relationships between the bonds. The validity of the CDM has been tested with a reduced implementation using commercial database software. The ease in both populating the database with data from the Protein Data Bank and formulating/executing queries supports the correctness of the model. The ability to conduct truly interactive analyses of protein structure is essential to fully capitalize on the explosion in postgenomic protein structure data.
Stabilizing roles of residual structure in the empty heme binding pockets and unfolded states of microsomal and mitochondrial apocytochrome b5
Authors: Cowley Aaron B. , Rivera Mario , Benson David R. 
Published: August 2004

AbstractThe microsomal (Mc) and mitochondrial (OM) isoforms of mammalian cytochrome b5are the products of different genes, which likely arose via duplication of a primordial gene and subsequent functional divergence. Despite sharing essentially identical folds, heme‐polypeptide interactions are stronger in OM b5s than in Mc b5s due to the presence of two conserved patches of hydrophobic amino acid side chains in the OM heme binding pockets. This is of fundamental interest in terms of understanding heme protein structure–function relationships, because stronger heme–polypeptide interactions in OM b5s in comparison to Mc b5s may represent a key source of their more negative reduction potentials. Herein we provide evidence that interactions amongst the amino acid side chains contributing to the hydrophobic patches in rat OM (rOM) b5persist when heme is removed, rendering the empty heme binding pocket of rOM apo‐b5more compact and less conformationally dynamic than that in bovine Mc (bMc) apo‐b5. This may contribute to the stronger heme binding by OM apo‐b5by reducing the entropic penalty associated with polypeptide folding. We also show that when bMc apo‐b5unfolds it adopts a structure that is more compact and contains greater nonrandom secondary structure content than unfolded rOM apo‐b5. We propose that a more robust β‐sheet in Mc apo‐b5s compensates for the absence of the hydrophobic packing interactions that stabilize the heme binding pocket in OM apo‐b5s.
Crystal structure of a dimeric form of streptococcal pyrogenic exotoxin A (SpeA1)
Authors: Baker Matthew D. , Gendlina Inessa , Collins Carleen M. , Acharya K. Ravi 
Published: August 2004

AbstractStreptococcal pyrogenic exotoxin A (SpeA1) is a bacterial superantigen associated with scarlet fever and streptococcal toxic shock syndrome (STSS). SpeA1 is found in both monomeric and dimeric forms, and previous work suggested that the dimer results from an intermolecular disulfide bond between the cysteines at positions 90 of each monomer. Here, we present the crystal structure of the dimeric form of SpeA1. The toxin crystallizes in the orthorhombic space group P212121, with two dimers in the crystallographic asymmetric unit. The final structure has a crystallographic R‐factor of 21.52% for 7248 protein atoms, 136 water molecules, and 4 zinc atoms (one zinc atom per molecule). The implications of SpeA1 dimer on MHC class II and T‐cell receptor recognition are discussed.
Assimilation, Faith and Identity: Educational Implications of Change and Continuity
Authors: Johnson Helen 
Published: August 2004

In England, the presence of an established church places its adherents within the social mainstream. Other religious groups have been tolerated though suffering social and educational disadvantages. With the passage of time through the nineteenth and twentieth centuries, minority religious groups such as Irish Catholics have been assimilated into the host culture, and allowed to have their own schools.However, it would appear that contemporary movements of people to the United Kingdom have retained loyalties not only to their own religion, but, in some instances to their own language, which they perceive as a vital element of their own culture and identity. Demands for schools, within the state‐funded system, for minority religious groups have not lessened. As faith schools in England increase in number, their role in a multicultural society becomes increasingly problematic. Lessons about changing models of assimilation and identity can be learnt from a brief review of the historic Irish Catholic experience that, in turn, can illuminate the current experience of a Greek Orthodox school in south London.
Successful treatment of oesophageal candidiasis by micafungin: a novel systemic antifungal agent
Authors: Pettengell K. , Mynhardt J. , Kluyts T. , Lau W. , Facklam D. , Buell D. ,   the FK463 South African Study Group
Published: August 2004

SummaryAim : To determine the minimum effective dose and safety of micafungin in the treatment of HIV‐related oesophageal candidiasis.Method : A total of 120 patients were enrolled in this open label study of the effects of daily 1 h infusions of micafungin on endoscopically proven fungal oesophagitis. Patients were randomly assigned to receive 12.5, 25, 50, 75 and 100 mg of micafungin daily. Response was evaluated clinically and endoscopically.Results : The protocol defined minimum effective dose of micafungin was 12.5 mg. The percentage of patients experiencing clearing of physical signs and symptoms showed a dose–response relationship and reached 94.7% in the 100 mg dose group. All patients in the 50, 75 and 100 mg dose groups achieved an endoscopically verified improvement in oesophagitis. Adverse effects of micafungin were generally mild and not dose‐related. No serious renal, hepatic or drug‐related infusion reactions were encountered.Conclusion : Micafungin was found to be effective, well‐tolerated and safe. The minimum effective dose was found to be 12.5 mg and a significant linear trend in the successful treatment of oesophageal candidiasis was observed across the doses used with 75 and 100 mg dose levels achieving high rates of clinical and endoscopic cure.
Erythropoietin increases platelet reactivity and platelet counts in patients with alcoholic liver cirrhosis: a randomized, double‐blind, placebo‐controlled study
Authors: Homoncik M. , Jilma‐Stohlawetz P. , Schmid M. , Ferlitsch A. , Peck‐Radosavljevic M. 
Published: August 2004

SummaryBackground: Patients with liver cirrhosis have a complex haemostasis disturbance including thrombocytopenia and abnormal bleeding time. Erythropoietin is the primary stimulator for erythrocyte production and also induces megakaryocyte formation. In healthy men erythropoietin increased platelet count and platelet reactivity.Aim: As patients with liver cirrhosis often undergo invasive procedures, we were interested to study whether erythropoietin could improve platelet function in addition to thrombocytopenia.Methods: In total, 22 thrombocytopenic (platelet counts < 120 g/L) patients with alcoholic liver cirrhosis received either 100 IE/kg erythropoietin or placebo on days 1, 3 and 5 in a 2:1 randomized, placebo‐controlled double‐blind fashion. Platelet counts and platelet reactivity (activator‐stimulated expression of P‐selectin on platelets measured by flow cytometry) were determined on study days 1, 3, 5 and 9.Results: Median platelet count was 80 g/L which is borderline for major elective surgical interventions. Baseline values were not different between groups (P > 0.05). Treatment with erythropoietin increased platelet count by 25% (P = 0.01) and platelet reactivity twofold (P < 0.01) vs. baseline. The increase in platelet count vs. baseline was more pronounced in patients with platelet counts <80 g/L. No significant effect was observed in the placebo group.Conclusions: Treatment with erythropoietin significantly increased platelet counts and platelet reactivity in patients with alcoholic liver cirrhosis. Preoperative treatment with erythropoietin is therefore expected to yield higher platelet levels and better platelet function.