bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mclip: motif detection based on cliques of gapped local profile-to-profile alignments
Authors: Frickey Tancred , Weiller Georg 
Published: November 2006

AbstractSummary: A multitude of motif-finding tools have been published, which can generally be assigned to one of three classes: expectation-maximization, Gibbs-sampling or enumeration. Irrespective of this grouping, most motif detection tools only take into account similarities across ungapped sequence regions, possibly causing short motifs located peripherally and in varying distance to a ‘core’ motif to be missed. We present a new method, adding to the set of expectation-maximization approaches, that permits the use of gapped alignments for motif elucidation.Availability: The program is available for download from:Contact: Georp.Weiller@anu.edu.auSupplementary information:
GOlorize: a Cytoscape plug-in for network visualization with Gene Ontology-based layout and coloring
Authors: Garcia Olivier , Saveanu Cosmin , Cline Melissa , Fromont-Racine Micheline , Jacquier Alain , Schwikowski Benno , Aittokallio Tero 
Published: November 2006

AbstractSummary: We have implemented a graph layout algorithm that exposes Gene Ontology (GO) class structure on the network nodes. It can be used in conjunction with BiNGO plug-in to Cytoscape, which finds the GO categories over-represented in a given network. Our plug-in, named GOlorize, first highlights the class members with category-specific color-coding and then constructs an enhanced visualization of the network using a class-directed layout algorithmAvailability:Contact: teanai@pasteur.frSupplementary information: Installation instructions and tutorial at
Cochlear Implantation in a Patient With Bilateral Deep Brain Stimulators
Authors: St. Martin Michele B. , Hirsch Barry E. 
Published: November 2006

AbstractObjective: We report the case of a patient successfully implanted with a Nucleus Contour cochlear implant after placement of a deep brain stimulator for Parkinson disease.Methods: The authors conducted a case report and literature review.Results: Successful hookup and mapping of the device was performed 1 month after implantation without evidence of aberrant activity of the deep brain stimulators.Conclusions: To our knowledge, this is the first reported case of successful implantation of both a cochlear implant and a deep brain stimulator in the same patient. We have outlined one approach to avoiding detrimental interactions between cochlear implant and deep brain stimulator devices.
To be named or not to be named—Heteropodarke pleijeli sp. n. (Annelida, Polychaeta)
Authors: Muona Jyrki 
Published: November 2006

Abstract Heteropodarke pleijeli n. sp. (Annelida, Polychaeta, Hesionidae) is described from Papua New Guinea. This taxon was characterized in a PhyloCode context by Pleijel in 1999 and again in 2000. The valid name for this annelid will be decided by the zoological community in the future, but the description provided here is regarded as the only available and thus valid one.© The Willi Hennig Society 2006.
High‐level serum B‐cell activating factor and promoter polymorphisms in patients with idiopathic thrombocytopenic purpura
Authors: Emmerich Florian , Bal Gürkan , Barakat Alaa , Milz Julian , Mühle Caroline , Martinez‐Gamboa Lorena , Dörner Thomas , Salama Abdulgabar 
Published: November 2006

SummaryIdiopathic thrombocytopenic purpura (ITP) is an autoimmune disorder in which platelets are opsonised by autoantibodies and destroyed by macrophages. Therefore, ITP represents a prototype of a B‐cell‐mediated autoimmune disorder. B‐cell activating factor (BAFF) is a member of the tumour necrosis factor family and an important regulator of B‐cell development. BAFF levels were determined in serum samples from 53 patients with ITP. Serum BAFF levels in patients with an active ITP were increased when compared with the healthy control group (median 1620 pg/ml vs. 977 pg/ml; P < 0·001). Moreover, immunosuppressive treatment was associated with strongly suppressed BAFF levels (median 629 pg/ml; P < 0·01). In addition, a polymorphic site was detected in the BAFF promoter region (−871) that appeared to occur more frequently in ITP patients than in healthy persons. This promoter variant was associated with very high BAFF levels in ITP patients. Our data suggest that BAFF is an important pathogenetic factor in the development of ITP.
Haematopoietic progenitor cells utilise conventional PKC to suppress PKB/Akt activity in response to c‐Kit stimulation
Authors: Edling Charlotte E. , Pedersen Malin , Carlsson Leif , Rönnstrand Lars , Palmer Ruth H. , Hallberg Bengt 
Published: November 2006

SummaryReceptor tyrosine kinase (RTK) c‐Kit signalling is crucial for the proliferation, survival and differentiation of haematopoietic stem cells (HSCs). To further understand the mechanisms underlying these events we explored how the downstream mediators interact. The present study investigated the function of conventional protein kinase Cs (c‐PKC) in c‐Kit mediated signalling pathways in HSC‐like cell lines. This analysis supported earlier findings, that steel factor (SF) activates c‐PKC, extracellular signal‐regulated kinase (Erk) and protein kinase B (PKB). The present results were consistent with an important role of c‐PKC in the positive activation of Erk and for proliferation. Further, it was observed that c‐PKC negatively regulated PKB activity upon SF stimulation, indicating that c‐PKC acts as a suppressor of c‐Kit signalling. Finally, these observations were extended to show that c‐PKC mediated the phosphorylation of the endogenous c‐Kit receptor on serine 746, resulting in decreased overall tyrosine phosphorylation of c‐Kit upon SF stimulation. This report showed that this specific feedback mechanism of c‐PKC mediated phosphorylation of the c‐Kit receptor has consequences for both proliferation and survival of HSC‐like cell lines.
A comparison of the binding of secretory component to immunoglobulin A (IgA) in human colostral S‐IgA1 and S‐IgA2
Authors: Almogren Adel , Senior Bernard W. , Kerr Michael A. 
Published: November 2006

SummaryA detailed investigation of the binding of secretory component to immunoglobulin A (IgA) in human secretory IgA2 (S‐IgA2) was made possible by the development of a new method of purifying S‐IgA1, S‐IgA2 and free secretory component from human colostrum using thiophilic gel chromatography and chromatography on Jacalin‐agarose. Sodium dodecyl sulphate–polyacrylamide gel electrophoresis of unreduced pure S‐IgA2 revealed that, unlike in S‐IgA1, a significant proportion of the secretory component was bound non‐covalently in S‐IgA2. When S‐IgA1 was incubated with a protease purified from Proteus mirabilis the secretory component, but not the α‐chain, was cleaved. This is in contrast to serum IgA1, in which the α‐chain was cleaved under the same conditions – direct evidence that secretory component does protect the α‐chain from proteolytic cleavage in S‐IgA. Comparisons between the products of cleavage with P. mirabilis protease of free secretory component and bound secretory component in S‐IgA1 and S‐IgA2 also indicated that, contrary to the general assumption, the binding of secretory component to IgA is different in S‐IgA2 from that in S‐IgA1.
Effects of wounding, fruit age and wetness duration on the development of cherry brown rot in the UK
Authors: Xu X.‐M. , Bertone C. , Berrie A. 
Published: November 2006

This research investigated the effects of wounding, fruit age and wetness duration on the development of cherry brown rot. Both Monilinia laxa and M. fructigena infected wounded detached cherry fruits, but M. laxa caused more infections than M. fructigena and only M. laxa efficiently infected intact detached fruits. Results from field monitoring and controlled inoculation in a polyethylene tunnel showed that the susceptibility of fruits to infection by M. laxa increased with fruit maturity. Infection of attached intact fruits by M. laxa was not affected by the length (3–24 h) of the wet period tested.
Efficacy and safety of preemptive anti‐CMV therapy with valganciclovir after kidney transplantation
Authors: Lopau Kai , Greser Alexandra , Wanner Christoph 
Published: November 2006

Abstract: Background: CMV infections still pose a potentially serious threat to kidney transplant recipients and have a significant impact on graft as well as patient survival. The antiviral agent valganciclovir (VGCV) has a greater bioavailability after oral administration than oral ganciclovir (GCV) and can be considered a substitute for GCV. The substance is approved in North America and Europe for anti‐CMV prophylaxis after organ transplantation. In this pilot study, we examined if VGCV could also be administered in preemptive treatment of CMV infections.Methods: Twenty‐eight renal transplant recipients suffering from 32 asymptomatic episodes of CMV infection were treated with VGCV and followed up. CMV infection was diagnosed by routine controls of pp65‐antigenemia in pre‐defined intervals. All patients received sequential quadruple immunosuppression. VGCV was given for up to 12 wk in a dosage adapted to renal graft function. Efficacy and safety parameters were monitored for 16 wk.Results: Twenty‐seven episodes of CMV antigenemia, two patients progressing to CMV syndrome and three patients progressing to CMV disease were treated. Primary efficiency was 79%, Four patients relapsed and were treated with a second course resulting in serological recovery. Two patients did not respond to oral VCGV and were switched to another antiviral agent. Graft function remained stable during and after treatment. Serious side effects were seen in seven patients, four patients complained of diarrhea and gastrointestinal pain, three patients suffered from leucopenia, in one of these treatment had to be temporary paused. Fifty‐nine percent of all episodes were treated in a completely ambulatory setting.Conclusions: VGCV can be considered as an option also for preemptive treatment of CMV infections after renal transplantation. The antiviral potency seems to be adequate, potential side effects are comparable with IV GCV. Because of the improved pharmacokinetics of VGCV the substance can be used to abbreviate or even completely avoid in‐hospital care of CMV infections.
Changes in Hospitalisation Rates and Costs in New South Wales, 1996–97 and 2000–01
Authors: Walker Agnes , Thurecht Linc , Harding Ann 
Published: November 2006

AbstractChanges in hospital admission rates and costs in New South Wales (NSW) between 1996‐97 and 2000–01 were examined by age, hospital type and socioeconomic status. A novel method led to a more accurate assessment of hospital patients' socio‐economic status than was previously possible. Use of unit record hospitals data and full population Census data allowed very high levels of disaggregation. Considerable increases in the baby boomer and frail aged populations led to higher hospital admission rates over the period. This was driven by the private sector, which saw its admission rates increase by 20 per cent (with the public sector rate declining by 6per cent). Public hospital admission rates by age were found to be up to 40 per cent greater for the poorest 20 per cent of the population than for the richest 20 per cent‐with a reversal of the pattern for private hospitals (up to 45 per cent greater for the richest 20 per cent than for the poorest 20 per cent). In a period when total NSW hospital expenditures increased by 21 per cent, we found that ‘per admission costs’ in the inpatient non‐psychiatric sub‐sector changed little.
A NOTE ON ‘AN INFRAMARGINAL ANALYSIS OF THE RICARDIAN MODEL’
Authors: Zhang Dingsheng , Shi Heling 
Published: November 2006

Abstract.  This is a note about Cheng et al.'s paper, in which we consider a dual structure of division of labour and trade that is missed in the model of Cheng et al. Though the inclusion of the dual structure will not change the main results in the paper by Cheng et al., it explores an interesting way to use a general equilibrium model to describe a dual structure with underemployment in a transitional period of economic development.
Population ecology and conservation of endangered megafauna: the case of European bison in Białowieża Primeval Forest, Poland
Authors: Mysterud A. , Bartoń K. A. , Jędrzejewska B. , Krasiński Z. A. , Niedziałkowska M. , Kamler J. F. , Yoccoz N. G. , Stenseth N. C. 
Published: November 2006

AbstractThe European bison Bison bonasus is an example of nearly extinct ‘charismatic megafauna’. The Białowieża Primeval Forest in Poland is among the few places where they still live in the wild. The management of this free‐living herd has to reconcile to the conservation needs of a species and the economic and environmental objectives of their habitat: protected as well as commercial woodlands of Białowieża. Here we present a detailed account of the population development and analyse variation in vital rates based on monitoring that started in 1952 and continued until 2002. The population was allowed to grow freely until 1970, when removal started with the aim to stabilize population size. We found that recruitment rate, but not mortality, was density dependent, suggesting that the population density was not very high relative to resource levels. Winters with much snow and cold temperature had a strong negative effect on survival. May temperature of the previous year positively affected recruitment rates. Masting (oak seed) also positively affected recruitment rates, which provides a rare account of masting affecting the performance of a large ruminant. Sex ratio of offspring was even and was not strongly affected by density or climate. We use an age‐structured matrix model to show how this knowledge of intrinsic and extrinsic factors affecting vital rates may help managerial decisions by providing explicit links between given environmental conditions and the population growth rates.
The polybasic sequence in the C2B domain of rabphilin is required for the vesicle docking step in PC12 cells
Authors: Tsuboi Takashi , Kanno Eiko , Fukuda Mitsunori 
Published: November 2006

AbstractRabphilin is generally thought to be involved in the regulation of secretory vesicle exocytosis in neurons and neuroendocrine cells, and it has recently been hypothesized that the C2B domain of rabphilin promotes the docking of dense‐core vesicles to the plasma membrane through simultaneous interaction with a vesicle protein, Rab3A/27A, and a plasma membrane protein, SNAP‐25 (synaptosome‐associated protein of 25 kDa). However, the physiological significance of the rabphilin–SNAP‐25 interaction in the vesicle‐docking step has never been elucidated. In this study we demonstrated by a mutation analysis that the polybasic sequence (587 KKAKHKTQIKKK 598) in the C2B domain of rabphilin is required for SNAP‐25 binding, and that the Asp residues in the Ca2+‐binding loop 3 (D628 and D630) of the C2B domain are not required. We also investigated the effect of Lys→Gln (KQ) mutations in the polybasic sequence of the C2B domain on vesicle dynamics by total internal reflection fluorescence microscopy in individual PC12 cells. A rabphilin(KQ) mutant that completely lacks SNAP‐25‐binding activity significantly decreased the number of plasma‐membrane‐docked vesicles and strongly inhibited high‐KCl‐induced dense‐core vesicle exocytosis. These results indicate that the polybasic sequence in the C2B domain functions as an effector domain for SNAP‐25 and controls the number of ‘releasable’ vesicles docked to the plasma membrane.
Dual role of CaMKII‐dependent SAP97 phosphorylation in mediating trafficking and insertion of NMDA receptor subunit NR2A
Authors: Mauceri D. , Gardoni F. , Marcello E. , Di Luca M. 
Published: November 2006

AbstractSynapse Associated Protein 97 (SAP97), a member of membrane‐associated guanylate kinase (MAGUK) protein family, has been involved in the correct targeting and clustering of ionotropic glutamate receptors (iGluRs) at postsynaptic sites. Calcium/calmodulin kinase II (CaMKII) phosphorylates SAP97 on two major sites in vivo; one located in the N‐terminal domain (Ser39) and the other in the first postsynaptic density disc large ZO1 (PDZ) domain (Ser232). CaMKII‐mediated phosphorylation of SAP97‐Ser39 is necessary and sufficient to drive SAP97 to the postsynaptic compartment in cultured hippocampal neurons. CaMKII‐dependent phosphorylation of Ser232 disrupts SAP97 interaction with NR2A subunit, thereby regulating synaptic targeting of this NMDA receptor subunit. Here we show by means of phospho‐specific antibodies that SAP97‐Ser39 phosphorylation represents the driving force to release SAP97/NR2A complex from the endoplasmic reticulum. Ser39 phosphorylation does not interfere with SAP97 capability to bind NR2A. On the contrary, SAP97‐Ser232 phosphorylation occurs within the postsynaptic compartment and is responsible for both the disruption of NR2A/SAP97 complex and, consequently, for NR2A insertion in the postsynaptic membrane. Thus, CaMKII‐dependent phosphorylation of SAP97 in different time frames and locations within the neurons controls both NR2A trafficking and insertion.
The effect of queuing representations on modeling transit signal priority systems in mixed mode operation
Authors: Lin Wei‐Hua 
Published: November 2006

AbstractThis paper examines quantitatively the effect of modeling assumptions on transit signal priority (TSP) control in mixed mode operation. The primary sources of delays to buses at intersections are queues formed at intersections (queuing delay) and traffic signals (signal delay). We show that models based on point queues and models based on spatial queues would lead to different control strategies and yield different results for the benefit to buses in terms of delay reduction. Situations in which the spatial content of queues is crucial to modeling TSP systems are identified in the paper. We conclude that given that models with the spatial queue representation are more realistic in capturing the queuing dynamics at intersections they should be incorporated in the decision‐making process for initiating priority calls in a TSP system.
A multicriteria approach for corporate decisions in sustainable planning policy
Authors: Henn Annette , Patz Renate 
Published: November 2006

AbstractUnder the current conditions of urban and regional renewal, it is a challenge and opportunity to find such decisions in planning policy supporting sustainable development. Redevelopment of former open‐cast mines and shrinking processes in cities are typical examples. Decision making in such a planning context considers complex tasks and involves preferential selection among different, usually competing alternatives. They result from demands of different spatial functions and the necessity to conserve the natural environment and landscape. The modeling of a planning process requires an adequate definition of the problem, identification of the main decision criteria and possible courses of action. Following environmental and institutional economic theory we use the idea of involving stakeholders. Determining and understanding the demands of stakeholders may lead to a successful management of environmental, social, human, and economic tasks. We propose a multicriteria approach to formulate a planning problem as a multiobjective optimization problem.
A financial resource allocation model for regional water systems
Authors: Rogers Jeffrey W. , Louis Garrick E. 
Published: November 2006

AbstractThe public water supply sector is facing significant external pressures for change from decreasing water resource availability, stricter water quality regulations, decreasing federal subsidies, increasing public scrutiny, decreasing financial health, and increasing infrastructure replacement costs. These forces necessitate greater accountability by community water systems (CWS) to their stakeholders.This paper presents a method for comparative efficiency analysis to improve the accountability of CWS to their stakeholders while maintaining the level of service. The method is achieved through three objectives, namely: (1) to construct standard efficiency metric parameters based on the techniques of data envelopment analysis; (2) to incorporate these uniform efficiency metric parameters into a transparent decision support system (DSS) based on the standard linear programming resource allocation problem; and (3) to utilize the DSS to determine the efficient allocation of limited budgetary resources among CWS operating as a regional water system (RWS).The paper is a significant departure, in three ways, from the current planning and management approach, which treats CWS as independent entities. First, it provides an open and transparent method for planning and management of CWS; second, it provides a uniform and consistent method for evaluating relative efficiencies across the CWS. Third, the DSS facilitates comparative efficiency analysis across the RWS, and guides financial allocation decisions among CWS operating as a RWS.
An overview of the Portuguese wind power sector
Authors: Ferreira Paula , Araújo Madalena , O'Kelly M. E. J. 
Published: November 2006

AbstractThe present situation of electricity production from renewable energy sources (RES) in Portugal is analyzed, giving particular attention to the wind power sector due to its increasing importance. The evolution of the electricity system is presented along with the strategies for the sector, and future prospects for the RES. Although the interest of private companies in the wind sector is high, the administrative and grid barriers represent major obstacles to wind power development. The problem of wind intermittency and uncertainty is also discussed. The improvement of interconnection capacity and the increase of power reserve are identified as key requirements for ensuring the security of supply. A clear understanding of all these aspects is fundamental for integrated, multidimensional wind power planning.
Towards establishing the use of holons as an enquiry method
Authors: Bell Gary , Warwick Jon 
Published: November 2006

AbstractThis paper argues the need for utilizing holons as an enquiry method to identify problems associated with messy situations. We demonstrate the use of holons through an investigation of a department within a UK university. Similar work was conducted by the university higher management using its quality management and enhancement procedures. We employ the case study research method to assess the explanatory capability of both approaches and conclude that there is evidence to support the use of holons for enquiry purposes and that the holons provide a structure for both soft and hard systems modeling.
The influence of the business cycle on bankruptcy probability
Authors: Hol Suzan 
Published: November 2006

AbstractTwo fields of research on default prediction are combined on a unique dataset covering all limited liability firms in Norway. This is done by empirically testing a bankruptcy prediction function where unlisted firms are evaluated on the basis of both their financial statement analysis and movements in the business cycle. This combination is found to improve the default prediction compared with financial statements alone. The GDP gap, a production index and the money supply M1 in combination with some financial health indicators for individual firms are found to be significant predictors on default for Norwegian firms during both recovery and expansion in the 1990s.