bluuebunny/crossref_metadata_2025_split huggingface dataset:
Neuronal nitric oxide synthase does not contribute to the modulation of pulmonary vascular tone in fetal lambs with congenital diaphragmatic hernia (nNOS in CDH lambs)
Authors: Roessingh Anthony S. de Buys , de Lagausie Pascal , Ibrahima Taline , Duong‐Quy Sy , Schneider Jean‐Christophe , Huang Xiao‐Lin , Mercier Jean‐Christophe , Aigrain Yves , Boulanger Chantal , Dinh‐Xuan Anh Tuan 
Published: February 2008

AbstractAimThe aim of this study was to determine the presence of the neuronal nitric oxide synthase (nNOS) in near full‐term lambs with congenital diaphragmatic hernia (CDH) and its role in the modulation of pulmonary vascular basal tone.MethodsWe surgically created diaphragmatic hernia on the 85th day of gestation. On the 135th, catheters were used to measure pulmonary pressure and blood flow. We tested the effects of 7‐nitroindazole (7‐NINA), a specific nNOS antagonist and of N‐nitro‐l‐arginine (l‐NNA), a nonspecific nitric oxide synthase antagonist. In vitro, we tested the effects of the same drugs on isolated pulmonary vessels. The presence of nNOS protein in the lungs was detected by Western blot analysis.ResultsNeither 7‐NINA nor l‐NNA modified pulmonary vascular basal tone in vivo. After l‐NNA injection, acetylcholine (ACh) did not decrease significantly pulmonary vascular resistance (PVR). In vitro, l‐NNA increased the cholinergic contractile‐response elicited by electric field stimulation (EFS) of vascular rings from lambs with diaphragmatic hernia.ConclusionWe conclude that nNOS protein is present in the lungs and pulmonary artery of near full‐term lamb fetuses with diaphragmatic hernia, but that it does not contribute to the reduction of pulmonary vascular tone at birth. Pediatr Pulmonol. 2008; 43:313–321. © 2008 Wiley‐Liss, Inc.
Modules for cloning‐free chromatin tagging in Saccharomyces cerevisae
Authors: Rohner Sabine , Gasser Susan M. , Meister Peter 
Published: February 2008

AbstractWe describe a straightforward two‐step PCR‐based method to insert arrays of lac or tet operators (lacO or tetO) at specific loci in the budding yeast genome. The method entails insertion of a marker generated by PCR with classical long primers recognizing the locus of interest, followed by the replacement of this marker by a linearized plasmid bearing an array of lacI‐ or tetR‐binding motifs. Using this technique, loci located either in the yeast genome or on yeast artificial chromosomes can be efficiently tagged. We provide a set of plasmids with different markers for cloning‐free integration of lacO or tetO repeats into the yeast genome. Copyright © 2008 John Wiley & Sons, Ltd.
The role of OXA-1 β-lactamase Asp66 in the stabilization of the active-site carbamate group and in substrate turnover
Authors: Leonard David A. , Hujer Andrea M. , Smith Brian A. , Schneider Kyle D. , Bethel Christopher R. , Hujer Kristine M. , Bonomo Robert A. 
Published: February 2008

The OXA-1 β-lactamase is one of the few class D enzymes that has an aspartate residue at position 66, a position that is proximal to the active-site residue Ser67. In class A β-lactamases, such as TEM-1 and SHV-1, residues adjacent to the active-site serine residue play a crucial role in inhibitor resistance and substrate selectivity. To probe the role of Asp66 in substrate affinity and catalysis, we performed site-saturation mutagenesis at this position. Ampicillin MIC (minimum inhibitory concentration) values for the full set of Asp66 mutants expressed in Escherichia coli DH10B ranged from ≤8 μg/ml for cysteine, proline and the basic amino acids to ≥256 μg/ml for asparagine, leucine and the wild-type aspartate. Replacement of aspartic acid by asparagine at position 66 also led to a moderate enhancement of extended-spectrum cephalosporin resistance. OXA-1 shares with other class D enzymes a carboxylated residue, Lys70, that acts as a general base in the catalytic mechanism. The addition of 25 mM bicarbonate to Luria–Bertani-broth agar resulted in a ≥16-fold increase in MICs for most OXA-1 variants with amino acid replacements at position 66 when expressed in E. coli. Because Asp66 forms hydrogen bonds with several other residues in the OXA-1 active site, we propose that this residue plays a role in stabilizing the CO2 bound to Lys70 and thereby profoundly affects substrate turnover.
Post-transcriptional regulation of CLMP mRNA is controlled by tristetraprolin in response to TNFα via c-Jun N-terminal kinase signalling
Authors: Sze Kit-Ling , Lui Wing-Yee , Lee Will M. 
Published: February 2008

During spermatogenesis, extensive restructuring of blood–testis barrier takes place to facilitate the migration of preleptotene/leptotene spermatocytes from the basal to the adluminal compartment in the seminiferous epithelium. However, the biochemical mechanisms involved in this event remain elusive. Recent studies have shown that pro-inflammatory cytokine TNFα (tumour necrosis factor α) plays a crucial role in this event by inhibiting the expression of tight junction proteins in Sertoli cells. In the present study, we sought to examine the detailed mechanism on how TNFα affects the expression of CLMP (coxsackie- and adenovirus-receptor-like membrane protein), a newly identified tight junction transmembrane protein, in the testis. Addition of TNFα (10 ng/ml) to Sertoli cell culture (TM4 cells) significantly reduced the steady-state CLMP mRNA and protein levels. In an mRNA stability assay, it was shown that the rate of CLMP mRNA degradation was significantly increased when cells treated with TNFα were compared with vehicle. Blockage of the JNK (c-Jun N-terminal kinase) signalling pathway by SP600125 significantly abolished the TNFα-mediated destabilization of CLMP mRNA. Activation of the JNK signalling pathway by TNFα up-regulated the expression of an RNA-binding protein, TTP (tristetraprolin). TTP was present in the RNA–protein complex in the RNA EMSA (electrophoretic mobility shift assay) and decreased the CLMP 3′-UTR (untranslated region)-dependent luciferase activity. Taken together, these results suggest that the TNFα-mediated mRNA degradation of the CLMP gene is controlled by TTP through the JNK signalling cascade.
Automated image alignment for 2D gel electrophoresis in a high-throughput proteomics pipeline
Authors: Dowsey Andrew W. , Dunn Michael J. , Yang Guang-Zhong 
Published: March 2008

Abstract
Motivation: The quest for high-throughput proteomics has revealed a number of challenges in recent years. Whilst substantial improvements in automated protein separation with liquid chromatography and mass spectrometry (LC/MS), aka ‘shotgun’ proteomics, have been achieved, large-scale open initiatives such as the Human Proteome Organization (HUPO) Brain Proteome Project have shown that maximal proteome coverage is only possible when LC/MS is complemented by 2D gel electrophoresis (2-DE) studies. Moreover, both separation methods require automated alignment and differential analysis to relieve the bioinformatics bottleneck and so make high-throughput protein biomarker discovery a reality. The purpose of this article is to describe a fully automatic image alignment framework for the integration of 2-DE into a high-throughput differential expression proteomics pipeline.
Results: The proposed method is based on robust automated image normalization (RAIN) to circumvent the drawbacks of traditional approaches. These use symbolic representation at the very early stages of the analysis, which introduces persistent errors due to inaccuracies in modelling and alignment. In RAIN, a third-order volume-invariant B-spline model is incorporated into a multi-resolution schema to correct for geometric and expression inhomogeneity at multiple scales. The normalized images can then be compared directly in the image domain for quantitative differential analysis. Through evaluation against an existing state-of-the-art method on real and synthetically warped 2D gels, the proposed analysis framework demonstrates substantial improvements in matching accuracy and differential sensitivity. High-throughput analysis is established through an accelerated GPGPU (general purpose computation on graphics cards) implementation.
Availability: Supplementary material, software and images used in the validation are available at http://www.proteomegrid.org/rain/
Contact: g.z.yang@imperial.ac.uk
Supplementary information: Supplementary data are available at Bioinformatics online.
In silico Biochemical Reaction Network Analysis (IBRENA): a package for simulation and analysis of reaction networks
Authors: Liu Gang , Neelamegham Sriram 
Published: March 2008

Abstract
Summary: We present In silico Biochemical Reaction Network Analysis (IBRENA), a software package which facilitates multiple functions including cellular reaction network simulation and sensitivity analysis (both forward and adjoint methods), coupled with principal component analysis, singular-value decomposition and model reduction. The software features a graphical user interface that aids simulation and plotting of in silico results. While the primary focus is to aid formulation, testing and reduction of theoretical biochemical reaction networks, the program can also be used for analysis of high-throughput genomic and proteomic data.
Availability: The software package, manual and examples are available at http://www.eng.buffalo.edu/~neel/ibrena
Contact: neel@eng.buffalo.edu
ISD: a software package for Bayesian NMR structure calculation
Authors: Rieping Wolfgang , Nilges Michael , Habeck Michael 
Published: March 2008

Abstract
Summary: The conventional approach to calculating biomolecular structures from nuclear magnetic resonance (NMR) data is often viewed as subjective due to its dependence on rules of thumb for deriving geometric constraints and suitable values for theory parameters from noisy experimental data. As a result, it can be difficult to judge the precision of an NMR structure in an objective manner. The inferential structure determination (ISD) framework, which has been introduced recently, addresses this problem by using Bayesian inference to derive a probability distribution that represents both the unknown structure and its uncertainty. It also determines additional unknowns, such as theory parameters, that normally need to be chosen empirically. Here we give an overview of the ISD software package, which implements this methodology.
Availability: http://www.bioc.cam.ac.uk/isd
Contact: wolfgang.rieping@bioc.cam.ac.uk, michael.habeck@tuebingen.mpg.de
Physical factors mediate effects of grazing by a non-indigenous snail species on saltmarsh cordgrass (Spartina alterniflora) in New England marshes
Authors: Tyrrell Megan C. , Dionne Michele , Edgerly Jessica A. 
Published: February 2008

Abstract
Tyrrell, M. C., Dionne, M., and Edgerly, J. A. 2008. Physical factors mediate effects of grazing by a non-indigenous snail species on saltmarsh cordgrass (Spartina alterniflora) in New England marshes. – ICES Journal of Marine Science, 65: 746–752. In the southeastern US, grazing by a common indigenous littorinid snail has caused large declines in the biomass of saltmarsh cordgrass (Spartina alterniflora). In northeastern marshes, a closely related but non-indigenous snail may also negatively affect production of this key marsh-building plant. We manipulated densities of the gastropod Littorina littorea at two sites to investigate the effect of its grazing on plant production and sediment accumulation. The effects of the manipulation differed between sites. The site with longer inundation periods, lower elevation, and poorer drainage attributable to smaller sediment grain size had more stressful conditions for S. alterniflora. At that site, protection from snail grazing resulted in higher end-of-season plant biomass than all the other treatments and controls. Rates of sediment accumulation were also lower at that site, and the difference between sites increased as the season progressed. At the site where physical conditions were benign, snail manipulation had no effect on S. alterniflora biomass. The nature of the physical conditions at a site may influence the susceptibility of S. alterniflora to grazing pressure by this ubiquitous snail species. Accelerating anthropogenic impacts, such as sea-level rise, could further stress saltmarsh plants, leaving them increasingly susceptible to herbivory.
A Homolog ofScRAD5Is Involved in DNA Repair and Homologous Recombination in Arabidopsis
Authors: Chen I-Peng , Mannuss Anja , Orel Nadiya , Heitzeberg Fabian , Puchta Holger 
Published: March 2008

AbstractRad5 is the key component in the Rad5-dependent error-free branch of postreplication repair in yeast (Saccharomyces cerevisiae). Rad5 is a member of the Snf2 ATPase/helicase family, possessing as a characteristic feature, a RING-finger domain embedded in the Snf2-helicase domain and a HIRAN domain. Yeast mutants are sensitive to DNA-damaging agents and reveal differences in homologous recombination. By sequence comparisons we were able to identify two homologs (AtRAD5a and AtRAD5b) in the Arabidopsis thaliana genome, sharing about 30% identity and 45% similarity to yeast Rad5. AtRad5a and AtRad5b have the same kind of domain organization with a higher degree of similarity to each other than to ScRad5. Surprisingly, both genes differ in function: whereas two independent mutants of Atrad5a are hypersensitive to the cross-linking agents mitomycin C and cis-platin and to a lesser extent to the methylating agent, methyl methane sulfonate, the Atrad5b mutants did not exhibit any sensitivity to all DNA-damaging agents tested. An Atrad5a/Atrad5b double mutant resembles the sensitivity phenotype of the Atrad5a single mutants. Moreover, in contrast to Atrad5b, the two Atrad5a mutants are deficient in homologous recombination after treatment with the double-strand break-inducing agent bleomycin. Our results suggest that the RAD5-dependent error-free branch of postreplication repair is conserved between yeast and plants, and that AtRad5a might be functionally homologous to ScRad5.
Architects about briefing
Authors: Bogers Tetske , van Meel Juriaan J. , van der Voordt Theo J.M. 
Published: March 2008

PurposeThis paper aims to provide a better understanding of how architects perceive and use briefing documents. It discusses what type of briefing information architects find relevant for their design process, and how and when briefing information should be presented. It also gives recommendations for clients and consultants that produce the brief.Design/methodology/approachThe article is based on a review of briefing literature, six exploratory interviews with two clients, two architects and two consultants, 18 in‐depth interviews with Dutch architects, and a workshop with Dutch experts on briefing.FindingsA brief (or “program of requirements”) is a crucial means of communication in the interaction between clients and architects. A good brief explains what the client needs, desires and expects from a project. This is all crucial information for the design process. In the interviews, however, many architects indicated that, in daily practice, briefing documents are not as useful as they should be. In their opinion, briefs are often too long, containing overly‐detailed specifications, that are not always clear, consistent or complete.Practical implicationsIn addition to the analysis of architects' complaints, six recommendations are given with respect to the briefing process, the contents and structure of the brief, and the status of the brief.Originality/valueMost publications on briefing focus on the client and brief writing at the start of a project. The present paper discusses the opinions and experiences of the architect and the use of the brief in the design process.
Brand familiarity: its effects on satisfaction evaluations
Authors: Tam Jackie L.M. 
Published: March 2008

PurposeThe purpose of this paper is to examine the moderating effects of brand familiarity on satisfaction evaluations and behavioral intentions.Design/methodology/approachA longitudinal survey involving pre‐purchase measures and post‐purchase measures was conducted with consumers in a restaurant setting. The hypotheses were assessed through LISREL methodology.FindingsThe results showed that there are some similarities and differences among customers with different levels of brand familiarity regarding satisfaction formation and behavioral intentions.Research limitations/implicationsA self‐reported item was used to measure brand familiarity. Although there was some evidence to support that the measure captured what it was intended to measure, it would be desirable to develop a multi‐item scale for this construct. There is also a need to extend the findings to other service industries.Practical implicationsMarketers should familiarize customers with a service while capturing opportunities to create a positive experience to gain customers' future purchases.Originality/valueThe study offers some insights into the effects of brand familiarity on satisfaction evaluations and behavioral intentions. It is particularly relevant for marketing services that are high in experience qualities.
The notion of internal market orientation and employee job satisfaction: some preliminary evidence
Authors: Gounaris Spiros 
Published: March 2008

PurposeThe purpose of this paper is to examine the impact of Internal Market Orientation (IMO) on the application of internal marketing practices and employee job satisfaction.Design/methodology/approachData were secured through personal interviews with hotel managers and employees from 20 different five‐star hotels. Hierarchical regression analysis is used to examine the hypotheses put forward in the study.FindingsJob satisfaction is positively related with the practice of internal marketing. However, IMO is also a significant variable in explaining employee job‐satisfaction while moderating the relationship between internal marketing and job satisfaction.Research limitations/implicationsDrawing the analogy from the market‐orientation research stream, this study reveals the importance of developing an internal‐market orientation before internal marketing practices can be truly effective.Practical implicationsService providers seeking differentiation through customer service and delight have to pay attention to their employees' needs and develop an internal‐market orientation to complement their customer‐orientation.Originality/valueThe paper is important for both scholars and practitioners. It introduces the notion of IMO and its impact on employee job‐satisfaction.
State reform in Greece: responding to old and new challenges
Authors: Spanou Calliope 
Published: March 2008

PurposeThe paper attempts to assess the impact of reforms of the last 25 years on Greek administration and more specifically on its Napoleonic features. Given that those have been reshaped by country specific socio‐political dynamics, the analysis starts by pointing out the Napoleonic features but also specific features its Greek variant. These form the context of reforms undertaken and determine their trajectories as well as their limitations.Design/methodology/approachThis paper examines four basic reform areas linked to important features of Napoleonic states: centrality of the state, centralised bureaucratic structures, labour relations in the public sector, and citizens‐administration relations. The rationale of reforms is discussed in relation to NPM trends but also to domestic challenges and priorities.FindingsThe significance of reforms undertaken varies. The state's presence in the economy has been significantly reduced and decentralisation reforms are more important politically than administratively. Citizens' rights and service delivery have been conceived rather as forms of democratisation and modernisation than as managerial reforms. Only recently labour relations in the public sector have been partly challenged while other reform aspects such as “agencification”, systematically by‐passing existing bureaucratic structures start to be part of the picture. Change has been incremental and followed pre‐established paths. The “Napoleonic” features of the state have not been seriously affected and reforms have hardly been reshaped by the new managerial paradigm. While the state remains the main reform actor and the law a typical policy instrument, a distinctive reform path emerges in Greece, as defined by the apparently contradictory rationale of a number of initiatives responding to old as much to new challenges.Originality/valueProvides a brief account of important aspects of the Greek variant of the Napoleonic state and the context of recent reforms. Features and limits of reforms are also discussed. Finally, a tentative assessment answers the central question of the paper.
Failed policies but institutional innovation through “layering” and “diffusion” in Spanish central administration
Authors: Parrado Salvador 
Published: March 2008

PurposeThis paper aims to show that the Spanish central administration, as a representative of the Napoleonic tradition, has undergone considerable managerial changes in non‐autonomous and semi‐autonomous agencies characterised by their direct involvement in service delivery in spite of the failure of macro‐changes and radical reforms of public administration.Design/methodology/approachThis paper provides case studies of “paths” of changes in three organisations.FindingsThrough “layering” and “diffusion” of institutions as social mechanisms included in the historical new institutionalism account for innovation, specific organisations like the tax agency, social security and property registry have become more managerial in a state dominated by public law.Research limitations/implicationsMore in‐depth case studies would make possible generalisation of how small changes can produce similar impacts or results than reform efforts at the macro‐level.Originality/valueThe use of historical neo‐institutionalism and the exam of mechanisms as “layering” and “diffusion” for explaining change is presented.
The trickiness of IT enhanced competence management
Authors: McHenry Joyce E.H. , Strønen Fred H. 
Published: March 2008

PurposeThe purpose of this paper is to develop a critical understanding of IT enhanced competence management and its promise to bridge operational and strategic functions with the aim of revealing potential hidden challenges.Design/methodology/approachEmpirical data were gathered through interviews and observations during a longitudinal field study over a two year period in a large Norwegian IT consulting firm that has adopted a competence IT tool throughout the entire organisation. The investigation was conducted from a practice‐based approach to studying competence management.FindingsIt was found that IT enhanced competence management that aims to bridge the individual and organisational purposes, is mediated by a universal‐stock versus contextualist approach to competence development. This results in four possible alternatives to IT enhanced competence management. In this study the contextual competence assessment for individual purposes has been objectified for organisational purposes, causing confusion about the value of IT enhanced competence management.Research limitations/implicationsThis study has been conducted in only one large IT firm in Norway. Further research is needed to support the finding that it is beneficial to remain in either the contextual or the universal‐stock orientation to competence development when using the same assessments for individual‐operational and organisational‐strategic purposes.Practical implicationsThe trickiness of IT enhanced competence management lies in the four hidden belief structures about competence that influence both the design and use of IT enhanced competence tools. Insight gained from this paper may help managers to reflect on their assumptions about competence and may contribute to successful IT enhanced competence management.Originality/valueThe research clarifies possible pitfalls when aiming to satisfy multiple purposes in the design and use of a competence IT tool.