bluuebunny/crossref_metadata_2025 huggingface dataset:
Two-frequency acousto-optic modulator driver to improve the beam pointing stability during intensity ramps
Authors: Fröhlich B. , Lahaye T. , Kaltenhäuser B. , Kübler H. , Müller S. , Koch T. , Fattori M. , Pfau T.
Published: April 2007

We report on a scheme to improve the pointing stability of the first order beam diffracted by an acousto-optic modulator (AOM). Due to thermal effects inside the crystal, the angular position of the beam can change by as much as 1mrad when the radio-frequency power in the AOM is reduced to decrease the first order beam intensity. This is done, for example, to perform forced evaporative cooling in ultracold atom experiments using far-off-resonant optical traps. We solve this problem by driving the AOM with two radio frequencies f1 and f2. The power of f2 is adjusted relative to the power of f1 to keep the total power constant. Using this, the beam displacement is decreased by a factor of 20. The method is simple to implement in existing experimental setups, without any modification of the optics.
Quiet boom could revive supersonic air travel
Authors: Feder Toni
Published: April 2007

Realizing overland supersonic flight is likely to proceed at a subsonic pace.
Structural basis for PRYSPRY-mediated tripartite motif (TRIM) protein function
Authors: James Leo C. , Keeble Anthony H. , Khan Zahra , Rhodes David A. , Trowsdale John
Published: March 2007

The human tripartite motif (TRIM) family comprises 70 members, including HIV restriction factor TRIM5α and disease-associated proteins TRIM20 (pyrin) and TRIM21. TRIM proteins have conserved domain architecture but diverse cellular roles. Here, we describe how the C-terminal PRYSPRY domain mediates diverse TRIM functions. The crystal structure of TRIM21 PRYSPRY in complex with its target IgG Fc reveals a canonical binding interface comprised of two discrete pockets formed by antibody-like variable loops. Alanine scanning of this interface has identified the hot-spot residues that control TRIM21 binding to Fc; the same hot-spots control HIV/murine leukemia virus restriction by TRIM5α and mediate severe familial Mediterranean fever in TRIM20/pyrin. Characterization of the IgG binding site for TRIM21 PRYSPRY reveals TRIM21 as a superantigen analogous to bacterial protein A and suggests that an antibody bipolar bridging mechanism may contribute to the pathogenic accumulation of anti-TRIM21 autoantibody immune complex in autoimmune disease.
Faithful modeling of transient expression and its application to elucidating negative feedback regulation
Authors: Rubinstein Amir , Gurevich Vyacheslav , Kasulin-Boneh Zohar , Pnueli Lilach , Kassir Yona , Pinter Ron Y.
Published: March 2007

Modeling and analysis of genetic regulatory networks is essential both for better understanding their dynamic behavior and for elucidating and refining open issues. We hereby present a discrete computational model that effectively describes the transient and sequential expression of a network of genes in a representative developmental pathway. Our model system is a transcriptional cascade that includes positive and negative feedback loops directing the initiation and progression through meiosis in budding yeast. The computational model allows qualitative analysis of the transcription of early meiosis-specific genes, specifically,
Ime2
and their master activator,
Ime1
. The simulations demonstrate a robust transcriptional behavior with respect to the initial levels of Ime1 and Ime2. The computational results were verified experimentally by deleting various genes and by changing initial conditions. The model has a strong predictive aspect, and it provides insights into how to distinguish among and reason about alternative hypotheses concerning the mode by which negative regulation through Ime1 and Ime2 is accomplished. Some predictions were validated experimentally, for instance, showing that the decline in the transcription of
IME1
depends on Rpd3, which is recruited by Ime1 to its promoter. Finally, this general model promotes the analysis of systems that are devoid of consistent quantitative data, as is often the case, and it can be easily adapted to other developmental pathways.
Deletion of the orphan nuclear receptor COUP-TFII in uterus leads to placental deficiency
Authors: Petit Fabrice G. , Jamin Soazik P. , Kurihara Isao , Behringer Richard R. , DeMayo Francesco J. , Tsai Ming-Jer , Tsai Sophia Y.
Published: April 2007

COUP-TFII (NR2F2), chicken ovalbumin upstream promoter–transcription factor II, is an orphan nuclear receptor of the steroid/thyroid hormone receptor superfamily. The
Coup-tfII
-null mutant mice die during the early embryonic development because of angiogenesis and heart defects. To analyze the physiological function of COUP-TFII during organogenesis, we used the cre/loxP system to conditionally inactivate COUP-TFII in the ovary and uterus. Homozygous adult female mutants with specific inactivation of the
Coup-tfII
gene in uterine stromal and smooth muscle cells have severely impaired placental formation, leading to miscarriage at days 10–12 of pregnancy. Deletion of the
Coup-tfII
gene resulted in an increase in trophoblast giant cell differentiation, a reduction of the spongiotrophoblast layer, and an absence of labyrinth formation causing an improper vascularization of the placenta. This study describes an important maternal role of COUP-TFII in regulating the placentation. The endometrial COUP-TFII might modulate the signaling between the uterus and the extraembryonic tissue for the proper formation of the placenta.
PROTMAP2D: visualization, comparison and analysis of 2D maps of protein structure
Authors: Pietal Michal J. , Tuszynska Irina , Bujnicki Janusz M.
Published: March 2007

Motivation: Protein structure comparison is a fundamental problem in structural biology and bioinformatics. Two-dimensional maps of distances between residues in the structure contain sufficient information to restore the 3D representation, while maps of contacts reveal characteristic patterns of interactions between secondary and super-secondary structures and are very attractive for visual analysis. The overlap of 2D maps of two structures can be easily calculated, providing a sensitive measure of protein structure similarity. PROTMAP2D is a software tool for calculation of contact and distance maps based on user-defined criteria, quantitative comparison of pairs or series of contact maps (e.g. alternative models of the same protein, model versus native structure, different trajectories from molecular dynamics simulations, etc.) and visualization of the results.

Availability: PROTMAP2D for Windows / Linux / MacOSX is freely available for academic users from http://genesilico.pl/protmap2d.htm

Contact: iamb@genesilico.pl

Supplementary information: Supplementary data are available at Bioinformatics online.
Rearrangement of competing U2 RNA helices within the spliceosome promotes multiple steps in splicing
Authors: Perriman Rhonda J. , Ares Manuel
Published: April 2007

Nuclear pre-messenger RNA (pre-mRNA) splicing requires multiple spliceosomal small nuclear RNA (snRNA) and pre-mRNA rearrangements. Here we reveal a new snRNA conformational switch in which successive roles for two competing U2 helices, stem IIa and stem IIc, promote distinct splicing steps. When stem IIa is stabilized by loss of stem IIc, rapid ATP-independent and Cus2p-insensitive prespliceosome formation occurs. In contrast, hyperstabilized stem IIc improves the first splicing step on aberrant branchpoint pre-mRNAs and rescues temperature-sensitive U6–U57C, a U6 mutation that also suppresses first-step splicing defects of branchpoint mutations. A second, later role for stem IIa is revealed by its suppression of a cold-sensitive allele of the second-step splicing factor PRP16. Our data expose a spliceosomal progression cycle of U2 stem IIa formation, disruption by stem IIc, and then reformation of stem IIa before the second catalytic step. We propose that the competing stem IIa and stem IIc helices are key spliceosomal RNA elements that optimize juxtaposition of the proper reactive sites during splicing.
Using Genetically Engineered Kinases to Screen for Novel Protein Kinase Substrates: Phosphorylation of Substrates in Cell Lysates with Exogenous Kinase
Authors: Eblen Scott T. , Kumar N. Vinay , Weber Michael J.
Published: April 2007

INTRODUCTION

This protocol describes a method for detection of direct substrates of a protein kinase in cell lysates or fractions. The approach involves the addition of recombinant mutant kinase and [γ-32P]ATP analog to cell lysates. This technique has been successfully used for the phosphorylation of extracellular signal-regulated kinase 2 (ERK2) substrates in cell lysates from SKOV-3 ovarian cells; however, the methodology can be applied to other protein kinases as well.
Impairment of the Photorespiratory Pathway Accelerates Photoinhibition of Photosystem II by Suppression of Repair But Not Acceleration of Damage Processes in Arabidopsis
Authors: Takahashi Shunichi , Bauwe Hermann , Badger Murray
Published: March 2007

Oxygenation of ribulose-1,5-bisphosphate catalyzed by Rubisco produces glycolate-2-P. The photorespiratory pathway, which consists of photorespiratory carbon and nitrogen cycles, metabolizes glycolate-2-P to the Calvin cycle intermediate glycerate-3-P and is proposed to be important for avoiding photoinhibition of photosystem II (PSII), especially in C3 plants. We show here that mutants of Arabidopsis (Arabidopsis thaliana) with impairment of ferredoxin-dependent glutamate synthase, serine hydroxymethyltransferase, glutamate/malate transporter, and glycerate kinase had accelerated photoinhibition of PSII by suppression of the repair of photodamaged PSII and not acceleration of the photodamage to PSII. We found that suppression of the repair process was attributable to inhibition of the synthesis of the D1 protein at the level of translation. Our results suggest that the photorespiratory pathway helps avoid inhibition of the synthesis of the D1 protein, which is important for the repair of photodamaged PSII upon interruption of the Calvin cycle.
Herbivory Rapidly Activates MAPK Signaling in Attacked and Unattacked Leaf Regions but Not between Leaves ofNicotiana attenuata
Authors: Wu Jianqiang , Hettenhausen Christian , Meldau Stefan , Baldwin Ian T.
Published: March 2007

Mitogen-activated protein kinase (MAPK) signaling plays a central role in transducing extracellular stimuli into intracellular responses, but its role in mediating plant responses to herbivore attack remains largely unexplored. When Manduca sexta larvae attack their host plant, Nicotiana attenuata, the plant's wound response is reconfigured at transcriptional, phytohormonal, and defensive levels due to the introduction of oral secretions (OS) into wounds during feeding. We show that OS dramatically amplify wound-induced MAPK activity and that fatty acid–amino acid conjugates in M. sexta OS are the elicitors. Virus-induced gene silencing of salicylic acid–induced protein kinase (SIPK) and wound-induced protein kinase revealed their importance in mediating wound and OS-elicited hormonal responses and transcriptional regulation of defense-related genes. We found that after applying OS to wounds created in one portion of a leaf, SIPK is activated in both wounded and specific unwounded regions of the leaf but not in phylotactically connected adjacent leaves. We propose that M. sexta attack elicits a mobile signal that travels to nonwounded regions of the attacked leaf where it activates MAPK signaling and, thus, downstream responses; subsequently, a different signal is transported by the vascular system to systemic leaves to initiate defense responses without activating MAPKs in systemic leaves.
Levels of strategy and performance in UK small retail businesses
Authors: Megicks Phil
Published: April 2007

Purpose

This study aims to investigate the way in which small retailer performance is influenced by strategy at different levels. It also aims to propose that business level strategy is more important to success than functional level strategy in small retail firms, as this is what enables them to distinguish their business from competitors and effectively set about competing in their markets.

Design/methodology/approach

Data were collected from a mail survey of 305 independent retailers in the UK. Multivariate statistical methods were used to develop appropriate variables and explore the relationships between level of strategy and performance.

Findings

The results indicate that business level strategy variables have a significant influence on performance whereas functional levels do not when their combined effects are analysed using hierarchical regression modelling.

Research limitations/implications

The caveats normally associated with survey methods apply, as do those related to the use of cross‐sectional, self‐report, and managerial perceptions data. Implications for retail strategy theory and small retailers' performance are addressed.

Practical implications

The importance of business level strategy generally and its specific elements are considered with a view to providing guidance to management decision makers and policy advisors.

Originality/value

Reliable measures for retail strategy variables are developed in the paper. The research distinguishes the performance effects of retail business strategy from retail functional strategy and supports the view that business strategy decisions are superior in their market significance over operational retail mix decisions.
A holistic framework for the strategic management of first tier managers
Authors: Peach Martins Lola
Published: April 2007

Purpose

The intention of this research paper is to shed light on the key factors influencing the human resource management (HRM) performance of first tier managers (FTMs), and the vital importance that a holistic strategic framework can have in this regard.

Design/methodology/approach

The research paper uses an up‐to‐date historical approach and, additionally, draws on detailed case study evidence from an aerospace manufacturing/engineering company via manually and electronically analysed in‐depth semi‐structured interview and company documentation.

Findings

The case study findings reveal that the FTM's HRM performance is greatly influenced by a group of four key factors, and their interrelationships.

Research limitations/implications

The literature survey was mainly industry‐specific (manufacturing), and the sample was restricted to one sector (aerospace), as well as one case study organisation. Furthermore, the views of FTMs' staff are not directly represented.

Originality/value

The FTMs' HRM role shows no signs of abating; in addition, questions regarding their performance of this role have increasingly emerged. This has become more evident as organisations have continued to expand the FTMs' role by devolving greater HRM responsibilities to them, and their performance of the role demonstrates that many FTMs are ill equipped to perform their HRM duties to the required standard. However, the vital importance that a holistic strategic framework (which encompasses the four key factors influencing their performance) can have on their performance of this role is not acknowledged. The present research paper, gives an empirical example of a case study, and therefore provides a springboard to address the weakness in the literature.
The fee tendering and service quality issue revisited
Authors: Hoxley Michael
Published: April 2007

Purpose

It is a little over 20 years since mandatory fee scales were abolished by UK professional bodies. During this period fee levels have fluctuated with economic demand, and new procurement strategies such as partnering have been developed, but there is still a widespread view in industry that fee levels are too low. This view is shared by many professionals, and perhaps more surprisingly by clients, even in the current construction and property boom. The purpose of this paper is to report research on the link between competitive fee tendering and clients' perceptions of service quality in the UK property industry. The main hypothesis is that there is a causal relationship between service quality and the method of appointment of the professional.

Design/methodology/approach

The research involved unstructured interviews with clients and professionals and a postal questionnaire study of one 133 UK based clients. The questionnaire study was a repeat of a similar survey conducted eight years previously in very different economic conditions. The public and private sector clients each assessed the service quality received from a professional using a measurement scale developed from the generic service industry instrument SERVQUAL. The scale is used to test the main hypothesis and four sub‐hypotheses. There were twice as many private sector clients completing the questionnaires as there were public sector clients and the largest group of professionals assessed were General Practice Chartered Surveyors.

Findings

The results of the recent study are similar to the earlier one (in that evidence of the predicted relationship is not provided by the data) but there are some interesting differences in the results of both studies – fee tendering has declined in popularity, direct appointment has increased, but less than 5 per cent of the commissions were let on a partnered basis.

Practical implications

Property managers and other professionals may wish to make use of the service quality measurement scale in order assess the service they provide to clients.

Originality/value

The research provides confirmation that clients do not perceive that a lower standard of service quality is provided for fee‐tendered commissions. It also extends the already substantial body of research based upon the SERVQUAL measurement technique.
Analysis and optimization of dynamically loaded porous metal sliding bearings under conditions of elastohydrodynamic lubrication
Authors: Marinković Aleksandar , Rosić Božidar , Petropoulos Georgios
Published: April 2007

Purpose

This paper aims to develop a simulating model of a journal porous metal bearing under elastohydrodynamic conditions and combined (radial, friction and thermal) load distribution and to carry out structural optimization.

Design/methodology/approach

The structure analysis is carried out for each kind of load separately and for the combined load distribution of the bearing, where a dynamically loaded porous metal bearing is simulated. This simulating model is developed by finite elements method using the structure analysis module of the CATIA V5 software. Further, a parameter optimization of a porous metal bearing is presented considering the elastic deformations of the bearing shell.

Findings

It is revealed that the bearing, even at points with maximum displacements, could not reach the mounting clearance value during its operational life. Relatively small bearing dimensions produce very high values of eigenfrequency response (over 150 kHz) and common dynamic loads met in all sorts of sliding bearing are not dangerous for bearing damage compared with static loads. In the stage of structural optimization based on the correlation between stress and geometric bearing parameters like wall thickness and outer diameter, the influence of finite element dimension on calculated results can be also analyzed and a proper choice of the latter is achieved.

Research limitations/implications

The present porous bearing optimization model with the aid of CATIA V5 module for optimum design uses only single objective optimization. For a complete optimum design a multi‐objective optimization has to be carried out.

Practical implications

The analysis under dynamic load conditions proved that relatively small dimensions of bearing commonly used in micro technique and precision mechanics result in extended safe and reliable operation.

Originality/value

This paper provides a methodology for bearing stress and deformation analysis in the elastic range and on the basis of this analysis it is possible to develop an optimization model for porous bearings offering help to designers for the selection of optimal bearing dimensions considering the bearing load caused by dynamic radial force, friction and temperature variation.
Industrial sector and financial distress
Authors: Smith Malcolm , Liou Dah‐Kwei
Published: April 2007

Purpose

A number of authors have noted that industrial sector is a significant factor in the design and construction of failure prediction models, suggesting that organisational structures dictate the construction of separate models for different sectors. However, most modellers have been content to amalgamate sub‐sectors of the “manufacturing” classification (often because of otherwise facing sample size difficulties) to produce a single manufacturing sector model. This paper seeks to examine the differences that exist across the manufacturing sector to identify those sub‐sectors for which such amalgamation is inadvisable.

Design/methodology/approach

The paper examines the correlation of traditional financial ratios with sector performance for a large sample of UK companies. A proprietary Z‐score failure prediction model is used to evaluate the solvency of 340 manufacturing companies, in order to determine the pattern of misclassification errors, and their association with industrial sector.

Findings

The paper identifies sub‐sectors whose inclusion would make traditional models vulnerable to error, and makes suggestions regarding their continued inclusion for modelling purposes.

Research limitations/implications

The paper makes suggestions for data selection in the construction of failure prediction models.

Practical implications

The classificatory ability of failure prediction models should be improved, notably through a reduction in the incidence of Type 2 errors. Users of financial models for evaluating companies as investments and/or their worthiness as suppliers or creditors will have more reliable information at their disposal.

Originality/value

Contribution to knowledge of the explanatory factors associated with corporate failure.
CONTEXT: the shared knowledge enigma
Authors: Bennet Alex , Bennet David
Published: April 2007

Purpose

The purpose of this paper is to present a systems perspective of context avenues that impact the knowledge‐sharing process.

Design/methodology/approach

Following a brief introduction of the meaning of context, an example of face‐to‐face interaction is used to explore the term “context‐sensitive” in terms of sharing knowledge in a one‐way single exchange from a source to a perceiver. Eight different context avenues are presented, their relationship to the conscious and unconscious mind addressed, and their impact on the sharing of knowledge considered.

Findings

The authors posit that there are eight primary context avenues that potentially impact the creation of knowledge in terms of shared understanding and meaning, and that the higher the number of related patterns forwarded through content and context the greater the resonance of shared understanding. Further, that the unconscious mind plays a significant role in embedding context and creating meaning.

Originality/value

This paper provides a shift in perception from the transmission of information to the sharing and re‐creation of knowledge in terms of shared understanding and meaning. It also presents a new model of context avenues impacting the sharing of knowledge.
Using RP to promote collaborative design of customised medical implants
Authors: Truscott Michèle , de Beer Deon , Vicatos George , Hosking Keith , Barnard Ludrick , Booysen Gerrie , Ian Campbell R.
Published: April 2007

Purpose

The last decade has seen major advances in rapid prototyping (RP), with it becoming a multi‐disciplinary technology, crossing various research fields, and connecting continents. Process and material advancements open up new applications and manufacturing (through RP) is serving non‐traditional industries. RP technology is used to support rapid product development (RPD). The purpose of this paper is to describe how the Integrated Product Development research group of the Central University of Technology, Free State, South Africa is applying various CAD/CAM/RP technologies to support a medical team from the Grootte Schuur and Vincent Palotti hospitals in Cape Town, to save limbs – as a last resort at a stage where conventional medical techniques or practices may not apply any longer.

Design/methodology/approach

The paper uses action research to justify the proposal of a new method to use CAD/CAM/RP related technologies to substitute lost/damaged bone regions through the use of CT to CAD to.STL manipulation.

Findings

A case study where RP related technologies were used to support medical product development for a patient with severe injuries from a road accident is discussed.

Originality/value

The paper considers current available technologies, and discusses new advancements in direct metal freeform fabrication, and its potential to revolutionise the medical industry.
Meeting the needs of the workplace and the learner through work‐based learning
Authors: Rhodes Garth , Shiel Gillian
Published: April 2007

Purpose

The purpose of this paper is to discuss the value and learning potential of work‐based projects to both worker‐researchers and their organisations.

Design/methodology/approach

Within the School of Health, Community and Education Studies at Northumbria University, work‐based learning (WBL) programmes are becoming increasingly important as a vehicle to enable individuals to gain academic credit and qualifications through developing their personal and professional repertoire of skills and knowledge, and also as a mechanism to improve organisational practice/change. To this end the School has used work‐based projects (WBPs) to work innovatively in partnership with employers. Three short case studies are used to explore how WBPs have been used effectively to meet the particular needs of both the workplace and the learner and to discuss the challenges that these initiatives pose in higher education (HE).

Findings

The paper finds that a number of identified issues currently challenging the authors' approaches to WBL have a wider resonance across the WBL community: issues concerning individuals undertaking work‐based‐learning who are unfamiliar with academic learning and how they can be supported to use the skills of enquiry as a tool to implement change in practice; the complexities of using WBL approaches within multi‐ professional groups at differing stages in the continuum from novice to expert and who present individual diverse entry behaviour and learning needs; and the challenges facing the WBL academic working, to recognise and assess the diverse learning acquired throughout the WBL journey so that it can be formally recognised within an HE setting.

Originality/value

The interrelation between action learning, action research and WBPs is introduced and discussed and the impact of the WBL process on the learner, the HE academic and the organisation scrutinised.
Sustainable development cognitive map: a new method of evaluating student understanding
Authors: Lourdel Nathalie , Gondran Natacha , Laforest Valérie , Debray Bruno , Brodhag Christian
Published: April 2007

Purpose

Owing to its complexity, sustainable development (SD) cannot be simply integrated as a supplementary course within the engineer's curricula. The first aim of this paper is to focus on how to reflect pedagogically this complexity. After dealing with these questions, the paper aims to present a tool that can evaluate the student's understanding of SD concepts.

Design/methodology/approach

A method of analysis of a student's sustainability's comprehension, based on cognitive maps, has been developed. The students are asked to write and connect by arrows all the terms that they associate to the concept of SD. The assessment of the aforementioned cognitive maps is based on an approach via semantic category.

Findings

This study shows that the students' perception of SD before the training seems mainly focalised on environmental and economical aspects. After the SD course, an increase of the number of words quoted is noted for each category (social and cultural aspects; stakeholders, principles of SD and allusions to complexity, temporal and spatial dimensions). Their vision seems richer and wider. The training seemed successful to help the students who did not associate SD to diverse dimension to improve this perception.

Practical implications

This cognitive map method can be a useful tool to improve learning in quantitative terms but also in qualitative terms. Identifying knowledge gaps and misunderstood ideas allows the improvement in the training.

Originality/value

This study presents a new method that can be used to evaluate the impact of training sessions on students. Another advantage is to analyse how the student's knowledge are interconnected. This seems particularly interesting because the study of this transdisciplinary concept as well, necessitates an integrated vision.
Rural‐based universities in South Africa
Authors: Nkomo Mokubung , Sehoole Chika
Published: April 2007

Purpose

The purpose of this paper is to focus on how two rural‐based universities in South Africa can contribute towards sustainable development especially in their immediate rural communities. It addresses the following questions: what conditions or policy frameworks exist that can engender a sustainable development trajectory? How can rural‐based universities reconstitute themselves so they can become effective agents for sustainable rural development? Historically, because of apartheid policies, these and other black universities were on the margins of the knowledge production process and have not effectively engaged in real development activities that would meaningfully improve the livelihoods of rural dwellers. The research identified policy and legislative instruments and strategies that can promote a dynamic interaction with other institutions thus empowering and promoting sustainability. The aim of the paper is to raise awareness about existing possibilities at the disposal of these institutions.

Design/methodology/approach

The paper is the outcome of two research initiatives: one was a doctoral study by one of the authors, and the other was a study conducted at both universities. Both studies involved extensive interviews with a wide spectrum of stakeholders (local and provincial authorities, members of the business and university communities). Both also involved document analyses.

Findings

That rural‐based universities are advantageously situated and possess a variety of characteristics that can enable them to effectively contribute to sustainable development. These include their strategic location within the rural communities; reinventing their mission orientation so as to enhance their research capacity; expanding their intellectual/entrepreneurial/social capital; and the establishment of strong collaborative relationships.

Practical implications

The first aim of the paper is to raise the awareness of policy makers and other stakeholders about the strategic value of these institutions. The awareness should lead to a series of engagements with appropriate individuals with the view to develop appropriate strategies for application.

Originality/value

The contribution of rural‐based universities to sustainable development has not been sufficiently researched in South Africa and, therefore, the study fills the gap by adding valuable knowledge, new perspectives, and presents possibilities for consideration.
New product development in Chinese SMEs
Authors: Mu Jifeng , Peng Gang , Tan Yi
Published: April 2007

Purpose

The importance of innovation to the performance of firms has led to numerous studies conducted to identify the critical successful factors in new product development (NPD). However, most of these studies were conducted within the context of the developed economies or for large enterprises; relatively little is known about how firms, especially small and medium‐size enterprises (SMEs), develop new products in many of the emerging markets. This paper tries to bridge the gap by examining the key success factors of NPD in Chinese SMEs. Different from the traditional approach regarding the success factors in each stage of NPD as homogeneous, the key success factors in each stage of the NPD process are examined from a managerial perspective.

Design/methodology/approach

The data used in this study were collected through a multi‐stage procedure including in‐depth field interviews and surveys. Two rounds of pretests were used to refine the measurements, and the 74 questionnaires retuned in the third round were used to analyze the key success factors for NPD through score ranking and principal component analysis.

Findings

Chinese SMEs do not regard financial return as the primary criterion in the idea‐generation stage. Although the key success factors are relatively quite different in various stages, technological, marketing, commercial, and managerial factors are important across all stages.

Research limitations/implications

The samples were from Beijing Incubator Alliances, which might not be representative.

Practical implications

The results will be interesting to both researchers and managers who want to know how the Chinese SMEs develop their new products.

Originality/value

Very few studies were conducted on how the Chinese SMEs develop new products, and this research contributed to this important topic. Various success factors were examined for each stage of the NPD process from a managerial perspective, rather than viewing the success factors in each stage of NPD as homogeneous, as most previous research has suggested.
Energy vulnerability and its management
Authors: Percebois Jacques
Published: April 2007

Purpose

The purpose of the paper is to clarify the distinction between vulnerability and energy dependence of a country and to present simple indicators that are used to analyse energy vulnerability.

Design/methodology/approach

This paper introduces the different facets of the energy vulnerability concept and discusses the options available to manage risks arising from energy vulnerability.

Findings

The concept of energy vulnerability takes various forms and cannot be reduced to appreciating the degree of dependency of a country concerning energy supplies.

Originality/value

The contribution of the paper lies in offering a coherent set of indicators for analysing the energy vulnerability issue and in identifying a potential research area of developing a composite indicator of vulnerability similar to that of the human development indicator.
CO migration pathways in cytochrome P450cam studied by molecular dynamics simulations
Authors: Mouawad Liliane , Tetreau Catherine , Abdel‐Azeim Safwat , Perahia David , Lavalette Daniel
Published: March 2007

Previous laser flash photolysis investigations between 100 and 300 K have shown that the kinetics of CO rebinding with cytochrome P450cam(camphor) consist of up to four different processes revealing a complex internal dynamics after ligand dissociation. In the present work, molecular dynamics simulations were undertaken on the ternary complex P450cam(cam)(CO) to explore the CO migration pathways, monitor the internal cavities of the protein, and localize the CO docking sites. One trajectory of 1 nsec with the protein in a water box and 36 trajectories of 1 nsec in the vacuum were calculated. In each trajectory, the protein contained only one CO ligand on which no constraints were applied. The simulations were performed at 200, 300, and 320 K. The results indicate the presence of seven CO docking sites, mainly hydrophobic, located in the same moiety of the protein. Two of them coincide with xenon binding sites identified by crystallography. The protein matrix exhibits eight persistent internal cavities, four of which corresponding to the ligand docking sites. In addition, it was observed that water molecules entering the protein were mainly attracted into the polar pockets, far away from the CO docking sites. Finally, the identified CO migration pathways provide a consistent interpretation of the experimental rebinding kinetics.
Exploring subdomain cooperativity in T4 lysozyme I: Structural and energetic studies of a circular permutant and protein fragment
Authors: Cellitti Jason , Llinas Manuel , Echols Nathaniel , Shank Elizabeth A. , Gillespie Blake , Kwon Ester , Crowder Scott M. , Dahlquist Frederick W. , Alber Tom , Marqusee Susan
Published: March 2007

Small proteins are generally observed to fold in an apparent two‐state manner. Recently, however, more sensitive techniques have demonstrated that even seemingly single‐domain proteins are actually made up of smaller subdomains. T4 lysozyme is one such protein. We explored the relative autonomy of its two individual subdomains and their contribution to the overall stability of T4 lysozyme by examining a circular permutation (CP13*) that relocates the N‐terminal A‐helix, creating subdomains that are contiguous in sequence. By determining the high‐resolution structure of CP13* and characterizing its energy landscape using native state hydrogen exchange (NSHX), we show that connectivity between the subdomains is an important determinant of the energetic cooperativity but not structural integrity of the protein. The circular permutation results in a protein more easily able to populate a partially unfolded form in which the C‐terminal subdomain is folded and the N‐terminal subdomain is unfolded. We also created a fragment model of this intermediate and demonstrate using X‐ray crystallography that its structure is identical to the corresponding residues in the full‐length protein with the exception of a small network of hydrophobic interactions. In sum, we conclude that the C‐terminal subdomain dominates the energetics of T4 lysozyme folding, and the A‐helix serves an important role in coupling the two subdomains.
Exploring subdomain cooperativity in T4 lysozyme II: Uncovering the C‐terminal subdomain as a hidden intermediate in the kinetic folding pathway
Authors: Cellitti Jason , Bernstein Rachel , Marqusee Susan
Published: March 2007

Intermediates along a protein's folding pathway can play an important role in its biology. Previous kinetics studies have revealed an early folding intermediate for T4 lysozyme, a small, well‐characterized protein composed of an N‐terminal and a C‐terminal subdomain. Pulse‐labeling hydrogen exchange studies suggest that residues from both subdomains contribute to the structure of this intermediate. On the other hand, equilibrium native state hydrogen experiments have revealed a high‐energy, partially unfolded form of the protein that has an unstructured N‐terminal subdomain and a structured C‐terminal subdomain. To resolve this discrepancy between kinetics and equilibrium data, we performed detailed kinetics analyses of the folding and unfolding pathways of T4 lysozyme, as well as several point mutants and large‐scale variants. The data support the argument for the presence of two distinct intermediates, one present on each side of the rate‐limiting transition state barrier. The effects of circular permutation and site‐specific mutations in the wild‐type and circular permutant background, as well as a fragment containing just the C‐terminal subdomain, support a model for the unfolding intermediate with an unfolded N‐terminal and a folded C‐terminal subdomain. Our results suggest that the partially unfolded form identified by native state hydrogen exchange resides on the folded side of the rate‐limiting transition state and is, therefore, under most conditions, a “hidden” intermediate.
The first step of hen egg white lysozyme fibrillation, irreversible partial unfolding, is a two‐state transition
Authors: Xu Ming , Shashilov Victor A. , Ermolenkov Vladimir V. , Fredriksen Laura , Zagorevski Dmitri , Lednev Igor K.
Published: March 2007

Amyloid fibril depositions are associated with many neurodegenerative diseases as well as amyloidosis. The detailed molecular mechanism of fibrillation is still far from complete understanding. In our previous study of in vitro fibrillation of hen egg white lysozyme, an irreversible partially unfolded intermediate was characterized. A similarity of unfolding kinetics found for the secondary and tertiary structure of lysozyme using deep UV resonance Raman (DUVRR) and tryptophan fluorescence spectroscopy leads to a hypothesis that the unfolding might be a two‐state transition. In this study, chemometric analysis, including abstract factor analysis (AFA), target factor analysis (TFA), evolving factor analysis (EFA), multivariate curve resolution–alternating least squares (ALS), and genetic algorithm, was employed to verify that only two principal components contribute to the DUVRR and fluorescence spectra of soluble fraction of lysozyme during the fibrillation process. However, a definite conclusion on the number of conformers cannot be made based solely on the above spectroscopic data although chemometric analysis suggested the existence of two principal components. Therefore, electrospray ionization mass spectrometry (ESI‐MS) was also utilized to address the hypothesis. The protein ion charge state distribution (CSD) envelopes of the incubated lysozyme were well fitted with two principal components. Based on the above analysis, the partial unfolding of lysozyme during in vitro fibrillation was characterized quantitatively and proven to be a two‐state transition. The combination of ESI‐MS and Raman and fluorescence spectroscopies with advanced statistical analysis was demonstrated to be a powerful methodology for studying protein structural transformations.
Estrogen receptor–ligand complexes measured by chip‐based nanoelectrospray mass spectrometry: An approach for the screening of endocrine disruptors
Authors: Bovet Cédric , Wortmann Arno , Eiler Sylvia , Granger Florence , Ruff Marc , Gerrits Bertran , Moras Dino , Zenobi Renato
Published: March 2007

In the present report, a method based on chip‐based nanoelectrospray mass spectrometry (nanoESI‐MS) is described to detect noncovalent ligand binding to the human estrogen receptor α ligand‐binding domain (hERα LBD). This system represents an important environmental interest, because a wide variety of molecules, known as endocrine disruptors, can bind to the estrogen receptor (ER) and induce adverse health effects in wildlife and humans. Using proper experimental conditions, the nanoESI‐MS approach allowed for the detection of specific ligand interactions with hERα LBD. The relative gas‐phase stability of selected hERα LBD–ligand complexes did not mirror the binding affinity in solution, a result that demonstrates the prominent role of hydrophobic contacts for stabilizing ER–ligand complexes in solution. The best approach to evaluate relative solution‐binding affinity by nanoESI‐MS was to perform competitive binding experiments with 17β‐estradiol (E2) used as a reference ligand. Among the ligands tested, the relative binding affinity for hERα LBD measured by nanoESI‐MS was 4‐hydroxtamoxifen ≈ diethylstilbestrol > E2 >> genistein >> bisphenol A, consistent with the order of the binding affinities in solution. The limited reproducibility of the bound to free protein ratio measured by nanoESI‐MS for this system only allowed the binding constants (Kd) to be estimated (low nanomolar range for E2). The specificity of nanoESI‐MS combined with its speed (1 min/ligand), low sample consumption (90 pmol protein/ligand), and its sensitivity for ligand (30 ng/mL) demonstrates that this technique is a promising method for screening suspected endocrine disrupting compounds and to qualitatively evaluate their binding affinity.
Ligand binding and allostery can emerge simultaneously
Authors: Liang Jing , Kim Jin Ryoun , Boock Jason T. , Mansell Thomas J. , Ostermeier Marc
Published: March 2007

A heterotropic allosteric effect involves an effector molecule that is distinct from the substrate or ligand of the protein. How heterotropic allostery originates is an unanswered question. We have previously created several heterotropic allosteric enzymes by recombining the genes for TEM1 β‐lactamase (BLA) and maltose binding protein (MBP) to create BLAs that are positively or negatively regulated by maltose. We show here that one of these engineered enzymes has ∼106 M−1 affinity for Zn2+, a property that neither of the parental proteins possesses. Furthermore, Zn2+ is a negative effector that noncompetitively switches off β‐lactam hydrolysis activity. Mutagenesis experiments indicate that the Zn2+‐binding site does not involve a histidine or a cysteine, which is atypical of natural Zn2+‐binding sites. These studies also implicate helices 1 and 12 of the BLA domain in allosteric signal propagation. These results support a model for the evolution of heterotropic allostery in which effector affinity and allosteric signaling emerge simultaneously.
Structural factors affecting the choice between latency transition and polymerization in inhibitory serpins
Authors: Yi Ji‐Yeun , Im Hana
Published: March 2007

Plasminogen activator inhibitor‐1 (PAI‐1), a member of the serine protease inhibitor (serpin) protein family, is unique among the serpins in its conformational lability. This lability allows spontaneous conversion of the active form to a more stable, latent conformation under physiological conditions. In other serpins, polymerization, rather than latency transition, is induced under pathological conditions or upon heat treatment. To identify specific factors promoting latency conversion in PAI‐1, we mutated PAI‐1 at various positions and compared the effects with those of equivalent mutations in α1‐antitrypsin, the archetypal serpin. Mutations that improved interactions with the turn between helix F and the third strand of β‐sheet A (thFs3A) or the fifth strand of β‐sheet A (s5A), which are near the site of latency transition‐associated insertion of the reactive center loop, retarded latency conversion but did not greatly increase structural stability. Mutations that decreased interactions with s2C facilitated conformational conversion, possibly by releasing the reactive center loop from β‐sheet C. Mutations of Thr93 that filled a hydrophobic surface pocket on s2A dramatically increased structural stability but had a negligible effect on the conformational transition. Our results suggest that the structural features controlling latency transition in PAI‐1 are highly localized, whereas the conformational strain of the native forms of other inhibitory serpins is distributed throughout the molecule and induces polymerization.
Solution structure of human sorting nexin 22
Authors: Song Jikui , Zhao Kate Qin , Newman Carrie L. Loushin , Vinarov Dmitriy A. , Markley John L.
Published: March 2007

The sorting nexins (SNXs) constitute a large group of PX domain‐containing proteins that play critical roles in protein trafficking. We report here the solution structure of human sorting nexin 22 (SNX22). Although SNX22 has <30% sequence identity with any PX domain protein of known structure, it was found to contain the α/β fold and compact structural core characteristic of PX domains. Analysis of the backbone dynamics of SNX22 by NMR relaxation measurements revealed that the two walls of the ligand binding cleft undergo internal motions: on the picosecond timescale for the β1/β2 loop and on the micro‐ to millisecond timescale for the loop between the polyproline motif and helix α2. Regions of the SNX22 structure that differ from those of other PX domains include the loop connecting strands β1 and β2 and the loop connecting helices α1 and α2, which appear to be more mobile than corresponding loops in other known structures. The interaction of dibutanoyl‐phosphatidylinositol‐3‐phosphate (dibutanoyl‐PtdIns(3)P) with SNX22 was investigated by an NMR titration experiment, which identified the binding site in a basic cleft and indicated that ligand binding leads only to a local structural rearrangement as has been found with other PX domains. Because motions in the loops are damped out when dibutanoyl‐PtdIns(3)P binds, entropic effects could contribute to the lower affinity of SNX22 for this ligand compared to other PX domains.