bluuebunny/crossref_metadata_2025 huggingface dataset:
PromoterExplorer: an effective promoter identification method based on the AdaBoost algorithm
Authors: Xie Xudong , Wu Shuanhu , Lam Kin-Man , Yan Hong
Published: September 2006

Motivation: Promoter prediction is important for the analysis of gene regulations. Although a number of promoter prediction algorithms have been reported in literature, significant improvement in prediction accuracy remains a challenge. In this paper, an effective promoter identification algorithm, which is called PromoterExplorer, is proposed. In our approach, we analyze the different roles of various features, that is, local distribution of pentamers, positional CpG island features and digitized DNA sequence, and then combine them to build a high-dimensional input vector. A cascade AdaBoost-based learning procedure is adopted to select the most ‘informative’ or ‘discriminating’ features to build a sequence of weak classifiers, which are combined to form a strong classifier so as to achieve a better performance. The cascade structure used for identification can also reduce the false positive.

Results: PromoterExplorer is tested based on large-scale DNA sequences from different databases, including the EPD, DBTSS, GenBank and human chromosome 22. Experimental results show that consistent and promising performance can be achieved.

Contact:  h.yan@cityu.edu.hk
GATHER: a systems approach to interpreting genomic signatures
Authors: Chang Jeffrey T. , Nevins Joseph R.
Published: September 2006

Motivation: Understanding the full meaning of the biology captured in molecular profiles, within the context of the entire biological system, cannot be achieved with a simple examination of the individual genes in the signature. To facilitate such an understanding, we have developed GATHER, a tool that integrates various forms of available data to elucidate biological context within molecular signatures produced from high-throughput post-genomic assays.

Results: Analyzing the Rb/E2F tumor suppressor pathway, we show that GATHER identifies critical features of the pathway. We further show that GATHER identifies common biology in a series of otherwise unrelated gene expression signatures that each predict breast cancer outcome. We quantify the performance of GATHER and find that it successfully predicts 90% of the functions over a broad range of gene groups. We believe that GATHER provides an essential tool for extracting the full value from molecular signatures generated from genome-scale analyses.

Availability: GATHER is available at

Contact:  j.nevins@duke.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Software for dynamic analysis of tracer-based metabolomic data: estimation of metabolic fluxes and their statistical analysis
Authors: Selivanov Vitaly A. , Marin Silvia , Lee Paul W. N. , Cascante Marta
Published: September 2006

Motivation: Metabolic flux analysis of biochemical reaction networks using isotope tracers requires software tools that can analyze the dynamics of isotopic isomer (isotopomer) accumulation in metabolites and reveal the underlying kinetic mechanisms of metabolism regulation. Since existing tools are restricted by the isotopic steady state and remain disconnected from the underlying kinetic mechanisms, we have recently developed a novel approach for the analysis of tracer-based metabolomic data that meets these requirements. The present contribution describes the last step of this development: implementation of (i) the algorithms for the determination of the kinetic parameters and respective metabolic fluxes consistent with the experimental data and (ii) statistical analysis of both fluxes and parameters, thereby lending it a practical application.

Results: The C++ applications package for dynamic isotopomer distribution data analysis was supplemented by (i) five distinct methods for resolving a large system of differential equations; (ii) the ‘simulated annealing’ algorithm adopted to estimate the set of parameters and metabolic fluxes, which corresponds to the global minimum of the difference between the computed and measured isotopomer distributions; and (iii) the algorithms for statistical analysis of the estimated parameters and fluxes, which use the covariance matrix evaluation, as well as Monte Carlo simulations.

An example of using this tool for the analysis of 13C distribution in the metabolites of glucose degradation pathways has demonstrated the evaluation of optimal set of parameters and fluxes consistent with the experimental pattern, their range and statistical significance, and also the advantages of using dynamic rather than the usual steady-state method of analysis.

Availability: Software is available free from

Contact:  martacascante@ub.edu
A Paranasal Tumor Associated With Tumor‐Induced Osteomalacia
Authors: Inokuchi Go , Tanimoto Hitoshi , Ishida Haruhiko , Sugimoto Toshitsugu , Yamauchi Mika , Miyauchi Akimitsu , Nibu Ken‐ichi
Published: September 2006

Background: Tumor‐induced osteomalacia (TIO) is an extremely rare paraneoplastic syndrome associated with mesenchymal tumors in the craniofacial region.

Methods: We treated a 24‐year‐old Japanese woman with paranasal sinus tumor and a low serum phosphate level who presented with nasal obstruction and systemic bone fractures. Serum fibroblast growth factor 23 (FGF‐23) was measured before and after surgery.

Results: After surgery, her symptoms were resolved and the serum phosphate and FGF‐23 levels became normalized.

Conclusion: FGF‐23 is thought to be a useful diagnostic marker in patients with craniofacial tumors associated with multiple systemic fractures.
Risk Acceptance in Laryngeal Transplantation
Authors: Reynolds Christopher C. , Martinez Serge A. , Furr Allen , Cunningham Michael , Bumpous Jeffrey M. , Lentsch Eric J. , Banis Joseph C. , Vasilic Dalibor , Storey Barckley , Wiggins Osborne , Maldonado Claudio , Perez‐Abadia Gustavo , Barker John H.
Published: September 2006

Purpose: Advancements in the fields of head and neck surgery and immunology have paved the way for new quality of life‐improving procedures such as larynx transplantation. To quantitatively assess the risks versus benefits in larynx transplantation, we used a questionnaire‐based survey (Louisville Instrument For Transplantation [LIFT]) to measure the degree of risk individuals are willing to accept to receive different types of transplantation procedures.

Methods: The LIFT contains 237 standardized questions incorporating standard gamble and time tradeoff outcome measures as well as questions assessing body image perception, depression, self‐esteem, optimism, socially desirable responding, and demographics. Respondents were questioned on the extent to which they would trade off specific numbers of life‐years, or sustain other costs, in exchange for receiving seven different types of transplant procedures. For this study, we questioned 243 individuals in three study populations with differing life experiences: healthy individuals, organ transplant recipients, and laryngectomees.

Results: All populations questioned perceived risks differently based on their varied life experiences and would accept differing degrees of risk for the different transplant procedures. Organ transplant recipients were the most risk‐tolerant group, whereas laryngectomees were the least risk‐tolerant.

Conclusions: By questioning individuals with life experiences directly relevant to the risks and benefits associated with larynx transplantation, this study provides an empiric basis for assessing risk versus benefit in this new quality of life‐improving procedure.
Fluorescent Retrograde Axonal Tracing of the Facial Nerve
Authors: O'Malley Matthew R. , Wittkopf Justin E. , Cutler Jeffrey L. , Labadie Robert F. , Hackett Troy A. , Haynes David S.
Published: September 2006

Objective: The objective of this study was to investigate retrograde fluorescent axonal labeling of motor nerves as an aid to surgical dissection in otolaryngology–head and neck surgery.

Methods: Cholera toxin B subunit conjugated to a fluorescent dye was injected into the facial musculature of New Zealand white rabbits. At variable time points after injection, the facial nerves were harvested and analyzed for fluorescence in the peripheral axon.

Results: All injected animals demonstrated axonal fluorescence. No animal demonstrated facial weakness. Fluorescence was detected a maximum of 20 mm from the distal end of the nerve. Time periods greater than 48 hours did not substantially increase transport distance.

Conclusions: Cholera toxin B subunit fluorescent conjugates, when administered intramuscularly, reliably label the distal portion of the facial nerve. In vivo labeling of a motor nerve may have significant potential for identifying a nerve in surgery. This work represents a preliminary investigation into the adaptation of in vivo fluorescence techniques as an aid to surgical dissection. Further research to refine this technique should be supported.
Surgical Treatment of Chronic Recurrent Rhinosinusitis: A Preliminary Report
Authors: Bhattacharyya Neil
Published: September 2006

Objective: The objective of this study was to determine if endoscopic sinus surgery (ESS) is effective in the management of chronic recurrent rhinosinusitis (CRRS).

Methods: A consecutive series of patients with CRRS diagnosed according to stringent criteria was prospectively examined before and at least 1 year after ESS. Paranasal sinus computed tomography scans were staged and ESS was performed targeting radiographic disease and the ostiomeatal complex. Preoperative and postoperative disease severities in terms of symptom scores, medicine utilization, and resource factors were assessed using the rhinosinusitis symptom inventory (RSI). Improvements in RSI symptom domains, medical and economic resource factors were determined using effect sizes and statistical comparison before and after ESS.

Results: Nineteen patients (mean age, 42.3 years) completed the study with a mean follow up of 19.1 months. The mean Lund score was 3.42 (standard deviation, 4.09). Statistically significant decreases in nasal (−36.1), facial (−28.4), oropharyngeal (−34.6), systemic (−24.7), and total (−31.9) RSI symptom domain scores were observed (all P < .003) with effect sizes ranging from 0.87 to 1.63 (strong surgical effect). Statistically significant decreases in antihistamine use (−30%, P = .031), number of workdays missed as a result of CRRS (−1.9, P = .035), and number of acute infectious episodes (−2.5, P = .006) were also observed. However, declines in weeks of antibiotic use (−2.8 weeks, P = .293) and number of antibiotic courses (−1.7, P = .118) were not significant.

Conclusions: Patients with CRRS may substantially benefit both symptomatically and medically from ESS. Although surgery should be used cautiously in treating CRRS, further trials of ESS for CRRS are warranted.
Useful Landmarks in Arytenoid Adduction and Laryngeal Reinnervation Surgery
Authors: Armin Bob B. , Head Christian , Berke Gerald S. , Chhetri Dinesh K.
Published: September 2006

Objective: Knowledge of the location of the muscular process of the arytenoid cartilage and the recurrent laryngeal nerve is essential to performing a successful arytenoid adduction and laryngeal reinnervation surgery. We describe external landmarks useful in locating these structures.

Study Design: Cadaveric laryngeal dissection.

Methods: Posterior laryngeal dissection was performed in 16 human larynges. The position of the muscular process of the arytenoid was measured bilaterally relative to the inferior and superior borders of the thyroid lamina. The recurrent laryngeal nerve was followed distally from slightly below the level of the cricothyroid joint to its genu where its vertical course changes to an oblique intralaryngeal course.

Results: The muscular process of the arytenoid was usually found halfway between the roots of the superior and inferior cornu of the thyroid lamina. The recurrent laryngeal nerve was found just deep to the cricothyroid joint and lateral to the posterior cricoarytenoid muscle. There were no other nerves in this area.

Conclusions: This study finds that the superior and inferior borders of the thyroid lamina are useful intraoperative landmarks to locate the muscular process of the arytenoid. The cricothyroid joint provides a good starting point to locate the recurrent laryngeal nerve, which can be identified slightly deeper between it and the posterior cricoarytenoid muscle.
Analysis of the Long‐Term Hearing Results after the Surgical Repair of Aural Atresia
Authors: Chang Sun O. , Choi Byung Yoon , Hur Dong Gu
Published: September 2006

Objectives: Careful surgical candidate selection guarantees a high probability of serviceable hearing postoperatively in congenital aural atresia (CAA) patients. The authors analyzed hearing results after CAA surgery with long‐term follow‐up (F/U) with respect to several clinical factors.

Study Design: This was a retrospective study.

Methods: The medical records of 93 CAA patients (100 ears) who underwent operations from January 1987 through December 2002 at Seoul National University Hospital were reviewed. Mean duration was 56.9 months. The authors evaluated the results of hearing after surgery over 3 year F/U with a view to clarifying the factors accounting for unsuccessful results.

Results: Approximately 64% of patients treated surgically achieved a considerable hearing gain over long‐term F/U. Postoperative hearing remained relatively stable over the period from 6 months to 3 years postoperatively, yielding only 2.75 dB of aggravation. However, hearing results in revision cases deteriorated with time, which led to statistically higher air‐conduction thresholds than those of primary cases at the 1 and 3 year F/Us. Resultantly, only 26.6% of patients having achieved a poor hearing gain post first surgery benefited from revision audiologically. The severity of microtia was found to help predict poor long‐term hearing outcomes after CAA surgery.

Conclusions: Nonrevision cases and cases with mild microtia appear to have acceptable and stable long‐term hearing results. Disappointing long‐term hearing results in revision, and severe microtia cases should lead to considerations of alternative options in these cases, such as bone‐anchored hearing aids, which offer reliable and stable results.
Chemopreventive Effect of Celecoxib in Oral Precancers and Cancers
Authors: Feng Lining , Wang Zhi
Published: September 2006

Objectives: Oral cancer has become an important health care problem in many countries. Because this disease develops slowly, early detection and intervention can greatly affect ultimate outcome. Celecoxib is a cyclooxygenase‐2 inhibitor with significantly less toxicity. This study investigated the possibility of using it for chemoprevention of oral cancer at the early stages.

Study Design: Randomized animal study.

Methods: Dysplastic lesions were induced in the buccal pouches of 47 hamsters by a 5 week painting of 9,10‐dimethl‐1,2‐benzanthrancene (DMBA). Basal diets or diets containing 500 or 1,500 ppm of Celecoxib were orally given for 7 weeks. The T50 (50% incidence; i.e., the time to appearance of tumors in 50% of the hamsters) was observed, and volume of tumors was measured on day 1, 9, 19, 28, 35, and 48 with the Celecoxib treatment.

Results: The T50 was 9, 19, and 28 days with the treatment in the control group, in the 500 ppm group, and in the 1,500 ppm group, respectively. It indicated that the Celecoxib treatment could delay progression of early lesion. The tumor measurement showed that this treatment was also effective in delaying tumor growth in both treatment groups. There was a difference in the treatment efficacy between the 500 ppm and 1,500 ppm of Celecoxib, indicating a dose‐dependent efficacy.

Conclusions: Celecoxib is effective in delaying onset of early lesions induced by DMBA and in slowing growth of the tumors in hamster cheek pouches during the postinitiation stage. Its treatment efficacy appears to be dose dependent.
Age‐Dependent Degeneration of the Stria Vascularis in Human Cochleae
Authors: Suzuki Teruhisa , Nomoto Yukio , Nakagawa Takayuki , Kuwahata Naofumi , Ogawa Hiroshi , Suzuki Yukie , Ito Juichi , Omori Koichi
Published: September 2006

Objective: Aging is a common cause of acquired hearing impairments. This study investigated age‐related morphologic changes in human cochleae, with a particular focus on degeneration of the stria vascularis (SV) and the spiral ganglion (SG).

Study Design: Retrospective case review.

Methods: The study group comprised 91 temporal bones from individuals aged 10 to 85 years who had no history or audiometric findings suggestive of specific causes of cochlear degeneration. We quantified the SV and SG atrophy at each cochlear turn using morphometric measurements. Correlations of the SV and SG atrophy with age, audiometric patterns of hearing loss, and auditory thresholds were statistically investigated.

Result: The SV and the SG both showed a tendency for progressive atrophy to develop with age. However, statistically significant correlations were observed between aging and SV atrophy only in the apical and basal cochlear turns. These findings were consistent with those reported previously in gerbils. No significant correlations were detected between SV or SG atrophy and audiometric findings.

Conclusion: SV atrophy appears to be the most prominent anatomic characteristic of aged human cochleae.
Sensorineural Hearing Loss in Vogt‐Koyanagi‐Harada Syndrome
Authors: Ondrey Frank G. , Moldestad Eric , Mastroianni Mary Ann , Pikus Anita , Sklare Daniel , Vernon Estelle , Nusenblatt Robert , Smith Janine
Published: September 2006

Background: Vogt‐Koyanagi‐Harada (VKH) syndrome is a systemic condition characterized by ocular inflammatory disease as well as skin, ear, and meningeal manifestations. Patients with VKH often report tinnitus and hearing loss, but these symptoms tend to be given secondary consideration because most undergo treatment with steroids to prevent blindness resulting from granulomatous uveitis, exudative retinal detachment, and optic nerve inflammation.

Methods/Study Design: In the current retrospective review, 24 patients with this syndrome were screened for auditory system abnormalities. All patients denied history of noise exposure or ototoxic agent exposure. The age range of the patients was 13 to 42 years.

Results: Three patients reported tinnitus and two patients reported sudden hearing loss. One patient experienced vertigo and aural fullness. Eight of 24 patients had pure‐tone thresholds greater than 25 dB hearing loss at two or more frequencies. Five of 24 of these patients experienced hearing loss outside of the 95% confidence interval for published age‐matched control populations. There was sloping sensorineural hearing loss at 4 kHz and above in five of 24 patients. All eight patients with hearing loss experienced some degree of hearing loss at 4 kHz or above. Three patients had mild to moderate low‐frequency sensorineural hearing loss. There were no tympanometric abnormalities suggestive of conductive involvement. Abnormal acoustic reflex decay was observed in one patient.

Conclusions: We conclude that a significant number of patients with VKH experience sensorineural hearing loss and that every patient with VKH should undergo a review of systems for auditory abnormalities and referral for audiologic testing if symptomatic. It is possible that untreated patients may experience worse symptoms.
The Efficacy of Mitomycin‐C in the Treatment of Laryngotracheal Stenosis
Authors: Simpson C Blake , James Joshua C.
Published: September 2006

Objective: The purpose of this study is to evaluate whether the addition of topical mitomycin‐C (MMC) application to the wound site after endoscopic treatment of laryngotracheal stenosis (LTS) resulted in measurable improvement in clinical outcomes.

Study Design and Setting: A retrospective chart review of patients with LTS treated by the senior author over a 6‐year period was performed. The treatment groups were stratified into two main categories: 1) endoscopic treatment alone and 2) endoscopic treatment + topical MMC. The “symptom‐free” interval was determined (in months) for each subject using a two‐tailed t test for statistical analysis of the control/study groups.

Results: Sixty‐seven procedures were performed in 36 patients with LTS with a mean of 1.86 surgical treatments per patient. The mean duration of the symptom‐free interval after endoscopic treatment for LTS was 4.9 months in the endoscopic‐only treatment group and 23.2 months in the endoscopic group receiving topical MMC. The symptom‐free interval observed in the MMC group was significantly longer than the control subjects (P = 1 × 10−11).

Conclusions: The results of this study suggest that MMC is an effective adjuvant in the treatment of LTS. The results of this study provide strong supporting evidence that topical MMC is an effective adjuvant in the treatment of LTS.
Management of the Radial Forearm Free Flap Donor Site With the Vacuum‐Assisted Closure (VAC) System
Authors: Andrews Brian T. , Smith Russell B. , Chang Kristi E. , Scharpf Joseph , Goldstein David P. , Funk Gerry F.
Published: September 2006

Introduction: The radial forearm free flap is a popular reconstructive flap in modern head and neck surgery. Poor wound healing at the forearm donor site is common and frequently results in tendon exposure. The Vacuum‐Assisted Closure (VAC) system (Kinetic Concepts Inc., San Antonio, TX) is a topical negative pressure dressing that has been shown to improve skin graft viability when used as a bolster dressing. In this study, we investigated the use of the VAC system in the management of the radial forearm free flap donor site.

Methods: A retrospective chart review was performed on all subjects who underwent a radial forearm free flap reconstruction in which the VAC system was used as a bolster dressing at the donor site from January 1, 2003, through March 31, 2005.

Results: Thirty‐four consecutive subjects were included in the study. Exposed tendon did not occur in 14 (0%) subjects in which the VAC bolster was used for a minimum of 6 days. Eleven of the 20 subjects (55%) who used the VAC bolster for 5 days demonstrated small amounts of tendon exposure (<2 cm) on follow‐up clinic examination. The minimum follow up for all subjects was 4 months.

Conclusion: This study demonstrates that the VAC system is a feasible alternative to conventional bolster dressing in the management of the radial forearm free flap skin‐grafted donor site. Based on this study, when used for a minimum of 6 days, the VAC bolster dressing eliminated tendon exposure at the forearm donor site.
Eukaryotic expression: developments for structural proteomics
Authors: Aricescu A. R. , Assenberg R. , Bill R. M. , Busso D. , Chang V. T. , Davis S. J. , Dubrovsky A. , Gustafsson L. , Hedfalk K. , Heinemann U. , Jones I. M. , Ksiazek D. , Lang C. , Maskos K. , Messerschmidt A. , Macieira S. , Peleg Y. , Perrakis A. , Poterszman A. , Schneider G. , Sixma T. K. , Sussman J. L. , Sutton G. , Tarboureich N. , Zeev-Ben-Mordehai T. , Jones E. Yvonne
Published: September 2006

The production of sufficient quantities of protein is an essential prelude to a structure determination, but for many viral and human proteins this cannot be achieved using prokaryotic expression systems. Groups in the Structural Proteomics In Europe (SPINE) consortium have developed and implemented high-throughput (HTP) methodologies for cloning, expression screening and protein production in eukaryotic systems. Studies focused on three systems: yeast (Pichia pastoris and Saccharomyces cerevisiae), baculovirus-infected insect cells and transient expression in mammalian cells. Suitable vectors for HTP cloning are described and results from their use in expression screening and protein-production pipelines are reported. Strategies for co-expression, selenomethionine labelling (in all three eukaryotic systems) and control of glycosylation (for secreted proteins in mammalian cells) are assessed.
SPINE bioinformatics and data-management aspects of high-throughput structural biology
Authors: Albeck S. , Alzari P. , Andreini C. , Banci L. , Berry I. M. , Bertini I. , Cambillau C. , Canard B. , Carter L. , Cohen S. X. , Diprose J. M. , Dym O. , Esnouf R. M. , Felder C. , Ferron F. , Guillemot F. , Hamer R. , Ben Jelloul M. , Laskowski R. A. , Laurent T. , Longhi S. , Lopez R. , Luchinat C. , Malet H. , Mochel T. , Morris R. J. , Moulinier L. , Oinn T. , Pajon A. , Peleg Y. , Perrakis A. , Poch O. , Prilusky J. , Rachedi A. , Ripp R. , Rosato A. , Silman I. , Stuart D. I. , Sussman J. L. , Thierry J.-C. , Thompson J. D. , Thornton J. M. , Unger T. , Vaughan B. , Vranken W. , Watson J. D. , Whamond G. , Henrick K.
Published: September 2006

SPINE (Structural Proteomics In Europe) was established in 2002 as an integrated research project to develop new methods and technologies for high-throughput structural biology. Development areas were broken down into workpackages and this article gives an overview of ongoing activity in the bioinformatics workpackage. Developments cover target selection, target registration, wet and dry laboratory data management and structure annotation as they pertain to high-throughput studies. Some individual projects and developments are discussed in detail, while those that are covered elsewhere in this issue are treated more briefly. In particular, this overview focuses on the infrastructure of the software that allows the experimentalist to move projects through different areas that are crucial to high-throughput studies, leading to the collation of large data sets which are managed and eventually archived and/or deposited.
Co-expression of protein complexes in prokaryotic and eukaryotic hosts: experimental procedures, database tracking and case studies
Authors: Romier Christophe , Ben Jelloul Marouane , Albeck Shira , Buchwald Gretel , Busso Didier , Celie Patrick H. N. , Christodoulou Evangelos , De Marco Valeria , van Gerwen Suzan , Knipscheer Puck , Lebbink Joyce H. , Notenboom Valerie , Poterszman Arnaud , Rochel Natacha , Cohen Serge X. , Unger Tamar , Sussman Joel L. , Moras Dino , Sixma Titia K. , Perrakis Anastassis
Published: September 2006

Structure determination and functional characterization of macromolecular complexes requires the purification of the different subunits in large quantities and their assembly into a functional entity. Although isolation and structure determination of endogenous complexes has been reported, much progress has to be made to make this technology easily accessible. Co-expression of subunits within hosts such as Escherichia coli and insect cells has become more and more amenable, even at the level of high-throughput projects. As part of SPINE (Structural Proteomics In Europe), several laboratories have investigated the use co-expression techniques for their projects, trying to extend from the common binary expression to the more complicated multi-expression systems. A new system for multi-expression in E. coli and a database system dedicated to handle co-expression data are described. Results are also reported from various case studies investigating different methods for performing co-expression in E. coli and insect cells.
Recombinant protein expression and solubility screening in Escherichia coli: a comparative study
Authors: Berrow Nick S. , Büssow K. , Coutard B. , Diprose J. , Ekberg M. , Folkers G. E. , Levy N. , Lieu V. , Owens R. J. , Peleg Y. , Pinaglia C. , Quevillon-Cheruel S. , Salim L. , Scheich C. , Vincentelli R. , Busso Didier
Published: September 2006

Producing soluble proteins in Escherichia coli is still a major bottleneck for structural proteomics. Therefore, screening for soluble expression on a small scale is an attractive way of identifying constructs that are likely to be amenable to structural analysis. A variety of expression-screening methods have been developed within the Structural Proteomics In Europe (SPINE) consortium and to assist the further refinement of such approaches, eight laboratories participating in the network have benchmarked their protocols. For this study, the solubility profiles of a common set of 96 His6-tagged proteins were assessed by expression screening in E. coli. The level of soluble expression for each target was scored according to estimated protein yield. By reference to a subset of the proteins, it is demonstrated that the small-scale result can provide a useful indicator of the amount of soluble protein likely to be produced on a large scale (i.e. sufficient for structural studies). In general, there was agreement between the different groups as to which targets were not soluble and which were the most soluble. However, for a large number of the targets there were wide discrepancies in the results reported from the different screening methods, which is correlated with variations in the procedures and the range of parameters explored. Given finite resources, it appears that the question of how to most effectively explore `expression space' is similar to several other multi-parameter problems faced by crystallographers, such as crystallization.
Advances in e‐democracy: overview
Authors: Gunter Barrie
Published: September 2006

Purpose

The purpose of this paper is to introduce the theme of this special issue, “Advances in e‐democracy: engaging citizens and electorates”.

Design/methodology/approach

An overview is provided of developments in e‐government before providing a summary discussion of the papers that are presented in this issue.

Findings

While governments around the world, not least in the UK, have been enthusiastic about the use of information and communication technologies to provide better citizen access to government and public services, there is still much to be learned about how these online services can be effectively implemented and will be taken up.

Originality/value

This paper provides a primer for the remainder of this issue which combines research reports from academics working in the e‐democracy field and from practitioners in government and commercial service suppliers.
Benchmarking e‐government policy within the e‐Europe programme
Authors: Wauters Patrick
Published: September 2006

Purpose

The paper aims to provide a benchmark study of the European Union (EU) e‐government policy within the e‐Europe programme. The main objective of the European strategy for the development of e‐government was that the member states should ensure “online public services”. To monitor this policy the European Commission defined two indicators.

Design/methodology/approach

The European Commission developed a list of 20 basic public services. The Commission and Capgemini defined a framework to evaluate the online availability of each of the services in each of the EU member states, plus Norway, Iceland and Switzerland.

Findings

The study finds that since 2001 a considerable improvement in online public service provision was measured, even so the 2004 result of 65 per cent online sophistication of public service delivery in the EU still shows an important gap with the 100 per cent objective, the result was considered a positive. When considering the different types of public services, income generating services including income tax, VAT and corporate tax are by far the most developed online. The new member countries seem to be only two years behind in the development of online public service. The most advanced countries exceed 80 per cent but seem to evolve to a “plateau”. They have developed their most feasible services, demanding less effort, now only the “hard” ones are undeveloped, mostly services delivered at a decentralised level.

Research limitations/implications

The study provides information on the online development of public services, i.e. the provision and interactivity of public services through the internet. It does not analyse the provision of services through other channels, neither the quality of the service delivery, nor the use or impact of these new ways of public service supply. Therefore a new EU e‐government measurement system must change the focus from “availability” of e‐government services, to “use” and desired positive “impact” of e‐government programmes.

Originality/value

This study provides the only available data measured scientifically over a longer period concerning the development of e‐government in the EU.
Online campaign communication and the phenomenon of blogging
Authors: Stanyer James
Published: September 2006

Purpose

In light of the phenomenon of blogging in the 2004 US presidential campaign, this article aims to examine blogging during the 2005 British general election campaign. The article seeks to establish how widespread blogging was, the extent of bloggers' partisanship, what issues blogs were concerned with, what the purpose of the messages posted by the bloggers were, and what if any impact blogs had beyond the immediate community of users.

Design/methodology/approach

These questions were addressed through a content analysis of over 300 blogs and 1,300 posted messages, by additional searches of the Lexis‐Nexis newspaper archive, and via the use of internet poll data on blogging.

Findings

The research showed that blogging in the UK is in its infancy. There were few bloggers posting messages about the campaign and few people accessed blogs regularly. Most of the comments posted focused on campaign issues and were observational. While some of the bloggers exhibited an overt partisan identity, most did not. There was also some evidence of partisan networks, with blogs of a particular partisan/ideological position hyperlinking to others with a similar outlook. However, unlike the 2004 US presidential election campaign, blogs had no impact on the campaign news agenda.

Research limitations/implications

Despite extensive research it is difficult to ascertain whether the sample of blogs examined in the research represented the entirety of the election campaign blogosphere. Nevertheless, the findings provide important insights into the evolving online election communication environment in the UK.

Originality/value

The study is the first to examine systematically the blogging about the general election campaigns in the UK.
Developing local e‐democracy in Bristol
Authors: Hilton Stephen
Published: September 2006

Purpose

Bristol City Council has received national and international recognition for its local e‐democracy work. This paper seeks to tell the story of three phases of development of local e‐democracy in Bristol. In summarising findings from the national evaluation of the Local E‐democracy Project, the paper also aims to consider stage four – where Bristol's e‐democracy programme is headed next.

Design/methodology/approach

Bristol acted as a lead authority on the evaluation of the Local E‐democracy National Project. This was a large multi‐method academic study, which set out to examine the aspirations and experiences of a variety of “actors” involved in more than 20 e‐democracy pilot projects across England. Professors Stephen Coleman of the Oxford Internet Institute and Ann Macintosh of the International Tele‐democracy Centre at Napier University undertook the evaluation, working with Bristol City Council as part of an E‐democracy Experts Group.

Findings

Findings from the national evaluation have been published in reports covering “top‐down” (authority‐led) and “ground‐up” (community‐led) approaches to local e‐democracy. This paper applies evaluation findings to Bristol City Council's experiences. It highlights how authorities can use e‐democracy to move between information sharing and consultation and then to creating space and conditions for ground‐up participation.

Research limitations/implications

The paper focuses on common themes, rather than an in‐depth account of all of the national evaluation findings as they relate to each project that was considered. As a case study, this paper concerns the particular experiences of Bristol City Council.

Practical implications

The study offers insight aimed at local authority e‐democracy practitioners.

Originality/value

Over the past five years, Bristol City Council has accumulated considerable practical experience of local e‐democracy. The authority has benefited from a close association with leading academic experts, leaving it perhaps uniquely positioned to share learning from critical self‐reflection.
Spacecraft vibration reduction using pulse modulated command input and smart materials
Authors: Hu Qinglei
Published: September 2006

Purpose

To provide an approach to active vibration reduction of flexible spacecraft actuated by on‐off thrusters during attitude control for spacecraft designers, which can help them analysis and design the attitude control system.

Design/methodology/approach

The new approach includes attitude controller acting on the rigid hub, designed by using pulse‐width pulse‐frequency modulation integrated with component command technique, and the piezoelectric material elements as sensors/actuators bonded on the surface of the beam appendages for active vibration suppression of flexible appendages, designed by optimal positive position feedback (OPPF) control technique. The OPPF compensator is devised by setting up a cost function to be minimized by feedback gains, which are subject to the stability criterion at the same time, and an extension to the conventional positive position feedback control design approach is investigated.

Findings

Numerical simulations for the flexible spacecraft show that the precise attitude control and vibration suppression can be accomplished using the derived vibration attenuator and attitude control controller.

Research limitations/implications

Studies on how to control the on‐off actuated system under impulse disturbances are left for future work.

Practical implications

An effective method is proposed for the spacecraft engineers planning to design attitude control system for actively suppressing the vibration and at the same time quickly and precisely responding to the attitude control command.

Originality/value

The advantage in this scheme is that the controllers are designed separately, allowing the two objectives to be satisfied independently of one another. It fulfils a useful source of theoretical analysis for the attitude control system design and offers practical help for the spacecraft designers.
Environmentally sustainable food production and marketing
Authors: Bhaskaran Suku , Polonsky Michael , Cary John , Fernandez Shadwell
Published: September 2006

Purpose

To identify and analyse the beliefs of value‐chain intermediaries regarding the production and marketing of food products conforming to environmentally sustainable standards.

Design/methodology/approach

The methodology was in‐depth, semi‐structured, face‐to‐face interviews with senior managers of food companies across the value chain.

Findings

In Australia, the demand for foods that are produced under environmentally sustainable standards has been slow to take‐off because customers do not perceive these products as offering any special benefits; customers distrust the claims made by organisations; these products are much more expensive than traditional products, and the implementation of environmental standards is expensive. Customers claim that the use of different terminologies such as organic, green and environmentally friendly in promoting food products is confusing.

Research limitations/implications

Findings are not generalisable because the study is based on a small sample.

Practical implications

Value‐chain intermediaries are unlikely to voluntarily adopt environmental standards because of low demand for such foods and the high costs of adopting and monitoring environmentally sustainable production and marketing regimes.

Originality/value

The story supports previous research findings from the USA and EU.
Cutting the bull: an effective business writing approach
Authors: Landale Anthony
Published: September 2006

Purpose

The purpose of this paper is to consider how effective training can address the issue of long‐winded and impenetrable business writing.

Design/methdology/approach

The paper reviews the key elements of the award‐winning Writing Dynamics approach and how it is being applied at The City of Edinburgh Council to improve the service this Council provides to its community.

Findings

Professional writers in particular are found to spend far more time in planning and editing than one might expect and there are some extremely practical techniques that can speed up and improve the writing process.

Practical implications

With people in business being bombarded by ever‐increasing amounts of information it has never been so important for people to get their message across clearly and persuasively. The conclusion that this article draws is that here is a method that is both extremely practical and beneficial for writers and readers alike.

Originality/value

This paper will be of particular value to training managers who want to know how a writing course can impact on their organisation's written communication as well as evidence of it having done so. It will also be of real interest to managers, marketeers and all staff who want to improve both the quality and speed of any business writing that is core to their work.
Beyond rule following: decoding leadership ethics
Authors: Wildermuth Cristina , Wildermuth Mel
Published: September 2006

Purpose

The purpose of the paper is to help leaders gain awareness of areas that can lead to problems in ethical decision making. Instead of simple “black and white” decisions, leaders face a myriad “grey” situations that cannot be addressed via blind application of company policy. The areas of focus are time, proximity, competitiveness, and personality.

Design/methodology/approach

The reader will learn about the “Urgency&Proximity Model” (U&PM); which describes how the urgency of an ethical decision and the proximity between the moral agent and the people involved in the situation impact the moral agent's decision‐making process. The authors incorporate the “Five Factor Model” of personality into the U&PM, raising possible connections between personality and moral reasoning.

Findings

The findings indicate that company policies lend themselves only to the simplest decisions, not ethical dilemmas. Thus keeping in mind the U&PM model, organizational competition, and one's own personality (from the WorkPlace Big Five Profile™) can form an ethical basis for moral decisions.

Research limitations/implications

Additional research is needed to connect the aspects of personality to the U&PM.

Practical implications

Leaders are advised to increase self‐awareness, consider their personality traits, and position the moral dilemma being addressed in the U&PM.

Originality/value

This paper is only an introductory examination of ethical decision making based on urgency, proximity, competition, and personality. The concept should be further investigated because of the impact these factors can have on leadership decision making.
Aggregation consistency and frequency of Chinese words and characters
Authors: Arsenault Clément
Published: September 2006

Purpose

Aims to measure syllable aggregation consistency of Romanized Chinese data in the title fields of bibliographic records. Also aims to verify if the term frequency distributions satisfy conventional bibliometric laws.

Design/methodology/approach

Uses Cooper's interindexer formula to evaluate aggregation consistency within and between two sets of Chinese bibliographic data. Compares the term frequency distributions of polysyllabic words and monosyllabic characters (for vernacular and Romanized data) with the Lotka and the generalised Zipf theoretical distributions. The fits are tested with the Kolmogorov‐Smirnov test.

Findings

Finds high internal aggregation consistency within each data set but some aggregation discrepancy between sets. Shows that word (polysyllabic) distributions satisfy Lotka's law but that character (monosyllabic) distributions do not abide by the law.

Research limitations/implications

The findings are limited to only two sets of bibliographic data (for aggregation consistency analysis) and to one set of data for the frequency distribution analysis. Only two bibliometric distributions are tested. Internal consistency within each database remains fairly high. Therefore the main argument against syllable aggregation does not appear to hold true. The analysis revealed that Chinese words and characters behave differently in terms of frequency distribution but that there is no noticeable difference between vernacular and Romanized data. The distribution of Romanized characters exhibits the worst case in terms of fit to either Lotka's or Zipf's laws, which indicates that Romanized data in aggregated form appear to be a preferable option.

Originality/value

Provides empirical data on consistency and distribution of Romanized Chinese titles in bibliographic records.
Evaluating library software and its fitness for purpose
Authors: Joint Nicholas
Published: September 2006

Purpose

To adapt general principles used for evaluating software quality to more specific requirements characteristic of information retrieval and educational applications in library environments.

Design/methodology/approach

A conceptual paper based on existing software evaluation models, but one which tries to add some important refinements to key aspects of these received concepts.

Findings

That the application of engineering concepts to technologically mediated tasks where crucial system outputs consist of the facilitation of specific mental events in the user of the system (e.g. “learning outcomes”) can be problematic. In such scenarios it may be valuable to avoid incorporating the production of specific mental events into the “objective functionality” of the software in question. Rather, it is suggested that the creation of these outputs should be left to the user, not to the mechanised routines of the system (i.e. these mental system outputs should be facilitated by the system as part of the “subjective functionality” of the overall design).

Research limitations/implications

These are purely conceptual approaches to library and e‐learning software that should be tested by practical case study investigation (e.g. comparative user evaluations both of software designed along general quality models standards, and of software designed to the model suggested here).

Practical implications

You can get better results in terms of human outputs and benefits (i.e. better learning outcomes, or a higher level of engagement with effective information retrieval) by means of simple, minimalist implementations of information technology and educational technology‐based systems.

Originality/value

This library and information science paper attempts to use ideas from software engineering and software evaluation to create an original perspective on real‐life problems in the sphere of information retrieval technology and educational technology.