bluuebunny/crossref_metadata_2025_split huggingface dataset:
Colonial competitive algorithm
Authors: Atashpaz Gargari Esmaeil , Hashemzadeh Farzad , Rajabioun Ramin , Lucas Caro 
Published: August 2008

PurposeThis paper aims to describe colonial competitive algorithm (CCA), a novel socio‐politically inspired optimization strategy, and how it is used to solve real world engineering problems by applying it to the problem of designing a multivariable proportional‐integral‐derivative (PID) controller. Unlike other evolutionary optimization algorithms, CCA is inspired from a socio‐political process – the competition among imperialists and colonies. In this paper, CCA is used to tune the parameters of a multivariable PID controller for a typical distillation column process.Design/methodology/approachThe controller design objective was to tune the PID controller parameters so that the integral of absolute errors, overshoots and undershoots be minimized. This multi‐objective optimization problem is converted to a mono‐objective one by adding up all the objective functions in which the absolute integral of errors is emphasized to be reduced as long as the overshoots and undershoots remain acceptable.FindingsSimulation results show that the controller tuning approach, proposed in this paper, can be easily and successfully applied to the problem of designing MIMO controller for control processes. As a result not only was the controlled process able to significantly reduce the coupling effect, but also the response speed was significantly increased. Also a genetic algorithm (GA) and an analytical method are used to design the controller parameters and are compared with CCA. The results showed that CCA had a higher convergence rate than GA, reaching to a better solution.Originality/valueThe proposed PID controller tuning approach is interesting for the design of controllers for industrial and chemical processes, e.g. MIMO evaporator plant. Also the proposed evolutionary algorithm, CCA, can be used in diverse areas of optimization problems including, industrial planning, resource allocation, scheduling, decision making, pattern recognition and machine learning.
Pedestrian tracking using single camera with new extended Kalman filter
Authors: Sadoghi Yazdi Hadi , Ebrahim Hosseini Seyyed 
Published: August 2008

PurposeThe purpose of this paper is to present research in the area of the signal processing and application into pedestrian tracking in the video scene.Design/methodology/approachThe paper describes the design of a new extended Kalman filter (EKF) in the high‐dimensional space (HDS) and studies of mean square error and variance analysis of error. A design algorithm is implemented in MATLAB software and tested. The data set includes many hours of captured films.FindingsThis paper includes a new derivation of the EKF and its implementation into the video scene.Practical implicationsThe proposed algorithm can be used to track each video application.Originality/valueThe Kalman filter in the HDS is presented for the first time. Also, the application of the proposed method is applied in pedestrian tracking and counting.
A multi‐agent approach to TS‐fuzzy modeling and predictive control of constrained nonlinear system
Authors: Nasr Hichem Ben , Faouzi M'Sahli 
Published: August 2008

PurposeThe paper aims to present a new concept based on a multi‐agent approach in the area of nonlinear model predictive control (MPC) for fast systems.Design/methodology/approachA contribution to decentralized implementation of MPC is made. The control of the nonlinear system subject to constraints is achieved via a set of actions taken from different agents. The actions are based on an analytical solution and a neural network is used to monitor the closed system using a supervisory loop concept.FindingsThe high online computational need to solve an optimal control actions in nonlinear MPC, which results in a non‐convex optimization, is compared with the new proposed concept. Simulation results show that this approach has very remarkable performances in time computing and target arrival.Research limitations/implicationsIn practice, each MPC problem of the individual agent in multi‐agent MPC can run in parallel at the same time, instead of in serial, one agent after another. A parallel processor can be useful for real time implementation. However, it is estimated that how much time can be gained by performing the computations in parallel instead of in serial.Practical implicationsThe proposed concept discussed in the paper has the potential to be applied to systems with rapid dynamics.Originality/valueThe multi‐agent MPC compares favorably with respect to a numerical optimization routine and also offers a solution for non‐convex optimization problems in single‐input single‐output systems.
Constrained optimization with an improved particle swarm optimization algorithm
Authors: Muñoz Zavala Angel E. , Hernández Aguirre Arturo , Villa Diharce Enrique R. , Botello Rionda Salvador 
Published: August 2008

PurposeThe purpose of this paper is to present a new constrained optimization algorithm based on a particle swarm optimization (PSO) algorithm approach.Design/methodology/approachThis paper introduces a hybrid approach based on a modified ring neighborhood with two new perturbation operators designed to keep diversity. A constraint handling technique based on feasibility and sum of constraints violation is adopted. Also, a special technique to handle equality constraints is proposed.FindingsThe paper shows that it is possible to improve PSO and keeping the advantages of its social interaction through a simple idea: perturbing the PSO memory.Research limitations/implicationsThe proposed algorithm shows a competitive performance against the state‐of‐the‐art constrained optimization algorithms.Practical implicationsThe proposed algorithm can be used to solve single objective problems with linear or non‐linear functions, and subject to both equality and inequality constraints which can be linear and non‐linear. In this paper, it is applied to various engineering design problems, and for the solution of state‐of‐the‐art benchmark problems.Originality/valueA new neighborhood structure for PSO algorithm is presented. Two perturbation operators to improve PSO algorithm are proposed. A special technique to handle equality constraints is proposed.
Swarm‐based spatial sorting
Authors: Amos Martyn , Don Oliver 
Published: August 2008

PurposeThe purpose of this paper is to present an algorithm for spatially sorting objects into an annular structure.Design/methodology/approachA swarm‐based model that requires only stochastic agent behaviour coupled with a pheromone‐inspired “attraction‐repulsion” mechanism.FindingsThe algorithm consistently generates high‐quality annular structures, and is particularly powerful in situations where the initial configuration of objects is similar to those observed in nature.Research limitations/implicationsExperimental evidence supports previous theoretical arguments about the nature and mechanism of spatial sorting by insects.Practical implicationsThe algorithm may find applications in distributed robotics.Originality/valueThe model offers a powerful minimal algorithmic framework, and also sheds further light on the nature of attraction‐repulsion algorithms and underlying natural processes.
Fragment‐HMM: A new approach to protein structure prediction
Authors: Li Shuai Cheng , Bu Dongbo , Xu Jinbo , Li Ming 
Published: August 2008

AbstractWe designed a simple position‐specific hidden Markov model to predict protein structure. Our new framework naturally repeats itself to converge to a final target, conglomerating fragment assembly, clustering, target selection, refinement, and consensus, all in one process. Our initial implementation of this theory converges to within 6 Å of the native structures for 100% of decoys on all six standard benchmark proteins used in ROSETTA (discussed by Simons and colleagues in a recent paper), which achieved only 14%–94% for the same data. The qualities of the best decoys and the final decoys our theory converges to are also notably better.
Male vocal behavior and phylogeny in deer
Authors: Cap Henri , Deleporte Pierre , Joachim Jean , Reby David 
Published: August 2008

AbstractThe phylogenetic relationships among 11 species of the Cervidae family were inferred from an analysis of male vocalizations. Eighteen characters, including call types (e.g. antipredator barks, mating loudcalls) and acoustic characteristics (call composition, fundamental frequency and formant frequencies), were used for phylogeny inference. The resulting topology and the phylogenetic consistency of behavioral characters were compared with those of current molecular phylogenies of Cervidae and with separate and simultaneous parsimony analyses of molecular and behavioral data. Our results indicate that male vocalizations constitute plausible phylogenetic characters in this taxon. Evolutionary scenarios for the vocal characters are discussed in relation with associated behaviors.
Increased death risk and altered cancer incidence pattern in patients with isolated or combined autoimmune primary adrenocortical insufficiency
Authors: Bensing Sophie , Brandt Lena , Tabaroj Farnoush , Sjöberg Olof , Nilsson Bo , Ekbom Anders , Blomqvist Paul , Kämpe Olle 
Published: August 2008

SummaryObjectives  Primary adrenocortical insufficiency is mostly caused by an autoimmune destruction of the adrenal cortex. The disease may appear isolated or as a part of an autoimmune polyendocrine syndrome (APS). APS1 is a rare hereditary disorder with a broad spectrum of clinical manifestations. In APS2, primary adrenocortical insufficiency is often combined with autoimmune thyroid disease and/or type 1 diabetes. We analysed mortality and cancer incidence in primary adrenocortical insufficiency patients during 40 years. Data were compared with the general Swedish population.Design and patients  A population based cohort study including all patients with autoimmune primary adrenocortical insufficiency (3299) admitted to Swedish hospitals 1964–2004.Measurements  Mortality risk was calculated as the standardized mortality ratio (SMR) and cancer incidence as the standardized incidence ratio (SIR).Results  A more than 2‐fold increased mortality risk was observed in both women (SMR 2·9, 95% CI 2·7–3·0) and men (SMR 2·5, 95% CI 2·3–2·7). Highest risks were observed in patients diagnosed in childhood. SMR was higher in APS1 patients (SMR 4·6, 95% CI 3·5–6·0) compared with patients with APS2 (SMR 2·1, 95% CI 1·9–2·4). Cancer incidence was increased (SIR 1·3, 95% CI 1·2–1·5). When tumours observed during the first year of follow‐up were excluded, only the cancer risk among APS1 patients remained increased. Cause‐specific cancer incidence analysis revealed significantly higher incidences of oral cancer, nonmelanoma skin cancer, and male genital system cancer among patients. Breast cancer incidence was lower than in the general population.Conclusions  Our study shows a reduced life expectancy and altered cancer incidence pattern in patients with autoimmune primary adrenocortical insufficiency.
Cultural characteristics of salmonid alphaviruses – influence of cell line and temperature
Authors: Graham D A , Wilson C , Jewhurst H , Rowley H 
Published: August 2008

AbstractLaboratory studies were carried out to investigate the cultural characteristics of salmonid alphaviruses (SAV) from Atlantic salmon (AS, Salmo salar) and rainbow trout (RT, Oncorhynchus mykiss), particularly in relation to cell line and temperature. In an initial study, SAV was isolated from 12 viraemic sera and passaged in Chinook salmon embryo (CHSE‐214) cells at 15 °C. Geometric mean titres (GMT) after initial isolation were found to be significantly higher (P < 0.05) relative to those after two or four passages. Primary isolation of SAV was conducted from 12 viraemic sera (six AS and six RT) in seven different cell lines at 15 °C: CHSE‐214, rainbow trout gonad (RTG‐2), TO (derived from Atlantic salmon head kidney leucocytes), salmon head kidney (SHK‐1), blue fin‐2 (BF‐2), fat head minnow (FHM) and Epithelioma papulosum cyprini (EPC). Overall, significant differences were found between cell lines in both the numbers of strains where growth was detected and in the GMT obtained. For both AS and RT strains, GMT values were significantly (P < 0.01) higher in both TO and BF‐2 cells relative to the others, including CHSE‐214 and RTG‐2, the cell lines conventionally used for SAV. The effects of temperature of incubation (4, 10, 15 and 20 °C) on growth in TO, CHSE‐214 and RTG‐2 were investigated. In TO and RTG‐2 growth was optimal at 15 °C, whereas in CHSE‐214 results at 10 and 15 °C were more similar. Little or no growth was detected at 4 or 20 °C.
Sortase‐mediated assembly and surface topology of adhesive pneumococcal pili
Authors: Fälker Stefan , Nelson Aaron L. , Morfeldt Eva , Jonas Kristina , Hultenby Kjell , Ries Johannes , Melefors Öjar , Normark Staffan , Henriques‐Normark Birgitta 
Published: August 2008

SummaryThe rlrA genetic islet encodes an extracellular pilus in the Gram‐positive pathogen Streptococcus pneumoniae. Of the three genes for structural subunits, rrgB encodes the major pilin, while rrgA and rrgC encode ancillary pilin subunits decorating the pilus shaft and tip. Deletion of all three pilus‐associated sortase genes, srtB, srtC and srtD, completely prevents pilus biogenesis. Expression of srtB alone is sufficient to covalently associate RrgB subunits to one another as well as linking the RrgA adhesin and the RrgC subunit into the polymer. The active‐site cysteine residue of SrtB (Cys 177) is crucial for incorporating RrgC, even when the two other sortase genes are expressed. SrtC is redundant to SrtB in permitting RrgB polymerization, and in linking RrgA to the RrgB filament, but SrtC is insufficient to incorporate RrgC. In contrast, expression of srtD alone fails to mediate RrgB polymerization, and a srtD mutant assembles heterotrimeric pilus indistinguishable from wild type. Topological studies demonstrate that pilus antigens are localized to symmetric foci at the cell surface in the presence of all three sortases. This symmetric focal presentation is abrogated in the absence of either srtB or srtD, while deletion of srtC had no effect. In addition, strains expressing srtB alone or srtC alone also displayed disrupted antigen localization, despite polymerizing subunits. Our data suggest that both SrtB and SrtC act as pilus subunit polymerases, with SrtB processing all three pilus subunit proteins, while SrtC only RrgB and RrgA. In contrast, SrtD does not act as a pilus subunit polymerase, but instead is required for wild‐type focal presentation of the pilus at the cell surface.
Quantitative RNA expression analysis with Affymetrix Tiling 1.0R arrays identifies new E2F target genes
Authors: Naouar Naïra , Vandepoele Klaas , Lammens Tim , Casneuf Tineke , Zeller Georg , Van Hummelen Paul , Weigel Detlef , Rätsch Gunnar , Inzé Dirk , Kuiper Martin , De Veylder Lieven , Vuylsteke Marnik 
Published: August 2008

SummaryThe Affymetrix ATH1 array provides a robust standard tool for transcriptome analysis, but unfortunately does not represent all of the transcribed genes in Arabidopsis thaliana. Recently, Affymetrix has introduced its Arabidopsis Tiling 1.0R array, which offers whole‐genome coverage of the sequenced Col‐0 reference strain. Here, we present an approach to exploit this platform for quantitative mRNA expression analysis, and compare the results with those obtained using ATH1 arrays. We also propose a method for selecting unique tiling probes for each annotated gene or transcript in the most current genome annotation, TAIR7, generating Chip Definition Files for the Tiling 1.0R array. As a test case, we compared the transcriptome of wild‐type plants with that of transgenic plants overproducing the heterodimeric E2Fa‐DPa transcription factor. We show that with the appropriate data pre‐processing, the estimated changes per gene for those with significantly different expression levels is very similar for the two array types. With the tiling arrays we could identify 368 new E2F‐regulated genes, with a large fraction including an E2F motif in the promoter. The latter groups increase the number of excellent candidates for new, direct E2F targets by almost twofold, from 181 to 334.
Strawberry Tree Blight in Spain, a New Disease Caused by various Phytophthora Species
Authors: Moralejo E. , Belbahri L. , Calmin G. , García‐Muñoz J. A. , Lefort F. , Descals E. 
Published: August 2008

AbstractDuring surveys for Phytophthora ramorum in garden centres in Majorca, Spain, 31 isolates of Phytophthora were recovered from potted strawberry trees (Arbutus unedo) showing leaf and twig blights. Many isolates of Phytophthora syringae and Phytophthora citrophthora as well as single isolates of P. ramorum, Phytophthora tropicalis and Phytophthora nicotianae were identified on morphological features and on the sequences of the internal transcribed spacer regions from ribosomal DNA genes. Phytophthora syringae was collected most frequently in late autumn and winter, whereas P. citrophthora was dominant during late summer and autumn. In vitro pathogenicity of P. syringae and P. citrophthora was compared with that of P. ramorum by inoculating intact detached leaves of A. unedo with zoospores and twigs with mycelial plugs. In addition, in vitro sporangial production was examined on inoculated excised leaves and on agar plugs at 12, 15 and 20°C. Phytophthora citrophthora produced the largest lesions both on leaves and on twigs at all temperatures. Phytophthora ramorum formed lesions comparable in size to those of P. syringae, but it significantly produced more sporangia on excised leaves and agar plugs. In a log inoculation assay, P. syringae caused large lesions in the inner bark, whereas those of P. ramorum were moderate. Strawberry tree blight has not yet been observed in natural ecosystems in the western Mediterranean areas. Possible biological and environmental limitations hindering disease spread in the wild are discussed.
INTRAOPERATIVE METHYLENE BLUE SENTINEL LYMPH NODE MAPPING IN COLORECTAL CANCER
Authors: Chan Siew H. , Ng Colin , Looi Lai M. 
Published: August 2008

Background:  Isosulfan blue is not available for clinical use in Malaysia. This study describes the use of methylene blue as an alternative to isosulfan blue in colorectal sentinel node mapping.Methods:  Methylene blue dye was injected around colonic and rectal tumours and the first blue‐stained nodes were suture tagged and harvested after standard colorectal resection. Standard histopathological examination was then carried out to detect nodal metastasis. All negative sentinel lymph nodes (SLN) were subjected to 10 further step sectioning and immunoperoxidase staining for cytokeratin 20 to detect tumour deposits.Results:  Thirty‐one patients were enrolled from August 2005 to July 2006. Twenty‐five attempts at identifying the SLN were successful (80.7%). Of the 18 (58.1%) who had nodal metastases (stage III), 3 had negative SLN but positive other lymph nodes (false‐negative rate of 21.4%). In one (4%), the SLN was the exclusive site of metastasis.Conclusion:  Methylene blue can be used as an alternative sentinel node marker for rectal cancer (above the peritoneal reflection) and colonic cancer.
THE QUEENSLAND TRAUMA PLAN PROJECT
Authors: FitzGerald Gerry , Tippett Vivienne , Schuetz Michael , Pollard Cliff 
Published: August 2008

Background:  The aim of this paper is to outline the development of ‘A Trauma Plan for Queensland’. Injury is one of Australia’s National Health Priorities. The full impact of injury, including early death, reduction in quality of life and the social and emotional costs to individuals and the community are immeasurable. The direct health‐care costs alone amounted to A$4.13bn in 2000–2001. Queensland has one of the highest rates of injury in Australia. An estimated 1500 Queenslanders die each year as a result of major traumatic injury and it is the single most common cause of death between the ages of 1 and 35 years.Methods:  The Queensland Trauma Plan was based on a detailed analysis of the management and outcome of trauma in Queensland and used an extensive process of stakeholder consultation to identify proposals for system improvement. Sequential workshops helped identify the issues and strategies for system improvement. These proposals were condensed into a high‐level strategic plan, which has now been endorsed by the Queensland Government.Results:  The Trauma Plan identifies service enhancements and the improved coordination required to support ongoing policy development, research and education. The Plan outlines a future direction for the development of trauma services and the system and structures required to support that development.Conclusion:  The Trauma Plan holds potential as a model for the development of future trauma services and injury prevention programmes. The process shows the value of engagement of clinicians and others into the policy development and planning processes. The outcome reinforces the value of taking a whole of community, coordinated and collaborative approach to injury prevention and management.
PAROTIDECTOMY: PREOPERATIVE INVESTIGATIONS AND OUTCOMES IN A SINGLE SURGEON PRACTICE
Authors: Burgess Adele N. , Serpell Jonathan W. 
Published: August 2008

Background:  The aim of this study was to assess the value of fine‐needle aspiration cytology (FNAC) as a preoperative evaluation for parotid tumours.Methods:  Prospectively collected data on 77 patients, collected on a parotid database, were retrospectively analysed. Preoperative investigations were carried out and cytology, histopathology and clinical outcomes were evaluated.Results:  The most common histopathology was benign lesions (89.6%), including pleomorphic adenoma (55.8%) and Warthin’s tumour (11.7%). Melanoma (3.9%) and lymphoma (2.6%) were the commonest malignancies. Preoperative investigations included FNAC in 72 of the 77 patients (93.5%). FNAC had a sensitivity and specificity for benign tumours of 92.3 and 75%, respectively. FNAC for malignant tumours had a sensitivity of 75% and specificity of 93.8%. FNAC accurately diagnosed cell type in 85.9% of specimens for benign lesions, but only 50% for malignancy. Complications included wound infections (10.4%), salivary fistulas (6.5%) and temporary partial facial palsies in six patients (7.8%).Conclusion:  We conclude FNAC assists in preoperative assessment and surgical planning for parotidectomy. This confirms the usefulness of FNAC as a preoperative assessment of parotid masses.
Doctors' attitudes towards invasive prenatal diagnosis
Authors: Pitukkijronnakorn Somsri , Manonai Jittima , Chittacharoen Apichart 
Published: August 2008

AbstractAim:  To assess the influence of a doctor's gender, age group, religion and invasive prenatal diagnosis (PND) knowledge on their attitude towards invasive PND.Methods:  All non–obstetric and gynecologic doctors were surveyed using a structured questionnaire. The questionnaire enquired about demographic information, and doctors' knowledge, attitude and experience regarding invasive PND for themselves, and their spouses, relatives, friends, colleagues and patients.Results:  Responses from the 289 respondents revealed that two‐thirds of respondents knew only a little about invasive PND. Most males and females were in the 31–39 and ≤30‐year‐old groups, respectively. There were no statistically significant differences in gender, age group, religion and invasive PND knowledge when recommending of invasive PND. If fetal anomalies were detected, most of the females in the Buddhist group (P < 0.05), males with quite a lot of PND knowledge group (p < 0.05) and younger doctors group (P < 0.05) would their own terminate pregnancies, or those of wives and relatives.Conclusion:  Attitudes towards invasive PND and pregnancy termination was influenced by gender, age group, religion and PND knowledge. Females and younger doctors from both gender groups tended to recommend the termination of pregnancy if they found fetal anomalies.