bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development of a method to improve the definition and alignment of intangible project outcomes and tangible project outputs
Authors: Nogeste Kersti , Walker Derek H.T. 
Published: April 2008

PurposeThe purpose of this paper is to describe a doctoral research study, including a summary of key literature review topics, the application of an action research methodology, key research findings and potential areas of future research.Design/methodology/approachResearch reported in this paper was based upon a series of five cycles of action research.FindingsAn Outcome Profile™ template can be used to guide project stakeholders through the process of identifying, defining and aligning intangible project outcomes with tangible project outputs.Practical implicationsThe research study will advance general management and project management research and practice by providing organisations with an improved template and method for linking project stakeholders' outcomes and benefits‐based perspective of project success with the more traditional project management outputs‐based perspective of project success. The research study, in itself provides a “how‐to” guide.Originality/valueThis paper alerts practitioners and academics to this recent research work to improve the definition of intangible project outcomes; to better determine what value a given project is expected to deliver.
Computational intelligence in multiple sequence alignment
Authors: Bi Chengpeng 
Published: April 2008

PurposeMultiple sequence alignment (MSA) is one of essential bioinformatics methods for decoding cis‐regulatory elements in gene regulation, predicting structure and function of proteins and RNAs, reconstructing phylogenetic tree, and other common tasks in biomolecular sequence analysis. The purpose of this paper is to describe briefly the basic concepts and formulations of gapped MSA and un‐gapped motif discovery approaches, and then review computational intelligence (CI) applications in MSA and motif‐finding problems.Design/methodology/approachThis paper performs exhaustive literature review on the MSA and motif discovery using CI techniques.FindingsAlthough CI‐based MSA algorithms were developed nearly a decade ago, most recent CI effort seems attempted to tackle the NP‐complete motif discovery problem. Applications of various CI techniques to solve motif discovery problem, including neural networks, self‐organizing map, genetic algorithms, swarm intelligence and combinations thereof, are surveyed. Finally, the paper concludes with discussion and perspective.Practical implicationsThe algorithms and software discussed in this paper can be used to align DNA, RNA and protein sequences, discover motifs, predict functions and structures of protein and RNA sequences, and estimate phylogenetic tree.Originality/valueThe paper contributes to the first comprehensive survey of CI techniques that are applied to MSA and motif discovery.
A decentralization approach for swarm intelligence algorithms in networks applied to multi swarm PSO
Authors: Janson Stefan , Merkle Daniel , Middendorf Martin 
Published: April 2008

PurposeThe purpose of this paper is to present an approach for the decentralization of swarm intelligence algorithms that run on computing systems with autonomous components that are connected by a network. The approach is applied to a particle swarm optimization (PSO) algorithm with multiple sub‐swarms. PSO is a nature inspired metaheuristic where a swarm of particles searches for an optimum of a function. A multiple sub‐swarms PSO can be used for example in applications where more than one optimum has to be found.Design/methodology/approachIn the studied scenario the particles of the PSO algorithm correspond to data packets that are sent through the network of the computing system. Each data packet contains among other information the position of the corresponding particle in the search space and its sub‐swarm number. In the proposed decentralized PSO algorithm the application specific tasks, i.e. the function evaluations, are done by the autonomous components of the system. The more general tasks, like the dynamic clustering of data packets, are done by the routers of the network.FindingsSimulation experiments show that the decentralized PSO algorithm can successfully find a set of minimum values for the used test functions. It was also shown that the PSO algorithm works well for different type of networks, like scale‐free network and ring like networks.Originality/valueThe proposed decentralization approach is interesting for the design of optimization algorithms that can run on computing systems that use principles of self‐organization and have no central control.
Selection methods for extended least squares support vector machines
Authors: Valyon József , Horváth Gábor 
Published: April 2008

PurposeThe purpose of this paper is to present extended least squares support vector machines (LS‐SVM) where data selection methods are used to get sparse LS‐SVM solution, and to overview and compare the most important data selection approaches.Design/methodology/approachThe selection methods are compared based on their theoretical background and using extensive simulations.FindingsThe paper shows that partial reduction is an efficient way of getting a reduced complexity sparse LS‐SVM solution, while partial reduction exploits full knowledge contained in the whole training data set. It also shows that the reduction technique based on reduced row echelon form (RREF) of the kernel matrix is superior when compared to other data selection approaches.Research limitations/implicationsData selection for getting a sparse LS‐SVM solution can be done in the different representations of the training data: in the input space, in the intermediate feature space, and in the kernel space. Selection in the kernel space can be obtained by finding an approximate basis of the kernel matrix.Practical implicationsThe RREF‐based method is a data selection approach with a favorable property: there is a trade‐off tolerance parameter that can be used for balancing complexity and accuracy.Originality/valueThe paper gives contributions to the construction of high‐performance and moderate complexity LS‐SVMs.
Social networks in simulated multi‐robot environment
Authors: Rodić Daniel , Engelbrecht Andries P. 
Published: April 2008

PurposeThe purpose of this paper is to present a novel approach to coordination of multi‐agent teams, and in particular multi‐robot teams. The new approach is based on models of organisational sociology, namely the concept of social networks. The social relationships used in the model that is presented in this paper are trust and kinship relationships, but modified for use in heterogeneous multi‐robot teams.Design/methodology/approachThe coordination of a robot team is achieved through task allocation. The proposed task allocation mechanism was tested in the multi‐robot team task allocation simulation.FindingsThe social networks‐based task allocation algorithm has performed according to expectations and the obtained results are very promising. Some intriguing similarities with higher mammalian societies were observed and they are discussed in this paper. The social networks‐based approach also exhibited the ability to learn and store information using social networks.Research limitations/implicationsThe research focused on simulated environments and further research is envisaged in the physical environments to confirm the applicability of the presented approach.Practical implicationsIn this paper, the proposed coordination was applied to simulated multi‐robot teams. It is important to note that the proposed coordination model is not robot specific, but can also be applied to almost any multi‐agent system without major modifications.Originality/valueThe paper emphasizes applicability of considering multi‐robot teams as socially embodied agents. It also presents a novel and efficient approach to task allocation.
A comprehensive mathematical framework for bridging a gap between two approaches to creating a meaning‐understanding web
Authors: Fomichov Vladimir 
Published: April 2008

PurposeSince, the middle of the 1990s, UNO has been funding a large‐scale project aimed at designing a family of natural language (NL) processing systems transforming the sentences in various NLs into the expressions of a new language‐intermediary called the Universal Networking Language (UNL) and vice versa. The purpose of the paper is to propose a constructive way of developing a semantic networking language (SNL) of a new generation and, as a consequence, to bridge a gap between UNL‐based studies and Semantic Web projects.Design/methodology/approachThe methodological basis of the paper is a new theory of designing semantic‐syntactic analyzers of NL texts elaborated by the author of the paper and called the theory of K‐representations (knowledge representations). One of its basic components is a mathematical model describing a system of ten partial operations on conceptual structures and determining a new class of formal languages called restricted standard knowledge languages (RSK‐languages).FindingsIt is shown that the expressive possibilities of RSK‐languages surpass the expressive possibilities of UNL from the standpoint of representing the meanings of discourses, compound goals, descriptions of sets, definitions of notions. It is proposed to use the definition of the class of RSK‐languages as a model of a SNL of a new generation in comparison with UNL.Practical implicationsIt is also proposed to use the definition of RSK‐languages for building semantic annotations of arbitrary web‐documents and web‐services.Originality/valueThe paper describes an original approach to representing conceptual structure of NL texts.
Expression of RUNX3 in salivary adenoid cystic carcinoma: Implications for tumor progression and prognosis
Authors: He Jian‐Feng , Ge Ming‐Hua , Zhu Xin , Chen Chao , Tan Zhuo , Li Yi‐Ning , Gu Zhi‐Yuan 
Published: April 2008

Runt‐related transcription factor‐3 (RUNX3), being a tumor suppressor gene in gastric cancer, plays an important role in inhibiting cellular growth by participating in the transforming growth factor‐β‐dependent apoptosis. The aim of this study was to determine the expression of RUNX3 in normal salivary glands and adenoid cystic carcinomas (ACCs), comparing the results with clinicopathological factors and patient survival. The quantitative reverse transcription–polymerase chain reaction (RT‐PCR) analysis and Western blot analysis revealed the expression of RUNX3 both in normal salivary glands and ACCs. Nuclear and cytoplasmic immunoreactivities against RUNX3 in ductal luminal cells and acinous cells, but immunonegative in myoepithelial cells, were detected in normal salivary glands. In ACC, the RUNX3 immunostaining was shown in the cytoplasm of tumor cells; however, no nuclear location of RUNX3 was found. Lower RUNX3 expression showed significant correlation to distant metastasis and histological growth pattern (P = 0.009 and P = 0.025, respectively). On univariate analysis, low level of RUNX3 immunolabeling (P = 0.012), stage T4 (P = 0.017), lymph node involvement (P = 0.007), and distant metastasis (P < 0.001) were significantly associated with decreased overall survival. Multivariate analysis showed only distant metastasis had an independent prognostic effect on overall survival (P = 0.043). Our results demonstrate the expression of RUNX3 in normal salivary glands and salivary ACCs. The low level of RUNX3 protein in salivary ACCs might play a pivotal role in tumor progression and have prognostic values in ACCs. (Cancer Sci 2008; 99: 1334–1340)
The Arabidopsis GSQ5/DOG1 Cvi allele is induced by the ABA‐mediated sugar signalling pathway, and enhances sugar sensitivity by stimulating ABI4 expression
Authors: Teng Sheng , Rognoni Sara , Bentsink Leónie , Smeekens Sjef 
Published: April 2008

Summary ABI4 encodes an AP2 family transcription factor that is a central regulator in sugar responsive gene expression in plants. Sugar‐induced ABI4 regulates plant genes essential for photosynthesis, and carbon, nitrogen and lipid metabolism. ABI4 activity is induced via the ABA‐mediated sugar signalling pathway, which is initiated by the glucose sensing protein hexokinase. Natural variation in sugar sensitivity was used to identify new loci involved in sugar signalling. Five quantitative trait loci (QTLs) for glucose sensitivity (GSQ1–GSQ5) were identified in a Ler/Cvi recombinant inbred line (RIL) population. The GSQ3, GSQ4 and GSQ5 loci are positioned in regions not previously associated with known sugar‐sensing genes. GSQ5 was fine mapped and cloned using a candidate‐gene approach. The GSQ5 locus was shown to encode the DELAY OF GERMINATION 1 (DOG1) gene. DOG1 was previously identified as a major locus in seed dormancy control. Glucose addition induced the expression of the GSQ5/DOG1 Cvi allele, whereas the Ler and Col alleles did not respond to glucose. Positive feedback was observed between the ABA‐mediated sugar signalling pathway and the GSQ5/DOG1 Cvi allele. Expression of the GSQ5/DOG1 Cvi allele requires the ABA‐mediated sugar signalling pathway, of which ABI4 is an important component. In addition, sugar induction of ABI4 was promoted by the GSQ5/DOG1 Cvi allele.
The cytoplasmic‐localized, cytoskeletal‐associated RNA binding protein OsTudor‐SN: evidence for an essential role in storage protein RNA transport and localization
Authors: Wang Changlin , Washida Haruhiko , Crofts Andrew J. , Hamada Shigeki , Katsube‐Tanaka Tomoyuki , Kim Dongwook , Choi Sang‐Bong , Modi Mahendra , Singh Salvinder , Okita Thomas W. 
Published: April 2008

SummaryPrevious studies have demonstrated that the major storage protein RNAs found in the rice endosperm are transported as particles via actomyosin to specific subdomains of the cortical endoplasmic reticulum. In this study, we examined the potential role of OsTudor‐SN, a major cytoskeletal‐associated RNA binding protein, in RNA transport and localization. OsTudor‐SN molecules occur as high‐molecular‐weight forms, the integrity of which are sensitive to RNase. Immunoprecipitation followed by RT‐PCR showed that OsTudor‐SN binds prolamine and glutelin RNAs. Immunofluorescence studies using affinity‐purified antibodies show that OsTudor‐SNs exists as particles in the cytoplasm, and are distributed to both the protein body endoplasmic reticulum (ER) and cisternal ER. Examination of OsTudor‐SN particles in transgenic rice plants expressing GFP‐tagged prolamine RNA transport particles showed co‐localization of OsTudor‐SN and GFP, suggesting a role in RNA transport. Consistent with this view, GFP‐tagged OsTudor‐SN is observed in living endosperm sections as moving particles, a property inhibited by microfilament inhibitors. Downregulation of OsTudor‐SN by antisense and RNAi resulted in a decrease in steady state prolamine RNA and protein levels, and a reduction in the number of prolamine protein bodies. Collectively, these results show that OsTudor‐SN is a component of the RNA transport particle, and may control storage protein biosynthesis by regulating one or more processes leading to the transport, localization and anchoring of their RNAs to the cortical ER.
Region‐selective alterations of glucose oxidation and amino acid synthesis in the thiamine‐deficient rat brain: a re‐evaluation using 1H/13C nuclear magnetic resonance spectroscopy
Authors: Navarro Darren , Zwingmann Claudia , Butterworth Roger F. 
Published: April 2008

AbstractThiamine deficiency provides an effective model of selective neuronal cell death. 1H and 13C‐NMR was used to investigate the effects of thiamine deficiency on the synthesis of amino acids derived from [1‐13C]glucose in vulnerable (medial thalamus; MT) compared to non‐vulnerable (frontal cortex; FC) brain regions. Following 11 days of thiamine deficiency, a time‐point associated with the absence of significant neuronal cell death, regional concentrations of glutamate, glutamine and GABA remained unaffected in FC and MT; however, decreased levels of aspartate in MT at this time‐point were a predictor of regional vulnerability. De novo synthesis of glutamate and GABA were unaffected at 11 days of thiamine deficiency, while synthesis of [2‐13C]aspartate was significantly impaired. Glucose loading, which has been shown to exacerbate symptoms in patients with thiamine deficiency, resulted in further decreases of TCA cycle flux and reduced de novo synthesis of glutamate, aspartate and GABA in thiamine‐deficient (TD) rats. Isotopomer analysis revealed that impaired TCA cycle flux and decreased aspartate synthesis due to thiamine deficiency occurred principally in neurons. Glucose loading deteriorated TD‐related decreases in TCA cycle flux, and concomitantly reduced synthesis of aspartate and glutamate in MT.
FasL shedding is reduced by hypothermia in experimental stroke
Authors: Liu Liping , Kim Jong Youl , Koike Maya A. , Yoon Yone Jung , Tang Xian Nan , Ma Hualong , Lee Hokyou , Steinberg Gary K. , Lee Jong Eun , Yenari Midori A. 
Published: April 2008

AbstractProtection by mild hypothermia has previously been associated with better mitochondrial preservation and suppression of the intrinsic apoptotic pathway. It is also known that the brain may undergo apoptotic death via extrinsic, or receptor‐mediated pathways, such as that triggered by Fas/FasL. Male Sprague‐Dawley rats subjected to 2 h middle cerebral artery occlusion with 2 h intraischemic mild hypothermia (33°C) were assayed for Fas, FasL and caspase‐8 expression. Ischemia increased Fas, but decreased FasL by ∼ 50–60% at 6 and 24 h post‐insult. Mild hypothermia significantly reduced expression of Fas and processed caspase‐8 both by ∼ 50%, but prevented ischemia‐induced FasL decreases. Fractionation revealed that soluble/shed FasL (sFasL) was decreased by hypothermia, while membrane‐bound FasL (mFasL) increased. To more directly assess the significance of the Fas/FasL pathway in ischemic stroke, primary neuron cultures were exposed to oxygen glucose deprivation. Since FasL is cleaved by matrix metalloproteinases (MMPs), and mild hypothermia decreases MMP expression, treatment with a pan‐MMP inhibitor also decreased sFasL. Thus, mild hypothermia is associated with reduced Fas expression and caspase‐8 activation. Hypothermia prevented total FasL decreases, and most of it remained membrane‐bound. These findings reveal new observations regarding the effect of mild hypothermia on the Fas/FasL and MMP systems.
Mechanisms of non‐steroid anti‐inflammatory drugs action on ASICs expressed in hippocampal interneurons
Authors: Dorofeeva Natalia A. , Barygin Oleg I. , Staruschenko Alexander , Bolshakov Konstantin V. , Magazanik Lev G. 
Published: April 2008

AbstractThe inhibitory action of non‐steroid anti‐inflammatory drugs was investigated on acid‐sensing ionic channels (ASIC) in isolated hippocampal interneurons and on recombinant ASICs expressed in Chinese hamster ovary (CHO) cells. Diclofenac and ibuprofen inhibited proton‐induced currents in hippocampal interneurons (IC50 were 622 ± 34 μM and 3.42 ± 0.50 mM, respectively). This non‐competitive effect was fast and fully reversible for both drugs. Aspirin and salicylic acid at 500 μM were ineffective. Diclofenac and ibuprofen decreased the amplitude of proton‐evoked currents and slowed the rates of current decay with a good correlation between these effects. Simultaneous application of acid solution and diclofenac was required for its inhibitory effect. Unlike amiloride, the action of diclofenac was voltage‐independent and no competition between two drugs was found. Analysis of the action of diclofenac and ibuprofen on activation and desensitization of ASICs showed that diclofenac but not ibuprofen shifted the steady‐state desensitization curve to more alkaline pH values. The reason for this shift was slowing down the recovery from desensitization of ASICs. Thus, diclofenac may serve as a neuroprotective agent during pathological conditions associated with acidification.
Spastin oligomerizes into a hexamer and the mutant spastin (E442Q) redistribute the wild‐type spastin into filamentous microtubule
Authors: Pantakani D. V. Krishna , Swapna Lakshmipuram S. , Srinivasan Narayanaswamy , Mannan Ashraf U. 
Published: April 2008

AbstractSpastin, a member of the ATPases associated with various cellular activities (AAA) family of proteins, is the most frequently mutated in hereditary spastic paraplegia. The defining feature of the AAA proteins is a structurally conserved AAA domain which assembles into an oligomer. By chemical cross‐linking and gel filtration chromatography, we show that spastin oligomerizes into a hexamer. Furthermore, to gain a comprehensive overview of the oligomeric structure of spastin, we generated a structural model of the AAA domain of spastin using template structure of VPS4B and p97/VCP. The generated model of spastin provided us with a framework to classify the identified missense mutations in the AAA domain from hereditary spastic paraplegia patients into different structural/functional groups. Finally, through co‐localization studies in mammalian cells, we show that E442Q mutant spastin acts in a dominant negative fashion and causes redistribution of both wild‐type spastin monomer and spastin interacting protein, RTN1 into filamentous microtubule bundles.
High cholesterol‐induced neuroinflammation and amyloid precursor protein processing correlate with loss of working memory in mice
Authors: Thirumangalakudi Lakshmi , Prakasam Annamalai , Zhang Ran , Bimonte‐Nelson Heather , Sambamurti Kumar , Kindy Mark S. , Bhat Narayan R. 
Published: April 2008

AbstractRecent findings suggest that hypercholesterolemia may contribute to the onset of Alzheimer’s disease‐like dementia but the underlying mechanisms remain unknown. In this study, we evaluated the cognitive performance in rodent models of hypercholesterolemia in relation to neuroinflammatory changes and amyloid precursor protein (APP) processing, the two key parameters of Alzheimer’s disease pathogenesis. Groups of normal C57BL/6 and low density lipoprotein receptor (LDLR)‐deficient mice were fed a high fat/cholesterol diet for an 8‐week period and tested for memory in a radial arm maze. It was found that the C57BL/6 mice receiving a high fat diet were deficient in handling an increasing working memory load compared with counterparts receiving a control diet while the hypercholesterolemic LDLR−/− mice showed impaired working memory regardless of diet. Immunohistochemical analysis revealed the presence of activated microglia and astrocytes in the hippocampi from high fat‐fed C57BL/6 mice and LDLR−/− mice. Consistent with a neuroinflammatory response, the hyperlipidemic mice showed increased expression of cytokines/mediators including tumor necrosis factor‐α, interleukin‐1β and ‐6, nitric oxide synthase 2, and cycloxygenase 2. There was also an induced expression of the key APP processing enzyme i.e. β‐site APP cleaving enzyme 1 in both high fat/cholesterol‐fed C57BL/6 and LDLR−/− mice accompanied by an increased generation of C‐terminal fragments of APP. Although ELISA for beta‐amyloid failed to record significant changes in the non‐transgenic mice, a threefold increase in beta‐amyloid 40 accumulation was apparent in a strain of transgenic mice expressing wild‐type human APP on high fat/cholesterol diet. The findings link hypercholesterolemia with cognitive dysfunction potentially mediated by increased neuroinflammation and APP processing in a non‐transgenic mouse model.