Prediction of MHC class II-binding peptides using an evolutionary algorithm and artificial neural network

Motivation: Prediction methods for identifying binding peptides could minimize the number of peptides required to be synthesized and assayed, and thereby facilitate the identification of potential T-cell epitopes. We developed a bioinformatic method for the prediction of peptide binding to MHC class II molecules. Results: Experimental binding data and expert knowledge of anchor positions and binding motifs were combined with an evolutionary algorithm (EA) and an artificial neural network (ANN): binding data extraction --> peptide alignment --> ANN training and classification. This method, termed PERUN, was implemented for the prediction of peptides that bind to HLA-DR4(B1*0401). The respective positive predictive values of PERUN predictions of high-, moderate-, low- and zero-affinity binder-a were assessed as 0.8, 0.7, 0.5 and 0.8 by cross-validation, and 1.0, 0.8, 0.3 and 0.7 by experimental binding. This illustrates the synergy between experimentation and computer modeling, and its application to the identification of potential immunotheraaeutic peptides.

Long-term quantification of the release of monomers from dental resin composites and a resin-modified glass ionomer cement

This study quantified the release of monomers from polymerized specimens of four commercially available resin composites and one glass ionomer cement immersed in water:ethanol solutions. Individual standard curves were prepared from five monomers: (1) triethylene glycol dimethacrylate (TEGDMA), (2) 2-hydroxy-ethyl methacrylate (HEMA), (3) urethane dimethacrylate (UDMA), (4) bisphenol A glycidyl dimethacrylate (BISGMA), and (5) bisphenol A. The concentration of the monomers was determined at Days 1, 7, 30, and 90 with the use of electrospray ionization/mass spectrometry. Data were expressed in mean mumol per mm(2) surface area of specimen and analyzed with Scheffe's test (P < 0.05). The following monomers were found in water: monomers (1) and (2) from Delton sealant, monomer (5) from ScotchBond Multipurpose Adhesive and Delton sealant, monomer (3) from Definite and monomer (4) from Fuji II LC, ScotchBond Multipurpose Adhesive, Synergy and Definite. All these monomers increased in concentration over time, with the exception of monomer (1) from Delton sealant. Monomers (3) and (5) were found in extracts of materials despite their absence from the manufacturer's published composition. All monomers were released in significantly higher concentrations in water:ethanol solutions than in water. The greatest release of monomers occurred in the first day. The effect of the measured concentrations of monomers (1-5) on human genes, cells, or tissues needs to be considered with the use of a biological model. (C) 2002 Wiley Periodicals, Inc.

Influence of HIV-1 coinfection on effective management of abnormal vaginal discharge

Background: Reports on microbiologic cure rates following syndromic management (SM) of women with nonulcerative sexually transmitted infections (STIs) are limited. Goal. The goal of the study was to determine the effectiveness of the drugs used in SM of nonulcerative STIs and bacterial vaginosis in women and to compare the response among those with and without HIV-1 coinfection. Study Design: This was a cohort study of women with nonulcerative STIs who were treated according to local SM protocols. Results: Of 692 women recruited, 415 (80%) returned 8 to 10 days later, and 290 (70%) consented to a second examination, in which specimens were obtained. Clinical cure was reported by 67%, and microbiologic cure ranged from 80% to 89% for the three discharge-causing STIs and was independent of HIV-1 status. Only 38% of those with bacterial vaginosis were cured, and HIV-1-infected women were less likely to be cured (28% versus 52%; P < 0.001). Conclusions: Clinical and microbiologic response to SM of the nonulcerative STIs was not affected by HIV-1 coinfection, but cure rates for bacterial vaginosis were reduced.

Identification of the regulatory subunit of Arabidopsis thaliana acetohydroxyacid synthase and reconstitution with its catalytic subunit

Acetohydroxyacid synthase (EC 4.1.3.18; AHAS) catalyzes the initial step in the formation of the branched-chain amino acids. The enzyme from most bacteria is composed of a catalytic subunit, and a smaller regulatory subunit that is required for full activity and for sensitivity to feedback regulation by valine. A similar arrangement was demonstrated recently for yeast AHAS, and a putative regulatory subunit of tobacco AHAS has also been reported. In this latter case, the enzyme reconstituted from its purified subunits remained insensitive to feedback inhibition, unlike the enzyme extracted from native plant sources. Here we have cloned, expressed in Escherichia coil, and purified the AHAS regulatory subunit of Ambidopsis thaliana. Combining the protein with the purified A. thaliana catalytic subunit results in an activity stimulation that is sensitive to inhibition by valine, leucine, and isoleucine. Moreover, there is a strong synergy between the effects of leucine and valine, which closely mimics the properties of the native enzyme. The regulatory subunit contains a sequence repeat of approximately 180 residues, and we suggest that one repeat binds leucine while the second binds valine or isoleucine. This proposal is supported by reconstitution studies of the individual repeats, which were also cloned, expressed, and purified. The structure and properties of the regulatory subunit are reminiscent of the regulatory domain of threonine deaminase (EC 4.2.1.16), and it is suggested that the two proteins are evolutionarily related.

Mobile digital technology: Emerging issues for marketing

The growth of direct marketing has been attributed to rapid advances in technology and the changing market context. The fundamental ability of direct marketers to communicate with consumers and to elicit a response, combined with the ubiquitous nature and power of mobile digital technology, provides a synergy that will increase the potential for the success of direct marketing. The aim of this paper is to provide an analytical framework identifying the developments in the digital environment from e-marketing to m-marketing, and to alert direct marketers to the enhanced capabilities available to them.

Regulatory interactions in Arabidopsis thaliana acetohydroxyacid synthase

Acetohydroxyacid synthase (AHAS; EC 4.1.3.18) contains catalytic and regulatory subunits, the latter being required for sensitivity to feedback regulation by leucine, valine and isoleucine. The regulatory subunit of Arabidopsis thaliana AHAS possesses a sequence repeat and we have suggested preciously that one repeat binds leucine while the second binds valine or isoleucine, with synergy between the two sites. We have mutated four residues in each repeat, based on a model of the regulatory subunit. The data confirm that there are separate leucine and valine/isoleucine sites, and suggest a complex pathway for regulatory signal transmission to the catalytic subunit. (C) 2002 Published by Elsevier Science B.V. on behalf of the Federation of European Biochemical Societies.

Combining nonthermal technologies to control foodborne microorganisms

Novel nonthermal processes, such as high hydrostatic pressure (HHP), pulsed electric fields (PEFs), ionizing radiation and ultrasonication, are able to inactivate microorganisms at ambient or sublethal temperatures. Many of these processes require very high treatment intensities, however, to achieve adequate microbial destruction in low-acid foods. Combining nonthermal processes with conventional preservation methods enhances their antimicrobial effect so that lower process intensities can be used. Combining two or more nonthermal processes can also enhance microbial inactivation and allow the use of lower individual treatment intensities. For conventional preservation treatments, optimal microbial control is achieved through the hurdle concept, with synergistic effects resulting from different components of the microbial cell being targeted simultaneously. The mechanisms of inactivation by nonthermal processes are still unclear; thus, the bases of synergistic combinations remain speculative. This paper reviews literature on the antimicrobial efficiencies of nonthermal processes combined with conventional and novel nonthermal technologies. Where possible, the proposed mechanisms of synergy is mentioned. (C) 2003 Elsevier Science B.V. All rights reserved.

'Localizing the national' - The rediscovery and reshaping of local campaigning in Australia

Pippa Norris provides a schematic account of the evolution of campaigning through premodern, modern and postmodern stages. In particular she points to an emerging postmodern phase of electioneering characterized by a renewed emphasis upon direct forms of engagement which resonate with an earlier period in which campaigns were locally fought and largely dependent upon the canvassing efforts of party workers and volunteers. Norris's analysis offers a useful prism with which to view recent developments in electioneering in Australia. In the past several elections the rival Labor and Liberal parties have attempted to achieve a synergy between their centrally conducted and constituency-level campaigns by ensuring that their national campaigns are locally relevant and address local concerns. Their efforts to 'localize the national' meld the use of sophisticated software with elements of a traditional 'meet and greet' politics and suggest that local campaigning may now have a new shape and importance.

Impairment in the cervical flexors: a comparison of whiplash and insidious onset neck pain patients

There has been little investigation into whether or not differences exist in the nature of physical impairment associated with neck pain of whiplash and insidious origin. This study examined the neck flexor synergy during performance of the cranio-cervical flexion test, a test targeting the action of the deep neck flexors. Seventy-five volunteer subjects participated in this study and were equally divided between Group 1, asymptomatic control subjects, Group 2, subjects with insidious onset neck pain and Group 3, subjects with neck pain following a whiplash injury. The cranio-cervical flexion test was performed in five progressive stages of increasing cranio-cervical flexion range. Subjects' performance was guided by feedback from a pressure sensor inserted behind the neck which monitored the slight flattening of the cervical lordosis which occurs with the contraction of longus colli. Myoelectric signals (EMG) were detected from the muscles during performance of the test. The results indicated that both the insidious onset neck pain and whiplash groups had higher measures of EMG signal amplitude (normalized root mean square) in the sternocleidomastoid during each stage of the test compared to the control subjects (all P

Profile of paediatric occupational therapy practice in Australia

Background: The purpose of the present study was to describe a profile of Australian paediatric occupational therapy practice in terms of theories, assessments and interventions used with the most frequently seen client groups. Methods: An ex post facto survey design was utilised. A purpose-designed survey was mailed to 600 occupational therapists identified by OT Australia as working in paediatrics. Results: The response rate was 55% (n = 330). Respondents in the sample worked chiefly with children with developmental delays, learning disabilities, neurological impairments, and infants/toddlers. Theoretical models used by paediatric clinicians that were common to the most frequently seen client groups focused on sensory integration/multisensory approaches, occupational performance, and client-centred practice. Assessment tools most frequently used were the Test of Visual Motor Integration, Sensory Profile, Bruininks-Oseretsky Test of Motor Proficiency, Handwriting Speed Test, and Motor-Free Visual Perception Test. The most often used treatment methods across the four most frequently seen client groups were parent/caregiver education, sensory integration/stimulation techniques, and managing activities of daily living. Conclusions: Paediatric occupational therapists appeared to draw on a range of theoretical models. With the exception of the Sensory Profile, the assessment and treatment methods most frequently used are not congruent with the most commonly used theoretical models. It is critical that the assessment and treatment methods used are conceptually consistent with the theoretical models that guide practice. Occupational therapists need to examine the evidence and determine whether their clinical practice is grounded in the best contemporary theoretical models, assessments and interventions.