Predictive vaccinology: Optimisation of predictions using support vector machine classifiers

Promiscuous human leukocyte antigen (HLA) binding peptides are ideal targets for vaccine development. Existing computational models for prediction of promiscuous peptides used hidden Markov models and artificial neural networks as prediction algorithms. We report a system based on support vector machines that outperforms previously published methods. Preliminary testing showed that it can predict peptides binding to HLA-A2 and -A3 super-type molecules with excellent accuracy, even for molecules where no binding data are currently available.

Optimisation of poly-b-hydroxyalkanoate analysis using gas chromatography for enhanced biological phosphorus removal systems

Poly-beta-hydroxyalkanoate (PHA) is a polymer commonly used in carbon and energy storage for many different bacterial cells. Polyphosphate accumulating organisms (PAOs) and glycogen accumulating organisms (GAOs), store PHA anaerobically through metabolism of carbon substrates such as acetate and propionate. Although poly-beta-hydroxybutyrate (PHB)and poly-beta-hydroxyvalerate (PHV) are commonly quantified using a previously developed gas chromatography (GC) method, poly-beta-hydroxy-2-methyl valerate (PH2MV) is seldom quantified despite the fact that it has been shown to be a key PHA fraction produced when PAOs or GAOs metabolise propionate. This paper presents two GC-based methods modified for extraction and quantification of PHB, PHV and PH2MV from enhanced biological phosphorus removal (EBPR) systems. For the extraction Of PHB and PHV from acetate fed PAO and GAO cultures, a 3% sulfuric acid concentration and a 2-20 h digestion time is recommended, while a 10% sulfuric acid solution digested for 20 h is recommended for PHV and PH2MV analysis from propionate fed EBPR systems. (c) 2005 Elsevier B.V. All rights reserved.

Mathematical modelling and optimisation of a water heat pump

The purpose of the work described here has been to seek methods of narrowing the present gap between currently realised heat pump performance and the theoretical limit. The single most important pre-requisite to this objective is the identification and quantitative assessment of the various non-idealities and degradative phenomena responsible for the present shortfall. The use of availability analysis has been introduced as a diagnostic tool, and applied to a few very simple, highly idealised Rankine cycle optimisation problems. From this work, it has been demonstrated that the scope for improvement through optimisation is small in comparison with the extensive potential for improvement by reducing the compressor's losses. A fully instrumented heat pump was assembled and extensively tested. This furnished performance data, and led to an improved understanding of the systems behaviour. From a very simple analysis of the resulting compressor performance data, confirmation of the compressor's low efficiency was obtained. In addition, in order to obtain experimental data concerning specific details of the heat pump's operation, several novel experiments were performed. The experimental work was concluded with a set of tests which attempted to obtain definitive performance data for a small set of discrete operating conditions. These tests included an investigation of the effect of two compressor modifications. The resulting performance data was analysed by a sophisticated calculation which used that measurements to quantify each dagradative phenomenon occurring in that compressor, and so indicate where the greatest potential for improvement lies. Finally, in the light of everything that was learnt, specific technical suggestions have been made, to reduce the losses associated with both the refrigerant circuit and the compressor.

The characterisation and optimisation of modified herbaceous grasses for identifying pyrolisis-oil quality traits

The primary objective of this work is to relate the biomass fuel quality to fast pyrolysis-oil quality in order to identify key biomass traits which affect pyrolysis-oil stability. During storage the pyrolysis-oil becomes more viscous due to chemical and physical changes, as reactions and volatile losses occur due to aging. The reason for oil instability begins within the pyrolysis reactor during pyrolysis in which the biomass is rapidly heated in the absence of oxygen, producing free radical volatiles which are then quickly condensed to form the oil. The products formed do not reach thermodynamic equilibrium and in tum the products react with each other to try to achieve product stability. The first aim of this research was to develop and validate a rapid screening method for determining biomass lignin content in comparison to traditional, time consuming and hence costly wet chemical methods such as Klason. Lolium and Festuca grasses were selected to validate the screening method, as these grass genotypes exhibit a low range of Klason /Acid Digestible Fibre lignin contents. The screening methodology was based on the relationship between the lignin derived products from pyrolysis and the lignin content as determined by wet chemistry. The second aim of the research was to determine whether metals have an affect on fast pyrolysis products, and if any clear relationships can be deduced to aid research in feedstock selection for fast pyrolysis processing. It was found that alkali metals, particularly Na and K influence the rate and yield of degradation as well the char content. Pre-washing biomass with water can remove 70% of the total metals, and improve the pyrolysis product characteristics by increasing the organic yield, the temperature in which maximum liquid yield occurs and the proportion of higher molecular weight compounds within the pyrolysis-oil. The third aim identified these feedstock traits and relates them to the pyrolysis-oil quality and stability. It was found that the mineral matter was a key determinant on pyrolysis-oil yield compared to the proportion of lignin. However the higher molecular weight compounds present in the pyrolysis-oil are due to the lignin, and can cause instability within the pyrolysis-oil. The final aim was to investigate if energy crops can be enhanced by agronomical practices to produce a biomass quality which is attractive to the biomass conversion community, as well as giving a good yield to the farmers. It was found that the nitrogen/potassium chloride fertiliser treatments enhances Miscanthus qualities, by producing low ash, high volatiles yields with acceptable yields for farmers. The progress of senescence was measured in terms of biomass characteristics and fast pyrolysis product characteristics. The results obtained from this research are in strong agreement with published literature, and provides new information on quality traits for biomass which affects pyrolysis and pyrolysis-oils.

Supply chain optimisation of pyrolysis plant deployment using goal programming

This paper presents a goal programming model to optimise the deployment of pyrolysis plants in Punjab, India. Punjab has an abundance of waste straw and pyrolysis can convert this waste into alternative bio-fuels, which will facilitate the provision of valuable energy services and reduce open field burning. A goal programming model is outlined and demonstrated in two case study applications: small scale operations in villages and large scale deployment across Punjab's districts. To design the supply chain, optimal decisions for location, size and number of plants, downstream energy applications and feedstocks processed are simultaneously made based on stakeholder requirements for capital cost, payback period and production cost of bio-oil and electricity. The model comprises quantitative data obtained from primary research and qualitative data gathered from farmers and potential investors. The Punjab district of Fatehgarh Sahib is found to be the ideal location to initially utilise pyrolysis technology. We conclude that goal programming is an improved method over more conventional methods used in the literature for project planning in the field of bio-energy. The model and findings developed from this study will be particularly valuable to investors, plant developers and municipalities interested in waste to energy in India and elsewhere. © 2014 Elsevier Ltd. All rights reserved.

Pharmaceutical process optimisation of bulk lyophilisates:implications of powder handling

Lyophilisation or freeze drying is the preferred dehydrating method for pharmaceuticals liable to thermal degradation. Most biologics are unstable in aqueous solution and may use freeze drying to prolong their shelf life. Lyophilisation is however expensive and has seen lots of work aimed at reducing cost. This thesis is motivated by the potential cost savings foreseen with the adoption of a cost efficient bulk drying approach for large and small molecules. Initial studies identified ideal formulations that adapted well to bulk drying and further powder handling requirements downstream in production. Low cost techniques were used to disrupt large dried cakes into powder while the effects of carrier agent concentration were investigated for powder flowability using standard pharmacopoeia methods. This revealed superiority of crystalline mannitol over amorphous sucrose matrices and established that the cohesive and very poor flow nature of freeze dried powders were potential barriers to success. Studies from powder characterisation showed increased powder densification was mainly responsible for significant improvements in flow behaviour and an initial bulking agent concentration of 10-15 %w/v was recommended. Further optimisation studies evaluated the effects of freezing rates and thermal treatment on powder flow behaviour. Slow cooling (0.2 °C/min) with a -25°C annealing hold (2hrs) provided adequate mechanical strength and densification at 0.5-1 M mannitol concentrations. Stable bulk powders require powder transfer into either final vials or intermediate storage closures. The targeted dosing of powder formulations using volumetric and gravimetric powder dispensing systems where evaluated using Immunoglobulin G (IgG), Lactate Dehydrogenase (LDH) and Beta Galactosidase models. Final protein content uniformity in dosed vials was assessed using activity and protein recovery assays to draw conclusions from deviations and pharmacopeia acceptance values. A correlation between very poor flowability (p<0.05), solute concentration, dosing time and accuracy was revealed. LDH and IgG lyophilised in 0.5 M and 1 M mannitol passed Pharmacopeia acceptance values criteria with 0.1-4 while formulations with micro collapse showed the best dose accuracy (0.32-0.4% deviation). Bulk mannitol content above 0.5 M provided no additional benefits to dosing accuracy or content uniformity of dosed units. This study identified considerations which included the type of protein, annealing, cake disruption process, physical form of the phases present, humidity control and recommended gravimetric transfer as optimal for dispensing powder. Dosing lyophilised powders from bulk was demonstrated as practical, time efficient, economical and met regulatory requirements in cases. Finally the use of a new non-destructive technique, X-ray microcomputer tomography (MCT), was explored for cake and particle characterisation. Studies demonstrated good correlation with traditional gas porosimetry (R2 = 0.93) and morphology studies using microscopy. Flow characterisation from sample sizes of less than 1 mL was demonstrated using three dimensional X-ray quantitative image analyses. A platinum-mannitol dispersion model used revealed a relationship between freezing rate, ice nucleation sites and variations in homogeneity within the top to bottom segments of a formulation.

Integrated optimisation of surface roughness and tool performance when face milling 416 SS

Tool life is an important factor to be considered during the optimisation of a machining process since cutting parameters can be adjusted to optimise tool changing, reducing cost and time of production. Also the performance of a tool is directly linked to the generated surface roughness and this is important in cases where there are strict surface quality requirements. The prediction of tool life and the resulting surface roughness in milling operations has attracted considerable research efforts. The research reported herein is focused on defining the influence of milling cutting parameters such as cutting speed, feed rate and axial depth of cut, on three major tool performance parameters namely, tool life, material removal and surface roughness. The research is seeking to define methods that will allow the selection of optimal parameters for best tool performance when face milling 416 stainless steel bars. For this study the Taguchi method was applied in a special design of an orthogonal array that allows studying the entire parameter space with only a number of experiments representing savings in cost and time of experiments. The findings were that the cutting speed has the most influence on tool life and surface roughness and very limited influence on material removal. By last tool life can be judged either from tool life or volume of material removal.

Message passing for distributed optimisation of power allocation with renewable resources

The increase in renewable energy generators introduced into the electricity grid is putting pressure on its stability and management as predictions of renewable energy sources cannot be accurate or fully controlled. This, with the additional pressure of fluctuations in demand, presents a problem more complex than the current methods of controlling electricity distribution were designed for. A global approximate and distributed optimisation method for power allocation that accommodates uncertainties and volatility is suggested and analysed. It is based on a probabilistic method known as message passing [1], which has deep links to statistical physics methodology. This principled method of optimisation is based on local calculations and inherently accommodates uncertainties; it is of modest computational complexity and provides good approximate solutions.We consider uncertainty and fluctuations drawn from a Gaussian distribution and incorporate them into the message-passing algorithm. We see the effect that increasing uncertainty has on the transmission cost and how the placement of volatile nodes within a grid, such as renewable generators or consumers, effects it.

Perceptions and experiences of the implementation, management, use and optimisation of electronic prescribing systems in hospital settings:protocol for a systematic review of qualitative studies

Introduction: There is increasing evidence that electronic prescribing (ePrescribing) or computerised provider/physician order entry (CPOE) systems can improve the quality and safety of healthcare services. However, it has also become clear that their implementation is not straightforward and may create unintended or undesired consequences once in use. In this context, qualitative approaches have been particularly useful and their interpretative synthesis could make an important and timely contribution to the field. This review will aim to identify, appraise and synthesise qualitative studies on ePrescribing/CPOE in hospital settings, with or without clinical decision support. Methods and analysis: Data sources will include the following bibliographic databases: MEDLINE, MEDLINE In Process, EMBASE, PsycINFO, Social Policy and Practice via Ovid, CINAHL via EBSCO, The Cochrane Library (CDSR, DARE and CENTRAL databases), Nursing and Allied Health Sources, Applied Social Sciences Index and Abstracts via ProQuest and SCOPUS. In addition, other sources will be searched for ongoing studies (ClinicalTrials.gov) and grey literature: Healthcare Management Information Consortium, Conference Proceedings Citation Index (Web of Science) and Sociological abstracts. Studies will be independently screened for eligibility by 2 reviewers. Qualitative studies, either standalone or in the context of mixed-methods designs, reporting the perspectives of any actors involved in the implementation, management and use of ePrescribing/CPOE systems in hospital-based care settings will be included. Data extraction will be conducted by 2 reviewers using a piloted form. Quality appraisal will be based on criteria from the Critical Appraisal Skills Programme checklist and Standards for Reporting Qualitative Research. Studies will not be excluded based on quality assessment. A postsynthesis sensitivity analysis will be undertaken. Data analysis will follow the thematic synthesis method. Ethics and dissemination: The study does not require ethical approval as primary data will not be collected. The results of the study will be published in a peer-reviewed journal and presented at relevant conferences.

Optimisation of chromatographic separation of oxidised phospholipids and detection with targeted approaches provides greater coverage of the oxidised lipidome

Phospholipid oxidation by adventitious damage generates a wide variety of products with potentially novel biological activities that can modulate inflammatory processes associated with various diseases. To understand the biological importance of oxidised phospholipids (OxPL) and their potential role as disease biomarkers requires precise information about the abundance of these compounds in cells and tissues. There are many chemiluminescence and spectrophotometric assays available for detecting oxidised phospholipids, but they all have some limitations. Mass spectrometry coupled with liquid chromatography is a powerful and sensitive approach that can provide detailed information about the oxidative lipidome, but challenges still remain. The aim of this work is to develop improved methods for detection of OxPLs by optimisation of chromatographic separation through testing several reverse phase columns and solvent systems, and using targeted mass spectrometry approaches. Initial experiments were carried out using oxidation products generated in vitro to optimise the chromatography separation parameters and mass spectrometry parameters. We have evaluated the chromatographic separation of oxidised phosphatidylcholines (OxPCs) and oxidised phosphatidylethanolamines (OXPEs) using C8, C18 and C30 reverse phase, polystyrene – divinylbenzene based monolithic and mixed – mode hydrophilic interaction (HILIC) columns, interfaced with mass spectrometry. Our results suggest that the monolithic column was best able to separate short chain OxPCs and OxPEs from long chain oxidised and native PCs and PEs. However, variation in charge of polar head groups and extreme diversity of oxidised species make analysis of several classes of OxPLs within one analytical run impractical. We evaluated and optimised the chromatographic separation of OxPLs by serially coupling two columns: HILIC and monolith column that provided us the larger coverage of OxPL species in a single analytical run.

Optimisation of a droplet digital PCR assay for the diagnosis of Schistosoma japonicum infection: A duplex approach with DNA binding dye chemistry

Schistosomiasis is a chronically debilitating helminth infection with a significant socio-economic and public health impact. Accurate diagnostics play a pivotal role in achieving current schistosomiasis control and elimination goals. However, many of the current diagnostic procedures, which rely on detection of schistosome eggs, have major limitations including lack of accuracy and the inability to detect pre-patent infections. DNA-based detection methods provide a viable alternative to the current tests commonly used for schistosomiasis diagnosis. Here we describe the optimisation of a novel droplet digital PCR (ddPCR) duplex assay for the diagnosis of Schistosoma japonicum infection which provides improved detection sensitivity and specificity. The assay involves the amplification of two specific and abundant target gene sequences in S. japonicum; a retrotransposon (SjR2) and a portion of a mitochondrial gene (nad1). The assay detected target sequences in different sources of schistosome DNA isolated from adult worms, schistosomules and eggs, and exhibits a high level of specificity, thereby representing an ideal tool for the detection of low levels of parasite DNA in different clinical samples including parasite cell free DNA in the host circulation and other bodily fluids. Moreover, being quantitative, the assay can be used to determine parasite infection intensity and, could provide an important tool for the detection of low intensity infections in low prevalence schistosomiasis-endemic areas.

Optimisation of digitally coded test vectors for mixed-signal components

International audience

Comparação entre métodos para mensuração da potência aeróbia em atletas tetraplégicos= : Comparison of methods for aerobic power assessment in athletes with tetraplegia

Universidade Estadual de Campinas . Faculdade de Educação Física

Validity and reliability of methods for the detection of secondary caries around amalgam restorations in primary teeth

Secondary caries has been reported as the main reason for restoration replacement. The aim of this in vitro study was to evaluate the performance of different methods - visual inspection, laser fluorescence (DIAGNOdent), radiography and tactile examination - for secondary caries detection in primary molars restored with amalgam. Fifty-four primary molars were photographed and 73 suspect sites adjacent to amalgam restorations were selected. Two examiners evaluated independently these sites using all methods. Agreement between examiners was assessed by the Kappa test. To validate the methods, a caries-detector dye was used after restoration removal. The best cut-off points for the sample were found by a Receiver Operator Characteristic (ROC) analysis, and the area under the ROC curve (Az), and the sensitivity, specificity and accuracy of the methods were calculated for enamel (D2) and dentine (D3) thresholds. These parameters were found for each method and then compared by the McNemar test. The tactile examination and visual inspection presented the highest inter-examiner agreement for the D2 and D3 thresholds, respectively. The visual inspection also showed better performance than the other methods for both thresholds (Az = 0.861 and Az = 0.841, respectively). In conclusion, the visual inspection presented the best performance for detecting enamel and dentin secondary caries in primary teeth restored with amalgam.

Reliability and discriminatory power of methods for dental plaque quantification

OBJECTIVE: This in situ study evaluated the discriminatory power and reliability of methods of dental plaque quantification and the relationship between visual indices (VI) and fluorescence camera (FC) to detect plaque. MATERIAL AND METHODS: Six volunteers used palatal appliances with six bovine enamel blocks presenting different stages of plaque accumulation. The presence of plaque with and without disclosing was assessed using VI. Images were obtained with FC and digital camera in both conditions. The area covered by plaque was assessed. Examinations were done by two independent examiners. Data were analyzed by Kruskal-Wallis and Kappa tests to compare different conditions of samples and to assess the inter-examiner reproducibility. RESULTS: Some methods presented adequate reproducibility. The Turesky index and the assessment of area covered by disclosed plaque in the FC images presented the highest discriminatory powers. CONCLUSION: The Turesky index and images with FC with disclosing present good reliability and discriminatory power in quantifying dental plaque.