Manufacture of a human mesenchymal stem cell population using an automated cell culture platform.

PubMed

Thomas, Robert James; Chandra, Amit; Liu, Yang; Hourd, Paul C; Conway, Paul P; Williams, David J

2007-09-01

Tissue engineering and regenerative medicine are rapidly developing fields that use cells or cell-based constructs as therapeutic products for a wide range of clinical applications. Efforts to commercialise these therapies are driving a need for capable, scaleable, manufacturing technologies to ensure therapies are able to meet regulatory requirements and are economically viable at industrial scale production. We report the first automated expansion of a human bone marrow derived mesenchymal stem cell population (hMSCs) using a fully automated cell culture platform. Differences in cell population growth profile, attributed to key methodological differences, were observed between the automated protocol and a benchmark manual protocol. However, qualitatively similar cell output, assessed by cell morphology and the expression of typical hMSC markers, was obtained from both systems. Furthermore, the critical importance of minor process variation, e.g. the effect of cell seeding density on characteristics such as population growth kinetics and cell phenotype, was observed irrespective of protocol type. This work highlights the importance of careful process design in therapeutic cell manufacture and demonstrates the potential of automated culture for future optimisation and scale up studies required for the translation of regenerative medicine products from the laboratory to the clinic.

Design Optimisation of a Magnetic Field Based Soft Tactile Sensor

PubMed Central

Raske, Nicholas; Kow, Junwai; Alazmani, Ali; Ghajari, Mazdak; Culmer, Peter; Hewson, Robert

2017-01-01

This paper investigates the design optimisation of a magnetic field based soft tactile sensor, comprised of a magnet and Hall effect module separated by an elastomer. The aim was to minimise sensitivity of the output force with respect to the input magnetic field; this was achieved by varying the geometry and material properties. Finite element simulations determined the magnetic field and structural behaviour under load. Genetic programming produced phenomenological expressions describing these responses. Optimisation studies constrained by a measurable force and stable loading conditions were conducted; these produced Pareto sets of designs from which the optimal sensor characteristics were selected. The optimisation demonstrated a compromise between sensitivity and the measurable force, a fabricated version of the optimised sensor validated the improvements made using this methodology. The approach presented can be applied in general for optimising soft tactile sensor designs over a range of applications and sensing modes. PMID:29099787

Automation of Silica Bead-based Nucleic Acid Extraction on a Centrifugal Lab-on-a-Disc Platform

NASA Astrophysics Data System (ADS)

Kinahan, David J.; Mangwanya, Faith; Garvey, Robert; Chung, Danielle WY; Lipinski, Artur; Julius, Lourdes AN; King, Damien; Mohammadi, Mehdi; Mishra, Rohit; Al-Ofi, May; Miyazaki, Celina; Ducrée, Jens

2016-10-01

We describe a centrifugal microfluidic ‘Lab-on-a-Disc’ (LoaD) technology for DNA purification towards eventual integration into a Sample-to-Answer platform for detection of the pathogen Escherichia coli O157:H7 from food samples. For this application, we use a novel microfluidic architecture which combines ‘event-triggered’ dissolvable film (DF) valves with a reaction chamber gated by a centrifugo-pneumatic siphon valve (CPSV). This architecture permits comprehensive flow control by simple changes in the speed of the platform innate spindle motor. Even before method optimisation, characterisation by DNA fluorescence reveals an extraction efficiency of 58%, which is close to commercial spin columns.

Producing a glycosylating Escherichia coli cell factory: The placement of the bacterial oligosaccharyl transferase pglB onto the genome.

PubMed

Strutton, Benjamin; Jaffé, Stephen R P; Pandhal, Jagroop; Wright, Phillip C

2018-01-01

Although Escherichia coli has been engineered to perform N-glycosylation of recombinant proteins, an optimal glycosylating strain has not been created. By inserting a codon optimised Campylobacter oligosaccharyltransferase onto the E. coli chromosome, we created a glycoprotein platform strain, where the target glycoprotein, sugar synthesis and glycosyltransferase enzymes, can be inserted using expression vectors to produce the desired homogenous glycoform. To assess the functionality and glycoprotein producing capacity of the chromosomally based OST, a combined Western blot and parallel reaction monitoring mass spectrometry approach was applied, with absolute quantification of glycoprotein. We demonstrated that chromosomal oligosaccharyltransferase remained functional and facilitated N-glycosylation. Although the engineered strain produced less total recombinant protein, the glycosylation efficiency increased by 85%, and total glycoprotein production was enhanced by 17%. Copyright © 2017 Elsevier Inc. All rights reserved.

ATNT: an enhanced system for expression of polycistronic secondary metabolite gene clusters in Aspergillus niger.

PubMed

Geib, Elena; Brock, Matthias

2017-01-01

Fungi are treasure chests for yet unexplored natural products. However, exploitation of their real potential remains difficult as a significant proportion of biosynthetic gene clusters appears silent under standard laboratory conditions. Therefore, elucidation of novel products requires gene activation or heterologous expression. For heterologous gene expression, we previously developed an expression platform in Aspergillus niger that is based on the transcriptional regulator TerR and its target promoter P terA . In this study, we extended this system by regulating expression of terR  by the doxycycline inducible Tet-on system. Reporter genes cloned under the control of the target promoter P terA remained silent in the absence of doxycycline, but were strongly expressed when doxycycline was added. Reporter quantification revealed that the coupled system results in about five times higher expression rates compared to gene expression under direct control of the Tet-on system. As production of secondary metabolites generally requires the expression of several biosynthetic genes, the suitability of the self-cleaving viral peptide sequence P2A was tested in this optimised expression system. P2A allowed polycistronic expression of genes required for Asp-melanin formation in combination with the gene coding for the red fluorescent protein tdTomato. Gene expression and Asp-melanin formation was prevented in the absence of doxycycline and strongly induced by addition of doxycycline. Fluorescence studies confirmed the correct subcellular localisation of the respective enzymes. This tightly regulated but strongly inducible expression system enables high level production of secondary metabolites most likely even those with toxic potential. Furthermore, this system is compatible with polycistronic gene expression and, thus, suitable for the discovery of novel natural products.

Fabrication and optimisation of a fused filament 3D-printed microfluidic platform

NASA Astrophysics Data System (ADS)

Tothill, A. M.; Partridge, M.; James, S. W.; Tatam, R. P.

2017-03-01

A 3D-printed microfluidic device was designed and manufactured using a low cost (2000) consumer grade fusion deposition modelling (FDM) 3D printer. FDM printers are not typically used, or are capable, of producing the fine detailed structures required for microfluidic fabrication. However, in this work, the optical transparency of the device was improved through manufacture optimisation to such a point that optical colorimetric assays can be performed in a 50 µl device. A colorimetric enzymatic cascade assay was optimised using glucose oxidase and horseradish peroxidase for the oxidative coupling of aminoantipyrine and chromotropic acid to produce a blue quinoneimine dye with a broad absorbance peaking at 590 nm for the quantification of glucose in solution. For comparison the assay was run in standard 96 well plates with a commercial plate reader. The results show the accurate and reproducible quantification of 0-10 mM glucose solution using a 3D-printed microfluidic optical device with performance comparable to that of a plate reader assay.

Conversion of DST Group Shape Optimisation Software for Increased Portability across Computing Platforms

DTIC Science & Technology

2016-05-01

reduction achieved is small due to the starting shape being near optimal. The general arrangement and x-y coordinate system are shown in Figure 23...Optimization, Vol. 28, pp. 55–68, 2004. [3] M Heller, J Calero, S Barter , RJ Wescott, J Choi. Fatigue life extension program for LAU-7 missile launcher

Influence of platform design of six different drug-eluting stents in provisional coronary bifurcation stenting by rePOT sequence: a comparative bench analysis.

PubMed

Derimay, François; Souteyrand, Geraud; Motreff, Pascal; Rioufol, Gilles; Finet, Gerard

2017-10-13

The rePOT (proximal optimisation technique) sequence proved significantly more effective than final kissing balloon (FKB) with two drug-eluting stents (DES) in a bench test. We sought to validate efficacy experimentally in a large range of latest-generation DES. On left main fractal coronary bifurcation bench models, five samples of each of the six main latest-generation DES (Coroflex ISAR, Orsiro, Promus PREMIER, Resolute Integrity, Ultimaster, XIENCE Xpedition) were implanted on rePOT (initial POT, side branch inflation, final POT). Proximal elliptical ratio, side branch obstruction (SBO), stent overstretch and strut malapposition were quantified on 2D and 3D OCT. Results were compared to FKB with Promus PREMIER. Whatever the design, rePOT maintained vessel circularity compared to FKB: elliptical ratio, 1.02±0.01 to 1.04±0.01 vs. 1.26±0.02 (p<0.05). Global strut malapposition was much lower: 2.6±1.4% to 0.1±0.2% vs. 40.4±8.4% for FKB (p<0.05). However, only Promus PREMIER and XIENCE Xpedition achieved significantly less SBO: respectively, 5.6±3.5% and 10.0±5.3% vs. 23.5±5.7% for FKB (p<0.05). Platform design differences had little influence on the excellent results of rePOT versus FKB. RePOT optimised strut apposition without proximal elliptical deformation in the six main latest-generation DES. Thickness and design characteristics seemed relevant for optimising SBO.

Optimised laser microdissection of the human ocular surface epithelial regions for microarray studies

PubMed Central

2013-01-01

Background The most important challenge of performing insitu transcriptional profiling of the human ocular surface epithelial regions is obtaining samples in sufficient amounts, without contamination from adjacent tissue, as the region of interest is microscopic and closely apposed to other tissues regions. We have effectively collected ocular surface (OS) epithelial tissue samples from the Limbal Epithelial Crypt (LEC), limbus, cornea and conjunctiva of post-mortem cadaver eyes with laser microdissection (LMD) technique for gene expression studies with spotted oligonucleotide microarrays and Gene 1.0 ST arrays. Methods Human donor eyes (4 pairs for spotted oligonucleotide microarrays, 3 pairs for Gene 1.0 ST arrays) consented for research were included in this study with due ethical approval of the Nottingham Research Ethics Committee. Eye retrieval was performed within 36 hours of post-mortem period. The dissected corneoscleral buttons were immersed in OCT media and frozen in liquid nitrogen and stored at −80°C till further use. Microscopic tissue sections of interest were taken on PALM slides and stained with Toluidine Blue for laser microdissection with PALM microbeam systems. Optimisation of the laser microdissection technique was crucial for efficient and cost effective sample collection. Results The starting concentration of RNA as stipulated by the protocol of microarray platforms was taken as the cut-off concentration of RNA samples in our studies. The area of LMD tissue processed for spotted oligonucleotide microarray study ranged from 86,253 μm2 in LEC to 392,887 μm2 in LEC stroma. The RNA concentration of the LMD samples ranged from 22 to 92 pg/μl. The recommended starting concentration of the RNA samples used for Gene 1.0 ST arrays was 6 ng/5 μl. To achieve the desired RNA concentration the area of ocular surface epithelial tissue sample processed for the Gene 1.0 ST array experiments was approximately 100,0000 μm2 to 130,0000 μm2. RNA concentration of these samples ranged from 10.88 ng/12 μl to 25.8 ng/12 μl, with the RNA integrity numbers (RIN) for these samples from 3.3 to 7.9. RNA samples with RIN values below 2, that had failed to amplify satisfactorily were discarded. Conclusions The optimised protocol for sample collection and laser microdissection improved the RNA yield of the insitu ocular surface epithelial regions for effective microarray studies on spotted oligonucleotide and affymetrix platforms. PMID:24160452

Improving linear transport infrastructure efficiency by automated learning and optimised predictive maintenance techniques (INFRALERT)

NASA Astrophysics Data System (ADS)

Jiménez-Redondo, Noemi; Calle-Cordón, Alvaro; Kandler, Ute; Simroth, Axel; Morales, Francisco J.; Reyes, Antonio; Odelius, Johan; Thaduri, Aditya; Morgado, Joao; Duarte, Emmanuele

2017-09-01

The on-going H2020 project INFRALERT aims to increase rail and road infrastructure capacity in the current framework of increased transportation demand by developing and deploying solutions to optimise maintenance interventions planning. It includes two real pilots for road and railways infrastructure. INFRALERT develops an ICT platform (the expert-based Infrastructure Management System, eIMS) which follows a modular approach including several expert-based toolkits. This paper presents the methodologies and preliminary results of the toolkits for i) nowcasting and forecasting of asset condition, ii) alert generation, iii) RAMS & LCC analysis and iv) decision support. The results of these toolkits in a meshed road network in Portugal under the jurisdiction of Infraestruturas de Portugal (IP) are presented showing the capabilities of the approaches.

Next generation bone tissue engineering: non-viral miR-133a inhibition using collagen-nanohydroxyapatite scaffolds rapidly enhances osteogenesis

NASA Astrophysics Data System (ADS)

Mencía Castaño, Irene; Curtin, Caroline M.; Duffy, Garry P.; O'Brien, Fergal J.

2016-06-01

Bone grafts are the second most transplanted materials worldwide at a global cost to healthcare systems valued over $30 billion every year. The influence of microRNAs in the regenerative capacity of stem cells offers vast therapeutic potential towards bone grafting; however their efficient delivery to the target site remains a major challenge. This study describes how the functionalisation of porous collagen-nanohydroxyapatite (nHA) scaffolds with miR-133a inhibiting complexes, delivered using non-viral nHA particles, enhanced human mesenchymal stem cell-mediated osteogenesis through the novel focus on a key activator of osteogenesis, Runx2. This study showed enhanced Runx2 and osteocalcin expression, as well as increased alkaline phosphatase activity and calcium deposition, thus demonstrating a further enhanced therapeutic potential of a biomaterial previously optimised for bone repair applications. The promising features of this platform offer potential for a myriad of applications beyond bone repair and tissue engineering, thus presenting a new paradigm for microRNA-based therapeutics.

AlphaMate: a program for optimising selection, maintenance of diversity, and mate allocation in breeding programs.

PubMed

Gorjanc, Gregor; Hickey, John M

2018-05-02

AlphaMate is a flexible program that optimises selection, maintenance of genetic diversity, and mate allocation in breeding programs. It can be used in animal and cross- and self-pollinating plant populations. These populations can be subject to selective breeding or conservation management. The problem is formulated as a multi-objective optimisation of a valid mating plan that is solved with an evolutionary algorithm. A valid mating plan is defined by a combination of mating constraints (the number of matings, the maximal number of parents, the minimal/equal/maximal number of contributions per parent, or allowance for selfing) that are gender specific or generic. The optimisation can maximize genetic gain, minimize group coancestry, minimize inbreeding of individual matings, or maximize genetic gain for a given increase in group coancestry or inbreeding. Users provide a list of candidate individuals with associated gender and selection criteria information (if applicable) and coancestry matrix. Selection criteria and coancestry matrix can be based on pedigree or genome-wide markers. Additional individual or mating specific information can be included to enrich optimisation objectives. An example of rapid recurrent genomic selection in wheat demonstrates how AlphaMate can double the efficiency of converting genetic diversity into genetic gain compared to truncation selection. Another example demonstrates the use of genome editing to expand the gain-diversity frontier. Executable versions of AlphaMate for Windows, Mac, and Linux platforms are available at http://www.AlphaGenes.roslin.ed.ac.uk/AlphaMate. gregor.gorjanc@roslin.ed.ack.uk.

Improved expression of recombinant plant-made hEGF.

PubMed

Thomas, David Rhys; Walmsley, Amanda Maree

2014-11-01

The yield of recombinant hEGF was increased approximately tenfold through a range of optimisations. Further, the recombinant protein was found to have biological activity comparable to commercial hEGF. Human epidermal growth factor (hEGF) is a powerful mitogen that can enhance the healing of a wide range of injuries, including burns, cuts, diabetic ulcers and gastric ulcers. However, despite its clinical value, hEGF is only consistently used for the treatment of chronic diabetic ulcers due to its high cost. In this study, hEGF was transiently expressed in Nicotiana benthamiana plants and targeted to the apoplast, ER and vacuole. Several other approaches were also included in a stepwise fashion to identify the optimal conditions for the expression of recombinant hEGF. Expression was found to be highest in the vacuole, while targeting hEGF to the ER caused a decrease in total soluble protein (TSP). Using a codon optimised sequence was found to increase vacuolar targeted hEGF yield by ~34 %, while it was unable to increase the yield of ER targeted hEGF. The use of the P19 silencing inhibitor was able to further increase expression by over threefold, and using 5-week-old plants significantly increased expression compared to 4- or 6-week-old-plants. The combined effect of these optimisations increased expression tenfold over the initial apoplast targeted construct to an average yield of 6.24 % of TSP. The plant-made hEGF was then shown to be equivalent to commercial E. coli derived hEGF in its ability to promote the proliferation of mouse keratinocytes. This study supports the potential for plants to be used for the commercial production of hEGF, and identifies a potential limitation for the further improvement of recombinant protein yields.

Mediating human stem cell behaviour via defined fibrous architectures by melt electrospinning writing.

PubMed

Eichholz, Kian F; Hoey, David A

2018-05-29

The architecture within which cells reside is key to mediating their specific functions within the body. In this study, we use melt electrospinning writing (MEW) to fabricate cell micro-environments with various fibrous architectures to study their effect on human stem cell behaviour. We designed, built and optimised a MEW apparatus and used it to fabricate four different platform designs of 10.4±2μm fibre diameter, with angles between fibres on adjacent layers of 90°, 45°, 10° and R (random). Mechanical characterisation was conducted via tensile testing, and human skeletal stem cells (hSSCs) were seeded to scaffolds to study the effect of architecture on cell morphology and mechanosensing (nuclear YAP). Cell morphology was significantly altered between groups, with cells on 90° scaffolds having a lower aspect ratio, greater spreading, greater cytoskeletal tension and nuclear YAP expression. Long term cell culture studies were then conducted to determine the differentiation potential of scaffolds in terms of alkaline phosphatase activity, collagen and mineral production. Across these studies, an increased cell spreading in 3-dimensions is seen with decreasing alignment of architecture correlated with enhanced osteogenesis. This study therefore highlights the critical role of fibrous architecture in regulating stem cell behaviour with implications for tissue engineering and disease progression. This is the first study which has investigated the effect of controlled fibrous architectures fabricated via melt electrospinning writing on cell behaviour and differentiation. After optimising the process and characterising scaffolds via SEM and tensile testing, cells were seeded to fibrous scaffolds with various micro-architectures and studied in terms of cell morphology. Nuclear YAP expression was further investigated as a marker of cell shape, cytoskeletal tension and differentiation potential. In agreement with these early markers, long term cell culture studies revealed for the first time that a 90° fibrous architecture is optimal for the osteogenic differentiation of skeletal stem cells. This is the first study to investigate the effect of controlled fibrous material architectures fabricated via melt electrospinning writing on cell shape, mechanosignalling and differentiation. After optimising the biofabrication process and characterising scaffolds via SEM and tensile testing, cells were seeded to fibrous scaffolds with various micro-architectures and studied in terms of cell shape. Nuclear YAP expression was further investigated as a marker of cytoskeletal tension and differentiation potential. In agreement with these early markers, long term cell culture studies revealed for the first time that a 90° fibrous architecture is optimal for the osteogenic differentiation of skeletal stem cells, by driving a spread morphology and nuclear translocation of YAP in 3 dimensions . Copyright © 2018 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Systems Biology of Recombinant Protein Production in Bacillus megaterium

NASA Astrophysics Data System (ADS)

Biedendieck, Rebekka; Bunk, Boyke; Fürch, Tobias; Franco-Lara, Ezequiel; Jahn, Martina; Jahn, Dieter

Over the last two decades the Gram-positive bacterium Bacillus megaterium was systematically developed to a useful alternative protein production host. Multiple vector systems for high yield intra- and extracellular protein production were constructed. Strong inducible promoters were combined with DNA sequences for optimised ribosome binding sites, various leader peptides for protein export and N- as well as C-terminal affinity tags for affinity chromatographic purification of the desired protein. High cell density cultivation and recombinant protein production were successfully tested. For further system biology based control and optimisation of the production process the genomes of two B. megaterium strains were completely elucidated, DNA arrays designed, proteome, fluxome and metabolome analyses performed and all data integrated using the bioinformatics platform MEGABAC. Now, solid theoretical and experimental bases for primary modeling attempts of the production process are available.

A wireless energy transfer platform, integrated at the bedside.

PubMed

De Clercq, Hans; Puers, Robert

2013-01-01

This paper presents the design of a wireless energy transfer platform, integrated at the bedside. The system contains a matrix of identical inductive power transmitters, which are optimised to provide power to a wearable sensor network, with the purpose of wirelessly recording vital signals over an extended period of time. The magnetic link, operates at a transfer frequency of 6.78MHz and is able to transfer a power of 3.3mW to the remote side at an inter-coil distance of 100mm. The total efficiency of the power link is 26%. Moreover, the platform is able to dynamically determine the position of freely moving sensor nodes and selectively induce a magnetic field in the area where the sensor nodes are positioned. As a result, the patient will not be subjected to unnecessary radiation and the specific absorption rate standards are met more easily.

Optimisation of Over-Expression in E. coli and Biophysical Characterisation of Human Membrane Protein Synaptogyrin 1

PubMed Central

Löw, Christian; Jegerschöld, Caroline; Kovermann, Michael; Moberg, Per; Nordlund, Pär

2012-01-01

Progress in functional and structural studies of integral membrane proteins (IMPs) is lacking behind their soluble counterparts due to the great challenge in producing stable and homogeneous IMPs. Low natural abundance, toxicity when over-expressed and potential lipid requirements of IMPs are only a few reasons for the limited progress. Here, we describe an optimised workflow for the recombinant over-expression of the human tetraspan vesicle protein (TVP) synaptogyrin in Escherichia coli and its biophysical characterisation. TVPs are ubiquitous and abundant components of vesicles. They are believed to be involved in various aspects of the synaptic vesicle cycle, including vesicle biogenesis, exocytosis and endocytotic recycling. Even though TVPs are found in most cell types, high-resolution structural information for this class of membrane proteins is still missing. The optimisation of the N-terminal sequence of the gene together with the usage of the recently developed Lemo21(DE3) strain which allows the balancing of the translation with the membrane insertion rate led to a 50-fold increased expression rate compared to the classical BL21(DE3) strain. The protein was soluble and stable in a variety of mild detergents and multiple biophysical methods confirmed the folded state of the protein. Crosslinking experiments suggest an oligomeric architecture of at least four subunits. The protein stability is significantly improved in the presence of cholesteryl hemisuccinate as judged by differential light scattering. The approach described here can easily be adapted to other eukaryotic IMPs. PMID:22675529

Controlled hydrostatic pressure stress downregulates the expression of ribosomal genes in preimplantation embryos: a possible protection mechanism?

PubMed

Bock, I; Raveh-Amit, H; Losonczi, E; Carstea, A C; Feher, A; Mashayekhi, K; Matyas, S; Dinnyes, A; Pribenszky, C

2016-04-01

The efficiency of various assisted reproductive techniques can be improved by preconditioning the gametes and embryos with sublethal hydrostatic pressure treatment. However, the underlying molecular mechanism responsible for this protective effect remains unknown and requires further investigation. Here, we studied the effect of optimised hydrostatic pressure treatment on the global gene expression of mouse oocytes after embryonic genome activation. Based on a gene expression microarray analysis, a significant effect of treatment was observed in 4-cell embryos derived from treated oocytes, revealing a transcriptional footprint of hydrostatic pressure-affected genes. Functional analysis identified numerous genes involved in protein synthesis that were downregulated in 4-cell embryos in response to hydrostatic pressure treatment, suggesting that regulation of translation has a major role in optimised hydrostatic pressure-induced stress tolerance. We present a comprehensive microarray analysis and further delineate a potential mechanism responsible for the protective effect of hydrostatic pressure treatment.

Heterologous expression of Aspergillus terreus fructosyltransferase in Kluyveromyces lactis.

PubMed

Spohner, Sebastian C; Czermak, Peter

2016-06-25

Fructo-oligosaccharides are prebiotic and hypocaloric sweeteners that are usually extracted from chicory. They can also be produced from sucrose using fructosyltransferases, but the only commercial enzyme suitable for this purpose is Pectinex Ultra, which is produced with Aspergillus aculeatus. Here we used the yeast Kluyveromyces lactis to express a secreted recombinant fructosyltransferase from the inulin-producing fungus Aspergillus terreus. A synthetic codon-optimised version of the putative β-fructofuranosidase ATEG 04996 (XP 001214174.1) from A. terreus NIH2624 was secreted as a functional protein into the extracellular medium. At 60°C, the purified A. terreus enzyme generated the same pattern of oligosaccharides as Pectinex Ultra, but at lower temperatures it also produced oligomers with up to seven units. We achieved activities of up to 986.4U/mL in high-level expression experiments, which is better than previous reports of optimised Aspergillus spp. fermentations. Copyright © 2016 Elsevier B.V. All rights reserved.

The 5C Concept and 5S Principles in Inflammatory Bowel Disease Management

PubMed Central

Hibi, Toshifumi; Panaccione, Remo; Katafuchi, Miiko; Yokoyama, Kaoru; Watanabe, Kenji; Matsui, Toshiyuki; Matsumoto, Takayuki; Travis, Simon; Suzuki, Yasuo

2017-01-01

Abstract Background and Aims The international Inflammatory Bowel Disease [IBD] Expert Alliance initiative [2012–2015] served as a platform to define and support areas of best practice in IBD management to help improve outcomes for all patients with IBD. Methods During the programme, IBD specialists from around the world established by consensus two best practice charters: the 5S Principles and the 5C Concept. Results The 5S Principles were conceived to provide health care providers with key guidance for improving clinical practice based on best management approaches. They comprise the following categories: Stage the disease; Stratify patients; Set treatment goals; Select appropriate treatment; and Supervise therapy. Optimised management of patients with IBD based on the 5S Principles can be achieved most effectively within an optimised clinical care environment. Guidance on optimising the clinical care setting in IBD management is provided through the 5C Concept, which encompasses: Comprehensive IBD care; Collaboration; Communication; Clinical nurse specialists; and Care pathways. Together, the 5C Concept and 5S Principles provide structured recommendations on organising the clinical care setting and developing best-practice approaches in IBD management. Conclusions Consideration and application of these two dimensions could help health care providers optimise their IBD centres and collaborate more effectively with their multidisciplinary team colleagues and patients, to provide improved IBD care in daily clinical practice. Ultimately, this could lead to improved outcomes for patients with IBD. PMID:28981622

Subnanomolar indazole-5-carboxamide inhibitors of monoamine oxidase B (MAO-B) continued: indications of iron binding, experimental evidence for optimised solubility and brain penetration.

PubMed

Tzvetkov, Nikolay T; Antonov, Liudmil

2017-12-01

Pharmacological and physicochemical studies of N-unsubstituted indazole-5-carboxamides (subclass I) and their structurally optimised N1-methylated analogues (subclass II), initially developed as drug and radioligand candidates for the treatment and diagnosis of Parkinson's disease (PD), are presented. The compounds are highly brain permeable, selective, reversible, and competitive monoamine oxidase B (MAO-B) inhibitors with improved water-solubility and subnanomolar potency (pIC 50  >8.8). Using a well-validated, combined X-ray/modelling technology platform, we performed a semi-quantitative analysis of the binding modes of all compounds and investigated the role of the indazole N1 position for their MAO-B inhibitory activity. Moreover, compounds NTZ-1006, 1032, and 1441 were investigated for their ability to bind Fe 2+ and Fe 3+ ions using UV-visible spectroscopy.

Facial Expression Training Optimises Viewing Strategy in Children and Adults

PubMed Central

Pollux, Petra M. J.; Hall, Sophie; Guo, Kun

2014-01-01

This study investigated whether training-related improvements in facial expression categorization are facilitated by spontaneous changes in gaze behaviour in adults and nine-year old children. Four sessions of a self-paced, free-viewing training task required participants to categorize happy, sad and fear expressions with varying intensities. No instructions about eye movements were given. Eye-movements were recorded in the first and fourth training session. New faces were introduced in session four to establish transfer-effects of learning. Adults focused most on the eyes in all sessions and increased expression categorization accuracy after training coincided with a strengthening of this eye-bias in gaze allocation. In children, training-related behavioural improvements coincided with an overall shift in gaze-focus towards the eyes (resulting in more adult-like gaze-distributions) and towards the mouth for happy faces in the second fixation. Gaze-distributions were not influenced by the expression intensity or by the introduction of new faces. It was proposed that training enhanced the use of a uniform, predominantly eyes-biased, gaze strategy in children in order to optimise extraction of relevant cues for discrimination between subtle facial expressions. PMID:25144680

Enhanced expression of codon optimized Mycobacterium avium subsp. paratuberculosis antigens in Lactobacillus salivarius

USDA-ARS?s Scientific Manuscript database

We have previously identified the mycobacterial high G+C codon usage bias as a limiting factor in heterologous expression of MAP proteins from Lb.salivarius, and demonstrated that codon optimisation of a synthetic coding gene greatly enhances MAP protein production. Here, we effectively demonstrate ...

A high-resolution x-ray spectrometer for a kaon mass measurement

NASA Astrophysics Data System (ADS)

Phelan, Kevin; Suzuki, Ken; Zmeskal, Johann; Tortorella, Daniele; Bühler, Matthias; Hertrich, Theo

2017-02-01

The ASPECT consortium (Adaptable Spectrometer Enabled by Cryogenic Technology) is currently constructing a generalised cryogenic platform for cryogenic detector work which will be able to accommodate a wide range of sensors. The cryogenics system is based on a small mechanical cooler with a further adiabatic demagnetisation stage and will work with cryogenic detectors at sub-Kelvin temperatures. The commercial aim of the consortium is to produce a compact, user-friendly device with an emphasis on reliability and portability which can easily be transported for specialised on-site work, such as beam-lines or telescope facilities. The cryogenic detector platform will accommodate a specially developed cryogenic sensor, either a metallic magnetic calorimeter or a magnetic penetration-depth thermometer. The detectors will be designed to work in various temperatures regions with an emphasis on optimising the various detector resolutions for specific temperatures. One resolution target is of about 10 eV at the energies range typically created in kaonic atoms experiments (soft x-ray energies). A following step will see the introduction of continuous, high-power, sub-Kelvin cooling which will bring the cryogenic basis for a high resolution spectrometer system to the market. The scientific goal of the project will produce an experimental set-up optimised for kaon-mass measurements performing high-resolution x-ray spectroscopy on a beam-line provided foreseeably by the J-PARC (Tokai, Japan) or DAΦNE (Frascati, Italy) facilities.

Absolute counting of neutrophils in whole blood using flow cytometry.

PubMed

Brunck, Marion E G; Andersen, Stacey B; Timmins, Nicholas E; Osborne, Geoffrey W; Nielsen, Lars K

2014-12-01

Absolute neutrophil count (ANC) is used clinically to monitor physiological dysfunctions such as myelosuppression or infection. In the research laboratory, ANC is a valuable measure to monitor the evolution of a wide range of disease states in disease models. Flow cytometry (FCM) is a fast, widely used approach to confidently identify thousands of cells within minutes. FCM can be optimised for absolute counting using spiked-in beads or by measuring the sample volume analysed. Here we combine the 1A8 antibody, specific for the mouse granulocyte protein Ly6G, with flow cytometric counting in straightforward FCM assays for mouse ANC, easily implementable in the research laboratory. Volumetric and Trucount™ bead assays were optimized for mouse neutrophils, and ANC values obtained with these protocols were compared to ANC measured by a dual-platform assay using the Orphee Mythic 18 veterinary haematology analyser. The single platform assays were more precise with decreased intra-assay variability compared with ANC obtained using the dual protocol. Defining ANC based on Ly6G expression produces a 15% higher estimate than the dual protocol. Allowing for this difference in ANC definition, the flow cytometry counting assays using Ly6G can be used reliably in the research laboratory to quantify mouse ANC from a small volume of blood. We demonstrate the utility of the volumetric protocol in a time-course study of chemotherapy induced neutropenia using four drug regimens. © 2014 International Society for Advancement of Cytometry.

Effectiveness of an implementation optimisation intervention aimed at increasing parent engagement in HENRY, a childhood obesity prevention programme - the Optimising Family Engagement in HENRY (OFTEN) trial: study protocol for a randomised controlled trial.

PubMed

Bryant, Maria; Burton, Wendy; Cundill, Bonnie; Farrin, Amanda J; Nixon, Jane; Stevens, June; Roberts, Kim; Foy, Robbie; Rutter, Harry; Hartley, Suzanne; Tubeuf, Sandy; Collinson, Michelle; Brown, Julia

2017-01-24

Family-based interventions to prevent childhood obesity depend upon parents' taking action to improve diet and other lifestyle behaviours in their families. Programmes that attract and retain high numbers of parents provide an enhanced opportunity to improve public health and are also likely to be more cost-effective than those that do not. We have developed a theory-informed optimisation intervention to promote parent engagement within an existing childhood obesity prevention group programme, HENRY (Health Exercise Nutrition for the Really Young). Here, we describe a proposal to evaluate the effectiveness of this optimisation intervention in regard to the engagement of parents and cost-effectiveness. The Optimising Family Engagement in HENRY (OFTEN) trial is a cluster randomised controlled trial being conducted across 24 local authorities (approximately 144 children's centres) which currently deliver HENRY programmes. The primary outcome will be parental enrolment and attendance at the HENRY programme, assessed using routinely collected process data. Cost-effectiveness will be presented in terms of primary outcomes using acceptability curves and through eliciting the willingness to pay for the optimisation from HENRY commissioners. Secondary outcomes include the longitudinal impact of the optimisation, parent-reported infant intake of fruits and vegetables (as a proxy to compliance) and other parent-reported family habits and lifestyle. This innovative trial will provide evidence on the implementation of a theory-informed optimisation intervention to promote parent engagement in HENRY, a community-based childhood obesity prevention programme. The findings will be generalisable to other interventions delivered to parents in other community-based environments. This research meets the expressed needs of commissioners, children's centres and parents to optimise the potential impact that HENRY has on obesity prevention. A subsequent cluster randomised controlled pilot trial is planned to determine the practicality of undertaking a definitive trial to robustly evaluate the effectiveness and cost-effectiveness of the optimised intervention on childhood obesity prevention. ClinicalTrials.gov identifier: NCT02675699 . Registered on 4 February 2016.

Expressing the human proteome for affinity proteomics: optimising expression of soluble protein domains and in vivo biotinylation.

PubMed

Keates, Tracy; Cooper, Christopher D O; Savitsky, Pavel; Allerston, Charles K; Phillips, Claire; Hammarström, Martin; Daga, Neha; Berridge, Georgina; Mahajan, Pravin; Burgess-Brown, Nicola A; Müller, Susanne; Gräslund, Susanne; Gileadi, Opher

2012-06-15

The generation of affinity reagents to large numbers of human proteins depends on the ability to express the target proteins as high-quality antigens. The Structural Genomics Consortium (SGC) focuses on the production and structure determination of human proteins. In a 7-year period, the SGC has deposited crystal structures of >800 human protein domains, and has additionally expressed and purified a similar number of protein domains that have not yet been crystallised. The targets include a diversity of protein domains, with an attempt to provide high coverage of protein families. The family approach provides an excellent basis for characterising the selectivity of affinity reagents. We present a summary of the approaches used to generate purified human proteins or protein domains, a test case demonstrating the ability to rapidly generate new proteins, and an optimisation study on the modification of >70 proteins by biotinylation in vivo. These results provide a unique synergy between large-scale structural projects and the recent efforts to produce a wide coverage of affinity reagents to the human proteome. Copyright © 2011 Elsevier B.V. All rights reserved.

Expressing the human proteome for affinity proteomics: optimising expression of soluble protein domains and in vivo biotinylation

PubMed Central

Keates, Tracy; Cooper, Christopher D.O.; Savitsky, Pavel; Allerston, Charles K.; Phillips, Claire; Hammarström, Martin; Daga, Neha; Berridge, Georgina; Mahajan, Pravin; Burgess-Brown, Nicola A.; Müller, Susanne; Gräslund, Susanne; Gileadi, Opher

2012-01-01

The generation of affinity reagents to large numbers of human proteins depends on the ability to express the target proteins as high-quality antigens. The Structural Genomics Consortium (SGC) focuses on the production and structure determination of human proteins. In a 7-year period, the SGC has deposited crystal structures of >800 human protein domains, and has additionally expressed and purified a similar number of protein domains that have not yet been crystallised. The targets include a diversity of protein domains, with an attempt to provide high coverage of protein families. The family approach provides an excellent basis for characterising the selectivity of affinity reagents. We present a summary of the approaches used to generate purified human proteins or protein domains, a test case demonstrating the ability to rapidly generate new proteins, and an optimisation study on the modification of >70 proteins by biotinylation in vivo. These results provide a unique synergy between large-scale structural projects and the recent efforts to produce a wide coverage of affinity reagents to the human proteome. PMID:22027370

The 5C Concept and 5S Principles in Inflammatory Bowel Disease Management.

PubMed

Hibi, Toshifumi; Panaccione, Remo; Katafuchi, Miiko; Yokoyama, Kaoru; Watanabe, Kenji; Matsui, Toshiyuki; Matsumoto, Takayuki; Travis, Simon; Suzuki, Yasuo

2017-10-27

The international Inflammatory Bowel Disease [IBD] Expert Alliance initiative [2012-2015] served as a platform to define and support areas of best practice in IBD management to help improve outcomes for all patients with IBD. During the programme, IBD specialists from around the world established by consensus two best practice charters: the 5S Principles and the 5C Concept. The 5S Principles were conceived to provide health care providers with key guidance for improving clinical practice based on best management approaches. They comprise the following categories: Stage the disease; Stratify patients; Set treatment goals; Select appropriate treatment; and Supervise therapy. Optimised management of patients with IBD based on the 5S Principles can be achieved most effectively within an optimised clinical care environment. Guidance on optimising the clinical care setting in IBD management is provided through the 5C Concept, which encompasses: Comprehensive IBD care; Collaboration; Communication; Clinical nurse specialists; and Care pathways. Together, the 5C Concept and 5S Principles provide structured recommendations on organising the clinical care setting and developing best-practice approaches in IBD management. Consideration and application of these two dimensions could help health care providers optimise their IBD centres and collaborate more effectively with their multidisciplinary team colleagues and patients, to provide improved IBD care in daily clinical practice. Ultimately, this could lead to improved outcomes for patients with IBD. Copyright © 2017 European Crohn’s and Colitis Organisation (ECCO). Published by Oxford University Press. All rights reserved. For permissions, please email: journals.permissions@oup.com

Energy and wear optimisation of train longitudinal dynamics and of traction and braking systems

NASA Astrophysics Data System (ADS)

Conti, R.; Galardi, E.; Meli, E.; Nocciolini, D.; Pugi, L.; Rindi, A.

2015-05-01

Traction and braking systems deeply affect longitudinal train dynamics, especially when an extensive blending phase among different pneumatic, electric and magnetic devices is required. The energy and wear optimisation of longitudinal vehicle dynamics has a crucial economic impact and involves several engineering problems such as wear of braking friction components, energy efficiency, thermal load on components, level of safety under degraded or adhesion conditions (often constrained by the current regulation in force on signalling or other safety-related subsystem). In fact, the application of energy storage systems can lead to an efficiency improvement of at least 10% while, as regards the wear reduction, the improvement due to distributed traction systems and to optimised traction devices can be quantified in about 50%. In this work, an innovative integrated procedure is proposed by the authors to optimise longitudinal train dynamics and traction and braking manoeuvres in terms of both energy and wear. The new approach has been applied to existing test cases and validated with experimental data provided by Breda and, for some components and their homologation process, the results of experimental activities derive from cooperation performed with relevant industrial partners such as Trenitalia and Italcertifer. In particular, simulation results are referred to the simulation tests performed on a high-speed train (Ansaldo Breda Emu V250) and on a tram (Ansaldo Breda Sirio Tram). The proposed approach is based on a modular simulation platform in which the sub-models corresponding to different subsystems can be easily customised, depending on the considered application, on the availability of technical data and on the homologation process of different components.

Pathway activity inference for multiclass disease classification through a mathematical programming optimisation framework.

PubMed

Yang, Lingjian; Ainali, Chrysanthi; Tsoka, Sophia; Papageorgiou, Lazaros G

2014-12-05

Applying machine learning methods on microarray gene expression profiles for disease classification problems is a popular method to derive biomarkers, i.e. sets of genes that can predict disease state or outcome. Traditional approaches where expression of genes were treated independently suffer from low prediction accuracy and difficulty of biological interpretation. Current research efforts focus on integrating information on protein interactions through biochemical pathway datasets with expression profiles to propose pathway-based classifiers that can enhance disease diagnosis and prognosis. As most of the pathway activity inference methods in literature are either unsupervised or applied on two-class datasets, there is good scope to address such limitations by proposing novel methodologies. A supervised multiclass pathway activity inference method using optimisation techniques is reported. For each pathway expression dataset, patterns of its constituent genes are summarised into one composite feature, termed pathway activity, and a novel mathematical programming model is proposed to infer this feature as a weighted linear summation of expression of its constituent genes. Gene weights are determined by the optimisation model, in a way that the resulting pathway activity has the optimal discriminative power with regards to disease phenotypes. Classification is then performed on the resulting low-dimensional pathway activity profile. The model was evaluated through a variety of published gene expression profiles that cover different types of disease. We show that not only does it improve classification accuracy, but it can also perform well in multiclass disease datasets, a limitation of other approaches from the literature. Desirable features of the model include the ability to control the maximum number of genes that may participate in determining pathway activity, which may be pre-specified by the user. Overall, this work highlights the potential of building pathway-based multi-phenotype classifiers for accurate disease diagnosis and prognosis problems.

Modelling and strategy optimisation for a kind of networked evolutionary games with memories under the bankruptcy mechanism

NASA Astrophysics Data System (ADS)

Fu, Shihua; Li, Haitao; Zhao, Guodong

2018-05-01

This paper investigates the evolutionary dynamic and strategy optimisation for a kind of networked evolutionary games whose strategy updating rules incorporate 'bankruptcy' mechanism, and the situation that each player's bankruptcy is due to the previous continuous low profits gaining from the game is considered. First, by using semi-tensor product of matrices method, the evolutionary dynamic of this kind of games is expressed as a higher order logical dynamic system and then converted into its algebraic form, based on which, the evolutionary dynamic of the given games can be discussed. Second, the strategy optimisation problem is investigated, and some free-type control sequences are designed to maximise the total payoff of the whole game. Finally, an illustrative example is given to show that our new results are very effective.

Efficient characterisation of large deviations using population dynamics

NASA Astrophysics Data System (ADS)

Brewer, Tobias; Clark, Stephen R.; Bradford, Russell; Jack, Robert L.

2018-05-01

We consider population dynamics as implemented by the cloning algorithm for analysis of large deviations of time-averaged quantities. We use the simple symmetric exclusion process with periodic boundary conditions as a prototypical example and investigate the convergence of the results with respect to the algorithmic parameters, focussing on the dynamical phase transition between homogeneous and inhomogeneous states, where convergence is relatively difficult to achieve. We discuss how the performance of the algorithm can be optimised, and how it can be efficiently exploited on parallel computing platforms.

Optimization of physical conditions for the production of thermostable T1 lipase in Pichia guilliermondii strain SO using response surface methodology.

PubMed

Abu, Mary Ladidi; Nooh, Hisham Mohd; Oslan, Siti Nurbaya; Salleh, Abu Bakar

2017-11-10

Pichia guilliermondii was found capable of expressing the recombinant thermostable lipase without methanol under the control of methanol dependent alcohol oxidase 1 promoter (AOXp 1). In this study, statistical approaches were employed for the screening and optimisation of physical conditions for T1 lipase production in P. guilliermondii. The screening of six physical conditions by Plackett-Burman Design has identified pH, inoculum size and incubation time as exerting significant effects on lipase production. These three conditions were further optimised using, Box-Behnken Design of Response Surface Methodology, which predicted an optimum medium comprising pH 6, 24 h incubation time and 2% inoculum size. T1 lipase activity of 2.0 U/mL was produced with a biomass of OD 600 23.0. The process of using RSM for optimisation yielded a 3-fold increase of T1 lipase over medium before optimisation. Therefore, this result has proven that T1 lipase can be produced at a higher yield in P. guilliermondii.

Highly active promoters and native secretion signals for protein production during extremely low growth rates in Aspergillus niger.

PubMed

Wanka, Franziska; Arentshorst, Mark; Cairns, Timothy C; Jørgensen, Thomas; Ram, Arthur F J; Meyer, Vera

2016-08-20

The filamentous ascomycete Aspergillus niger is used in many industrial processes for the production of enzymes and organic acids by batch and fed-batch cultivation. An alternative technique is continuous cultivation, which promises improved yield and optimized pipeline efficiency. In this work, we have used perfusion (retentostat) cultivation to validate two promoters that are suitable for A. niger continuous cultivation of industrially relevant products. Firstly, promoters of genes encoding either an antifungal protein (Panafp) or putative hydrophobin (PhfbD) were confirmed as active throughout retentostat culture by assessing mRNA and protein levels using a luciferase (mluc) reporter system. This demonstrated the anafp promoter mediates a high but temporally variable expression profile, whereas the hfbD promoter mediates a semi-constant, moderate-to-high protein expression during retentostat culture. In order to assess whether these promoters were suitable to produce heterologous proteins during retentostat cultivation, the secreted antifungal protein (AFP) from Aspergillus giganteus, which has many potential biotechnological applications, was expressed in A. niger during retentostat cultivation. Additionally, this assay was used to concomitantly validate that native secretion signals encoded in anafp and hfbD genes can be harnessed for secretion of heterologous proteins. Afp mRNA and protein abundance were comparable to luciferase measurements throughout retentostat cultivation, validating the use of Panafp and PhfbD for perfusion cultivation. Finally, a gene encoding the highly commercially relevant thermal hysteresis protein (THP) was expressed in this system, which did not yield detectable protein. Both hfbD and anafp promoters are suitable for production of useful products in A. niger during perfusion cultivation. These findings provide a platform for further optimisations for high production of heterologous proteins with industrial relevance.

Understanding ageing in older Australians: The contribution of the Dynamic Analyses to Optimise Ageing (DYNOPTA) project to the evidenced base and policy

PubMed Central

Anstey, Kaarin J; Bielak, Allison AM; Birrell, Carole L; Browning, Colette J; Burns, Richard A; Byles, Julie; Kiley, Kim M; Nepal, Binod; Ross, Lesley A; Steel, David; Windsor, Timothy D

2014-01-01

Aim To describe the Dynamic Analyses to Optimise Ageing (DYNOPTA) project and illustrate its contributions to understanding ageing through innovative methodology, and investigations on outcomes based on the project themes. DYNOPTA provides a platform and technical expertise that may be used to combine other national and international datasets. Method The DYNOPTA project has pooled and harmonized data from nine Australian longitudinal studies to create the largest available longitudinal dataset (N=50652) on ageing in Australia. Results A range of findings have resulted from the study to date, including methodological advances, prevalence rates of disease and disability, and mapping trajectories of ageing with and without increasing morbidity. DYNOPTA also forms the basis of a microsimulation model that will provide projections of future costs of disease and disability for the baby boomer cohort. Conclusion DYNOPTA contributes significantly to the Australian evidence-base on ageing to inform key social and health policy domains. PMID:22032767

A software platform for phase contrast x-ray breast imaging research.

PubMed

Bliznakova, K; Russo, P; Mettivier, G; Requardt, H; Popov, P; Bravin, A; Buliev, I

2015-06-01

To present and validate a computer-based simulation platform dedicated for phase contrast x-ray breast imaging research. The software platform, developed at the Technical University of Varna on the basis of a previously validated x-ray imaging software simulator, comprises modules for object creation and for x-ray image formation. These modules were updated to take into account the refractive index for phase contrast imaging as well as implementation of the Fresnel-Kirchhoff diffraction theory of the propagating x-ray waves. Projection images are generated in an in-line acquisition geometry. To test and validate the platform, several phantoms differing in their complexity were constructed and imaged at 25 keV and 60 keV at the beamline ID17 of the European Synchrotron Radiation Facility. The software platform was used to design computational phantoms that mimic those used in the experimental study and to generate x-ray images in absorption and phase contrast modes. The visual and quantitative results of the validation process showed an overall good correlation between simulated and experimental images and show the potential of this platform for research in phase contrast x-ray imaging of the breast. The application of the platform is demonstrated in a feasibility study for phase contrast images of complex inhomogeneous and anthropomorphic breast phantoms, compared to x-ray images generated in absorption mode. The improved visibility of mammographic structures suggests further investigation and optimisation of phase contrast x-ray breast imaging, especially when abnormalities are present. The software platform can be exploited also for educational purposes. Copyright © 2015 Elsevier Ltd. All rights reserved.

Sputnik: a database platform for comparative plant genomics.

PubMed

Rudd, Stephen; Mewes, Hans-Werner; Mayer, Klaus F X

2003-01-01

Two million plant ESTs, from 20 different plant species, and totalling more than one 1000 Mbp of DNA sequence, represents a formidable transcriptomic resource. Sputnik uses the potential of this sequence resource to fill some of the information gap in the un-sequenced plant genomes and to serve as the foundation for in silicio comparative plant genomics. The complexity of the individual EST collections has been reduced using optimised EST clustering techniques. Annotation of cluster sequences is performed by exploiting and transferring information from the comprehensive knowledgebase already produced for the completed model plant genome (Arabidopsis thaliana) and by performing additional state of-the-art sequence analyses relevant to today's plant biologist. Functional predictions, comparative analyses and associative annotations for 500 000 plant EST derived peptides make Sputnik (http://mips.gsf.de/proj/sputnik/) a valid platform for contemporary plant genomics.

Sputnik: a database platform for comparative plant genomics

PubMed Central

Rudd, Stephen; Mewes, Hans-Werner; Mayer, Klaus F.X.

2003-01-01

Two million plant ESTs, from 20 different plant species, and totalling more than one 1000 Mbp of DNA sequence, represents a formidable transcriptomic resource. Sputnik uses the potential of this sequence resource to fill some of the information gap in the un-sequenced plant genomes and to serve as the foundation for in silicio comparative plant genomics. The complexity of the individual EST collections has been reduced using optimised EST clustering techniques. Annotation of cluster sequences is performed by exploiting and transferring information from the comprehensive knowledgebase already produced for the completed model plant genome (Arabidopsis thaliana) and by performing additional state of-the-art sequence analyses relevant to today's plant biologist. Functional predictions, comparative analyses and associative annotations for 500 000 plant EST derived peptides make Sputnik (http://mips.gsf.de/proj/sputnik/) a valid platform for contemporary plant genomics. PMID:12519965

Investigating the Trade-Off Between Power Generation and Environmental Impact of Tidal-Turbine Arrays Using Array Layout Optimisation and Habitat Sustainability Modelling.

NASA Astrophysics Data System (ADS)

du Feu, R. J.; Funke, S. W.; Kramer, S. C.; Hill, J.; Piggott, M. D.

2016-12-01

The installation of tidal turbines into the ocean will inevitably affect the environment around them. However, due to the relative infancy of this sector the extent and severity of such effects is unknown. The layout of an array of turbines is an important factor in determining not only the array's final yield but also how it will influence regional hydrodynamics. This in turn could affect, for example, sediment transportation or habitat suitability. The two potentially competing objectives of extracting energy from the tidal current, and of limiting any environmental impact consequent to influencing that current, are investigated here. This relationship is posed as a multi-objective optimisation problem. OpenTidalFarm, an array layout optimisation tool, and MaxEnt, habitat sustainability modelling software, are used to evaluate scenarios off the coast of the UK. MaxEnt is used to estimate the likelihood of finding a species in a given location based upon environmental input data and presence data of the species. Environmental features which are known to impact habitat, specifically those affected by the presence of an array, such as bed shear stress, are chosen as inputs. MaxEnt then uses a maximum-entropy modelling approach to estimate population distribution across the modelled area. OpenTidalFarm is used to maximise the power generated by an array, or multiple arrays, through adjusting the position and number of turbines within them. It uses a 2D shallow water model with turbine arrays represented as adjustable friction fields. It has the capability to also optimise for user created functionals that can be expressed mathematically. This work uses two functionals; power extracted by the array, and the suitability of habitat as predicted by MaxEnt. A gradient-based local optimisation is used to adjust the array layout at each iteration. This work presents arrays that are optimised for both yield and the viability of habitat for chosen species. In each scenario studied, a range of array formations is found expressing varying preferences for either functional. Further analyses then allow for the identification of trade-offs between the two key societal objectives of energy production and conservation. This in turn produces information valuable to stakeholders and policymakers when making decisions on array design.

Modulation aware cluster size optimisation in wireless sensor networks

NASA Astrophysics Data System (ADS)

Sriram Naik, M.; Kumar, Vinay

2017-07-01

Wireless sensor networks (WSNs) play a great role because of their numerous advantages to the mankind. The main challenge with WSNs is the energy efficiency. In this paper, we have focused on the energy minimisation with the help of cluster size optimisation along with consideration of modulation effect when the nodes are not able to communicate using baseband communication technique. Cluster size optimisations is important technique to improve the performance of WSNs. It provides improvement in energy efficiency, network scalability, network lifetime and latency. We have proposed analytical expression for cluster size optimisation using traditional sensing model of nodes for square sensing field with consideration of modulation effects. Energy minimisation can be achieved by changing the modulation schemes such as BPSK, 16-QAM, QPSK, 64-QAM, etc., so we are considering the effect of different modulation techniques in the cluster formation. The nodes in the sensing fields are random and uniformly deployed. It is also observed that placement of base station at centre of scenario enables very less number of modulation schemes to work in energy efficient manner but when base station placed at the corner of the sensing field, it enable large number of modulation schemes to work in energy efficient manner.

Optimal bioprocess design through a gene regulatory network - growth kinetic hybrid model: Towards Replacing Monod kinetics.

PubMed

Tsipa, Argyro; Koutinas, Michalis; Usaku, Chonlatep; Mantalaris, Athanasios

2018-05-02

Currently, design and optimisation of biotechnological bioprocesses is performed either through exhaustive experimentation and/or with the use of empirical, unstructured growth kinetics models. Whereas, elaborate systems biology approaches have been recently explored, mixed-substrate utilisation is predominantly ignored despite its significance in enhancing bioprocess performance. Herein, bioprocess optimisation for an industrially-relevant bioremediation process involving a mixture of highly toxic substrates, m-xylene and toluene, was achieved through application of a novel experimental-modelling gene regulatory network - growth kinetic (GRN-GK) hybrid framework. The GRN model described the TOL and ortho-cleavage pathways in Pseudomonas putida mt-2 and captured the transcriptional kinetics expression patterns of the promoters. The GRN model informed the formulation of the growth kinetics model replacing the empirical and unstructured Monod kinetics. The GRN-GK framework's predictive capability and potential as a systematic optimal bioprocess design tool, was demonstrated by effectively predicting bioprocess performance, which was in agreement with experimental values, when compared to four commonly used models that deviated significantly from the experimental values. Significantly, a fed-batch biodegradation process was designed and optimised through the model-based control of TOL Pr promoter expression resulting in 61% and 60% enhanced pollutant removal and biomass formation, respectively, compared to the batch process. This provides strong evidence of model-based bioprocess optimisation at the gene level, rendering the GRN-GK framework as a novel and applicable approach to optimal bioprocess design. Finally, model analysis using global sensitivity analysis (GSA) suggests an alternative, systematic approach for model-driven strain modification for synthetic biology and metabolic engineering applications. Copyright © 2018. Published by Elsevier Inc.

DNA vaccination for cervical cancer: Strategic optimisation of RALA mediated gene delivery from a biodegradable microneedle system.

PubMed

Cole, Grace; Ali, Ahlam A; McCrudden, Cian M; McBride, John W; McCaffrey, Joanne; Robson, Tracy; Kett, Vicky L; Dunne, Nicholas J; Donnelly, Ryan F; McCarthy, Helen O

2018-06-01

Dissolvable microneedles can be employed to deliver DNA to antigen presenting cells within the skin. However, this technology faces two main challenges: the poor transfection efficacy of pDNA following release from the microneedle matrix, and the limited loading capacity of the micron-scale devices. Two-tier delivery systems combining microneedle platforms and DNA delivery vectors have increased efficacy but the challenge of increasing the loading capacity remains. This study utilised lyophilisation to increase the loading of RALA/pDNA nanoparticles within dissolvable PVA microneedles. As a result, delivery was significantly enhanced in vivo into an appropriate range for DNA vaccination (∼50 μg per array). Furthermore, modifying the manufacturing process was not detrimental to the microneedle mechanical properties or cargo functionality. It was demonstrated that arrays retained mechanical and functional stability over short term storage, and were able to elicit gene expression in vitro and in vivo. Finally, treatment with this novel formulation significantly retarded the growth of established tumours, and proved superior to standard intramuscular injection in a preclinical model of cervical cancer. Copyright © 2018 Elsevier B.V. All rights reserved.

Offshore Energy Mapping for Northeast Atlantic and Mediterranean: MARINA PLATFORM project

NASA Astrophysics Data System (ADS)

Kallos, G.; Galanis, G.; Spyrou, C.; Kalogeri, C.; Adam, A.; Athanasiadis, P.

2012-04-01

Deep offshore ocean energy mapping requires detailed modeling of the wind, wave, tidal and ocean circulation estimations. It requires also detailed mapping of the associated extremes. An important issue in such work is the co-generation of energy (generation of wind, wave, tides, currents) in order to design platforms on an efficient way. For example wind and wave fields exhibit significant phase differences and therefore the produced energy from both sources together requires special analysis. The other two sources namely tides and currents have different temporal scales from the previous two. Another important issue is related to the estimation of the environmental frequencies in order to avoid structural problems. These are issues studied at the framework of the FP7 project MARINA PLATFORM. The main objective of the project is to develop deep water structures that can exploit the energy from wind, wave, tidal and ocean current energy sources. In particular, a primary goal will be the establishment of a set of equitable and transparent criteria for the evaluation of multi-purpose platforms for marine renewable energy. Using these criteria, a novel system set of design and optimisation tools will be produced addressing new platform design, component engineering, risk assessment, spatial planning, platform-related grid connection concepts, all focussed on system integration and reducing costs. The University of Athens group is in charge for estimation and mapping of wind, wave, tidal and ocean current resources, estimate available energy potential, map extreme event characteristics and provide any additional environmental parameter required.

Efficient processing of multiple nested event pattern queries over multi-dimensional event streams based on a triaxial hierarchical model.

PubMed

Xiao, Fuyuan; Aritsugi, Masayoshi; Wang, Qing; Zhang, Rong

2016-09-01

For efficient and sophisticated analysis of complex event patterns that appear in streams of big data from health care information systems and support for decision-making, a triaxial hierarchical model is proposed in this paper. Our triaxial hierarchical model is developed by focusing on hierarchies among nested event pattern queries with an event concept hierarchy, thereby allowing us to identify the relationships among the expressions and sub-expressions of the queries extensively. We devise a cost-based heuristic by means of the triaxial hierarchical model to find an optimised query execution plan in terms of the costs of both the operators and the communications between them. According to the triaxial hierarchical model, we can also calculate how to reuse the results of the common sub-expressions in multiple queries. By integrating the optimised query execution plan with the reuse schemes, a multi-query optimisation strategy is developed to accomplish efficient processing of multiple nested event pattern queries. We present empirical studies in which the performance of multi-query optimisation strategy was examined under various stream input rates and workloads. Specifically, the workloads of pattern queries can be used for supporting monitoring patients' conditions. On the other hand, experiments with varying input rates of streams can correspond to changes of the numbers of patients that a system should manage, whereas burst input rates can correspond to changes of rushes of patients to be taken care of. The experimental results have shown that, in Workload 1, our proposal can improve about 4 and 2 times throughput comparing with the relative works, respectively; in Workload 2, our proposal can improve about 3 and 2 times throughput comparing with the relative works, respectively; in Workload 3, our proposal can improve about 6 times throughput comparing with the relative work. The experimental results demonstrated that our proposal was able to process complex queries efficiently which can support health information systems and further decision-making. Copyright © 2016 Elsevier B.V. All rights reserved.

The chemiluminescence based Ziplex automated workstation focus array reproduces ovarian cancer Affymetrix GeneChip expression profiles.

PubMed

Quinn, Michael C J; Wilson, Daniel J; Young, Fiona; Dempsey, Adam A; Arcand, Suzanna L; Birch, Ashley H; Wojnarowicz, Paulina M; Provencher, Diane; Mes-Masson, Anne-Marie; Englert, David; Tonin, Patricia N

2009-07-06

As gene expression signatures may serve as biomarkers, there is a need to develop technologies based on mRNA expression patterns that are adaptable for translational research. Xceed Molecular has recently developed a Ziplex technology, that can assay for gene expression of a discrete number of genes as a focused array. The present study has evaluated the reproducibility of the Ziplex system as applied to ovarian cancer research of genes shown to exhibit distinct expression profiles initially assessed by Affymetrix GeneChip analyses. The new chemiluminescence-based Ziplex gene expression array technology was evaluated for the expression of 93 genes selected based on their Affymetrix GeneChip profiles as applied to ovarian cancer research. Probe design was based on the Affymetrix target sequence that favors the 3' UTR of transcripts in order to maximize reproducibility across platforms. Gene expression analysis was performed using the Ziplex Automated Workstation. Statistical analyses were performed to evaluate reproducibility of both the magnitude of expression and differences between normal and tumor samples by correlation analyses, fold change differences and statistical significance testing. Expressions of 82 of 93 (88.2%) genes were highly correlated (p < 0.01) in a comparison of the two platforms. Overall, 75 of 93 (80.6%) genes exhibited consistent results in normal versus tumor tissue comparisons for both platforms (p < 0.001). The fold change differences were concordant for 87 of 93 (94%) genes, where there was agreement between the platforms regarding statistical significance for 71 (76%) of 87 genes. There was a strong agreement between the two platforms as shown by comparisons of log2 fold differences of gene expression between tumor versus normal samples (R = 0.93) and by Bland-Altman analysis, where greater than 90% of expression values fell within the 95% limits of agreement. Overall concordance of gene expression patterns based on correlations, statistical significance between tumor and normal ovary data, and fold changes was consistent between the Ziplex and Affymetrix platforms. The reproducibility and ease-of-use of the technology suggests that the Ziplex array is a suitable platform for translational research.

Design and Development of ChemInfoCloud: An Integrated Cloud Enabled Platform for Virtual Screening.

PubMed

Karthikeyan, Muthukumarasamy; Pandit, Deepak; Bhavasar, Arvind; Vyas, Renu

2015-01-01

The power of cloud computing and distributed computing has been harnessed to handle vast and heterogeneous data required to be processed in any virtual screening protocol. A cloud computing platorm ChemInfoCloud was built and integrated with several chemoinformatics and bioinformatics tools. The robust engine performs the core chemoinformatics tasks of lead generation, lead optimisation and property prediction in a fast and efficient manner. It has also been provided with some of the bioinformatics functionalities including sequence alignment, active site pose prediction and protein ligand docking. Text mining, NMR chemical shift (1H, 13C) prediction and reaction fingerprint generation modules for efficient lead discovery are also implemented in this platform. We have developed an integrated problem solving cloud environment for virtual screening studies that also provides workflow management, better usability and interaction with end users using container based virtualization, OpenVz.

Fast multi-core based multimodal registration of 2D cross-sections and 3D datasets.

PubMed

Scharfe, Michael; Pielot, Rainer; Schreiber, Falk

2010-01-11

Solving bioinformatics tasks often requires extensive computational power. Recent trends in processor architecture combine multiple cores into a single chip to improve overall performance. The Cell Broadband Engine (CBE), a heterogeneous multi-core processor, provides power-efficient and cost-effective high-performance computing. One application area is image analysis and visualisation, in particular registration of 2D cross-sections into 3D image datasets. Such techniques can be used to put different image modalities into spatial correspondence, for example, 2D images of histological cuts into morphological 3D frameworks. We evaluate the CBE-driven PlayStation 3 as a high performance, cost-effective computing platform by adapting a multimodal alignment procedure to several characteristic hardware properties. The optimisations are based on partitioning, vectorisation, branch reducing and loop unrolling techniques with special attention to 32-bit multiplies and limited local storage on the computing units. We show how a typical image analysis and visualisation problem, the multimodal registration of 2D cross-sections and 3D datasets, benefits from the multi-core based implementation of the alignment algorithm. We discuss several CBE-based optimisation methods and compare our results to standard solutions. More information and the source code are available from http://cbe.ipk-gatersleben.de. The results demonstrate that the CBE processor in a PlayStation 3 accelerates computational intensive multimodal registration, which is of great importance in biological/medical image processing. The PlayStation 3 as a low cost CBE-based platform offers an efficient option to conventional hardware to solve computational problems in image processing and bioinformatics.

Signal Enhancement Strategies for Refractive Index-Sensitive Nanobiosensor.

PubMed

Syahir, Amir; Kajikawa, Kotaro; Mihara, Hisakazu

2018-01-01

Direct bio-monitoring essentially involves optical means since photon has insignificant effects over biomolecules. Over the years, laser induced surface Plasmon resonance method with various modifications as well as versatile localized Plasmon excited by incoherent light have facilitated in recording many nanobiological activities. Yet, monitoring interactions of small molecules including drugs requires signal amplification and improvement on signal-to-noise ratio. This paper focused on how the refractive index based nanobio-sensoring gold platform can produce more efficient, adaptable and more practical detection techniques to observe molecular interactions at high degree of sensitivity. It discusses surface chemistry approach, optimisation of the refractive index of gold platform and manipulation of gold geometry augmenting signal quality. In a normal-incidence reflectivity, r0 can be calculated using the Fresnel equation. Particularly at λ = 470 nm the ratio of r / r0 showed significant amplitude reduction mainly stemmed from the imaginary part of the Au refractive index. Hence, the fraction of reduction, Δr = 1 - r / r0. Experimentally, in a common reference frame reflectivity of a bare gold surface, R0 is compared with the reflectivity of gold surface in the presence of biolayer, R. The reduction rate (%) of reflectivity, ΔR = 1 - R / R0 is denoted as the AR signal. The method therefore enables quantitative measurement of the surface-bound protein by converting ΔR to the thickness, d, and subsequently the protein mass. We discussed four strategies to improve the AR signal by changing the effective refractive index of the biosensing platform. They are; a) Thickness optimisation of Au thin layer, b) Au / Ag bimetallic layer, c) composing alloy or Au composite, and d) Au thinlayer with nano or micro holes. As the result we successfully 'move' the refractive index, ε of the AR platform (gold only) to ε = -0.948 + 3.455i, a higher sensitivity platform. This was done by composing Au-Ag2O composite with ratio = 1:1. The results were compared to the potential sensitivity improvement of the AR substrate using other that could be done by further tailoring the ε advanced method. We suggested four strategies in order to realize this purpose. It is apparent that sensitivity has been improved through Au/Ag bimetallic layer or Au-Ag2O composite thin layer, This study is an important step towards fabrication of sensitive surface for detection of biomolecular interactions. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

On-line data collection platform for national dose surveys in diagnostic and interventional radiology.

PubMed

Vassileva, J; Simeonov, F; Avramova-Cholakova, S

2015-07-01

According to the Bulgarian regulation for radiation protection at medical exposure, the National Centre of Radiobiology and Radiation Protection (NCRRP) is responsible for performing national dose surveys in diagnostic and interventional radiology and nuclear medicine and for establishing of national diagnostic reference levels (DRLs). The next national dose survey is under preparation to be performed in the period of 2015-16, with the aim to cover conventional radiography, mammography, conventional fluoroscopy, interventional and fluoroscopy guided procedures and CT. It will be performed electronically using centralised on-line data collection platform established by the NCRRP. The aim is to increase the response rate and to improve the accuracy by reducing human errors. The concept of the on-line dose data collection platform is presented. Radiological facilities are provided with a tool to determine local typical patient doses, and the NCRRP to establish national DRLs. Future work will include automatic retrieval of dose data from hospital picture archival and communicating system. The on-line data collection platform is expected to facilitate the process of dose audit and optimisation of radiological procedures in Bulgarian hospitals. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Strategies for comparing gene expression profiles from different microarray platforms: application to a case-control experiment.

PubMed

Severgnini, Marco; Bicciato, Silvio; Mangano, Eleonora; Scarlatti, Francesca; Mezzelani, Alessandra; Mattioli, Michela; Ghidoni, Riccardo; Peano, Clelia; Bonnal, Raoul; Viti, Federica; Milanesi, Luciano; De Bellis, Gianluca; Battaglia, Cristina

2006-06-01

Meta-analysis of microarray data is increasingly important, considering both the availability of multiple platforms using disparate technologies and the accumulation in public repositories of data sets from different laboratories. We addressed the issue of comparing gene expression profiles from two microarray platforms by devising a standardized investigative strategy. We tested this procedure by studying MDA-MB-231 cells, which undergo apoptosis on treatment with resveratrol. Gene expression profiles were obtained using high-density, short-oligonucleotide, single-color microarray platforms: GeneChip (Affymetrix) and CodeLink (Amersham). Interplatform analyses were carried out on 8414 common transcripts represented on both platforms, as identified by LocusLink ID, representing 70.8% and 88.6% of annotated GeneChip and CodeLink features, respectively. We identified 105 differentially expressed genes (DEGs) on CodeLink and 42 DEGs on GeneChip. Among them, only 9 DEGs were commonly identified by both platforms. Multiple analyses (BLAST alignment of probes with target sequences, gene ontology, literature mining, and quantitative real-time PCR) permitted us to investigate the factors contributing to the generation of platform-dependent results in single-color microarray experiments. An effective approach to cross-platform comparison involves microarrays of similar technologies, samples prepared by identical methods, and a standardized battery of bioinformatic and statistical analyses.

Evaluation of high throughput gene expression platforms using a genomic biomarker signature for prediction of skin sensitization.

PubMed

Forreryd, Andy; Johansson, Henrik; Albrekt, Ann-Sofie; Lindstedt, Malin

2014-05-16

Allergic contact dermatitis (ACD) develops upon exposure to certain chemical compounds termed skin sensitizers. To reduce the occurrence of skin sensitizers, chemicals are regularly screened for their capacity to induce sensitization. The recently developed Genomic Allergen Rapid Detection (GARD) assay is an in vitro alternative to animal testing for identification of skin sensitizers, classifying chemicals by evaluating transcriptional levels of a genomic biomarker signature. During assay development and biomarker identification, genome-wide expression analysis was applied using microarrays covering approximately 30,000 transcripts. However, the microarray platform suffers from drawbacks in terms of low sample throughput, high cost per sample and time consuming protocols and is a limiting factor for adaption of GARD into a routine assay for screening of potential sensitizers. With the purpose to simplify assay procedures, improve technical parameters and increase sample throughput, we assessed the performance of three high throughput gene expression platforms--nCounter®, BioMark HD™ and OpenArray®--and correlated their performance metrics against our previously generated microarray data. We measured the levels of 30 transcripts from the GARD biomarker signature across 48 samples. Detection sensitivity, reproducibility, correlations and overall structure of gene expression measurements were compared across platforms. Gene expression data from all of the evaluated platforms could be used to classify most of the sensitizers from non-sensitizers in the GARD assay. Results also showed high data quality and acceptable reproducibility for all platforms but only medium to poor correlations of expression measurements across platforms. In addition, evaluated platforms were superior to the microarray platform in terms of cost efficiency, simplicity of protocols and sample throughput. We evaluated the performance of three non-array based platforms using a limited set of transcripts from the GARD biomarker signature. We demonstrated that it was possible to achieve acceptable discriminatory power in terms of separation between sensitizers and non-sensitizers in the GARD assay while reducing assay costs, simplify assay procedures and increase sample throughput by using an alternative platform, providing a first step towards the goal to prepare GARD for formal validation and adaption of the assay for industrial screening of potential sensitizers.

Stably engineered nanobubbles and ultrasound - An effective platform for enhanced macromolecular delivery to representative cells of the retina.

PubMed

Thakur, Sachin S; Ward, Micheal S; Popat, Amirali; Flemming, Nicole B; Parat, Marie-Odile; Barnett, Nigel L; Parekh, Harendra S

2017-01-01

Herein we showcase the potential of ultrasound-responsive nanobubbles in enhancing macromolecular permeation through layers of the retina, ultimately leading to significant and direct intracellular delivery; this being effectively demonstrated across three relevant and distinct retinal cell lines. Stably engineered nanobubbles of a highly homogenous and echogenic nature were fully characterised using dynamic light scattering, B-scan ultrasound and transmission electron microscopy (TEM). The nanobubbles appeared as spherical liposome-like structures under TEM, accompanied by an opaque luminal core and darkened corona around their periphery, with both features indicative of efficient gas entrapment and adsorption, respectively. A nanobubble +/- ultrasound sweeping study was conducted next, which determined the maximum tolerated dose for each cell line. Detection of underlying cellular stress was verified using the biomarker heat shock protein 70, measured before and after treatment with optimised ultrasound. Next, with safety to nanobubbles and optimised ultrasound demonstrated, each human or mouse-derived cell population was incubated with biotinylated rabbit-IgG in the presence and absence of ultrasound +/- nanobubbles. Intracellular delivery of antibody in each cell type was then quantified using Cy3-streptavidin. Nanobubbles and optimised ultrasound were found to be negligibly toxic across all cell lines tested. Macromolecular internalisation was achieved to significant, yet varying degrees in all three cell lines. The results of this study pave the way towards better understanding mechanisms underlying cellular responsiveness to ultrasound-triggered drug delivery in future ex vivo and in vivo models of the posterior eye.

Stably engineered nanobubbles and ultrasound - An effective platform for enhanced macromolecular delivery to representative cells of the retina

PubMed Central

Thakur, Sachin S.; Ward, Micheal S.; Popat, Amirali; Flemming, Nicole B.; Parat, Marie-Odile; Barnett, Nigel L.

2017-01-01

Herein we showcase the potential of ultrasound-responsive nanobubbles in enhancing macromolecular permeation through layers of the retina, ultimately leading to significant and direct intracellular delivery; this being effectively demonstrated across three relevant and distinct retinal cell lines. Stably engineered nanobubbles of a highly homogenous and echogenic nature were fully characterised using dynamic light scattering, B-scan ultrasound and transmission electron microscopy (TEM). The nanobubbles appeared as spherical liposome-like structures under TEM, accompanied by an opaque luminal core and darkened corona around their periphery, with both features indicative of efficient gas entrapment and adsorption, respectively. A nanobubble +/- ultrasound sweeping study was conducted next, which determined the maximum tolerated dose for each cell line. Detection of underlying cellular stress was verified using the biomarker heat shock protein 70, measured before and after treatment with optimised ultrasound. Next, with safety to nanobubbles and optimised ultrasound demonstrated, each human or mouse-derived cell population was incubated with biotinylated rabbit-IgG in the presence and absence of ultrasound +/- nanobubbles. Intracellular delivery of antibody in each cell type was then quantified using Cy3-streptavidin. Nanobubbles and optimised ultrasound were found to be negligibly toxic across all cell lines tested. Macromolecular internalisation was achieved to significant, yet varying degrees in all three cell lines. The results of this study pave the way towards better understanding mechanisms underlying cellular responsiveness to ultrasound-triggered drug delivery in future ex vivo and in vivo models of the posterior eye. PMID:28542473

Optimisation of multiplet identifier processing on a PLAYSTATION® 3

NASA Astrophysics Data System (ADS)

Hattori, Masami; Mizuno, Takashi

2010-02-01

To enable high-performance computing (HPC) for applications with large datasets using a Sony® PLAYSTATION® 3 (PS3™) video game console, we configured a hybrid system consisting of a Windows® PC and a PS3™. To validate this system, we implemented the real-time multiplet identifier (RTMI) application, which identifies multiplets of microearthquakes in terms of the similarity of their waveforms. The cross-correlation computation, which is a core algorithm of the RTMI application, was optimised for the PS3™ platform, while the rest of the computation, including data input and output remained on the PC. With this configuration, the core part of the algorithm ran 69 times faster than the original program, accelerating total computation speed more than five times. As a result, the system processed up to 2100 total microseismic events, whereas the original implementation had a limit of 400 events. These results indicate that this system enables high-performance computing for large datasets using the PS3™, as long as data transfer time is negligible compared with computation time.

Continuous measurement of breast tumor hormone receptor expression: a comparison of two computational pathology platforms

PubMed Central

Ahern, Thomas P.; Beck, Andrew H.; Rosner, Bernard A.; Glass, Ben; Frieling, Gretchen; Collins, Laura C.; Tamimi, Rulla M.

2017-01-01

Background Computational pathology platforms incorporate digital microscopy with sophisticated image analysis to permit rapid, continuous measurement of protein expression. We compared two computational pathology platforms on their measurement of breast tumor estrogen receptor (ER) and progesterone receptor (PR) expression. Methods Breast tumor microarrays from the Nurses’ Health Study were stained for ER (n=592) and PR (n=187). One expert pathologist scored cases as positive if ≥1% of tumor nuclei exhibited stain. ER and PR were then measured with the Definiens Tissue Studio (automated) and Aperio Digital Pathology (user-supervised) platforms. Platform-specific measurements were compared using boxplots, scatter plots, and correlation statistics. Classification of ER and PR positivity by platform-specific measurements was evaluated with areas under receiver operating characteristic curves (AUC) from univariable logistic regression models, using expert pathologist classification as the standard. Results Both platforms showed considerable overlap in continuous measurements of ER and PR between positive and negative groups classified by expert pathologist. Platform-specific measurements were strongly and positively correlated with one another (rho≥0.77). The user-supervised Aperio workflow performed slightly better than the automated Definiens workflow at classifying ER positivity (AUCAperio=0.97; AUCDefiniens=0.90; difference=0.07, 95% CI: 0.05, 0.09) and PR positivity (AUCAperio=0.94; AUCDefiniens=0.87; difference=0.07, 95% CI: 0.03, 0.12). Conclusion Paired hormone receptor expression measurements from two different computational pathology platforms agreed well with one another. The user-supervised workflow yielded better classification accuracy than the automated workflow. Appropriately validated computational pathology algorithms enrich molecular epidemiology studies with continuous protein expression data and may accelerate tumor biomarker discovery. PMID:27729430

On the performance of energy detection-based CR with SC diversity over IG channel

NASA Astrophysics Data System (ADS)

Verma, Pappu Kumar; Soni, Sanjay Kumar; Jain, Priyanka

2017-12-01

Cognitive radio (CR) is a viable 5G technology to address the scarcity of the spectrum. Energy detection-based sensing is known to be the simplest method as far as hardware complexity is concerned. In this paper, the performance of spectrum sensing-based energy detection technique in CR networks over inverse Gaussian channel for selection combining diversity technique is analysed. More specifically, accurate analytical expressions for the average detection probability under different detection scenarios such as single channel (no diversity) and with diversity reception are derived and evaluated. Further, the detection threshold parameter is optimised by minimising the probability of error over several diversity branches. The results clearly show the significant improvement in the probability of detection when optimised threshold parameter is applied. The impact of shadowing parameters on the performance of energy detector is studied in terms of complimentary receiver operating characteristic curve. To verify the correctness of our analysis, the derived analytical expressions are corroborated via exact result and Monte Carlo simulations.

A detailed transcript-level probe annotation reveals alternative splicing based microarray platform differences

PubMed Central

Lee, Joseph C; Stiles, David; Lu, Jun; Cam, Margaret C

2007-01-01

Background Microarrays are a popular tool used in experiments to measure gene expression levels. Improving the reproducibility of microarray results produced by different chips from various manufacturers is important to create comparable and combinable experimental results. Alternative splicing has been cited as a possible cause of differences in expression measurements across platforms, though no study to this point has been conducted to show its influence in cross-platform differences. Results Using probe sequence data, a new microarray probe/transcript annotation was created based on the AceView Aug05 release that allowed for the categorization of genes based on their expression measurements' susceptibility to alternative splicing differences across microarray platforms. Examining gene expression data from multiple platforms in light of the new categorization, genes unsusceptible to alternative splicing differences showed higher signal agreement than those genes most susceptible to alternative splicing differences. The analysis gave rise to a different probe-level visualization method that can highlight probe differences according to transcript specificity. Conclusion The results highlight the need for detailed probe annotation at the transcriptome level. The presence of alternative splicing within a given sample can affect gene expression measurements and is a contributing factor to overall technical differences across platforms. PMID:17708771

Public Health Platforms: An Emerging Informatics Approach to Health Professional Learning and Development

PubMed Central

Gray, Kathleen

2016-01-01

Health informatics has a major role to play in optimising the management and use of data, information and knowledge in health systems. As health systems undergo digital transformation, it is important to consider informatics approaches not only to curriculum content but also to the design of learning environments and learning activities for health professional learning and development. An example of such an informatics approach is the use of large-scale, integrated public health platforms on the Internet as part of health professional learning and development. This article describes selected examples of such platforms, with a focus on how they may influence the direction of health professional learning and development. Significance for public health The landscape of healthcare systems, public health systems, health research systems and professional education systems is fragmented, with many gaps and silos. More sophistication in the management of health data, information, and knowledge, based on public health informatics expertise, is needed to tackle key issues of prevention, promotion and policy-making. Platform technologies represent an emerging large-scale, highly integrated informatics approach to public health, combining the technologies of Internet, the web, the cloud, social technologies, remote sensing and/or mobile apps into an online infrastructure that can allow more synergies in work within and across these systems. Health professional curricula need updating so that the health workforce has a deep and critical understanding of the way that platform technologies are becoming the foundation of the health sector. PMID:27190977

Statistical analysis of an RNA titration series evaluates microarray precision and sensitivity on a whole-array basis

PubMed Central

Holloway, Andrew J; Oshlack, Alicia; Diyagama, Dileepa S; Bowtell, David DL; Smyth, Gordon K

2006-01-01

Background Concerns are often raised about the accuracy of microarray technologies and the degree of cross-platform agreement, but there are yet no methods which can unambiguously evaluate precision and sensitivity for these technologies on a whole-array basis. Results A methodology is described for evaluating the precision and sensitivity of whole-genome gene expression technologies such as microarrays. The method consists of an easy-to-construct titration series of RNA samples and an associated statistical analysis using non-linear regression. The method evaluates the precision and responsiveness of each microarray platform on a whole-array basis, i.e., using all the probes, without the need to match probes across platforms. An experiment is conducted to assess and compare four widely used microarray platforms. All four platforms are shown to have satisfactory precision but the commercial platforms are superior for resolving differential expression for genes at lower expression levels. The effective precision of the two-color platforms is improved by allowing for probe-specific dye-effects in the statistical model. The methodology is used to compare three data extraction algorithms for the Affymetrix platforms, demonstrating poor performance for the commonly used proprietary algorithm relative to the other algorithms. For probes which can be matched across platforms, the cross-platform variability is decomposed into within-platform and between-platform components, showing that platform disagreement is almost entirely systematic rather than due to measurement variability. Conclusion The results demonstrate good precision and sensitivity for all the platforms, but highlight the need for improved probe annotation. They quantify the extent to which cross-platform measures can be expected to be less accurate than within-platform comparisons for predicting disease progression or outcome. PMID:17118209

Optimising parameters for the differentiation of SH-SY5Y cells to study cell adhesion and cell migration.

PubMed

Dwane, Susan; Durack, Edel; Kiely, Patrick A

2013-09-11

Cell migration is a fundamental biological process and has an important role in the developing brain by regulating a highly specific pattern of connections between nerve cells. Cell migration is required for axonal guidance and neurite outgrowth and involves a series of highly co-ordinated and overlapping signalling pathways. The non-receptor tyrosine kinase, Focal Adhesion Kinase (FAK) has an essential role in development and is the most highly expressed kinase in the developing CNS. FAK activity is essential for neuronal cell adhesion and migration. The objective of this study was to optimise a protocol for the differentiation of the neuroblastoma cell line, SH-SY5Y. We determined the optimal extracellular matrix proteins and growth factor combinations required for the optimal differentiation of SH-SY5Y cells into neuronal-like cells and determined those conditions that induce the expression of FAK. It was confirmed that the cells were morphologically and biochemically differentiated when compared to undifferentiated cells. This is in direct contrast to commonly used differentiation methods that induce morphological differentiation but not biochemical differentiation. We conclude that we have optimised a protocol for the differentiation of SH-SY5Y cells that results in a cell population that is both morphologically and biochemically distinct from undifferentiated SH-SY5Y cells and has a distinct adhesion and spreading pattern and display extensive neurite outgrowth. This protocol will provide a neuronal model system for studying FAK activity during cell adhesion and migration events.

Fast multi-core based multimodal registration of 2D cross-sections and 3D datasets

PubMed Central

2010-01-01

Background Solving bioinformatics tasks often requires extensive computational power. Recent trends in processor architecture combine multiple cores into a single chip to improve overall performance. The Cell Broadband Engine (CBE), a heterogeneous multi-core processor, provides power-efficient and cost-effective high-performance computing. One application area is image analysis and visualisation, in particular registration of 2D cross-sections into 3D image datasets. Such techniques can be used to put different image modalities into spatial correspondence, for example, 2D images of histological cuts into morphological 3D frameworks. Results We evaluate the CBE-driven PlayStation 3 as a high performance, cost-effective computing platform by adapting a multimodal alignment procedure to several characteristic hardware properties. The optimisations are based on partitioning, vectorisation, branch reducing and loop unrolling techniques with special attention to 32-bit multiplies and limited local storage on the computing units. We show how a typical image analysis and visualisation problem, the multimodal registration of 2D cross-sections and 3D datasets, benefits from the multi-core based implementation of the alignment algorithm. We discuss several CBE-based optimisation methods and compare our results to standard solutions. More information and the source code are available from http://cbe.ipk-gatersleben.de. Conclusions The results demonstrate that the CBE processor in a PlayStation 3 accelerates computational intensive multimodal registration, which is of great importance in biological/medical image processing. The PlayStation 3 as a low cost CBE-based platform offers an efficient option to conventional hardware to solve computational problems in image processing and bioinformatics. PMID:20064262

Towards optimised information about clinical trials; identification and validation of key issues in collaboration with cancer patient advocates.

PubMed

Dellson, P; Nilbert, M; Bendahl, P-O; Malmström, P; Carlsson, C

2011-07-01

Clinical trials are crucial to improve cancer treatment but recruitment is difficult. Optimised patient information has been recognised as a key issue. In line with the increasing focus on patients' perspectives in health care, we aimed to study patients' opinions about the written information used in three clinical trials for breast cancer. Primary data collection was done in focus group interviews with breast cancer patient advocates. Content analysis identified three major themes: comprehensibility, emotions and associations, and decision making. Based on the advocates' suggestions for improvements, 21 key issues were defined and validated through a questionnaire in an independent group of breast cancer patient advocates. Clear messages, emotionally neutral expressions, careful descriptions of side effects, clear comparisons between different treatment alternatives and information about the possibility to discontinue treatment were perceived as the most important issues. Patients' views of the information in clinical trials provide new insights and identify key issues to consider in optimising future written information and may improve recruitment to clinical cancer trials. © 2010 Blackwell Publishing Ltd.

Species-specific vesicular monoamine transporter 2 (VMAT2) expression in mammalian pancreatic beta cells: implications for optimising radioligand-based human beta cell mass (BCM) imaging in animal models

PubMed Central

Hartwig, N. R.; Kalmbach, N.; Klietz, M.; Anlauf, M.; Eiden, L. E.; Weihe, E.

2014-01-01

Aims/hypothesis Imaging of beta cell mass (BCM) is a major challenge in diabetes research. The vesicular monoamine transporter 2 (VMAT2) is abundantly expressed in human beta cells. Radiolabelled analogues of tetrabenazine (TBZ; a low-molecular-weight, cell-permeant VMAT2-selective ligand) have been employed for pancreatic islet imaging in humans. Since reports on TBZ-based VMAT2 imaging in rodent pancreas have been fraught with confusion, we compared VMAT2 gene expression patterns in the mouse, rat, pig and human pancreas, to identify appropriate animal models with which to further validate and optimise TBZ imaging in humans. Methods We used a panel of highly sensitive VMAT2 antibodies developed against equivalently antigenic regions of the transporter from each species in combination with immunostaining for insulin and species-specific in situ hybridisation probes. Individual pancreatic islets were obtained by laser-capture microdissection and subjected to analysis of mRNA expression of VMAT2. Results The VMAT2 protein was not expressed in beta cells in the adult pancreas of common mouse or rat laboratory strains, in contrast to its expression in beta cells (but not other pancreatic endocrine cell types) in the pancreas of pigs and humans. VMAT2- and tyrosine hydroxylase co-positive (catecholaminergic) innervation was less abundant in humans than in rodents. VMAT2-positive mast cells were identified in the pancreas of all species. Conclusions/interpretation Primates and pigs are suitable models for TBZ imaging of beta cells. Rodents, because of a complete lack of VMAT2 expression in the endocrine pancreas, are a ‘null’ model for assessing interference with BCM measurements by VMAT2-positive mast cells and sympathetic innervation in the pancreas. PMID:23404442

Continuous measurement of breast tumour hormone receptor expression: a comparison of two computational pathology platforms.

PubMed

Ahern, Thomas P; Beck, Andrew H; Rosner, Bernard A; Glass, Ben; Frieling, Gretchen; Collins, Laura C; Tamimi, Rulla M

2017-05-01

Computational pathology platforms incorporate digital microscopy with sophisticated image analysis to permit rapid, continuous measurement of protein expression. We compared two computational pathology platforms on their measurement of breast tumour oestrogen receptor (ER) and progesterone receptor (PR) expression. Breast tumour microarrays from the Nurses' Health Study were stained for ER (n=592) and PR (n=187). One expert pathologist scored cases as positive if ≥1% of tumour nuclei exhibited stain. ER and PR were then measured with the Definiens Tissue Studio (automated) and Aperio Digital Pathology (user-supervised) platforms. Platform-specific measurements were compared using boxplots, scatter plots and correlation statistics. Classification of ER and PR positivity by platform-specific measurements was evaluated with areas under receiver operating characteristic curves (AUC) from univariable logistic regression models, using expert pathologist classification as the standard. Both platforms showed considerable overlap in continuous measurements of ER and PR between positive and negative groups classified by expert pathologist. Platform-specific measurements were strongly and positively correlated with one another (r≥0.77). The user-supervised Aperio workflow performed slightly better than the automated Definiens workflow at classifying ER positivity (AUC Aperio =0.97; AUC Definiens =0.90; difference=0.07, 95% CI 0.05 to 0.09) and PR positivity (AUC Aperio =0.94; AUC Definiens =0.87; difference=0.07, 95% CI 0.03 to 0.12). Paired hormone receptor expression measurements from two different computational pathology platforms agreed well with one another. The user-supervised workflow yielded better classification accuracy than the automated workflow. Appropriately validated computational pathology algorithms enrich molecular epidemiology studies with continuous protein expression data and may accelerate tumour biomarker discovery. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/.

aGEM: an integrative system for analyzing spatial-temporal gene-expression information

PubMed Central

Jiménez-Lozano, Natalia; Segura, Joan; Macías, José Ramón; Vega, Juanjo; Carazo, José María

2009-01-01

Motivation: The work presented here describes the ‘anatomical Gene-Expression Mapping (aGEM)’ Platform, a development conceived to integrate phenotypic information with the spatial and temporal distributions of genes expressed in the mouse. The aGEM Platform has been built by extending the Distributed Annotation System (DAS) protocol, which was originally designed to share genome annotations over the WWW. DAS is a client-server system in which a single client integrates information from multiple distributed servers. Results: The aGEM Platform provides information to answer three main questions. (i) Which genes are expressed in a given mouse anatomical component? (ii) In which mouse anatomical structures are a given gene or set of genes expressed? And (iii) is there any correlation among these findings? Currently, this Platform includes several well-known mouse resources (EMAGE, GXD and GENSAT), hosting gene-expression data mostly obtained from in situ techniques together with a broad set of image-derived annotations. Availability: The Platform is optimized for Firefox 3.0 and it is accessed through a friendly and intuitive display: http://agem.cnb.csic.es Contact: natalia@cnb.csic.es Supplementary information: Supplementary data are available at http://bioweb.cnb.csic.es/VisualOmics/aGEM/home.html and http://bioweb.cnb.csic.es/VisualOmics/index_VO.html and Bioinformatics online. PMID:19592395

Genome and epigenome engineering CRISPR toolkit for in vivo modulation of cis-regulatory interactions and gene expression in the chicken embryo.

PubMed

Williams, Ruth M; Senanayake, Upeka; Artibani, Mara; Taylor, Gunes; Wells, Daniel; Ahmed, Ahmed Ashour; Sauka-Spengler, Tatjana

2018-02-23

CRISPR/Cas9 genome engineering has revolutionised all aspects of biological research, with epigenome engineering transforming gene regulation studies. Here, we present an optimised, adaptable toolkit enabling genome and epigenome engineering in the chicken embryo, and demonstrate its utility by probing gene regulatory interactions mediated by neural crest enhancers. First, we optimise novel efficient guide-RNA mini expression vectors utilising chick U6 promoters, provide a strategy for rapid somatic gene knockout and establish a protocol for evaluation of mutational penetrance by targeted next-generation sequencing. We show that CRISPR/Cas9-mediated disruption of transcription factors causes a reduction in their cognate enhancer-driven reporter activity. Next, we assess endogenous enhancer function using both enhancer deletion and nuclease-deficient Cas9 (dCas9) effector fusions to modulate enhancer chromatin landscape, thus providing the first report of epigenome engineering in a developing embryo. Finally, we use the synergistic activation mediator (SAM) system to activate an endogenous target promoter. The novel genome and epigenome engineering toolkit developed here enables manipulation of endogenous gene expression and enhancer activity in chicken embryos, facilitating high-resolution analysis of gene regulatory interactions in vivo . © 2018. Published by The Company of Biologists Ltd.

Payload Instrument Design Rules for Safe and Efficient Flight Operations

NASA Astrophysics Data System (ADS)

Montagnon, E.; Ferri, P.

2004-04-01

Payload operations are often being neglected in favour of optimisation of scientific performance of the instrument design. This has major drawbacks in terms of cost, safety, efficiency of operations and finally science return. By taking operational aspects into account in the early phases of the instrument design, with a minimum more cultural than financial or technological additional effort, many problems can be avoided or minimized, with significant benefits to be gained in the mission execution phases. This paper presents possible improvements based on the use of the telemetry and telecommand packet standard, proper sharing of autonomy functions between instrument and platform, and enhanced interface documents.

The tensor network theory library

NASA Astrophysics Data System (ADS)

Al-Assam, S.; Clark, S. R.; Jaksch, D.

2017-09-01

In this technical paper we introduce the tensor network theory (TNT) library—an open-source software project aimed at providing a platform for rapidly developing robust, easy to use and highly optimised code for TNT calculations. The objectives of this paper are (i) to give an overview of the structure of TNT library, and (ii) to help scientists decide whether to use the TNT library in their research. We show how to employ the TNT routines by giving examples of ground-state and dynamical calculations of one-dimensional bosonic lattice system. We also discuss different options for gaining access to the software available at www.tensornetworktheory.org.

Optimisation of intradermal DNA electrotransfer for immunisation.

PubMed

Vandermeulen, Gaëlle; Staes, Edith; Vanderhaeghen, Marie Lise; Bureau, Michel Francis; Scherman, Daniel; Préat, Véronique

2007-12-04

The development of DNA vaccines requires appropriate delivery technologies. Electrotransfer is one of the most efficient methods of non-viral gene transfer. In the present study, intradermal DNA electrotransfer was first optimised. Strong effects of the injection method and the dose of DNA on luciferase expression were demonstrated. Pre-treatments were evaluated to enhance DNA diffusion in the skin but neither hyaluronidase injection nor iontophoresis improved efficiency of intradermal DNA electrotransfer. Then, DNA immunisation with a weakly immunogenic model antigen, luciferase, was investigated. After intradermal injection of the plasmid encoding luciferase, electrotransfer (HV 700 V/cm 100 micros, LV 200 V/cm 400 ms) was required to induce immune response. The response was Th1-shifted compared to immunisation with the luciferase recombinant protein. Finally, DNA electrotransfer in the skin, the muscle or the ear pinna was compared. Muscle DNA electrotransfer resulted in the highest luciferase expression and the best IgG response. Nevertheless electrotransfer into the skin, the muscle and the ear pinna all resulted in IFN-gamma secretion by luciferase-stimulated splenocytes suggesting that an efficient Th1 response was induced in all case.

Sybil--efficient constraint-based modelling in R.

PubMed

Gelius-Dietrich, Gabriel; Desouki, Abdelmoneim Amer; Fritzemeier, Claus Jonathan; Lercher, Martin J

2013-11-13

Constraint-based analyses of metabolic networks are widely used to simulate the properties of genome-scale metabolic networks. Publicly available implementations tend to be slow, impeding large scale analyses such as the genome-wide computation of pairwise gene knock-outs, or the automated search for model improvements. Furthermore, available implementations cannot easily be extended or adapted by users. Here, we present sybil, an open source software library for constraint-based analyses in R; R is a free, platform-independent environment for statistical computing and graphics that is widely used in bioinformatics. Among other functions, sybil currently provides efficient methods for flux-balance analysis (FBA), MOMA, and ROOM that are about ten times faster than previous implementations when calculating the effect of whole-genome single gene deletions in silico on a complete E. coli metabolic model. Due to the object-oriented architecture of sybil, users can easily build analysis pipelines in R or even implement their own constraint-based algorithms. Based on its highly efficient communication with different mathematical optimisation programs, sybil facilitates the exploration of high-dimensional optimisation problems on small time scales. Sybil and all its dependencies are open source. Sybil and its documentation are available for download from the comprehensive R archive network (CRAN).

Intracerebral transplants of primary muscle cells: a potential 'platform' for transgene expression in the brain

NASA Technical Reports Server (NTRS)

Jiao, S.; Schultz, E.; Wolff, J. A.

1992-01-01

After the transplantation of rat primary muscle cells into the caudate or cortex of recipient rats, the muscle cells were able to persist for at least 6 months. Muscle cells transfected with expression plasmids prior to transplantation were able to express reporter genes in the brains for at least 2 months. These results suggest that muscle cells might be a useful 'platform' for transgene expression in the brain.

Reprogramming Microbes for the Remote Detection of Environmental Threats

DTIC Science & Technology

2013-10-15

Riboswitches consist of an aptamer that recognizes the ligand and an expression platform that couples ligand binding to a change in gene expression. Using in...vitro selection, it is possible to screen large (~10^13 member) libraries of RNA sequences to discover new aptamers . However, limitations in...consist of an aptamer that recognizes the ligand and an expression platform that couples ligand binding to a change in gene expression. Using in

Optimising parameters for the differentiation of SH-SY5Y cells to study cell adhesion and cell migration

PubMed Central

2013-01-01

Background Cell migration is a fundamental biological process and has an important role in the developing brain by regulating a highly specific pattern of connections between nerve cells. Cell migration is required for axonal guidance and neurite outgrowth and involves a series of highly co-ordinated and overlapping signalling pathways. The non-receptor tyrosine kinase, Focal Adhesion Kinase (FAK) has an essential role in development and is the most highly expressed kinase in the developing CNS. FAK activity is essential for neuronal cell adhesion and migration. Results The objective of this study was to optimise a protocol for the differentiation of the neuroblastoma cell line, SH-SY5Y. We determined the optimal extracellular matrix proteins and growth factor combinations required for the optimal differentiation of SH-SY5Y cells into neuronal-like cells and determined those conditions that induce the expression of FAK. It was confirmed that the cells were morphologically and biochemically differentiated when compared to undifferentiated cells. This is in direct contrast to commonly used differentiation methods that induce morphological differentiation but not biochemical differentiation. Conclusions We conclude that we have optimised a protocol for the differentiation of SH-SY5Y cells that results in a cell population that is both morphologically and biochemically distinct from undifferentiated SH-SY5Y cells and has a distinct adhesion and spreading pattern and display extensive neurite outgrowth. This protocol will provide a neuronal model system for studying FAK activity during cell adhesion and migration events. PMID:24025096

OptiPhy, a technical-economic optimisation model for improving the management of plant protection practices in agriculture: a decision-support tool for controlling the toxicity risks related to pesticides.

PubMed

Mghirbi, Oussama; LE Grusse, Philippe; Fabre, Jacques; Mandart, Elisabeth; Bord, Jean-Paul

2017-03-01

The health, environmental and socio-economic issues related to the massive use of plant protection products are a concern for all the stakeholders involved in the agricultural sector. These stakeholders, including farmers and territorial actors, have expressed a need for decision-support tools for the management of diffuse pollution related to plant protection practices and their impacts. To meet the needs expressed by the public authorities and the territorial actors for such decision-support tools, we have developed a technical-economic model "OptiPhy" for risk mitigation based on indicators of pesticide toxicity risk to applicator health (IRSA) and to the environment (IRTE), under the constraint of suitable economic outcomes. This technical-economic optimisation model is based on linear programming techniques and offers various scenarios to help the different actors in choosing plant protection products, depending on their different levels of constraints and aspirations. The health and environmental risk indicators can be broken down into sub-indicators so that management can be tailored to the context. This model for technical-economic optimisation and management of plant protection practices can analyse scenarios for the reduction of pesticide-related risks by proposing combinations of substitution PPPs, according to criteria of efficiency, economic performance and vulnerability of the natural environment. The results of the scenarios obtained on real ITKs in different cropping systems show that it is possible to reduce the PPP pressure (TFI) and reduce toxicity risks to applicator health (IRSA) and to the environment (IRTE) by up to approximately 50 %.

Enhancement of γ-aminobutyric acid production in recombinant Corynebacterium glutamicum by co-expressing two glutamate decarboxylase genes from Lactobacillus brevis.

PubMed

Shi, Feng; Jiang, Junjun; Li, Yongfu; Li, Youxin; Xie, Yilong

2013-11-01

γ-Aminobutyric acid (GABA), a non-protein amino acid, is a bioactive component in the food, feed and pharmaceutical fields. To establish an effective single-step production system for GABA, a recombinant Corynebacterium glutamicum strain co-expressing two glutamate decarboxylase (GAD) genes (gadB1 and gadB2) derived from Lactobacillus brevis Lb85 was constructed. Compared with the GABA production of the gadB1 or gadB2 single-expressing strains, GABA production by the gadB1-gadB2 co-expressing strain increased more than twofold. By optimising urea supplementation, the total production of L-glutamate and GABA increased from 22.57 ± 1.24 to 30.18 ± 1.33 g L⁻¹, and GABA production increased from 4.02 ± 0.95 to 18.66 ± 2.11 g L⁻¹ after 84-h cultivation. Under optimal urea supplementation, L-glutamate continued to be consumed, GABA continued to accumulate after 36 h of fermentation, and the pH level fluctuated. GABA production increased to a maximum level of 27.13 ± 0.54 g L⁻¹ after 120-h flask cultivation and 26.32 g L⁻¹ after 60-h fed-batch fermentation. The conversion ratio of L-glutamate to GABA reached 0.60-0.74 mol mol⁻¹. By co-expressing gadB1 and gadB2 and optimising the urea addition method, C. glutamicum was genetically improved for de novo biosynthesis of GABA from its own accumulated L-glutamate.

Expression stability of two housekeeping genes (18S rRNA and G3PDH) during in vitro maturation of follicular oocytes in buffalo (Bubalus bubalis).

PubMed

Aswal, Ajay Pal Singh; Raghav, Sarvesh; De, Sachinandan; Thakur, Manish; Goswami, Surender Lal; Datta, Tirtha Kumar

2008-01-15

The present study was undertaken to evaluate the expression stability of two housekeeping genes (HKGs), 18S rRNA and G3PDH during in vitro maturation (IVM) of oocytes in buffalo, which qualifies their use as internal controls for valid qRT-PCR estimation of other oocyte transcripts. A semi quantitative RT-PCR system was used with optimised qRT-PCR parameters at exponential PCR cycle for evaluation of temporal expression pattern of these genes over 24 h of IVM. 18S rRNA was found more stable in its expression pattern than G3PDH.

Recognition of cyclic-di-GMP by a riboswitch conducts translational repression through masking the ribosome-binding site distant from the aptamer domain.

PubMed

Inuzuka, Saki; Kakizawa, Hitoshi; Nishimura, Kei-Ichiro; Naito, Takuto; Miyazaki, Katsushi; Furuta, Hiroyuki; Matsumura, Shigeyoshi; Ikawa, Yoshiya

2018-06-01

The riboswitch is a class of RNA-based gene regulatory machinery that is dependent on recognition of its target ligand by RNA tertiary structures. Ligand recognition is achieved by the aptamer domain, and ligand-dependent structural changes of the expression platform then usually mediate termination of transcription or translational initiation. Ligand-dependent structural changes of the aptamer domain and expression platform have been reported for several riboswitches with short (<40 nucleotides) expression platforms. In this study, we characterized structural changes of the Vc2 c-di-GMP riboswitch that represses translation of downstream open reading frames in a ligand-dependent manner. The Vc2 riboswitch has a long (97 nucleotides) expression platform, but its structure and function are largely unknown. Through mutational analysis and chemical probing, we identified its secondary structures that are possibly responsible for switch-OFF and switch-ON states of translational initiation. © 2018 Molecular Biology Society of Japan and John Wiley & Sons Australia, Ltd.

Comparative assessment of two interfaces for delivering a multimedia medical course in the French-speaking Virtual Medical University (UMVF).

PubMed

Brunetaud, Jean Marc; Leroy, Nicolas; Pelayo, Sylvia; Wascat, Caroline; Renard, Jean Marie; Prin, Lionel; Beuscart-Zéphir, Marie Catherine

2003-01-01

The UMVF aims at helping medical students during their normal curriculum via the facilities provided by Internet based techniques. This paper describes a comparative assessment of two interfaces delivering a multimedia course: a conventional web server (WS) and an integrated e-learning platform in the form of a Virtual Campus (VC). Eleven students were arbitrarily divided into two groups. We used a qualitative method for comparing their acceptance of the on line course provided by the two different interfaces. The two groups were globally satisfied. However, a decrease in satisfaction was noted at the end of the experimentation in the VC group. This may be explained by a more complex Graphical User Interface (GUI) of the VC and some constraints which do not exist with the WS. The current e-learning platforms are probably not optimised for working conditions where presential and virtual activities are mixed. We think that a new type of "light" platforms should be developed for these specific working conditions. Students of the two groups also had limitations about the multimedia environment. They may change their opinion if they get more accustomed with the multimedia environment and if their teachers make a more adequate use of the multimedia techniques.

Disease activity-guided dose optimisation of adalimumab and etanercept is a cost-effective strategy compared with non-tapering tight control rheumatoid arthritis care: analyses of the DRESS study.

PubMed

Kievit, Wietske; van Herwaarden, Noortje; van den Hoogen, Frank Hj; van Vollenhoven, Ronald F; Bijlsma, Johannes Wj; van den Bemt, Bart Jf; van der Maas, Aatke; den Broeder, Alfons A

2016-11-01

A disease activity-guided dose optimisation strategy of adalimumab or etanercept (TNFi (tumour necrosis factor inhibitors)) has shown to be non-inferior in maintaining disease control in patients with rheumatoid arthritis (RA) compared with usual care. However, the cost-effectiveness of this strategy is still unknown. This is a preplanned cost-effectiveness analysis of the Dose REduction Strategy of Subcutaneous TNF inhibitors (DRESS) study, a randomised controlled, open-label, non-inferiority trial performed in two Dutch rheumatology outpatient clinics. Patients with low disease activity using TNF inhibitors were included. Total healthcare costs were measured and quality adjusted life years (QALY) were based on EQ5D utility scores. Decremental cost-effectiveness analyses were performed using bootstrap analyses; incremental net monetary benefit (iNMB) was used to express cost-effectiveness. 180 patients were included, and 121 were allocated to the dose optimisation strategy and 59 to control. The dose optimisation strategy resulted in a mean cost saving of -€12 280 (95 percentile -€10 502; -€14 104) per patient per 18 months. There is an 84% chance that the dose optimisation strategy results in a QALY loss with a mean QALY loss of -0.02 (-0.07 to 0.02). The decremental cost-effectiveness ratio (DCER) was €390 493 (€5 085 184; dominant) of savings per QALY lost. The mean iNMB was €10 467 (€6553-€14 037). Sensitivity analyses using 30% and 50% lower prices for TNFi remained cost-effective. Disease activity-guided dose optimisation of TNFi results in considerable cost savings while no relevant loss of quality of life was observed. When the minimal QALY loss is compensated with the upper limit of what society is willing to pay or accept in the Netherlands, the net savings are still high. NTR3216; Post-results. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/.

The effects of platform motion and target orientation on the performance of trackball manipulation.

PubMed

Yau, Yi-Jan; Chao, Chin-Jung; Feng, Wen-Yang; Hwang, Sheue-Ling

2011-08-01

The trackball has been widely employed as a control/command input device on moving vehicles, but few studies have explored the effects of platform motion on its manipulation. Fewer still have considered this issue in designing the user interface and the arrangement of console location and orientation simultaneously. This work describes an experiment carried out to investigate the performance of trackball users on a simple point-and-click task in a motion simulator. By varying the orientation of onscreen targets, the effect of cursor movement direction on performance is investigated. The results indicate that the platform motion and target orientation both significantly affect the time required to point and click, but not the accuracy of target selection. The movement times were considerably longer under rolling and pitching motions and for targets located along the diagonal axes of the interface. Subjective evaluations carried out by the participants agree with these objective results. These findings could be used to optimise console and graphical menu design for use on maritime vessels. STATEMENT OF RELEVANCE: In military situations, matters of life or death may be decided in milliseconds. Any delay or error in classification and identification will thus affect the safety of the ship and its crew. This study demonstrates that performance of manipulating a trackball is affected by the platform motion and target orientation. The results of the present study can guide the arrangement of consoles and the design of trackball-based graphical user interfaces on maritime vessels.

A novel swarm intelligence algorithm for finding DNA motifs.

PubMed

Lei, Chengwei; Ruan, Jianhua

2009-01-01

Discovering DNA motifs from co-expressed or co-regulated genes is an important step towards deciphering complex gene regulatory networks and understanding gene functions. Despite significant improvement in the last decade, it still remains one of the most challenging problems in computational molecular biology. In this work, we propose a novel motif finding algorithm that finds consensus patterns using a population-based stochastic optimisation technique called Particle Swarm Optimisation (PSO), which has been shown to be effective in optimising difficult multidimensional problems in continuous domains. We propose to use a word dissimilarity graph to remap the neighborhood structure of the solution space of DNA motifs, and propose a modification of the naive PSO algorithm to accommodate discrete variables. In order to improve efficiency, we also propose several strategies for escaping from local optima and for automatically determining the termination criteria. Experimental results on simulated challenge problems show that our method is both more efficient and more accurate than several existing algorithms. Applications to several sets of real promoter sequences also show that our approach is able to detect known transcription factor binding sites, and outperforms two of the most popular existing algorithms.

Antero-posterior (AP) pelvis x-ray imaging on a trolley: Impact of trolley design, mattress design and radiographer practice on image quality and radiation dose.

PubMed

Tugwell, J R; England, A; Hogg, P

2017-08-01

Physical and technical differences exist between imaging on an x-ray tabletop and imaging on a trolley. This study evaluates how trolley imaging impacts image quality and radiation dose for an antero-posterior (AP) pelvis projection whilst subsequently exploring means of optimising this imaging examination. An anthropomorphic pelvis phantom was imaged on a commercially available trolley under various conditions. Variables explored included two mattresses, two image receptor holder positions, three source to image distances (SIDs) and four mAs values. Image quality was evaluated using relative visual grading analysis with the reference image acquired on the x-ray tabletop. Contrast to noise ratio (CNR) was calculated. Effective dose was established using Monte Carlo simulation. Optimisation scores were derived as a figure of merit by dividing effective dose with visual image quality scores. Visual image quality reduced significantly (p < 0.05) whilst effective dose increased significantly (p < 0.05) for images acquired on the trolley using identical acquisition parameters to the reference image. The trolley image with the highest optimisation score was acquired using 130 cm SID, 20 mAs, the standard mattress and platform not elevated. A difference of 12.8 mm was found between the image with the lowest and highest magnification factor (18%). The acquisition parameters used for AP pelvis on the x-ray tabletop are not transferable to trolley imaging and should be modified accordingly to compensate for the differences that exist. Exposure charts should be developed for trolley imaging to ensure optimal image quality at lowest possible dose. Crown Copyright © 2017. Published by Elsevier Ltd. All rights reserved.

MICROARRAY QUALITY CONTROL PROJECT: A COMPREHENSIVE GENE EXPRESSION TECHNOLOGY SURVEY DEMONSTRATES MEASURABLE CONSISTENCY AND CONCORDANT RESULTS BETWEEN PLATFORMS

EPA Science Inventory

Over the last decade, the introduction of microarray technology has had a profound impact on gene expression research. The publication of studies with dissimilar or altogether contradictory results, obtained using different microarray platforms to analyze identical RNA samples, h...

Too much data, but little inter-changeability: a lesson learned from mining public data on tissue specificity of gene expression.

PubMed

Li, Shuyu; Li, Yiqun Helen; Wei, Tao; Su, Eric Wen; Duffin, Kevin; Liao, Birong

2006-10-25

The tissue expression pattern of a gene often provides an important clue to its potential role in a biological process. A vast amount of gene expression data have been and are being accumulated in public repository through different technology platforms. However, exploitations of these rich data sources remain limited in part due to issues of technology standardization. Our objective is to test the data comparability between SAGE and microarray technologies, through examining the expression pattern of genes under normal physiological states across variety of tissues. There are 42-54% of genes showing significant correlations in tissue expression patterns between SAGE and GeneChip, with 30-40% of genes whose expression patterns are positively correlated and 10-15% of genes whose expression patterns are negatively correlated at a statistically significant level (p = 0.05). Our analysis suggests that the discrepancy on the expression patterns derived from technology platforms is not likely from the heterogeneity of tissues used in these technologies, or other spurious correlations resulting from microarray probe design, abundance of genes, or gene function. The discrepancy can be partially explained by errors in the original assignment of SAGE tags to genes due to the evolution of sequence databases. In addition, sequence analysis has indicated that many SAGE tags and Affymetrix array probe sets are mapped to different splice variants or different sequence regions although they represent the same gene, which also contributes to the observed discrepancies between SAGE and array expression data. To our knowledge, this is the first report attempting to mine gene expression patterns across tissues using public data from different technology platforms. Unlike previous similar studies that only demonstrated the discrepancies between the two gene expression platforms, we carried out in-depth analysis to further investigate the cause for such discrepancies. Our study shows that the exploitation of rich public expression resource requires extensive knowledge about the technologies, and experiment. Informatic methodologies for better interoperability among platforms still remain a gap. One of the areas that can be improved practically is the accurate sequence mapping of SAGE tags and array probes to full-length genes.

Functional comparison of microarray data across multiple platforms using the method of percentage of overlapping functions.

PubMed

Li, Zhiguang; Kwekel, Joshua C; Chen, Tao

2012-01-01

Functional comparison across microarray platforms is used to assess the comparability or similarity of the biological relevance associated with the gene expression data generated by multiple microarray platforms. Comparisons at the functional level are very important considering that the ultimate purpose of microarray technology is to determine the biological meaning behind the gene expression changes under a specific condition, not just to generate a list of genes. Herein, we present a method named percentage of overlapping functions (POF) and illustrate how it is used to perform the functional comparison of microarray data generated across multiple platforms. This method facilitates the determination of functional differences or similarities in microarray data generated from multiple array platforms across all the functions that are presented on these platforms. This method can also be used to compare the functional differences or similarities between experiments, projects, or laboratories.

An open source web interface for linking models to infrastructure system databases

NASA Astrophysics Data System (ADS)

Knox, S.; Mohamed, K.; Harou, J. J.; Rheinheimer, D. E.; Medellin-Azuara, J.; Meier, P.; Tilmant, A.; Rosenberg, D. E.

2016-12-01

Models of networked engineered resource systems such as water or energy systems are often built collaboratively with developers from different domains working at different locations. These models can be linked to large scale real world databases, and they are constantly being improved and extended. As the development and application of these models becomes more sophisticated, and the computing power required for simulations and/or optimisations increases, so has the need for online services and tools which enable the efficient development and deployment of these models. Hydra Platform is an open source, web-based data management system, which allows modellers of network-based models to remotely store network topology and associated data in a generalised manner, allowing it to serve multiple disciplines. Hydra Platform uses a web API using JSON to allow external programs (referred to as `Apps') to interact with its stored networks and perform actions such as importing data, running models, or exporting the networks to different formats. Hydra Platform supports multiple users accessing the same network and has a suite of functions for managing users and data. We present ongoing development in Hydra Platform, the Hydra Web User Interface, through which users can collaboratively manage network data and models in a web browser. The web interface allows multiple users to graphically access, edit and share their networks, run apps and view results. Through apps, which are located on the server, the web interface can give users access to external data sources and models without the need to install or configure any software. This also ensures model results can be reproduced by removing platform or version dependence. Managing data and deploying models via the web interface provides a way for multiple modellers to collaboratively manage data, deploy and monitor model runs and analyse results.

The growing impact of lyophilized cell-free protein expression systems

PubMed Central

Hunt, J. Porter; Yang, Seung Ook; Wilding, Kristen M.; Bundy, Bradley C.

2017-01-01

ABSTRACT Recently reported shelf-stable, on-demand protein synthesis platforms are enabling new possibilities in biotherapeutics, biosensing, biocatalysis, and high throughput protein expression. Lyophilized cell-free protein expression systems not only overcome cold-storage limitations, but also enable stockpiling for on-demand synthesis and completely sterilize the protein synthesis platform. Recently reported high-yield synthesis of cytotoxic protein Onconase from lyophilized E. coli extract preparations demonstrates the utility of lyophilized cell-free protein expression and its potential for creating on-demand biotherapeutics, vaccines, biosensors, biocatalysts, and high throughput protein synthesis. PMID:27791452

Optimising molecular diagnostic capacity for effective control of tuberculosis in high-burden settings.

PubMed

Sabiiti, W; Mtafya, B; Kuchaka, D; Azam, K; Viegas, S; Mdolo, A; Farmer, E C W; Khonga, M; Evangelopoulos, D; Honeyborne, I; Rachow, A; Heinrich, N; Ntinginya, N E; Bhatt, N; Davies, G R; Jani, I V; McHugh, T D; Kibiki, G; Hoelscher, M; Gillespie, S H

2016-08-01

The World Health Organization's 2035 vision is to reduce tuberculosis (TB) associated mortality by 95%. While low-burden, well-equipped industrialised economies can expect to see this goal achieved, it is challenging in the low- and middle-income countries that bear the highest burden of TB. Inadequate diagnosis leads to inappropriate treatment and poor clinical outcomes. The roll-out of the Xpert(®) MTB/RIF assay has demonstrated that molecular diagnostics can produce rapid diagnosis and treatment initiation. Strong molecular services are still limited to regional or national centres. The delay in implementation is due partly to resources, and partly to the suggestion that such techniques are too challenging for widespread implementation. We have successfully implemented a molecular tool for rapid monitoring of patient treatment response to anti-tuberculosis treatment in three high TB burden countries in Africa. We discuss here the challenges facing TB diagnosis and treatment monitoring, and draw from our experience in establishing molecular treatment monitoring platforms to provide practical insights into successful optimisation of molecular diagnostic capacity in resource-constrained, high TB burden settings. We recommend a holistic health system-wide approach for molecular diagnostic capacity development, addressing human resource training, institutional capacity development, streamlined procurement systems, and engagement with the public, policy makers and implementers of TB control programmes.

The road map towards providing a robust Raman spectroscopy-based cancer diagnostic platform and integration into clinic

NASA Astrophysics Data System (ADS)

Lau, Katherine; Isabelle, Martin; Lloyd, Gavin R.; Old, Oliver; Shepherd, Neil; Bell, Ian M.; Dorney, Jennifer; Lewis, Aaran; Gaifulina, Riana; Rodriguez-Justo, Manuel; Kendall, Catherine; Stone, Nicolas; Thomas, Geraint; Reece, David

2016-03-01

Despite the demonstrated potential as an accurate cancer diagnostic tool, Raman spectroscopy (RS) is yet to be adopted by the clinic for histopathology reviews. The Stratified Medicine through Advanced Raman Technologies (SMART) consortium has begun to address some of the hurdles in its adoption for cancer diagnosis. These hurdles include awareness and acceptance of the technology, practicality of integration into the histopathology workflow, data reproducibility and availability of transferrable models. We have formed a consortium, in joint efforts, to develop optimised protocols for tissue sample preparation, data collection and analysis. These protocols will be supported by provision of suitable hardware and software tools to allow statistically sound classification models to be built and transferred for use on different systems. In addition, we are building a validated gastrointestinal (GI) cancers model, which can be trialled as part of the histopathology workflow at hospitals, and a classification tool. At the end of the project, we aim to deliver a robust Raman based diagnostic platform to enable clinical researchers to stage cancer, define tumour margin, build cancer diagnostic models and discover novel disease bio markers.

Dynamic in-situ sensing of fluid-dispersed 2D materials integrated on microfluidic Si chip.

PubMed

Hogan, Benjamin T; Dyakov, Sergey A; Brennan, Lorcan J; Younesy, Salma; Perova, Tatiana S; Gun'ko, Yurii K; Craciun, Monica F; Baldycheva, Anna

2017-02-10

In this work, we propose a novel approach for wafer-scale integration of 2D materials on CMOS photonic chip utilising methods of synthetic chemistry and microfluidics technology. We have successfully demonstrated that this approach can be used for integration of any fluid-dispersed 2D nano-objects on silicon-on-insulator photonics platform. We demonstrate for the first time that the design of an optofluidic waveguide system can be optimised to enable simultaneous in-situ Raman spectroscopy monitoring of 2D dispersed flakes during the device operation. Moreover, for the first time, we have successfully demonstrated the possibility of label-free 2D flake detection via selective enhancement of the Stokes Raman signal at specific wavelengths. We discovered an ultra-high signal sensitivity to the xyz alignment of 2D flakes within the optofluidic waveguide. This in turn enables precise in-situ alignment detection, for the first practicable realisation of 3D photonic microstructure shaping based on 2D-fluid composites and CMOS photonics platform, while also representing a useful technological tool for the control of liquid phase deposition of 2D materials.

Exploring Plant Co-Expression and Gene-Gene Interactions with CORNET 3.0.

PubMed

Van Bel, Michiel; Coppens, Frederik

2017-01-01

Selecting and filtering a reference expression and interaction dataset when studying specific pathways and regulatory interactions can be a very time-consuming and error-prone task. In order to reduce the duplicated efforts required to amass such datasets, we have created the CORNET (CORrelation NETworks) platform which allows for easy access to a wide variety of data types: coexpression data, protein-protein interactions, regulatory interactions, and functional annotations. The CORNET platform outputs its results in either text format or through the Cytoscape framework, which is automatically launched by the CORNET website.CORNET 3.0 is the third iteration of the web platform designed for the user exploration of the coexpression space of plant genomes, with a focus on the model species Arabidopsis thaliana. Here we describe the platform: the tools, data, and best practices when using the platform. We indicate how the platform can be used to infer networks from a set of input genes, such as upregulated genes from an expression experiment. By exploring the network, new target and regulator genes can be discovered, allowing for follow-up experiments and more in-depth study. We also indicate how to avoid common pitfalls when evaluating the networks and how to avoid over interpretation of the results.All CORNET versions are available at http://bioinformatics.psb.ugent.be/cornet/ .

Production of therapeutic proteins in algae, analysis of expression of seven human proteins in the chloroplast of Chlamydomonas reinhardtii

PubMed Central

Rasala, Beth A; Muto, Machiko; Lee, Philip A; Jager, Michal; Cardoso, Rosa MF; Behnke, Craig A; Kirk, Peter; Hokanson, Craig A; Crea, Roberto; Mendez, Michael; Mayfield, Stephen P

2010-01-01

Summary Recombinant proteins are widely used today in many industries, including the biopharmaceutical industry, and can be expressed in bacteria, yeasts, mammalian and insect cell cultures, or in transgenic plants and animals. In addition, transgenic algae have also been shown to support recombinant protein expression, both from the nuclear and chloroplast genomes. However, to date, there are only a few reports on recombinant proteins expressed in the algal chloroplast. It is unclear if this is due to few attempts or to limitations of the system that preclude expression of many proteins. Thus, we sought to assess the versatility of transgenic algae as a recombinant protein production platform. To do this, we tested whether the algal chloroplast could support the expression of a diverse set of current or potential human therapeutic proteins. Of the seven proteins chosen, greater than 50% expressed at levels sufficient for commercial production. Three expressed at 2% to 3% of total soluble protein, while a forth protein accumulated to similar levels when translationally fused to a well-expressed serum amyloid protein. All of the algal chloroplast-expressed proteins are soluble and showed biological activity comparable to that of the same proteins expressed using traditional production platforms. Thus, the success rate, expression levels, and bioactivty achieved demonstrate the utility of C. reinhardtii as a robust platform for human therapeutic protein production. PMID:20230484

Profound Effect of Profiling Platform and Normalization Strategy on Detection of Differentially Expressed MicroRNAs – A Comparative Study

PubMed Central

Meyer, Swanhild U.; Kaiser, Sebastian; Wagner, Carola; Thirion, Christian; Pfaffl, Michael W.

2012-01-01

Background Adequate normalization minimizes the effects of systematic technical variations and is a prerequisite for getting meaningful biological changes. However, there is inconsistency about miRNA normalization performances and recommendations. Thus, we investigated the impact of seven different normalization methods (reference gene index, global geometric mean, quantile, invariant selection, loess, loessM, and generalized procrustes analysis) on intra- and inter-platform performance of two distinct and commonly used miRNA profiling platforms. Methodology/Principal Findings We included data from miRNA profiling analyses derived from a hybridization-based platform (Agilent Technologies) and an RT-qPCR platform (Applied Biosystems). Furthermore, we validated a subset of miRNAs by individual RT-qPCR assays. Our analyses incorporated data from the effect of differentiation and tumor necrosis factor alpha treatment on primary human skeletal muscle cells and a murine skeletal muscle cell line. Distinct normalization methods differed in their impact on (i) standard deviations, (ii) the area under the receiver operating characteristic (ROC) curve, (iii) the similarity of differential expression. Loess, loessM, and quantile analysis were most effective in minimizing standard deviations on the Agilent and TLDA platform. Moreover, loess, loessM, invariant selection and generalized procrustes analysis increased the area under the ROC curve, a measure for the statistical performance of a test. The Jaccard index revealed that inter-platform concordance of differential expression tended to be increased by loess, loessM, quantile, and GPA normalization of AGL and TLDA data as well as RGI normalization of TLDA data. Conclusions/Significance We recommend the application of loess, or loessM, and GPA normalization for miRNA Agilent arrays and qPCR cards as these normalization approaches showed to (i) effectively reduce standard deviations, (ii) increase sensitivity and accuracy of differential miRNA expression detection as well as (iii) increase inter-platform concordance. Results showed the successful adoption of loessM and generalized procrustes analysis to one-color miRNA profiling experiments. PMID:22723911

Chicken ovalbumin upstream promoter-transcription factor II regulates nuclear receptor, myogenic, and metabolic gene expression in skeletal muscle cells.

PubMed

Crowther, Lisa M; Wang, Shu-Ching Mary; Eriksson, Natalie A; Myers, Stephen A; Murray, Lauren A; Muscat, George E O

2011-02-24

We demonstrate that chicken ovalbumin upstream promoter-transcription factor II (COUP-TFII) mRNA is more abundantly expressed (than COUP-TFI mRNA) in skeletal muscle C2C12 cells and in (type I and II) skeletal muscle tissue from C57BL/10 mice. Consequently, we have utilized the ABI TaqMan Low Density Array (TLDA) platform to analyze gene expression changes specifically attributable to ectopic COUP-TFII (relative to vector only) expression in muscle cells. Utilizing a TLDA-based platform and 5 internal controls, we analyze the entire NR superfamily, 96 critical metabolic genes, and 48 important myogenic regulatory genes on the TLDA platform utilizing 5 internal controls. The low density arrays were analyzed by rigorous statistical analysis (with Genorm normalization, Bioconductor R, and the Empirical Bayes statistic) using the (integromics) statminer software. In addition, we validated the differentially expressed patho-physiologically relevant gene (identified on the TLDA platform) glucose transporter type 4 (Glut4). We demonstrated that COUP-TFII expression increased the steady state levels of Glut4 mRNA and protein, while ectopic expression of truncated COUP-TFII lacking helix 12 (COUP-TFΔH12) reduced Glut4 mRNA expression in C2C12 cells. Moreover, COUP-TFII expression trans-activated the Glut4 promoter (-997/+3), and ChIP analysis identified selective recruitment of COUP-TFII to a region encompassing a highly conserved SP1 binding site (in mouse, rat, and human) at nt positions -131/-118. Mutation of the SpI site ablated COUP-TFII mediated trans-activation of the Glut4 promoter. In conclusion, this study demonstrates that in skeletal muscle cells, COUP-TFII regulates several nuclear hormone receptors, and critical metabolic and muscle specific genes.

High-Throughput Protein Expression Using a Combination of Ligation-Independent Cloning (LIC) and Infrared Fluorescent Protein (IFP) Detection

PubMed Central

Dortay, Hakan; Akula, Usha Madhuri; Westphal, Christin; Sittig, Marie; Mueller-Roeber, Bernd

2011-01-01

Protein expression in heterologous hosts for functional studies is a cumbersome effort. Here, we report a superior platform for parallel protein expression in vivo and in vitro. The platform combines highly efficient ligation-independent cloning (LIC) with instantaneous detection of expressed proteins through N- or C-terminal fusions to infrared fluorescent protein (IFP). For each open reading frame, only two PCR fragments are generated (with three PCR primers) and inserted by LIC into ten expression vectors suitable for protein expression in microbial hosts, including Escherichia coli, Kluyveromyces lactis, Pichia pastoris, the protozoon Leishmania tarentolae, and an in vitro transcription/translation system. Accumulation of IFP-fusion proteins is detected by infrared imaging of living cells or crude protein extracts directly after SDS-PAGE without additional processing. We successfully employed the LIC-IFP platform for in vivo and in vitro expression of ten plant and fungal proteins, including transcription factors and enzymes. Using the IFP reporter, we additionally established facile methods for the visualisation of protein-protein interactions and the detection of DNA-transcription factor interactions in microtiter and gel-free format. We conclude that IFP represents an excellent reporter for high-throughput protein expression and analysis, which can be easily extended to numerous other expression hosts using the setup reported here. PMID:21541323

Improving Vector Evaluated Particle Swarm Optimisation by Incorporating Nondominated Solutions

PubMed Central

Lim, Kian Sheng; Ibrahim, Zuwairie; Buyamin, Salinda; Ahmad, Anita; Naim, Faradila; Ghazali, Kamarul Hawari; Mokhtar, Norrima

2013-01-01

The Vector Evaluated Particle Swarm Optimisation algorithm is widely used to solve multiobjective optimisation problems. This algorithm optimises one objective using a swarm of particles where their movements are guided by the best solution found by another swarm. However, the best solution of a swarm is only updated when a newly generated solution has better fitness than the best solution at the objective function optimised by that swarm, yielding poor solutions for the multiobjective optimisation problems. Thus, an improved Vector Evaluated Particle Swarm Optimisation algorithm is introduced by incorporating the nondominated solutions as the guidance for a swarm rather than using the best solution from another swarm. In this paper, the performance of improved Vector Evaluated Particle Swarm Optimisation algorithm is investigated using performance measures such as the number of nondominated solutions found, the generational distance, the spread, and the hypervolume. The results suggest that the improved Vector Evaluated Particle Swarm Optimisation algorithm has impressive performance compared with the conventional Vector Evaluated Particle Swarm Optimisation algorithm. PMID:23737718

Improving Vector Evaluated Particle Swarm Optimisation by incorporating nondominated solutions.

PubMed

Lim, Kian Sheng; Ibrahim, Zuwairie; Buyamin, Salinda; Ahmad, Anita; Naim, Faradila; Ghazali, Kamarul Hawari; Mokhtar, Norrima

2013-01-01

The Vector Evaluated Particle Swarm Optimisation algorithm is widely used to solve multiobjective optimisation problems. This algorithm optimises one objective using a swarm of particles where their movements are guided by the best solution found by another swarm. However, the best solution of a swarm is only updated when a newly generated solution has better fitness than the best solution at the objective function optimised by that swarm, yielding poor solutions for the multiobjective optimisation problems. Thus, an improved Vector Evaluated Particle Swarm Optimisation algorithm is introduced by incorporating the nondominated solutions as the guidance for a swarm rather than using the best solution from another swarm. In this paper, the performance of improved Vector Evaluated Particle Swarm Optimisation algorithm is investigated using performance measures such as the number of nondominated solutions found, the generational distance, the spread, and the hypervolume. The results suggest that the improved Vector Evaluated Particle Swarm Optimisation algorithm has impressive performance compared with the conventional Vector Evaluated Particle Swarm Optimisation algorithm.

Development of a Web-Enabled Informatics Platform for Manipulation of Gene Expression Data

DTIC Science & Technology

2004-12-01

genomic platforms such as metabolomics and proteomics , and to federated databases for knowledge management. A successful SBIR Phase I completed...measurements that require sophisticated bioinformatic platforms for data archival, management, integration, and analysis if researchers are to derive...web-enabled bioinformatic platform consisting of a Laboratory Information Management System (LIMS), an Analysis Information Management System (AIMS

Critical stages of a biodetection platform development from sensor chip fabrication to surface chemistry and assay development

NASA Astrophysics Data System (ADS)

Uludag, Yildiz

2014-06-01

Once viewed solely as a tool to analyse biomolecular interactions, biosensors are gaining widespread interest for diagnostics, biological defense, environmental and quality assurance in agriculture/food industries. Advanced micro fabrication techniques have facilitated integration of microfluidics with sensing functionalities on the same chip making system automation more convenient1. Biosensor devices relying on lab-on-a-chip technologies and nanotechnology has attracted much of attention in recent years for biological defense research and development. However, compared with the numerous publications and patents available, the commercialization of biosensors technology has significantly lagged behind the research output. This paper reviews the reasons behind the slow commercialisation of biosensors with an insight to the critical stages of a biosensor development from the sensor chip fabrication to surface chemistry applications and nanotechnology applications in sensing with case studies. In addition, the paper includes the description of a new biodetection platform based on Real-time Electrochemical ProfilingTM (REPTM) that comprises novel electrode arrays and nanoparticle based sensing. The performance of the REPTM platform has been tested for the detection of Planktothrix agardhii, one of the toxic bloom-forming cyanobacteria, usually found in shallow fresh water sources that can be used for human consumption. The optimised REPTM assay allowed the detection of P. agardhii DNA down to 6 pM. This study, showed the potential of REPTM as a new biodetection platform for toxic bacteria and hence further studies will involve the development of a portable multi-analyte biosensor based on REPTM technology for on-site testing.

Intra-Platform Repeatability and Inter-Platform Comparability of MicroRNA Microarray Technology

PubMed Central

Sato, Fumiaki; Tsuchiya, Soken; Terasawa, Kazuya; Tsujimoto, Gozoh

2009-01-01

Over the last decade, DNA microarray technology has provided a great contribution to the life sciences. The MicroArray Quality Control (MAQC) project demonstrated the way to analyze the expression microarray. Recently, microarray technology has been utilized to analyze a comprehensive microRNA expression profiling. Currently, several platforms of microRNA microarray chips are commercially available. Thus, we compared repeatability and comparability of five different microRNA microarray platforms (Agilent, Ambion, Exiqon, Invitrogen and Toray) using 309 microRNAs probes, and the Taqman microRNA system using 142 microRNA probes. This study demonstrated that microRNA microarray has high intra-platform repeatability and comparability to quantitative RT-PCR of microRNA. Among the five platforms, Agilent and Toray array showed relatively better performances than the others. However, the current lineup of commercially available microRNA microarray systems fails to show good inter-platform concordance, probably because of lack of an adequate normalization method and severe divergence in stringency of detection call criteria between different platforms. This study provided the basic information about the performance and the problems specific to the current microRNA microarray systems. PMID:19436744

Microfluidic platform combining droplets and magnetic tweezers: application to HER2 expression in cancer diagnosis.

PubMed

Ferraro, Davide; Champ, Jérôme; Teste, Bruno; Serra, Marco; Malaquin, Laurent; Viovy, Jean-Louis; de Cremoux, Patricia; Descroix, Stephanie

2016-05-09

The development of precision medicine, together with the multiplication of targeted therapies and associated molecular biomarkers, call for major progress in genetic analysis methods, allowing increased multiplexing and the implementation of more complex decision trees, without cost increase or loss of robustness. We present a platform combining droplet microfluidics and magnetic tweezers, performing RNA purification, reverse transcription and amplification in a fully automated and programmable way, in droplets of 250nL directly sampled from a microtiter-plate. This platform decreases sample consumption about 100 fold as compared to current robotized platforms and it reduces human manipulations and contamination risk. The platform's performance was first evaluated on cell lines, showing robust operation on RNA quantities corresponding to less than one cell, and then clinically validated with a cohort of 21 breast cancer samples, for the determination of their HER2 expression status, in a blind comparison with an established routine clinical analysis.

Prefocal station mechanical design concept study for the E-ELT

NASA Astrophysics Data System (ADS)

Jolley, Paul; Brunetto, Enzo; Frank, Christoph; Lewis, Steffan; Marchetti, Enrico

2016-07-01

The Nasmyth platforms of the E-ELT will contain one Prefocal Station (PFS) each. The main PFS functional requirements are to provide a focal plane to the three Nasmyth focal stations and the Coudé focus, optical sensing supporting telescope low order optimisation and seeing limited image quality, and optical sensing supporting characterising and phasing of M1 and other telescope subsystems. The PFS user requirements are used to derive the PFS technical requirements specification that will form the basis for design, development and production of the system. This specification process includes high-level architectural decisions and technical performance budget allocations. The mechanical design concepts reported here have been developed in order to validate key system specifications and associated technical budgets.

Design of optimised backstepping controller for the synchronisation of chaotic Colpitts oscillator using shark smell algorithm

NASA Astrophysics Data System (ADS)

Fouladi, Ehsan; Mojallali, Hamed

2018-01-01

In this paper, an adaptive backstepping controller has been tuned to synchronise two chaotic Colpitts oscillators in a master-slave configuration. The parameters of the controller are determined using shark smell optimisation (SSO) algorithm. Numerical results are presented and compared with those of particle swarm optimisation (PSO) algorithm. Simulation results show better performance in terms of accuracy and convergence for the proposed optimised method compared to PSO optimised controller or any non-optimised backstepping controller.

Evaluation of external RNA controls for the standardisation of gene expression biomarker measurements.

PubMed

Devonshire, Alison S; Elaswarapu, Ramnath; Foy, Carole A

2010-11-24

Gene expression profiling is an important approach for detecting diagnostic and prognostic biomarkers, and predicting drug safety. The development of a wide range of technologies and platforms for measuring mRNA expression makes the evaluation and standardization of transcriptomic data problematic due to differences in protocols, data processing and analysis methods. Thus, universal RNA standards, such as those developed by the External RNA Controls Consortium (ERCC), are proposed to aid validation of research findings from diverse platforms such as microarrays and RT-qPCR, and play a role in quality control (QC) processes as transcriptomic profiling becomes more commonplace in the clinical setting. Panels of ERCC RNA standards were constructed in order to test the utility of these reference materials (RMs) for performance characterization of two selected gene expression platforms, and for discrimination of biomarker profiles between groups. The linear range, limits of detection and reproducibility of microarray and RT-qPCR measurements were evaluated using panels of RNA standards. Transcripts of low abundance (≤ 10 copies/ng total RNA) showed more than double the technical variability compared to higher copy number transcripts on both platforms. Microarray profiling of two simulated 'normal' and 'disease' panels, each consisting of eight different RNA standards, yielded robust discrimination between the panels and between standards with varying fold change ratios, showing no systematic effects due to different labelling and hybridization runs. Also, comparison of microarray and RT-qPCR data for fold changes showed agreement for the two platforms. ERCC RNA standards provide a generic means of evaluating different aspects of platform performance, and can provide information on the technical variation associated with quantification of biomarkers expressed at different levels of physiological abundance. Distinct panels of standards serve as an ideal quality control tool kit for determining the accuracy of fold change cut-off threshold and the impact of experimentally-derived noise on the discrimination of normal and disease profiles.

A high performance data parallel tensor contraction framework: Application to coupled electro-mechanics

NASA Astrophysics Data System (ADS)

Poya, Roman; Gil, Antonio J.; Ortigosa, Rogelio

2017-07-01

The paper presents aspects of implementation of a new high performance tensor contraction framework for the numerical analysis of coupled and multi-physics problems on streaming architectures. In addition to explicit SIMD instructions and smart expression templates, the framework introduces domain specific constructs for the tensor cross product and its associated algebra recently rediscovered by Bonet et al. (2015, 2016) in the context of solid mechanics. The two key ingredients of the presented expression template engine are as follows. First, the capability to mathematically transform complex chains of operations to simpler equivalent expressions, while potentially avoiding routes with higher levels of computational complexity and, second, to perform a compile time depth-first or breadth-first search to find the optimal contraction indices of a large tensor network in order to minimise the number of floating point operations. For optimisations of tensor contraction such as loop transformation, loop fusion and data locality optimisations, the framework relies heavily on compile time technologies rather than source-to-source translation or JIT techniques. Every aspect of the framework is examined through relevant performance benchmarks, including the impact of data parallelism on the performance of isomorphic and nonisomorphic tensor products, the FLOP and memory I/O optimality in the evaluation of tensor networks, the compilation cost and memory footprint of the framework and the performance of tensor cross product kernels. The framework is then applied to finite element analysis of coupled electro-mechanical problems to assess the speed-ups achieved in kernel-based numerical integration of complex electroelastic energy functionals. In this context, domain-aware expression templates combined with SIMD instructions are shown to provide a significant speed-up over the classical low-level style programming techniques.

expVIP: a Customizable RNA-seq Data Analysis and Visualization Platform1[OPEN

PubMed Central

2016-01-01

The majority of transcriptome sequencing (RNA-seq) expression studies in plants remain underutilized and inaccessible due to the use of disparate transcriptome references and the lack of skills and resources to analyze and visualize these data. We have developed expVIP, an expression visualization and integration platform, which allows easy analysis of RNA-seq data combined with an intuitive and interactive interface. Users can analyze public and user-specified data sets with minimal bioinformatics knowledge using the expVIP virtual machine. This generates a custom Web browser to visualize, sort, and filter the RNA-seq data and provides outputs for differential gene expression analysis. We demonstrate expVIP’s suitability for polyploid crops and evaluate its performance across a range of biologically relevant scenarios. To exemplify its use in crop research, we developed a flexible wheat (Triticum aestivum) expression browser (www.wheat-expression.com) that can be expanded with user-generated data in a local virtual machine environment. The open-access expVIP platform will facilitate the analysis of gene expression data from a wide variety of species by enabling the easy integration, visualization, and comparison of RNA-seq data across experiments. PMID:26869702

Detection and characterization of invasive circulating tumor cells derived from men with metastatic castration-resistant prostate cancer.

PubMed

Friedlander, Terence W; Ngo, Vy T; Dong, Huan; Premasekharan, Gayatri; Weinberg, Vivian; Doty, Shaun; Zhao, Qiang; Gilbert, Elizabeth G; Ryan, Charles J; Chen, Wen-Tien; Paris, Pamela L

2014-05-15

The Vitatex cell-adhesion matrix (CAM) platform allows for isolation of invasive circulating tumor cells (iCTCs). Here we sought to determine the utility of prostate-specific membrane antigen (PSMA) as a metastatic castration-resistant prostate cancer (mCRPC) iCTC biomarker, to identify solitary cells and clusters of iCTCs expressing either epithelial, mesenchymal, or stem cell markers, and to explore the feasibility of iCTC epigenomic analysis. CTCs were isolated and enumerated simultaneously using the Vitatex and CellSearch platforms in 23 men with mCRPC. CAM-avid iCTCs were identified as nucleated cells capable of CAM uptake, but without detectable expression of hematopoietic lineage (HL) markers including CD45. iCTCs were enumerated immunocytochemically (ICC) and by flow cytometry. Whole-genome methylation status was determined for iCTCs using the Illumina HumanMethylation27 BeadChip. Thirty-four samples were collected for iCTC analysis. A median of 27 (range 0-800) and 23 (range 2-390) iCTCs/mL were detected by ICC and flow, respectively. In a subset of 20 samples, a median of seven CTCs/mL (range 0-85) were detected by the CellSearch platform compared to 26 by the CAM platform. iCTC clusters were observed in 17% of samples. iCTCs expressing PSMA as well as markers of EMT and stemness were detectable. The iCTC methylation profile highly resembled mCRPC. More CTCs were recovered using the CAM platform than the CellSearch platform, and the CAM platform allowed for the detection of iCTC clusters, iCTCs expressing EMT and stem-cell markers, and characterization of the iCTC methylome. Correlation with clinical data in future studies may yield further insight into the functional significance of these findings. © 2013 UICC.

[Construction of 2-dimensional tumor microvascular architecture phenotype in non-small cell lung cancer].

PubMed

Liu, Jin-kang; Wang, Xiao-yi; Xiong, Zeng; Zhou, Hui; Zhou, Jian-hua; Fu, Chun-yan; Li, Bo

2008-08-01

To construct a technological platform of 2-dimensional tumor microvascular architecture phenotype (2D-TAMP) expression. Thirty samples of non-small cell lung cancer (NSCLC) were collected after surgery. The corresponding sections of tumor tissue specimens to the slice of CT perfusion imaging were selected. Immunohistochemical staining,Gomori methenamine silver stain, and electron microscope observation were performed to build a technological platform of 2D-TMAP expression by detecting the morphology and the integrity of basement membrane of microvasculature, microvascular density, various microvascular subtype, the degree of the maturity and lumenization of microvasculature, and the characteristics of immunogenetics of microvasculature. The technological platform of 2D-TMAP expression was constructed successfully. There was heterogeneity in 2D-TMAP expression of non-small cell lung cancer. The microvascular of NSCLC had certain characteristics. 2D-TMAP is a key technology that can be used to observe the overall state of micro-environment in tumor growth.

A measure of the signal-to-noise ratio of microarray samples and studies using gene correlations.

PubMed

Venet, David; Detours, Vincent; Bersini, Hugues

2012-01-01

The quality of gene expression data can vary dramatically from platform to platform, study to study, and sample to sample. As reliable statistical analysis rests on reliable data, determining such quality is of the utmost importance. Quality measures to spot problematic samples exist, but they are platform-specific, and cannot be used to compare studies. As a proxy for quality, we propose a signal-to-noise ratio for microarray data, the "Signal-to-Noise Applied to Gene Expression Experiments", or SNAGEE. SNAGEE is based on the consistency of gene-gene correlations. We applied SNAGEE to a compendium of 80 large datasets on 37 platforms, for a total of 24,380 samples, and assessed the signal-to-noise ratio of studies and samples. This allowed us to discover serious issues with three studies. We show that signal-to-noise ratios of both studies and samples are linked to the statistical significance of the biological results. We showed that SNAGEE is an effective way to measure data quality for most types of gene expression studies, and that it often outperforms existing techniques. Furthermore, SNAGEE is platform-independent and does not require raw data files. The SNAGEE R package is available in BioConductor.

HEx: A heterologous expression platform for the discovery of fungal natural products

PubMed Central

Schlecht, Ulrich; Horecka, Joe; Lin, Hsiao-Ching; Naughton, Brian; Miranda, Molly; Li, Yong Fuga; Hennessy, James R.; Vandova, Gergana A.; Steinmetz, Lars M.; Sattely, Elizabeth; Khosla, Chaitan; Hillenmeyer, Maureen E.

2018-01-01

For decades, fungi have been a source of U.S. Food and Drug Administration–approved natural products such as penicillin, cyclosporine, and the statins. Recent breakthroughs in DNA sequencing suggest that millions of fungal species exist on Earth, with each genome encoding pathways capable of generating as many as dozens of natural products. However, the majority of encoded molecules are difficult or impossible to access because the organisms are uncultivable or the genes are transcriptionally silent. To overcome this bottleneck in natural product discovery, we developed the HEx (Heterologous EXpression) synthetic biology platform for rapid, scalable expression of fungal biosynthetic genes and their encoded metabolites in Saccharomyces cerevisiae. We applied this platform to 41 fungal biosynthetic gene clusters from diverse fungal species from around the world, 22 of which produced detectable compounds. These included novel compounds with unexpected biosynthetic origins, particularly from poorly studied species. This result establishes the HEx platform for rapid discovery of natural products from any fungal species, even those that are uncultivable, and opens the door to discovery of the next generation of natural products. PMID:29651464

Cross-platform evaluation of commercial real-time SYBR green RT-PCR kits for sensitive and rapid detection of European bat Lyssavirus type 1.

PubMed

Picard-Meyer, Evelyne; Peytavin de Garam, Carine; Schereffer, Jean Luc; Marchal, Clotilde; Robardet, Emmanuelle; Cliquet, Florence

2015-01-01

This study evaluates the performance of five two-step SYBR Green RT-qPCR kits and five one-step SYBR Green qRT-PCR kits using real-time PCR assays. Two real-time thermocyclers showing different throughput capacities were used. The analysed performance evaluation criteria included the generation of standard curve, reaction efficiency, analytical sensitivity, intra- and interassay repeatability as well as the costs and the practicability of kits, and thermocycling times. We found that the optimised one-step PCR assays had a higher detection sensitivity than the optimised two-step assays regardless of the machine used, while no difference was detected in reaction efficiency, R (2) values, and intra- and interreproducibility between the two methods. The limit of detection at the 95% confidence level varied between 15 to 981 copies/µL and 41 to 171 for one-step kits and two-step kits, respectively. Of the ten kits tested, the most efficient kit was the Quantitect SYBR Green qRT-PCR with a limit of detection at 95% of confidence of 20 and 22 copies/µL on the thermocyclers Rotor gene Q MDx and MX3005P, respectively. The study demonstrated the pivotal influence of the thermocycler on PCR performance for the detection of rabies RNA, as well as that of the master mixes.

Development and characterisation of chitosan films impregnated with insulin loaded PEG-b-PLA nanoparticles (NPs): a potential approach for buccal delivery of macromolecules.

PubMed

Giovino, Concetta; Ayensu, Isaac; Tetteh, John; Boateng, Joshua S

2012-05-30

Mucoadhesive chitosan based films, incorporated with insulin loaded nanoparticles (NPs) made of poly(ethylene glycol)methyl ether-block-polylactide (PEG-b-PLA) have been developed and characterised. Blank-NPs were prepared by double emulsion solvent evaporation technique with varying concentrations of the copolymer (5 and 10%, w/v). The optimised formulation was loaded with insulin (model protein) at initial loadings of 2, 5 and 10% with respect to copolymer weight. The developed NPs were analysed for size, size distribution, surface charge, morphology, encapsulation efficiency and drug release. NPs showing negative (ζ)-potential (<-6 mV) with average diameter> 300 nm and a polydispersity index (P.I.) of ≈ 0.2, irrespective of formulation process, were achieved. Insulin encapsulation efficiencies of 70% and 30% for NPs-Insulin-2 and NPs-Insulin-5 were obtained, respectively. The in vitro release behaviour of both formulations showed a classic biphasic sustained release of protein over 5 weeks which was influenced by pH of the release medium. Optimised chitosan films embedded with 3mg of insulin loaded NPs were produced by solvent casting with homogeneous distribution of NPs in the mucoadhesive matrix, which displayed excellent physico-mechanical properties. The drug delivery system has been designed as a novel platform for potential buccal delivery of macromolecules. Copyright © 2012 Elsevier B.V. All rights reserved.

Cross-Platform Evaluation of Commercial Real-Time SYBR Green RT-PCR Kits for Sensitive and Rapid Detection of European Bat Lyssavirus Type 1

PubMed Central

Picard-Meyer, Evelyne; Peytavin de Garam, Carine; Schereffer, Jean Luc; Marchal, Clotilde; Robardet, Emmanuelle; Cliquet, Florence

2015-01-01

This study evaluates the performance of five two-step SYBR Green RT-qPCR kits and five one-step SYBR Green qRT-PCR kits using real-time PCR assays. Two real-time thermocyclers showing different throughput capacities were used. The analysed performance evaluation criteria included the generation of standard curve, reaction efficiency, analytical sensitivity, intra- and interassay repeatability as well as the costs and the practicability of kits, and thermocycling times. We found that the optimised one-step PCR assays had a higher detection sensitivity than the optimised two-step assays regardless of the machine used, while no difference was detected in reaction efficiency, R 2 values, and intra- and interreproducibility between the two methods. The limit of detection at the 95% confidence level varied between 15 to 981 copies/µL and 41 to 171 for one-step kits and two-step kits, respectively. Of the ten kits tested, the most efficient kit was the Quantitect SYBR Green qRT-PCR with a limit of detection at 95% of confidence of 20 and 22 copies/µL on the thermocyclers Rotor gene Q MDx and MX3005P, respectively. The study demonstrated the pivotal influence of the thermocycler on PCR performance for the detection of rabies RNA, as well as that of the master mixes. PMID:25785274

hydroPSO: A Versatile Particle Swarm Optimisation R Package for Calibration of Environmental Models

NASA Astrophysics Data System (ADS)

Zambrano-Bigiarini, M.; Rojas, R.

2012-04-01

Particle Swarm Optimisation (PSO) is a recent and powerful population-based stochastic optimisation technique inspired by social behaviour of bird flocking, which shares similarities with other evolutionary techniques such as Genetic Algorithms (GA). In PSO, however, each individual of the population, known as particle in PSO terminology, adjusts its flying trajectory on the multi-dimensional search-space according to its own experience (best-known personal position) and the one of its neighbours in the swarm (best-known local position). PSO has recently received a surge of attention given its flexibility, ease of programming, low memory and CPU requirements, and efficiency. Despite these advantages, PSO may still get trapped into sub-optimal solutions, suffer from swarm explosion or premature convergence. Thus, the development of enhancements to the "canonical" PSO is an active area of research. To date, several modifications to the canonical PSO have been proposed in the literature, resulting into a large and dispersed collection of codes and algorithms which might well be used for similar if not identical purposes. In this work we present hydroPSO, a platform-independent R package implementing several enhancements to the canonical PSO that we consider of utmost importance to bring this technique to the attention of a broader community of scientists and practitioners. hydroPSO is model-independent, allowing the user to interface any model code with the calibration engine without having to invest considerable effort in customizing PSO to a new calibration problem. Some of the controlling options to fine-tune hydroPSO are: four alternative topologies, several types of inertia weight, time-variant acceleration coefficients, time-variant maximum velocity, regrouping of particles when premature convergence is detected, different types of boundary conditions and many others. Additionally, hydroPSO implements recent PSO variants such as: Improved Particle Swarm Optimisation (IPSO), Fully Informed Particle Swarm (FIPS), and weighted FIPS (wFIPS). Finally, an advanced sensitivity analysis using the Latin Hypercube One-At-a-Time (LH-OAT) method and user-friendly plotting summaries facilitate the interpretation and assessment of the calibration/optimisation results. We validate hydroPSO against the standard PSO algorithm (SPSO-2007) employing five test functions commonly used to assess the performance of optimisation algorithms. Additionally, we illustrate how the performance of the optimization/calibration engine is boosted by using several of the fine-tune options included in hydroPSO. Finally, we show how to interface SWAT-2005 with hydroPSO to calibrate a semi-distributed hydrological model for the Ega River basin in Spain, and how to interface MODFLOW-2000 and hydroPSO to calibrate a groundwater flow model for the regional aquifer of the Pampa del Tamarugal in Chile. We limit the applications of hydroPSO to study cases dealing with surface water and groundwater models as these two are the authors' areas of expertise. However, based on the flexibility of hydroPSO we believe this package can be implemented to any model code requiring some form of parameter estimation.

Review of sample preparation strategies for MS-based metabolomic studies in industrial biotechnology.

PubMed

Causon, Tim J; Hann, Stephan

2016-09-28

Fermentation and cell culture biotechnology in the form of so-called "cell factories" now play an increasingly significant role in production of both large (e.g. proteins, biopharmaceuticals) and small organic molecules for a wide variety of applications. However, associated metabolic engineering optimisation processes relying on genetic modification of organisms used in cell factories, or alteration of production conditions remain a challenging undertaking for improving the final yield and quality of cell factory products. In addition to genomic, transcriptomic and proteomic workflows, analytical metabolomics continues to play a critical role in studying detailed aspects of critical pathways (e.g. via targeted quantification of metabolites), identification of biosynthetic intermediates, and also for phenotype differentiation and the elucidation of previously unknown pathways (e.g. via non-targeted strategies). However, the diversity of primary and secondary metabolites and the broad concentration ranges encompassed during typical biotechnological processes means that simultaneous extraction and robust analytical determination of all parts of interest of the metabolome is effectively impossible. As the integration of metabolome data with transcriptome and proteome data is an essential goal of both targeted and non-targeted methods addressing production optimisation goals, additional sample preparation steps beyond necessary sampling, quenching and extraction protocols including clean-up, analyte enrichment, and derivatisation are important considerations for some classes of metabolites, especially those present in low concentrations or exhibiting poor stability. This contribution critically assesses the potential of current sample preparation strategies applied in metabolomic studies of industrially-relevant cell factory organisms using mass spectrometry-based platforms primarily coupled to liquid-phase sample introduction (i.e. flow injection, liquid chromatography, or capillary electrophoresis). Particular focus is placed on the selectivity and degree of enrichment attainable, as well as demands of speed, absolute quantification, robustness and, ultimately, consideration of fully-integrated bioanalytical solutions to optimise sample handling and throughput. Copyright © 2016 Elsevier B.V. All rights reserved.

Improving the pharmacokinetic properties of biologics by fusion to an anti-HSA shark VNAR domain

PubMed Central

Müller, Mischa R.; Saunders, Kenneth; Grace, Christopher; Jin, Macy; Piche-Nicholas, Nicole; Steven, John; O’Dwyer, Ronan; Wu, Leeying; Khetemenee, Lam; Vugmeyster, Yulia; Hickling, Timothy P.; Tchistiakova, Lioudmila; Olland, Stephane; Gill, Davinder; Jensen, Allan; Barelle, Caroline J.

2012-01-01

Advances in recombinant antibody technology and protein engineering have provided the opportunity to reduce antibodies to their smallest binding domain components and have concomitantly driven the requirement for devising strategies to increase serum half-life to optimise drug exposure, thereby increasing therapeutic efficacy. In this study, we adopted an immunization route to raise picomolar affinity shark immunoglobulin new antigen receptors (IgNARs) to target human serum albumin (HSA). From our model shark species, Squalus acanthias, a phage display library encompassing the variable binding domain of IgNAR (VNAR) was constructed, screened against target, and positive clones were characterized for affinity and specificity. N-terminal and C-terminal molecular fusions of our lead hit in complex with a naïve VNAR domain were expressed, purified and exhibited the retention of high affinity binding to HSA, but also cross-selectivity to mouse, rat and monkey serum albumin both in vitro and in vivo. Furthermore, the naïve VNAR had enhanced pharmacokinetic (PK) characteristics in both N- and C-terminal orientations and when tested as a three domain construct with naïve VNAR flanking the HSA binding domain at both the N and C termini. Molecules derived from this platform technology also demonstrated the potential for clinical utility by being available via the subcutaneous route of delivery. This study thus demonstrates the first in vivo functional efficacy of a VNAR binding domain with the ability to enhance PK properties and support delivery of multifunctional therapies. PMID:23676205

Improving the pharmacokinetic properties of biologics by fusion to an anti-HSA shark VNAR domain.

PubMed

Müller, Mischa R; Saunders, Kenneth; Grace, Christopher; Jin, Macy; Piche-Nicholas, Nicole; Steven, John; O'Dwyer, Ronan; Wu, Leeying; Khetemenee, Lam; Vugmeyster, Yulia; Hickling, Timothy P; Tchistiakova, Lioudmila; Olland, Stephane; Gill, Davinder; Jensen, Allan; Barelle, Caroline J

2012-01-01

Advances in recombinant antibody technology and protein engineering have provided the opportunity to reduce antibodies to their smallest binding domain components and have concomitantly driven the requirement for devising strategies to increase serum half-life to optimise drug exposure, thereby increasing therapeutic efficacy. In this study, we adopted an immunization route to raise picomolar affinity shark immunoglobulin new antigen receptors (IgNARs) to target human serum albumin (HSA). From our model shark species, Squalus acanthias, a phage display library encompassing the variable binding domain of IgNAR (VNAR) was constructed, screened against target, and positive clones were characterized for affinity and specificity. N-terminal and C-terminal molecular fusions of our lead hit in complex with a naïve VNAR domain were expressed, purified and exhibited the retention of high affinity binding to HSA, but also cross-selectivity to mouse, rat and monkey serum albumin both in vitro and in vivo. Furthermore, the naïve VNAR had enhanced pharmacokinetic (PK) characteristics in both N- and C-terminal orientations and when tested as a three domain construct with naïve VNAR flanking the HSA binding domain at both the N and C termini. Molecules derived from this platform technology also demonstrated the potential for clinical utility by being available via the subcutaneous route of delivery. This study thus demonstrates the first in vivo functional efficacy of a VNAR binding domain with the ability to enhance PK properties and support delivery of multifunctional therapies.

Warpage optimisation on the moulded part with straight-drilled and conformal cooling channels using response surface methodology (RSM) and glowworm swarm optimisation (GSO)

NASA Astrophysics Data System (ADS)

Hazwan, M. H. M.; Shayfull, Z.; Sharif, S.; Nasir, S. M.; Zainal, N.

2017-09-01

In injection moulding process, quality and productivity are notably important and must be controlled for each product type produced. Quality is measured as the extent of warpage of moulded parts while productivity is measured as a duration of moulding cycle time. To control the quality, many researchers have introduced various of optimisation approaches which have been proven enhanced the quality of the moulded part produced. In order to improve the productivity of injection moulding process, some of researches have proposed the application of conformal cooling channels which have been proven reduced the duration of moulding cycle time. Therefore, this paper presents an application of alternative optimisation approach which is Response Surface Methodology (RSM) with Glowworm Swarm Optimisation (GSO) on the moulded part with straight-drilled and conformal cooling channels mould. This study examined the warpage condition of the moulded parts before and after optimisation work applied for both cooling channels. A front panel housing have been selected as a specimen and the performance of proposed optimisation approach have been analysed on the conventional straight-drilled cooling channels compared to the Milled Groove Square Shape (MGSS) conformal cooling channels by simulation analysis using Autodesk Moldflow Insight (AMI) 2013. Based on the results, melt temperature is the most significant factor contribute to the warpage condition and warpage have optimised by 39.1% after optimisation for straight-drilled cooling channels and cooling time is the most significant factor contribute to the warpage condition and warpage have optimised by 38.7% after optimisation for MGSS conformal cooling channels. In addition, the finding shows that the application of optimisation work on the conformal cooling channels offers the better quality and productivity of the moulded part produced.

Imaging grafted cells with [18F]FHBG using an optimized HSV1-TK mammalian expression vector in a brain injury rodent model.

PubMed

Salabert, Anne-Sophie; Vaysse, Laurence; Beaurain, Marie; Alonso, Mathieu; Arribarat, Germain; Lotterie, Jean-Albert; Loubinoux, Isabelle; Tafani, Mathieu; Payoux, Pierre

2017-01-01

Cell transplantation is an innovative therapeutic approach after brain injury to compensate for tissue damage. To have real-time longitudinal monitoring of intracerebrally grafted cells, we explored the feasibility of a molecular imaging approach using thymidine kinase HSV1-TK gene encoding and [18F]FHBG as a reporter probe to image enzyme expression. A stable neuronal cell line expressing HSV1-TK was developed with an optimised mammalian expression vector to ensure long-term transgene expression. After [18F]FHBG incubation under defined parameters, calibration ranges from 1 X 104 to 3 X 106 Neuro2A-TK cells were analysed by gamma counter or by PET-camera. In parallel, grafting with different quantities of [18F]FHBG prelabelled Neuro2A-TK cells was carried out in a rat brain injury model induced by stereotaxic injection of malonate toxin. Image acquisition of the rats was then performed with PET/CT camera to study the [18F]FHBG signal of transplanted cells in vivo. Under the optimised incubation conditions, [18F]FHBG cell uptake rate was around 2.52%. In-vitro calibration range analysis shows a clear linear correlation between the number of cells and the signal intensity. The PET signal emitted into rat brain correlated well with the number of cells injected and the number of surviving grafted cells was recorded via the in-vitro calibration range. PET/CT acquisitions also allowed validation of the stereotaxic injection procedure. Technique sensitivity was evaluated under 5 X 104 grafted cells in vivo. No [18F]FHBG or [18F]metabolite release was observed showing a stable cell uptake even 2 h post-graft. The development of this kind of approach will allow grafting to be controlled and ensure longitudinal follow-up of cell viability and biodistribution after intracerebral injection.

e-Collaboration for Earth observation (E-CEO): the Cloud4SAR interferometry data challenge

NASA Astrophysics Data System (ADS)

Casu, Francesco; Manunta, Michele; Boissier, Enguerran; Brito, Fabrice; Aas, Christina; Lavender, Samantha; Ribeiro, Rita; Farres, Jordi

2014-05-01

The e-Collaboration for Earth Observation (E-CEO) project addresses the technologies and architectures needed to provide a collaborative research Platform for automating data mining and processing, and information extraction experiments. The Platform serves for the implementation of Data Challenge Contests focusing on Information Extraction for Earth Observations (EO) applications. The possibility to implement multiple processors within a Common Software Environment facilitates the validation, evaluation and transparent peer comparison among different methodologies, which is one of the main requirements rose by scientists who develop algorithms in the EO field. In this scenario, we set up a Data Challenge, referred to as Cloud4SAR (http://wiki.services.eoportal.org/tiki-index.php?page=ECEO), to foster the deployment of Interferometric SAR (InSAR) processing chains within a Cloud Computing platform. While a large variety of InSAR processing software tools are available, they require a high level of expertise and a complex user interaction to be effectively run. Computing a co-seismic interferogram or a 20-years deformation time series on a volcanic area are not easy tasks to be performed in a fully unsupervised way and/or in very short time (hours or less). Benefiting from ESA's E-CEO platform, participants can optimise algorithms on a Virtual Sandbox environment without being expert programmers, and compute results on high performing Cloud platforms. Cloud4SAR requires solving a relatively easy InSAR problem by trying to maximize the exploitation of the processing capabilities provided by a Cloud Computing infrastructure. The proposed challenge offers two different frameworks, each dedicated to participants with different skills, identified as Beginners and Experts. For both of them, the contest mainly resides in the degree of automation of the deployed algorithms, no matter which one is used, as well as in the capability of taking effective benefit from a parallel computing environment.

A Novel Software Platform Extending Advances in Monitoring Technologies to On-demand Decision Support

NASA Astrophysics Data System (ADS)

Ormerod, R.; Scholl, M.

2017-12-01

Rapid evolution is occurring in the monitoring and assessment of air emissions and their impacts. The development of next generation lower cost sensor technologies creates the potential for much more intensive and far-reaching monitoring networks that provide spatially rich data. While much attention at present is being directed at the types and performance characteristics of sensor technologies, it is important also that the full potential of rich data sources be realized. Parallel to sensor developments, software platforms to display and manage data in real time are increasingly common adjuncts to sensor networks. However, the full value of data can be realized by extending platform capabilities to include complex scientific functions that are integrated into an action-oriented management framework. Depending on the purpose and nature of a monitoring network, there will be a variety of potential uses of the data or its derivatives, for example: statistical analysis for policy development, event analysis, real-time issue management including emergency response and complaints, and predictive management. Moving these functions into an on-demand, optionally mobile, environment greatly increases the value and accessibility of the data. Increased interplay between monitoring data and decision-making in an operational environment is optimised by a system that is designed with equal weight on technical robustness and user experience. A system now being used by several regulatory agencies and a larger number of industries in the US, Latin America, Europe, Australia and Asia has been developed to provide a wide range of on-demand decision-support in addition to the basic data collection, display and management that most platforms offer. With stable multi-year operation, the platform, known as Envirosuite, is assisting organisations to both reduce operating costs and improve environmental performance. Some current examples of its application across a range of applications for regulatory and industry organisations is described and demonstrated.

Comparative venom gland transcriptomics of Naja kaouthia (monocled cobra) from Malaysia and Thailand: elucidating geographical venom variation and insights into sequence novelty

PubMed Central

Chanhome, Lawan; Tan, Nget Hong

2017-01-01

Background The monocled cobra (Naja kaouthia) is a medically important venomous snake in Southeast Asia. Its venom has been shown to vary geographically in relation to venom composition and neurotoxic activity, indicating vast diversity of the toxin genes within the species. To investigate the polygenic trait of the venom and its locale-specific variation, we profiled and compared the venom gland transcriptomes of N. kaouthia from Malaysia (NK-M) and Thailand (NK-T) applying next-generation sequencing (NGS) technology. Methods The transcriptomes were sequenced on the Illumina HiSeq platform, assembled and followed by transcript clustering and annotations for gene expression and function. Pairwise or multiple sequence alignments were conducted on the toxin genes expressed. Substitution rates were studied for the major toxins co-expressed in NK-M and NK-T. Results and discussion The toxin transcripts showed high redundancy (41–82% of the total mRNA expression) and comprised 23 gene families expressed in NK-M and NK-T, respectively (22 gene families were co-expressed). Among the venom genes, three-finger toxins (3FTxs) predominated in the expression, with multiple sequences noted. Comparative analysis and selection study revealed that 3FTxs are genetically conserved between the geographical specimens whilst demonstrating distinct differential expression patterns, implying gene up-regulation for selected principal toxins, or alternatively, enhanced transcript degradation or lack of transcription of certain traits. One of the striking features that elucidates the inter-geographical venom variation is the up-regulation of α-neurotoxins (constitutes ∼80.0% of toxin’s fragments per kilobase of exon model per million mapped reads (FPKM)), particularly the long-chain α-elapitoxin-Nk2a (48.3%) in NK-T but only 1.7% was noted in NK-M. Instead, short neurotoxin isoforms were up-regulated in NK-M (46.4%). Another distinct transcriptional pattern observed is the exclusively and abundantly expressed cytotoxin CTX-3 in NK-T. The findings suggested correlation with the geographical variation in proteome and toxicity of the venom, and support the call for optimising antivenom production and use in the region. Besides, the current study uncovered full and partial sequences of numerous toxin genes from N. kaouthia which have not been reported hitherto; these include N. kaouthia-specific l-amino acid oxidase (LAAO), snake venom serine protease (SVSP), cystatin, acetylcholinesterase (AChE), hyaluronidase (HYA), waprin, phospholipase B (PLB), aminopeptidase (AP), neprilysin, etc. Taken together, the findings further enrich the snake toxin database and provide deeper insights into the genetic diversity of cobra venom toxins. PMID:28392982

A native IP satellite communications system

NASA Astrophysics Data System (ADS)

Koudelka, O.; Schmidt, M.; Ebert, J.; Schlemmer, H.; Kastner-Puschl, S.; Riedler, W.

2004-08-01

≪ In the framework of ESA's ARTES-5 program the Institute of Applied Systems Technology (Joanneum Research) in cooperation with the Department of Communications and Wave Propagation has developed a novel meshed satellite communications system which is optimised for Internet traffic and applications (L*IP—Local Network Interconnection via Satellite Systems Using the IP Protocol Suite). Both symmetrical and asymmetrical connections are supported. Bandwidth on demand and guaranteed quality of service are key features of the system. A novel multi-frequency TDMA access scheme utilises efficient methods of IP encapsulation. In contrast to other solutions it avoids legacy transport network techniques. While the DVB-RCS standard is based on ATM or MPEG transport cells, the solution of the L*IP system uses variable-length cells which reduces the overhead significantly. A flexible and programmable platform based on Linux machines was chosen to allow the easy implementation and adaptation to different standards. This offers the possibility to apply the system not only to satellite communications, but provides seamless integration with terrestrial fixed broadcast wireless access systems. The platform is also an ideal test-bed for a variety of interactive broadband communications systems. The paper describes the system architecture and the key features of the system.

Community engagement for paediatric MDR-TB clinical trials: principles to support ethical trial implementation.

PubMed

Hoddinott, G; Staples, S; Brown, R; Simwinga, M; Mubekapi-Musadaidzwa, C; Hesseling, A C; Hendricks, G; De Koker, P; McKenna, L

2018-05-01

The paediatric tuberculosis (TB) prevention and treatment landscape is moving into a new and exciting era, with knowledge from clinical trials offering real benefit to children. Community engagement is key to optimising the success of these trials. However, the clinical profile, epidemiology and social perceptions for paediatric multidrug-resistant TB (MDR-TB) complicate the operationalisation of this community engagement. We reflect on a diversity of recent experiences attempting to implement this type of research and the community engagement around it. We describe four recommendations and argue that these should guide the implementation of the community engagement agenda in the new landscape of paediatric MDR-TB clinical trials. Specifically, we argue for 1) dynamic, long-term continuity in community engagement platforms; 2) tiers of TB and research literacy; 3) multiple separate and joint platforms for holding 'stakes'; and 4) addressing the social/structural implications of family participation. We conclude that community-level stakeholders, such as health workers, parents and children, are willing to collaborate in paediatric MDR-TB clinical trials. Using these recommendations, there is considerable opportunity for effective community engagement in this new era of paediatric MDR-TB research.

Using Optimisation Techniques to Granulise Rough Set Partitions

NASA Astrophysics Data System (ADS)

Crossingham, Bodie; Marwala, Tshilidzi

2007-11-01

This paper presents an approach to optimise rough set partition sizes using various optimisation techniques. Three optimisation techniques are implemented to perform the granularisation process, namely, genetic algorithm (GA), hill climbing (HC) and simulated annealing (SA). These optimisation methods maximise the classification accuracy of the rough sets. The proposed rough set partition method is tested on a set of demographic properties of individuals obtained from the South African antenatal survey. The three techniques are compared in terms of their computational time, accuracy and number of rules produced when applied to the Human Immunodeficiency Virus (HIV) data set. The optimised methods results are compared to a well known non-optimised discretisation method, equal-width-bin partitioning (EWB). The accuracies achieved after optimising the partitions using GA, HC and SA are 66.89%, 65.84% and 65.48% respectively, compared to the accuracy of EWB of 59.86%. In addition to rough sets providing the plausabilities of the estimated HIV status, they also provide the linguistic rules describing how the demographic parameters drive the risk of HIV.

Propagation of evanescent waves in multimode chalcogenide fiber immersed in an aqueous acetone solution: theory and experiment

NASA Astrophysics Data System (ADS)

Korsakova, S. V.; Romanova, E. A.; Velmuzhov, A. P.; Kotereva, T. V.; Sukhanov, M. V.; Shiryaev, V. S.

2017-04-01

Chalcogenide fibers are considered as a base for creation of a fiber-optical platform for the mid-IR evanescent wave spectroscopy. In this work, transmittance of a multimode fiber made of Ge26As17Se25Te32 glass, immersed into an aqueous acetone solution was measured in the range of wavelengths 5 - 9 microns at various concentrations of the solution. A theoretical approach based on electromagnetic theory of optical fibers has been applied for analysis of evanescent modes propagation in the fiber. Attenuation coefficients calculated for each HE1m evanescent mode increase with the mode radial order m. This effect can be used for optimisation of the fiber-optic sensing elements for the mid-IR spectroscopy.

A lab-on-a-chip-based multiplex platform to detect potential fraud of introducing pig, dog, cat, rat and monkey meat into the food chain.

PubMed

Razzak, Md Abdur; Hamid, Sharifah Bee Abd; Ali, Md Eaqub

2015-01-01

Food forgery has posed considerable risk to public health, religious rituals, personal budget and wildlife. Pig, dog, cat, rat and monkey meat are restricted in most religions, but their sporadic adulteration are rampant. Market controllers need a low-cost but reliable technique to track and trace suspected species in the food chain. Considering the need, here we documented a lab-on-a-chip-based multiplex polymerase chain reaction (PCR) assay for the authentication of five non-halal meat species in foods. Using species-specific primers, 172, 163, 141, 129 and 108-bp sites of mitochondrial ND5, ATPase 6 and cytochrome b genes were amplified to detect cat, dog, pig, monkey and rat species under complex matrices. Species-specificity was authenticated against 20 different species with the potential to be used in food. The targets were stable under extreme sterilisation (121°C at 45 psi for 2.5 h) which severely degrades DNA. The assay was optimised under the backgrounds of various commercial meat products and validated for the analysis of meatballs, burgers and frankfurters, which are popular fast food items across the globe. The assay was tested to detect 0.1% suspected meats under commercial backgrounds of marketed foods. Instead of simplex PCR which detects only one species at a time, such a multiplex platform can reduce cost by at least fivefolds by detecting five different species in a single assay platform.

Functional testing of topical skin formulations using an optimised ex vivo skin organ culture model.

PubMed

Sidgwick, G P; McGeorge, D; Bayat, A

2016-07-01

A number of equivalent-skin models are available for investigation of the ex vivo effect of topical application of drugs and cosmaceuticals onto skin, however many have their drawbacks. With the March 2013 ban on animal models for cosmetic testing of products or ingredients for sale in the EU, their utility for testing toxicity and effect on skin becomes more relevant. The aim of this study was to demonstrate proof of principle that altered expression of key gene and protein markers could be quantified in an optimised whole tissue biopsy culture model. Topical formulations containing green tea catechins (GTC) were investigated in a skin biopsy culture model (n = 11). Punch biopsies were harvested at 3, 7 and 10 days, and analysed using qRT-PCR, histology and HPLC to determine gene and protein expression, and transdermal delivery of compounds of interest. Reduced gene expression of α-SMA, fibronectin, mast cell tryptase, mast cell chymase, TGF-β1, CTGF and PAI-1 was observed after 7 and 10 days compared with treated controls (p < 0.05). Histological analysis indicated a reduction in mast cell tryptase and chymase positive cell numbers in treated biopsies compared with untreated controls at day 7 and day 10 (p < 0.05). Determination of transdermal uptake indicated that GTCs were detected in the biopsies. This model could be adapted to study a range of different topical formulations in both normal and diseased skin, negating the requirement for animal models in this context, prior to study in a clinical trial environment.

Analysis of optimisation method for a two-stroke piston ring using the Finite Element Method and the Simulated Annealing Method

NASA Astrophysics Data System (ADS)

Kaliszewski, M.; Mazuro, P.

2016-09-01

Simulated Annealing Method of optimisation for the sealing piston ring geometry is tested. The aim of optimisation is to develop ring geometry which would exert demanded pressure on a cylinder just while being bended to fit the cylinder. Method of FEM analysis of an arbitrary piston ring geometry is applied in an ANSYS software. The demanded pressure function (basing on formulae presented by A. Iskra) as well as objective function are introduced. Geometry definition constructed by polynomials in radial coordinate system is delivered and discussed. Possible application of Simulated Annealing Method in a piston ring optimisation task is proposed and visualised. Difficulties leading to possible lack of convergence of optimisation are presented. An example of an unsuccessful optimisation performed in APDL is discussed. Possible line of further optimisation improvement is proposed.

Development of an IP-Free Biotechnology Platform for Constitutive Production of HPV16 L1 Capsid Protein Using the Pichia pastoris PGK1 Promoter.

PubMed

Mariz, F C; Coimbra, E C; Jesus, A L S; Nascimento, L M; Torres, F A G; Freitas, A C

2015-01-01

The human papillomavirus (HPV) L1 major capsid protein, which forms the basis of the currently available vaccines against cervical cancer, self-assembles into virus-like particles (VLPs) when expressed heterologously. We report the development of a biotechnology platform for HPV16 L1 protein expression based on the constitutive PGK1 promoter (PPGK1) from the methylotrophic yeast Pichia pastoris. The L1 gene was cloned under regulation of PPGK1 into pPGKΔ3 expression vector to achieve intracellular expression. In parallel, secretion of the L1 protein was obtained through the use of an alternative vector called pPGKΔ3α, in which a codon optimized α-factor signal sequence was inserted. We devised a work-flow based on the detection of the L1 protein by dot blot, colony blot, and western blot to classify the positive clones. Finally, intracellular HPV VLPs assembly was demonstrated for the first time in yeast cells. This study opens up perspectives for the establishment of an innovative platform for the production of HPV VLPs or other viral antigens for vaccination purposes, based on constitutive expression in P. pastoris.

Engineering modular ‘ON’ RNA switches using biological components

PubMed Central

Ceres, Pablo; Trausch, Jeremiah J.; Batey, Robert T.

2013-01-01

Riboswitches are cis-acting regulatory elements broadly distributed in bacterial mRNAs that control a wide range of critical metabolic activities. Expression is governed by two distinct domains within the mRNA leader: a sensory ‘aptamer domain’ and a regulatory ‘expression platform’. Riboswitches have also received considerable attention as important tools in synthetic biology because of their conceptually simple structure and the ability to obtain aptamers that bind almost any conceivable small molecule using in vitro selection (referred to as SELEX). In the design of artificial riboswitches, a significant hurdle has been to couple the two domains enabling their efficient communication. We previously demonstrated that biological transcriptional ‘OFF’ expression platforms are easily coupled to diverse aptamers, both biological and SELEX-derived, using simple design rules. Here, we present two modular transcriptional ‘ON’ riboswitch expression platforms that are also capable of hosting foreign aptamers. We demonstrate that these biological parts can be used to facilely generate artificial chimeric riboswitches capable of robustly regulating transcription both in vitro and in vivo. We expect that these modular expression platforms will be of great utility for various synthetic biological applications that use RNA-based biosensors. PMID:23999097

Gene expression platform for synthetic biology in the human pathogen Streptococcus pneumoniae.

PubMed

Sorg, Robin A; Kuipers, Oscar P; Veening, Jan-Willem

2015-03-20

The human pathogen Streptococcus pneumoniae (pneumococcus) is a bacterium that owes its success to complex gene expression regulation patterns on both the cellular and the population level. Expression of virulence factors enables a mostly hazard-free presence of the commensal, in balance with the host and niche competitors. Under specific circumstances, changes in this expression can result in a more aggressive behavior and the reversion to the invasive form as pathogen. These triggering conditions are very difficult to study due to the fact that environmental cues are often unknown or barely possible to simulate outside the host (in vitro). An alternative way of investigating expression patterns is found in synthetic biology approaches of reconstructing regulatory networks that mimic an observed behavior with orthogonal components. Here, we created a genetic platform suitable for synthetic biology approaches in S. pneumoniae and characterized a set of standardized promoters and reporters. We show that our system allows for fast and easy cloning with the BglBrick system and that reliable and robust gene expression after integration into the S. pneumoniae genome is achieved. In addition, the cloning system was extended to allow for direct linker-based assembly of ribosome binding sites, peptide tags, and fusion proteins, and we called this new generally applicable standard "BglFusion". The gene expression platform and the methods described in this study pave the way for employing synthetic biology approaches in S. pneumoniae.

The Corn Smut ('Huitlacoche') as a New Platform for Oral Vaccines.

PubMed

Juárez-Montiel, Margarita; Romero-Maldonado, Andrea; Monreal-Escalante, Elizabeth; Becerra-Flora, Alicia; Korban, Schuyler S; Rosales-Mendoza, Sergio; Jiménez-Bremont, Juan Francisco

2015-01-01

The development of new alternative platforms for subunit vaccine production is a priority in the biomedical field. In this study, Ustilago maydis, the causal agent of common corn smut or 'huitlacoche'has been genetically engineered to assess expression and immunogenicity of the B subunit of the cholera toxin (CTB), a relevant immunomodulatory agent in vaccinology. An oligomeric CTB recombinant protein was expressed in corn smut galls at levels of up to 1.3 mg g-1 dry weight (0.8% of the total soluble protein). Mice orally immunized with 'huitlacoche'-derived CTB showed significant humoral responses that were well-correlated with protection against challenge with the cholera toxin (CT). These findings demonstrate the feasibility of using edible corn smut as a safe, effective, and low-cost platform for production and delivery of a subunit oral vaccine. The implications of this platform in the area of molecular pharming are discussed.

The Corn Smut (‘Huitlacoche’) as a New Platform for Oral Vaccines

PubMed Central

Juárez-Montiel, Margarita; Romero-Maldonado, Andrea; Monreal-Escalante, Elizabeth; Becerra-Flora, Alicia; Korban, Schuyler S.; Rosales-Mendoza, Sergio; Jiménez-Bremont, Juan Francisco

2015-01-01

The development of new alternative platforms for subunit vaccine production is a priority in the biomedical field. In this study, Ustilago maydis, the causal agent of common corn smut or ‘huitlacoche’has been genetically engineered to assess expression and immunogenicity of the B subunit of the cholera toxin (CTB), a relevant immunomodulatory agent in vaccinology. An oligomeric CTB recombinant protein was expressed in corn smut galls at levels of up to 1.3 mg g-1 dry weight (0.8% of the total soluble protein). Mice orally immunized with ‘huitlacoche’-derived CTB showed significant humoral responses that were well-correlated with protection against challenge with the cholera toxin (CT). These findings demonstrate the feasibility of using edible corn smut as a safe, effective, and low-cost platform for production and delivery of a subunit oral vaccine. The implications of this platform in the area of molecular pharming are discussed. PMID:26207365

A comprehensive comparison of RNA-Seq-based transcriptome analysis from reads to differential gene expression and cross-comparison with microarrays: a case study in Saccharomyces cerevisiae

PubMed Central

Nookaew, Intawat; Papini, Marta; Pornputtapong, Natapol; Scalcinati, Gionata; Fagerberg, Linn; Uhlén, Matthias; Nielsen, Jens

2012-01-01

RNA-seq, has recently become an attractive method of choice in the studies of transcriptomes, promising several advantages compared with microarrays. In this study, we sought to assess the contribution of the different analytical steps involved in the analysis of RNA-seq data generated with the Illumina platform, and to perform a cross-platform comparison based on the results obtained through Affymetrix microarray. As a case study for our work we, used the Saccharomyces cerevisiae strain CEN.PK 113-7D, grown under two different conditions (batch and chemostat). Here, we asses the influence of genetic variation on the estimation of gene expression level using three different aligners for read-mapping (Gsnap, Stampy and TopHat) on S288c genome, the capabilities of five different statistical methods to detect differential gene expression (baySeq, Cuffdiff, DESeq, edgeR and NOISeq) and we explored the consistency between RNA-seq analysis using reference genome and de novo assembly approach. High reproducibility among biological replicates (correlation ≥0.99) and high consistency between the two platforms for analysis of gene expression levels (correlation ≥0.91) are reported. The results from differential gene expression identification derived from the different statistical methods, as well as their integrated analysis results based on gene ontology annotation are in good agreement. Overall, our study provides a useful and comprehensive comparison between the two platforms (RNA-seq and microrrays) for gene expression analysis and addresses the contribution of the different steps involved in the analysis of RNA-seq data. PMID:22965124

An approach to optimised control of HVAC systems in indoor swimming pools

NASA Astrophysics Data System (ADS)

Ribeiro, Eliseu M. A.; Jorge, Humberto M. M.; Quintela, Divo A. A.

2016-04-01

Indoor swimming pools are recognised as having a high level of energy consumption and present a great potential for energy saving. The energy is spent in several ways such as evaporation heat loss from the pool, high rates of ventilation required to guarantee the indoor air quality, and ambient temperatures with expressive values (typically 28-30°C) required to maintain conditions of comfort. This paper presents an approach to optimising control of heat ventilation and air conditioning systems that could be implemented in a building energy management system. It is easily adapted to any kind of pool and results in significant energy consumption reduction. The development and validation of the control model were carried out with a building thermal simulation software. The use of this control model in the case study building could reduce the energy efficiency index by 7.14 points (7.4% of total) which adds up to an energy cost saving of 15,609€ (7.5% of total).

Engineering synthetic TALE and CRISPR/Cas9 transcription factors for regulating gene expression.

PubMed

Kabadi, Ami M; Gersbach, Charles A

2014-09-01

Engineered DNA-binding proteins that can be targeted to specific sites in the genome to manipulate gene expression have enabled many advances in biomedical research. This includes generating tools to study fundamental aspects of gene regulation and the development of a new class of gene therapies that alter the expression of endogenous genes. Designed transcription factors have entered clinical trials for the treatment of human diseases and others are in preclinical development. High-throughput and user-friendly platforms for designing synthetic DNA-binding proteins present innovative methods for deciphering cell biology and designing custom synthetic gene circuits. We review two platforms for designing synthetic transcription factors for manipulating gene expression: Transcription activator-like effectors (TALEs) and the RNA-guided clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 system. We present an overview of each technology and a guide for designing and assembling custom TALE- and CRISPR/Cas9-based transcription factors. We also discuss characteristics of each platform that are best suited for different applications. Copyright © 2014 Elsevier Inc. All rights reserved.

Multidisciplinary design optimisation of a recurve bow based on applications of the autogenetic design theory and distributed computing

NASA Astrophysics Data System (ADS)

Fritzsche, Matthias; Kittel, Konstantin; Blankenburg, Alexander; Vajna, Sándor

2012-08-01

The focus of this paper is to present a method of multidisciplinary design optimisation based on the autogenetic design theory (ADT) that provides methods, which are partially implemented in the optimisation software described here. The main thesis of the ADT is that biological evolution and the process of developing products are mainly similar, i.e. procedures from biological evolution can be transferred into product development. In order to fulfil requirements and boundary conditions of any kind (that may change at any time), both biological evolution and product development look for appropriate solution possibilities in a certain area, and try to optimise those that are actually promising by varying parameters and combinations of these solutions. As the time necessary for multidisciplinary design optimisations is a critical aspect in product development, ways to distribute the optimisation process with the effective use of unused calculating capacity, can reduce the optimisation time drastically. Finally, a practical example shows how ADT methods and distributed optimising are applied to improve a product.

Performance comparison of two microarray platforms to assess differential gene expression in human monocyte and macrophage cells

PubMed Central

Maouche, Seraya; Poirier, Odette; Godefroy, Tiphaine; Olaso, Robert; Gut, Ivo; Collet, Jean-Phillipe; Montalescot, Gilles; Cambien, François

2008-01-01

Background In this study we assessed the respective ability of Affymetrix and Illumina microarray methodologies to answer a relevant biological question, namely the change in gene expression between resting monocytes and macrophages derived from these monocytes. Five RNA samples for each type of cell were hybridized to the two platforms in parallel. In addition, a reference list of differentially expressed genes (DEG) was generated from a larger number of hybridizations (mRNA from 86 individuals) using the RNG/MRC two-color platform. Results Our results show an important overlap of the Illumina and Affymetrix DEG lists. In addition, more than 70% of the genes in these lists were also present in the reference list. Overall the two platforms had very similar performance in terms of biological significance, evaluated by the presence in the DEG lists of an excess of genes belonging to Gene Ontology (GO) categories relevant for the biology of monocytes and macrophages. Our results support the conclusion of the MicroArray Quality Control (MAQC) project that the criteria used to constitute the DEG lists strongly influence the degree of concordance among platforms. However the importance of prioritizing genes by magnitude of effect (fold change) rather than statistical significance (p-value) to enhance cross-platform reproducibility recommended by the MAQC authors was not supported by our data. Conclusion Functional analysis based on GO enrichment demonstrates that the 2 compared technologies delivered very similar results and identified most of the relevant GO categories enriched in the reference list. PMID:18578872

FaceTOON: a unified platform for feature-based cartoon expression generation

NASA Astrophysics Data System (ADS)

Zaharia, Titus; Marre, Olivier; Prêteux, Françoise; Monjaux, Perrine

2008-02-01

This paper presents the FaceTOON system, a semi-automatic platform dedicated to the creation of verbal and emotional facial expressions, within the applicative framework of 2D cartoon production. The proposed FaceTOON platform makes it possible to rapidly create 3D facial animations with a minimum amount of user interaction. In contrast with existing commercial 3D modeling softwares, which usually require from the users advanced 3D graphics skills and competences, the FaceTOON system is based exclusively on 2D interaction mechanisms, the 3D modeling stage being completely transparent for the user. The system takes as input a neutral 3D face model, free of any facial feature, and a set of 2D drawings, representing the desired facial features. A 2D/3D virtual mapping procedure makes it possible to obtain a ready-for-animation model which can be directly manipulated and deformed for generating expressions. The platform includes a complete set of dedicated tools for 2D/3D interactive deformation, pose management, key-frame interpolation and MPEG-4 compliant animation and rendering. The proposed FaceTOON system is currently considered for industrial evaluation and commercialization by the Quadraxis company.

Comparative immune responses of corals to stressors associated with offshore reef-based tourist platforms

PubMed Central

Lamb, Joleah B; van Oppen, Madeleine J H; Willis, Bette L; Bourne, David G

2015-01-01

Abstract Unravelling the contributions of local anthropogenic and seasonal environmental factors in suppressing the coral immune system is important for prioritizing management actions at reefs exposed to high levels of human activities. Here, we monitor health of the model coral Acropora millepora adjacent to a high-use and an unused reef-based tourist platform, plus a nearby control site without a platform, over 7 months spanning a typical austral summer. Comparisons of temporal patterns in a range of biochemical and genetic immune parameters (Toll-like receptor signalling pathway, lectin–complement system, prophenoloxidase-activating system and green fluorescent protein-like proteins) among healthy, injured and diseased corals revealed that corals exhibit a diverse array of immune responses to environmental and anthropogenic stressors. In healthy corals at the control site, expression of genes involved in the Toll-like receptor signalling pathway (MAPK p38, MEKK1, cFos and ATF4/5) and complement system (C3 and Bf) was modulated by seasonal environmental factors in summer months. Corals at reef platform sites experienced additional stressors over the summer, as evidenced by increased expression of various immune genes, including MAPK p38 and MEKK1. Despite increased expression of immune genes, signs of white syndromes were detected in 31% of study corals near tourist platforms in the warmest summer month. Evidence that colonies developing disease showed reduced expression of genes involved in the complement pathway prior to disease onset suggests that their immune systems may have been compromised. Responses to disease and physical damage primarily involved the melanization cascade and GFP-like proteins, and appeared to be sufficient for recovery when summer heat stress subsided. Overall, seasonal and anthropogenic factors may have interacted synergistically to overwhelm the immune systems of corals near reef platforms, leading to increased disease prevalence in summer at these sites. PMID:27293717

Novel Single-Cell Analysis Platform Based on a Solid-State Zinc-Coadsorbed Carbon Quantum Dots Electrochemiluminescence Probe for the Evaluation of CD44 Expression on Breast Cancer Cells.

PubMed

Qiu, Youyi; Zhou, Bin; Yang, Xiaojuan; Long, Dongping; Hao, Yan; Yang, Peihui

2017-05-24

A novel single-cell analysis platform was fabricated using solid-state zinc-coadsorbed carbon quantum dot (ZnCQDs) nanocomposites as an electrochemiluminescence (ECL) probe for the detection of breast cancer cells and evaluation of the CD44 expression level. Solid-state ZnCQDs nanocomposite probes were constructed through the attachment of ZnCQDs to gold nanoparticles and then the loading of magnetic beads to amplify the ECL signal, exhibiting a remarkable 120-fold enhancement of the ECL intensity. Hyaluronic acid (HA)-functionalized solid-state probes were used to label a single breast cancer cell by the specific recognition of HA with CD44 on the cell surface, revealing more stable, sensitive, and effective tagging in comparison with the water-soluble CQDs. This strategy exhibited a good analytical performance for the analysis of MDA-MB-231 and MCF-7 single cells with linear range from 1 to 18 and from 1 to 12 cells, respectively. Furthermore, this single-cell analysis platform was used for evaluation of the CD44 expression level of these two cell lines, in which the MDA-MB-231 cells revealed a 2.8-5.2-fold higher CD44 expression level. A total of 20 single cells were analyzed individually, and the distributions of the ECL intensity revealed larger variations, indicating the high cellular heterogeneity of the CD44 expression level on the same cell line. The as-proposed single-cell analysis platform might provide a novel protocol to effectively study the individual cellular function and cellular heterogeneity.

Protocol: optimising hydroponic growth systems for nutritional and physiological analysis of Arabidopsis thaliana and other plants

PubMed Central

2013-01-01

Background Hydroponic growth systems are a convenient platform for studying whole plant physiology. However, we found through trialling systems as they are described in the literature that our experiments were frequently confounded by factors that affected plant growth, including algal contamination and hypoxia. We also found the way in which the plants were grown made them poorly amenable to a number of common physiological assays. Results The drivers for the development of this hydroponic system were: 1) the exclusion of light from the growth solution; 2) to simplify the handling of individual plants, and 3) the growth of the plant to allow easy implementation of multiple assays. These aims were all met by the use of pierced lids of black microcentrifuge tubes. Seed was germinated on a lid filled with an agar-containing germination media immersed in the same solution. Following germination, the liquid growth media was exchanged with the experimental solution, and after 14-21 days seedlings were transferred to larger tanks with aerated solution where they remained until experimentation. We provide details of the protocol including composition of the basal growth solution, and separate solutions with altered calcium, magnesium, potassium or sodium supply whilst maintaining the activity of the majority of other ions. We demonstrate the adaptability of this system for: gas exchange measurement on single leaves and whole plants; qRT-PCR to probe the transcriptional response of roots or shoots to altered nutrient composition in the growth solution (we demonstrate this using high and low calcium supply); producing highly competent mesophyll protoplasts; and, accelerating the screening of Arabidopsis transformants. This system is also ideal for manipulating plants for micropipette techniques such as electrophysiology or SiCSA. Conclusions We present an optimised plant hydroponic culture system that can be quickly and cheaply constructed, and produces plants with similar growth kinetics to soil-grown plants, but with the advantage of being a versatile platform for a myriad of physiological and molecular biological measurements on all plant tissues at all developmental stages. We present ‘tips and tricks’ for the easy adoption of this hydroponic culture system. PMID:23379342

Methylene blue not ferrocene: Optimal reporters for electrochemical detection of protease activity.

PubMed

González-Fernández, Eva; Avlonitis, Nicolaos; Murray, Alan F; Mount, Andrew R; Bradley, Mark

2016-10-15

Electrochemical peptide-based biosensors are attracting significant attention for the detection and analysis of proteins. Here we report the optimisation and evaluation of an electrochemical biosensor for the detection of protease activity using self-assembled monolayers (SAMs) on gold surfaces, using trypsin as a model protease. The principle of detection was the specific proteolytic cleavage of redox-tagged peptides by trypsin, which causes the release of the redox reporter, resulting in a decrease of the peak current as measured by square wave voltammetry. A systematic enhancement of detection was achieved through optimisation of the properties of the redox-tagged peptide; this included for the first time a side-by-side study of the applicability of two of the most commonly applied redox reporters used for developing electrochemical biosensors, ferrocene and methylene blue, along with the effect of changing both the nature of the spacer and the composition of the SAM. Methylene blue-tagged peptides combined with a polyethylene-glycol (PEG) based spacer were shown to be the best platform for trypsin detection, leading to the highest fidelity signals (characterised by the highest sensitivity (signal gain) and a much more stable background than that registered when using ferrocene as a reporter). A ternary SAM (T-SAM) configuration, which included a PEG-based dithiol, minimised the non-specific adsorption of other proteins and was sensitive towards trypsin in the clinically relevant range, with a Limit of Detection (LoD) of 250pM. Kinetic analysis of the electrochemical response with time showed a good fit to a Michaelis-Menten surface cleavage model, enabling the extraction of values for kcat and KM. Fitting to this model enabled quantitative determination of the solution concentration of trypsin across the entire measurement range. Studies using an enzyme inhibitor and a range of real world possible interferents demonstrated a selective response to trypsin cleavage. This indicates that a PEG-based peptide, employing methylene blue as redox reporter, and deposited on an electrode as a ternary SAM configuration, is a suitable platform to develop clinically-relevant and quantitative electrochemical peptide-based protease biosensing. Copyright © 2015 The Authors. Published by Elsevier B.V. All rights reserved.

Guidelines for whole genome bisulphite sequencing of intact and FFPET DNA on the Illumina HiSeq X Ten.

PubMed

Nair, Shalima S; Luu, Phuc-Loi; Qu, Wenjia; Maddugoda, Madhavi; Huschtscha, Lily; Reddel, Roger; Chenevix-Trench, Georgia; Toso, Martina; Kench, James G; Horvath, Lisa G; Hayes, Vanessa M; Stricker, Phillip D; Hughes, Timothy P; White, Deborah L; Rasko, John E J; Wong, Justin J-L; Clark, Susan J

2018-05-28

Comprehensive genome-wide DNA methylation profiling is critical to gain insights into epigenetic reprogramming during development and disease processes. Among the different genome-wide DNA methylation technologies, whole genome bisulphite sequencing (WGBS) is considered the gold standard for assaying genome-wide DNA methylation at single base resolution. However, the high sequencing cost to achieve the optimal depth of coverage limits its application in both basic and clinical research. To achieve 15× coverage of the human methylome, using WGBS, requires approximately three lanes of 100-bp-paired-end Illumina HiSeq 2500 sequencing. It is important, therefore, for advances in sequencing technologies to be developed to enable cost-effective high-coverage sequencing. In this study, we provide an optimised WGBS methodology, from library preparation to sequencing and data processing, to enable 16-20× genome-wide coverage per single lane of HiSeq X Ten, HCS 3.3.76. To process and analyse the data, we developed a WGBS pipeline (METH10X) that is fast and can call SNPs. We performed WGBS on both high-quality intact DNA and degraded DNA from formalin-fixed paraffin-embedded tissue. First, we compared different library preparation methods on the HiSeq 2500 platform to identify the best method for sequencing on the HiSeq X Ten. Second, we optimised the PhiX and genome spike-ins to achieve higher quality and coverage of WGBS data on the HiSeq X Ten. Third, we performed integrated whole genome sequencing (WGS) and WGBS of the same DNA sample in a single lane of HiSeq X Ten to improve data output. Finally, we compared methylation data from the HiSeq 2500 and HiSeq X Ten and found high concordance (Pearson r > 0.9×). Together we provide a systematic, efficient and complete approach to perform and analyse WGBS on the HiSeq X Ten. Our protocol allows for large-scale WGBS studies at reasonable processing time and cost on the HiSeq X Ten platform.

Patient-specific optimisation of administered activity and acquisition times for 18F-FDG PET imaging.

PubMed

Wickham, Fred; McMeekin, Helena; Burniston, Maria; McCool, Daniel; Pencharz, Deborah; Skillen, Annah; Wagner, Thomas

2017-12-01

The purpose of this study is to identify a method for optimising the administered activity and acquisition time for 18 F-FDG PET imaging, yielding images of consistent quality for patients with varying body sizes and compositions, while limiting radiation doses to patients and staff. Patients referred for FDG scans had bioimpedance measurements. They were injected with 3 MBq/kg of 18 F up to 370 MBq and scanned on a Siemens Biograph mCT at 3 or 4 min per bed position. Data were rebinned to simulate 2- and 1-min acquisitions. Subjective assessments of image quality made by an experienced physician were compared with objective measurements based on signal-to-noise ratio and noise equivalent counts (NEC). A target objective measure of image quality was identified. The activity and acquisition time required to achieve this were calculated for each subject. Multiple regression analysis was used to identify expressions for the activity and acquisition time required in terms of easily measurable patient characteristics. One hundred and eleven patients were recruited, and subjective and objective assessments of image quality were compared for 321 full and reduced time scans. NEC-per-metre was identified as the objective measure which best correlated with the subjective assessment (Spearman rank correlation coefficient 0.77) and the best discriminator for images with a subjective assessment of "definitely adequate" (area under the ROC curve 0.94). A target of 37 Mcount/m was identified. Expressions were identified in terms of patient sex, height and weight for the activity and acquisition time required to achieve this target. Including measurements of body composition in these expressions was not useful. Using these expressions would reduce the mean activity administered to this patient group by 66 MBq compared to the current protocol. Expressions have been identified for the activity and acquisition times required to achieve consistent image quality in FDG imaging with reduced patient and staff doses. These expressions might need to be adapted for other systems and reconstruction protocols.

Optimisation in radiotherapy. III: Stochastic optimisation algorithms and conclusions.

PubMed

Ebert, M

1997-12-01

This is the final article in a three part examination of optimisation in radiotherapy. Previous articles have established the bases and form of the radiotherapy optimisation problem, and examined certain types of optimisation algorithm, namely, those which perform some form of ordered search of the solution space (mathematical programming), and those which attempt to find the closest feasible solution to the inverse planning problem (deterministic inversion). The current paper examines algorithms which search the space of possible irradiation strategies by stochastic methods. The resulting iterative search methods move about the solution space by sampling random variates, which gradually become more constricted as the algorithm converges upon the optimal solution. This paper also discusses the implementation of optimisation in radiotherapy practice.

Global transcriptomic profiling demonstrates induction of oxidative stress and of compensatory cellular stress responses in brown trout exposed to glyphosate and Roundup.

PubMed

Uren Webster, Tamsyn M; Santos, Eduarda M

2015-01-31

Glyphosate, the active ingredient in Roundup formulations, is the most widely used herbicide worldwide, and as a result contaminates surface waters and has been detected in food residues, drinking water and human urine, raising concerns for potential environmental and human health impacts. Research has shown that glyphosate and Roundup can induce a broad range of biological effects in exposed organisms, particularly via generation of oxidative stress. However, there has been no comprehensive investigation of the global molecular mechanisms of toxicity of glyphosate and Roundup for any species. We aimed to characterise and compare the global mechanisms of toxicity of glyphosate and Roundup in the liver of brown trout (Salmo trutta), an ecologically and economically important vertebrate species, using RNA-seq on an Illumina HiSeq 2500 platform. To do this, we exposed juvenile female brown trout to 0, 0.01, 0.5 and 10 mg/L of glyphosate and Roundup (glyphosate acid equivalent) for 14 days, and sequenced 6 replicate liver samples from each treatment. We assembled the brown trout transcriptome using an optimised de novo approach, and subsequent differential expression analysis identified a total of 1020 differentially-regulated transcripts across all treatments. These included transcripts encoding components of the antioxidant system, a number of stress-response proteins and pro-apoptotic signalling molecules. Functional analysis also revealed over-representation of pathways involved in regulating of cell-proliferation and turnover, and up-regulation of energy metabolism and other metabolic processes. These transcriptional changes are consistent with generation of oxidative stress and the widespread induction of compensatory cellular stress response pathways. The mechanisms of toxicity identified were similar across both glyphosate and Roundup treatments, including for environmentally relevant concentrations. The significant alterations in transcript expression observed at the lowest concentrations tested raises concerns for the potential toxicity of this herbicide to fish populations inhabiting contaminated rivers.

Optimisation on processing parameters for minimising warpage on side arm using response surface methodology (RSM) and particle swarm optimisation (PSO)

NASA Astrophysics Data System (ADS)

Rayhana, N.; Fathullah, M.; Shayfull, Z.; Nasir, S. M.; Hazwan, M. H. M.; Sazli, M.; Yahya, Z. R.

2017-09-01

This study presents the application of optimisation method to reduce the warpage of side arm part. Autodesk Moldflow Insight software was integrated into this study to analyse the warpage. The design of Experiment (DOE) for Response Surface Methodology (RSM) was constructed and by using the equation from RSM, Particle Swarm Optimisation (PSO) was applied. The optimisation method will result in optimised processing parameters with minimum warpage. Mould temperature, melt temperature, packing pressure, packing time and cooling time was selected as the variable parameters. Parameters selection was based on most significant factor affecting warpage stated by previous researchers. The results show that warpage was improved by 28.16% for RSM and 28.17% for PSO. The warpage improvement in PSO from RSM is only by 0.01 %. Thus, the optimisation using RSM is already efficient to give the best combination parameters and optimum warpage value for side arm part. The most significant parameters affecting warpage are packing pressure.

Metaheuristic optimisation methods for approximate solving of singular boundary value problems

NASA Astrophysics Data System (ADS)

Sadollah, Ali; Yadav, Neha; Gao, Kaizhou; Su, Rong

2017-07-01

This paper presents a novel approximation technique based on metaheuristics and weighted residual function (WRF) for tackling singular boundary value problems (BVPs) arising in engineering and science. With the aid of certain fundamental concepts of mathematics, Fourier series expansion, and metaheuristic optimisation algorithms, singular BVPs can be approximated as an optimisation problem with boundary conditions as constraints. The target is to minimise the WRF (i.e. error function) constructed in approximation of BVPs. The scheme involves generational distance metric for quality evaluation of the approximate solutions against exact solutions (i.e. error evaluator metric). Four test problems including two linear and two non-linear singular BVPs are considered in this paper to check the efficiency and accuracy of the proposed algorithm. The optimisation task is performed using three different optimisers including the particle swarm optimisation, the water cycle algorithm, and the harmony search algorithm. Optimisation results obtained show that the suggested technique can be successfully applied for approximate solving of singular BVPs.

Optimisation study of a vehicle bumper subsystem with fuzzy parameters

NASA Astrophysics Data System (ADS)

Farkas, L.; Moens, D.; Donders, S.; Vandepitte, D.

2012-10-01

This paper deals with the design and optimisation for crashworthiness of a vehicle bumper subsystem, which is a key scenario for vehicle component design. The automotive manufacturers and suppliers have to find optimal design solutions for such subsystems that comply with the conflicting requirements of the regulatory bodies regarding functional performance (safety and repairability) and regarding the environmental impact (mass). For the bumper design challenge, an integrated methodology for multi-attribute design engineering of mechanical structures is set up. The integrated process captures the various tasks that are usually performed manually, this way facilitating the automated design iterations for optimisation. Subsequently, an optimisation process is applied that takes the effect of parametric uncertainties into account, such that the system level of failure possibility is acceptable. This optimisation process is referred to as possibility-based design optimisation and integrates the fuzzy FE analysis applied for the uncertainty treatment in crash simulations. This process is the counterpart of the reliability-based design optimisation used in a probabilistic context with statistically defined parameters (variabilities).

Silica Vesicle Nanovaccine Formulations Stimulate Long-Term Immune Responses to the Bovine Viral Diarrhoea Virus E2 Protein

PubMed Central

Mody, Karishma T.; Mahony, Donna; Cavallaro, Antonino S.; Zhang, Jun; Zhang, Bing; Mahony, Timothy J.; Yu, Chengzhong; Mitter, Neena

2015-01-01

Bovine Viral Diarrhoea Virus (BVDV) is one of the most serious pathogen, which causes tremendous economic loss to the cattle industry worldwide, meriting the development of improved subunit vaccines. Structural glycoprotein E2 is reported to be a major immunogenic determinant of BVDV virion. We have developed a novel hollow silica vesicles (SV) based platform to administer BVDV-1 Escherichia coli-expressed optimised E2 (oE2) antigen as a nanovaccine formulation. The SV-140 vesicles (diameter 50 nm, wall thickness 6 nm, perforated by pores of entrance size 16 nm and total pore volume of 0.934 cm3g-1) have proven to be ideal candidates to load oE2 antigen and generate immune response. The current study for the first time demonstrates the ability of freeze-dried (FD) as well as non-FD oE2/SV140 nanovaccine formulation to induce long-term balanced antibody and cell mediated memory responses for at least 6 months with a shortened dosing regimen of two doses in small animal model. The in vivo ability of oE2 (100 μg)/SV-140 (500 μg) and FD oE2 (100 μg)/SV-140 (500 μg) to induce long-term immunity was compared to immunisation with oE2 (100 μg) together with the conventional adjuvant Quil-A from the Quillaja saponira (10 μg) in mice. The oE2/SV-140 as well as the FD oE2/SV-140 nanovaccine generated oE2-specific antibody and cell mediated responses for up to six months post the final second immunisation. Significantly, the cell-mediated responses were consistently high in mice immunised with oE2/SV-140 (1,500 SFU/million cells) at the six-month time point. Histopathology studies showed no morphological changes at the site of injection or in the different organs harvested from the mice immunised with 500 μg SV-140 nanovaccine compared to the unimmunised control. The platform has the potential for developing single dose vaccines without the requirement of cold chain storage for veterinary and human applications. PMID:26630001

Modern multicore and manycore architectures: Modelling, optimisation and benchmarking a multiblock CFD code

NASA Astrophysics Data System (ADS)

Hadade, Ioan; di Mare, Luca

2016-08-01

Modern multicore and manycore processors exhibit multiple levels of parallelism through a wide range of architectural features such as SIMD for data parallel execution or threads for core parallelism. The exploitation of multi-level parallelism is therefore crucial for achieving superior performance on current and future processors. This paper presents the performance tuning of a multiblock CFD solver on Intel SandyBridge and Haswell multicore CPUs and the Intel Xeon Phi Knights Corner coprocessor. Code optimisations have been applied on two computational kernels exhibiting different computational patterns: the update of flow variables and the evaluation of the Roe numerical fluxes. We discuss at great length the code transformations required for achieving efficient SIMD computations for both kernels across the selected devices including SIMD shuffles and transpositions for flux stencil computations and global memory transformations. Core parallelism is expressed through threading based on a number of domain decomposition techniques together with optimisations pertaining to alleviating NUMA effects found in multi-socket compute nodes. Results are correlated with the Roofline performance model in order to assert their efficiency for each distinct architecture. We report significant speedups for single thread execution across both kernels: 2-5X on the multicore CPUs and 14-23X on the Xeon Phi coprocessor. Computations at full node and chip concurrency deliver a factor of three speedup on the multicore processors and up to 24X on the Xeon Phi manycore coprocessor.

Assessment of factors affecting Agrobacterium-mediated genetic transformation of the unicellular green alga, Chlorella vulgaris.

PubMed

Cha, Thye San; Yee, Willy; Aziz, Ahmad

2012-04-01

The successful establishment of an Agrobacterium-mediated transformation method and optimisation of six critical parameters known to influence the efficacy of Agrobacterium T-DNA transfer in the unicellular microalga Chlorella vulgaris (UMT-M1) are reported. Agrobacterium tumefaciens strain LBA4404 harbouring the binary vector pCAMBIA1304 containing the gfp:gusA fusion reporter and a hygromycin phosphotransferase (hpt) selectable marker driven by the CaMV35S promoter were used for transformation. Transformation frequency was assessed by monitoring transient β-glucuronidase (GUS) expression 2 days post-infection. It was found that co-cultivation temperature at 24°C, co-cultivation medium at pH 5.5, 3 days of co-cultivation, 150 μM acetosyringone, Agrobacterium density of 1.0 units (OD(600)) and 2 days of pre-culture were optimum variables which produced the highest number of GUS-positive cells (8.8-20.1%) when each of these parameters was optimised individually. Transformation conducted with the combination of all optimal parameters above produced 25.0% of GUS-positive cells, which was almost a threefold increase from 8.9% obtained from un-optimised parameters. Evidence of transformation was further confirmed in 30% of 30 randomly-selected hygromycin B (20 mg L(-1)) resistant colonies by polymerase chain reaction (PCR) using gfp:gusA and hpt-specific primers. The developed transformation method is expected to facilitate the genetic improvement of this commercially-important microalga.

Production of membrane proteins without cells or detergents.

PubMed

Rajesh, Sundaresan; Knowles, Timothy; Overduin, Michael

2011-04-30

The production of membrane proteins in cellular systems is besieged by several problems due to their hydrophobic nature which often causes misfolding, protein aggregation and cytotoxicity, resulting in poor yields of stable proteins. Cell-free expression has emerged as one of the most versatile alternatives for circumventing these obstacles by producing membrane proteins directly into designed hydrophobic environments. Efficient optimisation of expression and solubilisation conditions using a variety of detergents, membrane mimetics and lipids has yielded structurally and functionally intact membrane proteins, with yields several fold above the levels possible from cell-based systems. Here we review recently developed techniques available to produce functional membrane proteins, and discuss amphipols, nanodisc and styrene maleic acid lipid particle (SMALP) technologies that can be exploited alongside cell-free expression of membrane proteins. Copyright © 2010 Elsevier B.V. All rights reserved.

Value in cardiovascular care.

PubMed

Bradley, Steven M; Strauss, Craig E; Ho, P Michael

2017-08-01

Healthcare value, defined as health outcomes achieved relative to the costs of care, has been proposed as a unifying approach to measure improvements in the quality and affordability of healthcare. Although value is of increasing interest to payers, many providers remain unfamiliar with how value differs from other approaches to the comparison of cost and outcomes (ie, cost-effectiveness analysis). While cost-effectiveness studies can be used by policy makers and payers to inform decisions about coverage and reimbursement for new therapies, the assessment of healthcare can guide improvements in the delivery of healthcare to achieve better outcomes at lower cost. Comparison on value allows for the identification of healthcare delivery organisations or care delivery settings where patient outcomes have been optimised at a lower cost. Gaps remain in the measurement of healthcare value, particularly as it relates to patient-reported health status (symptoms, functional status and health-related quality of life). The use of technology platforms that capture health status measures with minimal disruption to clinical workflow (ie, web portals, automated telephonic systems and tablets to facilitate capture outside of in-person clinical interaction) is facilitating use of health status measures to improve clinical care and optimise patient outcomes. Furthermore, the use of a value framework has catalysed quality improvement efforts and research to seek better patient outcomes at lower cost. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2017. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

The QCDOC Project

NASA Astrophysics Data System (ADS)

Boyle, P.; Chen, D.; Christ, N.; Clark, M.; Cohen, S.; Cristian, C.; Dong, Z.; Gara, A.; Joo, B.; Jung, C.; Kim, C.; Levkova, L.; Liao, X.; Liu, G.; Li, S.; Lin, H.; Mawhinney, R.; Ohta, S.; Petrov, K.; Wettig, T.; Yamaguchi, A.

2005-03-01

The QCDOC project has developed a supercomputer optimised for the needs of Lattice QCD simulations. It provides a very competitive price to sustained performance ratio of around $1 USD per sustained Megaflop/s in combination with outstanding scalability. Thus very large systems delivering over 5 TFlop/s of performance on the evolution of a single lattice is possible. Large prototypes have been built and are functioning correctly. The software environment raises the state of the art in such custom supercomputers. It is based on a lean custom node operating system that eliminates many unnecessary overheads that plague other systems. Despite the custom nature, the operating system implements a standards compliant UNIX-like programming environment easing the porting of software from other systems. The SciDAC QMP interface adds internode communication in a fashion that provides a uniform cross-platform programming environment.

[In vitro evaluation of the gels properties prepared thermosensitive polymers as vehicles for administration substance by injection].

PubMed

Karolewicz, Bozena; Owczarek, Artur; Pluta, Janusz

2011-01-01

The aim of this study was to prepare a thermoresponsive formulations, which are a carrier for substance administered directly into site of action and which obtain sol-gel transitions at physiological ranges of temperature. The investigated formulations of liquid consistency at room temperature were obtained in sterile conditions on the basis of nonionic polymers Pluronic F-127, Pluronic F-68 and anionic polymer hyaluronic acid in different concentrations. The sol-gel transition temperature of the formulations was investigated and their physicochemical properties such as pH, density, osmotic pressure, sol-gel transition temperature, texture and release of vancomycin hydrochloride were studied. In vitro release experiments indicated that the optimised platform was able to prolong vancomycin hydrochloride release and their physico-chemical properties allow for application by injection form.

Virtual Engine a Tool for Truck Reliability Increase

NASA Astrophysics Data System (ADS)

Stodola, Jiri; Novotny, Pavel

2017-06-01

The internal combustion engine development process requires CAD models which deliver results for the concept phase at a very early stage and which can be further detailed on the same program platform as the development process progresses. The vibratory and acoustic behaviour of the powertrain is highly complex, consisting of many components that are subject to loads that vary greatly in magnitude and which operate at a wide range of speeds. The interaction of the crank and crankcase is a major problem for powertrain designers when optimising the vibration and noise characteristics of the powertrain. The Finite Element Method (FEM) and Multi-Body Systems (MBS) are suitable for the creation of 3-D calculation models. Non-contact measurements make it possible to verify complex calculation models. All numerical simulations and measurements are performed on a Diesel six-cylinder in-line engine.

Clofazimine drug susceptibility testing for Mycobacterium tuberculosis: the case of using the right diluent.

PubMed

Sng, Li-Hwei; Peh, Justine Woei Ling; Lee Kee, Melody Tai; Ya'akob, Nurhazirah Bte Mohd; Ong, Rick Twee-Hee; Wong, Christopher W; Chee, Cynthia Bin Eng; Wang, Yee Tang

2018-06-08

Accurate and reliable drug susceptibility testing (DST) is essential for the effective treatment and control of tuberculosis. With the increase in drug-resistant organisms, newer and less conventional antimicrobial agents are used for treatment. Recently, we found an unprecedented rise in the number of clofazimine-resistant Mycobacterium tuberculosis isolates in our laboratory. An investigation found that this phenomenon was due to a change in the method of drug preparation. We performed studies to assess the impact of water and dimethyl sulfoxide (DMSO) as a final diluent for clofazimine drug testing. Based on our findings, the use of DMSO as a solvent for M. tuberculosis DST was optimised using the BACTEC MGIT 960 platform. Copyright © 2018 Royal College of Pathologists of Australasia. Published by Elsevier B.V. All rights reserved.

Population Fisher information matrix and optimal design of discrete data responses in population pharmacodynamic experiments.

PubMed

Ogungbenro, Kayode; Aarons, Leon

2011-08-01

In the recent years, interest in the application of experimental design theory to population pharmacokinetic (PK) and pharmacodynamic (PD) experiments has increased. The aim is to improve the efficiency and the precision with which parameters are estimated during data analysis and sometimes to increase the power and reduce the sample size required for hypothesis testing. The population Fisher information matrix (PFIM) has been described for uniresponse and multiresponse population PK experiments for design evaluation and optimisation. Despite these developments and availability of tools for optimal design of population PK and PD experiments much of the effort has been focused on repeated continuous variable measurements with less work being done on repeated discrete type measurements. Discrete data arise mainly in PDs e.g. ordinal, nominal, dichotomous or count measurements. This paper implements expressions for the PFIM for repeated ordinal, dichotomous and count measurements based on analysis by a mixed-effects modelling technique. Three simulation studies were used to investigate the performance of the expressions. Example 1 is based on repeated dichotomous measurements, Example 2 is based on repeated count measurements and Example 3 is based on repeated ordinal measurements. Data simulated in MATLAB were analysed using NONMEM (Laplace method) and the glmmML package in R (Laplace and adaptive Gauss-Hermite quadrature methods). The results obtained for Examples 1 and 2 showed good agreement between the relative standard errors obtained using the PFIM and simulations. The results obtained for Example 3 showed the importance of sampling at the most informative time points. Implementation of these expressions will provide the opportunity for efficient design of population PD experiments that involve discrete type data through design evaluation and optimisation.

Nucleic acid programmable protein array a just-in-time multiplexed protein expression and purification platform.

PubMed

Qiu, Ji; LaBaer, Joshua

2011-01-01

Systematic study of proteins requires the availability of thousands of proteins in functional format. However, traditional recombinant protein expression and purification methods have many drawbacks for such study at the proteome level. We have developed an innovative in situ protein expression and capture system, namely NAPPA (nucleic acid programmable protein array), where C-terminal tagged proteins are expressed using an in vitro expression system and efficiently captured/purified by antitag antibodies coprinted at each spot. The NAPPA technology presented in this chapter enable researchers to produce and display fresh proteins just in time in a multiplexed high-throughput fashion and utilize them for various downstream biochemical researches of interest. This platform could revolutionize the field of functional proteomics with it ability to produce thousands of spatially separated proteins in high density with narrow dynamic rand of protein concentrations, reproducibly and functionally. Copyright © 2011 Elsevier Inc. All rights reserved.

CAMELOT: Computational-Analytical Multi-fidElity Low-thrust Optimisation Toolbox

NASA Astrophysics Data System (ADS)

Di Carlo, Marilena; Romero Martin, Juan Manuel; Vasile, Massimiliano

2018-03-01

Computational-Analytical Multi-fidElity Low-thrust Optimisation Toolbox (CAMELOT) is a toolbox for the fast preliminary design and optimisation of low-thrust trajectories. It solves highly complex combinatorial problems to plan multi-target missions characterised by long spirals including different perturbations. To do so, CAMELOT implements a novel multi-fidelity approach combining analytical surrogate modelling and accurate computational estimations of the mission cost. Decisions are then made using two optimisation engines included in the toolbox, a single-objective global optimiser, and a combinatorial optimisation algorithm. CAMELOT has been applied to a variety of case studies: from the design of interplanetary trajectories to the optimal de-orbiting of space debris and from the deployment of constellations to on-orbit servicing. In this paper, the main elements of CAMELOT are described and two examples, solved using the toolbox, are presented.

Boundary element based multiresolution shape optimisation in electrostatics

NASA Astrophysics Data System (ADS)

Bandara, Kosala; Cirak, Fehmi; Of, Günther; Steinbach, Olaf; Zapletal, Jan

2015-09-01

We consider the shape optimisation of high-voltage devices subject to electrostatic field equations by combining fast boundary elements with multiresolution subdivision surfaces. The geometry of the domain is described with subdivision surfaces and different resolutions of the same geometry are used for optimisation and analysis. The primal and adjoint problems are discretised with the boundary element method using a sufficiently fine control mesh. For shape optimisation the geometry is updated starting from the coarsest control mesh with increasingly finer control meshes. The multiresolution approach effectively prevents the appearance of non-physical geometry oscillations in the optimised shapes. Moreover, there is no need for mesh regeneration or smoothing during the optimisation due to the absence of a volume mesh. We present several numerical experiments and one industrial application to demonstrate the robustness and versatility of the developed approach.

A CONCEPTUAL FRAMEWORK FOR MANAGING RADIATION DOSE TO PATIENTS IN DIAGNOSTIC RADIOLOGY USING REFERENCE DOSE LEVELS.

PubMed

Almén, Anja; Båth, Magnus

2016-06-01

The overall aim of the present work was to develop a conceptual framework for managing radiation dose in diagnostic radiology with the intention to support optimisation. An optimisation process was first derived. The framework for managing radiation dose, based on the derived optimisation process, was then outlined. The outset of the optimisation process is four stages: providing equipment, establishing methodology, performing examinations and ensuring quality. The optimisation process comprises a series of activities and actions at these stages. The current system of diagnostic reference levels is an activity in the last stage, ensuring quality. The system becomes a reactive activity only to a certain extent engaging the core activity in the radiology department, performing examinations. Three reference dose levels-possible, expected and established-were assigned to the three stages in the optimisation process, excluding ensuring quality. A reasonably achievable dose range is also derived, indicating an acceptable deviation from the established dose level. A reasonable radiation dose for a single patient is within this range. The suggested framework for managing radiation dose should be regarded as one part of the optimisation process. The optimisation process constitutes a variety of complementary activities, where managing radiation dose is only one part. This emphasises the need to take a holistic approach integrating the optimisation process in different clinical activities. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Micro-algae come of age as a platform for recombinant protein production

PubMed Central

Specht, Elizabeth; Miyake-Stoner, Shigeki

2010-01-01

A complete set of genetic tools is still being developed for the micro-alga Chlamydomonas reinhardtii. Yet even with this incomplete set, this photosynthetic single-celled plant has demonstrated significant promise as a platform for recombinant protein expression. In recent years, techniques have been developed that allow for robust expression of genes from both the nuclear and plastid genome. With these advances, many research groups have examined the pliability of this and other micro-algae as biological machines capable of producing recombinant peptides and proteins. This review describes recent successes in recombinant protein production in Chlamydomonas, including production of complex mammalian therapeutic proteins and monoclonal antibodies at levels sufficient for production at economic parity with existing production platforms. These advances have also shed light on the details of algal protein production at the molecular level, and provide insight into the next steps for optimizing micro-algae as a useful platform for the production of therapeutic and industrially relevant recombinant proteins. PMID:20556634

Microfluidic platform combining droplets and magnetic tweezers: application to HER2 expression in cancer diagnosis

PubMed Central

Ferraro, Davide; Champ, Jérôme; Teste, Bruno; Serra, Marco; Malaquin, Laurent; Viovy, Jean-Louis; de Cremoux, Patricia; Descroix, Stephanie

2016-01-01

The development of precision medicine, together with the multiplication of targeted therapies and associated molecular biomarkers, call for major progress in genetic analysis methods, allowing increased multiplexing and the implementation of more complex decision trees, without cost increase or loss of robustness. We present a platform combining droplet microfluidics and magnetic tweezers, performing RNA purification, reverse transcription and amplification in a fully automated and programmable way, in droplets of 250nL directly sampled from a microtiter-plate. This platform decreases sample consumption about 100 fold as compared to current robotized platforms and it reduces human manipulations and contamination risk. The platform’s performance was first evaluated on cell lines, showing robust operation on RNA quantities corresponding to less than one cell, and then clinically validated with a cohort of 21 breast cancer samples, for the determination of their HER2 expression status, in a blind comparison with an established routine clinical analysis. PMID:27157697

Microfluidic platform combining droplets and magnetic tweezers: application to HER2 expression in cancer diagnosis

NASA Astrophysics Data System (ADS)

Ferraro, Davide; Champ, Jérôme; Teste, Bruno; Serra, Marco; Malaquin, Laurent; Viovy, Jean-Louis; de Cremoux, Patricia; Descroix, Stephanie

2016-05-01

The development of precision medicine, together with the multiplication of targeted therapies and associated molecular biomarkers, call for major progress in genetic analysis methods, allowing increased multiplexing and the implementation of more complex decision trees, without cost increase or loss of robustness. We present a platform combining droplet microfluidics and magnetic tweezers, performing RNA purification, reverse transcription and amplification in a fully automated and programmable way, in droplets of 250nL directly sampled from a microtiter-plate. This platform decreases sample consumption about 100 fold as compared to current robotized platforms and it reduces human manipulations and contamination risk. The platform’s performance was first evaluated on cell lines, showing robust operation on RNA quantities corresponding to less than one cell, and then clinically validated with a cohort of 21 breast cancer samples, for the determination of their HER2 expression status, in a blind comparison with an established routine clinical analysis.

Basis for the development of sustainable optimisation indicators for activated sludge wastewater treatment plants in the Republic of Ireland.

PubMed

Gordon, G T; McCann, B P

2015-01-01

This paper describes the basis of a stakeholder-based sustainable optimisation indicator (SOI) system to be developed for small-to-medium sized activated sludge (AS) wastewater treatment plants (WwTPs) in the Republic of Ireland (ROI). Key technical publications relating to best practice plant operation, performance audits and optimisation, and indicator and benchmarking systems for wastewater services are identified. Optimisation studies were developed at a number of Irish AS WwTPs and key findings are presented. A national AS WwTP manager/operator survey was carried out to verify the applied operational findings and identify the key operator stakeholder requirements for this proposed SOI system. It was found that most plants require more consistent operational data-based decision-making, monitoring and communication structures to facilitate optimised, sustainable and continuous performance improvement. The applied optimisation and stakeholder consultation phases form the basis of the proposed stakeholder-based SOI system. This system will allow for continuous monitoring and rating of plant performance, facilitate optimised operation and encourage the prioritisation of performance improvement through tracking key operational metrics. Plant optimisation has become a major focus due to the transfer of all ROI water services to a national water utility from individual local authorities and the implementation of the EU Water Framework Directive.

Integrative set enrichment testing for multiple omics platforms

PubMed Central

2011-01-01

Background Enrichment testing assesses the overall evidence of differential expression behavior of the elements within a defined set. When we have measured many molecular aspects, e.g. gene expression, metabolites, proteins, it is desirable to assess their differential tendencies jointly across platforms using an integrated set enrichment test. In this work we explore the properties of several methods for performing a combined enrichment test using gene expression and metabolomics as the motivating platforms. Results Using two simulation models we explored the properties of several enrichment methods including two novel methods: the logistic regression 2-degree of freedom Wald test and the 2-dimensional permutation p-value for the sum-of-squared statistics test. In relation to their univariate counterparts we find that the joint tests can improve our ability to detect results that are marginal univariately. We also find that joint tests improve the ranking of associated pathways compared to their univariate counterparts. However, there is a risk of Type I error inflation with some methods and self-contained methods lose specificity when the sets are not representative of underlying association. Conclusions In this work we show that consideration of data from multiple platforms, in conjunction with summarization via a priori pathway information, leads to increased power in detection of genomic associations with phenotypes. PMID:22118224

Strategic deployment of CHO expression platforms to deliver Pfizer's Monoclonal Antibody Portfolio.

PubMed

Scarcelli, John J; Shang, Tanya Q; Iskra, Tim; Allen, Martin J; Zhang, Lin

2017-11-01

Development of stable cell lines for expression of large-molecule therapeutics represents a significant portion of the time and effort required to advance a molecule to enabling regulatory toxicology studies and clinical evaluation. Our development strategy employs two different approaches for cell line development based on the needs of a particular project: a random integration approach for projects where high-level expression is critical, and a site-specific integration approach for projects in which speed and reduced employee time spend is a necessity. Here we describe both our random integration and site-specific integration platforms and their applications in support of monoclonal antibody development and production. We also compare product quality attributes of monoclonal antibodies produced with a nonclonal cell pool or clonal cell lines derived from the two platforms. Our data suggests that material source (pools vs. clones) does not significantly alter the examined product quality attributes. Our current practice is to leverage this observation with our site-specific integration platform, where material generated from cell pools is used for an early molecular assessment of a given candidate to make informed decisions around development strategy. © 2017 American Institute of Chemical Engineers Biotechnol. Prog., 33:1463-1467, 2017. © 2017 American Institute of Chemical Engineers.

Designing for scale: optimising the health information system architecture for mobile maternal health messaging in South Africa (MomConnect)

PubMed Central

Seebregts, Christopher; Dane, Pierre; Parsons, Annie Neo; Fogwill, Thomas; Rogers, Debbie; Bekker, Marcha; Shaw, Vincent; Barron, Peter

2018-01-01

MomConnect is a national initiative coordinated by the South African National Department of Health that sends text-based mobile phone messages free of charge to pregnant women who voluntarily register at any public healthcare facility in South Africa. We describe the system design and architecture of the MomConnect technical platform, planned as a nationally scalable and extensible initiative. It uses a health information exchange that can connect any standards-compliant electronic front-end application to any standards-compliant electronic back-end database. The implementation of the MomConnect technical platform, in turn, is a national reference application for electronic interoperability in line with the South African National Health Normative Standards Framework. The use of open content and messaging standards enables the architecture to include any application adhering to the selected standards. Its national implementation at scale demonstrates both the use of this technology and a key objective of global health information systems, which is to achieve implementation scale. The system’s limited clinical information, initially, allowed the architecture to focus on the base standards and profiles for interoperability in a resource-constrained environment with limited connectivity and infrastructural capacity. Maintenance of the system requires mobilisation of national resources. Future work aims to use the standard interfaces to include data from additional applications as well as to extend and interface the framework with other public health information systems in South Africa. The development of this platform has also shown the benefits of interoperability at both an organisational and technical level in South Africa. PMID:29713506

Designing for scale: optimising the health information system architecture for mobile maternal health messaging in South Africa (MomConnect).

PubMed

Seebregts, Christopher; Dane, Pierre; Parsons, Annie Neo; Fogwill, Thomas; Rogers, Debbie; Bekker, Marcha; Shaw, Vincent; Barron, Peter

2018-01-01

MomConnect is a national initiative coordinated by the South African National Department of Health that sends text-based mobile phone messages free of charge to pregnant women who voluntarily register at any public healthcare facility in South Africa. We describe the system design and architecture of the MomConnect technical platform, planned as a nationally scalable and extensible initiative. It uses a health information exchange that can connect any standards-compliant electronic front-end application to any standards-compliant electronic back-end database. The implementation of the MomConnect technical platform, in turn, is a national reference application for electronic interoperability in line with the South African National Health Normative Standards Framework. The use of open content and messaging standards enables the architecture to include any application adhering to the selected standards. Its national implementation at scale demonstrates both the use of this technology and a key objective of global health information systems, which is to achieve implementation scale. The system's limited clinical information, initially, allowed the architecture to focus on the base standards and profiles for interoperability in a resource-constrained environment with limited connectivity and infrastructural capacity. Maintenance of the system requires mobilisation of national resources. Future work aims to use the standard interfaces to include data from additional applications as well as to extend and interface the framework with other public health information systems in South Africa. The development of this platform has also shown the benefits of interoperability at both an organisational and technical level in South Africa.

Development and optimisation of atorvastatin calcium loaded self-nanoemulsifying drug delivery system (SNEDDS) for enhancing oral bioavailability: in vitro and in vivo evaluation.

PubMed

Kassem, Abdulsalam M; Ibrahim, Hany M; Samy, Ahmed M

2017-05-01

The objective of this study was to develop and optimise self-nanoemulsifying drug delivery system (SNEDDS) of atorvastatin calcium (ATC) for improving dissolution rate and eventually oral bioavailability. Ternary phase diagrams were constructed on basis of solubility and emulsification studies. The composition of ATC-SNEDDS was optimised using the Box-Behnken optimisation design. Optimised ATC-SNEDDS was characterised for various physicochemical properties. Pharmacokinetic, pharmacodynamic and histological findings were performed in rats. Optimised ATC-SNEDDS resulted in droplets size of 5.66 nm, zeta potential of -19.52 mV, t 90 of 5.43 min and completely released ATC within 30 min irrespective of pH of the medium. Area under the curve of optimised ATC-SNEDDS in rats was 2.34-folds higher than ATC suspension. Pharmacodynamic studies revealed significant reduction in serum lipids of rats with fatty liver. Photomicrographs showed improvement in hepatocytes structure. In this study, we confirmed that ATC-SNEDDS would be a promising approach for improving oral bioavailability of ATC.

Control of SIV infection and subsequent induction of pandemic H1N1 immunity in rhesus macaques using an Ad5 [E1-, E2b-] vector platform.

PubMed

Gabitzsch, Elizabeth S; Balint-Junior, Joseph P; Xu, Younong; Balcaitis, Stephanie; Sanders-Beer, Brigitte; Karl, Julie; Weinhold, Kent J; Paessler, Slobodan; Jones, Frank R

2012-11-26

Anti-vector immunity mitigates immune responses induced by recombinant adenovirus vector vaccines, limiting their prime-boost capabilities. We have developed a novel gene delivery and expression platform (Ad5 [E1-, E2b-]) that induces immune responses despite pre-existing and/or developed concomitant Ad5 immunity. In the present study, we evaluated if this new Ad5 platform could overcome the adverse condition of pre-existing Ad5 immunity to induce effective immune responses in prime-boost immunization regimens against two different infectious diseases in the same animal. Ad5 immune rhesus macaques (RM) were immunized multiple times with the Ad5 [E1-, E2b-] platform expressing antigens from simian immunodeficiency virus (SIV). Immunized RM developed cell-mediated immunity against SIV antigens Gag, Pol, Nef and Env as well as antibody against Env. Vaccinated and vector control RMs were challenged intra-rectally with homologous SIVmac239. During a 7-week follow-up, there was perturbation of SIV load in some immunized RM. At 7 weeks post-challenge, eight immunized animals (53%) did not have detectable SIV, compared to two RM controls (13%) (P<0.02; log-rank Mantel-Cox test). There was no correlation of protective MHC contributing to infection control. The RM without detectable circulating SIV, now hyper immune to Ad5, were then vaccinated with the same Ad5 [E1-, E2b-] platform expressing H1N1 influenza hemagglutinin (HA). Thirty days post Ad5 [E1-, E2b-]-HA vaccination, significant levels of influenza neutralizing antibody were induced in all animals that increased after an Ad5 [E1-, E2b-]-HA homologous boost. These data demonstrate the versatility of this new vector platform to immunize against two separate disease targets in the same animal despite the presence of immunity against the delivery platform, permitting homologous repeat immunizations with an Ad5 gene delivery platform. Copyright © 2012 Elsevier Ltd. All rights reserved.

Developing Ubiquitous Sensor Network Platform Using Internet of Things: Application in Precision Agriculture.

PubMed

Ferrández-Pastor, Francisco Javier; García-Chamizo, Juan Manuel; Nieto-Hidalgo, Mario; Mora-Pascual, Jerónimo; Mora-Martínez, José

2016-07-22

The application of Information Technologies into Precision Agriculture methods has clear benefits. Precision Agriculture optimises production efficiency, increases quality, minimises environmental impact and reduces the use of resources (energy, water); however, there are different barriers that have delayed its wide development. Some of these main barriers are expensive equipment, the difficulty to operate and maintain and the standard for sensor networks are still under development. Nowadays, new technological development in embedded devices (hardware and communication protocols), the evolution of Internet technologies (Internet of Things) and ubiquitous computing (Ubiquitous Sensor Networks) allow developing less expensive systems, easier to control, install and maintain, using standard protocols with low-power consumption. This work develops and test a low-cost sensor/actuator network platform, based in Internet of Things, integrating machine-to-machine and human-machine-interface protocols. Edge computing uses this multi-protocol approach to develop control processes on Precision Agriculture scenarios. A greenhouse with hydroponic crop production was developed and tested using Ubiquitous Sensor Network monitoring and edge control on Internet of Things paradigm. The experimental results showed that the Internet technologies and Smart Object Communication Patterns can be combined to encourage development of Precision Agriculture. They demonstrated added benefits (cost, energy, smart developing, acceptance by agricultural specialists) when a project is launched.

Rational Design of Photonic Dust from Nanoporous Anodic Alumina Films: A Versatile Photonic Nanotool for Visual Sensing

PubMed Central

Chen, Yuting; Santos, Abel; Wang, Ye; Kumeria, Tushar; Ho, Daena; Li, Junsheng; Wang, Changhai; Losic, Dusan

2015-01-01

Herein, we present a systematic study on the development, optimisation and applicability of interferometrically coloured distributed Bragg reflectors based on nanoporous anodic alumina (NAA-DBRs) in the form of films and nanoporous microparticles as visual/colorimetric analytical tools. Firstly, we synthesise a complete palette of NAA-DBRs by galvanostatic pulse anodisation approach, in which the current density is altered in a periodic fashion in order to engineer the effective medium of the resulting photonic films in depth. NAA-DBR photonic films feature vivid colours that can be tuned across the UV-visible-NIR spectrum by structural engineering. Secondly, the effective medium of the resulting photonic films is assessed systematically by visual analysis and reflectometric interference spectroscopy (RIfS) in order to establish the most optimal nanoporous platforms to develop visual/colorimetric tools. Then, we demonstrate the applicability of NAA-DBR photonic films as a chemically selective sensing platform for visual detection of mercury(II) ions. Finally, we generate a new nanomaterial, so-called photonic dust, by breaking down NAA-DBRs films into nanoporous microparticles. The resulting microparticles (μP-NAA-DBRs) display vivid colours and are sensitive towards changes in their effective medium, opening new opportunities for developing advanced photonic nanotools for a broad range of applications. PMID:26245759

Rational Design of Photonic Dust from Nanoporous Anodic Alumina Films: A Versatile Photonic Nanotool for Visual Sensing

NASA Astrophysics Data System (ADS)

Chen, Yuting; Santos, Abel; Wang, Ye; Kumeria, Tushar; Ho, Daena; Li, Junsheng; Wang, Changhai; Losic, Dusan

2015-08-01

Herein, we present a systematic study on the development, optimisation and applicability of interferometrically coloured distributed Bragg reflectors based on nanoporous anodic alumina (NAA-DBRs) in the form of films and nanoporous microparticles as visual/colorimetric analytical tools. Firstly, we synthesise a complete palette of NAA-DBRs by galvanostatic pulse anodisation approach, in which the current density is altered in a periodic fashion in order to engineer the effective medium of the resulting photonic films in depth. NAA-DBR photonic films feature vivid colours that can be tuned across the UV-visible-NIR spectrum by structural engineering. Secondly, the effective medium of the resulting photonic films is assessed systematically by visual analysis and reflectometric interference spectroscopy (RIfS) in order to establish the most optimal nanoporous platforms to develop visual/colorimetric tools. Then, we demonstrate the applicability of NAA-DBR photonic films as a chemically selective sensing platform for visual detection of mercury(II) ions. Finally, we generate a new nanomaterial, so-called photonic dust, by breaking down NAA-DBRs films into nanoporous microparticles. The resulting microparticles (μP-NAA-DBRs) display vivid colours and are sensitive towards changes in their effective medium, opening new opportunities for developing advanced photonic nanotools for a broad range of applications.

Fusing Bluetooth Beacon Data with Wi-Fi Radiomaps for Improved Indoor Localization

PubMed Central

Kanaris, Loizos; Kokkinis, Akis; Liotta, Antonio; Stavrou, Stavros

2017-01-01

Indoor user localization and tracking are instrumental to a broad range of services and applications in the Internet of Things (IoT) and particularly in Body Sensor Networks (BSN) and Ambient Assisted Living (AAL) scenarios. Due to the widespread availability of IEEE 802.11, many localization platforms have been proposed, based on the Wi-Fi Received Signal Strength (RSS) indicator, using algorithms such as K-Nearest Neighbour (KNN), Maximum A Posteriori (MAP) and Minimum Mean Square Error (MMSE). In this paper, we introduce a hybrid method that combines the simplicity (and low cost) of Bluetooth Low Energy (BLE) and the popular 802.11 infrastructure, to improve the accuracy of indoor localization platforms. Building on KNN, we propose a new positioning algorithm (dubbed i-KNN) which is able to filter the initial fingerprint dataset (i.e., the radiomap), after considering the proximity of RSS fingerprints with respect to the BLE devices. In this way, i-KNN provides an optimised small subset of possible user locations, based on which it finally estimates the user position. The proposed methodology achieves fast positioning estimation due to the utilization of a fragment of the initial fingerprint dataset, while at the same time improves positioning accuracy by minimizing any calculation errors. PMID:28394268

Fusing Bluetooth Beacon Data with Wi-Fi Radiomaps for Improved Indoor Localization.

PubMed

Kanaris, Loizos; Kokkinis, Akis; Liotta, Antonio; Stavrou, Stavros

2017-04-10

Indoor user localization and tracking are instrumental to a broad range of services and applications in the Internet of Things (IoT) and particularly in Body Sensor Networks (BSN) and Ambient Assisted Living (AAL) scenarios. Due to the widespread availability of IEEE 802.11, many localization platforms have been proposed, based on the Wi-Fi Received Signal Strength (RSS) indicator, using algorithms such as K -Nearest Neighbour (KNN), Maximum A Posteriori (MAP) and Minimum Mean Square Error (MMSE). In this paper, we introduce a hybrid method that combines the simplicity (and low cost) of Bluetooth Low Energy (BLE) and the popular 802.11 infrastructure, to improve the accuracy of indoor localization platforms. Building on KNN, we propose a new positioning algorithm (dubbed i-KNN) which is able to filter the initial fingerprint dataset (i.e., the radiomap), after considering the proximity of RSS fingerprints with respect to the BLE devices. In this way, i-KNN provides an optimised small subset of possible user locations, based on which it finally estimates the user position. The proposed methodology achieves fast positioning estimation due to the utilization of a fragment of the initial fingerprint dataset, while at the same time improves positioning accuracy by minimizing any calculation errors.

Developing Ubiquitous Sensor Network Platform Using Internet of Things: Application in Precision Agriculture

PubMed Central

Ferrández-Pastor, Francisco Javier; García-Chamizo, Juan Manuel; Nieto-Hidalgo, Mario; Mora-Pascual, Jerónimo; Mora-Martínez, José

2016-01-01

The application of Information Technologies into Precision Agriculture methods has clear benefits. Precision Agriculture optimises production efficiency, increases quality, minimises environmental impact and reduces the use of resources (energy, water); however, there are different barriers that have delayed its wide development. Some of these main barriers are expensive equipment, the difficulty to operate and maintain and the standard for sensor networks are still under development. Nowadays, new technological development in embedded devices (hardware and communication protocols), the evolution of Internet technologies (Internet of Things) and ubiquitous computing (Ubiquitous Sensor Networks) allow developing less expensive systems, easier to control, install and maintain, using standard protocols with low-power consumption. This work develops and test a low-cost sensor/actuator network platform, based in Internet of Things, integrating machine-to-machine and human-machine-interface protocols. Edge computing uses this multi-protocol approach to develop control processes on Precision Agriculture scenarios. A greenhouse with hydroponic crop production was developed and tested using Ubiquitous Sensor Network monitoring and edge control on Internet of Things paradigm. The experimental results showed that the Internet technologies and Smart Object Communication Patterns can be combined to encourage development of Precision Agriculture. They demonstrated added benefits (cost, energy, smart developing, acceptance by agricultural specialists) when a project is launched. PMID:27455265

A generic flexible and robust approach for intelligent real-time video-surveillance systems

NASA Astrophysics Data System (ADS)

Desurmont, Xavier; Delaigle, Jean-Francois; Bastide, Arnaud; Macq, Benoit

2004-05-01

In this article we present a generic, flexible and robust approach for an intelligent real-time video-surveillance system. A previous version of the system was presented in [1]. The goal of these advanced tools is to provide help to operators by detecting events of interest in visual scenes and highlighting alarms and compute statistics. The proposed system is a multi-camera platform able to handle different standards of video inputs (composite, IP, IEEE1394 ) and which can basically compress (MPEG4), store and display them. This platform also integrates advanced video analysis tools, such as motion detection, segmentation, tracking and interpretation. The design of the architecture is optimised to playback, display, and process video flows in an efficient way for video-surveillance application. The implementation is distributed on a scalable computer cluster based on Linux and IP network. It relies on POSIX threads for multitasking scheduling. Data flows are transmitted between the different modules using multicast technology and under control of a TCP-based command network (e.g. for bandwidth occupation control). We report here some results and we show the potential use of such a flexible system in third generation video surveillance system. We illustrate the interest of the system in a real case study, which is the indoor surveillance.

In-Vivo Real-Time Control of Protein Expression from Endogenous and Synthetic Gene Networks

PubMed Central

Orabona, Emanuele; De Stefano, Luca; Ferry, Mike; Hasty, Jeff; di Bernardo, Mario; di Bernardo, Diego

2014-01-01

We describe an innovative experimental and computational approach to control the expression of a protein in a population of yeast cells. We designed a simple control algorithm to automatically regulate the administration of inducer molecules to the cells by comparing the actual protein expression level in the cell population with the desired expression level. We then built an automated platform based on a microfluidic device, a time-lapse microscopy apparatus, and a set of motorized syringes, all controlled by a computer. We tested the platform to force yeast cells to express a desired fixed, or time-varying, amount of a reporter protein over thousands of minutes. The computer automatically switched the type of sugar administered to the cells, its concentration and its duration, according to the control algorithm. Our approach can be used to control expression of any protein, fused to a fluorescent reporter, provided that an external molecule known to (indirectly) affect its promoter activity is available. PMID:24831205

Multiplex cDNA quantification method that facilitates the standardization of gene expression data

PubMed Central

Gotoh, Osamu; Murakami, Yasufumi; Suyama, Akira

2011-01-01

Microarray-based gene expression measurement is one of the major methods for transcriptome analysis. However, current microarray data are substantially affected by microarray platforms and RNA references because of the microarray method can provide merely the relative amounts of gene expression levels. Therefore, valid comparisons of the microarray data require standardized platforms, internal and/or external controls and complicated normalizations. These requirements impose limitations on the extensive comparison of gene expression data. Here, we report an effective approach to removing the unfavorable limitations by measuring the absolute amounts of gene expression levels on common DNA microarrays. We have developed a multiplex cDNA quantification method called GEP-DEAN (Gene expression profiling by DCN-encoding-based analysis). The method was validated by using chemically synthesized DNA strands of known quantities and cDNA samples prepared from mouse liver, demonstrating that the absolute amounts of cDNA strands were successfully measured with a sensitivity of 18 zmol in a highly multiplexed manner in 7 h. PMID:21415008

Application of Three Existing Stope Boundary Optimisation Methods in an Operating Underground Mine

NASA Astrophysics Data System (ADS)

Erdogan, Gamze; Yavuz, Mahmut

2017-12-01

The underground mine planning and design optimisation process have received little attention because of complexity and variability of problems in underground mines. Although a number of optimisation studies and software tools are available and some of them, in special, have been implemented effectively to determine the ultimate-pit limits in an open pit mine, there is still a lack of studies for optimisation of ultimate stope boundaries in underground mines. The proposed approaches for this purpose aim at maximizing the economic profit by selecting the best possible layout under operational, technical and physical constraints. In this paper, the existing three heuristic techniques including Floating Stope Algorithm, Maximum Value Algorithm and Mineable Shape Optimiser (MSO) are examined for optimisation of stope layout in a case study. Each technique is assessed in terms of applicability, algorithm capabilities and limitations considering the underground mine planning challenges. Finally, the results are evaluated and compared.

The baculovirus expression vector system: A commercial manufacturing platform for viral vaccines and gene therapy vectors.

PubMed

Felberbaum, Rachael S

2015-05-01

The baculovirus expression vector system (BEVS) platform has become an established manufacturing platform for the production of viral vaccines and gene therapy vectors. Nine BEVS-derived products have been approved - four for human use (Cervarix(®), Provenge(®), Glybera(®) and Flublok(®)) and five for veterinary use (Porcilis(®) Pesti, BAYOVAC CSF E2(®), Circumvent(®) PCV, Ingelvac CircoFLEX(®) and Porcilis(®) PCV). The BEVS platform offers many advantages, including manufacturing speed, flexible product design, inherent safety and scalability. This combination of features and product approvals has previously attracted interest from academic researchers, and more recently from industry leaders, to utilize BEVS to develop next generation vaccines, vectors for gene therapy, and other biopharmaceutical complex proteins. In this review, we explore the BEVS platform, detailing how it works, platform features and limitations and important considerations for manufacturing and regulatory approval. To underscore the growth in opportunities for BEVS-derived products, we discuss the latest product developments in the gene therapy and influenza vaccine fields that follow in the wake of the recent product approvals of Glybera(®) and Flublok(®), respectively. We anticipate that the utility of the platform will expand even further as new BEVS-derived products attain licensure. Finally, we touch on some of the areas where new BEVS-derived products are likely to emerge. Copyright © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Process for Assembly and Transformation into Saccharomyces cerevisiae of a Synthetic Yeast Artificial Chromosome Containing a Multigene Cassette to Express Enzymes That Enhance Xylose Utilization Designed for an Automated Platform.

PubMed

Hughes, Stephen R; Cox, Elby J; Bang, Sookie S; Pinkelman, Rebecca J; López-Núñez, Juan Carlos; Saha, Badal C; Qureshi, Nasib; Gibbons, William R; Fry, Michelle R; Moser, Bryan R; Bischoff, Kenneth M; Liu, Siqing; Sterner, David E; Butt, Tauseef R; Riedmuller, Steven B; Jones, Marjorie A; Riaño-Herrera, Néstor M

2015-12-01

A yeast artificial chromosome (YAC) containing a multigene cassette for expression of enzymes that enhance xylose utilization (xylose isomerase [XI] and xylulokinase [XKS]) was constructed and transformed into Saccharomyces cerevisiae to demonstrate feasibility as a stable protein expression system in yeast and to design an assembly process suitable for an automated platform. Expression of XI and XKS from the YAC was confirmed by Western blot and PCR analyses. The recombinant and wild-type strains showed similar growth on plates containing hexose sugars, but only recombinant grew on D-xylose and L-arabinose plates. In glucose fermentation, doubling time (4.6 h) and ethanol yield (0.44 g ethanol/g glucose) of recombinant were comparable to wild type (4.9 h and 0.44 g/g). In whole-corn hydrolysate, ethanol yield (0.55 g ethanol/g [glucose + xylose]) and xylose utilization (38%) for recombinant were higher than for wild type (0.47 g/g and 12%). In hydrolysate from spent coffee grounds, yield was 0.46 g ethanol/g (glucose + xylose), and xylose utilization was 93% for recombinant. These results indicate introducing a YAC expressing XI and XKS enhanced xylose utilization without affecting integrity of the host strain, and the process provides a potential platform for automated synthesis of a YAC for expression of multiple optimized genes to improve yeast strains. © 2015 Society for Laboratory Automation and Screening.

Comparative Evaluation of Recombinant Protein Production in Different Biofactories: The Green Perspective

PubMed Central

Capaldi, Stefano

2014-01-01

In recent years, the production of recombinant pharmaceutical proteins in heterologous systems has increased significantly. Most applications involve complex proteins and glycoproteins that are difficult to produce, thus promoting the development and improvement of a wide range of production platforms. No individual system is optimal for the production of all recombinant proteins, so the diversity of platforms based on plants offers a significant advantage. Here, we discuss the production of four recombinant pharmaceutical proteins using different platforms, highlighting from these examples the unique advantages of plant-based systems over traditional fermenter-based expression platforms. PMID:24745008

Optimisation of high-quality total ribonucleic acid isolation from cartilaginous tissues for real-time polymerase chain reaction analysis.

PubMed

Peeters, M; Huang, C L; Vonk, L A; Lu, Z F; Bank, R A; Helder, M N; Doulabi, B Zandieh

2016-11-01

Studies which consider the molecular mechanisms of degeneration and regeneration of cartilaginous tissues are seriously hampered by problematic ribonucleic acid (RNA) isolations due to low cell density and the dense, proteoglycan-rich extracellular matrix of cartilage. Proteoglycans tend to co-purify with RNA, they can absorb the full spectrum of UV light and they are potent inhibitors of polymerase chain reaction (PCR). Therefore, the objective of the present study is to compare and optimise different homogenisation methods and RNA isolation kits for an array of cartilaginous tissues. Tissue samples such as the nucleus pulposus (NP), annulus fibrosus (AF), articular cartilage (AC) and meniscus, were collected from goats and homogenised by either the MagNA Lyser or Freezer Mill. RNA of duplicate samples was subsequently isolated by either TRIzol (benchmark), or the RNeasy Lipid Tissue, RNeasy Fibrous Tissue, or Aurum Total RNA Fatty and Fibrous Tissue kits. RNA yield, purity, and integrity were determined and gene expression levels of type II collagen and aggrecan were measured by real-time PCR. No differences between the two homogenisation methods were found. RNA isolation using the RNeasy Fibrous and Lipid kits resulted in the purest RNA (A260/A280 ratio), whereas TRIzol isolations resulted in RNA that is not as pure, and show a larger difference in gene expression of duplicate samples compared with both RNeasy kits. The Aurum kit showed low reproducibility. For the extraction of high-quality RNA from cartilaginous structures, we suggest homogenisation of the samples by the MagNA Lyser. For AC, NP and AF we recommend the RNeasy Fibrous kit, whereas for the meniscus the RNeasy Lipid kit is advised.Cite this article: M. Peeters, C. L. Huang, L. A. Vonk, Z. F. Lu, R. A. Bank, M. N. Helder, B. Zandieh Doulabi. Optimisation of high-quality total ribonucleic acid isolation from cartilaginous tissues for real-time polymerase chain reaction analysis. Bone Joint Res 2016;5:560-568. DOI: 10.1302/2046-3758.511.BJR-2016-0033.R3. © 2016 Peeters et al.

Optimisation of high-quality total ribonucleic acid isolation from cartilaginous tissues for real-time polymerase chain reaction analysis

PubMed Central

Peeters, M.; Huang, C. L.; Vonk, L. A.; Lu, Z. F.; Bank, R. A.; Doulabi, B. Zandieh

2016-01-01

Objectives Studies which consider the molecular mechanisms of degeneration and regeneration of cartilaginous tissues are seriously hampered by problematic ribonucleic acid (RNA) isolations due to low cell density and the dense, proteoglycan-rich extracellular matrix of cartilage. Proteoglycans tend to co-purify with RNA, they can absorb the full spectrum of UV light and they are potent inhibitors of polymerase chain reaction (PCR). Therefore, the objective of the present study is to compare and optimise different homogenisation methods and RNA isolation kits for an array of cartilaginous tissues. Materials and Methods Tissue samples such as the nucleus pulposus (NP), annulus fibrosus (AF), articular cartilage (AC) and meniscus, were collected from goats and homogenised by either the MagNA Lyser or Freezer Mill. RNA of duplicate samples was subsequently isolated by either TRIzol (benchmark), or the RNeasy Lipid Tissue, RNeasy Fibrous Tissue, or Aurum Total RNA Fatty and Fibrous Tissue kits. RNA yield, purity, and integrity were determined and gene expression levels of type II collagen and aggrecan were measured by real-time PCR. Results No differences between the two homogenisation methods were found. RNA isolation using the RNeasy Fibrous and Lipid kits resulted in the purest RNA (A260/A280 ratio), whereas TRIzol isolations resulted in RNA that is not as pure, and show a larger difference in gene expression of duplicate samples compared with both RNeasy kits. The Aurum kit showed low reproducibility. Conclusion For the extraction of high-quality RNA from cartilaginous structures, we suggest homogenisation of the samples by the MagNA Lyser. For AC, NP and AF we recommend the RNeasy Fibrous kit, whereas for the meniscus the RNeasy Lipid kit is advised. Cite this article: M. Peeters, C. L. Huang, L. A. Vonk, Z. F. Lu, R. A. Bank, M. N. Helder, B. Zandieh Doulabi. Optimisation of high-quality total ribonucleic acid isolation from cartilaginous tissues for real-time polymerase chain reaction analysis. Bone Joint Res 2016;5:560–568. DOI: 10.1302/2046-3758.511.BJR-2016-0033.R3. PMID:27881439

83. GENERAL VIEW FROM NORTH END OF GUN HILL PLATFORM ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

83. GENERAL VIEW FROM NORTH END OF GUN HILL PLATFORM OF 3RD AVENUE EL SHOWING THE SOUTHBOUND TRACK APPROACH INTO GUN HILL STATION. 7TH AVENUE EXPRESS EL ABOVE. - Interborough Rapid Transit Company, Third Avenue Elevated Line, Borough of the Bronx, New York County, NY

An efficient fermentation method for the degradation of cyanogenic glycosides in flaxseed.

PubMed

Wu, C-F; Xu, X-M; Huang, S-H; Deng, M-C; Feng, A-J; Peng, J; Yuan, J-P; Wang, J-H

2012-01-01

Recently, flaxseed has become increasingly popular in the health food market because it contains a considerable amount of specific beneficial nutrients such as lignans and omega-3 fatty acids. However, the presence of cyanogenic glycosides (CGs) in flaxseed severely limits the exploitation of its health benefits and nutritive value. We, therefore, developed an effective fermentation method, optimised by response surface methodology (RSM), for degrading CGs with an enzymatic preparation that includes 12.5% β-glucosidase and 8.9% cyanide hydratase. These optimised conditions resulted in a maximum CG degradation level of 99.3%, reducing the concentration of cyanide in the flaxseed power from 1.156 to 0.015 mg g(-1) after 48 h of fermentation. The avoidance of steam heat to evaporate hydrocyanic acid (HCN) results in lower energy consumption and no environmental pollution. In addition, the detoxified flaxseed retained the beneficial nutrients, lignans and fatty acids at the same level as untreated flaxseed, and this method could provide a new means of removing CGs from other edible plants, such as cassava, almond and sorghum by simultaneously expressing cyanide hydratase and β-glucosidase.

CubiCal - Fast radio interferometric calibration suite exploiting complex optimisation

NASA Astrophysics Data System (ADS)

Kenyon, J. S.; Smirnov, O. M.; Grobler, T. L.; Perkins, S. J.

2018-05-01

It has recently been shown that radio interferometric gain calibration can be expressed succinctly in the language of complex optimisation. In addition to providing an elegant framework for further development, it exposes properties of the calibration problem which can be exploited to accelerate traditional non-linear least squares solvers such as Gauss-Newton and Levenberg-Marquardt. We extend existing derivations to chains of Jones terms: products of several gains which model different aberrant effects. In doing so, we find that the useful properties found in the single term case still hold. We also develop several specialised solvers which deal with complex gains parameterised by real values. The newly developed solvers have been implemented in a Python package called CubiCal, which uses a combination of Cython, multiprocessing and shared memory to leverage the power of modern hardware. We apply CubiCal to both simulated and real data, and perform both direction-independent and direction-dependent self-calibration. Finally, we present the results of some rudimentary profiling to show that CubiCal is competitive with respect to existing calibration tools such as MeqTrees.

Sensor selection cost optimisation for tracking structurally cyclic systems: a P-order solution

NASA Astrophysics Data System (ADS)

Doostmohammadian, M.; Zarrabi, H.; Rabiee, H. R.

2017-08-01

Measurements and sensing implementations impose certain cost in sensor networks. The sensor selection cost optimisation is the problem of minimising the sensing cost of monitoring a physical (or cyber-physical) system. Consider a given set of sensors tracking states of a dynamical system for estimation purposes. For each sensor assume different costs to measure different (realisable) states. The idea is to assign sensors to measure states such that the global cost is minimised. The number and selection of sensor measurements need to ensure the observability to track the dynamic state of the system with bounded estimation error. The main question we address is how to select the state measurements to minimise the cost while satisfying the observability conditions. Relaxing the observability condition for structurally cyclic systems, the main contribution is to propose a graph theoretic approach to solve the problem in polynomial time. Note that polynomial time algorithms are suitable for large-scale systems as their running time is upper-bounded by a polynomial expression in the size of input for the algorithm. We frame the problem as a linear sum assignment with solution complexity of ?.

Implementation of a Multiplex and Quantitative Proteomics Platform for Assessing Protein Lysates Using DNA-Barcoded Antibodies.

PubMed

Lee, Jinho; Geiss, Gary K; Demirkan, Gokhan; Vellano, Christopher P; Filanoski, Brian; Lu, Yiling; Ju, Zhenlin; Yu, Shuangxing; Guo, Huifang; Bogatzki, Lisa Y; Carter, Warren; Meredith, Rhonda K; Krishnamurthy, Savitri; Ding, Zhiyong; Beechem, Joseph M; Mills, Gordon B

2018-06-01

Molecular analysis of tumors forms the basis for personalized cancer medicine and increasingly guides patient selection for targeted therapy. Future opportunities for personalized medicine are highlighted by the measurement of protein expression levels via immunohistochemistry, protein arrays, and other approaches; however, sample type, sample quantity, batch effects, and "time to result" are limiting factors for clinical application. Here, we present a development pipeline for a novel multiplexed DNA-labeled antibody platform which digitally quantifies protein expression from lysate samples. We implemented a rigorous validation process for each antibody and show that the platform is amenable to multiple protocols covering nitrocellulose and plate-based methods. Results are highly reproducible across technical and biological replicates, and there are no observed "batch effects" which are common for most multiplex molecular assays. Tests from basal and perturbed cancer cell lines indicate that this platform is comparable to orthogonal proteomic assays such as Reverse-Phase Protein Array, and applicable to measuring the pharmacodynamic effects of clinically-relevant cancer therapeutics. Furthermore, we demonstrate the potential clinical utility of the platform with protein profiling from breast cancer patient samples to identify molecular subtypes. Together, these findings highlight the potential of this platform for enhancing our understanding of cancer biology in a clinical translation setting. © 2018 by The American Society for Biochemistry and Molecular Biology, Inc.

Economic impact of optimising antiretroviral treatment in human immunodeficiency virus-infected adults with suppressed viral load in Spain, by implementing the grade A-1 evidence recommendations of the 2015 GESIDA/National AIDS Plan.

PubMed

Ribera, Esteban; Martínez-Sesmero, José Manuel; Sánchez-Rubio, Javier; Rubio, Rafael; Pasquau, Juan; Poveda, José Luis; Pérez-Mitru, Alejandro; Roldán, Celia; Hernández-Novoa, Beatriz

2018-03-01

The objective of this study is to estimate the economic impact associated with the optimisation of triple antiretroviral treatment (ART) in patients with undetectable viral load according to the recommendations from the GeSIDA/PNS (2015) Consensus and their applicability in the Spanish clinical practice. A pharmacoeconomic model was developed based on data from a National Hospital Prescription Survey on ART (2014) and the A-I evidence recommendations for the optimisation of ART from the GeSIDA/PNS (2015) consensus. The optimisation model took into account the willingness to optimise a particular regimen and other assumptions, and the results were validated by an expert panel in HIV infection (Infectious Disease Specialists and Hospital Pharmacists). The analysis was conducted from the NHS perspective, considering the annual wholesale price and accounting for deductions stated in the RD-Law 8/2010 and the VAT. The expert panel selected six optimisation strategies, and estimated that 10,863 (13.4%) of the 80,859 patients in Spain currently on triple ART, would be candidates to optimise their ART, leading to savings of €15.9M/year (2.4% of total triple ART drug cost). The most feasible strategies (>40% of patients candidates for optimisation, n=4,556) would be optimisations to ATV/r+3TC therapy. These would produce savings between €653 and €4,797 per patient per year depending on baseline triple ART. Implementation of the main optimisation strategies recommended in the GeSIDA/PNS (2015) Consensus into Spanish clinical practice would lead to considerable savings, especially those based in dual therapy with ATV/r+3TC, thus contributing to the control of pharmaceutical expenditure and NHS sustainability. Copyright © 2016 Elsevier España, S.L.U. and Sociedad Española de Enfermedades Infecciosas y Microbiología Clínica. All rights reserved.

Optimisation of the hybrid renewable energy system by HOMER, PSO and CPSO for the study area

NASA Astrophysics Data System (ADS)

Khare, Vikas; Nema, Savita; Baredar, Prashant

2017-04-01

This study is based on simulation and optimisation of the renewable energy system of the police control room at Sagar in central India. To analyse this hybrid system, the meteorological data of solar insolation and hourly wind speeds of Sagar in central India (longitude 78°45‧ and latitude 23°50‧) have been considered. The pattern of load consumption is studied and suitably modelled for optimisation of the hybrid energy system using HOMER software. The results are compared with those of the particle swarm optimisation and the chaotic particle swarm optimisation algorithms. The use of these two algorithms to optimise the hybrid system leads to a higher quality result with faster convergence. Based on the optimisation result, it has been found that replacing conventional energy sources by the solar-wind hybrid renewable energy system will be a feasible solution for the distribution of electric power as a stand-alone application at the police control room. This system is more environmentally friendly than the conventional diesel generator. The fuel cost reduction is approximately 70-80% more than that of the conventional diesel generator.

Optimisation of nano-silica modified self-compacting high-Volume fly ash mortar

NASA Astrophysics Data System (ADS)

Achara, Bitrus Emmanuel; Mohammed, Bashar S.; Fadhil Nuruddin, Muhd

2017-05-01

Evaluation of the effects of nano-silica amount and superplasticizer (SP) dosage on the compressive strength, porosity and slump flow on high-volume fly ash self-consolidating mortar was investigated. Multiobjective optimisation technique using Design-Expert software was applied to obtain solution based on desirability function that simultaneously optimises the variables and the responses. A desirability function of 0.811 gives the optimised solution. The experimental and predicted results showed minimal errors in all the measured responses.

Multiobjective optimisation of bogie suspension to boost speed on curves

NASA Astrophysics Data System (ADS)

Milad Mousavi-Bideleh, Seyed; Berbyuk, Viktor

2016-01-01

To improve safety and maximum admissible speed on different operational scenarios, multiobjective optimisation of bogie suspension components of a one-car railway vehicle model is considered. The vehicle model has 50 degrees of freedom and is developed in multibody dynamics software SIMPACK. Track shift force, running stability, and risk of derailment are selected as safety objective functions. The improved maximum admissible speeds of the vehicle on curves are determined based on the track plane accelerations up to 1.5 m/s2. To attenuate the number of design parameters for optimisation and improve the computational efficiency, a global sensitivity analysis is accomplished using the multiplicative dimensional reduction method (M-DRM). A multistep optimisation routine based on genetic algorithm (GA) and MATLAB/SIMPACK co-simulation is executed at three levels. The bogie conventional secondary and primary suspension components are chosen as the design parameters in the first two steps, respectively. In the last step semi-active suspension is in focus. The input electrical current to magnetorheological yaw dampers is optimised to guarantee an appropriate safety level. Semi-active controllers are also applied and the respective effects on bogie dynamics are explored. The safety Pareto optimised results are compared with those associated with in-service values. The global sensitivity analysis and multistep approach significantly reduced the number of design parameters and improved the computational efficiency of the optimisation. Furthermore, using the optimised values of design parameters give the possibility to run the vehicle up to 13% faster on curves while a satisfactory safety level is guaranteed. The results obtained can be used in Pareto optimisation and active bogie suspension design problems.

Advanced treatment planning using direct 4D optimisation for pencil-beam scanned particle therapy

NASA Astrophysics Data System (ADS)

Bernatowicz, Kinga; Zhang, Ye; Perrin, Rosalind; Weber, Damien C.; Lomax, Antony J.

2017-08-01

We report on development of a new four-dimensional (4D) optimisation approach for scanned proton beams, which incorporates both irregular motion patterns and the delivery dynamics of the treatment machine into the plan optimiser. Furthermore, we assess the effectiveness of this technique to reduce dose to critical structures in proximity to moving targets, while maintaining effective target dose homogeneity and coverage. The proposed approach has been tested using both a simulated phantom and a clinical liver cancer case, and allows for realistic 4D calculations and optimisation using irregular breathing patterns extracted from e.g. 4DCT-MRI (4D computed tomography-magnetic resonance imaging). 4D dose distributions resulting from our 4D optimisation can achieve almost the same quality as static plans, independent of the studied geometry/anatomy or selected motion (regular and irregular). Additionally, current implementation of the 4D optimisation approach requires less than 3 min to find the solution for a single field planned on 4DCT of a liver cancer patient. Although 4D optimisation allows for realistic calculations using irregular breathing patterns, it is very sensitive to variations from the planned motion. Based on a sensitivity analysis, target dose homogeneity comparable to static plans (D5-D95  <5%) has been found only for differences in amplitude of up to 1 mm, for changes in respiratory phase  <200 ms and for changes in the breathing period of  <20 ms in comparison to the motions used during optimisation. As such, methods to robustly deliver 4D optimised plans employing 4D intensity-modulated delivery are discussed.

Optimisation of immunofluorescence methods to determine MCT1 and MCT4 expression in circulating tumour cells.

PubMed

Kershaw, Stephen; Cummings, Jeffrey; Morris, Karen; Tugwood, Jonathan; Dive, Caroline

2015-05-10

The monocarboxylate transporter-1 (MCT1) represents a novel target in rational anticancer drug design while AZD3965 was developed as an inhibitor of this transporter and is undergoing Phase I clinical trials ( http://www.clinicaltrials.gov/show/NCT01791595 ). We describe the optimisation of an immunofluorescence (IF) method for determination of MCT1 and MCT4 in circulating tumour cells (CTC) as potential prognostic and predictive biomarkers of AZD3965 in cancer patients. Antibody selectivity was investigated by western blotting (WB) in K562 and MDAMB231 cell lines acting as positive controls for MCT1 and MCT4 respectively and by flow cytometry also employing the control cell lines. Ability to detect MCT1 and MCT4 in CTC as a 4(th) channel marker utilising the Veridex™ CellSearch system was conducted in both human volunteer blood spiked with control cells and in samples collected from small cell lung cancer (SCLC) patients. Experimental conditions were established which yielded a 10-fold dynamic range (DR) for detection of MCT1 over MCT4 (antibody concentration 6.25 μg/mL; integration time 0.4 seconds) and a 5-fold DR of MCT4 over MCT 1 (8 μg/100 μL and 0.8 seconds). The IF method was sufficiently sensitive to detect both MCT1 and MCT4 in CTCs harvested from cancer patients. The first IF method has been developed and optimised for detection of MCT 1 and MCT4 in cancer patient CTC.

Mutual information-based LPI optimisation for radar network

NASA Astrophysics Data System (ADS)

Shi, Chenguang; Zhou, Jianjiang; Wang, Fei; Chen, Jun

2015-07-01

Radar network can offer significant performance improvement for target detection and information extraction employing spatial diversity. For a fixed number of radars, the achievable mutual information (MI) for estimating the target parameters may extend beyond a predefined threshold with full power transmission. In this paper, an effective low probability of intercept (LPI) optimisation algorithm is presented to improve LPI performance for radar network. Based on radar network system model, we first provide Schleher intercept factor for radar network as an optimisation metric for LPI performance. Then, a novel LPI optimisation algorithm is presented, where for a predefined MI threshold, Schleher intercept factor for radar network is minimised by optimising the transmission power allocation among radars in the network such that the enhanced LPI performance for radar network can be achieved. The genetic algorithm based on nonlinear programming (GA-NP) is employed to solve the resulting nonconvex and nonlinear optimisation problem. Some simulations demonstrate that the proposed algorithm is valuable and effective to improve the LPI performance for radar network.

A novel global Harmony Search method based on Ant Colony Optimisation algorithm

NASA Astrophysics Data System (ADS)

Fouad, Allouani; Boukhetala, Djamel; Boudjema, Fares; Zenger, Kai; Gao, Xiao-Zhi

2016-03-01

The Global-best Harmony Search (GHS) is a stochastic optimisation algorithm recently developed, which hybridises the Harmony Search (HS) method with the concept of swarm intelligence in the particle swarm optimisation (PSO) to enhance its performance. In this article, a new optimisation algorithm called GHSACO is developed by incorporating the GHS with the Ant Colony Optimisation algorithm (ACO). Our method introduces a novel improvisation process, which is different from that of the GHS in the following aspects. (i) A modified harmony memory (HM) representation and conception. (ii) The use of a global random switching mechanism to monitor the choice between the ACO and GHS. (iii) An additional memory consideration selection rule using the ACO random proportional transition rule with a pheromone trail update mechanism. The proposed GHSACO algorithm has been applied to various benchmark functions and constrained optimisation problems. Simulation results demonstrate that it can find significantly better solutions when compared with the original HS and some of its variants.

Towards microfluidic technology-based MALDI-MS platforms for drug discovery: a review.

PubMed

Winkle, Richard F; Nagy, Judit M; Cass, Anthony Eg; Sharma, Sanjiv

2008-11-01

Microfluidic methods have found applications in various disciplines. It has been predicted that the microfluidic technology would be useful in performing routine steps in drug discovery ranging from target identification to lead optimisation in which the number of compounds evaluated in this regard determines the success of combinatorial screening. The sheer size of the parameter space that can be explored often poses an enormous challenge. We set out to find how close we are towards the use of integrated matrix-assisted laser desorption/ionisation mass spectrometry (MALDI-MS) microfluidic systems for drug discovery. In this article we review the latest applications of microfluidic technology in the area of MALDI-MS and drug discovery. Our literature survey revealed microfluidic technologies-based approaches for various stages of drug discovery; however, they are in still in developmental stages. Furthermore, we speculate on how these technologies could be used in the future.

Patient-tailored Drug-eluting Stent Choice - A Solution for Patients with Diabetes: Proceedings of Two Satellite Symposia Held at EuroPCR in May 2015 in Paris.

PubMed

Mountfort, Katrina; Mehran, Roxana; Colombo, Antonio; Stella, Pieter; Romaguera, Rafael; Sardella, Gennaro

2015-09-01

Although second-generation drug-eluting stents (DES) have improved outcomes in percutaneous coronary interventions (PCIs), important unmet needs remain. Two symposia at EuroPCR 2015 focused on two challenging scenarios. First, patients with diabetes mellitus (DM) have generally inferior outcomes following PCI. The Cre8™ stent (manufactured by CID Spa, member of Alvimedica Group) has shown unique efficacy in subpopulations of patients with DM during clinical trials. A live case in a patient with diabetes illustrated the challenges of complex multivessel disease. Second, optimising stent selection towards devices that have demonstrated complete and early endothelialisation offers the potential to reduce the duration of dual antiplatelet therapy. The Cre8™ DES features a polymer-free platform and has been associated with low rates of in-stent thrombosis.

DLR MiroSurge: a versatile system for research in endoscopic telesurgery.

PubMed

Hagn, Ulrich; Konietschke, R; Tobergte, A; Nickl, M; Jörg, S; Kübler, B; Passig, G; Gröger, M; Fröhlich, F; Seibold, U; Le-Tien, L; Albu-Schäffer, A; Nothhelfer, A; Hacker, F; Grebenstein, M; Hirzinger, G

2010-03-01

Research on surgical robotics demands systems for evaluating scientific approaches. Such systems can be divided into dedicated and versatile systems. Dedicated systems are designed for a single surgical task or technique, whereas versatile systems are designed to be expandable and useful in multiple surgical applications. Versatile systems are often based on industrial robots, though, and because of this, are hardly suitable for close contact with humans. To achieve a high degree of versatility the Miro robotic surgery platform (MRSP) consists of versatile components, dedicated front-ends towards surgery and configurable interfaces for the surgeon. This paper presents MiroSurge, a configuration of the MRSP that allows for bimanual endoscopic telesurgery with force feedback. While the components of the MiroSurge system are shown to fulfil the rigid design requirements for robotic telesurgery with force feedback, the system remains versatile, which is supposed to be a key issue for the further development and optimisation.

Design of a wideband CMOS impedance spectroscopy ASIC analog front-end for multichannel biosensor interfaces.

PubMed

Valente, Virgilio; Dai Jiang; Demosthenous, Andreas

2015-08-01

This paper presents the preliminary design and simulation of a flexible and programmable analog front-end (AFE) circuit with current and voltage readout capabilities for electric impedance spectroscopy (EIS). The AFE is part of a fully integrated multifrequency EIS platform. The current readout comprises of a transimpedance stage and an automatic gain control (AGC) unit designed to accommodate impedance changes larger than 3 order of magnitude. The AGC is based on a dynamic peak detector that tracks changes in the input current over time and regulates the gain of a programmable gain amplifier in order to optimise the signal-to-noise ratio. The system works up to 1 MHz. The voltage readout consists of a 2 stages of fully differential current-feedback instrumentation amplifier which provide 100 dB of CMRR and a programmable gain up to 20 V/V per stage with a bandwidth in excess of 10MHz.

Effect of Hyaluronic Acid on the Self Assembling Behaviour of PEO-PPO Copolymers in Aqueous Solution

NASA Astrophysics Data System (ADS)

Mayol, L.; Borzacchiello, A.; Quaglia, F.; La Rotonda, M. I.; Ambrosio, L.

2008-07-01

The influence of hyaluronic acid (HA) on the self assembling properties of pluronic (PEO-PPO-PEO block copolymers) blends has been studied with the aim of engineering thermosensitive and mucoadhesive polymeric platforms for drug delivery. The gelation temperature (Tgel), viscoelastic properties and mucoadhesive force of the systems were investigated and optimised by means of rheological analyses. Pluronic micellar radius was evaluated by Photon Correlation Spectroscopy (PCS). The addition of Low Molecular Weight HA did not hamper the self assembling process of pluronics just delaying the gelation temperature of few Celsius degrees. Furthermore, HA presence led to a strong increase of the pluronics gel rheological properties. PCS results show, in formulations containing HA, aggregates with hydrodynamic diameters values much higher than those of pluronic micelles. Mucoadhesive experiments indicate the possibility of interactions between the pluronic/HA gel and mucus glycoproteins.

Ubiquitin promoter-terminator cassette promotes genetically stable expression of the taste-modifying protein miraculin in transgenic lettuce.

PubMed

Hirai, Tadayoshi; Shohael, Abdullah Mohammad; Kim, You-Wang; Yano, Megumu; Ezura, Hiroshi

2011-12-01

Lettuce is a commercially important leafy vegetable that is cultivated worldwide, and it is also a target crop for plant factories. In this study, lettuce was selected as an alternative platform for recombinant miraculin production because of its fast growth, agronomic value, and wide availability. The taste-modifying protein miraculin is a glycoprotein extracted from the red berries of the West African native shrub Richadella dulcifica. Because of its limited natural availability, many attempts have been made to produce this protein in suitable alternative hosts. We produced transgenic lettuce with miraculin gene driven either by the ubiquitin promoter/terminator cassette from lettuce or a 35S promoter/nos terminator cassette. Miraculin gene expression and miraculin accumulation in both cassettes were compared by quantitative real-time PCR analysis, Western blotting, and enzyme-linked immunosorbent assay. The expression level of the miraculin gene and protein in transgenic lettuce was higher and more genetically stable in the ubiquitin promoter/terminator cassette than in the 35S promoter/nos terminator cassette. These results demonstrated that the ubiquitin promoter/terminator cassette is an efficient platform for the genetically stable expression of the miraculin protein in lettuce and hence this platform is of benefit for recombinant miraculin production on a commercial scale.

CGI: Java Software for Mapping and Visualizing Data from Array-based Comparative Genomic Hybridization and Expression Profiling

PubMed Central

Gu, Joyce Xiuweu-Xu; Wei, Michael Yang; Rao, Pulivarthi H.; Lau, Ching C.; Behl, Sanjiv; Man, Tsz-Kwong

2007-01-01

With the increasing application of various genomic technologies in biomedical research, there is a need to integrate these data to correlate candidate genes/regions that are identified by different genomic platforms. Although there are tools that can analyze data from individual platforms, essential software for integration of genomic data is still lacking. Here, we present a novel Java-based program called CGI (Cytogenetics-Genomics Integrator) that matches the BAC clones from array-based comparative genomic hybridization (aCGH) to genes from RNA expression profiling datasets. The matching is computed via a fast, backend MySQL database containing UCSC Genome Browser annotations. This program also provides an easy-to-use graphical user interface for visualizing and summarizing the correlation of DNA copy number changes and RNA expression patterns from a set of experiments. In addition, CGI uses a Java applet to display the copy number values of a specific BAC clone in aCGH experiments side by side with the expression levels of genes that are mapped back to that BAC clone from the microarray experiments. The CGI program is built on top of extensible, reusable graphic components specifically designed for biologists. It is cross-platform compatible and the source code is freely available under the General Public License. PMID:19936083

CGI: Java software for mapping and visualizing data from array-based comparative genomic hybridization and expression profiling.

PubMed

Gu, Joyce Xiuweu-Xu; Wei, Michael Yang; Rao, Pulivarthi H; Lau, Ching C; Behl, Sanjiv; Man, Tsz-Kwong

2007-10-06

With the increasing application of various genomic technologies in biomedical research, there is a need to integrate these data to correlate candidate genes/regions that are identified by different genomic platforms. Although there are tools that can analyze data from individual platforms, essential software for integration of genomic data is still lacking. Here, we present a novel Java-based program called CGI (Cytogenetics-Genomics Integrator) that matches the BAC clones from array-based comparative genomic hybridization (aCGH) to genes from RNA expression profiling datasets. The matching is computed via a fast, backend MySQL database containing UCSC Genome Browser annotations. This program also provides an easy-to-use graphical user interface for visualizing and summarizing the correlation of DNA copy number changes and RNA expression patterns from a set of experiments. In addition, CGI uses a Java applet to display the copy number values of a specific BAC clone in aCGH experiments side by side with the expression levels of genes that are mapped back to that BAC clone from the microarray experiments. The CGI program is built on top of extensible, reusable graphic components specifically designed for biologists. It is cross-platform compatible and the source code is freely available under the General Public License.

The moving platform after-effect reveals dissociation between what we know and how we walk.

PubMed

Reynolds, R; Bronstein, A

2007-01-01

Gait adaptation is crucial for coping with varying terrain and biological needs. It is also important that any acquired adaptation is expressed only in the appropriate context. Here we review a recent series of experiments which demonstrate inappropriate expression of gait adaptation. We showed that a brief period of walking onto a platform previously experienced as moving results in a large forward sway despite full awareness of the changing context. The adaptation mechanisms involved in this paradigm are extremely fast, just 1-2 discrete exposures to the moving platform results in a motor after-effect. This after-effect still occurs even if subjects deliberately attempt to suppress it. However it disappears when the location or method of gait is altered, indicating that after-effect expression is context dependent. Conversely, making gait self-initiated increased sway during the after-effect. This after-effect demonstrates a profound dissociation between knowledge and action. The absence of generalisation suggests a simple form of motor learning. However, persistent expression of gait after-effects may be dependent on an intact cerebral cortex. The fact that the after-effect is greater during self-initiated gait, and is context dependent, would be consistent with the involvement of supraspinal areas.

Visual grading characteristics and ordinal regression analysis during optimisation of CT head examinations.

PubMed

Zarb, Francis; McEntee, Mark F; Rainford, Louise

2015-06-01

To evaluate visual grading characteristics (VGC) and ordinal regression analysis during head CT optimisation as a potential alternative to visual grading assessment (VGA), traditionally employed to score anatomical visualisation. Patient images (n = 66) were obtained using current and optimised imaging protocols from two CT suites: a 16-slice scanner at the national Maltese centre for trauma and a 64-slice scanner in a private centre. Local resident radiologists (n = 6) performed VGA followed by VGC and ordinal regression analysis. VGC alone indicated that optimised protocols had similar image quality as current protocols. Ordinal logistic regression analysis provided an in-depth evaluation, criterion by criterion allowing the selective implementation of the protocols. The local radiology review panel supported the implementation of optimised protocols for brain CT examinations (including trauma) in one centre, achieving radiation dose reductions ranging from 24 % to 36 %. In the second centre a 29 % reduction in radiation dose was achieved for follow-up cases. The combined use of VGC and ordinal logistic regression analysis led to clinical decisions being taken on the implementation of the optimised protocols. This improved method of image quality analysis provided the evidence to support imaging protocol optimisation, resulting in significant radiation dose savings. • There is need for scientifically based image quality evaluation during CT optimisation. • VGC and ordinal regression analysis in combination led to better informed clinical decisions. • VGC and ordinal regression analysis led to dose reductions without compromising diagnostic efficacy.

A Face Attention Technique for a Robot Able to Interpret Facial Expressions

NASA Astrophysics Data System (ADS)

Simplício, Carlos; Prado, José; Dias, Jorge

Automatic facial expressions recognition using vision is an important subject towards human-robot interaction. Here is proposed a human face focus of attention technique and a facial expressions classifier (a Dynamic Bayesian Network) to incorporate in an autonomous mobile agent whose hardware is composed by a robotic platform and a robotic head. The focus of attention technique is based on the symmetry presented by human faces. By using the output of this module the autonomous agent keeps always targeting the human face frontally. In order to accomplish this, the robot platform performs an arc centered at the human; thus the robotic head, when necessary, moves synchronized. In the proposed probabilistic classifier the information is propagated, from the previous instant, in a lower level of the network, to the current instant. Moreover, to recognize facial expressions are used not only positive evidences but also negative.

Self-Expression on Social Media: Do Tweets Present Accurate and Positive Portraits of Impulsivity, Self-Esteem, and Attachment Style?

PubMed

Orehek, Edward; Human, Lauren J

2017-01-01

Self-expression values are at an all-time high, and people are increasingly relying upon social media platforms to express themselves positively and accurately. We examined whether self-expression on the social media platform Twitter elicits positive and accurate social perceptions. Eleven perceivers rated 128 individuals (targets; total dyadic impressions = 1,408) on their impulsivity, self-esteem, and attachment style, based solely on the information provided in targets' 10 most recent tweets. Targets were on average perceived normatively and with distinctive self-other agreement, indicating both positive and accurate social perceptions. There were also individual differences in how positively and accurately targets were perceived, which exploratory analyses indicated may be partially driven by differential word usage, such as the use of positive emotion words and self- versus other-focus. This study demonstrates that self-expression on social media can elicit both positive and accurate perceptions and begins to shed light on how to curate such perceptions.

The Role of MTurk in Education Research: Advantages, Issues, and Future Directions

ERIC Educational Resources Information Center

Follmer, D. Jake; Sperling, Rayne A.; Suen, Hoi K.

2017-01-01

The advent of online platforms such as Amazon's Mechanical Turk (MTurk) has expanded considerably researchers' options for collecting research data. Many researchers, however, express understandable skepticism of the viability of using platforms such as MTurk. In this article, we provide a background on the use of MTurk as a mechanism for…

The Use of a Virtual Online Debating Platform to Facilitate Student Discussion of Potentially Polarising Topics.

PubMed

McGreevy, Paul D; Tzioumis, Vicky; Degeling, Chris; Johnson, Jane; Brown, Robert; Sands, Mike; Starling, Melissa J; Phillips, Clive J C

2017-09-02

The merits of students exchanging views through the so-called human continuum exercise (HCE) are well established. The current article describes the creation of the virtual human continuum (VHC), an online platform that facilitates the same teaching exercise. It also reports feedback on the VHC from veterinary science students ( n = 38). First-year Doctor of Veterinary Medicine students at the University of Sydney, Australia, trialed the platform and provided feedback. Most students agreed or strongly agreed that the VHC offered: a non-threatening environment for discussing emotive and challenging issues; and an opportunity to see how other people form ideas. It also made them think about how to express their ideas and make arguments; and left them feeling more comfortable about expressing their views using it than they would discussing ideas face-to-face (98%, 84%, 79% and 76%, respectively). All respondents agreed or strongly agreed that the VHC encouraged them to consider other opinions. These data suggest that the transition of the HCE to an online platform facilitates dialogue on difficult ethical issues in a supportive environment.

Comparison of the Predictive Accuracy of DNA Array-Based Multigene Classifiers across cDNA Arrays and Affymetrix GeneChips

PubMed Central

Stec, James; Wang, Jing; Coombes, Kevin; Ayers, Mark; Hoersch, Sebastian; Gold, David L.; Ross, Jeffrey S; Hess, Kenneth R.; Tirrell, Stephen; Linette, Gerald; Hortobagyi, Gabriel N.; Symmans, W. Fraser; Pusztai, Lajos

2005-01-01

We examined how well differentially expressed genes and multigene outcome classifiers retain their class-discriminating values when tested on data generated by different transcriptional profiling platforms. RNA from 33 stage I-III breast cancers was hybridized to both Affymetrix GeneChip and Millennium Pharmaceuticals cDNA arrays. Only 30% of all corresponding gene expression measurements on the two platforms had Pearson correlation coefficient r ≥ 0.7 when UniGene was used to match probes. There was substantial variation in correlation between different Affymetrix probe sets matched to the same cDNA probe. When cDNA and Affymetrix probes were matched by basic local alignment tool (BLAST) sequence identity, the correlation increased substantially. We identified 182 genes in the Affymetrix and 45 in the cDNA data (including 17 common genes) that accurately separated 91% of cases in supervised hierarchical clustering in each data set. Cross-platform testing of these informative genes resulted in lower clustering accuracy of 45 and 79%, respectively. Several sets of accurate five-gene classifiers were developed on each platform using linear discriminant analysis. The best 100 classifiers showed average misclassification error rate of 2% on the original data that rose to 19.5% when tested on data from the other platform. Random five-gene classifiers showed misclassification error rate of 33%. We conclude that multigene predictors optimized for one platform lose accuracy when applied to data from another platform due to missing genes and sequence differences in probes that result in differing measurements for the same gene. PMID:16049308

Transcriptome-wide analysis supports environmental adaptations of two Pinus pinaster populations from contrasting habitats.

PubMed

Cañas, Rafael A; Feito, Isabel; Fuente-Maqueda, José Francisco; Ávila, Concepción; Majada, Juan; Cánovas, Francisco M

2015-11-06

Maritime pine (Pinus pinaster Aiton) grows in a range of different climates in the southwestern Mediterranean region and the existence of a variety of latitudinal ecotypes or provenances is well established. In this study, we have conducted a deep analysis of the transcriptome in needles from two P. pinaster provenances, Leiria (Portugal) and Tamrabta (Morocco), which were grown in northern Spain under the same conditions. An oligonucleotide microarray (PINARRAY3) and RNA-Seq were used for whole-transcriptome analyses, and we found that 90.95% of the data were concordant between the two platforms. Furthermore, the two methods identified very similar percentages of differentially expressed genes with values of 5.5% for PINARRAY3 and 5.7% for RNA-Seq. In total, 6,023 transcripts were shared and 88 differentially expressed genes overlapped in the two platforms. Among the differentially expressed genes, all transport related genes except aquaporins were expressed at higher levels in Tamrabta than in Leiria. In contrast, genes involved in secondary metabolism were expressed at higher levels in Tamrabta, and photosynthesis-related genes were expressed more highly in Leiria. The genes involved in light sensing in plants were well represented in the differentially expressed groups of genes. In addition, increased levels of hormones such as abscisic acid, gibberellins, jasmonic and salicylic acid were observed in Leiria. Both transcriptome platforms have proven to be useful resources, showing complementary and reliable results. The results presented here highlight the different abilities of the two maritime pine populations to sense environmental conditions and reveal one type of regulation that can be ascribed to different genetic and epigenetic backgrounds.

On the design and optimisation of new fractal antenna using PSO

NASA Astrophysics Data System (ADS)

Rani, Shweta; Singh, A. P.

2013-10-01

An optimisation technique for newly shaped fractal structure using particle swarm optimisation with curve fitting is presented in this article. The aim of particle swarm optimisation is to find the geometry of the antenna for the required user-defined frequency. To assess the effectiveness of the presented method, a set of representative numerical simulations have been done and the results are compared with the measurements from experimental prototypes built according to the design specifications coming from the optimisation procedure. The proposed fractal antenna resonates at the 5.8 GHz industrial, scientific and medical band which is suitable for wireless telemedicine applications. The antenna characteristics have been studied using extensive numerical simulations and are experimentally verified. The antenna exhibits well-defined radiation patterns over the band.

mirEX: a platform for comparative exploration of plant pri-miRNA expression data.

PubMed

Bielewicz, Dawid; Dolata, Jakub; Zielezinski, Andrzej; Alaba, Sylwia; Szarzynska, Bogna; Szczesniak, Michal W; Jarmolowski, Artur; Szweykowska-Kulinska, Zofia; Karlowski, Wojciech M

2012-01-01

mirEX is a comprehensive platform for comparative analysis of primary microRNA expression data. RT-qPCR-based gene expression profiles are stored in a universal and expandable database scheme and wrapped by an intuitive user-friendly interface. A new way of accessing gene expression data in mirEX includes a simple mouse operated querying system and dynamic graphs for data mining analyses. In contrast to other publicly available databases, the mirEX interface allows a simultaneous comparison of expression levels between various microRNA genes in diverse organs and developmental stages. Currently, mirEX integrates information about the expression profile of 190 Arabidopsis thaliana pri-miRNAs in seven different developmental stages: seeds, seedlings and various organs of mature plants. Additionally, by providing RNA structural models, publicly available deep sequencing results, experimental procedure details and careful selection of auxiliary data in the form of web links, mirEX can function as a one-stop solution for Arabidopsis microRNA information. A web-based mirEX interface can be accessed at http://bioinfo.amu.edu.pl/mirex.

Integrative Data Analysis of Multi-Platform Cancer Data with a Multimodal Deep Learning Approach.

PubMed

Liang, Muxuan; Li, Zhizhong; Chen, Ting; Zeng, Jianyang

2015-01-01

Identification of cancer subtypes plays an important role in revealing useful insights into disease pathogenesis and advancing personalized therapy. The recent development of high-throughput sequencing technologies has enabled the rapid collection of multi-platform genomic data (e.g., gene expression, miRNA expression, and DNA methylation) for the same set of tumor samples. Although numerous integrative clustering approaches have been developed to analyze cancer data, few of them are particularly designed to exploit both deep intrinsic statistical properties of each input modality and complex cross-modality correlations among multi-platform input data. In this paper, we propose a new machine learning model, called multimodal deep belief network (DBN), to cluster cancer patients from multi-platform observation data. In our integrative clustering framework, relationships among inherent features of each single modality are first encoded into multiple layers of hidden variables, and then a joint latent model is employed to fuse common features derived from multiple input modalities. A practical learning algorithm, called contrastive divergence (CD), is applied to infer the parameters of our multimodal DBN model in an unsupervised manner. Tests on two available cancer datasets show that our integrative data analysis approach can effectively extract a unified representation of latent features to capture both intra- and cross-modality correlations, and identify meaningful disease subtypes from multi-platform cancer data. In addition, our approach can identify key genes and miRNAs that may play distinct roles in the pathogenesis of different cancer subtypes. Among those key miRNAs, we found that the expression level of miR-29a is highly correlated with survival time in ovarian cancer patients. These results indicate that our multimodal DBN based data analysis approach may have practical applications in cancer pathogenesis studies and provide useful guidelines for personalized cancer therapy.

The High-Throughput Protein Sample Production Platform of the Northeast Structural Genomics Consortium

PubMed Central

Xiao, Rong; Anderson, Stephen; Aramini, James; Belote, Rachel; Buchwald, William A.; Ciccosanti, Colleen; Conover, Ken; Everett, John K.; Hamilton, Keith; Huang, Yuanpeng Janet; Janjua, Haleema; Jiang, Mei; Kornhaber, Gregory J.; Lee, Dong Yup; Locke, Jessica Y.; Ma, Li-Chung; Maglaqui, Melissa; Mao, Lei; Mitra, Saheli; Patel, Dayaban; Rossi, Paolo; Sahdev, Seema; Sharma, Seema; Shastry, Ritu; Swapna, G.V.T.; Tong, Saichu N.; Wang, Dongyan; Wang, Huang; Zhao, Li; Montelione, Gaetano T.; Acton, Thomas B.

2014-01-01

We describe the core Protein Production Platform of the Northeast Structural Genomics Consortium (NESG) and outline the strategies used for producing high-quality protein samples. The platform is centered on the cloning, expression and purification of 6X-His-tagged proteins using T7-based Escherichia coli systems. The 6X-His tag allows for similar purification procedures for most targets and implementation of high-throughput (HTP) parallel methods. In most cases, the 6X-His-tagged proteins are sufficiently purified (> 97% homogeneity) using a HTP two-step purification protocol for most structural studies. Using this platform, the open reading frames of over 16,000 different targeted proteins (or domains) have been cloned as > 26,000 constructs. Over the past nine years, more than 16,000 of these expressed protein, and more than 4,400 proteins (or domains) have been purified to homogeneity in tens of milligram quantities (see Summary Statistics, http://nesg.org/statistics.html). Using these samples, the NESG has deposited more than 900 new protein structures to the Protein Data Bank (PDB). The methods described here are effective in producing eukaryotic and prokaryotic protein samples in E. coli. This paper summarizes some of the updates made to the protein production pipeline in the last five years, corresponding to phase 2 of the NIGMS Protein Structure Initiative (PSI-2) project. The NESG Protein Production Platform is suitable for implementation in a large individual laboratory or by a small group of collaborating investigators. These advanced automated and/or parallel cloning, expression, purification, and biophysical screening technologies are of broad value to the structural biology, functional proteomics, and structural genomics communities. PMID:20688167

Modular programming for tuberculosis control, the "AuTuMN" platform.

PubMed

Trauer, James McCracken; Ragonnet, Romain; Doan, Tan Nhut; McBryde, Emma Sue

2017-08-07

Tuberculosis (TB) is now the world's leading infectious killer and major programmatic advances will be needed if we are to meet the ambitious new End TB Targets. Although mathematical models are powerful tools for TB control, such models must be flexible enough to capture the complexity and heterogeneity of the global TB epidemic. This includes simulating a disease that affects age groups and other risk groups differently, has varying levels of infectiousness depending upon the organ involved and varying outcomes from treatment depending on the drug resistance pattern of the infecting strain. We adopted sound basic principles of software engineering to develop a modular software platform for simulation of TB control interventions ("AuTuMN"). These included object-oriented programming, logical linkage between modules and consistency of code syntax and variable naming. The underlying transmission dynamic model incorporates optional stratification by age, risk group, strain and organ involvement, while our approach to simulating time-variant programmatic parameters better captures the historical progression of the epidemic. An economic model is overlaid upon this epidemiological model which facilitates comparison between new and existing technologies. A "Model runner" module allows for predictions of future disease burden trajectories under alternative scenario situations, as well as uncertainty, automatic calibration, cost-effectiveness and optimisation. The model has now been used to guide TB control strategies across a range of settings and countries, with our modular approach enabling repeated application of the tool without the need for extensive modification for each application. The modular construction of the platform minimises errors, enhances readability and collaboration between multiple programmers and enables rapid adaptation to answer questions in a broad range of contexts without the need for extensive re-programming. Such features are particularly important in simulating an epidemic as complex and diverse as TB.

A cross-sectional study of the presence of United Kingdom (UK) plastic surgeons on social media.

PubMed

Mabvuure, Nigel Tapiwa; Rodrigues, Jeremy; Klimach, Stefan; Nduka, Charles

2014-03-01

To determine the uptake and usage of websites and social media (SM) by UK consultant (attending) plastic surgeons. Professional profiles of full BAPRAS members were searched on Facebook, Twitter, LinkedIn, RealSelf, YouTube, ResearchGate in May 2013. Additional surgeons were identified from the follower lists of @BAPRASvoice and @BAAPSMedia. Website ownership was determined on Google. Searches were repeated three times. Dual BAAPS-BAPRAS members were identified from www.baaps.org.uk. There were 156 (48.3%) dual BAAPS-BAPRAS members and 36 BAPRAS-only members. Fifty seven (18%) surgeons had no account on any platform whereas 266 (82%) were on at least one platform. One hundred and sixty four (51%) had personal websites whilst 37 (11%) had profiles on partnership websites. One hundred and sixteen (36%) had no website presence whilst 2% had websites under construction. The platform most surgeons use is LinkedIn (52%) whilst smaller proportions used Facebook (4%) and Twitter (22%). Surgeons had a mean of 126 (range: 0-3270) Twitter followers and 368 (range: 7-3786) fans/'likes' of their Facebook profiles. Time spent in postgraduate practice was not predictive of website ownership or SM use. However, dual BAAPS-BAPRAS members were significantly more likely to own a personal website, Twitter, RealSelf and YouTube accounts. There has been an increase in the uptake of social media by UK plastic surgeons, especially in those with aesthetic surgery interests. However, very few surgeons have optimised their web presence. Continued education and appropriate usage guidance may promote uptake, particularly by reconstructive surgeons. Copyright © 2013 British Association of Plastic, Reconstructive and Aesthetic Surgeons. Published by Elsevier Ltd. All rights reserved.

A Droplet Microfluidic Platform for Automating Genetic Engineering.

PubMed

Gach, Philip C; Shih, Steve C C; Sustarich, Jess; Keasling, Jay D; Hillson, Nathan J; Adams, Paul D; Singh, Anup K

2016-05-20

We present a water-in-oil droplet microfluidic platform for transformation, culture and expression of recombinant proteins in multiple host organisms including bacteria, yeast and fungi. The platform consists of a hybrid digital microfluidic/channel-based droplet chip with integrated temperature control to allow complete automation and integration of plasmid addition, heat-shock transformation, addition of selection medium, culture, and protein expression. The microfluidic format permitted significant reduction in consumption (100-fold) of expensive reagents such as DNA and enzymes compared to the benchtop method. The chip contains a channel to continuously replenish oil to the culture chamber to provide a fresh supply of oxygen to the cells for long-term (∼5 days) cell culture. The flow channel also replenished oil lost to evaporation and increased the number of droplets that could be processed and cultured. The platform was validated by transforming several plasmids into Escherichia coli including plasmids containing genes for fluorescent proteins GFP, BFP and RFP; plasmids with selectable markers for ampicillin or kanamycin resistance; and a Golden Gate DNA assembly reaction. We also demonstrate the applicability of this platform for transformation in widely used eukaryotic organisms such as Saccharomyces cerevisiae and Aspergillus niger. Duration and temperatures of the microfluidic heat-shock procedures were optimized to yield transformation efficiencies comparable to those obtained by benchtop methods with a throughput up to 6 droplets/min. The proposed platform offers potential for automation of molecular biology experiments significantly reducing cost, time and variability while improving throughput.

Radiation dose optimisation for conventional imaging in infants and newborns using automatic dose management software: an application of the new 2013/59 EURATOM directive.

PubMed

Alejo, L; Corredoira, E; Sánchez-Muñoz, F; Huerga, C; Aza, Z; Plaza-Núñez, R; Serrada, A; Bret-Zurita, M; Parrón, M; Prieto-Areyano, C; Garzón-Moll, G; Madero, R; Guibelalde, E

2018-04-09

Objective: The new 2013/59 EURATOM Directive (ED) demands dosimetric optimisation procedures without undue delay. The aim of this study was to optimise paediatric conventional radiology examinations applying the ED without compromising the clinical diagnosis. Automatic dose management software (ADMS) was used to analyse 2678 studies of children from birth to 5 years of age, obtaining local diagnostic reference levels (DRLs) in terms of entrance surface air kerma. Given local DRL for infants and chest examinations exceeded the European Commission (EC) DRL, an optimisation was performed decreasing the kVp and applying the automatic control exposure. To assess the image quality, an analysis of high-contrast resolution (HCSR), signal-to-noise ratio (SNR) and figure of merit (FOM) was performed, as well as a blind test based on the generalised estimating equations method. For newborns and chest examinations, the local DRL exceeded the EC DRL by 113%. After the optimisation, a reduction of 54% was obtained. No significant differences were found in the image quality blind test. A decrease in SNR (-37%) and HCSR (-68%), and an increase in FOM (42%), was observed. ADMS allows the fast calculation of local DRLs and the performance of optimisation procedures in babies without delay. However, physical and clinical analyses of image quality remain to be needed to ensure the diagnostic integrity after the optimisation process. Advances in knowledge: ADMS are useful to detect radiation protection problems and to perform optimisation procedures in paediatric conventional imaging without undue delay, as ED requires.

SemanticSCo: A platform to support the semantic composition of services for gene expression analysis.

PubMed

Guardia, Gabriela D A; Ferreira Pires, Luís; da Silva, Eduardo G; de Farias, Cléver R G

2017-02-01

Gene expression studies often require the combined use of a number of analysis tools. However, manual integration of analysis tools can be cumbersome and error prone. To support a higher level of automation in the integration process, efforts have been made in the biomedical domain towards the development of semantic web services and supporting composition environments. Yet, most environments consider only the execution of simple service behaviours and requires users to focus on technical details of the composition process. We propose a novel approach to the semantic composition of gene expression analysis services that addresses the shortcomings of the existing solutions. Our approach includes an architecture designed to support the service composition process for gene expression analysis, and a flexible strategy for the (semi) automatic composition of semantic web services. Finally, we implement a supporting platform called SemanticSCo to realize the proposed composition approach and demonstrate its functionality by successfully reproducing a microarray study documented in the literature. The SemanticSCo platform provides support for the composition of RESTful web services semantically annotated using SAWSDL. Our platform also supports the definition of constraints/conditions regarding the order in which service operations should be invoked, thus enabling the definition of complex service behaviours. Our proposed solution for semantic web service composition takes into account the requirements of different stakeholders and addresses all phases of the service composition process. It also provides support for the definition of analysis workflows at a high-level of abstraction, thus enabling users to focus on biological research issues rather than on the technical details of the composition process. The SemanticSCo source code is available at https://github.com/usplssb/SemanticSCo. Copyright © 2017 Elsevier Inc. All rights reserved.

Analytical formulation of impulsive collision avoidance dynamics

NASA Astrophysics Data System (ADS)

Bombardelli, Claudio

2014-02-01

The paper deals with the problem of impulsive collision avoidance between two colliding objects in three dimensions and assuming elliptical Keplerian orbits. Closed-form analytical expressions are provided that accurately predict the relative dynamics of the two bodies in the encounter b-plane following an impulsive delta-V manoeuvre performed by one object at a given orbit location prior to the impact and with a generic three-dimensional orientation. After verifying the accuracy of the analytical expressions for different orbital eccentricities and encounter geometries the manoeuvre direction that maximises the miss distance is obtained numerically as a function of the arc length separation between the manoeuvre point and the predicted collision point. The provided formulas can be used for high-accuracy instantaneous estimation of the outcome of a generic impulsive collision avoidance manoeuvre and its optimisation.

Improving access to medicines for non-communicable diseases in rural India: a mixed methods study protocol using quasi-experimental design.

PubMed

Prashanth, N S; Elias, Maya Annie; Pati, Manoj Kumar; Aivalli, Praveenkumar; Munegowda, C M; Bhanuprakash, Srinath; Sadhana, S M; Criel, Bart; Bigdeli, Maryam; Devadasan, Narayanan

2016-08-22

India has the distinction of financing its healthcare mainly through out-of-pocket expenses by individual families contributing to catastrophic health expenditure and impoverishment. Nearly 70 % of the expenditure is on medicines purchased at private pharmacies. Patients with chronic ailments are especially affected, as they often need lifelong medicines. Over the past years in India, there have been several efforts to improve drug availability at government primary health centres. In this study, we aim to understand health system factors that affect utilisation and access to generic medicines for people with non-communicable diseases. This study aims to understand if (and how) a package of interventions targeting primary health centres and community participation platforms affect utilisation and access to generic medicines for people with non-communicable diseases in the current district context in India. This study will employ a quasi-experimental design and a qualitative theory-driven approach. PHCs will be randomly assigned to one of three arms of the intervention. In one arm, PHCs will receive inputs to optimise service delivery for non-communicable diseases, while the second arm will receive an additional package of interventions to strengthen community participation platforms for improving non-communicable disease care. The third arm will be the control. We will conduct household and facility surveys, before and after the intervention and will estimate the effect of the intervention by difference-in-difference analysis. Sample size for measuring effects was calculated based on obtaining at least 30 households for each primary health centre spread across three distance-based clusters. Primary outcomes include availability and utilisation of medicines at primary health centres and out-of-pocket expenditure for medicines by non-communicable disease households. Focus group discussions with patients and in-depth interviews with health workers will also be conducted. Qualitative and process documentation data will be used to explain how the intervention could have worked. By taking into consideration several health system building blocks and trying to understand how they interact, our study aims to generate evidence for health planners on how to optimise health services to improve access to medicines. Protocol registered on Clinical Trials Registry of India with registration identifier number CTRI/2015/03/005640 on 17(th) March 2015.

Integration of Monte-Carlo ray tracing with a stochastic optimisation method: application to the design of solar receiver geometry.

PubMed

Asselineau, Charles-Alexis; Zapata, Jose; Pye, John

2015-06-01

A stochastic optimisation method adapted to illumination and radiative heat transfer problems involving Monte-Carlo ray-tracing is presented. A solar receiver shape optimisation case study illustrates the advantages of the method and its potential: efficient receivers are identified using a moderate computational cost.

The Energy-Efficient Quarry: Towards improved understanding and optimisation of energy use and minimisation of CO2 generation in the aggregates industry.

NASA Astrophysics Data System (ADS)

Hill, Ian; White, Toby; Owen, Sarah

2014-05-01

Extraction and processing of rock materials to produce aggregates is carried out at some 20,000 quarries across the EU. All stages of the processing and transport of hard and dense materials inevitably consume high levels of energy and have consequent significant carbon footprints. The FP7 project "the Energy Efficient Quarry" (EE-Quarry) has been addressing this problem and has devised strategies, supported by modelling software, to assist the quarrying industry to assess and optimise its energy use, and to minimise its carbon footprint. Aggregate quarries across Europe vary enormously in the scale of the quarrying operations, the nature of the worked mineral, and the processing to produce a final market product. Nevertheless most quarries involve most or all of a series of essential stages; deposit assessment, drilling and blasting, loading and hauling, and crushing and screening. The process of determining the energy-efficiency of each stage is complex, but is broadly understood in principle and there are numerous sources of information and guidance available in the literature and on-line. More complex still is the interaction between each of these stages. For example, using a little more energy in blasting to increase fragmentation may save much greater energy in later crushing and screening, but also generate more fines material which is discarded as waste and the embedded energy in this material is lost. Thus the calculation of the embedded energy in the waste material becomes an input to the determination of the blasting strategy. Such feedback loops abound in the overall quarry optimisation. The project has involved research and demonstration operations at a number of quarries distributed across Europe carried out by all partners in the EE-Quarry project, working in collaboration with many of the major quarrying companies operating in the EU. The EE-Quarry project is developing a sophisticated modelling tool, the "EE-Quarry Model" available to the quarrying industry on a web-based platform. This tool guides quarry managers and operators through the complex, multi-layered, iterative, process of assessing the energy efficiency of their own quarry operation. They are able to evaluate the optimisation of the energy-efficiency of the overall quarry through examining both the individual stages of processing, and the interactions between them. The project is also developing on-line distance learning modules designed for Continuous Professional Development (CPD) activities for staff across the quarrying industry in the EU and beyond. The presentation will describe development of the model, and the format and scope of the resulting software tool and its user-support available to the quarrying industry.

Topology optimisation for natural convection problems

NASA Astrophysics Data System (ADS)

Alexandersen, Joe; Aage, Niels; Andreasen, Casper Schousboe; Sigmund, Ole

2014-12-01

This paper demonstrates the application of the density-based topology optimisation approach for the design of heat sinks and micropumps based on natural convection effects. The problems are modelled under the assumptions of steady-state laminar flow using the incompressible Navier-Stokes equations coupled to the convection-diffusion equation through the Boussinesq approximation. In order to facilitate topology optimisation, the Brinkman approach is taken to penalise velocities inside the solid domain and the effective thermal conductivity is interpolated in order to accommodate differences in thermal conductivity of the solid and fluid phases. The governing equations are discretised using stabilised finite elements and topology optimisation is performed for two different problems using discrete adjoint sensitivity analysis. The study shows that topology optimisation is a viable approach for designing heat sink geometries cooled by natural convection and micropumps powered by natural convection.

A supportive architecture for CFD-based design optimisation

NASA Astrophysics Data System (ADS)

Li, Ni; Su, Zeya; Bi, Zhuming; Tian, Chao; Ren, Zhiming; Gong, Guanghong

2014-03-01

Multi-disciplinary design optimisation (MDO) is one of critical methodologies to the implementation of enterprise systems (ES). MDO requiring the analysis of fluid dynamics raises a special challenge due to its extremely intensive computation. The rapid development of computational fluid dynamic (CFD) technique has caused a rise of its applications in various fields. Especially for the exterior designs of vehicles, CFD has become one of the three main design tools comparable to analytical approaches and wind tunnel experiments. CFD-based design optimisation is an effective way to achieve the desired performance under the given constraints. However, due to the complexity of CFD, integrating with CFD analysis in an intelligent optimisation algorithm is not straightforward. It is a challenge to solve a CFD-based design problem, which is usually with high dimensions, and multiple objectives and constraints. It is desirable to have an integrated architecture for CFD-based design optimisation. However, our review on existing works has found that very few researchers have studied on the assistive tools to facilitate CFD-based design optimisation. In the paper, a multi-layer architecture and a general procedure are proposed to integrate different CFD toolsets with intelligent optimisation algorithms, parallel computing technique and other techniques for efficient computation. In the proposed architecture, the integration is performed either at the code level or data level to fully utilise the capabilities of different assistive tools. Two intelligent algorithms are developed and embedded with parallel computing. These algorithms, together with the supportive architecture, lay a solid foundation for various applications of CFD-based design optimisation. To illustrate the effectiveness of the proposed architecture and algorithms, the case studies on aerodynamic shape design of a hypersonic cruising vehicle are provided, and the result has shown that the proposed architecture and developed algorithms have performed successfully and efficiently in dealing with the design optimisation with over 200 design variables.

Optimisation of SOA-REAMs for hybrid DWDM-TDMA PON applications.

PubMed

Naughton, Alan; Antony, Cleitus; Ossieur, Peter; Porto, Stefano; Talli, Giuseppe; Townsend, Paul D

2011-12-12

We demonstrate how loss-optimised, gain-saturated SOA-REAM based reflective modulators can reduce the burst to burst power variations due to differential access loss in the upstream path in carrier distributed passive optical networks by 18 dB compared to fixed linear gain modulators. We also show that the loss optimised device has a high tolerance to input power variations and can operate in deep saturation with minimal patterning penalties. Finally, we demonstrate that an optimised device can operate across the C-Band and also over a transmission distance of 80 km. © 2011 Optical Society of America

A targeted gene expression platform allows for rapid analysis of chemical-induced antioxidant mRNA expression in zebrafish larvae.

PubMed

Mills, Margaret G; Gallagher, Evan P

2017-01-01

Chemical-induced oxidative stress and the biochemical pathways that protect against oxidative damage are of particular interest in the field of toxicology. To rapidly identify oxidative stress-responsive gene expression changes in zebrafish, we developed a targeted panel of antioxidant genes using the Affymetrix QuantiGene Plex (QGP) platform. The genes contained in our panel include eight putative Nrf2 (Nfe2l2a)-dependent antioxidant genes (hmox1a, gstp1, gclc, nqo1, prdx1, gpx1a, sod1, sod2), a stress response gene (hsp70), an inducible DNA damage repair gene (gadd45bb), and three reference genes (actb1, gapdh, hprt1). We tested this platform on larval zebrafish exposed to tert-butyl hydroperoxide (tBHP) and cadmium (Cd), two model oxidative stressors with different modes of action, and compared our results with those obtained using the more common quantitative PCR (qPCR) method. Both methods showed that exposure to tBHP and Cd induced expression of prdx1, gstp1, and hmox1a (2- to 12-fold increase via QGP), indicative of an activated Nrf2 response in larval zebrafish. Both compounds also elicited a general stress response as reflected by elevation of hsp70 and gadd45bb, with Cd being the more potent inducer. Transient changes were observed in sod2 and gpx1a expression, whereas nqo1, an Nrf2-responsive gene in mammalian cells, was minimally affected by either tBHP or Cd chemical exposures. Developmental expression analysis of the target genes by QGP revealed marked upregulation of sod2 between 0-96hpf, and to a lesser extent, of sod1 and gstp1. Once optimized, QGP analysis of these experiments was accomplished more rapidly, using far less tissue, and at lower total costs than qPCR analysis. In summary, the QGP platform as applied to higher-throughput zebrafish studies provides a reasonable cost-effective alternative to qPCR or more comprehensive transcriptomics approaches to rapidly assess the potential for chemicals to elicit oxidative stress as a mechanism of chemical toxicity.

Multi-Objectivising Combinatorial Optimisation Problems by Means of Elementary Landscape Decompositions.

PubMed

Ceberio, Josu; Calvo, Borja; Mendiburu, Alexander; Lozano, Jose A

2018-02-15

In the last decade, many works in combinatorial optimisation have shown that, due to the advances in multi-objective optimisation, the algorithms from this field could be used for solving single-objective problems as well. In this sense, a number of papers have proposed multi-objectivising single-objective problems in order to use multi-objective algorithms in their optimisation. In this article, we follow up this idea by presenting a methodology for multi-objectivising combinatorial optimisation problems based on elementary landscape decompositions of their objective function. Under this framework, each of the elementary landscapes obtained from the decomposition is considered as an independent objective function to optimise. In order to illustrate this general methodology, we consider four problems from different domains: the quadratic assignment problem and the linear ordering problem (permutation domain), the 0-1 unconstrained quadratic optimisation problem (binary domain), and the frequency assignment problem (integer domain). We implemented two widely known multi-objective algorithms, NSGA-II and SPEA2, and compared their performance with that of a single-objective GA. The experiments conducted on a large benchmark of instances of the four problems show that the multi-objective algorithms clearly outperform the single-objective approaches. Furthermore, a discussion on the results suggests that the multi-objective space generated by this decomposition enhances the exploration ability, thus permitting NSGA-II and SPEA2 to obtain better results in the majority of the tested instances.

Optimising ICT Effectiveness in Instruction and Learning: Multilevel Transformation Theory and a Pilot Project in Secondary Education

ERIC Educational Resources Information Center

Mooij, Ton

2004-01-01

Specific combinations of educational and ICT conditions including computer use may optimise learning processes, particularly for learners at risk. This position paper asks which curricular, instructional, and ICT characteristics can be expected to optimise learning processes and outcomes, and how to best achieve this optimization. A theoretical…

Zinc Fingers, TALEs, and CRISPR Systems: A Comparison of Tools for Epigenome Editing.

PubMed

Waryah, Charlene Babra; Moses, Colette; Arooj, Mahira; Blancafort, Pilar

2018-01-01

The completion of genome, epigenome, and transcriptome mapping in multiple cell types has created a demand for precision biomolecular tools that allow researchers to functionally manipulate DNA, reconfigure chromatin structure, and ultimately reshape gene expression patterns. Epigenetic editing tools provide the ability to interrogate the relationship between epigenetic modifications and gene expression. Importantly, this information can be exploited to reprogram cell fate for both basic research and therapeutic applications. Three different molecular platforms for epigenetic editing have been developed: zinc finger proteins (ZFs), transcription activator-like effectors (TALEs), and the system of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and CRISPR-associated (Cas) proteins. These platforms serve as custom DNA-binding domains (DBDs), which are fused to epigenetic modifying domains to manipulate epigenetic marks at specific sites in the genome. The addition and/or removal of epigenetic modifications reconfigures local chromatin structure, with the potential to provoke long-lasting changes in gene transcription. Here we summarize the molecular structure and mechanism of action of ZF, TALE, and CRISPR platforms and describe their applications for the locus-specific manipulation of the epigenome. The advantages and disadvantages of each platform will be discussed with regard to genomic specificity, potency in regulating gene expression, and reprogramming cell phenotypes, as well as ease of design, construction, and delivery. Finally, we outline potential applications for these tools in molecular biology and biomedicine and identify possible barriers to their future clinical implementation.

An integrated biotechnology platform for developing sustainable chemical processes.

PubMed

Barton, Nelson R; Burgard, Anthony P; Burk, Mark J; Crater, Jason S; Osterhout, Robin E; Pharkya, Priti; Steer, Brian A; Sun, Jun; Trawick, John D; Van Dien, Stephen J; Yang, Tae Hoon; Yim, Harry

2015-03-01

Genomatica has established an integrated computational/experimental metabolic engineering platform to design, create, and optimize novel high performance organisms and bioprocesses. Here we present our platform and its use to develop E. coli strains for production of the industrial chemical 1,4-butanediol (BDO) from sugars. A series of examples are given to demonstrate how a rational approach to strain engineering, including carefully designed diagnostic experiments, provided critical insights about pathway bottlenecks, byproducts, expression balancing, and commercial robustness, leading to a superior BDO production strain and process.

Bringing metabolic networks to life: convenience rate law and thermodynamic constraints

PubMed Central

Liebermeister, Wolfram; Klipp, Edda

2006-01-01

Background Translating a known metabolic network into a dynamic model requires rate laws for all chemical reactions. The mathematical expressions depend on the underlying enzymatic mechanism; they can become quite involved and may contain a large number of parameters. Rate laws and enzyme parameters are still unknown for most enzymes. Results We introduce a simple and general rate law called "convenience kinetics". It can be derived from a simple random-order enzyme mechanism. Thermodynamic laws can impose dependencies on the kinetic parameters. Hence, to facilitate model fitting and parameter optimisation for large networks, we introduce thermodynamically independent system parameters: their values can be varied independently, without violating thermodynamical constraints. We achieve this by expressing the equilibrium constants either by Gibbs free energies of formation or by a set of independent equilibrium constants. The remaining system parameters are mean turnover rates, generalised Michaelis-Menten constants, and constants for inhibition and activation. All parameters correspond to molecular energies, for instance, binding energies between reactants and enzyme. Conclusion Convenience kinetics can be used to translate a biochemical network – manually or automatically - into a dynamical model with plausible biological properties. It implements enzyme saturation and regulation by activators and inhibitors, covers all possible reaction stoichiometries, and can be specified by a small number of parameters. Its mathematical form makes it especially suitable for parameter estimation and optimisation. Parameter estimates can be easily computed from a least-squares fit to Michaelis-Menten values, turnover rates, equilibrium constants, and other quantities that are routinely measured in enzyme assays and stored in kinetic databases. PMID:17173669

A domain specific language for performance portable molecular dynamics algorithms

NASA Astrophysics Data System (ADS)

Saunders, William Robert; Grant, James; Müller, Eike Hermann

2018-03-01

Developers of Molecular Dynamics (MD) codes face significant challenges when adapting existing simulation packages to new hardware. In a continuously diversifying hardware landscape it becomes increasingly difficult for scientists to be experts both in their own domain (physics/chemistry/biology) and specialists in the low level parallelisation and optimisation of their codes. To address this challenge, we describe a "Separation of Concerns" approach for the development of parallel and optimised MD codes: the science specialist writes code at a high abstraction level in a domain specific language (DSL), which is then translated into efficient computer code by a scientific programmer. In a related context, an abstraction for the solution of partial differential equations with grid based methods has recently been implemented in the (Py)OP2 library. Inspired by this approach, we develop a Python code generation system for molecular dynamics simulations on different parallel architectures, including massively parallel distributed memory systems and GPUs. We demonstrate the efficiency of the auto-generated code by studying its performance and scalability on different hardware and compare it to other state-of-the-art simulation packages. With growing data volumes the extraction of physically meaningful information from the simulation becomes increasingly challenging and requires equally efficient implementations. A particular advantage of our approach is the easy expression of such analysis algorithms. We consider two popular methods for deducing the crystalline structure of a material from the local environment of each atom, show how they can be expressed in our abstraction and implement them in the code generation framework.

Automated model optimisation using the Cylc workflow engine (Cyclops v1.0)

NASA Astrophysics Data System (ADS)

Gorman, Richard M.; Oliver, Hilary J.

2018-06-01

Most geophysical models include many parameters that are not fully determined by theory, and can be tuned to improve the model's agreement with available data. We might attempt to automate this tuning process in an objective way by employing an optimisation algorithm to find the set of parameters that minimises a cost function derived from comparing model outputs with measurements. A number of algorithms are available for solving optimisation problems, in various programming languages, but interfacing such software to a complex geophysical model simulation presents certain challenges. To tackle this problem, we have developed an optimisation suite (Cyclops) based on the Cylc workflow engine that implements a wide selection of optimisation algorithms from the NLopt Python toolbox (Johnson, 2014). The Cyclops optimisation suite can be used to calibrate any modelling system that has itself been implemented as a (separate) Cylc model suite, provided it includes computation and output of the desired scalar cost function. A growing number of institutions are using Cylc to orchestrate complex distributed suites of interdependent cycling tasks within their operational forecast systems, and in such cases application of the optimisation suite is particularly straightforward. As a test case, we applied the Cyclops to calibrate a global implementation of the WAVEWATCH III (v4.18) third-generation spectral wave model, forced by ERA-Interim input fields. This was calibrated over a 1-year period (1997), before applying the calibrated model to a full (1979-2016) wave hindcast. The chosen error metric was the spatial average of the root mean square error of hindcast significant wave height compared with collocated altimeter records. We describe the results of a calibration in which up to 19 parameters were optimised.

Reliability of clinical impact grading by healthcare professionals of common prescribing error and optimisation cases in critical care patients.

PubMed

Bourne, Richard S; Shulman, Rob; Tomlin, Mark; Borthwick, Mark; Berry, Will; Mills, Gary H

2017-04-01

To identify between and within profession-rater reliability of clinical impact grading for common critical care prescribing error and optimisation cases. To identify representative clinical impact grades for each individual case. Electronic questionnaire. 5 UK NHS Trusts. 30 Critical care healthcare professionals (doctors, pharmacists and nurses). Participants graded severity of clinical impact (5-point categorical scale) of 50 error and 55 optimisation cases. Case between and within profession-rater reliability and modal clinical impact grading. Between and within profession rater reliability analysis used linear mixed model and intraclass correlation, respectively. The majority of error and optimisation cases (both 76%) had a modal clinical severity grade of moderate or higher. Error cases: doctors graded clinical impact significantly lower than pharmacists (-0.25; P < 0.001) and nurses (-0.53; P < 0.001), with nurses significantly higher than pharmacists (0.28; P < 0.001). Optimisation cases: doctors graded clinical impact significantly lower than nurses and pharmacists (-0.39 and -0.5; P < 0.001, respectively). Within profession reliability grading was excellent for pharmacists (0.88 and 0.89; P < 0.001) and doctors (0.79 and 0.83; P < 0.001) but only fair to good for nurses (0.43 and 0.74; P < 0.001), for optimisation and error cases, respectively. Representative clinical impact grades for over 100 common prescribing error and optimisation cases are reported for potential clinical practice and research application. The between professional variability highlights the importance of multidisciplinary perspectives in assessment of medication error and optimisation cases in clinical practice and research. © The Author 2017. Published by Oxford University Press in association with the International Society for Quality in Health Care. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com

Optimisation of lateral car dynamics taking into account parameter uncertainties

NASA Astrophysics Data System (ADS)

Busch, Jochen; Bestle, Dieter

2014-02-01

Simulation studies on an active all-wheel-steering car show that disturbance of vehicle parameters have high influence on lateral car dynamics. This motivates the need of robust design against such parameter uncertainties. A specific parametrisation is established combining deterministic, velocity-dependent steering control parameters with partly uncertain, velocity-independent vehicle parameters for simultaneous use in a numerical optimisation process. Model-based objectives are formulated and summarised in a multi-objective optimisation problem where especially the lateral steady-state behaviour is improved by an adaption strategy based on measurable uncertainties. The normally distributed uncertainties are generated by optimal Latin hypercube sampling and a response surface based strategy helps to cut down time consuming model evaluations which offers the possibility to use a genetic optimisation algorithm. Optimisation results are discussed in different criterion spaces and the achieved improvements confirm the validity of the proposed procedure.

Distributed optimisation problem with communication delay and external disturbance

NASA Astrophysics Data System (ADS)

Tran, Ngoc-Tu; Xiao, Jiang-Wen; Wang, Yan-Wu; Yang, Wu

2017-12-01

This paper investigates the distributed optimisation problem for the multi-agent systems (MASs) with the simultaneous presence of external disturbance and the communication delay. To solve this problem, a two-step design scheme is introduced. In the first step, based on the internal model principle, the internal model term is constructed to compensate the disturbance asymptotically. In the second step, a distributed optimisation algorithm is designed to solve the distributed optimisation problem based on the MASs with the simultaneous presence of disturbance and communication delay. Moreover, in the proposed algorithm, each agent interacts with its neighbours through the connected topology and the delay occurs during the information exchange. By utilising Lyapunov-Krasovskii functional, the delay-dependent conditions are derived for both slowly and fast time-varying delay, respectively, to ensure the convergence of the algorithm to the optimal solution of the optimisation problem. Several numerical simulation examples are provided to illustrate the effectiveness of the theoretical results.

An effective pseudospectral method for constraint dynamic optimisation problems with characteristic times

NASA Astrophysics Data System (ADS)

Xiao, Long; Liu, Xinggao; Ma, Liang; Zhang, Zeyin

2018-03-01

Dynamic optimisation problem with characteristic times, widely existing in many areas, is one of the frontiers and hotspots of dynamic optimisation researches. This paper considers a class of dynamic optimisation problems with constraints that depend on the interior points either fixed or variable, where a novel direct pseudospectral method using Legendre-Gauss (LG) collocation points for solving these problems is presented. The formula for the state at the terminal time of each subdomain is derived, which results in a linear combination of the state at the LG points in the subdomains so as to avoid the complex nonlinear integral. The sensitivities of the state at the collocation points with respect to the variable characteristic times are derived to improve the efficiency of the method. Three well-known characteristic time dynamic optimisation problems are solved and compared in detail among the reported literature methods. The research results show the effectiveness of the proposed method.

Medicines optimisation: priorities and challenges.

PubMed

Kaufman, Gerri

2016-03-23

Medicines optimisation is promoted in a guideline published in 2015 by the National Institute for Health and Care Excellence. Four guiding principles underpin medicines optimisation: aim to understand the patient's experience; ensure evidence-based choice of medicines; ensure medicines use is as safe as possible; and make medicines optimisation part of routine practice. Understanding the patient experience is important to improve adherence to medication regimens. This involves communication, shared decision making and respect for patient preferences. Evidence-based choice of medicines is important for clinical and cost effectiveness. Systems and processes for the reporting of medicines-related safety incidents have to be improved if medicines use is to be as safe as possible. Ensuring safe practice in medicines use when patients are transferred between organisations, and managing the complexities of polypharmacy are imperative. A medicines use review can help to ensure that medicines optimisation forms part of routine practice.

Optimization of upcyte® human hepatocytes for the in vitro micronucleus assay.

PubMed

Nörenberg, Astrid; Heinz, Stefan; Scheller, Katharina; Hewitt, Nicola J; Braspenning, Joris; Ott, Michael

2013-12-12

"Upcyte(®) human hepatocytes" have the unique property of combining proliferation with the expression of drug metabolising activities. In our current study, we evaluated whether these cells would be suitable for early in vitro micronucleus (MN) tests. A treatment period of 96 h without a recovery period was most reliable for detecting MN formation in upcyte(®) hepatocytes from Donor 740. The basal MN rate in upcyte(®) hepatocytes varied considerably between donors (7-28%); therefore, modifications to the assay medium were tested to determine whether they could decrease inherent MN formation. Optimal medium supplements were 10 ng/ml oncostatin M for the pre-culture and recovery periods and 25 ng/ml epidermal growth factor and 10 ng/ml oncostatin M for the treatment period. Using the optimised conditions and outcome criteria, the upcyte(®) hepatocyte MN assay could correctly identify directly acting (e.g. mitomycin C, etoposide) and metabolically activated genotoxins (e.g. benzo[a]pyrene, cyclophosphamide). "True negative" and "false positive" compounds were also correctly identified as negative. The basal %MN in upcyte(®) hepatocytes from Donor 740 treated with DMSO, cyclophosphamide or MMC, was essentially unaffected by the growth stage ranging from population doublings of 14-61, suggesting that billions of cells could be produced from a single donor for standardised drug toxicity testing. In conclusion, we have established and optimised an in vitro MN test by using upcyte(®) hepatocytes to correctly identify known direct and metabolically activated genotoxicants as well as "false positives" and true negative compounds. The almost unlimited supply of cells from a single donor and optimised test conditions increase reproducibility in early and more predictive in vitro MN tests. Copyright © 2013 Elsevier B.V. All rights reserved.

Cell population heterogeneity and evolution towards drug resistance in cancer: Biological and mathematical assessment, theoretical treatment optimisation.

PubMed

Chisholm, Rebecca H; Lorenzi, Tommaso; Clairambault, Jean

2016-11-01

Drug-induced drug resistance in cancer has been attributed to diverse biological mechanisms at the individual cell or cell population scale, relying on stochastically or epigenetically varying expression of phenotypes at the single cell level, and on the adaptability of tumours at the cell population level. We focus on intra-tumour heterogeneity, namely between-cell variability within cancer cell populations, to account for drug resistance. To shed light on such heterogeneity, we review evolutionary mechanisms that encompass the great evolution that has designed multicellular organisms, as well as smaller windows of evolution on the time scale of human disease. We also present mathematical models used to predict drug resistance in cancer and optimal control methods that can circumvent it in combined therapeutic strategies. Plasticity in cancer cells, i.e., partial reversal to a stem-like status in individual cells and resulting adaptability of cancer cell populations, may be viewed as backward evolution making cancer cell populations resistant to drug insult. This reversible plasticity is captured by mathematical models that incorporate between-cell heterogeneity through continuous phenotypic variables. Such models have the benefit of being compatible with optimal control methods for the design of optimised therapeutic protocols involving combinations of cytotoxic and cytostatic treatments with epigenetic drugs and immunotherapies. Gathering knowledge from cancer and evolutionary biology with physiologically based mathematical models of cell population dynamics should provide oncologists with a rationale to design optimised therapeutic strategies to circumvent drug resistance, that still remains a major pitfall of cancer therapeutics. This article is part of a Special Issue entitled "System Genetics" Guest Editor: Dr. Yudong Cai and Dr. Tao Huang. Copyright © 2016 Elsevier B.V. All rights reserved.

Chimaeric Virus-Like Particles Derived from Consensus Genome Sequences of Human Rotavirus Strains Co-Circulating in Africa

PubMed Central

Jere, Khuzwayo C.; O'Neill, Hester G.; Potgieter, A. Christiaan; van Dijk, Alberdina A.

2014-01-01

Rotavirus virus-like particles (RV-VLPs) are potential alternative non-live vaccine candidates due to their high immunogenicity. They mimic the natural conformation of native viral proteins but cannot replicate because they do not contain genomic material which makes them safe. To date, most RV-VLPs have been derived from cell culture adapted strains or common G1 and G3 rotaviruses that have been circulating in communities for some time. In this study, chimaeric RV-VLPs were generated from the consensus sequences of African rotaviruses (G2, G8, G9 or G12 strains associated with either P[4], P[6] or P[8] genotypes) characterised directly from human stool samples without prior adaptation of the wild type strains to cell culture. Codon-optimised sequences for insect cell expression of genome segments 2 (VP2), 4 (VP4), 6 (VP6) and 9 (VP7) were cloned into a modified pFASTBAC vector, which allowed simultaneous expression of up to four genes using the Bac-to-Bac Baculovirus Expression System (BEVS; Invitrogen). Several combinations of the genome segments originating from different field strains were cloned to produce double-layered RV-VLPs (dRV-VLP; VP2/6), triple-layered RV-VLPs (tRV-VLP; VP2/6/7 or VP2/6/7/4) and chimaeric tRV-VLPs. The RV-VLPs were produced by infecting Spodoptera frugiperda 9 and Trichoplusia ni cells with recombinant baculoviruses using multi-cistronic, dual co-infection and stepwise-infection expression strategies. The size and morphology of the RV-VLPs, as determined by transmission electron microscopy, revealed successful production of RV-VLPs. The novel approach of producing tRV-VLPs, by using the consensus insect cell codon-optimised nucleotide sequence derived from dsRNA extracted directly from clinical specimens, should speed-up vaccine research and development by by-passing the need to adapt rotaviruses to cell culture. Other problems associated with cell culture adaptation, such as possible changes in epitopes, can also be circumvented. Thus, it is now possible to generate tRV-VLPs for evaluation as non-live vaccine candidates for any human or animal field rotavirus strain. PMID:25268783

Domain selection combined with improved cloning strategy for high throughput expression of higher eukaryotic proteins

PubMed Central

Chen, Yunjia; Qiu, Shihong; Luan, Chi-Hao; Luo, Ming

2007-01-01

Background Expression of higher eukaryotic genes as soluble, stable recombinant proteins is still a bottleneck step in biochemical and structural studies of novel proteins today. Correct identification of stable domains/fragments within the open reading frame (ORF), combined with proper cloning strategies, can greatly enhance the success rate when higher eukaryotic proteins are expressed as these domains/fragments. Furthermore, a HTP cloning pipeline incorporated with bioinformatics domain/fragment selection methods will be beneficial to studies of structure and function genomics/proteomics. Results With bioinformatics tools, we developed a domain/domain boundary prediction (DDBP) method, which was trained by available experimental data. Combined with an improved cloning strategy, DDBP had been applied to 57 proteins from C. elegans. Expression and purification results showed there was a 10-fold increase in terms of obtaining purified proteins. Based on the DDBP method, the improved GATEWAY cloning strategy and a robotic platform, we constructed a high throughput (HTP) cloning pipeline, including PCR primer design, PCR, BP reaction, transformation, plating, colony picking and entry clones extraction, which have been successfully applied to 90 C. elegans genes, 88 Brucella genes, and 188 human genes. More than 97% of the targeted genes were obtained as entry clones. This pipeline has a modular design and can adopt different operations for a variety of cloning/expression strategies. Conclusion The DDBP method and improved cloning strategy were satisfactory. The cloning pipeline, combined with our recombinant protein HTP expression pipeline and the crystal screening robots, constitutes a complete platform for structure genomics/proteomics. This platform will increase the success rate of purification and crystallization dramatically and promote the further advancement of structure genomics/proteomics. PMID:17663785

Integrative multi-platform meta-analysis of gene expression profiles in pancreatic ductal adenocarcinoma patients for identifying novel diagnostic biomarkers.

PubMed

Irigoyen, Antonio; Jimenez-Luna, Cristina; Benavides, Manuel; Caba, Octavio; Gallego, Javier; Ortuño, Francisco Manuel; Guillen-Ponce, Carmen; Rojas, Ignacio; Aranda, Enrique; Torres, Carolina; Prados, Jose

2018-01-01

Applying differentially expressed genes (DEGs) to identify feasible biomarkers in diseases can be a hard task when working with heterogeneous datasets. Expression data are strongly influenced by technology, sample preparation processes, and/or labeling methods. The proliferation of different microarray platforms for measuring gene expression increases the need to develop models able to compare their results, especially when different technologies can lead to signal values that vary greatly. Integrative meta-analysis can significantly improve the reliability and robustness of DEG detection. The objective of this work was to develop an integrative approach for identifying potential cancer biomarkers by integrating gene expression data from two different platforms. Pancreatic ductal adenocarcinoma (PDAC), where there is an urgent need to find new biomarkers due its late diagnosis, is an ideal candidate for testing this technology. Expression data from two different datasets, namely Affymetrix and Illumina (18 and 36 PDAC patients, respectively), as well as from 18 healthy controls, was used for this study. A meta-analysis based on an empirical Bayesian methodology (ComBat) was then proposed to integrate these datasets. DEGs were finally identified from the integrated data by using the statistical programming language R. After our integrative meta-analysis, 5 genes were commonly identified within the individual analyses of the independent datasets. Also, 28 novel genes that were not reported by the individual analyses ('gained' genes) were also discovered. Several of these gained genes have been already related to other gastroenterological tumors. The proposed integrative meta-analysis has revealed novel DEGs that may play an important role in PDAC and could be potential biomarkers for diagnosing the disease.

Controlled positioning of analytes and cells on a plasmonic platform for glycan sensing using surface enhanced Raman spectroscopy.

PubMed

Tabatabaei, Mohammadali; Wallace, Gregory Q; Caetano, Fabiana A; Gillies, Elizabeth R; Ferguson, Stephen S G; Lagugné-Labarthet, François

2016-01-01

The rise of molecular plasmonics and its application to ultrasensitive spectroscopic measurements has been enabled by the rational design and fabrication of a variety of metallic nanostructures. Advanced nano and microfabrication methods are key to the development of such structures, allowing one to tailor optical fields at the sub-wavelength scale, thereby optimizing excitation conditions for ultrasensitive detection. In this work, the control of both analyte and cell positioning on a plasmonic platform is enabled using nanofabrication methods involving patterning of fluorocarbon (FC) polymer (C 4 F 8 ) thin films on a plasmonic platform fabricated by nanosphere lithography (NSL). This provides the possibility to probe biomolecules of interest in the vicinity of cells using plasmon-mediated surface enhanced spectroscopies. In this context, we demonstrate the surface enhanced biosensing of glycan expression in different cell lines by surface enhanced Raman spectroscopy (SERS) on these plasmonic platforms functionalized with 4-mercaptophenylboronic acid (4-MPBA) as the Raman reporter. These cell lines include human embryonic kidney (HEK 293), C2C12 mouse myoblasts, and HeLa (Henrietta Lacks) cervical cancer cells. A distinct glycan expression is observed for cancer cells compared to other cell lines by confocal SERS mapping. This suggests the potential application of these versatile SERS platforms for differentiating cancerous from non-cancerous cells.

A comparison of the enzymatic properties of three recombinant isoforms of thrombolytic and antibacterial protein--Destabilase-Lysozyme from medicinal leech.

PubMed

Kurdyumov, Alexey S; Manuvera, Valentin A; Baskova, Isolda P; Lazarev, Vassili N

2015-11-21

Destabilase-Lysozyme (mlDL) is a multifunctional i-type enzyme that has been found in the secretions from the salivary glands of medicinal leeches. mlDL has been shown to exhibit isopeptidase, muramidase and antibacterial activity. This enzyme attracts interest because it expresses thrombolytic activity through isopeptidolysis of the ε-(γ-Glu)-Lys bonds that cross-link polypeptide chains in stabilised fibrin. To date, three isoforms of mlDL have been identified. The enzymatic properties of pure mlDL isoforms have not yet been described because only destabilase complexes containing other proteins could be isolated from the salivary gland secretion and because low product yield from the generation of recombinant proteins has made comprehensive testing difficult. In the present study, we optimised the procedures related to the expression, isolation and purification of active mlDL isoforms (mlDL-Ds1, mlDL-Ds2, mlDL-Ds3) using an Escherichia coli expression system, and we detected and compared their muramidase, lytic, isopeptidase and antimicrobial activities. After optimisation, the product yield was 30 mg per litre of culture. The data obtained in our study led to the suggestion that the recombinant mlDL isoforms isolated from inclusion bodies form stable oligomeric complexes. Analyses of the tested activities revealed that all isoforms exhibited almost identical patterns of pH and ionic strength effects on the activities. We determined that mlDL-Ds1, 2, 3 possessed non-enzymatic antibacterial activity independent of their muramidase activity. For the first time, we demonstrated the fibrinolytic activity of the recombinant mlDL and showed that only intact proteins possessed this activity, suggesting their enzymatic nature. The recombinant Destabilase-Lysozyme isoforms obtained in our study may be considered potential thrombolytic agents that act through a mechanism different from that of common thrombolytics.

Tissue and Animal Models of Sudden Cardiac Death

PubMed Central

Sallam, Karim; Li, Yingxin; Sager, Philip T.; Houser, Steven R.; Wu, Joseph C.

2015-01-01

Sudden Cardiac Death (SCD) is a common cause of death in patients with structural heart disease, genetic mutations or acquired disorders affecting cardiac ion channels. A wide range of platforms exist to model and study disorders associated with SCD. Human clinical studies are cumbersome and are thwarted by the extent of investigation that can be performed on human subjects. Animal models are limited by their degree of homology to human cardiac electrophysiology including ion channel expression. Most commonly used cellular models are cellular transfection models, which are able to mimic the expression of a single ion channel offering incomplete insight into changes of the action potential profile. Induced pluripotent stem cell derived Cardiomyocytes (iPSC-CMs) resemble, but are not identical, to adult human cardiomyocytes, and provide a new platform for studying arrhythmic disorders leading to SCD. A variety of platforms exist to phenotype cellular models including conventional and automated patch clamp, multi-electrode array, and computational modeling. iPSC-CMs have been used to study Long QT syndrome, catecholaminergic polymorphic ventricular tachycardia, hypertrophic cardiomyopathy and other hereditary cardiac disorders. Although iPSC-CMs are distinct from adult cardiomyocytes, they provide a robust platform to advance the science and clinical care of SCD. PMID:26044252

Large-scale production of tannase using the yeast Arxula adeninivorans.

PubMed

Böer, Erik; Breuer, Friederike Sophie; Weniger, Michael; Denter, Sylvia; Piontek, Michael; Kunze, Gotthard

2011-10-01

Tannase (tannin acyl hydrolase, EC 3.1.1.20) hydrolyses the ester and depside bonds of gallotannins and gallic acid esters and is an important industrial enzyme. In the present study, transgenic Arxula adeninivorans strains were optimised for tannase production. Various plasmids carrying one or two expression modules for constitutive expression of tannase were constructed. Transformant strains that overexpress the ATAN1 gene from the strong A. adeninivorans TEF1 promoter produce levels of up to 1,642 U L(-1) when grown in glucose medium in shake flasks. The effect of fed-batch fermentation on tannase productivity was then investigated in detail. Under these conditions, a transgenic strain containing one ATAN1 expression module produced 51,900 U of tannase activity per litre after 142 h of fermentation at a dry cell weight of 162 g L(-1). The highest yield obtained from a transgenic strain with two ATAN1 expression modules was 31,300 U after 232 h at a dry cell weight of 104 g L(-1). Interestingly, the maximum achieved yield coefficients [Y(P/X)] for the two strains were essentially identical.

Multi-Optimisation Consensus Clustering

NASA Astrophysics Data System (ADS)

Li, Jian; Swift, Stephen; Liu, Xiaohui

Ensemble Clustering has been developed to provide an alternative way of obtaining more stable and accurate clustering results. It aims to avoid the biases of individual clustering algorithms. However, it is still a challenge to develop an efficient and robust method for Ensemble Clustering. Based on an existing ensemble clustering method, Consensus Clustering (CC), this paper introduces an advanced Consensus Clustering algorithm called Multi-Optimisation Consensus Clustering (MOCC), which utilises an optimised Agreement Separation criterion and a Multi-Optimisation framework to improve the performance of CC. Fifteen different data sets are used for evaluating the performance of MOCC. The results reveal that MOCC can generate more accurate clustering results than the original CC algorithm.

Optimised collision avoidance for an ultra-close rendezvous with a failed satellite based on the Gauss pseudospectral method

NASA Astrophysics Data System (ADS)

Chu, Xiaoyu; Zhang, Jingrui; Lu, Shan; Zhang, Yao; Sun, Yue

2016-11-01

This paper presents a trajectory planning algorithm to optimise the collision avoidance of a chasing spacecraft operating in an ultra-close proximity to a failed satellite. The complex configuration and the tumbling motion of the failed satellite are considered. The two-spacecraft rendezvous dynamics are formulated based on the target body frame, and the collision avoidance constraints are detailed, particularly concerning the uncertainties. An optimisation solution of the approaching problem is generated using the Gauss pseudospectral method. A closed-loop control is used to track the optimised trajectory. Numerical results are provided to demonstrate the effectiveness of the proposed algorithms.

Design criteria for synthetic riboswitches acting on transcription

PubMed Central

Wachsmuth, Manja; Domin, Gesine; Lorenz, Ronny; Serfling, Robert; Findeiß, Sven; Stadler, Peter F; Mörl, Mario

2015-01-01

Riboswitches are RNA-based regulators of gene expression composed of a ligand-sensing aptamer domain followed by an overlapping expression platform. The regulation occurs at either the level of transcription (by formation of terminator or antiterminator structures) or translation (by presentation or sequestering of the ribosomal binding site). Due to a modular composition, these elements can be manipulated by combining different aptamers and expression platforms and therefore represent useful tools to regulate gene expression in synthetic biology. Using computationally designed theophylline-dependent riboswitches we show that 2 parameters, terminator hairpin stability and folding traps, have a major impact on the functionality of the designed constructs. These have to be considered very carefully during design phase. Furthermore, a combination of several copies of individual riboswitches leads to a much improved activation ratio between induced and uninduced gene activity and to a linear dose-dependent increase in reporter gene expression. Such serial arrangements of synthetic riboswitches closely resemble their natural counterparts and may form the basis for simple quantitative read out systems for the detection of specific target molecules in the cell. PMID:25826571

The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements

PubMed Central

2012-01-01

Over the last decade, the introduction of microarray technology has had a profound impact on gene expression research. The publication of studies with dissimilar or altogether contradictory results, obtained using different microarray platforms to analyze identical RNA samples, has raised concerns about the reliability of this technology. The MicroArray Quality Control (MAQC) project was initiated to address these concerns, as well as other performance and data analysis issues. Expression data on four titration pools from two distinct reference RNA samples were generated at multiple test sites using a variety of microarray-based and alternative technology platforms. Here we describe the experimental design and probe mapping efforts behind the MAQC project. We show intraplatform consistency across test sites as well as a high level of interplatform concordance in terms of genes identified as differentially expressed. This study provides a resource that represents an important first step toward establishing a framework for the use of microarrays in clinical and regulatory settings. PMID:16964229

New and improved tools and methods for enhanced biosynthesis of natural products in microorganisms.

PubMed

Wang, Zhiqing; Cirino, Patrick C

2016-12-01

Engineering efficient biosynthesis of natural products in microorganisms requires optimizing gene expression levels to balance metabolite flux distributions and to minimize accumulation of toxic intermediates. Such metabolic optimization is challenged with identifying the right gene targets, and then determining and achieving appropriate gene expression levels. After decades of having a relatively limited set of gene regulation tools available, metabolic engineers are recently enjoying an ever-growing repertoire of more precise and tunable gene expression platforms. Here we review recent applications of natural and designed transcriptional and translational regulatory machinery for engineering biosynthesis of natural products in microorganisms. Customized trans-acting RNAs (sgRNA, asRNA and sRNA), along with appropriate accessory proteins, are allowing for unparalleled tuning of gene expression. Meanwhile metabolite-responsive transcription factors and riboswitches have been implemented in strain screening and evolution, and in dynamic gene regulation. Further refinements and expansions on these platform technologies will circumvent many long-term obstacles in natural products biosynthesis. Copyright © 2016 Elsevier Ltd. All rights reserved.

Cretaceous tropical carbonate platform changes used as paleoclimatic and paleoceanic indicators: the three lower Cretaceous platform crises

NASA Astrophysics Data System (ADS)

Arnaud-Vanneau, A.; Vrielynck, B.

2009-04-01

Carbonate platform sediments are of biogenic origin. More commonly the bioclasts are fragments of shells and skeletons. The bioclastic composition of a limestone may reflect the nature of biota inhabiting the area and a carbonate platform can be estimated as a living factory, which reflects the prevailing ecological factors. The rate of carbonate production is highest in the tropics, in oligotrophic environments, and in the photic zone. The rate of carbonate production varies greatly with temperature and nutrient input. Three types of biotic carbonate platform can be distinguished. The highest carbonate production is linked to oligotrophic carbonate platform characterized by the presence of assemblages with hermatypic corals. This type of platform is developed in shallow marine environment, nutrient poor water and warm tropical sea. A less efficient production of carbonate platform is related to mesotrophic environments in cooler and/or deeper water and associated to nutrient flux with, sometime, detrital input. The biota includes red algae, solitary coral and branching ahermatypic corals, common bryozoans, crinoids and echinoids. The less productive carbonate platform is the eutrophic muddy platform where the mud is due to the intense bacterial activity, probably related to strong nutrient flux. All changes of type of carbonate platform can be related to climatic and oceanic changes. Three platform crises occurred during lower Cretaceous time. They are followed by important turnover of microfauna (large benthic foraminifers) and microflora (marine algae). They start with the demise of the previous oligotrophic platform, they continue with oceanic perturbations, expression of which was the widespread deposition of organic-rich sediments, well expressed during Late Aptian/Albian and Cenomanian Turonian boundary and the replacement of previous oligotrophic platforms by mesotrophic to eutrophic platforms. The first crisis occurred during Valanginian and Hauterivian time and is related to the opening of the North Atlantic and the neocimerian tectonic phase. It could be linked to cooling periods. Geographically, the warm oligotrophic tropical carbonate platforms of the northern Tethyan margin migrated towards the equator from more than 500kms. The Upper Valanginian-Hauterivian mesotrophic to eutrophic carbonate platforms are muddier and microbially dominated (algal mats, oolites). 60% of benthic foraminifers living in carbonate platform became extinct. The second crisis occurred during Late Aptian to Albian time. It is coeval to the increasing plate movement and the opening of the central Atlantic Ocean. It is linked to massive detrital input on both margins of the Tethys. Tropical carbonate platform are mostly mesotrophic to eutrophic with abundance of opportunistic species such as Orbitolina, which took advantage of abundance of clastic grains. 50% of benthic foraminifers living in carbonate platform became extinct. The last crisis coincides with the Cenomanian-Turonian boundary. This period corresponds to a rapid northward movement of Africa and Spain and the opening of the North-South Atlantic connection. At the boundary we note the disappearance of organisms such as large benthic foraminifers, corals and rudists, which had a symbiotic relationship with green algae. More than 90% of large benthic foraminifers living in carbonate platform became extinct, but this extinction is not available for small size benthic foraminifers, which had not symbiosis.

Improving target coverage and organ-at-risk sparing in intensity-modulated radiotherapy for cervical oesophageal cancer using a simple optimisation method.

PubMed

Lu, Jia-Yang; Cheung, Michael Lok-Man; Huang, Bao-Tian; Wu, Li-Li; Xie, Wen-Jia; Chen, Zhi-Jian; Li, De-Rui; Xie, Liang-Xi

2015-01-01

To assess the performance of a simple optimisation method for improving target coverage and organ-at-risk (OAR) sparing in intensity-modulated radiotherapy (IMRT) for cervical oesophageal cancer. For 20 selected patients, clinically acceptable original IMRT plans (Original plans) were created, and two optimisation methods were adopted to improve the plans: 1) a base dose function (BDF)-based method, in which the treatment plans were re-optimised based on the original plans, and 2) a dose-controlling structure (DCS)-based method, in which the original plans were re-optimised by assigning additional constraints for hot and cold spots. The Original, BDF-based and DCS-based plans were compared with regard to target dose homogeneity, conformity, OAR sparing, planning time and monitor units (MUs). Dosimetric verifications were performed and delivery times were recorded for the BDF-based and DCS-based plans. The BDF-based plans provided significantly superior dose homogeneity and conformity compared with both the DCS-based and Original plans. The BDF-based method further reduced the doses delivered to the OARs by approximately 1-3%. The re-optimisation time was reduced by approximately 28%, but the MUs and delivery time were slightly increased. All verification tests were passed and no significant differences were found. The BDF-based method for the optimisation of IMRT for cervical oesophageal cancer can achieve significantly better dose distributions with better planning efficiency at the expense of slightly more MUs.

Hypoxia-inducible tumour-specific promoters as a dual-targeting transcriptional regulation system for cancer gene therapy

PubMed Central

Javan, Bita; Shahbazi, Majid

2017-01-01

Transcriptional targeting is the best approach for specific gene therapy. Hypoxia is a common feature of the tumour microenvironment. Therefore, targeting gene expression in hypoxic cells by placing transgene under the control of a hypoxia-responsive promoter can be a good strategy for cancer-specific gene therapy. The hypoxia-inducible gene expression system has been investigated more in suicide gene therapy and it can also be of great help in knocking down cancer gene therapy with siRNAs. However, this system needs to be optimised to have maximum efficacy with minimum side effects in normal tissues. The combination of tissue-/tumour-specific promoters with HRE core sequences has been found to enhance the specificity and efficacy of this system. In this review, hypoxia-inducible gene expression system as well as gene therapy strategies targeting tumour hypoxia will be discussed. This review will also focus on hypoxia-inducible tumour-specific promoters as a dual-targeting transcriptional regulation systems developed for cancer-specific gene therapy. PMID:28798809

Living biointerfaces based on non-pathogenic bacteria support stem cell differentiation

NASA Astrophysics Data System (ADS)

Hay, Jake J.; Rodrigo-Navarro, Aleixandre; Hassi, Karoliina; Moulisova, Vladimira; Dalby, Matthew J.; Salmeron-Sanchez, Manuel

2016-02-01

Lactococcus lactis, a non-pathogenic bacteria, has been genetically engineered to express the III7-10 fragment of human fibronectin as a membrane protein. The engineered L. lactis is able to develop biofilms on different surfaces (such as glass and synthetic polymers) and serves as a long-term substrate for mammalian cell culture, specifically human mesenchymal stem cells (hMSC). This system constitutes a living interface between biomaterials and stem cells. The engineered biofilms remain stable and viable for up to 28 days while the expressed fibronectin fragment induces hMSC adhesion. We have optimised conditions to allow long-term mammalian cell culture, and found that the biofilm is functionally equivalent to a fibronectin-coated surface in terms of osteoblastic differentiation using bone morphogenetic protein 2 (BMP-2) added to the medium. This living bacteria interface holds promise as a dynamic substrate for stem cell differentiation that can be further engineered to express other biochemical cues to control hMSC differentiation.

Hes1 expression is reduced in Tbx1 null cells and is required for the development of structures affected in 22q11 deletion syndrome

PubMed Central

van Bueren, Kelly Lammerts; Papangeli, Irinna; Rochais, Francesca; Pearce, Kerra; Roberts, Catherine; Calmont, Amelie; Szumska, Dorota; Kelly, Robert G.; Bhattacharya, Shoumo; Scambler, Peter J.

2010-01-01

22q11 deletion syndrome (22q11DS) is characterised by aberrant development of the pharyngeal apparatus and the heart with haploinsufficiency of the transcription factor TBX1 being considered the major underlying cause of the disease. Tbx1 mutations in mouse phenocopy the disorder. In order to identify the transcriptional dysregulation in Tbx1-expressing lineages we optimised fluorescent-activated cell sorting of β-galactosidase expressing cells (FACS-Gal) to compare the expression profile of Df1/Tbx1lacZ (effectively Tbx1 null) and Tbx1 heterozygous cells isolated from mouse embryos. Hes1, a major effector of Notch signalling, was identified as downregulated in Tbx1−/− mutants. Hes1 mutant mice exhibited a partially penetrant range of 22q11DS-like defects including pharyngeal arch artery (PAA), outflow tract, craniofacial and thymic abnormalities. Similar to Tbx1 mice, conditional mutagenesis revealed that Hes1 expression in embryonic pharyngeal ectoderm contributes to thymus and pharyngeal arch artery development. These results suggest that Hes1 acts downstream of Tbx1 in the morphogenesis of pharyngeal-derived structures. PMID:20122914

A novel approach for discovering condition-specific correlations of gene expressions within biological pathways by using cloud computing technology.

PubMed

Chang, Tzu-Hao; Wu, Shih-Lin; Wang, Wei-Jen; Horng, Jorng-Tzong; Chang, Cheng-Wei

2014-01-01

Microarrays are widely used to assess gene expressions. Most microarray studies focus primarily on identifying differential gene expressions between conditions (e.g., cancer versus normal cells), for discovering the major factors that cause diseases. Because previous studies have not identified the correlations of differential gene expression between conditions, crucial but abnormal regulations that cause diseases might have been disregarded. This paper proposes an approach for discovering the condition-specific correlations of gene expressions within biological pathways. Because analyzing gene expression correlations is time consuming, an Apache Hadoop cloud computing platform was implemented. Three microarray data sets of breast cancer were collected from the Gene Expression Omnibus, and pathway information from the Kyoto Encyclopedia of Genes and Genomes was applied for discovering meaningful biological correlations. The results showed that adopting the Hadoop platform considerably decreased the computation time. Several correlations of differential gene expressions were discovered between the relapse and nonrelapse breast cancer samples, and most of them were involved in cancer regulation and cancer-related pathways. The results showed that breast cancer recurrence might be highly associated with the abnormal regulations of these gene pairs, rather than with their individual expression levels. The proposed method was computationally efficient and reliable, and stable results were obtained when different data sets were used. The proposed method is effective in identifying meaningful biological regulation patterns between conditions.

Fabrication of Organic Radar Absorbing Materials: A Report on the TIF Project

DTIC Science & Technology

2005-05-01

thickness, permittivity and permeability. The ability to measure the permittivity and permeability is an essential requirement for designing an optimised...absorber. And good optimisations codes are required in order to achieve the best possible absorber designs . In this report, the results from a...through measurement of their conductivity and permittivity at microwave frequencies. Methods were then developed for optimising the design of

Quality assurance after process changes of the production of a therapeutic antibody.

PubMed

Brass, J M; Krummen, K; Moll-Kaufmann, C

1996-12-01

Process development for the production of a therapeutic humanised antibody is a very complex operation. It involves recombinant genetics, verification of a strong expression system, gene amplification, characterisation of a stable host cell expression system, optimisation and design of the mammalian cell culture fermentation system and development of an efficient recovery process resulting in high yields and product quality. Rapid progress in the field and the wish of some pharmaceutical companies for outsourcing their production are the driving forces for process changes relatively late in the development phase. This literature survey is aimed at identifying the limits of acceptable process changes in up scaling of the fermentation and down stream processing of biopharmaceuticals and defining the demand in production validation to prove product equivalency and identity of the isolated, purified therapeutic antibody.

Epigenetically regulated imprinted genes and foetal programming.

PubMed

Keverne, Eric B

2010-11-01

Genomic imprinting is a widespread epigenetic phenomenon in mammals and many imprinted genes are expressed in the developing hypothalamus and placenta. The placenta and brain are very different structures with very different roles, but in the pregnant mother they functionally interact coordinating and ensuring the provision of nutrients, timing of parturition and priming of hypothalamus for maternal care and nurturing. This interaction has been evolutionarily fine-tuned to optimise infant survival such that when resources are poor, the mother 'informs' this condition to the foetus producing a thrifty phenotype that is adapted to survive scarce resources after birth.

The plastid genome as a platform for the expression of microbial resistance genes

USDA-ARS?s Scientific Manuscript database

In recent years, our fundamental understanding of host-microbe interaction has developed considerably. We have begun to tease out the genetic components that influence host resistance to microbial colonization. The use of advancing molecular technologies such as microarray expression profiling and...

The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements

EPA Science Inventory

Over the last decade, the introduction of microarray technology has had a profound impact on gene expression research. The publication of studies with dissimilar or altogether contradictory results, obtained using different microarray platforms to analyze identical RNA samples, ...

A farm platform approach to optimizing temperate grazing-livestock systems: metrics for trade-off assessments and future innovations

NASA Astrophysics Data System (ADS)

Harris, Paul; Takahashi, Taro; Blackwell, Martin; Cardenas, Laura; Collins, Adrian; Dungait, Jennifer; Eisler, Mark; Hawkins, Jane; Misselbrook, Tom; Mcauliffe, Graham; Mcfadzean, Jamie; Murray, Phil; Orr, Robert; Jordana Rivero, M.; Wu, Lianhai; Lee, Michael

2017-04-01

Global agriculture is at a critical juncture when competing requirements for maximal production and minimal pollution have led to the concept of sustainable intensification. Livestock production, especially ruminant livestock is central to this debate. Ruminants make an important contribution to global food security by converting feed that is unsuitable for human consumption to high value protein, demand for which is currently increasing at an unprecedented rate. Sustainable intensification of ruminant livestock production may be applied to pastoral grazing, mixed-cropping, feedlot and housed production systems. All these systems have associated environmental risks such as water and air pollution, greenhouse gas emissions and soil degradation, as well as issues affecting production efficiency, product quality and consumer acceptability, such as reduced animal fertility, health and welfare, reflected in the development of agricultural sustainability policies. Further, in many societies livestock represent a resource far greater than just food, e.g. fibre, draught, fertiliser, fuel, bank and social. These challenges necessitate multidisciplinary solutions that can only be properly researched, implemented and tested in real-world production systems which are suited to their geographical and climatic production practice, e.g. temperate grassland. The North Wyke Farm Platform (http://www.rothamsted.ac.uk/farmplatform) was established during 2010 as a UK national capability for collaborative research, training and knowledge exchange in agro-environmental sciences. Its remit is to research agricultural productivity and ecosystem responses to different management practices for beef and sheep production in lowland temperate grasslands. Following construction, a typical beef and sheep system based on permanent pasture receiving chemical fertilisers on first grade pasture (>60% perennial ryegrass) was implemented across the 67.2 ha farm platform in order to obtain baseline data on hydrology, emissions, nutrient cycling, biodiversity, productivity and livestock welfare/health for 2 years (April 2011 to March 2013). Since April 2013, the platform has been progressively modified across three distinct ca. 22 ha farmlets with the underlying principle being to improve the sustainability (economic, social and environmental) by comparing contrasting pasture-based systems (permanent pasture, grass and clover swards, and reseeding of high quality germplasm on a regular cycle). This modification or transitional period ended in July 2015, when the platform assumed full post-baseline status. In this paper, we summarise the sustainability trade-off metrics developed to compare the three systems, together with the farm platform data collections used to create them; collections that can be viewed as 'big data' when considered in their entirety. We concentrate on the baseline and transitional periods and discuss the potential innovations to optimise grazing livestock systems utilising an experimental farm platform approach.

A Method for Decentralised Optimisation in Networks

NASA Astrophysics Data System (ADS)

Saramäki, Jari

2005-06-01

We outline a method for distributed Monte Carlo optimisation of computational problems in networks of agents, such as peer-to-peer networks of computers. The optimisation and messaging procedures are inspired by gossip protocols and epidemic data dissemination, and are decentralised, i.e. no central overseer is required. In the outlined method, each agent follows simple local rules and seeks for better solutions to the optimisation problem by Monte Carlo trials, as well as by querying other agents in its local neighbourhood. With proper network topology, good solutions spread rapidly through the network for further improvement. Furthermore, the system retains its functionality even in realistic settings where agents are randomly switched on and off.

Thermal buckling optimisation of composite plates using firefly algorithm

NASA Astrophysics Data System (ADS)

Kamarian, S.; Shakeri, M.; Yas, M. H.

2017-07-01

Composite plates play a very important role in engineering applications, especially in aerospace industry. Thermal buckling of such components is of great importance and must be known to achieve an appropriate design. This paper deals with stacking sequence optimisation of laminated composite plates for maximising the critical buckling temperature using a powerful meta-heuristic algorithm called firefly algorithm (FA) which is based on the flashing behaviour of fireflies. The main objective of present work was to show the ability of FA in optimisation of composite structures. The performance of FA is compared with the results reported in the previous published works using other algorithms which shows the efficiency of FA in stacking sequence optimisation of laminated composite structures.

Distributed convex optimisation with event-triggered communication in networked systems

NASA Astrophysics Data System (ADS)

Liu, Jiayun; Chen, Weisheng

2016-12-01

This paper studies the distributed convex optimisation problem over directed networks. Motivated by practical considerations, we propose a novel distributed zero-gradient-sum optimisation algorithm with event-triggered communication. Therefore, communication and control updates just occur at discrete instants when some predefined condition satisfies. Thus, compared with the time-driven distributed optimisation algorithms, the proposed algorithm has the advantages of less energy consumption and less communication cost. Based on Lyapunov approaches, we show that the proposed algorithm makes the system states asymptotically converge to the solution of the problem exponentially fast and the Zeno behaviour is excluded. Finally, simulation example is given to illustrate the effectiveness of the proposed algorithm.

Evaluation of the External RNA Controls Consortium (ERCC) reference material using a modified Latin square design.

PubMed

Pine, P Scott; Munro, Sarah A; Parsons, Jerod R; McDaniel, Jennifer; Lucas, Anne Bergstrom; Lozach, Jean; Myers, Timothy G; Su, Qin; Jacobs-Helber, Sarah M; Salit, Marc

2016-06-24

Highly multiplexed assays for quantitation of RNA transcripts are being used in many areas of biology and medicine. Using data generated by these transcriptomic assays requires measurement assurance with appropriate controls. Methods to prototype and evaluate multiple RNA controls were developed as part of the External RNA Controls Consortium (ERCC) assessment process. These approaches included a modified Latin square design to provide a broad dynamic range of relative abundance with known differences between four complex pools of ERCC RNA transcripts spiked into a human liver total RNA background. ERCC pools were analyzed on four different microarray platforms: Agilent 1- and 2-color, Illumina bead, and NIAID lab-made spotted microarrays; and two different second-generation sequencing platforms: the Life Technologies 5500xl and the Illumina HiSeq 2500. Individual ERCC controls were assessed for reproducible performance in signal response to concentration among the platforms. Most demonstrated linear behavior if they were not located near one of the extremes of the dynamic range. Performance issues with any individual ERCC transcript could be attributed to detection limitations, platform-specific target probe issues, or potential mixing errors. Collectively, these pools of spike-in RNA controls were evaluated for suitability as surrogates for endogenous transcripts to interrogate the performance of the RNA measurement process of each platform. The controls were useful for establishing the dynamic range of the assay, as well as delineating the useable region of that range where differential expression measurements, expressed as ratios, would be expected to be accurate. The modified Latin square design presented here uses a composite testing scheme for the evaluation of multiple performance characteristics: linear performance of individual controls, signal response within dynamic range pools of controls, and ratio detection between pairs of dynamic range pools. This compact design provides an economical sample format for the evaluation of multiple external RNA controls within a single experiment per platform. These results indicate that well-designed pools of RNA controls, spiked into samples, provide measurement assurance for endogenous gene expression studies.

SEVIRI 4D-var assimilation analysing the April 2010 Eyjafjallajökull ash dispersion

NASA Astrophysics Data System (ADS)

Lange, Anne Caroline; Elbern, Hendrik

2016-04-01

We present first results of four dimensional variational (4D-var) data assimilation analysis applying SEVIRI observations to the Eulerian regional chemistry and aerosol transport model EURAD-IM (European Air Pollution Dispersion - Inverse Model). Optimising atmospheric dispersion models in terms of volcanic ash transport predictions by observations is especially essential for the aviation industry and associated interests. Remote sensing satellite observations are instrumental for ash detection and monitoring. We choose volcanic ash column retrievals of the Spinning Enhanced Visible and Infrared Imager (SEVIRI) because as infrared instrument on the geostationary satellite Meteosat Second Generation it delivers measurements with high temporal resolution during day and night. The retrieval method relies on the reverse absorption effect. In the framework of the national initiative ESKP (Earth System Knowledge Platform) and the European ACTRIS-2 (Aerosol, Clouds, and Trace gases Research InfraStructure) project, we developed new modules (forward and adjoint) within the EURAD-IM, which are able to process SEVIRI ash column data as observational input to the 4D-var system. The focus of the 4D-var analysis is on initial value optimisation of the volcanic ash clouds that were emitted during the explosive Eyjafjallajökull eruption in April 2010. This eruption caused high public interest because of air traffic closures and it was particularly well observed from many different observation systems all over Europe. Considering multiple observation periods simultaneously in one assimilation window generates a continuous trajectory in the phase space and ensures that past observations are considered within their uncertainties. Results are validated mainly by lidar (LIght Detection And Ranging) observations, both ground and satellite based.

Optimising the visual feedback technique for improving upright stance maintenance by delaying its display: behavioural effects on healthy adults.

PubMed

Rougier, P

2004-04-01

The visual feedback technique (VFB) is recognized by several studies as a valuable tool for re-establishing the balance functions. However, one former study has highlighted the fact that the increased control induced by this technique infer both favourable (the amplitudes of the horizontal motions of the centre of gravity (CoG(h)) are diminished) and unfavourable features (the vertical difference between the CoG(h) motions and centre of pressure (CoP) trajectories are enhanced). One means to decrease these CoP-CoG(v) motions is to delay their display on the screen of the monitor. To assess these behavioural effects, 16 healthy adults were evaluated with various delays from 0 to 1200 ms. CoP displacements, measured through a force platform, were decomposed into two elementary motions: CoG(h) and the difference CoP-CoG(v). A fractional Brownian motion modelling of these motions allowed to determine from which distance and for how long the corrective process takes over and to what extent the motion is controlled. Compared to the VFB real time condition, increasing the delay induces some effects mainly on the CoP-CoG(v) motions which are largely diminished, the most striking effect appearing for delays exceeding 600 ms. Despite the lower forces these reduced amplitudes infer to control body sways, the amplitudes of the CoG(h) motions tend to increase slightly. Considered as a whole, whilst retaining the beneficial aspects of VFB without delay and significantly suppressing the unfavourable features, the data suggests that the method of delaying the screen display optimises the VFB technique.

High Quality Genomic Copy Number Data from Archival Formalin-Fixed Paraffin-Embedded Leiomyosarcoma: Optimisation of Universal Linkage System Labelling

PubMed Central

Salawu, Abdulazeez; Ul-Hassan, Aliya; Hammond, David; Fernando, Malee; Reed, Malcolm; Sisley, Karen

2012-01-01

Most soft tissue sarcomas are characterized by genetic instability and frequent genomic copy number aberrations that are not subtype-specific. Oligonucleotide microarray-based Comparative Genomic Hybridisation (array CGH) is an important technique used to map genome-wide copy number aberrations, but the traditional requirement for high-quality DNA typically obtained from fresh tissue has limited its use in sarcomas. Although large archives of Formalin-fixed Paraffin-embedded (FFPE) tumour samples are available for research, the degradative effects of formalin on DNA from these tissues has made labelling and analysis by array CGH technically challenging. The Universal Linkage System (ULS) may be used for a one-step chemical labelling of such degraded DNA. We have optimised the ULS labelling protocol to perform aCGH on archived FFPE leiomyosarcoma tissues using the 180k Agilent platform. Preservation age of samples ranged from a few months to seventeen years and the DNA showed a wide range of degradation (when visualised on agarose gels). Consistently high DNA labelling efficiency and low microarray probe-to-probe variation (as measured by the derivative log ratio spread) was seen. Comparison of paired fresh and FFPE samples from identical tumours showed good correlation of CNAs detected. Furthermore, the ability to macro-dissect FFPE samples permitted the detection of CNAs that were masked in fresh tissue. Aberrations were visually confirmed using Fluorescence in situ Hybridisation. These results suggest that archival FFPE tissue, with its relative abundance and attendant clinical data may be used for effective mapping for genomic copy number aberrations in such rare tumours as leiomyosarcoma and potentially unravel clues to tumour origins, progression and ultimately, targeted treatment. PMID:23209738

A comparison of sample preparation methods for extracting volatile organic compounds (VOCs) from equine faeces using HS-SPME.

PubMed

Hough, Rachael; Archer, Debra; Probert, Christopher

2018-01-01

Disturbance to the hindgut microbiota can be detrimental to equine health. Metabolomics provides a robust approach to studying the functional aspect of hindgut microorganisms. Sample preparation is an important step towards achieving optimal results in the later stages of analysis. The preparation of samples is unique depending on the technique employed and the sample matrix to be analysed. Gas chromatography mass spectrometry (GCMS) is one of the most widely used platforms for the study of metabolomics and until now an optimised method has not been developed for equine faeces. To compare a sample preparation method for extracting volatile organic compounds (VOCs) from equine faeces. Volatile organic compounds were determined by headspace solid phase microextraction gas chromatography mass spectrometry (HS-SPME-GCMS). Factors investigated were the mass of equine faeces, type of SPME fibre coating, vial volume and storage conditions. The resultant method was unique to those developed for other species. Aliquots of 1000 or 2000 mg in 10 ml or 20 ml SPME headspace were optimal. From those tested, the extraction of VOCs should ideally be performed using a divinylbenzene-carboxen-polydimethysiloxane (DVB-CAR-PDMS) SPME fibre. Storage of faeces for up to 12 months at - 80 °C shared a greater percentage of VOCs with a fresh sample than the equivalent stored at - 20 °C. An optimised method for extracting VOCs from equine faeces using HS-SPME-GCMS has been developed and will act as a standard to enable comparisons between studies. This work has also highlighted storage conditions as an important factor to consider in experimental design for faecal metabolomics studies.

Optimisation and Characterisation of Anti-Fouling Ternary SAM Layers for Impedance-Based Aptasensors

PubMed Central

Miodek, Anna; Regan, Edward M.; Bhalla, Nikhil; Hopkins, Neal A.E.; Goodchild, Sarah A.; Estrela, Pedro

2015-01-01

An aptasensor with enhanced anti-fouling properties has been developed. As a case study, the aptasensor was designed with specificity for human thrombin. The sensing platform was developed on screen printed electrodes and is composed of a self-assembled monolayer made from a ternary mixture of 15-base thiolated DNA aptamers specific for human thrombin co-immobilised with 1,6-hexanedithiol (HDT) and further passivated with 1-mercapto-6-hexanol (MCH). HDT binds to the surface by two of its thiol groups forming alkyl chain bridges and this architecture protects from non-specific attachment of molecules to the electrode surface. Using Electrochemical Impedance Spectroscopy (EIS), the aptasensor is able to detect human thrombin as variations in charge transfer resistance (Rct) upon protein binding. After exposure to a high concentration of non-specific Bovine Serum Albumin (BSA) solution, no changes in the Rct value were observed, highlighting the bio-fouling resistance of the surface generated. In this paper, we present the optimisation and characterisation of the aptasensor based on the ternary self-assembled monolayer (SAM) layer. We show that anti-fouling properties depend on the type of gold surface used for biosensor construction, which was also confirmed by contact angle measurements. We further studied the ratio between aptamers and HDT, which can determine the specificity and selectivity of the sensing layer. We also report the influence of buffer pH and temperature used for incubation of electrodes with proteins on detection and anti-fouling properties. Finally, the stability of the aptasensor was studied by storage of modified electrodes for up to 28 days in different buffers and atmospheric conditions. Aptasensors based on ternary SAM layers are highly promising for clinical applications for detection of a range of proteins in real biological samples. PMID:26426017

Strategy for the lowering and the assessment of exposure to nanoparticles at workspace - Case of study concerning the potential emission of nanoparticles of Lead in an epitaxy laboratory

NASA Astrophysics Data System (ADS)

Artous, Sébastien; Zimmermann, Eric; Douissard, Paul-Antoine; Locatelli, Dominique; Motellier, Sylvie; Derrough, Samir

2015-05-01

The implementation in many products of manufactured nanoparticles is growing fast and raises new questions. For this purpose, the CEA - NanoSafety Platform is developing various research topics for health and safety, environment and nanoparticles exposure in professional activities. The containment optimisation for the exposition lowering, then the exposure assessment to nanoparticles is a strategy for safety improvement at workplace and workspace. The lowering step consists in an optimisation of dynamic and static containment at workplace and/or workspace. Generally, the exposure risk due to the presence of nanoparticles substances does not allow modifying the parameters of containment at workplace and/or workspace. Therefore, gaseous or nanoparticulate tracers are used to evaluate performances of containment. Using a tracer allows to modify safely the parameters of the dynamic containment (ventilation, flow, speed) and to study several configurations of static containment. Moreover, a tracer allows simulating accidental or incidental situation. As a result, a safety procedure can be written more easily in order to manage this type of situation. The step of measurement and characterization of aerosols can therefore be used to assess the exposition at workplace and workspace. The case of study, aim of this paper, concerns the potential emission of Lead nanoparticles at the exhaust of a furnace in an epitaxy laboratory. The use of Helium tracer to evaluate the performance of containment is firstly studied. Secondly, the exposure assessment is characterised in accordance with the French guide “recommendations for characterizing potential emissions and exposure to aerosols released from nanomaterials in workplace operations”. Thirdly the aerosols are sampled, on several places, using collection membranes to try to detect traces of Lead in air.

Optimisation and Characterisation of Anti-Fouling Ternary SAM Layers for Impedance-Based Aptasensors.

PubMed

Miodek, Anna; Regan, Edward M; Bhalla, Nikhil; Hopkins, Neal A E; Goodchild, Sarah A; Estrela, Pedro

2015-09-29

An aptasensor with enhanced anti-fouling properties has been developed. As a case study, the aptasensor was designed with specificity for human thrombin. The sensing platform was developed on screen printed electrodes and is composed of a self-assembled monolayer made from a ternary mixture of 15-base thiolated DNA aptamers specific for human thrombin co-immobilised with 1,6-hexanedithiol (HDT) and further passivated with 1-mercapto-6-hexanol (MCH). HDT binds to the surface by two of its thiol groups forming alkyl chain bridges and this architecture protects from non-specific attachment of molecules to the electrode surface. Using Electrochemical Impedance Spectroscopy (EIS), the aptasensor is able to detect human thrombin as variations in charge transfer resistance (Rct) upon protein binding. After exposure to a high concentration of non-specific Bovine Serum Albumin (BSA) solution, no changes in the Rct value were observed, highlighting the bio-fouling resistance of the surface generated. In this paper, we present the optimisation and characterisation of the aptasensor based on the ternary self-assembled monolayer (SAM) layer. We show that anti-fouling properties depend on the type of gold surface used for biosensor construction, which was also confirmed by contact angle measurements. We further studied the ratio between aptamers and HDT, which can determine the specificity and selectivity of the sensing layer. We also report the influence of buffer pH and temperature used for incubation of electrodes with proteins on detection and anti-fouling properties. Finally, the stability of the aptasensor was studied by storage of modified electrodes for up to 28 days in different buffers and atmospheric conditions. Aptasensors based on ternary SAM layers are highly promising for clinical applications for detection of a range of proteins in real biological samples.

Shelf architectures of an isolated Late Cretaceous carbonate platform margin, Galala Mountains (Eastern Desert, Egypt)

NASA Astrophysics Data System (ADS)

Scheibner, C.; Marzouk, A. M.; Kuss, J.

2001-12-01

An asymmetrical carbonate platform margin to basin transect has been investigated in the Upper Campanian-Maastrichtian succession of the Galala Mountains, northern Egypt. Identification of systems tracts and their lateral correlation was possible in slope sections only, whereas the monotonous chalk-marl alternations of the basinal sections could not be subdivided with respect to sequence stratigraphic terminology. The platform asymmetry is expressed by varying large-scale depositional architectures exhibiting a rimmed platform with a sigmoidal slope curvature in south-easterly dip-sections and a ramp with a linear slope curvature in south-westerly dip-sections. The rimmed platform is subdivided into a gentle upper slope and a steep lower slope. The platform formed as a result of the initial topography that was controlled by the tectonic uplift of the Northern Galala/Wadi Araba Syrian Arc structure. The calculated angles of the steep lower slope of the rimmed part range from 5 to 8°, whereas the ramp part has an angle of less than 0.1°.

Optimising operational amplifiers by evolutionary algorithms and gm/Id method

NASA Astrophysics Data System (ADS)

Tlelo-Cuautle, E.; Sanabria-Borbon, A. C.

2016-10-01

The evolutionary algorithm called non-dominated sorting genetic algorithm (NSGA-II) is applied herein in the optimisation of operational transconductance amplifiers. NSGA-II is accelerated by applying the gm/Id method to estimate reduced search spaces associated to widths (W) and lengths (L) of the metal-oxide-semiconductor field-effect-transistor (MOSFETs), and to guarantee their appropriate bias levels conditions. In addition, we introduce an integer encoding for the W/L sizes of the MOSFETs to avoid a post-processing step for rounding-off their values to be multiples of the integrated circuit fabrication technology. Finally, from the feasible solutions generated by NSGA-II, we introduce a second optimisation stage to guarantee that the final feasible W/L sizes solutions support process, voltage and temperature (PVT) variations. The optimisation results lead us to conclude that the gm/Id method and integer encoding are quite useful to accelerate the convergence of the evolutionary algorithm NSGA-II, while the second optimisation stage guarantees robustness of the feasible solutions to PVT variations.

A Bayesian Approach for Sensor Optimisation in Impact Identification

PubMed Central

Mallardo, Vincenzo; Sharif Khodaei, Zahra; Aliabadi, Ferri M. H.

2016-01-01

This paper presents a Bayesian approach for optimizing the position of sensors aimed at impact identification in composite structures under operational conditions. The uncertainty in the sensor data has been represented by statistical distributions of the recorded signals. An optimisation strategy based on the genetic algorithm is proposed to find the best sensor combination aimed at locating impacts on composite structures. A Bayesian-based objective function is adopted in the optimisation procedure as an indicator of the performance of meta-models developed for different sensor combinations to locate various impact events. To represent a real structure under operational load and to increase the reliability of the Structural Health Monitoring (SHM) system, the probability of malfunctioning sensors is included in the optimisation. The reliability and the robustness of the procedure is tested with experimental and numerical examples. Finally, the proposed optimisation algorithm is applied to a composite stiffened panel for both the uniform and non-uniform probability of impact occurrence. PMID:28774064

Optimisation of active suspension control inputs for improved vehicle handling performance

NASA Astrophysics Data System (ADS)

Čorić, Mirko; Deur, Joško; Kasać, Josip; Tseng, H. Eric; Hrovat, Davor

2016-11-01

Active suspension is commonly considered under the framework of vertical vehicle dynamics control aimed at improvements in ride comfort. This paper uses a collocation-type control variable optimisation tool to investigate to which extent the fully active suspension (FAS) application can be broaden to the task of vehicle handling/cornering control. The optimisation approach is firstly applied to solely FAS actuator configurations and three types of double lane-change manoeuvres. The obtained optimisation results are used to gain insights into different control mechanisms that are used by FAS to improve the handling performance in terms of path following error reduction. For the same manoeuvres the FAS performance is compared with the performance of different active steering and active differential actuators. The optimisation study is finally extended to combined FAS and active front- and/or rear-steering configurations to investigate if they can use their complementary control authorities (over the vertical and lateral vehicle dynamics, respectively) to further improve the handling performance.

Structural-electrical coupling optimisation for radiating and scattering performances of active phased array antenna

NASA Astrophysics Data System (ADS)

Wang, Congsi; Wang, Yan; Wang, Zhihai; Wang, Meng; Yuan, Shuai; Wang, Weifeng

2018-04-01

It is well known that calculating and reducing of radar cross section (RCS) of the active phased array antenna (APAA) are both difficult and complicated. It remains unresolved to balance the performance of the radiating and scattering when the RCS is reduced. Therefore, this paper develops a structure and scattering array factor coupling model of APAA based on the phase errors of radiated elements generated by structural distortion and installation error of the array. To obtain the optimal radiating and scattering performance, an integrated optimisation model is built to optimise the installation height of all the radiated elements in normal direction of the array, in which the particle swarm optimisation method is adopted and the gain loss and scattering array factor are selected as the fitness function. The simulation indicates that the proposed coupling model and integrated optimisation method can effectively decrease the RCS and that the necessary radiating performance can be simultaneously guaranteed, which demonstrate an important application value in engineering design and structural evaluation of APAA.

DryLab® optimised two-dimensional high performance liquid chromatography for differentiation of ephedrine and pseudoephedrine based methamphetamine samples.

PubMed

Andrighetto, Luke M; Stevenson, Paul G; Pearson, James R; Henderson, Luke C; Conlan, Xavier A

2014-11-01

In-silico optimised two-dimensional high performance liquid chromatographic (2D-HPLC) separations of a model methamphetamine seizure sample are described, where an excellent match between simulated and real separations was observed. Targeted separation of model compounds was completed with significantly reduced method development time. This separation was completed in the heart-cutting mode of 2D-HPLC where C18 columns were used in both dimensions taking advantage of the selectivity difference of methanol and acetonitrile as the mobile phases. This method development protocol is most significant when optimising the separation of chemically similar chemical compounds as it eliminates potentially hours of trial and error injections to identify the optimised experimental conditions. After only four screening injections the gradient profile for both 2D-HPLC dimensions could be optimised via simulations, ensuring the baseline resolution of diastereomers (ephedrine and pseudoephedrine) in 9.7 min. Depending on which diastereomer is present the potential synthetic pathway can be categorized.

Effect of microculture on cell metabolism and biochemistry: do cells get stressed in microchannels?

PubMed

Su, Xiaojing; Theberge, Ashleigh B; January, Craig T; Beebe, David J

2013-02-05

Microfluidics is emerging as a promising platform for cell culture, enabling increased microenvironment control and potential for integrated analysis compared to conventional macroculture systems such as well plates and Petri dishes. To advance the use of microfluidic devices for cell culture, it is necessary to better understand how miniaturization affects cell behavior. In particular, microfluidic devices have significantly higher surface-area-to-volume ratios than conventional platforms, resulting in lower volumes of media per cell, which can lead to cell stress. We investigated cell stress under a variety of culture conditions using three cell lines: parental HEK (human embryonic kidney) cells and transfected HEK cells that stably express wild-type (WT) and mutant (G601S) human ether-a-go-go related gene (hERG) potassium channel protein. These three cell lines provide a unique model system through which to study cell-type-specific responses in microculture because mutant hERG is known to be sensitive to environmental conditions, making its expression a particularly sensitive readout through which to compare macro- and microculture. While expression of WT-hERG was similar in microchannel and well culture, the expression of mutant G601S-hERG was reduced in microchannels. Expression of the endoplasmic reticulum (ER) stress marker immunoglobulin binding protein (BiP) was upregulated in all three cell lines in microculture. Using BiP expression, glucose consumption, and lactate accumulation as readouts we developed methods for reducing ER stress including properly increasing the frequency of media replacement, reducing cell seeding density, and adjusting the serum concentration and buffering capacity of culture medium. Indeed, increasing the buffering capacity of culture medium or frequency of media replacement partially restored the expression of the G601S-hERG in microculture. This work illuminates how biochemical properties of cells differ in macro- and microculture and suggests strategies that can be used to modify cell culture protocols for future studies involving miniaturized culture platforms.

Expedite the Processing of Unpressurized Payloads to the International Space Station Using the ExPRESS Pallet

NASA Technical Reports Server (NTRS)

Bacskay, Allen S.; Gilbert, Paul A. (Technical Monitor)

2002-01-01

The Expedite the PRocessing of Experiments to Space Station (ExPRESS) Pallet will be used as an experiment platform for external/unpressurized payloads to be flown aboard the International Space Station (ISS). The purpose of the ExPRESS Pallet is to provide an easy access to the ISS for Scientific Investigators that require an external platform for their experiment hardware. As the name of the ExPRESS Pallet implies, the objective of the ExPRESS program is to provide a simplified integration process in a short time period (24 months) for payloads to be flown on the ISS. The ExPRESS Pallet provides unique opportunities for research across many science disciplines, including earth observation, communications, solar and deep space viewing, and long-term exposure. The ExPRESS Pallet provides access to Ram, Wake, Nadir, Zenith and Earth Limb for viewing and exposure to the space environment. The ExPRESS Pallet will provide standard physical payload interfaces, and a standard integration template. The ExPS consists of the Pallet structure, payload Adapters, a subsystem assembly that includes data controller, power distribution and conversion, and Extra Vehicular Robotics compatibility. The ExPRESS Pallet provides the capability to changeout payloads on-orbit via the ExPRESS Pallet Adapter (ExPA). The following paragraphs will describe the Services and Accommodations available to the Payload developers by the ExPRESS Pallet and a brief description of the Integration process. More detailed information on the ExPRESS Pallet can be found in the ExPRESS Pallet Payload Accommodations Handbook, SSP 52000-PAH-EPP.

The yellow fever 17D virus as a platform for new live attenuated vaccines.

PubMed

Bonaldo, Myrna C; Sequeira, Patrícia C; Galler, Ricardo

2014-01-01

The live-attenuated yellow fever 17D virus is one of the most outstanding human vaccines ever developed. It induces efficacious immune responses at a low production cost with a well-established manufacture process. These advantages make the YF17D virus attractive as a vector for the development of new vaccines. At the beginning of vector development studies, YF17D was genetically manipulated to express other flavivirus prM and E proteins, components of the viral envelope. While these 17D recombinants are based on the substitution of equivalent YF17D genes, other antigens from unrelated pathogens have also been successfully expressed and delivered by recombinant YF17D viruses employing alternative strategies for genetic manipulation of the YF17D genome. Herein, we discuss these strategies in terms of possibilities of single epitope or larger sequence expression and the main properties of these replication-competent viral platforms.

A multiplexable TALE-based binary expression system for in vivo cellular interaction studies.

PubMed

Toegel, Markus; Azzam, Ghows; Lee, Eunice Y; Knapp, David J H F; Tan, Ying; Fa, Ming; Fulga, Tudor A

2017-11-21

Binary expression systems have revolutionised genetic research by enabling delivery of loss-of-function and gain-of-function transgenes with precise spatial-temporal resolution in vivo. However, at present, each existing platform relies on a defined exogenous transcription activator capable of binding a unique recognition sequence. Consequently, none of these technologies alone can be used to simultaneously target different tissues or cell types in the same organism. Here, we report a modular system based on programmable transcription activator-like effector (TALE) proteins, which enables parallel expression of multiple transgenes in spatially distinct tissues in vivo. Using endogenous enhancers coupled to TALE drivers, we demonstrate multiplexed orthogonal activation of several transgenes carrying cognate variable activating sequences (VAS) in distinct neighbouring cell types of the Drosophila central nervous system. Since the number of combinatorial TALE-VAS pairs is virtually unlimited, this platform provides an experimental framework for highly complex genetic manipulation studies in vivo.

The yellow fever 17D virus as a platform for new live attenuated vaccines

PubMed Central

Bonaldo, Myrna C; Sequeira, Patrícia C; Galler, Ricardo

2014-01-01

The live-attenuated yellow fever 17D virus is one of the most outstanding human vaccines ever developed. It induces efficacious immune responses at a low production cost with a well-established manufacture process. These advantages make the YF17D virus attractive as a vector for the development of new vaccines. At the beginning of vector development studies, YF17D was genetically manipulated to express other flavivirus prM and E proteins, components of the viral envelope. While these 17D recombinants are based on the substitution of equivalent YF17D genes, other antigens from unrelated pathogens have also been successfully expressed and delivered by recombinant YF17D viruses employing alternative strategies for genetic manipulation of the YF17D genome. Herein, we discuss these strategies in terms of possibilities of single epitope or larger sequence expression and the main properties of these replication-competent viral platforms. PMID:24553128

Shape Optimisation of Holes in Loaded Plates by Minimisation of Multiple Stress Peaks

DTIC Science & Technology

2015-04-01

UNCLASSIFIED UNCLASSIFIED Shape Optimisation of Holes in Loaded Plates by Minimisation of Multiple Stress Peaks Witold Waldman and Manfred...minimising the peak tangential stresses on multiple segments around the boundary of a hole in a uniaxially-loaded or biaxially-loaded plate . It is based...RELEASE UNCLASSIFIED UNCLASSIFIED Shape Optimisation of Holes in Loaded Plates by Minimisation of Multiple Stress Peaks Executive Summary Aerospace

Navigating catastrophes: Local but not global optimisation allows for macro-economic navigation of crises

NASA Astrophysics Data System (ADS)

Harré, Michael S.

2013-02-01

Two aspects of modern economic theory have dominated the recent discussion on the state of the global economy: Crashes in financial markets and whether or not traditional notions of economic equilibrium have any validity. We have all seen the consequences of market crashes: plummeting share prices, businesses collapsing and considerable uncertainty throughout the global economy. This seems contrary to what might be expected of a system in equilibrium where growth dominates the relatively minor fluctuations in prices. Recent work from within economics as well as by physicists, psychologists and computational scientists has significantly improved our understanding of the more complex aspects of these systems. With this interdisciplinary approach in mind, a behavioural economics model of local optimisation is introduced and three general properties are proven. The first is that under very specific conditions local optimisation leads to a conventional macro-economic notion of a global equilibrium. The second is that if both global optimisation and economic growth are required then under very mild assumptions market catastrophes are an unavoidable consequence. Third, if only local optimisation and economic growth are required then there is sufficient parametric freedom for macro-economic policy makers to steer an economy around catastrophes without overtly disrupting local optimisation.

Optimisation techniques in vaginal cuff brachytherapy.

PubMed

Tuncel, N; Garipagaoglu, M; Kizildag, A U; Andic, F; Toy, A

2009-11-01

The aim of this study was to explore whether an in-house dosimetry protocol and optimisation method are able to produce a homogeneous dose distribution in the target volume, and how often optimisation is required in vaginal cuff brachytherapy. Treatment planning was carried out for 109 fractions in 33 patients who underwent high dose rate iridium-192 (Ir(192)) brachytherapy using Fletcher ovoids. Dose prescription and normalisation were performed to catheter-oriented lateral dose points (dps) within a range of 90-110% of the prescribed dose. The in-house vaginal apex point (Vk), alternative vaginal apex point (Vk'), International Commission on Radiation Units and Measurements (ICRU) rectal point (Rg) and bladder point (Bl) doses were calculated. Time-position optimisations were made considering dps, Vk and Rg doses. Keeping the Vk dose higher than 95% and the Rg dose less than 85% of the prescribed dose was intended. Target dose homogeneity, optimisation frequency and the relationship between prescribed dose, Vk, Vk', Rg and ovoid diameter were investigated. The mean target dose was 99+/-7.4% of the prescription dose. Optimisation was required in 92 out of 109 (83%) fractions. Ovoid diameter had a significant effect on Rg (p = 0.002), Vk (p = 0.018), Vk' (p = 0.034), minimum dps (p = 0.021) and maximum dps (p<0.001). Rg, Vk and Vk' doses with 2.5 cm diameter ovoids were significantly higher than with 2 cm and 1.5 cm ovoids. Catheter-oriented dose point normalisation provided a homogeneous dose distribution with a 99+/-7.4% mean dose within the target volume, requiring time-position optimisation.

Mining the archives: a cross-platform analysis of gene expression profiles in archival formalin-fixed paraffin-embedded (FFPE) tissue.

EPA Science Inventory

Formalin-fixed paraffin-embedded (FFPE) tissue samples represent a potentially invaluable resource for genomic research into the molecular basis of disease. However, use of FFPE samples in gene expression studies has been limited by technical challenges resulting from degradation...

CRTP-13: ABC-GCB Expression Signatures in Human B-cell Lymphoma on the NanoString Platform | Frederick National Laboratory for Cancer Research

Cancer.gov

The CLIA Molecular Diagnostics Laboratory within the Cancer Research Technology Program will perform messenger RNA isolation and expression analysis specific to a 20-gene panel on formalin-fixed paraffin-embedded (FFPE) patient samples using the Nano

The optimal design of stepped wedge trials with equal allocation to sequences and a comparison to other trial designs.

PubMed

Thompson, Jennifer A; Fielding, Katherine; Hargreaves, James; Copas, Andrew

2017-12-01

Background/Aims We sought to optimise the design of stepped wedge trials with an equal allocation of clusters to sequences and explored sample size comparisons with alternative trial designs. Methods We developed a new expression for the design effect for a stepped wedge trial, assuming that observations are equally correlated within clusters and an equal number of observations in each period between sequences switching to the intervention. We minimised the design effect with respect to (1) the fraction of observations before the first and after the final sequence switches (the periods with all clusters in the control or intervention condition, respectively) and (2) the number of sequences. We compared the design effect of this optimised stepped wedge trial to the design effects of a parallel cluster-randomised trial, a cluster-randomised trial with baseline observations, and a hybrid trial design (a mixture of cluster-randomised trial and stepped wedge trial) with the same total cluster size for all designs. Results We found that a stepped wedge trial with an equal allocation to sequences is optimised by obtaining all observations after the first sequence switches and before the final sequence switches to the intervention; this means that the first sequence remains in the control condition and the last sequence remains in the intervention condition for the duration of the trial. With this design, the optimal number of sequences is [Formula: see text], where [Formula: see text] is the cluster-mean correlation, [Formula: see text] is the intracluster correlation coefficient, and m is the total cluster size. The optimal number of sequences is small when the intracluster correlation coefficient and cluster size are small and large when the intracluster correlation coefficient or cluster size is large. A cluster-randomised trial remains more efficient than the optimised stepped wedge trial when the intracluster correlation coefficient or cluster size is small. A cluster-randomised trial with baseline observations always requires a larger sample size than the optimised stepped wedge trial. The hybrid design can always give an equally or more efficient design, but will be at most 5% more efficient. We provide a strategy for selecting a design if the optimal number of sequences is unfeasible. For a non-optimal number of sequences, the sample size may be reduced by allowing a proportion of observations before the first or after the final sequence has switched. Conclusion The standard stepped wedge trial is inefficient. To reduce sample sizes when a hybrid design is unfeasible, stepped wedge trial designs should have no observations before the first sequence switches or after the final sequence switches.

Comparison of reverse transcription-quantitative polymerase chain reaction methods and platforms for single cell gene expression analysis.

PubMed

Fox, Bridget C; Devonshire, Alison S; Baradez, Marc-Olivier; Marshall, Damian; Foy, Carole A

2012-08-15

Single cell gene expression analysis can provide insights into development and disease progression by profiling individual cellular responses as opposed to reporting the global average of a population. Reverse transcription-quantitative polymerase chain reaction (RT-qPCR) is the "gold standard" for the quantification of gene expression levels; however, the technical performance of kits and platforms aimed at single cell analysis has not been fully defined in terms of sensitivity and assay comparability. We compared three kits using purification columns (PicoPure) or direct lysis (CellsDirect and Cells-to-CT) combined with a one- or two-step RT-qPCR approach using dilutions of cells and RNA standards to the single cell level. Single cell-level messenger RNA (mRNA) analysis was possible using all three methods, although the precision, linearity, and effect of lysis buffer and cell background differed depending on the approach used. The impact of using a microfluidic qPCR platform versus a standard instrument was investigated for potential variability introduced by preamplification of template or scaling down of the qPCR to nanoliter volumes using laser-dissected single cell samples. The two approaches were found to be comparable. These studies show that accurate gene expression analysis is achievable at the single cell level and highlight the importance of well-validated experimental procedures for low-level mRNA analysis. Copyright © 2012 Elsevier Inc. All rights reserved.

Uncovering stem-cell heterogeneity in the microniche with label-free microfluidics

NASA Astrophysics Data System (ADS)

Sohn, Lydia L.

2013-03-01

Better suited for large number of cells from bulk tissue, traditional cell-screening techniques, such as fluorescence-activated cell sorting (FACS) and magnetic-activated cell sorting (MACS), cannot easily screen stem or progenitor cells from minute populations found in their physiological niches. Furthermore, they rely upon irreversible antibody binding, potentially altering cell properties, including gene expression and regenerative capacity. We have developed a label-free, single-cell analysis microfluidic platform capable of quantifying cell-surface marker expression of functional organ stem cells directly isolated from their micro-anatomical niche. With this platform, we have screened single quiescent muscle stem (satellite) cells derived from single myofibers, and we have uncovered an important heterogeneity in the surface-marker expression of these cells. By sorting the screened cells with our microfluidic device, we have determined what this heterogeneity means in terms of muscle stem-cell functionality. For instance, we show that the levels of beta1-integrin can predict the differentiation capacity of quiescent satellite cells, and in contrast to recent literature, that some CXCR4 + cells are not myogenic. Our results provide the first direct demonstration of a microniche-specific variation in gene expression in stem cells of the same lineage. Overall, our label-free, single-cell analysis and cell-sorting platform could be extended to other systems involving rare-cell subsets. This work was funded by the W. M. Keck Foundation, NIH, and California Institute of Regenerative Medicine

Use of the Uteroglobin Platform for the Expression of a Bivalent Antibody against Oncofetal Fibronectin in Escherichia coli

PubMed Central

Ventura, Elisa; Riondato, Mattia; Sambuceti, Gianmario; Salis, Annalisa; Damonte, Gianluca; Cordazzo, Cinzia; Besir, Hüseyin; Pistoia, Vito; Zardi, Luciano

2013-01-01

Escherichia coli is a robust, economic and rapid expression system for the production of recombinant therapeutic proteins. However, the expression in bacterial systems of complex molecules such as antibodies and fusion proteins is still affected by several drawbacks. We have previously described a procedure based on uteroglobin (UG) for the engineering of very soluble and stable polyvalent and polyspecific fusion proteins in mammalian cells (Ventura et al. 2009. J. Biol. Chem. 284∶26646–26654.) Here, we applied the UG platform to achieve the expression in E. coli of a bivalent human recombinant antibody (L19) toward the oncofetal fibronectin (B-FN), a pan-tumor target. Purified bacterial L19-UG was highly soluble, stable, and, in all molecules, the L19 moiety maintained its immunoreactivity. About 50–70% of the molecules were covalent homodimer, however after refolding with the redox couple reduced-glutathione/oxidized-glutathione (GSH/GSSG), 100% of molecules were covalent dimers. Mass spectrometry studies showed that the proteins produced by E. coli and mammalian cells have an identical molecular mass and that both proteins are not glycosylated. L19-UG from bacteria can be freeze-dried without any loss of protein and immunoreactivity. In vivo, in tumor-bearing mice, radio-iodinated L19-UG selectively accumulated in neoplastic tissues showing the same performance of L19-UG from mammalian cells. The UG-platform may represent a general procedure for production of various biological therapeutics in E. coli. PMID:24367567

Cross-platform single cell analysis of kidney development shows stromal cells express Gdnf.

PubMed

Magella, Bliss; Adam, Mike; Potter, Andrew S; Venkatasubramanian, Meenakshi; Chetal, Kashish; Hay, Stuart B; Salomonis, Nathan; Potter, S Steven

2018-02-01

The developing kidney provides a useful model for study of the principles of organogenesis. In this report we use three independent platforms, Drop-Seq, Chromium 10x Genomics and Fluidigm C1, to carry out single cell RNA-Seq (scRNA-Seq) analysis of the E14.5 mouse kidney. Using the software AltAnalyze, in conjunction with the unsupervised approach ICGS, we were unable to identify and confirm the presence of 16 distinct cell populations during this stage of active nephrogenesis. Using a novel integrative supervised computational strategy, we were able to successfully harmonize and compare the cell profiles across all three technological platforms. Analysis of possible cross compartment receptor/ligand interactions identified the nephrogenic zone stroma as a source of GDNF. This was unexpected because the cap mesenchyme nephron progenitors had been thought to be the sole source of GDNF, which is a key driver of branching morphogenesis of the collecting duct system. The expression of Gdnf by stromal cells was validated in several ways, including Gdnf in situ hybridization combined with immunohistochemistry for SIX2, and marker of nephron progenitors, and MEIS1, a marker of stromal cells. Finally, the single cell gene expression profiles generated in this study confirmed and extended previous work showing the presence of multilineage priming during kidney development. Nephron progenitors showed stochastic expression of genes associated with multiple potential differentiation lineages. Copyright © 2017 Elsevier Inc. All rights reserved.

Effect of preventive (beta blocker) treatment, behavioural migraine management, or their combination on outcomes of optimised acute treatment in frequent migraine: randomised controlled trial.

PubMed

Holroyd, Kenneth A; Cottrell, Constance K; O'Donnell, Francis J; Cordingley, Gary E; Drew, Jana B; Carlson, Bruce W; Himawan, Lina

2010-09-29

To determine if the addition of preventive drug treatment (β blocker), brief behavioural migraine management, or their combination improves the outcome of optimised acute treatment in the management of frequent migraine. Randomised placebo controlled trial over 16 months from July 2001 to November 2005. Two outpatient sites in Ohio, USA. 232 adults (mean age 38 years; 79% female) with diagnosis of migraine with or without aura according to International Headache Society classification of headache disorders criteria, who recorded at least three migraines with disability per 30 days (mean 5.5 migraines/30 days), during an optimised run-in of acute treatment. Addition of one of four preventive treatments to optimised acute treatment: β blocker (n=53), matched placebo (n=55), behavioural migraine management plus placebo (n=55), or behavioural migraine management plus β blocker (n=69). The primary outcome was change in migraines/30 days; secondary outcomes included change in migraine days/30 days and change in migraine specific quality of life scores. Mixed model analysis showed statistically significant (P≤0.05) differences in outcomes among the four added treatments for both the primary outcome (migraines/30 days) and the two secondary outcomes (change in migraine days/30 days and change in migraine specific quality of life scores). The addition of combined β blocker and behavioural migraine management (-3.3 migraines/30 days, 95% confidence interval -3.2 to -3.5), but not the addition of β blocker alone (-2.1 migraines/30 days, -1.9 to -2.2) or behavioural migraine management alone (-2.2 migraines migraines/30 days, -2.0 to -2.4), improved outcomes compared with optimised acute treatment alone (-2.1 migraines/30 days, -1.9 to -2.2). For a clinically significant (≥50% reduction) in migraines/30 days, the number needed to treat for optimised acute treatment plus combined β blocker and behavioural migraine management was 3.1 compared with optimised acute treatment alone, 2.6 compared with optimised acute treatment plus β blocker, and 3.1 compared with optimised acute treatment plus behavioural migraine management. Results were consistent for the two secondary outcomes, and at both month 10 (the primary endpoint) and month 16. The addition of combined β blocker plus behavioural migraine management, but not the addition of β blocker alone or behavioural migraine management alone, improved outcomes of optimised acute treatment. Combined β blocker treatment and behavioural migraine management may improve outcomes in the treatment of frequent migraine. Clinical trials NCT00910689.

Comparison of the genetic algorithm and incremental optimisation routines for a Bayesian inverse modelling based network design

NASA Astrophysics Data System (ADS)

Nickless, A.; Rayner, P. J.; Erni, B.; Scholes, R. J.

2018-05-01

The design of an optimal network of atmospheric monitoring stations for the observation of carbon dioxide (CO2) concentrations can be obtained by applying an optimisation algorithm to a cost function based on minimising posterior uncertainty in the CO2 fluxes obtained from a Bayesian inverse modelling solution. Two candidate optimisation methods assessed were the evolutionary algorithm: the genetic algorithm (GA), and the deterministic algorithm: the incremental optimisation (IO) routine. This paper assessed the ability of the IO routine in comparison to the more computationally demanding GA routine to optimise the placement of a five-member network of CO2 monitoring sites located in South Africa. The comparison considered the reduction in uncertainty of the overall flux estimate, the spatial similarity of solutions, and computational requirements. Although the IO routine failed to find the solution with the global maximum uncertainty reduction, the resulting solution had only fractionally lower uncertainty reduction compared with the GA, and at only a quarter of the computational resources used by the lowest specified GA algorithm. The GA solution set showed more inconsistency if the number of iterations or population size was small, and more so for a complex prior flux covariance matrix. If the GA completed with a sub-optimal solution, these solutions were similar in fitness to the best available solution. Two additional scenarios were considered, with the objective of creating circumstances where the GA may outperform the IO. The first scenario considered an established network, where the optimisation was required to add an additional five stations to an existing five-member network. In the second scenario the optimisation was based only on the uncertainty reduction within a subregion of the domain. The GA was able to find a better solution than the IO under both scenarios, but with only a marginal improvement in the uncertainty reduction. These results suggest that the best use of resources for the network design problem would be spent in improvement of the prior estimates of the flux uncertainties rather than investing these resources in running a complex evolutionary optimisation algorithm. The authors recommend that, if time and computational resources allow, that multiple optimisation techniques should be used as a part of a comprehensive suite of sensitivity tests when performing such an optimisation exercise. This will provide a selection of best solutions which could be ranked based on their utility and practicality.

Business analysis for a sustainable, multi-stakeholder ecosystem for leveraging the Electronic Health Records for Clinical Research (EHR4CR) platform in Europe.

PubMed

Dupont, Danielle; Beresniak, Ariel; Sundgren, Mats; Schmidt, Andreas; Ainsworth, John; Coorevits, Pascal; Kalra, Dipak; Dewispelaere, Marc; De Moor, Georges

2017-01-01

The Electronic Health Records for Clinical Research (EHR4CR) technological platform has been developed to enable the trustworthy reuse of hospital electronic health records data for clinical research. The EHR4CR platform can enhance and speed up clinical research scenarios: protocol feasibility assessment, patient identification for recruitment in clinical trials, and clinical data exchange, including for reporting serious adverse events. Our objective was to seed a multi-stakeholder ecosystem to enable the scalable exploitation of the EHR4CR platform in Europe, and to assess its economic sustainability. Market analyses were conducted by a multidisciplinary task force to define an EHR4CR emerging ecosystem and multi-stakeholder value chain. This involved mapping stakeholder groups and defining their unmet needs, incentives, potential barriers for adopting innovative solutions, roles and interdependencies. A comprehensive business model, value propositions, and sustainability strategies were developed accordingly. Using simulation modelling (including Monte Carlo simulations) and a 5-year horizon, the potential financial outcomes of the business model were forecasted from the perspective of an EHR4CR service provider. A business ecosystem was defined to leverage the EHR4CR multi-stakeholder value chain. Value propositions were developed describing the expected benefits of EHR4CR solutions for all stakeholders. From an EHR4CR service provider's viewpoint, the business model simulation estimated that a profitability ratio of up to 1.8 could be achieved at year 1, with potential for growth in subsequent years depending on projected market uptake. By enhancing and speeding up existing processes, EHR4CR solutions promise to transform the clinical research landscape. The ecosystem defined provides the organisational framework for optimising the value and benefits for all stakeholders involved, in a sustainable manner. Our study suggests that the exploitation of EHR4CR solutions appears profitable and sustainable in Europe, with a growth potential depending on the rates of market and hospital adoption. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Biomarker discovery for colon cancer using a 761 gene RT-PCR assay.

PubMed

Clark-Langone, Kim M; Wu, Jenny Y; Sangli, Chithra; Chen, Angela; Snable, James L; Nguyen, Anhthu; Hackett, James R; Baker, Joffre; Yothers, Greg; Kim, Chungyeul; Cronin, Maureen T

2007-08-15

Reverse transcription PCR (RT-PCR) is widely recognized to be the gold standard method for quantifying gene expression. Studies using RT-PCR technology as a discovery tool have historically been limited to relatively small gene sets compared to other gene expression platforms such as microarrays. We have recently shown that TaqMan RT-PCR can be scaled up to profile expression for 192 genes in fixed paraffin-embedded (FPE) clinical study tumor specimens. This technology has also been used to develop and commercialize a widely used clinical test for breast cancer prognosis and prediction, the Onco typeDX assay. A similar need exists in colon cancer for a test that provides information on the likelihood of disease recurrence in colon cancer (prognosis) and the likelihood of tumor response to standard chemotherapy regimens (prediction). We have now scaled our RT-PCR assay to efficiently screen 761 biomarkers across hundreds of patient samples and applied this process to biomarker discovery in colon cancer. This screening strategy remains attractive due to the inherent advantages of maintaining platform consistency from discovery through clinical application. RNA was extracted from formalin fixed paraffin embedded (FPE) tissue, as old as 28 years, from 354 patients enrolled in NSABP C-01 and C-02 colon cancer studies. Multiplexed reverse transcription reactions were performed using a gene specific primer pool containing 761 unique primers. PCR was performed as independent TaqMan reactions for each candidate gene. Hierarchal clustering demonstrates that genes expected to co-express form obvious, distinct and in certain cases very tightly correlated clusters, validating the reliability of this technical approach to biomarker discovery. We have developed a high throughput, quantitatively precise multi-analyte gene expression platform for biomarker discovery that approaches low density DNA arrays in numbers of genes analyzed while maintaining the high specificity, sensitivity and reproducibility that are characteristics of RT-PCR. Biomarkers discovered using this approach can be transferred to a clinical reference laboratory setting without having to re-validate the assay on a second technology platform.

Developing a new production host from a blueprint: Bacillus pumilus as an industrial enzyme producer.

PubMed

Küppers, Tobias; Steffen, Victoria; Hellmuth, Hendrik; O'Connell, Timothy; Bongaerts, Johannes; Maurer, Karl-Heinz; Wiechert, Wolfgang

2014-03-24

Since volatile and rising cost factors such as energy, raw materials and market competitiveness have a significant impact on the economic efficiency of biotechnological bulk productions, industrial processes need to be steadily improved and optimized. Thereby the current production hosts can undergo various limitations. To overcome those limitations and in addition increase the diversity of available production hosts for future applications, we suggest a Production Strain Blueprinting (PSB) strategy to develop new production systems in a reduced time lapse in contrast to a development from scratch.To demonstrate this approach, Bacillus pumilus has been developed as an alternative expression platform for the production of alkaline enzymes in reference to the established industrial production host Bacillus licheniformis. To develop the selected B. pumilus as an alternative production host the suggested PSB strategy was applied proceeding in the following steps (dedicated product titers are scaled to the protease titer of Henkel's industrial production strain B. licheniformis at lab scale): Introduction of a protease production plasmid, adaptation of a protease production process (44%), process optimization (92%) and expression optimization (114%). To further evaluate the production capability of the developed B. pumilus platform, the target protease was substituted by an α-amylase. The expression performance was tested under the previously optimized protease process conditions and under subsequently adapted process conditions resulting in a maximum product titer of 65% in reference to B. licheniformis protease titer. In this contribution the applied PSB strategy performed very well for the development of B. pumilus as an alternative production strain. Thereby the engineered B. pumilus expression platform even exceeded the protease titer of the industrial production host B. licheniformis by 14%. This result exhibits a remarkable potential of B. pumilus to be the basis for a next generation production host, since the strain has still a large potential for further genetic engineering. The final amylase titer of 65% in reference to B. licheniformis protease titer suggests that the developed B. pumilus expression platform is also suitable for an efficient production of non-proteolytic enzymes reaching a final titer of several grams per liter without complex process modifications.

Evaluation of commercially available small RNASeq library preparation kits using low input RNA.

PubMed

Yeri, Ashish; Courtright, Amanda; Danielson, Kirsty; Hutchins, Elizabeth; Alsop, Eric; Carlson, Elizabeth; Hsieh, Michael; Ziegler, Olivia; Das, Avash; Shah, Ravi V; Rozowsky, Joel; Das, Saumya; Van Keuren-Jensen, Kendall

2018-05-05

Evolving interest in comprehensively profiling the full range of small RNAs present in small tissue biopsies and in circulating biofluids, and how the profile differs with disease, has launched small RNA sequencing (RNASeq) into more frequent use. However, known biases associated with small RNASeq, compounded by low RNA inputs, have been both a significant concern and a hurdle to widespread adoption. As RNASeq is becoming a viable choice for the discovery of small RNAs in low input samples and more labs are employing it, there should be benchmark datasets to test and evaluate the performance of new sequencing protocols and operators. In a recent publication from the National Institute of Standards and Technology, Pine et al., 2018, the investigators used a commercially available set of three tissues and tested performance across labs and platforms. In this paper, we further tested the performance of low RNA input in three commonly used and commercially available RNASeq library preparation kits; NEB Next, NEXTFlex, and TruSeq small RNA library preparation. We evaluated the performance of the kits at two different sites, using three different tissues (brain, liver, and placenta) with high (1 μg) and low RNA (10 ng) input from tissue samples, or 5.0, 3.0, 2.0, 1.0, 0.5, and 0.2 ml starting volumes of plasma. As there has been a lack of robust validation platforms for differentially expressed miRNAs, we also compared low input RNASeq data with their expression profiles on three different platforms (Abcam Fireplex, HTG EdgeSeq, and Qiagen miRNome). The concordance of RNASeq results on these three platforms was dependent on the RNA expression level; the higher the expression, the better the reproducibility. The results provide an extensive analysis of small RNASeq kit performance using low RNA input, and replication of these data on three downstream technologies.

Optimisation of wire-cut EDM process parameter by Grey-based response surface methodology

NASA Astrophysics Data System (ADS)

Kumar, Amit; Soota, Tarun; Kumar, Jitendra

2018-03-01

Wire electric discharge machining (WEDM) is one of the advanced machining processes. Response surface methodology coupled with Grey relation analysis method has been proposed and used to optimise the machining parameters of WEDM. A face centred cubic design is used for conducting experiments on high speed steel (HSS) M2 grade workpiece material. The regression model of significant factors such as pulse-on time, pulse-off time, peak current, and wire feed is considered for optimising the responses variables material removal rate (MRR), surface roughness and Kerf width. The optimal condition of the machining parameter was obtained using the Grey relation grade. ANOVA is applied to determine significance of the input parameters for optimising the Grey relation grade.

Dengue E Protein Domain III-Based DNA Immunisation Induces Strong Antibody Responses to All Four Viral Serotypes

PubMed Central

Chan, Kuan Rong; Tan, Hwee Cheng; Bestagno, Marco; Ooi, Eng Eong; Burrone, Oscar R.

2015-01-01

Dengue virus (DENV) infection is a major emerging disease widely distributed throughout the tropical and subtropical regions of the world affecting several millions of people. Despite constants efforts, no specific treatment or effective vaccine is yet available. Here we show a novel design of a DNA immunisation strategy that resulted in the induction of strong antibody responses with high neutralisation titres in mice against all four viral serotypes. The immunogenic molecule is an engineered version of the domain III (DIII) of the virus E protein fused to the dimerising CH3 domain of the IgG immunoglobulin H chain. The DIII sequences were also codon-optimised for expression in mammalian cells. While DIII alone is very poorly secreted, the codon-optimised fusion protein is rightly expressed, folded and secreted at high levels, thus inducing strong antibody responses. Mice were immunised using gene-gun technology, an efficient way of intradermal delivery of the plasmid DNA, and the vaccine was able to induce neutralising titres against all serotypes. Additionally, all sera showed reactivity to a recombinant DIII version and the recombinant E protein produced and secreted from mammalian cells in a mono-biotinylated form when tested in a conformational ELISA. Sera were also highly reactive to infective viral particles in a virus-capture ELISA and specific for each serotype as revealed by the low cross-reactive and cross-neutralising activities. The serotype specific sera did not induce antibody dependent enhancement of infection (ADE) in non-homologous virus serotypes. A tetravalent immunisation protocol in mice showed induction of neutralising antibodies against all four dengue serotypes as well. PMID:26218926

A Novel Dual Expression Platform for High Throughput Functional Screening of Phage Libraries in Product like Format.

PubMed

Xiao, Xiaodong; Chen, Yan; Mugabe, Sheila; Gao, Changshou; Tkaczyk, Christine; Mazor, Yariv; Pavlik, Peter; Wu, Herren; Dall'Acqua, William; Chowdhury, Partha Sarathi

2015-01-01

High throughput screenings of single chain Fv (scFv) antibody phage display libraries are currently done as soluble scFvs produced in E.coli. Due to endotoxin contaminations from bacterial cells these preparations cannot be reliably used in mammalian cell based assays. The monovalent nature and lack of Fc in soluble scFvs prevent functional assays that are dependent on target cross linking and/or Fc functions. A convenient approach is to convert scFvs into scFv.Fc fusion proteins and express them in mammalian cell lines for screening. This approach is low throughput and is only taken after primary screening of monovalent scFvs that are expressed in bacteria. There is no platform at present that combines the benefits of both bacterial and mammalian expression system for screening phage library output. We have, therefore, developed a novel dual expression vector, called pSplice, which can be used to express scFv.Fc fusion proteins both in E.coli and mammalian cell lines. The hallmark of the vector is an engineered intron which houses the bacterial promoter and signal peptide for expression and secretion of scFv.Fc in E.coli. When the vector is transfected into a mammalian cell line, the intron is efficiently spliced out resulting in a functional operon for expression and secretion of the scFv.Fc fusion protein into the culture medium. By applying basic knowledge of mammalian introns and splisosome, we designed this vector to enable screening of phage libraries in a product like format. Like IgG, the scFv.Fc fusion protein is bi-valent for the antigen and possesses Fc effector functions. Expression in E.coli maintains the speed of the bacterial expression platform and is used to triage clones based on binding and other assays that are not sensitive to endotoxin. Triaged clones are then expressed in a mammalian cell line without the need for any additional cloning steps. Conditioned media from the mammalian cell line containing the fusion proteins are then used for different types of cell based assays. Thus this system retains the speed of the current screening system for phage libraries and adds additional functionality to it.

A multifunctional material based on co-electrospinning for developing biosensors with optical oxygen transduction.

PubMed

Ramon-Marquez, Teresa; Medina-Castillo, Antonio L; Nagiah, Naveen; Fernandez-Gutierrez, Alberto; Fernandez-Sanchez, Jorge F

2018-07-26

A multifunctional material based on co-electrospinning has been developed as a basic material for the development of biosensors with optical oxygen transduction. It is based on coaxial nanofibres: inner fibres containing an oxygen sensitive dye and outer fibres containing aldehyde groups to allow the formation of Schiff bases with the amino groups of the enzyme. The resulting material preserves the oxygen sensing properties of the inner optical transducer as well as exhibits a high capacity for immobilizing molecules on its surface. Uricase has been selected as model enzyme and several parameters (temperature, pH, reaction time, buffer, and enzyme concentration) have been optimised to demonstrate the versatility of this novel multifunctional material in the development of biosensors with optical oxygen transduction for determining uric acid in serum samples. It suggests that the proposed multifunctional material can provide a promising multifunctional platform for biosensing applications. Copyright © 2018 Elsevier B.V. All rights reserved.

Intersections of lung progenitor cells, lung disease and lung cancer.

PubMed

Kim, Carla F

2017-06-30

The use of stem cell biology approaches to study adult lung progenitor cells and lung cancer has brought a variety of new techniques to the field of lung biology and has elucidated new pathways that may be therapeutic targets in lung cancer. Recent results have begun to identify the ways in which different cell populations interact to regulate progenitor activity, and this has implications for the interventions that are possible in cancer and in a variety of lung diseases. Today's better understanding of the mechanisms that regulate lung progenitor cell self-renewal and differentiation, including understanding how multiple epigenetic factors affect lung injury repair, holds the promise for future better treatments for lung cancer and for optimising the response to therapy in lung cancer. Working between platforms in sophisticated organoid culture techniques, genetically engineered mouse models of injury and cancer, and human cell lines and specimens, lung progenitor cell studies can begin with basic biology, progress to translational research and finally lead to the beginnings of clinical trials. Copyright ©ERS 2017.

Tier-2 Optimisation for Computational Density/Diversity and Big Data

NASA Astrophysics Data System (ADS)

Fay, R. B.; Bland, J.

2014-06-01

As the number of cores on chip continues to trend upwards and new CPU architectures emerge, increasing CPU density and diversity presents multiple challenges to site administrators. These include scheduling for massively multi-core systems (potentially including Graphical Processing Units (GPU), integrated and dedicated) and Many Integrated Core (MIC)) to ensure a balanced throughput of jobs while preserving overall cluster throughput, as well as the increasing complexity of developing for these heterogeneous platforms, and the challenge in managing this more complex mix of resources. In addition, meeting data demands as both dataset sizes increase and as the rate of demand scales with increased computational power requires additional performance from the associated storage elements. In this report, we evaluate one emerging technology, Solid State Drive (SSD) caching for RAID controllers, with consideration to its potential to assist in meeting evolving demand. We also briefly consider the broader developing trends outlined above in order to identify issues that may develop and assess what actions should be taken in the immediate term to address those.

Systematic Optimization of Long Gradient Chromatography Mass Spectrometry for Deep Analysis of Brain Proteome

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Hong; Yang, Yanling; Li, Yuxin

2015-02-06

Development of high resolution liquid chromatography (LC) is essential for improving the sensitivity and throughput of mass spectrometry (MS)-based proteomics. Here we present systematic optimization of a long gradient LC-MS/MS platform to enhance protein identification from a complex mixture. The platform employed an in-house fabricated, reverse phase column (100 μm x 150 cm) coupled with Q Exactive MS. The column was capable of achieving a peak capacity of approximately 700 in a 720 min gradient of 10-45% acetonitrile. The optimal loading level was about 6 micrograms of peptides, although the column allowed loading as many as 20 micrograms. Gas phasemore » fractionation of peptide ions further increased the number of peptide identification by ~10%. Moreover, the combination of basic pH LC pre-fractionation with the long gradient LC-MS/MS platform enabled the identification of 96,127 peptides and 10,544 proteins at 1% protein false discovery rate in a postmortem brain sample of Alzheimer’s disease. As deep RNA sequencing of the same specimen suggested that ~16,000 genes were expressed, current analysis covered more than 60% of the expressed proteome. Further improvement strategies of the LC/LC-MS/MS platform were also discussed.« less

High-throughput, luciferase-based reverse genetics systems for identifying inhibitors of Marburg and Ebola viruses.

PubMed

Uebelhoer, Luke S; Albariño, César G; McMullan, Laura K; Chakrabarti, Ayan K; Vincent, Joel P; Nichol, Stuart T; Towner, Jonathan S

2014-06-01

Marburg virus (MARV) and Ebola virus (EBOV), members of the family Filoviridae, represent a significant challenge to global public health. Currently, no licensed therapies exist to treat filovirus infections, which cause up to 90% mortality in human cases. To facilitate development of antivirals against these viruses, we established two distinct screening platforms based on MARV and EBOV reverse genetics systems that express secreted Gaussia luciferase (gLuc). The first platform is a mini-genome replicon to screen viral replication inhibitors using gLuc quantification in a BSL-2 setting. The second platform is complementary to the first and expresses gLuc as a reporter gene product encoded in recombinant infectious MARV and EBOV, thereby allowing for rapid quantification of viral growth during treatment with antiviral compounds. We characterized these viruses by comparing luciferase activity to virus production, and validated luciferase activity as an authentic real-time measure of viral growth. As proof of concept, we adapt both mini-genome and infectious virus platforms to high-throughput formats, and demonstrate efficacy of several antiviral compounds. We anticipate that both approaches will prove highly useful in the development of anti-filovirus therapies, as well as in basic research on the filovirus life cycle. Published by Elsevier B.V.

Finding the rhythm of sudden cardiac death: new opportunities using induced pluripotent stem cell-derived cardiomyocytes.

PubMed

Sallam, Karim; Li, Yingxin; Sager, Philip T; Houser, Steven R; Wu, Joseph C

2015-06-05

Sudden cardiac death is a common cause of death in patients with structural heart disease, genetic mutations, or acquired disorders affecting cardiac ion channels. A wide range of platforms exist to model and study disorders associated with sudden cardiac death. Human clinical studies are cumbersome and are thwarted by the extent of investigation that can be performed on human subjects. Animal models are limited by their degree of homology to human cardiac electrophysiology, including ion channel expression. Most commonly used cellular models are cellular transfection models, which are able to mimic the expression of a single-ion channel offering incomplete insight into changes of the action potential profile. Induced pluripotent stem cell-derived cardiomyocytes resemble, but are not identical, adult human cardiomyocytes and provide a new platform for studying arrhythmic disorders leading to sudden cardiac death. A variety of platforms exist to phenotype cellular models, including conventional and automated patch clamp, multielectrode array, and computational modeling. Induced pluripotent stem cell-derived cardiomyocytes have been used to study long QT syndrome, catecholaminergic polymorphic ventricular tachycardia, hypertrophic cardiomyopathy, and other hereditary cardiac disorders. Although induced pluripotent stem cell-derived cardiomyocytes are distinct from adult cardiomyocytes, they provide a robust platform to advance the science and clinical care of sudden cardiac death. © 2015 American Heart Association, Inc.

Bacterial cell-free expression technology to in vitro systems engineering and optimization.

PubMed

Caschera, Filippo

2017-06-01

Cell-free expression system is a technology for the synthesis of proteins in vitro . The system is a platform for several bioengineering projects, e.g. cell-free metabolic engineering, evolutionary design of experiments, and synthetic minimal cell construction. Bacterial cell-free protein synthesis system (CFPS) is a robust tool for synthetic biology. The bacteria lysate, the DNA, and the energy module, which are the three optimized sub-systems for in vitro protein synthesis, compose the integrated system. Currently, an optimized E. coli cell-free expression system can produce up to ∼2.3 mg/mL of a fluorescent reporter protein. Herein, I will describe the features of ATP-regeneration systems for in vitro protein synthesis, and I will present a machine-learning experiment for optimizing the protein yield of E. coli cell-free protein synthesis systems. Moreover, I will introduce experiments on the synthesis of a minimal cell using liposomes as dynamic containers, and E. coli cell-free expression system as biochemical platform for metabolism and gene expression. CFPS can be further integrated with other technologies for novel applications in environmental, medical and material science.

yStreX: yeast stress expression database

PubMed Central

Wanichthanarak, Kwanjeera; Nookaew, Intawat; Petranovic, Dina

2014-01-01

Over the past decade genome-wide expression analyses have been often used to study how expression of genes changes in response to various environmental stresses. Many of these studies (such as effects of oxygen concentration, temperature stress, low pH stress, osmotic stress, depletion or limitation of nutrients, addition of different chemical compounds, etc.) have been conducted in the unicellular Eukaryal model, yeast Saccharomyces cerevisiae. However, the lack of a unifying or integrated, bioinformatics platform that would permit efficient and rapid use of all these existing data remain an important issue. To facilitate research by exploiting existing transcription data in the field of yeast physiology, we have developed the yStreX database. It is an online repository of analyzed gene expression data from curated data sets from different studies that capture genome-wide transcriptional changes in response to diverse environmental transitions. The first aim of this online database is to facilitate comparison of cross-platform and cross-laboratory gene expression data. Additionally, we performed different expression analyses, meta-analyses and gene set enrichment analyses; and the results are also deposited in this database. Lastly, we constructed a user-friendly Web interface with interactive visualization to provide intuitive access and to display the queried data for users with no background in bioinformatics. Database URL: http://www.ystrexdb.com PMID:25024351

Systemic solutions for multi-benefit water and environmental management.

PubMed

Everard, Mark; McInnes, Robert

2013-09-01

The environmental and financial costs of inputs to, and unintended consequences arising from narrow consideration of outputs from, water and environmental management technologies highlight the need for low-input solutions that optimise outcomes across multiple ecosystem services. Case studies examining the inputs and outputs associated with several ecosystem-based water and environmental management technologies reveal a range from those that differ little from conventional electro-mechanical engineering techniques through methods, such as integrated constructed wetlands (ICWs), designed explicitly as low-input systems optimising ecosystem service outcomes. All techniques present opportunities for further optimisation of outputs, and hence for greater cumulative public value. We define 'systemic solutions' as "…low-input technologies using natural processes to optimise benefits across the spectrum of ecosystem services and their beneficiaries". They contribute to sustainable development by averting unintended negative impacts and optimising benefits to all ecosystem service beneficiaries, increasing net economic value. Legacy legislation addressing issues in a fragmented way, associated 'ring-fenced' budgets and established management assumptions represent obstacles to implementing 'systemic solutions'. However, flexible implementation of legacy regulations recognising their primary purpose, rather than slavish adherence to detailed sub-clauses, may achieve greater overall public benefit through optimisation of outcomes across ecosystem services. Systemic solutions are not a panacea if applied merely as 'downstream' fixes, but are part of, and a means to accelerate, broader culture change towards more sustainable practice. This necessarily entails connecting a wider network of interests in the formulation and design of mutually-beneficial systemic solutions, including for example spatial planners, engineers, regulators, managers, farming and other businesses, and researchers working on ways to quantify and optimise delivery of ecosystem services. Copyright © 2013 Elsevier B.V. All rights reserved.

Topology optimisation of micro fluidic mixers considering fluid-structure interactions with a coupled Lattice Boltzmann algorithm

NASA Astrophysics Data System (ADS)

Munk, David J.; Kipouros, Timoleon; Vio, Gareth A.; Steven, Grant P.; Parks, Geoffrey T.

2017-11-01

Recently, the study of micro fluidic devices has gained much interest in various fields from biology to engineering. In the constant development cycle, the need to optimise the topology of the interior of these devices, where there are two or more optimality criteria, is always present. In this work, twin physical situations, whereby optimal fluid mixing in the form of vorticity maximisation is accompanied by the requirement that the casing in which the mixing takes place has the best structural performance in terms of the greatest specific stiffness, are considered. In the steady state of mixing this also means that the stresses in the casing are as uniform as possible, thus giving a desired operating life with minimum weight. The ultimate aim of this research is to couple two key disciplines, fluids and structures, into a topology optimisation framework, which shows fast convergence for multidisciplinary optimisation problems. This is achieved by developing a bi-directional evolutionary structural optimisation algorithm that is directly coupled to the Lattice Boltzmann method, used for simulating the flow in the micro fluidic device, for the objectives of minimum compliance and maximum vorticity. The needs for the exploration of larger design spaces and to produce innovative designs make meta-heuristic algorithms, such as genetic algorithms, particle swarms and Tabu Searches, less efficient for this task. The multidisciplinary topology optimisation framework presented in this article is shown to increase the stiffness of the structure from the datum case and produce physically acceptable designs. Furthermore, the topology optimisation method outperforms a Tabu Search algorithm in designing the baffle to maximise the mixing of the two fluids.

Person-centred medicines optimisation policy in England: an agenda for research on polypharmacy.

PubMed

Heaton, Janet; Britten, Nicky; Krska, Janet; Reeve, Joanne

2017-01-01

Aim To examine how patient perspectives and person-centred care values have been represented in documents on medicines optimisation policy in England. There has been growing support in England for a policy of medicines optimisation as a response to the rise of problematic polypharmacy. Conceptually, medicines optimisation differs from the medicines management model of prescribing in being based around the patient rather than processes and systems. This critical examination of current official and independent policy documents questions how central the patient is in them and whether relevant evidence has been utilised in their development. A documentary analysis of reports on medicines optimisation published by the Royal Pharmaceutical Society (RPS), The King's Fund and National Institute for Health and Social Care Excellence since 2013. The analysis draws on a non-systematic review of research on patient experiences of using medicines. Findings The reports varied in their inclusion of patient perspectives and person-centred care values, and in the extent to which they drew on evidence from research on patients' experiences of polypharmacy and medicines use. In the RPS report, medicines optimisation is represented as being a 'step change' from medicines management, in contrast to the other documents which suggest that it is facilitated by the systems and processes that comprise the latter model. Only The King's Fund report considered evidence from qualitative studies of people's use of medicines. However, these studies are not without their limitations. We suggest five ways in which researchers could improve this evidence base and so inform the development of future policy: by facilitating reviews of existing research; conducting studies of patient experiences of polypharmacy and multimorbidity; evaluating medicines optimisation interventions; making better use of relevant theories, concepts and tools; and improving patient and public involvement in research and in guideline development.

Comprehensive Assessments of RNA-seq by the SEQC Consortium: FDA-Led Efforts Advance Precision Medicine.

PubMed

Xu, Joshua; Gong, Binsheng; Wu, Leihong; Thakkar, Shraddha; Hong, Huixiao; Tong, Weida

2016-03-15

Studies on gene expression in response to therapy have led to the discovery of pharmacogenomics biomarkers and advances in precision medicine. Whole transcriptome sequencing (RNA-seq) is an emerging tool for profiling gene expression and has received wide adoption in the biomedical research community. However, its value in regulatory decision making requires rigorous assessment and consensus between various stakeholders, including the research community, regulatory agencies, and industry. The FDA-led SEquencing Quality Control (SEQC) consortium has made considerable progress in this direction, and is the subject of this review. Specifically, three RNA-seq platforms (Illumina HiSeq, Life Technologies SOLiD, and Roche 454) were extensively evaluated at multiple sites to assess cross-site and cross-platform reproducibility. The results demonstrated that relative gene expression measurements were consistently comparable across labs and platforms, but not so for the measurement of absolute expression levels. As part of the quality evaluation several studies were included to evaluate the utility of RNA-seq in clinical settings and safety assessment. The neuroblastoma study profiled tumor samples from 498 pediatric neuroblastoma patients by both microarray and RNA-seq. RNA-seq offers more utilities than microarray in determining the transcriptomic characteristics of cancer. However, RNA-seq and microarray-based models were comparable in clinical endpoint prediction, even when including additional features unique to RNA-seq beyond gene expression. The toxicogenomics study compared microarray and RNA-seq profiles of the liver samples from rats exposed to 27 different chemicals representing multiple toxicity modes of action. Cross-platform concordance was dependent on chemical treatment and transcript abundance. Though both RNA-seq and microarray are suitable for developing gene expression based predictive models with comparable prediction performance, RNA-seq offers advantages over microarray in profiling genes with low expression. The rat BodyMap study provided a comprehensive rat transcriptomic body map by performing RNA-Seq on 320 samples from 11 organs in either sex of juvenile, adolescent, adult and aged Fischer 344 rats. Lastly, the transferability study demonstrated that signature genes of predictive models are reciprocally transferable between microarray and RNA-seq data for model development using a comprehensive approach with two large clinical data sets. This result suggests continued usefulness of legacy microarray data in the coming RNA-seq era. In conclusion, the SEQC project enhances our understanding of RNA-seq and provides valuable guidelines for RNA-seq based clinical application and safety evaluation to advance precision medicine.

A new web-based modelling tool (Websim-MILQ) aimed at optimisation of thermal treatments in the dairy industry.

PubMed

Schutyser, M A I; Straatsma, J; Keijzer, P M; Verschueren, M; De Jong, P

2008-11-30

In the framework of a cooperative EU research project (MILQ-QC-TOOL) a web-based modelling tool (Websim-MILQ) was developed for optimisation of thermal treatments in the dairy industry. The web-based tool enables optimisation of thermal treatments with respect to product safety, quality and costs. It can be applied to existing products and processes but also to reduce time to market for new products. Important aspects of the tool are its user-friendliness and its specifications customised to the needs of small dairy companies. To challenge the web-based tool it was applied for optimisation of thermal treatments in 16 dairy companies producing yoghurt, fresh cream, chocolate milk and cheese. Optimisation with WebSim-MILQ resulted in concrete improvements with respect to risk of microbial contamination, cheese yield, fouling and production costs. In this paper we illustrate the use of WebSim-MILQ for optimisation of a cheese milk pasteurisation process where we could increase the cheese yield (1 extra cheese for each 100 produced cheeses from the same amount of milk) and reduced the risk of contamination of pasteurised cheese milk with thermoresistent streptococci from critical to negligible. In another case we demonstrate the advantage for changing from an indirect to a direct heating method for a UHT process resulting in 80% less fouling, while improving product quality and maintaining product safety.

A brief understanding of process optimisation in microwave-assisted extraction of botanical materials: options and opportunities with chemometric tools.

PubMed

Das, Anup Kumar; Mandal, Vivekananda; Mandal, Subhash C

2014-01-01

Extraction forms the very basic step in research on natural products for drug discovery. A poorly optimised and planned extraction methodology can jeopardise the entire mission. To provide a vivid picture of different chemometric tools and planning for process optimisation and method development in extraction of botanical material, with emphasis on microwave-assisted extraction (MAE) of botanical material. A review of studies involving the application of chemometric tools in combination with MAE of botanical materials was undertaken in order to discover what the significant extraction factors were. Optimising a response by fine-tuning those factors, experimental design or statistical design of experiment (DoE), which is a core area of study in chemometrics, was then used for statistical analysis and interpretations. In this review a brief explanation of the different aspects and methodologies related to MAE of botanical materials that were subjected to experimental design, along with some general chemometric tools and the steps involved in the practice of MAE, are presented. A detailed study on various factors and responses involved in the optimisation is also presented. This article will assist in obtaining a better insight into the chemometric strategies of process optimisation and method development, which will in turn improve the decision-making process in selecting influential extraction parameters. Copyright © 2013 John Wiley & Sons, Ltd.

Optimized optical devices for edge-coupling-enabled silicon photonics platform

NASA Astrophysics Data System (ADS)

Png, Ching Eng; Ang, Thomas Y. L.; Ong, Jun Rong; Lim, Soon Thor; Sahin, Ezgi; Chen, G. F. R.; Tan, D. T. H.; Guo, Tina X.; Wang, Hong

2018-02-01

We present a library of high-performance passive and active silicon photonic devices at the C-band that is specifically designed and optimized for edge-coupling-enabled silicon photonics platform. These devices meet the broadband (100 nm), low-loss (< 2dB per device), high speed (>= 25 Gb/s), and polarization diversity requirements (TE and TM polarization extinction ratio <= 25 dB) for optical communication applications. Ultra-low loss edge couplers, broadband directional couplers, high-extinction ratio polarization beam splitters (PBSs), and high-speed modulators are some of the devices within our library. In particular, we have designed and fabricated inverse taper fiber-to-waveguide edge couplers of tip widths ranging from 120 nm to 200 nm, and we obtained a low coupling loss of 1.80+/-0.28 dB for 160 nm tip width. To achieve polarization diversity operation for inverse tapers, we have experimentally realized different designs of polarization beam splitters (PBS). Our optimized PBS has a measured extinction ratio of <= 25 dB for both the quasiTE modes, and quasi-TM modes. Additionally, a broadband (100 nm) directional coupler with a 50/50 power splitting ratio was experimentally realized on a small footprint of 20×3 μm2 . Last but not least, high-speed silicon modulators with a range of carrier doping concentrations and offset of the PN junction can be used to optimise the modulation efficiency, and insertion losses for operation at 25 GHz.

Complete Genome Sequence of Kluyveromyces lactis Strain GG799, a Common Yeast Host for Heterologous Protein Expression

PubMed Central

Chuzel, Léa; Ganatra, Mehul B.; Schermerhorn, Kelly M.; Gardner, Andrew F.; Anton, Brian P.

2017-01-01

ABSTRACT We report the genome sequence of the dairy yeast Kluyveromyces lactis strain GG799 obtained using the Pacific Biosciences RS II platform. K. lactis strain GG799 is a common host for the expression of proteins at both laboratory and industrial scales. PMID:28751387

OVERVIEW OF AN INTERLABORATORY COLLABORATION ON EVALUATING THE EFFECTS OF MODEL HEPATOTOXICANTS ON HEPATIC GENE EXPRESSION

EPA Science Inventory

Evaluating the Effects of Methapyrilene and Clofibrate on Hepatic Gene Expression: A Collaboration Between Laboratories and a Comparison of Platform and Analytical Approaches

Roger G. Ulrich1, John C. Rockett2, G. Gordon Gibson3 and Syril Pettit4

1 Rosetta Inpharmat...

The Plant Genome Integrative Explorer Resource: PlantGenIE.org.

PubMed

Sundell, David; Mannapperuma, Chanaka; Netotea, Sergiu; Delhomme, Nicolas; Lin, Yao-Cheng; Sjödin, Andreas; Van de Peer, Yves; Jansson, Stefan; Hvidsten, Torgeir R; Street, Nathaniel R

2015-12-01

Accessing and exploring large-scale genomics data sets remains a significant challenge to researchers without specialist bioinformatics training. We present the integrated PlantGenIE.org platform for exploration of Populus, conifer and Arabidopsis genomics data, which includes expression networks and associated visualization tools. Standard features of a model organism database are provided, including genome browsers, gene list annotation, Blast homology searches and gene information pages. Community annotation updating is supported via integration of WebApollo. We have produced an RNA-sequencing (RNA-Seq) expression atlas for Populus tremula and have integrated these data within the expression tools. An updated version of the ComPlEx resource for performing comparative plant expression analyses of gene coexpression network conservation between species has also been integrated. The PlantGenIE.org platform provides intuitive access to large-scale and genome-wide genomics data from model forest tree species, facilitating both community contributions to annotation improvement and tools supporting use of the included data resources to inform biological insight. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.

Assessment of a novel multi-array normalization method based on spike-in control probes suitable for microRNA datasets with global decreases in expression.

PubMed

Sewer, Alain; Gubian, Sylvain; Kogel, Ulrike; Veljkovic, Emilija; Han, Wanjiang; Hengstermann, Arnd; Peitsch, Manuel C; Hoeng, Julia

2014-05-17

High-quality expression data are required to investigate the biological effects of microRNAs (miRNAs). The goal of this study was, first, to assess the quality of miRNA expression data based on microarray technologies and, second, to consolidate it by applying a novel normalization method. Indeed, because of significant differences in platform designs, miRNA raw data cannot be normalized blindly with standard methods developed for gene expression. This fundamental observation motivated the development of a novel multi-array normalization method based on controllable assumptions, which uses the spike-in control probes to adjust the measured intensities across arrays. Raw expression data were obtained with the Exiqon dual-channel miRCURY LNA™ platform in the "common reference design" and processed as "pseudo-single-channel". They were used to apply several quality metrics based on the coefficient of variation and to test the novel spike-in controls based normalization method. Most of the considerations presented here could be applied to raw data obtained with other platforms. To assess the normalization method, it was compared with 13 other available approaches from both data quality and biological outcome perspectives. The results showed that the novel multi-array normalization method reduced the data variability in the most consistent way. Further, the reliability of the obtained differential expression values was confirmed based on a quantitative reverse transcription-polymerase chain reaction experiment performed for a subset of miRNAs. The results reported here support the applicability of the novel normalization method, in particular to datasets that display global decreases in miRNA expression similarly to the cigarette smoke-exposed mouse lung dataset considered in this study. Quality metrics to assess between-array variability were used to confirm that the novel spike-in controls based normalization method provided high-quality miRNA expression data suitable for reliable downstream analysis. The multi-array miRNA raw data normalization method was implemented in an R software package called ExiMiR and deposited in the Bioconductor repository.

Assessment of a novel multi-array normalization method based on spike-in control probes suitable for microRNA datasets with global decreases in expression

PubMed Central

2014-01-01

Background High-quality expression data are required to investigate the biological effects of microRNAs (miRNAs). The goal of this study was, first, to assess the quality of miRNA expression data based on microarray technologies and, second, to consolidate it by applying a novel normalization method. Indeed, because of significant differences in platform designs, miRNA raw data cannot be normalized blindly with standard methods developed for gene expression. This fundamental observation motivated the development of a novel multi-array normalization method based on controllable assumptions, which uses the spike-in control probes to adjust the measured intensities across arrays. Results Raw expression data were obtained with the Exiqon dual-channel miRCURY LNA™ platform in the “common reference design” and processed as “pseudo-single-channel”. They were used to apply several quality metrics based on the coefficient of variation and to test the novel spike-in controls based normalization method. Most of the considerations presented here could be applied to raw data obtained with other platforms. To assess the normalization method, it was compared with 13 other available approaches from both data quality and biological outcome perspectives. The results showed that the novel multi-array normalization method reduced the data variability in the most consistent way. Further, the reliability of the obtained differential expression values was confirmed based on a quantitative reverse transcription–polymerase chain reaction experiment performed for a subset of miRNAs. The results reported here support the applicability of the novel normalization method, in particular to datasets that display global decreases in miRNA expression similarly to the cigarette smoke-exposed mouse lung dataset considered in this study. Conclusions Quality metrics to assess between-array variability were used to confirm that the novel spike-in controls based normalization method provided high-quality miRNA expression data suitable for reliable downstream analysis. The multi-array miRNA raw data normalization method was implemented in an R software package called ExiMiR and deposited in the Bioconductor repository. PMID:24886675

Oracle Database 10g: a platform for BLAST search and Regular Expression pattern matching in life sciences.

PubMed

Stephens, Susie M; Chen, Jake Y; Davidson, Marcel G; Thomas, Shiby; Trute, Barry M

2005-01-01

As database management systems expand their array of analytical functionality, they become powerful research engines for biomedical data analysis and drug discovery. Databases can hold most of the data types commonly required in life sciences and consequently can be used as flexible platforms for the implementation of knowledgebases. Performing data analysis in the database simplifies data management by minimizing the movement of data from disks to memory, allowing pre-filtering and post-processing of datasets, and enabling data to remain in a secure, highly available environment. This article describes the Oracle Database 10g implementation of BLAST and Regular Expression Searches and provides case studies of their usage in bioinformatics. http://www.oracle.com/technology/software/index.html.

The multifunctional nuclear pore complex: a platform for controlling gene expression

PubMed Central

Ptak, Christopher; Aitchison, John D.; Wozniak, Richard W.

2014-01-01

In addition to their established roles in nucleocytoplasmic transport, the intimate association of nuclear pore complexes (NPCs) with chromatin has long led to speculation that these structures influence peripheral chromatin structure and regulate gene expression. These ideas have their roots in morphological observations, however recent years have seen the identification of physical interactions between NPCs, chromatin, and the transcriptional machinery. Key insights into the molecular functions of specific NPC proteins have uncovered roles for these proteins in transcriptional activation and elongation, mRNA processing, as well as chromatin structure and localization. Here, we review recent studies that provide further molecular detail on the role of specific NPC components as distinct platforms for these chromatin dependent processes. PMID:24657998

Implementation and comparative analysis of the optimisations produced by evolutionary algorithms for the parameter extraction of PSP MOSFET model

NASA Astrophysics Data System (ADS)

Hadia, Sarman K.; Thakker, R. A.; Bhatt, Kirit R.

2016-05-01

The study proposes an application of evolutionary algorithms, specifically an artificial bee colony (ABC), variant ABC and particle swarm optimisation (PSO), to extract the parameters of metal oxide semiconductor field effect transistor (MOSFET) model. These algorithms are applied for the MOSFET parameter extraction problem using a Pennsylvania surface potential model. MOSFET parameter extraction procedures involve reducing the error between measured and modelled data. This study shows that ABC algorithm optimises the parameter values based on intelligent activities of honey bee swarms. Some modifications have also been applied to the basic ABC algorithm. Particle swarm optimisation is a population-based stochastic optimisation method that is based on bird flocking activities. The performances of these algorithms are compared with respect to the quality of the solutions. The simulation results of this study show that the PSO algorithm performs better than the variant ABC and basic ABC algorithm for the parameter extraction of the MOSFET model; also the implementation of the ABC algorithm is shown to be simpler than that of the PSO algorithm.

Reference voltage calculation method based on zero-sequence component optimisation for a regional compensation DVR

NASA Astrophysics Data System (ADS)

Jian, Le; Cao, Wang; Jintao, Yang; Yinge, Wang

2018-04-01

This paper describes the design of a dynamic voltage restorer (DVR) that can simultaneously protect several sensitive loads from voltage sags in a region of an MV distribution network. A novel reference voltage calculation method based on zero-sequence voltage optimisation is proposed for this DVR to optimise cost-effectiveness in compensation of voltage sags with different characteristics in an ungrounded neutral system. Based on a detailed analysis of the characteristics of voltage sags caused by different types of faults and the effect of the wiring mode of the transformer on these characteristics, the optimisation target of the reference voltage calculation is presented with several constraints. The reference voltages under all types of voltage sags are calculated by optimising the zero-sequence component, which can reduce the degree of swell in the phase-to-ground voltage after compensation to the maximum extent and can improve the symmetry degree of the output voltages of the DVR, thereby effectively increasing the compensation ability. The validity and effectiveness of the proposed method are verified by simulation and experimental results.

Biomimetic High Density Lipoprotein Nanoparticles For Nucleic Acid Delivery

PubMed Central

McMahon, Kaylin M.; Mutharasan, R. Kannan; Tripathy, Sushant; Veliceasa, Dorina; Bobeica, Mariana; Shumaker, Dale K.; Luthi, Andrea J.; Helfand, Brian T.; Ardehali, Hossein; Mirkin, Chad A.; Volpert, Olga; Thaxton, C. Shad

2014-01-01

We report a gold nanoparticle-templated high density lipoprotein (HDL AuNP) platform for gene therapy which combines lipid-based nucleic acid transfection strategies with HDL biomimicry. For proof-of-concept, HDL AuNPs are shown to adsorb antisense cholesterylated DNA. The conjugates are internalized by human cells, can be tracked within cells using transmission electron microscopy (TEM), and regulate target gene expression. Overall, the ability to directly image the AuNP core within cells, the chemical tailorability of the HDL AuNP platform, and the potential for cell-specific targeting afforded by HDL biomimicry make this platform appealing for nucleic acid delivery. PMID:21319839

Computational aero-acoustics for fan duct propagation and radiation. Current status and application to turbofan liner optimisation

NASA Astrophysics Data System (ADS)

Astley, R. J.; Sugimoto, R.; Mustafi, P.

2011-08-01

Novel techniques are presented to reduce noise from turbofan aircraft engines by optimising the acoustic treatment in engine ducts. The application of Computational Aero-Acoustics (CAA) to predict acoustic propagation and absorption in turbofan ducts is reviewed and a critical assessment of performance indicates that validated and accurate techniques are now available for realistic engine predictions. A procedure for integrating CAA methods with state of the art optimisation techniques is proposed in the remainder of the article. This is achieved by embedding advanced computational methods for noise prediction within automated and semi-automated optimisation schemes. Two different strategies are described and applied to realistic nacelle geometries and fan sources to demonstrate the feasibility of this approach for industry scale problems.

Integrative analysis of RUNX1 downstream pathways and target genes

PubMed Central

Michaud, Joëlle; Simpson, Ken M; Escher, Robert; Buchet-Poyau, Karine; Beissbarth, Tim; Carmichael, Catherine; Ritchie, Matthew E; Schütz, Frédéric; Cannon, Ping; Liu, Marjorie; Shen, Xiaofeng; Ito, Yoshiaki; Raskind, Wendy H; Horwitz, Marshall S; Osato, Motomi; Turner, David R; Speed, Terence P; Kavallaris, Maria; Smyth, Gordon K; Scott, Hamish S

2008-01-01

Background The RUNX1 transcription factor gene is frequently mutated in sporadic myeloid and lymphoid leukemia through translocation, point mutation or amplification. It is also responsible for a familial platelet disorder with predisposition to acute myeloid leukemia (FPD-AML). The disruption of the largely unknown biological pathways controlled by RUNX1 is likely to be responsible for the development of leukemia. We have used multiple microarray platforms and bioinformatic techniques to help identify these biological pathways to aid in the understanding of why RUNX1 mutations lead to leukemia. Results Here we report genes regulated either directly or indirectly by RUNX1 based on the study of gene expression profiles generated from 3 different human and mouse platforms. The platforms used were global gene expression profiling of: 1) cell lines with RUNX1 mutations from FPD-AML patients, 2) over-expression of RUNX1 and CBFβ, and 3) Runx1 knockout mouse embryos using either cDNA or Affymetrix microarrays. We observe that our datasets (lists of differentially expressed genes) significantly correlate with published microarray data from sporadic AML patients with mutations in either RUNX1 or its cofactor, CBFβ. A number of biological processes were identified among the differentially expressed genes and functional assays suggest that heterozygous RUNX1 point mutations in patients with FPD-AML impair cell proliferation, microtubule dynamics and possibly genetic stability. In addition, analysis of the regulatory regions of the differentially expressed genes has for the first time systematically identified numerous potential novel RUNX1 target genes. Conclusion This work is the first large-scale study attempting to identify the genetic networks regulated by RUNX1, a master regulator in the development of the hematopoietic system and leukemia. The biological pathways and target genes controlled by RUNX1 will have considerable importance in disease progression in both familial and sporadic leukemia as well as therapeutic implications. PMID:18671852

Modeling and analysis of a flywheel microvibration isolation system for spacecrafts

NASA Astrophysics Data System (ADS)

Wei, Zhanji; Li, Dongxu; Luo, Qing; Jiang, Jianping

2015-01-01

The microvibrations generated by flywheels running at full speed onboard high precision spacecrafts will affect stability of the spacecraft bus and further degrade pointing accuracy of the payload. A passive vibration isolation platform comprised of multi-segment zig-zag beams is proposed to isolate disturbances of the flywheel. By considering the flywheel and the platform as an integral system with gyroscopic effects, an equivalent dynamic model is developed and verified through eigenvalue and frequency response analysis. The critical speeds of the system are deduced and expressed as functions of system parameters. The vibration isolation performance of the platform under synchronal and high-order harmonic disturbances caused by the flywheel is investigated. It is found that the speed range within which the passive platform is effective and the disturbance decay rate of the system are greatly influenced by the locations of the critical speeds. Structure optimization of the platform is carried out to enhance its performance. Simulation results show that a properly designed vibration isolation platform can effectively reduce disturbances emitted by the flywheel operating above the critical speeds of the system.

The Trip Itinerary Optimization Platform: A Framework for Personalized Travel Information

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kwasnik, Ted; Carmichael, Scott P.; Arent, Douglas J

The New Concepts Incubator team at the National Renewable Energy Laboratory (NREL) developed a three-stage online platform for travel diary collection, personal travel plan optimization and travel itinerary visualization. In the first stage, users provide a travel diary for the previous day through an interactive map and calendar interface and survey for travel attitudes and behaviors. One or more days later, users are invited via email to engage in a second stage where they view a personal mobility dashboard displaying recommended travel itineraries generated from a novel framework that optimizes travel outcomes over a sequence of interrelated trips. A weekmore » or more after viewing these recommended travel itineraries on the dashboard, users are emailed again to engage in a third stage where they complete a final survey about travel attitudes and behaviors. A usability study of the platform conducted online showed that, in general, users found the system valuable for informing their travel decisions. A total of 274 individuals were recruited through Amazon Mechanical Turk, an online survey platform, to participate in a transportation study using this platform. On average, the platform distilled 65 feasible travel plans per individual into two recommended itineraries, each optimal according to one or more outcomes and dependent on the fixed times and locations from the travel diary. For 45 percent of users, the trip recommendation algorithm returned only a single, typically automobile-centric, itinerary because there were no other viable alternative transportation modes available. Platform users generally agreed that the dashboard was enjoyable and easy to use, and that it would be a helpful tool in adopting new travel behaviors. Users generally agreed most that the time, cost and user preferred recommendations 'made sense' to them, and were most willing to implement these itineraries. Platform users typically expressed low willingness to try the carbon and calories optimized itineraries. Of the platform users who viewed the dashboard, 13 percent reported changing their travel behavior, most adopting the time, calories or carbon optimized itineraries. While the algorithm incorporates a wealth of travel data obtained from online APIs pertaining to a travelers route such as historic traffic condition data, public transit time-tables, and bike path routes, open-ended responses from users expressed an interest in the integration of even more fine-grained traffic data and the ability to dynamically model the effect of changes in travel times. Users also commonly expressed concerns over the safety of walking and biking recommendations. Responses indicate that more information about the amenities available to cyclists and pedestrians (sidewalks, shade from trees, access to food) and routes that avoid areas of perceived elevated danger would reduce barriers to implementing these recommendations. More accurate representations of personal vehicle trips (based on vehicle make and model, implications of parking) and the identification of routes that optimize caloric intensity (seeking out elevation changes or longer walks to public transit) are promising avenues for future research.« less

Chronic sleep restriction induces changes in the mandibular condylar cartilage of rats: roles of Akt, Bad and Caspase-3.

PubMed

Zhu, Yong; Wu, Gaoyi; Zhu, Guoxiong; Ma, Chuan; Zhao, Huaqiang

2014-01-01

The aim of the present study was to observe changes in the temporomandibular joint (TMJ) of rats that had been subjected to chronic sleep restriction and to investigate whether Akt, Bad and Caspase3 play a role in the mechanism underlying the changes. One hundred and eighty male Wistar rats were randomly divided into three groups (n = 60 in each): cage control group, large-platform control group, and sleep restriction group. Each group was divided into three subgroups (n = 20 in each) of three different time points (7, 14 and 21 days), respectively. The modified multiple platform method was used to induce chronic sleep restriction. The TMJ tissue histology was studied by staining with haematoxylin and eosin. The expression of Akt, p-Aktser473, Bad, p-Badser136 and Caspase3 proteins was detected by immunohistochemistry and western blotting. The expression of Akt, Bad and Caspase3 mRNAs was measured by real-time quantitative polymerase chain reaction (RT-qPCR). Compared with the large-platform and cage control groups, condylar cartilage pathological alterations were found in the sleep restriction group. There were significantly decreased expression levels of Akt, p-Aktser473 and p-Badser136 and significantly increased expression levels of Bad and Caspase3 after sleep restriction. These data suggest that sleep restriction may induce pathological alterations in the condylar cartilage of rats. Alterations in Akt, Bad and Caspase3 may be associated with the potential mechanism by which chronic sleep restriction influences the condylar cartilage.

Chronic sleep restriction induces changes in the mandibular condylar cartilage of rats: roles of Akt, Bad and Caspase-3

PubMed Central

Zhu, Yong; Wu, Gaoyi; Zhu, Guoxiong; Ma, Chuan; Zhao, Huaqiang

2014-01-01

Aims: The aim of the present study was to observe changes in the temporomandibular joint (TMJ) of rats that had been subjected to chronic sleep restriction and to investigate whether Akt, Bad and Caspase3 play a role in the mechanism underlying the changes. Main methods: One hundred and eighty male Wistar rats were randomly divided into three groups (n = 60 in each): cage control group, large-platform control group, and sleep restriction group. Each group was divided into three subgroups (n = 20 in each) of three different time points (7, 14 and 21 days), respectively. The modified multiple platform method was used to induce chronic sleep restriction. The TMJ tissue histology was studied by staining with haematoxylin and eosin. The expression of Akt, p-Aktser473, Bad, p-Badser136 and Caspase3 proteins was detected by immunohistochemistry and western blotting. The expression of Akt, Bad and Caspase3 mRNAs was measured by real-time quantitative polymerase chain reaction (RT-qPCR). Key findings: Compared with the large-platform and cage control groups, condylar cartilage pathological alterations were found in the sleep restriction group. There were significantly decreased expression levels of Akt, p-Aktser473 and p-Badser136 and significantly increased expression levels of Bad and Caspase3 after sleep restriction. Significance: These data suggest that sleep restriction may induce pathological alterations in the condylar cartilage of rats. Alterations in Akt, Bad and Caspase3 may be associated with the potential mechanism by which chronic sleep restriction influences the condylar cartilage. PMID:25356113

Is ICRP guidance on the use of reference levels consistent?

PubMed

Hedemann-Jensen, Per; McEwan, Andrew C

2011-12-01

In ICRP 103, which has replaced ICRP 60, it is stated that no fundamental changes have been introduced compared with ICRP 60. This is true except that the application of reference levels in emergency and existing exposure situations seems to be applied inconsistently, and also in the related publications ICRP 109 and ICRP 111. ICRP 103 emphasises that focus should be on the residual doses after the implementation of protection strategies in emergency and existing exposure situations. If possible, the result of an optimised protection strategy should bring the residual dose below the reference level. Thus the reference level represents the maximum acceptable residual dose after an optimised protection strategy has been implemented. It is not an 'off-the-shelf item' that can be set free of the prevailing situation. It should be determined as part of the process of optimising the protection strategy. If not, protection would be sub-optimised. However, in ICRP 103 some inconsistent concepts have been introduced, e.g. in paragraph 279 which states: 'All exposures above or below the reference level should be subject to optimisation of protection, and particular attention should be given to exposures above the reference level'. If, in fact, all exposures above and below reference levels are subject to the process of optimisation, reference levels appear superfluous. It could be considered that if optimisation of protection below a fixed reference level is necessary, then the reference level has been set too high at the outset. Up until the last phase of the preparation of ICRP 103 the concept of a dose constraint was recommended to constrain the optimisation of protection in all types of exposure situations. In the final phase, the term 'dose constraint' was changed to 'reference level' for emergency and existing exposure situations. However, it seems as if in ICRP 103 it was not fully recognised that dose constraints and reference levels are conceptually different. The use of reference levels in radiological protection is reviewed. It is concluded that the recommendations in ICRP 103 and related ICRP publications seem to be inconsistent regarding the use of reference levels in existing and emergency exposure situations.

Shift of microRNA profile upon orthotopic xenografting of glioblastoma spheroid cultures.

PubMed

Halle, Bo; Thomassen, Mads; Venkatesan, Ranga; Kaimal, Vivek; Marcusson, Eric G; Munthe, Sune; Sørensen, Mia D; Aaberg-Jessen, Charlotte; Jensen, Stine S; Meyer, Morten; Kruse, Torben A; Christiansen, Helle; Schmidt, Steffen; Mollenhauer, Jan; Schulz, Mette K; Andersen, Claus; Kristensen, Bjarne W

2016-07-01

Glioblastomas always recur despite surgery, radiotherapy and chemotherapy. A key player in the therapeutic resistance may be immature tumor cells with stem-like properties (TSCs) escaping conventional treatment. A group of promising molecular targets are microRNAs (miRs). miRs are small non-coding RNAs exerting post-transcriptional regulation of gene expression. In this study we aimed to identify over-expressed TSC-related miRs potentially amenable for therapeutic targeting. We used non-differentiated glioblastoma spheroid cultures (GSCs) containing TSCs and compared these to xenografts using a NanoString nCounter platform. This revealed 19 over-expressed miRs in the non-differentiated GSCs. Additionally, non-differentiated GSCs were compared to neural stem cells (NSCs) using a microarray platform. This revealed four significantly over-expressed miRs in the non-differentiated GSCs in comparison to the NSCs. The three most over-expressed miRs in the non-differentiated GSCs compared to xenografts were miR-126, -137 and -128. KEGG pathway analysis suggested the main biological function of these over-expressed miRs to be cell-cycle arrest and diminished proliferation. To functionally validate the profiling results suggesting association of these miRs with stem-like properties, experimental over-expression of miR-128 was performed. A consecutive limiting dilution assay confirmed a significantly elevated spheroid formation in the miR-128 over-expressing cells. This may provide potential therapeutic targets for anti-miRs to identify novel treatment options for GBM patients.

Bioinformatics on the cloud computing platform Azure.

PubMed

Shanahan, Hugh P; Owen, Anne M; Harrison, Andrew P

2014-01-01

We discuss the applicability of the Microsoft cloud computing platform, Azure, for bioinformatics. We focus on the usability of the resource rather than its performance. We provide an example of how R can be used on Azure to analyse a large amount of microarray expression data deposited at the public database ArrayExpress. We provide a walk through to demonstrate explicitly how Azure can be used to perform these analyses in Appendix S1 and we offer a comparison with a local computation. We note that the use of the Platform as a Service (PaaS) offering of Azure can represent a steep learning curve for bioinformatics developers who will usually have a Linux and scripting language background. On the other hand, the presence of an additional set of libraries makes it easier to deploy software in a parallel (scalable) fashion and explicitly manage such a production run with only a few hundred lines of code, most of which can be incorporated from a template. We propose that this environment is best suited for running stable bioinformatics software by users not involved with its development.

Employing metabolic engineered lipolytic microbial platform for 1-alkene one-step conversion.

PubMed

Wang, Juli; Yu, Haiying; Zhu, Kun

2018-05-01

1-Alkenes are traditionally used as basic chemicals with great importance. Biosynthetic 1-alkenes also have the potential to serve as biofuels. In this study, we engineered a Pseudomonas lipolytic microbial platform for 1-alkene production using hydrophobic substrate as sole carbon source. Fatty acid decarboxylase UndA and UndB were cloned and expressed, which successfully produced 1-alkenes. Optimal culturing temperature and the interruption of competitive pathway were proven to be beneficial to 1-alkene synthesis. Chromosomal integration of UndB conferred 177.8 mg/L 1-alkenes (mainly 1-undecene) in lauric acid medium and 128.9 mg/L 1-alkenes (mainly 1-pentadecene) in palm oil medium. Thioesterase expression, adjustments of fatty acid degradation pathway and a second copy of UndB improved 1-alkene titer to 1102.6 mg/L using lauric acid and 778.4 mg/L using palm oil. All in all, this study offers the first demonstration of lipolytic microbial 1-alkene producing platform with highest reported 1-alkene product titer up to date. Copyright © 2018 Elsevier Ltd. All rights reserved.

Bioinformatics on the Cloud Computing Platform Azure

PubMed Central

Shanahan, Hugh P.; Owen, Anne M.; Harrison, Andrew P.

2014-01-01

We discuss the applicability of the Microsoft cloud computing platform, Azure, for bioinformatics. We focus on the usability of the resource rather than its performance. We provide an example of how R can be used on Azure to analyse a large amount of microarray expression data deposited at the public database ArrayExpress. We provide a walk through to demonstrate explicitly how Azure can be used to perform these analyses in Appendix S1 and we offer a comparison with a local computation. We note that the use of the Platform as a Service (PaaS) offering of Azure can represent a steep learning curve for bioinformatics developers who will usually have a Linux and scripting language background. On the other hand, the presence of an additional set of libraries makes it easier to deploy software in a parallel (scalable) fashion and explicitly manage such a production run with only a few hundred lines of code, most of which can be incorporated from a template. We propose that this environment is best suited for running stable bioinformatics software by users not involved with its development. PMID:25050811

A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control consortium

PubMed Central

2014-01-01

We present primary results from the Sequencing Quality Control (SEQC) project, coordinated by the United States Food and Drug Administration. Examining Illumina HiSeq, Life Technologies SOLiD and Roche 454 platforms at multiple laboratory sites using reference RNA samples with built-in controls, we assess RNA sequencing (RNA-seq) performance for junction discovery and differential expression profiling and compare it to microarray and quantitative PCR (qPCR) data using complementary metrics. At all sequencing depths, we discover unannotated exon-exon junctions, with >80% validated by qPCR. We find that measurements of relative expression are accurate and reproducible across sites and platforms if specific filters are used. In contrast, RNA-seq and microarrays do not provide accurate absolute measurements, and gene-specific biases are observed, for these and qPCR. Measurement performance depends on the platform and data analysis pipeline, and variation is large for transcript-level profiling. The complete SEQC data sets, comprising >100 billion reads (10Tb), provide unique resources for evaluating RNA-seq analyses for clinical and regulatory settings. PMID:25150838

Influence of the platform jitter on intensity fluctuation for laser launch system

NASA Astrophysics Data System (ADS)

Zhang, Pengfei; Qiao, Chunhong; Huang, Tong; Zhang, Jinghui; Fan, Chengyu

2017-10-01

The jitter of the transmitting system can cause the light intensity fluctuation at the target position of the laser transmission, which affects the performance of the laser communication, imaging and the adaptive optical system. In this paper, the platform jitter is modeled by Gaussian random fluctuation phase and the analytic expression of the system jitter effect on the fluctuation of light intensity is obtained under the vacuum condition based on extended Huygens-Fresnel principle. The numerical simulation is compared with the theoretical expression and the consistency is obtained. At the same time, the influence of the jitter of the launch system on the intensity fluctuation of the target system under different turbulence conditions is analyzed by numerical simulation. The result show that normalized intensity fluctuation variance induced by platform jitter seems to be unrestricted. The jitter of the transmitting system has a more important influence on the fluctuation of the target position caused by the atmospheric turbulence, as the jitter increase. This result provides a reference for the application of the actual laser transmission system.

Droplet-based microfluidics platform for measurement of rapid erythrocyte water transport

PubMed Central

Jin, Byung-Ju; Esteva-Font, Cristina; Verkman, A.S.

2015-01-01

Cell membrane water permeability is an important determinant of epithelial fluid secretion, tissue swelling, angiogenesis, tumor spread and other biological processes. Cellular water channels, the aquaporins, are important drug targets. Water permeability is generally measured from the kinetics of cell volume change in response to an osmotic gradient. Here, we developed a microfluidics platform in which cells expressing a cytoplasmic, volume-sensing fluorescent dye are rapidly subjected to an osmotic gradient by solution mixing inside a ~ 0.1 nL droplet surrounded by oil. Solution mixing time was < 10 ms. Osmotic water permeability was deduced from a single, time-integrated fluorescence image of an observation area in which time after mixing is determined by spatial position. Water permeability was accurately measured in aquaporin-expressing erythrocytes with half-times for osmotic equilibration down to < 50 ms. Compared with conventional water permeability measurements using costly stopped-flow instrumentation, the microfluidics platform here utilizes sub-microliter blood sample volume, does not suffer from mixing artifact, and replaces challenging kinetic measurements by a single image capture using a standard laboratory fluorescence microscope. PMID:26159099

A Neuron-Based Screening Platform for Optimizing Genetically-Encoded Calcium Indicators

PubMed Central

Schreiter, Eric R.; Hasseman, Jeremy P.; Tsegaye, Getahun; Fosque, Benjamin F.; Behnam, Reza; Shields, Brenda C.; Ramirez, Melissa; Kimmel, Bruce E.; Kerr, Rex A.; Jayaraman, Vivek; Looger, Loren L.; Svoboda, Karel; Kim, Douglas S.

2013-01-01

Fluorescent protein-based sensors for detecting neuronal activity have been developed largely based on non-neuronal screening systems. However, the dynamics of neuronal state variables (e.g., voltage, calcium, etc.) are typically very rapid compared to those of non-excitable cells. We developed an electrical stimulation and fluorescence imaging platform based on dissociated rat primary neuronal cultures. We describe its use in testing genetically-encoded calcium indicators (GECIs). Efficient neuronal GECI expression was achieved using lentiviruses containing a neuronal-selective gene promoter. Action potentials (APs) and thus neuronal calcium levels were quantitatively controlled by electrical field stimulation, and fluorescence images were recorded. Images were segmented to extract fluorescence signals corresponding to individual GECI-expressing neurons, which improved sensitivity over full-field measurements. We demonstrate the superiority of screening GECIs in neurons compared with solution measurements. Neuronal screening was useful for efficient identification of variants with both improved response kinetics and high signal amplitudes. This platform can be used to screen many types of sensors with cellular resolution under realistic conditions where neuronal state variables are in relevant ranges with respect to timing and amplitude. PMID:24155972

Retention prediction and separation optimization under multilinear gradient elution in liquid chromatography with Microsoft Excel macros.

PubMed

Fasoula, S; Zisi, Ch; Gika, H; Pappa-Louisi, A; Nikitas, P

2015-05-22

A package of Excel VBA macros have been developed for modeling multilinear gradient retention data obtained in single or double gradient elution mode by changing organic modifier(s) content and/or eluent pH. For this purpose, ten chromatographic models were used and four methods were adopted for their application. The methods were based on (a) the analytical expression of the retention time, provided that this expression is available, (b) the retention times estimated using the Nikitas-Pappa approach, (c) the stepwise approximation, and (d) a simple numerical approximation involving the trapezoid rule for integration of the fundamental equation for gradient elution. For all these methods, Excel VBA macros have been written and implemented using two different platforms; the fitting and the optimization platform. The fitting platform calculates not only the adjustable parameters of the chromatographic models, but also the significance of these parameters and furthermore predicts the analyte elution times. The optimization platform determines the gradient conditions that lead to the optimum separation of a mixture of analytes by using the Solver evolutionary mode, provided that proper constraints are set in order to obtain the optimum gradient profile in the minimum gradient time. The performance of the two platforms was tested using experimental and artificial data. It was found that using the proposed spreadsheets, fitting, prediction, and optimization can be performed easily and effectively under all conditions. Overall, the best performance is exhibited by the analytical and Nikitas-Pappa's methods, although the former cannot be used under all circumstances. Copyright © 2015 Elsevier B.V. All rights reserved.

An optimized protocol for generation and analysis of Ion Proton sequencing reads for RNA-Seq.

PubMed

Yuan, Yongxian; Xu, Huaiqian; Leung, Ross Ka-Kit

2016-05-26

Previous studies compared running cost, time and other performance measures of popular sequencing platforms. However, comprehensive assessment of library construction and analysis protocols for Proton sequencing platform remains unexplored. Unlike Illumina sequencing platforms, Proton reads are heterogeneous in length and quality. When sequencing data from different platforms are combined, this can result in reads with various read length. Whether the performance of the commonly used software for handling such kind of data is satisfactory is unknown. By using universal human reference RNA as the initial material, RNaseIII and chemical fragmentation methods in library construction showed similar result in gene and junction discovery number and expression level estimated accuracy. In contrast, sequencing quality, read length and the choice of software affected mapping rate to a much larger extent. Unspliced aligner TMAP attained the highest mapping rate (97.27 % to genome, 86.46 % to transcriptome), though 47.83 % of mapped reads were clipped. Long reads could paradoxically reduce mapping in junctions. With reference annotation guide, the mapping rate of TopHat2 significantly increased from 75.79 to 92.09 %, especially for long (>150 bp) reads. Sailfish, a k-mer based gene expression quantifier attained highly consistent results with that of TaqMan array and highest sensitivity. We provided for the first time, the reference statistics of library preparation methods, gene detection and quantification and junction discovery for RNA-Seq by the Ion Proton platform. Chemical fragmentation performed equally well with the enzyme-based one. The optimal Ion Proton sequencing options and analysis software have been evaluated.

End-to-end automated microfluidic platform for synthetic biology: from design to functional analysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Linshiz, Gregory; Jensen, Erik; Stawski, Nina

Synthetic biology aims to engineer biological systems for desired behaviors. The construction of these systems can be complex, often requiring genetic reprogramming, extensive de novo DNA synthesis, and functional screening. Here, we present a programmable, multipurpose microfluidic platform and associated software and apply the platform to major steps of the synthetic biology research cycle: design, construction, testing, and analysis. We show the platform’s capabilities for multiple automated DNA assembly methods, including a new method for Isothermal Hierarchical DNA Construction, and for Escherichia coli and Saccharomyces cerevisiae transformation. The platform enables the automated control of cellular growth, gene expression induction, andmore » proteogenic and metabolic output analysis. Finally, taken together, we demonstrate the microfluidic platform’s potential to provide end-to-end solutions for synthetic biology research, from design to functional analysis.« less

End-to-end automated microfluidic platform for synthetic biology: from design to functional analysis

DOE PAGES

Linshiz, Gregory; Jensen, Erik; Stawski, Nina; ...

2016-02-02

Synthetic biology aims to engineer biological systems for desired behaviors. The construction of these systems can be complex, often requiring genetic reprogramming, extensive de novo DNA synthesis, and functional screening. Here, we present a programmable, multipurpose microfluidic platform and associated software and apply the platform to major steps of the synthetic biology research cycle: design, construction, testing, and analysis. We show the platform’s capabilities for multiple automated DNA assembly methods, including a new method for Isothermal Hierarchical DNA Construction, and for Escherichia coli and Saccharomyces cerevisiae transformation. The platform enables the automated control of cellular growth, gene expression induction, andmore » proteogenic and metabolic output analysis. Finally, taken together, we demonstrate the microfluidic platform’s potential to provide end-to-end solutions for synthetic biology research, from design to functional analysis.« less

Development of a gene synthesis platform for the efficient large scale production of small genes encoding animal toxins.

PubMed

Sequeira, Ana Filipa; Brás, Joana L A; Guerreiro, Catarina I P D; Vincentelli, Renaud; Fontes, Carlos M G A

2016-12-01

Gene synthesis is becoming an important tool in many fields of recombinant DNA technology, including recombinant protein production. De novo gene synthesis is quickly replacing the classical cloning and mutagenesis procedures and allows generating nucleic acids for which no template is available. In addition, when coupled with efficient gene design algorithms that optimize codon usage, it leads to high levels of recombinant protein expression. Here, we describe the development of an optimized gene synthesis platform that was applied to the large scale production of small genes encoding venom peptides. This improved gene synthesis method uses a PCR-based protocol to assemble synthetic DNA from pools of overlapping oligonucleotides and was developed to synthesise multiples genes simultaneously. This technology incorporates an accurate, automated and cost effective ligation independent cloning step to directly integrate the synthetic genes into an effective Escherichia coli expression vector. The robustness of this technology to generate large libraries of dozens to thousands of synthetic nucleic acids was demonstrated through the parallel and simultaneous synthesis of 96 genes encoding animal toxins. An automated platform was developed for the large-scale synthesis of small genes encoding eukaryotic toxins. Large scale recombinant expression of synthetic genes encoding eukaryotic toxins will allow exploring the extraordinary potency and pharmacological diversity of animal venoms, an increasingly valuable but unexplored source of lead molecules for drug discovery.

Nanobarcode gene expression monitoring system for potential miniaturized space applications

NASA Astrophysics Data System (ADS)

Ruan, Weiming; Eastman, P. Scott; Cooke, Patrick A.; Park, Jennifer S.; Chu, Julia S. F.; Gray, Joe W.; Li, Song; Chen, Fanqing Frank

Manned mission to space has been threatened by various cosmos risks including radiation, mirogravity, vacuum, confinement, etc., which may cause genetic variations of astronauts and eventually lead to damages of their health. Thus, the development of small biomedical devices, which can monitor astronaut gene expression changes, is useful for future long-term space missions. Using magnetic microbeads packed with nanocrystal quantum dots at controlled ratios, we were able to generate highly multiplexed nanobarcodes, which can encode a flexible panel of genes. Also, by using a reporter quantum dot, this nanobarcode platform can monitor and quantify gene expression level with improved speed and sensitivity. As a comparison, we studied TGF-β1 induced transcription changes in human bone marrow mesenchymal stem cells with both the nanobarcode microbead system and the Affymetrix GeneChip ® HTA system, which is currently considered as the industrial standard. Though using only 1/20 of the sample RNA, the nanobarcode system showed sensitivity equivalent to Affymetrix GeneChip ® system. The coefficient of variation, dynamic range, and accuracy of the nanobarcodes measurement is equivalent to that of the GeneChip ® HTA system. Therefore, this newly invented nanobarcode microbead platform is thought to be sensitive, flexible, cost-effective and accurate in a level equivalent to the conventional methods. As an extension of the use of this new platform, spacecrafts may carry this miniaturized system as a diagnostic tool for the astronauts.

Delivery of Small Interfering RNA by Peptide-Targeted Mesoporous Silica Nanoparticle-Supported Lipid Bilayers

PubMed Central

Ashley, Carlee E.; Carnes, Eric C.; Epler, Katharine E.; Padilla, David P.; Phillips, Genevieve K.; Castillo, Robert E.; Wilkinson, Dan C.; Wilkinson, Brian S.; Burgard, Cameron A.; Sewell, Robin M.; Townson, Jason L.; Chackerian, Bryce; Willman, Cheryl L.; Peabody, David S.; Wharton, Walker; Brinker, C. Jeffrey

2012-01-01

The therapeutic potential of small interfering RNAs (siRNAs) is severely limited by the availability of delivery platforms that protect siRNA from degradation, deliver it to the target cell with high specificity and efficiency, and promote its endosomal escape and cytosolic dispersion. Here we report that mesoporous silica nanoparticle-supported lipid bilayers (or ‘protocells’), exhibit multiple properties that overcome many of the limitations of existing delivery platforms. Protocells have a 10- to 100-fold greater capacity for siRNA than corresponding lipid nanoparticles and are markedly more stable when incubated under physiological conditions. Protocells loaded with a cocktail of siRNAs bind to cells in a manner dependent on the presence of an appropriate targeting peptide and, through an endocytic pathway followed by endosomal disruption, promote delivery of the silencing nucleotides to the cytoplasm. The expression of each of the genes targeted by the siRNAs was shown to be repressed at the protein level, resulting in a potent induction of growth arrest and apoptosis. Incubation of control cells that lack expression of the antigen recognized by the targeting peptide with siRNA-loaded protocells induced neither repression of protein expression nor apoptosis, indicating the precise specificity of cytotoxic activity. In terms of loading capacity, targeting capabilities, and potency of action, protocells provide unique attributes as a delivery platform for therapeutic oligonucleotides. PMID:22309035

Cytokine treatment optimises the immunotherapeutic effects of umbilical cord-derived MSC for treatment of inflammatory liver disease.

PubMed

de Witte, Samantha F H; Merino, Ana M; Franquesa, Marcella; Strini, Tanja; van Zoggel, Johanna A A; Korevaar, Sander S; Luk, Franka; Gargesha, Madhu; O'Flynn, Lisa; Roy, Debashish; Elliman, Steve J; Newsome, Philip N; Baan, Carla C; Hoogduijn, Martin J

2017-06-08

Mesenchymal stromal cells (MSC) possess immunomodulatory properties and low immunogenicity, both crucial properties for their development into an effective cellular immunotherapy. They have shown benefit in clinical trials targeting liver diseases; however the efficacy of MSC therapy will benefit from improvement of the immunomodulatory and immunogenic properties of MSC. MSC derived from human umbilical cords (ucMSC) were treated for 3 days in vitro with various inflammatory factors, interleukins, vitamins and serum deprivation. Their immunogenicity and immunomodulatory capacity were examined by gene-expression analysis, surface-marker expressions, IDO activity, PGE 2 secretion and inhibition of T cell proliferation and IFNγ production. Furthermore, their activation of NK cell cytotoxicity was investigated via CD107a expression on NK cells. The immunomodulatory capacity, biodistribution and survival of pre-treated ucMSC were investigated in a CCl 4 -induced liver disease mouse model. In addition, capacity of pre-treated MSC to ameliorate liver inflammation was examined in an ex vivo liver inflammation co-culture model. IFN-γ and a multiple cytokine cocktail (MC) consisting of IFN-γ, TGFβ and retinoic acid upregulated the expression of immunomodulatory factor PD-L1 and IDO activity. Subsequently, both treatments enhanced the capacity of ucMSC to inhibit CD4 and CD8 T cell proliferation and IFN-γ production. The susceptibility of ucMSC for NK cell lysis was decreased by IFN-β, TGFβ and MC treatment. In vivo, no immunomodulation was observed by the ucMSC. Four hours after intravenous infusion in mice with CCl 4 -induced inflammatory liver injury, the majority of ucMSC were trapped in the lungs. Rapid clearance of ucMSC(VitB 6 ), ucMSC(Starv + VitB 6 ) and ucMSC(MC) and altered bio-distribution of ucMSC(TGFβ) compared to untreated ucMSC was observed. In the ex vivo co-culture system with inflammatory liver slices ucMSC(MC) showed significantly enhanced modulatory capacity compared to untreated ucMSC. The present study demonstrates the responsiveness of ucMSC to in vitro optimisation treatment. The observed improvements in immunomodulatory capacity as well as immunogenicity after MC treatment may improve the efficacy of ucMSC as immunotherapy targeted towards liver inflammation.

Covering Chemical Diversity of Genetically-Modified Tomatoes Using Metabolomics for Objective Substantial Equivalence Assessment

PubMed Central

Hirai, Tadayoshi; Oikawa, Akira; Matsuda, Fumio; Fukushima, Atsushi; Arita, Masanori; Watanabe, Shin; Yano, Megumu; Hiwasa-Tanase, Kyoko; Ezura, Hiroshi; Saito, Kazuki

2011-01-01

As metabolomics can provide a biochemical snapshot of an organism's phenotype it is a promising approach for charting the unintended effects of genetic modification. A critical obstacle for this application is the inherently limited metabolomic coverage of any single analytical platform. We propose using multiple analytical platforms for the direct acquisition of an interpretable data set of estimable chemical diversity. As an example, we report an application of our multi-platform approach that assesses the substantial equivalence of tomatoes over-expressing the taste-modifying protein miraculin. In combination, the chosen platforms detected compounds that represent 86% of the estimated chemical diversity of the metabolites listed in the LycoCyc database. Following a proof-of-safety approach, we show that % had an acceptable range of variation while simultaneously indicating a reproducible transformation-related metabolic signature. We conclude that multi-platform metabolomics is an approach that is both sensitive and robust and that it constitutes a good starting point for characterizing genetically modified organisms. PMID:21359231

C to VHDL compiler

NASA Astrophysics Data System (ADS)

Berdychowski, Piotr P.; Zabolotny, Wojciech M.

2010-09-01

The main goal of C to VHDL compiler project is to make FPGA platform more accessible for scientists and software developers. FPGA platform offers unique ability to configure the hardware to implement virtually any dedicated architecture, and modern devices provide sufficient number of hardware resources to implement parallel execution platforms with complex processing units. All this makes the FPGA platform very attractive for those looking for efficient heterogeneous, computing environment. Current industry standard in development of digital systems on FPGA platform is based on HDLs. Although very effective and expressive in hands of hardware development specialists, these languages require specific knowledge and experience, unreachable for most scientists and software programmers. C to VHDL compiler project attempts to remedy that by creating an application, that derives initial VHDL description of a digital system (for further compilation and synthesis), from purely algorithmic description in C programming language. This idea itself is not new, and the C to VHDL compiler combines the best approaches from existing solutions developed over many previous years, with the introduction of some new unique improvements.

Development of the hard and soft constraints based optimisation model for unit sizing of the hybrid renewable energy system designed for microgrid applications

NASA Astrophysics Data System (ADS)

Sundaramoorthy, Kumaravel

2017-02-01

The hybrid energy systems (HESs) based electricity generation system has become a more attractive solution for rural electrification nowadays. Economically feasible and technically reliable HESs are solidly based on an optimisation stage. This article discusses about the optimal unit sizing model with the objective function to minimise the total cost of the HES. Three typical rural sites from southern part of India have been selected for the application of the developed optimisation methodology. Feasibility studies and sensitivity analysis on the optimal HES are discussed elaborately in this article. A comparison has been carried out with the Hybrid Optimization Model for Electric Renewable optimisation model for three sites. The optimal HES is found with less total net present rate and rate of energy compared with the existing method

Optimisation of a Generic Ionic Model of Cardiac Myocyte Electrical Activity

PubMed Central

Guo, Tianruo; Al Abed, Amr; Lovell, Nigel H.; Dokos, Socrates

2013-01-01

A generic cardiomyocyte ionic model, whose complexity lies between a simple phenomenological formulation and a biophysically detailed ionic membrane current description, is presented. The model provides a user-defined number of ionic currents, employing two-gate Hodgkin-Huxley type kinetics. Its generic nature allows accurate reconstruction of action potential waveforms recorded experimentally from a range of cardiac myocytes. Using a multiobjective optimisation approach, the generic ionic model was optimised to accurately reproduce multiple action potential waveforms recorded from central and peripheral sinoatrial nodes and right atrial and left atrial myocytes from rabbit cardiac tissue preparations, under different electrical stimulus protocols and pharmacological conditions. When fitted simultaneously to multiple datasets, the time course of several physiologically realistic ionic currents could be reconstructed. Model behaviours tend to be well identified when extra experimental information is incorporated into the optimisation. PMID:23710254

Load-sensitive dynamic workflow re-orchestration and optimisation for faster patient healthcare.

PubMed

Meli, Christopher L; Khalil, Ibrahim; Tari, Zahir

2014-01-01

Hospital waiting times are considerably long, with no signs of reducing any-time soon. A number of factors including population growth, the ageing population and a lack of new infrastructure are expected to further exacerbate waiting times in the near future. In this work, we show how healthcare services can be modelled as queueing nodes, together with healthcare service workflows, such that these workflows can be optimised during execution in order to reduce patient waiting times. Services such as X-ray, computer tomography, and magnetic resonance imaging often form queues, thus, by taking into account the waiting times of each service, the workflow can be re-orchestrated and optimised. Experimental results indicate average waiting time reductions are achievable by optimising workflows using dynamic re-orchestration. Crown Copyright © 2013. Published by Elsevier Ireland Ltd. All rights reserved.

Optimal integrated management of groundwater resources and irrigated agriculture in arid coastal regions

NASA Astrophysics Data System (ADS)

Grundmann, J.; Schütze, N.; Heck, V.

2014-09-01

Groundwater systems in arid coastal regions are particularly at risk due to limited potential for groundwater replenishment and increasing water demand, caused by a continuously growing population. For ensuring a sustainable management of those regions, we developed a new simulation-based integrated water management system. The management system unites process modelling with artificial intelligence tools and evolutionary optimisation techniques for managing both water quality and water quantity of a strongly coupled groundwater-agriculture system. Due to the large number of decision variables, a decomposition approach is applied to separate the original large optimisation problem into smaller, independent optimisation problems which finally allow for faster and more reliable solutions. It consists of an analytical inner optimisation loop to achieve a most profitable agricultural production for a given amount of water and an outer simulation-based optimisation loop to find the optimal groundwater abstraction pattern. Thereby, the behaviour of farms is described by crop-water-production functions and the aquifer response, including the seawater interface, is simulated by an artificial neural network. The methodology is applied exemplarily for the south Batinah re-gion/Oman, which is affected by saltwater intrusion into a coastal aquifer system due to excessive groundwater withdrawal for irrigated agriculture. Due to contradicting objectives like profit-oriented agriculture vs aquifer sustainability, a multi-objective optimisation is performed which can provide sustainable solutions for water and agricultural management over long-term periods at farm and regional scales in respect of water resources, environment, and socio-economic development.

Optimisation of Fabric Reinforced Polymer Composites Using a Variant of Genetic Algorithm

NASA Astrophysics Data System (ADS)

Axinte, Andrei; Taranu, Nicolae; Bejan, Liliana; Hudisteanu, Iuliana

2017-12-01

Fabric reinforced polymeric composites are high performance materials with a rather complex fabric geometry. Therefore, modelling this type of material is a cumbersome task, especially when an efficient use is targeted. One of the most important issue of its design process is the optimisation of the individual laminae and of the laminated structure as a whole. In order to do that, a parametric model of the material has been defined, emphasising the many geometric variables needed to be correlated in the complex process of optimisation. The input parameters involved in this work, include: widths or heights of the tows and the laminate stacking sequence, which are discrete variables, while the gaps between adjacent tows and the height of the neat matrix are continuous variables. This work is one of the first attempts of using a Genetic Algorithm ( GA) to optimise the geometrical parameters of satin reinforced multi-layer composites. Given the mixed type of the input parameters involved, an original software called SOMGA (Satin Optimisation with a Modified Genetic Algorithm) has been conceived and utilised in this work. The main goal is to find the best possible solution to the problem of designing a composite material which is able to withstand to a given set of external, in-plane, loads. The optimisation process has been performed using a fitness function which can analyse and compare mechanical behaviour of different fabric reinforced composites, the results being correlated with the ultimate strains, which demonstrate the efficiency of the composite structure.

Robustness analysis of bogie suspension components Pareto optimised values

NASA Astrophysics Data System (ADS)

Mousavi Bideleh, Seyed Milad

2017-08-01

Bogie suspension system of high speed trains can significantly affect vehicle performance. Multiobjective optimisation problems are often formulated and solved to find the Pareto optimised values of the suspension components and improve cost efficiency in railway operations from different perspectives. Uncertainties in the design parameters of suspension system can negatively influence the dynamics behaviour of railway vehicles. In this regard, robustness analysis of a bogie dynamics response with respect to uncertainties in the suspension design parameters is considered. A one-car railway vehicle model with 50 degrees of freedom and wear/comfort Pareto optimised values of bogie suspension components is chosen for the analysis. Longitudinal and lateral primary stiffnesses, longitudinal and vertical secondary stiffnesses, as well as yaw damping are considered as five design parameters. The effects of parameter uncertainties on wear, ride comfort, track shift force, stability, and risk of derailment are studied by varying the design parameters around their respective Pareto optimised values according to a lognormal distribution with different coefficient of variations (COVs). The robustness analysis is carried out based on the maximum entropy concept. The multiplicative dimensional reduction method is utilised to simplify the calculation of fractional moments and improve the computational efficiency. The results showed that the dynamics response of the vehicle with wear/comfort Pareto optimised values of bogie suspension is robust against uncertainties in the design parameters and the probability of failure is small for parameter uncertainties with COV up to 0.1.

Expressive Arts Project for Young Children with Disabilities. Final Report.

ERIC Educational Resources Information Center

Hutinger, Patricia L.

This final report describes activities and accomplishments of the Expressive Arts Project for Young Children with Disabilities, which developed and evaluated a CD-ROM, ArtSpace. The program, developed on a Macintosh platform, allows the child to either view or make art. It offers real time video, music especially produced to accompany images,…

RNase One Gene Isolation, Expression, and Affinity Purification Models Research Experimental Progression and Culminates with Guided Inquiry-Based Experiments

ERIC Educational Resources Information Center

Bailey, Cheryl P.

2009-01-01

This new biochemistry laboratory course moves through a progression of experiments that generates a platform for guided inquiry-based experiments. RNase One gene is isolated from prokaryotic genomic DNA, expressed as a tagged protein, affinity purified, and tested for activity and substrate specificity. Student pairs present detailed explanations…

PET/PDT theranostics: synthesis and biological evaluation of a peptide-targeted gallium porphyrin.

PubMed

Bryden, Francesca; Savoie, Huguette; Rosca, Elena V; Boyle, Ross W

2015-03-21

The development of novel theranostic agents is an important step in the pathway towards personalised medicine, with the combination of diagnostic and therapeutic modalities into a single treatment agent naturally lending itself to the optimisation and personalisation of treatment. In pursuit of the goal of a molecular theranostic suitable for use as a PET radiotracer and a photosensitiser for PDT, a novel radiolabelled peptide-porphyrin conjugate targeting the α6β1-integrin has been developed. (69/71)Ga and (68)Ga labelling of an azide-functionalised porphyrin has been carried out in excellent yields, with subsequent bioconjugation to an alkyne-functionalised peptide demonstrated. α6β1-integrin expression of two cell lines has been evaluated by flow cytometry, and therapeutic potential of the conjugate demonstrated. Evaluation of the phototoxicity of the porphyrin-peptide theranostic conjugate in comparison to an untargeted control porphyrin in vitro, demonstrated significantly enhanced activity for a cell line with higher α6β1-integrin expression when compared with a cell line exhibiting lower α6β1-integrin expression.

Global preamplification simplifies targeted mRNA quantification

PubMed Central

Kroneis, Thomas; Jonasson, Emma; Andersson, Daniel; Dolatabadi, Soheila; Ståhlberg, Anders

2017-01-01

The need to perform gene expression profiling using next generation sequencing and quantitative real-time PCR (qPCR) on small sample sizes and single cells is rapidly expanding. However, to analyse few molecules, preamplification is required. Here, we studied global and target-specific preamplification using 96 optimised qPCR assays. To evaluate the preamplification strategies, we monitored the reactions in real-time using SYBR Green I detection chemistry followed by melting curve analysis. Next, we compared yield and reproducibility of global preamplification to that of target-specific preamplification by qPCR using the same amount of total RNA. Global preamplification generated 9.3-fold lower yield and 1.6-fold lower reproducibility than target-specific preamplification. However, the performance of global preamplification is sufficient for most downstream applications and offers several advantages over target-specific preamplification. To demonstrate the potential of global preamplification we analysed the expression of 15 genes in 60 single cells. In conclusion, we show that global preamplification simplifies targeted gene expression profiling of small sample sizes by a flexible workflow. We outline the pros and cons for global preamplification compared to target-specific preamplification. PMID:28332609

Spotting and validation of a genome wide oligonucleotide chip with duplicate measurement of each gene

DOE Office of Scientific and Technical Information (OSTI.GOV)

Thomassen, Mads; Skov, Vibe; Eiriksdottir, Freyja

2006-06-16

The quality of DNA microarray based gene expression data relies on the reproducibility of several steps in a microarray experiment. We have developed a spotted genome wide microarray chip with oligonucleotides printed in duplicate in order to minimise undesirable biases, thereby optimising detection of true differential expression. The validation study design consisted of an assessment of the microarray chip performance using the MessageAmp and FairPlay labelling kits. Intraclass correlation coefficient (ICC) was used to demonstrate that MessageAmp was significantly more reproducible than FairPlay. Further examinations with MessageAmp revealed the applicability of the system. The linear range of the chips wasmore » three orders of magnitude, the precision was high, as 95% of measurements deviated less than 1.24-fold from the expected value, and the coefficient of variation for relative expression was 13.6%. Relative quantitation was more reproducible than absolute quantitation and substantial reduction of variance was attained with duplicate spotting. An analysis of variance (ANOVA) demonstrated no significant day-to-day variation.« less

Neurotrophin Expression in Lymphocytes: a Powerful Indicator of Degeneration in Parkinson's Disease, Amyotrophic Lateral Sclerosis and Ataxia.

PubMed

Sadanand, Anjana; Janardhanan, Anjali; Vanisree, A J; Pavai, Thamil

2018-02-01

Deregulated neurotrophin is an etiological factor in the pathology of neurodegenerative diseases (ND) that are clinically different entities but characterised by similar limb dysfunction. Earlier validation of peripheral biomarkers can provide significant translational benefit to ND patients. We analysed brain-derived neurotrophic factor (BDNF)-tropomyosin possessing tyrosine-related kinase (Trk B) and its key downstream proteins which are implicated in ND such as Parkinson's disease (PD), amyotrophic lateral sclerosis (ALS) and ataxia. Blood from ND patients with PD, ALS and Ataxia with movement dysfunctions were obtained to analyse mRNA and protein expressions of the above mentioned factors in lymphocytes. The mRNA and protein expression of BDNF-Trk B and its key downstream molecules showed a significant variation when compared to control and among NDs. The study intends to show that on identifying the variation of these key molecules in the blood samples of patients with ND can serve as early diagnostic candidates. Thus by intervening, the neurotrophins and their pathways can help in early diagnosis and optimising levels of diagnostic certainty.

Cdk1 activity acts as a quantitative platform for coordinating cell cycle progression with periodic transcription

PubMed Central

Banyai, Gabor; Baïdi, Feriel; Coudreuse, Damien; Szilagyi, Zsolt

2016-01-01

Cell proliferation is regulated by cyclin-dependent kinases (Cdks) and requires the periodic expression of particular gene clusters in different cell cycle phases. However, the interplay between the networks that generate these transcriptional oscillations and the core cell cycle machinery remains largely unexplored. In this work, we use a synthetic regulable Cdk1 module to demonstrate that periodic expression is governed by quantitative changes in Cdk1 activity, with different clusters directly responding to specific activity levels. We further establish that cell cycle events neither participate in nor interfere with the Cdk1-driven transcriptional program, provided that cells are exposed to the appropriate Cdk1 activities. These findings contrast with current models that propose self-sustained and Cdk1-independent transcriptional oscillations. Our work therefore supports a model in which Cdk1 activity serves as a quantitative platform for coordinating cell cycle transitions with the expression of critical genes to bring about proper cell cycle progression. PMID:27045731

Cross-platform normalization of microarray and RNA-seq data for machine learning applications

PubMed Central

Thompson, Jeffrey A.; Tan, Jie

2016-01-01

Large, publicly available gene expression datasets are often analyzed with the aid of machine learning algorithms. Although RNA-seq is increasingly the technology of choice, a wealth of expression data already exist in the form of microarray data. If machine learning models built from legacy data can be applied to RNA-seq data, larger, more diverse training datasets can be created and validation can be performed on newly generated data. We developed Training Distribution Matching (TDM), which transforms RNA-seq data for use with models constructed from legacy platforms. We evaluated TDM, as well as quantile normalization, nonparanormal transformation, and a simple log2 transformation, on both simulated and biological datasets of gene expression. Our evaluation included both supervised and unsupervised machine learning approaches. We found that TDM exhibited consistently strong performance across settings and that quantile normalization also performed well in many circumstances. We also provide a TDM package for the R programming language. PMID:26844019

Reservoir optimisation using El Niño information. Case study of Daule Peripa (Ecuador)

NASA Astrophysics Data System (ADS)

Gelati, Emiliano; Madsen, Henrik; Rosbjerg, Dan

2010-05-01

The optimisation of water resources systems requires the ability to produce runoff scenarios that are consistent with available climatic information. We approach stochastic runoff modelling with a Markov-modulated autoregressive model with exogenous input, which belongs to the class of Markov-switching models. The model assumes runoff parameterisation to be conditioned on a hidden climatic state following a Markov chain, whose state transition probabilities depend on climatic information. This approach allows stochastic modeling of non-stationary runoff, as runoff anomalies are described by a mixture of autoregressive models with exogenous input, each one corresponding to a climate state. We calibrate the model on the inflows of the Daule Peripa reservoir located in western Ecuador, where the occurrence of El Niño leads to anomalously heavy rainfall caused by positive sea surface temperature anomalies along the coast. El Niño - Southern Oscillation (ENSO) information is used to condition the runoff parameterisation. Inflow predictions are realistic, especially at the occurrence of El Niño events. The Daule Peripa reservoir serves a hydropower plant and a downstream water supply facility. Using historical ENSO records, synthetic monthly inflow scenarios are generated for the period 1950-2007. These scenarios are used as input to perform stochastic optimisation of the reservoir rule curves with a multi-objective Genetic Algorithm (MOGA). The optimised rule curves are assumed to be the reservoir base policy. ENSO standard indices are currently forecasted at monthly time scale with nine-month lead time. These forecasts are used to perform stochastic optimisation of reservoir releases at each monthly time step according to the following procedure: (i) nine-month inflow forecast scenarios are generated using ENSO forecasts; (ii) a MOGA is set up to optimise the upcoming nine monthly releases; (iii) the optimisation is carried out by simulating the releases on the inflow forecasts, and by applying the base policy on a subsequent synthetic inflow scenario in order to account for long-term costs; (iv) the optimised release for the first month is implemented; (v) the state of the system is updated and (i), (ii), (iii), and (iv) are iterated for the following time step. The results highlight the advantages of using a climate-driven stochastic model to produce inflow scenarios and forecasts for reservoir optimisation, showing potential improvements with respect to the current management. Dynamic programming was used to find the best possible release time series given the inflow observations, in order to benchmark any possible operational improvement.

Cancer theranostics: Multifunctional gold nanoparticles for diagnostics and therapy

NASA Astrophysics Data System (ADS)

Conde, Joao Diogo Osorio de Castro

The use of gold nanoparticles (AuNPs) has been gaining momentum in molecular diagnostics due to their unique physico-chemical properties these systems present huge advantages, such as increased sensitivity, reduced cost and potential for single-molecule characterisation. Because of their versatility and easy of functionalisation, multifunctional AuNPs have also been proposed as optimal delivery systems for therapy (nanovectors). Being able to produce such systems would mean the dawn of a new age in theranostics (diagnostics and therapy)driven by nanotechnology vehicles. Nanotechnology can be exploit for cancer theranostics via the development of diagnostics systems such as colorimetric and imunoassays, and in therapy approaches through gene therapy, drug delivery and tumour targeting systems. The unique characteristics of nanoparticles in the nanometre range, such as high surface-tovolume ratio or shape/size-dependent optical properties, are drastically different from those of their bulk materials and hold pledge in the clinical field for disease therapeutics. This PhD project intends to optimise a gold-nanoparticle based technique for the detection of oncogenes' transcripts (c-Myc and BCR-ABL) that can be used for the evaluation of the expression profile in cancer cells, while simultaneously developing an innovative platform of multifunctional gold nanoparticles (tumour markers, cell penetrating peptides, fluorescent dyes) loaded with siRNA capable of silencing the selected proto-oncogenes, which can be used to evaluate the level of expression and determine the efficiency of silencing. In order to achieve this goal we developed effective conjugation strategies to combine, in a highly controlled way, biomolecules to the surface of AuNPs with specific functions such as: ssDNA oligos to detect specific sequences and for mRNA quantification; Biofunctional spacers: Poly(ethylene glycol) (PEG) spacers used to increase solubility and biocompatibility and confer chemical functionality; Cell penetrating peptides: to overcome the lipophilic barrier of the cellular membranes and deliver molecules into cells using TAT peptide to achieve cytoplasm and nucleus; Quaternary ammonium: to introduce stable positively charged in gold nanoparticles surface; and RNA interference: siRNA complementary to a master regulator gene, the proto-oncogene c-Myc, that is implicated in cell growth, proliferation, loss of differentiation, and cell death. In order to establish that they are viable alternatives to the available methods, these innovative nanoparticles were extensively characterized on their chemical functionalization, ease of uptake, cellular toxicity and inflammation, and knockdown of MYC protein expression in several cancer cell lines and in in vivo models.

The Imperative to Integrate Air Force Command and Control Systems into Maritime Plans

DTIC Science & Technology

2014-08-01

coopera- tion with existing C2 plans? Table. Components of C2 systems and plans C2 Systems C2 Plans People Competencies Platforms Technologies Doctrine...Intent Authorities Functions Tasks Effects C2 Systems The requirements for such a system can be expressed in terms of its components: people ...competencies, platforms, technologies, and doc- trine. The people connect to the human elements of war and leverage their particular knowledge and skills that

On the dynamic rounding-off in analogue and RF optimal circuit sizing

NASA Astrophysics Data System (ADS)

Kotti, Mouna; Fakhfakh, Mourad; Fino, Maria Helena

2014-04-01

Frequently used approaches to solve discrete multivariable optimisation problems consist of computing solutions using a continuous optimisation technique. Then, using heuristics, the variables are rounded-off to their nearest available discrete values to obtain a discrete solution. Indeed, in many engineering problems, and particularly in analogue circuit design, component values, such as the geometric dimensions of the transistors, the number of fingers in an integrated capacitor or the number of turns in an integrated inductor, cannot be chosen arbitrarily since they have to obey to some technology sizing constraints. However, rounding-off the variables values a posteriori and can lead to infeasible solutions (solutions that are located too close to the feasible solution frontier) or degradation of the obtained results (expulsion from the neighbourhood of a 'sharp' optimum) depending on how the added perturbation affects the solution. Discrete optimisation techniques, such as the dynamic rounding-off technique (DRO) are, therefore, needed to overcome the previously mentioned situation. In this paper, we deal with an improvement of the DRO technique. We propose a particle swarm optimisation (PSO)-based DRO technique, and we show, via some analog and RF-examples, the necessity to implement such a routine into continuous optimisation algorithms.

PGA/MOEAD: a preference-guided evolutionary algorithm for multi-objective decision-making problems with interval-valued fuzzy preferences

NASA Astrophysics Data System (ADS)

Luo, Bin; Lin, Lin; Zhong, ShiSheng

2018-02-01

In this research, we propose a preference-guided optimisation algorithm for multi-criteria decision-making (MCDM) problems with interval-valued fuzzy preferences. The interval-valued fuzzy preferences are decomposed into a series of precise and evenly distributed preference-vectors (reference directions) regarding the objectives to be optimised on the basis of uniform design strategy firstly. Then the preference information is further incorporated into the preference-vectors based on the boundary intersection approach, meanwhile, the MCDM problem with interval-valued fuzzy preferences is reformulated into a series of single-objective optimisation sub-problems (each sub-problem corresponds to a decomposed preference-vector). Finally, a preference-guided optimisation algorithm based on MOEA/D (multi-objective evolutionary algorithm based on decomposition) is proposed to solve the sub-problems in a single run. The proposed algorithm incorporates the preference-vectors within the optimisation process for guiding the search procedure towards a more promising subset of the efficient solutions matching the interval-valued fuzzy preferences. In particular, lots of test instances and an engineering application are employed to validate the performance of the proposed algorithm, and the results demonstrate the effectiveness and feasibility of the algorithm.

Optimisation of the Management of Higher Activity Waste in the UK - 13537

DOE Office of Scientific and Technical Information (OSTI.GOV)

Walsh, Ciara; Buckley, Matthew

2013-07-01

The Upstream Optioneering project was created in the Nuclear Decommissioning Authority (UK) to support the development and implementation of significant opportunities to optimise activities across all the phases of the Higher Activity Waste management life cycle (i.e. retrieval, characterisation, conditioning, packaging, storage, transport and disposal). The objective of the Upstream Optioneering project is to work in conjunction with other functions within NDA and the waste producers to identify and deliver solutions to optimise the management of higher activity waste. Historically, optimisation may have occurred on aspects of the waste life cycle (considered here to include retrieval, conditioning, treatment, packaging, interimmore » storage, transport to final end state, which may be geological disposal). By considering the waste life cycle as a whole, critical analysis of assumed constraints may lead to cost savings for the UK Tax Payer. For example, it may be possible to challenge the requirements for packaging wastes for disposal to deliver an optimised waste life cycle. It is likely that the challenges faced in the UK are shared in other countries. It is therefore likely that the opportunities identified may also apply elsewhere, with the potential for sharing information to enable value to be shared. (authors)« less

Optimisation of active suspension control inputs for improved performance of active safety systems

NASA Astrophysics Data System (ADS)

Čorić, Mirko; Deur, Joško; Xu, Li; Tseng, H. Eric; Hrovat, Davor

2018-01-01

A collocation-type control variable optimisation method is used to investigate the extent to which the fully active suspension (FAS) can be applied to improve the vehicle electronic stability control (ESC) performance and reduce the braking distance. First, the optimisation approach is applied to the scenario of vehicle stabilisation during the sine-with-dwell manoeuvre. The results are used to provide insights into different FAS control mechanisms for vehicle performance improvements related to responsiveness and yaw rate error reduction indices. The FAS control performance is compared to performances of the standard ESC system, optimal active brake system and combined FAS and ESC configuration. Second, the optimisation approach is employed to the task of FAS-based braking distance reduction for straight-line vehicle motion. Here, the scenarios of uniform and longitudinally or laterally non-uniform tyre-road friction coefficient are considered. The influences of limited anti-lock braking system (ABS) actuator bandwidth and limit-cycle ABS behaviour are also analysed. The optimisation results indicate that the FAS can provide competitive stabilisation performance and improved agility when compared to the ESC system, and that it can reduce the braking distance by up to 5% for distinctively non-uniform friction conditions.

Design optimisation of powers-of-two FIR filter using self-organising random immigrants GA

NASA Astrophysics Data System (ADS)

Chandra, Abhijit; Chattopadhyay, Sudipta

2015-01-01

In this communication, we propose a novel design strategy of multiplier-less low-pass finite impulse response (FIR) filter with the aid of a recent evolutionary optimisation technique, known as the self-organising random immigrants genetic algorithm. Individual impulse response coefficients of the proposed filter have been encoded as sum of signed powers-of-two. During the formulation of the cost function for the optimisation algorithm, both the frequency response characteristic and the hardware cost of the discrete coefficient FIR filter have been considered. The role of crossover probability of the optimisation technique has been evaluated on the overall performance of the proposed strategy. For this purpose, the convergence characteristic of the optimisation technique has been included in the simulation results. In our analysis, two design examples of different specifications have been taken into account. In order to substantiate the efficiency of our proposed structure, a number of state-of-the-art design strategies of multiplier-less FIR filter have also been included in this article for the purpose of comparison. Critical analysis of the result unambiguously establishes the usefulness of our proposed approach for the hardware efficient design of digital filter.

A New Multiconstraint Method for Determining the Optimal Cable Stresses in Cable-Stayed Bridges

PubMed Central

Asgari, B.; Osman, S. A.; Adnan, A.

2014-01-01

Cable-stayed bridges are one of the most popular types of long-span bridges. The structural behaviour of cable-stayed bridges is sensitive to the load distribution between the girder, pylons, and cables. The determination of pretensioning cable stresses is critical in the cable-stayed bridge design procedure. By finding the optimum stresses in cables, the load and moment distribution of the bridge can be improved. In recent years, different research works have studied iterative and modern methods to find optimum stresses of cables. However, most of the proposed methods have limitations in optimising the structural performance of cable-stayed bridges. This paper presents a multiconstraint optimisation method to specify the optimum cable forces in cable-stayed bridges. The proposed optimisation method produces less bending moments and stresses in the bridge members and requires shorter simulation time than other proposed methods. The results of comparative study show that the proposed method is more successful in restricting the deck and pylon displacements and providing uniform deck moment distribution than unit load method (ULM). The final design of cable-stayed bridges can be optimised considerably through proposed multiconstraint optimisation method. PMID:25050400

A new multiconstraint method for determining the optimal cable stresses in cable-stayed bridges.

PubMed

Asgari, B; Osman, S A; Adnan, A

2014-01-01

Cable-stayed bridges are one of the most popular types of long-span bridges. The structural behaviour of cable-stayed bridges is sensitive to the load distribution between the girder, pylons, and cables. The determination of pretensioning cable stresses is critical in the cable-stayed bridge design procedure. By finding the optimum stresses in cables, the load and moment distribution of the bridge can be improved. In recent years, different research works have studied iterative and modern methods to find optimum stresses of cables. However, most of the proposed methods have limitations in optimising the structural performance of cable-stayed bridges. This paper presents a multiconstraint optimisation method to specify the optimum cable forces in cable-stayed bridges. The proposed optimisation method produces less bending moments and stresses in the bridge members and requires shorter simulation time than other proposed methods. The results of comparative study show that the proposed method is more successful in restricting the deck and pylon displacements and providing uniform deck moment distribution than unit load method (ULM). The final design of cable-stayed bridges can be optimised considerably through proposed multiconstraint optimisation method.

Optimisation and validation of a rapid and efficient microemulsion liquid chromatographic (MELC) method for the determination of paracetamol (acetaminophen) content in a suppository formulation.

PubMed

McEvoy, Eamon; Donegan, Sheila; Power, Joe; Altria, Kevin

2007-05-09

A rapid and efficient oil-in-water microemulsion liquid chromatographic method has been optimised and validated for the analysis of paracetamol in a suppository formulation. Excellent linearity, accuracy, precision and assay results were obtained. Lengthy sample pre-treatment/extraction procedures were eliminated due to the solubilising power of the microemulsion and rapid analysis times were achieved. The method was optimised to achieve rapid analysis time and relatively high peak efficiencies. A standard microemulsion composition of 33 g SDS, 66 g butan-1-ol, 8 g n-octane in 1l of 0.05% TFA modified with acetonitrile has been shown to be suitable for the rapid analysis of paracetamol in highly hydrophobic preparations under isocratic conditions. Validated assay results and overall analysis time of the optimised method was compared to British Pharmacopoeia reference methods. Sample preparation and analysis times for the MELC analysis of paracetamol in a suppository were extremely rapid compared to the reference method and similar assay results were achieved. A gradient MELC method using the same microemulsion has been optimised for the resolution of paracetamol and five of its related substances in approximately 7 min.

Optimisation of the supercritical extraction of toxic elements in fish oil.

PubMed

Hajeb, P; Jinap, S; Shakibazadeh, Sh; Afsah-Hejri, L; Mohebbi, G H; Zaidul, I S M

2014-01-01

This study aims to optimise the operating conditions for the supercritical fluid extraction (SFE) of toxic elements from fish oil. The SFE operating parameters of pressure, temperature, CO2 flow rate and extraction time were optimised using a central composite design (CCD) of response surface methodology (RSM). High coefficients of determination (R²) (0.897-0.988) for the predicted response surface models confirmed a satisfactory adjustment of the polynomial regression models with the operation conditions. The results showed that the linear and quadratic terms of pressure and temperature were the most significant (p < 0.05) variables affecting the overall responses. The optimum conditions for the simultaneous elimination of toxic elements comprised a pressure of 61 MPa, a temperature of 39.8ºC, a CO₂ flow rate of 3.7 ml min⁻¹ and an extraction time of 4 h. These optimised SFE conditions were able to produce fish oil with the contents of lead, cadmium, arsenic and mercury reduced by up to 98.3%, 96.1%, 94.9% and 93.7%, respectively. The fish oil extracted under the optimised SFE operating conditions was of good quality in terms of its fatty acid constituents.

Group search optimiser-based optimal bidding strategies with no Karush-Kuhn-Tucker optimality conditions

NASA Astrophysics Data System (ADS)

Yadav, Naresh Kumar; Kumar, Mukesh; Gupta, S. K.

2017-03-01

General strategic bidding procedure has been formulated in the literature as a bi-level searching problem, in which the offer curve tends to minimise the market clearing function and to maximise the profit. Computationally, this is complex and hence, the researchers have adopted Karush-Kuhn-Tucker (KKT) optimality conditions to transform the model into a single-level maximisation problem. However, the profit maximisation problem with KKT optimality conditions poses great challenge to the classical optimisation algorithms. The problem has become more complex after the inclusion of transmission constraints. This paper simplifies the profit maximisation problem as a minimisation function, in which the transmission constraints, the operating limits and the ISO market clearing functions are considered with no KKT optimality conditions. The derived function is solved using group search optimiser (GSO), a robust population-based optimisation algorithm. Experimental investigation is carried out on IEEE 14 as well as IEEE 30 bus systems and the performance is compared against differential evolution-based strategic bidding, genetic algorithm-based strategic bidding and particle swarm optimisation-based strategic bidding methods. The simulation results demonstrate that the obtained profit maximisation through GSO-based bidding strategies is higher than the other three methods.

Oracle Database 10g: a platform for BLAST search and Regular Expression pattern matching in life sciences

PubMed Central

Stephens, Susie M.; Chen, Jake Y.; Davidson, Marcel G.; Thomas, Shiby; Trute, Barry M.

2005-01-01

As database management systems expand their array of analytical functionality, they become powerful research engines for biomedical data analysis and drug discovery. Databases can hold most of the data types commonly required in life sciences and consequently can be used as flexible platforms for the implementation of knowledgebases. Performing data analysis in the database simplifies data management by minimizing the movement of data from disks to memory, allowing pre-filtering and post-processing of datasets, and enabling data to remain in a secure, highly available environment. This article describes the Oracle Database 10g implementation of BLAST and Regular Expression Searches and provides case studies of their usage in bioinformatics. http://www.oracle.com/technology/software/index.html PMID:15608287

Effect of Ganoderma Lucidum Preparation on the Behavior,Biochemistry,and Autoimmune Parameters of Mouse Models of APP/PS1 Double Transgenic Alzheimer's Disease.

PubMed

Qin, Chuan; Wu, Shanqiu; Chen, Baosheng; Wu, Xiaoxian; Qu, Kunyao; Liu, Junmin; Zhang, Guifang; Xu, Yanfeng; Shu, Shunli; Sun, Lihua; Li, Yanhong; Zhu, Hua; Huang, Lan; Ma, Chunmei; Xu, Yuhuan; Han, Yunlin; Lu, Yaozeng

2017-06-20

Objective To evaluate the efficacy of Ganoderma lucidum preparation on the behaviors,biochemistry,and autoimmunity parameters of mouse models of APP/PS-1 double transgenic Alzheimer's disease(AD).Methods A total of 44 4-month-old APP/PS-1 double transgenic AD mice were randomly divided into AD model group,Aricept group,Ganoderma lucidum middle-dose(LZ-M)group,and Ganoderma lucidum high-dose(LZ-H)group,with 11 mice in each group.In addition,10 4-month-old C57BL/6 mice were used as the control group.Water maze test was conducted to observe the behavior changes,and the protein expressions in brain tissues were detected by Western blot analysis.The autoimmune indicators were detected by indirect immunofluorescence method.Results In the navigation experiment,the time of finding the platform was gradually shortened since the 2 nd day in the control,LZ-H,and LZ-M groups,and the time of searching the platform in the AD model group gradually increased.On the 5 th day,the time of finding platform was significantly shorter in control group (t=5.607,P=0.000) and LZ-H group(t=2.750,P=0.010)than AD model group.In the space exploration experiment,the number of crossing the target platform(t=2.452,P=0.025)and the residence time in the target quadrant(t=2.530,P=0.020)in AD model group mice was significantly smaller/shorter than those in control group;in addition,the number of crossing the target platform in the AD model group was significantly smaller than that in LZ-H group(t=2.317,P=0.030)and LZ-M group(t=2.443,P=0.030),while the residence time in target quadrant decreased significantly(t=2.770,P=0.020)compared with LZ-H group;the number of crossing through the target platform quadrant(t=2.493,P=0.022)and residence time in the target quadrant(t=2.683,P=0.015)in LZ-H group were significantly higher than in Aricept group.Western blot analysis showed that the expression of ApoA1 in the brain tissues of mice in LZ-H and LZ-M groups were significantly higher than those in AD model group(P<0.01,P<0.05);Aβ-40 expression in LZ-H group was significantly lower than that in AD model group(P<0.05);the expressions of Syt1,ApoE,and ABCA1 in brain tissues of mice in LZ-H group were significantly higher than those in model group(P<0.01,P<0.05).The plasma IgG level in Aricept group(t=30.945,P=0.000),LZ-M group(t=25.639,P=0.000)and LZ-H group(t=4.689,P=0.001)were significantly higher than that in the control group.Conclusion Ganoderma lucidum preparation can improve behavior disorders of AD model mice,promote the expressions of ApoA1,ApoE and Syt1,inhibit the expression of Aβ-40 protein,and improve the autoimmune function.

Teaching individuals with intellectual disability to email across multiple device platforms.

PubMed

Cihak, David F; McMahon, Donald; Smith, Cate C; Wright, Rachel; Gibbons, Melinda M

2014-11-20

The purpose of this study was to examine the use of email by people with intellectual disability across multiple technological devices or platforms. Four individuals with intellectual disability participated in this study. Participants were taught how to access and send an email on a Windows desktop computer, laptop, and an iPad tablet device. Results indicated a functional relation. All participants acquired and generalized sending and receiving an email from multiple platforms. Conclusions are discussed about the importance of empowering people with intellectual disability by providing multiple means of expression, including the ability to communicate effectively using a variety of devices. Copyright © 2014 Elsevier Ltd. All rights reserved.

Evolving aerodynamic airfoils for wind turbines through a genetic algorithm

NASA Astrophysics Data System (ADS)

Hernández, J. J.; Gómez, E.; Grageda, J. I.; Couder, C.; Solís, A.; Hanotel, C. L.; Ledesma, JI

2017-01-01

Nowadays, genetic algorithms stand out for airfoil optimisation, due to the virtues of mutation and crossing-over techniques. In this work we propose a genetic algorithm with arithmetic crossover rules. The optimisation criteria are taken to be the maximisation of both aerodynamic efficiency and lift coefficient, while minimising drag coefficient. Such algorithm shows greatly improvements in computational costs, as well as a high performance by obtaining optimised airfoils for Mexico City's specific wind conditions from generic wind turbines designed for higher Reynolds numbers, in few iterations.

Exemples d’utilisation des techniques d’optimisation en calcul de structures de reacteurs

DTIC Science & Technology

2003-03-01

34~ optimisation g~om~trique (architecture fig~e) A la difference du secteur automobile et des avionneurs, la plupart des composants des r~acteurs n...utilise des lois de comportement mat~riaux non lin~aires ainsi que des hypotheses de grands d~placements. L𔄀tude d’optimisation consiste ý minimiser...un disque simple et d~cid6 de s~lectionner trois param~tes qui influent sur la rupture : 1𔄀paisseur de la toile du disque ElI, la hauteur L3 et la

Self-optimisation and model-based design of experiments for developing a C-H activation flow process.

PubMed

Echtermeyer, Alexander; Amar, Yehia; Zakrzewski, Jacek; Lapkin, Alexei

2017-01-01

A recently described C(sp 3 )-H activation reaction to synthesise aziridines was used as a model reaction to demonstrate the methodology of developing a process model using model-based design of experiments (MBDoE) and self-optimisation approaches in flow. The two approaches are compared in terms of experimental efficiency. The self-optimisation approach required the least number of experiments to reach the specified objectives of cost and product yield, whereas the MBDoE approach enabled a rapid generation of a process model.

Development and validation of a flax (Linum usitatissimum L.) gene expression oligo microarray

PubMed Central

2010-01-01

Background Flax (Linum usitatissimum L.) has been cultivated for around 9,000 years and is therefore one of the oldest cultivated species. Today, flax is still grown for its oil (oil-flax or linseed cultivars) and its cellulose-rich fibres (fibre-flax cultivars) used for high-value linen garments and composite materials. Despite the wide industrial use of flax-derived products, and our actual understanding of the regulation of both wood fibre production and oil biosynthesis more information must be acquired in both domains. Recent advances in genomics are now providing opportunities to improve our fundamental knowledge of these complex processes. In this paper we report the development and validation of a high-density oligo microarray platform dedicated to gene expression analyses in flax. Results Nine different RNA samples obtained from flax inner- and outer-stems, seeds, leaves and roots were used to generate a collection of 1,066,481 ESTs by massive parallel pyrosequencing. Sequences were assembled into 59,626 unigenes and 48,021 sequences were selected for oligo design and high-density microarray (Nimblegen 385K) fabrication with eight, non-overlapping 25-mers oligos per unigene. 18 independent experiments were used to evaluate the hybridization quality, precision, specificity and accuracy and all results confirmed the high technical quality of our microarray platform. Cross-validation of microarray data was carried out using quantitative qRT-PCR. Nine target genes were selected on the basis of microarray results and reflected the whole range of fold change (both up-regulated and down-regulated genes in different samples). A statistically significant positive correlation was obtained comparing expression levels for each target gene across all biological replicates both in qRT-PCR and microarray results. Further experiments illustrated the capacity of our arrays to detect differential gene expression in a variety of flax tissues as well as between two contrasted flax varieties. Conclusion All results suggest that our high-density flax oligo-microarray platform can be used as a very sensitive tool for analyzing gene expression in a large variety of tissues as well as in different cultivars. Moreover, this highly reliable platform can also be used for the quantification of mRNA transcriptional profiling in different flax tissues. PMID:20964859

Development and validation of a flax (Linum usitatissimum L.) gene expression oligo microarray.

PubMed

Fenart, Stéphane; Ndong, Yves-Placide Assoumou; Duarte, Jorge; Rivière, Nathalie; Wilmer, Jeroen; van Wuytswinkel, Olivier; Lucau, Anca; Cariou, Emmanuelle; Neutelings, Godfrey; Gutierrez, Laurent; Chabbert, Brigitte; Guillot, Xavier; Tavernier, Reynald; Hawkins, Simon; Thomasset, Brigitte

2010-10-21

Flax (Linum usitatissimum L.) has been cultivated for around 9,000 years and is therefore one of the oldest cultivated species. Today, flax is still grown for its oil (oil-flax or linseed cultivars) and its cellulose-rich fibres (fibre-flax cultivars) used for high-value linen garments and composite materials. Despite the wide industrial use of flax-derived products, and our actual understanding of the regulation of both wood fibre production and oil biosynthesis more information must be acquired in both domains. Recent advances in genomics are now providing opportunities to improve our fundamental knowledge of these complex processes. In this paper we report the development and validation of a high-density oligo microarray platform dedicated to gene expression analyses in flax. Nine different RNA samples obtained from flax inner- and outer-stems, seeds, leaves and roots were used to generate a collection of 1,066,481 ESTs by massive parallel pyrosequencing. Sequences were assembled into 59,626 unigenes and 48,021 sequences were selected for oligo design and high-density microarray (Nimblegen 385K) fabrication with eight, non-overlapping 25-mers oligos per unigene. 18 independent experiments were used to evaluate the hybridization quality, precision, specificity and accuracy and all results confirmed the high technical quality of our microarray platform. Cross-validation of microarray data was carried out using quantitative qRT-PCR. Nine target genes were selected on the basis of microarray results and reflected the whole range of fold change (both up-regulated and down-regulated genes in different samples). A statistically significant positive correlation was obtained comparing expression levels for each target gene across all biological replicates both in qRT-PCR and microarray results. Further experiments illustrated the capacity of our arrays to detect differential gene expression in a variety of flax tissues as well as between two contrasted flax varieties. All results suggest that our high-density flax oligo-microarray platform can be used as a very sensitive tool for analyzing gene expression in a large variety of tissues as well as in different cultivars. Moreover, this highly reliable platform can also be used for the quantification of mRNA transcriptional profiling in different flax tissues.

Identification of the contribution of contact and aerial biomechanical parameters in acrobatic performance

PubMed Central

Haering, Diane; Huchez, Aurore; Barbier, Franck; Holvoët, Patrice; Begon, Mickaël

2017-01-01

Introduction Teaching acrobatic skills with a minimal amount of repetition is a major challenge for coaches. Biomechanical, statistical or computer simulation tools can help them identify the most determinant factors of performance. Release parameters, change in moment of inertia and segmental momentum transfers were identified in the prediction of acrobatics success. The purpose of the present study was to evaluate the relative contribution of these parameters in performance throughout expertise or optimisation based improvements. The counter movement forward in flight (CMFIF) was chosen for its intrinsic dichotomy between the accessibility of its attempt and complexity of its mastery. Methods Three repetitions of the CMFIF performed by eight novice and eight advanced female gymnasts were recorded using a motion capture system. Optimal aerial techniques that maximise rotation potential at regrasp were also computed. A 14-segment-multibody-model defined through the Rigid Body Dynamics Library was used to compute recorded and optimal kinematics, and biomechanical parameters. A stepwise multiple linear regression was used to determine the relative contribution of these parameters in novice recorded, novice optimised, advanced recorded and advanced optimised trials. Finally, fixed effects of expertise and optimisation were tested through a mixed-effects analysis. Results and discussion Variation in release state only contributed to performances in novice recorded trials. Moment of inertia contribution to performance increased from novice recorded, to novice optimised, advanced recorded, and advanced optimised trials. Contribution to performance of momentum transfer to the trunk during the flight prevailed in all recorded trials. Although optimisation decreased transfer contribution, momentum transfer to the arms appeared. Conclusion Findings suggest that novices should be coached on both contact and aerial technique. Inversely, mainly improved aerial technique helped advanced gymnasts increase their performance. For both, reduction of the moment of inertia should be focused on. The method proposed in this article could be generalized to any aerial skill learning investigation. PMID:28422954

Multi-objective optimisation and decision-making of space station logistics strategies

NASA Astrophysics Data System (ADS)

Zhu, Yue-he; Luo, Ya-zhong

2016-10-01

Space station logistics strategy optimisation is a complex engineering problem with multiple objectives. Finding a decision-maker-preferred compromise solution becomes more significant when solving such a problem. However, the designer-preferred solution is not easy to determine using the traditional method. Thus, a hybrid approach that combines the multi-objective evolutionary algorithm, physical programming, and differential evolution (DE) algorithm is proposed to deal with the optimisation and decision-making of space station logistics strategies. A multi-objective evolutionary algorithm is used to acquire a Pareto frontier and help determine the range parameters of the physical programming. Physical programming is employed to convert the four-objective problem into a single-objective problem, and a DE algorithm is applied to solve the resulting physical programming-based optimisation problem. Five kinds of objective preference are simulated and compared. The simulation results indicate that the proposed approach can produce good compromise solutions corresponding to different decision-makers' preferences.

Cultural-based particle swarm for dynamic optimisation problems

NASA Astrophysics Data System (ADS)

Daneshyari, Moayed; Yen, Gary G.

2012-07-01

Many practical optimisation problems are with the existence of uncertainties, among which a significant number belong to the dynamic optimisation problem (DOP) category in which the fitness function changes through time. In this study, we propose the cultural-based particle swarm optimisation (PSO) to solve DOP problems. A cultural framework is adopted incorporating the required information from the PSO into five sections of the belief space, namely situational, temporal, domain, normative and spatial knowledge. The stored information will be adopted to detect the changes in the environment and assists response to the change through a diversity-based repulsion among particles and migration among swarms in the population space, and also helps in selecting the leading particles in three different levels, personal, swarm and global levels. Comparison of the proposed heuristics over several difficult dynamic benchmark problems demonstrates the better or equal performance with respect to most of other selected state-of-the-art dynamic PSO heuristics.

A shrinking hypersphere PSO for engineering optimisation problems

NASA Astrophysics Data System (ADS)

Yadav, Anupam; Deep, Kusum

2016-03-01

Many real-world and engineering design problems can be formulated as constrained optimisation problems (COPs). Swarm intelligence techniques are a good approach to solve COPs. In this paper an efficient shrinking hypersphere-based particle swarm optimisation (SHPSO) algorithm is proposed for constrained optimisation. The proposed SHPSO is designed in such a way that the movement of the particle is set to move under the influence of shrinking hyperspheres. A parameter-free approach is used to handle the constraints. The performance of the SHPSO is compared against the state-of-the-art algorithms for a set of 24 benchmark problems. An exhaustive comparison of the results is provided statistically as well as graphically. Moreover three engineering design problems namely welded beam design, compressed string design and pressure vessel design problems are solved using SHPSO and the results are compared with the state-of-the-art algorithms.

Achieving optimal SERS through enhanced experimental design

PubMed Central

Fisk, Heidi; Westley, Chloe; Turner, Nicholas J.

2016-01-01

One of the current limitations surrounding surface‐enhanced Raman scattering (SERS) is the perceived lack of reproducibility. SERS is indeed challenging, and for analyte detection, it is vital that the analyte interacts with the metal surface. However, as this is analyte dependent, there is not a single set of SERS conditions that are universal. This means that experimental optimisation for optimum SERS response is vital. Most researchers optimise one factor at a time, where a single parameter is altered first before going onto optimise the next. This is a very inefficient way of searching the experimental landscape. In this review, we explore the use of more powerful multivariate approaches to SERS experimental optimisation based on design of experiments and evolutionary computational methods. We particularly focus on colloidal‐based SERS rather than thin film preparations as a result of their popularity. © 2015 The Authors. Journal of Raman Spectroscopy published by John Wiley & Sons, Ltd. PMID:27587905

Microfluidic converging/diverging channels optimised for homogeneous extensional deformation.

PubMed

Zografos, K; Pimenta, F; Alves, M A; Oliveira, M S N

2016-07-01

In this work, we optimise microfluidic converging/diverging geometries in order to produce constant strain-rates along the centreline of the flow, for performing studies under homogeneous extension. The design is examined for both two-dimensional and three-dimensional flows where the effects of aspect ratio and dimensionless contraction length are investigated. Initially, pressure driven flows of Newtonian fluids under creeping flow conditions are considered, which is a reasonable approximation in microfluidics, and the limits of the applicability of the design in terms of Reynolds numbers are investigated. The optimised geometry is then used for studying the flow of viscoelastic fluids and the practical limitations in terms of Weissenberg number are reported. Furthermore, the optimisation strategy is also applied for electro-osmotic driven flows, where the development of a plug-like velocity profile allows for a wider region of homogeneous extensional deformation in the flow field.

Topology Optimisation of Wideband Coaxial-to-Waveguide Transitions

NASA Astrophysics Data System (ADS)

Hassan, Emadeldeen; Noreland, Daniel; Wadbro, Eddie; Berggren, Martin

2017-03-01

To maximize the matching between a coaxial cable and rectangular waveguides, we present a computational topology optimisation approach that decides for each point in a given domain whether to hold a good conductor or a good dielectric. The conductivity is determined by a gradient-based optimisation method that relies on finite-difference time-domain solutions to the 3D Maxwell’s equations. Unlike previously reported results in the literature for this kind of problems, our design algorithm can efficiently handle tens of thousands of design variables that can allow novel conceptual waveguide designs. We demonstrate the effectiveness of the approach by presenting optimised transitions with reflection coefficients lower than -15 dB over more than a 60% bandwidth, both for right-angle and end-launcher configurations. The performance of the proposed transitions is cross-verified with a commercial software, and one design case is validated experimentally.

Topology Optimisation of Wideband Coaxial-to-Waveguide Transitions.

PubMed

Hassan, Emadeldeen; Noreland, Daniel; Wadbro, Eddie; Berggren, Martin

2017-03-23

To maximize the matching between a coaxial cable and rectangular waveguides, we present a computational topology optimisation approach that decides for each point in a given domain whether to hold a good conductor or a good dielectric. The conductivity is determined by a gradient-based optimisation method that relies on finite-difference time-domain solutions to the 3D Maxwell's equations. Unlike previously reported results in the literature for this kind of problems, our design algorithm can efficiently handle tens of thousands of design variables that can allow novel conceptual waveguide designs. We demonstrate the effectiveness of the approach by presenting optimised transitions with reflection coefficients lower than -15 dB over more than a 60% bandwidth, both for right-angle and end-launcher configurations. The performance of the proposed transitions is cross-verified with a commercial software, and one design case is validated experimentally.

Strategic optimisation of microgrid by evolving a unitised regenerative fuel cell system operational criterion

NASA Astrophysics Data System (ADS)

Bhansali, Gaurav; Singh, Bhanu Pratap; Kumar, Rajesh

2016-09-01

In this paper, the problem of microgrid optimisation with storage has been addressed in an unaccounted way rather than confining it to loss minimisation. Unitised regenerative fuel cell (URFC) systems have been studied and employed in microgrids to store energy and feed it back into the system when required. A value function-dependent on line losses, URFC system operational cost and stored energy at the end of the day are defined here. The function is highly complex, nonlinear and multi dimensional in nature. Therefore, heuristic optimisation techniques in combination with load flow analysis are used here to resolve the network and time domain complexity related with the problem. Particle swarm optimisation with the forward/backward sweep algorithm ensures optimal operation of microgrid thereby minimising the operational cost of the microgrid. Results are shown and are found to be consistently improving with evolution of the solution strategy.

Optimal design and operation of a photovoltaic-electrolyser system using particle swarm optimisation

NASA Astrophysics Data System (ADS)

Sayedin, Farid; Maroufmashat, Azadeh; Roshandel, Ramin; Khavas, Sourena Sattari

2016-07-01

In this study, hydrogen generation is maximised by optimising the size and the operating conditions of an electrolyser (EL) directly connected to a photovoltaic (PV) module at different irradiance. Due to the variations of maximum power points of the PV module during a year and the complexity of the system, a nonlinear approach is considered. A mathematical model has been developed to determine the performance of the PV/EL system. The optimisation methodology presented here is based on the particle swarm optimisation algorithm. By this method, for the given number of PV modules, the optimal sizeand operating condition of a PV/EL system areachieved. The approach can be applied for different sizes of PV systems, various ambient temperatures and different locations with various climaticconditions. The results show that for the given location and the PV system, the energy transfer efficiency of PV/EL system can reach up to 97.83%.

Topology Optimisation of Wideband Coaxial-to-Waveguide Transitions

PubMed Central

Hassan, Emadeldeen; Noreland, Daniel; Wadbro, Eddie; Berggren, Martin

2017-01-01

To maximize the matching between a coaxial cable and rectangular waveguides, we present a computational topology optimisation approach that decides for each point in a given domain whether to hold a good conductor or a good dielectric. The conductivity is determined by a gradient-based optimisation method that relies on finite-difference time-domain solutions to the 3D Maxwell’s equations. Unlike previously reported results in the literature for this kind of problems, our design algorithm can efficiently handle tens of thousands of design variables that can allow novel conceptual waveguide designs. We demonstrate the effectiveness of the approach by presenting optimised transitions with reflection coefficients lower than −15 dB over more than a 60% bandwidth, both for right-angle and end-launcher configurations. The performance of the proposed transitions is cross-verified with a commercial software, and one design case is validated experimentally. PMID:28332585

VLSI Technology for Cognitive Radio

NASA Astrophysics Data System (ADS)

VIJAYALAKSHMI, B.; SIDDAIAH, P.

2017-08-01

One of the most challenging tasks of cognitive radio is the efficiency in the spectrum sensing scheme to overcome the spectrum scarcity problem. The popular and widely used spectrum sensing technique is the energy detection scheme as it is very simple and doesn’t require any previous information related to the signal. We propose one such approach which is an optimised spectrum sensing scheme with reduced filter structure. The optimisation is done in terms of area and power performance of the spectrum. The simulations of the VLSI structure of the optimised flexible spectrum is done using verilog coding by using the XILINX ISE software. Our method produces performance with 13% reduction in area and 66% reduction in power consumption in comparison to the flexible spectrum sensing scheme. All the results are tabulated and comparisons are made. A new scheme for optimised and effective spectrum sensing opens up with our model.

Achieving optimal SERS through enhanced experimental design.

PubMed

Fisk, Heidi; Westley, Chloe; Turner, Nicholas J; Goodacre, Royston

2016-01-01

One of the current limitations surrounding surface-enhanced Raman scattering (SERS) is the perceived lack of reproducibility. SERS is indeed challenging, and for analyte detection, it is vital that the analyte interacts with the metal surface. However, as this is analyte dependent, there is not a single set of SERS conditions that are universal. This means that experimental optimisation for optimum SERS response is vital. Most researchers optimise one factor at a time, where a single parameter is altered first before going onto optimise the next. This is a very inefficient way of searching the experimental landscape. In this review, we explore the use of more powerful multivariate approaches to SERS experimental optimisation based on design of experiments and evolutionary computational methods. We particularly focus on colloidal-based SERS rather than thin film preparations as a result of their popularity. © 2015 The Authors. Journal of Raman Spectroscopy published by John Wiley & Sons, Ltd.

A management and optimisation model for water supply planning in water deficit areas

NASA Astrophysics Data System (ADS)

Molinos-Senante, María; Hernández-Sancho, Francesc; Mocholí-Arce, Manuel; Sala-Garrido, Ramón

2014-07-01

The integrated water resources management approach has proven to be a suitable option for efficient, equitable and sustainable water management. In water-poor regions experiencing acute and/or chronic shortages, optimisation techniques are a useful tool for supporting the decision process of water allocation. In order to maximise the value of water use, an optimisation model was developed which involves multiple supply sources (conventional and non-conventional) and multiple users. Penalties, representing monetary losses in the event of an unfulfilled water demand, have been incorporated into the objective function. This model represents a novel approach which considers water distribution efficiency and the physical connections between water supply and demand points. Subsequent empirical testing using data from a Spanish Mediterranean river basin demonstrated the usefulness of the global optimisation model to solve existing water imbalances at the river basin level.

Microfluidic converging/diverging channels optimised for homogeneous extensional deformation

PubMed Central

Zografos, K.; Oliveira, M. S. N.

2016-01-01

In this work, we optimise microfluidic converging/diverging geometries in order to produce constant strain-rates along the centreline of the flow, for performing studies under homogeneous extension. The design is examined for both two-dimensional and three-dimensional flows where the effects of aspect ratio and dimensionless contraction length are investigated. Initially, pressure driven flows of Newtonian fluids under creeping flow conditions are considered, which is a reasonable approximation in microfluidics, and the limits of the applicability of the design in terms of Reynolds numbers are investigated. The optimised geometry is then used for studying the flow of viscoelastic fluids and the practical limitations in terms of Weissenberg number are reported. Furthermore, the optimisation strategy is also applied for electro-osmotic driven flows, where the development of a plug-like velocity profile allows for a wider region of homogeneous extensional deformation in the flow field. PMID:27478523

Crystal structure optimisation using an auxiliary equation of state

NASA Astrophysics Data System (ADS)

Jackson, Adam J.; Skelton, Jonathan M.; Hendon, Christopher H.; Butler, Keith T.; Walsh, Aron

2015-11-01

Standard procedures for local crystal-structure optimisation involve numerous energy and force calculations. It is common to calculate an energy-volume curve, fitting an equation of state around the equilibrium cell volume. This is a computationally intensive process, in particular, for low-symmetry crystal structures where each isochoric optimisation involves energy minimisation over many degrees of freedom. Such procedures can be prohibitive for non-local exchange-correlation functionals or other "beyond" density functional theory electronic structure techniques, particularly where analytical gradients are not available. We present a simple approach for efficient optimisation of crystal structures based on a known equation of state. The equilibrium volume can be predicted from one single-point calculation and refined with successive calculations if required. The approach is validated for PbS, PbTe, ZnS, and ZnTe using nine density functionals and applied to the quaternary semiconductor Cu2ZnSnS4 and the magnetic metal-organic framework HKUST-1.

Optimisation of confinement in a fusion reactor using a nonlinear turbulence model

NASA Astrophysics Data System (ADS)

Highcock, E. G.; Mandell, N. R.; Barnes, M.

2018-04-01

The confinement of heat in the core of a magnetic fusion reactor is optimised using a multidimensional optimisation algorithm. For the first time in such a study, the loss of heat due to turbulence is modelled at every stage using first-principles nonlinear simulations which accurately capture the turbulent cascade and large-scale zonal flows. The simulations utilise a novel approach, with gyrofluid treatment of the small-scale drift waves and gyrokinetic treatment of the large-scale zonal flows. A simple near-circular equilibrium with standard parameters is chosen as the initial condition. The figure of merit, fusion power per unit volume, is calculated, and then two control parameters, the elongation and triangularity of the outer flux surface, are varied, with the algorithm seeking to optimise the chosen figure of merit. A twofold increase in the plasma power per unit volume is achieved by moving to higher elongation and strongly negative triangularity.

Transcriptome interrogation of human myometrium identifies differentially expressed sense-antisense pairs of protein-coding and long non-coding RNA genes in spontaneous labor at term.

PubMed

Romero, Roberto; Tarca, Adi L; Chaemsaithong, Piya; Miranda, Jezid; Chaiworapongsa, Tinnakorn; Jia, Hui; Hassan, Sonia S; Kalita, Cynthia A; Cai, Juan; Yeo, Lami; Lipovich, Leonard

2014-09-01

To identify differentially expressed long non-coding RNA (lncRNA) genes in human myometrium in women with spontaneous labor at term. Myometrium was obtained from women undergoing cesarean deliveries who were not in labor (n = 19) and women in spontaneous labor at term (n = 20). RNA was extracted and profiled using an Illumina® microarray platform. We have used computational approaches to bound the extent of long non-coding RNA representation on this platform, and to identify co-differentially expressed and correlated pairs of long non-coding RNA genes and protein-coding genes sharing the same genomic loci. We identified co-differential expression and correlation at two genomic loci that contain coding-lncRNA gene pairs: SOCS2-AK054607 and LMCD1-NR_024065 in women in spontaneous labor at term. This co-differential expression and correlation was validated by qRT-PCR, an experimental method completely independent of the microarray analysis. Intriguingly, one of the two lncRNA genes differentially expressed in term labor had a key genomic structure element, a splice site, that lacked evolutionary conservation beyond primates. We provide, for the first time, evidence for coordinated differential expression and correlation of cis-encoded antisense lncRNAs and protein-coding genes with known as well as novel roles in pregnancy in the myometrium of women in spontaneous labor at term.

Digital detection of multiple minority mutants and expression levels of multiple colorectal cancer-related genes using digital-PCR coupled with bead-array.

PubMed

Huang, Huan; Li, Shuo; Sun, Lizhou; Zhou, Guohua

2015-01-01

To simultaneously analyze mutations and expression levels of multiple genes on one detection platform, we proposed a method termed "multiplex ligation-dependent probe amplification-digital amplification coupled with hydrogel bead-array" (MLPA-DABA) and applied it to diagnose colorectal cancer (CRC). CRC cells and tissues were sampled to extract nucleic acid, perform MLPA with sequence-tagged probes, perform digital emulsion polymerase chain reaction (PCR), and produce a hydrogel bead-array to immobilize beads and form a single bead layer on the array. After hybridization with fluorescent probes, the number of colored beads, which reflects the abundance of expressed genes and the mutation rate, was counted for diagnosis. Only red or green beads occurred on the chips in the mixed samples, indicating the success of single-molecule PCR. When a one-source sample was analyzed using mixed MLPA probes, beads of only one color occurred, suggesting the high specificity of the method in analyzing CRC mutation and gene expression. In gene expression analysis of a CRC tissue from one CRC patient, the mutant percentage was 3.1%, and the expression levels of CRC-related genes were much higher than those of normal tissue. The highly sensitive MLPA-DABA succeeds in the relative quantification of mutations and gene expressions of exfoliated cells in stool samples of CRC patients on the same chip platform. MLPA-DABA coupled with hydrogel bead-array is a promising method in the non-invasive diagnosis of CRC.

Design of the e-Vita diabetes mellitus study: effects and use of an interactive online care platform in patients with type 2 diabetes (e-VitaDM-1/ZODIAC-40)

PubMed Central

2014-01-01

Background Due to ongoing rise in need for care for people with chronic diseases and lagging increase in number of care providers, alternative forms of care provision and self-management support are needed. Empowering patients through an online care platform could help to improve patients’ self-management and reduce the burden on the healthcare system. Methods Access to laboratory results and educational modules on diabetes will be offered through a platform for subjects with type 2 diabetes mellitus treated in primary care. Differences in socio-demographic and clinical characteristics between subjects expressing interest vs. disinterest to use the platform will be explored. Platform usage will be tracked and compared. Patient satisfaction and quality of life will be measured by validated questionnaires and economic analyses will be performed. Discussion This study is designed to assess the feasibility of use of an online platform in routine primary healthcare for subjects with type 2 diabetes mellitus in the Netherlands, and to study effects of use of the platform on treatment satisfaction, quality of life and clinical parameters. Although providing access to a online platform is not a novel intervention, usage and effects have not yet been studied in this patient population. Trial registration Trial registration: NCT01570140. PMID:24593656

Microarray platform affords improved product analysis in mammalian cell growth studies

PubMed Central

Li, Lingyun; Migliore, Nicole; Schaefer, Eugene; Sharfstein, Susan T.; Dordick, Jonathan S.; Linhardt, Robert J.

2014-01-01

High throughput (HT) platforms serve as cost-efficient and rapid screening method for evaluating the effect of cell culture conditions and screening of chemicals. The aim of the current study was to develop a high-throughput cell-based microarray platform to assess the effect of culture conditions on Chinese hamster ovary (CHO) cells. Specifically, growth, transgene expression and metabolism of a GS/MSX CHO cell line, which produces a therapeutic monoclonal antibody, was examined using microarray system in conjunction with conventional shake flask platform in a non-proprietary medium. The microarray system consists of 60 nl spots of cells encapsulated in alginate and separated in groups via an 8-well chamber system attached to the chip. Results show the non-proprietary medium developed allows cell growth, production and normal glycosylation of recombinant antibody and metabolism of the recombinant CHO cells in both the microarray and shake flask platforms. In addition, 10.3 mM glutamate addition to the defined base media results in lactate metabolism shift in the recombinant GS/MSX CHO cells in the shake flask platform. Ultimately, the results demonstrate that the high-throughput microarray platform has the potential to be utilized for evaluating the impact of media additives on cellular processes, such as, cell growth, metabolism and productivity. PMID:24227746

User testing and performance evaluation of the Electronic Quality Improvement Platform for Plans and Pharmacies.

PubMed

Pringle, Janice L; Kearney, Shannon M; Grasso, Kim; Boyer, Annette D; Conklin, Mark H; Szymanski, Keith A

2015-01-01

To user-test and evaluate a performance information management platform that makes standardized, benchmarked medication use quality data available to both health plans and community pharmacy organizations. Multiple health/drug plans and multiple chain and independent pharmacies across the United States. During the first phase of the study, user experience was measured via user satisfaction surveys and interviews with key personnel (pharmacists, pharmacy leaders, and health plan leadership). Improvements were subsequently made to the platform based on these findings. During the second phase of the study, the platform was implemented in a greater number of pharmacies and by a greater number of payers. User experience was then reevaluated to gather information for further improvements. The surveys and interviews revealed that users found the Web-based platform easy to use and beneficial in terms of understanding and comparing performance metrics. Primary concerns included lack of access to real-time data and patient-specific data. Many users also expressed uncertainty as to how they could use the information and data provided by the platform. The study findings indicate that while information management platforms can be used effectively in both pharmacy and health plan settings, future development is needed to ensure that the provided data can be transferred to pharmacy best practices and improved quality care.

Design, Synthesis, and Biological Functionality of a Dendrimer-based Modular Drug Delivery Platform

PubMed Central

Mullen, Douglas G.; McNerny, Daniel Q.; Desai, Ankur; Cheng, Xue-min; DiMaggio, Stassi C.; Kotlyar, Alina; Zhong, Yueyang; Qin, Suyang; Kelly, Christopher V.; Thomas, Thommey P.; Majoros, Istvan; Orr, Bradford G.; Baker, James R.; Banaszak Holl, Mark M.

2011-01-01

A modular dendrimer-based drug delivery platform was designed to improve upon existing limitations in single dendrimer systems. Using this modular strategy, a biologically active platform containing receptor mediated targeting and fluorescence imaging modules was synthesized by coupling a folic acid (FA) conjugated dendrimer with a fluorescein isothiocyanate (FITC) conjugated dendrimer. The two different dendrimer modules were coupled via the 1,3-dipolar cycloaddition reaction (‘click’ chemistry) between an alkyne moiety on the surface of the first dendrimer and an azide moiety on the second dendrimer. Two simplified model systems were also synthesized to develop appropriate ‘click’ reaction conditions and aid in spectroscopic assignments. Conjugates were characterized by 1H NMR spectroscopy and NOESY. The FA-FITC modular platform was evaluated in vitro with a human epithelial cancer cell line (KB) and found to specifically target the over-expressed folic acid receptor. PMID:21425790

Synthetic biology platform technologies for antimicrobial applications.

PubMed

Braff, Dana; Shis, David; Collins, James J

2016-10-01

The growing prevalence of antibiotic resistance calls for new approaches in the development of antimicrobial therapeutics. Likewise, improved diagnostic measures are essential in guiding the application of targeted therapies and preventing the evolution of therapeutic resistance. Discovery platforms are also needed to form new treatment strategies and identify novel antimicrobial agents. By applying engineering principles to molecular biology, synthetic biologists have developed platforms that improve upon, supplement, and will perhaps supplant traditional broad-spectrum antibiotics. Efforts in engineering bacteriophages and synthetic probiotics demonstrate targeted antimicrobial approaches that can be fine-tuned using synthetic biology-derived principles. Further, the development of paper-based, cell-free expression systems holds promise in promoting the clinical translation of molecular biology tools for diagnostic purposes. In this review, we highlight emerging synthetic biology platform technologies that are geared toward the generation of new antimicrobial therapies, diagnostics, and discovery channels. Copyright © 2016 Elsevier B.V. All rights reserved.

Canarypox virus expressing infectious bursal disease VP2 protein as immunogen for chickens

PubMed Central

Zanetti, Flavia Adriana; Grand, María Daniela Conte; Mitarotonda, Romina Cristina; Taboga, Oscar Alberto; Calamante, Gabriela

2014-01-01

Canarypox viruses (CNPV) carrying the coding sequence of VP2 protein from infectious bursal disease virus (IBDV) were obtained. These viruses were able to express VP2 protein in vitro and to induce IBDV-neutralizing antibodies when inoculated in specific pathogen-free chickens demonstrating that CNPV platform is usefulness to develop immunogens for chickens. PMID:24948937

Lemna (duckweed) expressed hemagglutinin from avian influenza H5N1 protects chickens against H5N1 high pathogenicity avian influenza virus challenge

USDA-ARS?s Scientific Manuscript database

In the last two decades, transgenic plants have been explored as safe and cost effective alternative expression platforms for producing recombinant proteins. In this study, a synthetic hemagglutinin (HA) gene from the high pathogenicity avian influenza (HPAI) virus A/chicken/Indonesia/7/2003 (H5N1)...

Use of baculovirus expression system for generation of virus-like particles: successes and challenges.

PubMed

Liu, Fuxiao; Wu, Xiaodong; Li, Lin; Liu, Zengshan; Wang, Zhiliang

2013-08-01

The baculovirus expression system (BES) has been one of the versatile platforms for the production of recombinant proteins requiring multiple post-translational modifications, such as folding, oligomerization, phosphorylation, glycosylation, acylation, disulfide bond formation and proteolytic cleavage. Advances in recombinant DNA technology have facilitated application of the BES, and made it possible to express multiple proteins simultaneously in a single infection and to produce multimeric proteins sharing functional similarity with their natural analogs. Therefore, the BES has been used for the production of recombinant proteins and the construction of virus-like particles (VLPs), as well as for the development of subunit vaccines, including VLP-based vaccines. The VLP, which consists of one or more structural proteins but no viral genome, resembles the authentic virion but cannot replicate in cells. The high-quality recombinant protein expression and post-translational modifications obtained with the BES, along with its capacity to produce multiple proteins, imply that it is ideally suited to VLP production. In this article, we critically review the pros and cons of using the BES as a platform to produce both enveloped and non-enveloped VLPs. Copyright © 2013 Elsevier Inc. All rights reserved.

Preparation of highly multiplexed small RNA sequencing libraries.

PubMed

Persson, Helena; Søkilde, Rolf; Pirona, Anna Chiara; Rovira, Carlos

2017-08-01

MicroRNAs (miRNAs) are ~22-nucleotide-long small non-coding RNAs that regulate the expression of protein-coding genes by base pairing to partially complementary target sites, preferentially located in the 3´ untranslated region (UTR) of target mRNAs. The expression and function of miRNAs have been extensively studied in human disease, as well as the possibility of using these molecules as biomarkers for prognostication and treatment guidance. To identify and validate miRNAs as biomarkers, their expression must be screened in large collections of patient samples. Here, we develop a scalable protocol for the rapid and economical preparation of a large number of small RNA sequencing libraries using dual indexing for multiplexing. Combined with the use of off-the-shelf reagents, more samples can be sequenced simultaneously on large-scale sequencing platforms at a considerably lower cost per sample. Sample preparation is simplified by pooling libraries prior to gel purification, which allows for the selection of a narrow size range while minimizing sample variation. A comparison with publicly available data from benchmarking of miRNA analysis platforms showed that this method captures absolute and differential expression as effectively as commercially available alternatives.

In vivo genome editing of the albumin locus as a platform for protein replacement therapy

PubMed Central

Sharma, Rajiv; Anguela, Xavier M.; Doyon, Yannick; Wechsler, Thomas; DeKelver, Russell C.; Sproul, Scott; Paschon, David E.; Miller, Jeffrey C.; Davidson, Robert J.; Shivak, David; Zhou, Shangzhen; Rieders, Julianne; Gregory, Philip D.; Holmes, Michael C.; Rebar, Edward J.

2015-01-01

Site-specific genome editing provides a promising approach for achieving long-term, stable therapeutic gene expression. Genome editing has been successfully applied in a variety of preclinical models, generally focused on targeting the diseased locus itself; however, limited targeting efficiency or insufficient expression from the endogenous promoter may impede the translation of these approaches, particularly if the desired editing event does not confer a selective growth advantage. Here we report a general strategy for liver-directed protein replacement therapies that addresses these issues: zinc finger nuclease (ZFN) –mediated site-specific integration of therapeutic transgenes within the albumin gene. By using adeno-associated viral (AAV) vector delivery in vivo, we achieved long-term expression of human factors VIII and IX (hFVIII and hFIX) in mouse models of hemophilia A and B at therapeutic levels. By using the same targeting reagents in wild-type mice, lysosomal enzymes were expressed that are deficient in Fabry and Gaucher diseases and in Hurler and Hunter syndromes. The establishment of a universal nuclease-based platform for secreted protein production would represent a critical advance in the development of safe, permanent, and functional cures for diverse genetic and nongenetic diseases. PMID:26297739

A Novel Malaria Vaccine Candidate Antigen Expressed in Tetrahymena thermophila

PubMed Central

Eleni-Muus, Janna; Aldag, Ingo; Samuel, Kay; Creasey, Alison M.; Hartmann, Marcus W. W.; Cavanagh, David R.

2014-01-01

Development of effective malaria vaccines is hampered by the problem of producing correctly folded Plasmodium proteins for use as vaccine components. We have investigated the use of a novel ciliate expression system, Tetrahymena thermophila, as a P. falciparum vaccine antigen platform. A synthetic vaccine antigen composed of N-terminal and C-terminal regions of merozoite surface protein-1 (MSP-1) was expressed in Tetrahymena thermophila. The recombinant antigen was secreted into the culture medium and purified by monoclonal antibody (mAb) affinity chromatography. The vaccine was immunogenic in MF1 mice, eliciting high antibody titers against both N- and C-terminal components. Sera from immunized animals reacted strongly with P. falciparum parasites from three antigenically different strains by immunofluorescence assays, confirming that the antibodies produced are able to recognize parasite antigens in their native form. Epitope mapping of serum reactivity with a peptide library derived from all three MSP-1 Block 2 serotypes confirmed that the MSP-1 Block 2 hybrid component of the vaccine had effectively targeted all three serotypes of this polymorphic region of MSP-1. This study has successfully demonstrated the use of Tetrahymena thermophila as a recombinant protein expression platform for the production of malaria vaccine antigens. PMID:24489871

Coil optimisation for transcranial magnetic stimulation in realistic head geometry.

PubMed

Koponen, Lari M; Nieminen, Jaakko O; Mutanen, Tuomas P; Stenroos, Matti; Ilmoniemi, Risto J

Transcranial magnetic stimulation (TMS) allows focal, non-invasive stimulation of the cortex. A TMS pulse is inherently weakly coupled to the cortex; thus, magnetic stimulation requires both high current and high voltage to reach sufficient intensity. These requirements limit, for example, the maximum repetition rate and the maximum number of consecutive pulses with the same coil due to the rise of its temperature. To develop methods to optimise, design, and manufacture energy-efficient TMS coils in realistic head geometry with an arbitrary overall coil shape. We derive a semi-analytical integration scheme for computing the magnetic field energy of an arbitrary surface current distribution, compute the electric field induced by this distribution with a boundary element method, and optimise a TMS coil for focal stimulation. Additionally, we introduce a method for manufacturing such a coil by using Litz wire and a coil former machined from polyvinyl chloride. We designed, manufactured, and validated an optimised TMS coil and applied it to brain stimulation. Our simulations indicate that this coil requires less than half the power of a commercial figure-of-eight coil, with a 41% reduction due to the optimised winding geometry and a partial contribution due to our thinner coil former and reduced conductor height. With the optimised coil, the resting motor threshold of abductor pollicis brevis was reached with the capacitor voltage below 600 V and peak current below 3000 A. The described method allows designing practical TMS coils that have considerably higher efficiency than conventional figure-of-eight coils. Copyright © 2017 Elsevier Inc. All rights reserved.

Automatic optimisation of gamma dose rate sensor networks: The DETECT Optimisation Tool

NASA Astrophysics Data System (ADS)

Helle, K. B.; Müller, T. O.; Astrup, P.; Dyve, J. E.

2014-05-01

Fast delivery of comprehensive information on the radiological situation is essential for decision-making in nuclear emergencies. Most national radiological agencies in Europe employ gamma dose rate sensor networks to monitor radioactive pollution of the atmosphere. Sensor locations were often chosen using regular grids or according to administrative constraints. Nowadays, however, the choice can be based on more realistic risk assessment, as it is possible to simulate potential radioactive plumes. To support sensor planning, we developed the DETECT Optimisation Tool (DOT) within the scope of the EU FP 7 project DETECT. It evaluates the gamma dose rates that a proposed set of sensors might measure in an emergency and uses this information to optimise the sensor locations. The gamma dose rates are taken from a comprehensive library of simulations of atmospheric radioactive plumes from 64 source locations. These simulations cover the whole European Union, so the DOT allows evaluation and optimisation of sensor networks for all EU countries, as well as evaluation of fencing sensors around possible sources. Users can choose from seven cost functions to evaluate the capability of a given monitoring network for early detection of radioactive plumes or for the creation of dose maps. The DOT is implemented as a stand-alone easy-to-use JAVA-based application with a graphical user interface and an R backend. Users can run evaluations and optimisations, and display, store and download the results. The DOT runs on a server and can be accessed via common web browsers; it can also be installed locally.

[Public interactions, private censorship: the case of Facebook].

PubMed

Silveira, Sergio Amadeu da

2015-12-01

Facebook is examined as a transnational online social networking platform where public discussions and interactions take place. The study surveys the private control of cultural and political expressions exercised by the platform's managers, which can be defined as private censorship. Cases of removal of content are presented and Facebook's political control policies discussed. The article also shows how Facebook rules display highly discretionary components and an aesthetic that can be portrayed as a kind of biopolitics of the information-age society.

Optimisation of rocker sole footwear for prevention of first plantar ulcer: comparison of group-optimised and individually-selected footwear designs.

PubMed

Preece, Stephen J; Chapman, Jonathan D; Braunstein, Bjoern; Brüggemann, Gert-Peter; Nester, Christopher J

2017-01-01

Appropriate footwear for individuals with diabetes but no ulceration history could reduce the risk of first ulceration. However, individuals who deem themselves at low risk are unlikely to seek out bespoke footwear which is personalised. Therefore, our primary aim was to investigate whether group-optimised footwear designs, which could be prefabricated and delivered in a retail setting, could achieve appropriate pressure reduction, or whether footwear selection must be on a patient-by-patient basis. A second aim was to compare responses to footwear design between healthy participants and people with diabetes in order to understand the transferability of previous footwear research, performed in healthy populations. Plantar pressures were recorded from 102 individuals with diabetes, considered at low risk of ulceration. This cohort included 17 individuals with peripheral neuropathy. We also collected data from 66 healthy controls. Each participant walked in 8 rocker shoe designs (4 apex positions × 2 rocker angles). ANOVA analysis was then used to understand the effect of two design features and descriptive statistics used to identify the group-optimised design. Using 200 kPa as a target, this group-optimised design was then compared to the design identified as the best for each participant (using plantar pressure data). Peak plantar pressure increased significantly as apex position was moved distally and rocker angle reduced ( p  < 0.001). The group-optimised design incorporated an apex at 52% of shoe length, a 20° rocker angle and an apex angle of 95°. With this design 71-81% of peak pressures were below the 200 kPa threshold, both in the full cohort of individuals with diabetes and also in the neuropathic subgroup. Importantly, only small increases (<5%) in this proportion were observed when participants wore footwear which was individually selected. In terms of optimised footwear designs, healthy participants demonstrated the same response as participants with diabetes, despite having lower plantar pressures. This is the first study demonstrating that a group-optimised, generic rocker shoe might perform almost as well as footwear selected on a patient by patient basis in a low risk patient group. This work provides a starting point for clinical evaluation of generic versus personalised pressure reducing footwear.

A new compound arithmetic crossover-based genetic algorithm for constrained optimisation in enterprise systems

NASA Astrophysics Data System (ADS)

Jin, Chenxia; Li, Fachao; Tsang, Eric C. C.; Bulysheva, Larissa; Kataev, Mikhail Yu

2017-01-01

In many real industrial applications, the integration of raw data with a methodology can support economically sound decision-making. Furthermore, most of these tasks involve complex optimisation problems. Seeking better solutions is critical. As an intelligent search optimisation algorithm, genetic algorithm (GA) is an important technique for complex system optimisation, but it has internal drawbacks such as low computation efficiency and prematurity. Improving the performance of GA is a vital topic in academic and applications research. In this paper, a new real-coded crossover operator, called compound arithmetic crossover operator (CAC), is proposed. CAC is used in conjunction with a uniform mutation operator to define a new genetic algorithm CAC10-GA. This GA is compared with an existing genetic algorithm (AC10-GA) that comprises an arithmetic crossover operator and a uniform mutation operator. To judge the performance of CAC10-GA, two kinds of analysis are performed. First the analysis of the convergence of CAC10-GA is performed by the Markov chain theory; second, a pair-wise comparison is carried out between CAC10-GA and AC10-GA through two test problems available in the global optimisation literature. The overall comparative study shows that the CAC performs quite well and the CAC10-GA defined outperforms the AC10-GA.

A rapid, automated approach to optimisation of multiple reaction monitoring conditions for quantitative bioanalytical mass spectrometry.

PubMed

Higton, D M

2001-01-01

An improvement to the procedure for the rapid optimisation of mass spectrometry (PROMS), for the development of multiple reaction methods (MRM) for quantitative bioanalytical liquid chromatography/tandem mass spectrometry (LC/MS/MS), is presented. PROMS is an automated protocol that uses flow-injection analysis (FIA) and AppleScripts to create methods and acquire the data for optimisation. The protocol determines the optimum orifice potential, the MRM conditions for each compound, and finally creates the MRM methods needed for sample analysis. The sensitivities of the MRM methods created by PROMS approach those created manually. MRM method development using PROMS currently takes less than three minutes per compound compared to at least fifteen minutes manually. To further enhance throughput, approaches to MRM optimisation using one injection per compound, two injections per pool of five compounds and one injection per pool of five compounds have been investigated. No significant difference in the optimised instrumental parameters for MRM methods were found between the original PROMS approach and these new methods, which are up to ten times faster. The time taken for an AppleScript to determine the optimum conditions and build the MRM methods is the same with all approaches. Copyright 2001 John Wiley & Sons, Ltd.

Optimised analytical models of the dielectric properties of biological tissue.

PubMed

Salahuddin, Saqib; Porter, Emily; Krewer, Finn; O' Halloran, Martin

2017-05-01

The interaction of electromagnetic fields with the human body is quantified by the dielectric properties of biological tissues. These properties are incorporated into complex numerical simulations using parametric models such as Debye and Cole-Cole, for the computational investigation of electromagnetic wave propagation within the body. These parameters can be acquired through a variety of optimisation algorithms to achieve an accurate fit to measured data sets. A number of different optimisation techniques have been proposed, but these are often limited by the requirement for initial value estimations or by the large overall error (often up to several percentage points). In this work, a novel two-stage genetic algorithm proposed by the authors is applied to optimise the multi-pole Debye parameters for 54 types of human tissues. The performance of the two-stage genetic algorithm has been examined through a comparison with five other existing algorithms. The experimental results demonstrate that the two-stage genetic algorithm produces an accurate fit to a range of experimental data and efficiently out-performs all other optimisation algorithms under consideration. Accurate values of the three-pole Debye models for 54 types of human tissues, over 500 MHz to 20 GHz, are also presented for reference. Copyright © 2017 IPEM. Published by Elsevier Ltd. All rights reserved.

Advantages of Task-Specific Multi-Objective Optimisation in Evolutionary Robotics.

PubMed

Trianni, Vito; López-Ibáñez, Manuel

2015-01-01

The application of multi-objective optimisation to evolutionary robotics is receiving increasing attention. A survey of the literature reveals the different possibilities it offers to improve the automatic design of efficient and adaptive robotic systems, and points to the successful demonstrations available for both task-specific and task-agnostic approaches (i.e., with or without reference to the specific design problem to be tackled). However, the advantages of multi-objective approaches over single-objective ones have not been clearly spelled out and experimentally demonstrated. This paper fills this gap for task-specific approaches: starting from well-known results in multi-objective optimisation, we discuss how to tackle commonly recognised problems in evolutionary robotics. In particular, we show that multi-objective optimisation (i) allows evolving a more varied set of behaviours by exploring multiple trade-offs of the objectives to optimise, (ii) supports the evolution of the desired behaviour through the introduction of objectives as proxies, (iii) avoids the premature convergence to local optima possibly introduced by multi-component fitness functions, and (iv) solves the bootstrap problem exploiting ancillary objectives to guide evolution in the early phases. We present an experimental demonstration of these benefits in three different case studies: maze navigation in a single robot domain, flocking in a swarm robotics context, and a strictly collaborative task in collective robotics.

Optimisation of phenolic extraction from Averrhoa carambola pomace by response surface methodology and its microencapsulation by spray and freeze drying.

PubMed

Saikia, Sangeeta; Mahnot, Nikhil Kumar; Mahanta, Charu Lata

2015-03-15

Optimised of the extraction of polyphenol from star fruit (Averrhoa carambola) pomace using response surface methodology was carried out. Two variables viz. temperature (°C) and ethanol concentration (%) with 5 levels (-1.414, -1, 0, +1 and +1.414) were used to design the optimisation model using central composite rotatable design where, -1.414 and +1.414 refer to axial values, -1 and +1 mean factorial points and 0 refers to centre point of the design. The two variables, temperature of 40°C and ethanol concentration of 65% were the optimised conditions for the response variables of total phenolic content, ferric reducing antioxidant capacity and 2,2-diphenyl-1-picrylhydrazyl scavenging activity. The reverse phase-high pressure liquid chromatography chromatogram of the polyphenol extract showed eight phenolic acids and ascorbic acid. The extract was then encapsulated with maltodextrin (⩽ DE 20) by spray and freeze drying methods at three different concentrations. Highest encapsulating efficiency was obtained in freeze dried encapsulates (78-97%). The obtained optimised model could be used for polyphenol extraction from star fruit pomace and microencapsulates can be incorporated in different food systems to enhance their antioxidant property. Copyright © 2014 Elsevier Ltd. All rights reserved.

Analysis of power gating in different hierarchical levels of 2MB cache, considering variation

NASA Astrophysics Data System (ADS)

Jafari, Mohsen; Imani, Mohsen; Fathipour, Morteza

2015-09-01

This article reintroduces power gating technique in different hierarchical levels of static random-access memory (SRAM) design including cell, row, bank and entire cache memory in 16 nm Fin field effect transistor. Different structures of SRAM cells such as 6T, 8T, 9T and 10T are used in design of 2MB cache memory. The power reduction of the entire cache memory employing cell-level optimisation is 99.7% with the expense of area and other stability overheads. The power saving of the cell-level optimisation is 3× (1.2×) higher than power gating in cache (bank) level due to its superior selectivity. The access delay times are allowed to increase by 4% in the same energy delay product to achieve the best power reduction for each supply voltages and optimisation levels. The results show the row-level power gating is the best for optimising the power of the entire cache with lowest drawbacks. Comparisons of cells show that the cells whose bodies have higher power consumption are the best candidates for power gating technique in row-level optimisation. The technique has the lowest percentage of saving in minimum energy point (MEP) of the design. The power gating also improves the variation of power in all structures by at least 70%.

Novel algorithm implementations in DARC: the Durham AO real-time controller

NASA Astrophysics Data System (ADS)

Basden, Alastair; Bitenc, Urban; Jenkins, David

2016-07-01

The Durham AO Real-time Controller has been used on-sky with the CANARY AO demonstrator instrument since 2010, and is also used to provide control for several AO test-benches, including DRAGON. Over this period, many new real-time algorithms have been developed, implemented and demonstrated, leading to performance improvements for CANARY. Additionally, the computational performance of this real-time system has continued to improve. Here, we provide details about recent updates and changes made to DARC, and the relevance of these updates, including new algorithms, to forthcoming AO systems. We present the computational performance of DARC when used on different hardware platforms, including hardware accelerators, and determine the relevance and potential for ELT scale systems. Recent updates to DARC have included algorithms to handle elongated laser guide star images, including correlation wavefront sensing, with options to automatically update references during AO loop operation. Additionally, sub-aperture masking options have been developed to increase signal to noise ratio when operating with non-symmetrical wavefront sensor images. The development of end-user tools has progressed with new options for configuration and control of the system. New wavefront sensor camera models and DM models have been integrated with the system, increasing the number of possible hardware configurations available, and a fully open-source AO system is now a reality, including drivers necessary for commercial cameras and DMs. The computational performance of DARC makes it suitable for ELT scale systems when implemented on suitable hardware. We present tests made on different hardware platforms, along with the strategies taken to optimise DARC for these systems.

Generation of a new Gateway-compatible inducible lentiviral vector platform allowing easy derivation of co-transduced cells.

PubMed

De Groote, Philippe; Grootjans, Sasker; Lippens, Saskia; Eichperger, Chantal; Leurs, Kirsten; Kahr, Irene; Tanghe, Giel; Bruggeman, Inge; De Schamphelaire, Wouter; Urwyler, Corinne; Vandenabeele, Peter; Haustraete, Jurgen; Declercq, Wim

2016-01-01

In contrast to most common gene delivery techniques, lentiviral vectors allow targeting of almost any mammalian cell type, even non-dividing cells, and they stably integrate in the genome. Therefore, these vectors are a very powerful tool for biomedical research. Here we report the generation of a versatile new set of 22 lentiviral vectors with broad applicability in multiple research areas. In contrast to previous systems, our platform provides a choice between constitutive and/or conditional expression and six different C-terminal fusions. Furthermore, two compatible selection markers enable the easy derivation of stable cell lines co-expressing differently tagged transgenes in a constitutive or inducible manner. We show that all of the vector features are functional and that they contribute to transgene overexpression in proof-of-principle experiments.

Genomically Encoded Analog Memory with Precise In vivo DNA Writing in Living Cell Populations

PubMed Central

Farzadfard, Fahim; Lu, Timothy K.

2014-01-01

Cellular memory is crucial to many natural biological processes and for sophisticated synthetic-biology applications. Existing cellular memories rely on epigenetic switches or recombinases, which are limited in scalability and recording capacity. Here, we use the DNA of living cell populations as genomic ‘tape recorders’ for the analog and distributed recording of long-term event histories. We describe a platform for generating single-stranded DNA (ssDNA) in vivo in response to arbitrary transcriptional signals. When co-expressed with a recombinase, these intracellularly expressed ssDNAs target specific genomic DNA addresses, resulting in precise mutations that accumulate in cell populations as a function of the magnitude and duration of the inputs. This platform could enable long-term cellular recorders for environmental and biomedical applications, biological state machines, and enhanced genome engineering strategies. PMID:25395541

Grey-box state-space identification of nonlinear mechanical vibrations

NASA Astrophysics Data System (ADS)

Noël, J. P.; Schoukens, J.

2018-05-01

The present paper deals with the identification of nonlinear mechanical vibrations. A grey-box, or semi-physical, nonlinear state-space representation is introduced, expressing the nonlinear basis functions using a limited number of measured output variables. This representation assumes that the observed nonlinearities are localised in physical space, which is a generic case in mechanics. A two-step identification procedure is derived for the grey-box model parameters, integrating nonlinear subspace initialisation and weighted least-squares optimisation. The complete procedure is applied to an electrical circuit mimicking the behaviour of a single-input, single-output (SISO) nonlinear mechanical system and to a single-input, multiple-output (SIMO) geometrically nonlinear beam structure.

ExpressionDB: An open source platform for distributing genome-scale datasets.

PubMed

Hughes, Laura D; Lewis, Scott A; Hughes, Michael E

2017-01-01

RNA-sequencing (RNA-seq) and microarrays are methods for measuring gene expression across the entire transcriptome. Recent advances have made these techniques practical and affordable for essentially any laboratory with experience in molecular biology. A variety of computational methods have been developed to decrease the amount of bioinformatics expertise necessary to analyze these data. Nevertheless, many barriers persist which discourage new labs from using functional genomics approaches. Since high-quality gene expression studies have enduring value as resources to the entire research community, it is of particular importance that small labs have the capacity to share their analyzed datasets with the research community. Here we introduce ExpressionDB, an open source platform for visualizing RNA-seq and microarray data accommodating virtually any number of different samples. ExpressionDB is based on Shiny, a customizable web application which allows data sharing locally and online with customizable code written in R. ExpressionDB allows intuitive searches based on gene symbols, descriptions, or gene ontology terms, and it includes tools for dynamically filtering results based on expression level, fold change, and false-discovery rates. Built-in visualization tools include heatmaps, volcano plots, and principal component analysis, ensuring streamlined and consistent visualization to all users. All of the scripts for building an ExpressionDB with user-supplied data are freely available on GitHub, and the Creative Commons license allows fully open customization by end-users. We estimate that a demo database can be created in under one hour with minimal programming experience, and that a new database with user-supplied expression data can be completed and online in less than one day.

Optimisation of the Future Routine Orbit for Mars Express

NASA Technical Reports Server (NTRS)

Carranza, Manuel; Companys, Vincente

2007-01-01

Mars Express (MEX), the first planetary mission of the European Space Agency (ESA), reached Mars on December 25th 2003. Since then it is performing routine operations. Its operational phase had to cover one Martian year, with the possibility of an extension for a second Martian year (i.e. until November 2007). The end of the mission extension is approaching but, given the good health of the payload instruments and the high science return of the mission, there is a strong will to achieve further extensions. Mars Express is also seen as an important asset, capable to provide relay functions for future Martian missions. The ESA Science Program Committee has recently approved a second extension of the MEX mission until May 2009 and even further extensions are possible. Mars Express has an eccentric quasi-polar orbit with a period of approximately 6.72 hours and a pericentre height of about 300 km. Science observations are mainly performed at pericentre (but not only). In addition the orbit has a resonance of 11 revolutions per 3 Martian days. This means that ground tracks corresponding to orbits separated by 11 revolutions are adjacent, such that a given area can be covered by the on-board camera without leaving gaps. The J2 effect of Mars causes a drift of both ascending node and argument of pericentre. The drift of argument of pericentre makes it possible to observe periodically all Mars latitudes from close distance. Illumination conditions at pericentre are influenced by both the drift of the argument of pericentre and the drift of ascending node, as well as by the rotation of Mars around the Sun. The original MEX routine orbit was optimized for the duration of the nominal mission and extension, such that it produced a balanced share of day-side observations (for the optical instruments) and night-side observations (for the radar). The orbit was thus not optimized for the time beyond the assumed extension. Indeed, the evolution of the ascending node and argument of pericentre would cause in the following years a drift of the pericentre towards night-side observation conditions, hence uninteresting for the optical instruments. In order to prevent this an optimisation process for the future routine orbit has taken place. The share between day-side and night-side observations can be controlled by adjusting the drift of argument of pericentre and ascending node. This can in particular be achieved by changing the semimajor axis, eccentricity and/or inclination. A change of inclination is inefficient compared to a change in semimajor axis and eccentricity, and has therefore been discarded. An in-plane maneuvre can be performed to change both semi-major axis and eccentricity, and thus the period of the orbit. Although an apocentre manoeuvre is cheaper in terms of deltaV, it would result in raising the pericentre height, which is unfavourable for close observations. Hence a pericentre manoeuvre is proposed, which will increase the apocentre height. A repeat cycle is still required to allow mapping areas with adjacent ground tracks, so the change of semimajor axis must result in a new resonance. Resonances 18:5, 25:7 and 7:2 have been considered as potential candidates. The resulting long term evolution of the observation conditions has been analysed. Finally it has been decided to perform a change of orbit to reach the 18:5. Another aspect of the optimisation process is the control of the ground track. The previous MEX reference trajectory included regular maneuvres at every apocentre in order to adjust the orbital period, such that the separation of the ground tracks would be optimal, regardless of the latitude of pericentre. The implementation of the actual delatVs on-board was done partly by optimizing the attitude of reaction-wheel desaturation activities. Despite of it, this strategy has a significant propellant cost, because it prevents to optimize reaction wheel de-saturation activities to minimize propellant consumption. Therore, with the aim at preserving propellant resources for a long time extension it has been agreed to stop the ground-track control. This requires now a more accurate science operation planning, with improved attitude pointing control. Finally, the approach to phase Mars Express to provide back-up relay functions for NASA Phoenix landing is explained. In the context of the routine trajectory optimisation a new requirement for close fly-bys at Phobos, with different observation geometries, has been specified. The approach to fulfill this requirement is explained.

Do doctors' attachment styles and emotional intelligence influence patients' emotional expressions in primary care consultations? An exploratory study using multilevel analysis.

PubMed

Cherry, M Gemma; Fletcher, Ian; Berridge, Damon; O'Sullivan, Helen

2018-04-01

To investigate whether and how doctors' attachment styles and emotional intelligence (EI) might influence patients' emotional expressions in general practice consultations. Video recordings of 26 junior doctors consulting with 173 patients were coded using the Verona Coding Definition of Emotional Sequences (VR-CoDES). Doctors' attachment style was scored across two dimensions, avoidance and anxiety, using the Experiences in Close Relationships: Short Form questionnaire. EI was assessed with the Mayer-Salovey-Caruso Emotional Intelligence Test. Multilevel Poisson regressions modelled the probability of patients' expressing emotional distress, considering doctors' attachment styles and EI and demographic and contextual factors. Both attachment styles and EI were significantly associated with frequency of patients' cues, with patient- and doctor-level explanatory variables accounting for 42% of the variance in patients' cues. The relative contribution of attachment styles and EI varied depending on whether patients' presenting complaints were physical or psychosocial in nature. Doctors' attachment styles and levels of EI are associated with patients' emotional expressions in primary care consultations. Further research is needed to investigate how these two variables interact and influence provider responses and patient outcomes. Understanding how doctors' psychological characteristics influence PPC may help to optimise undergraduate and postgraduate medical education. Copyright © 2017 Elsevier B.V. All rights reserved.

The dominant expression of functional human lactoferrin in transgenic cloned goats using a hybrid lactoferrin expression construct.

PubMed

Yu, Huiqing; Chen, Jianquan; Sun, Wei; Liu, Siguo; Zhang, Aimin; Xu, Xujun; Wang, Xuebin; He, Zhuzi; Liu, Guohui; Cheng, Guoxiang

2012-10-31

Human Lactoferrin (hLF) is an iron-binding protein with multiple physiological functions. As the availability of natural hLF is limited, alternative means of producing this biopharmaceutical protein have been extensively studied. Here we report on the dominant expression of recombinant human lactoferrin (rhLF) in transgenic cloned goats using a novel optimised construct made by fusing a 3.3 kb hLF minigene to the regulatory elements of the β-casein gene. The transgenic goat produced more than 30 mg/ml rhLF in its milk, and rhLF expression was stable during the entire lactation cycle. The rhLF purification efficiency from whole goat milk is approximately 70%, and its purity is above 98%. Compared with natural hLF, the rhLF from transgenic goats has similar biological characteristics including molecular mass, N-terminal sequence, isoelectric point, immunoreactivity and digestive stability. More importantly, the purified rhLF showed specific anti-tumour activity in the mouse model of melanoma experimental metastasis. Therefore, our study shows that the large-scale production of functional rhLF in transgenic goat milk could be an economical and promising source of human therapeutic use in the future. Copyright © 2012. Published by Elsevier B.V.

Cloning, expression and characterisation of P450-Hal1 (CYP116B62) from Halomonas sp. NCIMB 172: A self-sufficient P450 with high expression and diverse substrate scope.

PubMed

Porter, Joanne L; Sabatini, Selina; Manning, Jack; Tavanti, Michele; Galman, James L; Turner, Nicholas J; Flitsch, Sabine L

2018-06-01

Cytochrome P450 monooxygenases are able to catalyse a range of synthetically challenging reactions ranging from hydroxylation and demethylation to sulfoxidation and epoxidation. As such they have great potential for biocatalytic applications but are underutilised due to often-poor expression, stability and solubility in recombinant bacterial hosts. The use of self-sufficient P450 s with fused haem and reductase domains has already contributed heavily to improving catalytic efficiency and simplifying an otherwise more complex multi-component system of P450 and redox partners. Herein, we present a new addition to the class VII family with the cloning, sequencing and characterisation of the self-sufficient CYP116B62 Hal1 from Halomonas sp. NCIMB 172, the genome of which has not yet been sequenced. Hal1 exhibits high levels of expression in a recombinant E. coli host and can be utilised from cell lysate or used in purified form. Hal1 favours NADPH as electron donor and displays a diverse range of activities including hydroxylation, demethylation and sulfoxidation. These properties make Hal1 suitable for future biocatalytic applications or as a template for optimisation through engineering. Copyright © 2018 Elsevier Inc. All rights reserved.

Isolation of 236U and 239,240Pu from seawater samples and its determination by Accelerator Mass Spectrometry.

PubMed

López-Lora, Mercedes; Chamizo, Elena; Villa-Alfageme, María; Hurtado-Bermúdez, Santiago; Casacuberta, Núria; García-León, Manuel

2018-02-01

In this work we present and evaluate a radiochemical procedure optimised for the analysis of 236 U and 239,240 Pu in seawater samples by Accelerator Mass Spectrometry (AMS). The method is based on Fe(OH) 3 co-precipitation of actinides and uses TEVA® and UTEVA® extraction chromatography resins in a simplified way for the final U and Pu purification. In order to improve the performance of the method, the radiochemical yields are analysed in 1 to 10L seawater volumes using alpha spectrometry (AS) and Inductively Coupled Plasma Mass Spectrometry (ICP-MS). Robust 80% plutonium recoveries are obtained; however, it is found that Fe(III) concentration in the precipitation solution and sample volume are the two critical and correlated parameters influencing the initial uranium extraction through Fe(OH) 3 co-precipitation. Therefore, we propose an expression that optimises the sample volume and Fe(III) amounts according to both the 236 U and 239,240 Pu concentrations in the samples and the performance parameters of the AMS facility. The method is validated for the current setup of the 1MV AMS system (CNA, Sevilla, Spain), where He gas is used as a stripper, by analysing a set of intercomparison seawater samples, together with the Laboratory of Ion Beam Physics (ETH, Zürich, Switzerland). Copyright © 2017 Elsevier B.V. All rights reserved.

An enhanced reliability-oriented workforce planning model for process industry using combined fuzzy goal programming and differential evolution approach

NASA Astrophysics Data System (ADS)

Ighravwe, D. E.; Oke, S. A.; Adebiyi, K. A.

2018-03-01

This paper draws on the "human reliability" concept as a structure for gaining insight into the maintenance workforce assessment in a process industry. Human reliability hinges on developing the reliability of humans to a threshold that guides the maintenance workforce to execute accurate decisions within the limits of resources and time allocations. This concept offers a worthwhile point of deviation to encompass three elegant adjustments to literature model in terms of maintenance time, workforce performance and return-on-workforce investments. These fully explain the results of our influence. The presented structure breaks new grounds in maintenance workforce theory and practice from a number of perspectives. First, we have successfully implemented fuzzy goal programming (FGP) and differential evolution (DE) techniques for the solution of optimisation problem in maintenance of a process plant for the first time. The results obtained in this work showed better quality of solution from the DE algorithm compared with those of genetic algorithm and particle swarm optimisation algorithm, thus expressing superiority of the proposed procedure over them. Second, the analytical discourse, which was framed on stochastic theory, focusing on specific application to a process plant in Nigeria is a novelty. The work provides more insights into maintenance workforce planning during overhaul rework and overtime maintenance activities in manufacturing systems and demonstrated capacity in generating substantially helpful information for practice.

STARNET 2: a web-based tool for accelerating discovery of gene regulatory networks using microarray co-expression data

PubMed Central

Jupiter, Daniel; Chen, Hailin; VanBuren, Vincent

2009-01-01

Background Although expression microarrays have become a standard tool used by biologists, analysis of data produced by microarray experiments may still present challenges. Comparison of data from different platforms, organisms, and labs may involve complicated data processing, and inferring relationships between genes remains difficult. Results STARNET 2 is a new web-based tool that allows post hoc visual analysis of correlations that are derived from expression microarray data. STARNET 2 facilitates user discovery of putative gene regulatory networks in a variety of species (human, rat, mouse, chicken, zebrafish, Drosophila, C. elegans, S. cerevisiae, Arabidopsis and rice) by graphing networks of genes that are closely co-expressed across a large heterogeneous set of preselected microarray experiments. For each of the represented organisms, raw microarray data were retrieved from NCBI's Gene Expression Omnibus for a selected Affymetrix platform. All pairwise Pearson correlation coefficients were computed for expression profiles measured on each platform, respectively. These precompiled results were stored in a MySQL database, and supplemented by additional data retrieved from NCBI. A web-based tool allows user-specified queries of the database, centered at a gene of interest. The result of a query includes graphs of correlation networks, graphs of known interactions involving genes and gene products that are present in the correlation networks, and initial statistical analyses. Two analyses may be performed in parallel to compare networks, which is facilitated by the new HEATSEEKER module. Conclusion STARNET 2 is a useful tool for developing new hypotheses about regulatory relationships between genes and gene products, and has coverage for 10 species. Interpretation of the correlation networks is supported with a database of previously documented interactions, a test for enrichment of Gene Ontology terms, and heat maps of correlation distances that may be used to compare two networks. The list of genes in a STARNET network may be useful in developing a list of candidate genes to use for the inference of causal networks. The tool is freely available at , and does not require user registration. PMID:19828039

Multiple response optimisation of processing and formulation parameters of pH sensitive sustained release pellets of capecitabine for targeting colon.

PubMed

Pandey, Sonia; Swamy, S M Vijayendra; Gupta, Arti; Koli, Akshay; Patel, Swagat; Maulvi, Furqan; Vyas, Bhavin

2018-04-29

To optimise the Eudragit/Surelease ® -coated pH-sensitive pellets for controlled and target drug delivery to the colon tissue and to avoid frequent high dosing and associated side effects which restrict its use in the colorectal-cancer therapy. The pellets were prepared using extrusion-spheronisation technique. Box-Behnken and 3 2 full factorial designs were applied to optimise the process parameters [extruder sieve size, spheroniser-speed, and spheroniser-time] and the coating levels [%w/v of Eudragit S100/Eudragit-L100 and Surelease ® ], respectively, to achieve the smooth optimised size pellets with sustained drug delivery without prior drug release in upper gastrointestinal tract (GIT). The design proposed the optimised batch by selecting independent variables at; extruder sieve size (X 1  = 1 mm), spheroniser speed (X 2  = 900 revolutions per minute, rpm), and spheroniser time (X 3  = 15 min) to achieve pellet size of 0.96 mm, aspect ratio of 0.98, and roundness 97.42%. The 16%w/v coating strength of Surelease ® and 13%w/v coating strength of Eudragit showed pH-dependent sustained release up to 22.35 h (t 99% ). The organ distribution study showed the absence of the drug in the upper part of GIT tissue and the presence of high level of capecitabine in the caecum and colon tissue. Thus, the presence of Eudragit coat prevent the release of drug in stomach and the inner Surelease ® coat showed sustained drug release in the colon tissue. The study demonstrates the potential of optimised Eudragit/Surelease ® -coated capecitabine-pellets for effective colon-targeted delivery system to avoid frequent high dosing and associated systemic side effects of drug.

Methodologie experimentale pour evaluer les caracteristiques des plateformes graphiques avioniques

NASA Astrophysics Data System (ADS)

Legault, Vincent

Within a context where the aviation industry intensifies the development of new visually appealing features and where time-to-market must be as short as possible, rapid graphics processing benchmarking in a certified avionics environment becomes an important issue. With this work we intend to demonstrate that it is possible to deploy a high-performance graphics application on an avionics platform that uses certified graphical COTS components. Moreover, we would like to bring to the avionics community a methodology which will allow developers to identify the needed elements for graphics system optimisation and provide them tools that can measure the complexity of this type of application and measure the amount of resources to properly scale a graphics system according to their needs. As far as we know, no graphics performance profiling tool dedicated to critical embedded architectures has been proposed. We thus had the idea of implementing a specialized benchmarking tool that would be an appropriate and effective solution to this problem. Our solution resides in the extraction of the key graphics specifications from an inherited application to use them afterwards in a 3D image generation application.

An improved predictive functional control method with application to PMSM systems

NASA Astrophysics Data System (ADS)

Li, Shihua; Liu, Huixian; Fu, Wenshu

2017-01-01

In common design of prediction model-based control method, usually disturbances are not considered in the prediction model as well as the control design. For the control systems with large amplitude or strong disturbances, it is difficult to precisely predict the future outputs according to the conventional prediction model, and thus the desired optimal closed-loop performance will be degraded to some extent. To this end, an improved predictive functional control (PFC) method is developed in this paper by embedding disturbance information into the system model. Here, a composite prediction model is thus obtained by embedding the estimated value of disturbances, where disturbance observer (DOB) is employed to estimate the lumped disturbances. So the influence of disturbances on system is taken into account in optimisation procedure. Finally, considering the speed control problem for permanent magnet synchronous motor (PMSM) servo system, a control scheme based on the improved PFC method is designed to ensure an optimal closed-loop performance even in the presence of disturbances. Simulation and experimental results based on a hardware platform are provided to confirm the effectiveness of the proposed algorithm.

Femtosecond optical injection of intact plant cells using a reconfigurable platform

NASA Astrophysics Data System (ADS)

Mitchell, Claire A.; Kalies, Stefan; Cizmar, Tomas; Bellini, Nicola; Kubasik-Thayil, Anisha; Heisterkamp, Alexander; Torrance, Lesley; Roberts, Alison G.; Gunn-Moore, Frank J.; Dholakia, Kishan

2014-03-01

The use of ultrashort-pulsed lasers for molecule delivery and transfection has proved to be a non-invasive and highly efficient technique for a wide range of mammalian cells. This present study investigates the effectiveness of femtosecond photoporation in plant cells, a hard-to-manipulate yet agriculturally relevant cell type, specifically suspension tobacco BY-2 cells. Both spatial and temporal shaping of the light field is employed to optimise the delivery of membrane impermeable molecules into plant cells using a reconfigurable optical system designed to be able to switch easily between different spatial modes and pulse durations. The use of a propagation invariant Bessel beam was found to increase the number of cells that could be viably optoinjected, when compared to the use of a Gaussian beam. Photoporation with a laser producing sub-12 fs pulses, coupled with a dispersion compensation system to retain the pulse duration at focus, reduced the power required for efficient optical injection by 1.5-1.8 times when compared to a photoporation with a 140 fs laser output.

Cameras and settings for optimal image capture from UAVs

NASA Astrophysics Data System (ADS)

Smith, Mike; O'Connor, James; James, Mike R.

2017-04-01

Aerial image capture has become very common within the geosciences due to the increasing affordability of low payload (<20 kg) Unmanned Aerial Vehicles (UAVs) for consumer markets. Their application to surveying has led to many studies being undertaken using UAV imagery captured from consumer grade cameras as primary data sources. However, image quality and the principles of image capture are seldom given rigorous discussion which can lead to experiments being difficult to accurately reproduce. In this contribution we revisit the underpinning concepts behind image capture, from which the requirements for acquiring sharp, well exposed and suitable imagery are derived. This then leads to discussion of how to optimise the platform, camera, lens and imaging settings relevant to image quality planning, presenting some worked examples as a guide. Finally, we challenge the community to make their image data open for review in order to ensure confidence in the outputs/error estimates, allow reproducibility of the results and have these comparable with future studies. We recommend providing open access imagery where possible, a range of example images, and detailed metadata to rigorously describe the image capture process.

Distribution uniformity of laser-accelerated proton beams

NASA Astrophysics Data System (ADS)

Zhu, Jun-Gao; Zhu, Kun; Tao, Li; Xu, Xiao-Han; Lin, Chen; Ma, Wen-Jun; Lu, Hai-Yang; Zhao, Yan-Ying; Lu, Yuan-Rong; Chen, Jia-Er; Yan, Xue-Qing

2017-09-01

Compared with conventional accelerators, laser plasma accelerators can generate high energy ions at a greatly reduced scale, due to their TV/m acceleration gradient. A compact laser plasma accelerator (CLAPA) has been built at the Institute of Heavy Ion Physics at Peking University. It will be used for applied research like biological irradiation, astrophysics simulations, etc. A beamline system with multiple quadrupoles and an analyzing magnet for laser-accelerated ions is proposed here. Since laser-accelerated ion beams have broad energy spectra and large angular divergence, the parameters (beam waist position in the Y direction, beam line layout, drift distance, magnet angles etc.) of the beamline system are carefully designed and optimised to obtain a radially symmetric proton distribution at the irradiation platform. Requirements of energy selection and differences in focusing or defocusing in application systems greatly influence the evolution of proton distributions. With optimal parameters, radially symmetric proton distributions can be achieved and protons with different energy spread within ±5% have similar transverse areas at the experiment target. Supported by National Natural Science Foundation of China (11575011, 61631001) and National Grand Instrument Project (2012YQ030142)

Optimised frequency modulation for continuous-wave optical magnetic resonance sensing using nitrogen-vacancy ensembles.

PubMed

El-Ella, Haitham A R; Ahmadi, Sepehr; Wojciechowski, Adam M; Huck, Alexander; Andersen, Ulrik L

2017-06-26

Magnetometers based on ensembles of nitrogen-vacancy centres are a promising platform for continuously sensing static and low-frequency magnetic fields. Their combination with phase-sensitive (lock-in) detection creates a highly versatile sensor with a sensitivity that is proportional to the derivative of the optical magnetic resonance lock-in spectrum, which is in turn dependant on the lock-in modulation parameters. Here we study the dependence of the lock-in spectral slope on the modulation of the spin-driving microwave field. Given the presence of the intrinsic nitrogen hyperfine spin transitions, we experimentally show that when the ratio between the hyperfine linewidth and their separation is ≳ 1/4, square-wave based frequency modulation generates the steepest slope at modulation depths exceeding the separation of the hyperfine lines, compared to sine-wave based modulation. We formulate a model for calculating lock-in spectra which shows excellent agreement with our experiments, and which shows that an optimum slope is achieved when the linewidth/separation ratio is ≲ 1/4 and the modulation depth is less then the resonance linewidth, irrespective of the modulation function used.

'Admit voluntary, schedule if tries to leave': placing Mental Health Acts in the context of mental health law and human rights.

PubMed

Wand, Anne; Wand, Timothy

2013-04-01

Most postgraduate training for clinicians in Australia and New Zealand regarding mental health legislation focuses on the relevant Mental Health Acts (MHAs) rather than the broader principles of mental health law. Key concepts include treatment in the least restrictive environment, voluntary access to mental health services, treatability, reciprocity and due process. Lack of awareness of these principles may result in a more risk-averse interpretation of MHAs, which is inconsistent with the spirit of mental health law and the promotion of human rights. The aim of this paper is to present some fundamental principles of mental health law, which are essential to proper clinical application of MHAs, and to demonstrate why they should form part of the curriculum for psychiatry training and continuing professional development for psychiatrists. A sound understanding of the principles of mental health law is essential for all clinicians who may be enacting aspects of MHAs. This provides the necessary platform to safeguard human rights and optimise the care of people with a mental illness.

Refinement of light-responsive transcript lists using rice oligonucleotide arrays: evaluation of gene-redundancy.

PubMed

Jung, Ki-Hong; Dardick, Christopher; Bartley, Laura E; Cao, Peijian; Phetsom, Jirapa; Canlas, Patrick; Seo, Young-Su; Shultz, Michael; Ouyang, Shu; Yuan, Qiaoping; Frank, Bryan C; Ly, Eugene; Zheng, Li; Jia, Yi; Hsia, An-Ping; An, Kyungsook; Chou, Hui-Hsien; Rocke, David; Lee, Geun Cheol; Schnable, Patrick S; An, Gynheung; Buell, C Robin; Ronald, Pamela C

2008-10-06

Studies of gene function are often hampered by gene-redundancy, especially in organisms with large genomes such as rice (Oryza sativa). We present an approach for using transcriptomics data to focus functional studies and address redundancy. To this end, we have constructed and validated an inexpensive and publicly available rice oligonucleotide near-whole genome array, called the rice NSF45K array. We generated expression profiles for light- vs. dark-grown rice leaf tissue and validated the biological significance of the data by analyzing sources of variation and confirming expression trends with reverse transcription polymerase chain reaction. We examined trends in the data by evaluating enrichment of gene ontology terms at multiple false discovery rate thresholds. To compare data generated with the NSF45K array with published results, we developed publicly available, web-based tools (www.ricearray.org). The Oligo and EST Anatomy Viewer enables visualization of EST-based expression profiling data for all genes on the array. The Rice Multi-platform Microarray Search Tool facilitates comparison of gene expression profiles across multiple rice microarray platforms. Finally, we incorporated gene expression and biochemical pathway data to reduce the number of candidate gene products putatively participating in the eight steps of the photorespiration pathway from 52 to 10, based on expression levels of putatively functionally redundant genes. We confirmed the efficacy of this method to cope with redundancy by correctly predicting participation in photorespiration of a gene with five paralogs. Applying these methods will accelerate rice functional genomics.

Single-cell real-time imaging of transgene expression upon lipofection

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fiume, Giuseppe; Di Rienzo, Carmine; NEST, Scuola Normale Superiore and Istituto Nanoscienze-CNR, Piazza San Silvestro 12, 56127, Pisa

2016-05-20

Here we address the process of lipofection by quantifying the expression of a genetically-encoded fluorescent reporter at the single-cell level, and in real-time, by confocal imaging in live cells. The Lipofectamine gold-standard formulation is compared to the alternative promising DC-Chol/DOPE formulation. In both cases, we report that only dividing cells are able to produce a detectable amount of the fluorescent reporter protein. Notably, by measuring fluorescence over time in each pair of daughter cells, we find that Lipofectamine-based transfection statistically yields a remarkably higher degree of “symmetry” in protein expression between daughter cells as compared to DC-Chol/DOPE. A model ismore » envisioned in which the degree of symmetry of protein expression is linked to the number of bioavailable DNA copies within the cell before nuclear breakdown. Reported results open new perspectives for the understanding of the lipofection mechanism and define a new experimental platform for the quantitative comparison of transfection reagents. -- Highlights: •The process of lipofection is followed by quantifying the transgene expression in real time. •The Lipofectamine gold-standard is compared to the promising DC-Chol/DOPE formulation. •We report that only dividing cells are able to produce the fluorescent reporter protein. •The degree of symmetry of protein expression in daughter cells is linked to DNA bioavailability. •A new experimental platform for the quantitative comparison of transfection reagents is proposed.« less

Micro-Analyzer: automatic preprocessing of Affymetrix microarray data.

PubMed

Guzzi, Pietro Hiram; Cannataro, Mario

2013-08-01

A current trend in genomics is the investigation of the cell mechanism using different technologies, in order to explain the relationship among genes, molecular processes and diseases. For instance, the combined use of gene-expression arrays and genomic arrays has been demonstrated as an effective instrument in clinical practice. Consequently, in a single experiment different kind of microarrays may be used, resulting in the production of different types of binary data (images and textual raw data). The analysis of microarray data requires an initial preprocessing phase, that makes raw data suitable for use on existing analysis platforms, such as the TIGR M4 (TM4) Suite. An additional challenge to be faced by emerging data analysis platforms is the ability to treat in a combined way those different microarray formats coupled with clinical data. In fact, resulting integrated data may include both numerical and symbolic data (e.g. gene expression and SNPs regarding molecular data), as well as temporal data (e.g. the response to a drug, time to progression and survival rate), regarding clinical data. Raw data preprocessing is a crucial step in analysis but is often performed in a manual and error prone way using different software tools. Thus novel, platform independent, and possibly open source tools enabling the semi-automatic preprocessing and annotation of different microarray data are needed. The paper presents Micro-Analyzer (Microarray Analyzer), a cross-platform tool for the automatic normalization, summarization and annotation of Affymetrix gene expression and SNP binary data. It represents the evolution of the μ-CS tool, extending the preprocessing to SNP arrays that were not allowed in μ-CS. The Micro-Analyzer is provided as a Java standalone tool and enables users to read, preprocess and analyse binary microarray data (gene expression and SNPs) by invoking TM4 platform. It avoids: (i) the manual invocation of external tools (e.g. the Affymetrix Power Tools), (ii) the manual loading of preprocessing libraries, and (iii) the management of intermediate files, such as results and metadata. Micro-Analyzer users can directly manage Affymetrix binary data without worrying about locating and invoking the proper preprocessing tools and chip-specific libraries. Moreover, users of the Micro-Analyzer tool can load the preprocessed data directly into the well-known TM4 platform, extending in such a way also the TM4 capabilities. Consequently, Micro Analyzer offers the following advantages: (i) it reduces possible errors in the preprocessing and further analysis phases, e.g. due to the incorrect choice of parameters or due to the use of old libraries, (ii) it enables the combined and centralized pre-processing of different arrays, (iii) it may enhance the quality of further analysis by storing the workflow, i.e. information about the preprocessing steps, and (iv) finally Micro-Analzyer is freely available as a standalone application at the project web site http://sourceforge.net/projects/microanalyzer/. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Optimisation of process parameters on thin shell part using response surface methodology (RSM)

NASA Astrophysics Data System (ADS)

Faiz, J. M.; Shayfull, Z.; Nasir, S. M.; Fathullah, M.; Rashidi, M. M.

2017-09-01

This study is carried out to focus on optimisation of process parameters by simulation using Autodesk Moldflow Insight (AMI) software. The process parameters are taken as the input in order to analyse the warpage value which is the output in this study. There are some significant parameters that have been used which are melt temperature, mould temperature, packing pressure, and cooling time. A plastic part made of Polypropylene (PP) has been selected as the study part. Optimisation of process parameters is applied in Design Expert software with the aim to minimise the obtained warpage value. Response Surface Methodology (RSM) has been applied in this study together with Analysis of Variance (ANOVA) in order to investigate the interactions between parameters that are significant to the warpage value. Thus, the optimised warpage value can be obtained using the model designed using RSM due to its minimum error value. This study comes out with the warpage value improved by using RSM.

Optimisation of warpage on thin shell part by using particle swarm optimisation (PSO)

NASA Astrophysics Data System (ADS)

Norshahira, R.; Shayfull, Z.; Nasir, S. M.; Saad, S. M. Sazli; Fathullah, M.

2017-09-01

As the product nowadays moving towards thinner design, causing the production of the plastic product facing a lot of difficulties. This is due to the higher possibilities of defects occur as the thickness of the wall gets thinner. Demand for technique in reducing the defects increasing due to this factor. These defects has seen to be occur due to several factors in injection moulding process. In the study a Moldflow software was used in simulating the injection moulding process. While RSM is used in producing the mathematical model to be used as the input fitness function for the Matlab software. Particle Swarm Optimisation (PSO) technique is used in optimising the processing condition to reduce the amount of shrinkage and warpage of the plastic part. The results shows that there are a warpage reduction of 17.60% in x direction, 18.15% in y direction and 10.25% reduction in z direction respectively. The results shows the reliability of this artificial method in minimising the product warpage.

Letter to the editor concerning the article "Effects of acoustic feedback training in elite-standard Para-Rowing" by Schaffert and Mattes (2015).

PubMed

Hill, Holger

2015-01-01

In a case study, Schaffert and Mattes reported the application of acoustic feedback (sonification) to optimise the time course of boat acceleration. The authors attributed an increased boat speed in the feedback condition to an optimised boat acceleration (mainly during the recovery phase). However, in rowing it is biomechanically impossible to increase the boat speed significantly by reducing the fluctuations in boat acceleration during the rowing cycle. To assess such a, potentially small, optimising effect experimentally, the confounding variables must be controlled very accurately (that is especially the propulsive forces must be kept constant between experimental conditions or the differences in propulsive forces between conditions must be much smaller than the effects on boat speed resulting from an optimised movement pattern). However, this was not controlled adequately by the authors. Instead, the presented boat acceleration data show that the increased boat speed under acoustic feedback was due to increased propulsive forces.

Optimisation of composite bone plates for ulnar transverse fractures.

PubMed

Chakladar, N D; Harper, L T; Parsons, A J

2016-04-01

Metallic bone plates are commonly used for arm bone fractures where conservative treatment (casts) cannot provide adequate support and compression at the fracture site. These plates, made of stainless steel or titanium alloys, tend to shield stress transfer at the fracture site and delay the bone healing rate. This study investigates the feasibility of adopting advanced composite materials to overcome stress shielding effects by optimising the geometry and mechanical properties of the plate to match more closely to the bone. An ulnar transverse fracture is characterised and finite element techniques are employed to investigate the feasibility of a composite-plated fractured bone construct over a stainless steel equivalent. Numerical models of intact and fractured bones are analysed and the mechanical behaviour is found to agree with experimental data. The mechanical properties are tailored to produce an optimised composite plate, offering a 25% reduction in length and a 70% reduction in mass. The optimised design may help to reduce stress shielding and increase bone healing rates. Copyright © 2016 Elsevier Ltd. All rights reserved.

Thermal energy and economic analysis of a PCM-enhanced household envelope considering different climate zones in Morocco

NASA Astrophysics Data System (ADS)

Kharbouch, Yassine; Mimet, Abdelaziz; El Ganaoui, Mohammed; Ouhsaine, Lahoucine

2018-07-01

This study investigates the thermal energy potentials and economic feasibility of an air-conditioned family household-integrated phase change material (PCM) considering different climate zones in Morocco. A simulation-based optimisation was carried out in order to define the optimal design of a PCM-enhanced household envelope for thermal energy effectiveness and cost-effectiveness of predefined candidate solutions. The optimisation methodology is based on coupling Energyplus® as a dynamic simulation tool and GenOpt® as an optimisation tool. Considering the obtained optimum design strategies, a thermal energy and economic analysis are carried out to investigate PCMs' integration feasibility in the Moroccan constructions. The results show that the PCM-integrated household envelope allows minimising the cooling/heating thermal energy demand vs. a reference household without PCM. While for the cost-effectiveness optimisation, it has been deduced that the economic feasibility is stilling insufficient under the actual PCM market conditions. The optimal design parameters results are also analysed.

Paediatric CT protocol optimisation: a design of experiments to support the modelling and optimisation process.

PubMed

Rani, K; Jahnen, A; Noel, A; Wolf, D

2015-07-01

In the last decade, several studies have emphasised the need to understand and optimise the computed tomography (CT) procedures in order to reduce the radiation dose applied to paediatric patients. To evaluate the influence of the technical parameters on the radiation dose and the image quality, a statistical model has been developed using the design of experiments (DOE) method that has been successfully used in various fields (industry, biology and finance) applied to CT procedures for the abdomen of paediatric patients. A Box-Behnken DOE was used in this study. Three mathematical models (contrast-to-noise ratio, noise and CTDI vol) depending on three factors (tube current, tube voltage and level of iterative reconstruction) were developed and validated. They will serve as a basis for the development of a CT protocol optimisation model. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Evolving optimised decision rules for intrusion detection using particle swarm paradigm

NASA Astrophysics Data System (ADS)

Sivatha Sindhu, Siva S.; Geetha, S.; Kannan, A.

2012-12-01

The aim of this article is to construct a practical intrusion detection system (IDS) that properly analyses the statistics of network traffic pattern and classify them as normal or anomalous class. The objective of this article is to prove that the choice of effective network traffic features and a proficient machine-learning paradigm enhances the detection accuracy of IDS. In this article, a rule-based approach with a family of six decision tree classifiers, namely Decision Stump, C4.5, Naive Baye's Tree, Random Forest, Random Tree and Representative Tree model to perform the detection of anomalous network pattern is introduced. In particular, the proposed swarm optimisation-based approach selects instances that compose training set and optimised decision tree operate over this trained set producing classification rules with improved coverage, classification capability and generalisation ability. Experiment with the Knowledge Discovery and Data mining (KDD) data set which have information on traffic pattern, during normal and intrusive behaviour shows that the proposed algorithm produces optimised decision rules and outperforms other machine-learning algorithm.

Multi-objective thermodynamic optimisation of supercritical CO2 Brayton cycles integrated with solar central receivers

NASA Astrophysics Data System (ADS)

Vasquez Padilla, Ricardo; Soo Too, Yen Chean; Benito, Regano; McNaughton, Robbie; Stein, Wes

2018-01-01

In this paper, optimisation of the supercritical CO? Brayton cycles integrated with a solar receiver, which provides heat input to the cycle, was performed. Four S-CO? Brayton cycle configurations were analysed and optimum operating conditions were obtained by using a multi-objective thermodynamic optimisation. Four different sets, each including two objective parameters, were considered individually. The individual multi-objective optimisation was performed by using Non-dominated Sorting Genetic Algorithm. The effect of reheating, solar receiver pressure drop and cycle parameters on the overall exergy and cycle thermal efficiency was analysed. The results showed that, for all configurations, the overall exergy efficiency of the solarised systems achieved at maximum value between 700°C and 750°C and the optimum value is adversely affected by the solar receiver pressure drop. In addition, the optimum cycle high pressure was in the range of 24.2-25.9 MPa, depending on the configurations and reheat condition.

An integrated and dynamic optimisation model for the multi-level emergency logistics network in anti-bioterrorism system

NASA Astrophysics Data System (ADS)

Liu, Ming; Zhao, Lindu

2012-08-01

Demand for emergency resources is usually uncertain and varies quickly in anti-bioterrorism system. Besides, emergency resources which had been allocated to the epidemic areas in the early rescue cycle will affect the demand later. In this article, an integrated and dynamic optimisation model with time-varying demand based on the epidemic diffusion rule is constructed. The heuristic algorithm coupled with the MATLAB mathematical programming solver is adopted to solve the optimisation model. In what follows, the application of the optimisation model as well as a short sensitivity analysis of the key parameters in the time-varying demand forecast model is presented. The results show that both the model and the solution algorithm are useful in practice, and both objectives of inventory level and emergency rescue cost can be controlled effectively. Thus, it can provide some guidelines for decision makers when coping with emergency rescue problem with uncertain demand, and offers an excellent reference when issues pertain to bioterrorism.

Losses of nutrients and anti-nutrients in red and white sorghum cultivars after decorticating in optimised conditions.

PubMed

Galán, María Gimena; Llopart, Emilce Elina; Drago, Silvina Rosa

2018-05-01

The aims were to optimise pearling process of red and white sorghum by assessing the effects of pearling time and grain moisture on endosperm yield and flour ash content and to assess nutrient and anti-nutrient losses produced by pearling different cultivars in optimised conditions. Both variables significantly affected both responses. Losses of ashes (58%), proteins (9.5%), lipids (54.5%), Na (37%), Mg (48.5%) and phenolic compounds (43%) were similar among red and white hybrids. However, losses of P (30% vs. 51%), phytic acid (47% vs. 66%), Fe (22% vs. 55%), Zn (32% vs. 62%), Ca (60% vs. 66%), K (46% vs. 61%) and Cu (51% vs. 71%) were lower for red than white sorghum due to different degree of extraction and distribution of components in the grain. Optimised pearling conditions were extrapolated to other hybrids, indicating these criteria could be applied at industrial level to obtain refined flours with proper quality and good endosperm yields.

Natural Erosion of Sandstone as Shape Optimisation.

PubMed

Ostanin, Igor; Safonov, Alexander; Oseledets, Ivan

2017-12-11

Natural arches, pillars and other exotic sandstone formations have always been attracting attention for their unusual shapes and amazing mechanical balance that leave a strong impression of intelligent design rather than the result of a stochastic process. It has been recently demonstrated that these shapes could have been the result of the negative feedback between stress and erosion that originates in fundamental laws of friction between the rock's constituent particles. Here we present a deeper analysis of this idea and bridge it with the approaches utilized in shape and topology optimisation. It appears that the processes of natural erosion, driven by stochastic surface forces and Mohr-Coulomb law of dry friction, can be viewed within the framework of local optimisation for minimum elastic strain energy. Our hypothesis is confirmed by numerical simulations of the erosion using the topological-shape optimisation model. Our work contributes to a better understanding of stochastic erosion and feasible landscape formations that could be found on Earth and beyond.

Optimisation of sensing time and transmission time in cognitive radio-based smart grid networks

NASA Astrophysics Data System (ADS)

Yang, Chao; Fu, Yuli; Yang, Junjie

2016-07-01

Cognitive radio (CR)-based smart grid (SG) networks have been widely recognised as emerging communication paradigms in power grids. However, a sufficient spectrum resource and reliability are two major challenges for real-time applications in CR-based SG networks. In this article, we study the traffic data collection problem. Based on the two-stage power pricing model, the power price is associated with the efficient received traffic data in a metre data management system (MDMS). In order to minimise the system power price, a wideband hybrid access strategy is proposed and analysed, to share the spectrum between the SG nodes and CR networks. The sensing time and transmission time are jointly optimised, while both the interference to primary users and the spectrum opportunity loss of secondary users are considered. Two algorithms are proposed to solve the joint optimisation problem. Simulation results show that the proposed joint optimisation algorithms outperform the fixed parameters (sensing time and transmission time) algorithms, and the power cost is reduced efficiently.

A generic methodology for the optimisation of sewer systems using stochastic programming and self-optimizing control.

PubMed

Mauricio-Iglesias, Miguel; Montero-Castro, Ignacio; Mollerup, Ane L; Sin, Gürkan

2015-05-15

The design of sewer system control is a complex task given the large size of the sewer networks, the transient dynamics of the water flow and the stochastic nature of rainfall. This contribution presents a generic methodology for the design of a self-optimising controller in sewer systems. Such controller is aimed at keeping the system close to the optimal performance, thanks to an optimal selection of controlled variables. The definition of an optimal performance was carried out by a two-stage optimisation (stochastic and deterministic) to take into account both the overflow during the current rain event as well as the expected overflow given the probability of a future rain event. The methodology is successfully applied to design an optimising control strategy for a subcatchment area in Copenhagen. The results are promising and expected to contribute to the advance of the operation and control problem of sewer systems. Copyright © 2015 Elsevier Ltd. All rights reserved.

Optimisation of synergistic biomass-degrading enzyme systems for efficient rice straw hydrolysis using an experimental mixture design.

PubMed

Suwannarangsee, Surisa; Bunterngsook, Benjarat; Arnthong, Jantima; Paemanee, Atchara; Thamchaipenet, Arinthip; Eurwilaichitr, Lily; Laosiripojana, Navadol; Champreda, Verawat

2012-09-01

Synergistic enzyme system for the hydrolysis of alkali-pretreated rice straw was optimised based on the synergy of crude fungal enzyme extracts with a commercial cellulase (Celluclast™). Among 13 enzyme extracts, the enzyme preparation from Aspergillus aculeatus BCC 199 exhibited the highest level of synergy with Celluclast™. This synergy was based on the complementary cellulolytic and hemicellulolytic activities of the BCC 199 enzyme extract. A mixture design was used to optimise the ternary enzyme complex based on the synergistic enzyme mixture with Bacillus subtilis expansin. Using the full cubic model, the optimal formulation of the enzyme mixture was predicted to the percentage of Celluclast™: BCC 199: expansin=41.4:37.0:21.6, which produced 769 mg reducing sugar/g biomass using 2.82 FPU/g enzymes. This work demonstrated the use of a systematic approach for the design and optimisation of a synergistic enzyme mixture of fungal enzymes and expansin for lignocellulosic degradation. Copyright © 2012 Elsevier Ltd. All rights reserved.

MiSTIC, an integrated platform for the analysis of heterogeneity in large tumour transcriptome datasets

PubMed Central

Sargeant, Tobias; Laperrière, David; Ismail, Houssam; Boucher, Geneviève; Rozendaal, Marieke; Lavallée, Vincent-Philippe; Ashton-Beaucage, Dariel; Wilhelm, Brian; Hébert, Josée; Hilton, Douglas J.

2017-01-01

Abstract Genome-wide transcriptome profiling has enabled non-supervised classification of tumours, revealing different sub-groups characterized by specific gene expression features. However, the biological significance of these subtypes remains for the most part unclear. We describe herein an interactive platform, Minimum Spanning Trees Inferred Clustering (MiSTIC), that integrates the direct visualization and comparison of the gene correlation structure between datasets, the analysis of the molecular causes underlying co-variations in gene expression in cancer samples, and the clinical annotation of tumour sets defined by the combined expression of selected biomarkers. We have used MiSTIC to highlight the roles of specific transcription factors in breast cancer subtype specification, to compare the aspects of tumour heterogeneity targeted by different prognostic signatures, and to highlight biomarker interactions in AML. A version of MiSTIC preloaded with datasets described herein can be accessed through a public web server (http://mistic.iric.ca); in addition, the MiSTIC software package can be obtained (github.com/iric-soft/MiSTIC) for local use with personalized datasets. PMID:28472340

MouSensor: A Versatile Genetic Platform to Create Super Sniffer Mice for Studying Human Odor Coding.

PubMed

D'Hulst, Charlotte; Mina, Raena B; Gershon, Zachary; Jamet, Sophie; Cerullo, Antonio; Tomoiaga, Delia; Bai, Li; Belluscio, Leonardo; Rogers, Matthew E; Sirotin, Yevgeniy; Feinstein, Paul

2016-07-26

Typically, ∼0.1% of the total number of olfactory sensory neurons (OSNs) in the main olfactory epithelium express the same odorant receptor (OR) in a singular fashion and their axons coalesce into homotypic glomeruli in the olfactory bulb. Here, we have dramatically increased the total number of OSNs expressing specific cloned OR coding sequences by multimerizing a 21-bp sequence encompassing the predicted homeodomain binding site sequence, TAATGA, known to be essential in OR gene choice. Singular gene choice is maintained in these "MouSensors." In vivo synaptopHluorin imaging of odor-induced responses by known M71 ligands shows functional glomerular activation in an M71 MouSensor. Moreover, a behavioral avoidance task demonstrates that specific odor detection thresholds are significantly decreased in multiple transgenic lines, expressing mouse or human ORs. We have developed a versatile platform to study gene choice and axon identity, to create biosensors with great translational potential, and to finally decode human olfaction. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.