994 resultados para threonine transfer RNA ligase


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All plants are typically confronted to simultaneous biotic and abiotic stress throughout their life cycle. Low inorganic phosphate (Pi) is the most common nutrient deficiency limiting plant growth in natural and agricultural ecosystems while insect herbivory accounts for major losses in plant productivity and impacts on ecological and evolutionary changes in plant populations. Here we report that plants experiencing Pi deficiency induce the jasmonic acid (JA) pathway and enhance their defence against insect herbivory. The phol mutant is impaired in the translocation of Pi from roots to shoots and shows the typical symptoms associated with Pi deficiency, including high anthocyanin and poor shoot growth. These phol shoot phenotypes were significantly attenuated by blocking the JA biosynthesis or signalling pathways. Wounded phol leaves hyper-accumulated JA in comparison to wild type, leading to increased resistance against the generalist herbivore Spodoptera littoralis. Pi deficiency also triggered enhanced resistance to herbivory in wild-type Arabidopsis as well as tomato and tobacco, revealing that the link between Pi deficiency and JA-mediated herbivory resistance is conserved in a diversity of plants, including crops. We performed a phol suppressor screen to identify new components involved in the adaptation of plants to Pi deficiency. We report that the THO RNA TRANSCRIPTION AND EXPORT (THO/TREX) complex is a crucial component involved in modulating the Pi- deficiency response. Knockout mutants of at least three members of the THO/TREX complex, including TEX1, HPR1, and TH06, can suppress the phol shoot phenotype. Grafting experiments showed that loss of function of TEX1 only in the root was sufficient to suppress the reduced shoot growth phenotype of phol while maintaining low Pi contents. This indicates that TEX1 is involved in a long distance root-to-shoot signalling component of the Pi-deficiency response. We identified a small MYB-like transcription factor, RAD LIKE 3 (RL3), as a potential downstream target of the THO/TREX complex. RL3 expression is induced in phol mutants but attenuated in phol-7 texl-4 double mutants. Identical to knockout mutants of the THO/TREX complex, rl3 mutants can suppress the phol shoot phenotypes. Interestingly, RL3 is induced during Pi deficiency and is described in the literature as likely being mobile. It is therefore a promising new candidate involved in the root-to-shoot Pi-deficiency signalling response. Finally, we report that PHOl and its homologue PH01:H3 are involved in the co-regulation of Pi and zinc (Zn) homeostasis. PH01;H3 is up-regulated in response to Zn deficiency and, like PHOl, is expressed in the root vascular cylinder and localizes to the Golgi when expressed transiently in tobacco cells. The phol;h3 mutant accumulates more Pi as compared to wild-type when grown in Zn-deficient medium, but this increase is abolished in the phol phol;h3 double mutant. These results suggest that PH01;H3 restricts the PHOl-mediated root-to-shoot Pi transfer in responsé to Zn deficiency. Résumé Au cours de leur cycle de vie, toutes les plantes sont généralement confrontées à divers stress biotiques et abiotiques. La carence nutritionnelle la plus fréquente, limitant la croissance des plantes dans les écosystèmes naturels et agricoles, est la faible teneur en phosphate inorganique (Pi). Au niveau des stress biotiques, les insectes herbivores sont responsables de pertes majeures de rendement et ont un impact considérable sur les changements écologiques et évolutifs dans les populations des plantes. Au cours de ce travail, nous avons mis en évidence que les plantes en situation de carence en Pi induisent la voie de l'acide jasmonique (JA) et augmentent leur défense contre les insectes herbivores. Le mutant phol est déficient dans le transport du phosphate des racines aux feuilles et démontre les symptômes typiques associés à la carence, tels que la forte concentration en anthocyane et une faible croissance foliaire. Ces phénotypes du mutant phol sont significativement atténués lors d'un blocage de la voie de la biosynthèse ou des voies de signalisation du JA. La blessure des feuilles induit une hyper-accumulation de JA chez phol, résultant en une augmentation de la résistance contre l'herbivore généraliste Spodoptera littoralis. Outre Arabidopsis, la carence en Pi induit une résistance accrue aux insectes herbivores aussi chez la tomate et le tabac. Cette découverte révèle que le lien entre la carence en Pi et la résistance aux insectes herbivores via le JA est conservé dans différentes espèces végétales, y compris les plantes de grandes cultures. Nous avons effectué un crible du suppresseur de phol afin d'identifier de nouveaux acteurs impliqués dans l'adaptation de la plante à la carence en Pi. Nous rapportons que le complexe nommé THO RNA TRANSCRIPTION AND EXPORT (THO/TREX) est un élément crucial participant à la réponse des feuilles à la carence en Pi. Les mutations d'au moins trois des membres que composent le complexe THO/TREX, incluant TEX1, HPR1 et 77/06, peuvent supprimer le phénotype de phol. Des expériences de greffes ont montré que la perte de fonction de TEX1, seulement dans la racine, est suffisante pour supprimer le phénotype de la croissance réduite des parties aériennes observé chez le mutant phol, tout en maintenant de faibles teneurs en Pi foliaire. Ceci indique que TEX1 est impliqué dans la signalisation longue distance entre les racines et les parties aériennes. Nous avons identifié un petit facteur de transcription proche de la famille des MYB, RAD LIKE 3 (RL3), comme une cible potentielle en aval du complexe THO / TREX. L'expression du gène RL3 est induite dans le mutant phol mais atténuée dans le double mutant phol-7 texl-4. Exactement comme les plantes mutées d'un des membres du complexe THO/TREX, le mutant rl3 peut supprimer le phénotype foliaire de phol. RL3 est induit au cours d'une carence en Pi et est décrit dans la littérature comme étant potentiellement mobile. Par conséquent, il serait un nouveau candidat potentiellement impliqué dans la réponse longue distance entre les racines et les parties aériennes lors d'un déficit en Pi. Enfin, nous reportons que PHOl et son homologue PHOl: H3 sont impliqués dans la co- régulation de l'homéostasie du Pi et du zinc (Zn). PHOl; H3 est sur-exprimé en réponse au déficit en Zn et, comme PHOl, est exprimé dans les tissus vasculaires des racines et se localise dans l'appareil de Golgi lorsqu'il est exprimé de manière transitoire dans des cellules de tabac. Le mutant phol; h3 accumule plus de Pi par rapport aux plantes sauvages lorsqu'il est cultivé sur un milieu déficient en Zn, mais cette augmentation en Pi est abolie dans le double mutant phol phol; h3. Ces résultats suggèrent qu'en réponse à une carence en Zn, PHOl; H3 limite l'action de PHOl et diminue le transfert du Pi des racines aux parties aériennes.

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Technical developments have made it possible to analyze very low amounts of DNA. This has many advantages, but the drawback of this technological progress is that interpretation of the results becomes increasingly complex: the number of mixed DNA profiles increased relatively to single source DNA profiles and stochastic effects in the DNA profile, such as drop-in and drop-out, are more frequently observed. Moreover, the relevance of low template DNA material regarding the activities alleged is not as straightforward as it was a few years ago, when for example large quantities of blood were recovered. The possibility of secondary and tertiary transfer is now becoming an issue. The purpose of this research is twofold: first, to study the transfer of DNA from the handler and secondly, to observe if handlers would transfer DNA from persons closely connected to them. We chose to mimic cases where the offender would attack a person with a knife. As a first approach, we envisaged that the defense would not give an alternative explanation for the origin of the DNA. In our transfer experiments (4 donors, 16 experiments each, 64 traces), 3% of the traces were single DNA profiles. Most of the time, the DNA profile of the person handling the knife was present as the major profile: in 83% of the traces the major contributor profile corresponded to the stabber's DNA profile (in single stains and mixtures). Mixture with no clear major/minor fraction (12%) were observed. 5% of the traces were considered of insufficient quality (more than 3 contributors, presence of a few minor peaks). In that case, we considered that the stabber's DNA was absent. In our experiments, no traces allowed excluding the stabber, however it must be noted that precautions were taken to minimize background DNA as knives were cleaned before the experiments. DNA profiles of the stabber's colleagues were not observed. We hope that this study will allow for a better understanding of the transfer mechanism and of how to assess and describe results given activity level propositions. In this preliminary research, we have focused on the transfer of DNA on the hand of the person. Besides, more research is needed to assign the probability of the results given an alternative activity proposed by the defense, for instance when the source of the DNA is not contested, but that the activities are.

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Treatment failure and symptomatic relapse are major concerns in American tegumentary leishmaniasis (TL). Such complications are seen frequently in Leishmania guyanensis infections, in which patients respond variously to first-line antileishmanials and are more prone to develop chronic cutaneous leishmaniasis. The factors underlying this pathology, however, are unknown. Recently, we reported that a double-stranded RNA virus, Leishmania RNA virus 1 (LRV1), nested within L. guyanensis parasites is able to exacerbate experimental murine leishmaniasis by inducing a hyperinflammatory response. This report investigates the prevalence of LRV1 in human L. guyanensis infection and its effect on treatment efficacy, as well as its correlation to symptomatic relapses after the completion of first-line treatment. In our cohort of 75 patients with a diagnosis of primary localized American TL, the prevalence of LRV1-positive L. guyanensis infection was elevated to 58%. All patients infected with LRV1-negative L. guyanensis were cured after 1 dose (22 of 31 [71%]) or 2 doses (31 of 31 [100%]) of pentamidine. In contrast, 12 of 44 LRV1-positive patients (27%) presented with persistent infection and symptomatic relapse that required extended therapy and the use of second-line drugs. Finally, LRV1 presence was associated with a significant increase in levels of intra-lesional inflammatory markers. In conclusion, LRV1 status in L. guyanensis infection is significantly predictive (P = .0009) of first-line treatment failure and symptomatic relapse and has the potential to guide therapeutic choices in American TL.

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The possibility of printing two-dimensional micropatterns of biomolecule solutions is of great interest in many fields of research in biomedicine, from cell-growth and development studies to the investigation of the mechanisms of communication between cells. Although laser-induced forward transfer (LIFT) has been extensively used to print micrometric droplets of biological solutions, the fabrication of complex patterns depends on the feasibility of the technique to print micron-sized lines of aqueous solutions. In this study we investigate such a possibility through the analysis of the influence of droplet spacing of a water and glycerol solution on the morphology of the features printed by LIFT. We prove that it is indeed possible to print long and uniform continuous lines by controlling the overlap between adjacent droplets. We show how, depending on droplet spacing, several printed morphologies are generated, and we offer, in addition, a simple explanation of the observed behavior based on the jetting dynamics characteristic of the LIFT of liquids.

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TRAF-interacting protein (TRIP) is a ubiquitously expressed nucleolar E3 ubiquitin ligase. Ubiquitination of proteins is a post-translational modification, which decides on the cellular fate of the protein. TRIP in vivo substrate has not been yet identified. However, TRIP has been shown to play an important role in cellular proliferation, especially in keratinocytes. TRIP was found to be up-regulated in basal cell carcinoma (BCC) at the mRNA level. This prompted us to elucidate its role in skin proliferative diseases such as cancer by analyzing its expression in BCCs at protein level and in squamous cell carcinoma (SCC) at mRNA and protein level. To that purpose, we performed a real-time PCR (qPCR) analysis followed by an immunohistochemistry (IHC) on formalin-fixed, paraffin-embedded (FFPE) biopsies. The real-time PCR was performed on 12 RNA samples of which 6 were extracted from SCC biopsies and 6 from normal human skin. The results were statistically insignificant. Further analyses are needed on new RNA samples. The IHC assay was performed on 20 biopsies from BCCs, 21 biopsies from SCCs and on 5 tissues from normal human skin. The results obtained showed an extensive expression of TRIP in keratinocytes nuclei. Due to various limitations related to the technique and to doubts about preservation of the antigens in the tissues from normal human skin, we could not highlight a clear difference in TRIP expression between the different tissues. In conclusion, further analyses are needed on new RNA samples (qPCR) and on better preserved FFPE tissues from normal skin (IHC) to assess TRIP relative expression in BCCs and SCCs versus normal human skin.

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Better models are needed for radiative heat transfer in boiler furnaces. If the process is known better, combustion in the furnace can be optimized to produce low emissions. It makes the process to be environmental friendly. Furthermore, if there is a better model of the furnace it can more fully explain what is happening inside the furnace. Using of the model one can quickly and easily analyze how it operates with bio fuels, moist fuels or difficult fuels and improve the operation. Models helps with better estimation of furnace dimensions and result in more accurate understanding of operation. Key component lacking in these models is radiative heat transfer in particle laden gases. If there are no particles than radiative heat transfer can be calculated approximately. There are two problems with current models when used with flow modeling. The first one is a need to account for a particle laden gas and the second one is an absence of a fast algorithm. Fast calculation is needed if radiative heat transfer calculation is done for a large CDF model. Computations slow down if time is required for calculating radiative properties over and over again. This thesis presents a band model for radiative heat transfer in boiler furnaces. Advantage is a quickness of calculation and account of particles in the process.

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We previously reported that A. hydrophila GalU mutants were still able to produce UDP-glucose introduced as a glucose residue in their lipopolysaccharide core. In this study, we found the unique origin of this UDP-glucose from a branched α-glucan surface polysaccharide. This glucan, surface attached through the O-antigen ligase (WaaL), is common to the mesophilic Aeromonas strains tested. The Aeromonas glucan is produced by the action of the glycogen synthase (GlgA) and the UDP-Glc pyrophosphorylase (GlgC), the latter wrongly indicated as an ADP-Glc pyrophosphorylase in the Aeromonas genomes available. The Aeromonas glycogen synthase is able to react with UDP or ADP-glucose, which is not the case of E. coli glycogen synthase only reacting with ADP-glucose. The Aeromonas surface glucan has a role enhancing biofilm formation. Finally, for the first time to our knowledge, a clear preference on behalf of bacterial survival and pathogenesis is observed when choosing to produce one or other surface saccharide molecules to produce (lipopolysaccharide core or glucan).

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The importance of the regional level in research has risen in the last few decades and a vast literature in the fields of, for instance, evolutionary and institutional economics, network theories, innovations and learning systems, as well as sociology, has focused on regional level questions. Recently the policy makers and regional actors have also began to pay increasing attention to the knowledge economy and its needs, in general, and the connectivity and support structures of regional clusters in particular. Nowadays knowledge is generally considered as the most important source of competitive advantage, but even the most specialised forms of knowledge are becoming a short-lived resource for example due to the accelerating pace of technological change. This emphasizes the need of foresight activities in national, regional and organizational levels and the integration of foresight and innovation activities. In regional setting this development sets great challenges especially in those regions having no university and thus usually very limited resources for research activities. Also the research problem of this dissertation is related to the need to better incorporate the information produced by foresight process to facilitate and to be used in regional practice-based innovation processes. This dissertation is a constructive case study the case being Lahti region and a network facilitating innovation policy adopted in that region. Dissertation consists of a summary and five articles and during the research process a construct or a conceptual model for solving this real life problem has been developed. It is also being implemented as part of the network facilitating innovation policy in the Lahti region.

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This thesis gathers knowledge about ongoing high-temperature reactor projects around the world. Methods for calculating coolant flow and heat transfer inside a pebble-bed reactor core are also developed. The thesis begins with the introduction of high-temperature reactors including the current state of the technology. Process heat applications that could use the heat from a high-temperature reactor are also introduced. A suitable reactor design with data available in literature is selected for the calculation part of the thesis. Commercial computational fluid dynamics software Fluent is used for the calculations. The pebble-bed is approximated as a packed-bed, which causes sink terms to the momentum equations of the gas flowing through it. A position dependent value is used for the packing fraction. Two different models are used to calculate heat transfer. First a local thermal equilibrium is assumed between the gas and solid phases and a single energy equation is used. In the second approach, separate energy equations are used for the phases. Information about steady state flow behavior, pressure loss, and temperature distribution in the core is obtained as results of the calculations. The effect of inlet mass flow rate to pressure loss is also investigated. Data found in literature and the results correspond each other quite well, considered the amount of simplifications in the calculations. The models developed in this thesis can be used to solve coolant flow and heat transfer in a pebble-bed reactor, although additional development and model validation is needed for better accuracy and reliability.

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Breast cancer is the most common diagnosed cancer and the leading cause of cancer death among females worldwide. It is considered a highly heterogeneous disease and it must be classified into more homogeneous groups. Hence, the purpose of this study was to classify breast tumors based on variations in gene expression patterns derived from RNA sequencing by using different class discovery methods. 42 breast tumors paired-samples were sequenced by Illumine Genome Analyzer and the data was analyzed and prepared by TopHat2 and htseq-count. As reported previously, breast cancer could be grouped into five main groups known as basal epithelial-like group, HER2 group, normal breast-like group and two Luminal groups with a distinctive expression profile. Classifying breast tumor samples by using PAM50 method, the most common subtype was Luminal B and was significantly associated with ESR1 and ERBB2 high expression. Luminal A subtype had ESR1 and SLC39A6 significant high expression, whereas HER2 subtype had a high expression of ERBB2 and CNNE1 genes and low luminal epithelial gene expression. Basal-like and normal-like subtypes were associated with low expression of ESR1, PgR and HER2, and had significant high expression of cytokeratins 5 and 17. Our results were similar compared with TGCA breast cancer data results and with known studies related with breast cancer classification. Classifying breast tumors could add significant prognostic and predictive information to standard parameters, and moreover, identify marker genes for each subtype to find a better therapy for patients with breast cancer.

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This dissertation is based on four articles dealing with modeling of ozonation. The literature part of this considers some models for hydrodynamics in bubble column simulation. A literature review of methods for obtaining mass transfer coefficients is presented. The methods presented to obtain mass transfer are general models and can be applied to any gas-liquid system. Ozonation reaction models and methods for obtaining stoichiometric coefficients and reaction rate coefficients for ozonation reactions are discussed in the final section of the literature part. In the first article, ozone gas-liquid mass transfer into water in a bubble column was investigated for different pH values. A more general method for estimation of mass transfer and Henry’s coefficient was developed from the Beltrán method. The ozone volumetric mass transfer coefficient and the Henry’s coefficient were determined simultaneously by parameter estimation using a nonlinear optimization method. A minor dependence of the Henry’s law constant on pH was detected at the pH range 4 - 9. In the second article, a new method using the axial dispersion model for estimation of ozone self-decomposition kinetics in a semi-batch bubble column reactor was developed. The reaction rate coefficients for literature equations of ozone decomposition and the gas phase dispersion coefficient were estimated and compared with the literature data. The reaction order in the pH range 7-10 with respect to ozone 1.12 and 0.51 the hydroxyl ion were obtained, which is in good agreement with literature. The model parameters were determined by parameter estimation using a nonlinear optimization method. Sensitivity analysis was conducted using object function method to obtain information about the reliability and identifiability of the estimated parameters. In the third article, the reaction rate coefficients and the stoichiometric coefficients in the reaction of ozone with the model component p-nitrophenol were estimated at low pH of water using nonlinear optimization. A novel method for estimation of multireaction model parameters in ozonation was developed. In this method the concentration of unknown intermediate compounds is presented as a residual COD (chemical oxygen demand) calculated from the measured COD and the theoretical COD for the known species. The decomposition rate of p-nitrophenol on the pathway producing hydroquinone was found to be about two times faster than the p-nitrophenol decomposition rate on the pathway producing 4- nitrocatechol. In the fourth article, the reaction kinetics of p-nitrophenol ozonation was studied in a bubble column at pH 2. Using the new reaction kinetic model presented in the previous article, the reaction kinetic parameters, rate coefficients, and stoichiometric coefficients as well as the mass transfer coefficient were estimated with nonlinear estimation. The decomposition rate of pnitrophenol was found to be equal both on the pathway producing hydroquinone and on the path way producing 4-nitrocathecol. Comparison of the rate coefficients with the case at initial pH 5 indicates that the p-nitrophenol degradation producing 4- nitrocathecol is more selective towards molecular ozone than the reaction producing hydroquinone. The identifiability and reliability of the estimated parameters were analyzed with the Marcov chain Monte Carlo (MCMC) method. @All rights reserved. No part of the publication may be reproduced, stored in a retrieval system, or transmitted, in any form or by any means, electronic, mechanical, photocopying, recording, or otherwise, without the prior permission of the author.

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Drug transporting membrane proteins are expressed in various human tissues and blood-tissue barriers, regulating the transfer of drugs, toxins and endogenous compounds into or out of the cells. Various in vitro and animal experiments suggest that P-glycoprotein (P-gp) forms a functional barrier between maternal and fetal blood circulation in the placenta thereby protecting the fetus from exposure to xenobiotics during pregnancy. The multidrug resistance-associated protein 1 (MRP1) is a relatively less studied transporter protein in the human placenta. The aim of this study series was to study the role of placental transporters, apical P-gp and basal MRP1, using saquinavir as a probe drug, and to study transfer of quetiapine and the role of P-gp in its transfer in the dually perfused human placenta/cotyledon. Furthermore, two ABCB1 (encoding P-gp) polymorphisms (c.3435C>T, p.Ile1145Ile and c.2677G>T/A, p.Ala893Ser/Thr) were studied to determine their impact on P-gp protein expression level and on the transfer of the study drugs. Also, the influence of the P-gp protein expression level on the transfer of the study drugs was addressed. Because P-gp and MRP1 are ATP-dependent drug-efflux pumps, it was studied whether exogenous ATP is needed for the function of ATP-dependent transporter in the present experimental model. The present results indicated that the addition of exogenous ATP was not necessary for transporter function in the perfused human placental cotyledon. Saquinavir and quetiapine were both found to cross the human placenta; transplacental transfer (TPTAUC %) for saquinavir was <0.5% and for quetiapine 3.7%. Pharmacologic blocking of P-gp led to disruption of the blood-placental barrier (BPB) and increased the placental transfer of P-gp substrate, saquinavir, into the fetal circulation by 6- to 8-fold. In reversed perfusions P-gp, MRP1 and possibly OATP2B1 had a negligible role in the fetal-to-maternal transfer of saquinavir. The TPTAUC % of saquinavir was about 100-fold greater from the fetal side to the maternal side compared with the maternal-to-fetal transfer. P-gp activity is not likely to modify the placental transfer of quetiapine. Higher P-gp protein expression levels were associated with the variant allele 3435T, but no correlation was found between the TPTAUC % of saquinavir and placental P-gp protein expression. The present results indicate that P-gp activity drastically affects the fetal exposure to saquinavir, and suggest that pharmacological blockade of the P-gp activity during pregnancy may pose an increased risk for adverse fetal outcome. The blockade of P-gp activity could be used in purpose to obtain higher drug concentration to the fetal side, for example, in prevention (to decrease virus transfer to fetal side) or in treating sick fetus.

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A rapid, expedient and enantioselective method for the synthesis of beta-hydroxy amines and monosubstituted aziridines in up to 99% e.e., via asymmetric transfer hydrogenation of a-amino ketones and cyclisation through treatment with tosyl chloride and base, is described. (1R,2R)-N-(para-toluenesulfonyl)-1,2-ethylenediamine with formic acid has been utilised as a ligand for the Ruthenium (II) catalysed enantioselective transfer hydrogenation of the ketones.The chiral 2-methyl aziridine, which is a potentially more efficient bonding agent for Rocket Solid Propellant has been successfully achieved.

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Data traffic caused by mobile advertising client software when it is communicating with the network server can be a pain point for many application developers who are considering advertising-funded application distribution, since the cost of the data transfer might scare their users away from using the applications. For the thesis project, a simulation environment was built to mimic the real client-server solution for measuring the data transfer over varying types of connections with different usage scenarios. For optimising data transfer, a few general-purpose compressors and XML-specific compressors were tried for compressing the XML data, and a few protocol optimisations were implemented. For optimising the cost, cache usage was improved and pre-loading was enhanced to use free connections to load the data. The data traffic structure and the various optimisations were analysed, and it was found that the cache usage and pre-loading should be enhanced and that the protocol should be changed, with report aggregation and compression using WBXML or gzip.

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This study illustrates the different types of plate heat exchangers that are commonly used in various domestic and industrial applications. The main purpose of this paper was to devise a methodology that is capable of calculating optimum number of plates in the design of a plate heat exchanger. To obtain the appropriate number of plates, typically several iterations must be made before a final acceptable design is completed, since plate amount depends on many factors such as, flow velocities, physical properties of the streams, flow channel geometry, allowable pressure drop, plate dimensions, and the gap between the plates. The methodology presented here can be used as a general guide for designing a plate heat exchanger. To investigate the effects of relevant parameters on the thermal-hydraulic design of a plate heat exchanger, several experiments were carried out for single-phase and counter flow arrangement with two brazed plate heat exchangers by varying the flow rates and the inlet temperatures of the fluid streams. The actual heat transfer coefficients obtained based on the experiment were nearly close to the calculated values and to improve the design, a correction factor was introduced. Besides, the effect of flow channel velocity on the pressure drop inside the unit is presented.