Interaction of peptides, peptidomimetics and other drug candidates with the DI/tripeptide transport system in intestinal epithelial cells, using the in vitro caco-2 cell culture system

An uptake system was developed using Caco-2 cell monolayers and the dipeptide, glycyl-[3H]L-proline, as a probe compound. Glycyl-[3H]L-proline uptake was via the di-/tripeptide transport system (DTS) and, exhibited concentration-, pH- and temperature-dependency. Dipeptides inhibited uptake of the probe, and the design of the system allowed competitors to be ranked against one another with respect to affinity for the transporter. The structural features required to ensure or increase interaction with the DTS were defined by studying the effect of a series of glycyl-L-proline and angiotensin-converting enzyme (ACE)-inhibitor (SQ-29852) analogues on the uptake of the probe. The SQ-29852 structure was divided into six domains (A-F) and competitors were grouped into series depending on structural variations within specific regions. Domain A was found to prefer a hydrophobic function, such as a phenyl group, and was intolerant to positive charges and H+ -acceptors and donors. SQ-29852 analogues were more tolerant of substitutions in the C domain, compared to glycyl-L-proline analogues, suggesting that interactions along the length of the SQ-29852 molecule may override the effects of substitutions in the C domain. SQ-29852 analogues showed a preference for a positive function, such as an amine group in this region, but dipeptide structures favoured an uncharged substitution. Lipophilic substituents in domain D increased affinity of SQ-29852 analogues with the DTS. A similar effect was observed for ACE-NEP inhibitor analogues. Domain E, corresponding to the carboxyl group was found to be tolerant of esterification for SQ-29852 analogues but not for dipeptides. Structural features which may increase interaction for one series of compounds, may not have the same effect for another series, indicating that the presence of multiple recognition sites on a molecule may override the deleterious effect of anyone change. Modifying current, poorly absorbed peptidomimetic structures to fit the proposed hypothetical model may improve oral bioavailability by increasing affinity for the DTS. The stereochemical preference of the transporter was explored using four series of compounds (SQ-29852, lysylproline, alanylproline and alanylalanine enantiomers). The L, L stereochemistry was the preferred conformation for all four series, agreeing with previous studies. However, D, D enantiomers were shown in some cases to be substrates for the DTS, although exhibiting a lower affinity than their L, L counterparts. All the ACE-inhibitors and β-lactam antibiotics investigated, produced a degree of inhibition of the probe, and thus show some affinity for the DTS. This contrasts with previous reports that found several ACE inhibitors to be absorbed via a passive process, thus suggesting that compounds are capable of binding to the transporter site and inhibiting the probe without being translocated into the cell. This was also shown to be the case for oligodeoxynucleotide conjugated to a lipophilic group (vitamin E), and highlights the possibility that other orally administered drug candidates may exert non-specific effects on the DTS and possibly have a nutritional impact. Molecular modelling of selected ACE-NEP inhibitors revealed that the three carbonyl functions can be oriented in a similar direction, and this conformation was found to exist in a local energy-minimised state, indicating that the carbonyls may possibly be involved in hydrogen-bond formation with the binding site of the DTS.

An opportunity for system dynamics in manufacturing system modelling

The computer simulation of manufacturing systems is commonly carried out using discrete event simulation (DES). Indeed, there appears to be a lack of applications of continuous simulation methods, particularly system dynamics (SD), despite evidence that this technique is suitable for industrial modelling. This paper investigates whether this is due to a decline in the general popularity of SD, or whether modelling of manufacturing systems represents a missed opportunity for SD. On this basis, the paper first gives a review of the concept of SD and fully describes the modelling technique. Following on, a survey of the published applications of SD in the 1990s is made by developing and using a structured classification approach. From this review, observations are made about the application of the SD method and opportunities for future research are suggested.

Design, synthesis and evaluation of dipeptides as probes for studies of gastrointestinal tract dipeptide transport system

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Modelling data and voice traffic over IP networks using continuous-time Markov models

Common approaches to IP-traffic modelling have featured the use of stochastic models, based on the Markov property, which can be classified into black box and white box models based on the approach used for modelling traffic. White box models, are simple to understand, transparent and have a physical meaning attributed to each of the associated parameters. To exploit this key advantage, this thesis explores the use of simple classic continuous-time Markov models based on a white box approach, to model, not only the network traffic statistics but also the source behaviour with respect to the network and application. The thesis is divided into two parts: The first part focuses on the use of simple Markov and Semi-Markov traffic models, starting from the simplest two-state model moving upwards to n-state models with Poisson and non-Poisson statistics. The thesis then introduces the convenient to use, mathematically derived, Gaussian Markov models which are used to model the measured network IP traffic statistics. As one of the most significant contributions, the thesis establishes the significance of the second-order density statistics as it reveals that, in contrast to first-order density, they carry much more unique information on traffic sources and behaviour. The thesis then exploits the use of Gaussian Markov models to model these unique features and finally shows how the use of simple classic Markov models coupled with use of second-order density statistics provides an excellent tool for capturing maximum traffic detail, which in itself is the essence of good traffic modelling. The second part of the thesis, studies the ON-OFF characteristics of VoIP traffic with reference to accurate measurements of the ON and OFF periods, made from a large multi-lingual database of over 100 hours worth of VoIP call recordings. The impact of the language, prosodic structure and speech rate of the speaker on the statistics of the ON-OFF periods is analysed and relevant conclusions are presented. Finally, an ON-OFF VoIP source model with log-normal transitions is contributed as an ideal candidate to model VoIP traffic and the results of this model are compared with those of previously published work.

Identification, mutagenesis, and transcriptional analysis of the methanesulfonate transport operon of methylosulfonomonas methylovora

Recently identified genes located downstream (3') of the msmEF (transport encoding) gene cluster, msmGH, and located 5' of the structural genes for methanesulfonate monooxygenase (MSAMO) are described from Methylosulfonomonas methylovora. Sequence analysis of the derived polypeptide sequences encoded by these genes revealed a high degree of identity to ABC-type transporters. MsmE showed similarity to a putative periplasmic substrate binding protein, MsmF resembled an integral membraneassociated protein, and MsmG was a putative ATP-binding enzyme. MsmH was thought to be the cognate permease component of the sulfonate transport system. The close association of these putative transport genes to the MSAMO structural genes msmABCD suggested a role for these genes in transport of methanesulfonic acid (MSA) into M. methylovora. msmEFGH and msmABCD constituted two operons for the coordinated expression of MSAMO and the MSA transporter systems. Reverse-transcription-PCR analysis of msmABCD and msmEFGH revealed differential expression of these genes during growth on MSA and methanol. The msmEFGH operon was constitutively expressed, whereas MSA induced expression of msmABCD. A mutant defective in msmE had considerably slower growth rates than the wild type, thus supporting the proposed role of MsmE in the transport of MSA into M. methylovora.

Interactions at the head-tape interface of a linear tape system

Many of the recent improvements in the capacity of data cartridge systems have been achieved through the use of narrower tracks, higher linear densities and continuous servo tracking with multi-channel heads. These changes have produced new tribological problems at the head/tape interface. It is crucial that the tribology of such systems is understood and this will continue since increasing storage capacities and faster transfer rates are constantly being sought. Chemical changes in the surface of single and dual layer MP tape have been correlated to signal performance. An accelerated tape tester, consisting of a custom made cycler ("loop tester"), was used to ascertain if results could be produced that were representative of a real tape drive system. A second set of experiments used a modified tape drive (Georgens cycler), which allowed the effects of the tape transport system on the tape surface to be studied. To isolate any effects on the tape surface due to the head/tape interface, read/write heads were not fitted to the cycler. Two further sets of experiments were conducted which included a head in the tape path. This allowed the effects of the head/tape interface on the physical and chemical properties of the head and tape surfaces to be investigated. It was during the final set of experiments that the effect on the head/tape interface, of an energised MR element, was investigated. The effect of operating each cycler at extreme relative humidity and temperature was investigated through the use of an environmental chamber. Extensive use was made of surface specific analytical techniques such as XPS, AFM, AES, and SEM to study the physical and chemical changes that occur at the head/tape interface. Results showed that cycling improved the signal performance of all the tapes tested. The data cartridge drive belt had an effect on the chemical properties of the tape surface on which it was in contact. Also binder degradation occurred for each tape and appeared to be greater at higher humidity. Lubricant was generally seen to migrate to the tape surface with cycling. Any surface changes likely to affect signal output occurred at the head surface rather than the tape.

Aspects of design for a spare parts provisioning system

This thesis describes an investigation by the author into the spares operation of compare BroomWade Ltd. Whilst the complete system, including the warehousing and distribution functions, was investigated, the thesis concentrates on the provisioning aspect of the spares supply problem. Analysis of the historical data showed the presence of significant fluctuations in all the measures of system performance. Two Industrial Dynamics simulation models were developed to study this phenomena. The models showed that any fluctuation in end customer demand would be amplified as it passed through the distributor and warehouse stock control systems. The evidence from the historical data available supported this view of the system's operation. The models were utilised to determine which parts of the total system could be expected to exert a critical influence on its performance. The lead time parameters of the supply sector were found to be critical and further study showed that the manner in which the lead time changed with work in progress levels was also an important factor. The problem therefore resolved into the design of a spares manufacturing system. Which exhibited the appropriate dynamic performance characteristics. The gross level of entity presentation, inherent in the Industrial Dynamics methodology, was found to limit the value of these models in the development of detail design proposals. Accordingly, an interacting job shop simulation package was developed to allow detailed evaluation of organisational factors on the performance characteristics of a manufacturing system. The package was used to develop a design for a pilot spares production unit. The need for a manufacturing system to perform successfully under conditions of fluctuating demand is not limited to the spares field. Thus, although the spares exercise provides an example of the approach, the concepts and techniques developed can be considered to have broad application throughout batch manufacturing industry.

A systems and cybernetic perspective on complex problem solving

This thesis is concerned with Organisational Problem Solving. The work reflects the complexities of organisational problem situations and the eclectic approach that has been necessary to gain an understanding of the processes involved. The thesis is structured into three main parts. Part I describes the author's understanding of problems and suitable approaches. Chapter 2 identifies the Transcendental Realist (TR) view of science (Harre 1970, Bhaskar 1975) as the best general framework for identifying suitable approaches to complex organisational problems. Chapter 3 discusses the relationship between Checkland's methodology (1972) and TR. The need to generate iconic (explanatory) models of the problem situation is identified and the ability of viable system modelling to supplement the modelling stage of the methodology is explored in Chapter 4. Chapter 5 builds further on the methodology to produce an original iconic model of the methodological process. The model characterises the mechanisms of organisational problem situations as well as desirable procedural steps. The Weltanschauungen (W's) or "world views" of key actors is recognised as central to the mechanisms involved. Part II describes the experience which prompted the theoretical investigation. Chapter 6 describes the first year of the project. The success of this stage is attributed to the predominance of a single W. Chapter 7 describes the changes in the organisation which made the remaining phase of the project difficult. These difficulties are attributed to a failure to recognise the importance of differing W's. Part III revisits the theoretical and organisational issues. Chapter 8 identifies a range of techniques embodying W's which are compatible with .the framework of Part I and which might usefully supplement it. Chapter 9 characterises possible W's in the sponsoring organisation. Throughout the work, an attempt 1s made to reflect the process as well as the product of the author's leaving.

Adaptive message rate control of infrastructured DSRC vehicle networks for coexisting road safety and non-safety applications

Intelligent transport system (ITS) has large potentials on road safety applications as well as nonsafety applications. One of the big challenges for ITS is on the reliable and cost-effective vehicle communications due to the large quantity of vehicles, high mobility, and bursty traffic from the safety and non-safety applications. In this paper, we investigate the use of dedicated short-range communications (DSRC) for coexisting safety and non-safety applications over infrastructured vehicle networks. The main objective of this work is to improve the scalability of communications for vehicles networks, ensure QoS for safety applications, and leave as much as possible bandwidth for non-safety applications. A two-level adaptive control scheme is proposed to find appropriate message rate and control channel interval for safety applications. Simulation results demonstrated that this adaptive method outperforms the fixed control method under varying number of vehicles. © 2012 Wenyang Guan et al.

Bayesian precalibration of a large stochastic microsimulation model

Calibration of stochastic traffic microsimulation models is a challenging task. This paper proposes a fast iterative probabilistic precalibration framework and demonstrates how it can be successfully applied to a real-world traffic simulation model of a section of the M40 motorway and its surrounding area in the U.K. The efficiency of the method stems from the use of emulators of the stochastic microsimulator, which provides fast surrogates of the traffic model. The use of emulators minimizes the number of microsimulator runs required, and the emulators' probabilistic construction allows for the consideration of the extra uncertainty introduced by the approximation. It is shown that automatic precalibration of this real-world microsimulator, using turn-count observational data, is possible, considering all parameters at once, and that this precalibrated microsimulator improves on the fit to observations compared with the traditional expertly tuned microsimulation. © 2000-2011 IEEE.

Integration of a graph-based model indexer in commercial modelling tools

Softeam has over 20 years of experience providing UML-based modelling solutions, such as its Modelio modelling tool, and its Constellation enterprise model management and collaboration environment. Due to the increasing number and size of the models used by Softeam’s clients, Softeam joined the MONDO FP7 EU research project, which worked on solutions for these scalability challenges and produced the Hawk model indexer among other results. This paper presents the technical details and several case studies on the integration of Hawk into Softeam’s toolset. The first case study measured the performance of Hawk’s Modelio support using varying amounts of memory for the Neo4j backend. In another case study, Hawk was integrated into Constellation to provide scalable global querying of model repositories. Finally, the combination of Hawk and the Epsilon Generation Language was compared against Modelio for document generation: for the largest model, Hawk was two orders of magnitude faster.

Transmission of image data over digital networks involving mobile terminals

There is a growing demand for data transmission over digital networks involving mobile terminals. An important class of data required for transmission over mobile terminals is image information such as street maps, floor plans and identikit images. This sort of transmission is of particular interest to the service industries such as the Police force, Fire brigade, medical services and other services. These services cannot be applied directly to mobile terminals because of the limited capacity of the mobile channels and the transmission errors caused by the multipath (Rayleigh) fading. In this research, transmission of line diagram images such as floor plans and street maps, over digital networks involving mobile terminals at transmission rates of 2400 bits/s and 4800 bits/s have been studied. A low bit-rate source encoding technique using geometric codes is found to be suitable to represent line diagram images. In geometric encoding, the amount of data required to represent or store the line diagram images is proportional to the image detail. Thus a simple line diagram image would require a small amount of data. To study the effect of transmission errors due to mobile channels on the transmitted images, error sources (error files), which represent mobile channels under different conditions, have been produced using channel modelling techniques. Satisfactory models of the mobile channel have been obtained when compared to the field test measurements. Subjective performance tests have been carried out to evaluate the quality and usefulness of the received line diagram images under various mobile channel conditions. The effect of mobile transmission errors on the quality of the received images has been determined. To improve the quality of the received images under various mobile channel conditions, forward error correcting codes (FEC) with interleaving and automatic repeat request (ARQ) schemes have been proposed. The performance of the error control codes have been evaluated under various mobile channel conditions. It has been shown that a FEC code with interleaving can be used effectively to improve the quality of the received images under normal and severe mobile channel conditions. Under normal channel conditions, similar results have been obtained when using ARQ schemes. However, under severe mobile channel conditions, the FEC code with interleaving shows better performance.

Molecular regulation of iron uptake in pseudomonas aeruginosa

The microbial demand for iron is often met by the elaboration of siderophores into the surrounding medium and expression of cognate outer membrane receptors for the ferric siderophore complexes. Conditions of iron limitation, such as those encountered in vivo, cause Pseudomonas aeruginosa to express two high-affinity iron-uptake systems based on pyoverdin and pyochelin. These systems will operate both in the organism's natural habitat, soil and water, where the solubility of iron at neutral pH is extremely low, and in the human host where the availability of free iron is too low to sustain bacterial growth due to the iron-binding glycoproteins transferrin and lactoferrin. Cross-feeding and radiolabelled iron uptake experiments demonstrated that pyoverdin biosynthesis and uptake were highly heterogeneous amongst P.aeruginosa strains, that growth either in the presence of pyoverdin or pyochelin resulted in induction of specific IROMPs, and that induction of iron uptake is siderophore-specific. The P.aeruginosa Tn5 mutant PH1 is deficient in ferripyoverdin uptake and resistant to pyocin Sa, suggesting that the site of interaction of pyocin Sa is a ferripyoverdin receptor. Additional Tn5 mutants appeared to exploit different strategies to achieve pyocin Sa-resistance, involving modifications in expression of pyoverdin-mediated iron uptake, indicating that complex regulatory systems exist to enable these organisms to compete effectively for iron. Modulation of expression of IROMPs prompted a study of the mechanism of uptake of a semi-synthetic C(7) α-formamido substituted cephalosporin BRL 41897A. Sensitivity to this agent correlated with expression of the 75 kDa ferri-pyochelin receptor and demonstrated the potential of high-affinity iron uptake systems for targeting of novel antibiotics. Studies with ferri-pyoverdin uptake-deficient mutant PH1 indicated that expression of outer membrane protein G (OprG), which is usually expressed under iron-rich conditions and repressed under iron-deficient conditions, was perturbed. Attempts were made to clone the oprG gene using a degenerate probe based on the N-terminal amino acid sequence. A strongly hybridising HindIll restriction fragment was cloned and sequenced, but failed to reveal an open reading frame correspondmg to OprG. However, there appears to be good evidence that a part of the gene codmg for the hydrophilic membrane-associated ATP-binding component of a hitherto uncharacterised periplasmic- binding-protein-dependent transport system has been isolated. The full organisation and sequence of the operon, and substrate for this putative transport system, are yet: to be elucidated,

Mechanism of uptake of the catecholic (7)-α-formamido cephalosporin BRL 41897A by klebsiella pneumoniae

The catecholic cephalosporin BRL 41897 A is resistant to β-lactamases and is taken up by bacteria via the iron transport system. The uptake of this antibiotic in E.coli uses the Fiu and Cir outer membrane proteins, whereas in P. aerugtnosa it enters via the pyochelin transport system. In this thesis mutants of K. pneumoniae resistant to BRL 41897A were isolated using TnphoA mutagenesis and used to study the mechanism of uptake of BRL 41897A by K. pneumoniae. The activity of BRL 41897A towards the parent strain (M10) was increased in iron depleted media, whereas no significant differences in the resistant (KSL) mutants were observed. Three mutants (KSL19, KSL38and KSL59) produced decreased amounts of certain iron-regulated outer membrane proteins. The uptake of 55Fe-BRL 41897A by M10 in iron-deficient medium was higher than in iron-rich medium. This result indicated the involvement of an iron transport system in the uptake of BRL 41897A by K. pneumoniae. Uptake by the KSL mutants in iron-deficient culture was higher than that by M10. This result, supported by analysis of outer membrane and periplasmic proteins of the KSL mutants, indicates that loss of one outer membrane protein can be compensated by over expression of other outer membrane and/or periplasmic proteins. However, the increased uptake of BRL 41897A by the KSL mutants did not reflect increased activity towards these strains, indicating that there are defects in the transport of BRL 41897A resulting in failure to reach the penicillin binding protein target sites in the cytoplasmic membrane. Southern blotting of chromosomal digests and sequencing in one mutant (KSL19) showed that only one copy of TnphoA was inserted into its chromosome. A putative TnphoA inserted gene in KSL19, designated kslA, carrying a signal sequence was identified. Transformation of a fragment containing the kslA gene into KSL19 cells restored the sensitivity to BRL 41897A to that of the parent strain. Data base peptide sequence searches revealed that the kslA gene in the KSL19 has some amino acid homology with the E. coli ExbD protein, which is involved in stabilisation of the TonB protein. 

Integrated logistics and supply chain management:the state of practice in Ireland

The Republic of Ireland and Northern Ireland were provided with aid to offset locational disadvantages in the run up to the Single European Market. Since then the Republic has emerged as the fastest growing member of the E.U. Success has not been underpinned by the transport system, suggesting that business has had to overcome locational disadvantages by strong performance elsewhere in the supply chain. The evidence indicates that there are Irish firms operating supply chain management techniques at a truly international standard. The problem is that there are so few in that category Meeting Ireland’s competitiveness challenge means closing the gap between the small group of large and foreign-owned firms, which display excellence in SCM, and the larger group of indigenous small and medium size businesses, which do not.