Action research: minimising the impact of disruptive incidents for rail passengers through improved sharing of information

This paper reports on an action research project based in the UK rail industry; it used a novel type of Soft Systems Methodology (known as PrOH Modelling) to facilitate change in a major Train Operating Company (TOC). The project looked at a number of different disruptive incidents to compare and contrast practice via the Mitigate, Prevent, React and Recover (MPRR) Framework. One incident is detailed in depth. The paper also looks at the general process of conducting action research. This work will be of interest for researchers in the rail sector and for those conducting operations action research projects.

The Nrf2-ARE activation protect neurones against oxidative stress

Oxidative stress has been implicated in the pathogenesis of many neurodegenerative diseases including Alzheimer’s disease. The transcription factor, Nrf2 (nuclear factor E2-related factor 2) that binds to the antioxidant responsive element (ARE) activates a battery of genes encoding enzymes and factors essential for neuronal survival. We have investigated the hypothesis that a downstream product of cyclooxygenase(COX-2), 15-deoxy-delta (12, 14)-prostagland in J2 (15d-PGJ2) has protective effects by activating the Nrf2 pathway during oxidative stress.Human neuroblastoma cells (SHSY5Y) were differentiated intoneuronal-like cells as described previously (Gimenez-Cassina et al.,2006). SHSY5Y cells were co-treated with 10 mM buthionine sulfoximine (BSO) 7 10 mM 15d-PGJ2. Cell viability was measured by MTT assay and cellular glutathione (GSH) levels were measured after treating cells for0.5-24 hours by GSH recycling assay. Cellular Nrf2 levels were determined by immunoblotting. IL-6 levels were measured by ELISA.15d-PGJ2 alone lowered GSH levels 30min after the treatment(12.870.64 nmol/mg protein) and returned to untreated control levels at 16hours (28.173.6 nmol/mg protein; Po0.01). Compared to intracellular GSH levels in untreated cells (27.871.8 nmol/mg protein) BSO treatment alone significantly decreased GSH (9.672.1 nmol/mg protein;Po0.001) but co-incubation with 15d-PGJ2 for 24 hours prevented the depletion elicited by BSO(21.372.7 nmol/mg protein). Compared to untreated cells BSO treatment decrease dIL-6 secretion (from 0.941.6ng/ml to 0.6971.3ng/ml) and total Nrf2 protein levels (by21%). Co-incubation with15d-PGJ2 for 24 hours with BSO did not change IL-6(0.6771.4ng/ml) or total Nrf2 level at any time point. This study suggests that neuronal toxicity resulting from glutathione depletion canbere stored by the induction of Nrf2-ARE pathway and the role of the Nrf2 signalling merits further investigation in neurodegenerative diseases.

Antimicrobial effect of Artemisia species on Pseudomonas aeruginosa

Antibiotic resistance has emerged as a severe problem in hospital-acquired infectious disease. The Gram-negative bacterium Pseudomonas aeruginosa is found to cause secondary infection in immune-compromised patients. Unfortunately, it is resistant to virtually all β-lactam antibiotics such as penicillin, cephalosporin and others. Researchers are seeking for new compounds to treat several antibiotic-resistant bacterial strains. Artemisia plant extracts are commonly used for their therapeutic properties by natives throughout dry regions of North and South America. Here, they are administered as an alternative medicine for stomach problems and other complex health issues. In this study, the antimicrobial effects of plant extracts from several Artemisia species as well as compounds dehydroleucodine and dehydroparishin-B (sesquiterpenes derived specifically from A. douglasiana) were used as treatments against the pathogenicity effects of P. aeruginosa. Results showed that both compounds effectively inhibit the secretion of LasB elastase, biofilm formation and type III secretion, but fail to control LasA protease. This is a significant observation because these virulent factors are crucial in establishing P.aeruginosa infection. The results from this study signify a plausible role for future alternative therapy in the biomedical field, which recommends DhL and DhP can be studied as key compounds against bacterial infections of Pseudomonas aeruginosa.

Regulation of Rab5 GTPase activity during Pseudomonas aeruginosa-macrophage interaction

Pseudomonas aeruginosa is a Gram-negative opportunistic pathogen. Several antibiotic resistant strains of P. aeruginosa are commonly found as secondary infection in immune-compromised patients leaving significant mortality and healthcare cost. Pseudomonas aeruginosa successfully avoids the process of phagocytosis, the first line of host defense, by secreting several toxic effectors. Effectors produced from P. aeruginosa Type III secretion system are critical molecules required to disrupt mammalian cell signaling and holds particular interest to the scientists studying host-pathogen interaction. Exoenzyme S (ExoS) is a bi-functional Type III effector that ADP-ribosylates several intracellular Ras (Rat sarcoma) and Rab (Response to abscisic acid) small GTPases in targeted host cells. The Rab5 protein acts as a rate limiting protein during phagocytosis by switching from a GDP- bound inactive form to a GTP-bound active form. Activation and inactivation of Rab5 protein is regulated by several Rab5-GAPs (GTPase Activating Proteins) and Rab5-GEFs (Rab5-Guanine nucleotide Exchange Factors). Some pathogenic bacteria have shown affinity for Rab proteins during infection and make their way inside the cell. This dissertation demonstrated that Rab5 plays a critical role during early steps of P. aeruginosa invasion in J774-Eclone macrophages. It was found that live, but not heat inactivated, P. aeruginosa inhibited phagocytosis that occurred in conjunction with down-regulation of Rab5 activity. Inactivation of Rab5 was dependent on ExoS ADP-ribosyltransferase activity, and more than one arginine sites in Rab5 are possible targets for ADP-ribosylation modification. However, the expression of Rin1, but not other Rab5GEFs (Rabex-5 and Rap6) reversed this down-regulation of Rab5 in vivo. Further studies revealed that the C-terminus of Rin1 carrying Rin1:Vps9 and Rin1:RA domains are required for optimal Rab5 activation in conjunction with active Ras. These observations demonstrate a novel mechanism of Rab5 targeting to phagosome via Rin1 during the phagocytosis of P. aeruginosa. The second part of this dissertation investigated antimicrobial activities of Dehydroleucodine (DhL), a secondary metabolite from Artemisia douglasiana, against P. aeruginosa growth and virulence. Populations of several P. aeruginosa strains were completely susceptible to DhL at a concentration between 0.48~0.96 mg/ml and treatment at a threshold concentration (0.12 mg/ml) inhibited growth and many virulent activities without damaging the integrity of the cell suggesting anti-Pseudomonas activity of DhL.

Use of Galleria mellonella as a model organism to study Legionella pneumophila infection.

Legionella pneumophila, the causative agent of a severe pneumonia named Legionnaires' disease, is an important human pathogen that infects and replicates within alveolar macrophages. Its virulence depends on the Dot/Icm type IV secretion system (T4SS), which is essential to establish a replication permissive vacuole known as the Legionella containing vacuole (LCV). L. pneumophila infection can be modeled in mice however most mouse strains are not permissive, leading to the search for novel infection models. We have recently shown that the larvae of the wax moth Galleria mellonella are suitable for investigation of L. pneumophila infection. G. mellonella is increasingly used as an infection model for human pathogens and a good correlation exists between virulence of several bacterial species in the insect and in mammalian models. A key component of the larvae's immune defenses are hemocytes, professional phagocytes, which take up and destroy invaders. L. pneumophila is able to infect, form a LCV and replicate within these cells. Here we demonstrate protocols for analyzing L. pneumophila virulence in the G. mellonella model, including how to grow infectious L. pneumophila, pretreat the larvae with inhibitors, infect the larvae and how to extract infected cells for quantification and immunofluorescence microscopy. We also describe how to quantify bacterial replication and fitness in competition assays. These approaches allow for the rapid screening of mutants to determine factors important in L. pneumophila virulence, describing a new tool to aid our understanding of this complex pathogen.

Cortactin recruitment by enterohemorrhagic Escherichia coli O157:H7 during infection in vitro and ex vivo

Enterohemorrhagic Escherichia coli (EHEC) O157:H7 is an important human pathogen that colonizes the gut mucosa via attaching and effacing (A/E) lesions; A/E lesion formation in vivo and ex vivo is dependent on the type III secretion system (T3SS) effector Tir. Infection of cultured cells by EHEC leads to induction of localized actin polymerization, which is dependent on Tir and a second T3SS effector protein, TccP, also known as EspF(U). Recently, cortactin was shown to bind both the N terminus of Tir and TccP via its SH3 domain and to play a role in EHEC-triggered actin polymerization in vitro. In this study, we investigated the recruitment of cortactin to the site of EHEC adhesion during infection of in vitro-cultured cells and mucosal surfaces ex vivo (using human terminal ileal in vitro organ cultures [IVOC]). We have shown that cortactin is recruited to the site of EHEC adhesion in vitro downstream of TccP and N-WASP. Deletion of the entire N terminus of Tir or replacing the N-terminal polyproline region with alanines did not abrogate actin polymerization or cortactin recruitment. In contrast, recruitment of cortactin to the site of EHEC adhesion in IVOC is TccP independent. These results imply that cortactin is recruited to the site of EHEC adhesion in vitro and ex vivo by different mechanisms and suggest that cortactin might have a role during EHEC infection of mucosal surfaces.

LtpD is a novel legionella pneumophila effector that binds phosphatidylinositol 3-phosphate and inositol monophosphatase IMPA1

The Dot/Icm type IV secretion system (T4SS) of Legionella pneumophila is crucial for the pathogen to survive in protozoa and cause human disease. Although more than 275 effector proteins are delivered into the host cell by the T4SS, the function of the majority is unknown. Here we have characterized the Dot/Icm effector LtpD. During infection, LtpD localized to the cytoplasmic face of the membrane of the Legionella-containing vacuole (LCV). In A549 lung epithelial cells, ectopically expressed LtpD localized to large vesicular structures that contained markers of endosomal compartments. Systematic analysis of LtpD fragments identified an internal 17-kDa fragment, LtpD_471-626, which was essential for targeting ectopically expressed LtpD to vesicular structures and for the association of translocated LtpD with the LCV. LtpD_471-626 bound directly to phosphatidylinositol 3-phosphate [PtdIns(3)P] in vitro and colocalized with the PtdIns(3)P markers FYVE and SetA in cotransfected cells. LtpD was also found to bind the host cell enzyme inositol (myo)-1 (or 4)-monophosphatase 1, an important phosphatase involved in phosphoinositide production. Analysis of the role of LtpD in infection showed that LtpD is involved in bacterial replication in THP-1 macrophages, the larvae of Galleria mellonella, and mouse lungs. Together, these data suggest that LtpD is a novel phosphoinositide- binding L. pneumophila effector that has a role in intracellular bacterial replication. © 2013, American Society for Microbiology.

Sistema avanzado de alarmas para el reactor RA6.

Los sistemas de alarmas constituyen un elemento clave en las plantas modernas de procesos industriales. A lo largo de los años, los mismos han ido evolucionando de la mano del importante desarrollo en la industria del software, para pasar de ser simples paneles de anunciación y lámparas cableadas hasta complejos sistemas inteligentes que asisten al operador en sus funciones de operación. En el desarrollo de este trabajo se planteó diseñar un Sistema Avanzado de Alarmas para el Reactor Nuclear de Investigación RA6 contemplando las nuevas tecnologías existentes para incorporar mejoras a la actual sala de control. Para ello se trabajó siguiendo la metodología propuesta por la guía de diseño de sistemas de alarmas ANSI / ISA- SP-18. Para asistir al diseño y la verificación del sistema se utilizó un modelo termohidráulico de la planta desarrollado en Matlab/Simulink. Entre las nuevas herramientas incorporadas en el prototipo final obtenido se pueden mencionar: creación de archivos históricos, asignación de prioridades, supresiones de alarmas según estado operativo, filtrado y agrupamiento de alarmas.

Sistema avanzado de alarmas para el reactor RA6.

Los sistemas de alarmas constituyen un elemento clave en las plantas modernas de procesos industriales. A lo largo de los años, los mismos han ido evolucionando de la mano del importante desarrollo en la industria del software, para pasar de ser simples paneles de anunciación y lámparas cableadas hasta complejos sistemas inteligentes que asisten al operador en sus funciones de operación. En el desarrollo de este trabajo se planteó diseñar un Sistema Avanzado de Alarmas para el Reactor Nuclear de Investigación RA6 contemplando las nuevas tecnologías existentes para incorporar mejoras a la actual sala de control. Para ello se trabajó siguiendo la metodología propuesta por la guía de diseño de sistemas de alarmas ANSI / ISA- SP-18. Para asistir al diseño y la verificación del sistema se utilizó un modelo termohidráulico de la planta desarrollado en Matlab/Simulink. Entre las nuevas herramientas incorporadas en el prototipo final obtenido se pueden mencionar: creación de archivos históricos, asignación de prioridades, supresiones de alarmas según estado operativo, filtrado y agrupamiento de alarmas.

Análise do custo-benefício de sistemas de cobertas em edificações comerciais para o clima de Natal/RN visando eficiência energética

This research consists in studying the influence of the various type of construction systems of roofs with their energy efficiency as well as on the cost benefit for the commercial buildings on the temperatures condition of the city of Natal/RN. The main goal of this research is to analyze the cost benefit of the construction systems of roofs available on the market, taking into consideration the energy efficiency of the commercial buildings artificially air conditioned in order to be used by the projectors and to be adequated to the temperatures condition of the city of Natal/RN. The method of valuation of the cost benefit of roof systems consists in six steps: Features and simulation of the reference building; Analyze of sensitivity; Analyzes, features and simulation of alternatives of roof construction systems; Analyze of the cost of implementation; Analyze of the benefits of the alternatives comparing to the base case; And finally the analyze of the cost benefit. The model type chosen as reference was stores with pre molded buildings and system of roof with fiber ciment and ceiling . The thermal results showed the influence of the roof system on the energy efficiency of the building. The Final results of the simulations of the alternatives comes to a conclusion that the absortance is the variable that presents the best cost benefit relation and the reduction on the thermal transmittance still has limitations because of the high cost

A bacterial acetyltransferase targets the protein kinase ZIP1, a positive regulator of plant immunity

Pseudomonas syringae is a model bacterial pathogen that penetrates the leaf to reach the plant apoplast, where it replicates causing disease. In order to do that, the pathogen must interfere and suppress a two-tiered plant defense response: PTI (PAMP-Triggered Immunity, or basal resistance) and ETI (Effector-Triggered Immunity). P. syringae uses a type III secretion system to directly deliver effector proteins inside the plant cell cytosol, many of which are known to suppress PTI, some of which are known to trigger ETI, and a handful of which are known to suppress ETI. Bacterial infection can also trigger a systemic plant defense response that protects the plant against additional pathogen attacks known as SAR (Systemic Acquired Resistance). We are particularly interested in the molecular and cellular mechanisms involved in effector-mediated defense evasion by P. syringae, in particular those involved in the suppression of ETI and SAR, and/or mediation of hormone signaling. Here we present data describing effector-mediated interference with plant immunity, by means of acetylation of a key positive regulator of local and systemic responses. Our work identifies a novel plant target for effector function, and characterizes its function. This work illustrates how analyzing the means by which a given effector interferes with its target can provide novel information regarding eukaryotic molecular mechanisms.

Análise do custo-benefício de sistemas de cobertas em edificações comerciais para o clima de Natal/RN visando eficiência energética

This research consists in studying the influence of the various type of construction systems of roofs with their energy efficiency as well as on the cost benefit for the commercial buildings on the temperatures condition of the city of Natal/RN. The main goal of this research is to analyze the cost benefit of the construction systems of roofs available on the market, taking into consideration the energy efficiency of the commercial buildings artificially air conditioned in order to be used by the projectors and to be adequated to the temperatures condition of the city of Natal/RN. The method of valuation of the cost benefit of roof systems consists in six steps: Features and simulation of the reference building; Analyze of sensitivity; Analyzes, features and simulation of alternatives of roof construction systems; Analyze of the cost of implementation; Analyze of the benefits of the alternatives comparing to the base case; And finally the analyze of the cost benefit. The model type chosen as reference was stores with pre molded buildings and system of roof with fiber ciment and ceiling . The thermal results showed the influence of the roof system on the energy efficiency of the building. The Final results of the simulations of the alternatives comes to a conclusion that the absortance is the variable that presents the best cost benefit relation and the reduction on the thermal transmittance still has limitations because of the high cost

Collaborative filtering and deep learning based recommendation system for cold start items

Recommender system is a specific type of intelligent systems, which exploits historical user ratings on items and/or auxiliary information to make recommendations on items to the users. It plays a critical role in a wide range of online shopping, e-commercial services and social networking applications. Collaborative filtering (CF) is the most popular approaches used for recommender systems, but it suffers from complete cold start (CCS) problem where no rating record are available and incomplete cold start (ICS) problem where only a small number of rating records are available for some new items or users in the system. In this paper, we propose two recommendation models to solve the CCS and ICS problems for new items, which are based on a framework of tightly coupled CF approach and deep learning neural network. A specific deep neural network SADE is used to extract the content features of the items. The state of the art CF model, timeSVD++, which models and utilizes temporal dynamics of user preferences and item features, is modified to take the content features into prediction of ratings for cold start items. Extensive experiments on a large Netflix rating dataset of movies are performed, which show that our proposed recommendation models largely outperform the baseline models for rating prediction of cold start items. The two proposed recommendation models are also evaluated and compared on ICS items, and a flexible scheme of model retraining and switching is proposed to deal with the transition of items from cold start to non-cold start status. The experiment results on Netflix movie recommendation show the tight coupling of CF approach and deep learning neural network is feasible and very effective for cold start item recommendation. The design is general and can be applied to many other recommender systems for online shopping and social networking applications. The solution of cold start item problem can largely improve user experience and trust of recommender systems, and effectively promote cold start items.

Comparative Genomics of Field Isolates of Mycobacterium bovis and M. caprae Provides Evidence for Possible Correlates with Bacterial Viability and Virulence

Mycobacteria of the Mycobacterium tuberculosis complex (MTBC) greatly affect humans and animals worldwide. The life cycle of mycobacteria is complex and the mechanisms resulting in pathogen infection and survival in host cells are not fully understood. Recently, comparative genomics analyses have provided new insights into the evolution and adaptation of the MTBC to survive inside the host. However, most of this information has been obtained using M. tuberculosis but not other members of the MTBC such as M. bovis and M. caprae. In this study, the genome of three M. bovis (MB1, MB3, MB4) and one M. caprae (MB2) field isolates with different lesion score, prevalence and host distribution phenotypes were sequenced. Genome sequence information was used for whole-genome and protein-targeted comparative genomics analysis with the aim of finding correlates with phenotypic variation with potential implications for tuberculosis (TB) disease risk assessment and control. At the whole-genome level the results of the first comparative genomics study of field isolates of M. bovis including M. caprae showed that as previously reported for M. tuberculosis, sequential chromosomal nucleotide substitutions were the main driver of the M. bovis genome evolution. The phylogenetic analysis provided a strong support for the M. bovis/M. caprae clade, but supported M. caprae as a separate species. The comparison of the MB1 and MB4 isolates revealed differences in genome sequence, including gene families that are important for bacterial infection and transmission, thus highlighting differences with functional implications between isolates otherwise classified with the same spoligotype. Strategic protein-targeted analysis using the ESX or type VII secretion system, proteins linking stress response with lipid metabolism, host T cell epitopes of mycobacteria, antigens and peptidoglycan assembly protein identified new genetic markers and candidate vaccine antigens that warrant further study to develop tools to evaluate risks for TB disease caused by M. bovis/M.caprae and for TB control in humans and animals.

New prophylactic and therapeutic treatments to combat pathogenic Enterohaemorrhagic Escherichia coli

Bacterial diarrhoeal diseases have significant influence on global human health, and are a leading cause of preventable death in the developing world. Enterohaemorrhagic Escherichia coli (EHEC), pathogenic strains of E. coli that carry potent toxins, have been associated with a high number of large-scale outbreaks caused by contaminated food and water sources. This pathotype produces diarrhoea and haemorrhagic colitis in infected humans, and in some patients leads to the development of haemolytic uremic syndrome (HUS), which can result in mortality and chronic kidney disease. A major obstacle to the treatment of EHEC infections is the increased risk of HUS development that is associated with antibiotic treatment, and rehydration and renal support are often the only options available. New treatments designed to prevent or clear E. coli infections and reduce symptoms of illness would therefore have large public health and economic impacts. The three main aims of this thesis were: to explore mouse models for pre-clinical evaluation in vivo of small compounds that inhibit a major EHEC colonisation factor, to assess the production and role of two proteins considered promising candidates for a broad-spectrum vaccine against pathogenic E. coli, and to investigate a novel compound that has recently been identified as a potential inhibitor of EHEC toxin production. As EHEC cannot be safely tested in humans due to the risk of HUS development, appropriate small animal models are required for in vivo testing of new drugs. A number of different mouse models have been developed to replicate different features of EHEC pathogenesis, several of which we investigated with a focus on colonisation mediated by the Type III Secretion System (T3SS), a needle-like structure that translocates bacterial proteins into host cells, resulting in a tight, intimate attachment between pathogen and host, aiding colonisation of the gastrointestinal tract. As E. coli models were found not to depend significantly on the T3SS for colonisation, the Citrobacter rodentium model, a natural mouse pathogen closely related to E. coli, was deemed the most suitable mouse model currently available for in vivo testing of T3SS-targeting compounds. Two bacterial proteins, EaeH (an outer membrane adhesin) and YghJ (a putative secreted lipoprotein), highly conserved surface-associated proteins recently identified as III protective antigens against E. coli infection of mice, were explored in order to determine their suitability as candidates for a human vaccine against pathogenic E. coli. We focused on the expression and function of these proteins in the EHEC O157:H7 EDL933 strain and the adherent-invasive E. coli (AIEC) LF82 strain. Although expression of EaeH by other E. coli pathotypes has recently been shown to be upregulated upon contact with host intestinal cells, no evidence of this upregulation could be demonstrated in our strains. Additionally, while YghJ was produced by the AIEC strain, it was not secreted by bacteria under conditions that other YghJ-expressing E. coli pathotypes do, despite the AIEC strain carrying all the genes required to encode the secretion system it is associated with. While our findings indicate that a vaccine that raises antibodies against EaeH and YghJ may have limited effect on the EHEC and AIEC strains we used, recent studies into these proteins in different E. coli pathogens have suggested they are still excellent candidates for a broadly effective vaccine against E. coli. Finally, we characterised a small lead compound, identified by high-throughput screening as a possible inhibitor of Shiga toxin expression. Shiga toxin production causes both the symptoms of illness and development of HUS, and thus reduction of toxin production, release, or binding to host receptors could therefore be an effective way to treat infections and decrease the risk of HUS. Inhibition of Shiga toxin production by this compound was confirmed, and was shown to be caused by an inhibitory effect on activation of the bacterial SOS response rather than on the Shiga toxin genes themselves. The bacterial target of this compound was identified as RecA, a major regulator of the SOS response, and we hypothesise that the compound binds covalently to its target, preventing oligomerisation of RecA into an activated filament. Altogether, the results presented here provide an improved understanding of these different approaches to combating EHEC infection, which will aid the development of safe and effective vaccines and anti-virulence treatments against EHEC.