Hazard and early warning analysis based on domain specific modeling technologies

An aim of proactive risk management strategies is the timely identification of safety related risks. One way to achieve this is by deploying early warning systems. Early warning systems aim to provide useful information on the presence of potential threats to the system, the level of vulnerability of a system, or both of these, in a timely manner. This information can then be used to take proactive safety measures. The United Nation’s has recommended that any early warning system need to have four essential elements, which are the risk knowledge element, a monitoring and warning service, dissemination and communication and a response capability. This research deals with the risk knowledge element of an early warning system. The risk knowledge element of an early warning system contains models of possible accident scenarios. These accident scenarios are created by using hazard analysis techniques, which are categorised as traditional and contemporary. The assumption in traditional hazard analysis techniques is that accidents are occurred due to a sequence of events, whereas, the assumption of contemporary hazard analysis techniques is that safety is an emergent property of complex systems. The problem is that there is no availability of a software editor which can be used by analysts to create models of accident scenarios based on contemporary hazard analysis techniques and generate computer code that represent the models at the same time. This research aims to enhance the process of generating computer code based on graphical models that associate early warning signs and causal factors to a hazard, based on contemporary hazard analyses techniques. For this purpose, the thesis investigates the use of Domain Specific Modeling (DSM) technologies. The contributions of this thesis is the design and development of a set of three graphical Domain Specific Modeling languages (DSML)s, that when combined together, provide all of the necessary constructs that will enable safety experts and practitioners to conduct hazard and early warning analysis based on a contemporary hazard analysis approach. The languages represent those elements and relations necessary to define accident scenarios and their associated early warning signs. The three DSMLs were incorporated in to a prototype software editor that enables safety scientists and practitioners to create and edit hazard and early warning analysis models in a usable manner and as a result to generate executable code automatically. This research proves that the DSM technologies can be used to develop a set of three DSMLs which can allow user to conduct hazard and early warning analysis in more usable manner. Furthermore, the three DSMLs and their dedicated editor, which are presented in this thesis, may provide a significant enhancement to the process of creating the risk knowledge element of computer based early warning systems.

Helicobacter pylori: comparative genomics and structure-function analysis of the flagellum biogenesis protein HP0958

Helicobacter pylori is a gastric pathogen which infects ~50% of the global population and can lead to the development of gastritis, gastric and duodenal ulcers and carcinoma. Genome sequencing of H. pylori revealed high levels of genetic variability; this pathogen is known for its adaptability due to mechanisms including phase variation, recombination and horizontal gene transfer. Motility is essential for efficient colonisation by H. pylori. The flagellum is a complex nanomachine which has been studied in detail in E. coli and Salmonella. In H. pylori, key differences have been identified in the regulation of flagellum biogenesis, warranting further investigation. In this study, the genomes of two H. pylori strains (CCUG 17874 and P79) were sequenced and published as draft genome sequences. Comparative studies identified the potential role of restriction modification systems and the comB locus in transformation efficiency differences between these strains. Core genome analysis of 43 H. pylori strains including 17874 and P79 defined a more refined core genome for the species than previously published. Comparative analysis of the genome sequences of strains isolated from individuals suffering from H. pylori related diseases resulted in the identification of “disease-specific” genes. Structure-function analysis of the essential motility protein HP0958 was performed to elucidate its role during flagellum assembly in H. pylori. The previously reported HP0958-FliH interaction could not be substantiated in this study and appears to be a false positive. Site-directed mutagenesis confirmed that the coiled-coil domain of HP0958 is involved in the interaction with RpoN (74-284), while the Zn-finger domain is required for direct interaction with the full length flaA mRNA transcript. Complementation of a non-motile hp0958-null derivative strain of P79 with site-directed mutant alleles of hp0958 resulted in cells producing flagellar-type extrusions from non-polar positions. Thus, HP0958 may have a novel function in spatial localisation of flagella in H. pylori

Antimicrobial activity of essential oils isolated from Portuguese endemic species of Thymus

Aims: Thymus species are wild species mostly found in the arid lands of Portugal. Possible antimicrobial properties of Thymus essential oils have been investigated. The chemical composition of the essential oils and the antimicrobial activity of Thymus mastichina (L) L. subsp. mastichina , T. camphoratus and T. lotocephalus from different regions of Portugal were analysed. Methods and Results: Hydrodistillation was used to isolate the essential oils and the chemical analyses were performed by gas chromatography (GC) and GC coupled to mass spectrometry. The antimicrobial activity was tested by the disc agar diffusion technique against Candida albicans , Escherichia coli , Listeria monocytogenes , Proteus mirabilis , Salmonella spp. and Staphylococcus aureus . Pure linalool, 1,8-cineole and a mixture (1:1) of these compounds were included. Linalool, 1,8-cineole or linalool/1,8-cineole and linalool/1,8-cineole/linalyl acetate were the major components of the essential oils, depending on the species or sampling place. The essential oils isolated from the Thymus species studied demonstrated antimicrobial activity but the micro-organisms tested had significantly different sensitivities. Conclusions: The antimicrobial activity of essential oils may be related to more than one component. Significance and Impact of the Study: Portuguese endemic species of Thymus can be used for essential oil production for food spoilage control, cosmetics and pharmaceutical use. Further studies will be required to elucidate the cell targets of the essential oil components.

Construction of bovine adenovirus type 3 E1 and E3, substitution plasmids and the sequencing analysis of DNA pol and pTP /

The relative ease to concentrate and purify adenoviruses, their well characterized mid-sized genome, and the ability to delete non-essential regions from their genome to accommodate foreign gene, made adenoviruses a suitable candidate for the construction of vectors. The use of adenoviral vectors in gene therapy, vaccination, and as a general vector system for expressing foreign genes have been documented for some time. In this study, the objective was to rescue a BAV3 E1 or E3 recombinant vector carrying the kanamycin resistant gene, a dominant selectable marker with useful applications in studying vectored gene expression in mammalian cells. To accomplish the objective of this study, more information about BAV3 DNA sequences was required in order to make the manipulation of the virus genome accessible. Therefore, sequencing of the BAV3 genome from 1 1 .7% to 30.8% was carried out. Analysis of the determined sequences revealed the primary structure of important viral gene products coded by E2 including BAV3 DNA pol and precursor to terminal protein. Comparative analysis of these proteins with their counterparts from human and non human adenoviruses revealed important insights as to the evolutionary lineage of BAV3. In order to insert the kanamycin resistance gene in either E1 or E3, it was necessary to delete BAV3 sequences to accommodate the foreign gene so as not to exceed the limit of the packaging capacity of the virus. To construct a recombinant BAV3 in which a foreign gene was inserted in the deleted E1 region, an E1 shuttle vector was constructed. This involved the deletion from the viral sequences a region between 1.3% to 9% and inserting the kanamycin resistance gene to replace the deletion. The E1 shuttle vector contained the left (0%- 53.9%) segment of the genome and was expected to generate BAV3 recombinants that can be grown and propagated in cells that can complement the missing E1 functions. To construct a similar shuttle vector for E3 deletion, DNA sequences extending from 78.9% to 82.5% (1281 bp) were deleted from within the E3 region that had been cloned into a plasmid vector. The deleted region corresponds to those that have been shown to be non-essential for viral replication in cell culture. The resulting plasmid was used to construct another recombinant plasmid with BAV3 DNA sequences extending from 37.1% to 100% and with a deletion of E3 sequences that were replaced by kanamycin resistance gene. This shuttle plasmid was used in cotransfections with digested viral DNA in an attempt to rescue a recombinant BAV3 carrying the kanamycin resistance gene to replace the deleted E3. In spite of repeated attempts of transfection, El or E3 recombinant BAV3 were not isolated. It seems that other approaches should be applied to make a final conclusion on BAV3 infectivity.

Investigation of high-efficiency Wireless Power Transfer criteria of resonantly-coupled loops and dipoles through analysis of the figure of merit

The efficiency of a Wireless Power Transfer (WPT) system is greatly dependent on both the geometry and operating frequency of the transmitting and receiving structures. By using Coupled Mode Theory (CMT), the figure of merit is calculated for resonantly-coupled loop and dipole systems. An in-depth analysis of the figure of merit is performed with respect to the key geometric parameters of the loops and dipoles, along with the resonant frequency, in order to identify the key relationships leading to high-efficiency WPT. For systems consisting of two identical single-turn loops, it is shown that the choice of both the loop radius and resonant frequency are essential in achieving high-efficiency WPT. For the dipole geometries studied, it is shown that the choice of length is largely irrelevant and that as a result of their capacitive nature, low-MHz frequency dipoles are able to produce significantly higher figures of merit than those of the loops considered. The results of the figure of merit analysis are used to propose and subsequently compare two mid-range loop and dipole WPT systems of equal size and operating frequency, where it is shown that the dipole system is able to achieve higher efficiencies than the loop system of the distance range examined.

Development of mint (Mentha piperita L.) grown on biosolids: evaluation of productivity and essential oil content

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Phytotoxic Activities of Mediterranean Essential Oils

Twelve essential oils from Mediterranean aromatic plants were tested for their phytotoxic activity, at different doses, against the germination and the initial radicle growth of seeds of Raphanus sativus, Lactuca sativa and Lepidium sativum. The essential oils were obtained from Hyssopus officinalis, Lavandula angustifolia, Majorana hortensis, Melissa officinalis, Ocimum basilicum, Origanum vulgare, Salvia officinalis and Thymus vulgaris (Lamiaceae), Verbena officinalis (Verbenaceae), Pimpinella anisum, Foeniculum vulgare and Carum carvi (Apiaceae). The germination and radicle growth of tested seeds were affected in different ways by the oils. Thyme, balm, vervain and caraway essential oils were more active against both germination and radicle elongation.

Attraction of fruit-eating bats with essential oils of fruits: A potential tool for forest restoration

Previous tests with essential oils from ripe chiropterochoric fruits suggested they can be used to attract and capture fruit-eating bats inside forest remnants. Here we evaluated the efficiency of these oils to attract frugivorous bats to open areas. We performed field tests with artificial fruits impregnated with essential oils of the genera Piper or Ficus that were attached to two groups of mist-nets set 50 m outside the border of a forest remnant. One group of artificial fruits received the corresponding oil isolated through hydrodistillation and the other received water only. Fruits with oils attracted significantly more fruit-eating bats, especially Artibeus lituratus that regularly crosses open habitats to reach other forest remnants. The highly significant attraction of A. lituratus by the oil of Piper was unexpected, since this bat is a specialist on Ficus fruits. We hypothesize that in habitats with no fruit available it is possible to attract frugivorous bats with the odor of several ripe fruit species. Furthermore, we verified that almost half of the individuals captured defecated seeds, indicating that the oils also attract recently fed bats, even when their preferred food is available nearby. This technique potentially may increase seed rain at specific locations, being particularly promising to restoration projects.

Characterization of the Pulp and Kernel Oils from Syagrus oleracea, Syagrus romanzoffiana, and Acrocomia aculeata

Vegetable oils are important sources of essential fatty acids. It is, therefore, important to characterize plant species that can be used as new oil sources. This study aimed to characterize the oils from guariroba (Syagrus oleracea), jeriva (Syagrus romanzoffiana), and macauba (Acrocomia aculeata). The physicochemical characterization was performed using official analytical methods for oils and fats, free fatty acids, peroxide value, refractive index, iodine value, saponification number, and unsaponifiable matter. The oxidative stability was determined using the Rancimat at 110 degrees C. The fatty acid composition was performed by gas chromatography. The results were submitted to Tukey's test for the medium to 5% using the ESTAT program. The pulp oils were more unsaturated than kernel oils, as evidenced by the higher refractive index and iodine value, especially the macauba pulp oil which gave 1.4556 and 80 g I(2)/100 g, respectively, for these indices. The kernel oils were less altered by oxidative process and had high induction period, free fatty acids below 0.5%, and peroxide value around 0.19 meq/kg. The guariroba kernel oil showed the largest induction period, 91.82 h.

Antimicrobial activity of essential oils from plants used in Brazilian popular medicine

Essential oils from, Salvia officinalis L. (SO), Mentha sylvestris L. (MS), Casearia sylvestris Sw. (CS), Mentha piperita L. (MP), Ocimum micrantum Willd. (OM) and Mentha arvensis L. (MA), plants used in Brazilian popular medicine were extracted using method I, as described in the Brazilian Pharmacopoeia, in order to obtain the phytochemical profile and to evaluate their antimicrobial activity against the following microorganisms: Bacillus subtilis, Staphylococcus aureus, Micrococcus luteus, Escherichia coli, Serratia marcescens, Candida albicans and Aspergilus oryzae. Test was made by means of the disk-plaque diffusion test in liquid medium using 1% essential oil. In the disk-plaque diffusion test, all the essential oils exhibited activity against B. subtilis, but OM showed the greatest inhibition zone and was the only one to show activity against S. aureus. Samples of SO, MS, MP, OM and MA were active against M. luteus, E. coli and S. marcescens, while A. oryzae was sensitive to MS, MP, OM and MA. No sample, however, was active against C. albicans. In the liquid medium test, significant results were observed for OM and MA, which inhibited the growth of all microorganisms for 24 hours, and OM continued active against E. coli and A. oryzae until the last reading.

Antimicrobial activity of the essential oils of some spice herbs

Essential oils were obtained from fennel seeds, dill, cumin and coriander. Their antimicrobial activity was tested on isolated clinical specimens of patients treated at the University Hospital of the School of Medicine of Botucatu, SP, UNESP. Microorganisms were grown in BHI (Brain Heart Infusion/Oxoid) at 37oC/18 hours and resuspended in 0,5 Mac Farland's Standard (1,5 x 108 CFU/mL). The diffusion method was performed, putting 10 μl of the essential oils on paper disks (6mm of diameter) (Blank Disks/CECON) at 37oC/24 hours. After this period, the disks were put on plates containing Mueller Hinton Agar (Oxoid) and inoculated with the microorganisms. After 48 hours at 37oC, inhibitory zones were measured (mm) for the respective oils and strains. The essential oil from Anethum graveolens showed antimicrobial activity against Staphylococcus aureus (inhibitory zone=18 mm), Salmonella sp. (=11 mm) and E. coli (10 mm). The Cuminum cyminum essential oil was effective against E. coli, P. aeruginosa and Salmonella sp. and their inhibitory zones were 18, 10 and 23 mm, respectively. Coriandrum sativum oil was active only against Salmonella sp. (18 mm) and Foeniculum vulgare inhibited only E. coli (9 mm).