'Malicious Code Execution Detection and Response Immune System inspired by the Danger Theory'

The analysis of system calls is one method employed by anomaly detection systems to recognise malicious code execution. Similarities can be drawn between this process and the behaviour of certain cells belonging to the human immune system, and can be applied to construct an artificial immune system. A recently developed hypothesis in immunology, the Danger Theory, states that our immune system responds to the presence of intruders through sensing molecules belonging to those invaders, plus signals generated by the host indicating danger and damage. We propose the incorporation of this concept into a responsive intrusion detection system, where behavioural information of the system and running processes is combined with information regarding individual system calls.

Trapping phosphorus (III) into polyoxometalates: synthesis, characterisation and electronic behaviour study

The introduction of electronically-active heteroanions into polyoxometalates (POMs) is one of the emerging topics in this field. The novel clusters have shown unprecedented intramolecular electron-transfer features that can be directly mediated by the incorporated heteroanions. In this thesis, we will focus on the study of phosphite (HPO32-) as new non-traditional heteroanions, discover HPO32- templated nanostructures, investigate their electronic behaviours as well as understand the self-assembly process of HPO32--templated species. The thesis starts with incorporating HPO32- into POM cages. The feasibility of this work was illustrated by the successful trapping of HPO32- into a “Trojan Horse” type {W18O56} nanocage. The reactivity of embedded {HPO3} was fully studied, showing the cluster undergoes a structural rearrangement in solution whereby the {HPO3} moieties dimerise to form a weakly interacting (O3PH···HPO3) moiety. In the crystalline state a temperature-dependent intramolecular redox reaction and structural rearrangement occurs. This rearrangement appears to proceed via an intermediate containing two different templates, a pyramidal {HPO3} and a tetrahedral {PO4} moiety. {HPO3} templated POM cages were then vigorously expanded and led to the isolation of five either fully oxidised or mixed-valence clusters trapped with mono-, di-, or tri- {HPO3}. Interestingly, an intriguing 3D honeycomb-like host-guest structure was also synthesised. The porous framework was self-aggregated by a tri-phopshite anion templated {W21} cluster with a {VO4} templated Wells-Dawson type {W18} acting as a guest species within the hexagonal channels. Based on this work, we further extended the templating anions to two different redox-active heteroanions, and discovered a unique mixed-heteroatom templated system built by pairing redox-active {HPIIIO3} with {TeO3}, {SeO3} or {AsO3}. Two molecular systems were developed, ie. “Trojan Horse” type [W18O56(HPO3)0.8(SeO3)1.2(H2O)2]8- and cross-shaped [H4P4X4W64O224]32-/36-, where X=TeIV, SeIV, AsIII. In the case of {W18(HPO3)0.8(SeO3)1.2}, the compound is found to be a mixture of heteroleptic {W18(HPO3)(SeO3)} and homoleptic {W18(SeO3)2} and {W18(HPO3)2}, identified by single crystal x-ray diffraction, NMR as well as high resolution mass spectrometry. The cluster exhibited similar temperature-dependent electronic features to “Trojan Horse” type {W18(HPO3)2O56}. However, due to the intrinsic reactivity difference between {HPO3} and {SeO3}, the thermal treatment leads to the formation of an unusual species [W18O55(PO4)(SeO3)]5-, in which {HPO3} was fully oxidised to {PO4} within the cage, whereas and lone-pair-containing {SeO3} heteroanions were kept intact inside the shell. This finding is extremely interesting, as it demonstrated that multiple and independent intramolecular electronic performance can be achieved by the coexistence of distinct heteroatoms within a single molecule. On the other hand, the cross-shaped [H4P4X4W64O224]32-/36- were constructed by four {W15(HPO3)(XO3)} building units linked by four {WO6} octahedra. Each building unit traps two different heteroatoms. It is interesting to note that the mixed heteroatom species show self-sorting, with a highly selective positional preference. Smaller ionic sized {HPO3} are self-organised into the uncapped side of {W15} cavity, whereas closed side are occupied by larger heteroatoms, which is surprisingly opposed to steric hindrance. Density functional theory (DFT) calculations are currently underway to have a full understanding of the preference of heteroatom substitutions. This series of clusters is of great interest in terms of achieving single molecule-based heteroatom-dependent multiple levels of electron transfer. It has opened a new way to design and synthesise POMs with higher diversity of electrical states, which may lead to a new type of Q-bits for quantum computing. The third chapter is focused on developing polyoxotungstate building blocks templated by {HPO3}. A series of building blocks, {W15O48(HPO3)2}, {W9O30(HPO3)} {W12O40(HPO3)2} and hexagonal {W6O18(HPO3)} have been obtained. The first four building blocks have been reported with {SeO3} and/or {TeO3} heteroanions. This result demonstrates {HPO3} has a similar reactivity as {SeO3} and {TeO3}, therefore studying the self-assembly of {HPO3}-based building blocks would be helpful to have a general understanding of pyramidal heteroatom-based molecular systems. The hexagonal {W6O18(HPO3)} is observed for the first time in polyoxotungstates, showing some of reactivity difference between {HPO3} and {SeO3} and {TeO3}. Furthermore, inorganic salts and pH values have some directing influence on the formation and transformation of various building blocks, resulting in the discovery of a family of {HPO3}-based clusters with nuclearity ranging from {W29} to {W106}. High resolution mass spectrometry was also carried out to investigate the cluster solution behaviour and also gain information of building block speciation. It is found that some clusters experienced decomposition, which gives rise to potential building blocks accountable for the self-assembly.

Bacterial community characterization of water and intestine of the shrimp Litopenaeus stylirostris in a biofloc system

Background Biofloc technology (BFT), a rearing method with little or no water exchange, is gaining popularity in aquaculture. In the water column, such systems develop conglomerates of microbes, algae and protozoa, together with detritus and dead organic particles. The intensive microbial community presents in these systems can be used as a pond water quality treatment system, and the microbial protein can serve as a feed additive. The current problem with BFT is the difficulty of controlling its bacterial community composition for both optimal water quality and optimal shrimp health. The main objective of the present study was to investigate microbial diversity of samples obtained from different culture environments (Biofloc technology and clear seawater) as well as from the intestines of shrimp reared in both environments through high-throughput sequencing technology. Results Analyses of the bacterial community identified in water from BFT and “clear seawater” (CW) systems (control) containing the shrimp Litopenaeus stylirostris revealed large differences in the frequency distribution of operational taxonomic units (OTUs). Four out of the five most dominant bacterial communities were different in both culture methods. Bacteria found in great abundance in BFT have two principal characteristics: the need for an organic substrate or nitrogen sources to grow and the capacity to attach to surfaces and co-aggregate. A correlation was found between bacteria groups and physicochemical and biological parameters measured in rearing tanks. Moreover, rearing-water bacterial communities influenced the microbiota of shrimp. Indeed, the biofloc environment modified the shrimp intestine microbiota, as the low level (27 %) of similarity between intestinal bacterial communities from the two treatments. Conclusion This study provides the first information describing the complex biofloc microbial community, which can help to understand the environment-microbiota-host relationship in this rearing system.

Quantifying the Resilience of an Urban Traffic-Electric Power Coupled System

Transportation system resilience has been the subject of several recent studies. To assess the resilience of a transportation network, however, it is essential to model its interactions with and reliance on other lifelines. In this work, a bi-level, mixed-integer, stochastic program is presented for quantifying the resilience of a coupled traffic-power network under a host of potential natural or anthropogenic hazard-impact scenarios. A two-layer network representation is employed that includes details of both systems. Interdependencies between the urban traffic and electric power distribution systems are captured through linking variables and logical constraints. The modeling approach was applied on a case study developed on a portion of the signalized traffic-power distribution system in southern Minneapolis. The results of the case study show the importance of explicitly considering interdependencies between critical infrastructures in transportation resilience estimation. The results also provide insights on lifeline performance from an alternative power perspective.

Protein disulfide isomerase as a target for besnoitiosis therapy : molecular characterization and studies of its role in infection and host immune response

Tese de Doutoramento em Ciências Veterinárias na especialidade de Sanidade Animal

mRNA-Seq and microarray development for the Grooved carpet shell clam, Ruditapes decussatus: a functional approach to unravel host -parasite interaction

Background The Grooved Carpet shell clam Ruditapes decussatus is the autochthonous European clam and the most appreciated from a gastronomic and economic point of view. The production is in decline due to several factors such as Perkinsiosis and habitat invasion and competition by the introduced exotic species, the manila clam Ruditapes philippinarum. After we sequenced R. decussatus transcriptome we have designed an oligo microarray capable of contributing to provide some clues on molecular response of the clam to Perkinsiosis. Results A database consisting of 41,119 unique transcripts was constructed, of which 12,479 (30.3%) were annotated by similarity. An oligo-DNA microarray platform was then designed and applied to profile gene expression in R. decussatus heavily infected by Perkinsus olseni. Functional annotation of differentially expressed genes between those two conditionswas performed by gene set enrichment analysis. As expected, microarrays unveil genes related with stress/infectious agents such as hydrolases, proteases and others. The extensive role of innate immune system was also analyzed and effect of parasitosis upon expression of important molecules such as lectins reviewed. Conclusions This study represents a first attempt to characterize Ruditapes decussatus transcriptome, an important marine resource for the European aquaculture. The trancriptome sequencing and consequent annotation will increase the available tools and resources for this specie, introducing the possibility of high throughput experiments such as microarrays analysis. In this specific case microarray approach was used to unveil some important aspects of host-parasite interaction between the Carpet shell clam and Perkinsus, two non-model species, highlighting some genes associated with this interaction. Ample information was obtained to identify biological processes significantly enriched among differentially expressed genes in Perkinsus infected versus non-infected gills. An overview on the genes related with the immune system on R. decussatus transcriptome is also reported.

Photochromism of the complex between 40-(2-hydroxyethoxy)-7-hydroxyflavylium and b-cyclodextrin, studied by 1H NMR, UVeVis, continuous irradiation and circular dichroism

1st International Caparica Conference on Chromogenic and Emissive Materials

HIV-1 infection: back and forth between virus and host.

The main obstacles to HIV-1 eradication are linked to the viral ability to evade immune system and establish a reservoir where virus is transcriptionally latent but able to replicate. IFN action and Restriction Factors (RFs) expression, dominant proteins that target multiple steps of the HIV-1 lifecycle, represent an early line of defence Because of their interplay with viral replication, we would like to study the relationship between RFs and the viral amount in latently infected cells.The first part of this project investigates the expression levels variations of a selected group of RFs (APOBEC3G, BST2, TRIM5α, MX2, SAMHD1, SERINC3/5, IFI16 and STING) in HIV-1 patients during the course of infection before and after ART administration by using Real Time qPCR. The second part of this study deals with the role of IFNα and IFNγ, and their role in the immune system disfunction that has been described during chronic inflammation associated to cancer, viral infection such as HIV-1, and autoimmune-disease. Immune Check Point proteins (ICPs) are a group of inhibitory receptors expressed on the cellular surface of immune cells and trigger immunosuppressive signaling pathways leading to T-cell exhaustion and the expression of immune checkpoint molecules (PD-1, PD-L1, TIGIT, LILRB2). The major aim of this project is to assess the clinical meaning of ICPs expression in HIV-1 chronically infected patients to better characterized their involvement in immune system disfunction.

Obesity And Inflammation And The Effect On The Hematopoietic System.

Bone marrow is organized in specialized microenvironments known as 'marrow niches'. These are important for the maintenance of stem cells and their hematopoietic progenitors whose homeostasis also depends on other cell types present in the tissue. Extrinsic factors, such as infection and inflammatory states, may affect this system by causing cytokine dysregulation (imbalance in cytokine production) and changes in cell proliferation and self-renewal rates, and may also induce changes in the metabolism and cell cycle. Known to relate to chronic inflammation, obesity is responsible for systemic changes that are best studied in the cardiovascular system. Little is known regarding the changes in the hematopoietic system induced by the inflammatory state carried by obesity or the cell and molecular mechanisms involved. The understanding of the biological behavior of hematopoietic stem cells under obesity-induced chronic inflammation could help elucidate the pathophysiological mechanisms involved in other inflammatory processes, such as neoplastic diseases and bone marrow failure syndromes.

The Value Of The 2005 International Society Of Urological Pathology (isup) Modified Gleason Grading System As A Predictor Of Biochemical Recurrence After Radical Prostatectomy.

To compare time and risk to biochemical recurrence (BR) after radical prostatectomy of two chronologically different groups of patients using the standard and the modified Gleason system (MGS). Cohort 1 comprised biopsies of 197 patients graded according to the standard Gleason system (SGS) in the period 1997/2004, and cohort 2, 176 biopsies graded according to the modified system in the period 2005/2011. Time to BR was analyzed with the Kaplan-Meier product-limit analysis and prediction of shorter time to recurrence using univariate and multivariate Cox proportional hazards model. Patients in cohort 2 reflected time-related changes: striking increase in clinical stage T1c, systematic use of extended biopsies, and lower percentage of total length of cancer in millimeter in all cores. The MGS used in cohort 2 showed fewer biopsies with Gleason score ≤ 6 and more biopsies of the intermediate Gleason score 7. Time to BR using the Kaplan-Meier curves showed statistical significance using the MGS in cohort 2, but not the SGS in cohort 1. Only the MGS predicted shorter time to BR on univariate analysis and on multivariate analysis was an independent predictor. The results favor that the 2005 International Society of Urological Pathology modified system is a refinement of the Gleason grading and valuable for contemporary clinical practice.

The Applicability Of Ordered Mesoporous Sba-15 And Its Hydrophobic Glutaraldehyde-bridge Derivative To Improve Ibuprofen-loading In Releasing System.

The mesoporous SBA-15 silica with uniform hexagonal pore, narrow pore size distribution and tuneable pore diameter was organofunctionalized with glutaraldehyde-bridged silylating agent. The precursor and its derivative silicas were ibuprofen-loaded for controlled delivery in simulated biological fluids. The synthesized silicas were characterized by elemental analysis, infrared spectroscopy, (13)C and (29)Si solid state NMR spectroscopy, nitrogen adsorption, X-ray diffractometry, thermogravimetry and scanning electron microscopy. Surface functionalization with amine containing bridged hydrophobic structure resulted in significantly decreased surface area from 802.4 to 63.0 m(2) g(-1) and pore diameter 8.0-6.0 nm, which ultimately increased the drug-loading capacity from 18.0% up to 28.3% and a very slow release rate of ibuprofen over the period of 72.5h. The in vitro drug release demonstrated that SBA-15 presented the fastest release from 25% to 27% and SBA-15GA gave near 10% of drug release in all fluids during 72.5 h. The Korsmeyer-Peppas model better fits the release data with the Fickian diffusion mechanism and zero order kinetics for synthesized mesoporous silicas. Both pore sizes and hydrophobicity influenced the rate of the release process, indicating that the chemically modified silica can be suggested to design formulation of slow and constant release over a defined period, to avoid repeated administration.

Electronic And Structural Study Of Pt-modified Au Vicinal Surfaces: A Model System For Pt-au Catalysts.

Two single crystalline surfaces of Au vicinal to the (111) plane were modified with Pt and studied using scanning tunneling microscopy (STM) and X-ray photoemission spectroscopy (XPS) in ultra-high vacuum environment. The vicinal surfaces studied are Au(332) and Au(887) and different Pt coverage (θPt) were deposited on each surface. From STM images we determine that Pt deposits on both surfaces as nanoislands with heights ranging from 1 ML to 3 ML depending on θPt. On both surfaces the early growth of Pt ad-islands occurs at the lower part of the step edge, with Pt ad-atoms being incorporated into the steps in some cases. XPS results indicate that partial alloying of Pt occurs at the interface at room temperature and at all coverage, as suggested by the negative chemical shift of Pt 4f core line, indicating an upward shift of the d-band center of the alloyed Pt. Also, the existence of a segregated Pt phase especially at higher coverage is detected by XPS. Sample annealing indicates that the temperature rise promotes a further incorporation of Pt atoms into the Au substrate as supported by STM and XPS results. Additionally, the catalytic activity of different PtAu systems reported in the literature for some electrochemical reactions is discussed considering our findings.

Inhibitory Effects Of A Cured Antibacterial Bonding System On Viability And Metabolic Activity Of Oral Bacteria.

To evaluate the antimicrobial efficacy of Clearfil SE Protect (CP) and Clearfil SE Bond (CB) after curing and rinsed against five individual oral microorganisms as well as a mixture of bacterial culture prepared from the selected test organisms. Bacterial suspensions were prepared from single species of Streptococcus mutans, Streptococcus sobrinus, Streptococcus gordonii, Actinomyces viscosus and Lactobacillus lactis, as well as mixed bacterial suspensions from these organisms. Dentin bonding system discs (6 mm×2 mm) were prepared, cured, washed and placed on the bacterial suspension of single species or multispecies bacteria for 15, 30 and 60 min. MTT, Live/Dead bacterial viability (antibacterial effect), and XTT (metabolic activity) assays were used to test the two dentin system's antibacterial effect. All assays were done in triplicates and each experiment repeated at least three times. Data were submitted to ANOVA and Scheffe's f-test (5%). Greater than 40% bacteria killing was seen within 15 min, and the killing progressed with increasing time of incubation with CP discs. However, a longer (60 min) period of incubation was required by CP to achieve similar antimicrobial effect against mixed bacterial suspension. CB had no significant effect on the viability or metabolic activity of the test microorganisms when compared to the control bacterial culture. CP was significantly effective in reducing the viability and metabolic activity of the test organisms. The results demonstrated the antimicrobial efficacy of CP both on single and multispecies bacterial culture. CP may be beneficial in reducing bacterial infections in cavity preparations in clinical dentistry.

Blockade Of Renin-angiotensin System Prevents Micturition Dysfunction In Renovascular Hypertensive Rats.

Association between hypertension and bladder symptoms has been described. We hypothesized that micturition dysfunction may be associated with renin-angiotensin system (RAS) acting in urethra. The effects of the anti-hypertensive drugs losartan (AT1 antagonist) and captopril (angiotensin-converting enzyme inhibitor) in comparison with atenolol (β1-adrenoceptor antagonist independently of RAS blockade) have been investigated in bladder and urethral dysfunctions during renovascular hypertension in rats. Two kidney-1 clip (2K-1C) rats were treated with losartan (30 mg/kg/day), captopril (50mg/kg/day) or atenolol (90 mg/kg/day) for eight weeks. Cystometric study, bladder and urethra smooth muscle reactivities, measurement of cAMP levels and p38 MAPK phosphorylation in urinary tract were determined. Losartan and captopril markedly reduced blood pressure in 2K-1C rats. The increases in non-voiding contractions, voiding frequency and bladder capacity in 2K-1C rats were prevented by treatments with both drugs. Likewise, losartan and captopril prevented the enhanced bladder contractions to electrical-field stimulation (EFS) and carbachol, along with the impaired relaxations to β-adrenergic-cAMP stimulation. Enhanced neurogenic contractions and impaired nitrergic relaxations were observed in urethra from 2K-1C rats. Angiotensin II also produced greater urethral contractions that were accompanied by higher phosphorylation of p38 MAPK in urethral tissues of 2K-1C rats. Losartan and captopril normalized the urethral dysfunctions in 2K-1C rats. In contrast, atenolol treatment largely reduced the blood pressure in 2K-1C rats but failed to affect the urinary tract smooth muscle dysfunction. The urinary tract smooth muscle dysfunction in 2K-1C rats takes place by local RAS activation irrespective of levels of arterial blood pressure.

Transmission Of Intra-cellular Genetic Information: A System Proposal.

One of the great challenges of the scientific community on theories of genetic information, genetic communication and genetic coding is to determine a mathematical structure related to DNA sequences. In this paper we propose a model of an intra-cellular transmission system of genetic information similar to a model of a power and bandwidth efficient digital communication system in order to identify a mathematical structure in DNA sequences where such sequences are biologically relevant. The model of a transmission system of genetic information is concerned with the identification, reproduction and mathematical classification of the nucleotide sequence of single stranded DNA by the genetic encoder. Hence, a genetic encoder is devised where labelings and cyclic codes are established. The establishment of the algebraic structure of the corresponding codes alphabets, mappings, labelings, primitive polynomials (p(x)) and code generator polynomials (g(x)) are quite important in characterizing error-correcting codes subclasses of G-linear codes. These latter codes are useful for the identification, reproduction and mathematical classification of DNA sequences. The characterization of this model may contribute to the development of a methodology that can be applied in mutational analysis and polymorphisms, production of new drugs and genetic improvement, among other things, resulting in the reduction of time and laboratory costs.