From genomes to vaccines via the proteome

An effective vaccine against schistosomiasis mansoni would be a valuable control tool and the high levels of protection elicited in rodents and primates by radiation-attenuated cercariae provide proof of principle. A major obstacle to vaccine development is the difficulty of identifying the antigens that mediate protection, not least because of the size of the genome at 280Mb DNA encoding 14,000 to 20,000 genes. The technologies collectively called proteomics, including 2D electrophoresis, liquid chromatography and mass spectrometry, now permit any protein to be identified provided there is extensive DNA data, and preferably a genome sequence. Applied to soluble (cytosolic) proteins from schistosomes, proteomics reveals the great similarity in composition between life cycle stages, with several WHO vaccine candidates amongst the most abundant constituents. The proteomic approach has been successfully applied to identify the secretions used by cercaria to penetrate host skin, the gut secretions of adult worms and the proteins exposed on the tegument surface. Soluble proteins can also be separated by 2D electrophoresis before western blotting to identify the full range of antigenic targets present in a parasite preparation. The next step is to discover which target proteins represent the weak points in the worm's defences.

Experimental transmission of the parasitic flagellates Trypanosoma cruzi and Trypanosoma rangeli between triatomine bugs or mice and captive neotropical bats

Trypanosoma cruzi and Trypanosoma rangeli-like trypanosomes have been found in a variety of neotropical bat species. In this study, bats (Artibeus lituratus, Carollia perspicillata, Desmodus rotundus, Glossophaga soricina, Molossus molossus, Phyllostomus hastatus) were maintained under controlled conditions, and experiments were conducted to determine how they might become infected naturally with trypanosomes. All bats were first screened for existing infections by hemoculture and the examination of blood smears, and only apparently uninfected animals were then used in the experiments. Proof was obtained that the triatomine bug Rhodnius prolixus would readily feed upon some of the bats, and two species became infected after being bitten by bugs infected with T. rangeli. Some bats also became infected by ingesting R. prolixus carrying T. cruzi, or following subcutaneous or intragastic inoculation with fecal suspensions of R. prolixus containing T. cruzi. P. hastatus became infected after ingesting mice carrying T. cruzi. All of the bats studied inhabit roosts that may be occupied by triatomine bugs and, with the exception of D. rotundus, all also feed to at least some extent upon insects. These findings provide further evidence of how bats may play significant roles in the epidemiology of T. cruzi and T. rangeli in the New World tropics.

Two approaches to discovering and developing new drugs for Chagas disease

This review will focus on two general approaches carried out at the Sandler Center, University of California, San Francisco, to address the challenge of developing new drugs for the treatment of Chagas disease. The first approach is target-based drug discovery, and two specific targets, cytochrome P450 CYP51 and cruzain (aka cruzipain), are discussed. A "proof of concept" molecule, the vinyl sulfone inhibitor K777, is now a clinical candidate. The preclinical assessment compliance for filing as an Investigational New Drug with the United States Food and Drug Administration (FDA) is presented, and an outline of potential clinical trials is given. The second approach to identifying new drug leads is parasite phenotypic screens in culture. The development of an assay allowing high throughput screening of Trypanosoma cruzi amastigotes in skeletal muscle cells is presented. This screen has the advantage of not requiring specific strains of parasites, so it could be used with field isolates, drug resistant strains or laboratory strains. It is optimized for robotic liquid handling and has been validated through a screen of a library of FDA-approved drugs identifying 65 hits.

The existence of nursing in caring for terminally ills’life: a phenomenological study

By taking care of cancer patients in their process of end of life, nursing experience situations of suffering before the anguish of others. This study aimed to understand the meaning and significance attributed by the nurses from the palliative care cancer hospital. This is a phenomenological research, grounded in Heidegger’s thinking, performed with 13 nurses, who work at Oncology hospitalward, through semi-structured interviews, which were analyzed according to the steps recommended by Josgrilberg. From understanding the statementsof the subjects, two ontological themesemerged: Feeling satisfaction and love in the care offered and Feeling anger and inabilitytowards terminally ill patients.We inferred that working in Oncology Ward is something rewarding for these professionals, but it entails physical and mental suffering, from feeling helpless before the death-dying process. Thus, we showedthat nursing professionals need to be recognized as human beings and as such, also deserving of care.

Life experiences of elderly with cancer pain: the existential comprehensive approach

OBJECTIVE Understanding the experiences of elderly with cancer pain. METHOD Qualitative research based on Heidegger's phenomenology. 12 elderly cancer patients from a city in northwest Paraná were interviewed from November 2013 to February 2014. RESULTS Analysis performed by vague, median and interpretive understanding which resulted in two ontological themes: Cancer pain: unveiling the imprisonment and impositions experienced by the elderly, and Unveiling the anguish of living with cancer pain; it revealed not only how the elderly experience pain in their daily lives, but also how hard it is to live with its particularities. CONCLUSION Cancer pain has biopsychosocial repercussions for the elderly, generating changes in their existence in the world, requiring holistic and authentic care.

Antioxidant compoundsand total antioxidant activity in fruits of acerola from cv. Flor Branca, Florida Sweet and BRS 366

Information on antioxidant properties at different ontological stages may help producers and food technologists to identify which cultivar and/or maturity stage are most adequate for their need, therefore this work aimed to study the changes in the antioxidant metabolism during acerola development. Fruit from cv. Flor Branca, BRS366 and Florida Sweet were harvested at different stages: immature green colored (I), physiologically mature with green color and maximum size (II), breaker (III) and full red ripe (IV). After harvest, fruits were selected, divided into four replications with 500 g each and evaluated regarding their titratable acidity, pH, soluble solids, total soluble sugar, vitamin C, polyphenol, anthocyanin, yellow flavonoid, total antioxidant activity and antioxidant enzyme activity. Anthocyanin and flavonoid were determined through LC-DAD-ESI/MS and all analysis followed a completely randomized factorial 3 x 4 design. Fruits of 'Florida Sweet' presented significantly higher soluble solids (9.46ºBrix). Vitamin C content decreased during ripening, but ripe 'BRS 366' fruits showed the greatest values (1363 mg.100 g-1) and highest TAA with 42.36 µM TEAC.g-1FW. Cyanidin 3-rhamnoside (520.76 mg.100 g-1 DM) and quercetin 3-rhamnoside (33.72 mg.100 g-1 DM) were the most abundant anthocyanin and yellow flavonoids found mainly in 'Flor Branca' fruit of acerola, whose antioxidant enzymes activities were also higher. Ripe 'Florida Sweet' fruit presents a great potential for fresh consumption, meanwhile physiologically mature 'BRS 366' fruit seems the best option for the bioactive compounds processing industry. As 'Flor Branca' fruit of acerola kept the highest activity levels, it could be an indicative of greater potential for postharvest conservation.

Expressiveness and definability in circumscription

We investigate expressiveness and definability issues with respect to minimal models, particularly in the scope of Circumscription. First, we give a proof of the failure of the Löwenheim-Skolem Theorem for Circumscription. Then we show that, if the class of P; Z-minimal models of a first-order sentence is Δ-elementary, then it is elementary. That is, whenever the circumscription of a first-order sentence is equivalent to a first-order theory, then it is equivalent to a finitely axiomatizable one. This means that classes of models of circumscribed theories are either elementary or not Δ-elementary. Finally, using the previous result, we prove that, whenever a relation Pi is defined in the class of P; Z-minimal models of a first-order sentence Φ and whenever such class of P; Z-minimal models is Δ-elementary, then there is an explicit definition ψ for Pi such that the class of P; Z-minimal models of Φ is the class of models of Φ ∧ ψ. In order words, the circumscription of P in Φ with Z varied can be replaced by Φ plus this explicit definition ψ for Pi.

The transcendence of time in the epistemology of observation from a phenomenological standpoint

In this article I deal with time as a notion of epistemological content associated though with the notion of a subjective consciousness co-constitutive of physical reality. In this phenomenologically grounded approach I attempt to establish a 'metaphysical' aspect of time, within a strictly epistemological context, in the sense of an underlying absolute subjectivity which is non-objectifiable within objective temporality and thus non-susceptible of any ontological designation. My arguments stem, on the one hand, from a version of quantum-mechanical theory (History Projection Operator theory, HPO theory) in view of its formal treatment of two different aspects of time within a quantum context. The discrete, partial-ordering properties (the notions of before and after) and the dynamical-parameter properties reflected in the wave equations of motion. On the other hand, to strengthen my arguments for a transcendental factor of temporality, I attempt an interpretation of some relevant conclusions in the work of J. Eccles ([5]) and of certain results of experimental research of S. Deahaene et al. ([2]) and others.

The relation between the general maxim of causality and the principle of uniformity in hume's theory of knowledge

ABSTRACT When Hume, in the Treatise on Human Nature, began his examination of the relation of cause and effect, in particular, of the idea of necessary connection which is its essential constituent, he identified two preliminary questions that should guide his research: (1) For what reason we pronounce it necessary that every thing whose existence has a beginning should also have a cause and (2) Why we conclude that such particular causes must necessarily have such particular effects? (1.3.2, 14-15) Hume observes that our belief in these principles can result neither from an intuitive grasp of their truth nor from a reasoning that could establish them by demonstrative means. In particular, with respect to the first, Hume examines and rejects some arguments with which Locke, Hobbes and Clarke tried to demonstrate it, and suggests, by exclusion, that the belief that we place on it can only come from experience. Somewhat surprisingly, however, Hume does not proceed to show how that derivation of experience could be made, but proposes instead to move directly to an examination of the second principle, saying that, "perhaps, be found in the end, that the same answer will serve for both questions" (1.3.3, 9). Hume's answer to the second question is well known, but the first question is never answered in the rest of the Treatise, and it is even doubtful that it could be, which would explain why Hume has simply chosen to remove any mention of it when he recompiled his theses on causation in the Enquiry concerning Human Understanding. Given this situation, an interesting question that naturally arises is to investigate the relations of logical or conceptual implication between these two principles. Hume seems to have thought that an answer to (2) would also be sufficient to provide an answer to (1). Henry Allison, in his turn, argued (in Custom and Reason in Hume, p. 94-97) that the two questions are logically independent. My proposal here is to try to show that there is indeed a logical dependency between them, but the implication is, rather, from (1) to (2). If accepted, this result may be particularly interesting for an interpretation of the scope of the so-called "Kant's reply to Hume" in the Second Analogy of Experience, which is structured as a proof of the a priori character of (1), but whose implications for (2) remain controversial.

The mathematics of McTaggart's paradox

Mc Taggart's celebrated proof of the unreality of time is a chain of implications whose final step asserts that the A-series (i.e. the classification of events as past, present or future) is intrinsically contradictory. This is widely believed to be the heart of the argument, and it is where most attempted refutations have been addressed; yet, it is also the only part of the proof which may be generalised to other contexts, since none of the notions involved in it is specifically temporal. In fact, as I show in the first part of the paper, McTaggart's refutation of the A-series can be easily interpreted in mathematical terms; subsequently, in order to strengthen my claim, I apply the same framework by analogy to the cases of space, modality, and personal identity. Therefore, either McTaggart's proof as a whole may be extended to each of these notions, or it must embed some distinctly temporal element in one of the steps leading up to the contradiction of the A-series. I conclude by suggesting where this element might lay, and by hinting at what I believe to be the true logical fallacy of the proof.

HILBERT BETWEEN THE FORMAL AND THE INFORMAL SIDE OF MATHEMATICS

Abstract: In this article we analyze the key concept of Hilbert's axiomatic method, namely that of axiom. We will find two different concepts: the first one from the period of Hilbert's foundation of geometry and the second one at the time of the development of his proof theory. Both conceptions are linked to two different notions of intuition and show how Hilbert's ideas are far from a purely formalist conception of mathematics. The principal thesis of this article is that one of the main problems that Hilbert encountered in his foundational studies consisted in securing a link between formalization and intuition. We will also analyze a related problem, that we will call "Frege's Problem", form the time of the foundation of geometry and investigate the role of the Axiom of Completeness in its solution.

Nuclear and mitochondrial DNA markers in traceability of retail beef samples

Several characteristics are important in a traceability system of animal products, such as age at slaughter, breed composition, besides information of the productive chain. In general, the certification agent records information about the animals and the system which it came from, although cannot guarantee that the slaughtering, meat processing and distribution are error proof. Besides, there is a differential price, at least at the international market, based on sex and breed composition of the animals. Genetic markers allow identification of characteristics controlled in the beef cattle traceability program, as sex and breed composition, in order to correctly identify and appraise the final product for the consumer. The hypothesis of this study was that the majority beef samples retailed in the local market originate from female with a great participation of zebu breeds. Therefore, the objective of this work was to characterize retail beef samples with DNA markers that identify cattle sex and breed composition. Within 10 beef shops localized in Pirassununga, SP, Brazil, 61 samples were collected, all were genotyped as harboring Bos taurus mitochondrial DNA and 18 were positive for the Y chromosome amplification (male). For the marker sat1711b-Msp I the frequency of the allele A was 0.278 and for the marker Lhr-Hha I the frequency of the allele T was 0.417. The results of sat1711b-Msp I and Lhr-Hha I allelic frequencies are suggestive that the proportion of indicus genome compared with the taurine genome in the market meat is smaller than the observed in the Nellore breed. The procedure described in this study identified sex and subspecies characteristics of beef meat samples, with potential application in meat products certification in special as an auxiliary tool in beef cattle traceability programs.

Differential gene expression profiles of hepatocellular carcinomas associated or not with viral infection

Chronic hepatitis B (HBV) and C (HCV) virus infections are the most important factors associated with hepatocellular carcinoma (HCC), but tumor prognosis remains poor due to the lack of diagnostic biomarkers. In order to identify novel diagnostic markers and therapeutic targets, the gene expression profile associated with viral and non-viral HCC was assessed in 9 tumor samples by oligo-microarrays. The differentially expressed genes were examined using a z-score and KEGG pathway for the search of ontological biological processes. We selected a non-redundant set of 15 genes with the lowest P value for clustering samples into three groups using the non-supervised algorithm k-means. Fisher’s linear discriminant analysis was then applied in an exhaustive search of trios of genes that could be used to build classifiers for class distinction. Different transcriptional levels of genes were identified in HCC of different etiologies and from different HCC samples. When comparing HBV-HCC vs HCV-HCC, HBV-HCC/HCV-HCC vs non-viral (NV)-HCC, HBC-HCC vs NV-HCC, and HCV-HCC vs NV-HCC of the 58 non-redundant differentially expressed genes, only 6 genes (IKBKβ, CREBBP, WNT10B, PRDX6, ITGAV, and IFNAR1) were found to be associated with hepatic carcinogenesis. By combining trios, classifiers could be generated, which correctly classified 100% of the samples. This expression profiling may provide a useful tool for research into the pathophysiology of HCC. A detailed understanding of how these distinct genes are involved in molecular pathways is of fundamental importance to the development of effective HCC chemoprevention and treatment.

Coping with genetic diversity: the contribution of pathogen and human genomics to modern vaccinology

Vaccine development faces major difficulties partly because of genetic variation in both infectious organisms and humans. This causes antigenic variation in infectious agents and a high interindividual variability in the human response to the vaccine. The exponential growth of genome sequence information has induced a shift from conventional culture-based to genome-based vaccinology, and allows the tackling of challenges in vaccine development due to pathogen genetic variability. Additionally, recent advances in immunogenetics and genomics should help in the understanding of the influence of genetic factors on the interindividual and interpopulation variations in immune responses to vaccines, and could be useful for developing new vaccine strategies. Accumulating results provide evidence for the existence of a number of genes involved in protective immune responses that are induced either by natural infections or vaccines. Variation in immune responses could be viewed as the result of a perturbation of gene networks; this should help in understanding how a particular polymorphism or a combination thereof could affect protective immune responses. Here we will present: i) the first genome-based vaccines that served as proof of concept, and that provided new critical insights into vaccine development strategies; ii) an overview of genetic predisposition in infectious diseases and genetic control in responses to vaccines; iii) population genetic differences that are a rationale behind group-targeted vaccines; iv) an outlook for genetic control in infectious diseases, with special emphasis on the concept of molecular networks that will provide a structure to the huge amount of genomic data.

Political economy of preferential trade agreement: the case of bilateral asymmetric negotiation

The purpose of this paper is to analyse the political economy of preferential trade agreements based on a sequential non-cooperative Stackelberg political game between a large economy and a small one, in which the political dispute of rival lobby groups defines the unilateral stance of both governments in the first stage; and the Stackelberg "coalition-proof" equilibrium defines the free trade agreement format in the second stage. Finally, a few modifications in the initial game structure are discussed in order to enhance the small economy's negotiation power. The political economy model is applied to FTAA case.