Bacterial peptidoglycan biosynthesis and recognition by the innate immune system

Dissertation presented to obtain the Ph.D degree in Biology

Improvements on the KNN classifier

Dissertação para obtenção do Grau de Mestre em Engenharia Informática

Synthesis of new enzyme stabilisers inspired by compatible solutes of hyperthermophilic microorganisms

Dissertation presented to obtain the Ph.D degree in Engineering Sciences and Technology.

Regulation and function of the cell wall polymer lipoteichoic acid in staphylococcus aureus

A thesis submitted for the Degree of Master in Medical microbiology

Fragilidade e pré-fragilidade em pessoas idosas residentes na comunidade

RESUMO: Objectivo: Este estudo tem como principal objectivo determinar perfis de fragilidade em pessoas idosas, residentes ma comunidade. Metodologia: Trata-se de um estudo de natureza não experimental, quantitativo, exploratório e descritivo, com uma amostra de conveniência, constituída por pessoas idosas (n=47), residentes na comunidade. As variáveis em análise foram o fenótipo de fragilidade, onde a força de preensão foi avaliada através de um dinamómetro portátil, a percepção de exaustão através da CES-D, a velocidade de marcha foi avaliada pelo Timed Up and Go Test, a actividade física através de uma escala simplificada, com base nos estudos de Grimby, e a perda de peso não intencional através de uma questão sobre perda de peso no último ano. As restantes variáveis foram avaliadas por questionário, à excepção da capacidade funcional, avaliada por uma escala com actividades básicas e instrumentais da vida diária assim como locomoção, e da força de membros inferiores, avaliada pelo teste de sentar e levantar da cadeira durante 30 segundos. Resultados: Verificou-se que a maioria da amostra era pré-frágil, com uma frequência próxima de fragilidade e uma quase inexistência de não fragilidade. Contribui para isto, essencialmente, a velocidade de marcha e perda de peso não intencional. Apesar de se encontrar uma grande presença de comorbilidade e independência com limitação nos indivíduos deste estudo, não se verifica uma relação de significância entre estas variáveis. Verificam-se relações significativas com a Hipertensão arterial e a percepção do estado de saúde. Conclusão: Não foi possível definir um perfil de fragilidade de forma consistente, devido à grande variabilidade de resultados encontrados e à não existência de correlações significativas, no que diz respeito à síndrome de fragilidade. -----------ABSTRACT: Objective: This study aims to determine profiles of fragility in elderly people, living in the community Methodology: This is a study of a non experimental, quantitative, exploratory and descriptive, with a convenience sample, consisting of elderly (n = 47), living in the community. The variables analyzed were the frailty phenotype where grip strength was measured using a handheld dynamometer, the perception of exhaustion through the CES-D, gait speed was assessed by the Timed Up and Go Test, physical activity through a simplified scale based on studies of Grimby and unintentional loss of weight through a question about weight loss in the last year.The remaining variables were assessed by questionnaire, with the exception of functional capacity assessed by a scale with basic and instrumental activities of daily living as well as locomotion, and lower limb strength, evaluated by sitting and rising from a chair for 30-second test. Results: It was found that most of the sample was pre-fragile with a frequency close to the fragility and almost no non-brittleness. Contribute to this, essentially, gait speed and unintentional weight loss. Despite being a large presence of comorbidity and independence in individuals with limitation of this study, no there is a significant relationship between this variables. There are significant relations with hypertension and the perception of health status. Conclusion: It was not possible to define a profile of fragility consistently, due to the great variability of results and the absence of significant correlations, with respect to the frailty syndrome.

Molecular detection of Treponema pallidum sp. pallidum in blood samples of VDRL-seroreactive women with lethal pregnancy outcomes: a retrospective observational study in northern Brazil

INTRODUCTION: Although control measures of maternal and congenital syphilis are available in Brazil, difficulties exist within the healthcare network in providing a laboratory diagnosis of the infection during the prenatal period. The objective of this study was to confirm the presence of Treponema pallidum by PCR in women with positive VDRL serology and lethal pregnancy outcomes, i.e., abortion, stillbirth and neonatal death. METHODS: A retrospective study was conducted on VDRLseroreactive women with lethal pregnancy outcomes admitted to the Fundação Santa Casa de Misericórdia do Pará (FSCM-PA) between January and July 2004. Serum samples and DNA from whole blood were obtained at the time of screening by the VDRL test. These samples were analyzed by IgG ELISA, IgM FTA-Abs and simple PCR (polA). RESULTS: During the study period, 0.7% (36/4,912) of women with lethal pregnancy outcomes presented a positive VDRL test. The polAgene was amplified in 72.7% (24/33) of these women, with 55.6% (20/36) and 94.4% (34/36) presenting IgM and IgG antibodies against T. pallidum, respectively. Comparison of these results showed a significant difference, with agreement between the PCR and IgM FTA-Abs results, suggesting that maternal syphilis was an active infection. No basic cause of death of the conceptus was reported in 97.2% (35/36) of cases. Among women who were submitted to the VDRL test during the prenatal period, only four of the nine seroreactive patients underwent treatment. CONCLUSIONS: The high frequency of syphilis in the group studied indicates the fragility of the service of infection diagnosis, treatment and monitoring, compromising epidemiological control.

A internet e o sistema de justiça

The subject of study of this Thesis aims to highlight and recognize as an object of reflection the undoubted relationship between the Internet and the Justice System, based on the issue of digital evidence. The simultaneously crossing of the juridical-legal implications and the more technical computer issues is the actual trigger for the discussion of the issues established. The Convention on Cybercrime of the Council of Europe of 23rd November 2001 and the Council Framework Decision n.° 2005/222/JHA of 24th February 2005 were avant-garde in terms of the international work about the crimes in the digital environment. In addition they enabled the harmonization of national legislations on the matter and, consequently, a greater flexibility in international judicial cooperation. Portugal, in compliance with these international studies, ratified, implemented and approved Law n. º 109/2009 of 15th September concerning the Cybercrime Act, establishing a more specific investigation and collection of evidence in electronic support when it comes to combating this type of crime, as it reinforced the Substantive Criminal Law and Procedural Nature. Nevertheless, the constant debates about the New Technologies of Information and Communication have not neglected the positive role of these tools for the user. However, they express a particular concern for their counterproductive effects; a special caution prevails on the part of the judge in assessing the digital evidence, especially circumstantial evidence, due to the its fragility. Indisputably, the practice of crimes through the computer universe, given its inexorable technical complexity, entails many difficulties for the forensic investigation, since the proofs hold temporary, changeable, volatile, and dispersed features. In this pillar, after the consummation of iter criminis, the Fundamental Rights of the suspects may be debated in the course of the investigation and the construction of iter probatorium. The intent of this Thesis is to contribute in a reflective way on the issues presented in order to achieve a bigger technical and legal awareness regarding the collection of digital proof, looking for a much lighter approach to its suitability in terms of evidentiary value.

Análise da qualidade do serviço numa empresa transportadora

Dissertação de mestrado integrado em Engenharia e Gestão Industrial

Comparative genomics reveals adaptations of a halotolerant thaumarchaeon in the interfaces of brine pools in the Red Sea

The bottom of the Red Sea harbors over 25 deep hypersaline anoxic basins that are geochemically distinct and characterized by vertical gradients of extreme physicochemical conditions. Because of strong changes in density, particulate and microbial debris get entrapped in the brine-seawater interface (BSI), resulting in increased dissolved organic carbon, reduced dissolved oxygen toward the brines and enhanced microbial activities in the BSI. These features coupled with the deep-sea prevalence of ammonia-oxidizing archaea (AOA) in the global ocean make the BSI a suitable environment for studying the osmotic adaptations and ecology of these important players in the marine nitrogen cycle. Using phylogenomic-based approaches, we show that the local archaeal community of five different BSI habitats (with up to 18.2% salinity) is composed mostly of a single, highly abundant Nitrosopumilus-like phylotype that is phylogenetically distinct from the bathypelagic thaumarchaea; ammonia-oxidizing bacteria were absent. The composite genome of this novel Nitrosopumilus-like subpopulation (RSA3) co-assembled from multiple single-cell amplified genomes (SAGs) from one such BSI habitat further revealed that it shares [sim]54% of its predicted genomic inventory with sequenced Nitrosopumilus species. RSA3 also carries several, albeit variable gene sets that further illuminate the phylogenetic diversity and metabolic plasticity of this genus. Specifically, it encodes for a putative proline-glutamate 'switch' with a potential role in osmotolerance and indirect impact on carbon and energy flows. Metagenomic fragment recruitment analyses against the composite RSA3 genome, Nitrosopumilus maritimus, and SAGs of mesopelagic thaumarchaea also reiterate the divergence of the BSI genotypes from other AOA.

Experimental procedures for the identification of material properties of intervertebal disc - a contribution for the development of biomimetic substitutes for the nucleus pulposus

Tese de Doutoramento em Engenharia Mecânica.

Dos ciclos e sistemas aos interstícios de Creixomil: entre o seu conhecimento e transformação potencial

Dissertação de mestrado integrado em Arquitectura (área de especialização em Território)

Estudos experimentais sôbre a origem do milho

1) It may seem rather strange that, in spite of the efforts of a considerable number of scientists, the problem of the origin of indian corn or maize still has remained an open question. There are no fossil remains or archaeological relics except those which are quite identical with types still existing. (Fig. 1). The main difficulty in finding the wild ancestor- which may still exist - results from the fact that it has been somewhat difficult to decide what it should be like and also where to look for it. 2) There is no need to discuss the literature since an excellent review has recently been published by MANGELSDORF and REEVES (1939). It may be sufficient to state that there are basically two hypotheses, that of ST. HILAIRE (1829) who considered Brazilian pod corn as the nearest relative of wild corn still existing, and that of ASCHERSON (1875) who considered Euchlaena from Central America as the wild ancestor of corn. Later hypotheses represent or variants of these two hypotheses or of other concepts, howewer generally with neither disproving their predecessors nor showing why the new hypotheses were better than the older ones. Since nearly all possible combinations of ideas have thus been put forward, it har- dly seems possible to find something theoretically new, while it is essential first to produce new facts. 3) The studies about the origin of maize received a new impulse from MANGELSDORF and REEVES'S experimental work on both Zea-Tripsacum and Zea-Euchlaena hybrids. Independently I started experiments in 1937 with the hope that new results might be obtained when using South American material. Having lost priority in some respects I decided to withold publication untill now, when I can put forward more concise ideas about the origin of maize, based on a new experimental reconstruction of the "wild type". 4) The two main aspects of MANGELSDORF and REEVES hypothesis are discussed. We agree with the authors that ST. HILAIRE's theory is probably correct in so far as the tunicata gene is a wild type relic gene, but cannot accept the reconstruction of wild corn as a homozygous pod corn with a hermaphroditic tassel. As shown experimentally (Fig. 2-3) these tassels have their central spike transformed into a terminal, many rowed ear with a flexible rachis, while possessing at the same time the lateral ear. Thus no explanation is given of the origin of the corn ear, which is the main feature of cultivated corn (BRIEGER, 1943). The second part of the hypothesis referring to the origin of Euchlaena from corn, inverting thus ASCHERSON's theory, cannot be accepted for several reasons, stated in some detail. The data at hand justify only the conclusion that both genera, Euchlaena and Zea, are related, and there is as little proof for considering the former as ancestor of the latter as there is for the new inverse theory. 5) The analysis of indigenous corn, which will be published in detail by BRIEGER and CUTLER, showed several very primitive characters, but no type was found which was in all characters sufficiently primitive. A genetical analysis of Paulista Pod Corn showed that it contains the same gene as other tunicates, in the IV chromosome, the segregation being complicated by a new gametophyte factor Ga3. The full results of this analysis shall be published elsewhere. (BRIEGER). Selection experiments with Paulista Pod Corn showed that no approximation to a wild ancestor may be obtained when limiting the studies to pure corn. Thus it seemed necessary to substitute "domesticated" by "wild type" modifiers, and the only means for achieving this substitution are hybridizations with Euchlaena. These hybrids have now been analysed init fourth generation, including backcrosses, and, again, the full data will be published elsewhere, by BRIEGER and ADDISON. In one present publication three forms obtained will be described only, which represent an approximation to wild type corn. 6) Before entering howewer into detail, some arguments against ST. HILAIRE's theory must be mentioned. The premendelian argument, referring to the instability of this character, is explained by the fact that all fertile pod corn plants are heterozygous for the dominant Tu factor. But the sterility of the homozygous TuTu, which phenotypically cannot be identified, is still unexplained. The most important argument against the acceptance of the Tunicata faetor as wild type relic gene was removed recently by CUTLER (not yet published) who showed that this type has been preserved for centuries by the Bolivian indians as a mystical "medicine". 7) The main botanical requirements for transforming the corn ear into a wild type structure are stated, and alternative solutions given. One series of these characters are found in Tripsacum and Euchlaena : 2 rows on opposite sides of the rachis, protection of the grains by scales, fragility of the rachis. There remains the other alternative : 4 rows, possibly forming double rows of female and male spikelets, protection of kernels by their glumes, separation of grains at their base from the cob which is thin and flexible. 8) Three successive stages in the reconstruction of wild corn, obtained experimentally, are discussed and illustrated, all characterized by the presence of the Tu gene. a) The structure of the Fl hybrids has already been described in 1943. The main features of the Tunicata hybrids (Fig. -8), when compared with non-tunicate hybrids (Fig. 5-6), consist in the absence of scaly protections, the fragility of the rachis and finally the differentiation of the double rows into one male and one female spikelet. As has been pointed out, these characters represent new phenotypic effects of the tunicate factor which do not appear in the presence of pure maize modifiers. b) The next step was observed among the first backcross to teosinte (Fig. 9). As shown in the photography, Fig. 9D, the features are essencially those of the Fl plants, except that the rachis is more teosinte like, with longer internodes, irregular four-row-arrangement and a complete fragility on the nodes. c) In the next generation a completely new type appeared (Fig. 10) which resembles neither corn nor teosinte, mainly in consequence of one character: the rachis is thin and flexible and not fragile, while the grains have an abscission layer at the base, The medium sized, pointed, brownish and hard granis are protected by their well developed corneous glumes. This last form may not yet be the nearest approach to a wild grass, and I shall try in further experiments to introduce other changes such as an increase of fertile flowers per spikelet, the reduction of difference between terminal and lateral inflorescences, etc.. But the nature of the atavistic reversion is alveadwy such that it alters considerably our expectation when looking for a still existing wild ancestor of corn. 9) The next step in our deductions must now consist in an reversion of our question. We must now explain how we may obtain domesticated corn, starting from a hypothetical wild plant, similar to type c. Of the several changes which must have been necessary to attract the attention of the Indians, the following two seem to me the most important: the disappearance of all abscission layers and the reduction of the glumes. This may have been brought about by an accumulation of mutations. But it seems much more probable to assume that some crossing with a tripsacoid grass or even with Tripsacum australe may have been responsible. In such a cross, the two types of abscission layer would be counterbalanced as shown by the Flhybrids of corn, Tripsacum and Euchlaena. Furthermore in later generations a.tu-allele of Tripsacum may become homozygous and substitute the wild tunicate factor of corn. The hypothesis of a hybrid origin of cultivated corn is not completely new, but has been discussed already by HARSHBERGER and COLLINS. Our hypothesis differs from that of MANGELSDORF and REEVES who assume that crosses with Tripsacum are responsible only for some features of Central and North American corn. 10) The following arguments give indirects evidence in support of our hypothesis: a) Several characters have been observed in indigenous corn from the central region of South America, which may be interpreted as "tripsacoid". b) Equally "zeoid" characters seem to be present in Tripsacum australe of central South-America. c) A system of unbalanced factors, combined by the in-tergeneric cross, may be responsible for the sterility of the wild type tunicata factor when homozygous, a result of the action of modifiers, brought in from Tripsacum together with the tuallele. d) The hybrid theory may explain satisfactorily the presence of so many lethals and semilethals, responsible for the phenomenon of inbreeding in cultivated corn. It must be emphasized that corn does not possess any efficient mechanism to prevent crossing and which could explain the accumulation of these mutants during the evolutionary process. Teosinte which'has about the same mechanism of sexual reproduction has not accumulated such genes, nor self-sterile plants in spite of their pronounced preference for crossing. 11) The second most important step in domestication must have consisted in transforming a four rowed ear into an ear with many rows. The fusion theory, recently revived byLANGHAM is rejected. What happened evidently, just as in succulent pXants (Cactus) or in cones os Gymnosperms, is that there has been a change in phyllotaxy and a symmetry of longitudinal rows superimposed on the original spiral arrangement. 12) The geographical distribution of indigenous corn in South America has been discussed. So far, we may distinguish three zones. The most primitive corn appears in the central lowlands of what I call the Central Triangle of South America: east of the Andies, south of the Amazone-Basin, Northwest of a line formed by the rivers São Prancisco-Paraná and including the Paraguay-Basin. The uniformity of the types found in this extremely large zone is astonishing (BRIEGER and CUTLER). To the west, there is the well known Andian region, characterized by a large number of extremely diverse types from small pop corn to large Cuszco, from soft starch to modified sweet corn, from large cylindrical ears to small round ears, etc.. The third region extends along the atlantic coast in the east, from the Caribean Sea to the Argentine, and is characterized by Cateto, an orange hard flint corn. The Andean types must have been obtained very early, and undoubtedly are the result of the intense Inca agriculture. The Cateto type may be obtained easily by crosses, for instance, of "São Paulo Pointed Pop" to some orange soft corn of the central region. The relation of these three South American zones to Central and North America are not discussed, and it seems essential first to study the intermediate region of Ecuador, Colombia and Venezuela. The geograprical distribution of chromosome knobs is rapidly discussed; but it seems that no conclusions can be drawn before a large number of Tripsacum species has been analysed.

Sobre os efeitos vasomotôres exercidos pela agua distilada e pelas soluções anisotonicas de clorêto de sodio

The writer reports experiments done with distilled water and hypotonic and hypertonic salt solutions of definite osmotic concentrations. The experiments were performed according to the Laewen-Trendelenburg technic using the vascular system of the frog's hind legs, and according to the Pissemski-Krawkow method using the capillaries of the rabbit's ear. Both preparations react to distilled water by marked vaso-constriction, the same phenomenon taking place in the case of the hypotonic salt solutions. The lower the concentration pf the hypotonic salt solution the stronger the vaso-constriction obtained. With hypertonic salt solutions was observed a strong but rather transient vaso-dilatation followed by secondary vaso-constriction. The later results were found only in the experiments with the frog's hind legs.

Regulació del factor de transcripció NFAT5 per les quinases WNK1, SPAK i OSR1 i cerca de quinases activadores de la pròpia WNK1 en resposta a estrés osmòtic

Estudi elaborat a partir d’una estada a la School of Life Sciences de la University of Dundee, Gran Bretanya, entre gener i març del 2007.L'estrès osmòtic causa rà pidament l'activació de la quinasa WNK1, que fosforila i activa a continuació les quinases SPAK i OSR1, que alhora regulen canals i transportadors d’ions preexistents a la membrana cel•lular. El factor de transcripció NFAT5 és el principal regulador de la resposta cel•lular transcripcional secundà ria a hipertonicitat i s’ha descrit que les quinases p38, Fyn, PKA, ERK/MEK i ATM estan involucrades en la seva regulació post-traduccional. No obstant, com que la funció d’aquestes quinases no explica totalment els mecanismes d'activació de NFAT5, s’ha estudiat si l’activitat transcripcional de NFAT5 pot estar regulada per WNK1, SPAK o OSR1. Així doncs, es va observar que l’activitat d’un reporter dependent de NFAT5 no es veu afectada per la presència de cap de les quinases anteriors, en la seva forma wild-type o dominant negatiu. D’altra banda, es va estudiar quin domini de WNK1 és necessari per a que pugui respondre a hipertonicitat i quines quinases poden estar involucrades en la fosforilació de la serina 382 de WNK1. En conclusió, les dades obtingudes apunten que l’activació de WNK1 en resposta a estrès osmòtic requereix la seva fosforilació en la serina 382 per quinases upstream com PAK2 o RSK i que també és necessari un dels seus dominis coiled-coil, almenys els aminoà cids 558 i 561. Aquests processos, però, semblen ser independents de l’activació de NFAT5 en resposta a hipertonicitat.   

Comparison of two osteoporotic fracture management pathways: experience at 1 year

Introduction: Osteoporosis presenting as low-impact fractures to traumatology units is often undiagnosed and under-treated. Results from the Osteocare study in Lausanne (a nurse based intervention, passive pathway) showed that only 19% of patients received management for osteoporosis, and in the literature [1], the rate is between 10-25%. We have evaluated a different management concept, based on the systematic assessment of patients with osteoporotic fractures during and after hospitalization (active pathway). Methods: Inpatients admitted to the Department of Musculoskeletal Medicine for a fragility fracture were identified by a nurse according to a predefined questionnaire and were then clinically evaluated by a doctor. Based on the results, a management plan was proposed to the patients. Patients could choose between follow up either by their GP or by the Centre of Bone Disease of the CHUV. For patients who chose follow-up in our Centre, we assessed their adherence to medical follow-up 1 year inclusion. The results of patients who had been evaluated in our cohort between the 1 November 2008 and the 1 December 2009 were analysed. Results: 573 inpatients received specific management of their osteoporotic fracture over 18 months. The mean age was 77 y (31-99), 81% were women (203 hip fractures, 40 pelvis fractures, 101 arm fractures, 57 vertebral fractures, 63 ankle fractures, and 25 others sites). During the study period, 303 patients received a proposition of a specific treatment. 39 (13%) chose a follow up with the GP, 19 (6%) dead and 245 (81%) preferred a follow up in our Centre. After 1 year, 166 (67%) patients are under follow up in our outpatient clinic. Conclusion: With an active clinical pathway that starts during the hospitalization, consisting on a nursing evaluation followed by a medical consultation by an expert in osteoporosis, the adherence increased from 19% to 67% in terms of follow up. These results lead us to propose a consultation with a doctor experienced in osteoporosis after all osteoporotic fractures.