Evolutionary dynamics of Chlamydia trachomatis genome and identification of molecular patterns of hypothetical protein coding genes

The obligate intracellular bacterium Chlamydia trachomatis is a human pathogen of major public health significance. Strains can be classified into 15 main serovars (A to L3) that preferentially cause ocular infections (A-C), genital infections (D-K) or lymphogranuloma venereum (LGV) (L1-L3), but the molecular basis behind their distinct tropism, ecological success and pathogenicity is not welldefined. Most chlamydial research demands culture in eukaryotic cell lines, but it is not known if stains become laboratory adapted. By essentially using genomics and transcriptomics, we aimed to investigate the evolutionary patterns underlying the adaptation of C. trachomatis to the different human tissues, given emphasis to the identification of molecular patterns of genes encoding hypothetical proteins, and to understand the adaptive process behind the C. trachomatis in vivo to in vitro transition. Our results highlight a positive selection-driven evolution of C. trachomatis towards nichespecific adaptation, essentially targeting host-interacting proteins, namely effectors and inclusion membrane proteins, where some of them also displayed niche-specific expression patterns. We also identified potential "ocular-specific" pseudogenes, and pointed out the major gene targets of adaptive mutations associated with LGV infections. We further observed that the in vivo-derived genetic makeup of C. trachomatis is not significantly compromised by its long-term laboratory propagation. In opposition, its introduction in vitro has the potential to affect the phenotype, likely yielding virulence attenuation. In fact, we observed a "genital-specific" rampant inactivation of the virulence gene CT135, which may impact the interpretation of data derived from studies requiring culture. Globally, the findings presented in this Ph.D. thesis contribute for the understanding of C.trachomatis adaptive evolution and provides new insights into the biological role of C. trachomatishypothetical proteins. They also launch research questions for future functional studies aiming toclarify the determinants of tissue tropism, virulence or pathogenic dissimilarities among C. trachomatisstrains.

Optimisation and design of post-tensioning anchorage corner blisters in concrete box girder bidges

The design of anchorage blisters of internal continuity post-tensioning tendons of bridges built by the cantilever method, presents some peculiarities, not only because they are intermediate anchorages but also because these anchorages are located in blisters, so the prestressing force has to be transferred from the blister the bottom slab and web of the girder. The high density of steel reinforcement in anchorage blisters is the most common reason for problems with concrete cast in situ, resulting in zones with low concrete compacity, leading to concrete crushing failures under the anchor plates. A solution may involve improving the concrete compression and tensile strength. To meet these requirements a high-performance fibre reinforced self-compacting mix- ture (HPFRC) was used in anchorage corner blisters of post-tensioning tendons, reducing the concrete cross-section and decreasing the reinforcement needed. To assess the ultimate capacity and the adequate serviceability of the local anchorage zone after reducing the minimum concrete cross-section and the confining reinforcement, specified by the anchorage device supplier for the particular tendon, load transfer tests were performed. To investigate the behaviour of anchorage blisters regarding the transmission of stresses to the web and the bottom slab of the girder, and the feasibility of using high performance concrete only in the blister, two half scale models of the inferior corner of a box girder existing bridge were studied: a reference specimen of ordinary reinforced concrete and a HPFRC blister specimen. The design of the reinforcement was based in the tensile forces obtained on strut-and-tie models. An experimental program was carried out to assess the models used in design and to study the feasibility of using high performance concrete only in the blister, either with casting in situ, or with precast solutions. A non-linear finite element analysis of the tested specimens was also performed and the results compared.

The World Health Organization Multi-Professional Patient Safety Curriculum : implementation of key modules and its impact on patient safety knowledge, skills, and attitudes of medical students at the University of Algarve

ABSTRACT - Objectives: We attempted to show how the implementation of the key elements of the World Health Organization Patient Safety Curriculum Guide Multi-professional Edition in an undergraduate curriculum affected the knowledge, skills, and attitudes towards patient safety in a graduate entry Portuguese Medical School. Methods: After receiving formal recognition by the WHO as a Complementary Test Site and approval of the organizational ethics committee , the validated pre-course questionnaires measuring the knowledge, skills, and attitudes to patient safety were administered to the 2nd and3rd year students pursuing a four-year course (N = 46). The key modules of the curriculum were implemented over the academic year by employing a variety of learning strategies including expert lecturers, small group problem-based teaching sessions, and Simulation Laboratory sessions. The identical questionnaires were then administered and the impact was measured. The Curriculum Guide was evaluated as a health education tool in this context. Results: A significant number of the respondents, 47 % (n = 22), reported having received some form of prior patient safety training. The effect on Patient Safety Knowledge was assessed by using the percentage of correct pre- and post-course answers to construct 2 × 2 contingency tables and by applying Fishers’ test (two-tailed). No significant differences were detected (p < 0.05). To assess the effect of the intervention on Patient Safety skills and attitudes, the mean and standard deviation were calculated for the pre and post-course responses, and independent samples were subjected to Mann-Whitney’s test. The attitudinal survey indicated a very high baseline incidence of desirable attitudes and skills toward patient safety. Significant changes were detected (p < 0.05) regarding what should happen if an error is made (p = 0.016), the role of healthcare organizations in error reporting (p = 0.006), and the extent of medical error (p = 0.005). Conclusions: The implementation of selected modules of the WHO Patient Safety Curriculum was associated with a number of positive changes regarding patient safety skills and attitudes, with a baseline incidence of highly desirable patient safety attitudes, but no measureable change on the patient safety knowledge, at the University of Algarve Medical School. The significance of these results is discussed along with implications and suggestions for future research.

Microlaparoscopy in gynecology: analysis of 16 cases and review of literature

Microlaparoscopy represents the development of endoscopic surgery towards a minimally invasive surgical procedure. The advantages include fewer surgical complications, faster return to daily activities, more comfortable postoperative recovery, and satisfactory aesthetic results. The possibility of performing surgery under sedation may result in shorter hospitalization, lower hospital costs, and easier anesthetic procedures. The authors report their preliminary experience with the use of microlaparoscopy, using optics and 2mm instruments, as well as a review of the literature since the introduction of this new technique. The report of these 16 cases demonstrates that microlaparoscopy is a feasible technique with satisfactory results. On the other hand, this new technique requires precise indications and a training period for the development of the skills necessary for performing these surgeries.

A study on the performance of technology transfer units

Universities are increasingly institutionalizing activities related to technology transfer and one of the main institutional mechanisms that has emerged is the “technology transfer unit” (TTU). Many of them are focusing their activities on the management of the university intellectual property. Studies have investigated factors that seem to affect their performance, but few have looked in detail at internal procedures and techniques that are used in their processes related to technology evaluation and licensing. The aim of this paper is to provide a comprehensive overview of some of the several steps that comprises the processes regarding technology evaluation and licensing, providing an analysis of the critical issues that affect each step of the process. A review of the literature was made, complemented with interviews to seven university TTUs, which was used as a check and a complement to the literature review and as way of perceiving from an insider perspective, the problems and issues that this paper wants to emphasize and to state clearly.

Methodology for real-time adaptation of tunnels support using the observational method

The observational method in tunnel engineering allows the evaluation in real time of the actual conditions of the ground and to take measures if its behavior deviates considerably from predictions. However, it lacks a consistent and structured methodology to use the monitoring data to adapt the support system in real time. The definition of limit criteria above which adaptation is required are not defined and complex inverse analysis procedures (Rechea et al. 2008, Levasseur et al. 2010, Zentar et al. 2001, Lecampion et al. 2002, Finno and Calvello 2005, Goh 1999, Cui and Pan 2012, Deng et al. 2010, Mathew and Lehane 2013, Sharifzadeh et al. 2012, 2013) may be needed to consistently analyze the problem. In this paper a methodology for the real time adaptation of the support systems during tunneling is presented. In a first step limit criteria for displacements and stresses are proposed. The methodology uses graphics that are constructed during the project stage based on parametric calculations to assist in the process and when these graphics are not available, since it is not possible to predict every possible scenario, inverse analysis calculations are carried out. The methodology is applied to the “Bois de Peu” tunnel which is composed by two tubes with over 500 m long. High uncertainty levels existed concerning the heterogeneity of the soil and consequently in the geomechanical design parameters. The methodology was applied in four sections and the results focus on two of them. It is shown that the methodology has potential to be applied in real cases contributing for a consistent approach of a real time adaptation of the support system and highlight the importance of the existence of good quality and specific monitoring data to improve the inverse analysis procedure.

Cognitive functioning and efficacy of cognitive intervention in Multiple Sclerosis

Tese de Doutoramento em Psicologia Clínica / Psicologia

Personal and Social Performance (PSP) scale for patients with schizophrenia: translation to Portuguese, cross-cultural adaptation and interrater reliability

INTRODUCTION: Schizophrenia is a chronic mental disorder associated with impairment in social functioning. The most widely used scale to measure social functioning is the GAF (Global Assessment of Functioning), but it has the disadvantage of measuring at the same time symptoms and functioning, as described in its anchors. OBJECTIVES:Translation and cultural adaptation of the PSP, proposing a final version in Portuguese for use in Brazil. METHODS: We performed five steps: 1) translation; 2) back translation; 3) formal assessment of semantic equivalence; 4) debriefing; 5) analysis by experts. Interrater reliability (Intraclass correlation, ICC) between two raters was also measured. RESULTS: The final version was applied by two independent investigators in 18 adults with schizophrenia (DSM-IV-TR). The interrater reliability (ICC) was 0.812 (p < 0.001). CONCLUSION: The translation and adaptation of the PSP had an adequate level of semantic equivalence between the Portuguese version and the original English version. There were no difficulties related to understanding the content expressed in the translated texts and terms. Its application was easy and it showed a good interrater reliability. The PSP is a valid instrument for the measurement of personal and social functioning in schizophrenia.

Effect of temperature on the survival and growth of freshwater prawns Macrobrachium borellii and Palaemonetes argentinus (Crustacea, Palaemonidae)

During the two-month rearing period, the effect of four water temperatures (15°C, 20°C, 25°C and 30°C) on survival rate, number of molts, and growth rate (molt increment and intermolt period) of juvenile Macrobrachium borellii Nobili, 1896 and Palaemonetes argentinus Nobili, 1901 prawns was evaluated in laboratory conditions. The two species showed some similarities in their both survival and growth pattern at different temperatures. The survival rate was highest at 20°C and 25°C, decreasing at the lowest temperature. The number of molts increased at higher temperatures, ranging the intermolt period from 22.2 days to 9.9 days, for M. borellii, and from 20.8 to 9.5 days for P. argentinus, corresponding those values to 15°C and 30°C, respectively. No difference between species was noted in the intermolt period. The size increment by molting increased significantly from 15°C to 25°C, whereas a reduction in the growth of prawns was observed at 30°C. Significant differences among temperatures were found in the slope of regressions between the size increment by molting and the cephalothorax length. M. borellii showed a significantly higher tolerance to elevated temperature and a faster growth (about twice at 25°C) than P. argentinus. These differences could provide M. borellii a competitive advantage for a better adaptation to the dynamic of freshwater environment, especially in areas with anthropogenic impact.

Transplantation tolerance induced by regulatory T cells: in vivo mechanisms and sites of action.

The mechanisms by which CD4(+)CD25(+)Foxp3(+) T (Treg) cells regulate effector T cells in a transplantation setting and their in vivo homeostasis still remain to be clarified. Using a mouse adoptive transfer model, we analyzed the in vivo expansion, trafficking, and effector function of alloreactive T cells and donor-specific Treg cells, in response to a full-thickness skin allograft. Fluorescent-labeled CD4(+)CD25(-) and antigen-specific Treg cells were transferred alone or co-injected into syngeneic BALB/c-Nude recipients transplanted with skins from (C57BL/6 x BALB/c) F1 donors. Treg cells divided in vivo, migrated and accumulated in the allograft draining lymph nodes as well as within the graft. The co-transfer of Treg cells did not modify the early activation and homing of CD4(+)CD25(-) T cells in secondary lymphoid organs. However, in the presence of Treg cells, alloreactive CD4(+)CD25(-) T cells produced significantly less IFN-gamma and were present in reduced numbers in the secondary lymphoid organs. Furthermore, time-course studies showed that Treg cells were recruited into the allograft at a very early stage after transplantation and effectively prevented the infiltration of effector T cells. In conclusion, suppression of rejection requires the early recruitment to the site of antigenic challenge of donor-specific Treg cells, which then mainly regulate the effector arm of T cell alloresponses.

Union Mediation and Adaptation to Reciprocal Loyalty Arrangements

This study assesses the industrial relations application of the „loyalty-exit-voice‟ proposition. The loyalty concept is linked to reciprocal employer-employee arrangements and examined as a job attribute in a vignette questionnaire distributed to low and medium-skilled employees. The responses provided by employees in three European countries indicate that reciprocal loyalty arrangements, which involve the exchange of higher effort for job security, are one of the most desirable job attributes. This attribute exerts a higher impact on the job evaluations provided by unionised workers, compared to their non-union counterparts. This pattern is robust to a number of methodological considerations. It appears to be an outcome of adaptation to union mediated cooperation. Overall the evidence suggests that the loyalty-job evaluation profiles of unionised workers are receptive to repeated interaction and negative shocks, such as unemployment experience. This is not the case for the non-union workers. Finally, unionised workers appear to „voice‟ a lower job satisfaction, but exhibit low „exit‟ intentions, compared to the non-unionised labour.

Mitochondrial targeting adaptation of the hominoid-specific glutamate dehydrogenase driven by positive Darwinian selection.

Many new gene copies emerged by gene duplication in hominoids, but little is known with respect to their functional evolution. Glutamate dehydrogenase (GLUD) is an enzyme central to the glutamate and energy metabolism of the cell. In addition to the single, GLUD-encoding gene present in all mammals (GLUD1), humans and apes acquired a second GLUD gene (GLUD2) through retroduplication of GLUD1, which codes for an enzyme with unique, potentially brain-adapted properties. Here we show that whereas the GLUD1 parental protein localizes to mitochondria and the cytoplasm, GLUD2 is specifically targeted to mitochondria. Using evolutionary analysis and resurrected ancestral protein variants, we demonstrate that the enhanced mitochondrial targeting specificity of GLUD2 is due to a single positively selected glutamic acid-to-lysine substitution, which was fixed in the N-terminal mitochondrial targeting sequence (MTS) of GLUD2 soon after the duplication event in the hominoid ancestor approximately 18-25 million years ago. This MTS substitution arose in parallel with two crucial adaptive amino acid changes in the enzyme and likely contributed to the functional adaptation of GLUD2 to the glutamate metabolism of the hominoid brain and other tissues. We suggest that rapid, selectively driven subcellular adaptation, as exemplified by GLUD2, represents a common route underlying the emergence of new gene functions.

Differential allocation and deployment of direct and indirect defences by Vicia sepium along elevation gradients

Dissecting drivers of plant defence investment remains central for understanding the assemblage of communities across different habitats. There is increasing evidence that direct defence strategies against herbivores, including secondary metabolites production, differ along ecological gradients in response to variation in biotic and abiotic conditions. In contrast, intraspecific variation in indirect defences remains unexplored. Here, we investigated variation in herbivory rate, resistance to herbivores, and indirect defences in ant-attracting Vicia species along the elevation gradient of the Alps. Specifically, we compared volatile organic compounds (VOCs) and ant attraction in high and low elevation ecotypes. Consistent with adaptation to the lower herbivory conditions that we detected at higher elevations in the field, high elevation plants were visited by fewer ants and were more susceptible to herbivore attack. In parallel, constitutive volatile organic compound production and subsequent ant attraction were lower in the high elevation ecotypes. We observed an elevation-driven trade-off between constitutive and inducible production of VOCs and ant attraction along the environmental cline. At higher elevations, inducible defences increased, while constitutive defence decreased, suggesting that the high elevation ecotypes compensate for lower indirect constitutive defences only after herbivore attack. Synthesis. Overall, direct and indirect defences of plants vary along elevation gradients. Our findings show that plant allocation to defences are subject to trade-offs depending on local conditions, and point to a feedback mechanism linking local herbivore pressure, predator abundance and the defence investment of plants.

Présentation de l'adaptation française de « l'échelle de coparentage » de McHale pour familles avec jeunes enfants [Presentation of the french adaptation of McHale's coparenting scale for families with young children.]

The aim of this paper is to present McHale's coparenting scale,a self-administered questionnaire enabling assessment of the quality of coparenting, and first steps in structural and construct validation of the French version. A total of 41 French speaking Swiss families and 84 US families completed this questionnaire and the Dyadic Adjustment Scale, a measure of marital satisfaction. The results of the Swiss families correspond to those of US families: first, items distributed into four factors (family integrity, conflict, affection and disparagement) and second, a partial link was found between quality of coparenting and marital adjustment. This finding supports the construct validity of the questionnaire, reflecting the established link between these two family sub-systems. Given that coparenting quality has a major influence on children's socio-affective development, the questionnaire will find great use in assessing not just negative features of coparenting, such as conflicts and disparagement, but also positive components such as warmth and support. This will be an important asset for research as well as clinical purposes.

Helminth Parasites of Conventionally Maintained Laboratory Mice: II- Inbred Strains with an Adaptation of the Anal Swab Technique

Worm burdens recovered from inbred mice strains, namely C57Bl/6, C57Bl/10, CBA, BALB/c, DBA/2 and C3H/He, conventionally maintained in two institutional animal houses in the State of Rio de Janeiro, RJ, Brazil, were analyzed and compared, regarding their prevalences and mean intensities.Three parasite species were observed: the nematodes Aspiculuris tetraptera, Syphacia obvelata and the cestode Vampirolepis nana. A modification of the anal swab technique is also proposed for the first time as an auxiliary tool for the detection of oxyurid eggs in mice