Computational design with flexible backbone sampling for protein remodeling and scaffolding of complex binding sites

Dissertation presented to obtain the Doutoramento (Ph.D.) degree in Biochemistry at the Instituto de Tecnologia Qu mica e Biol ogica da Universidade Nova de Lisboa

Chronic beryllium disease as a re-emerging occupational disorder possibly misdiagnosed as sarcoidosis : a Swiss study project

Background: Beryllium (Be) is increasingly used worldwide for numerous industrial applications. Occupational exposure to Be may lead to Be sensitization (BeS), a CD4-mediated immune response. BeS may progress to chronic beryllium disease (CBD), a granulomatous lung disorder closely resembling sarcoidosis. The recognition of CBD requires detection of Be exposure at occupational history, and detection of BeS on blood or BAL lymphocytes. Since methods for CBD detection are not routinely available in Switzerland, we hypothesized that CBD cases are not recognized but misdiagnosis as sarcoidosis. Objective: To present an ongoing Swiss study screening patients with sarcoidosis in search of Be exposure, BeS, and CBD. Methods: Both a prospective and a retrospective cohort are being studied. In the prospective cohort, the main steps include: 1) recruitment of 100 consecutive patients with newly diagnosed pulmonary sarcoidosis at 2 centers (Lausanne, Bern). 2) screening for possible occupational Be exposure by self-administered patient questionnaire. 3) standardized detailed occupational interview and clinical visit by occupational health specialist. If step 3 is positive, then 4) blood and BAL sampling for detection of BeS by specifically developed Elispot assay and CFSE flow cytometry, with subsequent comparison to the classical Be lymphocyte proliferation test. If step 4 is positive, then 5) review of medical records and diagnostic revision from sarcoidosis to CBD. 6) appropriate measures for exposure cessation and case reporting to SUVA as occupational disease. The retrospective cohort will include 400 patients with previously diagnosed pulmonary sarcoidosis, either treated or untreated, recruited through the SIOLD Registries. Steps 2 to 5 will be peformed as above, except for a) end of study after step 2 if screening questionnaire does not reveal Be exposure, and b) step 4 done on blood sample only (BAL not needed). Current status: Self-administered screening questionnaire and tools for standardized occupational interview have been developed. BeS testing has been implemented and undergoes validation. Inclusions in the prospective phase have started at both study sites. The retrospective phase is in preparation. Conclusion: The current study status allows to conclude to technical feasibility of the project. The prospective phase if this study is funded by the SUVA. The SIOLD Registries are supported by the Swiss Pulmonary League.

Coronary MR imaging using free-breathing 3D steady-state free precession with radial k-space sampling.

PURPOSE: To investigate the potential of free-breathing 3D steady-state free precession (SSFP) imaging with radial k-space sampling for coronary MR-angiography (MRA), coronary projection MR-angiography and coronary vessel wall imaging. MATERIALS AND METHODS: A navigator-gated free-breathing T2-prepared 3D SSFP sequence (TR = 6.1 ms, TE = 3.0 ms, flip angle = 120 degrees, field-of-view = 360 mm(2)) with radial k-space sampling (384 radials) was implemented for coronary MRA. For projection coronary MRA, this sequence was combined with a 2D selective aortic spin tagging pulse. Coronary vessel wall imaging was performed using a high-resolution inversion-recovery black-blood 3D radial SSFP sequence (384 radials, TR = 5.3 ms, TE = 2.7 ms, flip angle = 55 degrees, reconstructed resolution 0.35 x 0.35 x 1.2 mm(3)) and a local re-inversion pulse. Six healthy volunteers (two for each sequence) were investigated. Motion artifact level was assessed by two radiologists. Results: In coronary MRA, the coronary lumen was displayed with a high signal and high contrast to the surrounding lumen. Projection coronary MRA demonstrated selective visualization of the coronary lumen while surrounding tissue was almost completely suppressed. In coronary vessel wall imaging, the vessel wall was displayed with a high signal when compared to the blood pool and the surrounding tissue. No visible motion artifacts were seen. Conclusion: 3D radial SSFP imaging enables coronary MRA, coronary projection MRA and coronary vessel wall imaging with a low motion artifact level.

Rate of gene sequence evolution and species diversification in flowering plants: a re-evaluation

Barraclough and co-workers (in a paper published in 1996) observed that there was a significant positive correlation between the rate of evolution of the rbcL chloroplast gene within families of flowering plants and the number of species in those families. We tested three additional data sets of our own (based on both plastid and nuclear genes) and used methods designed specifically for the comparison of sister families (based on random speciation and extinction). We show that, over all sister groups, the correlation between the rate of gene evolution and an increased diversity is not always present. Despite tending towards a positive association, the observation of individual probabilities presents a U-shaped distribution of association (i.e. it can be either significantly positive or negative). We discuss the influence of both phylogenetic sampling and applied taxonomies on the results.

Liquid transportation and distribution during (re)wetting : impact on coated papers in printing

In many industrial applications, such as the printing and coatings industry, wetting of porous materials by liquids includes not only imbibition and permeation into the bulk but also surface spreading and evaporation. By understanding these phenomena, valuable information can be obtained for improved process control, runnability and printability, in which liquid penetration and subsequent drying play important quality and economic roles. Knowledge of the position of the wetting front and the distribution/degree of pore filling within the structure is crucial in describing the transport phenomena involved. Although exemplifying paper as a porous medium in this work, the generalisation to dynamic liquid transfer onto a surface, including permeation and imbibition into porous media, is of importance to many industrial and naturally occurring environmental processes. This thesis explains the phenomena in the field of heatset web offset printing but the content and the analyses are applicable in many other printing methods and also other technologies where water/moisture monitoring is crucial in order to have a stable process and achieve high quality end products. The use of near-infrared technology to study the water and moisture response of porous pigmented structures is presented. The use of sensitive surface chemical and structural analysis, as well as the internal structure investigation of a porous structure, to inspect liquid wetting and distribution, complements the information obtained by spectroscopic techniques. Strong emphasis has been put on the scale of measurement, to filter irrelevant information and to understand the relationship between interactions involved. The near-infrared spectroscopic technique, presented here, samples directly the changes in signal absorbance and its variation in the process at multiple locations in a print production line. The in-line non-contact measurements are facilitated by using several diffuse reflectance probes, giving the absolute water/moisture content from a defined position in the dynamic process in real-time. The nearinfrared measurement data illustrate the changes in moisture content as the paper is passing through the printing nips and dryer, respectively, and the analysis of the mechanisms involved highlight the roles of the contacting surfaces and the relative liquid carrier properties of both non-image and printed image areas. The thesis includes laboratory studies on wetting of porous media in the form of coated paper and compressed pigment tablets by mono-, dual-, and multi-component liquids, and paper water/moisture content analysis in both offline and online conditions, thus also enabling direct sampling of temporal water/moisture profiles from multiple locations. One main focus in this thesis was to establish a measurement system which is able to monitor rapid changes in moisture content of paper. The study suggests that near-infrared diffuse reflectance spectroscopy can be used as a moisture sensitive system and to provide accurate online qualitative indicators, but, also, when accurately calibrated, can provide quantification of water/moisture levels, its distribution and dynamic liquid transfer. Due to the high sensitivity, samples can be measured with excellent reproducibility and good signal to noise ratio. Another focus of this thesis was on the evolution of the moisture content, i.e. changes in moisture content referred to (re)wetting, and liquid distribution during printing of coated paper. The study confirmed different wetting phases together with the factors affecting each phase both for a single droplet and a liquid film applied on a porous substrate. For a single droplet, initial capillary driven imbibition is followed by equilibrium pore filling and liquid retreat by evaporation. In the case of a liquid film applied on paper, the controlling factors defining the transportation were concluded to be the applied liquid volume in relation to surface roughness, capillarity and permeability of the coating giving the liquid uptake capacity. The printing trials confirmed moisture gradients in the printed sheet depending on process parameters such as speed, fountain solution dosage and drying conditions as well as the printed layout itself. Uneven moisture distribution in the printed sheet was identified to be one of the sources for waving appearance and the magnitude of waving was influenced by the drying conditions.

PDFOS: PDF estimation based over-sampling for imbalanced two-class problems

This contribution proposes a novel probability density function (PDF) estimation based over-sampling (PDFOS) approach for two-class imbalanced classification problems. The classical Parzen-window kernel function is adopted to estimate the PDF of the positive class. Then according to the estimated PDF, synthetic instances are generated as the additional training data. The essential concept is to re-balance the class distribution of the original imbalanced data set under the principle that synthetic data sample follows the same statistical properties. Based on the over-sampled training data, the radial basis function (RBF) classifier is constructed by applying the orthogonal forward selection procedure, in which the classifier’s structure and the parameters of RBF kernels are determined using a particle swarm optimisation algorithm based on the criterion of minimising the leave-one-out misclassification rate. The effectiveness of the proposed PDFOS approach is demonstrated by the empirical study on several imbalanced data sets.

Poor performance of microbiological sampling in the prediction of recurrent arthroplasty infection

During a two-stage revision for prosthetic joint infections (PJI), joint aspirations, open tissue sampling and serum inflammatory markers are performed before re-implantation to exclude ongoing silent infection. We investigated the performance of these diagnostic procedures on the risk of recurrence of PJI among asymptomatic patients undergoing a two-stage revision. A total of 62 PJI were found in 58 patients. All patients had intra-operative surgical exploration during re-implantation, and 48 of them had intra-operative microbiological swabs. Additionally, 18 joint aspirations and one open biopsy were performed before second-stage reimplantation. Recurrence or persistence of PJI occurred in 12 cases with a mean delay of 218 days after re-implantation, but only four pre- or intraoperative invasive joint samples had grown a pathogen in cultures. In at least seven recurrent PJIs (58%), patients had a normal C-reactive protein (CRP, < 10 mg/l) level before re-implantation. The sensitivity, specificity, positive predictive and negative predictive values of pre-operative invasive joint aspiration and CRP for the prediction of PJI recurrence was 0.58, 0.88, 0.5, 0.84 and 0.17, 0.81, 0.13, 0.86, respectively. As a conclusion, pre-operative joint aspiration, intraoperative bacterial sampling, surgical exploration and serum inflammatory markers are poor predictors of PJI recurrence. The onset of reinfection usually occurs far later than reimplantation.

Classification criteria and commercial profile re-definition of the Family Farm Agriculture in Chile, Maule region

In Chile, small-scale farmers are classified according to old approaches from 1993 that do not include changes occurred in the last two decades. Maule is the region with most rural population in Chile which represents a significant stratum for development, innovation and competitiveness. This study explores a new approach of small-scale farmers -associated with Family Farm Agriculture (AFC) - classification in Chile and it describes a commercial profile or AFC-1 for famers of the Maule Region. A Cluster analysis to determine AFC-1 farmers is used. The analysis includes four association variables: Total Assets, Farm Income, Production Costs and Management Indicators. The results suggest that 16.4% of the farmers have a commercial profile and they could stay out support provided by the National Institute for Agricultural Development (INDAP). This group of farmers would not belong to AFC in short terms. This fact could bring restriction to AFC-1 farmers such as lack of credit access, less investment incentives and technical assistance. Thus, it would expect low process of technology adoption and welfare improvement. New agrarian policies must be warranted to support this important group of famers with a commercial profile.

Efficient sampling of band-limited signals from sine wave crossings

This correspondence presents an efficient method for reconstructing a band-limited signal in the discrete domain from its crossings with a sine wave. The method makes it possible to design A/D converters that only deliver the crossing timings, which are then used to interpolate the input signal at arbitrary instants. Potentially, it may allow for reductions in power consumption and complexity in these converters. The reconstruction in the discrete domain is based on a recently-proposed modification of the Lagrange interpolator, which is readily implementable with linear complexity and efficiently, given that it re-uses known schemes for variable fractional-delay (VFD) filters. As a spin-off, the method allows one to perform spectral analysis from sine wave crossings with the complexity of the FFT. Finally, the results in the correspondence are validated in several numerical examples.

Aquatic passive sampling of herbicides on naked particle loaded membranes: Accelerated measurement and empirical estimation of kinetic parameters

Water-sampler equilibrium partitioning coefficients and aqueous boundary layer mass transfer coefficients for atrazine, diuron, hexazionone and fluometuron onto C18 and SDB-RPS Empore disk-based aquatic passive samplers have been determined experimentally under a laminar flow regime (Re = 5400). The method involved accelerating the time to equilibrium of the samplers by exposing them to three water concentrations, decreasing stepwise to 50% and then 25% of the original concentration. Assuming first-order Fickian kinetics across a rate-limiting aqueous boundary layer, both parameters are determined computationally by unconstrained nonlinear optimization. In addition, a method of estimation of mass transfer coefficients-therefore sampling rates-using the dimensionless Sherwood correlation developed for laminar flow over a flat plate is applied. For each of the herbicides, this correlation is validated to within 40% of the experimental data. The study demonstrates that for trace concentrations (sub 0.1 mu g/L) and these flow conditions, a naked Empore disk performs well as an integrative sampler over short deployments (up to 7 days) for the range of polar herbicides investigated. The SDB-RPS disk allows a longer integrative period than the C18 disk due to its higher sorbent mass and/or its more polar sorbent chemistry. This work also suggests that for certain passive sampler designs, empirical estimation of sampling rates may be possible using correlations that have been available in the chemical engineering literature for some time.

Sampling information, length measurements, DNA alignments, models and phylogenetics trees for Oithona similis s.l.

Traditionally, many small-sized copepod species are considered to be widespread, bipolar or cosmopolitan. However, these large-scale distribution patterns need to be re-examined in view of increasing evidence of cryptic and pseudo-cryptic speciation in pelagic copepods. Here, we present a phylogeographic study of Oithona similis s.l. populations from the Arctic Ocean, the Southern Ocean and its northern boundaries, the North Atlantic and the Mediterrranean Sea. O. similis s.l. is considered as one of the most abundant species in temperate to polar oceans and acts as an important link in the trophic network between the microbial loop and higher trophic levels such as fish larvae. Two gene fragments were analysed: the mitochondrial cytochrome oxidase c subunit I (COI), and the nuclear ribosomal 28S genetic marker. Seven distinct, geographically delimitated, mitochondrial lineages could be identified, with divergences among the lineages ranging from 8 to 24 %, thus representing most likely cryptic or pseudocryptic species within O. similis s.l. Four lineages were identified within or close to the borders of the Southern Ocean, one lineage in the Arctic Ocean and two lineages in the temperate Northern hemisphere. Surprisingly the Arctic lineage was more closely related to lineages from the Southern hemisphere than to the other lineages from the Northern hemisphere, suggesting that geographic proximity is a rather poor predictor of how closely related the clades are on a genetic level. Molecular clock application revealed that the evolutionary history of O. similis s.l. is possibly closely associated with the reorganization of the ocean circulation in the mid Miocene and may be an example of allopatric speciation in the pelagic zone.

A meditation on boredom: Re-appraising its value through introspective phenomenology

Boredom is almost universally regarded as a dysphoric mental state, characterised by features such as disengagement and low arousal. However, in certain quarters (e.g., Zen Buddhism), boredom is seen as potentially having great value and even importance. The current study sought to explore boredom through a case study involving introspective phenomenology. The author created conditions in which he would experience boredom for an hour, and recorded his experience in real-time using a variant of the Experiencing Sampling Method. The data were analysed using an adaptation of Interpretative Phenomenological Analysis. The results indicated that the state of boredom contained three main sources of value: (a) altered perception of time; (b) awakened curiosity about the environment; and (c) exploration of self. Consequently, the paper offers a re-appraisal of boredom, suggesting that rather than necessarily being a negative state, if engaged with, boredom has the potential to be a positive and rewarding experience.

Corporeidade e cultura amazonica : re-flexões a partir do passaro junino do Para

Universidade Estadual de Campinas . Faculdade de Educação Física

Temporal variation of the phytoplankton community at short sampling intervals in the Mundaú reservoir, Northeastern Brazil

The aim of this study was to determine how abiotic factors drive the phytoplankton community in a water supply reservoir within short sampling intervals. Samples were collected at the subsurface (0.1 m) and bottom of limnetic (8 m) and littoral (2 m) zones in both the dry and rainy seasons. The following abiotic variables were analyzed: water temperature, dissolved oxygen, electrical conductivity, total dissolved solids, turbidity, pH, total nitrogen, nitrite, nitrate, total phosphorus, total dissolved phosphorus and orthophosphate. Phytoplankton biomass was determined from biovolume values. The role abiotic variables play in the dynamics of phytoplankton species was determined by means of Canonical Correspondence Analysis. Algae biomass ranged from 1.17×10(4) to 9.21×10(4) µg.L-1; cyanobacteria had biomass values ranging from 1.07×10(4) to 8.21×10(4) µg.L-1. High availability of phosphorous, nitrogen limitation, alkaline pH and thermal stability all favored cyanobacteria blooms, particularly during the dry season. Temperature, pH, total phosphorous and turbidity were key factors in characterizing the phytoplankton community between sampling times and stations. Of the species studied, Cylindrospermopsis raciborskii populations were dominant in the phytoplankton in both the dry and rainy seasons. We conclude that the phytoplankton was strongly influenced by abiotic variables, particularly in relation to seasonal distribution patterns.

Política de saúde e gestão no processo de (re)construção do SUS em município de grande porte: um estudo de caso de São Paulo, Brasil

O processo de (re)construção do SUS no Município de São Paulo, Brasil, foi analisado, no período de 2001- 2008, por meio de estudo de caso, utilizando-se distintas fontes: documentos; entrevistas com informantes-chave e observação participante. Os conceitos de política de saúde e de gestão em saúde foram utilizados na qualidade de categorias analíticas. Foram selecionadas e analisadas apenas políticas priorizadas pela gestão iniciada em 2001 e que tiveram sustentação até 2008. Discutem-se desafios para a (re)construção do SUS no município relacionados com o contexto político-institucional e com mudanças de estrutura implementadas. As reorganizações da Secretaria Municipal de Saúde de São Paulo propiciaram a constituição e manutenção de dois subsistemas municipais, um hospitalar e outro ambulatorial. Negociações entre os governos municipal, estadual e federal não avançaram para que o município assumisse a gestão de fato de todo sistema de saúde, constatando-se a coexistência de três subsistemas públicos de saúde paralelos: dois municipais e um estadual. A sustentação política do Programa Saúde da Família foi associada ao fato de que esse programa não se constituiu como marca da primeira gestão municipal e, ainda, de ser política prioritária e estimulada pelo governo federal.