Evaluation of Viral Load Thresholds for Predicting New World Health Organization Stage 3 and 4 Events in HIV-Infected Children Receiving Highly Active Antiretroviral Therapy

Background: This study evaluated a wide range of viral load (VL) thresholds to identify a cut-point that best predicts new clinical events in children on stable highly active antiretroviral therapy (HAART). Methods: Cox proportional hazards modeling was used to assess the adjusted risk for World Health Organization stage 3 or 4 clinical events (WHO events) as a function of time-varying CD4, VL, and hemoglobin values in a cohort study of Latin American children on HAART >= 6 months. Models were fit using different VL cut-points between 400 and 50,000 copies per milliliter, with model fit evaluated on the basis of the minimum Akaike information criterion value, a standard model fit statistic. Results: Models were based on 67 subjects with WHO events out of 550 subjects on study. The VL cut-points of >2600 and >32,000 copies per milliliter corresponded to the lowest Akaike information criterion values and were associated with the highest hazard ratios (2.0, P = 0.015; and 2.1, P = 0.0058, respectively) for WHO events. Conclusions: In HIV-infected Latin American children on stable HAART, 2 distinct VL thresholds (>2600 and >32,000 copies/mL) were identified for predicting children at significantly increased risk for HIV-related clinical illness, after accounting for CD4 level, hemoglobin level, and other significant factors.

Oral health profile in patients infected with HTLV-1: Clinical findings, proviral load, and molecular analysis from HTLV-1 in saliva

Human T-lymphotropic virus type 1 (HTLV-1) is associated with adult T-cell leukemia (ATL) and HTLV-1 associated myelopathy/tropical spastic paraparesis (HAM/TSP) and has also been implicated in several disorders, including periodontal disease. The proviral load is an important biological marker for understanding HTLV-1 pathogenesis and elucidating whether or not the virus is related to the clinical manifestation of the disease. This study describes the oral health profile of HTLV-1 carriers and HAM/TSP patients in order to investigate the association between the proviral load in saliva and the severity of the periodontal disease and to examine virus intra-host variations from peripheral blood mononuclear cells and saliva cells. It is a cross-sectional analytical study of 90 individuals carried out from November 2006 to May 2008. Of the patients, 60 were HTLV-1 positive and 30 were negative. Individuals from the HTLV-1 positive and negative groups had similar mean age and social-economic status. Data were analyzed using two available statistical software packages, STATA 8.0 and SPSS 11.0 to conduct frequency analysis. Differences of P?<?0.05 were considered statistically significant. HTLV-1 patients had poorer oral health status when compared to seronegative individuals. A weak positive correlation between blood and saliva proviral loads was observed. The mean values of proviral load in blood and saliva in patients with HAM/TSP was greater than those in HTLV-1 carriers. The HTLV-1 molecular analysis from PBMC and saliva specimens suggests that HTLV-1 in saliva is due to lymphocyte infiltration from peripheral blood. A direct relationship between the proviral load in saliva and oral manifestations was observed. J. Med. Virol. 84:1428-1436, 2012. (c) 2012 Wiley Periodicals, Inc.

CD3e expression in HTLV-1-infected individuals is associated with proviral load and Tax expression

Financial support: FUNDHERP, CTC, INCTC, FAPESP, CNPq and CAPES.

Influence of INF-gamma gene polymorphism in HTLV-1 proviral load

Financial Support FAPESP, CNPq, CTC/FUNDHERP and INCTC.

Microbial load in instruments used in surgeries classified as clean

Introduction / objectives The number of orthopedic surgery, especially surgery of total hip and knee, have been more frequent due to technological advances. This study aims to determine the microbial load in the instruments used in clean surgeries, quantifying and identifying the genus and species of microbial growth.Methods Orthopedic surgical instruments were immersed, after use, in sterile water, sonicated in ultrasonic washer and consecutively shaken. Then, the lavage was filtered through a 0.45micron membrane, the result was incubated in aerobic medium, anaerobic medium and medium for fungi and yeasts. Results In clean surgeries, results showed that 47% of used instruments had microbiological growth in the range of 1 to 100 CFU/instrument. The most prevalent organism was Staphylococcus coagulase negative (28%), followed by Bacillus subtilis (11%).This study refuted the hypothesis that clean surgeries happen in micro-organismsfree surgery field. Conclusion The microbiological findings reinforce the importance of antibiotic prophylaxis, practice already well established for this category of surgical procedure.

Two sequential PCR amplifications for detection of Schistosoma mansoni in stool samples with low parasite load

Schistosomiasis constitutes a major public health problem, with an estimated 200 million individuals infected worldwide and 700 million people living in risk areas. In Brazil there are areas of high, medium and low endemicity. Studies have shown that in endemic areas with a low prevalence of Schistosoma infection the sensitivity of parasitological methods is clearly reduced. Consequently diagnosis is often impeded due to the presence of false-negative results. The aim of this study is to present the PCR reamplification (Re-PCR) protocol for the detection of Schistosoma mansoni in samples with low parasite load (with less than 100 eggs per gram (epg) of feces). Three methods were used for the lysis of the envelopes of the S. mansoni eggs and two techniques of DNA extraction were carried out. Extracted DNA was quantified, and the results suggested that the extraction technique, which mixed glass beads with a guanidine isothiocyanate/phenol/chloroform (GT) solution, produced good results. PCR reamplification was conducted and detection sensitivity was found to be five eggs per 500 mg of artificially marked feces. The results achieved using these methods suggest that they are potentially viable for the detection of Schistosoma infection with low parasite load.

Enabling computationally intensive bioinformatics applications on the Grid platform

Bioinformatics is a recent and emerging discipline which aims at studying biological problems through computational approaches. Most branches of bioinformatics such as Genomics, Proteomics and Molecular Dynamics are particularly computationally intensive, requiring huge amount of computational resources for running algorithms of everincreasing complexity over data of everincreasing size. In the search for computational power, the EGEE Grid platform, world's largest community of interconnected clusters load balanced as a whole, seems particularly promising and is considered the new hope for satisfying the everincreasing computational requirements of bioinformatics, as well as physics and other computational sciences. The EGEE platform, however, is rather new and not yet free of problems. In addition, specific requirements of bioinformatics need to be addressed in order to use this new platform effectively for bioinformatics tasks. In my three years' Ph.D. work I addressed numerous aspects of this Grid platform, with particular attention to those needed by the bioinformatics domain. I hence created three major frameworks, Vnas, GridDBManager and SETest, plus an additional smaller standalone solution, to enhance the support for bioinformatics applications in the Grid environment and to reduce the effort needed to create new applications, additionally addressing numerous existing Grid issues and performing a series of optimizations. The Vnas framework is an advanced system for the submission and monitoring of Grid jobs that provides an abstraction with reliability over the Grid platform. In addition, Vnas greatly simplifies the development of new Grid applications by providing a callback system to simplify the creation of arbitrarily complex multistage computational pipelines and provides an abstracted virtual sandbox which bypasses Grid limitations. Vnas also reduces the usage of Grid bandwidth and storage resources by transparently detecting equality of virtual sandbox files based on content, across different submissions, even when performed by different users. BGBlast, evolution of the earlier project GridBlast, now provides a Grid Database Manager (GridDBManager) component for managing and automatically updating biological flatfile databases in the Grid environment. GridDBManager sports very novel features such as an adaptive replication algorithm that constantly optimizes the number of replicas of the managed databases in the Grid environment, balancing between response times (performances) and storage costs according to a programmed cost formula. GridDBManager also provides a very optimized automated management for older versions of the databases based on reverse delta files, which reduces the storage costs required to keep such older versions available in the Grid environment by two orders of magnitude. The SETest framework provides a way to the user to test and regressiontest Python applications completely scattered with side effects (this is a common case with Grid computational pipelines), which could not easily be tested using the more standard methods of unit testing or test cases. The technique is based on a new concept of datasets containing invocations and results of filtered calls. The framework hence significantly accelerates the development of new applications and computational pipelines for the Grid environment, and the efforts required for maintenance. An analysis of the impact of these solutions will be provided in this thesis. This Ph.D. work originated various publications in journals and conference proceedings as reported in the Appendix. Also, I orally presented my work at numerous international conferences related to Grid and bioinformatics.

Shear behavior of reinforced concrete slabs under concentrated load: an investigation through Sequentially Linear Analysis

ABSTRACT (italiano) Con crescente attenzione riguardo al problema della sicurezza di ponti e viadotti esistenti nei Paesi Bassi, lo scopo della presente tesi è quello di studiare, mediante la modellazione con Elementi Finiti ed il continuo confronto con risultati sperimentali, la risposta in esercizio di elementi che compongono infrastrutture del genere, ovvero lastre in calcestruzzo armato sollecitate da carichi concentrati. Tali elementi sono caratterizzati da un comportamento ed una crisi per taglio, la cui modellazione è, da un punto di vista computazionale, una sfida piuttosto ardua, a causa del loro comportamento fragile combinato a vari effetti tridimensionali. La tesi è incentrata sull'utilizzo della Sequentially Linear Analysis (SLA), un metodo di soluzione agli Elementi Finiti alternativo rispetto ai classici approcci incrementali e iterativi. Il vantaggio della SLA è quello di evitare i ben noti problemi di convergenza tipici delle analisi non lineari, specificando direttamente l'incremento di danno sull'elemento finito, attraverso la riduzione di rigidezze e resistenze nel particolare elemento finito, invece dell'incremento di carico o di spostamento. Il confronto tra i risultati di due prove di laboratorio su lastre in calcestruzzo armato e quelli della SLA ha dimostrato in entrambi i casi la robustezza del metodo, in termini di accuratezza dei diagrammi carico-spostamento, di distribuzione di tensioni e deformazioni e di rappresentazione del quadro fessurativo e dei meccanismi di crisi per taglio. Diverse variazioni dei più importanti parametri del modello sono state eseguite, evidenziando la forte incidenza sulle soluzioni dell'energia di frattura e del modello scelto per la riduzione del modulo elastico trasversale. Infine è stato effettuato un paragone tra la SLA ed il metodo non lineare di Newton-Raphson, il quale mostra la maggiore affidabilità della SLA nella valutazione di carichi e spostamenti ultimi insieme ad una significativa riduzione dei tempi computazionali. ABSTRACT (english) With increasing attention to the assessment of safety in existing dutch bridges and viaducts, the aim of the present thesis is to study, through the Finite Element modeling method and the continuous comparison with experimental results, the real response of elements that compose these infrastructures, i.e. reinforced concrete slabs subjected to concentrated loads. These elements are characterized by shear behavior and crisis, whose modeling is, from a computational point of view, a hard challenge, due to their brittle behavior combined with various 3D effects. The thesis is focused on the use of Sequentially Linear Analysis (SLA), an alternative solution technique to classical non linear Finite Element analyses that are based on incremental and iterative approaches. The advantage of SLA is to avoid the well-known convergence problems of non linear analyses by directly specifying a damage increment, in terms of a reduction of stiffness and strength in the particular finite element, instead of a load or displacement increment. The comparison between the results of two laboratory tests on reinforced concrete slabs and those obtained by SLA has shown in both the cases the robustness of the method, in terms of accuracy of load-displacements diagrams, of the distribution of stress and strain and of the representation of the cracking pattern and of the shear failure mechanisms. Different variations of the most important parameters have been performed, pointing out the strong incidence on the solutions of the fracture energy and of the chosen shear retention model. At last a confrontation between SLA and the non linear Newton-Raphson method has been executed, showing the better reliability of the SLA in the evaluation of the ultimate loads and displacements, together with a significant reduction of computational times.

Psychobiological correlates of allostatic load

Introduction: The term Clinimetric was introduced by Feinstein in 1982, who first noticed that despite all the improvements in the assessment methods, a number of clinical phenomena were still unconsidered during the evaluation process. Yet today clinical phenomena, such as stress, relevant in diseases progression and course, are not completely evaluated. Only recently, according to the clinimetric approach, Fava and colleagues have introduced specific criteria for evaluating the allostatic overload in clinical setting. Methods: Participants were 240 blood donors recruited from May 2007 to December 2009 in 4 different blood Centers (AVIS) in Italy. Blood samples from each participant were collected for laboratory test the same day the self-rating instruments were administered (Psychosocial Index, Symptom Questionnaire, Psychological well-being scales, Temperament and Character inventory, Self-Report Altruism scale). The study explore different aspects describing sample characteristics and correlates of stress in the total sample (part I), new selection criteria applied to existing instruments to identify individuals reporting allostatic load (part II), and differences on biological correlates between subjects with vs without AL. Results: Significant differences according to gender and past illnesses have been found in different dimensions of well-being and distress. Further, distress was explained for more than 60% by 4 main factors such as anxiety, somatic symptoms, environmental mastery and persistence. According to the new criteria, 98 donors reported AL. Allostatic load individuals reported to engage in less altruistic behaviours. Also they differ in personality traits and characters from controls. In the last part, results showed significant differences among donors according to allostatic load on diverse biological parameters (RBC, MCV, immune essay). Conclusion: This study presents obvious limitations due to its preliminary nature. Further research are need to confirm that these new criteria may lead to identify high risk individuals reporting not only stressful situations but also vulnerabilities.

Shear behaviour of reinforced cconcrete slab under concentrated load: an investigation through non-linear and sequentially linear analysis

English: The assessment of safety in existing bridges and viaducts led the Ministry of Public Works of the Netherlands to finance a specific campaing aimed at the study of the response of the elements of these infrastructures. Therefore, this activity is focused on the investigation of the behaviour of reinforced concrete slabs under concentrated loads, adopting finite element modeling and comparison with experimental results. These elements are characterized by shear behaviour and crisi, whose modeling is, from a computational point of view, a hard challeng, due to the brittle behavior combined with three-dimensional effects. The numerical modeling of the failure is studied through Sequentially Linear Analysis (SLA), an alternative Finite Element method, with respect to traditional incremental and iterative approaches. The comparison between the two different numerical techniques represents one of the first works and comparisons in a three-dimensional environment. It's carried out adopting one of the experimental test executed on reinforced concrete slabs as well. The advantage of the SLA is to avoid the well known problems of convergence of typical non-linear analysis, by directly specifying a damage increment, in terms of reduction of stiffness and resistance in particular finite element, instead of load or displacement increasing on the whole structure . For the first time, particular attention has been paid to specific aspects of the slabs, like an accurate constraints modeling and sensitivity of the solution with respect to the mesh density. This detailed analysis with respect to the main parameters proofed a strong influence of the tensile fracture energy, mesh density and chosen model on the solution in terms of force-displacement diagram, distribution of the crack patterns and shear failure mode. The SLA showed a great potential, but it requires a further developments for what regards two aspects of modeling: load conditions (constant and proportional loads) and softening behaviour of brittle materials (like concrete) in the three-dimensional field, in order to widen its horizons in these new contexts of study.

Influence of advanced load simulation models on fatigue design of jackets for offshore wind turbines.

Constant developments in the field of offshore wind energy have increased the range of water depths at which wind farms are planned to be installed. Therefore, in addition to monopile support structures suitable in shallow waters (up to 30 m), different types of support structures, able to withstand severe sea conditions at the greater water depths, have been developed. For water depths above 30 m, the jacket is one of the preferred support types. Jacket represents a lightweight support structure, which, in combination with complex nature of environmental loads, is prone to highly dynamic behavior. As a consequence, high stresses with great variability in time can be observed in all structural members. The highest concentration of stresses occurs in joints due to their nature (structural discontinuities) and due to the existence of notches along the welds present in the joints. This makes them the weakest elements of the jacket in terms of fatigue. In the numerical modeling of jackets for offshore wind turbines, a reduction of local stresses at the chord-brace joints, and consequently an optimization of the model, can be achieved by implementing joint flexibility in the chord-brace joints. Therefore, in this work, the influence of joint flexibility on the fatigue damage in chord-brace joints of a numerical jacket model, subjected to advanced load simulations, is studied.

The behaviour of osteocyte dendritic processes in bone under cyclic load (il comportamento dei processi dendritici degli osteociti nel tessuto osseo sottoposti a carico ciclico)

Bone is continually being removed and replaced through the actions of basic multicellular units (BMU). This constant upkeep is necessary to remove microdamage formed naturally due to fatigue and thus maintain the integrity of the bone. The repair process in bone is targeted, meaning that a BMU travels directly to the site of damage and repairs it. It is still unclear how targeted remodelling is stimulated and directed but it is highly likely that osteocytes play a role. A number of theories have been advanced to explain the microcrack osteocyte interaction but no complete mechanism has been demonstrated. Osteocytes are connected to each other by dendritic processes. The “scissors model" proposed that the rupture of these processes where they cross microcracks signals the degree of damage and the urgency of the necessary repair. In its original form it was proposed that under applied compressive loading, microcrack faces will be pressed together and undergo relative shear movement. If this movement is greater than the width of an osteocyte process, then the process will be cut in a “scissors like" motion, releasing RANKL, a cytokine known to be essential in the formation of osteoclasts from pre-osteoclasts. The main aim of this thesis was to investigate this theoretical model with a specific focus on microscopy and finite element modelling. Previous studies had proved that cyclic stress was necessary for osteocyte process rupture to occur. This was a divergence from the original “scissors model" which had proposed that the cutting of cell material occurred in one single action. The present thesis is the first study to show fatigue failure in cellular processes spanning naturally occurring cracks and it's the first study to estimate the cyclic strain range and relate it to the number of cycles to failure, for any type of cell. Rupture due to shear movement was ruled out as microcrack closing never occurred, as a result of plastic deformation of the bone. Fatigue failure was found to occur due to cyclic tensile stress in the locality of the damage. The strain range necessary for osteocyte process rupture was quantified. It was found that the lower the process strain range the greater the number of cycles to cell process failure. FEM modelling allowed to predict stress in the vicinity of an osteocyte process and to analyse its interaction with the bone surrounding it: simulations revealed evident creep effects in bone during cyclic loading. This thesis confirms and dismisses aspects of the “scissors model". The observations support the model as a viable mechanism of microcrack detection by the osteocyte network, albeit in a slightly modified form where cyclic loading is necessary and the method of rupture is fatigue failure due to cyclic tensile motion. An in depth study was performed focusing on microscopy analysis of naturally occurring cracks in bone and FEM simulation analysis of an osteocyte process spanning a microcrack in bone under cyclic load.