Relaxation of Adaptive Evolution during the HIV-1 Infection Owing to Reduction of CD4+T Cell Counts

Background: The first stages of HIV-1 infection are essential to establish the diversity of virus population within host. It has been suggested that adaptation to host cells and antibody evasion are the leading forces driving HIV evolution at the initial stages of AIDS infection. In order to gain more insights on adaptive HIV-1 evolution, the genetic diversity was evaluated during the infection time in individuals contaminated by the same viral source in an epidemic cluster. Multiple sequences of V3 loop region of the HIV-1 were serially sampled from four individuals: comprising a single blood donor, two blood recipients, and another sexually infected by one of the blood recipients. The diversity of the viral population within each host was analyzed independently in distinct time points during HIV-1 infection. Results: Phylogenetic analysis identified multiple HIV-1 variants transmitted through blood transfusion but the establishing of new infections was initiated by a limited number of viruses. Positive selection (d(N)/d(S)>1) was detected in the viruses within each host in all time points. In the intra-host viruses of the blood donor and of one blood recipient, X4 variants appeared respectively in 1993 and 1989. In both patients X4 variants never reached high frequencies during infection time. The recipient, who X4 variants appeared, developed AIDS but kept narrow and constant immune response against HIV-1 during the infection time. Conclusion: Slowing rates of adaptive evolution and increasing diversity in HIV-1 are consequences of the CD4+ T cells depletion. The dynamic of R5 to X4 shift is not associated with the initial amplitude of humoral immune response or intensity of positive selection.

SAG2A protein from Toxoplasma gondii interacts with both innate and adaptive immune compartments of infected hosts

Abstract Background Toxoplasma gondii is an intracellular parasite that causes relevant clinical disease in humans and animals. Several studies have been performed in order to understand the interactions between proteins of the parasite and host cells. SAG2A is a 22 kDa protein that is mainly found in the surface of tachyzoites. In the present work, our aim was to correlate the predicted three-dimensional structure of this protein with the immune system of infected hosts. Methods To accomplish our goals, we performed in silico analysis of the amino acid sequence of SAG2A, correlating the predictions with in vitro stimulation of antigen presenting cells and serological assays. Results Structure modeling predicts that SAG2A protein possesses an unfolded C-terminal end, which varies its conformation within distinct strain types of T. gondii. This structure within the protein shelters a known B-cell immunodominant epitope, which presents low identity with its closest phyllogenetically related protein, an orthologue predicted in Neospora caninum. In agreement with the in silico observations, sera of known T. gondii infected mice and goats recognized recombinant SAG2A, whereas no serological cross-reactivity was observed with samples from N. caninum animals. Additionally, the C-terminal end of the protein was able to down-modulate pro-inflammatory responses of activated macrophages and dendritic cells. Conclusions Altogether, we demonstrate herein that recombinant SAG2A protein from T. gondii is immunologically relevant in the host-parasite interface and may be targeted in therapeutic and diagnostic procedures designed against the infection.

Frequency and precision of feedback and the adaptive process of learning a dual motor task

This work investigated the effects of frequency and precision of feedback on the learning of a dual-motor task. One hundred and twenty adults were randomly assigned to six groups of different knowledge of results (KR), frequency (100%, 66% or 33%) and precision (specific or general) levels. In the stabilization phase, participants performed the dual task (combination of linear positioning and manual force control) with the provision of KR. Ten non-KR adaptation trials were performed for the same task, but with the introduction of an electromagnetic opposite traction force. The analysis showed a significant main effect for frequency of KR. The participants who received KR in 66% of the stabilization trials showed superior adaptation performance than those who received 100% or 33%. This finding reinforces that there is an optimal level of information, neither too high nor too low, for motor learning to be effective.

Cementum, apical morphology and hypercementosis: a probable adaptive response of the periodontal support tissues and potential orthodontic implications

Information about orthodontic movement of teeth with hypercementosis is scarce. As cementum deposition continues to occur, cementum is expected to change the shape of the root and apex over time, but this has not yet been demonstrated. Nor has it ever been established whether it increases or decreases the prevalence of root resorption during orthodontic treatment. The unique biological function of the interconnected network of cementocytes may play a role in orthodontic movement and its associated root resorptions, but no research has ever been conducted on the topic. Unlike cementum thickness and hypercementosis, root and apex shape has not yet been related to patient age. A study of the precise difference between increased cementum thickness and hypercementosis is warranted. Hypercementosis refers to excessive cementum formation above and beyond the extent necessary to fulfill its normal functions, resulting in abnormal thickening with macroscopic changes in the tooth root, which may require the delivery of forces that are different from conventional mechanics in their intensity, direction and distribution. What are the unique features and specificities involved in moving teeth that present with hypercementosis? Bodily movements would be expected to occur, since inclination might prove difficult to achieve, but would the root resorption index be higher or lower?

Adaptive immunity is related to coronary artery disease severity after acute coronary syndrome in subjects with metabolic syndrome

Metabolic syndrome (MetS) is an inflammatory state associated with high coronary disease risk. Inflammation and adaptive immunity modulate atherosclerosis and plaque instability. We examined early changes in anti-oxidized lowdensity lipoprotein (LDL) (anti-oxLDL) autoantibodies (Abs) in patients with MetS after an acute coronary syndrome (ACS). Patients of both genders (n=116) with MetS were prospectively included after an acute yocardial infarction (MI) or hospitalization due to unstable angina. Anti-oxLDL Abs (IgG class) were assayed at baseline, three and six weeks after ACS. The severity of coronary disease was evaluated by the Gensini score. We observed a decrease in anti-oxLDL Abs titers (p<0.002 vs. baseline), mainly in males (p=0.01), in those under 65 y (p=0.03), and in subjects with Gensini score above median (p=0.04). In conclusion, early decrease in circulating anti-oxLDL Abs is associated with coronary disease severity among subjects with MetS.

Dengue virus type 3 adaptive changes during epidemics in São Jose de Rio Preto, Brazil, 2006–2007

Global dengue virus spread in tropical and sub-tropical regions has become a major international public health concern. It is evident that DENV genetic diversity plays a significant role in the immunopathology of the disease and that the identification of polymorphisms associated with adaptive responses is important for vaccine development. The investigation of naturally occurring genomic variants may play an important role in the comprehension of different adaptive strategies used by these mutants to evade the human immune system. In order to elucidate this role we sequenced the complete polyprotein-coding region of thirty-three DENV-3 isolates to characterize variants circulating under high endemicity in the city of São José de Rio Preto, Brazil, during the onset of the 2006-07 epidemic. By inferring the evolutionary history on a local-scale and estimating rates of synonymous (dS) and nonsynonimous (dN) substitutions, we have documented at least two different introductions of DENV-3 into the city and detected 10 polymorphic codon sites under significant positive selection (dN/dS > 1) and 8 under significant purifying selection (dN/dS < 1). We found several polymorphic amino acid coding sites in the envelope (15), NS1 (17), NS2A (11), and NS5 (24) genes, which suggests that these genes may be experiencing relatively recent adaptive changes. Furthermore, some polymorphisms correlated with changes in the immunogenicity of several epitopes. Our study highlights the existence of significant and informative DENV variability at the spatio-temporal scale of an urban outbreak.

Human Abuses of Coral Reefs- Adaptive Responses and Regime Transitions

During the last few decades, coral reefs have become a disappearing feature of tropical marine environments, and those reefs that do remain are severely threatened. It is understood that humans have greately altered the environment under which these ecosystems previously have thrived and evoloved. Overharvesting of fish stocks, global warming and pollution are some of the most prominent threats, acting on coral reefs at several spatial and temporal scales. Presently, it is common that coral reefs have been degraded into alternative ecosystem regimes, such as macroalgae-dominated or sea urchin-barren. Although these ecosystems could potentially return to coral dominance in a long-term perspective, when considdering current conditions, it seems likely that they will persist in their degraded states. Thus, recovery of coral reefs cannot be taken for granted on a human timescale. Multiple stressors and disturbances, which are increasingly characteristic of coral reef environments today, are believed to act synergistically and produce ecological surprises. However, current knowledge of effects of compounded disturbances and stress is limited. Based on five papers, this thesis investigates the sublethal response of multiple stressors on coral physiology, as well as the effects of compounded stress and disturbance on coral reef structure and function. Adaptive responses to stress and disturbance in relation to prior experience are highlighted. The thesis further explores how inherent characteristics (traits) of corals and macroalgae may influence regime expression when faced with altered disturbance regimes, in particular overfishing, eutrophication, elevated temperature, and enhanced substrate availability. Finally, possibilities of affecting the resilience of macroalgae-dominaed reefs and shifting the community composition towards a coral-dominated regime are explored.

McMaster Model of Family Functioning: adattamento alla realtà italiana, implicazioni cliniche e di ricerca

Il presente lavoro comincia con una descrizione dettagliata del “McMaster Model of Family Functionig” (MMFF), modello che al suo interno integra una teoria multidimensionale sul funzionamento familiare, diversi strumenti di auto ed etero valutazione e chiare indicazioni terapeutiche racchiuse all’interno della “Problem Centered System Therapy of the Family” (PCSTF). Grazie alla sua completezza il Modello fornisce ai clinici metodi coerenti, pratici ed empiricamente validi per valutare e trattare le famiglie, essi inoltre, sono stati formulati in modo da essere adattabili a differenti setting clinici e di ricerca, applicabili ad un’ampia gamma di problematiche e verificabili empiricamente. Obiettivo finale della presente ricerca è stato quello di porre le basi per l’esportazione del MMFF in Italia e poter quindi procedere alla sua applicazione in ambito clinico. La ricerca è cominciata alla Brown University con la traduzione dall’inglese all’italiano del Family Assessment Device (FAD), uno degli strumenti di autovalutazione compresi nel MMFF, ed è in seguito continuata con la validazione del suddetto strumento in un campione di 317 soggetti appartenenti alla popolazione generale italiana. Il FAD si è dimostrato uno strumento valido ed affidabile, in grado quindi di fornire valutazioni stabili e coerenti anche nella sua versione italiana. Il passo successivo è stato caratterizzato dalla somministrazione di FAD, Symptom Questionnaire (SQ) e delle Psychological Well-Being scales (PWB) a 289 soggetti reclutati nella popolazione generale. In accordo con il modello bipsicosociale che vede l’ambiente familiare come il più immediato gruppo di influenza psicosociale dello stato di benessere o malessere dell’individuo, i nostri dati confermano una stretta relazione tra scarso funzionamento familiare, spesso espresso attraverso difficoltà di comunicazione, di problem solving e scarso coinvolgimento affettivo e distress psicologico esperito con sintomi depressivi, ansiogeni ed ostilità. I nostri dati sottoliano inoltre come un funzionamento familiare positivo sia altamente correlato ad elevati livelli di benessere psicologico. Obiettivo della parte finale del lavoro ed anche il più importante, è stato quello di esplorare l’efficacia della Problem Centered Systems Therapy of the Family nella gestione della perdita di efficacia degli antidepressivi nel trattamento della depressione ricorrente. 20 soggetti con diagnosi di depressione maggiore ricorrente secondo il DSM-IV sono stati randomizzati a due diverse condizioni di trattamento: 1) aumento del dosaggio dell’antidepressivo e clinical management, oppure 2) mantenimento dello stesso dosaggio di antidepressivo e PCSTF. I dati di questo studio mettono in evidenza come, nel breve termine, PCSTF e farmacoterapia sono ugualmente efficaci nel ridurre la sintomatologia depressiva. Diversamente, ad un follow-up di 12 mesi, la PCSTF si è dimostrata altamente superiore all’aumento del farmaco ner prevenire le ricadute. Nel gruppo sottoposto all’aumento del farmaco infatti ben 6 soggetti su 7 ricadono entro l’anno. Nel gruppo assegnato a terapia familiare invece solo 1 soggetto su 7 ricade. Questi risultati sono in linea con i dati della letteratura che sottolineano l’elevata probabilità di una seconda ricaduta dopo l’aumento dell’antidepressivo all’interno di una farmacoterapia di mantenimento e suggeriscono l’efficacia dell’utilizzo di strategie psicoterapiche nella prevenzione della ricaduta in pazienti con depressione ricorrente.

An adaptive solar radiation numerical model

[EN]A numerical model for the evaluation of solar radiation in different locations is presented. The solar radiation model is implemented taking into account the terrain surface using two-dimensional adaptive meshes of triangles that are constructed using a refinement/derefinement procedure in accordance with the variations of terrain surface and albedo. The selected methodology defines the terrain characteristics with a minimum number of points so that the computational cost is reduced for a given accuracy. The model can be used in atmospheric sciences as well as in other fields such as electrical engineering, since it allows the user to find the optimal location for maximum power generation in photovoltaic or solar thermal power plants...

Adaptive finite element simulation of stack pollutant emissions over complex terrains

[EN]A three-dimensional finite element model for the pollutant dispersion is presented. In these environmental processes over a complex terrain, a mesh generator capable of adapting itself to the topographic characteristics is essential. The first stage of the model consists on the construction of an adaptive tetrahedral mesh of a rectangular region bounded in its lower part by the terrain and in its upper part by a horizontal plane. Once the mesh is constructed, an adaptive local refinement of tetrahedra is used in order to capture the plume rise. Wind measurements are used to compute an interpolated wind field, that is modified by using a mass-consistent model and perturbing its vertical component to introduce the plume rise effect...

Adaptive multiscale biological signal processing

Biological processes are very complex mechanisms, most of them being accompanied by or manifested as signals that reflect their essential characteristics and qualities. The development of diagnostic techniques based on signal and image acquisition from the human body is commonly retained as one of the propelling factors in the advancements in medicine and biosciences recorded in the recent past. It is a fact that the instruments used for biological signal and image recording, like any other acquisition system, are affected by non-idealities which, by different degrees, negatively impact on the accuracy of the recording. This work discusses how it is possible to attenuate, and ideally to remove, these effects, with a particular attention toward ultrasound imaging and extracellular recordings. Original algorithms developed during the Ph.D. research activity will be examined and compared to ones in literature tackling the same problems; results will be drawn on the base of comparative tests on both synthetic and in-vivo acquisitions, evaluating standard metrics in the respective field of application. All the developed algorithms share an adaptive approach to signal analysis, meaning that their behavior is not dependent only on designer choices, but driven by input signal characteristics too. Performance comparisons following the state of the art concerning image quality assessment, contrast gain estimation and resolution gain quantification as well as visual inspection highlighted very good results featured by the proposed ultrasound image deconvolution and restoring algorithms: axial resolution up to 5 times better than algorithms in literature are possible. Concerning extracellular recordings, the results of the proposed denoising technique compared to other signal processing algorithms pointed out an improvement of the state of the art of almost 4 dB.

Adaptive T-spline refinement for isogeometric analysis in planar geometries

[EN]We present a new strategy, based on the meccano method [1, 2, 3], to construct a T-spline parameterization of 2D geometries for the application of isogeometric analysis. The proposed method only demands a boundary representation of the geometry as input data. The algorithm obtains, as a result, high quality parametric transformation between 2D objects and the parametric domain, the unit square. The key of the method lies in defining an isomorphic transformation between the parametric and physical T-mesh finding the optimal position of the interior nodes by applying a new T-mesh untangling and smoothing procedure. Bivariate T-spline representation is calculated by imposing the interpolation conditions on points sited both on the interior and on the boundary of the geometry…

Wind ensamble forecasting using an adaptive mass-consistent model

[EN]Ensemble forecasting [1] is a methodology to deal with uncertainties in the numerical wind prediction. In this work we propose to apply ensemble methods to the adaptive wind forecasting model presented in [2]. The wind _eld forecasting is based on a mass-consistent model and a log-linear wind pro_le using as input data the resulting forecast wind from Harmonie [3], a Non-Hydrostatic Dynamic model. The mass-consistent model parameters are estimated by using genetic algorithms [4]. The mesh is generated using the meccano method [5] and adapted to the geometry. The main source of uncertainties in this model is the parameter estimation and the in- trinsic uncertainties of the Harmonie Model…