Prediction of drug targets in human pathogens

The identification of new and druggable targets in bacteria is a critical endeavour in pharmaceutical research of novel antibiotics to fight infectious agents. The rapid emergence of resistant bacteria makes today's antibiotics more and more ineffective, consequently increasing the need for new pharmacological targets and novel classes of antibacterial drugs. A new model that combines the singular value decomposition technique with biological filters comprised of a set of protein properties associated with bacterial drug targets and similarity to protein-coding essential genes of E. coli has been developed to predict potential drug targets in the Enterobacteriaceae family [1]. This model identified 99 potential target proteins amongst the studied bacterial family, exhibiting eight different functions that suggest that the disruption of the activities of these proteins is critical for cells. Out of these candidates, one was selected for target confirmation. To find target modulators, receptor-based pharmacophore hypotheses were built and used in the screening of a virtual library of compounds. Postscreening filters were based on physicochemical and topological similarity to known Gram-negative antibiotics and applied to the retrieved compounds. Screening hits passing all filters were docked into the proteins catalytic groove and 15 of the most promising compounds were purchased from their chemical vendors to be experimentally tested in vitro. To the best of our knowledge, this is the first attempt to rationalize the search of compounds to probe the relevance of this candidate as a new pharmacological target.

Corrigendum to “Short-term changes in light distortion in orthokeratology subjects"

Artigo completo publicado na revista "BioMed Research International, (2015), 1-7" e disponível no RepositóriUM em: http://hdl.handle.net/1822/33375

Short-term corneal changes with gas-permeable contact lens wear in keratoconus subjects: a comparison of two fitting approaches

Purpose: To evaluate changes in anterior corneal topography and higher-order aberrations (HOA) after 14-days of rigid gas-permeable (RGP) contact lens (CL) wear in keratoconus subjects comparing two different fitting approaches. Methods: Thirty-one keratoconus subjects (50 eyes) without previous history of CL wear were recruited for the study. Subjects were randomly fitted to either an apical-touch or three-pointtouch fitting approach. The lens’ back optic zone radius (BOZR) was 0.4 mm and 0.1 mm flatter than the first definite apical clearance lens, respectively. Differences between the baseline and post-CL wear for steepest, flattest and average corneal power (ACP) readings, central corneal astigmatism (CCA), maximum tangential curvature (KTag), anterior corneal surface asphericity, anterior corneal surface HOA and thinnest corneal thickness measured with Pentacam were compared. Results: A statistically significant flattening was found over time on the flattest and steepest simulated keratometry and ACP in apical-touch group (all p < 0.01). A statistically significant reduction in KTag was found in both groups after contact lens wear (all p < 0.05). Significant reduction was found over time in CCA (p = 0.001) and anterior corneal asphericity in both groups (p < 0.001). Thickness at the thinnest corneal point increased significantly after CL wear (p < 0.0001). Coma-like and total HOA root mean square (RMS) error were significantly reduced following CL wearing in both fitting approaches (all p < 0.05). Conclusion: Short-term rigid gas-permeable CL wear flattens the anterior cornea, increases the thinnest corneal thickness and reduces anterior surface HOA in keratoconus subjects. Apicaltouch was associated with greater corneal flattening in comparison to three-point-touch lens wear.

Myeloid Sirtuin 2 expression does not impact long-term Mycobacterium tuberculosis control

Sirtuins (Sirts) regulate several cellular mechanisms through deacetylation of several transcription factors and enzymes. Recently, Sirt2 was shown to prevent the development of inflammatory processes and its expression favors acute Listeria monocytogenes infection. The impact of this molecule in the context of chronic infections remains unknown. We found that specific Sirt2 deletion in the myeloid lineage transiently increased Mycobacterium tuberculosis load in the lungs and liver of conditional mice. Sirt2 did not affect long-term infection since no significant differences were observed in the bacterial burden at days 60 and 120 post-infection. The initial increase in M. tuberculosis growth was not due to differences in inflammatory cell infiltrates in the lung, myeloid or CD4+ T cells. The transcription levels of IFN-?, IL-17, TNF, IL-6 and NOS2 were also not affected in the lungs by Sirt2-myeloid specific deletion. Overall, our results demonstrate that Sirt2 expression has a transitory effect in M. tuberculosis infection. Thus, modulation of Sirt2 activity in vivo is not expected to affect chronic infection with M. tuberculosis.

The Data Mining applied for the prediction of highway roughness due to overloaded trucks

Currently, the quality of the Indonesian national road network is inadequate due to several constraints, including overcapacity and overloaded trucks. The high deterioration rate of the road infrastructure in developing countries along with major budgetary restrictions and high growth in traffic have led to an emerging need for improving the performance of the highway maintenance system. However, the high number of intervening factors and their complex effects require advanced tools to successfully solve this problem. The high learning capabilities of Data Mining (DM) are a powerful solution to this problem. In the past, these tools have been successfully applied to solve complex and multi-dimensional problems in various scientific fields. Therefore, it is expected that DM can be used to analyze the large amount of data regarding the pavement and traffic, identify the relationship between variables, and provide information regarding the prediction of the data. In this paper, we present a new approach to predict the International Roughness Index (IRI) of pavement based on DM techniques. DM was used to analyze the initial IRI data, including age, Equivalent Single Axle Load (ESAL), crack, potholes, rutting, and long cracks. This model was developed and verified using data from an Integrated Indonesia Road Management System (IIRMS) that was measured with the National Association of Australian State Road Authorities (NAASRA) roughness meter. The results of the proposed approach are compared with the IIRMS analytical model adapted to the IRI, and the advantages of the new approach are highlighted. We show that the novel data-driven model is able to learn (with high accuracy) the complex relationships between the IRI and the contributing factors of overloaded trucks

Forecasting human entrances at a commercial store using facial recognition data

Dissertação de mestrado integrado em Engenharia e Gestão de Sistemas de Informação

Long-term prognosis of geriatric major depression in relation to cognition and white matter integrity: follow up of two cases

INTRODUCTION: The geriatric depression (GD) represents one of the most frequent psychiatric disorders in outpatient services specialized in old-age treatment. OBJECTIVE: The course of two illustrative cases of GD is discussed, highlighting its clinical picture after antidepressant treatment and underlining variables related to disease prognosis, treatment effectiveness and conversion to major cognitive disorders such as vascular dementia (VD). METHODS: The cognitive performance, depressive symptoms, autonomy and brain structural measurements as white matter hyperintensities (WMH) and hippocampal size, and microstructural integrity of WM with diffusion tensor imaging were followed during four years. RESULTS: Case 1, with a severe degree of WMH, was associated with worsening cognition and increasing functional disability. Case 2, with mild WMH, an improvement of cognitive functioning could be seen. CONCLUSIONS: The existence of different subtypes of GD, as presented in this report, points a pathophysiological heterogeneity of GD, and suggests a possible continuum vascular depression (VaDp) and vascular cognitive impairment (VCI).

Longitudinal evaluation, acceptability and long-term retention of knowledge on a horizontally integrated organic and functional systems course

Undergraduate medical education is moving from traditional disciplinary basic science courses into more integrated curricula. Integration models based on organ systems originated in the 1950s, but few longitudinal studies have evaluated their effectiveness. This article outlines the development and implementation of the Organic and Functional Systems (OFS) courses at the University of Minho in Portugal, using evidence collected over 10 years. It describes the organization of content, student academic performance and acceptability of the courses, the evaluation of preparedness for future courses and the retention of knowledge on basic sciences. Students consistently rated the OFS courses highly. Physician tutors in subsequent clinical attachments considered that students were appropriately prepared. Performance in the International Foundations of Medicine examination of a self-selected sample of students revealed similar performances in basic science items after the last OFS course and 4 years later, at the moment of graduation. In conclusion, the organizational and pedagogical approaches of the OFS courses achieve high acceptability by students and result in positive outcomes in terms of preparedness for subsequent training and long-term retention of basic science knowledge.

Development of computational and experimental methods for biomass composition and evaluation of its impact in genome-scale models prediction

The use of genome-scale metabolic models has been rapidly increasing in fields such as metabolic engineering. An important part of a metabolic model is the biomass equation since this reaction will ultimately determine the predictive capacity of the model in terms of essentiality and flux distributions. Thus, in order to obtain a reliable metabolic model the biomass precursors and their coefficients must be as precise as possible. Ideally, determination of the biomass composition would be performed experimentally, but when no experimental data are available this is established by approximation to closely related organisms. Computational methods however, can extract some information from the genome such as amino acid and nucleotide compositions. The main objectives of this study were to compare the biomass composition of several organisms and to evaluate how biomass precursor coefficients affected the predictability of several genome-scale metabolic models by comparing predictions with experimental data in literature. For that, the biomass macromolecular composition was experimentally determined and the amino acid composition was both experimentally and computationally estimated for several organisms. Sensitivity analysis studies were also performed with the Escherichia coli iAF1260 metabolic model concerning specific growth rates and flux distributions. The results obtained suggest that the macromolecular composition is conserved among related organisms. Contrasting, experimental data for amino acid composition seem to have no similarities for related organisms. It was also observed that the impact of macromolecular composition on specific growth rates and flux distributions is larger than the impact of amino acid composition, even when data from closely related organisms are used.

Plataforma de apoio à decisão nos cuidados de ginecologia e obstetrícia

Dissertação de mestrado integrado em Engenharia Biomédica (área de especialização em Informática Médica)

Myocardial repair with long-term and low-dose administration of a nitric oxide synthesis inhibitor. Myofibroblasts, type III collagen and fibronectin

OBJECTIVE: To study the healing process of the myocardium in hypertensive rats undergoing inhibition of nitric oxide synthesis. METHODS: Two groups of animals were studied: one received L-NAME, 12mg/kg/day, and the other was a control group. The presence of type III collagen, fibronectin, and alpha-smooth muscle actin-positive cells was assessed by immunohistochemistry. RESULTS: Fibronectin was seen in both early and late lesions, while type III collagen was seen mainly in areas of incomplete healing, situated among myocytes and around the intramyocardial branches of the coronary arteries. Areas representing early and late lesions showed a population of spindle-shaped cells. Immunohistochemistry showed that these cells were positive for alpha-smooth muscle actin. CONCLUSION: In the myocardium of hypertensive rats, the alpha-smooth muscle actin-positive cells are related to the accumulation of type III collagen and fibronectin in the areas of myocardial damage.

In-stent restenosis. Acute and long-term outcomes after excimer laser coronary angioplasty

OBJETIVE: With the increased use of intracoronary stents, in-stent restenosis has become a clinically significant drawback in invasive cardiology. We retrospectively assessed the short- and long-term outcomes after excimer laser coronary angioplasty of in-stent restenosis. METHODS: Twenty-five patients with 33 incidents of in-stent restenosis treated with excimer laser coronary angioplasty (ELCA) were analyzed. Sixty-six percent were males, mean age of 73±11 years, and 83% were functional class III-IV (NYHA). ELCA was performed using 23 concentric and 10 eccentric catheters with a diameter of 1.6-2.2 mm, followed by balloon angioplasty (PTCA) and ultrasound monitoring. The procedure was performed in the following vessels: left anterior descending artery, 10; left circumflex artery, 8; right coronary artery, 6; left main coronary artery, 2; and venous bypass graft, 7. RESULTS: The ELCA was successful in 71% of the cases, and PTCA was 100% successful. The diameter of the treated vessels was 3.44±0.5mm; the minimal luminal diameter (MLD) increased from 0.30mm pre-ECLA to 1.97mm post-ELCA, and to 2.94mm post-PTCA (p<0.001). The percent stenosis was reduced from 91.4±9.5% before ECLA to 42.3±14.9% after ELCA and to 14.6 ± 9.3% after PTCA (p<0.001). Seventeen (68%) patients were asymptomatic at 6 months and 15 (60%) at 1 year. New restenosis rates were 8/33 (24.2%) at 6 months and 9 /33 (27.3%) at 12 months. CONCLUSION: ELCA is safe and effective for the treatment of in-stent restenosis. In the present sample, a slight increase in new restenotic lesions between 6 and 12 months was found.

Immediate and long term evolution of valve replacement in children less than 12 years old

OBJECTIVE: The aim of this work was the follow-up and evaluation of valve replacement in children under 12 years of age. METHODS: Forty-four children less than 12 years old were underwent valve replacement at INCOR-HCFMUSP between January 1986 and December 1992. Forty (91%) were rheumatic, 39 (88.7%) were in functional classes II or IV, 19 (43.2%) were operated upon on an emergency basis, and 6 (13.6%) had atrial fibrillation. Biological prostheses (BP) were employed in 26 patients (59.1%), and mechanical prostheses (MP) in 18 (40.9%). Mitral valves were replaced in 30 (68.7%), aortic valves in 8 (18.2%), a tricuspid valve in 1 (2.3%), and double (aortic and mitral) valves in 5 (11.4) of the patients. RESULTS: Hospital mortality was of 4.5% (2 cases). The mean follow-up period was 5.8 years. Re-operations occurred in 63.3% of the patients with BP and in 12.5% of those with MP (p=0.002). Infectious endocarditis was present in 26.3% of the BP, but in none of the cases of MP (p=0.049). Thrombosis occurred in 2 (12.5%) and hemorrhage in one (6.5%) of the patients with a MP. Delayed mortality occurred in 5 (11.9%) of the patients over a mean period of 2.6 years; four had had BP and one had a MP (NS). Actuarial survival and re-operation-free curves after 10 years were respectively, 82.5±7.7 (SD)% and 20.6±15.9%. CONCLUSION: Patients with MP required fewer re-operation, had less infectious endocarditis and lower late mortality rates compared with patients with bioprostheses. The former, therefore, appear to be the best valve replacement for pediatric patients.

Heart transplantation in neonates and children. Intermediate-term results

OBJECTIVE: To assess intermediate-term outcome in children who have undergone orthotopic heart transplantation. METHODS: We carried out a longitudinal and prospective study between October '92 and June '99 comprising 20 patients with ages ranging from 12 days to 7 years (mean of 2.8 years). We employed a double immunosuppression protocol with cyclosporine and azathioprine and induction therapy with polyclonal antithymocyte serum. Survival and complications resulting from the immunosuppression protocol were analyzed. RESULTS:The double immunosuppression protocol and the induction therapy with polyclonal antithymocyte serum resulted in an actuarial survival curve of 90% and 78.2% at 1 and 6 years, respectively, with a mean follow-up period of 3.6 years. One patient died due to acute rejection 40 days after transplantation; another patient died 2 years after transplantation due to lymphoproliferative disorder; a third patient died because of primary failure of the graft; and a fourth patient died due to bronchopneumonia. The major complications were as follows: acute rejection, infection, nephrotoxicity, and systemic hypertension. The means of rejection and infection episodes per patient were 2.9 and 3.4, respectively. After one year of transplantation, a slight reduction in the creatinine clearance and systemic hypertension were observed in 7 (38.9%) patients. CONCLUSION: Heart transplantation made life possible for those patients with complex congenital heart diseases and cardiomyopathies in refractory congestive heart failure constituting a therapeutical option for this group of patients in the terminal phase.

Short-term follow-up of patients after aneurysmectomy of the left ventricle

OBJECTIVE: Left ventricular aneurysm is a complication of myocardial infarction that can best be treated by reconstructive surgeries that can restore ventricular geometry. We analyzed immediate results in a group of consecutive patients who underwent surgical correction of left ventricular aneurysms. METHODS: From January '90 to August '99, 94 patients - mean age 58.4 (ranging from 36 to 73 years), 65 (69.1%) males and 9 ( 30.8%) females - were operated upon. Pre-operative ejection fraction ranged from 0.22 to 0.58 (mean = 0.52), and the aneurysm was located in the antero-lateral area in 90.4% of the cases. Functional class III and IV (NYHA) was present in 82 (87.2%) patients, and 12 (12.7%) were in functional class I and II. Congestive heart failure was the most frequent cause (77.6%), occurring in isolation in 24.4% or associated with coronary artery diseases in 53.2%. RESULTS: Short-term follow-up showed a 7.4% mortality, and low cardiac output was the main cause of death. Coming off pump was uneventful in 73 patients (77.6%), with a 3.2% mortality and with the use of inotropics in 20 (21.3%). One patient (1%) did not come off the pump. CONCLUSION: Surgical correction was adequate in the immediate follow-up of operated patients, and mortality was higher in patients with higher functional class.