Use of virtual screening, flexible docking, and molecular interaction fields to design novel HMG-CoA reductase inhibitors for the treatment of hypercholesterolemia

Dietary changes associated with drug therapy can reduce high serum cholesterol levels and dramatically decrease the risk of coronary artery disease, stroke, and overall mortality. Statins are hypolipemic drugs that are effective in the reduction of cholesterol serum levels, attenuating cholesterol synthesis in liver by competitive inhibition regarding the substrate or molecular target HMG-CoA reductase. We have herewith used computer-aided molecular design tools, i.e., flexible docking, virtual screening in large data bases, molecular interaction fields to propose novel potential HMG-CoA reductase inhibitors that are promising for the treatment of hypercholesterolemia.

A New Family of Distance Functions for Perceptual Similarity Retrieval of Medical Images

A long-standing challenge of content-based image retrieval (CBIR) systems is the definition of a suitable distance function to measure the similarity between images in an application context which complies with the human perception of similarity. In this paper, we present a new family of distance functions, called attribute concurrence influence distances (AID), which serve to retrieve images by similarity. These distances address an important aspect of the psychophysical notion of similarity in comparisons of images: the effect of concurrent variations in the values of different image attributes. The AID functions allow for comparisons of feature vectors by choosing one of two parameterized expressions: one targeting weak attribute concurrence influence and the other for strong concurrence influence. This paper presents the mathematical definition and implementation of the AID family for a two-dimensional feature space and its extension to any dimension. The composition of the AID family with L (p) distance family is considered to propose a procedure to determine the best distance for a specific application. Experimental results involving several sets of medical images demonstrate that, taking as reference the perception of the specialist in the field (radiologist), the AID functions perform better than the general distance functions commonly used in CBIR.

Comparative study of Botox (R) injection treatment for upper eyelid retraction with 6-month follow-up in patients with thyroid eye disease in the congestive or fibrotic stage

Aim To compare morphometric data of the eyelid fissure and the levator muscle function (LF) before and up to 6 months after transcutaneous injection with five units of Botox (R) in patients with upper lid retraction (ULR) from congestive or fibrotic thyroid eye disease (TED). Methods Twenty-four patients with ULR from TED were submitted to transcutaneous injection of 5 units (0.1 ml) of Botox in one eye only. Patients were divided into two groups: 12 with congestive-stage TED (CG), and 12 with fibrotic-stage TED (FG). Bilateral lid fissure measurements using digital imaging and computer-aided analysis were taken at baseline and at regular intervals 2 weeks, 1 month, 3 months and 6 months after unilateral Botox injection. Mean values taken at different follow-up points were compared for the two groups. Results Most patients experienced marked improvement in ULR, with a mean reduction of 3.81 mm in FG and 3.05 mm in CG. The upper eyelid margin reflex distance, fissure height and total area of exposed interpalpebral fissure were significantly smaller during 1 month in CG and during 3 months in FG. Reduction in LF and in the difference between lateral and medial lid fissure measurements was observed in both groups. The treatment lasted significantly longer in FG than in CG. Conclusions A single 5-unit Botox injection improved ULR, reduced LF and produced an adequate lid contour in patients with congestive or fibrotic TED. The effect lasts longer in patients with fibrotic orbitopathy than in patients with congestive orbitopathy.

Is the Sciatic Functional Index always reliable and reproducible?

The Sciatic Functional Index (SFI) is a quite useful tool for the evaluation of functional recovery of the sciatic nerve of rats in a number of experimental injuries and treatments. Although it is an objective method, it depends on the examiner`s ability to adequately recognize and mark the previously established footprint key points, which is an entirely subjective step, thus potentially interfering with the calculations according to the mathematical formulae proposed by different authors. Thus, an interpersonal evaluation of the reproducibility of an SFI computer-aided method was carried out here to study data variability. A severe crush injury was produced on a 5 mm-long segment of the right sciatic nerve of 20 Wistar rats (a 5000 g load directly applied for 10 min) and the SH was measured by four different examiners (an experienced one and three newcomers) preoperatively and at weekly intervals from the 1st to the 8th postoperative week. Three measurements were made for each print and the average was calculated and used for statistical analysis. The results showed that interpersonal correlation was high (0.82) in the 3rd, 4th, 5th, 7th and 8th weeks, with an unexpected but significant (p < 0.01) drop in the 6th week. There was virtually no interpersonal correlation (correlation index close to 0) on the 1st and 2nd weeks, a period during which the variability between animals and examiners (p =0.24 and 0.32, respectively) was similar, certainly due to a poor definition of the footprints. The authors conclude that the SFI method studied here is only reliable from the 3rd week on after a severe lesion of the sciatic nerve of rats. (C) 2008 Elsevier B.V. All rights reserved.

Quantitative three-dimensional power Doppler angiography: a flow-free phantom experiment to evaluate the relationship between color gain, depth and signal artifact

Objectives To evaluate the presence of false flow three-dimensional (3D) power Doppler signals in `flow-free` models. Methods 3D power Doppler datasets were acquired from three different flow-free phantoms (muscle, air and water) with two different transducers and Virtual Organ Computer-aided AnaLysis was used to generate a sphere that was serially applied through the 3D dataset. The vascularization flow index was used to compare artifactual signals at different depths (from 0 to 6 cm) within the different phantoms and at different gain and pulse repetition frequency (PR F) settings. Results Artifactual Doppler signals were seen in all phantoms despite these being flow-free. The pattern was very similar and the degree of artifact appeared to be dependent on the gain and distance from the transducer. False signals were more evident in the far field and increased as the gain was increased, with false signals first appearing with a gain of 1 dB in the air and muscle phantoms. False signals were seen at a lower gain with the water phantom (-15 dB) and these were associated with vertical lines of Doppler artifact that were related to PRF, and disappeared when reflections were attenuated. Conclusions Artifactual Doppler signals are seen in flow-free phantoms and are related to the gain settings and the distance from the transducer. In the in-vivo situation, the lowest gain settings that allow the detection of blood flow and adequate definition of vessel architecture should be used, which invariably means using a setting near or below the middle of the range available. Additionally, observers should be aware of vertical lines when evaluating cystic or liquid-containing structures. Copyright (C) 2010 ISUOC. Published by John Wiley & Sons, Ltd.

A standardized measurement technique may improve the reliability of measurements of endometrial thickness and volume

Objective To investigate whether standardization of the multiplanar view (SMV) when evaluating the uterus using three-dimensional ultrasonography (3D-US) improves intra-and interobserver reliability and agreement with regard to endometrial measurement. Methods Two-dimensional (2D) and 3D-US was used to measure endometrial thickness by two observers in 30 women undergoing assisted reproduction treatment. Endometrial volume was measured with Virtual Organ Computer-aided AnaLysis (VOCAL (TM)) in the longitudinal (A) and coronal (C) planes using an unmodified multiplanar view (UMV) and a standardized multiplanar view (SMV). Measurement reliability was evaluated by intraclass correlation coefficient (ICC) and agreement was examined using Bland-Altman plots with limits of agreement (LoA). The ease of outlining the endometrial-myometrial interface was compared between the A-and C-planes using subjective assessment. Results Endometrial volume measurements using the SMV and A-plane were more reliable (intra-and interobserver ICCs, 0.979 and 0.975, respectively) than were measurements of endometrial thickness using 2D-US (intra-and interobserver ICCs, 0.742 and 0.702, respectively) or 3D-US (intra-and interobserver ICCs, 0.890 and 0.784, respectively). The LoAs were narrower for SMV than for UMV. Reliability and agreement were not much different between the A- and C-planes. However the observers agreed that delineating the endometrial-myometrial interface using the A-plane was easier (first and second observer, 50.0 and 46.7%, respectively) or `comparable` (50 and 53.3%, respectively), but never more difficult than using the C-plane. Conclusions Endometrial volume measurements are more reliable than endometrial thickness measurements and are best performed using SMV and the A-plane. Copyright (C) 2011 ISUOG. Published by John Wiley & Sons, Ltd.

Monolithic CAD/CAM Lithium Disilicate Versus Veneered Y-TZP Crowns: Comparison of Failure Modes and Reliability After Fatigue

Purpose: The aim of this research was to evaluate the fatigue behavior and reliability of monolithic computer-aided design/computer-assisted manufacture (CAD/CAM) lithium disilicate and hand-layer-veneered zirconia all-ceramic crowns. Materials and Methods: A CAD-based mandibular molar crown preparation, fabricated using rapid prototyping, served as the master die. Fully anatomically shaped monolithic lithium disilicate crowns (IPS e.max CAD, n = 19) and hand-layer-veneered zirconia-based crowns (IPS e.max ZirCAD/Ceram, n = 21) were designed and milled using a CAD/CAM system. Crowns were cemented on aged dentinlike composite dies with resin cement. Crowns were exposed to mouth-motion fatigue by sliding a WC-indenter (r = 3.18 mm) 0.7 mm lingually down the distobuccal cusp using three different step-stress profiles until failure occurred. Failure was designated as a large chip or fracture through the crown. If no failures occurred at high loads (> 900 N), the test method was changed to staircase r ratio fatigue. Stress level probability curves and reliability were calculated. Results: Hand-layer-veneered zirconia crowns revealed veneer chipping and had a reliability of < 0.01 (0.03 to 0.00, two-sided 90% confidence bounds) for a mission of 100,000 cycles and a 200-N load. None of the fully anatomically shaped CAD/CAM-fabricated monolithic lithium disilicate crowns failed during step-stress mouth-motion fatigue (180,000 cycles, 900 N). CAD/CAM lithium disilicate crowns also survived r ratio fatigue (1,000,000 cycles, 100 to 1,000 N). There appears to be a threshold for damage/bulk fracture for the lithium disilicate ceramic in the range of 1,100 to 1,200 N. Conclusion: Based on present fatigue findings, the application of CAD/CAM lithium disilicate ceramic in a monolithic/fully anatomical configuration resulted in fatigue-resistant crowns, whereas hand-layer-veneered zirconia crowns revealed a high susceptibility to mouth-motion cyclic loading with early veneer failures. Int J Prosthodont 2010; 23: 434-442.

Thermal/mechanical simulation and laboratory fatigue testing of an alternative yttria tetragonal zirconia polycrystal core-veneer all-ceramic layered crown design

This study evaluated the stress levels at the core layer and the veneer layer of zirconia crowns (comprising an alternative core design vs. a standard core design) under mechanical/thermal simulation, and subjected simulated models to laboratory mouth-motion fatigue. The dimensions of a mandibular first molar were imported into computer-aided design (CAD) software and a tooth preparation was modeled. A crown was designed using the space between the original tooth and the prepared tooth. The alternative core presented an additional lingual shoulder that lowered the veneer bulk of the cusps. Finite element analyses evaluated the residual maximum principal stresses fields at the core and veneer of both designs under loading and when cooled from 900 degrees C to 25 degrees C. Crowns were fabricated and mouth-motion fatigued, generating master Weibull curves and reliability data. Thermal modeling showed low residual stress fields throughout the bulk of the cusps for both groups. Mechanical simulation depicted a shift in stress levels to the core of the alternative design compared with the standard design. Significantly higher reliability was found for the alternative core. Regardless of the alternative configuration, thermal and mechanical computer simulations showed stress in the alternative core design comparable and higher to that of the standard configuration, respectively. Such a mechanical scenario probably led to the higher reliability of the alternative design under fatigue.

A Survey on Graphical Methods for Classification Predictive Performance Evaluation

Predictive performance evaluation is a fundamental issue in design, development, and deployment of classification systems. As predictive performance evaluation is a multidimensional problem, single scalar summaries such as error rate, although quite convenient due to its simplicity, can seldom evaluate all the aspects that a complete and reliable evaluation must consider. Due to this, various graphical performance evaluation methods are increasingly drawing the attention of machine learning, data mining, and pattern recognition communities. The main advantage of these types of methods resides in their ability to depict the trade-offs between evaluation aspects in a multidimensional space rather than reducing these aspects to an arbitrarily chosen (and often biased) single scalar measure. Furthermore, to appropriately select a suitable graphical method for a given task, it is crucial to identify its strengths and weaknesses. This paper surveys various graphical methods often used for predictive performance evaluation. By presenting these methods in the same framework, we hope this paper may shed some light on deciding which methods are more suitable to use in different situations.

An automatic correction method for the heel effect in digitized mammography images

The most significant radiation field nonuniformity is the well-known Heel effect. This nonuniform beam effect has a negative influence on the results of computer-aided diagnosis of mammograms, which is frequently used for early cancer detection. This paper presents a method to correct all pixels in the mammography image according to the excess or lack on radiation to which these have been submitted as a result of the this effect. The current simulation method calculates the intensities at all points of the image plane. In the simulated image, the percentage of radiation received by all the points takes the center of the field as reference. In the digitized mammography, the percentages of the optical density of all the pixels of the analyzed image are also calculated. The Heel effect causes a Gaussian distribution around the anode-cathode axis and a logarithmic distribution parallel to this axis. Those characteristic distributions are used to determine the center of the radiation field as well as the cathode-anode axis, allowing for the automatic determination of the correlation between these two sets of data. The measurements obtained with our proposed method differs on average by 2.49 mm in the direction perpendicular to the anode-cathode axis and 2.02 mm parallel to the anode-cathode axis of commercial equipment. The method eliminates around 94% of the Heel effect in the radiological image and the objects will reflect their x-ray absorption. To evaluate this method, experimental data was taken from known objects, but could also be done with clinical and digital images.

Gamma Knife(A (R)) 3-D Dose Distribution Mapping by Magnetic Resonance Imaging

In medical processes where ionizing radiation is used, dose planning and dose delivery are the key elements to patient safety and treatment success, particularly, when the delivered dose in a single session of treatment can be an order of magnitude higher than the regular doses of radiotherapy. Therefore, the radiation dose should be well defined and precisely delivered to the target while minimizing radiation exposure to surrounding normal tissues [1]. Several methods have been proposed to obtain three-dimensional (3-D) dose distribution [2, 3]. In this paper, we propose an alternative method, which can be easily implemented in any stereotactic radiosurgery center with a magnetic resonance imaging (MRI) facility. A phantom with or without scattering centers filled with Fricke gel solution is irradiated with Gamma Knife(A (R)) system at a chosen spot. The phantom can be a replica of a human organ such as head, breast or any other organ. It can even be constructed from a real 3-D MR image of an organ of a patient using a computer-aided construction and irradiated at a specific region corresponding to the tumor position determined by MRI. The spin-lattice relaxation time T (1) of different parts of the irradiated phantom is determined by localized spectroscopy. The T (1)-weighted phantom images are used to correlate the image pixels intensity to the absorbed dose and consequently a 3-D dose distribution with a high resolution is obtained.

In silico screening of HIV-1 non-nucleoside reverse transcriptase and protease inhibitors

Two targets, reverse transcriptase (RT) and protease from HIV-1, were used during the past two decades to the discovery of non-nucleoside reverse transcriptase inhibitors (NNRTI) and protease inhibitors (PI) that belong to the arsenal of the antiretroviral therapy. Herein these enzymes were chosen as templates for conducting a computer-aided ligand design. Ligand and structure-based drug designs were the starting points to select compounds from a database bearing more than five million compounds by means of cheminformatic tools. New promising lead structures are retrieved from the database, which are open to acquisition and test. Classes of molecules already described as NNRTI or PI in the literature also came out and were useful to prove the reliability of the workflow, and thus validating the work carried out so far. (c) 2007 Elsevier Masson SAS. All rights reserved.

Fragment-guided approach to incorporating structural information into a CoMFA study: BACE-1 as an example

Alzheimer`s disease is an ultimately fatal neurodegenerative disease, and BACE-1 has become an attractive validated target for its therapy, with more than a hundred crystal structures deposited in the PDB. In the present study, we present a new methodology that integrates ligand-based methods with structural information derived from the receptor. 128 BACE-1 inhibitors recently disclosed by GlaxoSmithKline R&D were selected specifically because the crystal structures of 9 of these compounds complexed to BACE-1, as well as five closely related analogs, have been made available. A new fragment-guided approach was designed to incorporate this wealth of structural information into a CoMFA study, and the methodology was systematically compared to other popular approaches, such as docking, for generating a molecular alignment. The influence of the partial charges calculation method was also analyzed. Several consistent and predictive models are reported, including one with r (2) = 0.88, q (2) = 0.69 and r (pred) (2) = 0.72. The models obtained with the new methodology performed consistently better than those obtained by other methodologies, particularly in terms of external predictive power. The visual analyses of the contour maps in the context of the enzyme drew attention to a number of possible opportunities for the development of analogs with improved potency. These results suggest that 3D-QSAR studies may benefit from the additional structural information added by the presented methodology.