Automatic design of decision-tree induction algorithms tailored to flexible-receptor docking data

Background: This paper addresses the prediction of the free energy of binding of a drug candidate with enzyme InhA associated with Mycobacterium tuberculosis. This problem is found within rational drug design, where interactions between drug candidates and target proteins are verified through molecular docking simulations. In this application, it is important not only to correctly predict the free energy of binding, but also to provide a comprehensible model that could be validated by a domain specialist. Decision-tree induction algorithms have been successfully used in drug-design related applications, specially considering that decision trees are simple to understand, interpret, and validate. There are several decision-tree induction algorithms available for general-use, but each one has a bias that makes it more suitable for a particular data distribution. In this article, we propose and investigate the automatic design of decision-tree induction algorithms tailored to particular drug-enzyme binding data sets. We investigate the performance of our new method for evaluating binding conformations of different drug candidates to InhA, and we analyze our findings with respect to decision tree accuracy, comprehensibility, and biological relevance. Results: The empirical analysis indicates that our method is capable of automatically generating decision-tree induction algorithms that significantly outperform the traditional C4.5 algorithm with respect to both accuracy and comprehensibility. In addition, we provide the biological interpretation of the rules generated by our approach, reinforcing the importance of comprehensible predictive models in this particular bioinformatics application. Conclusions: We conclude that automatically designing a decision-tree algorithm tailored to molecular docking data is a promising alternative for the prediction of the free energy from the binding of a drug candidate with a flexible-receptor.

Agar-Based Gel Electrolyte for Electrochromic Device Application

Gel Polymer Electrolytes (GPE) based on agar and containing LiClO4 have been prepared, characterized and applied to electrochromic devices. The ionic conductivity revealed the best result of 6.5 x 10(-5) S/cm for the sample with 17 wt.% of LiClO4, which increased to 5.4 x 10(-4) S/cm at 72 degrees C. TheGPE have been used in electrochromic devices (ECD) with K-glass/WO3/GPE/CeO2-TiO2/K-glass configuration. The ECD changed transmittance values up to 30% between the colored and transparent states. The charge density measurements revealed an increase of 5.5 to 7.5 mC/cm(2) from the first to 500th cycles and then a decrease to 4.4 mC/cm(2) during the next 4500 cycles. Coloration efficiency (eta) of 25 cm(2)/C was obtained.

Automatic aspect discrimination in data clustering

The attributes describing a data set may often be arranged in meaningful subsets, each of which corresponds to a different aspect of the data. An unsupervised algorithm (SCAD) that simultaneously performs fuzzy clustering and aspects weighting was proposed in the literature. However, SCAD may fail and halt given certain conditions. To fix this problem, its steps are modified and then reordered to reduce the number of parameters required to be set by the user. In this paper we prove that each step of the resulting algorithm, named ASCAD, globally minimizes its cost-function with respect to the argument being optimized. The asymptotic analysis of ASCAD leads to a time complexity which is the same as that of fuzzy c-means. A hard version of the algorithm and a novel validity criterion that considers aspect weights in order to estimate the number of clusters are also described. The proposed method is assessed over several artificial and real data sets.

Light emission and current rectification in a molecular device: Experiment and theory

We have investigated optical and transport properties of the molecular structure 2,3,4,5-tetraphenyl-1-phenylethynyl-cyclopenta-2,4-dienol experimentally and theoretically. The optical spectrum was calculated using Hartree-Fock-intermediate neglect of differential overlap-configuration interaction model. The experimental photoluminescence spectrum showed a peak around 470nm which was very well described by the modeling. Electronic transport measurements showed a diode-like effect with a strong current rectification. A phenomenological microscopic model based on non-equilibrium Green's function technique was proposed and a very good description electronic transport was obtained. (C) 2012 American Institute of Physics. [http://dx.doi.org/10.1063/1.4767457]

Use of a titanium device in lateral sinus floor elevation: an experimental study in monkeys

Aim: To evaluate the effect of a space-maintaining device fixed to the lateral wall of the maxillary sinus after the elevation of the sinus mucosa on bone filling of the sinus cavity. Material and methods: Immediately after the elevation of the maxillary sinus Schneiderian membrane accomplished through lateral antrostomy in four monkeys, a titanium device was affixed to the lateral sinus wall protruding into the sinus cavity to maintain the mucosa elevated without the use of grafting material. The healing of the tissue around the implants was evaluated after 3 and 6 months. Ground sections were prepared and analyzed histologically. Results: The void under the elevated sinus membrane, originally filled with the blood clot, was reduced after 3 as well as after 6 months of healing of about 56% and 40.5%, respectively. In seven out of eight cases, the devices had perforated the sinus mucosa. The formation of mineralized bone and bone marrow amounted to about 42% and 69% after 3 and 6 months, respectively. The connective tissue represented about 53% and 23% of the newly formed tissue after 3 and 6 months, respectively. Conclusions: New bone formation was found below the devices. However, shrinkage of the newly formed tissue was observed both after 3 and 6 months of healing. Hence, the space-maintaining function of the devices used in the present study has to be questioned.

Paper-Based Analytical Device for Electrochemical Flow-Injection Analysis of Glucose in Urine

This article describes a new design for a paper-based electrochemical system for flow injection analysis. Capillary wicking facilitates a gravity-driven flow of buffer solution continuously through paper and nitrocellulose, from a buffer reservoir at one end of the device to a sink at the other. A difference in height between the reservoir and the sink leads to a continuous and constant flow. The nitrocellulose lies horizontally on a working electrode, which consists of a thin platinum layer deposited on a solid support. The counter and reference electrodes are strategically positioned upstream in the buffer reservoir. A simple pipetting device was developed for reliable application of (sub)microliter volumes of sample without the need of commercial micropipets; this device did not damage the nitrocellulose membrane. Demonstration of the system for the determination of the concentration of glucose in urine resulted in a noninvasive, quantitative assay that could be used for diagnosis and monitoring of diabetes. This method does not require disposable test strips, with enzyme and electrodes, that are thrown away after each measurement Because of its low cost, this system could be used in medical environments that are resource-limited.

Influence of moisture and plaque on the performance of a laser fluorescence device in detecting caries lesions in primary teeth

The aim of this study was to evaluate the influence of dental plaque and moisture on performance of a laser fluorescence device in detecting occlusal and proximal caries lesions in primary teeth. Fifty-five occlusal and 58 proximal sites on primary molars were evaluated using a DIAGNOdent pen (LFpen) device. For the drying time study, the evaluations were performed in: (I) moist teeth; (II) teeth dried for 3 s, or (III) dried for 15 s. For the plaque study, the evaluations were done in sites: (I) without plaque; (II) with plaque, and (III) after cleaning. Evaluation of the teeth sections in stereomicroscope was the reference standard method. LF pen values, sensitivity, specificity, and accuracy were compared. The values obtained after 15 s of drying were higher than those obtained with moist teeth or dried for 3 s at both occlusal and proximal surfaces. However, there was no change in the performance in detecting caries lesions. With regard to the presence of plaque, there was no significant change in the readings of the device, but specificity was decreased in occlusal surfaces with plaque. At proximal surfaces, however, no significant differences were observed. In conclusion, the moisture conditions do not influence significantly the performance of the LFpen, but the presence of plaque can affect its performance in detecting occlusal caries lesions in primary teeth.

Endovascular repair of a traumatic arteriovenous fistula involving the iliac bifurcation using an iliac branch device

Endovascular techniques have shown to be useful in the management of vascular injuries because they transform a complex and potentially dangerous procedure into a safe one. We present the case of a 39-year-old man with congestive heart failure and abdominal bruit 11 years after an abdominal gunshot wound. Imaging studies revealed an arteriovenous fistula involving the left iliac artery bifurcation, and an iliac branch device was used to treat it. Symptoms resolved, and follow-up imaging showed patency of the graft and closure of the arteriovenous communication. To our knowledge, this is the first report of a nonaneurysmal disease treated with this device. (J Vasc Surg 2012;55:1474-6.)

Glass/PDMS hybrid microfluidic device integrating vertically aligned SWCNTs to ultrasensitive electrochemical determinations

This communication reports a promising platform for rapid, simple, direct, and ultrasensitive determination of serotonin. The method is related to integration of vertically aligned single-walled carbon nanotubes (SWCNTs) in electrochemical microfluidic devices. The required microfabrication protocol is simple and fast. In addition, the nanomaterial influenced remarkably the obtained limit-of-detection (LOD) values. Our system achieved a LOD of 0.2 nmol L-1 for serotonin, to the best of our knowledge one of the lowest values reported in the literature.

Development of a high sensitive automatic setup for screening of microcystins in surface waters by employing a LED-based photometric detector

In this manuscript, an automatic setup for screening of microcystins in surface waters by employing photometric detection is described. Microcystins are toxins delivered by cyanobacteria within an aquatic environment, which have been considered strongly poisonous for humans. For that reason, the World Health Organization (WHO) has proposed a provisional guideline value for drinking water of 1 mu g L-1. In this work, we developed an automated equipment setup, which allows the screening of water for concentration of microcystins below 0.1 mu g V. The photometric method was based on the enzyme-linked immunosorbent assay (ELISA) and the analytical signal was monitored at 458 nm using a homemade LED-based photometer. The proposed system was employed for the detection of microcystins in rivers and lakes waters. Accuracy was assessed by processing samples using a reference method and applying the paired t-test between results. No significant difference at the 95% confidence level was observed. Other useful features including a linear response ranging from 0.05 up to 2.00 mu g L-1 (R-2 =0.999) and a detection limit of 0.03 mu g L-1 microcystins were achieved. (C) 2011 Elsevier B.V. All rights reserved.

Performance of fixed-pressure valve with antisiphon device SPHERA (R) in hydrocephalus treatment and overdrainage prevention

Patients with hydrocephalus and risk factors for overdrainage may be submitted to ventricular shunt (VS) implant with antisiphon device. The objective of this study was to prospectively evaluate for two years the clinical and tomographic results of the implant of fixed-pressure valves with antisiphon device SPHERA (R) in 35 adult patients, with hydrocephalus and risk factors for overdrainage. Of these, 3 had congenital hydrocephalus in adult patients with very dilated ventricles (Evans index >50%), 3 had symptomatic overdrainage after previous VS implant (subdural hematoma, hygroma or slit ventricle syndrome), 1 had previous chronic subdural hematoma, 15 had normal pressure hydrocephalus with final lumbar pressure <5 cm H2O after tap test (40 mL), 6 had pseudotumor cerebri, and 7 had hydrocephalus due to other causes. Clinical improvement was observed and sustained in 94.3% of the patients during the two-year period with no computed tomography (CT) evidence of hypo or overdrainage, and no immediate early or late significant complications.

Automatic lumen segmentation in IVOCT images using binary morphological reconstruction

Abstract Background Atherosclerosis causes millions of deaths, annually yielding billions in expenses round the world. Intravascular Optical Coherence Tomography (IVOCT) is a medical imaging modality, which displays high resolution images of coronary cross-section. Nonetheless, quantitative information can only be obtained with segmentation; consequently, more adequate diagnostics, therapies and interventions can be provided. Since it is a relatively new modality, many different segmentation methods, available in the literature for other modalities, could be successfully applied to IVOCT images, improving accuracies and uses. Method An automatic lumen segmentation approach, based on Wavelet Transform and Mathematical Morphology, is presented. The methodology is divided into three main parts. First, the preprocessing stage attenuates and enhances undesirable and important information, respectively. Second, in the feature extraction block, wavelet is associated with an adapted version of Otsu threshold; hence, tissue information is discriminated and binarized. Finally, binary morphological reconstruction improves the binary information and constructs the binary lumen object. Results The evaluation was carried out by segmenting 290 challenging images from human and pig coronaries, and rabbit iliac arteries; the outcomes were compared with the gold standards made by experts. The resultant accuracy was obtained: True Positive (%) = 99.29 ± 2.96, False Positive (%) = 3.69 ± 2.88, False Negative (%) = 0.71 ± 2.96, Max False Positive Distance (mm) = 0.1 ± 0.07, Max False Negative Distance (mm) = 0.06 ± 0.1. Conclusions In conclusion, by segmenting a number of IVOCT images with various features, the proposed technique showed to be robust and more accurate than published studies; in addition, the method is completely automatic, providing a new tool for IVOCT segmentation.

Keratometry device for surgical support

Abstract Background High astigmatisms are usually induced during corneal suturing subsequent to tissue transplantation or any other surgery which involves corneal suturing. One of the reasons is that the procedure is intimately dependent on the surgeon's skill for suturing identical stitches. In order to evaluate the influence of the irregularity on suturing for the residual astigmatism, a prototype for ophthalmic surgical support has been developed. The final intention of this prototype is to be an evaluation tool for guided suture and as an outcome diminish the postoperative astigmatism. Methods The system consists of hand held ring with 36 infrared LEDs, that is to be projected onto the lachrymal film of the cornea. The image is reflected back through the optics of the ocular microscope and its distortion from the original circular shape is evaluated by developed software. It provides keratometric and circularity measurements during surgery in order to guide the surgeon for uniformity in suturing. Results The system is able to provide up to 23D of astigmatism (32D - 55D range) and is ± 0.25D accurate. It has been tested in 14 volunteer patients intraoperative and has been compared to a commercial keratometer Nidek Oculus Hand-held corneal topographer. The correlation factors are 0.92 for the astigmatism and 0.97 for the associated axis. Conclusion The system is potentially efficient for guiding the surgeon on uniformity of suturing, presenting preliminary data indicating an important decrease on the residual astigmatism, from an average of 8D - for patients not submitted to the prototype guidance - to 1.4D - for patients who have actually been submitted to the prototype guidance - after the first 24 hours post-surgery and in the subsequent weeks. It also indicates that the surgeon should achieve circularity greater or equal to 98% in order to avoid postoperative astigmatisms over 1D. Trial Registration Trial registration number: CAAE - 0212.0.004.000-09.

Performance of fixed-pressure valve with antisiphon device SPHERA® in hydrocephalus treatment and overdrainage prevention

Patients with hydrocephalus and risk factors for overdrainage may be submitted to ventricular shunt (VS) implant with antisiphon device. The objective of this study was to prospectively evaluate for two years the clinical and tomographic results of the implant of fixed-pressure valves with antisiphon device SPHERA® in 35 adult patients, with hydrocephalus and risk factors for overdrainage. Of these, 3 had congenital hydrocephalus in adult patients with very dilated ventricles (Evans index >50%), 3 had symptomatic overdrainage after previous VS implant (subdural hematoma, hygroma or slit ventricle syndrome), 1 had previous chronic subdural hematoma, 15 had normal pressure hydrocephalus with final lumbar pressure <5 cm H2O after tap test (40 mL), 6 had pseudotumor cerebri, and 7 had hydrocephalus due to other causes. Clinical improvement was observed and sustained in 94.3% of the patients during the two-year period with no computed tomography (CT) evidence of hypo or overdrainage, and no immediate early or late significant complications.

Estudo prospectivo da sensibilidade tátil em mãos de uma população brasileira usando pressure-specified sensory device

OBJETIVO: Avaliar os limiares de percepção da pressão em polpas de dois dedos (indicador e mínimo), em uma população brasileira, sem lesão nervosa ou neuropatia. MÉTODOS: Usamos Pressure-Specified Sensory Device, um equipamento computadorizado para obter limiares de percepção da pressão normal, tanto estáticos quanto dinâmicos, e discriminação de dois pontos. RESULTADOS: Testamos a sensibilidade nos dedos, em 30 voluntários. Os testes de significância foram realizados utilizando o teste t de Student. Os valores médios (g/mm²) para os limiares de pressão estática de um e dois pontos (s1PD, s2PD) e discriminação dinâmica de um e dois pontos (m1PD, m2PD) no dedo indicador dominante foram: s1PD = 0,4, m1PD = 0,4, s2PD = 0,48, m2PD = 0,51. CONCLUSÃO: Não há diferença significativa na sensibilidade entre as mãos dominante e não dominante.