A machine learning approach for genome-wide prediction of morbid and druggable human genes based on systems-level data

Background: The genome-wide identification of both morbid genes, i.e., those genes whose mutations cause hereditary human diseases, and druggable genes, i.e., genes coding for proteins whose modulation by small molecules elicits phenotypic effects, requires experimental approaches that are time-consuming and laborious. Thus, a computational approach which could accurately predict such genes on a genome-wide scale would be invaluable for accelerating the pace of discovery of causal relationships between genes and diseases as well as the determination of druggability of gene products.Results: In this paper we propose a machine learning-based computational approach to predict morbid and druggable genes on a genome-wide scale. For this purpose, we constructed a decision tree-based meta-classifier and trained it on datasets containing, for each morbid and druggable gene, network topological features, tissue expression profile and subcellular localization data as learning attributes. This meta-classifier correctly recovered 65% of known morbid genes with a precision of 66% and correctly recovered 78% of known druggable genes with a precision of 75%. It was than used to assign morbidity and druggability scores to genes not known to be morbid and druggable and we showed a good match between these scores and literature data. Finally, we generated decision trees by training the J48 algorithm on the morbidity and druggability datasets to discover cellular rules for morbidity and druggability and, among the rules, we found that the number of regulating transcription factors and plasma membrane localization are the most important factors to morbidity and druggability, respectively.Conclusions: We were able to demonstrate that network topological features along with tissue expression profile and subcellular localization can reliably predict human morbid and druggable genes on a genome-wide scale. Moreover, by constructing decision trees based on these data, we could discover cellular rules governing morbidity and druggability.

Determination of labile barium in petroleum-produced formation water using paper-based DGT samplers

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Synthesis of Fine Micro-sized BaZrO3 Powders Based on a Decaoctahedron Shape by the Microwave-Assisted Hydrothermal Method

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Investigations on the stability of plasma modified silicone surfaces

In this work it was investigated the effect of the exposure to different plasmas on the wettability of silicone samples. We have observed that oxygen. argon, and hydrogen glow discharges are quite effective in reducing the water contact angle of such polymer. However, indifferently to efficiency of the treatment, practically all the modified surfaces recovered great part of their original hydrophobicity. We have investigated this hydrophobic recovery using surface energy measurements and theoretical simulations based on the exponential decay of the population of polar groups on the surface. According to our results such recovery can be attributed to the decrease of polar species at the interface water-polymer surface.

On-line determination of Sb(III) and total Sb using baker's yeast immobilized on polyurethane foam and hydride generation inductively coupled plasma optical emission spectrometry

The yeast Saccharomyces cerevisiae was immobilized in cubes of polyurethane foam and the ability of this immobilized material to separate Sb(III) and Sb(V) was investigated. A method based on sequential determination of total Sb (after on-line reduction of Sb(V) to Sb(III) with thiourea) and Sb(Ill) (after on-line solid-liquid phase extraction) by hydride generation inductively coupled plasma optical emission spectrometry is proposed. A flow system assembled with solenoid valves was used to manage all stages of the process. The effects of pH, sample loading and elution flow rates on solid-liquid phase extraction of Sb(III) were evaluated. Also, the parameters related to online pre-reduction (reaction coil and flow rates) were optimized. Detection limits of 0.8 and 0.15 mu g L-1 were obtained for total Sb and Sb (III), respectively. The proposed method was applied to the analysis of river water and effluent samples. The results obtained for the determination of total Sb were in agreement with expected values, including the river water Standard Reference Material 1640 certified by the National Institute of Standards and Technology (NIST). Recoveries of Sb(III) and Sb(V) in spiked samples were between 81 19 and I I I 15% when 120 s of sample loading were used. (c) 2006 Elsevier B.V. All rights reserved.

Speciation analysis of Sn(II) and Sn(IV) using baker's yeast and inductively coupled plasma optical emission spectrometry

The use of Saccharomyces cerevisiae as a substrate to selectively retain Sn(II) and Sn(IV) has been investigated. Several factors affecting the retention of the analytes by yeast, such as pH, amount of biomass, temperature and time of contact were evaluated. Based on this study, a method for determination of Sn(II) and Sn(IV) combining inductively coupled plasma optical emission spectrometry (ICP OES) and solid phase extraction using Saccharomyces cerevisiae is proposed. The procedure consists of the selective retention of Sn(IV) by yeast at pH = 2.0 while Sn(II) remains in solution. Determination of tin in the solid phase was easily carried out by submitting a slurry of the yeast (0.5 g/40 mL) directly to ICP OES. The precision of the extraction procedure was characterized by an RSD lower than 4%. The detection limits of tin (3 sigma) in the solid phase and the liquid phase were 1.1 and 0.7 mu g L-1, respectively. The proposed approach was evaluated for determination of Sn(II) and Sn(IV) in spiked river water and real samples of industrial waste water (untreated and treated). For all samples, recoveries of spiked Sn(II) and Sn(IV) were between 85 and 112%.

Measurements of gunshot residues by sector field inductively coupled plasma mass spectrometry - Further studies with pistols

The most popular handgun in Brazil is the single round-barrel caliber 0.38 revolver. In recent years, however, owing to the modernization of police arms and their availability on the legal and illicit markets, pistols have become increasingly popular and currently represent about 20% of police seizures. In a previous paper we presented a novel collection method for gunshot residues (GSR) using a sampling procedure based on ethylenediamine-tetraacetic acid (EDTA) solution as a complexing agent on moistened swabs with subsequent detection using sector field-high resolution-inductively coupled plasma-mass spectrometry (SF-HR-ICP-MS). In the present paper, we discuss the capability of this methodology to identify antimony (Sb), barium (Ba) and lead (Pb) on the hands of volunteers after shot tests with 9 mm and 0.40 in. caliber pistols. Two types of munitions were tested: 9 mm Taurus and clean range. The use of a technique with high sensitivity, such as SF-HR-ICP-MS, permits the identification of low concentrations (less than 1 mu g/L) of metals in firearm residue and constitutes a powerful tool in forensic science. We also discuss the importance of the sampling procedure, including collection from a different body part than the gun hand of the suspect. Comparison of the analytical data obtained allows clear discrimination between samples from the hands of shooters and non-shooters. (C) 2007 Elsevier B.V.. All rights reserved.

Infrared spectroscopy investigation of various plasma-deposited polymer films irradiated with 170 keV He+ ions

This work illustrates the advantages of using p-polarized radiation at an incidence angle of 70 degrees in contrast to the conventional unpolarized beam at normal (or near-normal) incidence for the infrared spectroscopic study of polycarbosilane, polysilazane and polysiloxane thin films synthesized by plasma enhanced chemical vapor deposition (PECVD) and subsequently irradiated with 170 keV He+ ions at fluences from 1 x 10(14) to 1 x 10(16) cm(-2). Several bands not seen using the conventional mode could be observed in the polarized mode. (c) 2006 Elsevier B.V. All rights reserved.

Analysis of cement slurries by inductively coupled plasma optical emission spectrometry with axial viewing

The feasibility of Portland cement analysis by introduction of slurries in an inductively coupled plasma optical emission spectrometer (ICP-OES) with axial viewing has been evaluated. After a fast manual grinding of the cement samples, owing to the pulverized state of this material, 0.1% m/v slurries were prepared in 1% v/v HCl. The calibration was performed adopting two strategies: one based on slurries prepared from different masses (50, 75, 100 and 125 mg) of a Portland cement standard reference material (NIST SRM 1881), and the other one based on aqueous reference solutions. A complete analysis of cement for major (Al, Ca, Fe, Mg and Si), minor and trace elements (Mn, P, S, Sr and Ti) was accomplished. Both strategies led to accurate results for commercial Portland cement samples, except for Si and Ti. for which the calibration with aqueous reference solutions resulted in low values. Applying a paired t-test it was shown that most results were in agreement at a 95% confidence level with a conventional fusion decomposition procedure. The ICP-OES with axial viewing and end-on gas configuration for removal of the recombination plasma zone was effective for cement slurry analysis without any undesirable particle deposition in the pre-optics interface and without severe spectral interferences. (C) 2002 Elsevier B.V. B.V. All rights reserved.

A Simple Method Based on ICP-MS for Estimation of Background Levels of Arsenic, Cadmium, Copper, Manganese, Nickel, Lead, and Selenium in Blood of the Brazilian Population

Throughout the world, biomonitoring has become the standard for assessing exposure of individuals to toxic elements as well as for responding to serious environmental public health problems. However, extensive biomonitoring surveys require rapid and simple analytical methods. Thus, a simple and high-throughput method is proposed for the determination of arsenic (As), cadmium (Cd), copper (Cu), manganese (Mn), nickel (Ni), lead (Pb), and selenium (Se) in blood samples by using inductively coupled plasma-mass spectrometry (ICP-MS). Prior to analysis, 200 l of blood samples was mixed with 500 l of 10% v/v tetramethylammonium hydroxide (TMAH) solution, incubated for 10 min, and subsequently diluted to 10 ml with a solution containing 0.05% w/v ethylenediamine tetraacetic acid (EDTA) + 0.005% v/v Triton X-100. After that, samples were directly analyzed by ICP-MS (ELAN DRC II). Rhodium was selected as an internal standard with matrix-matching calibration. Method detection limits were 0.08, 0.04, 0.5, 0.09, 0.12, 0.04, and 0.1 g//L for As, Cd, Cu, Mn, Ni, Pb, and Se, respectively. Validation data are provided based on the analysis of blood samples from the trace elements inter-\comparison program operated by the Institut National de Sante Publique du Quebec, Canada. Additional validation was provided by the analysis of human blood samples by the proposed method and by using electrothermal atomic absorption spectrometry (ETAAS). The method was subsequently applied for the estimation of background metal blood values in the Brazilian population. In general, the mean concentrations of As, Cd, Cu, Mn, Ni, Pb, and Se in blood were 1.1, 0.4, 890, 9.6, 2.1, 65.4, and 89.3 g/L, respectively, and are in agreement with other global populations. Influences of age, gender, smoking habits, alcohol consumption, and geographical variation on the values were also considered. Smoking habits influenced the levels of Cd in blood. The levels of Cu, Mn, and Pb were significantly correlated with gender, whereas Cu and Pb were significantly correlated with age. There were also interesting differences in Mn and Se levels in the population living in the north of Brazil compared to the south.

Direct analysis of biodiesel microemulsions using an inductively coupled plasma mass spectrometry

An analytical procedure for direct introduction of biodiesel samples into an inductively coupled plasma mass spectrometer (ICP-MS) by using microemulsion for sample preparation was developed here. Cadmium, Co, Cu, Mn, Ni, Pb, Ti, and Zn were determined in biodiesel microemulsified samples prepared from different oleaginous sources (African palm, castor beans, palm, soybeans and an unknown oleaginous). Microemulsions were prepared using 0.25 mL Triton X-100, 0.25 mL 20% v v(-1) HNO(3), 0.50 mL biodiesel sample and 4.0 mL n-propanol. Argon-oxygen mixture was added to the plasma as auxiliary gas for correcting matrix effects caused by the high carbon load due to biodiesel microemulsions. The oxygen gas flow rate was set in 37.5 mL min(-1). The accuracy of the developed procedure was evaluated by applying addition-recovery experiments for biodiesel samples from different sources. Recoveries varied from 76.5 to 116.2% for all analytes but Zn in castor beans biodiesel sample (65.0 to 76.2%). Recoveries lower than 86.6% were obtained for palm biodiesel sample, probably due to matrix effects. Detection limits calculated by using oxygen in the composition of the auxiliary gas added to the plasma were higher than those calculated without using it, probably due to the highest formation of oxides. Despite oxides formation, best analytical performance was reached by using oxygen as auxiliary gas and by proper correction of transport interferences. The developed procedure based on microemulsion formation was suitable for direct introduction of biodiesel samples in ICP-MS. (C) 2010 Elsevier B.V. All rights reserved.

The workload and plasma ion concentration in a training match session of high-goal (elite) polo ponies

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Determinação de cetamina em plasma por HPLC: Aplicação em um estudo de farmacocinética de associação medicamentosa em cães

A S(+) cetamina é um fármaco amplamente utilizado na medicina para induzir anestesia e a associação com midazolam é empregada para minimizar seus efeitos adversos. Associações medicamentosas podem resultar em interações farmacocinéticas e a disponibilidade de métodos bioanalíticos para a determinação da cetamina em plasma constitui ferramenta útil para a avaliação do perfil cinético do fármaco administrado isoladamente ou em associação. O presente estudo teve como objetivo o desenvolvimento e validação de um método analítico para determinação da cetamina em plasma por cromatografia líquida de alta eficiência (HPLC) e a investigação do perfil farmacocinético da cetamina em quatro cães hígidos da raça Beagle. A S(+) cetamina (10mg/kg) foi administrada pela veia cefálica em dose única isoladamente (protocolo I) ou associada ao midazolam (0.2mg/kg) (protocolo II) em estudo cruzado com intervalo de uma semana para washout. Amostras seriadas de sangue foram coletadas no intervalo de oito horas e analisadas por HPLC para a avaliação do perfil farmacocinético utilizando modelo bicompartimental. O método bioanalítico apresentou limites de confiança aceitáveis para sua aplicação em estudos de farmacocinética e os parâmetros área sob a curva (ASC0-8), volume de distribuição (Vd), clearance total (Clt), meia vida de eliminação (t/12 ß), constante de eliminação (ß), meia vida de distribuição (t1/2α) e constante de distribuição (α) não mostraram diferenças estatísticas significativas entre os grupos (p < 0.05, Wilcoxon). Os resultados obtidos sugerem que a redução dos efeitos colaterais da cetamina decorrente do uso da associação cetamina-midazolam não está relacionada a alterações no perfil farmacocinético da cetamina.

A human retrieval study of plasma-sprayed hydroxyapatite-coated plateau root form implants after 2 months to 13 years in function

Calcium phosphate-based bioactive ceramics in various physical and chemical formulations have been extensively utilized as biomaterials for bone regeneration/conduction. However, the determination of their in vivo temporal behavior from the short to long term in humans has been a challenge due to the lack of physical reference for morphologic and morphometric evaluation. The present study evaluated bone morphology and morphometry (bone-to-implant contact [BIC]) around plasma-sprayed hydroxyapatite (PSHA)-coated endosseous implants that were retrieved due to prosthetic reasons while successfully in function at the posterior region of the jaws from as early as 2 months to ~13 years after a 6-month healing period after placement. Bone morphology was evaluated by light microscopy, and BIC was determined using computer software. Irrespective of the time in vivo, lamellar bone was observed in close contact with the implant PSHA-coated surface and between plateaus. BIC ranged from ~35-95%, was highly directional, and Haversian-like osteonic morphology between plateaus was observed for most implants. The PSHA coating was present with little variation in thickness between the samples retrieved regardless of time in vivo. © 2010 by Begell House, Inc.

Plasma treatment maintains surface energy of the implant surface and enhances osseointegration

The surface energy of the implant surface has an impact on osseointegration. In this study, 2 surfaces: nonwashed resorbable blasting media (NWRBM; control) and Ar-based nonthermal plasma 30 days (Plasma 30 days; experimental), were investigated with a focus on the surface energy. The surface energy was characterized by the Owens-Wendt-Rabel-Kaelble method and the chemistry by X-ray photoelectron spectroscopy (XPS). Five adult beagle dogs received 8 implants (n = 2 per surface, per tibia). After 2 weeks, the animals were euthanized, and half of the implants (n = 20) were removal torqued and the other half were histologically processed (n = 20). The bone-to-implant contact (BIC) and bone area fraction occupancy (BAFO) were evaluated on the histologic sections. The XPS analysis showed peaks of C, Ca, O, and P for the control and experimental surfaces. While no significant difference was observed for BIC parameter (P > 0.75), a higher level for torque (P < 0.02) and BAFO parameter (P < 0.01) was observed for the experimental group. The surface elemental chemistry was modified by the plasma and lasted for 30 days after treatment resulting in improved biomechanical fixation and bone formation at 2 weeks compared to the control group. © 2013 Fernando P. S. Guastaldi et al.