Random frog: An efficient reversible jump Markov Chain Monte Carlo-like approach for variable selection with applications to gene selection and disease classification

The identification of disease-relevant genes represents a challenge in microarray-based disease diagnosis where the sample size is often limited. Among established methods, reversible jump Markov Chain Monte Carlo (RJMCMC) methods have proven to be quite promising for variable selection. However, the design and application of an RJMCMC algorithm requires, for example, special criteria for prior distributions. Also, the simulation from joint posterior distributions of models is computationally extensive, and may even be mathematically intractable. These disadvantages may limit the applications of RJMCMC algorithms. Therefore, the development of algorithms that possess the advantages of RJMCMC methods and are also efficient and easy to follow for selecting disease-associated genes is required. Here we report a RJMCMC-like method, called random frog that possesses the advantages of RJMCMC methods and is much easier to implement. Using the colon and the estrogen gene expression datasets, we show that random frog is effective in identifying discriminating genes. The top 2 ranked genes for colon and estrogen are Z50753, U00968, and Y10871_at, Z22536_at, respectively. (The source codes with GNU General Public License Version 2.0 are freely available to non-commercial users at: http://code.google.com/p/randomfrog/.)     

Exhaled breath condensate: Determination of non-volatile compounds and their potential for clinical diagnosis and monitoring. A review

Exhaled breath condensate is a promising, non-invasive, diagnostic sample obtained by condensation of exhaled breath. Starting from a historical perspective of early attempts of breath testing towards the contemporary state-of-the-art breath analysis, this review article focuses mainly on the progress in determination of non-volatile compounds in exhaled breath condensate. The mechanisms by which the aerosols/droplets of non-volatile compounds are formed in the airways are discussed with methodological consequences for sampling. Dilution of respiratory droplets is a major problem for correct clinical interpretation of the measured data and there is an urgent need for standardization of EBC. This applies also for collection instrumentation and therefore various commercial and in-house built devices are described and compared with regard to their design, function and collection parameters. The analytical techniques and methods for determination of non-volatile compounds as potential markers of oxidative stress and lung inflammation are scrutinized with an emphasis on method suitability, sensitivity and appropriateness. The relevance of clinical findings for each group of possible non-volatile markers of selected pulmonary diseases and methodological recommendations with emphasis on interdisciplinary collaboration that is essential for future development into a fully validated clinical diagnostic tool are given.     

A rapid UPLC‐MS/MS method for the determination of oleanolic acid in rat plasma and liver tissue: application to plasma and liver pharmacokinetics

A reliable high‐throughput ultra‐high performance liquid chromatography–tandem mass spectrometry (UPLC‐MS/MS) method was developed and validated for oleanolic acid (OA) determination in rat plasma and liver tissue using glycyrrhetic acid as the internal standard (IS). Plasma and liver homogenate samples were prepared using solid‐phase extraction. Chromatographic separation was achieved on a C₁₈ column using an isocratic mobile phase system. The detection was performed by multiple reaction monitoring mode via positive electrospray ionization interface. The calibration curves showed good linearity (R² > 0.9997) within the tested concentration ranges. The lower limit of quantification for plasma and liver tissue was ≤0.75 ng/mL. The intra‐ and inter‐day precision and accuracy deviations were within ±15% in plasma and liver tissue. The mean extraction recoveries ranged from 80.8 to 87.0%. In addition, the carryover, matrix effect, stability and robustness involved in the method were also validated. The method was successfully applied to the plasma and hepatic pharmacokinetics of OA after oral administration to rats. Copyright © 2015 John Wiley & Sons, Ltd.     

Studies on oral bioavailability and first‐pass metabolism of withaferin A in rats using LC–MS/MS and Q‐TRAP

Withaferin A (WA) is one of the major bioactive steroidal lactones with extensive pharmacological activities present in the plant Withania somnifera. The absolute oral bioavailability of WA remains unknown and human‐related in vitro data are not available. Therefore, in the present study, the absolute oral bioavailability of WA in male rats and the in vitro screening of absorption factors by Q‐trap and LC–MS/MS analysis were conducted to explore possible clinical properties of WA. The developed and validated analytical methods were successfully applied to the pharmacokinetic studies and in vitro measurement of WA. The oral bioavailability was determined to be 32.4 ± 4.8% based on intravenous (5 mg/kg) and oral (10 mg/kg) administrations of WA in male rats. The in vitro results showed that WA could be easily transported across Caco‐2 cells and WA did not show as a substrate for P‐glycoprotein. Moreover, the stability of WA was similar between male rat and human in simulated gastric fluid (stable), in intestinal microflora solution (slow decrease) and in liver microsomes (rapid depletion, with a half‐life of 5.6 min). As such, the first‐pass metabolism of WA was further verified by rat intestine‐liver in situ perfusion, revealing that WA rapidly decreased and 27.1% remained within 1 h, while the content of three major metabolites (M1, M4, M5) identified by Q‐trap increased. This perfusion result is consistent with the oral bioavailability results in vivo. The first‐pass metabolism of WA might be the main barrier in achieving good oral bioavailability in male rats and it is predicted to be similar in humans. This study may hold clinical significance.     

A Near-Infrared-Controllable Artificial Metalloprotease Used for Degrading Amyloid-β Monomers and Aggregates

Proteolysis of amyloid-β (Aβ) is a promising approach against Alzheimer's disease. However, it is not feasible to employ natural hydrolases directly because of their cumbersome preparation and purification, poor stability, and hazardous immunogenicity. Therefore, artificial enzymes have been developed as potential alternatives to natural hydrolases. Since specific cleavage sites of Aβ are usually embedded inside the β-sheet structures that restrict access by artificial enzymes, this strongly hinders their efficiency for practical applications. Herein, we construct a NIR (near-IR) controllable artificial metalloprotease (MoS₂-Co) using a molybdenum disulfide nanosheet (MoS₂) and a cobalt complex of 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid (Codota). Evidenced by detailed experimental and theoretical studies, the NIR-enhanced MoS₂-Co can circumvent the restriction by simultaneously inhibition of β-sheet formation and destroying β-sheet structures of the preformed Aβ aggregates in living cell. Furthermore, our designed MoS₂-Co is an easy to graft Aβ-target agent that prevents misdirected or undesirable hydrolysis reactions, and has been demonstrated to cross the blood brain barrier. This method can be adapted for hydrolysis of other kinds of amyloids.     

The impact of blood on liver metabolite profiling – a combined metabolomic and proteomic approach

Metabolomics has entered the well‐established omic sciences as it is an indispensable information resource to achieve a global picture of biological systems. The aim of the present study was to estimate the influence of blood removal from mice liver as part of sample preparation for metabolomic and proteomic studies. For this purpose, perfused mice liver tissue (i.e. with blood removed) and unperfused mice liver tissue (i.e. containing blood) were compared by two‐dimensional gas chromatography time of flight mass spectrometry (GC × GC‐TOFMS) for the metabolomic part, and by liquid chromatography tandem mass spectrometry (LC‐MS/MS) for the proteomic part. Our data showed significant differences between the unperfused and perfused liver tissue samples. Furthermore, we also observed an overlap of blood and tissue metabolite profiles in our data, suggesting that the perfusion of liver tissue prior to analysis is beneficial for an accurate metabolic profile of this organ. Copyright © 2013 John Wiley & Sons, Ltd.     

Rapid and sensitive ultra‐high‐pressure liquid chromatography method for quantification of antichagasic benznidazole in plasma: application in a preclinical pharmacokinetic study

Benznidazole (BNZ) and nifurtimox are the only drugs available for treating Chagas disease. In this work, we validated a bioanalytical method for the quantification of BNZ in plasma aimed at improving sensitivity and time of analysis compared with the assays already published. Furthermore, we demonstrated the application of the method in a preclinical pharmacokinetic study after administration of a single oral dose of BNZ in Wistar rats. A Waters® Acquity UHPLC system equipped with a UV–vis detector was employed. The method was established using an Acquity® UHPLC HSS SB C₁₈ protected by an Acquity® UHPLC HSS SB C₁₈ VanGuard guard column and detection at 324 nm_. The mobile phase consisted of ultrapure water–acetonitrile (65:35), and elution was isocratic. The mobile phase flow rate was 0.55 mL/min, the volume of injection was 1 μL, and the run time was just 2 min. The samples were kept at 25°C until injection and the column at 45°C for the chromatographic separation. The sample preparation was performed by a rapid protein precipitation with acetonitrile. The linear concentration range was 0.15–20 µg/mL. The pharmacokinetic parameters of BNZ in rats were determined and the method was considered sensitive, fast and suitable for application in pharmacokinetic studies. Copyright © 2014 John Wiley & Sons, Ltd.     

Investigation into the structural composition of hydroalcoholic solutions as basis for the development of multiple suppression pulse sequences for NMR measurement of alcoholic beverages

An eight‐fold suppression pulse sequence was recently developed to improve sensitivity in ¹H NMR measurements of alcoholic beverages [Magn. Res. Chem. 2011 (49): 734–739]. To ensure that only one combined hydroxyl peak from water and ethanol appears in the spectrum, adjustment to a certain range of ethanol concentrations was required. To explain this observation, the structure of water–ethanol solutions was studied. Hydroalcoholic solutions showed extreme behavior at 25% vol, 46% vol, and 83% vol ethanol according to ¹H NMR experiments. Near‐infrared spectroscopy confirmed the occurrence of four significant compounds (‘individual’ ethanol and water structures as well as two water–ethanol complexes of defined composition – 1 : 1 and 1 : 3). The successful multiple suppression can be achieved for every kind of alcoholic beverage with different alcoholic strengths, when the final ethanol concentration is adjusted to a range between 25% vol and 46% vol (e.g. using dilution or pure ethanol addition). In this optimum region, an individual ethanol peak was not detected, because the ‘individual’ water structure and the 1 : 1 ethanol–water complex predominate. The nature of molecular association in ethanol–water solutions is essential to elucidate NMR method development for measurement of alcoholic beverages. The presented approach can be used to optimize other NMR suppression protocols for binary water–organic solvent mixtures, where hydrogen bonding plays a dominant role. Copyright © 2014 John Wiley & Sons, Ltd.     

大斯托克斯位移远红光至近红外荧光探针用于检测肝损伤过程中过氧化亚硝酸盐的动态变化

肝损伤是影响公众健康的重大问题之一, 已经引起了人们越来越多的关注. 而过表达的过氧化亚硝酸盐(ONOO^?)在肝损伤等疾病的发病机制中起着重要作用, 被认为是一种与早期肝损伤密切相关的生物活性分子. 因此, 为了探究ONOO^?在肝损伤过程中的作用, 开发可以实现肝损伤过程中ONOO^?高选择性和实时检测的分析方法具有重要意义. 本文报道了一种具有大斯托克斯位移的远红光至近红外(FR-NIR)ONOO^?荧光探针. 由于该探针具有大的斯托克斯位移, 可以有效消除光谱重叠和自吸收的干扰, 从而显著提高成像的信噪比. 此外, 该探针对ONOO^?具有高的灵敏度(检出限为25.8 nmol/L)和良好的选择性, 被成功用于药物诱导肝损伤过程中ONOO^?信号的成像检测.     

刀锋伪影校正技术在精神疾病患者海马MRI检查中的应用

为探讨磁共振刀锋伪影校正（BLADE）技术提升精神疾病患者海马磁共振图像质量的效果，本文分别使用结合了BLADE技术的BLADE T₂WI TSE、BLADE T₂WI FLAIR及传统T₂WI TSE、T₂WI FLAIR四种序列，对47例精神疾病患者和美国放射学院（ACR）标准模体在3.0 T磁共振成像（MRI）设备上分别进行常规海马斜冠状位扫描和ACR标准检测.患者的磁共振图像由2名放射科医师采用5分法对运动伪影、搏动伪影、颗粒度、海马磁共振图像质量进行评价，并应用Wilcoxon符号秩检验进行数据分析.模体图像通过识别图像的钻孔阵列和轮辐的数目，半定量评价各序列的高对比空间分辨力（HCSR）和低对比物体探测能力（LCD）.结果表明相比传统序列，结合BLADE技术的序列能够明显改善海马磁共振图像的运动伪影、搏动伪影（p<0.001），提高图像质量（p<0.05）；但在图像颗粒度方面，传统序列表现更优（p<0.001）.ACR模体半定量分析显示，结合BLADE技术序列与传统序列相比，在LCD检测方面结果更优、在HCSR检测方面结果相同或略逊.本文推荐将BLADE技术应用于不合作的精神疾病患者海马的MRI检查.