Comparative evaluation of software for retention time alignment of gas chromatography/time-of-flight mass spectrometry-based metabonomic data

In chromatography-based metabonomic research, retention time (RT) alignment of chromatographic peaks poses a challenge for the accurate profiling of biomarkers. Although a number of RT alignment software has been reported, the performance of these software packages have not been comprehensively evaluated. This study aimed to evaluate the RT alignment accuracy of publicly available and commercial RT alignment software. Two gas chromatography/mass spectrometry (GC/MS) datasets acquired from a mixture of standard metabolites and human bladder cancer urine samples, were used to assess three publicly available software packages, MetAlign, MZmine and TagFinder, and two commercial applications comprising the Calibration feature and Statistical Compare of ChromaTOF software. The overall RT alignment accuracies in aligning standard compounds mixture were 93, 92, 74, 73 and 42% for Calibration feature, MZmine, MetAlign, Statistical Compare and TagFinder, respectively. Additionally, unique trends were observed for the individual software with regards to the different experimental conditions related to extent and direction of RT shifts. Conflicting performance was observed for human urine samples suggesting that RT misalignments still occurred despite the use of RT alignment software. While RT alignment remains an inevitable step in data preprocessing, metabonomic researchers are recommended to perform manual check on the RT alignment of important biomarkers as part of their validation process.     

Evaluation of comprehensive two-dimensional gas chromatography coupled to time-of-flight mass spectrometry for the diagnosis of inherited metabolic disorders using an automated data processing strategy

Organic acidurias are a large group of inherited metabolic disorders (IMDs), commonly diagnosed by GC-MS analysis of organic acids in urine after acidic extraction and trimethylsilylation. In this study, a GC×GC-ToF-MS method has been optimized for the analysis of pathological metabolites in urine. An automated data processing strategy based on the use of mass spectra and GC retention times for the target search and quantification of pathological metabolites has been developed. Using this procedure, each unknown sample is automatically examined for the presence of markers of several diseases at the same time. The method has been applied for the analysis of 6 challenging proficiency testing samples from patients with IMDs (thymidine phosphorylase deficiency, mevalonic aciduria, hawkinsinuria, aromatic l-amino acid decarboxylase deficiency, propionic acidemia and medium-chain acyl-CoA dehydrogenase deficiency). Using the GC×GC-ToF-MS method, we were able to determine complete sets of markers for all the IMDs. The quality of the mass spectral matches for the pathological markers was higher than 800 (out of 1000).     

Membrane chromatography: Protein purification from E. coli lysate using newly designed and commercial anion-exchange stationary phases

This contribution describes the purification of anthrax protective antigen (PA) protein from Escherichia coli lysate using bind-and-elute chromatography with newly designed weak anion-exchange membranes. Protein separation performance of the new AEX membrane adsorber was compared with the commercial Sartobind^® D membrane adsorber and HiTrap™ DEAE FF resin column under preparative scale conditions. Dynamic protein binding capacities of all three stationary phases were determined using breakthrough curve analysis. The AEX membrane showed higher binding capacities than the Sartobind^® D membrane at equivalent volumetric throughput and higher capacities than the HiTrap™ DEAE FF resin column at 15 times higher volumetric throughput. Anion-exchange chromatography was performed using all three stationary phases to purify PA protein. Quantitative SDS-PAGE analysis of effluent fractions showed that the purity of PA protein was higher for membrane adsorbers than the HiTrap™ DEAE FF resin column and was the same for the new AEX membrane and Sartobind^® D membrane adsorbers. The effects of E. coli lysate load volume and volumetric flow rate on PA protein separation resolution using the membrane adsorbers were minor, and the peak elution profile remained un-changed even under conditions where >75% of the total protein dynamic binding capacity of the membranes had been utilized. PA protein peak resolution was higher using pH-gradient elution than with ionic strength gradient elution. Overall, the results clearly demonstrate that membrane chromatography is a high-capacity, high-throughput, high-resolution separation technique, and that resolution in membrane chromatography can be higher than resin column chromatography under preparative conditions and at much higher volumetric throughput.     

Sub-wavelength and non-periodic holes array based fully lensless imager

We present a novel concept for microscopic imaging. The proposed microscope-like device does not include an objective lens neither a condenser. Instead, a metallic plate of sub-wavelength hole-array with a varying pitch is used to illuminate the inspected object that is mounted very close to it. As a result, the transmitted spectrum through each hole differs from the others and therefore, each spot of the detected object is illuminated with a unique spectrum. By measuring a single spectrum that is the sum of all the spectra that are transmitted through the sample and by using spectral decomposition algorithms, the spatial transmission pattern of the object can be extracted.     

The analysis of the error statistics in a 5 × 40 Gbit/s fibre link with hybrid amplification

We quantify the error statistics and patterning effects in a 5 × 40 Gbit/s WDM RZ-OOK SMF/DCF fibre link using hybrid Raman/EDFA amplification. By extensive use of a numerical model, we determine how the error statistics change with the transmission distance. This knowledge is used as a basis for a constrained coding technique in order to improve the transmission error rate. We propose an adaptive constrained code for mitigation of the patterning effects and demonstrate that this approach can substantially reduce the bit error rate (BER) even for very large values of the channel BER (BER > 10^− 1). The proposed technique can be used in combination with forward error correction schemes (FEC) to extend the range of channel BERs that an FEC scheme is effective over.     

Partially coherent optical processor for enhancement of partial second order derivatives of an image: Analysis and implementation

We present an optical processor capable to perform partial second derivatives of an image working with partially coherent illumination. The proposed system utilizes a liquid crystal display, onto which images to be derived are displayed. The method is based on the capacity of these devices to generate simultaneously a contrast reverted replica of the image displayed on it. A positive replica of original image is obtained when the LCD is between crossed polarizers, while the negative one is obtained with the LCD is between parallel polarizers. Since the LCD is a diffraction element, both polarizer arrangements may be simultaneously implemented, for example, in a 4f optical processor using polarization filtering of the different diffraction orders. When three images (two replicas of original image displaced in opposite direction and the other one with contrast reverted and centered at the origin.) are imagined across a slightly defocused plane, one obtains an image with enhanced second derivatives in a given direction. No other incoherent (or partially coherent) optical system is presently known which can perform partial second-order derivatives of an image. Experimental results obtained are presented.     

Experimental opto-digital synthesis of encrypted sub-samples of an image to improve its decoded quality

We develop an experimental protocol to visualize decrypted images that otherwise would have been barely recognizable, while keeping the standard security levels. This image deterioration is partly due to the natural speckle noise as well as the practical limitations arising from the optical elements composing the setup. This protocol is based on an optical image synthesis with digital holography using enlarged sub-samples of an entire image together with a multiplexing technique. We implement the process using a Mach-Zehnder interferometer with a joint transform correlator encrypting architecture. As a result, we get smaller speckle patterns on the final assembled image and a spatial frequency enhancement with respect to the decoded image obtained with the conventional procedures.     

宽光谱膜厚监控系统中光谱实时测量技术研究

 在宽光谱膜厚监控系统中,利用光栅光谱仪分光,线阵CCD接收,完成光谱的一次性快速扫描来控制膜层厚度,达到实时监控的要求。而系统光谱扫描的准确性,直接影响膜厚实时监控的有效性。为了得到准确的光谱信息,首先确定CCD像素和光波波长的对应关系,基于特征谱线的离散关系,采用最小二乘拟合法建立了光谱标定函数,经实验,标定波长均方根误差为0.037 nm;对于CCD实时输出的光谱监控信号,利用小波阈值优化算法抑制信号中的随机噪声,保留了光谱信号的细节成分,峰值误差的最大值为1.0%,峰位误差的最大值为0.3%,满足了监控中光谱分辨率的要求。     

Thermographic signal reconstruction for vibrothermography

Vibrothermography, also known as thermosonics or sonic infrared, is a method of nondestructive evaluation that finds cracks or delaminations from the heat given off in response to vibration. In vibrothermography, finding cracks requires identifying and localizing pulsed surface and subsurface heat sources from a time sequence of infrared images. Traditionally this identification involves manually stepping through and studying the images. Careful observation of the heating and subsequent cooling is needed to distinguish cracks from false indications. In this paper, we present an algorithm that reduces the entire time sequence to a single static plot. The plot uses only a few coefficients per pixel to reconstruct the original sequence; this is possible because the reduction is based on a physical model. As an added bonus, the algorithm reduces noise and improves sensitivity. A single false-color image summarizes all the information from the entire sequence, simplifying the task of identifying cracks.