[Application of wavelet transform and neural network in the near-infrared spectrum analysis of oil shale].

In the present study, an innovative method is proposed, employing both wavelet transform and neural network, to analyze the near-infrared spectrum data in oil shale survey. The method entails using db8 wavelet at 3 levels decomposition to process raw data, using the transformed data as the input matrix, and creating the model through neural network. To verify the validity of the method, this study analyzes 30 synthesized oil shale samples, in which 20 samples are randomly selected for network training, the other 10 for model prediction, and uses the full spectrum and the wavelet transformed spectrum to carry out 10 network models, respectively. Results show that the mean speed of the full spectrum neural network modeling is 570.33 seconds, and the predicted residual sum of squares (PRESS) and correlation coefficient of prediction are 0.006 012 and 0.843 75, respectively. In contrast, the mean speed of the wavelet network modeling method is 3.15 seconds, and the mean PRESS and correlation coefficient of prediction are 0.002 048 and 0.953 19, respectively. These results demonstrate that the wavelet neural network modeling method is significantly superior to the full spectrum neural network modeling method. This study not only provides a new method for more efficient and accurate detection of the oil content of oil shale, but also indicates the potential for applying wavelet transform and neutral network in broad near-infrared spectrum analysis.

A quantitative assay to detect α-thalassemia deletions and triplications using multiplex nested real-time quantitative polymerase chain reaction.

Increasing evidence indicates that copy number variants (CNVs) have great relevance to common human diseases. In α-thalassemia, clinical phenotypes are related to genotypes, specifically copy number changes in the human α-globin gene cluster. Assays are available for high-throughput screening of unknown CNVs genome-wide and also for targeted CNV genotyping at loci associated with genetic disorders. Here we describe a universal quantitative approach based on nested real-time quantitative polymerase chain reaction for accurate determination of copy numbers at multiple particular gene loci. We used the α-globin gene as a model system, obtaining the reproducibility and sensitivity to analyze different gene copies and testing 95 DNA samples with 16 different known genotypes. Our results showed that this approach has high sensitivity and low standard deviations for correctly genotyping DNA samples containing different copy numbers of the α1 and α2 globin genes. Our method is rapid, simple, and reliable, and it could be used to simultaneously screen for α-thalassemia deletions or triplications. Moreover, it has potential as a versatile technology for the rapid genotyping of known CNVs in a targeted region.

Fluid pumping by liquid metal droplet utilizing ac electric field.

We report a unique phenomenon in which liquid metal droplets (LMDs) under a pure ac electric field pump fluid. Unlike the directional pumping that occurs upon reversing the electric field polarity under a dc signal, this phenomenon allows the direction of fluid motion to be switched by simply shifting the position of the LMD within the cylindrical chamber. The physical mechanism behind this phenomenon has been termed Marangoni flow, caused by nonlinear electrocapillary stress. Under the influence of a localized, asymmetric ac electric field, the polarizable surface of the position-offset LMD produces a net time-averaged interfacial tension gradient that scales with twice the field strength, and thus pumps fluid unidirectionally. However, the traditional linear RC circuit polarization model of the LMD/electrolyte interface fails to capture the correct pump-flow direction when the thickness of the LMD oxide skin is non-negligible compared to the Debye length. Therefore, we developed a physical description by treating the oxide layer as a distributed capacitance with variable thickness and connected with the electric double layer. The flow profile is visualized via microparticle imaging velocimetry, and excellent consistency is found with simulation results obtained from the proposed nonlinear model. Furthermore, we investigate the effects of relevant parameters on fluid pumping and discuss a special phenomenon that does not exist in dc control systems. To our knowledge, no previous work addresses LMDs in this manner and uses a zero-mean ac electric field to achieve stable, adjustable directional pumping of a low-conductivity solution.

Homogeneous label-free genotyping of single nucleotide polymorphism using ligation-mediated strand displacement amplification with DNAzyme-based chemiluminescence detection.

Genotyping of single nucleotide polymorphisms (SNPs) is a central challenge in disease diagnostics and personalized medicine. A novel label-free homogeneous SNP genotyping technique is developed on the basis of ligation-mediated strand displacement amplification (SDA) with DNAzyme-based chemiluminescence detection. Discrimination of single-base mismatches is first accomplished using DNA ligase to generate a ligation product between a discriminant probe and a common probe. The ligated product then initiates two consecutive SDA reactions to produce a great abundance of aptamer sequences against hemin, which can be probed by chemiluminscence detection. The developed strategy is demonstrated using a model SNP target of cytochrome P450 monooxygenase CYP2C19*2, a molecular marker for personalized medicines. The results reveal that the developed technique displays superb selectivity in discriminating single-base mismatches, very low detection limit as low as 0.1 fM, a wide dynamic range from 1 fM to 1 nM, and a high signal-to-background ratio of 150. Due to its label-free, homogeneous, and chemiluminescence-based detection format, this technique can be greatly robust, cost-efficient, readily automated, and scalable for parallel assays of hundreds of samples. The developed genotyping strategy might provide a robust, highly sensitive, and specific genotyping platform for genetic analysis and molecular diagnostics.

Rapid, accurate detection of TMPRSS6 gene causative mutations with a high-resolution melting assay.

Mutations of the TMPRSS6 gene are considered the major genetic factors for iron-refractory iron deficiency anemia (IRIDA). Artificial clone libraries containing 17 known mutations of the TMPRSS6 gene were used to develop a high-resolution melting (HRM) assay for the detection of 17 TMPRSS6 gene mutations. The melting temperatures and melting curves were able to distinguish the different genotypes of the 17 TMPRSS6 gene mutations. We used replicate experiments to evaluate the reproducibility of the assay, and the coefficients of variation were in the range 0.0091% to 0.0873%. A total of 145 Chinese patients with IDA were screened with this assay and no TMPRSS6 gene causative mutation was found in any patient. The HRM assay was proved to be rapid, accurate and cost-effective method to identify the TMPRSS6 gene mutations and can be used in the clinical diagnosis of IRIDA.

[Non-invasive prenatal genetic diagnosis using multiple displacement amplification].

OBJECTIVE: To investigate the feasibility of multiple displacement amplification (MDA) to apply in the non-invasive prenatal genetic diagnosis of Duchenne muscular dystrophy (DMD). METHODS: Maternal blood was obtained from 20 pregnant women at 7 to 25 weeks of gestation. After the discontinuous density gradient centrifugation with Percoll, the fetal nucleated red blood cells (NRBCs) were stained with Kleihauer test. All positive NRBCs were collected by micromanipulator and then performed with MDA. Sex and short tandern repeat (STR) analysis were determind from a small aliquot of the reaction. The origin of NRBCs was verified and prenatal diagnosis of DMD was made at the same time. RESULTS: The product length of MDA was >15 kb, while primer extension preamplification (PEP) is only about 1 kb. We completed non-invasive prenatal genetic diagnosis of 6 fetus at high risk of DMD using MDA. The results were all coincident with amniotic fluid control. CONCLUSION: The MDA method which provides a highly uniform representation across the genome, representing the entire genome with minimal amplification bias, shows good application prospects.

[Detection of fetal nucleated red blood cells in the maternal circulation by Kleihauer test].

Maternal blood was obtained from 18 pregnant women at 7 to 25 weeks of gestation. After Percoll discontinuous density gradient centifugation, the fetal nucleated red blood cells (NRBCs) were stained with Kleihauer test. Positive fetal cells appeared with an intense red cytoplasmic staining while maternal cells with adult haemoglobin were colourless. Individual positive NRBC was collected by micromanipulator and whole genome amplification was then performed to determine sex and STR status. This allowed the simultaneous verification of the fetal origin of NRBC and prenatal diagnosis of genetic diseases. The non-invasive prenatal genetic diagnosis of 9 fetuses at high risk of Duchenne muscular dystrophy (DMD) was completed successfully. The Kleihauer test is a rapid, simple and direct chemical staining method to select fetal cells and can be applied in prenatal diagnosis.