A template matching model for pattern recognition: Self-organization of templates and template matching by a disinhibitory neural network

A template matching model for pattern recognition is proposed. By following a previouslyproposed algorithm for synaptic modification (Hirai, 1980), the template of a stimulus pattern is selforganized as a spatial distribution pattern of matured synapses on the cells receiving modifiable synapses. Template matching is performed by the disinhibitory neural network cascaded beyond the neural layer composed of the cells receiving the modifiable synapses. The performance of the model has been simulated on a digital computer. After repetitive presentations of a stimulus pattern, a cell receiving the modifiable synapses comes to have the template of that pattern. And the cell in the latter layer of the disinhibitory bitory neural network that receives the disinhibitory input from that cell becomes electively sensitive to that pattern. Learning patterns are not restricted by previously learned ones. They can be subset or superset patterns of the ones previously learned. If an unknown pattern is presented to the model, no cell beyond the disinhibitory neural network will respond. However, if previously learned patterns are embedded in that pattern, the cells which have the templates of those patterns respond and are assumed to transmit the information to higher center. The computer simulation also shows that the model can organize a clean template under a noisy environment.     

A combinatorial synthesis of tyrphostins via the "directed sorting" method

Using solid-phase organic synthesis, we have prepared a 432-member (18 x 8 x 3) sample library based on the AG 490 "tyrphostin" template. By utilizing 432 reactors each equipped with a unique radiofrequency memory ID tag, the 432 products could be obtained as discrete entities (i.e., not as mixtures) via 18 + 8 + 3, or 29 reactions. Reading each ID tag after each reaction step permitted the "directed sorting" of reactors into appropriate reaction vessels containing multiple reactors. After synthesis, all products were cleaved from the solid-phase support and lyophilized to afford powders. Characterization of 5% of the library members by NMR and mass spectrometry provided verification of structure. In addition, TLC analysis of every library member provided evidence that most (or all) are composed of a single major organic compound. Some 88% of these samples were obtained in amounts of between 5 and 19 mg. Using this reaction sequence and the "directed sorting" approach, the synthesis of much larger AG 490-based libraries can be envisioned.     

Template matching as a tool for annotation of tomograms of stained biological structures

In recent years, electron tomography has improved our three-dimensional (3D) insight in the structural architecture of cells and organelles. For studies that involve the 3D imaging of stained sections, manual annotation of tomographic data has been an important method to help understand the overall 3D morphology of cellular compartments. Here, we postulate that template matching can provide a tool for more objective annotation and contouring of cellular structures. Also, this technique can extract information hitherto unharvested in tomographic studies. To evaluate the performance of template matching on tomograms of stained sections, we generated several templates representing a piece of microtubule or patches of membranes of different staining-thicknesses. These templates were matched to tomograms of stained electron microscopy sections. Both microtubules and ER-Golgi membranes could be detected using this method. By matching cuboids of different thicknesses, we were able to distinguish between coated and non-coated endosomal membrane-domains. Finally, heterogeneity in staining-thickness of endosomes could be observed. Template matching can be a useful addition to existing annotation-methods, and provide additional insights in cellular architecture.     

Solid phase DNA sequencing using the biotin-avidin system.

A novel method for solid-phase DNA sequencing is described. A plasmid vector, pRIT27, has been designed to allow directional immobilization of double stranded plasmid to avidin agarose. The strategy involves enzymatic incorporation of 11-bio-dUTP into the plasmid and strand specific elution using alkali. The immobilized single stranded DNA is used as template for sequencing reactions and the resulting labelled oligonucleotides are eluted by alkali. The affinity gel containing the immobilized template is consecutively used for the four different dideoxy-nucleotide reactions. The solid-phase technique can be used for both primer specific or extension specific labelling. The possibility to use the system in automated DNA sequencing is discussed.     

表面肌电信号的下肢痉挛信号的特征分析与识别

脑卒中患者康复治疗中会引起下肢肌肉痉挛,这种现象给患者的康复训练过程带来极大的危害,因此能够在训练过程中识别痉挛并及时中断训练具有重要的实际意义。本研究通对下肢表面肌电信号的采集,采用基于形状的模版匹配法来识别痉挛信号,并以皮尔逊相关系数来分析表征下肢痉挛信号的相关性大小。分析结果表明,通过仿真验证了模版匹配法在个人痉挛信号识别中的准确性,显示了在泛用痉挛信号识别中的可行性。     

TMaCS: A hybrid template matching and classification system for partially-automated particle selection

Selection of particle images from electron micrographs presents a bottleneck in determining the structures of macromolecular assemblies by single particle electron cryomicroscopy (cryo-EM). The problem is particularly important when an experimentalist wants to improve the resolution of a 3D map by increasing by tens or hundreds of thousands of images the size of the dataset used for calculating the map. Although several existing methods for automatic particle image selection work well for large protein complexes that produce high-contrast images, it is well known in the cryo-EM community that small complexes that give low-contrast images are often refractory to existing automated particle image selection schemes. Here we develop a method for partially-automated particle image selection when an initial 3D map of the protein under investigation is already available. Candidate particle images are selected from micrographs by template matching with template images derived from projections of the existing 3D map. The candidate particle images are then used to train a support vector machine, which classifies the candidates as particle images or non-particle images. In a final step in the analysis, the selected particle images are subjected to projection matching against the initial 3D map, with the correlation coefficient between the particle image and the best matching map projection used to assess the reliability of the particle image. We show that this approach is able to rapidly select particle images from micrographs of a rotary ATPase, a type of membrane protein complex involved in many aspects of biology.     

Enzymatic assay for deoxyribonucleoside triphosphates using synthetic oligonucleotides as template primers

The enzymatic assay for deoxyribonucleoside triphosphates has been improved by using synthetic oligonucleotides of a carefully defined sequence as template primers for DNA polymerase. High backgrounds, which limit the sensitivity of the assay when calf thymus DNA or alternating copolymers are used as template primers, were eliminated with these oligonucleotide template primers. Sensitivity was further increased by designing the template primer to incorporate multiple labeled deoxyribonucleotides per limiting unlabeled deoxyribonucleotide. Each of several DNA polymerases exhibited unique reaction characteristics with the oligonucleotide template primers, which was attributed to the differing exonuclease activities associated with these various enzymes. Assay optimization therefore included matching the polymerase with the template primer to obtain the lowest background reaction and highest sensitivity. This modified assay is particularly well suited for keeping cell sample size to a minimum in experimental protocols which generate large numbers of data points or require careful timing of sampling. With this technique, we measured the levels of all four deoxyribonucleoside triphosphates in extracts from as few as 2 x 10(4) cultured cells.     

Application of template matching technique to particle detection in electron micrographs

Template matching together with the comprehensive theory of image formation in electron microscope provides an optimal (in Bayesian sense) tool for solving one of the outstanding problems in single particle analysis, i.e., automatic selection of particle views from noisy micrograph fields. The method is based on the assumption that the reference three-dimensional structure is known and that the relevant parameters of the model of the image formation process can be estimated. In the first stage of the procedure, a set of possible particle views is generated using the available reference structure. The template images are constructed as linear combinations of available particle views using a clustering technique. Next, the micrograph noise characteristic is established using an automated contrast transfer function (CTF) estimation procedure. Finally, the CTF parameters calculated are used to construct a matched filter and correlation functions corresponding to the available template images are calculated. In order to alleviate the problem of the biased caused by varying image formation conditions, a decision making strategy based on the predicted distribution of correlation coefficients is proposed. It is demonstrated that due to the inclusion of CTF considerations, the template matching method performed very well in a broad range of microscopy conditions.     

A program for template matching of protein sequences

The matching of a template to a protein sequence is simplifiedby treating it as a special case of sequence alignment. Restrictionof the distances between motifs in the template controls againstspurious matches within very long sequences. The program usingthis algorithm is fast enough to be used in scanning large databasesfor sequences matching a complex template. Received on August 17, 1987; accepted on January 11, 1988     

Nanostructured conducting molecularly imprinted polymer for selective uptake/release of naproxen by the electrochemically controlled sorbent

A conducting molecularly imprinted polymer (CMIP) film, based on polypyrrole, was electrosynthesized for selective uptake/release and determination of naproxen. The film was prepared by incorporation of a template anion (naproxen) during the electropolymerization of pyrrole into a platinum electrode using the cyclic voltammetry method. Overoxidized polypyrrole films with cavities complementary to the template were used as a potential-induced selective recognition element in the solid-phase sorbent. Various important fabricating factors, which control the performance of the CMIP film, were investigated using fluorescence spectroscopy. The measured fluorescence intensities of released solutions were related to the concentrations of naproxen taken up into the films. Several key parameters such as applied potential and time for uptake and release were varied to achieve the optimal sorption procedure. The film template with naproxen exhibited excellent selectivity over some interference. The calibration graphs were linear in the ranges of 5×10(-8) to 3×10(-7)molml(-1) and 7×10(-6) to 8×10(-4)molml(-1), and the limit of detection was 1×10(-8)molml(-1). The CMIP films, as the electrochemically controlled solid-phase sorbent, were applied for the selective cleanup and quantification of trace amounts of naproxen from physiological samples. Scanning electron microscopy confirmed the nanostructure morphology of the films.     

一种QRS波群实时检测方法

结合模板匹配和改进的导数阈值法,提出了一种QRS波群实时检测方法CT2(combination method of template matching and improved derivative threshold)。首先,预采集一段ECG信号,使用高斯函数构造QRS模板;然后将实时采集的ECG信号使用CT2检测R波位置。为了比较算法检测精度和效率,使用CT2和基于小波模极大值的方法进行了对比。结果表明,CT2检测精度与基于小波模极大值的方法相当,但运算时间大大缩短,适于实时检测。     

SuperStar: a knowledge-based approach for identifying interaction sites in proteins.

An empirical method for identifying interaction sites in proteins is described and validated. The method is based entirely on experimental information about non-bonded interactions occurring in small-molecule crystal structures. These data are used in the form of scatterplots that show the experimentally observed distribution of one functional group (the "contact group" or "probe") around another. A template molecule (e.g. a protein binding site) is broken down into structure fragments and the scatterplots, showing the distribution of a chosen probe around these structure fragments, are superimposed on the corresponding parts of the template. The scatterplots are then translated into a three-dimensional map that shows the propensity of the probe at different positions around the template molecule. The method is illustrated for l -arabinose-binding protein, complexed with l -arabinose and with d -fucose, and for dihydrofolate reductase complexed with methotrexate. The method is validated on 122 X-ray structures of protein-ligand complexes. For all the binding sites of these proteins, propensity maps are generated for four different probes: a charged NH+3nitrogen, a carbonyl oxygen, a hydroxyl oxygen and a methyl carbon atom. Next, the maps are compared with the experimentally observed positions of ligand atoms of these types. For 74% of these ligand atoms (84% of the solvent-inaccessible ones) the calculated propensity of the matching probe at the experimental positions is higher than expected by chance. For 68% of the atoms (82% of the solvent-inaccessible ones) the propensity of the matching probe is higher than that of the other three probes. These results indicate that the approach generally gives good predictions for protein-ligand interactions. The potential applications of the propensity maps range from an aid in manual docking and structure-based drug design to their use in pharmacophore development.     

Computer-aided detection of pulmonary nodules using dynamic self-adaptive template matching and a FLDA classifier

Improving the performance of computer-aided detection (CAD) system for pulmonary nodules is still an important issue for its future clinical applications. This study aims to develop a new CAD scheme for pulmonary nodule detection based on dynamic self-adaptive template matching and Fisher linear discriminant analysis (FLDA) classifier. We first segment and repair lung volume by using OTSU algorithm and three-dimensional (3D) region growing. Next, the suspicious regions of interest (ROIs) are extracted and filtered by applying 3D dot filtering and thresholding method. Then, pulmonary nodule candidates are roughly detected with 3D dynamic self-adaptive template matching. Finally, we optimally select 11 image features and apply FLDA classifier to reduce false positive detections. The performance of the new method is validated by comparing with other methods through experiments using two groups of public datasets from Lung Image Database Consortium (LIDC) and ANODE09. By a 10-fold cross-validation experiment, the new CAD scheme finally has achieved a sensitivity of 90.24% and a false-positive (FP) of 4.54 FP/scan on average for the former dataset, and a sensitivity of 84.1% with 5.59 FP/scan for the latter. By comparing with other previously reported CAD schemes tested on the same datasets, the study proves that this new scheme can yield higher and more robust results in detecting pulmonary nodules.     

TAMS technology for simple and efficient in vitro site-directed mutagenesis and mutant screening

Site-directed mutagenesis is an invaluable tool for functional studies and genetic engineering. However, most current protocols require the target DNA to be cloned into a plasmid vector before mutagenesis can be performed, and none of them are effective for multiple-site mutagenesis. We now describe a method that allows mutagenesis on any DNA template (eg. cDNA, genomic DNA and plasmid DNA), and is highly efficient for multiple-site mutagenesis (up to 100%). The technology takes advantage of the requirement that, in order for DNA polymerases to elongate, it is crucial that the 3′ sequences of the primers match the template perfectly. When two outer mutagenic oligos are incorporated together with the desired mutagenic oligos into the newly synthesised mutant strand, they serve as anchors for PCR primers which have 3′ sequences matching the mutated nucleotides, thus amplifying the mutant strand only. The same principle can also be used for mutant screening.     

Collagen-based structures containing the peptoid residue N-isobutylglycine (Nleu): Synthesis and biophysical studies of Gly-Pro-Nleu sequences by circular dichroism,ultraviolet absorbance,and optical rotation

A peptoid residue N-isobutylglycine (Nleu) was introduced as a proline surrogate in collagen-like triple helical structures. A series of single chain and template-assembled collagen-based peptide-peptoid structures composed of Gly-Pro-Nleu sequences were prepared by solid-phase segment condensation methods. Both a synthetic route in solution and a solid phase method were employed to couple the KTA (cis,cis-1,3,5-trimethylcyclohexane-1,3,5-tricarboxylic acid, also known as the Kemp triacid) based template, KTA-(Gly-OH)₃, to peptide-peptoid chains. Biophysical studies using CD, uv absorbance, and optical rotation measurements demonstrated that these compounds form triple-helical structures when the chains are longer than critical lengths. Results from melting curve measurements indicated that the Gly-Pro-Nleu sequence is comparable to the Gly-Pro-Pro sequence in stabilizing a triple-helical conformation. The KTA-based template stabilized triple-helical structures as can be seen by the increased melting temperatures as compared to equivalent single chain molecules. In addition, the template reduced the minimum chain length necessary to form a triple helix from six to only three trimer repeats. © 1996 John Wiley & Sons, Inc.     

Quantitative analysis of human DNA sequences by PCR and solid-phase minisequencing

Reliable quantification by PCR requires careful experimental design and conditions, often involving sampling of the PCR reactions at different time points or amplifying multiple dilutions of a standard DNA. We describe here an accurate, quantitative and easily automatizable solid-phase method based on competetive PCR. The PCR products are analyzed by solid-phase minisequencing after capture of biotinylated PCR products in streptavidin-coated microtiter wells and single-nucleotide extension of a specific detection primer by a radioactively labelled nucleotide. The results are expressed as numeric cpm-values, and the incorporated label expresses the relative amount of sequence variants in the original template mixture. We have applied the method to determination of allele frequencies in pooled DNA samples, of mitochondrial heteroplasmy, of gene copy numbers, and to forensic DNA analysis.     

Allograft selection for distal femur through cutting contour registration

Allograft reconstruction is an acceptable procedure for the recovery of normal anatomy after the bone tumor resection. During the past few years, several automated methods have been proposed to select the best anatomically matching allograft from the virtual donor bone bank. The surface-based automated method uses the contralateral healthy bone to obtain the normal surface shape of the diseased bone, which could achieve good matching of the defect and the selected allograft. However, the surface-based method focuses on the matching of the whole bone so that the matching of the contact surface between the allograft and the recipient bone may not be optimal. To deal with the above problem, we propose a cutting contour based method for the allograft selection. Cutting contour from the recipient bone could reflect the structural information of the defect and is seldom influenced by tumor. Thus the cutting contour can be used as the matching template to find the optimal alignment of the recipient bone and the allograft. The proposed method is validated using the data of distal femurs where bone transplantation is commonly performed. Experimental results show that the proposed method generally outperforms the surface-based method within modest extra time. Overall, our contour-based method is an effective complementary technique for allograft selection in the virtual bone bank.     

Class-specific molecularly imprinted polymers for the selective extraction and determination of sulfonylurea herbicides in maize samples by high-performance liquid chromatography–tandem mass spectrometry

A novel method based on the molecularly imprinted solid-phase extraction (MISPE) procedure has been developed for the simultaneous determination of concentrations of sulfonylurea herbicides such as chlorsulfuron (CS), monosulfuron (MNS), and thifensulfuron methyl (TFM) in maize samples by liquid chromatography–tandem quadrupole mass spectrometry (LC–MS/MS). The molecularly imprinted polymer (MIP) for sulfonylurea herbicides was synthesized by precipitation polymerization using chlorsulfuron as the template molecule, 2-(diethylamino)ethyl methacrylate (DEAMA) as the functional monomer, and trimethylolpropane trimethacrylate (TRIM) as the cross-linker. The selectivities of the chlorsulfuron template and its analogs on the molecularly imprinted polymer were evaluated by high-performance liquid chromatography (HPLC). The extraction and purification procedures for the solid-phase extraction (SPE) cartridge with a molecularly imprinted polymer as the adsorbent for the selected sulfonylurea herbicides were then established. A molecularly imprinted solid-phase extraction method followed by high-performance liquid chromatography–tandem mass spectrometry for the determination of chlorsulfuron, monosulfuron, and thifensulfuron methyl was also established. The mean recoveries of these compounds in maize were in the range 75–110% and the limits of detection (LOD) of chlorsulfuron, monosulfuron, and thifensulfuron methyl were 0.02, 0.75, and 1.45 μg kg⁻¹, respectively. It was demonstrated that the MISPE–HPLC–MS/MS method could be applied to the determination of chlorsulfuron, monosulfuron, and thifensulfuron methyl in maize samples.     

Real-time turbidimetry of LAMP reaction for quantifying template DNA

Loop-mediated isothermal amplification (LAMP) is a nucleic acid amplification method that allows the synthesis of large amounts of DNA in a short period of time with high specificity. As the LAMP reaction progresses, the reaction by-product pyrophosphate ions bind to magnesium ions and form a white precipitate of magnesium pyrophosphate. We designed an apparatus capable of measuring the turbidity of multiple samples simultaneously while maintaining constant temperature to conduct real-time measurements of the changes in the turbidity of LAMP reactions. The time (Tt) required for the turbidity of the LAMP reaction solution to exceed a given value was dependent on the quantity of the initial template DNA. That is, a graph with the plot of Tt versus the log of the amount of initial template DNA was linear from 2 x 10(3) copies (0.01 pg/tube) to 2 x 10(9) copies (100 ng/tube) of template DNA. These results indicate that real-time turbidity measurements of the LAMP reaction permit the quantitative analysis of minute amounts of nucleic acids present in a sample, with a high precision over a wide range, using a simple apparatus reported in this study.