Abstract: The present invention provides methods, kits and compositions for the detection of an analyte. The invention is particularly suited for the detection and quantification of analytes in solution. In the methods of the invention a complex is formed between two or more analyte specific probes (ASP) and an analyte. The reactive moieties of the probes interact upon the binding of the analyte specific probes to the analyte. The reactive moieties generate a nucleic acid cleavage product which is detected and indicative of the presence of the analyte.

Abstract: Methods and systems for detecting pinholes in a film formed on a wafer or for monitoring a thermal process tool are provided. One method for detecting pinholes in a film formed on a wafer includes generating output responsive to light from the wafer using an inspection system. The output includes first output corresponding to defects on the wafer and second output that does not correspond to the defects. This method also includes detecting the pinholes in the film formed on the wafer using the second output. One method for monitoring a thermal process tool includes generating output responsive to light from a wafer using an inspection system. The output includes the first and second output described above. The wafer was processed by the thermal process tool prior to generating the output. The method also includes monitoring the thermal process tool using the second output.

Abstract: Computer-implemented methods and systems for determining a configuration for a light scattering inspection system are provided. One computer-implemented method includes determining a three-dimensional map of signal-to-noise ratio values for data that would be acquired for a specimen and a potential defect on the specimen by the light scattering inspection system across a scattering hemisphere of the inspection system. The method also includes determining one or more portions of the scattering hemisphere in which the signal-to-noise ratio values are higher than in other portions of the scattering hemisphere based on the three-dimensional map. In addition, the method includes determining a configuration for a detection subsystem of the inspection system based on the one or more portions of the scattering hemisphere.

Abstract: Provided herein are methods, compositions and kits for detecting a target nucleic acid. A target nucleic acid can be produced, for example, by a cleavage reaction in an assay for detection of biological samples. In one aspect, a described method comprises the following steps: hybridizing the target nucleic acid having a 5? end and a 3? end to a probe to form a circular hybridization complex; forming a covalent circular target nucleic acid using the probe as a template for nucleic acid synthesis; and detecting the covalent circular target nucleic acid.

Abstract: Methods and systems for inspection of a wafer are provided. One method includes illuminating the wafer with light at a first wavelength that penetrates into the wafer and light at a second wafer that does not substantially penetrate into the wafer. The method also includes generating output signals responsive to light from the wafer resulting from the illuminating step. In addition, the method includes detecting defects on the wafer using the output signals. The method further includes determining if the defects are subsurface defects or surface defects using the output signals.

Abstract: This method removes high frequency noise from shape data, significantly improves metrology system (10) performance and provides very compact representation of the shape. This model-based method for wafer shape reconstruction from data measured by a dimensional metrology system (10) is best accomplished using the set of Zernike polynomials (matrix L). The method is based on decomposition of the wafer shape over the complete set of the spatial function. A weighted least squares fit is used to provide the best linear estimates of the decomposition coefficients (Bnk). The method is operable with data that is not taken at regular data points and generates a reduced data field of Zernike coefficients compared to the large size of the original data field.

Abstract: The present invention provides protein kinase and protein phosphatase substrates, methods of detecting protein kinases and protein phosphatases, and kits for detection of protein kinases and protein phosphatases. The substrates, methods, and kits use multiple substrates that can easily be differentiated from all other substrates, thus enabling rapid and easy detection of protein kinase or protein phosphatase activities. The invention also provides methods of directionally cloning nucleic acids.

Abstract: Described are methods and compositions for generating short (cDNA) sequence tags derived from the extreme 5′ ends of eukaryotic mRNAs (“5′ SSTs”). The 5′ SSTs may be aligned with genomic DNA sequences to elucidate the borders of the genes with their corresponding promoters. Thus, the subject invention provides for identification of genes and promoters in genomic DNA sequence and for isolation of nucleic acid molecules encoding same. Vectors comprising such nucleic acid molecules are also provided as are methods of using such nucleic acid molecules, diagnostically, therapeutically and in industrial processes. Storage medium is provided having promoter and gene sequence information in computer readable form stored thereon. In addition, the inventeion provides novel reagents and methods for conducting mRNA expression analysis. The invention also provides reagents and methods for correlating genetic polymorphisms with phenotypic traits of interest.

Abstract: This method removes high frequency noise from shape data, significantly improves metrology system (10) performance and provides very compact representation of the shape. This model-based method for wafer shape reconstruction from data measured by a dimensional metrology system (10) is best accomplished using the set of Zernike polynomials (matrix L). The method is based on decomposition of the wafer shape over the complete set of the spatial function. A weighted least squares fit is used to provide the best linear estimates of the decomposition coefficients (Bnk). The method is operable with data that is not taken at regular data points and generates a reduced data field of Zernike coefficients compared to the large size of the original data field.

Abstract: A measurement station which rotates a wafer in a vertical plane and moves a scanning sensor linearly along an axis which is parallel to the wafer rotation plane, thus providing a spiral, or other, scan path across the wafer. The vertical orientation reduces errors from weight induced sagging, especially of large, e.g. 300 mm wafers. The measurement station includes wafer grippers which move in the wafer's plane for securing the wafer in position for rotation. The measurement station also includes master calibration gauges which simplify calibration and obviate the need for calibration test wafers. A technique for reducing vibration and assuring scan repeatability includes coasting of the wafer in rotation and coordinated linear probe motions for scanning. Probe measurement data obtained is digitized early and calibration, demodulation, filtering and other processing is done digitally.