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Reagents, methods, and libraries for bead-based sequencing

The present invention provides methods for determining a nucleic acid sequence by performing successive cycles of duplex extension along a single stranded template. The cycles comprise steps of extension, ligation, and, preferably, cleavage. In certain embodiments the methods make use of extension probes containing phosphorothiolate linkages and employ agents appropriate to cleave such linkages. In certain embodiments the methods make use of extension probes containing an abasic residue or a damaged base and employ agents appropriate to cleave linkages between a nucleoside and an abasic residue and/or agents appropriate to remove a damaged base from a nucleic acid. The invention provides methods of determining information about a sequence using at least two distinguishably labeled probe families. In certain embodiments the methods acquire less than 2 bits of information from each of a plurality of nucleotides in the template in each cycle. In certain embodiments the sequencing reactions are performed on templates attached to beads, which are immobilized in or on a semi-solid support. The invention further provides sets of labeled extension probes containing phosphorothiolate linkages or trigger residues that are suitable for use in the method. In addition, the invention includes performing multiple sequencing reactions on a single template by removing initializing oligonucleotides and extended strands and performing subsequent reactions using different initializing oligonucleotides. The invention further provides efficient methods for preparing templates, particularly for performing sequencing multiple different templates in parallel. The invention also provides methods for performing ligation and cleavage. The invention also provides new libraries of nucleic acid fragments containing paired tags, and methods of preparing microparticles having multiple different templates (e.g., containing paired tags) attached thereto and of sequencing the templates individually. The invention also provides automated sequencing systems, flow cells, image processing methods, and computer-readable media that store computer-executable instructions (e.g., to perform the image-processing methods) and/or sequence information. In certain embodiments the sequence information is stored in a database.
Owner:APPL BIOSYSTEMS INC

FPGA with register-intensive architecture

Field programmable gate arrays (FPGA's) may be structured in accordance with the disclosure to have a register-intensive architecture that provides, for each of plural function-spawning LookUp Tables (e.g. a 4-input, base LUT's) within a logic block, a plurality of in-block accessible registers. A register-feeding multiplexer means may be provided for allowing each of the plural registers to equivalently capture and store a result signal output by the corresponding, base LUT of the plural registers. Registerable, primary and secondary feedthroughs may be provided for each base LUT so that locally-acquired input signals of the LUT may be fed-through to the corresponding, in-block registers for register-recovery purposes without fully consuming (wasting) the lookup resources of the associated, base LUT. A multi-stage, input switch matrix (ISM) may be further provided for acquiring and routing input signals from adjacent, block-interconnect lines (AIL's) and/or block-intra-connect lines (e.g., FB's) to the base LUT's and/or their respective, registerable feedthroughs. Techniques are disclosed for utilizing the many in-block registers and/or the registerable feedthroughs and/or the multi-stage ISM's for efficiently implementing various circuit designs by appropriately configuring such register-intensive FPGA's.
Owner:LATTICE SEMICON CORP

Method and apparatus for interleaved processing of direct and indirect texture coordinates in a graphics system

InactiveUS7002591B1Efficient implementationIncrease in texture mapping hardware complexityCathode-ray tube indicators3D-image renderingPattern recognitionProcessing
A graphics system including a custom graphics and audio processor produces exciting 2D and 3D graphics and surround sound. The system includes a graphics and audio processor including a 3D graphics pipeline and an audio digital signal processor. The graphics pipeline renders and prepares images for display at least in part in response to polygon vertex attribute data and texel color data stored as a texture images in an associated memory. An efficient texturing pipeline arrangement achieves a relatively low chip-footprint by utilizing a single texture coordinate / data processing unit that interleaves the processing of logical direct and indirect texture coordinate data and a texture lookup data feedback path for “recirculating” indirect texture lookup data retrieved from a single texture retrieval unit back to the texture coordinate / data processing unit. Versatile indirect texture referencing is achieved by using the same texture coordinate / data processing unit to transform the recirculated texture lookup data into offsets that may be added to the texture coordinates of a direct texture lookup. A generalized indirect texture API function is provided that supports defining at least four indirect texture referencing operations and allows for selectively associating one of at least eight different texture images with each indirect texture defined. Retrieved indirect texture lookup data is processed as multi-bit binary data triplets of three, four, five, or eight bits. The data triplets are multiplied by a 3×2 texture coordinate offset matrix before being optionally combined with regular non-indirect coordinate data or coordinate data from a previous cycle / stage of processing. Values of the offset matrix elements are variable and may be dynamically defined for each cycle / stage using selected constants. Two additional variable matrix configurations are also defined containing element values obtained from current direct texture coordinates. Circuitry for optionally biasing and scaling retrieved texture data is also provided.
Owner:NINTENDO CO LTD

Apparatus and method for communicating voice and data between a customer premises and a central office

A method and apparatus are provided for communicating data across a communication link, in a manner that senses and dynamically adapts to the simultaneous transmission of voice information across the local loop. In accordance with one aspect of the invention, a method is provided for dynamically communicating data over a local loop using a modem comprising the steps of transmitting data in a full-band transmission state, sensing a band-limiting condition, and adjusting the transmission of data from the full-band transmission state to a bandlimited transmission state, in response to the sensing step. In accordance with the method, data may be transmitted by the modem across the local loop at the same time that voice information is communicated via telephone across the same local loop. A significant aspect of the present invention is the dynamic allocation of the data transmission bandwidth, whereby the invention senses a condition indicative of whether voice information is being communicated. If so, then the system shifts and / or narrows the data transmission bandwidth to allow for voice communications without interference from or with the data transmission. However, when no voice information is being communicated, the invention dynamically allocates the data transmission bandwidth to utilize at least a portion, if not all, of the frequency band otherwise used for communicating voice information.
Owner:PARADYNE CORP

Multi-parameter X-ray computed tomography

The present invention relates to the field of x-ray imaging. More particularly, embodiments of the invention relate to methods, systems, and apparatus for imaging, which can be used in a wide range of applications, including medical imaging, security screening, and industrial non-destructive testing to name a few. Specifically provided as embodiments of the invention are systems for x-ray imaging comprising: a) a first collimator-and-detector assembly having a first operable configuration to provide at least one first dataset comprising primary x-ray signals as a majority component of its data capable of being presented as a first image of an object subjected to x-ray imaging; b) a second collimator-and-detector assembly having a second operable configuration or wherein the first collimator-and-detector assembly is adjustable to a second configuration to provide at least one second dataset comprising primary and dark-field x-ray signals as a majority component of its data capable of being presented as a second image of the object; and c) a computer operably coupled with the collimator-and-detector assemblies comprising a computer readable medium embedded with processing means for combining the first dataset and the second dataset to extract the dark-field x-ray signals and produce a target image having higher contrast quality than the images based on the first or second dataset alone. Such systems can be configured to comprise at least two collimator-and-detector assemblies or configurations differing with respect to collimator height, collimator aperture, imaging geometry, or distance between an object subjected to the imaging and the collimator-and-detector assembly.
Owner:VIRGINIA TECH INTPROP INC
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