Abstract: The invention relates to methods for determining a haplotype for an organism by using a system for transforming SNP alleles found in sequence fragments into vertices in a graph with edges connecting vertices for alleles that appear together in a sequence fragment. A community detection operation can be used to infer the haplotype from the graph. The system may produce a report that includes the haplotype of the SNPs found in the genome of that organism.

Abstract: An optical modulator is disclosed that includes an optical resonator structure. The optical resonator structure includes at least one non-linear portion, the at least one non-linear portion comprising at least one radial junction region. The at least one radial junction region is formed between at least first and second materials, respectively, having different electronic conductivity characteristics. A principal axis of the at least one radial junction region is oriented along a radius of curvature of the at least one non-linear portion. The optical modulator includes an optical waveguide that is coupled to the at least one non-linear portion of the optical resonator structure.

Abstract: The invention provides systems and methods for calling variants in data from amplicon-based sequencing methods by aligning and assembling reads, associating the reads with their source amplicons, treating each amplicon as a separate sample or file, calling variants on the reads. A portion of each read is aligned to the primer binding site of the associated amplicons. Variants called at sites in the mapped portions of each read are discarded. The remaining variant calls are merged, to provide a set of variant calls across the original target region.

Abstract: Method and structural embodiments are described which provide an integrated structure using polysilicon material having different optical properties in different regions of the structure.

Abstract: An integrated structure and method of formation provide a lower level waveguide having a core of a first material and a higher level waveguide having a core of a second material and a coupling region for coupling the two waveguides together. The different core materials provided different coupled waveguides having different light loss characteristics.

Abstract: Systems and methods for monitoring pressure at a contact surface, for applications such as pressure sore prevention. The system includes a number of force sensors positioned at different locations in relation to the contact surface, the force sensors providing a signal in proportion to the amount of force detected. The system includes a controller for receiving the signals from the force sensors and determining values associated with each force sensor. The controller is configured for comparing a first one or more values associated with a first subset of force sensors with a second one or more values associated with a second subset of force sensors, determining from the comparing whether a threshold between said first one or more values and said second one or more values has been exceeded, and controlling, based on the determining, an indicator to provide an indication to the user.

Abstract: A functional electrical stimulation method for rehabilitating, treating, retraining, and/or otherwise improving upper extremity mobility and control in persons having impaired or disabled upper extremities due to stroke or spinal cord injury, comprising stimulation of the lumbricalis muscles.

Abstract: A system, method and computer program for enabling signings/dedications on a remote basis is provided. A first computer at a first location is associated with an individual from whom a signature or dedication is required. A second computer at a location where the signing or dedication is required is linked to the first computer so as to provide a two-way audiovisual communication system. The second computer is operate e to receive input from one or more individuals regarding their request for a signature and/or dedication, and to communicate the request to the first computer. The first computer is operable to permit the individual associated with the first computer to review the request, and based on such request provide a signature and/or personalized dedication as an input to an input device connected to the first computer. The first computer transmits the signature and/or personalized dedication from the first computer to the second computer.

Abstract: A system, method and computer program for enabling signings/dedications on a remote basis is provided. A first computer at a first location is associated with an individual from whom a signature or dedication is required. A second computer at a location where the signing or dedication is required is linked to the first computer so as to provide a two-way audiovisual communication system. The second computer is operate e to receive input from one or more individuals regarding their request for a signature and/or dedication, and to communicate the request to the first computer. The first computer is operable to permit the individual associated with the first computer to review the request, and based on such request provide a signature and/or personalized dedication as an input to an input device connected to the first computer. The first computer transmits the signature and/or personalized dedication from the first computer to the second computer.

Abstract: An optical resonator supports three resonance modes and having third-order optical nonlinearity. One or more waveguides are coupled to the three resonant modes. A waveguide input port is more strongly coupled to the first resonant mode than to the second and third resonant modes. A waveguide output port is more strongly coupled to at least one of the second and third resonant modes than to the first resonant mode. An optical filter has at least two optical resonators. The optical filter provides a passband having at least two poles and a transmission zero positioned outside the two poles. An optical demultiplexer includes first optical filter coupled in series with a second optical filter. Both optical filters provide a passband having at least two poles and a zero positioned outside the two poles. The zero of the first filter is located within the passband of the second filter.

Abstract: An optical coupler has a waveguide coupled to a grating of multiple scattering units, each scattering unit having a first scattering element formed of a shape in a polysilicon gate layer and a second scattering element formed of a shape in a body silicon layer of a metal-oxide-semiconductor (MOS) integrated circuit (IC). The couplers may be used in a system having a coupler on each of a first and second IC, infrared light being formed into a beam passing between the couplers. Vias may be interposed in third ICs between the first and second ICs. The couplers may be configured with nonuniform width of scattering elements to produce Gaussian or focused beams.

Abstract: A hitless tunable filter may include a ring resonator, a Mach-Zehnder coupler, and first and second phase shifters. The Mach-Zehnder coupler may include a switching arm that is coupled to the ring resonator at first and second coupling points. The first phase shifter may be used to introduce a first phase shift to light propagating through the ring resonator, while the second phase shifter may be used to introduce a second phase shift to light propagating through the Mach-Zehnder coupler. The Mach-Zehnder coupler may have a free spectral range substantially equal to a free spectral range of the ring resonator divided by a non-negative integer.

Abstract: Disclosed are resonant optical modulators, and methods of use thereof, that achieve constant photon populations in the resonator by simultaneously modulating at least two variable modulation parameters.

Abstract: A solid state waveguide coupler is provided including a first coupler end disposed on a solid state material substrate for connection to a first solid state waveguide located on the substrate and a second coupler end disposed on the substrate for connection to a second waveguide located on the substrate. A coupling span, comprising a waveguide material layer on the substrate, is disposed between the first and second coupler ends and tapers between a height of the first waveguide and a height of the second waveguide, tapers between a width of the first waveguide and a width of the second waveguide, and includes curved sidewalls along at least a portion of the tapered coupling span. In a method for fabricating the waveguide coupler, material is isotropically removed from a waveguide material layer on the substrate to produce tapered surfaces between the first waveguide and the second waveguide.

Abstract: Disclosed are optical modulators that have two coupling paths or structures between an input port to an output port, at least one of which includes an optical resonator.

Abstract: The invention generally relates, in one aspect, to an interferometer system. The interferometer system includes a splitter/combiner element (SCE), a first bi-directional optical path, and a second bi-directional optical path.

Abstract: Low-loss waveguide structures may comprise a multimode waveguide supporting a periodic light intensity pattern, and attachments disposed at the waveguide adjacent low-intensity regions of the light intensity pattern.

Abstract: The invention generally relates, in one aspect, to an interferometer system. The interferometer system includes a splitter/combiner element (SCE), a first bi-directional optical path, and a second bi-directional optical path.

Abstract: A maskless lithography system and method to expose a pattern on a wafer by propagating a photon beam through a waveguide on a substrate in a plane parallel to a top surface of the wafer.

Abstract: An optical waveguide having a core region with a substantially rectangular cross-section with a selected aspect ratio of width to height. Embodiments include devices incorporating the optical waveguide and methods for using the optical waveguide.