Abstract: Improved compositions, methods, apparatus, and kits for high-throughput nucleic acid amplification, detection and sequencing are disclosed. A nucleic acid cluster having an identifiable center is produced by generating on a solid support an immobilized nucleic acid complement from a template, one of which comprises a detectable label; and amplifying the complement and the template to obtain a nucleic acid cluster on the support, the cluster having a substantially central location marked by the detectable label and a surrounding region comprising immobilized copies. Also disclosed are nucleotide sequence determination in nucleic acid clusters so produced, center position annotation in the clusters, assignment of sequence information to overlapping clusters, and related compositions and methods.

Abstract: The invention provides a signal processor that receives a signal containing information about an acoustic signal that is generated by at least one acoustic transmitter, that travels through an aerated fluid in a container, and that is received by at least one acoustic receiver arranged in relation to the container, including inside the container; and determines the gas volume fraction of the aerated fluid based at least partly on the speed of sound measurement of the acoustic signal that travels through the aerated fluid in the container. The signal processor also sends an output signal containing information about the gas volume fraction of the aerated fluid. The signal processor may be configured together with at least one acoustic transmitter, the at least one acoustic receiver, or both.

Abstract: A composition including an optical substrate removably attached to an item. At least a portion of the substrate has a diffraction grating embedded therein or thereon. The grating has a resultant refractive index variation at a grating location. The grating provides an output optical signal indicative of a code when illuminated by an incident light signal.

Abstract: A side-hole optical cane for measuring pressure and/or temperature is disclosed. The side-hole cane has a light guiding core containing a sensor and a cladding containing symmetrical side-holes extending substantially parallel to the core. The side-holes cause an asymmetric stress across the core of the sensor creating a birefringent sensor. The sensor, preferably a Bragg grating, reflects a first and second wavelength each associated with orthogonal polarization vectors, wherein the degree of separation between the two is proportional to the pressure exerted on the core. The side-hole cane structure self-compensates and is insensitive to temperature variations when used as a pressure sensor, because temperature induces an equal shift in both the first and second wavelengths. Furthermore, the magnitude of these shifts can be monitored to deduce temperature, hence providing the side-hole cane additional temperature sensing capability that is unaffected by pressure.

Abstract: An apparatus is provided for performing an chemical, biochemical, or biological assay on a sample comprising: a microfluidic assay cartridge (1) that contains at least one sample inlet well (2) configured to receive a sample; and a microfluidic sub-unit (3) associated with the microfluidic assay cartridge (1) and comprising microfluidic channels (8), micro-valves (4, 4a, 9) and at least one separate and fluidicly-isolated isolation channel (5), and at least one hollow element (14); the at least one hollow element (14) being functionalized with a capture moiety or molecules (15) so as to form at least one reaction vessel (19); the microfluidic channels (8) and micro-valves (4, 4a, 9) configured to respond to signaling containing information about performing the assay and to controllably receive the sample and at least one reagent in the at least one reaction vessel (19), and to provide from the at least one reaction vessel (19) light containing information about the assay performed on the sample inside the at

Abstract: An optical reader system including a source light assembly that has a code-reading beam and a fluorescence-excitation beam that are configured to illuminate encoded substrates. The substrates have optically readable codes that provide output signals when the code-reading beam is incident thereon. The output signals are indicative of the codes. The reader system also includes a fluorescence detector that is configured to detect fluorescent signals from the substrates and code pickup optics that are configured to project the output signals from the optically readable codes onto a Fourier plane. The reader system also includes a code detector that is positioned to detect the output signals in the Fourier plane.

Abstract: A large diameter optical waveguide, grating, and laser includes a waveguide having at least one core surrounded by a cladding, the core propagating light in substantially a few transverse spatial modes; and having an outer waveguide dimension of said waveguide being greater than about 0.3 mm. At least one Bragg grating may be impressed in the waveguide. The waveguide may be axially compressed which causes the length of the waveguide to decrease without buckling. The waveguide may be used for any application where a waveguide needs to be compression tuned. Also, the waveguide exhibits lower mode coupling from the core to the cladding and allows for higher optical power to be used when writing gratings without damaging the waveguide. The waveguide may resemble a short “block” or a longer “cane” type, depending on the application and dimensions used.

Abstract: A large diameter optical waveguide, grating, and laser includes a waveguide having at least one core surrounded by a cladding, the core propagating light in substantially a few transverse spatial modes; and having an outer waveguide dimension of said waveguide being greater than about 0.3 mm. At least one Bragg grating may be impressed in the waveguide. The waveguide may be axially compressed which causes the length of the waveguide to decrease without buckling. The waveguide may be used for any application where a waveguide needs to be compression tuned. Also, the waveguide exhibits lower mode coupling from the core to the cladding and allows for higher optical power to be used when writing gratings without damaging the waveguide. The waveguide may resemble a short “block” or a longer “cane” type, depending on the application and dimensions used.

Abstract: An optical sensor formed from an optical waveguide having at least one core surrounded by a cladding and a large diameter generally D-shaped portion is disclosed. Axial or compressive strain across the D-shaped cross section may be determined by measuring the change in polarization or birefringence of the light output from the sensor. A layer responsive to a parameter may be disposed on a flat portion of the D-shaped portion of the sensor. The refractive index of the layer changes and/or the layer applies a strain on the sensor in response to the parameter. Changes in the refractive index of the layer alters the light output from the sensor, which is measured over time and correlated to the parameter.

Abstract: A large diameter optical waveguide, grating, and laser includes a waveguide having at least one core surrounded by a cladding, the core propagating light in substantially a few transverse spatial modes; and having an outer waveguide dimension of said waveguide being greater than about 0.3 mm. At least one Bragg grating may be impressed in the waveguide. The waveguide may be axially compressed which causes the length of the waveguide to decrease without buckling. The waveguide may be used for any application where a waveguide needs to be compression tuned. Also, the waveguide exhibits lower mode coupling from the core to the cladding and allows for higher optical power to be used when writing gratings without damaging the waveguide. The waveguide may resemble a short “block” or a longer “cane” type, depending on the application and dimensions used.

Abstract: An optical sensor formed from an optical waveguide having at least one core surrounded by a cladding and a large diameter generally D-shaped portion is disclosed. Axial or compressive strain across the D-shaped cross section may be determined by measuring the change in polarization or birefringence of the light output from the sensor. A layer responsive to a parameter may be disposed on a flat portion of the D-shaped portion of the sensor. The refractive index of the layer changes and/or the layer applies a strain on the sensor in response to the parameter. Changes in the refractive index of the layer alters the light output from the sensor, which is measured over time and correlated to the parameter.

Abstract: A method of identifying analytes that react with probes on encoded particles. The method includes providing a support substrate that has a plurality of the particles randomly distributed on the support substrate. The particles have elongated bodies with codes that extend along the corresponding bodies. The codes identify probes that are attached to the corresponding bodies, wherein at least some of the probes include fluorescent labels from reactions with the analytes. The method also includes detecting fluorescent signals that are emitted from the fluorescent labels. The fluorescent signals emit from random spatial locations along the support substrate. The method also includes detecting the codes of the particles at the random spatial locations along the support substrate and analyzing the codes and the fluorescent signals to identify the analytes that react with the probes on the particles.

Abstract: An optical reader system including a source light assembly that has a code-reading beam and a fluorescence-excitation beam that are configured to illuminate encoded substrates. The substrates have optically readable codes that provide output signals when the code-reading beam is incident thereon. The output signals are indicative of the codes. The reader system also includes a fluorescence detector that is configured to detect fluorescent signals from the substrates and code pickup optics that are configured to project the output signals from the optically readable codes onto a Fourier plane. The reader system also includes a code detector that is positioned to detect the output signals in the Fourier plane.

Abstract: A method of identifying analytes that react with probes on encoded particles. The method includes providing a support substrate that has a plurality of the particles randomly distributed on the support substrate. The particles have elongated bodies with codes that extend along the corresponding bodies. The codes identify probes that are attached to the corresponding bodies, wherein at least some of the probes include fluorescent labels from reactions with the analytes. The method also includes detecting fluorescent signals that are emitted from the fluorescent labels. The fluorescent signals emit from random spatial locations along the support substrate. The method also includes detecting the codes of the particles at the random spatial locations along the support substrate and analyzing the codes and the fluorescent signals to identify the analytes that react with the probes on the particles.

Abstract: An optical reader system that includes a plurality of substrates. The substrates have an optically readable code disposed therein and a source light assembly that is configured to illuminate the substrates with a code-reading beam and another beam for detecting another optically readable property of the substrate. The code-reading beam and the other beam form beam spots on the substrates that have different shapes. The system also includes a reader that is configured to receive output signals from the code-reading beam and the other beam when the substrates are illuminated. The output signals from the code-reading beam are indicative of the code.

Abstract: An encoded microparticle including an optical substrate comprising a material that permits light to propagate therethrough. The optical substrate has an elongated body that extends in a direction along a central axis. The optical substrate includes an outer region that extends about the central axis. The encoded microparticle also includes an optically detectable code that is disposed within the optical substrate and extends along the central axis. The outer region surrounds the optically detectable code about the central axis. The optically detectable code is readable when the light propagates through the outer region and is at least one of reflected or filtered by the optically detectable code. Said at least one of reflected or filtered light propagates through the outer region to be detected for reading the optically detectable code.

Abstract: A method of identifying an analyte. The method includes providing a plurality of microparticles. The microparticles have optically detectable codes extending along bodies of the corresponding microparticle. The microparticles have the chemical probes attached thereto. Each of the chemical probes is associated with a corresponding one of the codes. The method also includes selectively binding target analytes to the chemical probes on the microparticles to produce labeled microparticles and distributing the labeled microparticles to random locations of a substrate. The method also includes determining the codes for the labeled microparticles in the random array and code positions of the codes in the random array. The method further includes detecting the label on the labeled microparticles in the random array and label positions of the labels in the random array. The method also includes using the code positions and the label positions to analyze the target analyte.

Abstract: A method and apparatus for drug product tracking (or other pharmaceutical, health care or cosmetics products, and/or the packages or containers they are supplied with) using diffraction grating-based encoded optical identification elements 8 includes an optical substrate 10 having at least one diffraction grating 12 disposed therein. The grating 12 has one or more collocated pitches ? which represent a unique identification digital code that is detected when illuminated by incident light 24. The incident light 24 may be directed transversely from the side of the substrate 10 (or from an end) with a narrow band (single wavelength) or multiple wavelength source, and the code is represented by a spatial distribution of light or a wavelength spectrum, respectively, or a combination thereof. The encoded element 8 may be used to label any desired item, such as drugs or medicines, or other pharmaceutical or health care products or cosmetics.

Abstract: A method for fabricating microparticles. The method includes providing a removable substrate that has a photosensitive material. The substrate has a plurality of inner regions. Each inner region surrounds a corresponding outer region. The method also includes providing at least one optically detectable code within at least one of the inner regions of the substrate and etching lines into the substrate to create a plurality of microparticles having at least one optically detectable code therein. The microparticles have elongated bodies that extend in an axial direction. The optically detectable codes extend in the axial direction within the microparticles.

Abstract: A side-hole optical cane for measuring pressure and/or temperature is disclosed. The side-hole cane has a light guiding core containing a sensor and a cladding containing symmetrical side-holes extending substantially parallel to the core. The side-holes cause an asymmetric stress across the core of the sensor creating a birefringent sensor. The sensor, preferably a Bragg grating, reflects a first and second wavelength each associated with orthogonal polarization vectors, wherein the degree of separation between the two is proportional to the pressure exerted on the core. The side-hole cane structure self-compensates and is insensitive to temperature variations when used as a pressure sensor, because temperature induces an equal shift in both the first and second wavelengths. Furthermore, the magnitude of these shifts can be monitored to deduce temperature, hence providing the side-hole cane additional temperature sensing capability that is unaffected by pressure.