Abstract: In some embodiments, sample-derived characteristic determination may be facilitated via creation or use of anchor-based data structures. In some embodiments, an anchor and a seed length range may be obtained (e.g., for creating a reference data structure derived from reference data). Based on the anchor and the seed length range, reference seeds may be extracted from the reference data (e.g., such that each of the extracted reference seeds (i) is a data instance adjacent at least one instance of the anchor in the reference data and (ii) has a length within the seed length range). The reference data structure may be created with the extracted reference seeds, and unassembled sample data may be processed using the reference data structure, the anchor, and the seed length range to determine characteristics related to the unassembled sample data.

Abstract: The present invention relates to systems and methods capable of characterizing populations of organisms within a sample. The characterization may utilize probabilistic matching of short strings of sequencing information to identify genomes from a reference genomic database to which the short strings belong. The characterization may include identification of the microbial community of the sample to the species and/or sub-species and/or strain level with their relative concentrations or abundance. In addition, the system and methods may enable rapid identification of organisms including both pathogens and commensals in clinical samples, and the identification may be achieved by a comparison of many (e.g., hundreds to millions) metagenomic fragments, which have been captured from a sample and sequenced, to many (e.g., millions or billions) of archived sequence information of genomes (i.e., reference genomic databases).

Abstract: The present invention relates to systems and methods capable of characterizing populations of organisms within a sample. The characterization may utilize probabilistic matching of short strings of sequencing information to identify genomes from a reference genomic database to which the short strings belong. The characterization may include identification of the microbial community of the sample to the species and/or sub-species and/or strain level with their relative concentrations or abundance. In addition, the system and methods may enable rapid identification of organisms including both pathogens and commensals in clinical samples, and the identification may be achieved by a comparison of many (e.g., hundreds to millions) metagenomic fragments, which have been captured from a sample and sequenced, to many (e.g., millions or billions) of archived sequence information of genomes (i.e., reference genomic databases).

Abstract: The present invention relates to systems and methods capable of characterizing populations of organisms within a sample. The characterization may utilize probabilistic matching of short strings of sequencing information to identify genomes from a reference genomic database to which the short strings belong. The characterization may include identification of the microbial community of the sample to the species and/or sub-species and/or strain level with their relative concentrations or abundance. In addition, the system and methods may enable rapid identification of organisms including both pathogens and commensals in clinical samples, and the identification may be achieved by a comparison of many (e.g., hundreds to millions) metagenomic fragments, which have been captured from a sample and sequenced, to many (e.g., millions or billions) of archived sequence information of genomes (i.e., reference genomic databases).

Abstract: The present invention relates to systems and methods capable of characterizing populations of organisms within a sample. The characterization may utilize probabilistic matching of short strings of sequencing information to identify genomes from a reference genomic database to which the short strings belong. The characterization may include identification of the microbial community of the sample to the species and/or sub-species and/or strain level with their relative concentrations or abundance. In addition, the system and methods may enable rapid identification of organisms including both pathogens and commensals in clinical samples, and the identification may be achieved by a comparison of many (e.g., hundreds to millions) metagenomic fragments, which have been captured from a sample and sequenced, to many (e.g., millions or billions) of archived sequence information of genomes (i.e., reference genomic databases).

Abstract: The power handling capability of polymer fibers is increased by broadening an input intensity profile, which is typically Gaussian, without significantly decreasing the efficiency of coupling light into a polymer fiber. The method for increasing the power handling capability of polymer fibers includes the steps of: a) emitting light having a Gaussian intensity profile from a fiber light source; b) broadening the Gaussian intensity profile so that energy at the center of the Gaussian intensity profile is distributed to the perimeter to reduce the peak power intensity of the emitted light before it is launched into the polymer fiber; c) transmitting the emitted light into at least one polymer fiber. Preferably, a fused bundle is used to broaden the intensity profile and preferably the fused bundle has an angled input end face.

Abstract: An illumination system includes a light source and a tapered bundle of fused optical fibers having a light input end configured for receiving light, the light input end having a first cross sectional area and a first numerical aperture, the tapered bundle having an output end configured for outputting light, the output end having a second cross sectional area and a second numerical aperture. The bundle of fused optical fibers is tapered between the input end and the output end such that there is a difference in size between the first and second cross sectional areas, so that light exiting the output end has a higher numerical aperture. A first fiber optic light guide is coupled to the light source for receiving light from the light source and delivering light to the input end of the tapered bundle, or the light can be directly coupled into the tapered bundle.

Abstract: An electromagnetic radiation source, such as an arc lamp, is located at a point displaced from the optical axis of a concave toroidal reflecting surface. The concave primary reflector focuses the radiation from the source at an off-axis image point that is displaced from the optical axis. The use of a toroidal reflecting surface enhances the collection efficiency into a small target, such as an optical fiber, relative to a spherical reflecting surface by substantially reducing aberrations caused by the off-axis geometry. A second concave reflector is placed opposite to the first reflector to enhance further the total flux collected by a small target. In accordance with one embodiment, the present invention is directed to devices in which the square of the off-axis distance divided by the radius of curvature is equal to or less than the extent of the source of electromagnetic radiation (y02/r≦s0).

Abstract: A surgical tool with surgical field illuminator includes a light-conveying fiber optic member having a body portion, a light-receiving end optically connectable to a source of light, and a light-delivering end. A surgical tool can be attached to, or surround, part of the body portion of the fiber optic member, and the surgical tool can be connected to the body portion of the fiber optic member. A light-transmitting member is positioned adjacent the light-delivering end of the fiber optic member. A light-delivering port in the surgical tool can be provided. When the light-receiving end of the fiber optic member is optically connected to the source of light, light is transmitted through the fiber optic member to the light-delivering end of the fiber optic member, and through the light-transmitting member at a light density, to illuminate a surgical region adjacent the light-transmitting member.

Abstract: A method and apparatus for coupling high intensity light into a low melting temperature optical fiber which uses a high temperature, low NA optical fiber as a spatial filter between a source of high intensity light and a low melting temperature, low NA optical fiber. In an alternate embodiment, the spatial filter is composed of a fused bundle of optical fibers. The source of light may be a high intensity arc lamp or may be a high NA, high melting temperature optical fiber transmitting light from a remote light source.

Abstract: A method and apparatus which can couple a high intensity point source, such as from a single fiber, to a fiber bundle. A bundle of fibers is fed though a hole in the light post. A removable potting compound is applied to the tip of the bundle to hold the fibers together for polishing. The tip of the bundle is polished and then the potting compound is removed from the tip of the bundle. A window is placed over a light inlet of the hole so as to seal the bundle. A point source cable introduces a point source of light to the bundle of fibers. A ferrule is provided around the point source cable, having a diameter sized corresponding to a diameter of said light post. The ferrule and the bundle of fibers are clamped with a split sleeve which extends therebetween.

Abstract: The power handling capability of polymer fibers is increased by broadening an input intensity profile, which is typically Gaussian, without significantly decreasing the efficiency of coupling light into a polymer fiber. The method for increasing the power handling capability of polymer fibers includes the steps of: a) emitting light having a Gaussian intensity profile from a fiber light source; b) broadening the Gaussian intensity profile so that energy at the center of the Gaussian intensity profile is distributed to the perimeter to reduce the peak power intensity of the emitted light before it is launched into the polymer fiber; c) transmitting the emitted light into at least one polymer fiber. Preferably, a fused bundle is used to broaden the intensity profile and preferably the fused bundle has an angled input end face.

Abstract: A method and apparatus which can couple a high intensity point source, such as from a single fiber, to a fiber bundle. A bundle of fibers is fed though a hole in the light post. A removable potting compound is applied to the tip of the bundle to hold the fibers together for polishing. The tip of the bundle is polished and then the potting compound is removed from the tip of the bundle. A window is placed over a light inlet of the hole so as to seal the bundle. A point source cable introduces a point source of light to the bundle of fibers. A ferrule is provided around the point source cable, having a diameter sized corresponding to a diameter of said light post. The ferrule and the bundle of fibers are clamped with a split sleeve which extends therebetween.

Abstract: A device which adjusts the angle of illumination of light exiting a fiber optic light guide. A first light guide has a first numerical aperture for emitting light from a light source, and light exiting the first light guide has a first light intensity angular profile. A second light guide has a second numerical aperture for receiving the light from the first light guide, and light exiting the second light guide has a second light intensity angular profile. Light from the first light guide is dispersed by a device including at least a first surface interposed between the first light guide and the second light guide such that light from the first light guide having the first light intensity profile irradiates the first surface and the angular intensity profile of the light irradiating the second light guide is modified so as to cause the second light intensity angular profile to be modified. The first light guide preferably has a single fiber, and the second light guide preferably has a fiber bundle.

Abstract: The optical coupler couples light output from the single fiber optic into the fiber optic bundle while preserving the numerical aperture of the beam output from the single fiber optic. The optical coupler also preserves any uniformity in s the beam output from the single fiber optic. The optical coupler includes a collimating device such as a magnifying lens and a diffusing device such as a hemispherical lens array. The collimating device collimates the beam output from the single fiber optic into a parallel beam having a diameter substantially equal to a diameter of the fiber optic bundle. The diffuser device diverges the collimated beam for input into the fiber optic bundle by an amount sufficient to reproduce the numerical aperture of light output from the single fiber optic. A wide variety of optical diffuser devices are disclosed, including spherical convex lens arrays, cylindrical lens arrays, pyramidal lens arrays and fresnel lenses.

Abstract: The present invention comprises a system for condensing and collecting electromagnetic radiation having a primary reflector disposed on one side of an electromagnetic radiation source and a target disposed on the opposite side of the source. The primary reflector includes a concave reflecting surface portion, which preferably forms the entire surface of the reflector. The concave surface portion of the primary reflector, which is preferably of a substantially toroidal shape, defines an optical axis and a primary center of curvature disposed along the optical axis. The source of electromagnetic radiation is located approximately on the optical axis but axially offset a first distance from the center of curvature in a direction toward the concave surface portion.

Abstract: The present invention provides a compact surgical headlamp capable of dynamic adjustment of the resulting field of illumination, comprising at least a single core fiber optic delivery light guide, an adjustable light projection system, and a mounting mechanism for movably supporting the headlamp proximate to the surgeon's eyes. A receiving block is also provided for supporting the structure of the projection system and for coupling the delivery fiber thereto. The projection system comprises a cylindrical housing mount adapted with a centrally disposed cylindrical cavity for receiving the ferruled, output end of the delivery fiber and for allowing the light output therefrom to initially diverge within the cavity of the housing mount.

Abstract: An off-axis optical system for collecting and condensing electromagnetic radiation utilizes an ellipsoidal reflector or a portion thereof configured so that the effects of magnification and optical aberrations (caused by the off-axis arrangement and an aspherical source envelope) are minimized. This is accomplished by the utilization of a specially designed ellipsoidal reflector having primary and secondary focal points along the major axis of the reflector or an effective reflecting portion thereof defined as that portion which is both illuminated by the source and subtended by the acceptance cone of the target.