Abstract: The present invention provides methods and accompanying computer-based systems and computer-executable code stored on a computer-readable medium for constructing a model of a biological network. The invention further provides methods for performing sensitivity analysis on a biological network and for identifying major regulators of species in the network and of the network as a whole. In addition, the invention provides methods for identifying targets of a perturbation such as that resulting from exposure to a compound or an environmental change. The invention further provides methods for identifying phenotypic mediators that contribute to differences in phenotypes of biological systems.

Abstract: The invention relates to computer-implemented methods and systems for identifying regulatory relationships between expressed regulating polypeptides and targets of the regulatory activities of such regulating polypeptides. More specifically, the invention provides a new method for identifying regulatory dependencies between biochemical species in a cell. In particular embodiments, provided are computer-implemented methods for identifying a regulatory interaction between a transcription factor and a gene target of the transcription factor, or between a transcription factor and a set of gene targets of the transcription factor. Further provided are genome-scale methods for predicting regulatory interactions between a set of transcription factors and a corresponding set of transcriptional target substrates thereof.

Abstract: The present invention provides compounds that potentiate the activity of antibiotic agents, particularly quinolones such as norflaxin. The invention further provides compositions, e.g., pharmaceutical compositions, comprising the inventive compounds. The invention also provides compositions comprising an antibiotic (e.g., a quinolone) and a compound that potentiates activity of the antibiotic. The invention further provides methods of treating a subject comprising administering any of the inventive compounds or compositions to the subject. The invention also provides screening methods to identify compounds that potentiate the activity of an antibiotic, e.g., a quinolone.

Abstract: An improved fiber optic tap monitor has characteristics that are flatter over the wavelength range of interest. The polarization dependence of the characteristics of the tap monitor is reduced, and the package for the tap monitor is smaller. The tap monitor reduces the amount of light reflected back to the source. The tap monitor is also assembled in a manner to improve temperature stability, so that its characteristics over a range of temperatures are more nearly constant.

Abstract: The invention relates to an approach to angle tuning a thin film, interference filter device in which light is delivered to the filter from a fiber lying off-axis relative to the filter, and to a method of optically coupling such a device. The optical device comprises a lens unit having an optical axis and an adjustable effective focal length. The device also includes a first port disposed on a first side of the lens unit and on a first side of the optical axis, and an optical element disposed on the second side of the lens unit. The optical element has an optical characteristic that is dependent on the angle of incidence on the optical element. The lens unit has an adjustable focal length so light from the first port is incident on the optical element at a desired angle.

Abstract: Two sub-assemblies in a fiber optic device are fitted to mounting faces of a central section. The mounting faces are typically flat and mutually orthogonal, thus permitting the adjustment of the two sub-assemblies in decoupled degrees of freedom. This results in a simpler adjustment procedure for aligning the two sub-assemblies. Furthermore, the mounting of the sub-assemblies using the orthogonal mounting faces permits the use of relatively thin layers of adhesive that reduce misalignment problems arising from mismatched thermal expansion when the temperature changes.

Abstract: Generally, the present invention relates to a fiber optic device that is easier to align than conventional devices, and to a method for aligning such devices. An embodiment of the invention includes a first focusing element having an optical axis and a first focal length, and a first optical fiber optically coupled to a first side of the first focusing element. The first optical fiber is disposed at a first transverse distance from the optical axis so that light from the first optical fiber propagates on a second side of the first focusing element as a substantially collimated beam at a first angle to the optical axis. A wedged optical element is optically coupled to the second side of the first focusing element and deviates the substantially collimated beam so as to propagate in a direction substantially parallel to the optical axis.

Abstract: A particular focusing arrangement in a dual fiber collimator improves the transmission efficiency and ease of alignment of the collimator. In particular, the collimator includes two optical fibers mounted in a dual-fiber ferrule. The fiber end-faces are co-planar with the angle-polished end-face of the ferrule and displaced along the optical axis of the ferrule. The collimator unit also includes a first focusing element centered along the optical axis of the ferrule and positioned such that its back front focal point is between the two end faces of the fibers. An advantage provided by this arrangement is that by changing the fiber polish angle and polish azimuth, relative to a line connecting the fiber centers, superior coupling from one fiber to the other can be achieved, even with different working distances and at various wavelengths.

Abstract: An improved fiber optic tap monitor has characteristics that are flatter over the wavelength range of interest. The tap monitor includes a filter that reflects a major fraction of the light from a first fiber to a second fiber. A photodetector located behind the filter detects the light transmitted by the filter. The reflectance spectrum of the filter is selected to compensate for nonuniformities in the detection response characteristic of the photodetector over the wavelength range of interest, so that the overall response of the tap monitor is relatively flat.

Abstract: A particular focusing arrangement in a dual fiber collimator improves the transmission efficiency and ease of alignment of the collimator. In particular, the collimator includes two optical fibers mounted in a dual-fiber ferrule. The fiber end-faces are co-planar with the angle-polished end-face of the ferrule and displaced along the optical axis of the ferrule. The collimator unit also includes a first focusing element centered along the optical axis of the ferrule and positioned such that its back front focal point is between the two end faces of the fibers. An advantage provided by this arrangement is that by changing the fiber polish angle and polish azimuth, relative to a line connecting the fiber centers, superior coupling from one fiber to the other can be achieved, even with different working distances and at various wavelengths.

Abstract: Generally, the present invention relates to a new approach to angle tuning a thin film, interference filter device in which the light is delivered to the filter from a fiber lying off-axis relative to the filter, and to a method of optically coupling such a device. An embodiment of the invention is directed to an optical device comprising a lens unit having an optical axis and an adjustable effective focal length. The optical device includes a first port disposed on a first side of the lens unit and on a first side of the optical axis, and an optical element disposed on the second side of the lens unit, the optical element having an optical characteristic that is dependent on the angle of incidence on the optical element. Wherein the lens unit has an adjustable focal length adjusted so that light from the first port is incident on the optical element at a desired optical characteristic of the optical element.

Abstract: Two sub-assemblies in a fiber optic device are fitted to mounting faces of a central section. The mounting faces are typically flat and mutually orthogonal, thus permitting the adjustment of the two sub-assemblies in decoupled degrees of freedom. This results in a simpler adjustment procedure for aligning the two sub-assemblies. Furthermore, the mounting of the sub-assemblies using the orthogonal mounting faces permits the use of relatively thin layers of adhesive that reduce misalignment problems arising from mismatched thermal expansion when the temperature changes.

Abstract: Generally, the present invention relates to a method for aligning collimator sub-assemblies, disposed along a longitudinal axis. The invention arises from a realization that prohibiting the two collimator sub-assemblies from being adjusted in the same rotational degree of freedom leads to faster and easier alignment. In particular, the method includes rotating only one of the first and second sub-assemblies in a first plane defined by the longitudinal axis and a first axis perpendicular to the longitudinal axis. In some aspects of the invention, one of the first and second sub-assemblies are rotated in a second plane defined by the longitudinal axis and a second axis perpendicular to the both the longitudinal axis and the first axis. The sub-assemblies may also be translated in a direction parallel to the first axis and/or in a direction parallel to the second axis.

Abstract: Two sub-assemblies in a fiber optic device are fitted to respective end faces of a central section, along a longitudinal axis. The end faces of the central section are non-parallel. Butting the sub-assemblies to respective ends of the central section permits relative adjustment of the two sub-assemblies in substantially decoupled degrees of freedom. This results in a simpler adjustment procedure for aligning the two sub-assemblies. Furthermore, the mounting of the sub-assemblies using angled faces permits the use of relatively thin layers of adhesive that reduce misalignment problems arising from mismatched thermal expansion when the temperature changes.

Abstract: An improved fiber optic tap monitor has characteristics that are flatter over the wavelength range of interest. The polarization dependence of the characteristics of the tap monitor is reduced, and the package for the tap monitor is smaller. The tap monitor reduces the amount of light reflected back to the source. The tap monitor is also assembled in a manner to improve temperature stability, so that its characteristics over a range of temperatures are more nearly constant.

Abstract: Generally, the present invention relates to a fiber optic device that is easier to align than conventional devices, and to a method for aligning such devices. An embodiment of the invention includes a first focusing element having an optical axis and a first focal length, and a first optical fiber optically coupled to a first side of the first focusing element. The first optical fiber is disposed at a first transverse distance from the optical axis so that light from the first optical fiber propagates on a second side of the first focusing element as a substantially collimated beam at a first angle to the optical axis. A wedged optical element is optically coupled to the second side of the first focusing element and deviates the substantially collimated beam so as to propagate in a direction substantially parallel to the optical axis.

Abstract: An apparatus for providing focus and tracking error signals for controlling an application of a radiation beam to a data track of an optical storage medium is disclosed. The present invention describes a multi-element optical prism used in the optical head, which permits for a single return path, a reduced cross talk between focus and tracking error signals, and a reduced track offset.

Abstract: An apparatus for providing focus and tracking error signals for controlling an application of a radiation beam to a data track of an optical storage medium is disclosed. The present invention describes a multi-element optical prism having at least four separator elements with each separator element engaging at least three other separator elements and at least two separator elements surrounding two inner separator elements and engaging each other at spaced apart positions. This apparatus permits a single return path, a reduced cross talk between focus and tracking error signals, and a reduced track offset.

Abstract: A magnetooptical disk recording device has a far-field detector for detecting radial position of a laser beam with respect to tracks on the disk. The far-field detector has a reference line dividing first and second photo detectors. The reference line is centered radially with respect to center lines of the tracks. The reference line is also center lengthwise to be tangentially center with respect to a tangential point on the track. The detector is adjustable both radially and tangentially. The tangential adjustment is based upon sensing two low reflective calibration marks on the disk that indicate centering the laser beam, hence the track tangent point, on the reference line. The calibration is based upon obtaining minimum noise in the detector output signal that signifies that the laser beam is centered on the length of the detector reference line. The calibration marks are in a mirror area disposed at one radial extremity of the disk.

Abstract: A coarse position sensor is provided for an optical recording device to generate a substantially linear coarse position signal, indicative of the position of a coarse carriage along the range of its travel, and which also is substantially immune to environmental and device variations. The sensor includes a light source mounted to a drive frame at one end of the range of travel, a position sensitive device fixed to the frame at the opposite end of the range of travel and facing the light source, and a deflecting optical element mounted to the coarse carriage in the path of the light. As the coarse carriage travels along its stroke between the inner and outer diameters of the optical disk, the amount of deflection of the light beam on the position sensitive device from a reference location will change.