Abstract: The present invention relates to methods and compositions for the normalization of complex analyte mixtures. The invention allows the preparation of profiled samples from highly complex analyte mixtures, allowing the identification of relevant targets or biomarkers. The invention also relates to methods for producing devices, such as a support, suitable for normalization of complex analyte samples. The invention can be used for the normalization of any complex mixture, such as immunogenic libraries, particularly of human source, and to identify or produce biomarkers highly relevant to human traits or conditions.

Abstract: The present invention relates to an efficient mAb panel-based expression profiling technology platform suitable for global and accurate measurement of proteins, peptides and metabolites in complex mixtures. The platform is comprised of new and well established technologies that are coupled in a unique fashion to provide a novel platform technology for (i) the discovery of differentially displayed elements of complex protein, peptide and metabolite mixtures and (ii) the development of robust mAb based assays that detect the differentially expressed elements.

Abstract: A method or platform for monoclonal antibody based biomarker discovery is disclosed. The method according to the invention provides for the integration of analyte collection, hybridoma screening and nanovolume integrated mass spectrometry (NVIMS) to achieve a robust screening system that is capable, for example, of cutting 4-6 years off of the classical biomarker discovery and development process. The invention provides a platform for the rapid, high-throughput production, isolation and characterization of, e.g., disease specific biomarkers together with highly specific monoclonal antibodies. The method of the invention has a variety of applications such as, but not limited to, drug testing, biohazard applications, ecological applications, physiological applications and/or pathology screening applications. The method of the invention is also capable of being performed or used as or with a high-throughput screening process or system of the invention.

Abstract: A vacuum deposition system has been designed to produce thin film based demultiplexers with high throughput and production yields of greater than 25% for use in Dense Wavelength Division Multiplexer (DWDM) systems. The system employs a dense array of high yield fixtures and an ion assisted movable dual electron beam evaporation system. The fixture array increases acceptable yields of narrow band pass filters to 25–75% compared to less than 5% in conventional coating systems used for DWDM. The movable e-beam system allows critical symmetry to be maintained while eliminating significant delays resulting from deposition of two materials from a single electron gun. The vacuum deposition system will enable production of more than 15,000 50–200 GHZ filters which meet specifications for DWDM demultiplexers every 48 hours.

Abstract: A method of making an optical filter wheel of a device synchronizable with an internal, rotatable virtual reference wheel, created in a memory of a motor controller of the device, is disclosed. The method includes a single trigger event that initializes rotation of the virtual reference wheel. The controller determines the orientation of an optical filter wheel of the device and maintains an ongoing representation of said orientation over time. The controller controls the motor, which causes the filter wheel to become coincident with the virtual reference wheel after the trigger event. A self-contained light fixture is also disclosed, which includes an optical filter wheel driven by an electric motor that is synchronizable with an internal, rotatable virtual reference wheel of the fixture. The method and light fixture permits optical filter wheels of multiple light fixtures, which may be identical, to synchronize with one another.

Abstract: An optical filter using alternating layers of materials with “low” and “high” indices of refraction and deposited with atomic layer control has been developed. The multilayered thin film filter uses, but is not limited to, alternating amorphous layers of atomically controlled Si (n=3.56) as the high index material and diamond-like carbon (DLC, n=2.0) as the low index material. The Si layers are grown with a self-limiting pulsed molecular beam deposition process which results in layer-by-layer growth and thickness control to within one atomic layer. The DLC layers are produced using an ion-based process and made atomically smooth using a modified Chemical Reactive-Ion Surface Planarization (CRISP) process. Intrinsic stress is monitored using an in-situ cantilever-based intrinsic stress optical monitor and adjusted during filter fabrication by deposition parameter modification. The resulting filter has sufficient individual layer thickness control and surface roughness to enable ˜12.

Abstract: An optical filter using alternating layers of materials with “low” and “high” indices of refraction and deposited with atomic layer control has been developed. The multilayered thin film filter uses, but is not limited to, alternating amorphous layers of atomically controlled Si (n=3.56) as the high index material and diamond-like carbon (DLC, n=2.0) as the low index material. The Si layers are grown with a self-limiting pulsed molecular beam deposition process which results in layer-by-layer growth and thickness control to within one atomic layer. The DLC layers are produced using an ion-based process and made atomically smooth using a modified Chemical Reactive-Ion Surface Planarization (CRISP) process. Intrinsic stress is monitored using an in-situ cantilever-based intrinsic stress optical monitor and adjusted during filter fabrication by deposition parameter modification. The resulting filter has sufficient individual layer thickness control and surface roughness to enable ˜12.

Abstract: A method of constructing optical filters using alternating layers of materials with “low” and “high” indices of refraction and deposited with atomic layer control. The multilayered thin film filter uses, but is not limited to, alternating layers of single crystal, polycrystalline or amorphous materials grown with self-limiting epitaxial deposition processes well known to the semiconductor industry. The deposition process, such as atomic layer epitaxy (ALE), pulsed chemical beam epitaxy (PCB E), molecular layer epitaxy (MLE) or laser molecular beam epitaxy (laser MBE) can result in epitaxial layer by layer growth and thickness control to within one atomic layer. The alternating layers are made atomically smooth using a Chemical Reactive-Ion Surface Planarization (CRISP) process. Intrinsic stress is monitored using an in-situ cantilever based intrinsic stress optical monitor and adjusted during filter fabrication by deposition parameter modification.

Abstract: Methods and systems for comparing a first sequence and a second sequence, including associating errors with alignments of the first sequence and the second sequence, comparing the alignment errors to identify the alignment having the smallest error, and, based on the alignment having the smallest error, computing: a first percent identity relative to the first sequence, and a second percent identity relative to the second sequence.

Abstract: An oxygen ion process, Chemical Reactive-Ion Surface Planarization (CRISP), has been developed which enables planarization of thin film surfaces at the atomic level. Narrow/broad band filters produced with vacuum deposited multilayered thin films are designed to selectively reflect/transmit light at specific wavelengths. The optical performance is limited by the ability to control the individual layer thickness, the “roughness” of the individual layer surfaces and the stoichiometry of the layers. The process described herein will enable reduction of surface roughness at the interfaces of multilayered thin films to produce atomically smooth surfaces. The application of this process will result in the production of notch filters of less than 0.3 nm full width at half maximum (FWHM) centered at the desired wavelength.

Abstract: A vacuum deposition system has been designed to produce thin film based demultiplexers with high throughput and production yields of greater than 25% for use in Dense Wavelength Division Multiplexer (DWDM) systems. The system employs a dense array of high yield fixtures and an ion assisted movable dual electron beam evaporation system. The fixture array increases acceptable yields of narrow band pass filters to 25-75% compared to less than 5% in conventional coating systems used for DWDM. The movable e-beam system allows critical symmetry to be maintained while eliminating significant delays resulting from deposition of two materials from a single electron gun. The vacuum deposition system will enable production of more than 15,000 50-200 GHZ filters which meet specifications for DWDM demultiplexers every 48 hours.

Abstract: A substrate fixture has been designed, which significantly improves production yield of thin film based demultiplexer filters for use in Dense Wavelength Division Multiplexer (DWDM) systems. The fixture is comprised of a small area disk capable of rotational speeds greater than 1000 rpm with a dedicated concentric thin film quartz crystal thickness monitor and “clam shell” type shutter. The fixture is intended to be used in a vacuum deposition system, designed to perform optical coatings. The high-speed rotation and location of the fixture with respect to the deposition source guarantees coating thickness uniformity on substrates attached to the disk. The concentric quartz crystal thickness monitor (QCM) calibrated to the geometry or the deposition environment guarantees accurate thickness determination over the area of the disk to within 0.01 percent.

Abstract: An optical filter using alternating layers of materials with “low” and “high” indices of refraction and deposited with atomic layer control has been developed. The multilayered thin film filter uses, but is not limited to, alternating layers of single crystal, polycrystalline or amorphous materials grown with self-limiting epitaxial deposition processes well known to the semiconductor industry. The deposition process, such as atomic layer epitaxy (ALE), pulsed chemical beam epitaxy (PCBE), molecular layer epitaxy (MLE) or laser molecular beam epitaxy (laser MBE) can result in epitaxial layer by layer growth and thickness control to within one atomic layer. The alternating layers are made atomically smooth using the patent pending Chemical Reactive-Ion Surface Planarization (CRISP) process. Intrinsic stress is monitored using an in-situ cantilever-based intrinsic stress optical monitor and adjusted during filter fabrication by deposition parameter modification.

Abstract: An optical filter using alternating layers of materials with “low” and “high” indices of refraction and deposited with atomic layer control has been developed. The multilayered thin film filter uses, but is not limited to, alternating amorphous layers of atomically controlled Si (n=3.56) as the high index material and diamond-like carbon (DLC, n=2.0) as the low index material. The Si layers are grown with a self-limiting pulsed molecular beam deposition process which results in layer-by-layer growth and thickness control to within one atomic layer. The DLC layers are produced using an ion-based process and made atomically smooth using a modified Chemical Reactive-Ion Surface Planarization (CRISP) process. Intrinsic stress is monitored using an in-situ cantilever-based intrinsic stress optical monitor and adjusted during filter fabrication by deposition parameter modification.

Abstract: An oxygen ion process, Chemical Reactive-Ion Surface Planarization (CRISP), has been developed which enables planarization of thin film surfaces at the atomic level. Narrow/broad band filters produced with vacuum deposited multilayered thin films are designed to selectively reflect/transmit light at specific wavelengths. The optical performance is limited by the ability to control the individual layer thickness, the “roughness” of the individual layer surfaces and the stoichiometry of the layers. The process described herein will enable reduction of surface roughness at the interfaces of multilayered thin films to produce atomically smooth surfaces. The application of this process will result in the production of notch filters of less than 0.3 nm full width at half maximum (FWHM) centered at the desired wavelength.

Abstract: A proteome analyzer includes a separation cassette having a first dimension separation compartment for separation of protein samples by isoelectric focusing and a second dimension separation compartment for separation of protein samples by SDS-polymer network electrophoresis. The first dimension compartment is a reservoir in which a porous material having capillary channels is disposed. The protein samples are disposed in the capillary channels and, in the presence of a pH gradient, are focused spatially by isolectric focusing upon application of an electric field. The second dimension compartment consists of two glass or plastic plates separated by a separation medium. The separation medium is an ultra-thin layer of a low concentration linear polymer supported by an inert matrix. The spatially focused protein samples are contacted with the separation medium in the presence of an electric field to initiate second dimension separation.

Abstract: The present invention involves a variety of assay methods and devices for screening or diagnosing the occurrence of extrahepatic biliary atresia. In particular the methods and devices involve an antibody specifically for the detection of dipeptidyl peptidase IV in a test sample as indicative of extrahepatic biliary atresia.