Abstract: The present invention relates to antisense oligonucleotides that modulate the expression of and/or function of NANOG, in particular, by targeting natural antisense polynucleotides of NANOG. The invention also relates to the identification of these antisense oligonucleotides and their use in treating diseases and disorders associated with the expression of NANOG.

Abstract: Computer software products, methods, and systems are described which provide functionality to a user conducting experiments designed to detect and/or identify genetic sequences and other characteristics of a genetic sample, such as, for instance, gene copy number and aberrations thereof. The presently described software allows the user to interact with a graphical user interface which depicts the genetic information obtained from the experiment. The presently disclosed methods and software are related to bioinformatics and biological data analysis. Specifically, provided are methods, computer software products and systems for analyzing and visually depicting genotyping data on a screen or other visual projection. The presently disclosed methods and software allow the user conducting the experiment to differentially filter complex genetic data and information by varying genetic parameters and removing or highlighting visually various regions of genetic data of interest (CytoRegions).

Abstract: A disposable and inexpensive biological diagnostic cartridge for the amplification and detection of nucleic acids includes a configuration having a reaction pouch for amplification which is compressed by a flexible pump pouch for detection of the amplified reaction.

Abstract: A technique for sequencing nucleic acids in an automated or semi-automated manner is disclosed. Sample arrays of a multitude of nucleic acid sites are processed in multiple cycles to add nucleotides to the material to be sequenced, detect the nucleotides added to sites, and to de-block the added nucleotides of blocking agents and tags used to identify the last added nucleotide. Multiple parameters of the system are monitored to enable diagnosis and correction of problems as they occur during sequencing of the samples. Quality control routines are run during sequencing to determine quality of samples, and quality of the data collected.

Abstract: A method and system for optical angular momentum (OAM) spectroscopy includes generating a beam of light having a single OAM mode. A first spectrum of the beam of light is detected and the beam of light is passed through a gas to attenuate the beam of light in accordance with a presence and concentration of a respective gas. A second spectrum the beam of light is coherently detected and a difference between the first and second spectrum for the beam of light is analyzed to determine the presence and concentration of the respective gas.

Abstract: Systems and methods for improved measurement of absorbance/transmission through fluidic systems are described. Specifically, in one set of embodiments, optical elements are fabricated on one side of a transparent fluidic device opposite a series of fluidic channels. The optical elements may guide incident light passing through the device such that most of the light is dispersed away from specific areas of the device, such as intervening portions between the fluidic channels. By decreasing the amount of light incident upon these intervening portions, the amount of noise in the detection signal can be decreased when using certain optical detection systems.

Abstract: The present invention relates to antisense oligonucleotides that modulate the expression of and/or function of PAR4, in particular, by targeting natural antisense polynucleotides of PAR4. The invention also relates to the identification of these antisense oligonucleotides and their use in treating diseases and disorders associated with the expression of PAR4.

Abstract: Methods of determining a corrected analyte concentration in view of some error source are provided herein. The methods can be utilized for the determination of various analytes and/or various sources of error. In one example, the method can be configured to determine a corrected glucose concentration in view of an extreme level of hematocrit found within the sample. In other embodiments, methods are provided for identifying various system errors and/or defects. For example, such errors can include partial-fill or double-fill situations, high track resistance, and/or sample leakage. Systems are also provided for determining a corrected analyte concentration and/or detecting some system error.

Abstract: An apparatus for performing a thermocyclic process, such as amplifying DNA, includes a microfluidic chip with a channel formed therein and one or more thermal distribution elements disposed over portions of the chip. Each thermal distribution element is configured to distribute thermal energy from an external thermal energy source substantially uniformly over the portion of the chip covered by the thermal distribution element. The portion of the chip covered by the thermal distribution element thereby comprises a discrete temperature zone. Other temperature zones can be defined by other thermal distribution elements or by portions of the chip not covered by a thermal distribution element. The channel is configured so that a fluid flowing through the channel would enter and exit the different temperature zones a plurality of times, thereby alternately exposing the fluid to the temperature of each zone for a period of time required for the fluid to traverse the zone.

Abstract: A chip device for manipulating an object component is described, in which multiple liquid substances such as reagents required for a series of manipulations on a sample are stably secured in separated states throughout the manipulations within the device. The chip device includes a manipulation chip, magnetic particles, and a magnetic field application means. The manipulation chip includes a substrate, a groove formed in the surface of the substrate, and a manipulation medium accommodated in the groove such that gel phases and aqueous liquid phases are alternately disposed in the longitudinal direction of the groove and are in contact with each other. The magnetic particles are for capturing and carrying the object component. The magnetic field application means is capable of moving the magnetic particles in the longitudinal direction of the groove in the substrate by the application of a magnetic field to the substrate.

Abstract: Methods and systems to apply a plurality of test voltages to the test strip and measure a current transient output resulting from an electrochemical reaction in a test chamber of the test strip so that a glucose concentration can be determined that account for interferent substances in the body fluid sample. A method of determining blood glucose concentration with a glucose measurement system that includes a test strip and test meter. The test meter has a microcontroller configured to apply a plurality of test voltages to the test strip and measure a current transient output resulting from an electrochemical reaction in a test chamber of the test strip.

Abstract: Provided are methods, systems, and kits for diagnosing or monitoring systemic lupus erythematosus in an individual. In particular aspects, in a blood sample containing white blood cells from the individual, autoantibodies deposited on or contacting with the surface of a T lymphocyte in the sample are quantitated.

Abstract: The present invention relates to optical confinements, methods of preparing and methods of using them for analyzing molecules and/or monitoring chemical reactions. The apparatus and methods embodied in the present invention are particularly useful for high-throughput and low-cost single-molecular analysis.

Abstract: The object of the invention is the provision of methods for controlled production of continuous multi-component filaments or discreet structures using a multi-component liquid jet issuing from an orifice. A multi-component jet consists of two or more liquids. The liquids may be miscible or immiscible, and form a co-axially propagating flow along the central axis of a flow cell. The working distance between the exit orifice and a substrate can be as large as 50 mm, so that in-flight processing of the jet is possible. The coaxial flow consists of an outer sheath liquid and an inner sample liquid or composite of liquids. The flow cell and the exit channel of the deposition head are heated so that the pressurized sheath liquid temperature is raised to near or above the boiling point of the sheath liquid at the local atmospheric pressure. The jet exits the deposition head through the orifice, and the outer liquid is evaporated as the jet falls at atmospheric pressure.

Abstract: Microfluidic devices and methods for the encapsulation of particles within liquid droplets are disclosed. The new methods and devices form 1-100 picoliter-size monodisperse droplets containing the particles, such as single cells, encapsulated in individual liquid droplets. The particles can be encapsulated in droplets of a fluid by passing a fluid containing the particles through a high aspect-ratio microchannel to order the particles in the fluid, followed by forming the fluid into droplets. The resulting fraction of the liquid droplets with a single particle (e.g., a cell) is higher than the corresponding fraction of single-particle liquid droplets predicted by Poisson statistics.

Abstract: A hybridization system is provided, which comprises a biological chip having a substrate (1) with a probe dot matrix (3) and a cover plate (2) with at least two through-holes (4), where a hybrid chamber (5) is formed between the substrate (1) and the cover plate (2), at least two fluid channels (6) are interconnected respectively with the hybrid chamber (5) by the two through-holes (4), and a fluid control device is interconnected with the fluid channels (6). The biological chip hybridization system integrates hybridizing, cleaning and drying functions, uses power provided by the fluid control device as the drive force for promoting the liquid flow for automatically reciprocation flow in the fluid channels (6) and the chamber (5) to achieve a dynamic hybridization, thus improving the hybrid efficiency and uniformity, and achieving automatic control.

Abstract: An improved monocyte activation test is described that is better able to detect non-endotoxin pyrogens in medical products, in which a sample is incubated with a monocyte-containing reagent in an assay system comprising at least one surface comprising polypropylene. The invention also concerns assay systems for use in these tests that include at least one microtiter well having at least one interior surface comprising polypropylene and having a shape such that monocyte-containing reagent is concentrated in the well to provide greater cell to cell contact. The invention also relates to a diagnostic kit that can be used to test for the presence of non-endotoxin pyrogens in a sample.

Abstract: A microscope including a sample carrier configured to support a sample. Excitation light illuminates the sample via an excitation beam path, Detection light from the sample is guided to detection means via a detection beam path. Through an objective arranged along the optical axis, excitation light is guided in direction of the sample carrier and detection light coming from the sample is guided in direction of the detection means. Beam-splitting means separate excitation light and detection light. Also provided are means for generating a light sheet from excitation light, and means for illuminating the sample with this light sheet. The light sheet lies in a plane at a nonzero angle to the optical axis. The means for illuminating the sample include an optical-deflecting device arranged on or at the sample carrier, which deflects excitation light from the objective into the plane of the light sheet via an optically active surface.

Abstract: Presented herein is a method and devices for identifying biological molecules and cells labeled by small magnetic particles and by optically active dyes. The labeled molecules are typically presented in a biological fluid but are then magnetically guided into narrow channels by a sequential process of magnetically trapping and releasing the magnetic labels that is implemented by sequential synchronized reversing the magnetic fields of a regular array of patterned magnetic devices that exert forces on the magnetic particles. These devices, which may be bonded to a substrate, can be formed as parallel magnetic strips adjacent to current carrying lines or can be substantially of identical structure to trilayered MTJ cells. Once the magnetically labeled molecules have been guided into the appropriate channels, their optical labels can be detected by a process of optical excitation and de-excitation. The molecules are thereby identified and counted.

Abstract: A random access, high-throughput system and method for preparing a biological sample for polymerase chain reaction (PCR) testing are disclosed. The system includes a nucleic acid isolation/purification apparatus and a PCR apparatus. The nucleic acid isolation/purification apparatus magnetically captures nucleic acid (NA) solids from the biological sample and then suspends the NA in elution buffer solution. The PCR testing apparatus provides multiple cycles of the denaturing, annealing, and elongating thermal cycles. More particularly, the PCR testing apparatus includes a multi-vessel thermal cycler array that has a plurality of single-vessel thermal cyclers that is each individually-thermally-controllable so that adjacent single-vessel thermal cyclers can be heated or cooled to different temperatures corresponding to the different thermal cycles of the respective PCR testing process.

Abstract: System, including methods, apparatus, and kits, for forming and concentrating emulsions. An exemplary system may comprise a device including a sample well configured to receive sample-containing fluid, a continuous-phase well configured to receive continuous-phase fluid, a droplet well, and a channel network interconnecting the wells. The system also may comprise an instrument configured to operatively receive the device and to create (i) a first pressure differential to produce an emulsion collected in the droplet well and (ii) a second pressure differential to decrease a volume fraction of continuous-phase fluid in the emulsion, after the emulsion has been collected in the droplet well, by selectively driving continuous-phase fluid, relative to sample-containing droplets, from the droplet well.

Abstract: System, including methods and apparatus, for sample processing. In exemplary embodiments, the system comprises a plurality of devices to perform a protocol on sample holders supporting samples, and also comprises a control system that coordinates operation of the plurality of devices, such that the protocol is performed automatically. Each device of at least two of the plurality of devices may have one or more status lights configured to display a plurality of different visual indicators each indicating a different status of the device. The at least two devices may utilize a same indicator scheme as one another for each different status indicated by the visual indicators. In some embodiments, the indicator scheme is user-configurable. In some embodiments, the one or more status lights of at least one device are provided by one or more recessed light-emitting strips.

Abstract: System, including methods, apparatus, and kits, for forming emulsions. An exemplary system may comprise a device including a sample well configured to receive sample-containing fluid, a continuous-phase well configured to receive continuous-phase fluid, and a droplet well. The device also may include a channel network having a first channel, a second channel, and a third channel that meet one another in a droplet-generation region. The system also may comprise a holder for the device. The system further may comprise an instrument configured to operatively receive an assembly including the device and the holder and to drive sample-containing fluid from the sample well to the droplet-generation region via the first channel, continuous-phase fluid from the continuous-phase well to the droplet-generation region via the second channel, and sample-containing droplets from the droplet-generation region to the droplet well via the third channel.

Abstract: The present invention provides a novel technique by which the redox activity of a nucleic acid molecule can be evaluated. An evaluation method of the present invention includes: a detection step of electrochemically detecting a redox reaction to a substrate, the redox reaction being catalyzed by a nucleic acid molecule to be evaluated, using a device that electrochemically detects a redox reaction; and an evaluation step of evaluating redox activity of the nucleic acid molecule from a result of the detection of the redox reaction. As the device, a device in which a base provided with a detection portion is included, the detection portion includes an electrode system, and the nucleic acid molecule to be evaluated is arranged on the base is used. In the present invention, it is preferred that a plurality of kinds of nucleic acid molecule to be evaluated is arranged on the base, and the plurality of kinds of nucleic acid molecules to be evaluated is evaluated by a single device.

Abstract: An apparatus for purifying nucleic acid can include a disposable cartridge having a layered configuration, and a disposable syringe for coupling to the disposable cartridge such that a fluid can be delivered to or withdrawn fluid from the disposable cartridge using the syringe. At least one layer of the disposable cartridge can include a cut-out for forming a functional unit of the disposable cartridge, and at least one layer of the disposable cartridge can be joined to an adjacent layer of the disposable cartridge by an adhesive material layer. The functional unit can include a fluid channel between an access port on the first surface of the disposable cartridge and the fluid pouch. The apparatus can include a disposable silica-containing material for binding with the nucleic acid. The apparatus can include a heating element and a temperature sensor for heating the disposable silica-containing material.

Abstract: A system and method for processing and detecting nucleic acids from a set of biological samples, comprising: a capture plate and a capture plate module configured to facilitate binding of nucleic acids within the set of biological samples to magnetic beads; a molecular diagnostic module configured to receive nucleic acids bound to magnetic beads, isolate nucleic acids, and analyze nucleic acids, comprising a cartridge receiving module, a heating/cooling subsystem and a magnet configured to facilitate isolation of nucleic acids, a valve actuation subsystem configured to control fluid flow through a microfluidic cartridge for processing nucleic acids, and an optical subsystem for analysis of nucleic acids; a fluid handling system configured to deliver samples and reagents to components of the system to facilitate molecular diagnostic protocols; and an assay strip configured to combine nucleic acid samples with molecular diagnostic reagents for analysis of nucleic acids.

Abstract: A method of projection a production characteristic includes receiving down well video image data depicting multiphase flow within the well, determining a flow rate data of at least one phase of the multiphase flow based on the down well video image data, and projecting the production characteristic based at least in part on the determined flow rate using a well performance model.

Abstract: Methods and kits for sampling mucous from within a sinus to determine if a single sample includes one or more bacterial types indicating bacterial sinusitis.

Abstract: A biological fluid collection device that is adapted to receive a multi-component blood sample having a cellular portion and a plasma portion is disclosed. After collecting the blood sample, the biological fluid collection device is able to separate the plasma portion from the cellular portion. After separation, the biological fluid collection device is able to transfer the plasma portion of the blood sample to a point-of-care testing device. The biological fluid collection device also provides a closed sampling and transfer system that reduces the exposure of a blood sample and provides fast mixing of a blood sample with an anticoagulant. The biological fluid collection device is engageable with a testing device for closed transfer of a portion of the plasma portion from the biological fluid collection device to the testing device. The testing device is adapted to receive the plasma portion to analyze the blood sample and obtain test results.

Abstract: Nucleic acid from cells and viruses sampled from a variety of environments may purified and expressed utilizing microfluidic techniques. In accordance with one embodiment of the present invention, individual or small groups of cells or viruses may be isolated in microfluidic chambers by dilution, sorting, and/or segmentation. The isolated cells or viruses may be lysed directly in the microfluidic chamber, and the resulting nucleic acid purified by exposure to affinity beads. Subsequent elution of the purified nucleic acid may be followed by ligation and cell transformation, all within the same microfluidic chip. In one specific application, cell isolation, lysis, and nucleic acid purification may be performed utilizing a highly parallelized microfluidic architecture to construct gDNA and cDNA libraries.

Abstract: A method for performing polymerase chain reactions (PCR) for improving thermal non-uniformity is provided. The method includes measuring a first temperature, by a first sensor, of a first sample block sector of a sample block and measuring a second temperature, by a second sensor, of a second sample block sector of the sample block that is adjacent to the first sample block sector. The method further includes calculating, by a thermoelectric controller, a difference in temperature between the first temperature and the second temperature and adjusting, by the thermoelectric controller, the first temperature of the first sample block sector based on the difference in temperature by using one or more thermoelectric coolers. The one or more thermoelectric coolers is configured to heat or cool the first sample block sector by adjusting power output from the thermoelectric controller.

Abstract: Embodiments are directed to microfluidic refill cartridges and methods of assembling same. The microfluidic refill cartridges include a microfluidic delivery member that includes a filter for filtering fluid passed therethrough. The filter may be configured to block particles above a threshold size to prevent blockage in the nozzles. For instance, particles having a dimension that is larger than the diameter of the nozzles can block or reduce fluid flow through the nozzle.

Abstract: Fluidic devices and methods including those that provide storage and/or facilitate fluid handling of reagents are provided. Fluidic devices described herein may include channel segments positioned on two sides of an article, optionally connected by an intervening channel passing through the article. The channel segments may be used to store reagents in the device prior to first use by an end user. The stored reagents may include fluid plugs positioned in linear order so that during use, as fluids flow to a reaction site, they are delivered in a predetermined sequence. The specific geometries of the channel segments and the positions of the channel segments within the fluidic devices described herein may allow fluid reagents to be stored for extended periods of time without mixing, even during routine handling of the devices such as during shipping of the devices, and when the devices are subjected to physical shock or vibration.

Abstract: Methods and systems for controlling fluid flow through a cartridge for use in an assay of a fluid sample for detection of a target analyte. In one aspect, the cartridge includes a microfluidic device having a network of microfluidic channels, one or more reservoirs and one or more actuatable valves for controlling fluid flow from the reservoirs through the microfluidic channels. In some embodiments, the valve includes a deformable membrane movable between a closed configuration in which the membrane seals against the microfluidic device inhibiting fluid flow and an open configuration moved away from the microfluidic device to allow fluid flow through the microfluidic channels. Other valve embodiments utilize frangible membranes or user-removable membrane.

Abstract: A sample processing apparatus includes a laser triangulation system that locates the position of a lower end of a pipette tip. When the laser triangulation system identifies a discrepancy between the actual position of the lower end and the proper position of the lower end, the sample processing apparatus may undergo a compensating action to compensate for the discrepancy.

Abstract: Provided are a system for integrated analysis of a real-time polymerase chain reaction and a DNA chip and a method for integrated analysis using the same, and more particularly to an apparatus for integrated analysis of a real-time polymerase chain reaction and a DNA chip and a method for integrated analysis using the same. According to the method for integrated analysis of a biomaterial of the present invention, gene amplification proceeds and subsequently hybridization proceeds in a single reactor, thereby preventing contamination of the sample due to external factors, which may be caused while the sample is transferred for reaction, and automating a series of procedures such as injection of the sample, reaction of the biomaterial, and detection and analysis of results.

Abstract: Provided are methods for sequencing a nucleic acid with a sequencing enzyme, e.g., a polymerase or exonuclease. The sequencing enzyme can optionally be exchanged with a second sequencing enzyme, which continues the sequencing of the nucleic acid. In certain embodiments, a template is fixed to a surface through a template localizing moiety. The template localizing moiety can optionally anneal with the nucleic acid and/or associate with the sequencing enzyme. Also provided are compositions comprising a nucleic acid and a first sequencing enzyme, which can sequence the nucleic acid and optionally exchange with a second sequencing enzyme present in the composition. Compositions in which a template localizing moiety is immobilized on a surface are provided. Also provided are methods for using data from analytical reactions wherein two different enzymes are employed, e.g., at a same or different reaction regions.

Abstract: The invention relates to microscale cell separating apparatus which are able to separate cells on the basis of size of the cells, interaction of the cells with surfaces of the apparatus, or both. The apparatus comprises a stepped or sloped separation element (16) interposed between an inlet region (20) and an outlet region (22) of a void that can be filled with fluid. The void can be enclosed within a cover (12) and fluid flow through the void engages cells with the separation element. Only cells which have (or can deform to have) a characteristic dimension smaller than or equal to the distance between a step and the cover or body can pass onto or past a step. Modifications of surfaces within the apparatus can also inhibit passage of cells onto or past a step.

Abstract: The invention relates to microscale cell separating apparatus which are able to separate cells on the basis of size of the cells, interaction of the cells with surfaces of the apparatus, or both. The apparatus comprises a stepped or sloped separation element (16) interposed between an inlet region (20) and an outlet region (22) of a void that can be tilled with fluid. The void can be enclosed within a cover (12) and fluid flow through the void engages cells with the separation element. Only cells which have (or can deform to have) a characteristic dimension smaller than or equal to the distance between a step and the cover or body can pass onto or past a step. Modifications of surfaces within the apparatus can also inhibit passage of cells onto or past a step.

Abstract: The present invention relates to antisense oligonucleotides that modulate the expression of and/or function of ‘IQ motif containing GTPase activating protein’ (IQGAP), in particular, by targeting natural antisense polynucleotides of ‘IQ motif containing GTPase activating protein’ (IQGAP). The invention also relates to the identification of these antisense oligonucleotides and their use in treating diseases and disorders associated with the expression of IQGAP.

Abstract: Methods and microfluidic apparatus are disclosed for drug prediction. A microfluidic apparatus has (a) a plate, (b) a plurality of wells defined in the plate, (c) a plurality of closed microchannels defined in the plate, and (d) a sample platform defining a plurality of open microchannels, where the plurality of closed microchannels are each in communication with one of the plurality of wells and one of the plurality of open microchannels of the sample platform.

Abstract: The present invention provides a flow-channel device for detecting light emission, which suppresses a noise originating in unnecessary light emission, and can be simply bonded with the use of an organic material. The flow-channel device having a flow channel is structured by the bonding of at least two substrates, wherein at least any one substrate has a first groove which constitutes the flow channel, and a second groove for arranging an adhesive therein which contains an organic material, and a light-shielding layer is provided on an inner wall of the second groove so as to block a light emitted from the second groove from penetrating into the first groove.

Abstract: Universal reference dye mixtures for quantitative amplification, and uses thereof, are provided.

Abstract: Provided are compounds comprising oligonucleotides complementary to a fibronectin transcript. Certain such compounds are useful for hybridizing to a fibronectin transcript, including but not limited to a fibronectin transcript in a cell. Such hybridization results in modulation of splicing of the fibronectin transcript. Such compounds are used to treat one or more symptoms associated with fibrosis. Such compounds are used to treat one or more symptoms associated with renal fibrosis.

Abstract: Novel methods of generating a localized population of immobilized clonal amplicons on a support are provided.

Abstract: A nucleic acid extraction device, which can realize automation, ultra-miniaturization and super-high speed in the nucleic acid extraction reaction, has no limitation to the type of biological specimens that can be used, such as sputum, blood, cells, urine, saliva, tissues, etc., minimize the used amount of the sample solution, and also maintain and/or improve the nucleic acid extraction efficiency with reliability.

Abstract: The invention relates to a microfluidic circuit including at least one microchannel for the flow of a first fluid conveying drops or bubbles of at least one second fluid, characterized in that the height of the microchannel is sized so as to crush the drops or bubbles during the movement thereof, and in that the microchannel comprises at least one trough, extending at least partially in the direction of flow of the first fluid or an area for trapping drops or bubbles, said area or the trough having a height that is greater than the height of the microchannel, such that at least some of the drops or bubbles of the second fluid in the microchannel are drawn and guided into the trough or into the trapping area.

Abstract: Provided are devices and methods for effecting processing of samples, including essentially isothermal amplification of nucleic acids, at multiple reaction locations in a single device. In some embodiments, the disclosed devices and methods provide for effecting parallel sample processing in several hundred locations on a single device.

Abstract: The present invention is directed to methods and compositions for the use of micro sphere arrays to detect and quantify a number of nucleic acid reactions. The invention finds use in genotyping, i.e. the determination of the sequence of nucleic acids, particularly alterations such as nucleotide substitutions (mismatches) and single nucleotide polymorphisms (SNPs). Similarly, the invention finds use in the detection and quantification of a nucleic acid target using a variety of amplification techniques, including both signal amplification and target amplification. The methods and compositions of the invention can be used in nucleic acid sequencing reactions as well. All applications can include the use of adapter sequences to allow for universal arrays.

Abstract: A system for nucleic acid amplification of a sample comprises partitioning the sample into partitioned sections and performing PCR on the partitioned sections of the sample. Another embodiment of the invention provides a system for nucleic acid amplification and detection of a sample comprising partitioning the sample into partitioned sections, performing PCR on the partitioned sections of the sample, and detecting and analyzing the partitioned sections of the sample.