Abstract: The present invention describes microplates with arrays of wells containing magnetic inserts in the form of disks, cylinders or otherwise shaped materials with apertures in the centre for optical interrogation of the contacting solution. These inserts are capable of capturing ferro- and paramagnetic nano- and microparticles. The subject microplates find use in a variety of applications, including clinical and environmental assays, high throughput screening for genomics, proteomics and pharmaceutical applications, point-of-care in vitro diagnostics, molecular genetic analysis and nucleic acid diagnostics, cell separations, and bioresearch generally and high-throughput screening of materials for separation and catalysis.

Abstract: A high-throughput corrosion testing mechanism was developed for metals in a variety of environments in controlled, multiplexed microenvironments. Many parallel experiments can be conducted with microbial and environmental variables independently manipulated to identify the key determinants of corrosion progression. The synthetic assay design enables subsequent surface characterization of select samples within the array. In as little as one day, diverse corrosive environments can be compared quantitatively.

Abstract: Techniques for hydrogel microstructures with oil isolation for small reaction volumes include providing a hydrogel microstructure that has a plurality of pores and a hydrogel frame surrounding the pores. The microstructure has a volume in a range from about 1 picoliter to about 10,000 picoliters and is configured to repel an immiscible fluid. Each pore of the plurality of pores has a pore size configured to pass the target molecule in a first solution. The microstructure is contacted with the first solution, and with a second solution that includes a reactant molecule that reacts with the target molecule to produce an observable product molecule. The microstructure is encompassed with the immiscible fluid for an extended observation duration from about 1 to about 10,000 seconds, wherein the immiscible fluid does not pass into the pores but traps the product in the microstructure. The observable product molecule is measured at some time during the observation duration.

Abstract: A biological sample processing apparatus having an enclosure. A plurality of sample processing modules are held by the enclosure. Each sample processing module is configured to hold a removable sample cartridge and to only perform sample processing on a sample within the corresponding removable sample cartridge. Each sample processing module is configured to perform at least one of a plurality of testing processes on the sample within the removable sample cartridge. At least one module in the apparatus is configured to perform nucleic acid amplification and detection.

Abstract: A system for performing one or more microfluidic processes includes an integrated fluidic device comprising a plurality of well regions and a plurality of control valves and a workflow manager. The system also includes a transfer robot adapted to transfer the integrated fluidic device between a plurality of stations in response to a series of instructions from the workflow manager and a first station comprising a dispensing robot adapted to dispense at least one of a plurality of sample solutions and at least one of a plurality of reagents into the integrated fluidic device. The system further includes a second station comprising a fluidic controller unit and a third station comprising an inspection station.

Abstract: There are systems and methods for performing an assay to generate genotype information about a subject associated with a medical condition. There are also systems and method for generating and utilizing prognostic information associated with treating the patient with a medication based on the genotype information and an association of the genotype and metabolizing the medication. The genotype information includes data relating to SNP alleles in the patient's genotype and the association of the alleles and metabolism of a medication by the patient.

Abstract: Novel and improved systems and methods for high speed arraying, hybridization, quantitative development and/or assaying are provided. Some embodiments provide a web based arraying format. Some other embodiments provide a sheet based arraying format. Some embodiments use a drop on drop assaying or hybridization mode. In some embodiments, a substantially inert substrate is utilized. In some other embodiments, an interactive substrate is utilized.

Abstract: This disclosure relates generally to the prediction of a gene target of an enhancer based on genomic proximity and a comparison to a set of known enhancer-gene pairs. A gene can be selected a gene from a given cell type. A domain can be established bi-directionally around the gene, and enhancers located within the domain can be identified. The enhancers located within the domain can be considered to be in close genomic proximity to the gene. For each enhancer, a test pair of the enhancer and the gene can be established and compared to a set of known enhancer-gene pairs. The prediction can be established based on the comparison and the genomic proximity.

Abstract: This invention relates to determination of quantitative expression of plasma membrane proteins as biomarkers in the erythrocytes. The invention includes simple, quantitative assay platforms which can be made available in most diagnostic laboratories. The platform allows performing personalized, quantitative tests for the direct expression level of a wide range of membrane proteins from small volume blood samples and connecting them to individual genetic variability, disease conditions, disease stages and complications, treatment protocols, pharmacological responses, or toxic side effects.

Abstract: Biosensor components (chips) are described based on direct biocoating processes that result in the tenacious and stable, noncovalent (believed to be chemisorptive) binding of anchor substances such as avidin(s) other proteins having specific binding partners or oligo- or poly-nucleotides onto any piezo-electrically active crystal surface. The resulting platform technology can be developed for a variety of biosensors with specific applications in biological assays. The table mono layers of the anchor substances forms reactive layers, ready to bind a capture reagent such as a biot-inylated antibody for capture and detection of analytes in biologic fluid samples.

Abstract: The invention is a device for testing an individual for the presence of a entity. The entity can be a pathogen, toxin or drug. The device is adapted to collect from the individual the biological sample to be tested. The test device comprises noble metal nanoparticles (i.e. gold, silver or copper) to detect the entity. Test results are read from a window in the device. The current visual limit using aggregated noble metal nanoparticles is a clump having a diameter in a range of about 50 nm to about 75 nm. One or more ligands specific for the entity are attached to two or more metal nanoparticles. Each individual nanoparticle has a diameter in a range of about 15 nm to about 35 nm. Ligands attached to the nanoparticles and specific for the entity can be for example antibodies, antibody fragments, oligonucleotides, and aptamers. Different ligands specific for different sites on the entity may be used in order to increase the aggregation potential of the nanoparticles in the presence of the target.

Abstract: The methods of the present invention provide methods for manufacturing a master substrate and methods for manufacturing replica arrays from the master substrate. The methods may be used, for example, directly to manufacture or “print” peptide arrays from a DNA array; however, the methods are applicable to a wide range of manufacturing applications for use any time multiple copies of an array needs to be printed.

Abstract: Analysis of a system and/or sample involves the use of absorption-encoded micro beads. Each type of micro bead is encoded with amounts of the k dyes in a proportional relationship that is different from proportional relationships of the k dyes of others of the n types of absorption-encoded micro beads. A system and/or a sample can be analyzed using information obtained from detecting the one or more types of absorption-encoded micro beads.

Abstract: A micro-fluidic device for mapping a DNA or RNA strand labeled at a plurality of specific sites with labels suitable for generating a detection signal when interacting with a detector element, the device comprising: a micro-fluidic channel; and a plurality of detector elements for detecting the labels by acquiring the detection signals, the detector elements being positioned longitudinally along the micro-fluidic channel, each detector element having a width, successive detector elements being separated by an inter-detector gap having a width, wherein the widths of at least two of the detector elements are different and/or wherein the widths at least two of the inter-detector gaps are different.

Abstract: A method for analyzing a binding ability of protein to a compound, involves fractionating first and second groups of proteins into plural fractions using a carrier having the compound immobilized thereon; combining fractions, analyzing the combined fractions with mass spectrometry; based on the mass spectrometry information, obtaining, regarding each fraction, an intensity ratio between peaks derived from a protein in each of the groups of fractions; and comparing degrees of the binding ability of the plural kinds of proteins to the compound.

Abstract: Microfluidic devices and methods for using the same are provided. Aspects of the invention include microfluidic devices that include a separation medium and a pan-capture binding medium. The microfluidic devices are configured to subject a sample to two or more directionally distinct electric fields. Also provided are methods of using the devices as well as systems and kits that include the devices. The devices, systems and methods find use in a variety of different applications, including diagnostic and validation assays.

Abstract: Preeclampsia markers, preeclampsia marker panels, and methods for obtaining a preeclampsia marker level representation for a sample are provided. These compositions and methods find use in a number of applications, including, for example, diagnosing preeclampsia, prognosing a preeclampsia, monitoring a subject with preeclampsia, and determining a treatment for preeclampsia. In addition, systems, devices and kits thereof that find use in practicing the subject methods are provided.

Abstract: A method of detection of a target nucleic acid is provided. The method includes fractionating a sample into a plurality of sample volumes wherein more than 50% of the fractions contain no more than 1 target nucleic acid molecule per sample volumes, and subjecting the plurality of sample volumes to conditions for amplification. The method further includes detecting a change in ion concentration in a sample volume wherein a target nucleic acid is present, counting the number of fractions with an amplified target nucleic acid, and determining the quantity of target nucleic acid in the sample.

Abstract: Disclosed is a test device to detect pregnancy in a human female subject, the test device comprising: an assay means to measure the absolute or relative amount of hCG in a sample from the subject; an assay means to measure the absolute or relative amount of FSH in a sample from the subject; and an assay means to measure the absolute or relative amount of one or more progesterone metabolites in a sample from the subject.

Abstract: A method and apparatus for diagnosing cancer by using genetic information, the method comprising acquiring first gene expression data of a subject, for whom cancer is to be diagnosed, for a gene marker set including at least one gene marker; and determining a possibility of a presence of the cancer of the subject by using the acquired first gene expression data and pre-stored second gene expression data of a normal person group and a cancer patient group, wherein the gene marker set includes gene markers such as pyrroline-5-carboxylate reductase 1 (PYCR1), phosphoglycerate dehydrogenase (PHGDH), glutaminase 2 (liver, mitochondrial) (GLS2), and glutaminase (GLS) among others.

Abstract: A bio-disc device including new valve control means and fluid movement system, a bio-driver apparatus in which a controller disc including a controller for the bio-disc is installed, and an assay method using the same, which are suitable for labs-on-a-chips for various diagnostic assays, nucleic acid hybridization assays, and immunoassays, are provided. The bio-driver apparatus is compatible with general optical discs, including audio CDs, CD-Rs, game CDs, DVDs, etc., and the assay method is compatible with general optical disc drivers, including CD-ROMs, DVD players, etc. Thus, the bio-driver apparatus and the assay method offer and economical and convenient alternative to existing products. In addition, the bio-driver apparatus can be readily and easily applied in connection with a computer for remote diagnosis via the Internet.

Abstract: The present invention relates to systems and methods for minimizing or eliminating diffusion effects. Diffused regions of a segmented flow of multiple, miscible fluid species may be vented off to a waste channel, and non-diffused regions of fluid may be preferentially pulled off the channel that contains the segmented flow. Multiple fluid samples that are not contaminated via diffusion may be collected for analysis and measurement in a single channel. The systems and methods for minimizing or eliminating diffusion effects may be used to minimize or eliminate diffusion effects in a microfluidic system for monitoring the amplification of DNA molecules and the dissociation behavior of the DNA molecules.

Abstract: Apparatus, systems, and methods for detecting, screening and sampling of cells are disclosed.

Abstract: A microfluidic device comprising a microfluidic channel network sealed on one side by a membrane sheet, the sheet having PDMS defining at least the surface sealing the channel, the membrane sheet on its opposite side sealing one side of a pneumatic channel, the pneumatic channel arranged to enable pneumatic deflection of a deflectable portion of the membrane sheet into contact with an opposed surface to control flow in a channel of the network, the membrane sheet confining in a channel of the network at least one micro-particle, micro-length tube or glass nano reactor, functionalized with a capture agent, that has been inserted into that channel. A microfluidic device having a microfluidic channel containing at least two micro-particles, micro-length tubes or glass nano reactors, one functionalized with nucleic acid and another with antibody or antigen.

Abstract: The methods of the present invention provide methods for manufacturing a master substrate and methods for manufacturing replica arrays from the master substrate. The methods may be used, for example, directly to manufacture or “print” peptide arrays from a DNA array; however, the methods are applicable to a wide range of manufacturing applications for use any time multiple copies of an array needs to be printed.

Abstract: A system for performing biological reactions is provided. The system includes a chip including a substrate and a plurality of reaction sites. The plurality of reaction sites are each configured to include a liquid sample of at most one nanoliter. Further, the system includes a control system configured to initiate biological reactions within the liquid samples. The system further includes a detection system configured to detect biological reactions on the chip. According to various embodiments, the chip includes at least 20000 reaction sites. In other embodiments, the chip includes at least 30000 reaction sites.

Abstract: A luminescence detecting apparatus and method for analyzing luminescent samples is disclosed. Luminescent samples are placed in a plurality of sample wells in a tray, and the tray is placed in a visible-light impervious chamber containing a charge coupled device camera. The samples may be injected in the wells, and the samples may be injected with buffers and reagents, by an injector. In the chamber, light from the luminescent samples pass through a collimator, a Fresnel field lens, a filter, and a camera lens, whereupon a focused image is created by the optics on the charge-coupled device (CCD) camera. The use of a Fresnel field lens, in combination with a collimator and filter, reduces crosstalk between samples below the level attainable by the prior art. Preferred embodiments of the luminescence detecting apparatus and method disclosed include central processing control of all operations, multiple wavelength filter wheel, and robot handling of samples and reagents.

Abstract: Embodiments of the present disclosure generally pertain to systems and methods for performing amplicon rescue multiplex polymerase chain reaction (arm-PCR). In one embodiment, the system comprises a processor and a reader coupled to a control element. The control element is configured to control the operation of the processor and the reader based on a variety of settings. The processor is configured to receive a self-contained cassette for performing PCR amplification of DNA and/or RNA obtained from an organic specimen. The processor engages with the cassette and manipulates reagents within the cassette in order to amplify and detect the DNA from the specimen. The processor also causes the cassette to deposit the DNA on a microarray within the cassette. The reader is configured to receive the cassette after it has been processed by the processor and to capture an image of the microarray for transmission to the control element as test data.

Abstract: Provided herein are methods and systems of molecular profiling of diseases, such as cancer. In some embodiments, the molecular profiling can be used to identify treatments for a disease, such as treatments that were not initially identified as a treatment for the disease or not expected to be a treatment for a particular disease.

Abstract: A system and method for characterizing contributions to signal noise associated with charge-coupled devices adapted for use in biological analysis. Dark current contribution, readout offset contribution, photo response non-uniformity, and spurious charge contribution can be determined by the methods of the present teachings and used for signal correction by systems of the present teachings.

Abstract: Provided herein are methods and systems of molecular profiling of diseases, such as cancer. In some embodiments, the molecular profiling can be used to identify treatments for a disease, such as treatments that were not initially identified as a treatment for the disease or not expected to be a treatment for a particular disease.

Abstract: Disclosed herein are methods of treating a patient at risk of developing or having a neurofibromatosis or a sporadic schwannoma. In exemplary embodiments, the method involves administering to a subject in need an effective amount of a modulator of a target related to neurofibromatosis. Also disclosed are screening assays involving the implementation of Merlin-null Schwann cells, and to compounds identified using same.

Abstract: A detection device and associated systems and methods for detecting analytes from a multiplex reaction are described. In particular, a device for conducting at least one detection reaction using a modified ELISA method including a surface with a detection region and a reference region, a detection sensor, and a light source. The detection device may include a complementary metal-oxide-semiconductor (CMOS) image sensor. The device may be used to measure and report discrete quantities or combinations of discrete analytes, providing information to aid in the prognosis and/or diagnosis of altered states of health in vertebrates.

Abstract: The present invention provides a method for determining radioactivity in an ion-sensitive field effect transistor array, the method comprising the steps of incubating the array with electron-sensitive silver-halide material and then incubating the array with a developer solution reducing the silver halides that have been exposed to radioactivity to elemental silver and simultaneously measuring pH at each separate reaction chambers, wherein decrease of the pH indicates the presence of radioactivity in a reaction chamber.

Abstract: Disclosed herein are computer-based systems, media and methods of generating dynamic classifiers and uses thereof. The dynamic classifiers may be generated from a subset of cases and/or a subset of genes that have a molecular similarity to a subject suffering from a cancer. Thus, the dynamic classifiers may be subject-specific. The dynamic classifiers may be used in the diagnosis, prognosis and/or monitoring of a status or outcome of a cancer in a subject in need thereof.

Abstract: Methods and systems for manipulating drops in microfluidic channels are provided.

Abstract: An assay assembly includes an assay plate. The assay plate includes at least one hydrophobic area and a plurality of hydrophilic areas defined by the hydrophobic area, wherein the hydrophilic areas are defined as a plurality of assay areas. Due to the specialized structure of the assay plate, droplets around the assay areas are drawn to the assay area by pushing force of the hydrophobic area and the pulling force of the assay area. In addition, the shaker is coupled to the assay plate and configured for shaking the assay plate thereby droplets around the assay areas are further drawn to the assay area by shaking of the shaker. The present invention may improve the error-tolerance rate of the assay plate and be used for high-throughput screening.

Abstract: A nucleic acid sequence measuring method includes measuring fluorescence from the nucleic acid sequence measuring device supplied with a sample solution. The device includes a fluorescent probe added with a fluorescent molecule, and a quenching probe added with a quenching substance. The fluorescent probe and/or the quenching probe has a detection part detecting a particular nucleic acid sequence. Fluorescence from the fluorescent molecule is quenched by the quenching substance coupled with the fluorescent molecule when the hybridization between the detection target nucleic acid and the detection part has not occurred, and fluorescence is emitted from the fluorescent molecule separated from the quenching substance when the hybridization has occurred.

Abstract: A diagnostic tool and method of diagnosing brain injury and brain injury type (traumatic vs. ischemic) by detecting the level of expression of endothelial monocyte-activating polypeptide II (EMAP II) and comparing to a control. An increase of EMAP II indicates the presence of traumatic brain injury and a decrease of EMAP II indicates the presence of ischemic brain injury.

Abstract: An analytical assembly within a unified device structure for integration into an analytical system. The analytical assembly is scalable and includes a plurality of analytical devices, each of which includes a reaction cell, an optical sensor, and at least one optical element positioned in optical communication with both the reaction cell and the sensor and which delivers optical signals from the cell to the sensor. Additional elements are optionally integrated into the analytical assembly. Methods for forming and operating the analytical system are also disclosed.

Abstract: A system for determining the number of target nucleotide molecules in a sample includes a sample holder, an excitation optical system, an optical sensor, and an emission optical system. The sample holder is configured to receive an article comprising at least 20,000 separate reaction sites. The excitation optical system comprises a light source configured to simultaneously illuminate the at least 20,000 separate reaction sites. The optical sensor comprises a predetermined number of pixels, the predetermined number of pixels being at least 20 times the number of separate reaction sites. The emission optical system comprises a system working distance from the sample holder, wherein the working distance is less than or equal to 60 millimeters.

Abstract: The disclosure relates to a system diagnosis of a disease or a disease condition whereby a single sample is prepared from a biological specimen which integrates synchronously the methods of protection, isolation and alteration of a biological specimen or a bio-molecule to isolate and study tissues and bio-molecules including DNA, large RNA, small RNA, protein, lipid, carbohydrates, and other metabolite simultaneously or individually resulting in a comprehensive understanding of the cause, prevention, risk, seriousness, confirmation, treatment, triage, and prognosis of a disease or a disease condition.

Abstract: High throughput system for in vivo screens on vertebrate larvae. The system includes a source of vertebrate larvae in a liquid medium and loading tube means for aspirating a larva. A detector assembly is provided to differentiate passage of a larva from bubbles and/or debris. An imaging means is provided for both confocal imaging and wide-field fluorescence imaging of the larva. A laser is provided for optical manipulation of the larva.

Abstract: Disclosed herein are systems, devices, and methods for the electrochemical detection of a target using a helper oligonucleotide (each a helper oligo, or collectively, helper oligos).

Abstract: Methods and systems for colorimetric detection of a target. Nucleic acid is obtained from a sample potentially containing two pathogens of interest, and is contacted with a plurality of nanoparticles. A first portion of the plurality of nanoparticles are functionalized with oligonucleotides complementary to a first region of the first target and oligonucleotides complementary to a second region of the first target, and a second portion of the plurality of nanoparticles are functionalized with oligonucleotides complementary to a first region of the second target and oligonucleotides complementary to a second region of the second target. The presence of the target nucleic acid causes a detectable colorimetric change, thereby diagnosing the presence of the pathogen.

Abstract: Means of determining the condition of the oral cavity in a subject is provided. The condition of the oral cavity in the subject is determined by using an analytical tool comprising the following (A), (B), and (C): (A) a reagent for measuring one or more parameters that reflect the dental caries risk for a test sample obtained from the oral cavity, (B) a reagent for measuring one or more parameters that reflect the periodontal disease risk for the test sample obtained from the oral cavity, and (C) a reagent for measuring one or more parameters that reflect the degree of oral cleanliness for the test sample obtained from the oral cavity.

Abstract: The present invention relates to a method for specifically measuring sialylation of a biomolecule of interest without the interference of other biomolecules present in the sample.

Abstract: A graphene biosensor is formed on an electrically insulating substrate with a single-layer graphene sheet arranged between two metallic electrodes. The graphene sheet is in electrical contact with the metallic electrodes. The graphene sheet has perforations creating edges in the graphene sheet. The perforations may be holes on a micrometer scale or in a nanometer scale. The biosensor can be configured as an ISFET. The graphene sheet may comprise affinity probes immobilized on the edges for attaching specific molecules to the graphene sheet. Several graphene sheets may be arranged in a microarray with different affinity probes on different graphene sheets. The sensor may also be arranged on the distal end of a catheter for in situ measurements in a body vessel.

Abstract: There is provided an assay device comprising a lid and a base, said base comprising, a sample addition zone, a reaction zone and an absorbing zone, said components being in fluid connection and being part of a fluid passage leading from the sample addition zone to the absorbing zone, wherein: (a) a sample addition well is integrated in the lid, (b) the absorbing zone consists of an area on an non-porous substrate, having substantially perpendicular projections, said projections defining a volume, which together with the volume of the fluid passage defines the sample volume subjected to the assay, and (c) at least one filter is between the sample addition well and the sample addition zone. There is further provided methods for handling samples.

Abstract: The invention relates to the field of diagnostic methods, in particular to detection of biological molecules using mass spectroscopy (MS). Provided is an automated high-throughput method for quantitating a low molecular weight protein-bound biomarker directly in an isolated biological sample, comprising the steps of: (a) automated prepurification of the sample using an effective amount of an acid protease under conditions that allow for digestion of one or more binding proteins; (b) applying said protease-digested sample onto an on-line SPE column to capture at least part of said biomarker, followed by sequential washing of the solid phase; (c) eluting a fraction comprising said biomarker directly onto a liquid chromatography (LC) column comprising an apolar stationary phase and subjecting it to LC-MS or LC-MS-MS measurements to determine the amount of at least one biomarker; and (d) quantitating the biomarker(s).