Abstract: Methods of forming at least one nanochannel include: (a) providing a substrate having a thick single or a thick multi-layer overlayer; (b) milling at least one channel through the overlayer into the substrate; then (c) removing the overlayer; and (d) forming at least one nanochannel in the substrate having an average width and depth dimension that is less than about 10 nm in response to the milling and removing steps.

Abstract: A method of making a flowcell structure, the method comprising forming a first structure, forming a second structure and bonding the first structure to the second structure. Further, forming the first structure comprises forming one or more first bio-chemicals in a first substrate and printing a first glue layer on the first substrate. Forming the second structure comprises forming one or more second bio-chemicals in a second substrate.

Abstract: A data management system for a biological process, comprising: a. a single-use component, b. a tag assembly, including a non-volatile memory storage component, that is associated with the single-use component, c. the memory storage component including a unique identification and a memory, and at least one data element that describes a key performance, calibration or control parameter of the single-use component d. a memory reader useable to obtain the identification from the memory storage component.

Abstract: This disclosure provides, among other things, a method for analyzing a planar cellular sample. In some embodiments, the method comprises: (a) indirectly or directly attaching nucleic acid tags to binding sites in a planar cellular sample; (b) contacting the planar cellular sample with a solid support comprising an array of spatially addressed features that comprise oligonucleotides, wherein each oligonucleotide comprises a molecular barcode that identifies the feature in which the oligonucleotides is present; (c) hybridizing the nucleic acid tags, or a copy of the same, with the oligonucleotides to produce duplexes; and (d) extending the oligonucleotides in the duplexes to produce extension products that each comprises (i) a molecular barcode and (ii) a copy of a nucleic acid tag. Other embodiments, e.g., kits and the like, are also described.

Abstract: The invention provides methods and reagents for determination of risk and treatment of a vascular disorder such as abdominal aortic aneurysm (AAA) by detecting presence of gene polymorphisms and/or genetic profiles associated with an elevated or a reduced risk of the disorder. In an embodiment, the present invention provides methods and reagents for determining sequence variants in the genome of an individual which facilitate assessment of risk for developing such diseases.

Abstract: The present invention provides methods and compositions for prognosing treatment outcome in DLBCL patients, diagnosing DLBCL and monitoring efficacy of DLBCL treatment.

Abstract: Provided herein are reagents and kits for detection of multiple target sequences in a single-tube, single-color assay, and methods of use thereof. In particular, multiplex assays are provided for the detection of Mycobacterium tuberculosis complex target sequences (e.g., katG, rpoB, inhA promotor, pncA, etc.).

Abstract: The present disclosure describes methods, devices, reagents, and kits for the detection of one or more target molecules that may be present in a test sample. The described methods, devices, kits, and reagents facilitate the detection and quantification of a non-nucleic acid target (e.g., a protein target) in a test sample by detecting and quantifying a nucleic acid (i.e., an aptamer) where the aptamer-aptamer interactions are significantly reduced or eliminated while maintaining the aptamer-target interaction.

Abstract: The present invention relates to novel nucleic acid molecules, called aptamers, that bind specifically to a small molecule fluorophore and thereby enhance the fluorescence signal of the fluorophore upon exposure to radiation of suitable wavelength. Molecular complexes formed between the novel fluorophores, novel nucleic acid molecules, and their target molecules are described, and the use of multivalent aptamer constructs as fluorescent sensors for target molecules of interest are also described.

Abstract: Compositions, methods and kits are disclosed for high-sensitivity single molecule digital counting by the stochastic labeling of a collection of identical molecules by attachment of a diverse set of labels. Each copy of a molecule randomly chooses from a non-depleting reservoir of diverse labels. Detection may be by a variety of methods including hybridization based or sequencing. Molecules that would otherwise be identical in information content can be labeled to create a separately detectable product that is unique or approximately unique in a collection. This stochastic transformation relaxes the problem of counting molecules from one of locating and identifying identical molecules to a series of binary digital questions detecting whether preprogrammed labels are present. The methods may be used, for example, to estimate the number of separate molecules of a given type or types within a sample.

Abstract: Provided is a single-stranded nucleic acid aptamer specifically binding to Klebsiella pneumoniae, and a method for detecting Klebsiella pneumoniae by using the same. The aptamer of the present disclosure, and a method, a composition, a kit or a sensor of using the same may be used to specifically detect Klebsiella pneumoniae present in an aqueous environment, foods, and medical samples and also be applied in fields such as sanitary conditions of foods and medical diagnosis.

Abstract: Methods, compositions and arrays for non-random loading of single analyte molecules into array structures are provided. For example, methods are presented for providing a surface comprising the plurality of array regions by exposing the surface to a solution comprising polymerase enzymes where each polymerase enzyme is bound to a binding structure having several functional moieties. The functional moieties of the binding structure react with the binding elements on the array regions such that the functional moieties on the binding structure react with other available binding sites in an array region, preventing other polymerase-binding structures from loading, and resulting in a single polymerase molecule bound to each of these regions.

Abstract: The invention provides methods of and diagnostic kits for the detection of breast cancer, in particular luminal A breast cancer, or to assist in assessing the prognosis, or determine the efficacy of a treatment regimen for breast cancer comprising at least one oligonucleotide probe capable of binding to at least a portion of a circulating miRNA selected from the group comprising the miR-181a and miR-652 biomarkers. The invention also provides methods of identifying a therapeutic agent capable of preventing or treating cancers, including breast cancer, comprising testing the ability of the potential therapeutic agent to enhance the expression of at least one protein selected from the group comprising miR-181a and miR-652.

Abstract: Provided are methods and devices for detection of unlabeled nucleic acids. The detection methods are based on change of solubility of hydrophobic probes upon hybridization with a polynucleotide. In one embodiment, the probes are morpholino probes, having a fluorophore attached thereto. The morpholino probes are immobilized on a substrate that has fluorescence quenching functionality.

Abstract: The present disclosure generally relates to sequencing two or more genes expressed in a single cell in a high-throughput manner. More particularly, the present disclosure relates to a method for high-throughput sequencing of pairs of transcripts co expressed in single cells (e.g., antibody VH and VL coding sequence) to determine pairs of polypeptide chains that comprise immune receptors.

Abstract: Genetic markers associated with intellectual disability as well as compositions, methods and kits for screening for genetic markers of intellectual disability, diagnosing intellectual disability and identifying individuals with a predisposition for offspring suffering from intellectual disability are provided.

Abstract: This invention relates generally to composition and methods for characterizing a methylome which comprises all or substantially all methylation states of a genome. In particular, a plurality of oligonucleotides, each representing nearly every possible methylation state of the cytosine position of each CG dinucleotide pair within a target nucleic acid of interest, and methods of using the plurality are provided herein.

Abstract: The present disclosure relates to methods of determining a treatment course of action. In particular, the present disclosure relates to mutations in the gene encoding estrogen receptor and their association with responsiveness to estrogen therapies for cancer.

Abstract: The present invention relates to novel methods for the prevention, treatment and diagnosis of Alzheimer's disease. In addition, the invention relates to methods for assessing an individual's susceptibility or pre-disposition to Alzheimer's disease. The methods of the present invention involve the use of therapeutic targets and diagnostic and/or predictive markers within the mTOR signalling pathway. The methods also involve screening subjects for genetic polymorphisms associated with rapamycin-sensitive genes.

Abstract: The present invention is a novel protocol for the massively parallel production of improved MIPs. The molecular improvements to the MIP cover the manufacturing of the probes, the workflow, the addition of unique sequence elements which connote sample specificity, and a sequence tag which uniquely identifies a specific molecule present in the initial sample population. Lastly, this invention also is combined with an empirical optimization strategy that overcomes issues of both locus representation and allelic bias. This improved technique is scalable and can be utilized to amplify targets comprised of a single locus' amplicon up to targeting more than 1 million loci.

Abstract: The invention relates to a method for enriching one or more target sequences of a deoxyribonucleic acid (DNA) in a composition, comprising the steps of providing a composition comprising one or more deoxyribonucleic acid (DNA) molecules, hybridizing to said one or more DNA molecules, one or more target specific ribonucleic acid (RNA) hybridization probes, thereby forming one or more RNA/DNA hybrids, capturing the RNA/DNA hybrids with one or more antibodies being specific for such RNA/DNA hybrids, thereby forming one or more RNA/DNA/antibody hybrids, isolating the one or more RNA/DNA/antibody hybrids, amplifying the one or more DNA molecules of the one or more RNA/DNA/antibody hybrids if necessary, and, optionally, sequencing the one or more DNA molecules of the one or more RNA/DNA/antibody hybrids or the amplification product, wherein the sequencing is preferably done by means of next generation sequencing.

Abstract: This invention provides methods of using circulating diseased cells in the diagnosis, prognosis, or monitoring of diseases or conditions. The invention also provides methods of using circulating diseased cells to identify markers of diseases or conditions. This invention also provides methods for assessing the risk of developing a disease or condition, prognosing said disease, monitoring said disease progression or regression, assessing the efficacy of a treatment, or identifying a compound capable of ameliorating or treating said disease or condition.

Abstract: Compositions and methods for detecting bladder cancer are provided. In some embodiments, methods of monitoring recurrence of bladder cancer are provided. In some embodiments, the methods comprise detecting a set of markers consisting of CRH, IGF2, KRT20, and ANXA10.

Abstract: Disclosed are kits and methods for diagnosing a person with, or assessing a person's risk for developing, sarcoidosis and/or complicated sarcoidosis.

Abstract: It was determined whether SNPs in SLC4A5 are associated with salt sensitivity of blood pressure (BP). Subjects consumed an isocaloric constant diet with a randomized order of 7 days low Na+ (10 mmol/d) and 7 days high Na+ (300 mmol/d) intake. Salt sensitivity was defined as a ?7 mm Hg increase in mean arterial pressure (MAP). 35 polymorphisms in 17 candidate genes were assayed. Association analyses with salt sensitivity revealed three variants that associated with salt sensitivity, two in SLC4A5 (rs7571842, rs10177833; P<0.001), and one in GRK4 (rs1801058; P=0.020). Paradoxical changes in blood pressure in response to changes in salt intake were also found associated with a SNP for DRD2 (rs6276). In conclusion, SLC4A5 variants are strongly associated with salt sensitivity of BP in Caucasian and a DRD2 SNP is a marker for paradoxical response to salt intake.

Abstract: The present invention relates to systems and methods for performing isothermal amplification reactions. In particular, the present invention relates to denaturation methods for use in isothermal amplification reactions.

Abstract: The present invention relates to a method for producing pools of siRNA molecules suitable for RNA interference.

Abstract: The present invention provides a method and a reagent for detecting a digestive organ cancer, gastric cancer, colorectal cancer, pancreatic cancer, or biliary tract cancer patient by analyzing genes with expression levels (in peripheral blood) that vary in association with digestive organ cancer, gastric cancer, colorectal cancer, pancreatic cancer, or biliary tract cancer cases, compared with normal healthy subjects. Specifically, the method for detecting a digestive organ cancer, gastric cancer, colorectal cancer, pancreatic cancer, or biliary tract cancer patient based on expression profiles comprises obtaining the expression profile of at least one gene selected from the group consisting of probes corresponding to genes with expression levels (in peripheral blood) that vary in digestive organ cancer, gastric cancer, colorectal cancer, pancreatic cancer, and biliary tract cancer cases, compared with normal healthy subjects.

Abstract: The present invention provides a diagnostic agent for endometriosis for measuring the concentration of at least one miRNA selected from the group consisting of hsa-miR-708, hsa-miR-127-3p and hsa-miR-518d-3p in a sample derived from the blood of a subject, the agent containing an amplification primer for the miRNA as a main component. The present invention also provides a method of detecting endometriosis, including a step of measuring the concentration of at least one miRNA selected, from the group consisting of hsa-miR-708, hsa-miR-127-3p and hsa-miR-518d-3p in a sample derived from the blood of the subject. The diagnostic agent for endometriosis of the present invention and the diagnostic method using the agent are simple and low invasive and have high sensitivity and specificity.

Abstract: Disclosed herein are methods of detecting influenza virus in a sample from a subject. In some embodiments, the disclosed methods include contacting a sample with at least one primer 10-40 nucleotides in length wherein the at least one primer is capable of hybridizing to an influenza virus polymerase basic protein 1 (PB1) nucleic acid at least 70% identical to the nucleic acid sequence set forth as any one of SEQ ID NOs: 1-3, amplifying the PB1 nucleic acid or a portion thereof to produce an amplified PB1 nucleic acid, and detecting the amplified PB1 nucleic acid, wherein presence of the amplified PB1 nucleic acid indicates presence of influenza virus in the sample from the subject. In some examples, the primers comprise or consist of the nucleic acid sequence set forth as one of SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 9, or SEQ ID NO: 10.

Abstract: The instant invention is based, at least in part, on the identification of novel methods for the enzymatic enrichment of capped RNAs. The invention provides, e.g., methods for enrichment of capped RNAs, kits for making such capped RNAs, and compositions of enriched RNAs or cDNA libraries derived therefrom.

Abstract: The invention provides methods and materials related to a gene expression-based survival predictor for DLBCL patients.

Abstract: The present invention relates to assays, diagnostic kits and methods for the simultaneous real-time PCR detection of influenza viruses selected from influenza A subtypes H1 and/or H3 and/or influenza 2009 H1N1 and/or influenza B.

Abstract: The present invention provides a method and a reagent for detecting a digestive organ cancer, gastric cancer, colorectal cancer, pancreatic cancer, or biliary tract cancer patient by analyzing genes with expression levels (in peripheral blood) that vary in association with digestive organ cancer, gastric cancer, colorectal cancer, pancreatic cancer, or biliary tract cancer cases, compared with normal healthy subjects. Specifically, the method for detecting a digestive organ cancer, gastric cancer, colorectal cancer, pancreatic cancer, or biliary tract cancer patient based on expression profiles comprises obtaining the expression profile of at least one gene selected from the group consisting of probes corresponding to genes with expression levels (in peripheral blood) that vary in digestive organ cancer, gastric cancer, colorectal cancer, pancreatic cancer, and biliary tract cancer cases, compared with normal healthy subjects.

Abstract: The disclosure provides a plurality of nucleic acid sequences comprising multiple variants of a reference sequence. The disclosure further provides plasmids, cells, methods and kits comprising the same.

Abstract: Methods, kits and systems are disclosed for analyzing one or more molecules in a sample. Analyzing the one or more molecules may comprise quantitation of the one or more molecules. Individual molecules may quantitated by PCR, arrays, beads, emulsions, droplets, or sequencing. Quantitation of individual molecules may further comprise stochastic labeling of the one or more molecules with a plurality of oligonucleotide tags to produce one or more stochastically labeled molecules. The methods may further comprise amplifying, sequencing, detecting, and/or quantifying the stochastically labeled molecules. The molecules may be DNA, RNA and/or proteins.

Abstract: The present invention is directed to multiple a-lipoic acid-containing hydrophobic compounds (mALAs) capable of acting as scavengers of free radicals, metals and reactive oxygen species (ROS). Methods of synthesizing novel antioxidant mALAs, spontaneous emulsification or nanoprecipitaion thereof to produce antioxidant nanospheres and their use in preventing or treating diseases or conditions caused by oxidative stress and other free radical mediated conditions are also described. Another aspect of this invention is the use of these antioxidant nanospheres for the preparation of antioxidant particulate delivery system of therapeutic agents.

Abstract: Disclosed are primers, probes, and single nucleotide polymorphisms (SNP) specific to a distinct subclones of the E. coli sequence type 131 (ST131). Also disclosed are methods and assay kits useful in detecting the presence of the distinct subtype of E. coli and methods of treating a subject suffering from an infection from a subclone of ST131.

Abstract: The present invention provides a method and a reagent for detecting a digestive organ cancer, gastric cancer, colorectal cancer, pancreatic cancer, or biliary tract cancer patient by analyzing genes with expression levels (in peripheral blood) that vary in association with digestive organ cancer, gastric cancer, colorectal cancer, pancreatic cancer, or biliary tract cancer cases, compared with normal healthy subjects. Specifically, the method for detecting a digestive organ cancer, gastric cancer, colorectal cancer, pancreatic cancer, or biliary tract cancer patient based on expression profiles comprises obtaining the expression profile of at least one gene selected from the group consisting of probes corresponding to genes with expression levels (in peripheral blood) that vary in digestive organ cancer, gastric cancer, colorectal cancer, pancreatic cancer, and biliary tract cancer cases, compared with normal healthy subjects.

Abstract: Described herein are miRNA-based methods for prognosis of recurrence of melanoma and related methods and kits. The present invention addresses these and other needs by providing a method for predicting the likelihood of recurrence of melanoma (including distal metastasis and locoregional recurrence) in a subject diagnosed with melanoma. In a separate aspect, the invention provides a method for treatment of a melanoma recurrence (including distal metastasis and locoregional recurrence) in a subject in need thereof.

Abstract: Methods and kits for diagnosing or predicting head and neck squamous cell carcinoma (HNSCC) and for predicting responsivity to therapeutic regimens for treating HNSCC are disclosed.

Abstract: This invention provides high unit density arrays of microparticles and methods of assembling such arrays. The microparticles in the arrays may be functionalized with chemical or biological entities specific to a given target analyte. The high unit density arrays of this invention are formed on chips which may be combined to form multichip arrays according to the methods described herein. The chips and/or multichip arrays of this invention are useful for chemical and biological assays.

Abstract: The present invention provides methods for diagnosing whether a human subject has a prostate carcinoma, methods for differentiating a high grade prostate cancer from a low grade prostate cancer in a human subject having a prostate carcinoma, and kits for detecting prostate cancer cells in a sample from a human subject.

Abstract: The present invention relates to a method and kit for the classification and prognosis of wounds of mammalian, in particular in human. The method defines a molecular signature that enables one to characterize a pathological wound healing such as chronic or non-healing wound.

Abstract: A method for characterizing a cancer in a subject, comprising: (a) providing a biological sample from the subject; (b) determining expression levels of genes in the biological sample to obtain a gene expression profile for the subject, wherein the genes comprise members of a meta-signature associated with the cancer; and (c) comparing the profile of the subject to a reference, wherein the cancer is characterized based on a measurable difference in the expression levels of genes in the biological sample as compared to the reference.

Abstract: The present invention relates to nanocones and nanomaterials. In one embodiment, the present invention provides a method of fabricating an array of nanostructures on a flexible film, comprising self-assembling a layer of particles on a film, and fabricating an array of nanostructures by etching and/or modifying the film. In another embodiment, the present invention provides a microarray comprising a nanomaterial comprising a film configured for an array of one or more nanocones.

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: Methods and compositions for identifying, diagnosing, and treating neuroblastoma are disclosed.

Abstract: Disclosed herein are markers whose mutational status is associated with sensitivity to treatment with NAE inhibitors. Mutational status is determined by measurement of characteristics of markers associated with the marker genes. Compositions and methods are provided to assess markers of marker genes to predict response to NAE inhibition treatment.

Abstract: The present invention relates to diagnostic and prognostic methods and kits for determining genetic predisposition for at least one AChE-associated disorder, as well for diagnosing, prognosing and monitoring said disorders. The methods of the invention are based on detection of specific SNPs that modulate the interaction of different miRNAs to AChE 3?-UTR.