Abstract: Methods for processing data using information gained from examining biological materials identifies and characterized probes for Single Nucleotide Polymorphisms and identifies Off Target Variants.

Abstract: The inventions provided herein relate to detection reagents, compositions, methods, and kits comprising the detection reagents for use in detection, identification, and/or quantification of analytes in a sample. Such detection reagents and methods described herein allow multiplexing of many more labeled species in the same procedure than conventional methods, in which multiplexing is limited by the number of available and practically usable colors.

Abstract: Disclosed herein are novel compositions, methods, and systems for determining whether a subject has, or is at risk of developing, or is at a given stage of a condition afflicting a tissue of interest, or determining the tissue or cell provenance of a biological sample, based on expression level of one or more of the novel miRNA and isomiR sequences disclosed herein. The compositions, methods, and systems described herein can be used to diagnose a disease or disorder, or prognose a given stage and/or progression of the disease or disorder, or determine the identity of the tissue or cell in a sample. In some embodiments, the compositions, methods, and systems described herein can be used to develop a treatment for the disease or disorder. For example, in some embodiments, the novel miRNAs can be used as therapeutics for treatment of a disease or disorder.

Abstract: Methods for detecting nucleic acid sequences, where attenuator oligonucleotides are provided to reduce the number of detection products resulting from highly abundant sequences.

Abstract: Provided herein are methods and compositions for assessing the quality and potential of stem cells in a sample. Such methods and compositions are useful for helping to ensure the safety and quality of a population of stem cells before it is used in a subject.

Abstract: An image analysis apparatus and an image analysis method capable of appropriately analyzing whether an analysis target cell is an abnormal cell even when a subject has a chromosomal abnormality are provided. An image analysis apparatus 10 includes light sources 121 and 122 configured to irradiate light onto a sample 21 whose target portion is labeled, an imaging unit 154 for capturing light generated from the sample 21 by irradiation with light, and a processing unit 11 that processes the image captured by the imaging unit 154. The processing unit 11 acquires information on the chromosomal abnormality and analyzes the image based on the information on the acquired chromosome abnormality.

Abstract: Methods for treating sleep disorders and for reducing a risk associated with developing a sleep disorder in patients via therapeutic renal neuromodulation and associated systems are disclosed herein. Sympathetic nerve activity can contribute to several cellular and physiological conditions associated with sleep disorders as well as an increased risk of developing a sleep disorder. One aspect of the present technology is directed to methods for improving a patient's calculated risk score corresponding to a sleep disorder status in the patient. Other aspects are directed to reducing a likelihood of developing a sleep disorder in patients presenting one or more sleep disorder risk factors. Renal sympathetic nerve activity can be attenuated to improve a patient's sleep disorder status or risk of developing a sleep disorder. The attenuation can be achieved, for example, using an intravascularly positioned catheter carrying a therapeutic assembly configured to use, e.g.

Abstract: An object of this invention is to provide a streptavidin mutant reduced in affinity to the naturally-occurring biotin, and to provide a modified biotin which shows a high affinity to such streptavidin mutant reduced in affinity to the naturally-occurring biotin. This invention can provide a compound composed of a dimer of modified biotin, a streptavidin mutant, and usage of them.

Abstract: This invention relates to a binomial calculation of copy number of data obtained from a mixed sample having a first source and a second source.

Abstract: Disclosed herein are methods for identifying a genetic susceptibility to colon cancer in as subject, the method comprising determining the mRNA expression level of one or more of FSCN1, ZIC2, ZIC5, CRYBA2, MUC6, TRNP1 and SEMG1 in a colon tissue sample in the subject, where a ratio of the sample expression level of one or more genes in the panel to a reference expression level of one or more genes in the panel indicates cancer or and increased susceptibility of cancer. Disclosed herein are diagnostic devices comprising one or more biomarkers, wherein the biomarkers are FSCN1, ZIC2, ZIC5, CRYBA2, MUC6, TRNP1 and SEMG1; and a gene expression panel consisting of primers or probes for detecting FSCN1, ZIC2, ZIC5, CRYBA2, MUC6, TRNP1 and SEMG1 in a sample, and methods for assessing risk of developing colon cancer in a subject.

Abstract: Methods for imaging are described, including, but not limited to a method comprising: (1) contacting a sample being tested for the presence of one or more targets with one or more target-specific binding partners, wherein each target-specific binding partner is linked to a docking strand, and wherein target-specific binding partners of different specificity are linked to different docking strands, (2) optionally removing unbound target-specific binding partners, (3) contacting the sample with antigen-bound imager strands and antigen-specific binding partners linked (directly or indirectly) to optical labels, wherein the antigen-bound imager strands have complementarity to a docking strand, directly or indirectly, and wherein each antigen-specific binding partner is linked to one or more optical labels, and wherein antigen-specific binding partners of different specificity are linked to distinct optical labels, (4) optionally removing unbound antigen-bound imager strands and/or antigen-specific binding partner

Abstract: The present invention relates to a method for writing data comprising a sequence of bits, the data being written in a form of nucleic acid, by in-vitro enzymatically producing memory nucleic acid from a strand of memory writing substrate nucleic acid, wherein the strand of memory writing substrate nucleic acid comprises a plurality of spacer sections and memory writing sections sandwiched between the spacer sections. Each of the spacer sections comprises one or more nucleobases, and each of the memory writing sections comprises a nucleobase other than the nucleobases of an adjacent spacer section upstream of the memory writing section in a travel direction of an enzyme along the strand of memory writing substrate nucleic acid.

Abstract: Compositions, reactions mixtures, kits, and systems for detecting bacterial contamination are provided, as well as methods of using the same.

Abstract: An analytical system includes a laser disposed to direct light toward a microfluidic feature disposed in a feature layer of a multiple layer test cartridge, a sensor to receive reflections from capping layers disposed about the microfluidic feature in the feature layer, and a controller to determine a depth of the microfluidic feature as a function of the received reflections.

Abstract: The invention is directed to methods of assessing the safety of therapeutic compounds and therapeutic genetic manipulations, including integrating gene therapy vectors and genome editing. In particular, the invention provides a method, wherein the oncogenic potential of therapeutic compounds and therapeutic genetic manipulations, including integrating gene therapy vectors and genome editing, is determined by determining the percentage of differentiation blocked hematopoietic progenitor cells.

Abstract: The present disclosure provides reagents and methods for molecular proximity detection of specific endogenous nucleic acids in situ using RNA-guided nucleic acid binding proteins.

Abstract: Technology for a pillar structure for a biochip is disclosed. The pillar structure for a biochip includes: a substrate portion having a plate structure; an insertion pillar portion formed in one piece with the substrate portion and protruding downward from a lower surface of the substrate portion so as to be inserted into a well; and a compensation pillar portion formed in one piece with the substrate portion, the compensation pillar portion corresponding to the insertion pillar portion and protruding upward from an upper surface of the substrate portion. Therefore, when the pillar structure is cooled during an injection molding process, the substrate portion is prevented from being partially recessed, and when samples are analyzed using microscopic images, accuracy and reliability may be improved.

Abstract: The present disclosure relates to a method for detecting CpG methylation of SDC2 (Syndecan 2) gene, a kit for detecting CpG methylation of SDC2 (Syndecan 2) gene, and a method for detecting CpG methylation of SDC2 (Syndecan 2) gene for a colorectal cancer diagnosis.

Abstract: The invention is directed to methods for determining antigen-specific T cells. In some embodiments, methods of the invention may be implemented by the steps of reacting under interaction conditions one or more antigens with T cells in a plurality of subsets of a tissue sample, such as peripheral blood; sorting antigen-interacting T cells from other T cells; separately sequencing for each subset recombined nucleic acid encoding a segment of a TCR chain from a sample of T cells prior to exposure to antigen and from a sample of T cells isolated based on their interaction with antigen, thereby forming a clonotype profile for the former sample and the latter sample for each subset; and identifying as antigen-specific T cells those T cells associated with a clonotype whose frequency increases in the latter sample relative to its frequency in the former sample.

Abstract: A frequency of somatic mutations in a biological sample (e.g., plasma or serum) of a subject undergoing screening or monitoring for cancer, can be compared with that in the constitutional DNA of the same subject. A parameter can derived from these frequencies and used to determine a classification of a level of cancer. False positives can be filtered out by requiring any variant locus to have at least a specified number of variant sequence reads (tags), thereby providing a more accurate parameter. The relative frequencies for different variant loci can be analyzed to determine a level of heterogeneity of tumors in a patient.

Abstract: Provided herein are, inter alia, nucleic acids, methods, and kits for detecting unmethylated DNA in body fluid sample of a subject. The disclosure includes compositions, methods, and kits for detecting unmethylation at a CpG site in an insulin gene promoter of a subject.

Abstract: Methods for fabricating a biochip for detecting or sequencing biomolecules are shown. Such a biochip may for instance include: a base member; a dielectric layer deposited on the base member and having at least two rows of discrete recesses formed thereon; and two or more electrodes sandwiched between the base member and the dielectric layer and running under respective row of discrete recesses, the two or more electrodes separated from each other along lengths thereof by a portion of the dielectric layer; wherein the dielectric layer defines a continuous operation surface above the electrodes and on which the discrete recesses are deposited for detecting or sequencing of biomolecules, when an electric field is applied through the electrodes, a field gradient is created to draw a biomolecule towards a preferred part of the operation surface.

Abstract: A method for quantifying labels on a substrate is performed by an electronic device with one or more processors and memory. The method includes obtaining digital data corresponding to a multi-dimensional measurement over the substrate; identifying a first set of sub-portions of the digital data; and, for a respective sub-portion of the first set of sub-portions of the digital data: increasing a quantity of labels, and subtracting a reference signal distribution from the respective sub-portion to obtain subtracted sub-portion data. The method also includes obtaining subtracted digital data. The subtracted digital data includes the subtracted sub-portion data for the respective sub-portion. The method further includes identifying a second set of one or more sub-portions of the subtracted digital data; and, for a respective sub-portion of the second set of one or more sub-portions of the subtracted digital data, increasing a quantity of labels.

Abstract: Craftwork tools are described. The craftworks tools may include a stamp and a jig with matching alignment patterns. Methods of using same are also described. The method may include placing the jig on a stamp platform, aligning the stamp with the jig, placing cardstock or another substrate on the jig, inking the stamp, and closing the lid of the stamp platform to mark the cardstock with the stamp. The cardstock and the jig may then be rotated clockwise or counterclockwise on the stamp platform without rotating the stamp on the lid, the stamp may be re-inked and then the lid may be closed again to mark the cardstock with the stamp. Methods of using embossing tools are also described.

Abstract: Provided are compositions and methods for the conversion of thiolated nucleotides, and subsequent detection of the converted nucleotides in RNA or DNA. Also provided herein are compositions and methods for the metabolic labeling of RNA and DNA by incorporation of thiolated nucleotides, and their subsequent conversion and detection.

Abstract: The present invention provides a novel class of insecticides for control of disease vector insects, particularly mosquitoes. These insecticides prevent maturation or development of larvae into adult insects using interfering RNA (iRNA). The present invention further includes compositions comprising iRNA and methods of controlling, reducing, or treating an insect infestation with the iRNA or compositions described herein.

Abstract: The present disclosure provides methods and systems for determining and/or characterizing one or more haplotypes and/or phasing of haplotypes in a nucleic acid sample. In particular, the disclosure provides methods for determining a haplotype and/or phasing of haplotypes in a nucleic acid sample by incorporating synthetic polymorphisms into fragments of a nucleic acid sample and utilizing the synthetic polymorphisms in determining one or more haplotypes and/or phasing of haplotypes.

Abstract: The present disclosure is drawn to methods for detection, quantitation and analysis of nucleotides of interest, for example SNPs, in nucleic acid sequences of interest using universal FRET-based reporter primers.

Abstract: The invention refers to a novel method of preparing strand-specific RNA-sequencing libraries that can be used to identify DNA coding and non-coding strands that are transcribed to RNA. Such strand-specific RNA-sequencing libraries are especially useful in discovering anti-sense RNA and non-coding RNA. Random primer oligonucleotides, covalently coupled to a moiety, which blocks ligation, are used for RT reaction or the subsequent generation of the second DNA strand so that only one strand of the generated double-stranded DNA is ligated to sequencing adapters at the 5? nucleotide and sequenced by paired-end sequencing.

Abstract: Method of identifying a cognate nucleotide (i.e., the “next correct nucleotide”) for a primed template nucleic acid molecule. In some embodiments, an ordered or random array of primed target nucleic acids characterized by different cognate nucleotides can be evaluated using a single imaging step to identify different cognate nucleotides for a collection of different primed template nucleic acid molecules. An optional incorporation step can follow the identifying step. A polymerase different from the ones used in the binding and examination steps can be used to incorporate a nucleotide, such as a reversible terminator nucleotide, preliminary to identification of the next cognate nucleotide.

Abstract: The present invention provides systems and methods for identifying, isolating, and/or characterizing microRNAs, their targets, and microRNA response elements, and for predicting their biological function.

Abstract: A galactooligosaccharide composition comprising a mixture of disaccharides, trisaccharides, a tetrasaccharide and a pentasaccharide for use in preventing or treating cognitive dysfunction and/or emotional disturbances in neuropsychiatric illnesses or ageing.

Abstract: The present disclosure relates to RNA interference (RNAi) reagents for treatment of oculopharyngeal muscular dystrophy (OPMD), compositions comprising same, and use thereof to treat individuals suffering from OPMD or which are predisposed thereto.

Abstract: Methods and kits for detection and quantification of EGFRvIII in the peripheral blood for monitoring the therapy of GBM patients.

Abstract: The present disclosure relates to compositions and methods for cancer diagnosis, research and therapy, including but not limited to, cancer markers. In particular, the present disclosure relates to cancer markers as diagnostic markers and clinical targets for lung cancer.

Abstract: A sample capture unit comprising a housing defining an enclosed substrate chamber containing a substantially planar sample-capture substrate extending in a plane for receiving a skin-print thereon. The housing comprises: a first part having an aperture providing access to the substrate chamber for depositing a skin-print on the sample-capture substrate; and a second part movable relative to the first part, from a first position in which the aperture is uncovered so as to allow receipt of a sample on the sample-capture substrate, and into a second position in which the aperture is covered, thereby preventing access to the substrate chamber; the housing further comprises a retaining mechanism configured to retain the second part in the second position; and an element having a perimeter defined by a line of frangibility, which enables irreversible detachment of at least a part of the element so as to create an access port dimensioned to allow removal of the sample-capture substrate.

Abstract: This invention provides nucleoside polyphosphate analogues each of which comprises a tag comprising a plurality of Raman-scattering moieties; compounds comprising said nucleoside polyphosphate analogs. This invention also provides nucleotide polymerases with one or more attached and/or conjugated noble metal nanoparticles, wherein the noble metal nanoparticles are surface-enhanced Raman spectroscopy (SERS) substrates thereby creating a region of enhanced sensitivity for surface enhanced Raman spectroscopy (SERS) within or adjacent to the polymerase. This invention also provides a surface with regions of enhanced sensitivity for surface enhanced Raman spectroscopy comprising interspersed rough or nanostructured noble metal surface. This invention also provides methods for determining the sequence of a single stranded DNA or RNA polynucleotide using one or more of nucleoside polyphosphate analogues, polymerase with noble metal nanoparticles, and surface with noble metal.

Abstract: A method comprising the steps of: (a) collecting a stool sample with the analyte and transferring a defined amount of stool sample into a prepared vessel having a sieve filter and a predetermined amount of extraction solution; (b) suspending and extracting the stool sample in the extraction solution so that the analyte goes into solution; (c) filtering the extraction solution through the sieve filter and transferring a defined amount of extraction solution to a cellulosic fibrous web having predetermined absorbency; (d) rapid drying of the extraction solution on the cellulose fibrous web at ambient temperature by the capillary action of the fibrous web, wherein the fibrous web with the sample extraction solution represents a storage and transport form stable over days and weeks, on which analyte and digestive enzymes are physically separated from each other; (e) collecting and extracting the analyte from the fibrous web in a predetermined amount of assay buffer; (f) separating the fibrous web from the assay b

Abstract: The present invention provides a method of modifying a targeted site of a double stranded DNA of a monocot cell, comprising a step of contacting a complex wherein a nucleic acid sequence-recognizing module that specifically binds to a target nucleotide sequence in the given double stranded DNA and a nucleic acid base converting enzyme are bonded, with said double stranded DNA, to convert one or more nucleotides in the targeted site to other one or more nucleotides or delete one or more nucleotides, or insert one or more nucleotides into said targeted site, without cleaving at least one strand of said double stranded DNA in the targeted site, wherein the double stranded DNA is contacted with the complex by introducing a nucleic acid encoding the complex into the monocot cell.

Abstract: Provided herein are biological information pattern (BIP) arrays and related methods for reading out information stored in a biological medium. In this manner, encoded digital information in biomolecular medium can be used as a high data density storage medium that may be read-out and accessed in a label-free manner.

Abstract: The present disclosure provides compositions and methods that employ the compositions for conducting pairwise sequencing and for generating concatemer template molecules for pairwise sequencing. The concatemers can be generated using a rolling circle amplification reaction which is conducted either on-support, or conducted in-solution and then distributed onto a support. The rolling circle amplification reaction generates concatemers containing tandem copies of a sequence of interest and at least one universal adaptor sequence. An increase in the number of tandem copies in a given concatemer increases the number of sites along the concatemer for hybridizing to multiple sequencing primers which serve as multiple initiation sites for polymerase-catalyzed sequencing reactions. When the sequencing reaction employs detectably labeled nucleotides and/or detectably labeled multivalent molecules (e.g.

Abstract: The present application includes biomarkers, methods, devices, reagents, systems, and kits for the detection and diagnosis of lung cancer. In one aspect, the application provides biomarkers that can be used alone or in various combinations to diagnose lung cancer or permit the differential diagnosis of pulmonary nodules as benign or malignant. In another aspect, methods are provided for diagnosing lung cancer in an individual, where the methods include detecting, in a biological sample from an individual, at least one biomarker value corresponding to at least one biomarker selected from the group of biomarkers provided in Table 18, Table 20, or Table 21, wherein the individual is classified as having lung cancer, or the likelihood of the individual having lung cancer is determined, based on the at least one biomarker value.

Abstract: The present invention relates to a method of predicting the effectiveness of chemotherapy in a breast cancer patient, and more particularly, to a method for predicting the effectiveness of chemotherapy by measuring the expression levels of genes for predicting prognosis of breast cancer and a standard gene in a biological sample obtained from the breast cancer patient, and a method for predicting the difference between a patient group having a high effectiveness of chemotherapy and a patient group having a low effectiveness of chemotherapy. Therefore, the method of the present invention can accurately predict the effectiveness of chemotherapy for the breast cancer patient and can be used for the purpose of presenting clues about the direction of breast cancer treatment in the future.

Abstract: A device with integrated methods for carrying out reverse transcription polymerase chain reaction (RT-PCR) and/or array based analysis involving signal generating agents (gold nanoclusters) comprising a heating and cooling cycle based synthesis selectively with DIMA and protein as templates. The advancement is further directed to a portable device adapted for RT-PCR and array based gene and protein expression analyses based on a common detection agent involving luminescence of in-situ synthesized gold nanoclusters with adaptability for user friendly graphical user interface (GUI) for controlling, visualization and analysis of the data.

Abstract: Bistable devices are constructed using a polynucleotide platform for the sensing of molecular events such as binding or conformational changes of target molecules. Uses include measurement of target concentration, measuring the effect of environmental condition (such as heat, light, or pH) on the target, or screening a library for molecules that bind the target or modulate its biological function. Devices comprise three regions: a top lid, bottom lid, and flexible linker or hinge between them. A device has an open configuration in which the top and bottom lid are separated, and a closed configuration they are bound close together. Binding domains or variations of the target molecule are fixed to a device so that when the molecular event occurs, the device switches from open to closed, or vice versa, which generates a signal. Devices carry DNA tags to enable separation of open and closed devices, as well as barcoding for multiplexed detection.

Abstract: A method and apparatus for determining a presence of a microorganism in a sample is provided. The method includes storing electrophysiological and/or impedance signatures of a plurality of microorganisms in a memory of a processor. The method also includes obtaining a sample and generating an electrophysiological and/or impedance signature of the sample. The electrophysiological and/or impedance signature of the sample is compared with the electrophysiological and/or impedance signatures in the memory. A presence of one of the plurality of microorganisms in the sample is then identified based on a correlation between the electrophysiological and/or impedance signature of the sample and the electrophysiological and/or impedance signature of the one of the plurality of microorganisms. A method is also provided for determining a growth stage of a microorganism in a sample.

Abstract: At least one embodiment relates to a focusing arrangement for focusing particles or cells in a flow. The arrangement includes at least one channel for guiding the flow. The channel includes (i) at least one particle confinement structure having particle flow boundaries and (ii) at least one acoustic confinement structure having acoustic field boundaries adapted for confining acoustic fields. The acoustic field boundaries may be different from the particle flow boundaries, and the at least one acoustic confinement structure may be arranged with regard to the channel to at least partially confine acoustic fields in the channel.

Abstract: A volumetric microfluidic injector for capillary electrophoresis (CE) for highly repeatable sample injection has been designed and built to eliminate known injection bias in hydrodynamic injection. A defined volume from 1-10 nL or 0.1-100 nL of sample is confined in a defined region of a micro-valve PDMS microfluidic injector chip and electrophoretic potential is applied to drive sample into a separation device such as an embedded fused silica capillary for separation and detection. Using a 75 ?m ID capillary, the RSD of an absorbance peak area as low as 1.32% (n=11) is obtained. As a comparison, the time-dependent injection was tested using the same chip which resulted in an inferior repeatability.

Abstract: Provided are methods and systems for detecting formation of nucleotide-specific ternary complexes comprising a DNA polymerase, a nucleic acid, and a nucleotide complementary to the templated base of the primed template nucleic acid. The methods and systems facilitate determination of the next correct nucleotide without requiring chemical incorporation of the nucleotide into the primer. These results can even be achieved in procedures employing unlabeled, native nucleotides.

Abstract: A method for amplification of nucleic acids in which substantially use is made of the fact that a pre-defined nucleic acid chain (target sequence) can be multiplied/amplified in the presence of a target sequence-specific activator oligonucleotide. The target sequence-specific activator oligonucleotide causes the separation of re-synthesized complementary primer extension products by strand displacement, so that a new primer oligonucleotide can attach to the respective template strand. The thus formed complex of a primer oligonucleotide and a template strand can initiate a new primer extension reaction. The thus formed primer extension products in turn function as templates, so that an exponential amplification reaction results. Amplification of a particular target sequence takes place more efficiently in case of perfect match complementary base pair formation between the activator oligonucleotide and the corresponding target sequence.