Abstract: The present invention relates to a composition for detecting microbial contamination comprising a preparation for detecting nucleases, and a use thereof. A probe for measuring nucleic acid double-stranded nucleases, according to the present invention, may detect the comprehensive nucleic acid degradation capability of nucleases, whereby it is possible to quickly and precisely detect and quantify live microorganisms in a sample in a simple manner. Moreover, since the probe of the present invention is characterized in that signals of fluorescence consistently increase; is capable of measuring live microorganisms; and consists of a double-stranded nucleic acid, the probe is excellent for storage in a kit or a cartridge. As such, it is expected that the probe of the present invention may be used to easily and simply measure and compare the degree of contamination of microorganisms in an environment.

Abstract: This invention provides methods of using labeled nucleotide polyphosphate analogues to detect the identity or presence of a nucleotide at certain positions in nucleic acid sequences with single molecule sensitivity using nanopore detection, nucleotides and primer-conjugated nanopore proteins for use in such methods, and processes for producing such nucleotides and primer-conjugated nanopore proteins.

Abstract: The present invention relates to molecular microscopy or volumetric imaging by proximal unique molecular identifiers (“UID”) reaction (“VIPUR”) microscopy methods to record the cellular co-localization and/or spatial distributions of arbitrary nucleic acid sequences, or other biomolecules tagged with nucleic sequences. The method involves one or both of two DNA sequence-components such as an ?-UID, which may identify the targeted sequences-of-interest themselves and/or spatial beacons relative to which their distances are measured, and a- ?-UID, which labels ?-UID association events.

Abstract: Provided herein, in some embodiments, are novel compositions and improved methods for nucleic acid manipulation and analysis that can be applied to multiplex nucleic acid sequencing. In certain embodiments, the novel compositions and methods presented herein are more cost effective, more conducive to automation, and faster than traditional approaches. Also provided herein are novel blocking nucleic acids.

Abstract: The present invention provides a method of assessing whether an individual is at high risk or low risk of inflammatory bowel disease (IBD) progression by determining the expression level of two or more genes in a whole blood sample. Also provided are methods for treating IBD in an individual who is determined to be at high risk or low risk for IBD progression, and kits for assessing whether an individual is at high risk or low risk for IBD progression. Arrays, and methods of providing arrays, of patient-identified selected gene expression products from a whole blood sample of a patient are also provided.

Abstract: An apparatus configured for improving retention of non-adherent cells is disclosed. The apparatus includes a plate that includes a number of elements having a first surface energy arranged in an array with an overlay, on the plate, having a second surface energy. The first surface energy results in a hydrophilic surface and the second surface energy results in a hydrophobic surface. A diameter of the elements is at least 1 mm. A height of the overlay having the second surface energy, which results in a hydrophobic surface, is between 5% and 100% of the diameter of the elements. The apparatus also includes a wall circumferential to the plate. A method for performing multiple reactions with the apparatus is also disclosed.

Abstract: A method of diagnosing a disease associated with a DNA repeat sequence is disclosed. The method comprises: (a) determining the number of repeats of a DNA sequence in DNA molecules of a sample of the subject; and (b) determining the CpG methylation status of the DNA molecules, wherein the number of repeats of the DNA sequence and the CpG methylation status of the DNA molecules is indicative of the disease.

Abstract: Provided herein are systems and methods for generating an immune-oncology profile from a biological sample. The immune-oncology profile can include the proportion or percentage of immune cells, expression of immune escape genes, and/or mutational burden. The immune-oncology profile may allow the generation of classifiers for making prognostic or diagnostic predictions.

Abstract: The invention provides methods, compositions, kits and devices for the detection of target molecules. In some embodiments, the invention allows for multiplexed target molecule detection.

Abstract: The present invention provides a method of predicting the risk of reoccurrence of melanoma in a patient from whom melanoma tissue was previously removed which comprises the following: a. obtaining a RNA-containing sample of the previously removed melanoma tissue containing RNA from the patient; b. treating the sample to determine from the RNA contained in the sample the level of expression of a plurality of preselected genes; and c. comparing the level of expression of each gene of the plurality of pre-selected genes to a predetermined reference level of expression for each such gene; wherein a higher level of expression of the plurality of pre-selected genes in the sample as compared with the predetermined reference level of expression of such genes indicates that the patient has a reduced risk of reoccurrence of melanoma.

Abstract: The invention provides ubiquitin variants that specifically bind to HECT E3 ligases, and methods of using these variants to modulate the activity of HECT E3 ligases.

Abstract: The present disclosure relates to a method for predicting a recurrence and a progression of an urothelial cancer patient after a treatment including steps as follows. A urine sample is obtained from a subject. The urine sample is performing a serially centrifugation step to obtain a third precipitate. The third precipitate is resuspended with an extraction solvent to obtain a third mixture, and the third mixture is centrifuged to obtain a fourth supernatant. The fourth supernatant is analyzed by a mass spectrometry to detect whether there is a particular peptide therein.

Abstract: Embodiments of the present disclosure relate to methods for capturing and amplifying target polynucleotides on a solid surface, in particular in a well in a microarray, wherein the microarray may comprise a) a substrate comprising at least one well, a surface surrounding the well and an inner well surface; b) a first layer covering the inner well surface and comprising at least one first capture primer pair; and c) a second layer covering the first layer and the surface surrounding the well.

Abstract: The invention provides particle compositions having applications in nucleic acid analysis. Nucleic acid polymer particles of the invention allow polynucleotides to be attached throughout their volumes for higher loading capacities than those achievable solely with surface attachment. In one aspect, nucleic acid polymer particles of the invention comprise polyacrylamide particles with uniform size distributions having low coefficients of variations, which result in reduced particle-to-particle variation in analytical assays. Such particle compositions are used in various amplification reactions to make amplicon libraries from nucleic acid fragment libraries.

Abstract: Some embodiments described herein relate to solid-support based processes for the functionalization of immunoglobulins through the use of transglutaminase. Also provided are solid support compositions with bound antibody. The methods can be used, for example, in manufacturing processes or in drug screening.

Abstract: Disclosed herein are compositions and methods related to the elimination of molecules of a selected sequence from a nucleic acid sample or from an sequence dataset resulting from the sequencing of a sample, for example to exclude such molecules from downstream analysis or sequencing, or to exclude such sequences from a downstream data set.

Abstract: Compositions and methods are provided for ligating polynucleotides having a length that is greater than 8 nucleotides on an RNA splint. The ligation reaction provides consistent results in high or low ATP concentrations. The reaction can occur rapidly and is generally at least 10 fold more efficient than T4DNA ligase under optimal conditions for T4DNA ligase and the reaction time is less than 6 hours for example, less than 1 hour.

Abstract: Compositions and methods are provided for ligating polynucleotides having a length that is greater than 8 nucleotides on an RNA splint. The ligation reaction provides consistent results in high or low ATP concentrations. The reaction can occur rapidly and is generally at least 10 fold more efficient than T4DNA ligase under optimal conditions for T4DNA ligase and the reaction time is less than 6 hours for example, less than 1 hour.

Abstract: The present invention relates to methods and biomarkers (e.g., protein biomarkers) for detection of colorectal cancer in biological samples (e.g., tissue samples, biopsy samples, stool samples, blood samples, plasma samples, serum samples). In some embodiments, methods and biomarkers of the present invention find use in detection of colon cancer, providing a prognosis to colorectal cancer patients, and in companion diagnostics.

Abstract: Disclosed are methods and kits for improving global gene expression analysis for a population of RNA molecules derived from a human blood, plasma and/or serum sample. In an embodiment, the method comprises the step of selectively depleting 5?-RNAY4 fragments from the population of RNA molecules or selectively blocking 5?-RNAY4 fragments within the RNA population. The 5?-RNAY4 depleted or 5?-RNAY4 blocked population of RNA can be used in a variety of global gene expression analysis protocols, including next generation sequencing. In a further embodiment, the method comprises selectively depleting or blocking miR-486-5p fragments within the RNA population. The miR-486-5p depleted or miR-486-5p blocked population of RNA can also be used in global gene expression analysis protocols, including next generation sequencing.

Abstract: Provided is a fingerprint identification method and the method includes the follows. Source fingerprint data for fingerprint identification is acquired. Fingerprint data to be processed, whose fingerprint data value in a preset threshold range, is extracted from the source fingerprint data. A feature amplifying process is performed on the fingerprint data to be processed and fingerprint data obtained through the amplifying process is repaired to obtain target fingerprint data. Fingerprint simulation data is generated according to the target fingerprint data and the fingerprint simulation data is matched with pre-stored fingerprint verification data. The source fingerprint data is determined to be identified successfully, when the fingerprint simulation data matches the pre-stored fingerprint verification data successfully. A terminal is also provided.

Abstract: This invention provides a method of quantifying chimeric DNA in a cell-free DNA sample.

Abstract: An information processing apparatus and method are disclosed, each of which: using a set of normal data, learns a first model for determining the normal data; sets, out of a plurality of abnormality candidate areas, the abnormality candidate areas selected by a user as correct data and the abnormality candidate areas not selected by the user as incorrect data, to learn a second model for identifying the correct data and the incorrect data, each abnormality candidate area indicating a candidate area of an abnormality and detected based on the first model from each of a plurality of captured images; obtains the captured images; detects the abnormality candidate areas from the respective captured images, using the first model; determines whether the abnormality candidate areas detected belong to the correct data or the incorrect data, using the second model; and controls to output a determination.

Abstract: Provided herein are devices and methods suitable for sequencing, amplifying, analyzing, and performing sample preparation procedures for nucleic acids and other biomolecules.

Abstract: The present invention provides a primer for nucleic acid random fragmentation and a nucleic acid random fragmentation method. The primer consists of a plurality of upstream random primers and downstream random primers. The sequence composition of the upstream random primers is 5?-X-Y-3?, and the sequence composition of the downstream random primers is 5?-P-Y?-X?-close-3?, wherein Y and Y? are random sequences, X is all or part of sequences of a sequencing platform 5? end adaptor, X? is all or part of sequences of a sequencing platform 3? end adaptor, P is phosphorylation modification, and close is close modification. The primer of the present invention adopts double random anchoring of both the upstream random primers and the downstream random primers, and a DNA sample can be randomly broken.

Abstract: A microfluidic cartridge, configured to facilitate processing and detection of nucleic acids, comprising: a top layer comprising a set of cartridge-aligning indentations, a set of sample port-reagent port pairs, a shared fluid port, a vent region, a heating region, and a set of Detection chambers; an intermediate substrate, coupled to the top layer comprising a waste chamber; an elastomeric layer, partially situated on the intermediate substrate; and a set of fluidic pathways, each formed by at least a portion of the top layer and a portion of the elastomeric layer, wherein each fluidic pathway is fluidically coupled to a sample port-reagent port pair, the shared fluid port, and a Detection chamber, comprises a turnabout portion passing through the heating region, and is configured to be occluded upon deformation of the elastomeric layer, to transfer a waste fluid to the waste chamber, and to pass through the vent region.

Abstract: Provided herein, among other things, are compositions for improving signal-to-noise in hybridization to oligonucleotide arrays. In some embodiments, the composition may comprise a population of indexing oligonucleotides of formula X-Y, where the sequences of region X hybridize to an array and the sequences of region Y hybridize to distinct sites within a genomic region, transcript, set of transcripts, or complement of the same. Use of these oligonucleotides increases signal, reduces background and smoothens array hybridization analyses. Methods and kits that employ the compositions are also provided.

Abstract: Provided are a vesicular linker and a single-chain cyclic library constructed by using the linker. The library can be used for RNA sequencing and other sequencing platforms dependent on a single-stranded cyclic library, and has the advantages of high throughput sequencing, high accuracy and simple operations.

Abstract: Methods, systems, and apparatus, including computer programs encoded on computer storage media, for obtaining data defining a sequence for an aptamer, the aptamer comprising a string of nucleobases; encoding the data defining the sequence for the aptamer as a neural network input; and processing the neural network input using a neural network to generate an output that characterizes how strongly the aptamer binds to a particular target molecule, wherein the neural network has been configured through training to receive the data defining the sequence and to process the data to generate predicted outputs that characterize how strongly the aptamer binds to the particular target molecule.

Abstract: Thermal control devices adapted to provide improved control and efficiency in temperature cycling are provided herein. Such thermal control device can include a thermoelectric cooler controlled in coordination with another thermal manipulation device to control an opposing face of the thermoelectric cooler and/or a microenvironment. Some such thermal control devices include a first and second thermoelectric cooler separated by a thermal capacitor. The thermal control devices can be configured in a planar configuration with a means for thermally coupling with a planar reaction vessel of a sample analyzer for use in thermal cycling in a polymerase chain reaction of the fluid sample in the reaction vessel. Methods of thermal cycling using such a thermal control devices are also provided.

Abstract: Provided is a method for detecting a stem cell based on an undifferentiated sugar chain marker having a specific sugar chain structure, wherein the stem cell is detected by detecting podocalyxin contained in a culture supernatant or a lysate of cells by a “lectin-antibody sandwich method” using a combination of a lectin and an antibody and having high sensitivity, the method including steps of: contacting the culture supernatant or the lysate, a lectin capable of binding to a sugar chain represented by (Formula 1) or (Formula 2), and an antibody capable of binding to keratan sulfate to form a complex composed of the lectin, podocalyxin and the antibody; and detecting the complex. wherein R1 represents an OH group or any sugar chain and R2 represents an OH group or any sugar chain, protein, lipid, or another molecule. wherein R1 represents an OH group or any sugar chain and R2 represents an OH group or any sugar chain, protein, lipid, or another molecule.

Abstract: The present disclosure relates generally to method of preparing aptamers, aptamers, and uses thereof.

Abstract: The present invention relates generally to nucleic acid molecules in respect of which changes to DNA methylation levels are indicative of the onset or predisposition to the onset of a neoplasm. More particularly, the present invention is directed to nucleic acid molecules in respect of which changes to DNA methylation levels are indicative of the onset and/or progression of a large intestine or breast neoplasm, such as an adenoma or adenocarcinoma. The DNA methylation status of the present invention is useful in a range of applications including, but not limited to, those relating to the diagnosis and/or monitoring of colorectal or breast neoplasms, such as colorectal or breast adenocarcinomas. Accordingly, in a related aspect the present invention is directed to a method of screening for the onset, predisposition to the onset and/or progression of a neoplasm by screening for modulation in DNA methylation of one or more nucleic acid molecules.

Abstract: The invention provides in situ nucleic acid sequencing to be conducted in biological specimens that have been physically expanded. The invention leverages the techniques for expansion microscopy (ExM) to provide new methods for in situ sequencing of nucleic acids in a process referred to herein as “expansion sequencing” (ExSEQ).

Abstract: The present invention relates to the use of the biomarker Flattop (Fltp) for distinguishing mature ? cells from immature progenitor ? cells. The present invention further relates to a method for distinguishing a mature ? cell from an immature progenitor ? cell, the method comprising: determining the presence or absence of the biomarker Flattop (Fltp) in a ? cell; wherein the presence of Fltp in the cell indicates that the cell is a mature ? cell and wherein the absence of Fltp in the cell indicates that the cell is an immature progenitor ? cell. Furthermore, the present invention relates to a method of identifying a compound suitable for differentiating immature progenitor ? cells into mature ? cells as well as to a method of identifying a compound suitable for preventing the de-differentiating of mature ? cells.

Abstract: A method for determining the presence or amount of a target nucleic acid sequence in a sample, uses magnetic particles loaded with a probe and polystyrene particles loaded with a probe, in particular a different probe, for directly or indirectly detecting the presence or amount of the target nucleic acid sequence which is in particular indicative of a disease. The methods of the present invention allow for determining target nucleic acid sequences even in low abundance and in complex samples with advantageous sensitivity and, thus, represent promising approaches which can in particular be used in the diagnosis of several diseases and health conditions. A kit comprising a loaded magnetic particle and a loaded polystyrene particle is provided and can be used for the methods of the present invention, in particular for diagnosis or prognosis of a disease in a subject such as a human.

Abstract: A system and method for isolating and analyzing single cells, comprising: a substrate having a broad surface; a set of wells defined at the broad surface of the substrate, and a set of channels, defined by the wall, that fluidly couple each well to at least one adjacent well in the set of wells; and fluid delivery module defining an inlet and comprising a plate, removably coupled to the substrate, the plate defining a recessed region fluidly connected to the inlet and facing the broad surface of the substrate, the fluid delivery module comprising a cell capture mode.

Abstract: Described herein are nanopore biosensors based on a modified cytolysin protein. The nanopore biosensors accommodate macromolecules including proteins and nucleic acids, and may additionally comprise ligands with selective binding properties.

Abstract: The claimed invention relates to mobile computing monitoring of health statistics using chemically synthesized conjugate markers providing highly specific details of personal health states. Using portable computing and communications devices, commonly known as ‘smartphones’, personal health and wellness information is gathered from chemical markers and reported to the user. Chemical markers include chemicals which undergo a measurable color change when combined with body fluids such as saliva. Health information derived from chemical markers may be optically collected, locally reported and widely broadcast over a ‘cloud based’ internet data distribution system.

Abstract: Disclosed herein are methods and systems for detecting and/or quantifying cellular targets such as nucleic acids in cells, tissues, organs or organisms. Through sequential barcoding, it is possible to perform high-throughput profiling of a large number of targets, such as transcripts and/or DNA loci. In some embodiments, error correction is implemented through use of barcodes that can tolerate mistakes and missing data during sequential hybridization of probes to selected targets.

Abstract: The present invention provides a method by which lung squamous cell carcinoma can be detected in a simple and prompt manner with high detection performance; and the like. The method according to the present invention detects lung squamous cell carcinoma by an assessment including the steps of: (1) performing measurement of the desmoglein 3 content in a blood sample collected from a subject; and (2) comparing the desmoglein 3 content determined by the measurement with the desmoglein 3 content in a blood sample collected from a healthy individual so as to estimate the presence of lung squamous cell carcinoma in the subject when the desmoglein 3 content is higher in the blood sample collected from the subject.

Abstract: The present disclosure provides a system and method for the detection of rare mutations and copy number variations in cell free polynucleotides. Generally, the systems and methods comprise sample preparation, or the extraction and isolation of cell free polynucleotide sequences from a bodily fluid; subsequent sequencing of cell free polynucleotides by techniques known in the art; and application of bioinformatics tools to detect rare mutations and copy number variations as compared to a reference. The systems and methods also may contain a database or collection of different rare mutations or copy number variation profiles of different diseases, to be used as additional references in aiding detection of rare mutations, copy number variation profiling or general genetic profiling of a disease.

Abstract: The instant application provides methods of diagnosing and treating a subject having IBS. In certain embodiments, the methods also include diagnosing subjects who will respond to IBS treatment with rifaximin.

Abstract: Disclosed is a method for assessing heart failure in vitro including the steps of measuring in a sample the concentration of the marker IGFBP-7, of optionally measuring in the sample the concentration of one or more other marker(s) of heart failure, and of assessing heart failure by comparing the concentration determined in for IGFBP-7 and the concentration(s) determined for the optionally one or more other marker to the concentration of this marker or these markers as established in a reference population. Also disclosed are the use of IGFBP-7 as a marker protein in the assessment of heart failure, a marker combination comprising IGFBP-7 and a kit for measuring IGFBP-7.

Abstract: A material film is formed as a thin film having a thickness of 1 ?m on a surface of a glass substrate. A plurality of micro-chambers having a diameter of 5 ?m are formed in the material film to be arrayed at a high density. The respective chambers filled with an aqueous test solution have openings that are liquid-sealed by a lipid bilayer membrane to provide a high-density micro-chamber array. Significant downsizing of the micro-chambers enhances a change in concentration by a reaction of one biomolecule in the chamber and thereby increases the detection sensitivity. In the configuration that a large number of micro-chambers are formed at a high density, even in the case of an extremely slow reaction of the biomolecule, the reaction proceeds in any of the chambers. This configuration accordingly enables the reaction of the biomolecule to be detected with high sensitivity.

Abstract: Provided herein are methods for culturing patient-derived tumor cell spheroids in a three-dimensional microfluidic device. The method comprises mincing primary tumor sample in a medium supplemented with serum; treating the minced primary tumor sample with a composition comprising an enzyme; collecting tumor spheroids having a diameter of 10 ?m to 500 ?m from the enzyme treated sample; suspending the tumor spheroids in biocompatible gel; and culturing the tumor spheroids in a three dimensional microfluidic device. Methods for identifying an agent for treating cancer and microfluidic devices that allow for the simultaneous exposure of the cultured patient-derived primary tumor cell spheroids to a treatment of choice and to control treatment are also provided.

Abstract: Time-resolved nucleic acids include a long-lifetime FRET donor with an emission lifetime of at least one millisecond (such as a terbium complex), configured as a donor in a first FRET process, and at least one fluorescent dye with an emission lifetime of less than 100 nanoseconds configured as an acceptor in the FRET process. They can be configured as photonic wires, hybridization probes or beacons, and/or systems for computing logical operations.

Abstract: A system and method for isolating and analyzing single cells, including: a substrate having a broad surface; a set of wells defined at the broad surface of the substrate, and a set of channels, defined by the wall, that fluidly couple each well to at least one adjacent well in the set of wells; and fluid delivery module defining an inlet and comprising a plate, removably coupled to the substrate, the plate defining a recessed region fluidly connected to the inlet and facing the broad surface of the substrate, the fluid delivery module comprising a cell capture mode.

Abstract: Methods and devices are provided for preparing a protein array having a plurality of proteins. In one embodiment, the method includes providing a plurality of nucleic acids each having a predefined sequence and expressing in vitro a plurality of proteins from the plurality of nucleic acids. In another embodiment, protein arrays having a solid surface and a microvolume are also provided. The solid surface can have a plurality of anchor oligonucleotides capable of hybridizing with a plurality of nucleic acids. The microvolume can cover each of the plurality of anchor oligonucleotides and can be configured to produce a polypeptide from each of the plurality of nucleic acids.

Abstract: As a receptor layer, a film of a composite material of a base material such as a polymer and particles that adsorb an analyte is used. When the present invention is applied to a surface stress sensor or the like, the Young's modulus of the receptor layer, which significantly affects detection sensitivity, can be preset with a high degree of freedom, by independently selecting particles that adsorb a desired analyte and a base material that disperses said particles therein.