Abstract: A system (100) for classifying a biological test sample, including a database (112) populated with reference expression data. The reference expression data includes expression levels of a plurality of molecules (polynucleotides or polypeptides), including a set of marker molecules, in a plurality of reference samples. Each reference sample has a pre-assigned value for each of one or more clinically significant variables. The system includes at least one processor (110) and at least one storage medium containing program instructions for execution by said processor (110). The program instructions cause the processor to accept (122) input expression data including a test vector of expression levels of the marker molecules in the biological test sample; and pass the input expression data to one or more analysis programs (130a, 130b, 135).

Abstract: A microfluidic device is disclosed which comprises: (i) at least one reaction unit having a test chamber connected to at least one microchannel, wherein a surface of at least a portion of said reaction unit is attached to an isolated nucleic acid; and (ii) a flow-through channel having at least one inlet port and at least one outlet port, said flow-through channel and said microchannel being of dimensions to allow reactant diffusion to and from said reaction unit, wherein the diffusion time of said reactant along the microchannel is shorter than the flow time along the microchannel.

Abstract: Provided herein is a method for making a pool of probes by primer extension. In certain embodiments, the method comprises hybridizing a first population of oligonucleotides comprising a top strand sequence having the following formula V1-B-3? with a second population of oligonucleotides comprising a bottom strand sequence having the following formula V2?-B?-3? to provide a population of duplexes. After hybridizing, the 3? ends of the oligonucleotides in the duplexes are extended to produce a population of double stranded products comprising a top strand sequence having the following formula V1-B-V2, where V2 is complementary to V2?.

Abstract: The present invention relates to methods for the detection of nucleic acids of defined sequence, and compositions and kits for use in said methods. The methods employ nicking agent(s) and a sequential series of oligonucleotide probes to produce probe fragments in the presence of a target nucleic acid.

Abstract: The present application relates to secondary amine-substituted coumarin compounds and their uses as fluorescent labels. The compounds may be used as fluorescent labels for nucleotides in nucleic acid sequencing applications.

Abstract: The present disclosure provides, in one aspect, a target substance detection method in which a trapping substance that indirectly binds to both an immobilization side (support side) and a detection side (reporter side), which is a method for detecting a target substance in a sample. The method includes a reaction step of reacting the sample, a support including a first binding portion, a reporter substance including a second binding portion, a first trapping substance that includes a first binding partner portion capable of binding to the first binding portion and that can bind to the target substance, and a second trapping substance that includes a second binding partner portion capable of binding to the second binding portion and that can bind to the target substance; and a detection step of detecting a signal from the reporter substance.

Abstract: Methods and reagent for determining the presence and/or for quantifying the amount of a target nucleic acid sequences in a sample are provided. In some aspects, the methods comprise performing a melt analysis by detecting, a signal from a probe at a temperature that is lower than the Tm of the probe and a signal at a temperature that is higher than the Tm of the probe, without detecting a signal at the Tm of the probe.

Abstract: The present invention relates to a method for the isolation of a target nucleic acid region. In particular, said method comprises the steps of contacting a population of nucleic acid molecules with at least one Type II Cas protein-gRNA complex, wherein said gRNA comprises a guide segment that is complementary to the sequence comprised in the target region of at least one nucleic acid molecule, thereby forming a Type II Cas protein-gRNA-nucleic acid complex, contacting the population of nucleic acid molecules with at least one enzyme having exonuclease activity, and isolating the target nucleic acid region from the Type II Cas protein-gRNA-nucleic acid complex.

Abstract: Disclosed herein are methods for purifying RNA comprising poly A. Also disclosed herein are compositions such as surfaces and oligonucleotides for purifying RNA comprising polyA. Other embodiments are also disclosed. Commercially-available resins having polythymidine oligonucleotide ligands typically contain less than 30 thymidine (2?deoxy) residues and some commercial resin suppliers utilize a distribution of dT chain lengths, not of a discreet length.

Abstract: Specific single nucleotide polymorphisms (SNPs) in the human genome, and their association with deep vein thrombosis (DVT) and related pathologies, such as pulmonary embolism (PE), in relation with hormonal preparations (i.e. combined contraceptives, hormone replacement therapeutics) and hormone levels (i.e. during pregnancy and post-partum).

Abstract: The present invention is based on the identification of novel biomarkers predictive of responsiveness to anti-immune checkpoint therapies.

Abstract: The disclosure provides compositions and methods for amplifying and/or analyzing nucleic acids.

Abstract: The present application relates to new coumarin compounds and their uses as fluorescent labels. The compounds may be used as fluorescent labels for nucleotides in nucleic acid sequencing applications.

Abstract: The present application relates to detection units and methods for detecting one or more target analytes in a sample using a complex formed by a target and first and second probes, wherein the first probe is coupled to a detectable piece, the target is coupled to the first probe and the second probe, and the second probe is coupled to a solid support. Specific binding of the detectable piece to the target analyte can be distinguished from non-specific binding of the detectable piece by measuring the number of detectable pieces that leave their initial location after exposure to a disruptor that uncouples the detectable piece from the solid support.

Abstract: The invention provides eukaryotic cell-based screening methods to identify an aptamer that specifically binds a ligand, or a ligand that specifically binds an aptamer, using a polynucleotide cassette for the regulation of the expression of a reporter gene where the polynucleotide cassette contains a riboswitch in the context of a 5? intron-alternative exon-3? intron. The riboswitch comprises an effector region and an aptamer such that when the aptamer binds a ligand, reporter gene expression occurs.

Abstract: The present invention provides an isolated nucleic acid molecule comprising, or consisting of, the nucleic acid sequence of SEQ ID NO:1 or a nucleic acid sequence of at least 1800 bp having at least 80% identity to said sequence of SEQ ID NO:1, wherein said isolated nucleic acid molecule specifically leads to the expression in retinal ganglion cells of a gene when operatively linked to a nucleic acid sequence coding for said gene.

Abstract: Technology provided herein relates in part to methods, processes and apparatuses for non-invasive assessment of genetic variations. In particular the invention relates to methods and kits for detecting aneuploidy of a fetal chromosome by determining the amounts of differentially methylated regions in each of chromosomes 13, 18 and 21 in circulating cell-free nucleic acid from a human pregnant female.

Abstract: The present invention relates to a method for the sensitive identification of high-affinity complexes made of two ligands (2, 3, 4, 5, 6, 7) and one receptor (1). A large number of different ligands (2, 3, 4, 5, 6, 7) of a chemical library are hereby contacted with at least one receptor (1) in a solution. The ligands of the library have a single-strand DNA (8, 9) or RNA with a base length of 2 to 10 bases or alternatively more than 10 bases. In addition, the solution is incubated for a specific period of time and complexes made of two ligands (2, 3, 4, 5, 6, 7) and one receptor (1) are identified.

Abstract: The present disclosure provides methods of treating subjects having obesity, methods of identifying subjects having an increased risk of developing obesity, methods of detecting human G-protein coupled receptor 75 variant nucleic acid molecules and variant polypeptides, and GPR75 variant nucleic acid molecules and variant polypeptides.

Abstract: The present invention generally relates to systems and methods for the control of fluids and, in some cases, to systems and methods for flowing a fluid into and/or out of other fluids. As examples, fluid may be injected into a droplet contained within a fluidic channel, or a fluid may be injected into a fluidic channel to create a droplet. In some embodiments, electrodes may be used to apply an electric field to one or more fluidic channels, e.g., proximate an intersection of at least two fluidic channels. For instance, a first fluid may be urged into and/or out of a second fluid, facilitated by the electric field. The electric field, in some cases, may disrupt an interface between a first fluid and at least one other fluid. Properties such as the volume, flow rate, etc.

Abstract: Localized detection of RNA in a tissue sample that includes cells is accomplished on an array. The array include a number of features on a substrate. Each feature includes a different capture probe immobilized such that the capture probe has a free 3? end. Each feature occupies a distinct position on the array and has an area of less than about 1 mm2. Each capture probe is a nucleic acid molecule, which includes a positional domain including a nucleotide sequence unique to a particular feature, and a capture domain including a nucleotide sequence complementary to the RNA to be detected. The capture domain can be at a position 3? of the positional domain.

Abstract: The disclosure relates generally to molecular diagnostic devices configured to amplifying a single nucleotide polymorphism (SNP) locus and discriminate between two or more allelic variants of the SNP, indicating presence or absence of a target allele. In some embodiments, the molecular diagnostic devices are capable of detecting, at point-of-care, SNPs associated with resistance or susceptibility to antibiotic treatment of organism infections. In other aspects, the disclosure provides methods of treatment for disease or disorders (e.g. organism infections) where treatment is guided by presence or absence of an allele at a SNP locus as determined by such molecular diagnostic devices.

Abstract: Provided herein are methods and compositions for determining the susceptibility of Parkinson's disease patients to optimized drug therapy (ODT) and or deep brain stimulation (DBS) therapy.

Abstract: The present invention relates to compositions and methods comprising administering gene modifiers for treating ocular disease.

Abstract: A method of storing fluorescent dye-containing resin particles comprising adding the fluorescent dye-containing resin particles in a liquid comprising a buffer, a protein, and a surfactant, thereby obtaining a particle-containing liquid. The rate of change in the backscatter intensity (transmitted light) at the center of the height of the particle-containing liquid left to stand for 24 hours after the adding is not less than ?1% based on the particle-containing liquid immediately after the adding.

Abstract: The subject invention pertains to biomarkers for identifying a subject as having high risk of the development PE. The biomarkers presented herein include miRNAs, post-translational modification of histone proteins, amount, expression and/or activity of histone or DNA modifying enzymes and methylation of sites in the genomic DNA. In certain embodiments, increased miR-17, increased acetylation of H4 histone protein, decreased amount, expression and/or activity of HDACS mRNA or protein or increased methylation of DNA at the genomic site CYP19A1 in the blood, serum or plasma of a subject compared to that of a control subject is used to predict the development of PE in the subject. The invention also provides kits and reagents to conduct assays to quantify biomarkers described herein. The invention further provides the methods of treating and/or managing PE in a subject identified as having a high risk of the development of PE.

Abstract: A tomographic imaging method which includes the steps of activating fluorescence in a surface layer of a protein-marked or fluorescent dye-marked biological tissue sample not emitting fluorescence or only emitting specific fluorescence to acquire an activated surface of biological tissue sample; performing fluorescence excitation on the acquired surface biological tissue sample, and imaging the fluorescence to acquire a fluorescence image of the surface layer; cutting off the surface layer; exposing an inactivated new surface layer after cutting the surface layer; repeatedly performing activating, imaging and cutting off steps for the new surface layer to repeat tomographic imaging in such a manner till acquiring a two-dimensional image of each layer of the biological tissue sample; and overlapping the two-dimensional images to acquire a complete three-dimensional image of the biological tissue sample, thus acquiring three-dimensional structure information of the entire sample.

Abstract: Provided herein is technology relating compositions and methods for analysis of methylated DNA from a subject. The technology also relates to use of endogenous methylated DNAs as internal controls for marker gene methylation assays.

Abstract: Provided in the disclosure relates to a panel of gene expression markers for cancer patient treated or to be treated by karenitecin. The disclosure provides methods and compositions, e.g., kits, for evaluating gene expression levels of the markers and methods of using such gene expression levels to predict a cancer patient's response to karenitecin. Such information can be used in determining prognosis and treatment options for cancer patients.

Abstract: A micro alternating tangential flow (microATF) perfusion filter includes a hollow cylinder having a proximal end and a distal end. The proximal end is connected in series to a permeate chamber, followed by a retentate chamber. The proximal end either (i) terminates in or at the permeate chamber, or (ii) terminates in or at the retentate chamber. The portion of the proximal end within the permeate chamber, in a case of (ii), possesses at least one opening allowing fluid communication between an inside of the hollow cylinder and the permeate chamber. The microATF perfusion filter further includes an inlet, positioned over the retentate chamber, for communication with a source of positive or negative pressure, and an outlet, positioned in a wall of the permeate chamber, which can be connected to a check valve, which, in turn, can be connected to a hydrophobic fluid vent filter.

Abstract: A method and system for mapping fluid objects on a substrate using a microscope inspection system that includes a light source, imaging device, stage for moving a substrate disposed on the stage, and a control module. A computer analysis system includes an object identification module that identifies for each of the objects on the substrate, an object position on the substrate including a set of X, Y, and ? coordinates using algorithms, networks, machines and systems including artificial intelligence and image processing algorithms. At least one of the objects is fluid and has shifted from a prior position or deformed from a prior size.

Abstract: A test kit of the present invention includes an analysis chip and a pipette tip. The pipette tip includes: a first portion coming in contact with an insertion hole hermetic seal when the pipette tip is inserted into a pipette tip insertion portion so as to allow a liquid dispensation port to be positioned at or in the vicinity of a bottom surface of the pipette tip insertion portion; and a second portion positioned closer to the liquid dispensation port side than the first portion. The outer diameter of the second portion is formed to be equal to or greater than the outer diameter of the first portion and any portion between the first portion and the second portion.

Abstract: The disclosure provides methods and systems for nucleic acid amplification including isothermal nucleic acid amplification.

Abstract: The invention provides methods for simultaneously amplifying multiple nucleic acid regions of interest in one reaction volume as well as methods for selecting a library of primers for use in such amplification methods. The invention also provides library of primers with desirable characteristics, such as minimal formation of amplified primer dimers or other non-target amplicons.

Abstract: A structure for culturing cells includes growth medium regions on a surface of the structure. Each of the growth medium regions includes a growth medium surface configured to receive and promote growth in a cell that is being cultured. The structure includes a non-growth medium. The non-growth medium includes a non-growth medium surface configured to receive the cell that is being cultured.

Abstract: Disclosed herein are adapter nucleic acid sequences, double-stranded complexed nucleic acids, compositions, and methods for sequencing a double-stranded target nucleic acid with applications to error correction by duplex sequencing.

Abstract: Methods for detecting single nucleotide polymorphisms in nucleotide sequences using LAMP reactions are provided herein. Generally, two sets of LAMP primers, a wild-type primer that matches expected DNA sequences and an SNP primer that matches the expected SNP DNA are provided. One method includes providing the wild-type primer and the SNP primer in separate wells of a multi-well microfluidic array device, adding the sample nucleotide sequence into the wells seeded with the primers, and initiating LAMP reactions within the wells. The method includes observing the reaction differential between the primers and determining the status of the DNA with regard to that particular SNP. A second method includes providing the primers with tags in a mixture, adding the sample nucleotide sequence to the mixture, and initiating LAMP reactions.

Abstract: The disclosure provides for methods, compositions, and kits for normalizing nucleic acid libraries, for example sequencing libraries.

Abstract: The present disclosure provides methods and systems for nucleic acid sequencing. Such systems and methods may achieve context-independent incorporation, have reduced context-dependence or have context-dependence that is amenable to calibration and modeling. Such systems and methods may also reduce misincorporation.

Abstract: A particle or pollen sensor comprises an array of relative humidity sensors. A change in relative humidity is representative of a particle or pollen in contact with one or more of the sensors. A size and/or shape of a particle or pollen in contact with one or more of the sensors is optionally also determined based on the number and/or configuration of sensors. From this information, a particle or pollen type is determined.

Abstract: The present invention relates to RNAi agents, e.g., double stranded RNAi agents, targeting a xanthine dehydrogenase (XDH) gene, and methods of using such double stranded RNAi agents to inhibit expression of an XDH gene and methods of treating subjects having an XDH-associated disease.

Abstract: The present invention is directed to a method of treating cancer using interfering RNA duplexes to mediate gene silencing. The present invention is also directed to interfering RNA duplexes and vectors encoding such interfering RNA duplexes.

Abstract: A method of analysing nucleic acid using apparatus comprising a reaction chamber and plurality of sensors located in the base of the chamber, with each sensor preferably located within a respective well. The method comprises flowing a fluid containing the nucleic acid or fragments thereof into the reaction chamber. While the chamber is fully or at least partially sealed, amplification of the nucleic acid or said fragments is performed within the chamber using an amplification primer or primers whilst detecting the generation of amplicons using said sensors. Sequencing or hybridisation is then performed on the amplicons, and sequencing or hybridisation is detected using said sensors.

Abstract: The technology disclosed relates to constructing a convolutional neural network-based classifier for variant classification. In particular, it relates to training a convolutional neural network-based classifier on training data using a backpropagation-based gradient update technique that progressively match outputs of the convolutional neural network-based classifier with corresponding ground truth labels. The convolutional neural network-based classifier comprises groups of residual blocks, each group of residual blocks is parameterized by a number of convolution filters in the residual blocks, a convolution window size of the residual blocks, and an atrous convolution rate of the residual blocks, the size of convolution window varies between groups of residual blocks, the atrous convolution rate varies between groups of residual blocks. The training data includes benign training examples and pathogenic training examples of translated sequence pairs generated from benign variants and pathogenic variants.

Abstract: Provided herein are compositions, systems, and methods for detecting microorganisms. In particular, provided herein are compositions, systems, and methods for rapid, multiplex detection of microorganism in unpurified biological samples.

Abstract: High surface area coatings are applied to solid substrates to increase the surface area available for solid-phase synthesis of polymers. The high surface area coatings use three-dimensional space to provide more area for functional groups to bind polymers than an untreated solid substrate. The polymers may be oligonucleotides, polypeptides, or another type of polymer. The solid substrate is a rigid supportive layer made from a material such as glass, a silicon material, a metal material, and plastic. The coating may be thin films, hydrogels, microparticles. The coating may be made from a metal oxide, a high-? dielectric, a low-? dielectric, an etched metal, a carbon material, or an organic polymer. The functional groups may be hydroxyl groups, amine groups, thiolate groups, alkenes, n-alkenes, alkalines, N-Hydroxysuccinimide (NHS)-activated esters, polyaniline, aminosilane groups, silanized oxides, oligothiophenes, and diazonium compounds.

Abstract: Inputs from sensors (e.g., image and environmental sensors) are used for real-time optimization of plant growth in indoor farms by adjusting the light provided to the plants and other environmental factors. The sensors use wireless connectivity to create an Internet of Things network. The optimization is determined using machine-learning analysis and image recognition of the plants being grown. Once a machine-learning model has been generated and/or trained in the cloud, the model is deployed to an edge device located at the indoor farm to overcome connectivity issues between the sensors and the cloud. Plants in an indoor farm are continuously monitored and the light energy intensity and spectral output are automatically adjusted to optimal levels at optimal times to create better crops. The methods and systems are self-regulating in that light controls the plant's growth, and the plant's growth in-turn controls the spectral output and intensity of the light.

Abstract: This disclosure provides methods, systems, and compositions of matter for studying solvent accessibility and three-dimensional structure of biological molecules. A plasma can be used to generate marker radicals, which can interact with a biological molecule and mark the solvent-accessible portions of the biological molecule.

Abstract: Systems and methods for light based heating of light absorbing sources for modification of nucleic acids through fast thermal cycling of polymerase chain reaction are described.

Abstract: This disclosure provides systems and methods for sample processing and data analysis. Sample processing may include nucleic acid sample processing and subsequent sequencing. Some or all of a nucleic acid sample may be sequenced to provide sequence information, which may be stored or otherwise maintained in an electronic storage location. The sequence information may be analyzed with the aid of a computer processor, and the analyzed sequence information may be stored in an electronic storage location that may include a pool or collection of sequence information and analyzed sequence information generated from the nucleic acid sample. Methods and systems of the present disclosure can be used, for example, for the analysis of a nucleic acid sample, for producing one or more libraries, and for producing biomedical reports. Methods and systems of the disclosure can aid in the diagnosis, monitoring, treatment, and prevention of one or more diseases and conditions.