Abstract: An exemplary method and system is disclosed that facilitate the integration of multiplexed single-cell impedance cytometry in a high throughput format, which can be deployed upstream from microfluidic sample preparation and/or downstream to microfluidic cell separation. In exemplary method and system may employ impedance-based quantification of cell electrophysiology on the same microfluidic chip (i.e., “on-chip”) to provide distinguishing phenotypic information on the sample, without the need for additional sample handling, preparation or dilution steps as would be needed for other flow cytometry techniques.

Abstract: This disclosure provides systems and methods for molecular identification and polymer (e.g., nucleic acid) sequencing using nanopores. The polymer may be passed through or in proximity to the nanopore and various subunits of the polymer may affect the current flowing through the nanopore. The various subunits may be identified by measuring the current at a plurality of voltages applied across the nanopore and/or membrane. In some cases, the polymerization of tagged nucleotides presents tag molecules to the nanopore that can be identified by measuring the current at a plurality of voltages applied across the nanopore and/or membrane. Also provided herein are systems and methods for sequencing both the sense and anti-sense strand of a double stranded nucleic acid molecule with a nanopore and methods for using ribonucleic acid (RNA) speed bump molecules to slow the passage of a nucleic acid molecule through or in proximity to a nanopore.

Abstract: Disclosed herein, inter alia, are compounds, compositions, and methods of use thereof in the sequencing of a nucleic acid.

Abstract: The present disclosure provides resonator networks adapted to a variety of applications. The networks include fluorophores, quantum dots, dyes, plasmonic nanorods, or other optical resonators maintained in position relative to each other by a backbone (e.g., a backbone composed of DNA). The networks may exhibit optical absorption and re-emission according to specified temporal decay profiles, e.g., to provide temporally-multiplexed labels for imaging or flow cytometry. The networks can include resonators that exhibit a dark state, such that the behavior of the network can be modified by inducing the dark state in one or more resonators. Such networks could be configured as logic gates or other logical elements, e.g., to provide multiplexed detection of analytes by a single network, to permit the temporal decay profile of the network to be adjusted (e.g., to use the networks as a controllable random number generator), or to provide other benefits.

Abstract: Compositions comprising modified recombinant polymerizing enzymes are provided, along with nucleic acid molecules encoding the modified polymerizing enzymes. In some aspects, methods of using such polymerizing enzymes to synthesize a nucleic acid molecule or to sequence a nucleic acid template are provided.

Abstract: Systems and methods of the present disclosure enable automated nucleic acid extraction using components including a rotating platform and a magnetic extractor. A controller controls the components to identify a program associated with a well plate kit based on a well plate kit indicator, where each well plate in the well plate kit is associated with a step for extracting nucleic acid from a sample, and each well plate is loaded with a particular substance for processing each step. Positions on the rotating platform associated with each well plate in the well plate kit are determined. Using the positions and the program, the controller performs each step by determining a particular position for particular well plate of a particular step, controlling the rotating platform to position the particular well plate under the magnetic extractor, and controlling magnetic rods of the magnetic extractor according to the program.

Abstract: The present disclosure is directed, among other things, to automated systems and methods for analyzing, storing, and/or retrieving information associated with biological objects having irregular shapes. In some embodiments, the systems and methods partition an input image into a plurality of sub-regions based on localized colors, textures, and/or intensities in the input image, wherein each sub-region represents biologically meaningful data.

Abstract: The present invention relates to methods and compositions for determination of and uses of specific methylation patterns indicative of adenoma and carcinoma. In particular, the invention relates to analysis of defined CpG loci that are coordinately methylated in DNAs from cancer and adenoma samples, methods for identifying coordinately methylated loci, and methods of using analysis of coordinately methylated loci in one or more marker regions in the design of assays for adenoma and cancer.

Abstract: The present disclosure provides in vitro methods for predicting a compound's ability to inhibit multinucleate cell production resulting from post-mitotic cell fusion during a process of Daughter Number Variation (DNV) in mitosis. Compounds identified by this method can be used in cancer treatment, either alone or in combination with other known cancer drugs. The present invention also provides methods of personalized cancer treatment for a patient having a malignant tumor.

Abstract: The present disclosure relates to biomarkers and methods for determining or predicting survival of patients with low grade glioma (LGG) or pediatric neuroblastoma. Further disclosed are methods of diagnosing and treating patients with low grade glioma (LGG) or pediatric neuroblastoma.

Abstract: A system comprising a device or the device itself for measuring temperatures, comprising a sensor array plate, comprising on a first surface at least one temperature sensor arranged on at least one tongue that is surrounded by a cut-out leaving a bridge to the sensor array plate, wherein the at least one sensor has on both sides' spacer and a second surface opposite the first surface for connection to at least one operating plate of a thermocycler; and a pressure plate, comprising fins at the side for connection to the sensor array plate that align with the spacer of the sensor array plate when a pressure plate is arranged onto a sensor array plate.

Abstract: An array includes a support including a plurality of discrete wells, a gel material positioned in each of the plurality of discrete wells, and a quality control tracer grafted to the gel material in each of the plurality of discrete wells. The quality control tracer comprises (a) a cleavable nucleotide sequence comprising a cleavage site and (b) a detectable label; and in some aspects, is a cleavable nucleotide sequence with a detectable label and a non-reactive nucleotide sequence or a primer nucleotide sequence.

Abstract: A microfluidic device performs a method of partitioning droplets from a fluid reservoir containing particles that provides a non-Poissonian distribution of dispensed droplets containing a desired number of particles. Using an electrowetting on dielectric (EWOD) device, droplets are dispensed having a Poissonian distribution of dispensed droplets containing a desired number of particles, and the droplets are interrogated to determine whether each dispensed droplet has a desired number of particles. Droplets that contain the desired number of particles are moved by EWOD operation to a reaction area on the EWOD device, and droplets that do not contain the desired number of particles are rejected and moved by EWOD operation to a holding area on the EWOD device that is different and spaced apart from the reaction area. The result is that droplets in the reaction area have a non-Poissonian distribution of droplets containing the desired number of particles.

Abstract: A diagnostic process for disease detection using gene expression based PCA (Principal Component Analysis) classifier is provided. The present invention includes a method of diagnosing disease in a patient by performing a multilayer PCA classification that analyzes gene expression profiles of patients' biological samples to predict their class as disease or healthy, uses patients' biological samples to extract a set of fingerprint genes for specific disease and cell type which can be used as identification features, and classifies patient biological samples as disease or healthy based on differential gene expression profiles of the fingerprint genes.

Abstract: Provided herein are compositions and methods useful for the detection of MTB. In particular, provided herein are kits, reagents, reaction mixtures, and methods involving such for nucleic acid amplification and detection procedures, which specifically and sensitively detect MTB in samples.

Abstract: Provided herein are methods and systems for characterizing a nucleic acid molecule from a single cell. A method for characterizing a nucleic acid molecule from a single cell may comprise providing a partition (e.g., droplets or wells) comprising a single cell and a single bead. The single bead may comprise a nucleic acid barcode molecule. A nucleic acid molecule from the single cell and the nucleic acid barcode molecule may be used to generate a barcoded nucleic acid molecule for sequencing, which may be used to determine an epigenetic state or characteristic of the nucleic acid molecule as being associated with the single cell.

Abstract: A primer for isothermal amplification of nucleic acid and its application are described. The primer includes a forward primer and a reverse primer used for amplifying a target gene. The forward primer is a sequence with an exogenous self-paired hairpin structure at the 5? end, or a sequence with a hairpin structure matched with any source sequence in the target gene close to the forward primer end at the 5? end. Nucleic acid amplification technology using the primer of the invention can produce repeated tandem structure of the target gene, and the repetition times can be controlled precisely. The technology can also be applied to the third generation sequencing technology. The amplification steps are not only simple and fast, but also improve sequencing accuracy.

Abstract: The present invention is methods and assays for identifying single proteins from a sample, without the use of affinity reagents. The methods and assays combine endopeptidase-based component of conventional peptide mapping with single molecule labeling and a microreactor array platform. The invention also includes kits for performing the methods and assays.

Abstract: The invention discloses a soybean plant, or a part of said plant comprising the transgenic event CIGBDt-Def1 or the transgenic event CIGBIs-Def5, as well as a method for the detection of those events in soybean samples. It also provides a seed from a soybean plant comprising said transgenic events, and products obtained from a plant, or from soybean seeds, comprising one of said events. In addition, the invention is related to a method for the production of soybean plants resistant to glyphosate, and to diseases caused by fungi or oomycetes, comprising the introduction of one of the mentioned transgenic events in the genome of said plants. The increase in the yield of a soybean crop in the field can be achieved with the transgenic events of the invention.

Abstract: A new fluorescence detection method called pyrophosphorolysis activated fluorescence was developed to measure PAP amplification of nucleic acid. A fluorophore-quencher dual-attached blocked primer was used for PAP which has a fluorophore attached to a nucleotide in the internal region or at the 5? end and a quencher attached to a blocked nucleotide at the 3? end. Multiple fluorophore-quencher dual-labeled blocked primers were also used for multiplex PAP, which are attached with different fluorophores to distinguish multiple templates in a reaction.

Abstract: Disclosed herein are devices and methods for amplifying double stranded DNA molecules. Methods for amplifying apoptotic cell-free DNA molecules can include performing end-repair and dA tailing of the cfDNA molecules, attachment of single-stranded hairpin adaptors to both ends of the end-repaired cfDNA molecules to produce adaptor-tagged, single-stranded, covalently closed DNA molecules, and amplification of the adaptor-tagged, single-stranded, covalently closed DNA molecules by a combination of rolling circle amplification and multiple displacement amplification using a PrimPol enzyme, a DNA polymerase with strand displacement activity and free nucleotides.

Abstract: The present invention relates to methods, kits and systems for the prognosis of the disease outcome of breast cancer, said method comprising: (a) determining in a tumor sample from said patient the RNA expression levels of at least 2 of the following 9 genes: UBE2C, BIRC5, RACGAP1, DHCR7, STC2, AZGP1, RBBP8, IL6ST, and MGP (b) mathematically combining expression level values for the genes of the said set which values were determined in the tumor sample to yield a combined score, wherein said combined score is indicative of a prognosis of said patient; and kits and systems for performing said method.

Abstract: This disclosure provides for devices and methods for conduction assays for combinatorial libraries. The devices comprise a multiplicity of wells and a removable cap.

Abstract: The present invention relates to a diatomaceous earth composition with a low endotoxin content, comprising an agglomerated mixture of calcined diatomaceous earth particles and water, wherein the mass ratio of calcined diatomaceous earth particles and water is in the range of 1:1.0 to 1:2.0, and wherein the endotoxin content of the diatomaceous earth composition is equal to or less than 0.5 EU/mL. In a further aspect, the present invention relates to a method for producing the diatomaceous earth composition with a low endotoxin content. In another aspect, the present invention relates to the use of the diatomaceous earth composition with a low endotoxin content as a precoat agent for the precoat filtration in biopharmaceutical applications.

Abstract: The disclosure describes novel systems, methods, and compositions for the manipulation of nucleic acids in a targeted fashion. The disclosure describes non-naturally occurring, engineered CRISPR systems, components, and methods for targeted modification of nucleic acids such as DNA. Each system includes one or more protein components and one or more nucleic acid components that together target nucleic acids.

Abstract: The invention is directed to devices and methods for performing rapid low-cost bioassays in self-contained disposable cartridges that provide efficient mixing of sample and reactants under a layer of liquid wax. Some embodiments additionally use gravity assisted distribution of sample and assay reagents in conjunction with an appliance containing all necessary valves, pneumatic sources, heat sources and detection stations.

Abstract: A first aspect of the present invention is directed to a method for the detection of a compound of interest in a microfluidic system. A second aspect of the present invention relates to the use of the method according to the first aspect for monitoring a biological event. A further aspect of the present invention is directed to a microfluidic system and the use thereof for carrying out the method according to the first aspect.

Abstract: Methods and assays for diagnosis or prognosis of endometriosis include comparing an expression level or activity of miR-155 and JARID2 in a sample to detect a measurable difference. Therapeutic methods for treating endometriosis in a subject comprise identifying a subject as having a decreased expression level and/or activity of JARID2 in a sample obtained from the subject; and administering an agent that inhibits an activity of an miRNA that targets JARID2 or an agent that inhibits EZH2. Methods for screening for a compound useful for treating endometriosis are also provided and include contacting a cell with an effective amount of a test compound, and detecting whether the expression level or activity level of JARID2 or miR-155 in the cell is altered in the presence of the test compound.

Abstract: A sequencing system includes an automated sequencing instrument adapted to determine variant calls for one or more extracted polynucleotide samples with a performance of at least 98.5% raw read accuracy and a run time in a range of 5 hours to 14 hours to determine variant calls for 4 extracted polynucleotide samples using a targeted assay with one DNA pool per sample and an average amplicon size in a range of 100 to 120 bases.

Abstract: The disclosed methods for preparing cytological samples may include placing a cytological sample in a concave filter in a filtration system, applying a negative pressure to an outer side of the concave filter with a vacuum device to withdraw a liquid from the cytological sample, applying a sectionable matrix material over the filtered cellular material within the concave filter, and removing an assembly including the filtered cellular material and the sectionable matrix material from the filtration system. Various other related methods, systems, and materials are also disclosed.

Abstract: Applications of a ZmROA1 protein or substance regulating the content or activity of the ZmROA1 protein are provided. The ZmROA1 protein can be specified as follows: A1), A2) or A3): A1, the amino acid sequence is the amino acid sequence shown in SEQ ID NO: 3; A2, the protein, which is obtained by replacing and/or deleting and/or adding the amino acid sequence shown in SEQ ID NO: 3 through amino acid residues, is more than 80% identity to A1) and relates to plant root angle; A3, the fusion protein which is obtained by linking N-end or/and C-end of A1) or A2) to protein tags. ZmROA1 protein and its related biological materials can be used to regulate plant density tolerance and/or root angle, and the cultivation of new density-tolerant maize varieties, which helps improve maize harvest index for high and stable yield.

Abstract: The invention is directed to devices and methods for performing rapid low-cost bioassays in self-contained disposable cartridges that provide efficient mixing of sample and reactants under a layer of liquid wax. Some embodiments additionally use gravity assisted distribution of sample and assay reagents in conjunction with an appliance containing all necessary valves, pneumatic sources, heat sources and detection stations.

Abstract: Methods of stabilizing DNA-engineered crystals can include cross-linking the hybridized oligonucleotides. Stabilized crystals can have improved chemical and thermal stability.

Abstract: The present disclosure provides methods and processes for increasing the efficiency and accuracy of nucleic acid sequencing using techniques such as polymerase chain reaction (PCR). The methods described herein can be used to achieve clonal amplification even with a greater than Poisson distribution of beads and/or nucleic acid templates into an emulsion. A PCR method may comprise generating a partition (e.g., a droplet) comprising at least two beads and/or at least two nucleic acid molecules and generating clonal amplification products corresponding to the nucleic acid molecule, at least a subset of which may be attached to a bead.

Abstract: A magnetic digital microfluidic apparatus for manipulating a liquid droplet containing magnetic particles using a magnetic force, the apparatus comprising: a hydrophobic surface on which the liquid droplet containing magnetic particles can be moved using the magnetic force; and at least one surface energy trap provided to retain at least a portion of the liquid droplet thereon, the at least one surface energy trap comprising a layer of polydopamine. A method of magnetic digital microfluidic manipulation, the method comprising the steps of: a) contacting a liquid droplet on a hydrophobic surface with a polydopamine surface energy trap, the liquid droplet containing magnetic particles; b) retaining at least a portion of the liquid droplet on the surface energy trap; and c) moving at least the magnetic particles with a magnetic force.

Abstract: The present invention is directed to provide new PCR measuring method and device. As one embodiment of the present invention, a DNA detection method for detecting DNA in a droplet being present in oil, the droplet containing the DNA and a fluorescent labeled probe, the fluorescent labeled probe being hybridized to the DNA, the method including: a first step of amplifying the DNA in the droplet by a nucleic acid amplification reaction; and a second step of measuring a melting temperature of the fluorescent labeled probe and the DNA in the droplet is provided.

Abstract: The technology relates in part to methods and compositions for isothermal amplification of nucleic acids.

Abstract: The present invention provides materials and methods useful for error correction of nucleic acid molecules. In one embodiment of the invention, a first plurality of double-stranded nucleic acid molecules having a nucleotide mismatch are fragmented by exposure to a molecule having unidirectional mismatch endonuclease activity. The nucleic acid molecules are cut at the mismatch site or near the mismatch site, leaving a double-stranded nucleic acid molecule having a mismatch at the end or near end of the molecule. The nucleic acid molecule is then exposed to a molecule having unidirectional exonuclease activity to remove the mismatched nucleotide. The missing nucleotides can then be filled in by the action of, e.g., a molecule having DNA polymerase activity. The result is double-stranded nucleic acid molecules with a decreased frequency of nucleotide mismatches.

Abstract: The present disclosure describes significant methylation changes in multiple genes and multiple metabolites in body fluid in response to TBI. Gene pathways affected included several known to be involved in neurological and brain function. A large number of good to excellent biomarkers for the detection of TBI was identified. The combination of epigenomic, clinical and metabolomic markers in different combinations overall were highly accurate for the detection of pediatric concussion using Artificial Intelligence-based techniques.

Abstract: Methods and compositions for nucleic acid amplification, detection, and genotyping techniques are disclosed. In one embodiment, a nucleic acid molecule having a target-specific primer sequence; an anti-tag sequence 5? of the target-specific primer sequence; a tag sequence 5? of the anti-tag sequence; and a blocker between the anti-tag sequence and the tag sequence is disclosed. Compositions containing such a nucleic acid molecule and methods of using such a nucleic acid molecule are also disclosed.

Abstract: The application belongs to the technical field of animal or human antibodies, and discloses a TIM-3 nanobody, a preparation method thereof and use thereof. The nanobody is a TIM-3 nanobody with sequence of SEQ ID NO:1. TIM-3 antigen is a transient transfection expression by mammalian cells. TIM-3 antigen is used to screen the nanobody library repeatedly, specific phage of nanobody is obtained, and the target fragment is conducted sequencing. The application uses the HEK293 cell line to express antigen. Using the mammalian expression system to express human protein may maximumly guarantee the original structure of the protein, guarantee the protein to have a post-translational modification and specific modifications of eukaryotic proteins such as glycosylation, which makes the obtained protein have high activity. This method maximizes the original structure and activity of the protein; the nanobodies screened by the application can efficiently and specifically bind to the target.

Abstract: In traditional plant breeding approaches, chemical mutagenesis may be utilized to introduce nucleotide substitutions at random in the genome of a plant, i.e. without possibilities to control the sites of nucleotide changes. Because of genome complexities, the statistical probability is extremely little when it comes to finding a predetermined nucleotide substitution. The present invention, however, demonstrates how a novel, alternative use of digital polymerase chain reaction (dPCR), preferably droplet dPCR (ddPCR), is developed to exploit finding of specific nucleotide substitutions in mutated genes. The entire platform comprises a screening method with a library of mutagenized organisms, digital PCR-based systems and a set-up to propagate and analyze identified, mutated organisms.

Abstract: The present invention relates to a method for detecting nucleic acids by fluorescent PCR. The method combines primer-activated polymerization reaction and specific fluorescence-labeled probe, which detects the target nucleic acid with high selectivity and high specificity.

Abstract: Provided herein are methods and compositions for preparing nucleic acid templates wherein spatial-proximal and molecular contiguity of target nucleic acids is preserved, and the sequencing data obtained therefrom is used, but not limited to, identification of genomic variants, determination of contiguity information to inform assemblies of target nucleic acids de novo including deconvolution of haplotype phase information, and analyses of conformation and topology of target nucleic acids.

Abstract: In embodiments of field value search drill down, a search system exposes a search interface that displays one or more events returned as a search result set. A field-value pair can be emphasized in the field-value pairs of an event displayed in the search interface, and a menu is displayed with search options that are selectable to operate on the emphasized field-value pair of the event. The menu includes the search options to add search criteria of the emphasized field-value pair to a search command in a search bar of the search interface, exclude the search criteria of the emphasized field-value pair from a search, or create a new data search based on the emphasized field-value pair. A selection of one of the search options in the menu can be received, and the search command in the search bar is updated based on the search option that is selected.

Abstract: The present disclosure provides methods and compositions for the treatment of cancer. In some aspects, the present disclosure provides splice-switching oligonucleotides that downregulate AR expression and methods of using these splice-switching oligonucleotides to treat cancer, specifically castrate resistant prostate cancer.

Abstract: Filtration head (1) for a filter system, comprising base (2) including filter support (3) for removable filter element (4) and a fluid path from one side of filter element (4) on filter support (3), through filter element (4), and to drainage outlet (5) of base (2), and holder device (6) for removably attaching funnel (7) to base (2) to form a sample fluid reservoir on one side of filter element (4), wherein holder device (6) comprises ring-shaped element (8) configured to extend about bottom peripheral flange (7a) surrounding a lower end of funnel (7) and to selectively apply a biasing force on a radially outward protruding portion (7b) of bottom peripheral flange (7a) of funnel (7) to press funnel (7) against base (2). The filtration head allows the use of cardboard funnels without risk of liquid leakage between the funnel and the base.

Abstract: An object of the present invention is to prepare a functional intestinal organoid from pluripotent stem cells. An intestinal organoid is prepared from pluripotent stem cells, by the following steps (1) to (4): (1) differentiating pluripotent stem cells into endoderm-like cells; (2) differentiating the endoderm-like cells obtained in step (1) into intestinal stem cell-like cells; (3) culturing the intestinal stem cell-like cells obtained in step (2) to form spheroids; and (4) differentiating the spheroids formed in step (3) to form an intestinal organoid, the step including culture in the presence of a MEK1/2 inhibitor, a DNA methylation inhibitor, a TGF-? receptor inhibitor, and a ?-secretase inhibitor, in addition to an epidermal growth factor, a BMP inhibitor, and a Wnt signal activator.

Abstract: The present disclosure provides a “looping amplification” method to increase the specificity of nucleic acid amplification. This increased specificity facilitates multiplexing to a much higher degree than was previously possible.

Abstract: The present invention relates to methods for the treatment of cancer and inflammatory disease using antibodies (e.g. monoclonal antibodies), antibody fragments, and derivatives thereof that specifically bind KIR3DL2. The invention also relates to antibodies, cells producing such antibodies; methods of making such antibodies; fragments, variants, and derivatives of the antibodies; pharmaceutical compositions comprising the same.