Abstract: Described herein are engineered CCCTC-binding factor (CTCF) variants that can bind to mutant CTCF binding sequences and method of using the same.

Abstract: A method, implemented by a computer system, and a system of organizing data of a wide area motion imagery frame and a method and a system of retrieving objects that match a user defined AOI from an image in a WAMI frame in a WAMI collection are described. The method of organizing includes dividing, by the computer system, an image of a WAMI frame into a plurality of tiles, each tile in the plurality of tiles comprising a plurality of pixels and having a pixel width and a pixel height; storing, by the computer system, the plurality of tiles as objects in an OSD, each object having an object identifier (OID); collecting, by the computer system, object identifiers (OIDs) of the objects; and storing, by the computer system, the OIDs in the OSD.

Abstract: In embodiments there is described a method for reducing false positives and negatives in the detection of SARS-CoV-2 in suspected patients using mass spectroscopy employing the steps of mixing samples of collected saliva and nasopharyngeal secretions in a single sample container; adding universal transport medium to the mixed samples in said single sample container; transporting the single sample container at a temperature above 0° C. to a remote location; deactivation of viral content of the mixed sample; protein digestion of the mixed sample; concomitant separation of peptides, ionization by mass spectroscopy of the separated peptides, and comparison of peptide patterns to known SARS-CoV-2 peptides. Also set forth in an embodiment is a collection container for collecting saliva and/or sputum, as well as a swab member, with universal transport medium and/or virus inactivating agent housed in separate compartment communicable with sample compartment through a one-way valve.

Abstract: The invention generally relates to methods for maintaining the integrity and identification of a nucleic acid template in a multiplex sequencing reaction. In certain embodiments, methods of the invention involve obtaining a template nucleic acid, incorporating a pair of sequence identifiers into the template, and sequencing the template.

Abstract: Provided herein are modified Archaeal family B polymerases derived from species of the Archaeal microorganism Pyrococcus that exhibit improved incorporation of nucleotide analogues utilized in DNA sequencing.

Abstract: The present invention is directed to a phospholipid-based NIR molecular beacon, having a phospholipid moiety; with an NIR fluorophore moiety covalently linked to a phospholipid glycerol backbone and a quencher moiety covalently linked to the phospholipid glycerol backbone. Additionally, provided herein is methods of analyzing a sample for the presence of a phospholipase and methods of identifying the activity of a phospholipase in vivo utilizing phospholipid-based NIR molecular beacon.

Abstract: In a method p for controlling translocation of a target polymer molecule through a nanopore, a clamp is reversibly bound to a sequential plurality of polymer subunits along the target polymer molecule length and the molecule and clamp are disposed in an ionic solution that is in fluidic communication with the nanopore. A constant translocation force is applied across the nanopore to induce travel of the target polymer molecule into the nanopore, until the clamp abuts the nanopore aperture and stops further travel of the target polymer molecule into the nanopore. Then a voltage control pulse is applied across the nanopore and/or a thermal control pulse is applied at the nanopore, with a pulse duration that steps the clamp along the target polymer molecule by no more than one polymer subunit in a direction opposite that of travel into the nanopore. No fuel is provided to the clamp.

Abstract: The use of PHGDH as a biomarker for detecting the occurrence of epithelial-to-mesenchymal transition (EMT) in a subject, and the use of PHGDH modulators to treat cancer is disclosed herein. Also disclosed are various methods for detecting the occurrence of epithelial-to-mesenchymal transition (EMT) in a subject by measuring PHGDH expression and/or activity.

Abstract: A method and composition for extracting an analyte from a test sample such as grain, so as to determine whether the test sample is contaminated with a toxin. The method is particularly useful for detecting the presence in a batch of grain of a mycotoxin, such as for example aflatoxin, ochratoxin, T2, zearalanone, vomitoxin (deoxynivalenol a/k/a DON), patulin and fumonisin. Extraction is performed with use of a composition that includes a proteinaceous material, such as albumin, as an extraction agent.

Abstract: Methods and compositions for digital profiling of nucleic acid sequences present in a sample are provided.

Abstract: Provided herein are methods, compositions and kits for the generation of bisulfite-converted next generation sequencing (NGS) libraries. The methods, compositions and kits provided herein can be useful, for example, for the production of libraries from genomic DNA that allow for determination of the methylation status across the genome, i.e. the methylome. The methods, compositions and kits provided herein can also be utilized to query methylation status at a particular genomic locus or loci. Moreover, the methods provided herein can be employed for high-throughput sequencing of bisulfite-converted DNA while maintaining the directional (strandedness) information of the original nucleic acid sample.

Abstract: The present invention provides processes for determining accurate risk probabilities for chromosome dosage abnormalities. Specifically, the invention provides non-invasive evaluation of genomic variations through chromosome-selective sequencing and non-host fraction data analysis of maternal samples.

Abstract: The invention provides peptides that can reactivate p53 mutants efficiently and specifically, as well as methods that allow the identification, selection and isolation of such peptides, in a precise, cost and time effective manner. In particular, there are provided mutant p53 reactivating peptides that can restore the native wild type p53 folding, and hence the tumor suppressor activity, to the mutant p53 protein. Such peptides are useful for treating various conditions and diseases in which p53 is mutated.

Abstract: The present application relates to detection of changes in the number of nucleotides in short homopolymeric nucleic acid repeats, in particular in short homopolymeric microsatellites, for example for the purpose of diagnosing microsatellite instability (MSI) and/or mismatch repair (MMR-) deficiency in tumors. Accordingly, methods are provided for detecting changes in the number of nucleotides present in short homopolymeric nucleotide repeat sequences as well as kits and cartridges for automated detection of said changes.

Abstract: A method of maintaining contiguity in chromosomal DNA following treatment with a tagmentase. Conditions are selected such that the tagmentase does not release from the DNA, and thus forms a bridge linking DNA segments that have the same relationship (haplotype) as occurred in the genomic DNA. Thus the tagmentase step can occur in bulk (before partitions are formed). The resulting tagmentase-bridged DNA segments can be added to partitions maintaining the bridged segments until they are introduced into different partitions. Once in partitions, the contiguous DNA segments can be barcoded with a partition-specific barcode, thereby allowing for later identification of contiguous DNA after sequencing in bulk (after partitions contents are merged).

Abstract: The invention generally relates to sequencing library preparation methods. In certain embodiments, two or more template nucleic acids are joined together by a linking molecule, such as a PEG derivative. Identical copies of a nucleic acid fragment or both strands of a duplex fragment may be linked together. The linked nucleic acids are amplified, creating linked amplicons. Emulsion PCR with linked primers creates linked template nucleic acids for seeding sequencing clusters and errors can be readily identified by their presence on only one of the linked fragments.

Abstract: Providing herein, among other things, are kits, compositions and methods that relate to DNA fragmentation. An embodiment of a composition provides combining: one or more enzymes capable of nick translating activity, a dNTP mix comprising at least one dNTP having a modified base, and at least one modification-sensitive nicking endonuclease that is prevented from nicking DNA if its recognition site contains the modified base. When the composition is added to a sample comprising a double-stranded DNA template that comprises recognition sites for the modification-sensitive nicking endonuclease, a reaction mix was produced which could be incubated for any time period in excess of about 5 minutes to produce fragments of a desired size of the double-stranded DNA template. In this method, the fragments produced include the modified base and, as such, are not re-nicked by the nicking endonuclease.

Abstract: A semiconductor device includes a silicon carbide semiconductor layer, a termination region disposed in the silicon carbide semiconductor layer, an insulating film covering part of the termination region, an electrode disposed on the silicon carbide semiconductor layer, a seal ring disposed on remaining part of the termination region and surrounding the electrode, and a passivation film covering the insulating film and the seal ring. Assuming that an outer peripheral end of the seal ring and an outer peripheral end of the passivation film have distance L2 at a side of the silicon carbide semiconductor layer, the outer peripheral end of the seal ring and the outer peripheral end of the passivation film have distance L1 at a corner, and the outer peripheral end of the passivation film at the corner has radius of curvature R1, L1>L2 and R1?L2 are satisfied.

Abstract: Methods, devices, and kits are provided for performing PCR in <20 seconds per cycle, with improved efficiency and yield.

Abstract: The present invention provides a method of preparing a nucleic acid library, which includes providing a one or more nucleic acid samples, and a one or more of samples of solid state capture material; contacting each nucleic acid sample with a sample of capture material to provide captured nucleic acid samples; and pooling the captured nucleic acid samples to provide the nucleic acid library. The method is particularly suitable for preparing nucleic acids for sequencing, especially next generation sequencing and related methods such as genotyping-by-sequencing.

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 RAF gene fusions as diagnostic markers and clinical targets for cancer.

Abstract: This specification describes techniques for detecting abnormal data in a data set. One example method includes obtaining, by a data processing platform, a to-be-validated data group including to-be-validated data corresponding to a predetermined feature; obtaining, by the data processing platform, a comparison data group including historical data associated with the to-be-validated data group, wherein the historical and the to-be-validated data are from a same data source; performing, by the data processing platform, a two-group significance test on the to-be-validated data group and the comparison data group to generate a test result; and determining, by the data processing platform, whether there is abnormal data in the to-be-validated data group based on the test result.

Abstract: The invention relates to a method for preparing a strand-specific library from an nucleic acid or preferably RNA sample, for RNA comprising the steps of: (i) optionally fragmenting said RNA sample, (ii) generating a plurality of first cDNA strands by subjecting said fragmented RNA to reverse transcription by using a reverse transcriptase and first oligonucleotide primers, (iii) generating a plurality of second cDNA strands by using a DNA polymerase, second oligonucleotide primers, and the plurality of first cDNA strands, and (iv) ligating adapters to the 3? and 5? termini of the of double-stranded cDNA, (v) wherein the first cDNA strand allows no adapter ligation at its 5? terminus and said second cDNA strand allows adapter ligation at its 5? terminus, or vice versa, and, (v) optionally cloning, sequencing or otherwise using the strand-specific library.

Abstract: A method for determining the number of nucleic acid molecules (NAMs) in a group of NAMs, comprising i) obtaining an amplified and mutagenized group of NAMs that was produced by a. subjecting the group of NAMs to a chemical mutagenesis which mutates only select nucleic acid bases in the group of NAMs at a rate of 10% to 90% thus forming a group of mutagenized NAMs (mNAMs), and b. amplifying the group of mNAMs; ii) obtaining sequences of the mNAMs in the group of amplified mNAMs; and iii) counting the number of different sequences obtained in step (ii) to determine the number of unique mNAMs in the group of mNAMS, thereby determining the number of NAMs in the group of NAMs.

Abstract: The invention relates to a kit for use in a method for detecting genetic variation in one or more members of a population, comprising (a) an adaptor adapted for ligation to a plurality of nucleic acid fragments and (b) a set of primers for PCR amplification having a 5?-end and a 3?-end, wherein at least one of the primers comprises one or more selective nucleotides at the 3? end, and wherein the adaptor and/or at least one of the primers comprises a sample-specific identifier sequence capable of indicating sample origin of an amplification product.

Abstract: Methods of sequencing molecules based on luminescence lifetimes and/or intensities are provided. In some aspects, methods of sequencing nucleic acids involve determining the luminescence lifetimes, and optionally luminescence intensities, of a series of luminescently labeled nucleotides incorporated during a nucleic acid sequencing reaction.

Abstract: The present invention provides methods and systems for real-time measurements of PCR with multiplexing capability. Certain embodiments relate to methods and systems that use fluorescently encoded superparamagnetic microspheres for the immobilization of amplification products during the PCR process, and an imaging chamber of a measurement device that is also capable of controllable thermal cycling for assisting the PCR process.

Abstract: This specification describes techniques for detecting abnormal data in a data set. One example method includes obtaining, by a data processing platform, a to-be-validated data group including to-be-validated data corresponding to a predetermined feature; obtaining, by the data processing platform, a comparison data group including historical data associated with the to-be-validated data group, wherein the historical and the to-be-validated data are from a same data source; performing, by the data processing platform, a two-group significance test on the to-be-validated data group and the comparison data group to generate a test result; and determining, by the data processing platform, whether there is abnormal data in the to-be-validated data group based on the test result.

Abstract: Provided herein are artificial lung organoids. The artificial lung organoids may include an epithelial cell layer comprising mammalian lung epithelial cells, a stromal cell layer comprising mammalian lung fibroblast cells and an endothelial cell layer comprising mammalian endothelial cells. The artificial lung organoids may optionally include a porous membrane between said epithelial cell layer and said stromal cell layer and/or between said stromal cell layer and said endothelial lung cell layer.

Abstract: The present invention relates to a microfluidic assay system and associated reading device, as well as the individual components themselves. The present invention also relates to methods of conducting assays, using a disposable system and associated reading device, as well as kits for conducting assays.

Abstract: Single dye fluorescent staining and the combination of differences in both intensity and spectral emission permit determination of the minimum concentration of an antibiotic needed to inactivate bacteria (Minimum Inhibitory Concentration (MIC)), thereby providing a means for rapid Antibiotic Susceptibility Testing (AST). This allows for a quick and easy means for clinicians to determine a suitable treatment regimen for patients suffering from bacterial infections and those that eventually lead to sepsis.

Abstract: Described herein are biological devices and methods for using the same to produce oxidized zinc. The biological devices include microbial cells transformed with a DNA construct containing genes for producing a zinc-related protein, an alkaline phosphatase, and an alcohol dehydrogenase. In some instances, the biological devices also include a gene for lipase. The oxidized zinc compositions produced herein have numerous applications.

Abstract: Methods, kits, and compositions for evaluating the quality of nucleic acids within a biological sample for analysis in a molecular assay are provided.

Abstract: A method for detecting and quantifying additives in a complex aqueous fluid, and a method for detecting an inhibitor of mineral deposition or corrosion, injected in a gas or oil well. The invention also relates to a developer solution including a lanthanide and a chelating agent for detecting said additives or inhibitors.

Abstract: A PCR reaction vessel includes: a substrate; a channel formed on the substrate; a pair of filters, a first filter and a second filter, provided at respective ends of the channel; a pair of air communication ports, a first air communication port and a second air communication port, that communicate with the channel through the first filter and the second filter; a thermal cycle region formed between the first filter and the second filter in the channel; a branch point formed between the first filter and the second filter in the channel; a branched channel whose one end is connected to the branch point; and a sample introduction port formed at the other end of the branched channel.

Abstract: According to the present teachings, methods and compositions are provided that utilize at least one reference dye of formula (I): In some embodiments, a method comprises measuring a detection signal of a reporter dye and at least one reference dye of formula (I). In some embodiments, a composition comprises a reference dye of formula (1), a buffer, a selection of nucleotides and a protein.

Abstract: Provided herein are methods and composition for immune repertoire sequencing and single cell barcoding. The methods and compositions can be used to pair any two sequences originating from a single cell, such as heavy and light chain antibody sequences, for antibody discovery, disease and immune diagnostics, and low error sequencing.

Abstract: The present technology relates to methods for excluding Lynch syndrome as a possible diagnosis in patients suffering from colorectal cancers or endometrial cancers. These methods are based on detecting the methylation status of the MLH1 promoter ‘C’ region in colorectal and endometrial cancer patients using an improved and highly sensitive methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA) assay.

Abstract: A method to detect chromatin-interacting RNAs in any given state of a cell or tissue by examining global RNA interactions with DNA by deep sequencing. A method to generate a global view of chromatin-RNA interactome by mapping the binding locations on the genome of each detected chromatin interacting RNA.

Abstract: Multivalent binding compositions including a particle-nucleotide conjugate having a plurality of copies of a nucleotide attached to the particle are described. The multivalent binding compositions allow one to localize detectable signals to active regions of biochemical interaction, e.g., sites of protein-protein interaction, protein-nucleic acid interaction, nucleic acid hybridization, or enzymatic reaction, and can be used to identify sites of base incorporation in elongating nucleic acid chains during polymerase reactions and to provide improved base discrimination for sequencing and array based applications.

Abstract: Methods, primers and probes are provided for the isothermal amplification and detection, without denaturation, of double stranded nucleic acid targets for polymerase strand displacement amplification (“iSDA”). The methods and compositions disclosed are highly specific for nucleic acid targets with high sensitivity, specificity and speed that allow detection of clinical relevant target levels. The methods and compositions can easily be used to amplify or detect nucleic acid targets in biological samples.

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: The present disclosure relates to tagged multi-nucleotide compounds, which comprise a single tag moiety covalently linked to a plurality of nucleoside-5?-oligophosphate moieties. As disclosed herein, these tagged multi-nucleotide compounds have improved characteristics as polymerase substrates and can be used in a range of nucleic acid detection and sequencing methods, including nanopore sequencing-by-synthesis.

Abstract: A system and method for capturing and analyzing a set of cells, comprising: an array including a set of parallel pores, each pore including a chamber including a chamber inlet and a chamber outlet, and configured to hold a single cell, and a pore channel fluidly connected to the chamber outlet; an inlet channel fluidly connected to each chamber inlet of the set of parallel pores; an outlet channel fluidly connected to each pore channel of the set of parallel pores; a set of electrophoresis channels fluidly coupled to the outlet channel, configured to receive a sieving matrix for electrophoretic separation; and a set of electrodes including a first electrode and a second electrode, wherein the set of electrodes is configured to provide an electric field that facilitates electrophoretic analysis of the set of cells.

Abstract: The present invention relates, in part, to methods for large-scale purification of mRNA. The method includes, at least, a step of centrifuging an mRNA suspension in a centrifuge comprising a porous substrate at a speed sufficient to remove process contaminants and to precipitate purified mRNA composition onto the porous substrate.

Abstract: Systems and methods for provenance tracking and/or identification of a product using genetic material are claimed. In various embodiments, genetic material such as plasmids may be incorporated into and/or otherwise persistently associated with a product. The genetic material may be encoded with, among other things, information that may uniquely identify the product, provide details relating to the origins of the product, the handling, distribution, and/or chain of custody of the product, intellectual property rights and/or other rights associated with the product, and/or the like. By extracting and analyzing the genetic material from the product, information encoded in the genetic material may be obtained by an interested party.

Abstract: Described herein are fluid-manipulation-based devices and methods of use. Fluid manipulations according to devices and methods as described herein can be configured to perform assays on biological samples. Devices and methods as described herein can manipulate and analyze nanoliter volumes of fluid, microliter volumes of fluid, milliliter volumes of fluid, or greater. Embodiments of the present disclosure can enable random biological assays and rapid, simultaneous analysis of multiple biological samples.

Abstract: The invention generally relates to sequencing library preparation methods. In certain embodiments, two or more template nucleic acids are joined together by a linking molecule, such as a PEG derivative. Identical copies of a nucleic acid fragment or both strands of a duplex fragment may be linked together. The linked nucleic acids are amplified, creating linked amplicons. Emulsion PCR with linked primers creates linked template nucleic acids for seeding sequencing clusters and errors can be readily identified by their presence on only one of the linked fragments.

Abstract: A method of fabricating a nanoscale topography system for inducing unfolding of a DNA molecule for sequencing includes providing a substrate and creating trench walls on the substrate which define a trench therebetween. The method further includes depositing a layer of a block copolymer (BCP) in the trench and forming cylindrical domains by self-assembly of the BCP between the trench walls, removing a first portion of the cylindrical domains to create a vacant region in the trench, and depositing a subsequent layer of the BCP in the vacant region and forming spherical domains by self-assembly of the BCP between the trench walls adjacent a second portion of the cylindrical domains. The spherical domains form staggered post structures for unfolding the DNA molecule and the cylindrical domains form parallel channel structures for entry of the DNA molecule for sequencing.

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