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.

Abstract: A method of treating a patient having a cancer in which HER2, HER4, FGFR1, EPHA2 and/or FGFR3 is upregulated and/or in which HER2, HER4, FGFR1, EPHA2 and/or FGFR3 mediated-signaling is upregulated, the method comprising administering to the patient a compound comprising or consisting of an OPCML polypeptide (SEQ ID NO: 1), or a fragment thereof which comprises at least one Ig domain of OPCML, or a variant thereof having at least 90% sequence identity with the OPCML polypeptide or the fragment thereof, or a nucleic acid molecule which encodes the OPCML polypeptide or fragment or variant thereof.

Abstract: In some aspects, the present disclosure provides methods for enriching amplicons, or amplification products, comprising a concatemer of at least two or more copies of a target polynucleotide. In some embodiments, a method comprises sequencing the amplicons comprising at least two or more copies of a target polynucleotide. In some embodiments, the target polynucleotides comprise sequences resulting from chromosome rearrangement, including but not limited to point mutations, single nucleotide polymorphisms, insertions, deletions, and translocations including fusion genes. In some aspects, the present disclosure provides compositions and reaction mixtures useful in the described methods.

Abstract: Provided are vertical flow detection devices and related methods. The devices may comprise a membrane having a first surface and a second surface with a plurality of porous structures extending between the first and second surfaces to form fluid conduits from a first fluid chamber formed by the first surface and a second fluid chamber formed by the second fluid surface. A capture agent is immobilized on and/or in the membrane. A rigid porous membrane support mechanically supports the membrane and to provide a relatively uniform flow across the membrane. Various gaskets or holder elements are positioned around an outer edge of the membrane to prevent fluid leakage around the membrane. A fluid pump is configured to force a fluid sample flow in a direction from the first fluid chamber to the second fluid chamber.

Abstract: Provided herein are methods and systems for analysis of one or more single cells. The disclosed methods may comprise barcoding analytes from cell types of interest, while eliminating undesired cell types from analysis. Barcoding may comprise the use of a targeting agent. A targeting agent may be attached to an inhibitor or an activator, thereby inhibiting or activating analyte barcoding.

Abstract: This disclosure describes microfluidic tissue biopsy and immune response drug evaluation devices and systems. A microfluidic device can include an inlet channel having a first end configured to receive a fluid sample optionally containing a tissue sample. The microfluidic device can also include a tissue trapping region at the second end of the inlet channel downstream from the first end. The tissue trapping region can include one or more tissue traps configured to catch a tissue sample flowing through the inlet channel such that the fluid sample contacts the tissue trap. The microfluidic device can also include one or more channels providing an outlet.

Abstract: Provided herein are methods for identifying the presence or absence of a target nucleic acid from a microorganism using direct amplification without a step of extraction of the nucleic acids, but retaining substantially the same specificity and sensitivity of methods assaying extracted nucleic acids.

Abstract: Provided herein are compositions and methods for diagnosing and characterizing cancer. In particular, provided herein are compositions and methods for selecting MRI imaging methods for prostate tumors.

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: The application relates to methods and systems for proteomics and spatial mapping of biomolecules using a next generation sequencing readout to decipher biomolecular and cellular interaction networks. Specifically, disclosed are antenna networks generated by conjugating DNA antennas to proteins. The antennas carry a unique antenna identifier (UAI) sequence that can provide spatial location of the network, as well as biomolecules by transfer of the UAI to reporter oligonucleotides associated with other antennas and biomolecules. The methods and systems are also applicable to single cells.

Abstract: A communication interface buffer comprises: a data bus connection adapted to be coupled to a bus interface contact; and a ground. The communication interface buffer also comprises an output transistor with a first current terminal, a second current terminal and a control terminal, the first current terminal coupled to the data bus connection, the second current terminal coupled to ground, and the control terminal adapted to receive a drive signal. The communication interface buffer also comprises a control circuit coupled to the control terminal of the output transistor, wherein the control circuit is configured to: turn off the output transistor during a first interval that starts when the data bus connection is coupled to the bus interface contact; and turn on the output transistor after the first interval is complete.

Abstract: The present disclosure, at least in part, relates to an engineered RNA (e.g., microRNA and sgRNA), in the absence of an input signal, that is engineered to have a large enough energy gap between the formations of a first secondary structure, which is unrecognizable by an actuator, and a second secondary structure, which is recognizable by an actuator (e.g., Drosha and Cas protein).

Abstract: A method assessing tissue morphology using machine learning includes a step of training a machine learnable device to predict the status of a diagnostic feature in stained tissue samples. The machine learnable device is trained with a characterized set of digital images of stained tissue samples. Each digital image of the characterized set has a known status for the diagnostic feature and an extracted feature map provides values for a extracted feature over an associated 2-dimensional grid of spatial locations. A step of inputting the set of extracted feature maps is inputted into the machine learnable device to form associations therein between the set of extracted feature maps to and the known status for the diagnostic feature to form a trained machine learnable device. The status for the diagnostic feature of a stained tissue sample of unknown status for the diagnostic feature is predicted from the trained machine learnable device.

Abstract: Disclosed is a fluorescent composition for whole blood analysis capable of predicting the diagnosis, treatment and prognosis of diseases through blood analysis. In the case of using the fluorescent composition of exemplary embodiments of the present invention for whole blood analysis, the shape of a target material such as red blood cells and white blood cells may be maintained as it is and non-target biomaterials and the like may be dissolved to increase the sensitivity and affinity to the target and improve the staining efficiency of the blood cell nucleic acids, thereby increasing the fluorescent efficiency. Therefore, more accurate blood cell analysis is possible than conventional techniques, and through this, it is possible to accurately predict not only the diagnosis of the disease, but also the treatment method and prognosis.

Abstract: The present invention generally concerns an automated system capable of performing quantitative PCR (qPCR) analysis of a nucleic acid present in a biological sample together with preparation of a sequencing-ready nucleic acid library from the sample, either simultaneously or sequentially. In a further aspect, the present invention also provides a method for performing qPCR of a nucleic acid present in a biological sample together with simultaneous of sequential preparation of a sequencing-ready nucleic acid library from the sample. Finally, the present invention also provides removable cartridges for use in the automated systems and methods according to the invention.

Abstract: Aspects of the disclosure relate to methods of altering RNA splicing in a subject. In some embodiments, methods are provided for correcting splicing in a cell that contains a DYSF gene having a mutation that results in defective splicing.

Abstract: The present disclosure provides methods and systems for detecting multiple different nucleotides in a sample. In particular, the disclosure provides for detection of multiple different nucleotides in a sample utilizing fewer detection moieties than the number of nucleotides being detected and/or fewer imaging events than the number of nucleotides being detected.

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: The present disclosure provides methods and reagents for improving nanopore-based analyses of polymers. Specifically, the disclosure provides a method of analyzing a polymer that includes a polymer analyte that contains an end domain that has at least one charged moiety. The disclosure also provides a method of increasing the interaction rate between a polymer analyte and a nanopore, wherein the polymer analyte contains an end domain that has at least one charged moiety. The disclosure also provide compositions for use with the described methods, including adapter compositions that contain charged moieties, such as phosphate or sulfate groups, and that are configured to being linked to an polymer analyte domain.

Abstract: Transgenic INIR20 soybean plants comprising modifications of the MON87701 soybean locus which provide for facile excision of the modified MON87701 transgenic locus or portions thereof, methods of making such plants, and use of such plants to facilitate breeding are disclosed.

Abstract: Compositions and methods for improving cardiac structure and/or function in subjects in need thereof. The methods include administering to a subject a succinate dehydrogenase inhibitor in an amount and for a time effective to elicit an improvement in cardiac structure and/or function. The subjects include subjects suffering from cardiac damage, such as damage resulting from myocardial infarction or other cardiac events. Improvements in cardiac function include one or more of an increase in cardiomyocyte proliferation, an increase in ejection fraction, an increase in fractional shortening, a decrease in left ventricle internal diameter diastole, and a decrease in left ventricle internal diameter systole. Improvements in cardiac structure include one or more of decreased fibrosis, an increase in myocardial thickness, an increase in coronary artery formation, an increase in capillary density, an increase in revascularization, and a decrease in myocardial lesion size.

Abstract: Provided herein is technology related to the chemical modification and purification of DNA. Specifically, the technology provides methods for performing a bisulfite conversion reaction on small amounts of single-stranded, fragmented DNA and performing the subsequent desulfonation and purification steps on magnetic beads.

Abstract: The present invention provides a non-naturally occurring dendritic-like myeloid leukaemia cell according to ATCC Patent Deposit Designation PTA-123875, and methods and kits utilising such cells.

Abstract: In accordance with the present invention, a method for increasing the yield of rLV vector particles comprising a trans gene encoding a therapeutic protein or fragment thereof is disclosed. In one approach, cells are transfected with plasmids encoding the necessary components for rLV production using a calcium chloride transfection mix at pH 7.1 wherein the calcium chloride and plasmids form a complex which is added to the cells at a constant speed. The cells are then incubated for a suitable time period wherein virus particle media is collected at least twice during the incubation period and stored in a cold storage unit, thereby reducing virus inactivation.

Abstract: The invention relates to processes for performing biochemical reactions, such as in an aqueous in vitro reaction system. The processes involve macromolecules, particularly polypeptides, comprising one or more functional intrinsically disordered regions (IDRs). The invention also relates to IDR-macromolecules, including IDR-polypeptides, including macromolecules or polypeptides comprising a tagged amino acid sequence which comprises or consists of one or more functional IDRs. Such functional IDRs are capable of increasing the efficiency of the biochemical reaction. The invention relates to kits comprising any such macromolecules and polypeptides. The invention further relates to processes for stimulating or enhancing liquid-liquid demixing in a solution using any such macromolecules and polypeptides, including in combination with multivalent metal ions, thereby providing reagents capable of increasing the efficiency of a biochemical reaction.

Abstract: This application provides for methods of treatment for IBD, especially in subjects who have R. gnavus species or R. gnavus group IBD strains as a component of their microbiome. The application also provides for methods of diagnosing IBD, as well as kits for use in the claimed methods.

Abstract: A microfluidic analysis system (1) performs polymerase chain reaction (PCR) analysis on a bio sample. In a centrifuge (6) the sample is separated into DNA and RNA constituents. The vortex is created by opposing flow of a silicon oil primary carrier fluid effecting circulation by viscous drag. The bio sample exits the centrifuge enveloped in the primary carrier fluid. This is pumped by a flow controller (7) to a thermal stage (9). The thermal stage (9) has a number of microfluidic devices (70) each having thermal zones (71, 72, 73) in which the bio sample is heated or cooled by heat conduction to/from a thermal carrier fluid and the primary carrier fluid. Thus, the carrier fluids envelope the sample, control its flowrate, and control its temperature without need for moving parts at the micro scale.

Abstract: A dispersant system comprises a plurality of taggant vessels, each having a taggant that corresponds to a position in a tag string and a computer controller convert the tag string into a selection of a taggant set while computer-controlled valves allow or block a flow of taggants to a manifold output tube. From the output tube, a mix of the taggants flow to form a dispersant formed according to the tag string. A nozzle disperses the dispersant onto an object to be tagged, possibly atomized with air. The taggant can comprise a DNA taggant comprising a static portion and a dynamic portion that is unique to each tag string position. Tag strings for adjacent lots might have a low Hamming distances to reduce cross-contamination and/or have redundancy for error detection and correction and selected so that consumption of taggants evens out over the plurality of taggant vessels.

Abstract: Systems and methods for multiplexed cell sorting are provided herein. The disclosed cell sorting system is referred to as DNA gated sorting (DGS). An exemplary system provides a set of orthogonal sorting probes and release probes for sorting cells of one or more different cell types from a biological specimen.

Abstract: An endoscopic imaging system for use in a light deficient environment includes an imaging device having a tube, one or more image sensors, and a lens assembly including at least one optical elements that corresponds to the one or more image sensors. The endoscopic system includes a display for a user to visualize a scene and an image signal processing controller. The endoscopic system includes a light engine having an illumination source generating one or more pulses of electromagnetic radiation and a lumen transmitting one or more pulses of electromagnetic radiation to a distal tip of an endoscope.

Abstract: Disclosed is a method for determining the presence of Mycobacterium avium complex nucleic acids in a biological sample. In particular, the mig gene of M. avium and the DT1 gene of M. intracellulare are detected, preferably following amplification. In addition, the method distinguishes between species of M. avium and M. intracellulare. Also described are oligonucleotides that can be used as primers to amplify target genes such as mig and DT1 genes and as probes as well as kits containing the oligonucleotide.

Abstract: One embodiment provides methods to identify known and unknown gene fusions by creating a cDNA circle and analyzing the circle cDNA by amplification or sequencing. The circle cDNA is created in two approaches: 1) reverse transcribe a target RNA to cDNA, ligate the 3?end of the cDNA to its 5?end to form a circle cDNA, or 2). ligate the 3?end of target RNA to its 5? end to form a circle RNA, reverse transcribe the RNA to a cDNA, and ligate the cDNA to form a circle cDNA. The circle cDNA is amplified using a primer designed from a known sequence of a wild type target gene by rolling circle amplification or PCR methods. The known or unknown fusion gene sequences in the circle cDNA are amplified and identified by sequencing analysis.

Abstract: A method of tracking proximity relationships is disclosed, comprising: (a) introducing a body into a solution of bio-molecule(s), said body comprising at least two capture probes, wherein each capture probe comprises a barcode and a capture domain, and at least one capture probe is a releasable capture probe, connected to the body via at least one cleavable linker; (b) allowing at least two capture probes to bind to their respective target bio-molecule(s) via their respective capture domains; and (c) releasing the at least one releasable capture probe from the body by cleaving its at least one cleavable linker.

Abstract: Provided herein are methods of detecting an analyte of interest to interrogate spatial gene expression in a sample using RNA-templated ligation.

Abstract: A system and method for automatically calculating an accurate recommended dosage for hormone replacement therapy and automating the life cycle of a patient's treatment over time. The system and method can automatically acquire relevant patient parameters and apply a consistent formulaic approach to help reduce incorrect dosage determinations. A pellet insertion size may be determined and documented based on a calculated dosage, and an insertion side and lot numbers may be tracked and managed. In addition, corresponding revenues may be tracked and profitability may be reported for hormone replacement therapy practices.

Abstract: A machine learning (ML) architecture may be trained to determine an estimated epigenetic status at a target DNA locus based at least in part on epigenetic data associated with one or more other DNA loci. The ML architecture may additionally or alternatively be used to detect a failed epigenetic assay and/or determine a likelihood that a subject has falsified information provided about the subject.

Abstract: Personalized treatment plan generation from an inference engine of a system. The system may receive or retrieve data from a plurality of sources and parse the data to generate individual data fields defining characteristics of a patient. The inference engine may process the contents of the individual data fields in relation to rule blocks suggesting certain treatment actions and combinations thereof in response to satisfied conditions. The inference engine may implement machine learning to refine rule blocks and improve functioning of the system to optimize healthcare.

Abstract: The present disclosure provides method and products for the selective enrichment of one population of DNA in a mixed sample comprising multiple populations of DNA. In some embodiments, the mixed sample comprises one or more populations of microbial DNA and the mammalian host DNA, particularly including pathogenic microbial DNA mixed with mammalian host DNA in a clinical sample from an infected individual.

Abstract: The invention provides methods and compositions for separately denaturing a probe and target in hybridization applications. The invention may, for example, eliminate the use of, or reduce the dependence on formamide in hybridization applications. Compositions for use in the invention include an aqueous composition comprising at least one polar aprotic solvent in an amount effective to denature double-stranded nucleotide sequences.

Abstract: Methods, primers, sets of primers, probes, compositions, and kits for detecting presence or absence of SARS-CoV-2 in a sample are provided.

Abstract: To reduce an arithmetic processing load or an influence of noise at the time of virtual curve calculation processing, provided is a data processing device for a chromatograph, which is configured to execute data processing based on plot data measured by using a chromatograph, the data processing device including a virtual curve calculation data generator configured to obtain a smaller number of pieces of virtual curve calculation data than a number of pieces of the measured plot data; and an arithmetic processor (163) functioning as a virtual curve calculator configured to obtain a virtual curve based on the virtual curve calculation data.

Abstract: Disclosed is a substance which down-regulates the activity of a MAST gene, or the activity of a transcription or translation product of a MAST gene, for use in the prevent and/or treatment of an inflammatory skin condition in a mammalian subject.

Abstract: Embodiments of a system and method for characterizing a panel of conditions associated with a set of taxa related to microorganisms can include a taxonomic database including reference microbiome features for the set of taxa associated with the panel of conditions; a handling operable to collect a container including biological material from a user, the handling system comprising a sequencer system operable to determine a microorganism sequence dataset; and a panel characterization system operable to: determine user microbiome features for the set of taxa for the user based on the microorganism sequence dataset, generate a comparison between the user microbiome features and the reference microbiome features, and determine a panel characterization for the panel of conditions for the user based on the comparison; and a treatment system operable to promote a therapy for a condition of the panel of conditions based on the panel characterization.

Abstract: The present invention provides systems, apparatuses, and methods to detect the presence of fetal cells when mixed with a population of maternal cells in a sample and to test fetal abnormalities, e.g. aneuploidy. The present invention involves labeling regions of genomic DNA in each cell in said mixed sample with different labels wherein each label is specific to each cell and quantifying the labeled regions of genomic DNA from each cell in the mixed sample. More particularly the invention involves quantifying labeled DNA polymorphisms from each cell in the mixed sample.