Abstract: A method for compressing nucleic acid sequence data wherein each sequence read is associated with a molecular tag sequence, wherein a portion of the sequence reads alignments correspond to sequence reads mapped to a targeted fusion reference sequence includes determining a consensus sequence read for each family of sequence reads based on flow space signal measurements corresponding to the family of sequence reads, determining a consensus sequence alignment for each family of sequence reads, wherein a portion of the consensus sequence alignments correspond to the consensus sequence reads aligned with the targeted fusion reference sequence, generating a compressed data structure comprising consensus compressed data, the consensus compressed data including the consensus sequence read and the consensus sequence alignment for each family, and detecting a fusion using the consensus sequence reads and the consensus sequence alignments from the compressed data structure.

Abstract: A filter bag assembly includes: a flexible first sheet; a flexible second sheet overlying and secured to the first sheet so that a compartment is formed therebetween; a porous filter sheet disposed between the first sheet and the second sheet so as to divide the compartment into a first compartment and a second compartment; a first port secured to the second sheet so as to communicate directly with the first compartment; and a second port secured to the second sheet so as to communicate directly with the second compartment, the second port being spaced apart from the first port. The porous filter sheet is disposed so that fluid entering the first compartment through the first port must pass through the filter sheet before entering the second compartment or exiting through the second port.

Abstract: A method for compressing molecular tagged sequence data includes: grouping sequence reads associated with a molecular tag sequence to form a family of sequence reads, corresponding vectors of flow space signal measurements and corresponding sequence alignments, calculating an arithmetic mean of the corresponding vectors of flow space signal measurements to form a vector of consensus flow space signal measurements, calculating a standard deviation of the corresponding vectors of flow space signal measurements to form a vector of standard deviations, determining a consensus base sequence based on the vector of consensus flow space signal measurements, determining a consensus sequence alignment and generating a compressed data structure comprising consensus compressed data, the consensus compressed data including for each family, the consensus base sequence, the consensus sequence alignment, the vector of consensus flow space signal measurements, the vector of standard deviations and the number of members.

Abstract: Methods for forecasting case counts for a future date in one or more geographic areas of persons infected by a disease is disclosed. The presence of the disease in a biological sample is testable by a polymerase chain reaction (PCR) test. A load of one or more pathogens associated with the disease correlates with a PCR cycle which indicates presence of the one or more pathogens, and is referred to as a threshold cycle (Ct). Data relevant to forecasting the case counts including Ct data and other data is received. The Ct data comprises Ct values from PCR tests of biological samples from persons within the one or more geographic areas. Arrays of feature data for processing by a trained machine learning model are generated, comprising Ct features and other features obtained from the data. A forecasted number of infected persons are generated by processing the arrays using machine learning.

Abstract: A sensor apparatus includes a substrate, a semiconductor device disposed over the substrate, the semiconductor device having a surface electrode structure, and a saccharide coating formed over the surface electrode structure. The saccharide coating can be removed prior to use. The semiconductor device can further include a well and optionally a bead disposed in the well.

Abstract: Methods and apparatus relating to FET arrays for monitoring chemical and/or biological reactions such as nucleic acid sequencing-by-synthesis reactions. Some methods provided herein relate to improving signal (and also signal to noise ratio) from released hydrogen ions during nucleic acid sequencing reactions.

Abstract: A check valve assembly includes a first port fitting and a second port fitting with a base secured therebetween. The base has an annular sleeve encircling a seat, the seat having a central mounting hole and one or more flow channels passing therethrough. An umbrella valve includes a flexible sealing disk having an outer surface and an opposing inner surface, a mounting stem extending from the inner surface and projecting into the mounting hole of the base, the sealing disk being movable between a first position wherein at least a portion of the sealing disk sits on the seat so as to cover the one or more flow channels and a second position wherein the sealing disk is resiliently flexed so as to at least partially uncover the one or more flow channels. A retention plate is disposed between first port fitting and the seat of the base so that the retention plate sits against the outer surface of the sealing disk.

Abstract: The present invention provides lipid aggregate compositions having at least two cationic lipids in combination with one or optionally more than one non-cationic lipids for the in vitro and/or in vivo delivery of biologically active molecules including nucleic acids, specifically DNA and RNA, and proteins into cells and tissues. Methods are also provided that use the compounds of the present invention to deliver biologically active molecules, into cells and tissues to facilitate the expression of target proteins therein. In some non-limiting embodiments, the subject lipid aggregate compositions can be used to deliver nucleic acid molecules to facilitate the expression of proteins involved in cellular reprogramming and genome editing applications.

Abstract: A reagent container includes a base defining a plurality of wells having openings exposed at an upper surface of the base and a tube receptacle. The plurality of wells include a first set of wells and a second set of wells. Each well of the first set of wells has an opening to a well bore and a channel in communication with the well bore. The opening has a first portion disposed over the well bore and a second portion disposed over the channel. The first portion has a larger area than the second portion. An angle defined by tangents to the inner surface of the first and second portions at a junction between the first and second portions is at least 100° and not greater than 180°. The reagent container further includes a top coupled over the top surface of the base and defining windows providing access to the openings of the plurality of wells and the tube receptacle.

Abstract: A reagent solution includes water, a nucleotide, and tris(2-carboxyethyl)phosphine in a range of 0.5 ?M to 1000 ?M. The reagent solution can further include a non-ionic surfactant in an amount of 0.001% to 1% or a biocidal agent in an amount of 0.001% to 1%. The reagent solution can include salts, such as sodium chloride or magnesium sulfate.

Abstract: This disclosure relates to the field of fluorescent dyes, and in particular, compositions and methods for increasing fluorescent signals and the reduction of fluorescent quenching.

Abstract: A sample purification system includes a mixing zone; a settling zone in fluid communication with the mixing zone; a mixer element disposed in the mixing zone, the mixer element being configured to mix immiscible liquids to form a mixture; and a first acoustic wave settler configured to emit an acoustic wave into the mixture.

Abstract: Methods for evaluating microsatellite instability (MSI) analyze nucleic acid sequence reads corresponding to a plurality of marker regions for MSI. The marker regions may include long homopolymers and/or short tandem repeats (STRs). For a target homopolymer, a histogram of homopolymer signal values is calculated based on flow space signal measurements for the homopolymer region in the sequence reads. A score per marker based on features of the histogram of homopolymer signal values is determined for each marker region corresponding to the target homopolymers. For a target STR, the method includes calculating a histogram of repeat lengths for sequence reads corresponding to the marker region of the target STR. A score per STR marker is calculated based on features of the histogram of repeat lengths. A plurality of per marker scores may be combined to form a total MSI score for the sample.

Abstract: The present disclosure provides compositions, methods, kits, systems and apparatus that are useful for nucleic acid polymerization. In particular, recombinant polymerases and biologically active fragments thereof are provided that allow for nucleic acid amplification. In some aspects, the disclosure provides recombinant polymerases that yield lower systematic error rates and/or improved accuracy, when used in sequencing by synthesis reactions as compared to a control polymerase. In one aspect, the disclosure relates to recombinant polymerases useful for nucleic acid sequencing, genotyping, copy number variation analysis, paired-end sequencing and other forms of genetic analysis. In another aspect, the recombinant polymerases are useful for the amplification of nucleic acid templates during PCR, emPCR, isothermal amplification, recombinase polymerase amplification, rolling circle amplification, strand displacement amplification and proximity ligation amplification.

Abstract: A new class of pH sensitive fluorescent dyes and assays relating thereto are described. The dyes and assays are particularly suited for biological applications including phagocytosis and monitoring intracellular processes. The pH sensitive fluorescent dyes of the present invention include compounds of Formula I: wherein the variables are described throughout the application.

Abstract: A system for separating biological molecules includes a plurality of capillaries, a capillary mount, a plurality of optical fibers, a fiber mount, an optical detector, and a motion stage. The plurality of capillaries are configured to separate biological molecules in a sample. Each capillary comprising a detection portion configured to pass electromagnetic radiation into the capillary. The plurality of capillaries are coupled to the capillary mount such that the detection portions are fixedly located relative to one another. Each optical fiber includes a receiving end to receive emissions. The optical fibers are coupled to the fiber mount such that the receiving ends of the optical fibers are fixedly located relative to one another. The optical detector is configured to produce an alignment signal. The motion stage is configured to align the receiving ends of the optical fibers to the detection portions based on values of the alignment signal.

Abstract: This disclosure relates to the field of fluorescent dyes, and in particular, compositions and methods for increasing fluorescent signals and the reduction of fluorescent quenching.