Provided are systems and methods that allow for brightfield imaging in a flow cytometer, allowing for collection of fluorescence and high-quality image date. The disclosed technology also gives rise to an illumination pattern that allows a user to create different oblique or structured illumination profiles within a static system. With the disclosed approach, a user can illuminate a sample from a first direction (e.g., with laser illumination configured to give rise to one or more of fluorescence information and scattering information), collect scattering information from a second direction, collect fluorescence information from a third direction, and capture an image of the sample from a fourth direction. (Two or more of the foregoing can be accomplished simultaneously.) Also as described elsewhere herein, an illumination used to illuminate the sample for visual image capture can be communicated to the same through a lens that also collects fluorescence from the sample.
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.
C12Q 1/6874 - Methods for sequencing involving nucleic acid arrays, e.g. sequencing by hybridisation [SBH]
G01N 27/27 - Association of two or more measuring systems or cells, each measuring a different parameter, where the measurement results may be either used independently, the systems or cells being physically associated, or combined to produce a value for a furthe
3.
COMPOSITIONS AND METHODS FOR CULTURING AND EXPANDING CELLS
Provided herein are, inter alia, compositions, systems, kits, and methods for culturing and expanding cells (such as T cells, diploid or non-diploid cells), as well as methods for treating disorders (e.g., with T cells), and methods for producing biological molecules and compositions (e.g., proteins, viruses, viral particles or fragments thereof, etc.), including vaccines.
The present disclosure provides methods, compositions, kits and systems for nucleic acid amplification. In some embodiments, nucleic acid amplification methods include subjecting the nucleic acid to be amplified to partially denaturing conditions. In some embodiments, nucleic acid amplification methods include amplifying without fully denaturing the nucleic acid that is amplified. In some embodiments, the nucleic acid amplification method employs an enzyme that catalyzes homologous recombination and a polymerase. In some embodiments, methods for nucleic acid amplification can be conducted in a single reaction vessel and/or in a single continuous liquid phase of a reaction mixture, without need for compartmentalization of the reaction mixture or immobilization of reaction components. In some embodiments, methods for nucleic acid amplification comprise amplifying at least one polynucleotide onto a surface under isothermal amplification conditions, optionally in the presence of a polymer which can include a sieving agent and/or a diffusion-reducing agent.
The present disclosure provides compositions, methods, kits, systems and apparatus that are useful for nucleic acid polymerization. In particular, modified polymerases and biologically active fragments thereof are provided that allow for nucleic acid amplification. In some aspects, the disclosure provides modified polymerases having lower systematic error as compared to a reference polymerase. In one aspect, the disclosure relates to modified polymerases useful for nucleic acid sequencing, genotyping, copy number variation analysis, paired-end sequencing and other forms of genetic analysis. In some aspects, the disclosure relates to modified polymerases useful for the generation of nucleic acid libraries or nucleic acid templates. In some aspects, the disclosure relates to the identification of homologous amino acid mutations that can be transferred across classes or families of polymerases to provide novel polymerases with altered properties.
Disclosed is an integrated biocontainment cell sorter that isolates portions of the cell sorter that can create contamination. Two containment systems are utilized. A main cabinet containment system contains input samples. An aerosol management containment area includes a nozzle chamber with a nozzle and a sort chamber with sort plates and collection media that collect a droplet stream from the nozzle. The main cabinet is maintained at a first low pressure and clean air is recirculated under a positive pressure. The aerosol management containment area is kept at a second low pressure, which is lower than the first pressure, so that contamination does not leak from the aerosol management containment area into the main cabinet containment area. A sliding sash window is located over an access opening in the main cabinet and can be moved to access different portions of the main cabinet without changing the substantially constant first low pressure in the main cabinet.
Energy transfer dye pairs including a donor dye covalently attached to an acceptor dye through a linker, uses of the energy transfer dye pairs, for example, in conjugates of an energy transfer dye pair covalently attached to a quencher and an analyte (e.g., an oligonucleotide), for biological applications including, for example, amplification assays such as quantitative polymerase chain reaction (qPCR) and digital PCR (dPCR).
C09B 62/343 - Reactive dyes, i.e. dyes which form covalent bonds with the substrates or which polymerise with themselves with the reactive group directly attached to a heterocyclic ring to a five-membered ring
9.
COMPOSITIONS AND METHODS FOR ENHANCED FLUORESCENCE
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.
A coupling assembly includes: a tubular compression collar having a tubular body made of a resiliently flexible polymeric material and having an interior surface and an opposing exterior surface; an end of a tube disposed within a throughway of the compression collar; and a tube fitting disposed within the passageway of the tube. The tube fitting includes: a tubular stem; a flange radially outwardly projecting from an exterior surface of the stem; and an annular barb encircling and radially outwardly projecting from the exterior surface of the stem, the annular barb including a frustoconical outside face that extends along and outwardly slopes away from the stem as the outside face extends toward the flange. The compression collar radially inwardly compresses the tube against the annular barb of the tube fitting so that a liquid tight seal is formed between the tube and the tube fitting.
F16L 33/207 - Undivided rings, sleeves, or like members contracted on the hose or expanded inside the hose by means of tools; Arrangements using such members only a sleeve being contracted on the hose
F16L 33/22 - Arrangements for connecting hoses to rigid members; Rigid hose-connectors, i.e. single members engaging both hoses with means not mentioned in the preceding groups for gripping the hose between inner and outer parts
B29C 65/00 - Joining of preformed parts; Apparatus therefor
B29C 65/68 - Joining of preformed parts; Apparatus therefor by liberation of internal stresses, e.g. shrinking of one of the parts to be joined using auxiliary shrinkable element
B29C 65/56 - Joining of preformed parts; Apparatus therefor using mechanical means
A61M 39/12 - Tube connectors or tube couplings for joining a flexible tube to a rigid attachment
Provided herein, inter alia, are chemically defined components and compositions that substitute or partially substitute for albumin in cell culture media. The components and compositions may support cell cultures, protect cells, or enhance viability of cultured cells. Further provided are chemically defined culture media supplements for use in cell culture media containing albumin. The chemically defined culture media supplements may rescue cells from albumin-induced toxicity.
A method for coupling a tube to a tube fitting includes radially outwardly expanding a tubular compression collar from a constricted state to an expanded state, the compression collar having a throughway extending there through and being made of a resiliently flexible material. An end of the tube is inserted within the throughway of the expanded compression collar, the tube bounding a passage. A tube fitting is inserted within the passage of the tube. The compression collar is allowed to resiliently rebound back towards the constricted state so that the compression collar pushes the tube against the tube fitting.
F16L 33/207 - Undivided rings, sleeves, or like members contracted on the hose or expanded inside the hose by means of tools; Arrangements using such members only a sleeve being contracted on the hose
F16L 33/22 - Arrangements for connecting hoses to rigid members; Rigid hose-connectors, i.e. single members engaging both hoses with means not mentioned in the preceding groups for gripping the hose between inner and outer parts
B29C 65/00 - Joining of preformed parts; Apparatus therefor
B29C 65/68 - Joining of preformed parts; Apparatus therefor by liberation of internal stresses, e.g. shrinking of one of the parts to be joined using auxiliary shrinkable element
B29C 65/56 - Joining of preformed parts; Apparatus therefor using mechanical means
A61M 39/12 - Tube connectors or tube couplings for joining a flexible tube to a rigid attachment
13.
METHODS AND SYSTEMS TO DETECT LARGE REARRANGEMENTS IN BRCA1/2
A method for detecting large rearrangements in BRCA1 and BRCA2 genes includes amplifying a nucleic acid sample in the presence of a primer pool to produce amplicons, where the primer pool includes target specific primers targeting regions of exons of the BRCA1 and BRCA2 genes. The method further includes sequencing the amplicons to generate a plurality of reads, mapping the reads to a reference sequence, determining a number of reads per amplicon for the amplicons associated with the exons of the BRCA and the BRCA2 genes, determining exon copy numbers for the exons of the BRCA1 and BRCA2 genes based on the number of reads per amplicon, detecting an exon deletion or duplication based on the exon copy numbers, and detecting a whole gene deletion of the BRCA1 or BRCA2 gene based on the number of reads per amplicon associated with the exons of the BRCA1 and BRCA2 genes.
C12Q 1/6886 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
G16B 30/00 - ICT specially adapted for sequence analysis involving nucleotides or amino acids
G16B 40/00 - ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
The present disclosure generally relates to compositions and methods for the synthesis of nucleic acid molecules with low error rates. Provided, as examples, are compositions and methods for high throughput synthesis and assembly of nucleic acid molecules, in many instances, with high sequence fidelity. In many instances, thermostable mismatch recognition proteins (e.g., thermostable mismatch binding protein, thermostable mismatch endonucleases) will be present in compositions and use methods provided.
C07H 21/00 - Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids
A method of modeling a background signal when sequencing a polynucleotide strand using sequencing-by-synthesis includes: flowing a series of nucleotide flows onto a reactor array having multiple reaction confinement regions, one or more copies of the polynucleotide strand being located in a loaded reaction confinement region of the reactor array, the loaded reaction confinement region being located in a vicinity of one or more neighboring reaction confinement regions that may or may not be loaded; receiving output signals from the reactor array; and modeling a background signal for the loaded reaction confinement region using the received output signals and a model adapted to account at least for an exchange of ions between the one or more neighboring reaction confinement regions and a headspace adjacent the loaded reaction confinement region and the one or more neighboring reaction confinement regions.
G16B 5/00 - ICT specially adapted for modelling or simulations in systems biology, e.g. gene-regulatory networks, protein interaction networks or metabolic networks
C12Q 1/6874 - Methods for sequencing involving nucleic acid arrays, e.g. sequencing by hybridisation [SBH]
G16B 25/00 - ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression
G16B 30/00 - ICT specially adapted for sequence analysis involving nucleotides or amino acids
17.
TEMPERATURE INSULATED PACKAGING SYSTEMS AND RELATED METHODS
A temperature insulated packaging system includes a container having interior surface bounding an interior volume and a liner disposed within the interior volume and at least partially bounding a compartment configured to receive an item for temperature insulated shipping. The liner includes a first sleeve made of cellulose material and at least partially bounds a channel. The first sleeve has an outside wall disposed adjacent to the container and an opposing inside wall disposed adjacent to the compartment configured to receive the item for shipping, the channel being disposed between the inside wall and the outside wall. At least one insulation sheet is disposed within the channel of the first sleeve, the at least one insulation sheet being made of a cellulose material and having a plurality of recesses formed thereon.
B65D 81/38 - Containers, packaging elements, or packages, for contents presenting particular transport or storage problems, or adapted to be used for non-packaging purposes after removal of contents with thermal insulation
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.
G16H 50/80 - ICT specially adapted for medical diagnosis, medical simulation or medical data mining; ICT specially adapted for detecting, monitoring or modelling epidemics or pandemics for detecting, monitoring or modelling epidemics or pandemics, e.g. flu
G16H 50/20 - ICT specially adapted for medical diagnosis, medical simulation or medical data mining; ICT specially adapted for detecting, monitoring or modelling epidemics or pandemics for computer-aided diagnosis, e.g. based on medical expert systems
A chromatography system includes a first chromatography column and a panel having a top face and an opposing bottom face, a first cavity being formed on the panel so as to pass through the top face and be encircled by an inner surface. The panel bounds an inlet fluid channel having an end terminating at an inlet opening formed on the inner surface encircling the first cavity so that the inlet fluid channel communicates with the first cavity. The panel also bounds a plurality of first outlet fluid channels each having an end terminating at an outlet opening formed on the inner surface encircling the first cavity so that each of the plurality of first outlet fluid channels communicate with the first cavity, a first one of the plurality of first outlet fluid channels being in fluid communication with the first chromatography column. A first valve is rotatably disposed within the first cavity.
B01D 15/18 - Selective adsorption, e.g. chromatography characterised by constructional or operational features relating to flow patterns
B01D 15/14 - Selective adsorption, e.g. chromatography characterised by constructional or operational features relating to the introduction of the feed to the apparatus
20.
SYSTEMS AND METHODS FOR IDENTIFYING SEQUENCE VARIATION
Systems and method for determining variants can receive mapped reads, and call variants. In embodiments, flow space information for the reads can be aligned to a flow space representation of a corresponding portion of the reference. Reads spanning a position with a potential variant can be grouped and a score can be calculated for the variant. Based on the scores, a list of probable variants can be provided. In various embodiments, low frequency variants can be identified where multiple potential variants are present at a position.
C08B 37/00 - Preparation of polysaccharides not provided for in groups ; Derivatives thereof
G01N 33/532 - Production of labelled immunochemicals
G01N 33/543 - Immunoassay; Biospecific binding assay; Materials therefor with an insoluble carrier for immobilising immunochemicals
B01D 15/38 - Selective adsorption, e.g. chromatography characterised by the separation mechanism involving specific interaction not covered by one or more of groups , e.g. affinity, ligand exchange or chiral chromatography
G01N 33/554 - Immunoassay; Biospecific binding assay; Materials therefor with an insoluble carrier for immobilising immunochemicals the carrier being a biological cell or cell fragment, e.g. bacteria, yeast cells
G01N 33/569 - Immunoassay; Biospecific binding assay; Materials therefor for microorganisms, e.g. protozoa, bacteria, viruses
C07K 16/00 - Immunoglobulins, e.g. monoclonal or polyclonal antibodies
G01N 33/58 - Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving labelled substances
C07D 403/12 - Heterocyclic compounds containing two or more hetero rings, having nitrogen atoms as the only ring hetero atoms, not provided for by group containing two hetero rings linked by a chain containing hetero atoms as chain links
Methods, assays, compositions and kits for the ligation of short polynucleotides are presented herein. The short polynucleotides are optionally no more than 7 nucleotides in length, and can be as short as 3 or 4 nucleotides in length. The ligation is optionally performed by CV ligase.
A61J 1/14 - Containers specially adapted for medical or pharmaceutical purposes - Details; Accessories therefor
B65B 3/00 - Packaging plastic material, semiliquids, liquids or mixed solids and liquids, in individual containers or receptacles, e.g. bags, sacks, boxes, cartons, cans or jars
B65B 31/04 - Evacuating, pressurising or gasifying filled containers or wrappers by means of nozzles through which air or other gas, e.g. an inert gas, is withdrawn or supplied
B65D 8/00 - Containers having a curved cross-section formed by interconnecting or uniting two or more rigid, or substantially rigid, components made wholly or mainly of metal, plastics, wood or substitutes therefor
C12N 9/00 - Enzymes, e.g. ligases (6.); Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating, or purifying enzymes
C12Q 1/6876 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
Provided herein, are compositions, methods and kits for inducing an immune response in a subject. In aspects, a lipid composition is described, which includes at least one ionizable lipid comprising a charge (N), at least one peptide, and a nucleic acid molecule comprising a charge (P). In aspects, methods are provided for delivery of a payload to an immune cell using a lipid composition comprising at least one ionizable lipid, at least one endosomal release peptide, and a payload.
A61K 47/69 - Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the conjugate being characterised by physical or galenical forms, e.g. emulsion, particle, inclusion complex, stent or kit
A61K 47/58 - Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the non-active ingredient being a modifying agent the modifying agent being an organic macromolecular compound, e.g. an oligomeric, polymeric or dendrimeric molecule obtained by reactions only involving carbon-to-carbon unsaturated bonds, e.g. poly[meth]acrylate, polyacrylamide, polystyrene, polyvinylpyrrolidone, polyvinylalcohol or polystyrene sulfonic acid resin
Systems, methods, software and computer-usable media for annotating biomolecule-related data are disclosed. In certain exemplified embodiments, the biomolecules can be nucleic acids and the data can be sequence-related data. In various embodiments, systems can include one or more public or private biological attributes (e.g., annotation information databases, data storage devices and systems, etc.) sources, one or more genomic features data sources (e.g., genomic variant tools, genomic variant databases, genomic variant data storage devices and systems, etc.), a computing device (e.g., workstation, server, personal computer, mobile device, etc.) hosting an annotations module and/or a reporting module, and a client terminal.
G16B 40/00 - ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
G16B 50/00 - ICT programming tools or database systems specially adapted for bioinformatics
Methods for assessing genomic instability (GI) may include selectively amplifying nucleic acid sequences at targeted locations in a tumor sample genome by a targeted panel with a low sample input to generate a plurality of nucleic acid sequence reads; dividing the genome into segments having homogeneous copy numbers using log odds of heterozygous SNPs and CNV log ratios determined for the nucleic acid sequence reads; applying a threshold count to squared allelic log odds of each segment in autosomes of the genome to identify unbalanced copy number (UCN) segments; adding numbers of bases in the UCN segments to produce a sum of UCN bases; and dividing the sum of UCN bases by the total number of bases in all the segments identified in the autosomes of the sample genome to produce a ratio indicative of genomic instability. The ratio may be expressed as a percent to give a GI score.
The present disclosure provides apparatuses, systems, and methods for performing particle analysis through flow cytometry at comparatively high event rates and for gathering high resolution images of particles.
LIFE TECHNOLOGIES HOLDINGS PTE LIMITED (Singapore)
LIFE TECHNOLOGIES CORPORATION (USA)
Inventor
Chen, Ming Song
Chong, Chee Woei
Loh, Wuh Ken
Foo, Wern Yuh
Boo, Kuan Moon
Leclerc, Norbert
Uhlendorf, Kristina
Koellner, Reiner
Fuchs, Torsten
Breitfelder, Stefan
Abstract
A biological analysis system can include an excitation module and an emission module. The excitation module can include a collimator element for receiving excitation light from the excitation light source and transmitting collimated excitation light in a first direction, and a plurality of excitation mirrors arrayed along the excitation light path, each excitation mirror disposed at an acute angle relative to the first direction and configured to reflect collimated excitation light along a second direction. The emission module can be positioned to receive excitation light transmitted along the second direction and can include a sample block comprising a plurality of sample receptacles positioned to receive a beam of collimated excitation light, and a plurality of photodetectors configured to receive emission light transmitted from a respective sample receptacle in a direction transverse to the second direction of the excitation light path.
The present disclosure provides methods, compositions, kits, and systems useful in the determination and evaluation of the immune repertoire. In one aspect, target-specific primer panels provide for the effective amplification of sequences of B cell receptor heavy and light chains in a single assay, with improved sequencing accuracy and resolution over the repertoire. Variable regions associated with the immune cell receptor are resolved to effectively portray clonal diversity of a biological sample and/or differences associated with the immune cell repertoire of a biological sample.
C12Q 1/6883 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
31.
Apparatuses, Systems And Methods For Imaging Flow Cytometry
The present disclosure provides apparatuses, systems, and methods for performing particle analysis through flow cytometry at comparatively high event rates and for gathering high resolution images of particles.
A method for processing a fluid includes removably securing a retention member to a vessel that bounds a chamber; inserting a collapsible bag within the chamber of the vessel; securing the bag to the retention member so that the bag is supported within the chamber of the vessel; and dispensing a fluid into a compartment of the collapsible bag supported within the chamber of the vessel. The fluid can be mixed within bag while the bag is disposed within the vessel.
B01F 27/88 - Mixers with rotary stirring devices in fixed receptacles; Kneaders with stirrers rotating about a substantially vertical axis with a separate receptacle-stirrer unit that is adapted to be coupled to a drive mechanism
C12M 1/00 - Apparatus for enzymology or microbiology
C12M 1/06 - Apparatus for enzymology or microbiology with gas introduction means with agitator, e.g. impeller
B01F 23/233 - Mixing gases with liquids by introducing gases into liquid media, e.g. for producing aerated liquids using driven stirrers with completely immersed stirring elements
B01F 23/231 - Mixing gases with liquids by introducing gases into liquid media, e.g. for producing aerated liquids by bubbling
B01F 27/91 - Mixers with rotary stirring devices in fixed receptacles; Kneaders with stirrers rotating about a substantially vertical axis with propellers
B01F 27/213 - Mixers with rotary stirring devices in fixed receptacles; Kneaders characterised by their rotating shafts characterised by the connection with the drive
B01F 27/2121 - Mixers with rotary stirring devices in fixed receptacles; Kneaders characterised by their rotating shafts composed of interconnected parts
B01F 33/00 - Other mixers; Mixing plants; Combinations of mixers
B01F 33/501 - Movable mixing devices, i.e. readily shifted or displaced from one place to another, e.g. portable during use
B01F 35/41 - Mounting or supporting stirrer shafts or stirrer units on receptacles
B01F 35/45 - Closures or doors specially adapted for mixing receptacles; Operating mechanisms therefor
B01F 35/513 - Flexible receptacles, e.g. bags supported by rigid containers
B65B 1/02 - Machines characterised by the incorporation of means for making the containers or receptacles
33.
CENTRIFUGAL SEPARATORS AND SKID FOR SEPARATING BIOCOMPONENTS AND METHODS OF USE
A skid (700) for use in separating biocomponents includes a housing (701) bounding a compartment (708), the compartment being partially bounding by a mounting platform (709); and a loading assembly (800) secured to the housing so as to communicate with the compartment. The loading assembly (800) includes an alignment plate (808) having a top surface with cavity (814) recessed therein, the cavity communicating with the compartment; a drive rotor (15) rotatably disposed below the alignment plate and at least partially encircling the cavity, the drive rotor including one or more magnets; a motor (169) coupled to the drive rotor for selectively rotating the drive rotor about the cavity; and a mount at least partially encircling the drive rotor and communicating with the compartment, the mount including a mounting plate having one or more mounting elements upstanding therefrom, the mount being movable between a raised position wherein the mounting plate is aligned with the alignment plate and a second lowered position wherein the mounting plate is disposed at an elevation lower than the alignment plate.
A method for labeling sequence reads includes retrieving a sequence read having an associated flow measurement and an associated flow order; matching a sequence selected from a plurality of sequences with the sequence read, the sequence having a position within the sequence that has more than one acceptable variants; determining which variant of the more than one acceptable variants matches the sequence; generating a predicted flow measurement based on the matched sequence, the variant, and a flow order; and labeling the sequence read and associated flow measurement with the predicted flow measurement.
A method of conjugating a substrate includes exchanging a counter ion associated with a biomolecule with a lipophilic counter ion to form a biomolecule complex, dispersing the biomolecule complex in a nonaqueous solvent, and coupling the biomolecule complex to a substrate in the presence of the nonaqueous solvent.
A system facilitating parallel laboratory operations which includes a plurality of labware components, and a plurality of processing heads configured to interact with the plurality of labware components is described. The system further includes a first set of actuators coupled to the plurality of processing heads and configured to actuate the plurality of processing heads along a first directional axis. The system further includes a second set of actuators configured to translate the plurality of labware components along at least a second directional axis and a third directional axis. The second set of actuators may include one or more magnetic levitation systems configured to cause movement of the plurality of labware components along the second directional axis and the third directional axis.
A computer-implemented method for classifying alignments of paired nucleic acid sequence reads is disclosed. A plurality of paired nucleic acid sequence reads is received, wherein each read is comprised of a first tag and a second tag separated by an insert region. Potential alignments for the first and second tags of each read to a reference sequence is determined, wherein the potential alignments satisfies a minimum threshold mismatch constraint. Potential paired alignments of the first and second tags of each read are identified, wherein a distance between the first and second tags of each potential paired alignment is within an estimated insert size range. An alignment score is calculated for each potential paired alignment based on a distance between the first and second tags and a total number of mismatches for each tag.
G16B 40/00 - ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
G16B 30/00 - ICT specially adapted for sequence analysis involving nucleotides or amino acids
The present set of embodiments relate to a system, method, and apparatus for culturing cells within a cell culture vessel having a mixing element. The cell culture system includes a flexible portion and a mixing element disposed therein. The mixing element includes a suspended foldable portion. The system is configured to reduce shear stress on cells without compromising mixing efficiency. This reduction is accomplished by using a mixing element having a large surface area allowing for reduced rotational speeds. The system is collapsible for ease of transport and disposal. The flexible portion collapses and the foldable portion folds to minimize the volume of the system while not in operation.
C12M 1/06 - Apparatus for enzymology or microbiology with gas introduction means with agitator, e.g. impeller
C12M 1/00 - Apparatus for enzymology or microbiology
B01F 27/054 - Deformable stirrers, e.g. deformed by a centrifugal force applied during operation
B01F 27/072 - Stirrers characterised by their mounting on the shaft characterised by the disposition of the stirrers with respect to the rotating axis
B01F 27/2124 - Shafts with adjustable length, e.g. telescopic shafts
B01F 27/1125 - Stirrers characterised by the configuration of the stirrers with arms, paddles, vanes or blades with vanes or blades extending parallel or oblique to the stirrer axis
B01F 35/513 - Flexible receptacles, e.g. bags supported by rigid containers
A system and method of selecting genes for a gene panel, includes retrieving gene-disease associations of genes associated with diseases at a given level in the disease hierarchy from a disease association database. The disease association database stores disease information, gene information, phenotype information, associations between diseases in the disease hierarchy, gene-disease associations and strength parameters related to the gene-disease associations. For each gene associated with the diseases at the given level, the strength parameters are weighted and combined to determine a rank score for the each gene. The genes are ranked based on the rank scores to provide ranked gene information. The ranked gene information is linked with diseases at the higher levels of the disease hierarchy based on hierarchical relationships. The ranked gene information for gene-disease associations can be used to select genes for a gene panel design.
Systems and methods for automated laser microdissection are disclosed including automatic slide detection, position detection of cutting and capture lasers, focus optimization for cutting and capture lasers, energy and duration optimization for cutting and capture lasers, inspection and second phase capture and/or ablation in a quality control station and tracking information for linking substrate carrier or output microdissected regions with input sample or slide.
Systems and method for identifying variants associated with a genetic disease can include obtaining sequencing reads for a plurality of individuals for a list of variant positions. The reads can be compared to identify variants that are found in affected individuals and absent in non-affected individuals. Such variants can include loss of heterozygosity, trans-phased compound heterozygotes, increased frequency mitochondrial variants, homozygous recessive variants, de novo variants, sex-linked variants, and combinations thereof.
A quality control system for a qPCR receives signals resulting from operation of the qPCR system on an assay, and applies labeled data sets to a Support Vector Machine (SVM) to generate classifications for the signals to generate classifications that are utilized as operational feedback to the qPCR system.
Devices and methods for measuring the quantity of multiple analytes in a sample can include a device designed such that each of the analyte sensing elements is configured to measure the quantity of a predetermined analyte and machine executable instructions configured to select the proper analyte sensing element corresponding to the analyte to be measured.
Efficient methods for production of targeted libraries from complex samples is desirable for a variety of nucleic acid analyses. Provided are methods of selectively blocking abundant targets present in a sample for preparing libraries of target nucleic acid sequences, thereby allowing for rapid production of highly multiplexed targeted libraries and analysis of low frequency sequences, including sequencing applications. Methods optionally include use of unique tag sequences. Methods comprise contacting a nucleic acid sample with a plurality of target specific primers or adapters capable of amplification of one or more target nucleic acid sequences under conditions wherein the target nucleic acid(s) undergo a first amplification; digesting the resulting first amplification products; ligating the digested target amplicons or repairing the digested target amplicons; and amplifying the ligated or repaired products in a second amplification, thereby producing a library of target nucleic acid sequence. Each of the reactions further comprise target specific primers that are not capable of completely processing the workflow, resulting in non-useful amplicon production and thereby blocking selected target sequences, e.g., those present in high abundance in the sample. Provided methods may be carried out in a single, addition only workflow reaction, allowing for rapid production of highly multiplexed targeted libraries, optionally including unique tag sequences, which are optimized for detection of low frequency target sequences.
Cell culture media, concentrated media and feeds, methods of manufacturing cell culture media and feeds, and methods of culturing cells are provided. One or more small peptides, including dipeptides are added to the cell culture media to provide improved stability and improved conditions for culturing cells.
A method for correcting signal measurements comprises an artificial neural network (ANN). The ANN receives a plurality of signal measurements in a channel of an input layer. The ANN is applied to the signal measurements and produces a plurality of signal correction values. The signal correction values may be subtracted from the signal measurements to form corrected signal measurements. The corrected signal measurements may be provided to a base caller to produce a sequence of base calls. The ANN may comprise a convolutional neural network (CNN). The CNN may have a U-NET architecture that includes an encoder and a decoder. The U-NET may include a Convolutional Block Attention Module (CBAM). The CBAM may applied to the outputs of a last pooling layer of the encoder and provides refined feature maps to a first layer of the decoder. The input signal measurements may be generated by a nucleic acid sequencing instrument.
Provided are systems and methods for line volume calibration, and measurement of fluid samples delivered to an interrogation point. In various embodiments, a known fluid volume comprising a sample line fluid and a secondary fluid is delivered to a fluid boundary sensor. The fluid boundary sensor assists in determining the position of the boundaries between the various fluids, and the positions of these boundaries are used to determine the sample line fluid volume.
G01F 25/17 - Testing or calibration of apparatus for measuring volume, volume flow or liquid level or for metering by volume of flowmeters using calibrated reservoirs
G01F 15/00 - MEASURING VOLUME, VOLUME FLOW, MASS FLOW, OR LIQUID LEVEL; METERING BY VOLUME - Details of, or accessories for, apparatus of groups insofar as such details or appliances are not adapted to particular types of such apparatus
G01N 29/22 - Investigating or analysing materials by the use of ultrasonic, sonic or infrasonic waves; Visualisation of the interior of objects by transmitting ultrasonic or sonic waves through the object - Details
48.
METHODS, SYSTEMS, AND COMPUTER READABLE MEDIA FOR EVALUATING VARIANT LIKELIHOOD
A method comprises receiving an ensemble of sequencing reads based on measurements from a plurality of microwells of a sensor array; assigning measured values to the ensemble of sequencing reads; calculating model-predicted values utilizing a predictive model of nucleotide incorporations resulting from flows of nucleotide species according to a predetermined order; modifying at least some model-predicted values using a first bias for forward strands and a second bias for reverse strands, the modifying based on variations between model-predicted values for different hypothesized sequences obtained using the predictive model of nucleotide incorporations resulting from the flows of nucleotide species according to the predetermined order; calculating a measurement confidence value for each read in the ensemble of sequencing reads, the confidence value representing variations between the measured values and the modified model-predicted values; and identifying a plurality of reads in the ensemble as corresponding to a variant sequence.
G16B 20/20 - Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
G16B 30/00 - ICT specially adapted for sequence analysis involving nucleotides or amino acids
G16B 40/00 - ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
49.
LIQUID MIXING SYSTEM WITH VERTICALLY ADJUSTABLE MIXING ELEMENT AND METHOD OF USE
A liquid mixing system includes a support housing at least partially bounding a compartment. A mount is secured to the support housing. A drive motor assembly is configured to engage a drive shaft for moving the drive shaft within the compartment of the support housing. A four bar linkage system extends between the mount and the drive motor assembly, the four bar linkage system being movable between a first position wherein the drive motor assembly is disposed at a first elevation and a second position wherein the drive motor assembly is disposed at a second elevation that is different from the first elevation.
B01F 27/231 - Mixers with rotary stirring devices in fixed receptacles; Kneaders characterised by the orientation or disposition of the rotor axis with a variable orientation during mixing operation, e.g. with tiltable rotor axis
C12M 1/34 - Measuring or testing with condition measuring or sensing means, e.g. colony counters
C12M 1/00 - Apparatus for enzymology or microbiology
B01F 23/231 - Mixing gases with liquids by introducing gases into liquid media, e.g. for producing aerated liquids by bubbling
B01F 27/07 - Stirrers characterised by their mounting on the shaft
B01F 27/113 - Propeller-shaped stirrers for producing an axial flow, e.g. shaped like a ship or aircraft propeller
B01F 27/213 - Mixers with rotary stirring devices in fixed receptacles; Kneaders characterised by their rotating shafts characterised by the connection with the drive
B01F 27/2121 - Mixers with rotary stirring devices in fixed receptacles; Kneaders characterised by their rotating shafts composed of interconnected parts
A method for sequencing a nucleic acid template includes: (a) performing a first sequencing process including flowing nucleotides and/or reagents to the nucleic acid template according to a first predetermined ordering of nucleotides and/or reagents to obtain a first sequencing result; (b) after the first sequencing process, performing a second sequencing process including flowing nucleotides and/or reagents to the nucleic acid template according to a second predetermined ordering of nucleotides and/or reagents to obtain a second sequencing result, the second predetermined ordering of nucleotides and/or reagents being different from the first predetermined ordering of nucleotides and/or reagents and at least one of the first and second predetermined orderings of nucleotides and/or reagents being designed for repeat sequencing; and (c) determining a sequence of bases corresponding to at least a portion of the nucleic acid template using both the first sequencing result and the second sequencing result.
The present disclosure provides methods, compositions, kits, and systems useful in the determination and evaluation of the immune repertoire. In one aspect, methods provide for determining convergence of T cell receptor beta and T cell receptor gamma repertoires in samples prior to a treatment and predicting a subject's response to the treatment. In another aspect, methods provide predicting a subject's potential or predisposition to be protected from or vulnerable to an adverse event following a treatment.
C12Q 1/6883 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
In some embodiments, the present teachings provide compositions, systems, methods and kits for generating a population of nucleic acid fragments. In some embodiments, nucleic acids can be fragmented enzymatically. For example, methods for generating a population of nucleic acid fragments can include a nucleic acid nicking reaction. In one embodiment, the methods can include a nick translation reaction. A nicking reaction can introduce nicks at random positions on either strand of a double-stranded nucleic acid. A nick translation reaction can move the position of nicks to a new position so that the new positions of two of the nicks are aligned to create a double-stranded break. In some embodiments, methods for generating a population of nucleic acid fragments can include joining at least one end of a fragmented nucleic acid to one or more oligonucleotide adaptors.
C12P 19/40 - Nucleosides having a condensed ring system containing a six-membered ring having two nitrogen atoms in the same ring, e.g. purine nucleosides
C12N 15/10 - Processes for the isolation, preparation or purification of DNA or RNA
C12Q 1/6806 - Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
53.
Methods and systems for evaluating microsatellite instability status
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.
C12Q 1/6809 - Methods for determination or identification of nucleic acids involving differential detection
C12Q 1/6886 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
G16B 50/00 - ICT programming tools or database systems specially adapted for bioinformatics
G16B 20/00 - ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
Systems and methods for analyzing overlapping sequence information can obtain first and second overlapping sequence information for a polynucleotide, align the first and second sequence information, determine a degree of agreement between the first and second sequence information for a location along the polynucleotide, and determine a base call and a quality value for the location.
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.
A condenser bag includes a body bounding a channel that extends between an inlet opening at a first end and an outlet opening at an opposing second end, the body being comprised of a polymeric film; an intake port bounding a port opening that extends therethrough, the intake port being directly physically secured to the first end of the body so that the port opening communicates with the channel of the body; and a tubular transfer line having a first end directly mechanically coupled with the body at a first location located between the inlet opening and the outlet opening so as to communicate with the channel and an opposing second end directly mechanically coupled to the intake port so as to communicate with the port opening thereof.
B01D 53/00 - Separation of gases or vapours; Recovering vapours of volatile solvents from gases; Chemical or biological purification of waste gases, e.g. engine exhaust gases, smoke, fumes, flue gases or aerosols
57.
FLUID MIXING SYSTEMS WITH ADJUSTABLE MIXING ELEMENT
A fluid mixing system includes a support housing having an interior surface bounding a chamber. A flexible bag is disposed within the chamber of the support housing, the flexible bag having an interior surface bounding a compartment. An impeller is disposed within the chamber of the flexible bag. A drive shaft is coupled with the impeller such that rotation of the drive shaft facilitates rotation of the impeller. A drive motor assembly is coupled with the draft shaft and is adapted to rotate the drive shaft. An adjustable arm assembly is coupled with the drive motor assembly and is adapted to move the drive motor assembly which in turn moves the position of the drive shaft and impeller. An electrical controller can control movement of the adjustable arm.
C12M 1/00 - Apparatus for enzymology or microbiology
C12M 3/00 - Tissue, human, animal or plant cell, or virus culture apparatus
C12M 1/06 - Apparatus for enzymology or microbiology with gas introduction means with agitator, e.g. impeller
C12M 1/34 - Measuring or testing with condition measuring or sensing means, e.g. colony counters
B01F 27/61 - Mixers with rotary stirring devices in fixed receptacles; Kneaders with stirrers rotating about a horizontal or inclined axis about an inclined axis
B01F 27/07 - Stirrers characterised by their mounting on the shaft
B01F 27/113 - Propeller-shaped stirrers for producing an axial flow, e.g. shaped like a ship or aircraft propeller
B01F 27/213 - Mixers with rotary stirring devices in fixed receptacles; Kneaders characterised by their rotating shafts characterised by the connection with the drive
B01F 27/2121 - Mixers with rotary stirring devices in fixed receptacles; Kneaders characterised by their rotating shafts composed of interconnected parts
B01F 27/231 - Mixers with rotary stirring devices in fixed receptacles; Kneaders characterised by the orientation or disposition of the rotor axis with a variable orientation during mixing operation, e.g. with tiltable rotor axis
B01F 33/00 - Other mixers; Mixing plants; Combinations of mixers
B01F 35/513 - Flexible receptacles, e.g. bags supported by rigid containers
A filter assembly for separating microcarriers from a fluid medium includes a collapsible container bounding a sterile compartment adapted to hold a fluid. An inlet port is attached to the container through which fluid flows into the compartment. An outlet port is attached to the container through which fluid flows out of the compartment. A filter is disposed within the compartment, the filter dividing the compartment into an inlet chamber that is fluidly coupled with the inlet port and an outlet chamber that is fluidly coupled with the outlet port, the filter allowing a medium to pass therethrough but preventing microcarriers disposed in the medium from passing therethrough.
In some embodiments, the present inventions relates generally to compositions, methods and kits for use in discriminating sequence variation between different alleles. More specifically, in some embodiments, the present invention provides for compositions, methods and kits for quantitating rare (e.g., mutant) allelic variants, such as SNPs, or nucleotide (NT) insertions or deletions, in samples comprising abundant (e.g., wild type) allelic variants with high specificity and selectivity. In particular, in some embodiments, the invention relates to a highly selective method for mutation detection referred to as competitive allele-specific TaqMan PCR (“cast-PCR”).
C12Q 1/6886 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
Methods and systems for generating a computer-implemented interactive graphical user interface for facilitating finding appropriate antibody products utilizing visual evaluation of sequence information are disclosed. An antibody product listing within the graphical user interface is generated. The antibody product listing is responsive to a user interaction. The antibody product listing includes at least one antibody product including corresponding sequence information and product specifications. A sequence infographic is generated based on the corresponding sequence information, wherein the sequence infographic includes an amino acid sequence area of interest indicator. The sequence infographic is displayed aligned relative to a plurality of sequence infographics.
The present disclosure relates to temperature insulated packaging systems and related methods of manufacture and use that can be used for shipping perishable materials. An insulative insert is formed by folding one or more pieces of stock cellulose material along predetermined fold lines and folding slots to form an insert in a folded configuration suitable for insertion as an insulative liner within a container for use in shipment.
B65D 81/38 - Containers, packaging elements, or packages, for contents presenting particular transport or storage problems, or adapted to be used for non-packaging purposes after removal of contents with thermal insulation
62.
Systems, Devices And Methods For Cell Analysis Using ChemFET Sensor Arrays
Systems, devices and methods for cell analysis provide an end user with real-time cell analysis and imaging of single cells in a population. Various cell analysis systems can provide both optical imaging, as well as electroscopic imaging, which is an image of cellular response as detected by sensors covering a cell footprint or cellular efflux. An automated fluidic system can provide an end-user selected sequence of reagents to cells, while precision controlled sensor array device thermostatting, and analysis compartment environmental control provide consistency in the cell analysis system environment.
Provided herein is an electrophoresis separation medium comprising: (a) a non-crosslinked or sparsely cross-linked polymer or copolymer; (b) one or more denaturant compounds, in an amount sufficient to inhibit re-naturation of single stranded polynucleotides; (c) an aqueous solvent; (d) optionally, a wall-coating material suited to inhibition of electroosmotic flow; and (e) optionally, an organic water miscible solvent such as DMSO or acetonitrile, wherein the electrophoresis separation medium exhibits functional stability for at least seven days at 23° C.
Provided herein is an electrophoresis separation medium comprising: (a) a non-crosslinked or sparsely cross-linked polymer or copolymer; (b) one or more denaturant compounds, in an amount sufficient to inhibit re-naturation of single stranded polynucleotides; (c) an aqueous solvent; (d) optionally, a wall-coating material suited to inhibition of electroosmotic flow; and (e) optionally, an organic water miscible solvent such as DMSO or acetonitrile, wherein the electrophoresis separation medium exhibits functional stability for at least seven days at 23° C.
Also provided herein are sieving compositions, including polymer-based sieving compositions, for molecular sieving as well as related kits, devices and methods of use. Such compositions can be useful for separation of biomolecules such as nucleic acids, proteins, glycoproteins and glycans.
C12Q 1/689 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms for bacteria
C12Q 1/70 - Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving virus or bacteriophage
B01L 3/00 - Containers or dishes for laboratory use, e.g. laboratory glassware; Droppers
C12Q 1/6806 - Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
C12Q 1/6848 - Nucleic acid amplification reactions characterised by the means for preventing contamination or increasing the specificity or sensitivity of an amplification reaction
Disclosed is a method for determining the quality, expressed in terms of a quality value, of an RNA sample based on a multiplex fluorescent ratiometric method, wherein the ratio of small RNA to large and/or structured RNA in a sample is determined, thereby obtaining the quality value. Also disclosed is a method for determining the quality value of an RNA sample wherein the relationship of the intensity of the fluorescent signal corresponding to small RNA is compared to the intensity of the fluorescent signal corresponding to large and/or structured RNA in a sample. The relationship of the intensity of the two fluorescent signals is used to determine the amount of intact RNA present in the sample.
A system (1000) comprising first and second excitation sources (101a, 101b) with respective excitation wavelengths for exciting first second and third dyes in a sample (110) and further comprising a detector (115), first and second emission spectral elements (121a, 121b) for transmitting respective first and second emission wavelengths as well as a processor (130) for automatically operating the elements of the system. The first dye comprises a first absorption spectrum comprising a first maximum absorption wavelength and the second dye comprises a second absorption spectrum comprising a second maximum absorption wavelength that is equal to or substantially equal to the first maximum absorption wavelength. The second dye comprises a second emission spectrum comprising a second maximum emission wavelength and the third dye comprises a third emission spectrum comprising a third maximum emission wavelength that is equal to or substantially equal to the second maximum emission wavelength.
A method for nucleic acid sequencing includes receiving nucleic acid sequencing data from a sequencing instrument that receives and processes a sample nucleic acid in a sequencing-by-synthesis process. The method also includes generating a set of candidate sequences of bases for the observed or measured nucleic acid sequencing data by determining a predicted signal for candidate sequences using a simulation framework. The simulation framework incorporates an estimated carry forward rate (CFR), an estimated incomplete extension rate (IER), an estimated droop rate (DR), an estimated reactivated molecules rate (RMR), and an estimated termination failure rate (TFR), the RMR being greater than or equal to zero and the TFR being lesser than one. The method also includes identifying, from the set of candidate sequences of bases, a candidate sequence as corresponding to the sequence for the sample nucleic acid.
G16B 40/10 - Signal processing, e.g. from mass spectrometry [MS] or from PCR
G16B 5/00 - ICT specially adapted for modelling or simulations in systems biology, e.g. gene-regulatory networks, protein interaction networks or metabolic networks
G16B 20/00 - ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
G16B 25/00 - ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression
G16B 30/00 - ICT specially adapted for sequence analysis involving nucleotides or amino acids
68.
SYSTEMS AND METHODS FOR TRACKING VIEWING POSITION DURING SAMPLE ANALYSIS
A sample analyzer is configured to obtain first and second stage position data. The first stage position data indicates a first position of a movable stage in a first dimension, and the second stage position data indicates a second position of the movable stage in a second (perpendicular) dimension. The sample analyzer is configured to, based on the first and second stage position data, determine a viewing position of one or more viewing or imaging optics relative to the movable stage. The sample analyzer is configured to display a vessel map, which comprises a visual representation of a sample vessel associated with the movable stage. The sample analyzer is configured to display a viewing position marker overlaid on the vessel map. The viewing position marker indicates the viewing position of the one or more viewing or imaging optics relative to the sample vessel as represented by the vessel map.
Energy transfer dye pairs including a donor dye covalently attached to an acceptor dye through a linker, uses of the energy transfer dye pairs, for example, in conjugates of an energy transfer dye pair covalently attached to a quencher and an analyte (e.g., an oligonucleotide), for biological applications including, for example, amplification assays such as quantitative polymerase chain reaction (qPCR) and digital polymerase chain reaction (dPCR). Systems and methods include those in which (1) two dyes have the same excitation wavelength range, but different emission wavelength ranges and/or (2) two dyes have the same emission wavelength range, but different excitation wavelength ranges.
G01N 21/27 - Colour; Spectral properties, i.e. comparison of effect of material on the light at two or more different wavelengths or wavelength bands using photo-electric detection
A method for operating a bioreactor includes passing a drive shaft into a first tubular connector and a second tubular connector projecting from the first tubular connector, the first tubular connector and the second tubular connector being at least partially disposed within a container, the first tubular connector being more flexible than the second tubular connector, the second tubular connector having a length that comprises at least 20% of a combined length of the first tubular connector and the second tubular connector. Rotating the drive shaft so as to rotate the first tubular connector and the second tubular connector within the container.
B01F 27/2121 - Mixers with rotary stirring devices in fixed receptacles; Kneaders characterised by their rotating shafts composed of interconnected parts
B01F 35/513 - Flexible receptacles, e.g. bags supported by rigid containers
71.
SYSTEM FOR PORT AND TUBE HOLDER ASSEMBLY ATTACHMENT DEVICE
A tube holder assembly includes a base plate, an attachment plate, and an optional securing element. The base plate may include guides into which protrusions of the attachment plate slide to alter the positioning apparatus from an open position to a closed position. The base plate also includes receivers to receive tubular members, which have their movement restrained by the receivers and the securing elements in the closed position. The tube holder assembly may also include a latch to help maintain the closed position during operation.
A method for filtering a gas includes delivering a gas into a compartment of a gas filter assembly; applying a partial vacuum to the gas filter assembly so that the partial vacuum assists in drawing the gas through a porous filter body of the gas filter assembly that is at least partially disposed within the compartment of the gas filter assembly; and regulating the application of the partial vacuum based on a pressure reading of the gas upstream or downstream of the gas filter assembly.
B01D 46/58 - Filters or filtering processes specially modified for separating dispersed particles from gases or vapours with multiple filtering elements, characterised by their mutual disposition connected in parallel
B01D 5/00 - Condensation of vapours; Recovering volatile solvents by condensation
Embodiments herein provide methods of differentiating neural stem cells to neuronal cells while concomitantly retarding neural stem cell proliferation. Resultant cultures demonstrate reduced clumping of cells, increased purity of neuronal cells and accelerated electrophysiology as compared to control methods.
The method includes compressing numbers of reads data for targeted genes of a gene expression assay performed on a test sample. The targeted genes are organized into categories. Each category represents a functional context associated with the targeted genes in that category. The numbers of reads corresponding to targeted genes each category is compressed to form a compressed value for the category. The compressed value is compared to a baseline value for the category to determine an enrichment or a loss of a signature corresponding to the functional context of the category. The method may include analyzing information from multiple assays performed on the test sample, assigning a score value to each assay result and predicting a response to immune-oncology treatment based on the assigned scores.
A protein transfer system includes at least one base configured to receive one or more consumable protein transfer stacks and at least one lid configured to cover the base. The lid(s) comprise(s) one or more electrodes for supplying current to the one or more consumable protein transfer stacks. The protein transfer system further includes at least one voltage source configured to supply the current to the one or more consumable protein transfer stacks, one or more processors, and one or more hardware storage devices storing instructions that are executable by the one or more processors to configure the protein transfer system to control operation of the one or more voltage sources.
The present disclosure relates to recombinant nucleases, recombinant nucleases operatively linked to nucleic acid binding domains, and methods of making and using them.
A fluid manifold system includes a first manifold having portions of opposing flexible sheets welded together to form a fluid flow path therebetween, a fluid inlet communicating with the fluid flow path. The fluid flow path of the first manifold includes: a primary flow path communicating with the fluid inlet of the first manifold; and a plurality of spaced apart secondary flow paths that branch off of the primary flow path. Each secondary flow path has a first end communicating with the primary flow path and an opposing second end, each secondary flow path having a diameter that is smaller than a diameter of the primary flow path. The fluid manifold system also includes a plurality of tubular connectors with each tubular connector being secured to the first manifold at the second end of a corresponding one of the secondary flow paths.
B65B 1/04 - Methods of, or means for, filling the material into the containers or receptacles
B65B 3/00 - Packaging plastic material, semiliquids, liquids or mixed solids and liquids, in individual containers or receptacles, e.g. bags, sacks, boxes, cartons, cans or jars
B65B 3/02 - Machines characterised by the incorporation of means for making the containers or receptacles
B65B 3/04 - Methods of, or means for, filling the material into the containers or receptacles
B65B 51/02 - Applying adhesives or sealing liquids
B65B 51/22 - Applying or generating heat or pressure or combinations thereof by friction or ultrasonic or high-frequency electrical means
79.
Fluorometer display screen with graphical user interface
A fluidic coupler to engage a plurality of flow cells of a sensor device includes a body and a plurality of fluidics interfaces formed in the body. Each fluidic interface of the plurality of fluidics interfaces includes an opening, a first port in fluid communication with the opening, a second port, and a third port in fluidic communication with the second port.
The disclosure provides gene fusions, gene variants, and novel associations with disease states, as well as kits, probes, and methods of using the same.
C12Q 1/6886 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
G16B 20/20 - Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
82.
Fluorometer display screen with graphical user interface
The present disclosure provides apparatuses, systems, and methods for performing particle analysis through flow cytometry at comparatively high event rates and for gathering high resolution images of particles.
Life Technologies Holdings PTE Limited (Singapore)
Life Technologies Corporation (USA)
Inventor
Lim, Beng Heng
Loh, Wuh Ken
Kuah, Hwee Siong
Wong, Jing Han
Gangcuangco, Jefferson Cruz
Ong, Jin Xin
Lau, Soo Yong
Xu, Yanping
Shapiro, Victor
Teh, Zhi Da
Chong, Chee Woei
Boo, Kuan Moon
Abstract
A gel electrophoresis system includes a base module and a camera module. The base module includes a cassette slot for receiving a gel electrophoresis cassette, and a light element that functions to illuminate the gel electrophoresis cassette. The camera module is selectively attachable to and detachable from the base module. When attached to the base module, the camera module facilitates imaging of the gel electrophoresis cassette and provides additional imaging capabilities.
Methods and systems for improving computer efficiency by intelligently selecting subsets of possible short tandem repeat (STR) allele combinations for further deconvolution analysis are disclosed. In one embodiment, at each locus, for a currently analyzed contribution ratio scenario of a plurality of contribution ratio scenarios, a processor computes an adjusted evidence profile. For a first, or next, unidentified contributor having a pre-determined highest remaining contribution ratio in the currently analyzed contribution ratio scenario for the plurality of contributors, a processor computes a first range of expected peak heights using at least the pre-determined highest remaining contribution ratio, a selected degradation value, and a peak height ratio distribution. Also disclosed are methods and systems for intelligently estimating the number of contributors to a biological sample.
This disclosure relates to novel detergents for use in various procedures including, for example, nucleic acid amplification reactions such as polymerase chain reaction (PCR). Methods for preparing the modified detergents are also described.
C12Q 1/6848 - Nucleic acid amplification reactions characterised by the means for preventing contamination or increasing the specificity or sensitivity of an amplification reaction
C07C 229/12 - Compounds containing amino and carboxyl groups bound to the same carbon skeleton having amino and carboxyl groups bound to acyclic carbon atoms of the same carbon skeleton the carbon skeleton being acyclic and saturated having only one amino and one carboxyl group bound to the carbon skeleton the nitrogen atom of the amino group being further bound to acyclic carbon atoms or to carbon atoms of rings other than six-membered aromatic rings to carbon atoms of acyclic carbon skeletons
C07C 229/24 - Compounds containing amino and carboxyl groups bound to the same carbon skeleton having amino and carboxyl groups bound to acyclic carbon atoms of the same carbon skeleton the carbon skeleton being acyclic and saturated having more than one carboxyl group bound to the carbon skeleton, e.g. aspartic acid
C07D 207/16 - Carbon atoms having three bonds to hetero atoms with at the most one bond to halogen, e.g. ester or nitrile radicals
A high data rate integrated circuit, such as an integrated circuit including a large sensor array, may be implemented using clock multipliers in individual power domains, coupled to sets of transmitters, including a transmitter pair configuration. Reference clock distribution circuitry on the integrated circuit distributes a relatively low speed reference clock. In a transmitter pair configuration, each pair comprises a first transmitter and a second transmitter in a transmitter power domain. Also, each pair of transmitters includes a clock multiplier connected to the reference clock distribution circuitry, and disposed between the first and second transmitters, which produces a local transmit clock.
A system for performing biological reactions is provided. The system includes a chip including a substrate and a plurality of reaction sites. The plurality of reaction sites are each configured to include a liquid sample of at most one nanoliter. Further, the system includes a control system configured to initiate biological reactions within the liquid samples. The system further includes a detection system configured to detect biological reactions on the chip. According to various embodiments, the chip includes at least 20000 reaction sites. In other embodiments, the chip includes at least 30000 reaction sites.
The invention relates to the analysis of carbohydrates, such as N-glycans and O-glycans found on proteins. The invention relates, in part, to glycan labeling with formulas/compounds enhancing their detection and/or analysis by methods such as capillary electrophoresis, liquid chromatography and mass spectrometry. These detection methods may be useful in studying glycosylation patterns of biological or medical samples, or for assessing protein production, protein quality/purity, for comparing innovator and biosimilar glycosylated proteins, or for selecting proteins with the desired glycosylation.
A method for preparing a homopolymer recalibration panel includes: extracting, from a set of amplicons used in sequencing-by-synthesis, a set of candidate amplicons satisfying a first set of criteria, wherein the first set of criteria includes amplicons known to belong to high-confidence regions of a reference genome with no variants; and selecting, from the set of candidate amplicons, a reduced set of amplicons satisfying a second set of criteria, wherein the second set of criteria includes amplicons that together comprise at least a minimal threshold number of homopolymers of each homopolymer length between a predetermined minimal homopolymer length and a predetermined maximal homopolymer length for one or more of homopolymer types A, T, C, and G.
Provided herein are compositions and systems for use in polymerase-dependent, nucleotide transient-binding methods. The methods are useful for deducing the sequence of a template nucleic acid molecule and single nucleotide polymorphism (SNP) analyses. The methods rely on the fact that the polymerase transient-binding time for a complementary nucleotide is longer compared to that of a non-complementary nucleotide. The labeled nucleotides transiently-binds the polymerase in a template-dependent manner, but does not incorporate. The methods are conducted under any reaction condition that permits transient binding of a complementary or non-complementary nucleotide to a polymerase, and inhibits nucleotide incorporation.
A method for nucleic acid sequencing includes receiving a plurality of observed or measured signals indicative of a parameter observed or measured for a plurality of defined spaces; determining, for at least some of the defined spaces, whether the defined space comprises one or more sample nucleic acids; processing, for at least some of the defined spaces, the observed or measured signal to improve a quality of the observed or measured signal; generating, for at least some of the defined spaces, a set of candidate sequences of bases for the defined space using one or more metrics adapted to associate a score or penalty to the candidate sequences of bases; and selecting the candidate sequence leading to a highest score or a lowest penalty as corresponding to the correct sequence for the one or more sample nucleic acids in the defined space.
The instant technology relates to a production system to produce AAV vectors in a serum free suspension platform and at high titers. This technology uses reagents comprising media, cells, transfection reagent, AAV enhancer, and a lysis buffer, each of which is designed to provide maximal AAV production from suspension culture of mammalian cells, e.g. HEK293 cells. With this new system we are able to deliver up to about 2×1011 viral genomes per milliliter (vg/mL) of unconcentrated AAV vectors.
A rotor assembly includes a rotor plate to rotate around a first axis, a bucket attached to the rotor plate and to rotate around a second axis, and a stop plate to rotate around the first axis between an open position and a closed position. When in the closed position, the stop plate engages the bucket to fix an angular position of the bucket relative to a plane of rotation of the rotor assembly. The rotor assembly further includes a housing for a sensor array component, the housing disposed in the bucket and including a solution inlet, a solution outlet, a transfer basin, a solution retainer disposed between the solution outlet and the transfer basin, and a collection reservoir in fluid communication with the transfer basin. The solution inlet and the solution outlet to engage ports of a flow cell of a sensor array.
H02K 11/20 - Structural association of dynamo-electric machines with electric components or with devices for shielding, monitoring or protection for measuring, monitoring, testing, protecting or switching
B01L 3/00 - Containers or dishes for laboratory use, e.g. laboratory glassware; Droppers
B04B 5/04 - Radial chamber apparatus for separating predominantly liquid mixtures, e.g. butyrometers
F16K 99/00 - Subject matter not provided for in other groups of this subclass
C12Q 1/6874 - Methods for sequencing involving nucleic acid arrays, e.g. sequencing by hybridisation [SBH]
H02K 5/10 - Casings or enclosures characterised by the shape, form or construction thereof with arrangements for protection from ingress, e.g. of water or fingers
95.
Umbrella check valve assembly having retention plate
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.
The present disclosure relates, in some embodiments, to a system for measuring capillary electrophoresis current. The system includes a plurality of capillaries, where each capillary has a cathode end and an anode end. The system further includes a plurality of cathode buffers. Each of the cathode buffers is configured to be electrically isolated from the other cathode buffers. Further, each cathode buffer is associated with one capillary of the plurality of capillaries. The cathode end of each capillary is immersed in its associated cathode buffer. The system includes a plurality of current sensors, each current sensor associated with one capillary of the plurality of capillaries for measuring current. In some embodiments, the plurality of capillaries is four capillaries.
G01F 23/263 - Indicating or measuring liquid level or level of fluent solid material, e.g. indicating in terms of volume or indicating by means of an alarm by measuring physical variables, other than linear dimensions, pressure or weight, dependent on the level to be measured, e.g. by difference of heat transfer of steam or water by measuring variations of capacity or inductance of capacitors or inductors arising from the presence of liquid or fluent solid material in the electric or electromagnetic fields by measuring variations in capacitance of capacitors
G01R 19/25 - Arrangements for measuring currents or voltages or for indicating presence or sign thereof using digital measurement techniques
97.
AMINE-CONTAINING TRANSFECTION REAGENTS AND METHODS FOR MAKING AND USING SAME
There are provided for herein novel amine-containing transfection compounds and methods for making and using same. The compounds are generally obtained by reacting a primary amine with an unsaturated compound. Transfection complexes made using the amine-containing transfection compounds in combination with additional compounds to encapsulate biologically active agents such as nucleic acids are also provided for herein. Methods of using the transfection complexes for the in vivo or in vitro delivery of biologically active agents are also described. The transfection complexes of the present invention are highly potent, thereby allowing effective modulation of a biological activity at relatively low doses compared to analogous transfection compounds known in the art.
A61K 47/54 - Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the non-active ingredient being a modifying agent the modifying agent being an organic compound
C07C 227/06 - Formation of amino groups in compounds containing carboxyl groups by addition or substitution reactions, without increasing the number of carbon atoms in the carbon skeleton of the acid
C07D 211/28 - Heterocyclic compounds containing hydrogenated pyridine rings, not condensed with other rings with only hydrogen or carbon atoms directly attached to the ring nitrogen atom having no double bonds between ring members or between ring members and non-ring members with hydrocarbon or substituted hydrocarbon radicals directly attached to ring carbon atoms with substituted hydrocarbon radicals attached to ring carbon atoms with hydrocarbon radicals, substituted by nitrogen atoms to which a second hetero atom is attached
C07D 211/58 - Nitrogen atoms attached in position 4
C12N 15/88 - Introduction of foreign genetic material using processes not otherwise provided for, e.g. co-transformation using microencapsulation, e.g. using liposome vesicle
A61K 48/00 - Medicinal preparations containing genetic material which is inserted into cells of the living body to treat genetic diseases; Gene therapy
C07C 229/08 - Compounds containing amino and carboxyl groups bound to the same carbon skeleton having amino and carboxyl groups bound to acyclic carbon atoms of the same carbon skeleton the carbon skeleton being acyclic and saturated having only one amino and one carboxyl group bound to the carbon skeleton the nitrogen atom of the amino group being further bound to hydrogen atoms
C12N 15/113 - Non-coding nucleic acids modulating the expression of genes, e.g. antisense oligonucleotides
98.
METHODS, COMPOSITIONS, SYSTEMS, APPARATUSES AND KITS FOR NUCLEIC ACID AMPLIFICATION
A method of forming a polymer matrix array includes applying an aqueous solution into wells of a well array. The aqueous solution includes polymer precursors. The method further includes applying an immiscible fluid over the well array to isolate the aqueous solution within the wells of the well array and polymerizing the polymer precursors isolated in the wells of the well array to form the polymer matrix array. An apparatus includes a sensor array, a well array corresponding to the sensor array, and an array of polymer matrices disposed in the well array.
A method of forming a particle includes, in a disperse phase within an aqueous suspension, polymerizing a plurality of mer units of a hydrophilic monomer having a hydrophobic protection group, thereby forming a polymeric particle including a plurality of the hydrophobic protection groups. The method further includes converting the polymeric particle to a hydrophilic particle.
C08F 130/08 - Homopolymers of compounds having one or more unsaturated aliphatic radicals, each having only one carbon-to-carbon double bond, and containing phosphorus, selenium, tellurium, or a metal containing a metal containing silicon
C07F 7/18 - Compounds having one or more C—Si linkages as well as one or more C—O—Si linkages
C08F 2/20 - Suspension polymerisation with the aid of macromolecular dispersing agents
C08F 2/26 - Emulsion polymerisation with the aid of emulsifying agents anionic
C08F 230/08 - Copolymers of compounds having one or more unsaturated aliphatic radicals, each having only one carbon-to-carbon double bond, and containing phosphorus, selenium, tellurium, or a metal containing a metal containing silicon