Methods and systems for data distribution are described herein. In one aspect, a method can include receiving, by at least one worker node (WN) 110 of a plurality of WNs of a data distribution system, a job definition from a job manager, wherein the job definition comprises a set of processes to be performed on a set of data request; sending, by the WN 110 and to an extended binary access manager (BAMEx) 140, a request for the data; receiving, by the WN 110 and from the BAMEx 140, the data based on the request for the data; performing, by the WN 110, one or more processes according to the job definition; generating, by the WN 110, a set of results files comprising results of at least one of the performed one or more processes; and sending, by the WN 110, the set of results files to the BAMEx 140.
A method, composition and kit for determining the presence or absence of Salmonella sp., Shigella sp./Enteroinvasive Escherichia coli (EIEC), and Campylobacter sp. in a sample, comprising producing an amplicon by subjecting a reaction mixture including the sample and five primer pairs to reaction conditions suitable to amplify targeted nucleic acids. The five primer pairs include primer pair A that specifically hybridizes with a portion of Campylobacter coli genome, primer pair B that specifically hybridizes with a portion of Campylobacter jejuni genome, primer pair C that specifically hybridizes with a portion of Campylobacter upsaliensis genome, primer pair D that specifically hybridizes with a portion of Salmonella sp. genome, and primer pair E that specifically hybridizes with a portion of Shigella sp./EIEC genome; and determining the presence or absence of Campylobacter sp., Salmonella sp., and/or Shigella sp./Enteroinvasive Escherichia coli (EIEC) in the sample based on the amplicon.
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 1/6883 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
Methods and system are described for normalizing and creating correction factors for measurements in a fluorometer. To ensure that measurements across multiple channels can be properly compared, some kind of calibration must be done. The same calibrant can be run across all the channels and fluorescence measured. The fluorescence of one channel can be chosen as a reference. A correction factor can be calculated for each channel and used for an extended period of time, possibly even the lifetime of the instrument.
4.
SYSTEM AND METHOD FOR GENOTYPING STRUCTURAL VARIANTS
Methods for determining genotypes of structural variants in a sample genome, may include: amplifying nucleic acid sequences at targeted locations in the sample genome by a panel targeting a plurality of structural variant marker to generate sequence reads; mapping the sequence reads to a modified reference genome to produce aligned sequence reads, wherein the modified reference genome includes a wild-type target region and a structural variant target region; for each structural variant marker, determining a read count for a wild-type allele and a read count for a structural variant allele; determining a probability for each possible genotype, wherein the possible genotypes include a homozygous wild-type genotype, a heterozygous genotype and a homozygous structural variant genotype; and selecting the genotype with a maximum probability value to provide an estimated genotype corresponding to the structural variant marker of the sample.
LIFE TECHNOLOGIES HOLDINGS PTE LIMITED (Singapore)
LIFE TECHNOLOGIES CORPORATION (USA)
Inventor
Wei, Han
Chan, Chee Wai
Liaw, Wui Khen
Dong, Shan Hua
Goh, See Chen
Yeo, Huei Steven
Sicat, Jr., Harmon Cosme
Ling, Mio Xiu Lu
Mead, Josh M.
Makinen, Mikko
Lim, Beng Heng
Boo, Kuan Moon
Bong, Justina Linkai
Ng, Chye Sin
Lee, Wee Liam
Lim, Li Yang
Lee, Way Xuang
Abstract
An electroporation system including one or more of a pipette, a pipette tip, a pipette docking assembly, and a pulse generator. The pipette docking assembly includes a pipette station, a pipette station guard, and a reservoir (e.g., a buffer tube). A method for transfecting a cell with a payload including providing an electroporation system, providing the cell, providing the payload, introducing the cell and the payload into a pipette tip, and electroporating the cell within the pipette tip by operating the electroporation system.
6.
METHODS FOR DETECTING ALLELE DOSAGES IN POLYPLOID ORGANISMS
A method for determining a genotype of a sample of a polyploid organism, may include: amplifying nucleic acid sequences at targeted locations in a sample genome by a panel targeting a plurality of SNP markers to generate sequence reads; mapping the sequence reads to a reference genome for the polyploid organism; detecting variants in the aligned sequence reads to produce detected variants, wherein the detected variants include detected SNP's corresponding to the SNP markers; determining a probability for each alternate allele dosage of a plurality of possible allele dosages for a corresponding detected SNP, wherein the number of possible allele dosages is equal to a ploidy of the SNP marker plus one; and selecting the alternate allele dosage with a maximum probability value to provide an estimated allele dosage corresponding to the SNP marker, wherein the estimated allele dosage is indicative of the genotype for the SNP marker.
A bioreactor pod includes a pod base; a dual mode bioreactor operable in static and dynamic modes and insertable into the pod base; one or more portable and arrangeable pod modules; a stand for mounting pod components; a display including a user interface for transmitting user inputs and receiving outputs associated with the dual mode bioreactor, pod modules; and a controller for controlling the bioreactor and pod modules.
8.
COMPOSITIONS, KITS AND METHODS FOR DETECTION OF VIRAL VARIANT SEQUENCES
Disclosed are compositions, assays, methods, diagnostic methods, kits and diagnostic kits for the specific and differential detection of SARS-CoV-2, including SARS-CoV-2 variants, or other coronaviruses from samples including veterinary samples, clinical samples, food samples, forensic sample, an environmental sample (e.g., soil, dirt, garbage, sewage, air, or water), including food processing and manufacturing surfaces, or a biological sample.
C12Q 1/70 - Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving virus or bacteriophage
Systems and methods for measuring a foam layer in a fluid processing system are disclosed. The system includes a container having a chamber for containing a liquid and the foam layer. The system includes a first sensor positioned adjacent a top portion of the chamber. The first sensor is configured to measure a first distance between a top foam surface of the foam layer and the first sensor. The system includes a second sensor coupled to the container, the second sensor configured to measure a mass of the liquid. The system also includes a processor configured to perform the operations of calculating a thickness of the foam layer based on dimensions of the chamber of the container, the measured first distance between the top foam surface of the foam layer and the first sensor, and the mass of the liquid as measured by the second sensor.
G01F 17/00 - Methods or apparatus for determining the capacity of containers or cavities, or the volume of solid bodies
G01F 1/34 - Measuring the volume flow or mass flow of fluid or fluent solid material wherein the fluid passes through a meter in a continuous flow by using mechanical effects by measuring pressure or differential pressure
Various embodiments of a compression collar expander assembly for expanding a tubular compression collar are described. For example, the compression collar expander assembly can include a guide plate, a spindle plate, and a plurality of carriages movably disposed on a top surface of the guide plate. Each of the plurality of carriages can include a body, a guide projecting from the body, and a die set comprising a plurality of dies. Each die can include a base coupled to a corresponding one of the plurality of carriages and a prong upstanding from the base. In some embodiments, a tapered expander is configured to assist with expanding the plurality of dies.
Provided herein are ionizable lipids, compositions comprising the ionizable lipids, and methods of making and using the same. The ionizable lipids provided herein can be formulated in lipid compositions for the delivery of macromolecules, such as nucleic acids, in vitro, ex vivo, or in vivo.
C07D 265/30 - 1,4-Oxazines; Hydrogenated 1,4-oxazines not condensed with other rings
C07D 279/12 - 1,4-Thiazines; Hydrogenated 1,4-thiazines not condensed with other rings
C07D 295/145 - Heterocyclic compounds containing polymethylene-imine rings with at least five ring members, 3-azabicyclo [3.2.2] nonane, piperazine, morpholine or thiomorpholine rings, having only hydrogen atoms directly attached to the ring carbon atoms with substituted hydrocarbon radicals attached to ring nitrogen atoms substituted by carbon atoms having three bonds to hetero atoms with at the most one bond to halogen, e.g. ester or nitrile radicals with the ring nitrogen atoms and the carbon atoms with three bonds to hetero atoms attached to the same carbon chain, which is not interrupted by carbocyclic rings
A61K 48/00 - Medicinal preparations containing genetic material which is inserted into cells of the living body to treat genetic diseases; Gene therapy
12.
COMPOSITIONS, KITS, AND METHODS FOR DETECTION OF VARIANT STRAINS OF AFRICAN SWINE FEVER VIRUS
Disclosed are compositions, methods, systems, and kits for the detection of African swine fever virus (ASFV) in a test sample, and in particular for distinguishing between wild/reference type ASFV and mutant/variant strains of ASFV. A variant ASFV assay includes a first set of primers and a first probe that correspond to a first ASFV target, and a second set of primers and a second probe that correspond to a second ASFV target. The first and second probes are differentially labelled. The first ASFV target is a MGF360 gene and the second ASFV target is the CD2v gene. Absence of these targets, in conjunction with a positive determination for another generic ASFV target such as the p72 gene, is indicative of a vaccine-associated variant strain of ASFV.
C12Q 1/70 - Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving virus or bacteriophage
13.
CYCLE THRESHOLDS IN MACHINE LEARNING FOR FORECASTING INFECTION COUNTS
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 50/50 - ICT specially adapted for medical diagnosis, medical simulation or medical data mining; ICT specially adapted for detecting, monitoring or modelling epidemics or pandemics for simulation or modelling of medical disorders
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
Described herein are various methods and embodiments of a fluid processing system and foam breaker devices for at least reducing foam formation in a container of the fluid processing system. In some embodiments, the foam breaker device includes a mounting hub extending along a longitudinal axis of the foam breaker device. The mounting hub can include a coupling feature for coupling the foam breaker device to a drive shaft of the fluid processing system. The foam breaker device can also include a wall structure extending circumferentially from the mounting hub at an angle relative to the longitudinal axis of the foam breaker device. The wall structure can cause a reduction in the foam volume as a result of at least a part of the wall structure contacting the foam volume.
C12M 1/00 - Apparatus for enzymology or microbiology
B01D 45/00 - Separating dispersed particles from gases or vapours by gravity, inertia, or centrifugal forces
B01F 27/90 - Mixers with rotary stirring devices in fixed receptacles; Kneaders with stirrers rotating about a substantially vertical axis with paddles or arms
An in vitro method, composition and kit for determining the presence or absence of adenovirus, metapneumovirus, rhinovirus/enterovirus, and parainfluenza in a sample, including providing a reaction mixture containing the sample and at least one primer pair set. The primer pair set includes at least one primer pair A that specifically amplifies a portion of adenovirus genome; at least one primer pair B that specifically amplifies a portion of metapneumovirus genome; at least one primer pair C that specifically amplifies a portion of rhinovirus/enterovirus genome; and at least one primer pair D that specifically amplifies a portion of parainfluenza genome. The reaction mixture is subjected to reaction conditions suitable to amplify targeted nucleic acids, thereby generating at least one amplicon; wherein the presence or absence of at least one amplicon in the sample indicates the presence or absence of adenovirus, metapneumovirus, rhinovirus/enterovirus, and/or parainfluenza in the sample.
C12Q 1/70 - Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving virus or bacteriophage
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.
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
Disclosed are compositions, kits, and methods that enable intra-channel multiplexing by enabling determination of separate detectable signals, each associated with a different assay target, within the same detection channel. The multiple detectable signals can be separately resolved and independently analyzed to enable detection and/or quantification of each respective target. Enabling multiple targets to be assayed within the same detection channel increases the plexy of multiplex assays without relying on additional dyes and concomitant issues of increased spectral overlap.
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 47/64 - Drug-peptide, drug-protein or drug-polyamino acid conjugates, i.e. the modifying agent being a peptide, protein or polyamino acid which is covalently bonded or complexed to a therapeutically active agent
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
C07K 7/08 - Linear peptides containing only normal peptide links having 12 to 20 amino acids
C12N 15/87 - Introduction of foreign genetic material using processes not otherwise provided for, e.g. co-transformation
Systems and methods that enable analyte detection in a multiplexed amplification process can include obtaining, at multiple time points during the amplification process, composite emission signal data associated with a composite emission signal from at least a first probe type comprising a first label configured to generate a first emission signal and a second probe type comprising a second label configured to generate a second emission signal which has spectrally similar characteristics as said first emission signal, the first probe type and the second probe type differing in thermal and/or temporal properties; and determining, based at least partially on the composite emission signal data, emission signal data associated with a emission signal from a given probe type of the first probe type or the second probe type during the amplification process.
Apparatus, methods, and systems including a syringe for delivering a fluid. The syringe includes a syringe body, a piston, an insert, and a removable plunger. The piston is located in a lumen of the syringe body such that a bottom of the piston together with interior walls of the syringe define a working volume. The piston comprising a cavity. The insert is located at a desired position in the lumen. The insert narrowing the lumen and being configured to prevent retraction of the piston beyond the desired position. The removable plunger is configured to removably couple to the piston. The removable plunger includes a tip configured to couple with the cavity of the piston and move the piston when a force is applied at the plunger, and to decouple from the piston when the piston engages the insert at the desired position.
A61M 5/315 - Pistons; Piston-rods; Guiding, blocking or restricting the movement of the rod; Appliances on the rod for facilitating dosing
A61M 5/00 - Devices for bringing media into the body in a subcutaneous, intra-vascular or intramuscular way; Accessories therefor, e.g. filling or cleaning devices, arm rests
A61M 39/12 - Tube connectors or tube couplings for joining a flexible tube to a rigid attachment
Provided are methods and compositions for preparing a library of target nucleic acid sequences that are useful for assessing gene mutations for oncology biomarker profiling of samples. In particular, a target-specific primer panel is provided that allows for selective amplification of oncology biomarker target sequences in a sample. In one aspect, the invention relates to target-specific primers useful for selective amplification of one or more target sequences associated with oncology biomarkers from two or more sample types. In some aspects, amplified target sequences obtained using the disclosed methods, and compositions can be used in various processes including nucleic acid sequencing and used to detect the presence of genetic variants of one or more targeted sequences associated with oncology.
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
23.
METHODS FOR DEEP ARTIFICIAL NEURAL NETWORKS FOR SIGNAL ERROR CORRECTION
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.
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 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.
G01N 35/00 - Automatic analysis not limited to methods or materials provided for in any single one of groups ; Handling materials therefor
G01N 35/04 - Automatic analysis not limited to methods or materials provided for in any single one of groups ; Handling materials therefor using a plurality of sample containers moved by a conveyor system past one or more treatment or analysis stations - Details of the conveyor system
G01N 35/10 - Devices for transferring samples to, in, or from, the analysis apparatus, e.g. suction devices, injection devices
Systems and methods under the present disclosure include swabs and storage tubes for use in medical environments. The various embodiments can help prevent cross contamination in laboratories or make swabs and storage tubes more compatible with automated laboratory processes. Accurate positioning of swabs can help make any pipetting procedures more accurate, easier and quicker.
A61B 10/00 - Other methods or instruments for diagnosis, e.g. for vaccination diagnosis; Sex determination; Ovulation-period determination; Throat striking implements
B01L 3/00 - Containers or dishes for laboratory use, e.g. laboratory glassware; Droppers
A61B 10/02 - Instruments for taking cell samples or for biopsy
27.
INSULATED PACKAGING SYSTEM USING CELLULOSE MATERIALS
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 (100) is formed by folding one or more pieces of stock cellulose material along predetermined fold lines (122, 124) and folding slots (120) to form an insert in a folded configuration suitable for insertion as an insulative liner within a container for use in shipment.
B65D 5/50 - Internal supporting or protecting elements for contents
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
Systems and methods under the present disclosure include sample collection kits, such as for saliva or other fluids. In certain embodiments a detachable funnel can collect saliva from a user. A debris filter can be coupled to the funnel that extends into the test tube. The funnel can comprise or be coupled to a reagent cartridge that, when manipulated by a user, can break open and release reagent into the test tube for use in testing the saliva. Certain embodiments can comprise a casing that can house a test tube and tube cap, with a funnel configured to cover the entire top edge of the casing so as to protect the test tube and tube cap until used by a user.
A61B 10/00 - Other methods or instruments for diagnosis, e.g. for vaccination diagnosis; Sex determination; Ovulation-period determination; Throat striking implements
29.
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.
Embodiments of the invention are disclosed that provide improved computer systems, computerized methods, and computer program products for generating and evaluating automated predictions regarding whether a particular amplification curve from a qPCR assay indicates presence of a target molecule in a sample. In some embodiments, predictions are generated using deep learning networks. In some embodiments, curve-quality predictions are generated and used to assess whether an amplification prediction can be reliably made from a particular amplification curve or whether the curve reflects an anomaly in the qPCR assay. In various embodiments, prediction confidence data is also generated and used, along with prediction data, in an electronic user interface to improve qPCR measurement.
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.
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.
Methods, systems, and devices for analyzing a sample for the presence of a target protein are provided. A sample can be processed, the processing generating an amplification product of a template nucleic acid formed in response to a target protein being present in the sample. The amplification product can be contacted with a detection probe to generate a second product comprising a labeled nucleic acid. A lateral flow substrate can be contacted with the second product, the lateral flow substrate comprising a capture moiety configured to bind the labeled nucleic acid. The methods can be carried out in one or more chambers of a single device or multiple devices. Detection probe bound to amplicons of the template nucleic acid captured on the lateral flow substrate can be read visually or using a sensor.
THERMO SCIENTIFIC PORTABLE ANALYTICAL INSTRUMENTS INC. (USA)
LIFE TECHNOLOGIES CORPORATION (USA)
Inventor
Doherty, Walter
Lee, Lisa
Fisher, Brandon
Benson, Katelyn
Abstract
A modular accessory for orienting a light path at different angles to an optical axis of a spectrometer is described. The modular accessory includes an attachment module configured to couple to a Raman spectrometer. The attachment module attaches to a base module which includes a visible light imager. An objective module couples to the base module and includes an objective configured to provide an optical path for the sample light beam travelling from a sample along a light path to an objective lens of the objective, through the objective, and to the input for the sample light beam of the base module. The modules can provide tilt and swivel angles to orient the light path at different angles. Portable Raman systems including the modular accessory and a Raman spectrometer are also described as well as methods for using the systems.
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.
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 120 and a camera module 130. The base module 120 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 130 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.
Disclosed are compositions, kits, and methods for use in applications involving electrophoretic separation of nucleic acids, including capillary electrophoresis applications in which nucleic acid samples are labelled with dyes, size-separated, and subjected to short tandem repeat (STR) analysis. A sample containing DNA is mixed with a composition that includes at least one set of primers that target an STR region of the sample nucleic acid, a set of short quantification primers (QS primers) that target a first multi-copy sequence (QS sequence) of the sample nucleic acid, and a set of long quantification primers (QL primers) that target a second multi-copy sequence (QL sequence) of the sample nucleic acid, wherein the QS sequence is shorter than the QL sequence.
A manifestation of fluid potential noise is a periodic profile characterized by a periodic saw-tooth spike in a graph of average voltage across all columns of a sensor array as a function of time. This periodic profile is indicative of an adverse impact on the function of active sensor pixels that are proximal to reference pixels in sensor devices that include a large array of chemically-sensitive field effect transistor (ChemFET) sensors. Systems, devices, and methods are described that can mitigate the impact of reference pixels on fluid potential noise.
This disclosure describes master mix compositions, nucleic acid amplification kits, methods of manufacturing master mix compositions, and methods of using master mix compositions that minimize or eliminate the negative effects of contaminant nucleic acids. Conventional master mix compositions often include contaminant nucleic acids.
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
40.
METHODS FOR ELECTROSCOPIC IMAGING FOR ANALYSIS OF CELLS
Analyzing cells disposed on a sensor array surface of a ChemFET sensor array, may include flowing a solution having a step change in pH across the sensor array surface, wherein ChemFET sensors of the sensor array generate signals in response to the step change in pH to produce electroscopic image data. Multiple frames of the electroscopic image data are acquired during an acquisition time interval. Each frame corresponds to signal samples generated by the sensor array measured at a sampling time during the acquisition time interval. Each frame comprises pixels, wherein a given pixel in the frame corresponds to a signal sample from a given sensor in the sensor array. The electroscopic image data is segmented, based on characteristics of the signal samples, into cell regions corresponding to locations of the cells on the sensor array surface and background regions corresponding to areas on the sensor array having no cells.
Disclosed are compositions, kits, and methods for amplifying and quantifying a target nucleic acid from a sample. Compositions, kits, and methods enable the quantification of a target nucleic acid from a sample using an internal quantification standard disposed in the same reaction volume as the target nucleic acid, thereby eliminating the need for additional amplification reactions and processing to generate a standard curve. Compositions, kits, and methods also enable the comparison of target nucleic acid loads between two or more test samples by normalizing measured levels of the target nucleic acid in each sample according to relative levels of endogenous nucleic acid in each test sample.
The present disclosure generally relates to compositions, kits, and methods for the rapid detection of nucleic acid targets in a sample. In some embodiments, a detection reagent comprising at least two metal indicators is disclosed. In additional embodiments, kits and methodologies for detecting the presence or absence of a target nucleic acid sequence comprising the detection reagent comprising multiple metal indicators are provided.
Methods and systems for improving the scalability and associated efficacy of continuous transfection processes, such as continuous transient transfection processes. The continuous transfection system includes at least a first input line and a second input line, wherein the first input line and the second input line are configured for sterile, fluid connection to a first reagent housing and a second reagent housing, respectively, a mixing chamber that is fluidly connected to the at least first and second input lines, a delivery line fluidly connected to the mixing chamber, wherein the delivery line is configured for sterile, fluid connection to a cell culture vessel, and a flow rate control component, such as a pump operable to control flow rate of liquid into the at least first and second input lines, throughout the mixing chamber, and into the cell culture vessel.
Methods and systems are provided for genotyping a gene sequence. The method comprises obtaining first genotyping call data representing a query gene sequence. A numerical score is assigned to each of a plurality of allele calls of second genotyping call data by matching the first genotyping call data with the second genotyping call data, the second genotyping call data representing a plurality of candidate gene sequences. A match score is determined for each of the plurality of candidate gene sequences based on the numerical score assigned to each of the plurality of allele calls of the second genotyping call data, and a genotyping call is made for the query gene sequence based on a highest match score from among the match score determined for each of the plurality of candidate gene sequences.
LIFE TECHNOLOGIES HOLDINGS PTE LIMITED (Singapore)
LIFE TECHNOLOGIES CORPORATION (USA)
Inventor
Ling, Mio Xiu Lu
Sicat, Harmon Jr. Cosme
Mead, Joshua
Shi, Benyong
Ong, Li Yong
Kovarcik, Don Paul
Andronikou, Nektaria
Abstract
The present disclosure provides systems and methods of electroporation protocol optimization. Embodiments include electroporation machines capable of carrying out test protocols including multiple user-designated parameters. The protocols and parameters can be carried out on samples comprising cells, including portions of a sample, to determine optimum parameters for electroporation for different samples. The systems and methods of optimization preferably use electroporation cartridges, electroporation instruments and systems and methods of electroporation using these devices and systems. In some embodiments, electroporation cartridges comprise an electroporation chamber and electrodes.
An adjustable foam sensor system is disclosed. The adjustable foam sensor system can include an adjustable foam sensor coupled to a transition member with a foam probe extending from the transition member. The adjustable foam sensor system can also include an adjustable housing that can be coupled to a container interface for interfacing with a container of a fluid processing system. The adjustable housing can be configured to be compressed or extended in response to a force, which in turn can reposition or move the adjustable foam sensor in the container. A controller can automatically adjust the adjustable foam sensor based on sensed and/or determined fluid levels, as well as control the delivery of anti-foam for reducing foam in the container.
A bioprocessing control system can include an intelligent gateway. The gateway can receive, from a controller, a request for data associated with the plurality of bioprocessing instruments including a primary data set and a secondary data set. The primary data set includes a block of primary data measured by the plurality of bioprocessing instruments. The secondary data set has a lower priority than the primary data set. The gateway can cause the controller to control the bioprocessing instrument by at least: sending, to the controller in response to the request, the block of primary data. The gateway can send, to the controller during the sending the block of primary data and in response to the request, a portion of the secondary data set, thereby reducing a load on the controller.
G05B 19/042 - Programme control other than numerical control, i.e. in sequence controllers or logic controllers using digital processors
G05B 19/04 - Programme control other than numerical control, i.e. in sequence controllers or logic controllers
G06F 15/16 - Combinations of two or more digital computers each having at least an arithmetic unit, a program unit and a register, e.g. for a simultaneous processing of several programs
A bubble trap includes a body having an interior surface bounding a cavity that extends between an upper end and an opposing lower end, an axis extends centrally through the cavity of the body between the upper end and the lower end, a first plane extends through the body orthogonal to the axis so as to divide the body into an upper body portion and a lower body, the interior surface of the lower body portion having a constant first radius from a fixed first center point, the interior surface of the upper body portion not having a constant radius from a fixed center point. A tubular spout projects into the cavity at the lower end encircles a channel that communicates with the cavity. A liquid inlet port, a liquid outlet port, and a gas outlet port communicate with the cavity.
The instant technology generally relates to methods and compositions for expansion of mesenchymal stem cells in culture on a modified surface in the absence of a cell feeder layer and the absence of a cell adhesive coating on the surface. In some instances, the mesenchymal stem cells are expanded on the modified surface in a serum-free culture medium.
Disclosed are master mix compositions, kits, and related methods for use in amplifying a target nucleic acid. A master mix composition may be formulated to enable effective reaction mixture loading onto a dPCR plate, provide high proportion of valid/readable partitions, enable identification and distinguishing between amplified and unamplified partitions, enable detection of low abundance targets amidst high background levels of non-target nucleic acids and/or amidst inhibiting agents, and/or enable effective detection of low frequency mutant alleles.
The present disclosure relates to recombinant nucleases, recombinant nucleases operatively linked to nucleic acid binding domains, and methods of making and using them.
Prediction of a clinical response to a therapy of a subject with an autoimmune disease based on B cell immune repertoire may include determining a plurality of clone frequencies in a biological sample from the subject, wherein the clone frequencies include: IgM, IgD, IgG3, IgG4, IgA, IgM with first somatic hypermutation (SHM) level, IgG1 with second SHM level. A plurality of decision criteria may be applied to features including the plurality of clone frequencies. Each decision criterion applies at least one threshold to a feature, wherein the plurality of decision criteria provides a plurality of output values. The plurality of output values may be summed and a sigmoid transformation may be applied to the summed value to form a prediction value. The prediction value may be compared to a final threshold to identify the subject as a likely responder or non-responder to an autoimmune disease therapy.
G01N 33/50 - Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
G01N 33/68 - Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving proteins, peptides or amino acids
C12Q 1/6881 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for tissue or cell typing, e.g. human leukocyte antigen [HLA] probes
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
New lipids are provided that are useful for delivering macromolecules, such as nucleic acids, into eukaryotic cells and tissue. The lipids can be used alone, in combination with other lipids and/or in combination with other transfection enhancing reagents to prepare transfection complexes and complexes for in vivo delivery of bioactive agents.
C07D 295/125 - Heterocyclic compounds containing polymethylene-imine rings with at least five ring members, 3-azabicyclo [3.2.2] nonane, piperazine, morpholine or thiomorpholine rings, having only hydrogen atoms directly attached to the ring carbon atoms with substituted hydrocarbon radicals attached to ring nitrogen atoms substituted by singly or doubly bound nitrogen atoms with the ring nitrogen atoms and the substituent nitrogen atoms attached to the same carbon chain, which is not interrupted by carbocyclic rings
C07C 225/20 - Compounds containing amino groups and doubly-bound oxygen atoms bound to the same carbon skeleton, at least one of the doubly-bound oxygen atoms not being part of a —CHO group, e.g. amino ketones having amino groups bound to carbon atoms of rings other than six-membered aromatic rings of the carbon skeleton
A61K 48/00 - Medicinal preparations containing genetic material which is inserted into cells of the living body to treat genetic diseases; Gene therapy
54.
COMPOSITIONS, KITS, AND METHODS FOR DETECTION OF NUCLEIC ACID SEQUENCE LOADS
Disclosed are compositions, kits, and methods for quantifying a target nucleic acid from a sample. Compositions, kits, and methods enable the comparison of target nucleic acid loads between two or more test samples by normalizing measured levels (using a standard curve) of the target nucleic acid in each sample according to relative levels of endogenous nucleic acid in each test sample.
C12Q 1/70 - Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving virus or bacteriophage
55.
AZAINDOLE CYANINE DYES, USES, AND METHODS OF PREPARATION
The present disclosure relates to new and useful azaindole cyanine (pyrrolo pyridine cyanine) compounds. Use of the compounds as dyes that operate in the far-red and near-IR spectral region in biological imaging, and methods of making the compounds are also disclosed herein. The azaindole cyanine (pyrrolo pyridine cyanine) compounds have formulas (I) and (II).
C09B 23/08 - Methine or polymethine dyes, e.g. cyanine dyes characterised by the methine chain containing an odd number of CH groups more than three CH groups, e.g. polycarbocyanines
C09B 1/00 - Dyes with an anthracene nucleus not condensed with any other ring
G01N 21/00 - Investigating or analysing materials by the use of optical means, i.e. using sub-millimetre waves, infrared, visible or ultraviolet light
C07D 201/00 - Preparation, separation, purification, or stabilisation of unsubstituted lactams
C07D 471/00 - Heterocyclic compounds containing nitrogen atoms as the only ring hetero atoms in the condensed system, at least one ring being a six-membered ring with one nitrogen atom, not provided for by groups
C07D 519/00 - Heterocyclic compounds containing more than one system of two or more relevant hetero rings condensed among themselves or condensed with a common carbocyclic ring system not provided for in groups or
56.
DIBENZOXANTHENE QUENCHERS, USES, AND METHODS OF PREPARATION
The present disclosure relates to dibenzoxanthene compounds that are efficient quenchers of fluorescence, for example in the far red and near infrared spectrum. Applications using the dibenzoxanthene quenching compounds and methods of making same are also described. Also disclosed is a method of detecting or quantifying a target nucleic acid molecule in a sample by polymerase chain reaction (PCR). The compounds have the following formula (I).
G01N 33/542 - Immunoassay; Biospecific binding assay; Materials therefor with immune complex formed in liquid phase with steric inhibition or signal modification, e.g. fluorescent quenching
C09B 56/00 - Azo dyes containing other chromophoric systems
Provided are, inter alia, flow centration components (100) that can be used in flow cytometers and other applications. A flow centrator can define central axis (116), a proximal end (106), and a distal end (108), and having a central bore (112) extending within the flow centration component in the direction of the central axis; the flow centration component defining a splined outer surface that defines a plurality of circumferentially arranged bypass flute channels (126), the plurality of bypass flute channels extending in the direction of the central axis, and each of the bypass flute channels having a depth and a length. Also provided are related methods that utilize the disclosed components.
Provided are optical fiber alignment assemblies, comprising: a plurality of fiber channel members being arranged along a first vertical axis, each fiber channel member comprising a fiber channel configured to accommodate an optical fiber disposed therein, the plurality of fiber channels being parallel to one another, fiber channels adjacent to one another defining a spacing therebetween, the spacing being measured along the first vertical axis; a plurality of resilient members, a resilient member being disposed between adjacent fiber channel members; and an adjustment element, the adjustment element being configured to effect a force oriented along the first vertical axis, and the adjustment member being configured such that actuation of the adjustment member changes a compression of the plurality of resilient members so as to effect an essentially linear variation in the spacing between adjacent fiber channels. Also provided are related methods.
Provided are handling systems and methods for sample processing. The systems can include a sample container (106) and a probe (104). A system can be convertible between a loading state in which a user loads sample into the sample container, a sampling state in which relative motion between the sample container and the probe places the probe and sample container into fluid communication with one another so that the probe can aspirate sample from the sample container, and a washing state in which rinse fluid is expressed through the probe so as to remove unwanted material from within the probe, with the rinse fluid being collected by a wash manifold.
G01N 35/04 - Automatic analysis not limited to methods or materials provided for in any single one of groups ; Handling materials therefor using a plurality of sample containers moved by a conveyor system past one or more treatment or analysis stations - Details of the conveyor system
G01N 35/10 - Devices for transferring samples to, in, or from, the analysis apparatus, e.g. suction devices, injection devices
A01N 25/30 - Biocides, pest repellants or attractants, or plant growth regulators, characterised by their forms, or by their non-active ingredients or by their methods of application; Substances for reducing the noxious effect of the active ingredients to organisms other than pests characterised by the surfactants
A01N 59/08 - Alkali metal chlorides; Alkaline earth metal chlorides
A01P 1/00 - Disinfectants; Antimicrobial compounds or mixtures thereof
61.
COMPOSITIONS, KITS, AND METHODS FOR VARIANT-RESISTANT DETECTION OF TARGET VIRAL SEQUENCES
Disclosed are compositions, assays, methods, diagnostic methods, kits and diagnostic kits for the specific and differential detection of SARS-CoV-2, including SARS-CoV-2 variants, or other coronaviruses from samples including veterinary samples, clinical samples, food samples, forensic sample, an environmental sample (e.g., soil, dirt, garbage, sewage, air, or water), including food processing and manufacturing surfaces, or a biological sample.
Disclosed are compositions, assays, methods, diagnostic methods, kits and diagnostic kits for the specific and differential detection of SARS-CoV-2, including SARS-CoV-2 variants, or other coronaviruses from samples including veterinary samples, clinical samples, food samples, forensic sample, an environmental sample (e.g., soil, dirt, garbage, sewage, air, or water), including food processing and manufacturing surfaces, or a biological sample.
C12Q 1/70 - Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving virus or bacteriophage
C12Q 1/6888 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms
63.
SYSTEM AND METHOD FOR CONTAINMENT OF AEROSOL PARTICLES
An embodiment of a system is described that, comprises a containment assembly comprising a receptacle configured to hold a substrate, wherein the containment assembly is configured to extend the receptacle from a housing and retract receptacle into the housing; and an aerosol collector comprising a sample chamber, wherein the aerosol collector is configured to operatively couple to the containment assembly and receive the extended receptacle with the substrate in the sample compartment.
Disclosed are compositions, assays, methods, diagnostic methods, kits and diagnostic kits for the detection of target nucleic acids, including those from microbes and/or from infectious agents such as SARS-CoV-2 and other viruses. Embodiments described herein are designed to enable processing and analysis of the sample to detect target nucleic acids within the sample without requiring extraction and/or isolation of nucleic acid from the sample prior to subsequent processing steps. Samples analyzed can thus be "crude" biological samples that do not require pre-processing prior to placement in the workflow.
A method for determining a sequence of nucleic acids includes purifying the nucleic acids from a sample with a purification instrument in accordance with a purification plan of a run plan. The purified nucleic acids are disposed in a transfer plate. Disposition of the purified nucleic acids is stored in a transfer file. The method further includes transferring the transfer plate to a sequencing instrument; transferring the transfer file to the sequencing instrument; and sequencing the nucleic acids with the sequencing instrument in accordance with a sequencing plan of the run plan and based on the transfer file.
A reagent solution is an aqueous solution including 2-[4-(2-hydroxyethyl)piperazin-1-yl]ethanesulfonic acid in an amount of 1 mM to 200 mM, 2-(methacryloyloxy)ethyl]dimethyl-(3-sulfopropyl)ammonium hydroxide in an amount of 1 mM to 200 mM, and tris(hydroxymethyl)aminomethane in an amount of 1 mM to 200 mM.
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.
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.
LIFE TECHNOLOGIES HOLDINGS PTE LIMITED (Singapore)
Inventor
Ward, Michael D.
Kaduchak, Gregory
Zhu, Lingzhi
Abstract
Provided are laser sources, the laser sources comprising at least one diode; and an optic fiber of a predefined length disposed between the laser source and a position for a target such that the optic fiber communicates light pulses from the laser source as a source light to the position for the target, wherein the position is illuminated by the source light so as to reduce speckles in a captured image of the target. Also provided are methods for providing source light for generating an image, comprising: generating illumination with one or more laser diodes; and passing the illumination through an optic fiber having a plurality of bends therein such that source light is emitted from the optic fiber so as to illuminate a target with the source light, the source light reducing speckles in an image of the target.
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.
inter aliainter 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 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.
F16K 11/085 - Multiple-way valves, e.g. mixing valves; Pipe fittings incorporating such valves; Arrangement of valves and flow lines specially adapted for mixing fluid with all movable sealing faces moving as one unit comprising only taps or cocks with cylindrical plug
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 1/6881 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for tissue or cell typing, e.g. human leukocyte antigen [HLA] probes
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
74.
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.
B04B 5/04 - Radial chamber apparatus for separating predominantly liquid mixtures, e.g. butyrometers
B04B 1/08 - Centrifuges with rotary bowls provided with solid jackets for separating predominantly liquid mixtures with or without solid particles with inserted separating walls of conical shape
A method for sequencing a target polynucleotide includes detecting a first series of nucleotide incorporations complementary to at least a portion of the target polynucleotide. The first series of nucleotide incorporations forms a first complementary polynucleotide. The target nucleotide is secured to a substate disposed in a sequencing zone of an assembly. The method further includes moving the substrate to which the target nucleotide is secured to a templating zone of the assembly; removing the first complementary polynucleotide when the substrate is disposed at the templating zone of the assembly, the target polynucleotide remaining secured to the substrate; following the removing, moving the substrate to which the target polynucleotide is secured to the sequencing zone; and detecting a second series of nucleotide incorporations complementary to at least a portion of the target polynucleotide, the second series of nucleotide incorporations forming a second complementary polynucleotide.
A sequencing system includes an automated sequencing instrument adapted to determine variant calls for one or more extracted polynucleotide samples with a performance of at least 98.5% raw read accuracy and a total instrument run time in a range of 16 hours to 22 hours to determine variant calls when sequencing 6 cfTNA extracted polynucleotide samples using a targeted assay with one nucleic acid pool per sample.
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.
A system includes a pipetting system including a 3-axis gantry; a sled mechanism to select a magnetic comb from a set of magnetic combs; a fluorometer; and a set of receptacles to receive welled plates. A method for purifying nucleic acids includes applying a sample to a well of a multi-well plate, selecting a magnetic comb from a set of magnetic combs disposed on a gantry system, collecting magnetic beads using the magnetic comb, collecting nucleic acid using the magnetic beads, and eluting the nucleic acid from the beads.
LIFE TECHNOLOGIES HOLDINGS PTE LIMITED (Singapore)
Inventor
Luhr, Morten
Gordon, Michael
Sia, Ming Tiong
Chong, Kok Shyong
Soh, Woon Liang Terence
Lim, Seng Leong
Schroeder, Ida Caroline
Alfsnes, Katrine
Lim, Terry Jianhui
Bosnes, Marie
Neurauter, Axl Alois
Pedersen, Ketil Winther
Wilbur, Autumn Day
Zimmerman, Sean
Abstract
A bead processing assembly for use in attaching magnetic beads to biological cells and other biological materials and/or separating magnetic beads from biological cells and other biological materials includes a base assembly having a housing, a support panel disposed on the housing and having a front face, a first pinch valve at least partially outwardly projecting from the front face of the support panel, and a first pump at least partially outwardly projecting from the front face of the support panel. A rocker assembly is supported on the base assembly and includes a mount assembly supported on the base assembly, a platform assembly pivotably secured to the mount assembly, and a rocker drive for repeatedly rocking the platform assembly relative to the mount assembly.
Systems and methods for autofocus using artificial intelligence include (i) capturing a plurality of monochrome images over a nominal focus range, (ii) identifying one or more connected components within each monochrome image, (iii) sorting the identified connected components based on a number of pixels associated with each connected component, (iv) generating a focus quality estimate of at least a portion of the sorted connected components using a machine learning module, and (iv) calculating a target focus position based on the focus quality estimate of the evaluated connected components. The calculated target focus position can be used to perform cell counting using artificial intelligence, such as by (i) generating a seed likelihood image and a whole cell likelihood image based on output- a convolutional neural network and (ii) generating a mask indicative quantity and/or pixel locations of objects based on the seed likelihood image.
A method of testing a biological sample comprising deoxyribonucleic acid (DNA) molecules for presence of a plurality of alleles is described, wherein DNA fragments obtained using the biological sample and corresponding to different alleles have different, fragment sizes. A capillary electrophoresis (CE) instrument is used to obtain test fragment sizing data for the biological sample. A pre-computed model is used to dynamically determine one or more synthetic allelic ladders, where the pre-computed model is derived via analysis of a plurality of fragment sizing data sets obtained from a plurality of previous allelic ladder sample runs conducted using CE instruments. The one or more synthetic or experimentally derived allelic ladders are used to find a sufficient fit to the test fragment sizing data to identify which of the plurality of alleles are present in the biological sample. The statistical analysis may comprise a principal component analysis including two principal components.
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
G16H 10/40 - ICT specially adapted for the handling or processing of patient-related medical or healthcare data for data related to laboratory analysis, e.g. patient specimen analysis
82.
SYSTEMS, METHODS, AND AUTOMATION KITS FOR MAGNETIC ISOLATION AND/OR ENRICHMENT OF TARGET ANALYTES
An in-field modification kit configured to convert a manually operated magnet assembly to an at least partially automated system can include (i) a door assembly configured to selectively attach to a magnet assembly, (ii) an elevation system configured to secure to the magnet assembly and to engage at least a portion of the door assembly for selectively adjusting a distance between the door assembly and the magnet assembly, (iii) a circular reciprocation system configured to engage a fulcrum of the magnet assembly and to selectively rotate the magnet assembly, and (iv) a valve manifold operably connected to the elevation system and the circular reciprocation system for executing automated protocols of magnetic isolation and/or enrichment of target analytes.
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.
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).
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
C12Q 1/6818 - Hybridisation assays characterised by the detection means involving interaction of two or more labels, e.g. resonant energy transfer
1. A system (1000), comprising: a radiant source (101) characterized by an average excitation wavelength; a sample (110) disposed to receive radiation from the radiant source, the sample comprising:a first dye;a second dye; and a detector (115) configured to measure emissions from the sample; a first emission spectral element (121a) characterized by a first average emission wavelength; a second emission spectral element (121b) characterized by a second average emission wavelength that is different than the first average emission wavelength; at least one processor (130) comprising at least one memory including instructions to: illuminate the sample with the radiant source and, in response, (1) measure emissions from the sample using the detector and the first emission spectral element and (2) measure emissions from the sample using the detector and the second emission spectral element. A method corresponding to the above system.
LIFE TECHNOLOGIES HOLDINGS PTE LIMITED (Singapore)
Inventor
Murakami, Marie
Bulloch, Kyle
Olson, Neil
Winnick, Ross
Teo, Wei Fuh
Thacker, Michael
Abstract
The present disclosure provides systems for gel electrophoresis and electrotransfer comprising one or more chambers (10a, 10b) that can removably and interchangeably receive either an electrophoresis cassette, or an electrotransfer cassette, and provides an electrical interface for both electrophoresis and electrotransfer of biomolecules. The present disclosure also provides electrophoresis devices including clamps and electrotransfer cassettes and related devices. Methods for electrophoresis and electrotransfer using the systems and devices of the disclosure are also 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
C07H 1/00 - Processes for the preparation of sugar derivatives
C12N 15/00 - Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
88.
METHODS AND COMPOSITIONS FOR CULTIVATING PLURIPOTENT CELL SUSPENSIONS
Described herein are cell culture media and/or cell culture media supplements that comprise at least one GSK3 inhibitor, a ROCK inhibitor, and one or more mitogenic growth factors, and methods of culturing and/or expanding pluripotent stem cells in 3D culture formats in the compositions described herein.
Embodiments of the invention are disclosed that implement deep learning methods using artificial neural networks to provide improved automated predictions regarding whether a particular sample comprises a target molecule. In some embodiments, a convolutional neural network is used. In some embodiments, an artificial neural network is trained using a class-weighted error determination. These and other embodiments are disclosed herein.
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
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
90.
BASECALLER WITH DILATED CONVOLUTIONAL NEURAL NETWORK
A method of automatically sequencing or basecalling one or more DNA (deoxyribonucleic acid) molecules of a biological sample is described. The method comprises using a capillary electrophoresis genetic analyzer to measure the biological sample to obtain at least one input trace comprising digital data corresponding to fluorescence values for a plurality of scans. Scan labelling probabilities for the plurality of scans are generated using a trained artificial neural network comprising a plurality of layers including convolutional layers. A basecall sequence comprising a plurality of basecalls for the one or more DNA molecules based on the scan labelling probabilities for the plurality of scans is determined.
Disclosed is a system for use in a flow cytometer for unclogging obstructions in a nozzle from salt crystal formations and clumps of cells or debris. A nozzle system is moved to a docking station so that a nozzle tip is seated in the docking station. Deionized water is pushed through the nozzle in a reverse direction to a waste port so that the nozzle is flushed. The nozzle system can remain in the docked position during nonuse so that salt crystals do not form in or on the nozzle.
A system for generating a low-pulsatility fluid flow comprises: a first pressurized reservoir (106); a second pressurized reservoir (126); a fluid sensor (128) that generates a quantity signal in response to an amount of the fluid in the second pressurized reservoir (126); a peristaltic fluid pump (118) for pumping fluid from the first pressurized reservoir (106) to the second pressurized reservoir (126); and a peristaltic air pump for pumping air between the first pressurized reservoir (106) and the second pressurized reservoir (126). The system is configured to modulate the operation of the peristaltic fluid pump (118) in response to the fluid quantity signal generated by the fluid sensor (128) so as to maintain a predetermined amount of fluid in the second pressurized reservoir (126), and configured to pump air between the first pressurized reservoir (106) and the second pressurized reservoir (126) so as to maintain both pressurized reservoirs (106, 126) at a substantially even pressure so that fluid pulsations are reduced. The corresponding method of generating a low-pulsatile fluid flow is also disclosed.
in vitro in vitro in vitro (e.g., for therapeutic purposes). When administered to subjects who are afflicted with COVID-19, the compositions provided herein may facilitate recovery and/or ameliorate symptoms cause by SARS-CoV-2.
A powder mixing system (12) includes a conduit (40) having a first end and an opposing second end, the conduit bounding a passage; a fluid pump (80) fluid coupled with the conduit, the fluid pump being configured to pump a liquid through the passage of the conduit; and a tubular transfer member (190) in fluid communication with the conduit, the transfer member being configured to couple with a powder bag housing a powder. The mixing system further including: (1) an eductor coupled to the transfer member and disposed in-line with the conduit so that the liquid pumped through the conduit also passes through the eductor; and/or (2) an auger assembly comprising an auger blade, at least a portion of the auger assembly being rotatably disposed within the transfer member.
Compositions, assays, methods, diagnostic methods, kits, and diagnostic kits are disclosed for the specific and differential detection of SARS-CoV-2 and/or other viruses from samples, including veterinary samples, clinical samples, food samples, forensic sample, environmental samples (e.g., obtained from soil, garbage, sewage, air, water, food processing and manufacturing surfaces, or likewise), or biological sample obtained from a human or non-human animal.
C12Q 1/70 - Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving virus or bacteriophage
97.
FLUID MIXING SYSTEMS WITH MODULAR IMPELLERS AND RELATED METHODS
A mixing system for mixing a liquid includes a first impeller segment (170A) having a first mount (172A) and a first mixing blade (174A) secured to the first mount (172A) and a second impeller segment (170B) having a second mount (172B) and a first mixing blade (174B) secured to the second mount (172B), the second impeller segment (170B) being separate and discrete from the first impeller segment (170A). One or more drive members are secured to the first impeller segment (170A) and the second impeller segment (170B) for concurrently rotating the first impeller segment (170A) and the second impeller segment (170B) about a rotational axis (171). The first impeller segment (170A) and the second impeller segment (170B) are secured to the one or more drive members so that a plane (210) extending normal to the axis (171) of rotation intersects with the first mixing blade (174A) of the first impeller segment (170A) and the first mixing blade (174A) of the second impeller segment (170B).
The present disclosure provides methods for predicting clinical response to therapy of a subject with an autoimmune disease or disorder and/or methods for predicting prognosis of a subject with immunodeficiency (e.g., leukemia) based on characterizing the B cell immune repertoire of the subject. In one aspect, methods provide for determining frequency of class switch recombination and/or somatic hypermutation of B cell receptor repertoires in samples prior to a treatment and predicting a subject's prognosis and/or response to treatment based on the measured class switching and/or somatic hypermutation frequency. In another aspect, methods provide for determination of immune receptor class switching and/or somatic hypermutation frequency and treating a subject based on the resulting prediction of prognosis and/or response to treatment based on the measured class switching and/or somatic hypermutation frequency.
C12Q 1/6881 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for tissue or cell typing, e.g. human leukocyte antigen [HLA] probes
99.
UMBRELLA CHECK VALVE ASSEMBLY HAVING RETENTION PLATE
A check valve assembly includes a first port fitting having a tubular stem with a passage extending therethrough and a second port fitting having a tubular stem with a passage extending therethrough. A base is secured between the first port fitting and the second port fitting, the base having an annular sleeve encircling a seat, the seat having a central mounting hole passing therethrough 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 of the sealing disk 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 of the base 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.
Purifying target biomolecules, such as nucleic acids or proteins, from a biological source is a time intensive process and is typically performed by a skilled technician or scientist owing to the highly technical nature of the work. Systems, devices, and methods disclosed herein enable the automated bioprocessing and purification of target biomolecules from a biological source. For example, an instrument and disposable cartridge are provided for automatedly isolating and purifying nucleic acids (such as plasmid DNA from a bacterial culture) or for isolating protein from any biological sample. Such an exemplary instrument and cartridge can work in concert to timely release, mix, and move the target biomolecule and various reagents and buffers through a target biomolecule purification process, resulting in a purified target biomolecule with less manual oversight than traditional approaches.
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