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Небесная энциклопедия

Космические корабли и станции, автоматические КА и методы их проектирования, бортовые комплексы управления, системы и средства жизнеобеспечения, особенности технологии производства ракетно-космических систем

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Мониторинг СМИ

Мониторинг СМИ и социальных сетей. Сканирование интернета, новостных сайтов, специализированных контентных площадок на базе мессенджеров. Гибкие настройки фильтров и первоначальных источников.

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28-06-2012 дата публикации

Simultaneous determination of aneuploidy and fetal fraction

Номер: US20120165203A1

Автор: David A. COMSTOCK, Gabrielle HEILEK, Manjula CHINNAPPA, Richard P. Rava, Stephen Quake

Принадлежит: Verinata Health Inc

The invention provides compositions and methods for simultaneously determining the presence or absence of fetal aneuploidy and the relative amount of fetal nucleic acids in a sample obtained form a pregnant female. The method encompasses the use of sequencing technologies and exploits the occurrence of polymorphisms to provide a streamlined noninvasive process applicable to the practice of prenatal diagnostics.

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Номер записи: 1

26-07-2012 дата публикации

Assembly Error Detection

Номер: US20120191356A1

Автор: Laxmi P. Parida, Niina Haiminen

Принадлежит: International Business Machines Corp

A method for detecting errors in genetic sequence assemblies including defining an assembly (A) of a sequence of genetic data, collecting read data into a library of reads (L), plotting histograms of sizes or reads versus a number of reads per size, normalizing a distribution (D) with a coverage C to obtain D′ that has a mean (μ) and standard deviation (σ) and reserve positions (i) not used to obtain D′, collecting subset of reads (S i □ L) using A and D′, computing mean (μ i ) and standard deviation (√c i ·σ i ) using S i , outputting results to user on a display.

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Номер записи: 2

07-02-2013 дата публикации

Mitochondrial enhancement of cells

Номер: US20130034527A1

Автор: Lowell L. Wood, Roderick A. Hyde

Принадлежит: SEARETE LLC

Certain embodiments disclosed herein include, but are not limited to, at least one of compositions, methods, devices, systems, kits, or products regarding rejuvenation or preservation of stem cells. Certain embodiments disclosed herein include, but are not limited to, methods of modifying stem cells, or methods of administering modified stem cells to at least one biological tissue.

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Номер записи: 3

11-04-2013 дата публикации

Digital Holographic Method of Measuring Cellular Activity and Measuring Apparatus with Improved Stabililty

Номер: US20130088568A1

Автор: David D. Nolte

Принадлежит: PURDUE RESEARCH FOUNDATION

Motility contrast imaging (MCI) is a depth-resolved holographic technique to extract cellular and subcellular motion inside tissue. The holographic basis of the measurement technique makes it highly susceptible to mechanical motion. The motility contrast application, in particular, preferably includes increased mechanical stability because the signal is based on time-varying changes caused by cellular motion, which should not be confused with mechanical motion of the system. Apparatus for motility contrast imaging that provides increased mechanical stability is disclosed. It is based on common-path configurations, in which the signal and reference beams share optical elements in their paths to the detector. The two beams share mechanical motions in common, and hence these motions do not contribute to the signal.

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Номер записи: 4

18-04-2013 дата публикации

Digital Holographic Method of Measuring Cellular Activity and of Using Results to Screen Compounds

Номер: US20130096017A1

Автор: David D. Nolte, Kwan Jeong

Принадлежит: PURDUE RESEARCH FOUNDATION

Motility contrast imaging (MCI) is a depth-resolved holographic technique to extract cellular and subcellular motion inside tissue. The holographic basis of the measurement technique makes it highly susceptible to mechanical motion. The motility contrast application, in particular, preferably includes increased mechanical stability because the signal is based on time-varying changes caused by cellular motion, not to be confused with mechanical motion of the system. The use of the resulting spectrogram response signatures, or “fingerprint” data, of known compounds is disclosed to screen new compounds for leads as to those having potentially beneficial mechanisms of action. The “fingerprint” data of known toxic compounds can be used to screen new compounds for toxicity.

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Номер записи: 5

02-05-2013 дата публикации

Biological information processing method and device, recording medium and program

Номер: US20130110409A1

Автор: Kazuhiro Sakurada

Принадлежит: Sony Corp

Provided is a biological information processing method and a device, a recording medium and a program that are able to predict and control changes in the state of an organism. The expression level of molecules in an organism is measured over a specific time interval; the measured time-series data is divided into a periodic component, an environmental stimulus response component and a baseline component; constant regions of the time-series data are identified from variations in the baseline component or from the amplitude or periodic variations of the periodic component; and causal relation between the identified constant regions is identified. The relation between the external environment and variations in the internal environment is identified and from the identified causal relation between the constant regions, changes in the state of the organism are inferred.

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Номер записи: 6

30-05-2013 дата публикации

System and method including analytical units

Номер: US20130137110A1

Автор: Charles S. Kraihanzel

Принадлежит: Beckman Coulter Inc

Systems and methods for processing and analyzing samples are disclosed. The system may process samples, such as biological fluids, using assay cartridges which can be processed at different processing locations. In some cases, the system can be used for PCR processing. The different processing locations may include a preparation location where samples can be prepared and an analysis location where samples can be analyzed. To assist with the preparation of samples, the system may also include a number of processing stations which may include processing lanes. During the analysis of samples, in some cases, thermal cycler modules and an appropriate optical detection system can be used to detect the presence or absence of certain nucleic acid sequences in the samples. The system can be used to accurately and rapidly process samples.

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Номер записи: 7

27-06-2013 дата публикации

Fluid injection and safety system

Номер: US20130160532A1

Автор: Eugene Lim, Gil Rivas, Jeffrey T. Chiou, Michael Butler

Принадлежит: Optiscan Biomedical Corp

Various medical systems and methods are described, including a medical monitoring system. The medical monitoring system can have a fluid system configured to receive bodily fluid and optically analyze said fluid to determine analyte concentration. The fluid system can have a removable portion. The removable portion can have an opening with a port. The system can also have a container configured to contain anticoagulant. The container can have a portion configured to mate with the port of the removable portion. The container can be further configured to not fit into a conventional luer fitting. An anti-coagulant insertion apparatus is also described. The apparatus can have a syringe, a dock with a port, and an adapter configured to connect the syringe to the port. The dock can also have a tab configured to move with the port.

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Номер записи: 8

15-08-2013 дата публикации

System and method including analytical units

Номер: US20130209334A1

Автор: Alan N. Johnson, Brian D. Wilson, Daniel R. Schmidt, David L. Anderson, Joshua D. Wiltsie, Matthew D. Erickson, Michael J. Rosen

Принадлежит: Beckman Coulter Inc

Systems and methods for processing and analyzing samples are disclosed. The system may process samples, such as biological fluids, using assay cartridges which can be processed at different processing locations. In some cases, the system can be used for PCR processing. The different processing locations may include a preparation location where samples can be prepared and an analysis location where samples can be analyzed. To assist with the preparation of samples, the system may also include a number of processing stations which may include processing lanes. During the analysis of samples, in some cases, thermal cycler modules and an appropriate optical detection system can be used to detect the presence or absence of certain nucleic acid sequences in the samples. The system can be used to accurately and rapidly process samples.

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Номер записи: 9

26-09-2013 дата публикации

Method and system for detection of microbial growth in a specimen container

Номер: US20130252271A1

Автор: Michael Ullery

Принадлежит: Biomerieux Inc

A method for determining whether microbial growth is occurring within a specimen container includes steps of incubating the specimen container and obtaining a series of measurement data points while the specimen container is incubated and storing the data points in a machine-readable memory. The series of measurement data points represent a growth curve of microbial growth within the specimen container. The methods determine a positive condition of microbial growth within the container from the measurement data points.

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Номер записи: 10

27-03-2014 дата публикации

Information Processing Method

Номер: US20140088881A1

Автор: Babak Amirparviz, Ehsan Saeedi

Принадлежит: Google LLC

Systems, apparatus and methods including a contact lens that facilitates collection and/or processing of information associated with sensed features are provided. In one aspect, a system can include a contact lens and an analysis component external to the contact lens. The contact lens can include: a substrate; and a circuit, disposed on or within the substrate. The circuit can include: a plurality of sensors configured to sense respective features associated with a wearer of the contact lens; and a communication component configured to communicate information indicative of sensed features. The analysis component can be configured to: receive the information indicative of the sensed features; and generate statistical information based, at least, on the information indicative of the sensed features.

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Номер записи: 11

06-01-2022 дата публикации

Systems And User Interface For Collecting A Data Set In A Flow Cytometer

Номер: US20220003658A1

Автор: Rich Collin A.

Принадлежит:

Systems in a flow cytometer having an interrogation zone and illumination impinging the interrogation zone include: a lens subsystem including a collimating element that collimates light from the interrogation zone, a light dispersion element that disperses collimated light into a light spectrum, and a focusing lens that focuses the light spectrum onto an array of adjacent detection points; a detector array, including semiconductor detector devices, that collectively detects a full spectral range of input light signals, in which each detector device detects a subset spectral range of the full spectral range of light signals; and a user interface that enables a user to create a set of virtual detector channels by grouping detectors in the detector array, such that each virtual detector channel corresponds to a detector group and has a virtual detector channel range including the sum of subset spectral ranges of the detectors in the corresponding detector group. 19-. (canceled)10. A light detection system comprising:a plurality of user-configurable groups of photodetectors; anda plurality of detector channels, wherein each detector channel is assigned to one or more of the user-configurable groups of photodetectors.11. The light detection system according to claim 10 , wherein the light detection system is configured to:detect light from a sample irradiated with a light source; andgenerate a data signal from the detected light.12. The light detection system according to claim 11 , wherein the light detection system is operably coupled to a processor comprising memory having instructions stored thereon claim 11 , which when executed by the processor claim 11 , cause the processor to assign each detector channel to a user-configurable group of photodetectors before generating a data signal from the light detected from the irradiated sample.13. The light detection system according to claim 11 , wherein the light detection system is operably coupled to a processor ...

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Номер записи: 12

02-01-2020 дата публикации

MOLECULAR PROFILING OF TUMORS

Номер: US20200003796A1

Автор: Alarcon Arlet, Bender Ryan P., Loesch David M., McGinniss Matthew J., Pawlowski Traci, PENNY Robert J., von Hoff Daniel D., Wright Alan

Принадлежит:

Provided herein are methods and systems of molecular profiling of diseases, such as cancer. In some embodiments, the molecular profiling can be used to identify treatments for a disease, such as treatments that were not initially identified as a treatment for the disease or not expected to be a treatment for a particular disease. 1. A system for generating a report identifying at least one therapeutic agent for an individual with a cancer comprising:a. at least one device configured to assay a plurality of molecular targets in a biological sample from the individual to determine molecular profile test values for each of the plurality of molecular targets, wherein the molecular targets comprise ERBB2, PTEN, TOP2A, TOPO1 and TS; and i. a reference value for each of the plurality of molecular targets; and', 'ii. a listing of therapeutic agents with efficacy linked to a biological state of at least one member of the plurality of molecular targets;, 'b. at least one computer database comprisingc. a computer-readable program code comprising instructions to input the molecular profile test values and to compare each molecular profile test value with a corresponding reference value in (b)(i) to identify a biological state for each member of the plurality of molecular targets;d. a computer-readable program code comprising instructions to identify at least one therapeutic agent from the listing of therapeutic agents in (b)(ii), wherein the biological state identified in (c) for at least one member of the plurality of molecular targets provides an indication of likely benefit of the at least one therapeutic agent for treating the cancer; ande. a computer-readable program code comprising instructions to generate a report that comprises a listing of the at least one therapeutic agent identified in (d) and the biological state of each molecular target with efficacy linked thereto.2. The system of claim 1 , wherein the molecular profile test values are input into the system from a ...

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Номер записи: 13

18-01-2018 дата публикации

Systems and methods for nucleic acid-based identification

Номер: US20180018422A1

Автор: Chien-Wei Chang, Lori Hennessy, Robert Lagace

Принадлежит: Life Technologies Corp

Systems and methods for calculating a predictive index of identity of a nucleic acid sample using polymorphic genetic marker data are provided. In one embodiment, a predictive index of identity of the nucleic acid sample is calculated using a value from a second set of data from a polymorphic genetic marker that is not linked to a polymorphic genetic marker used to produce a first set of data. In another embodiment, the predictive index of identity is calculated using a value from a second set of data from a polymorphic genetic marker that is linked to a polymorphic genetic marker used to produce the first set of data. Systems and methods for generating an identifier for a biological sample and for verifying a relationship between a biological sample and an identifier are also provided. The identifier is an encoding of a set of values for polymorphic genetic markers.

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Номер записи: 14

21-01-2021 дата публикации

Personalized genetic testing

Номер: US20210017603A1

Автор: Christian Haudenschild, John West, Richard Chen

Принадлежит: Personalis Inc

The present disclosure provides methods and systems for personalized genetic testing of a subject. In some embodiments, a sequencing assay is performed on a biological sample from the subject, which then leads to genetic information related to the subject. Next, nucleic acid molecules are array-synthesized or selected based on the genetic information derived from data of the sequencing assay. At least some of the nucleic acid molecules may then be used in an assay which may provide additional information on one or more biological samples from the subject or a biological relative of the subject.

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Номер записи: 15

24-01-2019 дата публикации

Methods for fluorescence data correction

Номер: US20190026426A1

Автор: Martin Reijans, Wouter UTEN, Yves Antonius OZOG

Принадлежит: UgenTec NV

Method of processing real-time PCR data, comprising: c) receiving a plurality of fluorescence melting curve data of real time PCR-experiments performed by a real-time PCR device with at least two fluorescence channels, and configured to perform the following steps multiple times, while increasing a temperature: i) at first moments in time measuring a first temperature value and a first radiation value corresponding to a first fluorescence channel; ii) at second moments in time measuring a second temperature value and a second radiation value corresponding to a second fluorescence channel; d) storing the plurality of temperature values and radiation values; e) determining a plurality of time-shifted second radiation values by linearly interpolating between two measured second radiation values, using weighting factors defined by the measured temperature values; f) after performing step e), calculating color corrected first radiation values, and color corrected second radiation values.

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Номер записи: 16

23-01-2020 дата публикации

Rational design of microbial-based biotherapeutics

Номер: US20200027524A1

Автор: Danièl van der Lelie, Safiyh Taghavi

Принадлежит: Gusto Global LLC

Methods are provided for the rational design of stable communities of microbes for benefiting the health of a host organism, including human and/or animal health. The methods describe design of microbial consortia based on providing and/or complementing key functionalities lacking or underrepresented in the microbiome of an organism having a disorder or disease as compared to healthy subjects. The consortia are designed to possess metabolic interdependencies for improved engrafting, stability and performance of the consortium. Compositions that include the designed microbial consortia are provided for treatment of disorders/diseases involving chronic inflammation, infection, and the combination of chronic inflammation and infection including inflammatory bowel disease and related disorders. The compositions are also broadly applicable for the treatment of neurological, metabolic and oncology-related conditions.

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Номер записи: 17

24-04-2014 дата публикации

Using aggregated sensed data of individuals to predict whether an individual requires assistance from a responder

Номер: US20140115008A1

Автор: David Andre, Eric Teller, John A. Monocello, III, John M. Stivoric

Принадлежит: Bodymedia Inc

The methods and systems described herein may involve determining at least one lifeotype of at least one individual, analyzing the at least one lifeotype, and delivering content to at least one individual based on the analysis. The methods and systems described herein may involve providing a game, determining at least one lifeotype of at least one player of the game, analyzing the at least one lifeotype, and affecting the game play based on the analysis. The methods and systems described herein may involve providing an interactive space, determining at least one lifeotype of at least one individual in the space, analyzing the at least one lifeotype, and modifying at least one attribute of the space based on the analysis.

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Номер записи: 18

01-05-2014 дата публикации

Analysis system for analyzing biological samples, methods, and computer program product thereof

Номер: US20140117089A1

Автор: Anton Steimle, Bernhard Von Allmen

Принадлежит: Roche Diagnostics Operations Inc

An analysis system for analyzing biological samples, such as body fluids, methods implemented by the analysis system, and a computer program product for implementing the analysis system are disclosed. The system may include first and second lab devices, at least one of the lab devices may have a user identification component for identifying a user, a device identification component for identifying the lab device, and an interface component for sending a user identifier of the identified user and a device identifier of the lab device. The system may include a server computer having a server interface component for receiving the user identifier and the device identifier, and a processing component for determining a step of a workflow to be executed by the identified user, wherein the server interface component is operable to send a signal being indicative of a determined workflow to the lab device identified by the device identifier.

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Номер записи: 19

17-02-2022 дата публикации

Methods and Systems for Providing Labelled Biomolecules

Номер: US20220050097A1

Автор: Brent S. Gaylord, Eric Jensen, John Archdeacon, Olaf Zoellner

Принадлежит: Becton Dickinson and Co

Aspects of the present disclosure include systems for use in preparing a labelled biomolecule reagent. Systems according to certain embodiments include an input manager for receiving a request for a labelled biomolecule reagent, a memory for storing a dataset having a plurality of labelled biomolecule reagent storage identifiers, a processing module communicatively coupled to the memory and configured to identify one or more labelled biomolecule reagent storage identifiers from the dataset that corresponds to the labelled biomolecule reagent request and an output manager for providing the one or more identified labelled biomolecule reagent storage identifiers. A reagent preparatory apparatus for preparing the labelled biomolecule reagent from an activated biomolecule and activated label is also described. Methods for communicating and receiving a labelled biomolecule reagent request and preparing the subject labelled biomolecule reagents are also provided.

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Номер записи: 20

17-02-2022 дата публикации

Method to Use Gene Expression to Determine Likelihood of Clinical Outcome of Renal Cancer

Номер: US20220051755A9

Автор: BAEHNER Frederick L., BAKER Joffre, Cowens Wayne, Goddard Audrey, Kiefer Michael C., Knezevic Dejan, Maddala Tara, Shak Steven

Принадлежит: GENOMIC HEALTH, INC.

The present disclosure provides gene and gene sets, the expression of which is important in the classification and/or prognosis of cancer, in particular of renal cell carcinoma. 116.-. (canceled)17. A method of analyzing the expression of RNA transcripts of genes in a human renal cancer patient , the method comprising:measuring levels of RNA transcripts, in a renal tumor sample from the patient, of a panel of genes consisting of:a set of genes consisting of one or more angiogenesis genes selected from: ADD1, ANGPTL3, APOLD1, CEACAM1, EDNRB, EMCN, ENG, EPAS1, FLT1, JAG1, KDR, KL, LDB2, NOS3, NUDT6, PPAP2B, PRKCH, PTPRB, RGS5, SHANK3, SNRK, TEK, ICAM2, and VCAM1;a set of genes consisting of one or more immune response genes selected from: CCL5, CCR7, CD8A, CX3CL1, CXCL10, CXCL9, HLA-DPB1, IL6, IL8, and SPP1; anda set of genes consisting of one or more cell cycle genes selected from: BUB1, C13orf15, CCNB1, PTTG1, TPX2, LMNB1, and TUBB2A;EIF4BP1; anda set of genes consisting of one or more reference genes.18. The method of claim 17 , wherein the renal cancer is renal cell carcinoma (RCC).19. The method of claim 17 , wherein the RCC is clear cell renal cell carcinoma (ccRCC).20. The method of claim 17 , wherein the level of the RNA transcripts is measured by quantitative RT-PCR.21. The method of claim 17 , wherein the renal tumor sample is paraffin-embedded and fixed.22. The method of claim 17 , wherein the panel comprises at least two angiogenesis genes claim 17 , at least two immune response genes claim 17 , and at least two cell cycle genes.23. The method of claim 17 , wherein the at least one reference gene is selected from the group consisting of: AAMP claim 17 , ARF1 claim 17 , ATP5E claim 17 , EEF1A1 claim 17 , GPX1 claim 17 , RPS23 claim 17 , SDHA claim 17 , UBB claim 17 , RPLP1 claim 17 , GAPDH claim 17 , and beta-actin.24. A method of analyzing the expression of RNA transcripts of genes in a human renal cancer patient claim 17 , the method comprising:measuring ...

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Номер записи: 21

24-02-2022 дата публикации

METHODS AND SYSTEMS FOR GENETIC ANALYSIS

Номер: US20220056521A1

Автор: Bartha Gabor T., Chandratillake Gemma, Chen Richard, Garcia Sarah, Lam Hugo Yu Kor, Luo Shujun, Pratt Mark R., West John

Принадлежит:

This disclosure provides systems and methods for sample processing and data analysis. Sample processing may include nucleic acid sample processing and subsequent sequencing. Some or all of a nucleic acid sample may be sequenced to provide sequence information, which may be stored or otherwise maintained in an electronic storage location. The sequence information may be analyzed with the aid of a computer processor, and the analyzed sequence information may be stored in an electronic storage location that may include a pool or collection of sequence information and analyzed sequence information generated from the nucleic acid sample. Methods and systems of the present disclosure can be used, for example, for the analysis of a nucleic acid sample, for producing one or more libraries, and for producing biomedical reports. Methods and systems of the disclosure can aid in the diagnosis, monitoring, treatment, and prevention of one or more diseases and conditions. 1. A method of analyzing a nucleic acid sample isolated from a biological sample of an individual to detect a presence or an absence of cancer , comprising(a) contacting said nucleic acid sample with one or more capture probe sets to produce one or more capture probe hybridized nucleic acid molecules, wherein said one or more capture probe sets are configured to selectively enrich for an exome;(b) conducting one or more sequencing reactions on said one or more capture probe hybridized nucleic acid molecules to produce one or more sequencing reads;(c) analyzing said one or more sequencing reads, with the aid of a computer processor, to produce a unified assessment of a genetic state of said nucleic acid sample at each locus addressed by said sequencing reaction; and(d) generating a biomedical report that includes biomedical information of said subject, which biomedical information is indicative of said genetic state.2. The method of claim 1 , wherein said biomedical information of said subject is predictive claim ...

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Номер записи: 22

18-02-2021 дата публикации

METHODS AND SYSTEMS FOR GENETIC ANALYSIS

Номер: US20210047687A1

Автор: Bartha Gabor T., Chandratillake Gemma, Chen Richard, Garcia Sarah, Lam Hugo Yu Kor, Luo Shujun, Pratt Mark R., West John

Принадлежит:

This disclosure provides systems and methods for sample processing and data analysis. Sample processing may include nucleic acid sample processing and subsequent sequencing. Some or all of a nucleic acid sample may be sequenced to provide sequence information, which may be stored or otherwise maintained in an electronic storage location. The sequence information may be analyzed with the aid of a computer processor, and the analyzed sequence information may be stored in an electronic storage location that may include a pool or collection of sequence information and analyzed sequence information generated from the nucleic acid sample. Methods and systems of the present disclosure can be used, for example, for the analysis of a nucleic acid sample, for producing one or more libraries, and for producing biomedical reports. Methods and systems of the disclosure can aid in the diagnosis, monitoring, treatment, and prevention of one or more diseases and conditions. 129.-. (canceled)30. A method for sequencing a nucleic acid sample isolated from a body fluid of an individual , comprising: (i) exons,', '(ii) untranslated regions (UTRs), and', '(iii) one or more splice sites, one or more intronic regions, one or more regulatory regions, or a combination thereof; and, '(a) contacting said nucleic acid sample with one or more capture probe sets to produce one or more capture probe hybridized nucleic acid molecules, wherein said one or more capture probe sets are configured to selectively enrich for an exome, wherein said exome comprises(b) conducting one or more sequencing reactions on said one or more capture probe hybridized nucleic acid molecules to produce one or more sequencing reads.31. The method of claim 30 , wherein said one or more sequencing reactions produces at least 1 claim 30 ,000 claim 30 ,000 claim 30 ,000 sequencing reads.32. The method of claim 30 , wherein said one or more sequencing reads comprise paired end reads of at least 2×150 nucleotides.33. The ...

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Номер записи: 23

06-02-2020 дата публикации

SYSTEMS AND METHODS FOR ERROR CORRECTION IN DNA SEQUENCING

Номер: US20200043568A1

Автор: BLANCHARD ALAN, SIKORA Marcin

Принадлежит:

Disclosed are systems and methods for polynucleotide sequencing where detection and correction of base calling errors can be achieved without reliance on a reference sequence. In certain embodiments, redundant information can be introduced during measurement so as to allow such detection of errors. Such redundant information and measurements can be facilitated by encoding of nucleotide sequence being measured. Various examples of such encoding, redundancy introduction, and decoding are provided. 1. A method for configuring a detectable probe for sequencing a polynucleotide , comprising:arranging, using a processor, a number K of bases, each base being one of nucleotides A, C, G, and T;determining a number X of rounds of interrogation, a number N of different types of detectable labels in a set of detectable labels, a number S of offsets of the detectable probe relative to the polynucleotide, and a number of M measureable characteristics, wherein a combination of X, N, S and M meet a redundancy condition;assigning one or more detectable labels of the set of detectable labels to said arrangement of bases to form a labeled arrangement of bases; andgenerating the detectable probe using the labeled arrangement of bases.2. The method of claim 1 , wherein the assigning step assigns one detectable label to said arrangement of bases.3. The method of claim 1 , wherein the set of detectable labels comprises four or more different dyes.4. The method of claim 2 , wherein said one detectable label comprises one of four different dyes.5. The method of claim 4 , wherein said assigning of said label to said arrangement of bases further comprises:transforming said arrangement of bases to a numerical representation based on a map associating the bases A, C, G, and T with numerical values;multiplying the numerical representation and a generator vector based on a Galois field GF(4) multiplication table to form members of a product sequence;adding the members of the product sequence ...

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Номер записи: 24

03-03-2022 дата публикации

Lung Cancer Biomarkers and Uses Thereof

Номер: US20220065872A1

Автор: Brody Edward N., Ostroff Rachel M., Riel-Mehan Michael, STEWART Alex A. E., Williams Stephen Alaric

Принадлежит: SomaLogic, Inc.

The present application includes biomarkers, methods, devices, reagents, systems, and kits for the detection and diagnosis of non-small cell lung cancer and general cancer. In one aspect, the application provides biomarkers that can be used alone or in various combinations to diagnose non-small cell lung cancer or general cancer. In another aspect, methods are provided for diagnosing non-small cell lung cancer in an individual, where the methods include detecting, in a biological sample from an individual, at least one biomarker value corresponding to at least one biomarker selected from the group of biomarkers provided in Table 1, wherein the individual is classified as having lung cancer, or the likelihood of the individual having lung cancer is determined, based on the at least one biomarker value. In another aspect, methods are provided for diagnosing cancer in an individual, where the methods include detecting, in a biological sample from an individual, at least one biomarker value corresponding to at least one biomarker selected from the group of biomarkers provided in Table 19, wherein the individual is classified as having cancer, or the likelihood of the individual having cancer is determined, based on the at least one biomarker value.

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Номер записи: 25

13-02-2020 дата публикации

Method for Characterizing a Sample by Data Analysis

Номер: US20200051669A1

Автор: Huber Fritz, Kirchhöfer Renate, Pfahlert Volker

Принадлежит:

A method for characterizing a sample is disclosed, having the following steps: providing at least one analysis result having a plurality of values, wherein the analysis result was generated by the analysis of a sample by at least one analysis method; determining the value of at least one mathematic relation between at least two values of the plurality of values; generating a characterizing signature of the sample on the basis of the value of the at least one mathematic relation. Furthermore, a method for characterizing a system is disclosed in which method the preceding method is used. 1. A method for characterizing a system , comprising the following steps:providing a first analysis result having a plurality of values, wherein the first analysis result was generated by an analysis of a first sample taken from a system by an analysis method chosen from a group consisting of NMR spectroscopy, mass spectrometry, electron spin resonance, vibrational spectroscopy, UV/VIS spectroscopy, and fluorescence spectroscopy;determining a first set of values of a quotient between pairs of two values of a first plurality of values; a) determining a first deviation between the first set of values of the quotient and a first average correlation matrix that has been obtained by summing up a plurality of a second set of values of a quotient, wherein the second set of values of the quotient has been obtained by providing a second analysis result having a second plurality of values, wherein the second analysis result method is the same analysis used for the first analysis result, and determining the second set of values of a quotient between the first set of values;', 'b) determining a second deviation between the first set of values of the quotient and a second average correlation matrix that has been obtained by summing up a plurality of a third set of values of a quotient, wherein the third set of values of the quotient has been obtained by providing a third analysis result having a ...

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Номер записи: 26

10-03-2022 дата публикации

MICROBIAL STRAIN DESIGN SYSTEM AND METHODS FOR IMPROVED LARGE-SCALE PRODUCTION OF ENGINEERED NUCLEOTIDE SEQUENCES

Номер: US20220076177A1

Автор: FREWEN Barbara, KIMBALL Aaron

Принадлежит: Zymergen Inc.

The generation of a factory order includes receiving an expression indicating an operation on a first sequence operand and a second sequence operand. The first sequence operand represents multiple biological sequence parts, and the second sequence operand represents at least one biological sequence part. The expression is evaluated to a sequence specification, which represents modifications to at least one biological sequence, and comprises a data structure representing (a) the first and second sequence operands, (b) one or more first-level operations to be performed on one or more first-level sequence operands, and (c) one or more second-level operations, the execution of at least one of which resolves values of at least one of the first-level sequence operands. A factory order is generated based upon execution of at least one first-level operation and at least one second-level operation. 172.-. (canceled)73. A method comprising:(i) receiving, at a computing device, an expression indicating an operation on a first sequence operand and a second sequence operand, wherein the first sequence operand represents a plurality of biological sequence parts, and the second sequence operand represents at least one biological sequence part;(ii) executing, by a computing device, instructions to evaluate the expression to a sequence specification, wherein the sequence specification comprises a data structure representing (a) the first and second sequence operands, (b) one or more first-level operations to be performed on one or more first-level sequence operands, and (c) one or more second-level operations, the execution of at least one of which resolves a plurality of values of at least one of the one or more first-level sequence operands, wherein the sequence specification represents modifications to one or more biological sequences; and(iii) generating a factory order based upon execution, by a computing device, of one or more of the first-level operations and one or more of ...

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Номер записи: 27

04-03-2021 дата публикации

METHODS AND SYSTEMS FOR GENETIC ANALYSIS

Номер: US20210062258A1

Автор: Bartha Gabor T., Chandratillake Gemma, Chen Richard, Garcia Sarah, Lam Hugo Yu Kor, Luo Shujun, Pratt Mark R., West John

Принадлежит:

This disclosure provides systems and methods for sample processing and data analysis. Sample processing may include nucleic acid sample processing and subsequent sequencing. Some or all of a nucleic acid sample may be sequenced to provide sequence information, which may be stored or otherwise maintained in an electronic storage location. The sequence information may be analyzed with the aid of a computer processor, and the analyzed sequence information may be stored in an electronic storage location that may include a pool or collection of sequence information and analyzed sequence information generated from the nucleic acid sample. Methods and systems of the present disclosure can be used, for example, for the analysis of a nucleic acid sample, for producing one or more libraries, and for producing biomedical reports. Methods and systems of the disclosure can aid in the diagnosis, monitoring, treatment, and prevention of one or more diseases and conditions. 129.-. (canceled)30. A method for analyzing a nucleic acid sample isolated from a body fluid of an individual , comprising:(a) producing, with the aid of a computer processor, one or more capture probes, wherein the one or more capture probes are configured to hybridize to one or more polymorphisms, wherein the one or more polymorphisms are: (i) based on or extracted from one or more databases of polymorphisms, (ii) observed in a population of one or more samples, or (iii) a combination thereof;(b) contacting said nucleic acid sample with said one or more capture probes to produce one or more capture probe hybridized nucleic acid molecules; and(c) conducting a first assay on said one or more capture probe hybridized nucleic acid molecules, thereby analyzing the nucleic acid sample, wherein the first assay comprises a sequencing reaction.31. The method of claim 30 , wherein said sequencing reaction produces at least 1 claim 30 ,000 claim 30 ,000 claim 30 ,000 sequencing reads.32. The method of claim 30 , wherein ...

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Номер записи: 28

20-02-2020 дата публикации

METHOD OF DIAGNOSING CANCER USING MITOCHONDRIAL DNA HETEROGENEITY

Номер: US20200058398A1

Автор: Campo David S.

Принадлежит:

The present invention relates to diagnosing cancer based on measurements of sequence heterogeneity in mitochondrial genomic DNA. 1. A method of diagnosing a cancer in a patient , comprising:(a) providing a heterogeneity profile of mitochondrial DNA (mtDNA) obtained from a sample from a patient, wherein the heterogeneity profile comprises a level of genetic heterogeneity quantified at one or more nucleotide positions of a mtDNA genome;(b) classifying the patient heterogeneity profile as cancer-positive or cancer-negative based on the result of a machine learning classifier; and(c) diagnosing the presence or absence of cancer in the patient based on the classification.2. The method of claim 1 , wherein the machine learning algorithm is a random forest claim 1 , which has been trained with a data set comprising heterogeneity profiles of mtDNA genomes from positive control subjects diagnosed with the cancer and heterogeneity profiles of mtDNA genomes from negative control subjects diagnosed as not having the cancer;3. The method of claim 2 , wherein the level of genetic heterogeneity at each nucleotide position of the mtDNA genome from each patient and control subject is quantified by calculating Shannon entropy.4. The method of claim 3 , wherein the level of genetic heterogeneity at each nucleotide position is quantified by transforming the Shannon entropy level into a Z-score.5. The method of claim 1 , wherein the cancer is liver cancer.6. The method of claim 5 , wherein the liver cancer is hepatocellular carcinoma.7. The method of claim 2 , wherein the heterogeneity profiles comprise levels of entropy quantified at each nucleotide position of the mtDNA genomes of the patient claim 2 , the positive control subjects claim 2 , and the negative control subjects claim 2 , and wherein the mtDNA genomes are sequenced using next-generation sequencing.8. A system comprising:a memory; andat least one computing device to:obtain heterogeneity profile data including data ...

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Номер записи: 29

17-03-2022 дата публикации

PERSONALIZED GENETIC TESTING

Номер: US20220081716A1

Автор: Chen Richard, Haudenschild Christian, West John

Принадлежит:

The present disclosure provides methods and systems for personalized genetic testing of a subject. In some embodiments, a sequencing assay is performed on a biological sample from the subject, which then leads to genetic information related to the subject. Next, nucleic acid molecules are array-synthesized or selected based on the genetic information derived from data of the sequencing assay. At least some of the nucleic acid molecules may then be used in an assay which may provide additional information on one or more biological samples from the subject or a biological relative of the subject. 130-. (canceled)31. A method for personalized genetic testing , comprising:(a) sequencing nucleic acid molecules from at least one biological sample of a subject to generate sequencing data;(b) computer processing said sequencing data to identify a plurality of nucleic acid sequences having a set of genetic variants, wherein a genetic variant of said set of genetic variants is identified based on a number of reads comprising said genetic variant which exceed a first threshold;(c) obtaining a probe set comprising a plurality of nucleic acid probe molecules having said plurality of nucleic acid sequences or complements thereof, wherein said plurality of nucleic acid probe molecules are configured to selectively enrich or amplify sequences comprising said set of genetic variants over other sequences in said at least one biological sample;(d) using said probe set to selectively enrich or amplify sequences comprising said set of genetic variants over other sequences in an additional biological sample from said subject, to generate a sequencing library; and(e) subjecting said sequencing library to sequencing to identify a presence or absence of at least a subset of said set of genetic variants in said additional biological sample from said subject, wherein said genetic variant of said set of genetic variants is identified as present based on a number of reads comprising said ...

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Номер записи: 30

19-03-2015 дата публикации

Molecular profiling of tumors

Номер: US20150080268A1

Автор: Alan Wright, Arlet Alarcon, Daniel D. Von Hoff, David M. Loesch, Matthew J. McGinniss, Robert J. Penny, Ryan P. Bender, Traci Pawlowski

Принадлежит: Caris MPI Inc

Provided herein are methods and systems of molecular profiling of diseases, such as cancer. In some embodiments, the molecular profiling can be used to identify treatments for a disease, such as treatments that were not initially identified as a treatment for the disease or not expected to be a treatment for a particular disease.

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Номер записи: 31

18-03-2021 дата публикации

Normalizing chromosomes for the determination and verification of common and rare chromosomal aneuploidies

Номер: US20210082538A1

Автор: Richard P. Rava

Принадлежит: Verinata Health Inc

The present invention provides a method capable of detecting single or multiple fetal chromosomal aneuploidies in a maternal sample comprising fetal and maternal nucleic acids, and verifying that the correct determination has been made. The method is applicable to determining copy number variations (CNV) of any sequence of interest in samples comprising mixtures of genomic nucleic acids derived from two different genomes, and which are known or are suspected to differ in the amount of one or more sequence of interest. The method is applicable at least to the practice of noninvasive prenatal diagnostics, and to the diagnosis and monitoring of conditions associated with a difference in sequence representation in healthy versus diseased individuals.

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Номер записи: 32

31-03-2022 дата публикации

METHODS AND SYSTEMS FOR GENETIC ANALYSIS

Номер: US20220098662A1

Автор: Bartha Gabor T., Chandratillake Gemma, Chen Richard, Garcia Sarah, Lam Hugo Yu Kor, Luo Shujun, Pratt Mark R., West John

Принадлежит:

This disclosure provides systems and methods for sample processing and data analysis. Sample processing may include nucleic acid sample processing and subsequent sequencing. Some or all of a nucleic acid sample may be sequenced to provide sequence information, which may be stored or otherwise maintained in an electronic storage location. The sequence information may be analyzed with the aid of a computer processor, and the analyzed sequence information may be stored in an electronic storage location that may include a pool or collection of sequence information and analyzed sequence information generated from the nucleic acid sample. Methods and systems of the present disclosure can be used, for example, for the analysis of a nucleic acid sample, for producing one or more libraries, and for producing biomedical reports. Methods and systems of the disclosure can aid in the diagnosis, monitoring, treatment, and prevention of one or more diseases and conditions. 1. A method for analyzing nucleic acid samples isolated from an individual , comprising:(a) generating a first subset of nucleic acid molecules from a first nucleic acid sample obtained from said individual;(b) conducting a first sequencing assay on said first subset of nucleic acid molecules to yield a first result comprising a first nucleic acid sequence wherein said first sequencing assay comprises whole genome sequencing;(c) generating a second subset of nucleic acid molecules from a second nucleic acid sample of said individual by contacting said second nucleic acid sample with a plurality of capture probes, wherein said plurality of capture probes hybridize to one or more polymorphisms which are based on or extracted from one or more databases of polymorphisms, observed in a population of one or more samples, or a combination thereof;(d) conducting a second sequencing assay on said second subset of nucleic acid molecules to yield a second result comprising a second nucleic acid sequence.2. The method of ...

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Номер записи: 33

25-03-2021 дата публикации

AUTOMATED SAMPLE QUALITY ASSESSMENT

Номер: US20210088539A1

Автор: Brown Meredith V., Kennedy Adam D., Lawton Kay A., Lonergan Shaun, Mitchell Matthew W., Wulff Jacob Edward

Принадлежит:

A method of assessing the quality of a biological sample while maintaining the viability of the biological sample for intended use analysis is described herein. The method includes analyzing a biological sample obtained from a subject for an intended use, assessing the quality of the biological sample using one or more biomarkers of sample quality, and simultaneously performing intended use analysis on the same sample. Assessing the quality of the sample can include assessing compliance with sample handling protocols and assessing subject compliance. 1. A method of assessing the quality of a sample to determine the suitability of the sample for an intended use , the method comprising:analyzing the sample using biochemical analysis or metabolic profiling analysisassessing the quality of the sample using one or more biomarkers of sample quality to determine whether the sample meets an acceptance criteria for the intended use, andsimultaneously analyzing the sample for the intended use.2. The method of claim 1 , wherein assessing the quality of the sample comprises determining the level(s) of the one or more biomarkers of sample quality claim 1 , identifying aberrant sample quality biomarkers in the sample claim 1 , listing aberrant sample quality biomarkers claim 1 , and providing a sample quality assessment.3. The method of claim 1 , wherein for a sample that is determined to meet the acceptance criteria for the intended use claim 1 , the result of the biochemical analysis or metabolic profiling analysis is used for the intended use and for a sample that is determined to not meet quality acceptance criteria claim 1 , either not using the result of the biochemical analysis or metabolic profiling analysis for the intended use or modifying the result of the biochemical analysis or metabolic profiling analysis for the intended use based on the quality assessment analysis.4. The method of claim 1 , wherein determining whether a sample meets acceptance criteria for the ...

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Номер записи: 34

29-03-2018 дата публикации

Measurement of protein expression using reagents with barcoded oligonucleotide sequences

Номер: US20180088112A1

Автор: Brent Gaylord, Christina Chang, Christina Fan, Eleen Shum, Eric Jensen, Gretchen Yinbon Lam, James GHADIALI, Jason G. Vidal, Jody MARTIN, Jurg Rohrer, Nidhanjali Bansal, Olaf Zoellner

Принадлежит: Becton Dickinson and Co, Cellular Research Inc

Some embodiments disclosed herein provide a plurality of compositions each comprising a protein binding reagent conjugated with an oligonucleotide. The oligonucleotide comprises a unique identifier for the protein binding reagent it is conjugated with, and the protein binding reagent is capable of specifically binding to a protein target. Further disclosed are methods and kits for quantitative analysis of a plurality of protein targets in a sample and for simultaneous quantitative analysis of protein and nucleic acid targets in a sample. Also disclosed herein are systems and methods for preparing a labeled biomolecule reagent, including a labeled biomolecule agent comprising a protein binding reagent conjugated with an oligonucleotide.

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Номер записи: 35

19-06-2014 дата публикации

Molecular profiling of tumors

Номер: US20140172319A1

Автор: Alan Wright, Arlet Alarcon, Daniel D. Von Hoff, David M. Loesch, Matthew J. McGinniss, Robert J. Penny, Ryan P. Bender, Traci Pawlowski

Принадлежит: Caris MPI Inc

Provided herein are methods and systems of molecular profiling of diseases, such as cancer. In some embodiments, the molecular profiling can be used to identify treatments for a disease, such as treatments that were not initially identified as a treatment for the disease or not expected to be a treatment for a particular disease.

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Номер записи: 36

19-03-2020 дата публикации

Systems And User Interface For Collecting A Data Set In A Flow Cytometer

Номер: US20200088625A1

Автор: Rich Collin A.

Принадлежит:

Systems in a flow cytometer having an interrogation zone and illumination impinging the interrogation zone include: a lens subsystem including a collimating element that collimates light from the interrogation zone, a light dispersion element that disperses collimated light into a light spectrum, and a focusing lens that focuses the light spectrum onto an array of adjacent detection points; a detector array, including semiconductor detector devices, that collectively detects a full spectral range of input light signals, in which each detector device detects a subset spectral range of the full spectral range of light signals; and a user interface that enables a user to create a set of virtual detector channels by grouping detectors in the detector array, such that each virtual detector channel corresponds to a detector group and has a virtual detector channel range including the sum of subset spectral ranges of the detectors in the corresponding detector group. 19-. (canceled)10. A light detection system comprising:a plurality of user-configurable groups of photodetectors; anda plurality of detector channels, wherein each detector channel is assigned to one or more of the user-configurable groups of photodetectors.11. The light detection system according to claim 10 , wherein the light detection system is configured to:detect light from a sample irradiated with a light source; andgenerate a data signal from the detected light.12. The light detection system according to claim 11 , wherein the light detection system is operably coupled to a processor comprising memory having instructions stored thereon claim 11 , which when executed by the processor claim 11 , cause the processor to assign each detector channel to a user-configurable group of photodetectors before generating a data signal from the light detected from the irradiated sample.13. The light detection system according to claim 11 , wherein the light detection system is operably coupled to a processor ...

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Номер записи: 37

12-05-2022 дата публикации

METHOD AND APPARATUS FOR INVESTIGATING INTRA- AND/OR INTERMOLECULAR INTERACTIONS INVOLVING RNA

Номер: US20220148683A1

Автор: Bockelmann Ulrich

Принадлежит:

A method for investigating intra- and/or intermolecular interactions involving RNA is provided. The method includes a) synthesizing a RNA/DNA heteroduplex (RDH) comprising a RNA strand of interest paired to a DNA strand; b) binding a first end of the DNA strand and a corresponding first end of the RNA strand to a first element of a nanoscale manipulating device, and a second end of the DNA strand to a second element of the nanoscale manipulating device, leaving a second end of the RNA strand free; c) moving the first and second elements of the manipulating device apart from each other, stretching the DNA strand and causing the RNA strand to peel off the heteroduplex; and d) moving the first and second elements of the nanoscale manipulating device towards each other, allowing the DNA strand to relax and causing the RNA strand to bind again to it. Measurement of a force-displacement relationship during steps c) and d) provides information on intra- and/or intermolecular interactions involving the RNA strand. Also provided is an apparatus for carrying out the method. 1. A method for investigating intra- and/or intermolecular interactions involving RNA , the method comprising the steps of:a) synthesizing a RNA/DNA heteroduplex comprising a RNA strand of interest paired to a DNA strand, each of said strands having a first and a second end;b) binding a first end of the DNA strand and a corresponding first end of the RNA strand to a first element of a nanoscale manipulating device, and a second end of the DNA strand to a second element of the nanoscale manipulating device, leaving a second end of the RNA strand free;c) moving the first and second elements of the manipulating device apart from each other, stretching the DNA strand and causing the RNA strand to peel off the heteroduplex, while measuring a force-displacement relationship; andd) moving the first and second elements of the nanoscale manipulating device towards each other, allowing the DNA strand to relax and ...

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Номер записи: 38

26-06-2014 дата публикации

Data predicting the type of individual used with separate applications

Номер: US20140180720A1

Автор: David Andre, Eric Teller, John A. Monocello, III, John M. Stivoric

Принадлежит: Bodymedia Inc

The methods and systems described herein may involve determining at least one lifeotype of at least one individual, analyzing the at least one lifeotype, and delivering content to at least one individual based on the analysis. The methods and systems described herein may involve providing a game, determining at least one lifeotype of at least one player of the game, analyzing the at least one lifeotype, and affecting the game play based on the analysis. The methods and systems described herein may involve providing an interactive space, determining at least one lifeotype of at least one individual in the space, analyzing the at least one lifeotype, and modifying at least one attribute of the space based on the analysis.

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Номер записи: 39

26-06-2014 дата публикации

Determining an individuals daily routine

Номер: US20140180993A1

Автор: David Andre, Eric Teller, John A. Monocello, III, John M. Stivoric

Принадлежит: Bodymedia Inc

The methods and systems described herein may involve determining at least one lifeotype of at least one individual, analyzing the at least one lifeotype, and delivering content to at least one individual based on the analysis. The methods and systems described herein may involve providing a game, determining at least one lifeotype of at least one player of the game, analyzing the at least one lifeotype, and affecting the game play based on the analysis. The methods and systems described herein may involve providing an interactive space, determining at least one lifeotype of at least one individual in the space, analyzing the at least one lifeotype, and modifying at least one attribute of the space based on the analysis.

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Номер записи: 40

02-06-2022 дата публикации

DISTINGUISHING METHYLATION LEVELS IN COMPLEX BIOLOGICAL SAMPLES

Номер: US20220170113A1

Автор: Liu Li, Shen Min-Jui, Toung Jonathan, Zhang Ruoyu

Принадлежит: Illumina, Inc.

Provided herein is a method for distinguishing an aberrant methylation level for DNA from a first cell type, including steps of (a) providing a test data set that includes (i) methylation states for a plurality of sites from test genomic DNA from at least one test organism, and (ii) coverage at each of the sites for detection of the methylation states; (b) providing methylation states for the plurality of sites in reference genomic DNA from one or more reference individual organisms, (c) determining, for each of the sites, the methylation difference between the test genomic DNA and the reference genomic DNA, thereby providing a normalized methylation difference for each site; and (d) weighting the normalized methylation difference for each site by the coverage at each of the sites, thereby determining an aggregate coverage-weighted normalized methylation difference score. Also provided herein are sensitive methods for using genomic DNA methylation levels to distinguish cancer cells from normal cells and to classify different cancer types according to their tissues of origin. 110-. (canceled)11. A method for distinguishing an aberrant methylation level for DNA from a first cell type , the method comprising(a) providing, for a plurality of CpG sites in baseline genomic DNA from two or more normal individual baseline organisms, a mean methylation level and a standard deviation of methylation level for each CpG site in the baseline genomic DNA; 'methylation states for the plurality of CpG sites from a first test genomic DNA from an individual test organism, wherein the CpG sites are derived from a sample,', '(b) providing a test data set comprising(c) determining, for each of the CpG sites, the methylation difference between the first test genomic DNA and the baseline genomic DNA, thereby providing a normalized methylation difference for each CpG site; and(d) converting the normalized methylation difference for each CpG site into a one-sided p-value;(e) determining an ...

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Номер записи: 41

03-07-2014 дата публикации

Using data from a wearable device to determine, index, and present activities for types of individuals

Номер: US20140187872A1

Автор: David Andre, Eric Teller, John A. Monocello, III, John M. Stivoric

Принадлежит: Bodymedia Inc

The methods and systems described herein may involve determining at least one lifeotype of at least one individual, analyzing the at least one lifeotype, and delivering content to at least one individual based on the analysis. The methods and systems described herein may involve providing a game, determining at least one lifeotype of at least one player of the game, analyzing the at least one lifeotype, and affecting the game play based on the analysis. The methods and systems described herein may involve providing an interactive space, determining at least one lifeotype of at least one individual in the space, analyzing the at least one lifeotype, and modifying at least one attribute of the space based on the analysis.

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Номер записи: 42

26-04-2018 дата публикации

Methods and Systems for Predicting Colorectal Cancer Incidence and Mortality

Номер: US20180112274A1

Автор: James D. Otvos, Paulette Denise Chandler, Samia Mora

Принадлежит: Liposcience Inc

Disclosed are methods and systems that uses GlycA concentration in biosamples to evaluate risks of CRC incidence and mortality.

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Номер записи: 43

09-04-2020 дата публикации

METHOD FOR IDENTIFYING MICROORGANISMS BY MASS SPECTROMETRY

Номер: US20200111653A1

Автор: ARSAC Maud, COTTE-PATTAT Pierre-Jean, Desseree Denis, Strubel Grégory

Принадлежит: bioMerieux, Inc.

A method of identifying a microorganism by mass spectrometry, including acquiring at least one mass spectrum of said microorganism; for each acquired mass spectrum: detecting peaks of the spectrum in a predetermined mass range; generating a list of peaks identifying at most one peak in each interval of a predetermined subdivision of the range of mass-to-charge ratios, the width of the intervals of the subdivision logarithmically increasing along with the mass-to-charge ratio, and analyzing the list(s) of peaks obtained according to a knowledge base of previously-identified microorganisms and/or types of microorganisms. 2. The method of claim 1 , wherein the predetermined range of mass-to-charge ratios is in the range from 3 claim 1 ,000 Thomsons to 17 claim 1 ,000 Thomsons.3. The method of claim 1 , wherein there are from 900 to 1 claim 1 ,500 intervals.4. The method of claim 3 , wherein there are from 1 claim 3 ,200 to 1 claim 3 ,400 intervals.5. The method of claim 1 , wherein the peak kept in an interval of the subdivision is a maximum peak.6. The method of claim 1 , wherein the at least one mass spectrum of the sample of the microorganism was generated using MALDI-TOF spectrometry.8. The device of claim 7 , wherein the predetermined range of mass-to-charge ratios is in the range from 3 claim 7 ,000 Thomsons to 17 claim 7 ,000 Thomsons.9. The device of claim 7 , wherein there are from 900 to 1 claim 7 ,500 intervals.10. The device of claim 9 , wherein there are from 1 claim 9 ,200 to 1 claim 9 ,400 intervals.11. The device of claim 7 , wherein the peak kept in an interval of the subdivision is a maximum peak.12. The device of claim 7 , wherein the at least one mass spectrum of the sample of the microorganism was generated using MALDI-TOF spectrometry.13. The device of claim 7 , wherein the device further returns an identification decision to a user.14. The device of claim 7 , further comprising a mass spectrometer claim 7 , wherein the at least one mass spectrum ...

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Номер записи: 44

24-07-2014 дата публикации

Systems and methods for characterizing topological network perturbations

Номер: US20140207385A1

Автор: Alain SEWER, Florian Martin

Принадлежит: PHILIP MORRIS PRODUCTS SA

Systems, computerized methods and products are disclosed herein for determining metrics for nodes in a network model of a biological system. Such systems and computerized methods can be used to quantify the response of a biological system to one or more perturbations based on measured activity data of a subset of entities in the biological system. Based on the activity data and a network model of the biological system, centrality values representative of the relative importance of a node in the network are derived. The centrality values are used for characterizing topological perturbations in the network, such as for performing sensitivity analysis, visualizing topological effects of a perturbation in the biological system, or deriving a score quantifying the response of the biological system to a perturbation such as exposure to a chemical agent.

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Номер записи: 45

01-09-2022 дата публикации

Methods and systems for genetic analysis

Номер: US20220275445A1

Автор: Gabor T. Bartha, Gemma Chandratillake, Hugo Yu Kor Lam, John West, Mark R. Pratt, Richard Chen, Sarah Garcia, Shujun Luo

Принадлежит: Personalis Inc

This disclosure provides systems and methods for sample processing and data analysis. Sample processing may include nucleic acid sample processing and subsequent sequencing. Some or all of a nucleic acid sample may be sequenced to provide sequence information, which may be stored or otherwise maintained in an electronic storage location. The sequence information may be analyzed with the aid of a computer processor, and the analyzed sequence information may be stored in an electronic storage location that may include a pool or collection of sequence information and analyzed sequence information generated from the nucleic acid sample. Methods and systems of the present disclosure can be used, for example, for the analysis of a nucleic acid sample, for producing one or more libraries, and for producing biomedical reports. Methods and systems of the disclosure can aid in the diagnosis, monitoring, treatment, and prevention of one or more diseases and conditions.

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Номер записи: 46

01-09-2022 дата публикации

Methods and systems for genetic analysis

Номер: US20220275446A1

Автор: Christian Haudenschild, John West, Richard Chen

Принадлежит: Personalis Inc

This disclosure provides systems and methods for sample processing and data analysis. Sample processing may include nucleic acid sample processing and subsequent sequencing. Some or all of a nucleic acid sample may be sequenced to provide sequence information, which may be stored or otherwise maintained in an electronic storage location. The sequence information may be analyzed with the aid of a computer processor, and the analyzed sequence information may be stored in an electronic storage location that may include a pool or collection of sequence information and analyzed sequence information generated from the nucleic acid sample. Methods and systems of the present disclosure can be used, for example, for the analysis of a nucleic acid sample, for producing one or more libraries, and for producing biomedical reports. Methods and systems of the disclosure can aid in the diagnosis, monitoring, treatment, and prevention of one or more diseases and conditions.

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Номер записи: 47

23-04-2020 дата публикации

MEASUREMENT OF PROTEIN EXPRESSION USING REAGENTS WITH BARCODED OLIGONUCLEOTIDE SEQUENCES

Номер: US20200124601A1

Автор: Fan Christina, Zoellner Olaf

Принадлежит:

Some embodiments disclosed herein provide a plurality of compositions each comprising a protein binding reagent conjugated with an oligonucleotide. The oligonucleotide comprises a unique identifier for the protein binding reagent it is conjugated with, and the protein binding reagent is capable of specifically binding to a protein target. Further disclosed are methods and kits for quantitative analysis of a plurality of protein targets in a sample and for simultaneous quantitative analysis of protein and nucleic acid targets in a sample. Also disclosed herein are systems and methods for preparing a labeled biomolecule reagent, including a labeled biomolecule agent comprising a protein binding reagent conjugated with an oligonucleotide. 120.-. (canceled)21. A plurality of compositions each comprising an antibody associated with one or more oligonucleotides , wherein one of the at least one or more oligonucleotides comprises a target region and a unique identifier for the antibody that it is associated therewith , and the antibody is capable of specifically binding to a protein target , and the unique identifier is selected from a diverse set of unique identifiers comprising at least 100 different unique identifiers.22. The plurality of compositions of claim 21 , wherein the protein target is a cell-surface protein claim 21 , a cell marker claim 21 , a B-cell receptor claim 21 , a T-cell receptor claim 21 , an antibody claim 21 , a major histocompatibility complex claim 21 , a tumor antigen claim 21 , a receptor claim 21 , or a combination thereof.23. The plurality of compositions of claim 21 , wherein the unique identifier sequence comprises a nucleotide sequence of 25-45 nucleotides in length.24. The plurality of composition of claim 22 , comprising at least 100 compositions each comprising the antibody associated with one or more oligonucleotides.25. The plurality of composition of claim 24 , wherein at least 10 of the at least 100 compositions comprise different ...

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Номер записи: 48

03-06-2021 дата публикации

Method to Use Gene Expression to Determine Likelihood of Clinical Outcome of Renal Cancer

Номер: US20210166790A1

Автор: BAEHNER Frederick L., BAKER Joffre, Cowens Wayne, Goddard Audrey, Kiefer Michael C., Knezevic Dejan, Maddala Tara, Shak Steven

Принадлежит: GENOMIC HEALTH, INC.

The present disclosure provides gene and gene sets, the expression of which is important in the classification and/or prognosis of cancer, in particular of renal cell carcinoma. 116.-. (canceled)17. A method of analyzing the expression of RNA transcripts of genes in a human renal cancer patient , the method comprising:measuring levels of RNA transcripts, in a renal tumor sample from the patient, of a panel of genes consisting of:a set of genes consisting of one or more angiogenesis genes selected from: ADD1, ANGPTL3, APOLD1, CEACAM1, EDNRB, EMCN, ENG, EPAS1, FLT1, JAG1, KDR, KL, LDB2, NOS3, NUDT6, PPAP2B, PRKCH, PTPRB, RGS5, SHANK3, SNRK, TEK, ICAM2, and VCAM1;a set of genes consisting of one or more immune response genes selected from: CCL5, CCR7, CD8A, CX3CL1, CXCL10, CXCL9, HLA-DPB1, IL6, IL8, and SPP1; anda set of genes consisting of one or more cell cycle genes selected from: BUB1, C13orf15, CCNB1, PTTG1, TPX2, LMNB1, and TUBB2A;EIF4BP1; anda set of genes consisting of one or more reference genes.18. The method of claim 17 , wherein the renal cancer is renal cell carcinoma (RCC).19. The method of claim 17 , wherein the RCC is clear cell renal cell carcinoma (ccRCC).20. The method of claim 17 , wherein the level of the RNA transcripts is measured by quantitative RT-PCR.21. The method of claim 17 , wherein the renal tumor sample is paraffin-embedded and fixed.22. The method of claim 17 , wherein the panel comprises at least two angiogenesis genes claim 17 , at least two immune response genes claim 17 , and at least two cell cycle genes.23. The method of claim 17 , wherein the at least one reference gene is selected from the group consisting of: AAMP claim 17 , ARF1 claim 17 , ATP5E claim 17 , EEF1A1 claim 17 , GPX1 claim 17 , RPS23 claim 17 , SDHA claim 17 , UBB claim 17 , RPLP1 claim 17 , GAPDH claim 17 , and beta-actin.24. A method of analyzing the expression of RNA transcripts of genes in a human renal cancer patient claim 17 , the method comprising:measuring ...

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Номер записи: 49

17-05-2018 дата публикации

Methods and systems for high resolution melt analysis of a nucleic acid sequence

Номер: US20180136150A1

Автор: Charles Andre, David Cohen, Ian Kavanagh, Jaakko Kurkela, Jorma Mustola, Ossian Saris, Ville Vahervuori

Принадлежит: THERMO FISHER SCIENTIFIC OY

Described herein are methods and systems for analyzing and visualizing HRM data from a double-stranded nucleic acid. The HRM data is generally characterized by a plurality of data points each including a signal value associated with the concentration of a double-stranded nucleic acid in a sample and a temperature value associated with a the temperature of the sample. Embodiments of the invention analyze the HRM curves from samples using the first negative derivative of the HRM curve or a virtual standard. The first negative derivative plot method may be used to identify the melting temperature of a homogenous double-stranded nucleic acid in a sample, as well as the presence and melting temperature of heterogeneous double-stranded nucleic acids in the sample. Data points associated with the melting temperature are plotted on a scatter plot for analysis. The virtual standard allows for visualization of HRM data across data sets.

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Номер записи: 50

07-08-2014 дата публикации

Delivering content based on an individuals predicted type and stress-related state

Номер: US20140221730A1

Автор: David Andre, Eric Teller, John A. Monocello, III, John M. Stivoric

Принадлежит: Bodymedia Inc

The methods and systems described herein may involve determining at least one lifeotype of at least one individual, analyzing the at least one lifeotype, and delivering content to at least one individual based on the analysis. The methods and systems described herein may involve providing a game, determining at least one lifeotype of at least one player of the game, analyzing the at least one lifeotype, and affecting the game play based on the analysis. The methods and systems described herein may involve providing an interactive space, determining at least one lifeotype of at least one individual in the space, analyzing the at least one lifeotype, and modifying at least one attribute of the space based on the analysis.

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Номер записи: 51

07-08-2014 дата публикации

Systems, methods, and devices to determine an individuals mood

Номер: US20140222735A1

Автор: David Andre, Eric Teller, John A. Monocello, III, John M. Stivoric

Принадлежит: Bodymedia Inc

The methods and systems described herein may involve determining at least one lifeotype of at least one individual, analyzing the at least one lifeotype, and delivering content to at least one individual based on the analysis. The methods and systems described herein may involve providing a game, determining at least one lifeotype of at least one player of the game, analyzing the at least one lifeotype, and affecting the game play based on the analysis. The methods and systems described herein may involve providing an interactive space, determining at least one lifeotype of at least one individual in the space, analyzing the at least one lifeotype, and modifying at least one attribute of the space based on the analysis.

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Номер записи: 52

07-08-2014 дата публикации

Systems and methods using a wearable device to predict the individuals type and a suitable therapy regime

Номер: US20140222847A1

Автор: David Andre, Eric Teller, John A. Monocello, III, John M. Stivoric

Принадлежит: Bodymedia Inc

The methods and systems described herein may involve determining at least one lifeotype of at least one individual, analyzing the at least one lifeotype, and delivering content to at least one individual based on the analysis. The methods and systems described herein may involve providing a game, determining at least one lifeotype of at least one player of the game, analyzing the at least one lifeotype, and affecting the game play based on the analysis. The methods and systems described herein may involve providing an interactive space, determining at least one lifeotype of at least one individual in the space, analyzing the at least one lifeotype, and modifying at least one attribute of the space based on the analysis.

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Номер записи: 53

28-05-2015 дата публикации

Methods and systems for storing sequence read data

Номер: US20150149510A1

Автор: Caleb J. Kennedy, Niru Chennagiri

Принадлежит: Good Start Genetics Inc

The present invention generally relates to storing sequence read data. The invention can involve obtaining a plurality of sequence reads from a sample, identifying one or more sets of duplicative sequence reads within the plurality of sequence reads, and storing only one of the sequence reads from each set of duplicative sequence reads in a text file using nucleotide characters.

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Номер записи: 54

09-05-2019 дата публикации

METHOD FOR USING DNA TO STORE TEXT INFORMATION, DECODING METHOD THEREFOR AND APPLICATION THEREOF

Номер: US20190138909A1

Автор: Chen Shihong, CHEN Tai, LIU Longying, SHEN Yue, Wang Yun, Yang Huanming

Принадлежит:

A method for encoding and storing text information using DNA as a storage medium, a decoding method therefor and an application thereof. The method for using DNA to store text information comprises: encoding characters into computer binary digits by means of encoding, and converting the binary digits into DNA sequences by means of transcoding; and artificially synthesizing the DNA sequences encoded with character information, positioning the characters by means of a designed ligation adapter, and assembling the DNA sequences encoded with the character information according to a pre-set order. The method for using DNA to store text information has the advantages of a small storage volume, a large storage capacity, a strong stability and low maintenance costs. 19.-. (canceled)10. A method for storing text information by using DNA as a storage medium , comprising the steps of:(1) encoding a character into a computer binary digit by encoding;(2) converting the computer binary digit encoding the character into a DNA sequence, which is represented by the four deoxyribonucleotides A, T, G, and C, by transcoding;(3) synthesizing the DNA sequence encoding the character;(4) locating the DNA sequence encoding the character by a designed ligation adapter, ligating individual DNA sequences encoding individual characters according to the order of characters of the information to be stored, followed by assembling and storing.11. The method according to claim 10 , wherein the encoding is Unicode-ucs2 encoding.12. The method according to claim 11 , wherein the character is a Chinese character claim 11 , and wherein the Chinese character is encoded by a hexadecimal digit claim 11 , and the hexadecimal digit is converted into a 4-bit binary digit.13. The method according to claim 12 , wherein the 8-bit binary digit produces a 4-bit Hamming code for verification.14. The method according to claim 10 , wherein the transcoding is performed according to a principle that the binary digit 0 ...

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Номер записи: 55

10-06-2021 дата публикации

LABORATORY SYSTEM

Номер: US20210173769A1

Автор: Puig Albert

Принадлежит: ROCHE DIAGNOSTICS OPERATIONS, INC.

A laboratory system is disclosed. The laboratory system comprises a plurality of laboratories comprising one or more analytical instruments for performing a plurality of analytical tests (T-n) and providing analytical test results (TR-n) and a remote computer communicatively connected to the laboratories. Each of the laboratories is configured to define test result validation criteria (C-n) for validating at least one of the analytical test results (TR-n) associated with the respective analytical tests (T-n) of one of the plurality of laboratories. The remote computer is configured to define a plurality of profiles (P-n) of validation criteria, to assign the profiles (P-n) of test result validation criteria (C-n) to one or more of the laboratories (), and to perform an automatic validation of groups (G-n) of the analytical test results (TR-n) according to the profiles (P-n) of test result validation criteria (C-n). 1. A computer-implemented method for validating analytical test results provided by a laboratory system , wherein the laboratory system comprises a plurality of work areas , each work area comprising one or more analytical instruments designed for performing analytical tests of biological samples and providing analytical test results , the method performed by a remote computer connected to the plurality of work areas via a communication network comprising:defining test result validation criteria for the analytical tests;storing a test validation configuration comprising one or more test validation profiles, each test validation profile comprising one or more analytical test groups, each group comprising one or more analytical tests, for each analytical test group of the test validation profile, a set of test result validation criteria for the one or more analytical tests of this analytical test group, and a work area to which test validation profile is allocated; a) a test validation profile of the test validation configuration is allocated to a work area ...

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Номер записи: 56

25-05-2017 дата публикации

Gene mutations and copy number alterations of egfr, kras and met

Номер: US20170145516A1

Автор: AmirAli TALASAZ, Scott KOPETZ

Принадлежит: Guardant Health Inc, University of Texas System

Sequence variants and copy number variations in the EGFR, KRAS and MET genes are biomarkers for resistance to anti-EGFR therapies for cancer. This disclosure provides methods of detecting these biomarkers and using them in the diagnosis and treatment of cancer.

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Номер записи: 57

07-05-2020 дата публикации

METHODS TO DETERMINE TUMOR GENE COPY NUMBER BY ANALYSIS OF CELL-FREE DNA

Номер: US20200140960A1

Автор: Abdueva Diana, Chudova Darya, Eltoukhy Helmy, Talasaz AmirAli

Принадлежит:

Methods are provided herein to improve automatic detection of copy number variation in nucleic acid samples. These methods provide improved approaches for determining baseline copy number of genetic loci within a sample, reduce variation due to features of genetic loci, sample preparation, and probe exhaustion. 1. A system , comprising a controller comprising , or capable of accessing , computer-readable media comprising non-transitory computer-executable instructions which , when executed by one or more electronic processors , perform at least:(a) obtaining sequencing reads of polynucleotides derived from cell-free deoxyribonucleic acid (cfDNA) molecules of a bodily fluid sample of a subject, wherein the polynucleotides are enriched for a plurality of genetic loci using one or more oligonucleotide probes that are complementary to at least a portion of one or more genetic loci from the plurality of genetic loci;(b) generating from the sequencing reads a first data set of baselining genetic loci comprising, for each genetic locus of the plurality of genetic loci, a quantitative measure related to sequencing read coverage (“read coverage”) of the genetic locus;(c) correcting the first data set by performing saturation equilibrium correction and probe efficiency correction;(d) determining a baseline read coverage for the first data set, wherein the baseline read coverage relates to saturation equilibrium and probe efficiency; and(e) determining a copy number state for each genetic locus of the plurality of genetic loci relative to the baseline read coverage.2. The system of claim 1 , wherein the first data set comprises claim 1 , for each genetic locus of the plurality of genetic loci claim 1 , a quantitative measure related to guanine-cytosine content (“GC content”) of the genetic locus.3. The system of claim 2 , wherein claim 2 , prior to (c) claim 2 , genetic loci that are high-variance genetic loci are removed from the first data set claim 2 , wherein the removing ...

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Номер записи: 58

16-05-2019 дата публикации

Determining Characteristics of Enzyme Catalysis

Номер: US20190145894A1

Автор: Dushek Omer, Goyette Jesse

Принадлежит: OXFORD UNIVERSITY INNOVATION LIMITED

Embodiments of the present invention provide a computer-implemented method of determining characteristics of enzyme catalysis, comprising receiving, from a surface plasmon resonance (SPR) instrument, SPR data indicative of binding of anenzyme and a substrate, and determining one or more characteristics of the enzyme catalysis based on a multi-centre particle density (MPD) model and the SPR data. 1. A computer-implemented method of determining characteristics of enzyme catalysis , comprising:receiving, from a surface plasmon resonance (SPR) instrument, SPR data indicative of binding of an enzyme and a substrate;determining one or more characteristics of the enzyme catalysis based on a multi-centre particle density (MPD) model and the SPR data.2. The method of claim 1 , wherein determining the one or more characteristics comprises fitting the MPD model to the SPR data.3. The method of claim 1 , wherein one or more characteristics comprise one or more of catalytic rate (k*) claim 1 , association (k) and dissociation (k) of the enzyme.4. The method of claim 1 , wherein the one or more characteristics comprise reach length (L).5. The method of claim 1 , wherein the determining comprises determining catalytic rate (k) claim 1 , association (k) and dissociation (k) of the enzyme; and reach length (L).6. The method of claim 1 , wherein the determining the one or more characteristics of the enzyme catalysis comprises fitting the multi-centre particle density (MPD) model to the SPR data.7. The method of claim 1 , wherein the MPD model comprises a system of multi-centre particle distributions (MPD).9. The method of claim 7 , wherein each characteristic of the enzyme catalysis is associated with a respective MPD.10. The method of claim 1 , wherein the MPD model comprises a multi-centre particle distribution system of coupled partial differential equations.12. The method of claim 1 , wherein14. An apparatus for determining characteristics of enzyme catalysis claim 1 , comprising ...

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Номер записи: 59

17-06-2021 дата публикации

LIPOPROTEIN ANALYSIS BY DIFFERENTIAL CHARGED-PARTICLE MOBILITY

Номер: US20210181217A1

Автор: Benner W. Henry, Blanche Patricia J., Caulfield Michael P., Cornell Earl, Krauss Ronald, Lee Gloria Kwangja, Li Shuguang, Reitz Richard E

Принадлежит:

The invention provides methods of preparation of lipoproteins from a biological sample, including HDL, LDL, Lp(a), IDL, and VLDL, for diagnostic purposes utilizing differential charged particle mobility analysis methods. Further provided are methods for analyzing the size distribution of lipoproteins by differential charged particle mobility, which lipoproteins are prepared by methods of the invention. Further provided are methods for assessing lipid-related health risk, cardiovascular condition, risk of cardiovascular disease, and responsiveness to a therapeutic intervention, which methods utilize lipoprotein size distributions determined by methods of the invention. 1. A method for purifying lipoproteins for ion mobility analysis , the method comprising:admixing a solution comprising lipoproteins and non-lipoproteins with one or more lipoprotein-capture ligands capable of binding lipoproteins to form a lipoprotein/lipoprotein-capture ligand complex;isolating the lipoprotein/lipoprotein-capture ligand complex; andreleasing the lipoproteins from the lipoprotein/lipoprotein-capture ligand complex and subjecting the lipoproteins to ion mobility;wherein the method does not include centrifugation.2. The method of claim 1 , wherein the lipoproteins are selected from the group consisting of HDL claim 1 , LDL claim 1 , Lp(a) claim 1 , IDL and VLDL.3. The method of claim 1 , wherein the lipoprotein-capture ligand is selected from the group consisting of an aptamer and an antibody.4. The method of claim 1 , wherein the aptamer or antibody comprises a biotinylated aptamer or a biontinylated antibody.5. The method of claim 1 , wherein the lipoprotein-capture ligand is an aptamer.6. The method of claim 5 , wherein the aptamer comprises RNA or DNA.7. The method of claim 5 , wherein the aptamer binds Apo A1 claim 5 , Apo B claim 5 , or Apo(a).8. The method of claim 1 , wherein the lipoprotein-capture ligand is an antibody.9. The method of wherein the antibody complexes the ...

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Номер записи: 60

07-06-2018 дата публикации

Self correction for spatial orientation and motion of portable clinical analyzers

Номер: US20180157785A1

Автор: Gary Vandersleen, Graham Davis, Narendra Soman, Paul Wasserman, PIERRE Emeric

Принадлежит: ABBOTT POINT OF CARE INC

The present invention covers the integration and utility of accelerometer features into a clinical analysis system. For example, measurement of dynamic acceleration and orientation of a blood-testing instrument with respect to Earth's gravitational field may be used to determine reliability of a test procedure and optionally to provide corrective elements thereof.

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Номер записи: 61

30-05-2019 дата публикации

COGNITIVE CELL WITH CODED CHEMICALS FOR GENERATING OUTPUTS FROM ENVIRONMENTAL INPUTS AND METHOD OF USING SAME

Номер: US20190162714A1

Автор: Karimi Tahereh

Принадлежит: Cemvita Technologies LLC

A synthetic, cognitive cell, system, and method for automatically generating an output based on an environmental input is disclosed. The cognitive cell includes an operator including chemical agents, and a coded chemical including polymers. Each of the polymers includes a sequence of affinity blocks of molecular groups arranged in predetermined patterns to define a multi-layered base code. Each of the affinity blocks includes a monomer with a sidechain, the sidechains having affinities to each other. At least a portion of the affinity blocks forming a gate switch defining a bridge between the environmental inputs and the chemical agent whereby, upon exposure to the environmental inputs, the gate switches trigger the chemical agent to perform an operation. The coded chemical and at least one chemical agent are contained within a natural or synthetic membrane. 1. A synthetic cognitive cell for automatically generating an output based on an environmental input , the cognitive cell comprising:an operator comprising chemical agents; anda coded chemical comprising polymers, each of the polymers comprising a sequence of affinity blocks of molecular groups arranged in predetermined patterns to define a multi-layered base code, each of the affinity blocks comprises a monomer with a sidechain, the sidechains having affinities to each other, at least a portion of the affinity blocks forming a gate switch defining a bridge between the environmental inputs and the chemical agent whereby, upon exposure to the environmental inputs, the gate switches trigger the chemical agent to perform an operation,wherein the coded chemical and at least one chemical agent is contained within a natural or synthetic membrane.2. The synthetic cognitive cell of claim 1 , wherein the polymer is selected from the group consisting of natural or synthetic deoxyribonucleic acid (DNA) claim 1 , plasmid claim 1 , graphene claim 1 , aptamer claim 1 , synthetic polysaccharide claim 1 , enzyme sensitive ...

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Номер записи: 62

23-06-2016 дата публикации

Secondary structure defining database and methods for determining identity and geographic origin of an unknown bioagent thereby

Номер: US20160180020A1

Автор: David J. Ecker, John McNeil, Rangarajan Sampath, Richard H. Griffey, Stanley T. Crooke, Steven A. Hofstadler

Принадлежит: Ibis Biosciences Inc

The present invention relates generally to the field of investigational bioinformatics and more particularly to secondary structure defining databases. The present invention further relates to methods for interrogating a database as a source of molecular masses of known bioagents for comparing against the molecular mass of an unknown or selected bioagent to determine either the identity of the selected bioagent, and/or to determine the origin of the selected bioagent. The identification of the bioagent is important for determining a proper course of treatment and/or irradication of the bioagent in such cases as biological warfare. Furthermore, the determination of the geographic origin of a selected bioagent will facilitate the identification of potential criminal identity.

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Номер записи: 63

01-07-2021 дата публикации

Hardware Acceleration of Short Read Mapping for Genomic and Other Types of Analyses

Номер: US20210202036A1

Автор: Olson Corey B.

Принадлежит:

A scalable FPGA-based solution to the short read mapping problem in DNA sequencing is disclosed which greatly accelerates the task of aligning short length reads to a known reference genome. A representative system comprises one or more memory circuits storing a plurality of short reads and a reference genome sequence; and one or more field programmable gate arrays configured to select a short read; to extract a plurality of seeds from the short read, each seed comprising a genetic subsequence of the short read; for each seed, to determine at least one candidate alignment location (CAL) in the reference genome sequence to form a plurality of CALs; for each CAL, to determine a likelihood of the short read matching the reference genome sequence in the vicinity of the CAL; and to select one or more CALs having the currently greater likelihood of the short read matching the reference genome sequence. 120- (canceled)21. A method for acceleration in a system of short read mapping to a reference sequence for proteomic analysis , the system having at least one host computing system , one or more field programmable gate arrays , and one or more memory circuits , the method comprising:using the one or more field programmable gate arrays, selecting a short read from a plurality of short reads, each short read of the plurality of short reads comprising a protein sequence;using the one or more field programmable gate arrays, extracting a plurality of seeds from the selected short read, each seed of the plurality of seeds comprising a subsequence of the selected short read;using the one or more field programmable gate arrays, for each seed of the plurality of seeds, determining at least one candidate alignment location in the reference sequence to form a plurality of candidate alignment locations;using the one or more field programmable gate arrays, for each candidate alignment location of the plurality of candidate alignment locations, determining a likelihood of the selected ...

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Номер записи: 64

06-06-2019 дата публикации

Method and System for Assessment of Regulatory Variants in a Genome

Номер: US20190172556A1

Автор: Butte Atul J., Dudley Joel T., Karczewski Konrad J., Snyder Michael P.

Принадлежит: THE BOARD OF TRUSTEES OF THE LELAND STANFORD JUNIOR UNIVERSITY

The present invention provides methods embodied in a system that can be applied to genetic information comprising an individual genome to assess the regulatory impact of specific genetic variants and their possible impact on biological function or disease pathology. 1. A method of treating an individual based on genetic variants in transcription factor binding sites , comprising:obtaining genetic data from an individual by sequencing genetic material of the individual; receiving information regarding genome-wide quantitative and genetic profiles, information regarding genetic variants associated with disease conditions, information regarding DNA motifs associated with transcription factor binding, and molecular profiles of disease pathologies and storing this information using a computer system comprising a processor and a memory, wherein the quantitative and genetic profiles describe transcription factor binding and gene expression measured across a multitude of individual human genomes;', mapping the genetic variants associated with disease conditions to the DNA motifs associated with transcription factor binding; and', 'determining whether the genetic variants associated with disease conditions affect gene expression by identifying the effect on gene expression of the mapped genetic variants from the quantitative and genetic profiles;, 'identifying a set of candidate variants using a computer system with a processor and a memory, wherein the set of candidate variants are identified by, 'generating regulatory impact data for the set of candidate variants using a computer system comprising a processor and a memory, wherein the regulatory impact data indicates the clinical significance of the set of candidate variants, where the clinical significance identifies a disease associated with the effect of the set of candidate variants on gene expression based on the received molecular profiles of disease pathology; and', 'identifying the presence of at least one ...

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Номер записи: 65

13-06-2019 дата публикации

STAIN-FREE PROTEIN QUANTIFICATION AND NORMALIZATION

Номер: US20190178877A1

Автор: Freeby Steve, Liu Ning, McDonald Kevin, Paulus Aran, Posch Anton

Принадлежит:

Disclosed herein are methods of protein quantification and normalization using haloalkylated tryptophan fluorescence. Complex protein samples, i.e., samples that each contain 1,000 or more distinct proteins, from diverse sources that do not have common protein profiles are treated with a halo-substituted organic compound (i.e. haloalkane) that reacts with tryptophan residues to form fluorescent products. Irradiation of the samples with ultraviolet light and the detection and quantification of the resultant fluorescent emissions from all proteins in each sample are then used to obtain comparative values for total protein content among the various samples. The values thus obtained are found to be valid indications of comparative total protein content, despite the fact that the tryptophan levels vary widely among the various proteins in any single sample and the samples, due to the diversity of their origins, tend to differ among themselves in the identities and relative amounts of the proteins that they contain. Protein samples are also normalized to correct for differences in sample dilution, sample loading, and protein transfer inconsistencies, by using stain-free detection of total protein in each of the samples, or detection of subsamples within each sample. 1. A method of normalizing , using detected haloalkylated tryptophan fluorescence , the amount of protein in a first subsample of a protein sample to the amount of protein in a second subsample of the protein sample , the method comprising:quantifying the amount of haloalkylated tryptophan fluorescence detected from the first subsample;quantifying the amount of haloalkylated tryptophan fluorescence detected from the second subsample; andnormalizing the amount of protein in the first subsample to the amount of protein in the second subsample based on the amounts of haloalkylated tryptophan fluorescence detected from the first subsample and the second subsample.2. The method of claim 1 , wherein the first ...

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Номер записи: 66

04-06-2020 дата публикации

Measurement of protein expression using reagents with barcoded oligonucleotide sequences

Номер: US20200173992A1

Автор: Christina Fan, Olaf Zoellner

Принадлежит: Cellular Research Inc

Some embodiments disclosed herein provide a plurality of compositions each comprising a protein binding reagent conjugated with an oligonucleotide. The oligonucleotide comprises a unique identifier for the protein binding reagent it is conjugated with, and the protein binding reagent is capable of specifically binding to a protein target. Further disclosed are methods and kits for quantitative analysis of a plurality of protein targets in a sample and for simultaneous quantitative analysis of protein and nucleic acid targets in a sample. Also disclosed herein are systems and methods for preparing a labeled biomolecule reagent, including a labeled biomolecule agent comprising a protein binding reagent conjugated with an oligonucleotide.

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Номер записи: 67

18-09-2014 дата публикации

Multimode sensor devices

Номер: US20140278139A1

Автор: Andrew Cole Axley, Jung Ook Hong, Shelten Gee Jao Yuen

Принадлежит: Fitbit LLC

The disclosure provides BMDs that have multiple device modes depending on operational conditions of the devices, e.g., motion intensity, device placement, and/or activity type. The device modes are associated with various data processing algorithms. In some embodiments, the BMD is implemented as a wrist-worn or arm-worn device. In some embodiments, methods for tracking physiological metrics using the BMDs are provided. In some embodiments, the process or the BMD applies a time domain analysis on data provided by a sensor of the BMD when the data has a high signal (e.g., high signal-to-noise ratio), and applies a frequency domain analysis on the data when the data has a low signal, which contributes to improved accuracy and speed of biometric data.

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Номер записи: 68

20-06-2019 дата публикации

LIPOPROTEIN ANALYSIS BY DIFFERENTIAL CHARGED-PARTICLE MOBILITY

Номер: US20190187160A1

Автор: Benner W. Henry, Blanche Patricia J., Caulfield Michael P., Cornell Earl, Krauss Ronald, Lee Gloria Kwangja, Li Shuguang, Reitz Richard E.

Принадлежит:

The invention provides methods of preparation of lipoproteins from a biological sample, including HDL, LDL, Lp(a), IDL, and VLDL, for diagnostic purposes utilizing differential charged particle mobility analysis methods. Further provided are methods for analyzing the size distribution of lipoproteins by differential charged particle mobility, which lipoproteins are prepared by methods of the invention. Further provided are methods for assessing lipid-related health risk, cardiovascular condition, risk of cardiovascular disease, and responsiveness to a therapeutic intervention, which methods utilize lipoprotein size distributions determined by methods of the invention. 1. A system for analyzing size distribution of lipoproteins , the system comprising a processor and memory having machine instructions stored thereon , the instructions being executable by the processor to cause the processor to:collect, via an ion mobility analyzer configured to receive samples for differential charged-particle mobility analysis, differential ion mobility data for a sample having one or more lipoproteins;determine, using the differential ion mobility data, a lipoprotein particle size distribution for one or more lipoproteins, wherein determining the lipoprotein particle size distribution comprises determining a best fit for a set of one or more regions of interest for lipoprotein particle sizes;generate a visual representation of the lipoprotein particle size distribution; andoutput the visual representation via a display or a printer.2. The system of claim 1 , wherein the instructions are executable to cause the processor to generate a graphical representation of the lipoprotein particle size distribution as the visual representation.3. The system of claim 2 , wherein the instructions are further executable to cause the processor to determine a curve corresponding to the best fit claim 2 , and include the curve in the visual representation.4. The system of claim 1 , wherein the ...

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Номер записи: 69

13-07-2017 дата публикации

Systems and methods for versioning hosted software

Номер: US20170199734A1

Автор: Amitabh Shukla, Brijesh Krishnaswami, Yuandan Lou

Принадлежит: Life Technologies Corp

Systems and methods for performing a validated analysis can include access to first and second versions of an analysis engine. The first version of the analysis engine can be used to perform a previously validated analysis. After the second version is made available, the first version can be continued to be used while the second version undergoes validation. The user can initiate a migration from the first version to the second version when the validation is complete. Access to both versions can be maintained for a period of time to allow users to migrate on their own schedule, and a common login interface can direct the user to a default version or allow the user to select an alternate version.

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Номер записи: 70

06-08-2015 дата публикации

System and method including thermal cycler modules

Номер: US20150217291A1

Автор: Alan N. Johnson, Brian D. Wilson, Daniel R. Schmidt, David L. Yang, Garrick A. Maurer, Joshua D. Wiltsie, Mark F. Sauerburger, Matthew D. Erickson, Matthew S. Davis, Sami D. Alaruri, Thomas M. Stachelek

Принадлежит: Beckman Coulter Inc

Systems and methods for processing and analyzing samples are disclosed. The system may process samples, such as biological fluids, using assay cartridges which can be processed at different processing locations. In some cases, the system can be used for PCR processing. The different processing locations may include a preparation location where samples can be prepared and an analysis location where samples can be analyzed. To assist with the preparation of samples, the system may also include a number of processing stations which may include processing lanes. During the analysis of samples, in some cases, thermal cycler modules and an appropriate optical detection system can be used to detect the presence or absence of certain nucleic acid sequences in the samples. The system can be used to accurately and rapidly process samples.

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Номер записи: 71

05-08-2021 дата публикации

METHODS AND SYSTEMS FOR GENETIC ANALYSIS

Номер: US20210238677A1

Автор: Bartha Gabor T., Chandratillake Gemma, Chen Richard, Garcia Sarah, Lam Hugo Yu Kor, Luo Shujun, Pratt Mark R., West John

Принадлежит:

This disclosure provides systems and methods for sample processing and data analysis. Sample processing may include nucleic acid sample processing and subsequent sequencing. Some or all of a nucleic acid sample may be sequenced to provide sequence information, which may be stored or otherwise maintained in an electronic storage location. The sequence information may be analyzed with the aid of a computer processor, and the analyzed sequence information may be stored in an electronic storage location that may include a pool or collection of sequence information and analyzed sequence information generated from the nucleic acid sample. Methods and systems of the present disclosure can be used, for example, for the analysis of a nucleic acid sample, for producing one or more libraries, and for producing biomedical reports. Methods and systems of the disclosure can aid in the diagnosis, monitoring, treatment, and prevention of one or more diseases and conditions. 1. A method for processing nucleic acid samples from a subject , comprising:(a) generating at least a first subset of nucleic acid molecules and a second subset of nucleic acid molecules from at least one of said nucleic acid samples from said subject with the aid of pulldown probes that selectively enrich for one or more features in at least said first subset of nucleic acid molecules or said second subset of nucleic acid molecules such that said first subset of nucleic acid molecules and said second subset of nucleic acid molecules differ by said one or more features, wherein said one or more features comprise(s) one or more polymorphisms, wherein said at least one nucleic acid sample and at least one or more additional nucleic acid sample(s) are collected from said subject at different time points; and(b) combining at least said first subset of nucleic acid molecules and said second subset of nucleic acid molecules to produce a combined pool of nucleic acid molecules, and conducting one or more assays on at ...

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Номер записи: 72

04-08-2016 дата публикации

Molecular profiling of tumors

Номер: US20160224725A1

Автор: Alan Wright, Arlet Alarcon, Daniel D. Von Hoff, David M. Loesch, Matthew J. McGinniss, Robert J. Penny, Ryan P. Bender, Traci Pawlowski

Принадлежит: Caris MPI Inc

Provided herein are methods and systems of molecular profiling of diseases, such as cancer. In some embodiments, the molecular profiling can be used to identify treatments for a disease, such as treatments that were not initially identified as a treatment for the disease or not expected to be a treatment for a particular disease.

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Номер записи: 73

04-08-2016 дата публикации

Molecular profiling of tumors

Номер: US20160224727A1

Автор: Alan Wright, Arlet Alarcon, Daniel D. Von Hoff, David M. Loesch, Matthew J. McGinniss, Robert J. Penny, Ryan P. Bender, Traci Pawlowski

Принадлежит: Caris MPI Inc

Provided herein are methods and systems of molecular profiling of diseases, such as cancer. In some embodiments, the molecular profiling can be used to identify treatments for a disease, such as treatments that were not initially identified as a treatment for the disease or not expected to be a treatment for a particular disease.

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Номер записи: 74

04-08-2016 дата публикации

Molecular profiling of tumors

Номер: US20160224745A1

Автор: Alan Wright, Arlet Alarcon, Daniel D. Von Hoff, David M. Loesch, Matthew J. McGinniss, Robert J. Penny, Ryan P. Bender, Traci Pawlowski

Принадлежит: Caris MPI Inc

Provided herein are methods and systems of molecular profiling of diseases, such as cancer. In some embodiments, the molecular profiling can be used to identify treatments for a disease, such as treatments that were not initially identified as a treatment for the disease or not expected to be a treatment for a particular disease.

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Номер записи: 75

16-10-2014 дата публикации

Systems and methods making recommendations based on data from wearable devices

Номер: US20140310295A1

Автор: David Andre, Eric Teller, John A. Monocello, III, John M. Stivoric

Принадлежит: Bodymedia Inc

The methods and systems described herein may involve determining at least one lifeotype of at least one individual, analyzing the at least one lifeotype, and delivering content to at least one individual based on the analysis. The methods and systems described herein may involve providing a game, determining at least one lifeotype of at least one player of the game, analyzing the at least one lifeotype, and affecting the game play based on the analysis. The methods and systems described herein may involve providing an interactive space, determining at least one lifeotype of at least one individual in the space, analyzing the at least one lifeotype, and modifying at least one attribute of the space based on the analysis.

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Номер записи: 76

16-10-2014 дата публикации

Systems and methods making recommendations based on data from wearable devices

Номер: US20140310296A1

Автор: David Andre, Eric Teller, John A. Monocello, III, John M. Stivoric

Принадлежит: Bodymedia Inc

The methods and systems described herein may involve determining at least one lifeotype of at least one individual, analyzing the at least one lifeotype, and delivering content to at least one individual based on the analysis. The methods and systems described herein may involve providing a game, determining at least one lifeotype of at least one player of the game, analyzing the at least one lifeotype, and affecting the game play based on the analysis. The methods and systems described herein may involve providing an interactive space, determining at least one lifeotype of at least one individual in the space, analyzing the at least one lifeotype, and modifying at least one attribute of the space based on the analysis.

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Номер записи: 77

19-08-2021 дата публикации

METHOD AND APPARATUS FOR PROVIDING DATA PROCESSING AND CONTROL IN A MEDICAL COMMUNICATION SYSTEM

Номер: US20210251529A1

Автор: Hayter Gary Alan, McGarraugh Geoffrey V.

Принадлежит:

Methods and apparatus for providing data processing and control for use in a medical communication system are provided. 127-. (canceled)28. A method for determining a state of an analyte sensor , comprising:generating, by an analyte sensor positioned at least in part in contact with a fluid under a skin of a subject, a signal corresponding to a monitored analyte level;receiving, by one or more processors in communication with the analyte sensor, the signal corresponding to the monitored analyte level;performing, by the one or more processors, a first comparison of the signal to a first predetermined signal characteristic to determine whether the signal is indicative of the first predetermined signal characteristic;determining, by the one or more processors based on the first comparison, a state of the analyte sensor, wherein the state of the analyte sensor relates to a position of the analyte sensor; andtransmitting output data indicative of the state of the analyte sensor to a receiving device.29. The method of claim 28 , wherein the first predetermined signal characteristic comprises a transition above or below a first predetermined signal level.30. The method of claim 28 , wherein the first predetermined signal characteristic comprises a transition above or below a first predetermined signal rate of change.31. The method of claim 29 , wherein the first predetermined signal level corresponds to a first number of analog to digital converter counts.32. The method of claim 28 , further comprising:performing, by the one or more processors, a second comparison of the signal to a second predetermined signal characteristic, wherein the second predetermined signal characteristic is different from the first predetermined signal characteristic; anddetermining, by the one or more processors based on the second comparison, the state of the analyte sensor.33. The method of claim 32 , wherein the second predetermined signal characteristic comprises a transition above or below a ...

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Номер записи: 78

10-08-2017 дата публикации

Aptamers for use against autoantibody-associated diseases

Номер: US20170226513A1

Автор: Johannes Mueller

Принадлежит: Berlin Cures Holding AG

The present invention relates to new aptamer molecules for use in the treatment and/or diagnosis of autoimmune diseases associated with autoantibodies against G-protein coupled receptors, a pharmaceutical composition comprising such aptamer molecules, an apheresis column comprising such aptamer molecules and a method for the determination of nucleotide sequences for use as sequences of aptamer molecules.

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Номер записи: 79

09-08-2018 дата публикации

Method for selecting a transplantation donor or donor material using low or intermediate hla typing information

Номер: US20180225412A1

Автор: Daniel McCloskey

Принадлежит: Pirche AG

Aspects relate to a method for selecting a transplantation donor or selecting a mismatched allele group of a transplantation donor, wherein two-field specific HLA protein typing is unavailable for said donor(s) and/or recipient(s). Other aspects include computer-software and systems for carrying out said method.

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Номер записи: 80

25-07-2019 дата публикации

MULTI-LEVEL, LABORATORY-BASED SURVEILLANCE SYSTEM FOR DETECTION OF INTRAOPERATIVE "ESKAPE" BACTERIAL PATHOGENS FOR HCAI PREVENTION

Номер: US20190226004A1

Автор: Loftus Randy W.

Принадлежит:

The present invention provides systems and methods for surveillance, diagnosis, and evaluation of high risk bacterial transmission events. The systems and methods utilize software and computational systems that automate identification, surveillance, and communication. The invention further includes archival systems for use in the systems and methods that compile bacterial isolates linked to information about patients, pre-operative, intra-operative, or post-operative arenas, healthcare providers, and the like. 1. A method of preventing bacteria transmission comprising: obtaining infection risk information from one or more pre-operative, intra-operative, or post-operative arenas;', 'screening patients for development of or as having a high risk for development of infection, wherein said screening comprises processing the infection risk information; and', 'identifying one or more patients as being at risk for a particular post-operative infection based on said screening; and, 'identifying patients at risk of developing postoperative infections, wherein said identifying comprisesproviding one or more patients identified as being at risk for a particular post-operative infection with one or more treatments capable of treating or preventing said infection;obtaining physical samples from environment, patient, hand and other samples from the identified high risk patient, operating room, and hospital ward;wherein the method results in infection reduction.2. The method of claim 1 , wherein said identifying one or more patients further comprises generating an alert claim 1 , and delivering said alert to a healthcare provider.3. The method of claim 1 , wherein said processing comprises predictive modeling; and wherein said screening comprises an automatic process of detecting patients who develop infections and/or require the acquisition of patient cultures for assessment of infection.4. The method of claim 1 , further comprising: (a) using a collection kit for ordered ...

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Номер записи: 81

25-07-2019 дата публикации

SYSTEMS AND METHODS FOR BIOMETRIC DATA COLLECTIONS

Номер: US20190228247A1

Автор: Jovanovich Stevan B., KING David, Park Chungsoo Charles, Schueren Robert A.

Принадлежит:

A biometric biochemical analysis system includes a user interface module to provide instructions for collecting and handling biochemical sampling and processing related to biometric data gathering as well as capturing biometric data using digital data capturing devices. The user interface module and display are integrated with analysis and communications portions of the biometric biochemical analysis system to provide a portable system for multi-portion data collecting, storage, verification, and analysis. 1. A system comprising:(I) an authentication sub-system comprising a camera and/or a microphone, and(II) a biochemical analysis sub-system configured to perform a biochemical analysis on a biological sample provided to the biochemical analysis sub-system, and(III) a communications interface; (a) instruct an authenticated user to provide a biological sample to the biochemical analysis sub-system;', '(b) without further user input, automatically execute a biochemical analysis on the biological sample; and', '(c) communicate, through the communications interface, data obtained from the biochemical analysis to a server, wherein the server is configured to determine whether the communicated data match a record in a database., 'wherein the system is configured to2. The system of claim 1 , wherein the system is further configured to authenticate the user by facial recognition based on one or more images taken by the camera or by voice recognition based on voice sound picked up by the microphone claim 1 , wherein authentication proceeds without an active command from the user.3. The system of wherein the biochemical analysis sub-system comprises an electrophoresis analyzer.4. (canceled)5. The system of configured to operate the camera to periodically or continually scan the environment for a user that can be authenticated.6. The system of wherein the biochemical analysis comprises performing a biochemical reaction on an analyte in the biological sample to produce a ...

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Номер записи: 82

16-07-2020 дата публикации

METHOD AND APPARATUS FOR ANALYTE MEASUREMENTS USING CALIBRATION SETS

Номер: US20200227144A1

Автор: Callicoat David N., Soldo Monnett H.

Принадлежит:

Examples of methods and apparatus are described that permit an analyte concentration to be estimated from a measurement in the presence of compounds that interfere with the measurement. In one example, the method can reduce the error in the estimation of analyte concentration in the presence of interferents. The method can include the use of one or more calibration set to determine analyte concentration. From a sample measurement, each calibration set can be tested to determine if it is eligible to estimate the analyte concentration in the sample. An estimate of analyte concentration can then be produced, based at least in part on the eligible calibration sets and on the sample measurement. In some implementations, if no calibration sets are eligible, an action is taken such as not outputting an estimate, displaying an alarm or alert, or providing a notification. 1. A method for estimating a concentration of an analyte in a sample , the method comprising:receiving one or more calibration sets, each calibration set usable to estimate an analyte concentration for a sample;accessing a measurement of the sample;processing the measurement of the sample to reduce or minimize effects on the estimate of concentration of the analyte caused by one or more interferents;determining, for each of the one or more calibration sets, whether the calibration set is eligible to estimate analyte concentration from the processed measurement of the sample; anddetermining, via execution of instructions by a computing system comprising computing hardware, an estimated analyte concentration for the sample based at least in part on the processed measurement of the sample and the calibration sets determined to be eligible.2. The method of claim 1 , wherein the one or more calibration sets comprise a plurality of calibration sets.3. The method of claim 1 , wherein the sample includes at least one component of blood claim 1 , and wherein the analyte comprises glucose.4. The method of claim 1 , ...

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Номер записи: 83

16-07-2020 дата публикации

METHODS AND SYSTEMS FOR BIOLOGICAL SEQUENCE COMPRESSION TRANSFER AND ENCRYPTION

Номер: US20200228507A1

Автор: Anderson Jason Michael, Godinez-Moreno Ricardo, Olivares-Amaya Roberto, Quiroz-Zarate Alejandro, Sinclair David A

Принадлежит:

A device for compressing subject data. the device comprises a communication link, the communication link capable of receiving a set of subject data; a compression module, the compression module configured to apply a compression algorithm to the set of subject data, the compression algorithm compressing the set of subject data using a reference string of subject data; and a transmission module, the transmission module configured to transmit the compressed subject data. The device further comprising an encryption module for encrypting the subject data. 19-. (canceled)10. A device for encrypting subject data , the device comprising:a communication link, the communication link capable of receiving a set of subject data, the set of subject data including a plurality of subject data reads, the plurality of subject data reads having at least one data point;an encryption module, the encryption module encrypting the plurality of subject data reads using a single cipher encryption method; anda transmission module, the transmission module configured to transmit the encrypted subject data.11. The device of claim 10 , wherein the encryption module executes an encryption process claim 10 , the encryption process comprising the steps of:generating a plurality of random keys for each of the plurality of subject data reads, and assigning the plurality of random keys to each of the plurality of subject data reads, the random key including a plurality of key data points equal to the number of data points in the assigned subject data read;assigning numerical values to every data point, the numerical value based on the value of the data point;executing a modulo adding process to add the numerical values of the random key to the numerical values of the assigned subject data read; andgenerating an encrypted subject data read.12. The device of claim 11 , wherein the plurality of random keys are generated based on the received subject data reads.13. The device of claim 12 , wherein the ...

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Номер записи: 84

10-09-2015 дата публикации

Information processing apparatus

Номер: US20150254396A1

Автор: Akitsugu Tsuchiya, Keigo Tamura, Tomohiro Ogawa, Toshimasa Aoki

Принадлежит: Sony Computer Entertainment Inc

A communication section receives a connection request from a game controller to connect the game controller with an information processing apparatus. A registered user information holding section holds biometric information of a user registered in the information processing apparatus. A biometric authentication portion compares biometric information of a user included in a taken image with biometric information held in the registered user information holding section to determine whether the imaged user is a user registered in the information processing apparatus. After the imaged user is found to be a user registered in the information processing apparatus, a login controller executes login processing of the user, or to be more specific, stores information for identifying a device included in the taken image and information for identifying the user into a login user storage portion by relating these items of information with each other.

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Номер записи: 85

13-11-2014 дата публикации

System and method for aligning genome sequence in consideration of read quality

Номер: US20140336941A1

Автор: Minseo Park

Принадлежит: Samsung SDS Co Ltd

Provided are a system and/or apparatus, and a method, for aligning a genome sequence. The system and/or apparatus includes a corrector configured to correct quality of input reads, a seed generator configured to generate one or more seeds from the corrected reads, and an aligner configured to perform a global alignment operation of the corrected reads in a reference sequence using the generated seeds.

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Номер записи: 86

01-08-2019 дата публикации

BIOLOGICAL INFORMATION PROCESSING METHOD AND DEVICE, RECORDING MEDIUM AND PROGRAM

Номер: US20190237164A1

Автор: Sakurada Kazuhiro

Принадлежит:

Provided is a biological information processing method and a device, a recording medium and a program that are able to predict and control changes in the state of an organism. The expression level of molecules in an organism is measured over a specific time interval; the measured time-series data is divided into a periodic component, an environmental stimulus response component and a baseline component; constant regions of the time-series data are identified from variations in the baseline component or from the amplitude or periodic variations of the periodic component; and causal relation between the identified constant regions is identified. The relation between the external environment and variations in the internal environment is identified and from the identified causal relation between the constant regions, changes in the state of the organism are inferred. 1. A biological information processing method , comprising:acquiring environmental information associated with an environmental condition of a first organism;acquiring genetic information associated with a gene sequence of the first organism;acquiring epigenetic information associated with a temporal change of epigenetic modification in the first organism; andanalyzing similarity between the first organism and a second organism associated with the acquired environmental information, the genetic information and the epigenetic information.2. The method according to claim 1 , wherein the epigenetic modification includes DNA methylation or histone modification.3. The method according to claim 1 , wherein the temporal change of epigenetic modification is based on a temporal change of expression level of a biological molecule.4. The method according to claim 3 , wherein the biological molecule includes a blood molecule.5. The method according to claim 3 , wherein the temporal change of epigenetic modification is obtained on a basis of a temporal change of an amount of blood glucose measured by a glucose meter.6. ...

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Номер записи: 87

09-09-2021 дата публикации

SYSTEMS AND METHODS FOR AUTOMATIC DETECTION AND QUANTIFICATION OF PATHOLOGY USING DYNAMIC FEATURE CLASSIFICATION

Номер: US20210279872A1

Автор: Humphries Stephen M., Lynch David A.

Принадлежит:

Methods, devices, and systems are provided for quantifying an extent of various pathology patterns in scanned subject images. The detection and quantification of pathology is performed automatically and unsupervised via a trained system. The methods, devices, and systems described herein generate unique dictionaries of elements based on actual image data scans to automatically identify pathology of new image data scans of subjects. The automatic detection and quantification system can detect a number of pathologies including a usual interstitial pneumonia pattern on computed tomography images, which is subject to high inter-observer variation, in the diagnosis of idiopathic pulmonary fibrosis. 1. A computer-based diagnostic system comprising:a machine learning unit configured to classify a region of an organ of a patient as an abnormal image pattern based on a tomographic image of the organ using a plurality of trained neural networks to obtain a classification result, the abnormal image pattern corresponding to pathological tissue; and calculate a quantitative score based on the classification result, and', 'output the quantitative score via a display device,, 'processing circuitry configured to'} the trained neural networks correspond to a plurality of processing stages of the machine learning unit,', 'the trained neural networks are configured to delineate a plurality of respective regions of pathological tissue from regions of healthy tissue within a segment of the organ, and', 'the trained neural networks are further configured to classify each of the plurality of respective regions of pathological tissue as corresponding to the abnormal image pattern., 'wherein'}2. The computer-based diagnostic system of claim 1 , wherein the processing circuitry is further configured to generate an elements dictionary based on a plurality of sample image data scans received from a plurality of subjects.3. The computer-based diagnostic system of claim 2 , wherein the plurality ...

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Номер записи: 88

09-09-2021 дата публикации

PROTEIN STRUCTURE PREDICTION SYSTEM

Номер: US20210280268A1

Автор: Blattner Frederick R., DARNELL Steven J., LARSON Matthew R., MITCHELL Amanda E., SCHROEDER John L.

Принадлежит: DNASTAR, INC.

The present invention is an accelerated conformational sampling method for predicting target peptide and protein structures comprising a process of determining energy minimized synthetic templates using a simple system for modeling individual molecular bonds within the subject peptide or protein. Use of these synthetic templates greatly reduces the computational resources necessary for optimally determining structural features of the target peptide or protein. The present invention also provides methods for rapid and efficient analysis of the effect of mutations on target peptides and proteins. 1. A conformational sampling method for predicting the structure of an amino acid sequence , the amino acid sequence comprising a plurality of residues , comprising:a) creating a sequence profile matrix of the amino acid sequence;b) determining an alignment of each respective residue of the amino acid sequence against the sequence profile matrix;c) identifying internal contacts for one or more residues in the plurality of residues using the alignment;d) collecting the features of the sequence profile matrix and internal contacts for each residue in the plurality of residues into a collected feature matrix;e) aligning the collected feature matrix using one or more threading models with a structural feature database of original templates;f) selecting a plurality of optimally aligned original templates from the aligning e);g) calculating normal modes of motion for each original template in the plurality of optimally aligned original templates;h) perturbing each respective original template in the plurality of optimally aligned original templates, for each pair of calculated normal modes, thereby collectively creating a plurality of synthetic templates;i) scoring the energy difference between each original template and the corresponding synthetic template;j) selecting a subset of synthetic templates from the plurality of synthetic templates based on satisfaction of a ...

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Номер записи: 89

06-09-2018 дата публикации

Methods of Treating and Preventing Influenza Infections

Номер: US20180250383A1

Автор: Gerald W. Fischer, Luke T. Daum

Принадлежит: Longhorn Vaccines and Diagnostics LLC

The invention relates to composite antigens comprising a peptide with contiguous amino acid sequence derived from a plurality of antigenic epitopes of one or more pathogens that induces an immune response in a mammal that is protective against infection by the one or more pathogens. In addition, the invention relates to vaccines comprising composite antigens and to method for treating and preventing an infection.

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Номер записи: 90

21-10-2021 дата публикации

Energy Expenditure

Номер: US20210327556A1

Автор: Aaron B. Weast, Aaron K. Goodwin, James M. Mullin, John M. Schmitt

Принадлежит: Nike Inc

Aspects relate to calculating energy expenditure values from an apparatus configured to be worn on an appendage of a user. Steps counts may be quantified, such as by detecting arm swings peaks and bounce peaks in motion data. A search range of acceleration frequencies related to an expected activity may be established. Frequencies of acceleration data within a search range may be analyzed to identify one or more peaks, such as a bounce peak and an arm swing peak. Novel systems and methods may determine whether to utilize the arm swing data, bounce data, and/or other data or portions of data to quantify steps. The number of peaks (and types of peaks) may be used to choose a step frequency and step magnitude. At least a portion of the motion data may be classified into an activity category based upon the quantification of steps.

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Номер записи: 91

22-08-2019 дата публикации

Cell-free detection of methylated tumour dna

Номер: US20190256921A1

Автор: Christopher R. Mueller, Marc-Henri Stern

Принадлежит: INSTITUT CURIE, Institut National de la Sante et de la Recherche Medicale INSERM, Queens University at Kingston

Provided herein is a method for detecting a tumour that can be applied to cell-free samples, e.g., to cell-free detect circulating tumour DNA. The method utilizes detection of adjacent methylation signals within a single sequencing read as the basic positive tumour signal, thereby decreasing false positives. The method comprises extracting DNA from a cell-free sample obtained from a subject, bisulphite converting the DNA, amplifying regions methylated in cancer (e.g., CpG islands, CpG shores, and/or CpG shelves), generating sequencing reads, and detecting tumour signals. To increase sensitivity, biased primers designed based on bisulphite converted methylated sequences can be used. Target methylated regions can be selected from a pre-validated set according to the specific aim of the test. Absolute number, proportion, and/or distribution of tumour signals may be used for tumour detection or classification. The method is also useful in, e.g., predicting, prognosticating, and/or monitoring response to treatment, tumour load, relapse, cancer development, or risk.

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Номер записи: 92

22-08-2019 дата публикации

GENE MUTATIONS AND COPY NUMBER ALTERATIONS OF EGFR, KRAS AND MET

Номер: US20190256927A1

Автор: KOPETZ Scott, Talasaz AmirAli

Принадлежит:

Sequence variants and copy number variations in the EGFR, KRAS and MET genes are biomarkers for resistance to anti-EGFR therapies for cancer. This disclosure provides methods of detecting these biomarkers and using them in the diagnosis and treatment of cancer. 168-. (canceled)69. A method of treating a cancer in a subject , the method comprising administering to the subject a cancer treatment other than an anti-EGFR therapy , wherein the cancer comprises cancer cells , the cancer cells comprising an EGFR nucleotide sequence variant that encodes EGFR comprising a G465V , T130A , D1083N , I491R , K467I , K1061T , and/or V876M variation.70. The method of claim 69 , wherein the cancer has been determined to comprise cancer cells comprising the EGFR nucleotide sequence variant.71. The method of claim 69 , wherein the at least one EGFR nucleotide sequence variant includes at least one of G>T G465V claim 69 , A>G T130A claim 69 , G>A D1083N claim 69 , T>G I491R claim 69 , A>T K467I claim 69 , A>C K1061T claim 69 , and G>A V876M.72. The method of claim 69 , wherein the cancer is colorectal cancer or head and neck cancer.73. The method of claim 69 , wherein the subject has previously been treated with anti-EGFR therapy.74. The method of claim 69 , wherein the cancer comprises cancer cells comprising an EGFR gene amplification.75. The method of claim 69 , wherein the cancer is unresponsive to cetuximab.76. The method of claim 69 , wherein the subject is refractory to 5-FU-based therapy.77. The method of claim 69 , wherein the cancer cells further comprise a KRAS nucleotide sequence variant and/or a KRAS gene amplification.78. The method of claim 69 , wherein the cancer cells further comprise a KRAS nucleotide sequence variant that encodes a G12C claim 69 , G12R claim 69 , G13D claim 69 , or Q61H KRAS variant.79. The method of claim 69 , wherein the cancer cells do not comprise a KRAS nucleotide sequence variant.80. The method of claim 69 , wherein the cancer has been ...

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Номер записи: 93

27-09-2018 дата публикации

Attenuated virus mutated at sites of evolutionarily conserved rna structure

Номер: US20180273911A1

Автор: Eli Goz, Hadas Zur, Shimshi ATAR, Tamir Tuller

Принадлежит: Ramot at Tel Aviv University Ltd, Synvaccine Ltd, Yeda Research and Development Co Ltd

Attenuated viruses and methods of designing them are disclosed. In one embodiment, there is disclosed an attenuated form of a virulent virus comprising an RNA encoding a viral protein or a nucleic acid sequence transcribable to said RNA, wherein the folding energy or structure of the RNA is changed at positions of evolutionarily conserved RNA structures with respect to that of said RNA encoding said viral protein in the virulent virus so as to bring about attenuation of the virus.

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Номер записи: 94

25-11-2021 дата публикации

Methods, Devices and Systems for Analyte Monitoring Management

Номер: US20210366579A1

Автор: Erwin S. Budiman

Принадлежит: Abbott Diabetes Care Inc

Methods of analyte monitoring management are provided. The methods include indicating on a user interface a plurality of analyte management procedures available for user-selection, where the plurality of analyte management procedures relate to analyte management parameters. Embodiments include receiving an indication to initiate a first procedure of the plurality of analyte management procedures, where the first procedure is for determining a first analyte management parameter. The methods may further include outputting user-instructions associated with the first procedure; receiving analyte measurement data for the first procedure; estimating the first analyte management parameter based on the analyte measurement data; calculating a degree of certainty for the estimation of the first analyte management parameter; and, initiating an action in response to an event associated with a status of the estimation of the first analyte management parameter or the degree of certainty. Analyte monitoring devices and systems implementing the methods are also provided.

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Номер записи: 95

25-12-2014 дата публикации

System and method for aligning genome sequence considering mismatch

Номер: US20140379270A1

Автор: Min Seo PARK

Принадлежит: Samsung SDS Co Ltd

A system and method for aligning a genome sequence considering mismatches are provided. The system for aligning a genome sequence includes an error bound calculation unit configured to calculate an error bound of a read according to a length of the input read, a comparison unit configured to calculate an error number estimate of the read and compare the error bound with the calculated error number estimate, and an alignment unit configured to perform a global alignment of the input read with a reference sequence when the comparison result shows that the calculated error number estimate is less than or equal to the error bound.

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Номер записи: 96

25-12-2014 дата публикации

System and method for aligning genome sequence

Номер: US20140379271A1

Автор: Min Seo PARK

Принадлежит: Samsung SDS Co Ltd

A system and method for aligning a genome sequence are provided. The system for aligning a genome sequence includes a seed generation unit configured to generate a plurality of seeds from an input read, a filtering unit configured to map the generated seeds to a reference sequence and select target seeds for global alignment from the mapped seeds in consideration of gaps between the mapped seeds, and an alignment unit configured to perform a global alignment of the read with the reference sequence in mapping positions in which the selected seeds are mapped to the reference sequence.

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Номер записи: 97

04-10-2018 дата публикации

System and method for controlling information presented to user referring to contents

Номер: US20180285351A1

Автор: Hiroki Sato, Miaomei LEI, Toshinori Miyoshi, Yoshiki Niwa

Принадлежит: HITACHI LTD

Provided is a system which controls information presented to a user referring to contents including a plurality of elements, outputs the contents to an output device, obtains bioinformation of the user at a time when each of the elements included in the contents is output to the output device, calculates an understanding level of the user with respect to each of the elements included in the contents, based on each piece of the obtained bioinformation, determines the understanding type based on the calculated understanding level and a difficulty level indicated by the difficulty level information of the elements of which the understanding level is equal to or lower than a first threshold value, in a case where it is determined that the user does not understand the contents based on the calculated understanding level, and outputs the presented information which corresponds to the determined understanding type to the output device.

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Номер записи: 98

03-09-2020 дата публикации

Bambam: parallel comparative analysis of high-throughput sequencing data

Номер: US20200279617A1

Автор: David Haussler, John Zachary Sanborn

Принадлежит: UNIVERSITY OF CALIFORNIA

A differential sequence object is constructed on the basis of alignment of sub-strings via incremental synchronization of sequence strings using known positions of the sub-strings relative to a reference genome sequence. An output file is then generated that comprises only relevant changes with respect to the reference genome.

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Номер записи: 99

24-09-2020 дата публикации

System and method for modelling system behaviour

Номер: US20200302094A1

Автор: Nigel John Conrad Greenwood

Принадлежит: Evolving Machine Intelligence Pty Ltd

A method of modelling system behaviour of a physical system, the method including, in one or more electronic processing devices obtaining quantified system data measured for the physical system, the quantified system data being at least partially indicative of the system behaviour for at least a time period, forming at least one population of model units, each model unit including model parameters and at least part of a model, the model parameters being at least partially based on the quantified system data, each model including one or more mathematical equations for modelling system behaviour, for each model unit calculating at least one solution trajectory for at least part of the at least one time period; determining a fitness value based at least in part on the at least one solution trajectory; and, selecting a combination of model units using the fitness values of each model unit, the combination of model units representing a collective model that models the system behaviour.

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Номер записи: 100