Abstract: Techniques for generating therapy biomarker scores and visualizing same. The techniques include determining, using a patient's sequence data and distributions of biomarker values across one or more reference populations, a first set of normalized scores for a first set of biomarkers associated with a first therapy, and a second set of normalized scores for a second set of biomarkers associated with a second therapy, generating a graphical user interface (GUI) including a first portion associated with the first therapy and having at least one visual characteristic determined based on a normalized score of the respective biomarker in the first set of normalized scores; and a second portion associated with a second therapy and having at least one visual characteristic determined based on a normalized score of the respective biomarker in the second set of normalized scores; and displaying the generated GUI.

Abstract: Methods and systems for use in sperm analysis are described. A method for processing measured data comprising at least interferometric phase data of label-free sperm cell(s), the processing comprising determining topographic optical phase delay map of the label-free sperm, determining at least one physical parameter of the label-free sperm, and generating data indicative of sperm quality for the label-free sperm. A device comprising a flow channel comprising an inlet for receiving fluid containing cells, a selection zone and at least two outlets at said selection zone; and a flow-driving mechanism comprising a flow-driving unit configured and operable to generate flow of said fluid from said inlet towards at least first of said at least two outlets, and a collecting driving unit selectively operating along the direction of a second outlet of said at least two outlets to direct a portion of interest of said fluid towards said second outlet.

Abstract: Disclosed are new and improved methods and systems for nucleic acid sequence analysis that can analyze data indicative of natural by-products of nucleotide incorporation events without the need for exogenous labels or dyes to identify nucleic acid sequences of interest. In particular, the methods and systems of the present teachings can process such data and various forms thereof to align fragments of the nucleic acid(s) of interest, particularly those analyzed using an addition sequencing technique, for example, as occurs with the use of nucleotide flows.

Abstract: The present invention relates to methods of using cell-free DNA analysis for guiding treatment of advanced prostate cancer. In particular, liquid biopsies are collected from urine and/or plasma of patients for measuring copy number variation in cell-free DNA associated with metastatic prostate cancer. In particular, urine genomic abnormality (UGA) and plasma genomic abnormality (PGA) values are contemplated for use in predicting treatment responses in advanced prostate cancer patients and for use in making decisions related to androgen deprivation therapy (ADT) treatment outcomes in hormone sensitive stage and for starting or changing chemotherapy treatments in castrate resistant advanced cancer stage.

Abstract: The application relates to hepatic fibrosis, specifically to hepatic fibrosis that may appear in a patient infected with one or more hepatitis viruses and/or who is suffering from hepatitis, specifically chronic hepatitis. The application provides methods and means for determining the stage (or degree) of hepatic fibrosis of such a patient. Specifically, the methods and means of the application make it possible to determine whether or not the stage (or degree) of hepatic fibrosis of the patient has exceeded the stage of light fibrosis. The methods and means of the invention use a combination of biomarkers such as, in particular, the CXCL10 protein and hyaluronic acid (HA).

Abstract: An information processing method is executed by a computer having a control unit, wherein the control unit executes: acquiring a plurality of biological signals; detecting for each predetermined time unit a peak part of the respective biological signals; attaching identical identification information to one or a plurality of peak parts forming an identical peak when attaching peak identification information to each of the biological signals; and extracting a combination of corresponding peaks from at least two biological signals on the basis of the identification information of each time unit of the at least two biological signals.

Abstract: Disclosed is a method for predicting an in vivo concentration of an analyte, including: estimating an in vivo intrinsic spectrum of the analyte; and predicting the in vivo concentration of the analyte by using a concentration predicting algorithm based on the estimated in vivo intrinsic spectrum and an in vivo spectrum obtained during a section in which the in vivo concentration of the analyte is not substantially changed.

Abstract: A method determines an amino acid sequence that binds to a target molecule or a base sequence encoding the same. The method pans for bringing a library constructed by a display method, followed by incubation. The method sequences for analyzing a base sequence before panning step and the polypeptide group of the library after panning by a next-generation sequencer, or determining an amino acid sequence based on a base sequence obtained by analyzing the base sequence of a nucleic acid encoding all the polypeptides by a next-generation sequencer. The method scores for evaluating and scoring, based on the results of the sequencing step, an amplification ratio. The method determines a sequence for selecting a polypeptide with a high score and determines an amino acid sequence of the polypeptide or a base sequence as an amino acid sequence that binds to the target molecule or as a base sequence of a nucleic acid encoding the polypeptide.

Abstract: A system and method for molecular design and simulation is disclosed. In one aspect, a system for simulating a molecular structure includes a processor configured to simulate the molecular structure, a head-mounted display (HMD) configured to display the molecular structure, and at least one handheld input device. The input device may be configured to: receive input from a user, the input being indicative of movement of the handheld input device in 6 degrees-of-freedom (DoF), and selectively map, based on additional user input and at least one property of the molecular structure, one of the DoF to one of a plurality of defined techniques for altering the molecular structure. The processor may be configured to modify the molecular structure based on the received input as mapped to the selected defined technique.

Abstract: A method for estimating the affinity ? of a first DNA strand, or “probe”, to be hybridized with a second DNA strand, or “target”, to form a hybrid of length Lbp, the method comprising: in each division of a set of M divisions of the hybrid, counting the number of times in which each hybrid of a set of P DNA strand hybrids is present in the division, the hybrids being of length k less than the length Lbp, or “k-hybrids”; for each combination of mismatches of a set of L combinations of mismatches in a hybrid of length Lbp, determining whether the pair of mismatches is present in the hybrid; and calculating the affinity ? according to the relation: ? = ? m = 1 M ? ? p = 1 P ? x m , p · ? ^ m , p + ? .

Abstract: A method for increasing the number of analyte/assay combinations in a single chip or cartridge of an in vitro diagnostic system may include: prioritizing a set of analyte/assay combinations based on characteristics of each analyte in the set of analyte/assay combinations, wherein the characteristics comprise one selected from the group consisting of a prevalence of each analyte, a clinical relevance of each analyte, a clinical actionability of each analyte, a patient benefit, a cost savings, and any combination thereof; deriving an analyte/analyte interactivity for two or more analytes in the set of analyte/assay combinations; designing a plurality of candidate panel layouts based on panel layout rules, the prioritization of the set of analyte/assay combinations, and the analyte/analyte interactivity, wherein the panel layout comprises one or more chips each comprising a chamber with two or more analytes; and validating the plurality of candidate panel layouts to produce panel layout solutions.

Abstract: Three-dimensional modeling of patient-specific tumors. In an embodiment, patient-specific data, representing a tumor microenvironment and one or more metrics, are received. A patient-specific spatial model, representing the tumor microenvironment as a lattice comprising a plurality of elastic material points, is generated from the patient-specific data. Patient-specific drug interaction and metabolism models are also determined. The tumor microenvironment is then simulated, for one or more drug interventions, through a plurality of iterations in which each elastic material point is updated in each iteration based on computations of chemical diffusion, biochemical reactions, metabolism, drug interactions, growth and death, and mechanical forces. A report, comprising a three-dimensional representation of the patient-specific spatial model after one or more iterations, is generated for the drug intervention(s).

Abstract: System that automates analysis of mass spectrometry data for oligonucleotides to generate pharmacokinetic parameters and models. A user inputs an oligonucleotide sequence and a maximum number of nucleotides that may be lost during metabolism while retaining therapeutic effectiveness. The system calculates the possible active metabolites and develops a mass spectrum filter for the mass-to-charge ratio of ions for these metabolites. Full-scan spectra are analyzed to calculate the total concentration of these active molecules present in a time series of samples. Pharmacokinetic models and parameters are calculated from the time series of total concentration. Because full-scan spectra are captured, assumptions may be modified and analyses may be quickly rerun without collecting additional data. Overall pharmacokinetic analysis is therefore much more streamlined and efficient, reducing cost, delay, and the need for a mass spectrometrist who is highly skilled in spectral analysis.

Abstract: Disclosed is a method for predicting an in vivo concentration of an analyte, including: estimating an in vivo intrinsic spectrum of the analyte; and predicting the in vivo concentration of the analyte by using a concentration predicting algorithm based on the estimated in vivo intrinsic spectrum and an in vivo spectrum obtained during a section in which the in vivo concentration of the analyte is not substantially changed.

Abstract: A flexible system capable of utilizing data from different monitoring techniques and capable of providing assistance to patients with diabetes at several scalable levels, ranging from advice about long-term trends and prognosis to real-time automated closed-loop control (artificial pancreas). These scalable monitoring and treatment strategies are delivered by a unified system called the Diabetes Assistant (DiAs) platform. The system provides a foundation for implementation of various monitoring, advisory, and automated diabetes treatment algorithms or methods. The DiAs recommendations are tailored to the specifics of an individual patient, and to the patient risk assessment at any given moment. A central data exchange node or server collects patient data from individual DiAs devices and provides safety assurance, monitoring, telemedicine and database building for the DiAs system.

Abstract: A mobile measurement device comprising a computing device; one or more sensors that are coupled to the computing device using one or more corresponding compatible digital interfaces; and logic encoded with instructions which when executed perform determining and storing vascular function information and one or more of: values of metrics or parameters; physiological analysis of the parameters and the vascular function information; recommendations for actions that an individual or healthcare provider should take in response to the recommendations or parameters. Embodiments further include processes for using vascular function information collected from a mobile measurement device to generate the parameters, analysis, and recommendations.

Abstract: A computer-implemented method for a monitoring device being executed by a processor of the monitoring device comprises acquiring at least two kinds of physiological signals via a sensor of the monitoring device, obtaining a signal quality index of each of the at least two kinds of physiological signals by the processor of the monitoring device, providing a homologous physiological parameter value corresponding to each of the at least two kinds of physiological signals by the processor of the monitoring device, and fusing the homologous physiological parameter values based on the signal quality index of each of the at least two kinds of physiological signals and providing a fused value of the homologous physiological parameter values by the processor of the monitoring device. The disclosed physiological parameter processing method avoids disadvantages caused by relying on a single physiological signal.

Abstract: Computationally-efficient techniques facilitate secure crowdsourcing of genomic and phenotypic data, e.g., for large-scale association studies. In one embodiment, a method begins by receiving, via a secret sharing protocol, genomic and phenotypic data of individual study participants. Another data set, comprising results of pre-computation over random number data, e.g., mutually independent and uniformly-distributed random numbers and results of calculations over those random numbers, is also received via secret sharing. A secure computation then is executed against the secretly-shared genomic and phenotypic data, using the secretly-shared results of the pre-computation over random number data, to generate a set of genome-wide association study (GWAS) statistics. For increased computational efficiency, at least a part of the computation is executed over dimensionality-reduced genomic data.

Abstract: Systems and methods configured to process motion data associated with a user. The systems and methods are configured to receive motion data from a sensor, calculate motion attributes from the data, and classify the motion data using one or more mathematical models. Attributes may be calculated without classifying the motion data into an activity type (such as walking, running, swimming, or any specific or general activity). Attributes may be compared to activity models comprising motion data from several individuals, which may not include the user. Motion data within the models and attributes of the user may be independent of any activity type. Attributes may be compared to select an energy expenditure model from one or more energy expenditure models, which may be selected as a best-match to the one or more motion attributes. An energy expenditure associated with the motion of the user may then be calculated.

Abstract: The purpose of the present invention is to make it possible to efficiently generate information for cell analysis. A feature-group information generating unit generates, as feature-group information, information including values of N types of feature parameters (wherein N represents an integer having a value of 1 or more) about a morphological feature of a single cell of a plurality of cells or a morphological feature of a cell population based on data of one or more cell images included in a unit, the one or more cell images in the unit being selected from cell images capturing the cell population including the cells in accordance with a predetermined requirement.