Abstract: A computer implemented method for predicting an agronomical value and a breeding value of a plant belonging to a population, the method includes the steps of: obtaining at least some genotypic data from a subset of lines from the population, obtaining at least some phenotypic data from a subset of lines from the population, providing a statistical model receiving in input the genotypic data and phenotypic data, using the statistical model to output at least an agronomical value estimated for the plant. More particularly, the statistical model is a mixed model combining fixed effects and random effects.

Abstract: Disclosed herein are optimized guide RNAs (gRNAs) that have increased target binding specificity and reduced off-target binding. Further disclosed herein are methods of designing and using the optimized gRNAs.

Abstract: A genomic data analysis architecture includes a plurality of application nodes, each application node including a calculation system including at least one calculation node, the calculation system being constructed and arranged so as to carry out genomic calculations, a human-machine interface constructed and arranged so as to communicate with the calculation system, and a knowledge base access interface, and including a knowledge base constructed and arranged so as to communicate with the plurality of application nodes. The knowledge base contains genomic data.

Abstract: Methods, devices, and systems are provided that determine analyte trends according to different methods depending on whether a change-resistant state is active or not active. The method used when the change-resistant state is activated provides for different requirements for a resulting analyte trend to transition between states (e.g., level to non-level). Furthermore, in some aspects, methods, devices, and systems of selecting or modifying a response rate of an analyte monitoring device for an individual user are provided. User instructions for selecting or modifying a response rate of the device or system is received externally via a user interface or communication channel. The response rate of the analyte monitoring device or system is then selected or modified to the first response rate, and the device or system operated with the first response rate.

Abstract: A molecular state machine is implemented in a cell by designing the cell to use specific homology directed repair (“HDR”) templates for repairing double strand breaks in polynucleotides based on a current “state” of the cell. The state may be established by the presence of a molecule in the cell or by the availability of specific cut sites in the polynucleotides of the cell. Different HDR templates or different nucleases may be available for performing HDR based on the state. When the state is changed, the same signal or event will result in a different HDR template being incorporated into the existing polynucleotides of the cell. Signals that are internal or external to the cell may be used to change the state of the cell. The cell may create a log of molecular events, store binary data, or perform other synthetic biology/molecular computing functions based on state.

Abstract: The invention provides methods and reagents for diagnosing prostate cancer that are based on the detection of biomarkers in the circulating nucleic acids from a patient to be evaluated.

Abstract: The invention provides a method of determining turbidity and concentration simultaneously a sample by irradiating the sample with a single incident wavelength and simultaneously measuring wavelength shifted (IE) and unshifted (EE) light emitted. A relative volume of light emitted from two phases may be determined, wherein the two phases comprise a first Rayleigh and Mie scattering and fluorescent phase associated with suspended particles, and a second, non-scattering but fluorescent phase associated with suspending solution. Volumes of the phases and/or concentrations of specific fluorophores or Raman active species are calculated from the volume of light emitted by the first phase relative to the total volume of light emitted from the first and second phases.

Abstract: A wearable device supports continuous wearability and operation with a supplemental set of removable and replaceable batteries that recharge a first set of batteries powering the device. In an aspect, the wearable system includes a head portion coupled to an appendage of a user, where the head portion includes an electronic system powered by a first set of batteries, and a modular housing releasably engageable to the head portion that includes a second set of batteries. In this manner, the modular housing can be removed and recharged independent from the head portion, and then recoupled to the head portion to recharge the first set of batteries. Thus, in an aspect, the first set of batteries can continuously power the electronic system without a need for removal of the head portion. Such a system can be particularly advantageous for continuous, uninterrupted health and fitness monitoring.

Abstract: A method for allocating resources among multiple sub-models in a simulation of a biological cell is described herein. The method receives an initial state dataset including initial aggregate resources in a plurality of sub-models, which make up a whole cell model. The method calculates, at a first time step, an outcome of each of the sub-models, which includes a local production, a local consumption and local net value of at least one resource shared between at least two sub-models. The method calculates a subsequent state dataset based on the outcome of each of the sub-models. The subsequent state dataset includes subsequent aggregate resources, the local production, the local consumption and local net value. The method determines, at a second time step, a second outcome of each of the plurality of sub-models based on the subsequent aggregate resources and the local production, local consumption and local net value.

Abstract: Mathematical models for the analysis of signal data generated by sequencing of a polynucleotide strand using a pH-based method of detecting nucleotide incorporation(s). In an embodiment, the measured output signal from the reaction confinement region of a reactor array is mathematically modeled. The output signal may be modeled as a linear combination of one or more signal components, including a background signal component. This model is solved to determine the nucleotide incorporation signal. In another embodiment, the incorporation signal from the reaction confinement region of a reactor array is mathematically modeled.

Abstract: A system is provided with an insulin delivery device configured to deliver insulin to a user of the system and a computer-based control unit associated with the insulin delivery device. The computer-based control unit includes a user interface and a computer-based processor. The computer-based processor is configured to calculate a relative insulin on board value for a specific time by calculating a first value that represents a reference insulin on board value at the specific time, calculating a second value that represents an automated insulin on board value at the specific time, and subtracting one of the first and second values from the other. The automated insulin on board value represents at least one insulin delivery automatically specified by the computer-based control unit. Methods of use are also disclosed.

Abstract: Methods and systems and for calculating light projection obstruction in human vision analyses are described. The methods and systems include an integration of formulas, algorithms, databases, and interactive interfaces that capture, document, and deliver the results of human vision studies. The methods and systems calculate the amount of vision obstruction for a particular device by producing a rendered image having pixels and designating the pixels in the rendered image to have various colors. Certain types of colors are designated for representing objects in the rendered image to be visible to the user, and other types of colors are designated to represent objects that are obstructed in the rendered image. The methods and systems may also be integrated into, and displayed within, conventional virtual reality, augmented reality, and/or mixed reality equipment and/or systems.

Abstract: A method of predicting a phenotypical age of a subject based on a microflora taxonomic profile of a microbiota of the subject can include: isolating a plurality of microorganism nucleic acids of microorganisms from a sample of a microbiota of the subject; analyzing the plurality of microorganism nucleic acids to determine an amount of the microorganisms of the microbiota based on the plurality of microorganism nucleic acids; generating a taxonomic profile of the microbiota of the subject based on the amount of each of the microorganisms; processing the taxonomic profile of the microbiota with a computer configured with a machine learning platform in order to predict the phenotypical age of the subject; generating a report with the predicted phenotypical age of the subject; and providing the report to the subject.

Abstract: Mechanisms are provided to implement a genomic database curation (GDC) system. The GDC system generates a ground truth database based on a training subset of datasets from an uncurated large scale genomic database, and label metadata for the training subset. The GDC system trains at least one classification engine of the GDC system based on the training subset and the ground truth database at least by performing a machine learning operation on the at least one classification engine. The GDC system automatically applies the at least one trained classification engine on the uncurated large scale genomic database to generate an automatically curated large scale genomic database. A meta-classifier engine generates an output specifying at least one of significant gene signatures or gene pathways for at least one of diseases or drug agents based on the automatically curated large scale genomic database.

Abstract: Methods for non-invasive prenatal paternity testing are disclosed herein. The method uses genetic measurements made on plasma taken from a pregnant mother, along with genetic measurements of the alleged father, and genetic measurements of the mother, to determine whether or not the alleged father is the biological father of the fetus. This is accomplished by way of an informatics based method that can compare the genetic fingerprint of the fetal DNA found in maternal plasma to the genetic fingerprint of the alleged father.

Abstract: The present invention relates to a method of enhancing the detection of a signal from biomarker data in a subject or group of subjects.

Abstract: The present invention relates to a method and system for determining Copy Number Variations (CNVs) in a genomic test sample including target amplicons and a reference amplicons. Specifically, nucleic acid melting curves are generated for the test sample. A mathematical model is fitted to each of the nucleic acid melting curves to separate target and reference melting reactions within the measured nucleic acid melting curve. The fitting parameters of the mathematical model are calculated. A CNV of the test sample is determined based on the fitting parameters of the mathematical model corresponding to the target and reference melting reactions.

Abstract: The present invention provides a combination of genomic and computational technologies to provide rapid, portable sample analysis for sequencing or identifying a target sequence involving generating probes for use in analyzing a sample which may comprise a target sequence.

Abstract: A method can include storing input electrical signal data representing at least a given electrophysiological signal acquired from a patient. A non-local mean filter can be applied to the given electrophysiological signal, the non-local mean filter including a spatial filter component and an intensity filter component. The method can also include controlling parameters to establish weighting of each of the spatial filter component and the intensity filter component in response to a control input. Filtered signal data can be stored based on the applying and the controlling.

Abstract: Methods for non-invasive prenatal paternity testing are disclosed herein. The method uses genetic measurements made on plasma taken from a pregnant mother, along with genetic measurements of the alleged father, and genetic measurements of the mother, to determine whether or not the alleged father is the biological father of the fetus. This is accomplished by way of an informatics based method that can compare the genetic fingerprint of the fetal DNA found in maternal plasma to the genetic fingerprint of the alleged father.