Abstract: Embodiments herein described provide methods for determining phenotypic parameters of cell populations and expressing them in terms of tensors that can be compared with one another. Embodiments provide methods for determining phenotypic parameters of cell populations in response to an agent. Embodiments provide methods for comparing effects of an agent on phenotypic parameters to effects of reference standards whose in vivo effects are known. Embodiments provide methods for predicting the effect of an agent by the comparison with the known effects of reference standards. Embodiments provide methods for classifying agents by their effects on phenotypic parameters. Embodiments provide software and computer systems for calculating multiparametric tensors, compressing their complexity and comparing them after compression.

Abstract: Techniques described herein relate to systems and methods for parallel DNA molecules sequencing. A preprocessor can receive raw data frames from a sensor chip including 100,000 or more cells, where each raw data frame can include detection signals from the 100,000 or more cells at a given time during the formation of the 100,000 or more cells or during the DNA molecules sequencing using the 100,000 or more cells. The preprocessor can then extract relevant information for determining states of the cells from the raw data frames, generate one or more digested frames that includes the extracted information, and send the digested frames to a processor for processing, such as base determination. Because the number of digested frames sent to the processor is less than a number of the raw data frames and the digested frames include preprocessed data, the amount of data being transferred to the processor and the amount of data processing by the processor can be reduced.

Abstract: An advice system employs a genetic analysis of a patient to identify one or more characteristics of the patient. The advice system employs the characteristics to identify one or more attributes of a medical device that would desirably exist in a medical device that is to be prescribed for the patient. The advice system then identifies from the one or more attributes one or more medical devices from among a plurality of medical devices whose features at least in part meet the one or more attributes. The advice system then outputs a recommendation of the one or more medical devices. The system employs known genes that are expressive of certain traits in a person, with the known traits being interpreted or evaluated in terms of characteristics that are relevant in selecting a medical device from among a plurality of medical devices, such as patient interface devices or other devices.

Abstract: The invention relates to a computer implemented method of analysing data comprising measured values of characteristics of objects in samples, the data comprising —a first set of data (Xireference)? with measured values of characteristics of objects in reference samples; —a test set of data (Xitest) with measured values of the characteristics of objects in a test sample; characterised by the method comprising; —fitting a control model to the first set of data to determine control loadings (Pcontrol) each representing an independent correlation between characteristics; —projecting the first set of data (Xireference) onto the control loadings (Pcontrol) for determining a first set control scores (Tcontrol,ireference) and determining one or more confidence intervals for the first set of control scores (Tcontrol,ireference); —projecting the test data onto the control loadings (Pcontrol) for determining test control scores; —determining if the test control scores are within one or more the confidence intervals.

Abstract: Systems and methods for molecular structure generation and conformer elaboration, in which natural physical molecular movements can be combined with a molecular force field that constrains those movements, to rapidly produce conformational variants with relatively low energy. Construction and energy minimization of initial and subsequent 3D molecular models using force field parameters, are combined with alteration of the molecular model using biophysical transformations, to generate one or more conformations thereof. The biophysical transformations each include natural physical movements of parts of the molecule, such as rotation of atoms or bonds about a selected axis in the 3D molecular model. The selected axis can define ring components, selected bonds within a macrocyclic ring, selected bonds joining substituents or other portions of the molecule, or axes or lines defining one or more geometric features of the molecular model.

Abstract: Described are computer-implemented methods, systems, and media for de novo phased diploid assembly of nucleic acid sequence data generated from a nucleic acid sample of an individual utilizing nucleic acid tags to preserve long-range sequence context for the individual such that a subset of short-read sequence data derived from a common starting sequence shares a common tag. The phased diploid assembly is achieved without alignment to a reference sequence derived from organisms other than the individual. The methods, systems, and media described are computer-resource efficient, allowing scale-up.

Abstract: A method for sequencing biopolymers. The method includes selecting with a sequence generator module an input nucleotide sequence having plural k-mers; simulating with a deep learning simulator, actual electrical current signals corresponding to the input nucleotide sequence; identifying reads that correspond to the actual electrical current signals; and displaying the reads. The deep learning simulator includes a context-dependent deep learning model that takes into consideration a position of a k-mer of the plural k-mers on the input nucleotide sequence when calculating a corresponding actual electrical current.

Abstract: A method and system for determining interaction sites between biosequences is described herein. A dataset of contact data for a plurality of biomolecule pairs is obtained to account their frequency of occurrence. Statistical weights are determined for each frequency of occurrence. Each vector of a statistical residual vector space (SRV) is decomposed through principal component decomposition. The vectors of the SRV are re-projected back to a new SRV with a new set of coordinates. A feature vector is generated and inputted into a predictor for outputting a likelihood of an interaction site.

Abstract: Systems and methods are provided for evaluating an alarm condition for a monitored patient in a population of one or more patients. One or more physiological parameters pertaining to the patient, or physiological variables, are used to form a time series describing the patient status. A dimension parameter such as a time series roughness statistic or a fractal dimension is used to estimate a dimension decision statistic over time. The dimension decision statistic is used as a measure of physiological condition. The dimension decision statistic may be compared to a threshold to determine a region of operation for the dimension of the physiological variable. The dimension decision statistic is used in an embodiment in combination with the underlying raw physiological variable value to reduce the rate of false alarms, to increase the frequency of missed detections, and to aid diagnostic decision making and to aid the formation of a crisis action plan.

Abstract: Systems and methods are provided for training a classifier to discriminate between a first cancer condition associated with an oncogenic pathogenic infection a second cancer condition that is not associated with an oncogenic pathogenic infection. Systems and methods are provided for distinguishing cancers associated with oncogenic pathogenic infections that contribute to the cancer pathology and cancers that are not associated with oncogenic pathogenic infections. Systems and methods are provided for treating cancer based on whether the cancer is associated with an oncogenic pathogenic infection.

Abstract: Methods, systems and circuits evaluate a subject's risk of developing type 2 diabetes using defined mathematical models of short term risk (STR) and longer term risk of progression. The evaluations can stratify risk for patients having the same glucose measurement, particularly those with intermediate or low (normal) fasting plasma glucose (FPG) values. The STR or IR (insulin resistance) model(s) may include an inflammatory biomarker such as an NMR derived measurements of GlycA and a plurality of selected lipoprotein components of at least one biosample of the subject. Embodiments of the invention also provide methods, systems and circuits that generate STR scores as a marker of beta-cell dysfunction or impairment.

Abstract: A method for evaluating the ability of cells to grow into a sheet includes (1) a step of examining cell cultures growing into a sheet to determine their impedance and/or electrical resistance or numerical values relating thereto; (2) a step of comparing the numerical values determined by Step (1) with reference values; and (3) a step of judging, based on the results of comparison obtained in Step (2), the ability of cells to grow into a sheet.

Abstract: Features for a quantitative biological data analysis system are described. Index sort analysis can be performed using sort electronics on a flow cytometer or other particle analysis system or after an experiment using a workstation. The sort electronics on the cytometer or other particle analysis system may generate sort decision information for the events. The sort decision information may be transmitted from the sort electronics to the workstation that may differ from the sort identified by the workstation. The feature fuse the gate information with the sorting decision information to provide an accurate representation of the sorting.

Abstract: The present invention provides processes for determining accurate risk probabilities for chromosome dosage abnormalities. Specifically, the invention provides non-invasive evaluation of genomic variations through chromosome-selective sequencing and non-host fraction data analysis of maternal samples.

Abstract: A method for analyzing a bipartite graph data structure to condense reaction pathways of a metabolic network is described herein. A cell's metabolic network is structured as a bipartite graph, with molecule nodes representing the molecules within metabolism and edges connecting molecule nodes representing chemical reactions or processes. Molecule nodes within the bipartite graph are categorized according to the number of edges leading into and out of each node. If the structure of the bipartite graph indicates that the molecule node does not contribute to flux value solutions of a mathematical model of the metabolic network, then the node and its connected reaction pathway is blocked or removed from the bipartite graph. Thus the complexity of the bipartite graph may be reduced, and crucial nodes and pathways identified.

Abstract: A representation of a nucleic acid sequence encodes a particular gene having at least one intron. An intron signature value corresponding to the at least one intron is determined based on a first computational function applied to at least one portion of the representation of the nucleic acid sequence corresponding to the at least one intron. A protein signature value is determined, being based on a second computational function applied to a representation of a protein. In a database, an association is formed between the intron and protein signature values. This process is repeated for each of a plurality of nucleic acid sequences. Nucleic acid sequences in the database are ordered based on a sort of corresponding intron signature values. An ordering determined by the sort is used to determine or confirm a role or function of a portion of a given nucleic acid sequence.

Abstract: The subject disclosure presents systems and computer-implemented methods for determining an acoustic time-of-flight (TOF) of sound waves through a sample material with greater accuracy and in a more repeatable fashion, by invoking one or more of an envelope generation for an error function, fitting a non-linear curve to an ultrasound frequency sweep, or performing a clustered piece-wise linear regression on individual linear parts of the ultrasonic frequency sweep. The systems and methods are useful for, among other things, monitoring diffusion of fluids through porous materials, such as tissue samples.

Abstract: Provided herein are methods and arrangements and related cell-free biomolecular breadboards configured to design, build, implement, debug, and/or test a genetic circuit to be operated in a target environment, by testing in a cell-free system under conditions of the target environment, molecular components of the genetic circuit and/or combinations thereof to select the molecular components and/or combinations thereof of a genetic circuit operative in the target environment.

Abstract: Provided herein are novel methods, systems and processes for generating and analyzing sequence data for the determination of the presence or absence of one or more genetic variations within a genome of a subject.

Abstract: Provided is a method for quantifying A? in plasma by treating the plasma with MPP and/or TCEP, and a method for diagnosing, using the quantifying method, whether or not clinical cognitive deterioration and pathological A? accumulation occur. Through cut-off values of measured values measured by the method for quantifying A? according to the present subject matter, it is possible to identify normal, MCI and AD subjects and determine whether or not accumulation of A? in the brain occurs, and it is possible to predict progression to AD.