Abstract: A bioinformatics process which provides an improved means to detect NFkB cellular signaling pathway in a subject, such as a human, based on the expression levels of at least six unique target genes of the NFkB cellular signaling pathway measured in a sample. The invention includes an apparatus comprising a digital processor configured to perform such a method, a non-transitory storage medium storing instructions that are executable by a digital processing device to perform such a method, and a computer program comprising program code means for causing a digital processing device to perform such a method. Kits are also provided for measuring expression levels of unique sets of NFkB cellular signaling pathway target genes.

Abstract: Systems and methods for in silico prediction of HLA type of a patient are presented in which patient sequence reads and a reference sequence with known and distinct HLA alleles are used in a de Bruijn graph. A composite match score is then used to rank HLA alleles, thus providing a first HLA type. A second HLA type is identified by re-ranking using an adjusted composite match score.

Abstract: An Amplicon Sequencing Analysis Pipeline (ASAP) system (120, 600) characterizes a genetic sample. The ASAP system (120, 600) receives assay configuration data individually associating reference sequences and genetic characteristics. The ASAP system (120, 600) processes amplicon sequencing data and the reference sequences to characterize the genetic sample based on the individual associations between the reference sequences and the genetic characteristics in the assay configuration data. The ASAP (120, 600) system transfers genetic data indicating the genetic characteristics for the genetic sample and indicating interpretation metrics for amplicon sequencing read depth and quality related to the genetic characteristics.

Abstract: A method (10) for forming novel signatures of biological data is provided. The method comprises ranking features based on a trend value, which is created based on multiple signatures identified by a pattern discovery method. Furthermore, a device (30) and a computer program product (40), performing the steps according to the method (10) is provided. Uses of the method, for statistically analyzing clinical data, designing assays based on multiple molecular signatures and interpreting assays based on multiple molecular signatures are also provided.

Abstract: A methods and processors for generating a 3D-representation of a tooth-specific dental appliance are disclosed. The appliance has a grooved body and a pair of holding arms. The method includes acquiring a 3D-platform representation, acquiring a 3D-grooved body representation, and positioning the 3D-grooved body representation relative to the 3D-platform representation. The method also includes acquiring a first and second 3D-arm representations, each having a respective pair of platform anchor points and a respective adjustment anchor point. The method also includes individually positioning the first and second 3D-arm representations relative to the 3D-platform representation using the respective pairs of platform anchor points, thereby defining preliminary positions of the first and second 3D-arm representations.

Abstract: This invention provides, inter alia, a complement-inhibitor-based treatment plan coupled with a risk evaluation and management strategy (“REMS”) and a safety support program (“SSP”) for reinforcing the REMS. The REMS and SPP are implemented using one or more computer devices with software tools programmed to enforce conditions of the REMS and/or prompt follow-ups by registered nurses enrolled in the SSP. The software tool(s) determines whether a prescriber requesting the complement inhibitor has agreed to abide by the REMS, and can prompt a provider of the complement inhibitor to provide updated educational materials to the prescriber at predetermined times or intervals, to monitor the prescriber for compliance with the REMS, and/or to monitor patients for signs of adverse events. Using exemplary embodiments described herein, a risk of adverse events (especially, but not limited to, meningococcal infections) can be managed and an incidence of the adverse events can be reduced.

Abstract: A computer of a prediction-rule generating system includes an input unit configured to input time series data of an abundance proportion of microorganisms or nucleotide sequences included in activated sludge in which a water treatment is performed and water quality information indicating water quality after a water treatment associated with data at each time constituting the time series data, a principal component analyzing unit configured to perform principal component analysis on the input time series data and calculate principal component scores of data at each time constituting time series data, and a prediction rule generating unit configured to generate a prediction rule for predicting water quality after a water treatment from an abundance proportion of microorganisms or nucleotide sequences on the basis of the calculated principal component scores and the input water quality information indicating water quality after a water treatment.

Abstract: This invention relates to a method for measuring viscosity of a fluid using particle diffusometry (PD). The method finds practical applications in detecting structural and functional changes of a biomolecular composition by comparing the viscosity change as compared with the standard of the biomolecular composition. This method may also find uses in clinical diagnosis and quality control of clinical biological medicines, food and feeds during the process of manufacturing, distribution and consumption.

Abstract: Systems and methods for using a flow cell array are provided herein. A system includes at least one processor coupled to a memory and configured for determining placement of one or more reaction sites on a first component; providing a material for the one or more reaction sites in one or more surface channels of the first component; connecting the first component to a second component to form an array, wherein the one or more surface channels of the first component connect the one or more reaction sites with one or more vias, and wherein the second component comprises the one or more vias connected to multiple sub-surface channels; and aligning the one or more surface channels of the first component with the one or more vias of the second component to form a connection between the first component and the second component.

Abstract: Systems, computer program products, and methods for using a flow cell array are provided herein. A computer program product includes a computer readable storage medium having program instructions embodied therewith, the program instructions executable by a device to cause the device to deliver multiple items of chemical matter independently to multiple reaction sites of a flow cell array across multiple distinct instances of time; image multiple parallel chemical reactions at the multiple reaction sites of the flow cell array; and record an emission from each of the multiple chemical reactions site.

Abstract: Disclosed are gene signatures that may be used to predict the recurrence of colorectal cancer in a human patient. These signatures can be used to determine when to treat a patient with post-operative adjuvant chemotherapy, i.e., when a high risk of colorectal cancer recurrence is predicted.

Abstract: This invention provides, inter alia, a complement-inhibitor-based treatment plan coupled with a risk evaluation and management strategy (“REMS”) and a safety support program (“SSP”) for reinforcing the REMS. The REMS and SPP are implemented using one or more computer devices with software tools programmed to enforce conditions of the REMS and/or prompt follow-ups by registered nurses enrolled in the SSP. The software tool(s) determines whether a prescriber requesting the complement inhibitor has agreed to abide by the REMS, and can prompt a provider of the complement inhibitor to provide updated educational materials to the prescriber at predetermined times or intervals, to monitor the prescriber for compliance with the REMS, and/or to monitor patients for signs of adverse events. Using exemplary embodiments described herein, a risk of adverse events (especially, but not limited to, meningococcal infections) can be managed and an incidence of the adverse events can be reduced.

Abstract: The present disclosure relates to methods and devices for amplifying a plurality of targets in a single PCR run while distinguishing between clinically relevant amplification and amplification from other sources such as from background contamination. The methods and devices further enable discrimination between gram-positive, gram-negative and fungal infections as wells as identify antimicrobial resistance genes. When applying the methods and devices of the invention, the species or genus of an infection(s), and genus of a fungal co-infection(s) or category of bacterial (gram-positive or negative) co-infection(s) are identified. Species identification of co-infections can also be achieved. Further, when applying the methods and devices of the invention, organisms which are likely to be contaminating organisms from a blood draw are identified.

Abstract: The invention relates to a method for determining interaction kinetics for an analyte. The method comprises first contacting a solution containing the analyte with immobilized ligand, or analogue thereof, immobilized on an optical sensor surface; monitoring the binding of the analyte to the immobilized ligand or analogue, wherein the binding is measured as a resulting change in a property of the surface; and automatically determining the interaction kinetics, which determining step includes first defining parts of the dissociation phase that contains kinetic information for fitting. The invention further relates to an analytical system for studying molecular interactions, which system is capable of performing the novel method, as well as a computer program product for performing the steps of the method.

Abstract: The invention provides an unbiased method to assess the binding of a test compound to a multiplicity of proteins in the same sample, including samples from living cells by applying the unbiased determination technique of SWATH-MS or the biased technique of SRM-MS to a thermal shift assay to evaluate drug target interactions. In addition, the results created by SWATH-MS can be analyzed by SRM-MS in a biased manner to assess the binding of a test compound to a multiplicity of proteins in the same sample, including samples from living cells.

Abstract: The invention provides an unbiased method to assess the binding of a test compound to a multiplicity of proteins in the same sample, including samples from living cells by applying the unbiased determination technique of SWATH-MS or the biased technique of SRM-MS to a thermal shift assay to evaluate drug target interactions. In addition, the results created by SWATH-MS can be analyzed by SRM-MS in a biased manner to assess the binding of a test compound to a multiplicity of proteins in the same sample, including samples from living cells.

Abstract: The present invention provides a method to define normal maturation of the gut microbiota using a limited number of bacterial taxa found in the gut microbiota. Regressing the relative abundance of age-discriminatory taxa in their gut microbiota against the chronological age of each healthy subject at the time a sample of the gut microbiota was collected produces a regression model that may be used to characterize the maturity of another subject's gut microbiota to provide a measure of gastrointestinal health without having to query the whole microbiota. The present invention also provides composition and methods for preventing and/or treating a disease in a subject in need thereof.

Abstract: A computer-implemented method for determining minor variants. The method includes receiving electropherogram sequence data from a test sample, identifying any non-primary peaks in the electropherogram, and characterizing identified non-primary peaks using at least one signal feature. The method may further include analyzing the at least one signal feature across identified non-primary peaks to identify variant candidates, evaluating at least one peak characteristic of each of the identified variant candidates, and classifying variant candidates as bona fide variants based on the evaluation of peak characteristics.

Abstract: A method for at least one of characterizing, diagnosing, and treating an endocrine system condition in at least a subject, the method comprising: receiving an aggregate set of biological samples from a population of subjects; generating at least one of a microbiome composition dataset and a microbiome functional diversity dataset for the population of subjects; generating a characterization of the endocrine system condition based upon features extracted from at least one of the microbiome composition dataset and the microbiome functional diversity dataset; based upon the characterization, generating a therapy model configured to correct the endocrine system condition; and at an output device associated with the subject, promoting a therapy to the subject based upon the characterization and the therapy model.

Abstract: BioMEMS/NEMS appliance biologically monitors an individual, using biosensors to detect cellular components. Data is simulated or analyzed using systems-biology software, which provides diagnostic or therapeutic guidance.