Abstract: Disclosed herein are methods, non-transitory computer readable media, and systems for subphenotyping acute respiratory distress syndrome (ARDS) patients by analyzing electronic health data (EHR) using a subphenotype classifier. According to their classification, different treatments can be selected which are likely to be efficacious in treating ARDS. Such methods, non-transitory computer readable media, and systems are useful for rapid classification and guided treatment in critical care settings, such as in hospitals.

Abstract: A method for identifying a therapy recommendation for a subject exhibiting dysregulated host response is provided. A classification of the subject of subtype A, subtype B, or subtype C is obtained. The therapy recommendation for the subject is identified based at least in part on the classification. Responsive to the classification of the subject comprising subtype A, the therapy recommendation can be no immunosuppressive therapy. Responsive to the classification of the subject comprising subtype B, the therapy recommendation can be no therapy recommendation, immune stimulation therapy, suppression of immune regulation therapy, blocking of immune suppression therapy, blocking of complement activity therapy, and/or anti-inflammatory therapy.

Abstract: A method for determining at least one of a medical diagnosis recommendation and a medical intervention recommendation for a subject. At least one of electronic health record (EHR) data and biomarker data for the subject are input into a diagnostic/intervention recommendation model that comprises parameters and a function. The parameters are identified based on a training dataset that comprises a plurality of training samples. Each training sample is associated with a retrospective subject and includes at least one of EHR data and biomarker data for the retrospective subject. The function represents a relation between the at least one of EHR data and biomarker data for the subject received as inputs to the diagnostic/intervention recommendation model, and at least one of a medical diagnosis recommendation and intervention recommendation for the subject generated as an output of the model.

Abstract: Disclosed herein are various methods, systems, and compositions for the growth independent detection of cells such as microorganisms including bacteria. While existing cellular detection methodologies benefit from cell growth, the methods, systems, and compositions disclosed herein demonstrate embodiments that are independent of cell growth while still allowing for cell-based detection.

Abstract: Disclosed herein are materials and methods for achieving sequence-specific organism detection and/or phenotype(s) using sequence-specific oligonucleotides. Also disclosed are related kits, cultures, and cells for detecting and/or phenotyping microorganisms in a sequence-specific manner.

Abstract: Accurate measurements of the presence or absence of an analyte (e.g., MRSA) in a sample are provided. For example, the sample can be subjected to an activation reagent (potentially after an initial reagent has already been added), which can cause a flash signal that increases and then decreases over time. Signal data points can be measured from the flash signal using a detector. A quadratic regression function that fits the signal data points can be determined. An accuracy of the quadratic fit can be determined, as well as a signal-to-background ratio. A difference between a signal-to-background term and an accuracy term can be used as a score that is compared to a threshold to determine whether the analyte is present in the sample.

Abstract: Disclosed herein are various methods, systems, and compositions for the growth independent detection of cells such as microorganisms including bacteria. While existing cellular detection methodologies benefit from cell growth, the methods, systems, and compositions disclosed herein demonstrate embodiments that are independent of cell growth while still allowing for cell-based detection.

Abstract: Methods and systems are provided for packaging reporter nucleic acid molecules into non-replicative transduction particles for use as reporter molecules. The non-replicative transduction particles can be constructed from viruses and use viral transduction and replication systems. The reporter nucleic acid molecules include a reporter gene, such as a reporter molecule or selectable marker, for detecting target genes or cells. Methods and systems are provided for detection of cells and target nucleic acid molecules using the non-replicative transduction particles as reporter molecules.

Abstract: Disclosed herein are methods and compositions for determining the presence or absence of a mechanism of antimicrobial resistance in a sample.

Abstract: Systems and methods for detecting and/or identifying target cells (e.g., bacteria) using engineered transduction particles are described herein. In some embodiments, a method includes mixing a quantity of transduction particles within a sample. The transduction particles are associated with a target cell. The transduction particles are non-replicative, and are engineered to include a nucleic acid molecule formulated to cause the target cell to produce a series of reporter molecules. The sample and the transduction particles are maintained to express the series of the reporter molecules when target cell is present in the sample. A signal associated with a quantity of the reporter molecules is received. In some embodiments, a magnitude of the signal is independent from a quantity of the transduction particle above a predetermined quantity.

Abstract: Disclosed herein are materials and methods for achieving sequence-specific organism detection and/or phenotype(s) using sequence-specific oligonucleotides. Also disclosed are related kits, cultures, and cells for detecting and/or phenotyping microorganisms in a sequence-specific manner.

Abstract: Systems and methods for detecting and/or identifying target cells (e.g., bacteria) using engineered transduction particles are described herein. In some embodiments, a method includes mixing a quantity of transduction particles within a sample. The transduction particles are associated with a target cell. The transduction particles are non-replicative, and are engineered to include a nucleic acid molecule formulated to cause the target cell to produce a series of reporter molecules. The sample and the transduction particles are maintained to express the series of the reporter molecules when target cell is present in the sample. A signal associated with a quantity of the reporter molecules is received. In some embodiments, a magnitude of the signal is independent from a quantity of the transduction particle above a predetermined quantity.

Abstract: Disclosed herein are materials and methods for achieving sequence-specific organism detection and/or phenotype(s) using sequence-specific oligonucleotides. Also disclosed are related kits, cultures, and cells for detecting and/or phenotyping microorganisms in a sequence-specific manner.

Abstract: Methods and systems are provided for packaging reporter nucleic acid molecules into non-replicative transduction particles for use as reporter molecules. The non-replicative transduction particles can be constructed from viruses and use viral transduction and replication systems. The reporter nucleic acid molecules include a reporter gene, such as a reporter molecule or selectable marker, for detecting target genes or cells. Methods and systems are provided for detection of cells and target nucleic acid molecules using the non-replicative transduction particles as reporter molecules.

Abstract: Methods and systems are provided for packaging reporter nucleic acid molecules into non-replicative transduction particles for use as reporter molecules. The non-replicative transduction particles can be constructed from viruses and use viral transduction and replication systems. The reporter nucleic acid molecules include a reporter gene, such as a reporter molecule or selectable marker, for detecting target genes or cells. Methods and systems are provided for detection of cells and target nucleic acid molecules using the non-replicative transduction particles as reporter molecules.

Abstract: Disclosed herein are various methods, systems, and compositions for the growth independent detection of cells such as microorganisms including bacteria. While existing cellular detection methodologies benefit from cell growth, the methods, systems, and compositions disclosed herein demonstrate embodiments that are independent of cell growth while still allowing for cell-based detection.

Abstract: Disclosed herein are methods and compositions for determining the presence or absence of a mechanism of antimicrobial resistance in a sample.

Abstract: Disclosed herein are methods and compositions for determining the presence or absence of a mechanism of antimicrobial resistance in a sample.

Abstract: Methods and systems are provided for packaging reporter nucleic acid molecules into non-replicative transduction particles for use as reporter molecules. The non-replicative transduction particles can be constructed from viruses and use viral transduction and replication systems. The reporter nucleic acid molecules include a reporter gene, such as a reporter molecule or selectable marker, for detecting target genes or cells. Methods and systems are provided for detection of cells and target nucleic acid molecules using the non-replicative transduction particles as reporter molecules.

Abstract: Methods and systems are provided for packaging reporter nucleic acid molecules into non-replicative transduction particles for use as reporter molecules. The non-replicative transduction particles can be constructed from viruses and use viral transduction and replication systems. The reporter nucleic acid molecules include a reporter gene, such as a reporter molecule or selectable marker, for detecting target genes or cells. Methods and systems are provided for detection of cells and target nucleic acid molecules using the non-replicative transduction particles as reporter molecules.