Abstract: This invention relates to the identification of peptide binding to ligands, and in particular to identification of epitopes expressed by microorganisms and by mammalian cells. The present invention provides polypeptides comprising the epitopes, and vaccines, antibodies and diagnostic products that utilize or are developed using the epitopes.

Abstract: Characteristics of proteins, peptides, and/or peptoids can be determined via two-dimensional correlation spectroscopy and/or two-dimensional co-distribution spectroscopies. Spectral data of the proteins, peptides, and/or peptoids can be obtained with respect to an applied perturbation. two-dimensional co-distribution analysis can be applied to generate an asynchronous co-distribution plot for the proteins, peptides, and/or peptoids to define the population of proteins in solution. In the two-dimensional asynchronous plot, a cross peak can be identified as correlating with an auto peak in the two-dimensional correlation synchronous plot associated with aggregation of the proteins, peptides, and/or peptoids. The two-dimensional asynchronous cross peak can be used to determine an order of a distributed presence of spectral intensities with respect to the applied perturbation.

Abstract: A method of administering insulin includes receiving glucose measurements of a patient at a data processing device from a continuous glucose monitoring system. The glucose measurements are separated by a time interval. The method also includes receiving patient information at the data processing device and selecting a subcutaneous insulin treatment from a collection of subcutaneous insulin treatments. The selection is based on the glucose measurements and the patient information. The selection includes one or more of a subcutaneous standard program, a subcutaneous program without meal boluses, a meal-by-meal subcutaneous program without carbohydrate counting, a meal-by-meal subcutaneous program with carbohydrate counting, and a subcutaneous program for non-diabetic patients. The method also includes executing, using the data processing device, the selected subcutaneous insulin treatment.

Abstract: A system and method for identification of key driver responsible for bringing changes in a microbial population is provided. The method involves construction of microbial association networks with each microbial taxa as nodes and their associations as edges and subsequent identification of crucial ‘driver’ nodes involved in the studied disease progression. While comparing a particular node between two networks, this method takes individual nodes and their associations into account as well as the identity of their interacting partners. A taxon in the diseased state with an altered set of associations while still being increasingly important for the whole network necessarily holds a key significance in microbial interplay. Using this rationale, this methodology computes a score to quantify this change for each node and calculates its statistical significance.

Abstract: Disclosed herein are methods and systems for classifying cell labels, for example identifying a signal cell label. In some embodiments, the method comprises: obtaining sequencing data of barcoded targets created using targets in cells barcoded using barcodes, wherein a barcode comprises a cell label and a molecular label. After ranking the cell labels, a minimum of a second derivative plot of a cumulative sum plot can be determined. Using the methods, a cell label can be classified as a signal cell label or a noise cell label based on the number of molecular labels with distinct sequences associated with the cell label and a cell label threshold.

Abstract: Disclosed systems and methods relate to predicting the relative representation of genomic variants in an edited cell population, based on the editing cassette design representation in an editing cassette design library used to generate the edited cell population. A library of editing cassette designs is generated, and a feature vector, or sequence embedding, is developed for each design using natural language processing techniques. The feature vector may be based upon sequence attributes and editing kinetics of each cassette design as well as attributes that describe the library context. Features may include sequence embeddings generated from a neural network, linguistic-type distances, and statistical distance summaries thereof. The feature vectors are classified using one or more machine learning models, and the classified feature vectors are used to predict the representation of each design an edited cell population.

Abstract: The disclosure provides a process of designing and optimizing supramolecular therapeutics. The disclosure also provides a method for designing and optimizing antibody drug conjugates.

Abstract: Systems and methods are provided for microbial identification using cleavable tags. Control information is sent to a mass spectrometer to fragment one or more nucleic acid primers labeled with a first tag and monitor for an intensity of the first tag in a mass spectrometry (MS) method. An ion source provides a beam of ions from a polymerase chain reaction amplified sample that includes one or more nucleic acid primers labeled with the first tag. The first tag binds to one or more nucleic acid primers of a known microbe and is cleaved from the nucleic acid primers during the MS method. The mass spectrometer receives the beam of ions and is adapted to perform the MS method on the beam of ions. If the intensity of the first tag received from the mass spectrometer exceeds a threshold value, the known microbe is identified in the sample.

Abstract: Membrane protein expression can be predicted using statistical frameworks to provide an enhanced subset of sequences, out of an initial larger set of potentially expressing sequences, by using features derived from sequences and a model parameterized through a dataset of known expression levels. Also, membrane protein experimentation protocols can be designed using the statistical frameworks in concert known outcomes to identify which laboratory conditions are most likely to produce successful results.

Abstract: Disclosed are methods for identifying bio-molecules with desired properties (or which are most suitable for a round of directed evolution) from complex bio-molecule libraries or sets of such libraries. Some embodiments of the present disclosure provide methods for virtually screening proteins for beneficial properties. Some embodiments of the present disclosure provide methods for virtually screening enzymes for desired activity and/or selectivity for catalytic reactions involving particular substrates. Some embodiments combine screening and directed evolution to design and develop proteins and enzymes having desired properties. Systems and computer program products implementing the methods are also provided.

Abstract: The subject matter disclosed herein relates to methods of identifying pharmacophores and inhibitors against protein aggregation. The present disclosure also provides pharmacophores themselves and medical uses of agents in the treatment of diseases associated with protein aggregation.

Abstract: A system for determining user taste changes using a plurality of biological extraction data and artificial intelligence includes at least a computing device, wherein the computing device is designed and configured to receive, from a user, at least a first element of biological extraction data, calculate at least a first taste index of the user, wherein calculating further comprises training a first machine learning process as a function of training data correlating biological extraction data with taste indices, calculating the at least a first taste index as a function of the first machine learning process and the at least a first element of biological extraction data, generate a taste profile using the first taste index, and determine, using at least a second element of biological extraction data and a second machine learning process, at least a change in user taste profile.

Abstract: A system for generating first data including content data includes an interface for outputting the content data, a conversion unit to convert an intensity change indicative of a detected chemical substance contained in data from a sensor into the content data. The sensor includes a mass spectrometric type sensor capable of controlling sensitivity, resolution or selectivity, and a hardware unit that is configured to carry out an analysis of the data with initial setting conditions designed for scanning in a first range using a test sample prepared in advance, change the setting conditions for the sensor for use with the conversion unit, based on the analysis carried out automatically and periodically, the setting conditions including at least one of a voltage for ionizing and a voltage for scanning a spectrum region for detecting a chemical substance requested by an application.

Abstract: Disclosed herein are systems and methods for efficient 3D structure estimation from images of a transmissive object, including cryo-EM images. The method generally comprises, receiving a set of 2D images of a target specimen from an electron microscope, carrying out a reconstruction technique to determine a likely molecular structure, and outputting the estimated 3D structure of the specimen. The described reconstruction technique comprises: establishing a probabilistic model of the target structure; optimizing using stochastic optimization to determine which structure is most likely; and, optionally utilizing importance sampling to minimize computational burden.

Abstract: Biomarkers useful for diagnosing and assessing inflammatory disease activity, for prediction of risk for progressive spinal and joint damage, in particular for axial spondyloarthritis (axSpA) and ankylosing spondylitis (AS), and for generating a dataset are provided, along with kits for measuring expression of the biomarkers. The invention also provides predictive models, based on the biomarkers, as well as computer systems, and software embodiments of the models for scoring and optionally classifying samples.

Abstract: Methods for ex vivo perfusion of organs (and/or tissues) with a perfusate designed to condition the organ with the desired effect being that upon transplant, said organ, having been administered said perfusate, is less likely to experience delayed graft function, deleterious effects of ischemia/reperfusion injury, including inflammatory reactions, and/or other detrimental responses that can injure the organ or recipient including precipitating or enhancing an immunological reaction from the recipient with the potential of compromising the graft's and/or recipients short teen and/or long term health and proper functionality while monitoring, sustaining and/or restoring the viability of the organ and preserving the organ for storage and/or transport.

Abstract: A method and system for in-silico testing of actives on human skin is described. The present invention discloses a micro and macroscopic level model of the skins upper protective layer Stratum-Corneum. The invention presents a multi-scale modeling framework for the calculation of diffusion and release profile of different actives like drugs, particles and cosmetics through developed skin model using molecular dynamics simulations and computational fluid dynamics approach. The systems consist of a molecular model of the skin's upper layer stratum corneum and permeate molecules. The system also consists of a macroscopic transport model of stratum corneum. The transport model is used to generate the release profile of the active molecule.

Abstract: A method of making a synthetic foldable having a tertiary structure emulating the tertiary structure of a reference foldable protein is described. The method includes determining a folding nucleus peptide sequence associated with folding the reference foldable protein. The synthetic foldable protein is synthesized by including the determined folding nucleus peptide sequence and at least one repeat thereof in the peptide sequence of the synthetic foldable protein.

Abstract: A method and system of predicting a muscle characteristic using ultrasound. The characteristic may include a tenderness characteristic and/or a strength characteristic. An analysis of muscle structure is performed for a sample using ultrasound data of the sample. The analysis may include determining a relative number of bundles, fascicles, sarcomeres, fibers, and/or sheath thickness from the ultrasound data. Thereafter, the muscle characteristic is predicted for the sample based on the analysis.

Abstract: A method of administering insulin includes receiving glucose measurements of a patient at a data processing device from a continuous glucose monitoring system. The glucose measurements are separated by a time interval. The method also includes receiving patient information at the data processing device and selecting a subcutaneous insulin treatment from a collection of subcutaneous insulin treatments. The selection is based on the glucose measurements and the patient information. The selection includes one or more of a subcutaneous standard program, a subcutaneous program without meal boluses, a meal-by-meal subcutaneous program without carbohydrate counting, a meal-by-meal subcutaneous program with carbohydrate counting, and a subcutaneous program for non-diabetic patients. The method also includes executing, using the data processing device, the selected subcutaneous insulin treatment.