Abstract: The present invention relates to methods for predicting T cell epitopes useful for vaccination. In particular, the present invention relates to methods for predicting whether modifications in peptides or polypeptides such as tumor-associated neoantigens are immunogenic and, in particular, useful for vaccination, or for predicting which of such modifications are most immunogenic and, in particular, most useful for vaccination. The methods of the invention may be used, in particular, for the provision of vaccines which are specific for a patient's tumor and thus, in the context of personalized cancer vaccines.

Abstract: A method of administering insulin includes receiving blood glucose measurements of a patient at a data processing device from a glucometer. The blood 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 blood 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: This disclosure presents methods for antibody structure prediction and design. We utilize the growing number of antibody structures and sequences are used with powerful protein modeling methods to design and predict antibody structural models up to sub-angstrom accuracy. The invention also relates to systems and methods for generating an antibody library. Specifically, the invention relates to computer-implemented systems and methods for generating an antibody library for a predetermined epitope. The invention further relates to determining structural models of the interface between an antibody and its antigen. The invention also relates to determining structural models of an unbound complementarity determining region of an antibody.

Abstract: Methods and systems for obtaining inhibitors of human DNA methyltransferase 1 (DNMT1) are disclosed where the methods involve designing compounds that resemble the DNMT1 transition state.

Abstract: Computational methods are used to create cardiovascular simulations having desired hemodynamic features. Cardiovascular modeling methods produce descriptions of blood flow and pressure in the heart and vascular networks. Numerical methods optimize and solve nonlinear equations to find parameter values that result in desired hemodynamic characteristics including related flow and pressure at various locations in the cardiovascular system, movements of soft tissues, and changes for different physiological states. The modeling methods employ simplified models to approximate the behavior of more complex models with the goal of to reducing computational expense. The user describes the desired features of the final cardiovascular simulation and provides minimal input, and the system automates the search for the final patient-specific cardiovascular model.

Abstract: A method of administering insulin includes receiving blood glucose measurements of a patient at a data processing device from a glucometer. The blood 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 blood 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: This disclosure describes methods, kits, and systems for scoring the immune response to cancer through examination of tissue infiltrating lymphocytes (TILs). Methods of scoring the immune response in cancer using tissue infiltrating lymphocytes include detecting CD3, CD8, CD20, and FoxP3 within the sample and scoring the detection manually or scoring the digital images of the staining with the aid of image analysis and algorithms.

Abstract: An apparatus for identifying transition points in a chemical reaction, the apparatus comprising: a property value receiver, configured to receive a plurality of values of a physical property of the chemical reaction, a linear function calculator, associated with the property value receiver, configured to calculate a linear function connecting two of the received values, the two values pertaining to a start and end of a time period, a difference calculator, associated with the linear function calculator, configured to calculate a difference between the linear function and a plurality of the received values pertaining to the time period, and a transition point identifier, associated with the difference calculator, configured to identify at least one transition point of the chemical reaction, using the calculated difference.

Abstract: This invention relates to the identification of peptidase cleavage sites in proteins and in particular to identification protease cleavage by the endopeptidases. The present invention utilizes a bioinformatic methodology for prediction of peptidase cleavage sites based on principal component analysis and based on training sets obtained by experimental protein cleavage. This invention is not limited to training sets derived from CSL approaches, nor to any other experimental determination of cleavage site.

Abstract: An artificial intelligence engine architecture for generating candidate drugs is disclosed. In one embodiment, a method includes generating, via a creator module, a candidate drug compound including a sequence of a candidate drug compound, including the candidate drug compound as a node in a knowledge graph; generating, via a descriptor module, a description of the candidate drug compound at the node in the knowledge graph, wherein the description comprises drug compound structural information, drug compound activity information, and drug compound semantic information; based on the description, performing, via a scientist module, a benchmark analysis of a parameter of the creator module; and modifying, based on the benchmark analysis, the creator module to change the parameter in a desired way during a subsequent benchmark analysis.

Abstract: Systems, methods and non-transitory computer readable media identify favored polymer conformations. One or more residues are identified and may be replaced in the polymer, or the original primary sequence of the polymer may be retained. The conformations of residues in a subset of residues in a region of the identified one or more residues are altered. This conformational adjustment is repeated for other subsets of residues in the region of the identified one or more residues, and for other conformations, thereby deriving a plurality of polymer structures. A set of clusters is generated for each residue of the polymer using the conformationally adjusted structures, thereby creating sets of clusters. Structures in the plurality of structures are grouped into subgroups when the structures fall into the same clusters across a threshold number of the sets of clusters.

Abstract: The present invention is an accelerated conformational sampling method for predicting target peptide and protein structures comprising a process of determining energy minimized synthetic templates using a simple system for modeling individual molecular bonds within the subject peptide or protein. Use of these synthetic templates greatly reduces the computational resources necessary for optimally determining structural features of the target peptide or protein. The present invention also provides methods for rapid and efficient analysis of the effect of mutations on target peptides and proteins.

Abstract: Disclosed herein are methods, compositions, and systems for determining specific microbial taxa, within a complex consortia of mixed taxa, which are interacting with each other in an environment of interest. In some embodiments, after diluting a sample comprising multiple different taxa of microorganisms, dilutions of the sample are cultivated for determining taxonomic information and interactions of multiple taxa of microorganisms in the sample.

Abstract: In an embodiment, a computer-implemented method of selecting sampling locations in a field is disclosed. The method comprises receiving, by a processor, input data including a map for a management zone in a field indicating one or more values of a set of agricultural characteristics for each of a plurality of locations in the management zone. The method further comprises identifying, by the processor, a set of values for the set of agricultural characteristics for each of a group of locations in the management zone based on map. In addition, the method comprises normalizing a set of model values for the set of agricultural characteristics used by an agricultural modeling tool and the set of values of the set of agricultural characteristics for each of the group of locations in the management zone.

Abstract: Systems and methods include directing limited frequencies of microwave signals toward target molecules, driving a motion of the target molecules to impact molecular recognition. In one implementation, a microwave spectra associated with the rotational modes of a target molecule is obtained. From peaks in the spectra, a mode of molecular movement is identified and a microwave signal profile is generated for driving a motion of binding portions of the molecule associated with the identified mode. Microwave signals are generated based on the signal profile for output by antennas. For example, the microwave signals can be can be used to impede the binding of quorum sensing molecules by receptors of P. aeruginosa. In one implementation, the antennas can be placed in a catheter for placement in a patient. In another implementation, the antennas can be placed in a sleeve or other device for use adjacent to the skin of a patient.

Abstract: The present disclosure features a method of detecting and/or quantifying collagen VII or a fragment thereof in a sample, the method including contacting the sample with collagen IV or a fragment thereof which binds to collagen VII; and contacting the sample with an anti-collagen VII antibody, wherein the anti-collagen VII antibody binds to the NC2 domain of collagen VII; detecting binding of the anti-collagen VII antibody to thereby detect and/or quantify an amount of collagen VII or the fragment thereof in the sample. A method of evaluating or processing a collagen VII preparation is also provided.

Abstract: Methods and systems for performing a flow cytometry experiment can include evaluating one or more assignments of labels to a plurality of markers. Evaluating assignments of labels can include evaluating condition numbers for at least one spillover matrix. The method can further include selecting labels based at least in part on the evaluation of condition numbers. Methods and systems for performing a flow cytometry experiment can also include inputting data regarding markers, cell populations, labels, and cytometer configuration for a flow cytometry experiment, assigning labels to at least some of the markers, and running the flow cytometry experiment.

Abstract: Apparatus, systems, computer-readable media, articles of manufacture and methods for selecting an antibody. Apparatus, systems, computer-readable media, articles of manufacture and methods for producing the selected antibody. The selecting may include determining one or more physiochemical characteristics of the antibody. The determining may be based on antibody structural parameters.

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: Disclosed herein is a system and methods for determining the alleles, neoantigens, and vaccine composition as determined on the basis of an individual's tumor mutations. Also disclosed are systems and methods for obtaining high quality sequencing data from a tumor. Further, described herein are systems and methods for identifying somatic changes in polymorphic genome data. Finally, described herein are unique cancer vaccines.