Abstract: The present technology relates to systems, methods and devices for haptically-enabled virtual reality simulation of cerebral aneurysm clipping, wherein a user uses two physical stations during the simulation. The first station is a haptic and augmented reality station, and the second station is a haptic and virtual reality station.

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.

Abstract: The present invention discloses a method for evaluating vitality of a plant including (a) a step of measuring a delayed luminescence of a leaf of each plant of a group of plants subject to evaluation to obtain data of delayed luminescence amount, and (b) a step of processing data of a plurality of delayed luminescence amounts thus obtained to evaluate a plant exhibiting a delayed luminescence amount not less than a preset upper limit threshold as an individual of poor growth or evaluate a plant exhibiting a delayed luminescence amount not more than a preset lower limit threshold as an individual of good growth, and a measurement system and an evaluation system used for the method.

Abstract: Methods and systems are described to provide computerized trajectory-based methods to represent translocon-associated protein trajectories, provide proteins or protein sequences with desired translocon-associated biogenesis features, screening proteins or protein sequences to provide proteins or protein sequences with desired translocon-associated biogenesis features, screening translocon-associated biogenesis feature determinants to provide proteins or protein sequences with desired translocon-associated biogenesis features, identifying translocon-associated biogenesis feature determinants of a given protein sequence, computer-based protein sequence identification methods, computer-based methods for identifying correlations in a set of protein sequences, computer-based methods for identifying correlations between experimental data and computer-generated data in a protein sequence, and computer-based methods for determining which modifications of a protein sequence do not substantially affect a translocon-ass

Abstract: The invention provides a method of determining changes in a first set of residues r1 due to changes in a second set of residues r2 in a protein system comprising one or more proteins comprising r1 and r2. In exemplary embodiments, the method comprises optimizing a quality function Q by modifying one or more properties of r1 and r2 in a constrained environment in which all degrees of freedom of the system except those directly involved in the potential coupling between r1 and r2 are removed.

Abstract: The invention describes an explicit solvent all-atom molecular dynamics methodology (SILCS: Site Identification by Ligand Competitive Saturation) that uses small aliphatic and aromatic molecules plus water molecules to map the affinity pattern of a large molecule for hydrophobic groups, aromatic groups, hydrogen bond donors, and hydrogen bond acceptors. By simultaneously incorporating ligands representative of all these functionalities, the method is an in silico free energy-based competition assay that generates three-dimensional probability maps of fragment binding (FragMaps) indicating favorable fragment:large molecule interactions. The FragMaps may be used to qualitatively inform the design of small-molecule ligands or as scoring grids for high-throughput in silico docking that incorporates both an atomic-level description of solvation and the large molecule's flexibility.

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 function calculator, associated with the property value receiver, configured to calculate a function and verify that the function has a line of best fit with a same slope as 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 function calculator, configured to calculate a difference between the calculated function and a plurality of the received values pertaining to the time period having the start and end, 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: A method for labeling vessel branches forming first and second vessel systems. A 3D image is segmented to obtain vessel branches. First and second root points are then determined. Starting from the first root point, the vessel branches are traced to derive a tracing path and a break point is determined, that separates the tracing path into two portions. A region of interest in the 3D image is determined with respect to the break point, in which center lines are assigned to the first or second vessel system. A 3D cutting structure is generated based on distances measured from points on the center lines to the 3D cutting structure. Graph representations are constructed for the first and second vessel systems. The vessel branches are labeled with different labels based on the graph representations.

Abstract: The invention relates to the field of biotechnology. The method for determining the spatial and temporal distribution of the activity of a proteolytic enzyme in an in vitro heterogeneous system, such as blood or blood plasma, involves the introduction of a luminescent, fluorogenic or chromogenic substrate into a sample with the subsequent release of a detectable tag as the proteolytic enzyme cleaves the substrate, and the recording of the optical characteristics of the sample, which makes it possible to assess the spatial and temporal distribution of the activity of the enzyme. The device for the implementation of the above method comprises an in vitro system, a means for illuminating the sample, a recording means and a control means. A method for diagnosing homeostatic imbalances according to a change in the spatial and temporal distribution of the activity of a proteolytic enzyme in a blood sample is also proposed.

Abstract: The present invention provides methods and computational tools based, at least in part, on computer simulations that identify macromolecule binding regions and aggregation prone regions of a protein. Substitutions may then be made in these aggregation prone regions to engineer proteins with enhanced stability and/or a reduced propensity for aggregation. Similarly, substitutions may then be made in these macromolecule binding regions to engineer proteins with altered binding affinity for the macromolecule.

Abstract: Cell-bound complement activation product (CB-CAP) profiling and scoring serve as diagnostic biomarkers for patients to determine whether a patient who has not met at least four American College of Rheumatology (or similar e.g. SLICC) criteria for a definite Lupus diagnosis should be classified as exhibiting a pre-existing condition that this document refers to as pre-Lupus. This document also describes methods for determining whether a patient who has been determined to exhibit pre-Lupus has progressed to exhibiting definite Lupus.

Abstract: The present invention relates to a top-down symmetric deconstruction approach which provides a novel alternative means to successfully identify a useful polypeptide “building block” for subsequent “bottom-up” de novo design of target protein architecture. The present invention also pertains to a novel peptides isolated by top-down symmetric deconstruction which may be useful for design or directed evolution of novel proteins with novel functionalities.

Abstract: Methods and systems for biochemical data analysis are provided. A dataset can be received and a selection of a compare field can be used for creation of sub-groups of data to run statistical analysis on. The sub-groups of the dataset can be created based on the selection of the compare field. Statistical information about each sub-group of data can be calculated and displayed on a user display. Other information can be provided for further dataset refinements. A user may supply a control group selection, and such a selection may then result in an indication on the display of which population represents the control group. A user may supply information for further dataset filtering. Such information may be used to filter data, prior to creating the sub-groups for statistical analysis.

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: Described are methods for determination of peptide specific parameter(s) of a mixture comprising a target peptide and a related impurity (or impurities) to be used in a simulation model of chromatographic separation using mathematical model(s). Also described are chromatographic simulation methods using above determined parameters, as well as computer systems and computer programs for performing one or more of the above method(s).

Abstract: Methods and systems for evaluating biological dataset profiles relating to inflammatory cardiovascular conditions are provided, where datasets comprising information for multiple cellular parameters are compared and identified, and used in the evaluation of candidate pharmacologic agents for suitability as therapeutic agents.

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: Embodiments of a computer system, a method, and a computer-program product (e.g., software) for analyzing tandem-mass-spectrometry data are described. Using this analysis technique, unanticipated chemical modifications to peptides associated with proteins can be identified. In particular, a modification called a wild-card modification is used to identify the most likely chemical modifications in the peptides. A wild-card modification allows the addition of any mass, typically any integer atomic mass within a range, to any one amino acid residue within a candidate peptide.

Abstract: A method for simultaneously measuring the activities of multiple kinds of enzymes in single channel through concimitantly monitoring multiple wavelength absorbances is claimed; based on linear additivity of absorbances and the isoabsorbance wavelengths of chromogenic substrates and their chromogenic products, both the principles for the combination of chromogenic substrates required for simultaneously measuring the activities of multiple kinds of enzymes in single channel through concimitantly monitoring multiple wavelength absorbances and an approach for data processing to eliminate the interference of the overlapped absorbances are developed, kinetic analysis of reaction curves via numerical integration eliminates the interference of all substrates and products and estimates the maximal reaction rates of the enzymes to be measured, giving the linear ranges and the limits of quantification for simultaneously measuring the activities of multiple kinds of enzymes in single channel comparable to those by separa

Abstract: The present invention is directed to methods for determining the relative amount of wrongly disulphide bridged TNFR2:Fc in a sample of TNFR2:Fc, a fusion protein which is used in a variety of therapeutic applications. In addition, the invention pertains to a method for purifying TNFR2:Fc using said method for determining the percentage of wrongly disulphide bridged TNFR2:Fc, and to TNFR2:Fc compositions obtained thereby.