Abstract: The invention relates to a method for selecting compounds which can be used as additives in photopolymer formulations for producing light holographic media, and to photopolymer formulations which contain at least one softener which are selected according to the claimed method. The invention also relates to the use of photopolymer formulations for producing holographic media.

Abstract: Protein confidence values are calculated in proteomic analysis. A protein database is searched for proteins matching peptides found from mass spectrometry of a sample producing a set of proteins and a corresponding set of peptides. Peptide confidence values for the set of peptides are determined. Protein confidence values are calculated for the set of proteins based on the peptide confidence values. A protein is selected from the set of proteins with a largest protein confidence value, the largest protein confidence value is saved for the protein, the protein is removed from the set of proteins, and one or more peptides corresponding to the protein are removed from the set of peptides. Protein confidence values are recalculated for the set of proteins based on the peptide confidence values and an effect of removing the one or more peptides from the set of peptides.

Abstract: Systems and methods for searching conformation space of a polymer to determine a three-dimensional conformation of the polymer that satisfies a performance metric is provided. The polymer comprises a plurality of domains and at least a first hinge. Initial three-dimensional coordinates of the polymer are altered by pivoting the first domain with respect to the second domain about the first hinge thereby obtaining an altered set of three-dimensional coordinates for the polymer. In this altering, atoms within the first domain are held fixed with respect to each other and atoms within the second domain are also held fixed with respect to each other. The altered set of coordinates is scored against a performance metric. Additional instances of the altering and scoring are performed, if necessary, until the altered set of three-dimensional coordinates satisfy the performance metric.

Abstract: The present invention relates to a method for identifying target regions existing in the interface of monomers constituting the PilT protein with the view to design molecules potentially applicable in impairing the activity of this protein, thus controlling infectious processes. The method is characterized in (i) selecting at least one amino acid sequence constituting the PilT monomer; (ii) developing a three-dimensional computational model of the PilT homo-hexameric structure; (iii) analyzing and determining, with computer aid, the interface-forming residues (IFR) and their physicochemical and structural characteristics for all the chains of the models of hexameric complexes generated; (iv) selecting the regions to be used as therapeutic targets (and preferred therapeutic targets) in the interface between the monomers based on the intensity of determined parameters; (v) computer-aided design of molecules potentially capable of effecting bindings and/or interactions between target regions of the monomers.

Abstract: A method of determining kinetic parameters for a reversible molecular interaction between a ligand immobilized to a solid support surface and a binding partner to the ligand in solution, comprises sequentially, without intermediate regeneration or renewal of the immobilized ligand, flowing a plurality of fluid volumes containing different known concentrations of the binding partner over the solid support surface, monitoring the momentary amount of binding partner bound to the solid support surface related to time and solution concentration of binding partner and collecting the binding data, and determining the kinetic parameters by globally fitting a predetermined kinetic model for the interaction between the binding partner and the immobilized ligand to the collected binding data, which model allows for mass transport limitation at the solid support surface.

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: The present disclosure relates to methods and computational tools based, at least in part, on computer simulations that identify hot-spot amino acid residues and binding-region amino acid residues of a protein.

Abstract: The present invention provides compositions and methods for light-activated cation channel proteins and their uses within cell membranes and subcellular regions. The invention provides for proteins, nucleic acids, vectors and methods for genetically targeted expression of light-activated cation channels to specific cells or defined cell populations. In particular the invention provides millisecond-timescale temporal control of cation channels using moderate light intensities in cells, cell lines, transgenic animals, and humans. The invention provides for optically generating electrical spikes in nerve cells and other excitable cells useful for driving neuronal networks, drug screening, and therapy.

Abstract: A computerized procedure for aligning molecules for use in CoMFA or other 3D QSAR methodologies does not rely on fragmentation of the molecules instead, aligning molecules based upon comparison to identified template molecules. Initially an anchor bond is identified in the candidate and template molecule that have similar atoms at each end of the bonds. The anchor bond need not be an acyclic bond. The candidate molecule is overlaid onto the template molecule by aligning the anchor bonds. Starting and working away from the anchor bond, matching atoms or atom types between the candidate and template molecule are identified. Once all matching atoms have been identified, the 3D coordinates of the template atoms are assigned to the corresponding atoms in the candidate molecule to place the candidate molecule into alignment.

Abstract: A system for non-invasively measuring cardiac output, stroke volume, or both comprises a pulse oximeter, a data processor, and means for generating an output reporting measured one or more CO or SV values to a user. A method for non-invasively measuring cardiac output, stroke volume, or both comprises collecting plethysmographic waveform data of a patient, providing the plethysmographic waveform to a data processor, and calculating measured values for CO or SV. The data processor comprises a mathematical model of the cardiovascular system integrated in a dynamic state space model (DSSM).

Abstract: Provided herein are methods for measuring molecular flux rates of molecules of interest in a tissue sample in spatially-organized manner and generating output (e.g., an image, a heat map, a contour map, a table or a database) representing the molecular flux rates of each spatially-defined location of the sample. Provided herein are also the output, as well as systems and computer-readable medium with computer-executable instructions for determining molecular flux rates of molecules of interest in the sample.

Abstract: A method for computational drug design using an evolutionary algorithm, comprises evaluating virtual molecules according to vector distance (VD) to at least one achievement objective that defines a desired ideal molecule. In one method the invention comprises defining a set of n achievement objectives (OA1-n), where n is at least one; defining a population (PG=0) of at least one molecule; selecting an initial population (Pparent) of at least one molecule (I1-In) from the population (PG=0); and evaluating members (I1-In) of the initial population (Pparent) against at least one of the n achievement objectives (OA1-x), where x is from 1 to n.

Abstract: The present invention is directed to a computer implemented method for executing a procedure to select a water-soluble variant of a G Protein-Coupled Receptor (GPCR).

Abstract: The method according to the invention allows modelling of oil and the retention phenomenon in the source rock. Organic matter characterization experiments are used to establish the molecular model (MM) of the initial sample. The thermal cracking reaction of this molecular model is reproduced by dynamic molecular simulation computations with a reactive force field and validated by comparison with experimental data. The reaction mechanism permits a kinetic study by variation of the temperature parameter. The successive phase equilibrium assessments at various progress stages of the cracking reaction allow following the physicochemical evolution of the thermal maturation of the organic sample. The free hydrocarbons are not retained in the solid residue can be quantified throughout numerical modelling of the sample maturation.

Abstract: The present invention relates to screening methods and, in particular, to methods of screening anti-ligand libraries for identifying anti-ligands specific for differentially and/or infrequently expressed ligands. The method comprises the steps of providing a library of anti-ligands: providing a first subtractor ligand; providing a second target ligand; determining the amount of the first and second target ligands using one or more equations derived from the universal law of mass action; providing the determined amount of a first subtractor ligand; providing the determined amount of a second target ligand; providing separation means capable of use to isolate anti-ligand bound to the second target ligand from anti-ligand bound to the first subtractor ligand; exposing the library of to the first and second target ligands to permit binding of anti-ligands to ligands; and using the separation means to isolate the anti-ligand bound to second target ligand.

Abstract: A method and system for patient-specific simulation of cardiac electrophysiology is disclosed. A patient-specific anatomical heart model is generated from medical image data of a patient. A patient-specific cardiac electrophysiology model is generated based on simulated torso potentials and body surface potential measurements of the patient. Cardiac electrophysiology of the patient is simulated over time for the patient-specific anatomical heart model using the patient-specific electrophysiology model. One or more electrophysiology maps are generated based on the cardiac electrophysiology simulated using the patient-specific cardiac electrophysiology model.

Abstract: The present invention belongs to the field of functional proteomics and more particularly to the field of protein aggregation. The invention discloses a method for interfering with the function of a target protein and uses a non-naturally, user-designed molecule, designated as interferor, that has a specificity for a target protein and which induces aggregation upon contact with said target protein. The present invention also discloses such interferor molecules and their use in agrobiotech applications.

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: Systems and methods are provided for microbial identification using cleavable tags. Control information is sent to a mass spectrometer to select a peptide labeled with a first tag of a known microbe, fragment the labeled peptide of the known microbe, and monitor for an intensity of the first tag in an MRM method using a processor. An ion source provides a beam of ions from a sample that includes peptides labeled with the first tag. The first tag binds to a peptide of a known microbe and is cleaved from the peptide of the known microbe during mass spectrometry. The mass spectrometer receives the beam of ions and is adapted to perform the MRM 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 using the processor.

Abstract: The present specification discloses methods of characterizing a population of particles using a particle analyzer. Particles may be characterized by size, absolute number, whether the particle is non-proteinaceous or proteinaceous, whether a proteinaceous particle has or lacks a certain physical property, or any combination thereof.