Abstract: The human neural response is coupled with computer pattern analysis for robust single-event detection of significant non-stationary brain responses triggered upon occurrence of a task-relevant stimulus. Classifier performance is enhanced fusing together the outputs of multiple different classifiers albeit multiple spatial classifiers to extract a temporal pattern as the brain response evolves, time and frequency-based spatio-temporal classifiers, and/or EEG and pupillary classifiers.

Abstract: Multimodal optical spectroscopy systems and methods produce a spectroscopic event to obtain spectroscopic response data from biological tissue and compare the response data with preset criteria configured to correlate the measured response data and the most probable attributes of the tissue, thus facilitating classification of the tissue based on those attributes for subsequent biopsy or remedial measures as necessary.

Abstract: Multimodal optical spectroscopy systems and methods produce a spectroscopic event to obtain spectroscopic response data from biological tissue and compare the response data with an empirical equation configured to correlate the measured response data and the most probable attributes of the tissue, thus facilitating classification of the tissue based on those attributes for subsequent biopsy or remedial measures as necessary.

Abstract: An integrated system for modeling, simulating and analyzing chemical and biochemical reactions includes a modeling environment for constructing a model of a chemical or biochemical reaction. The system also includes a simulation engine accepting as input the constructed model of the chemical or biochemical reaction and generating as output an expected result. An analysis environment communicates with the simulation engine and displays the expected result.

Abstract: A method is provided for selecting two or more genes from gene expression data. In the method, gene expression data for a plurality of genes is provided, where the gene expression data include expression levels for each of the plurality of genes. The gene expression data is discretized. Based on the discretized gene expression data, the synergy among the plurality of genes with respect to a phenotype, for example, presence or absence of a disease in a tissue, is evaluated. Two or more genes whose synergy exceeds a predetermined threshold are selected. A system implementing the method is also provided.

Abstract: Techniques for medical infusions include determining a first infusion rate for administering a first medication to a patient. A fluid load is determined based at least in part on the first infusion rate. It is determined whether the fluid load exceeds a predetermined threshold based on a fluid maintenance rate. If it is determined that the fluid load exceeds the predetermined threshold, then an action is caused to inhibit administering the first medication to the patient at the first infusion rate.

Abstract: The invention relates to a method for optimizing a nucleotide sequence for expression of a protein on the basis of the amino acid sequence of the protein, in which for a particular region there is specification of a test sequence with m optimization positions on which the codon occupation is varied, a quality function being used to ascertain the optimal codon occupation on these optimization positions, and one or more codons of this optimal occupation being specified as codons of the optimized nucleotide sequence. These steps are iterated, with the codons of the optimized nucleotide sequence which are specified in the preceding steps remaining unchanged in subsequent iteration steps. The invention additionally relates to a device for carrying out this method.

Abstract: The present invention relates to the identification and use of protein expression profiles with clinical relevance to osteoarthritis (OA). In particular, the invention provides the identity of marker proteins whose expressions are correlated with OA, OA subtype, and/or OA progression. Methods and kits are described for using these protein expression profiles in the study and/or diagnosis of OA, in the determination of the degree of advancement of OA, and in the selection and/or monitoring of treatment regimens. The invention also relates to the screening of drugs that modulate expression of these proteins or nucleic acid molecules encoding these proteins, in particular for the development of disease-modifying OA agents.

Abstract: One embodiment of the present invention sets forth a technique for efficiently performing N-body computations using parallel computation systems. The technique involves a first processing step whereby a force matrix is partitioned into tiles, which are assigned to a one or more thread groups for processing. An off-diagonal tile may be aligned to include no diagonal cells, while an on-diagonal tile includes diagonal cells. One approach for computing either type of tile involves assigning each row from a tile to a thread within a thread group. Each thread operates on an offset pattern to avoid access conflicts to a shared memory. A net force for each atom within an N-body system is then computed by efficiently adding constituent forces stored within the force matrix using reduction operations on the force matrix.

Abstract: Systems and methods for determining free energy parameters for predicting binding affinities of nucleotide sequences are provided. The disclosed subject matter obtains phenotypic measurements for nucleotide sequences (for example a DNA sequence or RNA sequence), links the phenotypic measurements to the nucleotide sequences to obtain linked pairs of phenotypic measurements and nucleotide sequences, estimates a relationship between the phenotypic measurements and the nucleotide sequences using the linked pairs, and obtains sequence specific affinity parameters from the estimated relationship.

Abstract: One embodiment of the present invention sets forth a technique for efficiently performing N-body computations using parallel computation systems. The technique involves a first processing step whereby a force matrix is partitioned into tiles, which are assigned to a one or more thread groups for processing. An off-diagonal tile may be aligned to include no diagonal cells, while an on-diagonal tile includes diagonal cells. One approach for computing either type of tile involves assigning each row from a tile to a thread within a thread group. Each thread operates on an offset pattern to avoid access conflicts to a shared memory. A net force for each atom within an N-body system is then computed by efficiently adding constituent forces stored within the force matrix using reduction operations on the force matrix.

Abstract: One embodiment of the present invention sets forth a technique for efficiently performing N-body computations using parallel computation systems. The technique involves a first processing step whereby a force matrix is partitioned into tiles, which are assigned to a one or more thread groups for processing. An off-diagonal tile may be aligned to include no diagonal cells, while an on-diagonal tile includes diagonal cells. One approach for computing either type of tile involves assigning each row from a tile to a thread within a thread group. Each thread operates on an offset pattern to avoid access conflicts to a shared memory. A net force for each atom within an N-body system is then computed by efficiently adding constituent forces stored within the force matrix using reduction operations on the force matrix.

Abstract: A computer-implemented method for managing change of sets of processing information that describe a process flow includes receiving a first activity description describing a first activity for performing a process flow, receiving a first formula description describing a first input and an output of the process flow, receiving a second formula description describing a second input and the same output of the process flow, and associating the first activity description with one of the first formula description and the second formula description.

Abstract: A fluorescence analyzing method includes the steps of irradiating a board, to which oligonucleotide is fixed, with light for fluorescence measurement; focusing produced fluorescence to form an image; and detecting the fluorescence with a two-dimensional sensor. Here, the board is provided with plural regions to which the oligonucleotide is fixed, and the plural regions are spaced apart from one another on the board substantially equidistantly in the vertical and horizontal directions. A fluorescent image is detected in a condition where the following equation is satisfied: dd=ds×M/n where ds denotes the interval between the regions, M denotes the imaging magnification of an optical focusing/imaging system, dd denotes the pixel pitch of the two-dimensional sensor, and n denotes an integer (n=1, 2, 3, 4, 5).

Abstract: The invention provides a method for generating a database of candidate essential genes in Staphylococcus aureus, as well as otherwise important genes that, when mutated, lead to a growth attenuated phenotype. Such genes and mutants of such genes are important for identifying antibacterial agents suitable for treating and preventing S. aureus infections. The invention includes methods for confirming the essentiality or importance of candidate genes, as well as methods for utilizing those genes to screen for new antibacterial drugs. The invention also includes the antibacterial agents identified using the disclosed methods, as well as methods of using the same for treating and preventing Staphylococcus infection.

Abstract: The present invention is drawn to methods for designing synthetic nucleotide sequences encoding polypeptides of interest. The methods involve organizing a database of sequences as a set of N-length oligomer sequences and compiling a list of probability scores for each N-length sequence. The probability scores are used to substitute one or more higher-scoring sequences into the parent nucleotide sequence to generate an optimized sequence. The nucleotide sequence of interest may be further optimized by removing either or both of unintended open reading frames or undesired short DNA elements, and/or substituting oligomer sequences to achieve a specific G:C content. These methods may be used for optimizing expression of heterologous genes in any organism, particularly in plants. The method generates synthetic sequences with a composition similar to that of a target database.

Abstract: In particular, this invention provides novel methods of populating data structures for use in evolutionary modeling. In particular, this invention provides methods of populating a data structure with a plurality of character strings. The methods involve encoding two or more biological molecules into character strings to provide a collection of two or more different initial character strings; selecting at least two substrings from the pool of character strings; concatenating the substrings to form one or more product strings about the same length as one or more of the initial character strings; adding the product strings to a collection of strings; and optionally repeating this process using one or more of the product strings as an initial string in the collection of initial character strings.

Abstract: The invention provides an in silico model for determining a S. cerevisiae physiological function. The model includes a data structure relating a plurality of S. cerevisiae reactants to a plurality of S. cerevisiae reactions, a constraint set for the plurality of S. cerevisiae reactions, and commands for determining a distribution of flux through the reactions that is predictive of a S. cerevisiae physiological function. A model of the invention can further include a gene database containing information characterizing the associated gene or genes. The invention further provides methods for making an in silico S. cerevisiae model and methods for determining a S. cerevisiae physiological function using a model of the invention.

Abstract: Numerical determinations of the first derivatives of a melt curve data set are made. A model function, such as a Gaussian Mixture Model (GMM) function, with parameters determined using a Levenberg-Marquardt (LM) regression process is used to find an approximation to the first derivative curve. The maximum values of the numerically determined first derivative values are used as initial conditions for parameters of the model function. The determined parameters provide one or more fractional melting temperature values, which can be returned, for example, displayed or otherwise used for further processing.

Abstract: Provided herein are methods for evaluating associations between candidate genes and a trait of interest in a population. The methods include a combination of genome-wide association analysis and one or more of nested association mapping (NAM), expression QTL analysis (eQTL), and allele epistastic analysis (AEA). Markers are selected or prioritized if they are shown to be positively-correlated with a trait of interest using GWA and a combination of one or both of NAM and eQTL. Also provided are models for evaluating the association between a candidate marker and a trait in a nested population of organisms. These methods include single marker regression and multiple marker regression models. Markers identified using the methods of the invention can be used in marker assisted breeding and selection, as genetic markers for constructing linkage maps, for gene discovery, for identifying genes contributing to a trait of interest, and for generating transgenic organisms having a desired trait.