Abstract: The present disclosure presents novel shape comparison methods. Methods for determining shape similarity between a query molecule and a target molecule and methods for screening one or more molecules in a database based on shape similarity to a query molecule are described.

Abstract: The present invention embraces methods for identifying compounds that modulate the activity of telomerase. Compounds of the invention are identified by designing or screening for a compound which binds to at least one amino acid residue of the TRBD, “thumb,” “finger,” and/or “palm” domain; or FP-pocket, PT-pocket or Th-pocket of telomerase and testing the compound for its ability to modulate the activity of telomerase.

Abstract: The present invention relates generally to chemical agents useful in the prophylaxis and/or treatment of disease conditions and in particular chronic disease conditions such as inflammatory including allergic diseases, metastatic cancers and infection by pathogenic agents including bacteria, viruses or parasites. More particularly, the chemical agents contemplated by the present invention are selected from glycosaminoglycan (GAG) molecules derived from a larger GAG, GAG-like molecules which resemble GAGs in some of their characteristics but may be derived from a larger non-GAG polysaccharide and molecules having a GAG-like composite structure as well as agents which bind to the same sites as GAGs, GAG-like molecules or GAG-like composite molecules. The present invention also provides assays to identify GAG and GAG-like therapeutic agents including GAG-like composite structures as well as analogs, homologs and orthologs thereof.

Abstract: Co-administration of a lysostaphin or other anti-staphylococcal agent which cleaves cross-links of peptidoglycans of staphylococci cell walls such as lysostaphin and an antibiotic effective against staphylococci due to antibiotic activity mediated by cell-wall activity is effective against staphylococcal infection, even staphylococci that may be resistant to one or other of lysostaphin or the cell-wall active antibiotic. Co-administration simultaneously suppresses the generation of antibiotic-resistant mutant strains. Effective cell-wall active antibiotics include ?-lactams and glycopeptides.

Abstract: Methods related to the generation of shape signatures representing molecular shape, and using shape signatures in both ligand-based and receptor-based molecular design. Ray-tracing is used to explore the volume interior to a ligand, or the space exterior to a receptor site. Shape signatures are then probability distributions derived from the ray-traces. Shape signatures provide condensed descriptors of shape properties readily compared to each other to test for shape similarity or complementarity.

Abstract: An electroencephalogram interface system includes a biological signal detection section for detecting an electroencephalogram signal from a user and a control section for distinguishing a component of an event-related potential and causing a device to operate based on the distinguished event-related potential. An activation apparatus activates the control section and an output section for presenting a visual stimulation which flickers with a predetermined frequency based on a signal from the activation apparatus. The activation apparatus includes: a frequency analysis section for analyzing a frequency component of the electroencephalogram signal and detecting an intensity corresponding to the predetermined frequency; and a determination section for comparing the detected intensity of the predetermined frequency and a predetermined threshold, and if the intensity of the predetermined frequency is equal to or greater than a predetermined threshold, activating the control section.

Abstract: A method of determining aggregation rate data predicting an aggregation rate of a polypeptide defined by an amino acid sequence, the method comprising determining a hydrophobicity value, a charge value, and at least one shape propensity value for said sequence; identifying one or more aggregation-influencing patterns within said sequence; determining a pattern value for the sequence responsive to said identifying; and determining said aggregation rate data by determining a weighted combination of said hydrophobicity value, said charge value, said at least one shape propensity value, said pattern value and at least one factor extrinsic to said amino acid sequence.

Abstract: This application is based on the concept of the Proteomic Code, PC (discovered and described by Biro, 1981-2011, for review see ref 6) and making use of the biological observation, that co-locating amino acids [in interacting proteins] are coded by partially complementary codons. A method is provided to design and produce a special and distinct set of affinity oligopeptides (AffiSeq) using the PC principle. These designed and artificially produced affinity peptides will be used in any biotechnological or pharmacological applications which benefit of the specific and high affinity protein-protein interactions.

Abstract: A computer-implemented method for calculating a value representative of interaction (VRI) of a proposed ligand with a specified receptor. Hydrophobic interactions between one or more ligand atoms and one or more receptor atoms are scored by a method that awards a bonus for the presence of hydrophobic enclosure of one or more ligand atoms by the receptor. Also, charge-charge hydrogen bonds between a ligand and a receptor are scored by setting a default value for a charge-charge hydrogen bond and awarding a bonus above the default value when one or more specialized predetermined charge-charge hydrogen bond criteria is satisfied. Various charge-charge hydrogen bond criteria are used. Zwitterions, charge, salvation, geometry and electrostatic energy are accounted for.

Abstract: The present invention provides a method of predicting the mutual affinity of two molecules for each other in solution, by computing the configuration integrals of the free molecules and their bound complex as sums over local energy wells. The invention makes accurate calculations computationally tractable for a range of molecular systems by several means, including restraining the conformations of selected molecular components, and using a single conformation representative of an energy well to correct an efficient but less accurate energy model toward a slower but more accurate model.

Abstract: Generally, the present invention provides a number of procedures to spatially profile proteins by using hydrophobic moments. In all procedures, a hydrophobicity distribution of a protein is shifted and normalized. In one procedure, a shape or profile of a curve of a second-order moment of hydrophobicity is determined. A second procedure involves determining one or more ratios, such as the ratio of a distance at which the second order moment of hydrophobicity vanishes to the distance at which a zero-order moment of hydrophobicity vanishes. The distance at which a peak occurs in a profile of the zero- or second-order moment of hydrophobicity can also be used for comparison. For many of these procedures, a surface or profiling contour can be chosen and used to accumulate hydrophobicities and to determine the moments. These procedures can be combined to provide a good mathematical determination of whether a protein belongs to a particular class of proteins.

Abstract: The present invention provides a data processing system and a data collection method by which measurement data can be read in and transmitted easily, without connecting a terminal for transmitting data with various types of measurement apparatuses, and further provides a measurement apparatus to be used for the data processing system and the data collection method. The data processing system at least uses: a measurement apparatus (10) provided with a display screen (13); a terminal (20); and a server (30). The measurement apparatus (10) includes: a measurement portion for obtaining measurement data; a code transforming portion for transforming the measurement data into a bar code, a two-dimensional code (8) or a composite code; and a display portion for displaying the code on the display screen.

Abstract: The present invention relates to isolated Porphyromonas gingivalis polypeptides and nucleotides. The polypeptides include an amino acid sequence selected from the group consisting of: SEQ. ID. NO. 110; SEQ. ID. NO. 111; SEQ. ID. NO. 112; SEQ. ID. NO. 113; SEQ ID NO: 120; SEQ. ID. NO. 123; SEQ. ID. NO. 124; SEQ. ID. NO. 125; SEQ. ID. NO. 130; SEQ. ID. NO. 131; SEQ. ID. NO. 132; SEQ. ID. NO. 133; SEQ. ID. NO. 135; SEQ. ID. NO. 136; SEQ. ID. NO. 137; SEQ. ID. NO. 138; SEQ. ID. NO. 143; SEQ. ID. NO. 144; SEQ. ID. NO. 145; SEQ. ID. NO. 146; SEQ. ID. NO. 147; SEQ. ID. NO. 148; and amino acid sequences at least 95% identical thereto.

Abstract: A method of using a variable set from complete blood counts and blood chemistry panels to generate a machine learned algorithm for determining the effectiveness of thiopurine treatment on inflammatory bowel disease (IBD) patients using CART, boosted trees, random forest classification, RuleFit and/or logistic regression analysis.

Abstract: In a system having an interface which utilizes electroencephalogram, it is determined whether the user was looking at a menu or not based on the frequency of the user electroencephalogram, and the electroencephalogram is excluded from the subject of distinction in the case where the user is not looking at the menu. A distinction necessity determination apparatus 10 for determining whether or not to perform a distinction of an electroencephalogram signal in an electroencephalogram interface system 1 includes a frequency analysis section 11 for calculating a representative frequency at which frequency power of the electroencephalogram signal becomes maximal, and a determination section 12.

Abstract: A method for identifying or monitoring SLE in an individual is provided. The method includes quantitating complement component C4d on the surfaces of platelets and comparing the amounts of C4d to reference levels of C4d on platelets of individuals without SLE and/or on platelets of the individual obtained at a different time. Kits for use in the above-described methods are provided along with computer readable media tangibly embodying executable instructions to perform the methods.

Abstract: The present invention provides automated methods for cell body extension analysis, software for carrying out such methods, and detection devices comprising such software.

Abstract: Methods for treating cutaneous inflammation, are described. Also described is a method for inhibiting the mucus release into airways of a patient, a method for blocking IgE activation of a lymphocyte, a method for stabilizing the cell membrane of a lymphocyte, thereby preventing their further involvement in the increased inflammatory response to an IgE antigen challenge, and a method for inhibiting the migration of T-cells. Such methods involve administering to said patient a therapeutically effective amount of a peptide having the formula f-Met-Leu-X, wherein X is selected from the group consisting of Tyr, Tyr-Phe, Phe-Phe and Phe-Tyr.

Abstract: A method, computer system, and computer program product for determining N disulphide bond connections in a protein having 2N bonded sulphur atoms. Each sulphur atom is available for forming the N disulphide bond connections through use of an undirected graph having the 2N sulphur atoms as nodes and having an edge connecting each pair of nodes. Each sulphur atom is comprised by a cysteine of the protein. The cysteines are sequenced along a chain in the protein as ordered list of position indexes. A weight W of each edge between cysteine position indexes I1 and I2 is calculated as decreasing with increasing separation d between I1 and I2, wherein d is |I1?I2|/100. The N disulphide bond connections are determined by optimizing an objective function formed from the calculated weights W.

Abstract: Disclosed is a method and system for analyzing patient hospitalization data to determine a Nosocomial Infection Marker (NIM), the method comprising receiving from a database hospitalization data associated with at least one patient, calculating from the hospitalization data the number of specimens with non-duplicate hospital isolates (SNDHI) markers, calculating from the hospitalization data antibiotic utilization criteria (AUC) markers, and determining the nosocomial infection marker (NIM) for each patient, based upon the calculated SNDHI and AUC markers.