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.

Abstract: The invention relates to methods and systems for predicting or estimating the melting temperature of duplex nucleic acids, in the presence of divalent cations, particularly duplexes of oligonucleotides which may be used as, for example, but not limited to primers or probes in PCR and/or hybridization assays. The methods and algorithms use novel formulas, having terms and coefficients that are functions of the particular nucleotide sequence, to estimate the effect of divalent cation salt conditions on the melting temperature.

Abstract: The present invention relates to methods and compositions of modified variants of diphtheria toxin (DT) that reduce binding to vascular endothelium or vascular endothelial cells, and therefore, reduce the incidence of Vascular Leak Syndrome. One aspect of the present invention relates to a polypeptide toxophore from a modified DT, wherein the mutation is the substitution or deletion at least one amino acid residue at the amino acid residues 6-8, 28-30 or 289-291 of native DT. Another aspect of the present invention relates to a fusion protein which comprises a modified DT and a non-DT fragment. Another aspect of the present invention relates to the use of modified DT for the treatment of cancer.

Abstract: The present invention provides automated methods and associated software for determining the organization of a component of interest in individual cells by determining the amount or distribution of the cellular component of interest as a function of position relative to a reference component in the individual cells.

Abstract: The invention relates to the field of compounds, especially peptides or polypeptides, that have thrombopoietic activity. The peptides and polypeptides of the invention may be used to increase platelets or platelet precursors (e.g., megakaryocytes) in a mammal.

Abstract: Modeling of prognosis of survivability, side-effect, or both is provided. For example, RILI is predicted using bullae information. The amount, volume or ratio of Bullae, even alone, may indicate the likelihood of complication, such as the likelihood of significant (e.g., stage 3) pneumonitis. As another example, RILI is predicted using uptake values of an imaging agent. Standardized uptake from a functional image (e.g., FDG uptake from a positron emission image), alone or in combination with other features, may indicate the likelihood of side-effect. In another example, survivability, such as two-year survivability, is predicted using blood biomarkers. The characteristics of a patient's blood may be measured and, alone or in combination with other features, may indicate the likelihood of survival. The modeling may be for survivability, side-effect, or both and may use one or more of the blood biomarker, uptake value, and bullae features.

Abstract: A self-improving classification system classifies specimens based on class identifiers. The system stores specimen profiles in a database that is updated with additional specimen profiles and with follow-up data that corrects classification of specimens that were initially incorrectly classified. Algorithms use the updated database to discover new class identifiers, modify thresholds of known class identifiers, and drop unnecessary class identifiers to improve classification of specimens.

Abstract: A method of finding 3D similarities in protein structures of a first molecule and a second molecule. The method comprises providing preselected information regarding the first molecule and the second molecule. Comparing the first molecule and the second molecule using Longest Continuous Segments (LCS) analysis. Comparing the first molecule and the second molecule using Global Distance Test (GDT) analysis. Comparing the first molecule and the second molecule using Local Global Alignment Scoring function (LGA_S) analysis. Verifying constructed alignment and repeating the steps to find the regions of 3D similarities in protein structures.

Abstract: A method of obtaining information about a chemically active area of a target molecule, for example for drug discovery, comprising: providing a set of substantially rigid chemical gauges; reacting said target with a plurality of gauges of said set of gauges; assaying a binding of said gauges with said target to obtain a plurality of assay results; and analyzing said assay results to obtain information about said chemically active area.

Abstract: Methods for treating cutaneous inflammation are described. Also described is 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: The present invention provides a method for accurately and easily confirming that nucleic acid probes immobilized on a nucleic acid array are correctly arrayed on predetermined positions.

Abstract: Techniques for analyzing one or more protein structures. In one aspect of the invention, the technique comprises the following steps. A normalized second-order hydrophobic moment is determined for a protein structure. The normalized second-order hydrophobic moment is then used for analysis of the protein structure. A scoring function in accordance with the normalized second-order hydrophobic moment for the protein structure may be determined. A score for the protein structure may then be generated using the scoring function. The scoring function may represent an integral of the normalized second-order hydrophobic moment. The scores may be generated for a plurality of protein structures. The scores generated for the plurality of protein structures may then be compared.

Abstract: The present invention provides a method utilizing primary amino acid sequence of a protein, energy minimization, molecular dynamics and protein vibrational modes to predict three-dimensional structure of a protein. The present invention also determines possible intermediates in the protein folding pathway. The present invention has important applications to the design of novel drugs as well as protein engineering. The present invention predicts the three-dimensional structure of a protein independent of size of the protein, overcoming a significant limitation in the prior art.

Abstract: Methods of determining analyte concentration. The methods use a fraction of the predicted total charge, from analyte electrolysis, instead of using time, for determination of a data collection endpoint. The total charge is then extrapolated from the data collection endpoint. The analyte concentration is determined from the total charge.

Abstract: Methods and apparatus for screening large numbers of chemical compounds and performing a wide variety of fluorescent assays, including live cell assays. The methods utilize a laser linescan confocal microscope with high speed, high resolution and multi-wavelength capabilities and real time data-processing. Imaging may be done at video-rates and with use of ultraviolet illumination.

Abstract: A prediction method for predicting the effect of an amino acid modification on the rate of aggregation (solubility) of a reference polypeptide comprising: calculating the difference in hydrophobicity (?Hydr) between the reference polypeptide and a modified polypeptide, calculating the difference in ?-sheet propensity (??Gcoil-?+??G?-coil) between the reference polypeptide and modified polypeptide, calculating the difference in charge (? Charge) between the reference polypeptide and modified polypeptide, and calculating: [x*?Hydr]+[y*(??Gcoil-?+??G?-coil)]?[z*?Charge], wherein x, y and z are scaling factors.

Abstract: A method of simulating behaviour of a molecular system with m degrees of freedom over time comprising a partial momentum refreshment step and a molecular dynamics step, wherein the partial momentum refreshment step comprises: given a starting position q and a starting momentum p of the molecular system, partially refreshing the momentum to define refreshed momentum p? evaluating the shadow Hamiltonian 331 ?t at position q and momentum p?; and accepting or rejecting the refreshed momentum p? according to a Metropolis-type function and if p? is accepted using p? as the resulting momentum p and starting position q as the resulting position q or if it is rejected, using p as the resulting momentum p and starting position q as the resulting position; and wherein the molecular dynamics step comprises: given a starting position q and starting momentum p of the molecular system, running a molecular dynamics simulation over a fixed number of iterations and obtaining new position q? and new momentum p?; evaluating the

Abstract: The present invention presents a new approach to rapidly obtaining precise high-dimensional NMR spectral information, named “GFT NMR spectroscopy”, which is based on the phase sensitive joint sampling of the indirect dimensions spanning a subspace of a conventional NMR experiment. The phase-sensitive joint sampling of several indirect dimensions of a high-dimensional NMR experiment leads to largely reduced minimum measurement times when compared to FT NMR. This allows one to avoid the “sampling limited” data collection regime. Concomitantly, the analysis of the resulting chemical shift multiplets, which are edited by the G-matrix transformation, yields increased precision for the measurement of the chemical shifts. Additionally, methods of conducting specific GFT NMR experiments as well as methods of conducting a combination of GFT NMR experiments for rapidly obtaining precise chemical shift assignment and determining the structure of proteins or other molecules are disclosed.

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: Isolated peptides that are fragments of protein products arising from frameshift mutations in genes associated with cancer are disclosed. The isolated peptides of the invention are capable of eliciting T cell immunity against cells harboring genes with such frameshift mutations. Cancer vaccines and therapeutically effective compositions containing the peptides of the invention are also described.