Abstract: The present invention relates to the field of therapeutic methods, compositions and uses thereof, that affect, directly or indirectly, the behavior of LRP receptors. These compositions and methods result in the treatment of inflammatory, immunological and metabolic conditions. More particularly, the methods and compositions of the invention are directed to the identification of small molecules, drugs and/or pharmacological agents that affect the Wnt pathway by affecting normal complex formation among various signaling receptors, the LRP5 and LRP6 receptor, and related ligands.

Abstract: The mechanism by which the high bone mass (HBM) mutation (G171V) of the Wnt coreceptor LRP5 regulates the canonical Wnt signaling was investigated. The mutation was previously shown to reduce Dkk protein-1-mediated antagonism, suggesting that the first YWTD repeat domain where G171 is located may be responsible for Dkk protein-mediated antagonism. However, we found that the third YWTD repeat, but not the first repeat domain, is required for DKK1-mediated antagonism. Instead, we found that the G171V mutation disrupted the interaction of LRP5 with Mesd, a chaperon protein for LRP5/6 that is required for the coreceptors' transport to cell surfaces, resulting in less LRP5 molecules on the cell surface. Although the reduction in the level of cell surface LRP5 molecules led to a reduction in Wnt signaling in a paracrine paradigm, the mutation did not appear to affect the activity of coexpressed Wnt in an autocrine paradigm.

Abstract: The Wnt signaling pathways are involved in embryo development as well as in tumorigenesis. Dishevelled (Dvl) tranduces Wnt signals from the receptor Frizzled (Fz) to downstream components in canonical and non-canonical Wnt signaling pathways, and the Dvl PDZ domain plays an essential role in both pathways, and the Dvl PDZ domain binds directly to Fz receptors. In the present invention using NMR-assisted virtual ligand screening, several compounds were identified and were found to bind to the Dvl PDZ domain. Molecular dynamics simulation was used to analyze the binding between the PDZ domain and these compounds in detail. These compounds provide a basis for rational design of high-affinity inhibitors of the PDZ domain, which can block Wnt signaling by interrupting the Fz-Dvl interaction.

Abstract: Heterocyclic compounds having a relatively flexible backbone are used to create combinatorial libraries that permit screening for lead compounds and selection of drug candidates for a variety of uses in human and veterinary medicine as well as in agriculture. The compounds of the library generally differ in ring size and chirality of substituents on the ring. Also disclosed are methods for providing and screening these libraries, preferably in an automated or computerizable manner, such as by using a computer program to virtually screen the compounds in order to identify those that are predicted to have bioactive conformations that should give rise to desirable biological effects.

Abstract: Compositions and methods are provided for predicting inhibitors of protein targets related to treatment of infectious disease, for example, bacterial, viral, or parasitic diseases. Methods are provided for predicting inhibitors of protein targets related to treatment infectious disease, for example, microbial disease, utilizing a docking with dynamics protocol to identify inhibitors, or utilizing a protein structure energy function to identify peptide or peptidomimetic inhibitors.

Abstract: A sequencing method is presented in which a biomolecule is hybridized with a specially chosen pool of different probes of known sequence which can be electrically distinguished. The different probe types are tagged such that they can be distinguished from each other in a Hybridization Assisted Nanopore Sequencing (HANS) detection system, and their relative positions on the biomolecule can be determined as the biomolecule passes through a pore or channel. The methods eliminate, resolve, or greatly reduce ambiguities encountered in previous sequencing methods.

Abstract: Certain embodiments disclosed herein include, but are not limited to, at least one of compositions, methods, devices, systems, kits, or products regarding rejuvenation or preservation of stem cells. Certain embodiments disclosed herein include, but are not limited to, methods of modifying stem cells, or methods of administering modified stem cells to at least one biological tissue.

Abstract: A crystal comprising human isoglutaminyl cyclase having a characterised space group of P1211 and unit cell dimensions of +/?5% of a=126.51 ?, b=109.68 ?, c=159.53 ?, ?=90.0°, ?=104.9° and ?=90.0°.

Abstract: Rotamer libraries and methods of use thereof are provided.

Abstract: Systems and method for curation of mass spectral libraries. In general, the systems and methods provided herein (a) obtain an experimentally derived mass spectrum of a compound of interest; (b) identify a peak in the mass spectrum that represent an experimental m/z value for an ion fragment of the compound of interest; (c) remove from the mass spectrum any peak that does not correspond to the compound of interest; and (d) replace the experimental m/z value for the peak identified in step (b) with a calculated theoretical m/z value for the ion fragment.

Abstract: There is provided a compound found by screening a material for inhibiting a binding between a beta-amyloid 1-42 peptide and VEGF165, in which the inhibition material screened according to the present invention can improve effectiveness as a material for treating Alzheimer's disease.

Abstract: A method for designing primers, being capable of efficiently designing primers for a SELEX method is provided. The method for designing primers of the present invention includes the steps of: (S1) generating candidate primer sequences; (S2) evaluating the candidate primer sequences according to a predetermined criterion so as to select candidate primer sequences; (S3) based on the selected candidate primer sequences, generating random pools each containing a plurality of nucleic acid sequences that include random sequences and the candidate primer sequences; (S4) predicting a structure of each of the nucleic acid sequences in each of the random pools and evaluating the predicted structure according to a predetermined criterion so as to select a random pool; and (S5) determining that the candidate primer sequences in the selected random pool are employed as primer sequences. The respective steps are carried out using a computer.

Abstract: Disclosed herein are systems and uses of systems operating between fully quantum coherent and fully classical states. Such systems operate in what is termed the “Poised realm” and exhibit unique behaviors that can be applied to a number of useful applications.

Abstract: A method for treating, preventing or ameliorating a hyperliferative disease and/or disorder in a mammal, comprises administering a therapeutically effective amount of one or more compounds selected from the group consisting of a compound of Formula (III), a compound of Formula (IV), and a pharmaceutically acceptable salt of Formula (III) or Formula (IV): wherein R2 is selected from the group consisting of methyl, ethyl, n-propyl, isopropyl, n-butyl, vinyl and allyl.

Abstract: Naturally-occurring and modified recombinant nucleic acid molecules have been isolated that encode linear pre-cursors of cyclopeptides of the Caryophyllaceae (Ccps) and Caryophyllaceae-like (Clcps) type V1 class of cyclopeptides. Such nucleic acid molecules are useful for producing cyclopeptides and their linear precursors by recombinant methods.

Abstract: The invention relates to methods for the identification and use of introns with gene expression enhancing properties. The teaching of this invention enables the identification of introns causing intron-mediated enhancement (IME) of gene expression. The invention furthermore relates to recombinant expression construct and vectors comprising said IME-introns operably linked with a promoter sequence and a nucleic acid sequence. The present invention also relates to transgenic plants and plant cells transformed with these recombinant expression constructs or vectors, to cultures, parts or propagation material derived there from, and to the use of same for the preparation of foodstuffs, animal feeds, seed, pharmaceuticals or fine chemicals, to improve plant biomass, yield, or provide desirable phenotypes.

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: Disclosed herein are compositions and methods relating to modulators of Nod-like Receptors NOD1 (NLRC1) and NOD2 (NLRC2) signaling. Further provided are methods of identifying modulators of Nod-like Receptors NOD1 and NOD2 activity. Further provided are compositions and methods for treating or preventing inflammation, including diseases associated with inflammation such as inflammatory bowel diseases (Crohn's disease, ulcerative colitis), pancreatitis, arthritis, asthma, psoriasis. Alzheimer's disease, cardiovascular disease (arteritis), diabetes, and sepsis.

Abstract: The present invention relates to antisense oligonucleotides that modulate the expression of and/or function of a Lipid transport and metabolism gene, in particular, by targeting natural antisense polynucleotides of a Lipid transport and metabolism gene. The invention also relates to the identification of these antisense oligonucleotides and their use in treating diseases and disorders associated with the expression of a Lipid transport and metabolism genes.

Abstract: A promoter for differentiation of brain tumor initiating cells is provided.

Abstract: A program interface for diabetic users to streamline the process of carbohydrate counting of meals. The present invention helps diabetic patients keep track of their blood glucose levels and help the users to calculate their require insulin intake for each meal. The invention comprises of a database of foods which users can select from for the calculation of nutrition and carbohydrates. The users are able to select their assigned carbohydrate to insulin ratio for the calculation of the amount of insulin that is required for the meal. Essential data is then stored and accessible for future corrective analysis.

Abstract: Methods and systems for determining a set of control molecules for use in a combinatorial approach for the treatment of medical conditions, including providing one or more sets of control molecules, where each control molecule within the set acts on a set of targets and the number of control molecules within the one or more sets of control molecules is fewer than the number of targets within the sets of targets; and searching within the sets of control molecules to identify a subset of control molecules that together with a subset of targets form an artificial system to produce a biological effect through the modulation of the subset of targets.

Abstract: The instant invention provides methods and compositions for the diagnosis and treatment of cancer. The invention also provides method and compositions for determining if a subject is, or is at risk of becoming, chemoresistant.

Abstract: The present invention relates to systems and methods capable of characterizing populations of organisms within a sample. The characterization may utilize probabilistic matching of short strings of sequencing information to identify genomes from a reference genomic database to which the short strings belong. The characterization may include identification of the microbial community of the sample to the species and/or sub-species and/or strain level with their relative concentrations or abundance. In addition, the system and methods may enable rapid identification of organisms including both pathogens and commensals in clinical samples, and the identification may be achieved by a comparison of many (e.g., hundreds to millions) metagenomic fragments, which have been captured from a sample and sequenced, to many (e.g., millions or billions) of archived sequence information of genomes (i.e., reference genomic databases).

Abstract: The disclosure provides methods and kits for performing automated high-throughput assays to measure bactericidal activity in samples, such as plasma or sera from vaccinated subjects to evaluate the efficacy of vaccines against bacterial pathogens. The method combines obligatory linear-range data analysis, plate sealing and liquid volume handling for all assay steps to provide an automated, high-throughput measurement of bactericidal activity with favorable inter-assay and inter-operator variability.

Abstract: The present invention provides a novel mechanistic pathway and methods related to this pathway for the identification of compounds for the treatment of diseases involving cell proliferation, invasion and/or metastasis such as cancer. In particular, the instant invention relates to the phosphatase activity of Eya and the Eya-Six complex as a target for identifying novel therapeutic agents for the treatment of proliferative, invasive and/or metastatic disorders, and compositions identified using the methods disclosed herein.

Abstract: The invention relates to the X-ray crystal structure of PfA-M1 aminopeptidase alone, and in complex with the phosphinate dipeptide analogue hPheP[CH2]Phe. More specifically the present invention provides the structure coordinates of PfA-M1 and PfA-M1 in complex with Co4. The invention also includes the use of the X-ray crystal structures as drug target models for anti-malarial drug design and a method for identifying or designing novel anti-malarial drugs, for example using high-throughput chemical screening and medicinal chemistry methods. The invention further provides anti-malarial drugs identified or designed according to the aforementioned method and their use for obstructing protein metabolism and synthesis in a parasite by blocking the entrance of Hb-derived peptides and/or blocking the exit of released amino acids at the active site of PfA-M1 protease.

Abstract: The present invention relates to genetic markers whose expression is correlated with breast cancer. Specifically, the invention provides sets of markers whose expression patterns can be used to differentiate clinical conditions associated with breast cancer, such as the presence or absence of the estrogen receptor ESR1, and BRCA1 and sporadic tumors, and to provide information on the likelihood of tumor distant metastases within five years of initial diagnosis. The invention relates to methods of using these markers to distinguish these conditions. The invention also relates to kits containing ready-to-use microarrays and computer software for data analysis using the statistical methods disclosed herein.

Abstract: Provided are antibodies that bind to: a sulfonated epitope of the protein Sclerostin, to Sclerostin portions comprising a sulfonated amino acid and to dimerized forms of Sclerostin. Further provided are compositions and peptides comprising a sulfonated epitope of sclerostin. Also provided by this invention are methods for production of such antibodies, both active and passive, and methods for identifying antibodies specific for sulfonation sites in Sclerostin and other antibodies which discriminate between sulfonated and unsulfonated forms of sclerostin. Physical and virtual screening processes are provided in this invention for identifying compounds whichh disrupt or inhibit sulfonation and the interaction between Sclerostin and binding partners. The antibodies and compositions of the present invention are useful in diagnostic and therapeutic applications directed to Sclerostin-related disorders.

Abstract: The present invention relates to a method of identifying compounds useful in inhibiting protein kinase-like endoplasmic reticulum protein kinase (PERK). The method comprises providing a first model comprising PERK active domains, where the said active domains are selected from the group consisting of the peptide spanning from amino acid residue Asp144 to amino acid residue Ser191 of SEQ ID NO: 1 and a peptide comprising the amino acid residue at position 7 of SEQ ID NO: 1, providing one or more candidate compounds, evaluating contact between the candidate compounds and the first model to determine which of the one or more candidate compounds have an ability to bind to and/or fit in the first model, and identifying the compounds which, based on said evaluating, have the ability to bind to and/or fit in the first model as compounds potentially useful for inhibiting PERK.

Abstract: The preset invention relates to a process for discovering potential treatment strategy for a given disease, providing a niche for PPI network construction, target prioritization, and potential drug identification for a given disease, particular a cancer, based on the interaction between prioritized NPC targets (e.g. cliques and bottleneck genes) and drugs.

Abstract: The invention is related to various methods for inhibiting or reducing biofilm formation, treating a biofilm production-related disorder, preventing biofilm formation, and screening for neuraminidase inhibitors.

Abstract: The present invention relates to the field of medical treatments for diseases and disorders. More specifically, the present invention relates to the use of the lanthionine synthetase component C-like (LANCL) proteins as therapeutic targets for novel classes of anti-inflammatory, immune regulatory and antidiabetic drugs.

Abstract: Materials and Methods related to developing a unipolar depression (MDD) disease score in a subject using a multi-parameter system to measure a plurality of parameters, and an algorithm to calculate a score.

Abstract: The present invention provides an approach for the simultaneous determination of the activation states of a plurality of proteins in single cells. This approach permits the rapid detection of heterogeneity in a complex cell population based on activation states, and the identification of cellular subsets that exhibit correlated changes in activation within the cell population. Moreover, this approach allows the correlation of cellular activities or properties. In addition, the use of potentiators of cellular activation allows for characterization of such pathways and cell populations.

Abstract: Disclosed is a method for examining prognosis of breast cancer including the steps of: (A) extracting RNA from a specimen collected from a subject, (B) preparing a determination sample using the extracted RNA, (C) determining the expression level of each gene in the specific gene groups using the obtained determination sample, (D) analyzing the expression level of the determined each gene, and (E) examining prognosis of breast cancer, based on the obtained analysis result are performed.

Abstract: The present invention generally relates to methods of rapidly and efficiently searching biologically-related data space. More specifically, the invention includes methods of identifying bio-molecules with desired properties, or which are most suitable for acquiring such properties, from complex bio-molecule libraries or sets of such libraries. The invention also provides methods of modeling sequence-activity relationships. As many of the methods are computer-implemented, the invention additionally provides digital systems and software for performing these methods.

Abstract: Materials and Methods related to developing a unipolar depression (MDD) disease score in a subject using a multi-parameter system to measure a plurality of parameters, and an algorithm to calculate a score.

Abstract: A system and method to search spectral databases to identify unknown materials, specifically pathogenic microorganisms. A library is provided, having sublibraries containing reference data sets of known materials and test data sets, both generated by at least one spectroscopic data generating instrument. For each test data set, each sublibrary associated with the instrument used is searched. A set of scores for each searched sublibrary is produced, representing the likelihood of a match between the reference data set and test data set. Relative probability values are calculated for each searched sublibrary. All relative probability values are fused producing a set of final probability values, used in determining whether the unknown material is represented through a known material in the library. The known material represented in the libraries having the highest final probability value is reported, if the highest final probability value is greater than or equal to the minimum confidence value.

Abstract: A method for determining the presence of a copy number imbalance in genomic DNA of a test sample is provided. The method can separately measure hybridization of a single test sample to a first hybridization array and hybridization of a plurality of reference samples to a plurality of other, respective test arrays. A determination of copy number can be based on the best fit reference array, relative to the test array. The best fit can be determined based on the closest or most similar signal-to-noise ratio of the measured signals.

Abstract: The invention provides isolated pyruvate dehydrogenase kinase nucleic acids and their encoded polypeptides. The present invention provides methods and compositions relating to altering pyruvate dehydrogenase kinase levels in plants. The invention further provides recombinant expression cassettes, host cells, transgenic plants, and antibody compositions.

Abstract: A method for analyzing a mixture includes identifying a plurality of possible components of the mixture, calculating at least one feature for at least a portion of the plurality of possible components, and calculating a probability value for at least a portion of the plurality of possible components based on the at least one feature and at least one transfer function

Abstract: According to an embodiment of the present invention, it is possible to rapidly and accurately predict a class label of a predetermined test sample by extracting a disease-specific gene pair from gene pairs on a microarray data set representing an expression level for each of genes of a genome and for each of a plurality of samples by considering the correlation in a normal class and the correlation in a disease class, selecting a highest specific gene pair with the highest correlation among the extracted disease-specific genes, and predicting the class label of the predetermined test sample by using the selected highest specific gene pair.

Abstract: The present invention provides methods for identifying compounds that selectively bind one or more active sites within an ubiquitin conjugating enzyme. The compounds identified by the methods are useful in the treatment of disorders attributed to dysregulated ubiquitin conjugating enzyme function, specifically in hyperproliferative disorders.

Abstract: Disclosed is a method for detecting one or both of the native material in an object and any foreign material in the object by parallel-mode spectroscopy, comprising parallel-mode data acquisition, signal processing and data reduction and providing results. Parallel-mode data acquisition comprises producing an interrogating signal simultaneously containing electromagnetic radiation of sufficient bandwidth in the range of approximately 10 GHz to approximately 25 THz to allow simultaneous detection of a plurality of signals at a plurality of frequencies, each signal being at some amplitude, which collectively provide a unique spectral signature of a material whose detection is desired. The signal processing and data reduction comprises processing a signal resulting from exposing the object to the interrogating radiation to produce a three-dimensional data matrix representative of at least any foreign or native material associated with the object.

Abstract: Systems and methods for determining therapeutic potential. In at least one embodiment of a system of the present disclosure, the system comprises a detection platform, a computer processor and a database. The processor, in at least one embodiment of a method of the present disclosure, has and executes a software program operational to determine a binding characteristic of the detection agent and a stabilized diagnostic marker in each of the plurality of detection sites on the platform, compare the binding characteristic, and determining the stabilizing agent with the greatest effect on the binding characteristic between the detection agent and the diagnostic marker. Further, at least one embodiment of a system for determining the therapeutic potential of a therapeutic compound of the present disclosure is able to generate a binding record using the compared binding characteristics, and deliver the binding record to a recipient.

Abstract: The invention provides for a method for screening compounds that bind to and modulate the hair-specific G-protein coupled receptor, P2RY5. The invention further provides for methods for controlling hair growth by administering a P2RY5 modulating compound to a subject.

Abstract: The invention provides peptide epitopes for use in the prevention and/or treatment of influenza or for the development of such treatment or vaccine against influenza. The invention also relates to a method for evaluating the potential of a chemical entity, such as an antibody, to bind to a peptide epitope derived from the divalent sialoside binding site of hemagglutinin protein of influenza virus, and to conjugates containing one or more such peptide epitopes. The peptide epitopes of the invention are cyclic peptides comprising a 7-mer peptide derived from H1, H3 or H5 hemagglutinin of influenza virus. The 7-mer peptide has a sequence corresponding to the loop sequence at positions 220-226 of X31-hemagglutinin.

Abstract: Methods and devices for diagnosing, monitoring, or determining kidney transplant rejection or an associated disorder in a mammal are described. In particular, methods and devices for diagnosing, monitoring, or determining kidney transplant rejection or an associated disorder using measured concentrations of a combination of three or more analytes in a test sample taken from the mammal are described.

Abstract: DNA taggants in which the nucleotide sequences are defined according to combinatorial mathematical principles. Methods of defining nucleotide sequences of the combinatorial DNA taggants, and using such taggants for authentication and tracking and tracing an object or process are also disclosed.