Abstract: A method and evaluation kit are provided, in which a high-capacity urate transporter is identified to assist in the early treatment and prevention of urate transport-related disease and inflammation-related disease. The method can include a step for detecting variations in genes that encode ABCG2 protein. When a subject has an SNP of V12M, R113X, Q126X, Q141K, F2085, G268R, E334X, S441N, L447V, S486N, F506SfsX4, R575X, and/or C608X, it can be concluded that the subject has a factor that is capable of inducing urate transport failure, or a state or disease attributable to that failure. When a subject has an SNP of V12M, it can be concluded that, unlike the other SNPs, there is a possibility that the subject does not possess such a factor because, although this variation itself does not lead to a change in urate transport capability, said variation is related to linkage disequilibrium with other SNPs.

Abstract: The present invention relates to biomarkers that are useful in the prognosis of triple negative breast cancer patients. The biomarkers may be used to select treatment and to determine whether a treatment is effective or not. The biomarkers may also be used to select novel treatments and to screen for new potential compounds that may treat the triple negative breast cancer.

Abstract: The present invention relates to a method for the prognosis and/or risk assessment and/or monitoring of therapy and/or management of patients with COPD the method comprising the steps of: i) providing a sample of a bodily fluid from said patient, ii) determining in said sample the level of at least one biomarker, selected from the group consisting of pro-adrenomedullin (proADM), pronatriuretic peptide, pro-Vasopressin (proAVP) and Procalcitonin (PCT) or fragments thereof of at least 12 amino acids in length, iii) determining one, two or three of the BODE-index parameters body-mass index (BMI, parameter B), degree of airflow obstruction (FEV1, parameter O), dyspnea (parameter D) and exercise capacity (parameter E), iv) correlating said level of said at least one biomarker determined in step ii), in combination with said one, two or three BODE-index parameters determined in step iii) to the prognosis and/or risk assessment and/or monitoring of therapy and/or management of patients with COPD.

Abstract: The method of sub-classifying breast cancer tumors profiles the expression of the Raf kinase inhibitor protein (RKIP) from a tissue sample from a cancerous primary breast tumor. The RKIP expression is profiled using its mRNA or by immunohistochemical protein quantifying methods in order to detect the level of RKIP in the breast cancer tissue sample. Based upon the RKIP expression profile, a sub-classification of cancer type may then be assigned. An RKIP expression of approximately 10.31 indicates basal carcinoma, an RKIP expression of approximately 10.04 indicates Claudin-low carcinoma, an RKIP expression of approximately 10.47 indicates Luminal-A carcinoma, an RKIP expression of approximately 10.44 indicates Luminal-B carcinoma, an RKIP expression of approximately 10.25 indicates HER2+ carcinoma, an RKIP expression of approximately 10.43 indicates ER+ carcinoma, and an RKIP expression of approximately 10.30 indicates ER? carcinoma.

Abstract: The invention relates to novel cyclic compounds (cyclic peptides), linkers useful as beta-turn promoters in cyclic peptides, and methods for treatment of malignant cells in vitro or in vivo using one or more linear and cyclic peptides. The peptides can act as integrin interaction inhibitors and may be used in the treatment of cancers as monotherapies or in combination with other anti-cancer agents, such as proteasome inhibitors, inhibitors of autophagy, alkylating agents, MEK inhibitors, FAK/PYK2 inhibitors, and EGFR inhibitors. The invention further concerns a method of predicting the binding of a cyclic or linear HYD1 peptide to a cancer cell by assessing overexpression of biomarkers such as CD44, VLA-4 integrin, basigin, CD138 (syndecan 1), NCAM, ICAM1, ICAM3, and CD59.

Abstract: The invention provides devices and methods for self-administered noninvasive retrieval of biological materials of the uterus and/or cervix. The cervical device comprises a receptacle with a variable volume receptacle cavity, a controller configured to change the volume of the receptacle cavity, a surface for collection of biological materials, and a flexible pouch for generation of suction to facilitate efficient retrieval of biological materials. The biological materials retrieved include various biomarkers of diseases and disorders of reproduction, are directly isolated from a site of pathology, and are not metabolized or diluted. Information generated by analyzing these biological materials permits early diagnosis and prognosis assessments of disease and disorders of the female reproductive organs, irregularities of pregnancy, anomalies of the fetus in utero, and microbial infections.

Abstract: The present invention relates to a method for the in vitro diagnosis or prognosis of ovarian cancer, which includes a step of detecting at least one expression product of at least one HERV nucleic acid sequence, the use of said nucleic acid sequences, once isolated, as one or more molecular marker(s) and a kit including at least one specific binding partner of at least one of the expression products of the HERV nucleic acid sequences.

Abstract: A novel method that enables prostate cancer testing that is noninvasive and more accurate than conventional methods is disclosed. The present inventors intensively analyzed urine samples from prostate cancer patients, and non-cancer subjects, who are free of prostate cancer, and, as a result, newly discovered urinary peptides that can be used as indicators in prostate cancer testing. Use of these urinary peptides as indicators enables various prostate cancer-related tests including detection of prostate cancer, discrimination between prostate cancer and benign prostatic hyperplasia, monitoring of a therapeutic effect of prostate cancer therapy and monitoring of postoperative recurrence.

Abstract: Provided are methods of predicting the outcome of a chronic lymphocytic leukemia (CLL) in a subject. The methods comprise performing a polymerase chain reaction assay for an IGH locus on a nucleic acid from a biological sample from a subject with CLL, wherein the PCR assay amplifies a non-coding region of the IGH locus, sequencing a product from the PCR assay, and determining a level of mutation in the non-coding region of the IGH locus. An increased level of mutation in the non-coding region as compared to a control indicates a positive outcome for the subject with CLL. A decreased level or no mutation in the non-coding region as compared to a control indicates a poor outcome for the subject with CLL.

Abstract: Disclosed are nucleic acid sequences, including microRNA sequences and cDNA sequences, as well as vectors, DNA libraries, microarrays, and recombinant cells comprising the nucleic acid sequences described herein. Methods of determining the B cell stage from which a B cell malignancy is derived. Methods of identifying B cell malignancies are also provided. Methods of diagnosing B cell malignancies are provided. Such methods comprise, in certain embodiments, detecting one or more microRNAs or cDNAs as disclosed herein.

Abstract: The present disclosure provides methods of that include detecting in a biological sample from a patient having or suspected of having cancer the presence of a polypeptide having ROS1 kinase activity or a polynucleotide encoding the same and detecting in the biological sample the presence of a mutant EGFR polypeptide or a polynucleotide encoding the same. In some aspects, the disclosure provides methods of treating a patient for cancer that include determining that a biological sample from a tumor in the patient includes a polypeptide having ROS1 kinase activity or a polynucleotide encoding the same and a mutant EGFR polypeptide or a polynucleotide encoding the same and administering to the patient a therapeutically effective amount of a ROS1 inhibitor and an EGFR inhibitor, thereby treating the patient for cancer.

Abstract: Provided herein are methods to generate and screen peptides that exhibit drug like stabilities in vitro and in vivo. By selecting for enzyme resistance, Applicants are able to derive peptides that are not only stable to a broad spectrum of proteases, but also stable to other drug processing enzymes such as cytochrome P450s. This approach provides a general method to the rapid development of highly stable peptides for therapeutic development and diagnosis. The peptides are further modified for oral bioavailability.

Abstract: Methods for obtaining plants that exhibit useful traits by perturbation of plastid function in plants are provided. Methods for identifying genetic loci that provide for useful traits in plants and plants produced with those loci are also provided. In addition, plants that exhibit the useful traits, parts of the plants including seeds, and products of the plants are provided as well as methods of using the plants. Recombinant DNA vectors and transgenic plants comprising those vectors that provide for plastid perturbation are also provided.

Abstract: The invention relates to a method for detecting the presence or absence of a bacterial pathogen in a biological sample obtained from a human or animal subject, using an internal control. In particular, the invention relates to a method for detecting the presence or absence of Streptococcus equi in an equine sample using a control bacterial strain as internal control for DNA extraction and PCR. The invention also relates to host cells (such as bacterial cells) and nucleic acids for use as internal standard in said method in addition to diagnostic kits comprising said host cells and nucleic acids.

Abstract: A system and method for targeting relevant research activity for clinical application in response to diagnostic markers analyses is described. Diagnostic analysis is performed to detect the level of each of at least three diagnostic markers. The levels of the tested markers are used to identify relevant publications from among a large database of articles. The most relevant literature, such as, one which reports research and studies that have been conducted to identify, moderate, and define the mechanisms unique to individual and combinations of diagnostic markers for various disease states, is then provided to the patient and/or the patient's physician, optionally with a summarization of the treatment recommendations from the provided literature. The customized information delivery provides a range of published peer-reviewed therapeutic options and/or published research studies.

Abstract: This disclosure describes screening a population of transgenic plants derived from plant cells transformed with recombinant DNA for expression of proteins with homeobox domains to identify plant cells of specific transgenic events that are useful for imparting enhanced traits to transgenic crop plants. Traits include enhanced nitrogen use efficiency, increased yield, enhanced water use efficiency, enhanced tolerance to cold stress and/or improved seed compositions. Also disclosed are transgenic seeds for growing a transgenic plant having the recombinant DNA in its genome and exhibiting the screened enhance trait. Also disclosed are methods for generating seed and plants based on the transgenic events.

Abstract: A group of bacterial dihydroxy-acid dehydratases having a [2Fe-2S] cluster was discovered. Bacterial [2Fe-2S] DHADs were expressed as heterologous proteins in bacteria and yeast cells, providing DHAD activity for conversion of 2,3-dihydroxyisovalerate to ?-ketoisovalerate or 2,3-dihydroxymethylvalerate to ?-ketomethylvalerate. Isobutanol and other compounds may be synthesized in pathways that include bacterial [2Fe-2S] DHAD activity.

Abstract: Methods of making and using bacterial display polypeptide libraries using circularly permuted OmpX (CPX) variants are disclosed. The invention further relates to methods for enhancing the display of proteins and peptides at the surface of bacteria by optimizing linkers and incorporating mutations at positions 165 and 166 of CPX.

Abstract: Fluid-based no-moving part logic devices are constructed from complex sequences of micro- and nanofluidic channels, on-demand bubble/droplet modulators and generators for programming the devices, and micro- and nanofluidic droplet/bubble memory elements for storage and retrieval of biological or chemical elements. The input sequence of bubbles/droplets encodes information, with the output being another sequence of bubbles/droplets or on-chip chemical synthesis. For performing a set of reactions/tasks or process control, the modulators can be used to program the device by producing a precisely timed sequence of bubbles/droplets, resulting in a cascade of logic operations within the micro- or nanofluidic channel sequence, utilizing the generated droplets/bubbles as a control. The devices are based on the principle of minimum energy interfaces formed between the two fluid phases enclosed inside precise channel geometries.

Abstract: Processing personal compatibility matches includes a computer system receiving input of a first allele group determined to be present in a first person and a second allele group determined to be present in a second person. The first allele group and the second allele group are members of a set of allele groups for a human leukocyte antigen (HLA) gene. Each group of the set of allele groups is predefined to contain related alleles. By comparing the first allele group to the second allele group, a similarity of the first allele group to the second allele group may be determined. An indication of personal compatibility of the first person and the second person is inversely related to the determined similarity. The computer system can output the indication of personal compatibility to, for example, a matchmaker or a third-parting service.

Abstract: Analysis of a system and/or sample involves the use of absorption-encoded micro beads. Each type of micro bead is encoded with amounts of the k dyes in a proportional relationship that is different from proportional relationships of the k dyes of others of the n types of absorption-encoded micro beads. A system and/or a sample can be analyzed using information obtained from detecting the one or more types of absorption-encoded micro beads.

Abstract: A method is disclosed to obtain oligonucleotide sequences with high affinity to target molecules. By design, the oligonucleotides have a defined primary and secondary structure. The affinity for binding to target species is classified or quantified by assay measurements using physical measurements rather than being based primarily on separations. Targets include but are not limited to proteins, polymers, biological membranes including cells and organelles and small molecules.

Abstract: The present invention features improved methods of in vitro RNA display to allow reliable expression and selection of scFv antibody molecules from expression libraries. The improved methods, in part, involve the use of mildly reducing conditions, which favor of scFv intra-chain disulphide bond and thus correct folding of the scFv antibody molecules. Although particularly suited to expression and selection of scFv antibody molecules, the methods of the invention are also expedient for in vitro RNA display of all classes of protein.

Abstract: A sensor array includes resonator sensors having respective receptor materials disposed thereon. The receptor materials have a physical property relevant to their ability to bind or adsorb one or more analytes in a sample. The physical property of the receptor materials on the sensors systematically increases or decreases in degree from one sensor to the next in the array. The device also comprises at least one detector for detecting sensor responses when masses of the analytes are adsorbed or bound to the receptor materials on the sensors. With this graded panel of sensors in the array, the analytes may adsorb or bind to the functionalized sensors with a pattern of responses specific to each analyte.

Abstract: Disclosed embodiments concern an array for use in identifying or identifying and quantifying analytes in a sample using a macrocyclic sensor comprising a macrocyclic compound and a detectable moiety. The disclosed array may be used to discriminate among various analytes based on different features, such as post-translational modifications, isomeric post-translational modifications, and the peptide sequence around post-translational modifications. Also disclosed is a method for identifying analytes comprising a post-translational modification, as well as an enzymatic assay using the disclosed macrocyclic sensor.

Abstract: The systems and methods of the invention provide a guided approach to pyrosequencing (i.e., hybrid pyrosequencing). A de novo nucleic acid sequence may compared to a library of possible results and the next nucleotide to be dispensed is selected based on the comparison of the de novo sequence and the library of possible results. In another example, at least the first nucleotide to be dispensed is selected based on a query of a database(s) of non-sequence parameters (e.g., incidence of infection, diagnostic symptoms, sample source) and subsequent dispensations determined based on a comparison of the de novo sequence and the library of possible results (e.g., candidate sequences). The systems and methods of the invention may be performed using a droplet actuator.

Abstract: The invention relates to assays for measuring the effect of a inactive test substance on a lipid bilayer, kits for measuring the effects of test substances on lipid bilayers and an apparatus for performing a high through-put assay that measures the effect of test substances on a lipid bilayer.

Abstract: A method for encoding and identifying biological materials is disclosed. The method may include encoding and identifying plants from which controlled substances may be derived and other materials for which movement and distribution may need to be tracked. The biological material may be first encoded using DNA oligomers. A spray method or the use of an encoded substrate, both using these DNA oligomers for encoding the biological material, may be employed. The biological material, or a part of the biological material, may be first encoded by atomizing a solution containing DNA oligomers onto it and then dried by an appropriate method. Thereafter, the part of the encoded biological material, or the nitrocellulose substrate, may be dissolved with a buffer solution for extracting the DNA oligomers. Then, the dissolved solution may be used for generating a barcode by a suitable detection scheme.

Abstract: According to various embodiments, a method is provided that comprises washing an array of DNA-coated beads on a substrate, with a wash solution to remove stacked beads from the substrate. The wash solution can include inert solid beads in a carrier. The DNA-coated beads can have an average diameter and the solid beads in the wash solution can have an average diameter that is at least twice the diameter of the DNA-coated beads. The washing can form dislodged DNA-coated beads and a monolayer of DNA-coated beads. In some embodiments, first beads for forming an array are contacted with a poly(ethylene glycol) (PEG) solution comprising a PEG having a molecular weight of about 350 Da or less. In some embodiments, slides for forming bead arrays are provided as are systems for imaging the same.

Abstract: An analytical device such as a flow cytometer is provided in which a fluid sample flowing through a channel is focused into multiple, parallel particle streams by an acoustic wave field extending across the channel. Each stream is then presented to an individual detector to allow for simultaneous interrogation of the multiple streams and thus, high-throughput analysis of the fluid sample.

Abstract: The invention relates to compositions and methods to isolate nucleic acids, and the identification of polyadenylation sites in a gene of interest. In one aspect, the invention provides an oligonucleotide comprising at least one nucleic acid and an affinity moiety, wherein said nucleic acid is 30-60 nucleotides in length and said nucleic acid comprises 1-25 uracil and 5-50 thymine nucleotides.

Abstract: The invention relates to methods of identifying a binding partner of a target molecule within a plurality of analyte molecules, including a plurality of peptides and/or proteins. The target molecule is physically combined with a target labeling nucleic acid molecule. Each member of the plurality of analyte molecules is physically linked to an analyte labeling nucleic acid molecule, each analyte labeling nucleic acid molecule comprising a selected nucleotide sequence. This specific nucleotide sequence may include a sequence encoding a peptide/protein combined therewith. The target molecule is contacted with the analyte molecules and a complex between the target molecule and an analyte molecule forms. The mixture is subdivided into compartments. The target labeling nucleic acid molecule and the analyte labeling nucleic acid molecule are linked and the plurality of compartments allowed to disintegrate. The linked nucleic acid molecule is retrieved and the sequence determined.

Abstract: A process for the production of an antigen specific antigen binding domain using a transformed host containing an expressible DNA sequence encoding the antigen specific antigen binding domain, wherein the antigen specific antigen binding domain is derived from a variable region of the immunoglobulin isotype NAR found in fish.

Abstract: A method of preparing a species-specific phosphorylation site peptide array for a target organism comprising: a) selecting a plurality of known non-target organism (NTO) phosphorylation site sequences and cognate known NTO phosphorylation polypeptide sequences from one or more NTO, each of the known NTO phosphorylation site sequences comprising at least 5 residues and less than 30 residues; b) identifying a matching target organism (TO) phosphorylation site sequence and cognate TO phosphorylation polypeptide sequence for one or more of the known NTO phosphorylation site sequences; c) determining the matching TO phosphorylation site sequences that correspond to orthologue polypeptides of the cognate known NTO phosphorylation polypeptide sequences; d) selecting the matching TO phosphorylation site sequences determined to correspond to orthologue polypeptides for inclusion on the array; wherein the matching TO phosphorylation site sequences that correspond to orthologue polypeptides are determined by calculating

Abstract: Provided are a method of constructing a nucleic acid library, a method of determining a nucleic acid sequence of a nucleic acid sample, and a kit thereof. The method of constructing the nucleic acid library includes the following steps: subjecting a nucleic acid sample to a DOP-PCR amplification, to obtain a first PCR amplification product; subjecting the first PCR amplification product to a second PCR amplification using a DOP-Amp primer, to obtain a second PCR amplification product; and subjecting the second PCR amplification product to an adaptor-ligation PCR, to obtain a third PCR amplification product, wherein the third PCR amplification product constitutes the nucleic acid library.

Abstract: The present invention generally relates to methods and compositions used delivery of gene editing compositions including transcriptional effectors with parvovirus and preferred methods for making same.

Abstract: Provided herein are methods for assessing cancer, comprising analysis of sequence data from a set of cancer-related genes in a tumor sample from a subject, followed by monitoring of a subset of the set in circulating tumor-associated DNA in a fluid sample from the subject. Also provided are kits and systems for practicing any of them methods of the invention.

Abstract: The invention provides compositions and methods for diagnosing a patient as having a myeloproliferative disease by identifying mutations in the MPL gene or gene products.

Abstract: Provided herein is technology relating to detecting neoplasia and particularly, but not exclusively, to methods, compositions, and related uses for detecting premalignant and malignant neoplasms such as pancreatic and colorectal cancer.

Abstract: Embodiments described herein relate to methods, devices, and computer systems thereof for the derivation of T CAR libraries (Universal Subject or Individual Subject) for personalized treatment of disease in a subject. In certain embodiments, differential screening of normal and diseased tissue expression data is utilized to determine disease-specific antigens and thereby generate T CAR cells reactive to such antigens to form a disease-specific library. In certain embodiments, determination of the most effective T CAR clones from the disease-specific library is based on the subject's own disease-specific antigens. In certain embodiments, a subject is treated with a therapeutically effective amount of T CAR clones.

Abstract: A method of identifying a copy number variations reads includes mapping reads to a reference genome, computing coverage for a plurality of tiles, and normalizing the coverage for a tile based on a coverage mode across the plurality of tiles. The method further includes determining a score for the plurality of tiles being in a plurality of ploidy states, determining a maximum score path across the tiles and through the ploidy states, and providing a copy number determination based on the maximum score path.

Abstract: The present invention relates to a composition, a kit and a method for diagnosing ovarian cancer metastasis or predicting the risk of metastasis by detecting methylation levels at CpG sites of one or more gene promoters selected from the group consisting of AGR2 (anterior gradient 2), CA9 (carbonic adj anhydrase 9), GABRP (gamma-aminobutyric acid receptor pi subunit), IFITM1 (interferon-induced transmembrane 1) and MUC13 (mucin 13).

Abstract: Methods for determining the prognosis of a subject with oropharyngeal squamous cell carcinoma are described, as well as miRNAs and panels of prognostic miRNAs that are used in the methods.

Abstract: The present invention relates to methods for diagnosing, staging, prognosticating and treating melanoma based on evaluating the expression of specific patterns of oncogenic or suppressive microRNA (miR) molecules in a patient in need thereof.

Abstract: The present invention provides an apparatus for conducting biological assays which employs “virtual wells” in lieu of the physical wells of conventional array plates. Also provided are methods of processing a sample and/or culturing cells using the apparatus and systems described herein. In some embodiments, the apparatus includes a first structure having a sheet layer with a plurality of discrete through holes; and a second structure coupled to the first structure, the second structure including a base layer. At least a portion of a first surface of the sheet layer of the first structure is exposed from the second structure, and a second surface of the sheet layer, opposite to the first surface of the sheet layer, is embedded in the base layer of the second structure adjacent the first surface of the base layer.

Abstract: The present invention relates to methods of identifying IGF-IR modulators and hybrid-R modulators comprising contacting IGF-IR with a humanized anti-IGF-IR antibody and contacting hybrid-R with a humanized anti-hybrid-R antibody, respectively.

Abstract: A method of screening for template-fixed ?-hairpin mimetics and libraries including a plurality of these mimetics is provided. The template-fixed ?-hairpin mimetics are of the following general formula: R1-Cys-Z-Cys-R2??I wherein the two cysteine residues are bridged by a disulfide bond, thereby forming a cyclic peptide; R1 and R2 are di- or tripeptide moieties of certain types, as defined herein; and Z is a chain of n amino acid residues with n being an integer from 4 to 20 and with each of these n amino acid residues being, independently, derived from any naturally occurring L-?-amino acid.

Abstract: The invention relates to variants that predispose to risk of type 2 diabetes, basal cell carcinoma and breast cancer. It has been discovered that certain genetic variants confer risk of these diseases when inherited from one parent, but not the other. The invention provides methods of disease management, including diagnostic methods, utilizing such parental origin effects.

Abstract: Methods and devices for adding liquids to and washing a microfluidic element array are disclosed. The method and devices feature a microfluidic plate holder with a sloped wall for improved draining of liquid, a machine readable/writable identifier, plate leveling systems, liquid filling systems, a hydrophilic-liquid coating, and an automated washing station.

Abstract: Disclosed are compositions, kits, and methods for detecting, extracting, visualizing, and identifying a pathogenic protozoan. Quantitative real time polymerase chain reaction in connection with specifically designed oligonucleotide probes are used to detect a variety of pathogenic protozoans in patient samples.