Abstract: The invention is directed to methods for determining antigen-specific T cells. In some embodiments, methods of the invention may be implemented by the steps of reacting under interaction conditions one or more antigens with T cells in a plurality of subsets of a tissue sample, such as peripheral blood; sorting antigen-interacting T cells from other T cells; separately sequencing for each subset recombined nucleic acid encoding a segment of a TCR chain from a sample of T cells prior to exposure to antigen and from a sample of T cells isolated based on their interaction with antigen, thereby forming a clonotype profile for the former sample and the latter sample for each subset; and identifying as antigen-specific T cells those T cells associated with a clonotype whose frequency increases in the latter sample relative to its frequency in the former sample.

Abstract: The invention relates to methods of tagging analytes in a sample.

Abstract: Disclosed herein are double-stranded RNA nucleic acid molecules, which include at least one pyrazolotriazine nucleotide analog and have been modified to exhibit one of the following, increased on-target activity, increased target specificity, enhanced nuclease stability, reduced off target activity and/or reduced immunogenicity when compared to an unmodified or similarly modified dsRNA; pharmaceutical compositions comprising such molecules and methods of use thereof in therapy.

Abstract: The invention relates to an antigen binding site for binding to a P2X7 receptor, the antigen binding site being defined by general formula 1: FR1-CDR1-FR2-CDR2-FR3-CDR3-FR4

Abstract: Apparatus, systems and methods for pre-processing, analyzing, and storing genomic data through a scalable, distributed analysis system across a network is presented.

Abstract: Among other things, the present invention provides assay methods for detecting or quantifying one or more analytes in a sample, which involve the use of dissociable nanoparticles that comprise one or more signaling agents (e.g., the nanoparticles conceal or partially conceal the signaling agents).

Abstract: A method for analyzing water toxicity, the method including: exposure experiment, sample collection, transcriptome detection, metabolome detection, screening of differentially expressed genes, screening of differentially expressed metabolites, and identification of commonly changed biological pathways in both the transcriptome and the metabolome.

Abstract: Embodiments include methods, systems and computer program products for communicating the presence of a target DNA or RNA sequence. Aspects include receiving a plurality of images of a sample taken by a portable video capture device. Aspects also include calculating a change in position over time of microscopic beads coated with DNA probe sequence in a sample containing genetic material. Aspects also include determining whether the beads are displaying Brownian motion. Aspects also include, based upon a determination of that the beads are displaying Brownian motion, generating a negative output message and sending the negative output message to a portable display. Aspects also include, based upon a determination of that the beads are not displaying Brownian motion, generating a positive output message and sending the positive output message to a portable display.

Abstract: Provided herein is an all-in-one saliva collection apparatus that collects saliva to allow for the filtration of saliva in order to separate saliva components, such as extracellular proteins and nucleic acids that are not present in intact cells, from the intact cells and debris remaining in the extracted sample. The filtered saliva samples can be aliquoted into two fractions for protein and/or nucleic acid analysis. The present invention further describes long term storage at ambient temperatures of filtered salivary nucleic acids, and long term storage at ambient temperatures of filtered salivary proteins added to an ethanol solution. The filtered cell-free saliva samples have diagnostic usefulness.

Abstract: The present invention relates to a high throughput method for the identification and detection of molecular markers wherein restriction fragments are generated and suitable adaptors comprising (sample-specific) identifiers are ligated. The adapter-ligated restriction fragments may be selectively amplified with adaptor compatible primers carrying selective nucleotides at their 3? end. The amplified adapter-ligated restriction fragments are, at least partly, sequenced using high throughput sequencing methods and the sequence parts of the restriction fragments together with the sample-specific identifiers serve as molecular marker.

Abstract: Described herein are apparatus and methods for detecting substances of abuse or other analytes in liquids. For example, the apparatus and methods described herein can be used for real-time detection of analytes, such as substances of abuse. The methods comprise providing a detection area comprising a chromatographic membrane capable of receiving the liquid and allowing for migration of the liquid, the chromatographic membrane comprising an anti-analyte antibody-particle conjugate, an analyte-conjugate protein at a test line; exposing at least the first location of the apparatus to the liquid; and determining whether an interaction between the analyte-conjugate protein and the liquid occurs to detect the presence of the analyte. The chromatographic membrane may further comprise an anti-species antibody at a control line.

Abstract: The present invention relates to a composition for promoting hair growth or preventing hair loss and, specifically, to a composition, which has excellent stability for skin and no side effects, promotes hair growth, prevents hair loss through the delay of hair loss, and has an excellent hair growth effect.

Abstract: The present disclosure provides method and systems for improving nanopore-based analysis of polymers. The disclosure provides methods for selectively modifying one or more monomeric subunit(s) of a kind a pre-analyte polymer that results polymer analyte with a modified subunit. The polymer analyte produces a detectable signal in a nanopore-based system. The detectable signal, and/or its deviation from a reference signal, indicates the location of the modified subunit in the polymer analyte and, thus, permits the identification of the subunit at that location in the original pre-analyte polymer.

Abstract: Among others, the present invention provides apparatus for interacting with a biological subject to detect circulating tumor cells therein, comprising one device for sending a signal to the biological subject and optionally receiving a response to the signal from the biological entity.

Abstract: The present invention provides methods and apparatus for enhanced detection of a disease by among others enhancing the difference in a microscopic property of diseased cells and normal cells, thereby enhancing the detection sensitivity and specificity.

Abstract: The present application provides arrays for use in immunosignaturing and quality control of such arrays. Also disclosed are peptide arrays and uses thereof for diagnostics, therapeutics and research.

Abstract: Provided herein are compositions, compounds, and methods of modulating gene expression. In certain embodiments described herein is a composition, wherein the composition comprises an antagoNAT. In some embodiments, the antagoNAT is an oligonucleotide comprising modified and unmodified sugar subunits, wherein the antagoNAT hybridizes with a natural antisense transcript. Certain embodiments of the present invention provide a method for modulating gene expression in a cell comprising contacting the cell with an antagoNAT. In some embodiments, the method includes forming a hybrid comprising the antagoNAT and a natural antisense transcript of the gene, wherein the hybrid sterically blocks the normal function of the natural antisense transcript.

Abstract: The present invention relates to polynucleotide probes and antibodies for detecting Lrp4/Corin dopaminergic neuron progenitor cell markers, which enable the efficient separation of dopaminergic neuron progenitor cells; and methods for selecting the progenitor cells by the use thereof.

Abstract: The present invention relates to pyrazolotriazolyl nucleoside analogs, such as oligonucleotide comprising them, and uses in treatment of hepatitis C virus infections. Further the invention relates to a method for reducing gene expression in a cell comprising transfecting the cell with such an oligonucleotide.

Abstract: Methods for assessing the integrity of an RNA sample from a given tissue or blood type are disclosed.

Abstract: Network-based meta-analysis of four independent microarray studies identified the hepatocyte nuclear factor (HNF4A), a transcription factor associated with gluconeogenesis and diabetes, as a central regulatory hub gene upregulated in blood of PD patients. In parallel, the polypyrimidine tract binding protein 1 (PTBP1), involved in the stabilization and mRNA translation of insulin, was identified as the most downregulated gene. Using both markers, PD patients were classified with 90% sensitivity and 80% specificity. Longitudinal performance analysis demonstrated that relative abundance of HNF4A and PTBP1 mRNAs significantly decreased and increased, respectively, in PD patients during 3 years follow up period. The inverse regulation of HNF4A and PTBP1 provides a molecular rationale for the altered insulin signaling observed in PD patients. The longitudinally dynamic biomarkers identified in this study may be useful for monitoring disease-modifying therapies for PD.

Abstract: Provided herein are methods for processing biomass materials that are disposed in one or more structures or carriers, e.g., a bag, a shell, a net, a membrane, a mesh or any combination of these. Containing the material in this manner allows it to be readily added or removed at any point and in any sequence during processing.

Abstract: The present invention provides methods for constructing peptide construct sets and methods of use of these peptide construct sets in assay systems for peptide analysis, and in particular for use in high throughput peptide analysis. The methods allow for analysis of large sets of peptide constructs in a cost-effective manner, employing molecular biological techniques that are both robust and easily parallelized. Thus, the methods allow for the construction of peptide construct sets encompassing, e.g., the human proteome.

Abstract: Clinical management of human cancer is dependent on the accurate monitoring of residual and recurrent tumors. We have developed a method, called personalized analysis of rearranged ends (PARE), which can identify translocations in solid tumors. Analysis of four colorectal and two breast cancers revealed an average of nine rearranged sequences (range 4 to 15) per tumor. Polymerase chain reaction with primers spanning the breakpoints were able to detect mutant DNA molecules present at levels lower than 0.001% and readily identified mutated circulating DNA in patient plasma samples. This approach provides an exquisitely sensitive and broadly applicable approach for the development of personalized biomarkers to enhance the clinical management of cancer patients.

Abstract: The present invention pertains to the use of DNase to treat female infertility and the use of cfDNA as a marker of female infertility.

Abstract: The present invention relates to peptides, nucleic acids and cells for use in immunotherapeutic methods. In particular, the present invention relates to the immunotherapy of cancer. The present invention furthermore relates to tumor-associated T-helper cell peptide epitopes, alone or in combination with other tumor-associated peptides that serve as active pharmaceutical ingredients of vaccine compositions which stimulate anti-tumor immune responses. The present invention relates to novel peptide sequences and their variants derived from HLA class I and class II molecules of human tumor cells which can be used in vaccine compositions for eliciting anti-tumor immune responses.

Abstract: The invention provides an isolated, purified population of human cells comprising CD8+ T cells with reduced Cbl-b activity. The invention provides uses of such cells in methods for inducing or enhancing an anti-tumor immune response in a subject. These methods comprise: (a) providing a cell population, from a subject or from another source, which comprises CD8+ T cells, (b) reducing Cbl-b activity in the CD8+ T-cells, (c) administering the cells of step (b) to the subject. The invention provides methods for making CD8+ T cells that do not require stimulation through a co-receptor in order for the cell to become activated or proliferated in response to contact via its T cell receptor. Such methods are based upon reducing function of Cbl-b. The invention also provides methods for identifying agents which affect Cbl-b expression or activity.

Abstract: The present invention relates to agonists of Neprilysin and their use in preventing and treating pulmonary vascular remodeling. Also described are diagnostic and screening applications stemming from the inventor's discovery that Neprilysin is expressed at reduced levels in disease tissues.

Abstract: The use of a modulator of the Nav 1.9 sodium channel is described for treating an inflammatory skin disease. Also described, is a pharmaceutical composition including a modulator of the Nav 1.9 sodium channel, and in vitro diagnostic methods based on the detection or quantification of Nav 1.9.

Abstract: Methods and compositions disclosed herein generally relate to methods of improving clinical and economic outcomes to address adverse effects related to anesthesia, analgesics, opioids, and inadequate pain relief. Embodiments of the invention relate to the association between genes, specific polymorphisms of genes, and non-genetic factors with inadequate pain relief and anesthesia-, analgesic, and/or opioid-related adverse effects. Embodiments of the invention can be used to determine and manage patient risk factors for development of adverse perioperative effects and can allow for personalized anesthesia and pain management for improvement of pain control and reduction of anesthesia-, analgesic-, and opioid-related adverse outcomes. These methods and compositions apply to non-surgical pain management with opioids.

Abstract: The present disclosure relates generally to methods and materials for use in detecting abnormalities of the number of whole chromosomes or chromosome regions (aneuploidy). It has particular utility for assessing the risk of aneuploidy of eggs (i.e., oocytes), fertilized eggs or embryos developed therefrom in the context of in vitro fertilization.

Abstract: According to some aspects of the invention, provided herein are methods of amplifying nucleic acids using homopolymer-mediated ligation. The methods, in some embodiments, comprise adding a first homopolymer of at least 12 nucleotides to each 3? end of blunt-ended double-stranded nucleic acid containing a target nucleic acid, thereby producing a partially double-stranded nucleic acid.

Abstract: Disclosed are genes that, when overexpressed in cells expressing alpha-synuclein, either suppress or enhance alpha-synuclein mediated cellular toxicity. Compounds that modulate expression of these genes or activity of the encoded proteins can be used to inhibit alpha-synuclein mediated toxicity and used to treat or prevent synucleinopathies such as Parkinson's disease. Also disclosed are methods of identifying inhibitors of alpha-synuclein mediated toxicity.

Abstract: Described herein is a mutation that confers resistance to the treatment with a BTK inhibitor. Described herein is a modified PLC?2 polypeptide that is modified at amino acid position 742, 845, or 1140 and the modified PLC?2 polypeptide exhibits decreased inhibition (e.g., resistance) to a covalent and/or irreversible BTK inhibitor. Described herein are diagnostic methods for detecting the modified polypeptide and nucleic acid encoding the modified polypeptide and applications of the methods thereof. Described herein are compositions, combinations, and kits containing the modified polypeptide and methods of using the modified polypeptide. Also described herein are methods of using the modified polypeptide as screening agents for the identification and design of inhibitors of PLC?2.

Abstract: Methods are disclosed for identifying one or more proteins or polypeptides comprised by a sample. The methods comprise determining binding of each polypeptide with respect to each binding pool of a plurality of binding pools, wherein each binding pool comprises one or more probes which bind a structure comprised by a protein or polypeptide. In some aspects, polypeptides can be denatured and separated into individual polypeptide strands and immobilized on a solid support prior to determining binding of the binding pools. A protein, polypeptide or polypeptide strand can be identified by searching, in at least one database, for a protein or polypeptide sequence comprising binding pool targets either identical to or most similar to the binding pool targets comprised by the protein, polypeptide or polypeptide strand to be identified. Kits for identifying proteins, polypeptides and polypeptide strands are also disclosed.

Abstract: The present disclosure generally relates to compositions and methods for the genetic modification of cells. In particular, the disclosure relates to CRISPR reagents and the use of such reagents.

Abstract: A purified polynucleotide having a chain of nucleotides corresponding to a mutated sequence, which in a wild form encodes a polypeptide implicated in hereditary sensory defect wherein said mutated purified polynucleotide presents a mutation responsible for prelingual non-syndromic deafness selected from the group consisting of a specific deletion of at least one nucleotide.

Abstract: Disclosed herein is a composition comprising a substrate with functionalized surface covalently bound to an anti-infective agent, such as a quaternary phosphonium compound with anti-bacterial activity against a broad range of bacteria, methods of synthesizing an anti-infective composition, and its resultant antimicrobial performance.

Abstract: Methods and compositions for the diagnosis, prognosis and classification of cancer, especially colorectal cancer, are provided. For example, in certain aspects methods for cancer prognosis using expression or methylation analysis of selected biomarkers are described. Particular aspects of the present invention may include methods and biomarkers for diagnosing or detecting colorectal cancer or metastasis in a subject by measuring a level of expression of biomarker miRNA such as miR-885-5p in the sample from the subject and evaluating the risk of developing cancer or metastasis in the subject.

Abstract: The present invention provides for compositions and methods for diagnosing and treating Kawasaki disease. More specifically, the proteomes of patients with KD are enriched for the meprin A, filamin B, and filamin C, which serve as biomarkers (and potential therapeutic targets) for KD. Accordingly, detection of these biomarkers, using compositions and methods provided for herein, can inform the therapy delivered to the subject.

Abstract: The invention relates to a method for generating a DNA sequence coding for the heavy chain or the light chain of at least one antibody from RNA from a cell capable of producing an antibody. More particularly, the invention relates to the generation of a monoclonal antibody library. The invention also relates to the use of an antibody library for screening monoclonal antibodies, preferably human antibodies for treating cancer.

Abstract: Methods and kits for characterizing a subject having a steroid-dependent disease such as prostate cancer are described. A method of treating a steroid-dependent disease in a subject by obtaining a biological sample from the subject, determining if the HSD3B1(1245C) gene or 3?HSD1(367T) protein is expressed in the biological sample, and providing treatment other than or in addition to steroid ablation to the subject if the HSD3B1(1245C) gene or 3?HSD1(367T) protein is expressed is also described.

Abstract: This invention pertains to methods and compositions for the diagnosis and treatment of cardiovascular conditions. More specifically, the invention relates to isolated molecules that can be used to diagnose and/or treat cardiovascular conditions including cardiac hypertrophy, myocardial infarction, stroke, arteriosclerosis, and heart failure.

Abstract: The present disclosure provides a system and method for the detection of rare mutations and copy number variations in cell free polynucleotides. Generally, the systems and methods comprise sample preparation, or the extraction and isolation of cell free polynucleotide sequences from a bodily fluid; subsequent sequencing of cell free polynucleotides by techniques known in the art; and application of bioinformatics tools to detect rare mutations and copy number variations as compared to a reference. The systems and methods also may contain a database or collection of different rare mutations or copy number variation profiles of different diseases, to be used as additional references in aiding detection of rare mutations, copy number variation profiling or general genetic profiling of a disease.

Abstract: The present invention provides antigen-binding proteins capable of binding to KIR3D polypeptides. The antibodies have increased activity in the treatment of disorders characterized by KIR3DL2-expressing cells, particularly CD4+ T cells, including malignancies such as Mycosis Fungoides and Sézary Syndrome.

Abstract: The present invention relates to biomarkers for chemoradioresistant subtypes of cervical cancer. In particular the present invention relates to a method for predicting a predisposition to a chemoradioresistant cervical cancer in a subject, a method for diagnosing a chemoradioresistant cervical cancer in a subject, a method for predicting the likelihood of recurrence of cervical cancer in a cervical cancer patient under treatment, and a method for predicting the prognosis for a patient with a chemoradioresistant cervical cancer.

Abstract: A microarray-based assay is provided, which is used for analyzing molecular interactions, including polynucleotides, polypeptides, antibodies, small molecule compounds, peptides and carbohydrates. Such method comprises coupling a target molecule to a particle and then binding to a probe molecule on microarray. In particular, multiplexed genetic analysis of nucleic acid fragments can be implemented. Specific genes, single nucleotide polymorphisms or gene mutations, such as deletions, insertions, and indels, can be identified. Coupled with microarray, the particles, themselves or further modified, facilitate the detection of results with non-expensive devices or even naked eyes. This technology enables the detection and interpretation of molecular interactions in an efficient and cost effective way.

Abstract: This invention relates to humaneered anti-factor B antibodies and antigen-binding fragments thereof with modified glycosylation patterns. The humaneered anti-factor B antibodies and antigen-binding fragments thereof are derived from murine monoclonal antibody 1379, which binds factor B in the third short consensus repeat (“SCR”) domain and selectively inhibits activation of the alternative complement pathway by preventing formation of the C3bBb complex. The invention also relates to methods of treating diseases or disorders in which activation of the alternative complement pathway plays a role, and methods of selectively inhibiting activation of the alternative complement pathway in an individual in need thereof.

Abstract: A method for magnetic cellular manipulation may include contacting a composition with a biological sample to form a mixture. The composition may include a plurality of particles. Each particle in the plurality of particles may include a magnetic substrate. The magnetic substrate may be characterized by a magnetic susceptibility greater than zero. The composition may also include a chargeable silicon-containing compound. The chargeable silicon-containing compound may coat at least a portion of the magnetic substrate. The biological sample may include cells and/or cellular structures. The method may also include applying a magnetic field to the mixture to manipulate the composition.

Abstract: The invention relates to methods for conducting binding assays in an assay device that includes one or more storage and use zone. The storage zones of the assay device are configured to house one or more reagents used in an assay conducted in the use zone of the device.