Abstract: Methods for treating, preventing and predicting a subject's risk of developing breast cancer are provided.

Abstract: Embodiments of the present invention relate generally to non-invasive methods and tests that measure biomarkers (e.g., tumor antigens) and collect clinical parameters from patients, and computer-implemented machine learning methods, apparatuses, systems, and computer-readable media for assessing a likelihood that a patient has a disease, relative to a patient population or a cohort population. In one embodiment, a classifier is generated using a machine learning system based on training data from retrospective data and subset of inputs (e.g. at least two biomarkers and at least one clinical parameter), wherein each input has an associated weight and the classifier meets a predetermined Receiver Operator Characteristic (ROC) statistic, specifying a sensitivity and a specificity, for correct classification of patients.

Abstract: Aspects of the present disclosure provide methods for determining the eligibility of a subject having a malignancy for treatment with an anti-PD therapeutic agent based on a Combined Positive Score (CPS) for a tumor tissue sample from the subject. Compositions and kits or performing the disclosed methods are also provided.

Abstract: Disclosed are methods for diagnosing CAT1-related diseases, wherein the methods include detecting CAT1 in a cell by a BLV.RBD ligand, or a variant or a fragment thereof. Also disclosed is a BLV.RBD ligand, or a variant or a fragment thereof for use in the treatment of CAT1-related diseases and/or BLV infections.

Abstract: Provided herein are compositions and methods for detecting and/or targeting dysfunctional tumor antigen-specific CD8+ T cells in the tumor microenvironment for diagnostic, therapeutic and/or research applications. In particular, dysfunctional tumor antigen-specific CD8+ T cells are detected and/or targeted via their expression of cell surface receptors described herein, such as 4-1BB, LAG-3, or additional markers that correlate with 4-1BB and LAG-3 expression, such as markers differentially expressed on the surface of the T cells.

Abstract: Microscale and/or mesoscale condenser arrays that can facilitate microfluidic separation and/or purification of mesoscale and/or nanoscale particles and methods of operation are described herein. An apparatus comprises a condenser array comprising pillars arranged in a plurality of columns, wherein a pillar gap greater than or equal to about 0.5 micrometers is located between a first pillar of the pillars in a first column of the columns and a second pillar of the plurality of pillars in the first column, and wherein the first pillar is adjacent to the second pillar. The first ratio can be characterized by Dx/Dy is less than or equal to a first defined value, wherein Dx represents a first distance across the lattice in a first direction, wherein Dy represents a second distance across the lattice in a second direction, and wherein the first direction is orthogonal to the second direction.

Abstract: The invention described herein relates to methods of monitoring genotoxic stress in a test subject, specifically by detecting the expression level of microvesicle-associated H2AX from a biological sample.

Abstract: The present invention relates to a method of diagnosing Head and Neck Squamous Cell Carcinoma (HNSCC) in an individual. In addition, the present invention relates to a method of providing a survival prognosis to an individual suffering from Head and Neck Squamous Cell Carcinoma (HNSCC). Moreover, the present invention relates to a kit for performing the above-mentioned methods.

Abstract: This invention comprises compositions and methods to detect and treat gastrointestinal diseases.

Abstract: An immunoassay for the detection of an analyte in a sample includes a plurality of moieties capable of binding to the analyte. Capture moieties, which are not specific for the same epitope, are bound to a solid substrate, and at least one epitope-specific detection moiety is bound to a detectable marker. The detectable marker is a large particle marker having a particle size of ?50 nm and ?5000 nm.

Abstract: The state of protein phosphorylation and glycosylation can be key determinants of cellular physiology such as early stage cancer, but the development of phosphoproteins and/or glycoproteins in biofluids for disease diagnosis remains elusive. Here we demonstrate, for the first time, a strategy to isolate and identify phosphoproteins/glycoproteins in extracellular vesicles (EVs) from human plasma as potential markers to differentiate disease from healthy states. We identified close to 10,000 unique phosphopeptides in EVs by isolating from small volume of plasma samples. Using label-free quantitative phosphoproteomics, we identified 144 phosphoproteins in plasma EVs that are significantly higher in patients diagnosed with breast cancer than in healthy controls. Several novel biomarkers were validated in individual patients using Paralleled Reaction Monitoring for targeted quantitation. Similarly a group of glycoproteins in plasma EVs are identified.

Abstract: Described herein are methods for diagnosing high-risk cancer in a subject by detecting PolySialic Acid (polySia) in a biological sample obtained from the subject, or by detecting polySia and one or more tissue-specific markers in a biological sample obtained from the subject.

Abstract: Disclosed herein are monoclonal antibodies targeting specific tau epitopes, particularly, phosphorylated tau epitopes. Also disclosed are methods of detecting tau protein in a subject, comprising performing an assay using the antibodies or antigen binding fragments thereof on the subject or on a biological sample obtained from the subject. Assay kits containing the disclosed antibodies are also provided. Further, methods of treating or preventing a tauopathy in a subject by administering to the subject tau antibodies or antigen-binding fragments thereof are provided.

Abstract: Methods of testing tumor samples for mutational burden and/or for expression profiles permit the prediction of responsiveness of an individual to immunotherapy comprising PVSRIPO. Those predicted to respond are treated with PVSRIPO and those predicted not to respond are treated with other agents.

Abstract: The present invention relates to biomarkers of lung cancer, particularly to markers that enable distinguishing between subtypes of non-small cell lung cancer (NSCLC), particularly between adenocarcinoma (AC) and squamous cell carcinoma (SCC). In particular, the present invention relates to means and methods for diagnosing, assessing the level of severity and selecting methods of treating NSCLC.

Abstract: The instant disclosure provides biomarkers and methods for identifying subjects at risk of developing cytokine release syndrome (CRS), neurotoxicity, or both after adoptive immunotherapy to guide preemptive intervention, modified therapy, or the like. For example, adverse event biomarkers may be measured in a subject before pre-conditioning chemotherapy, before immunotherapy (e.g., adoptive immunotherapy infusion comprising a chimeric antigen receptor (CAR) modified T cell), or shortly after pre-conditioning chemotherapy and/or immunotherapy. Exemplary biomarkers include temperature, cytokine levels and endothelial activation biomarkers, such as angiopoietin 2, von Willebrand factor (vWF), ratio of angiopoietin 2 to angiopoietin 1, and ratio of ADAMTS13 to vWF. Also provided are methods of treating subjects identified as at risk of developing cytokine release syndrome (CRS), neurotoxicity, or both to minimize such potential adverse events.

Abstract: The present invention provides novel IgE antibodies useful for inhibiting or preventing metastatic cancer. Also provided are methods to inhibit tumor metastasis by modulating the activity of at least one non-tumor cell, treating a patient to inhibit or prevent tumor metastases of a primary solid tumor, treating metastatic carcinoma, reducing metastasis of carcinoma cells, and reducing the growth kinetics of a primary solid tumor or a metastasized cell or tumor.

Abstract: Disclosed herein are methods and devices for antigen-specific T cell identification or neoantigen identification. Also disclosed herein are devices for separating and isolating antigen-specific T cells or other particles of a certain size from a population of particles of different sizes. Also describe herein are methods and devices for the separation and isolation of barcoded T cells from other nanoparticles containing barcodes for subsequent analysis and further processing of a viable T cell.

Abstract: Methods of using detection of PD-L1 expression by circulating cancer cells in the screening, monitoring, treatment and diagnosis of cancer in subjects are disclosed. The methods are based on assaying one or more of circulating tumor cells (CTCs), epithelial to mesenchymal transition CTCs (EMTCTCs), cancer associated macrophage-like cells (CAMLs), and cancer associated vascular endothelial cells (CAVEs) isolated from a subject having cancer for PD-L1 expression.

Abstract: Described herein are methods of identifying immunologically protective neo-epitopes from the cancer tissue DNA of cancer patients using biophysical principles as well as bioinformatics techniques. The identification of immunologically protective neo-epitopes provides pharmaceutical compositions with a limited number of tumor-specific peptides suitable for personalized genomics-driven immunotherapy of human cancer. Specifically disclosed herein is a method of using the conformational stability of an epitope in an MHC protein-binding groove to predict immunogenicity of peptides in a putative neo-peptide set from a tumor from a cancer patient. Pharmaceutical compositions and methods of administration are also included.

Abstract: Disclosed herein are biomarkers for hepatocellular carcinoma and pancreatic cancer. The biomarkers may be laminin gamma 2 monomer, PIVKA-II, AFP, CEA, CA19-9, or combinations thereof. Also disclosed herein are methods of diagnosing, prognosing, classifying risk, and monitoring progression of hepatocellular carcinoma or pancreatic cancer by the detecting the level of laminin gamma 2 monomer, PIVKA-II, AFP, CEA, CA19-9, or combinations thereof.

Abstract: Herein are described methods of treating a human subject having acute myeloid leukemia (AML) that is refractory to induction therapy, wherein an MDM2 inhibitor is administered before or concurrently with chemotherapy, which may comprise induction therapy. Refractory AML may be predicted based on decreased expression of MTF2 in cells from a hematological sample obtained from the subject. Also provided are methods of predicting and treating AML responsive to MDM2/HDM2 inhibitors, based on MTF2 expression. One set of additional biomarkers useful in the predictions comprise one or more of H3K27me3, CD84, CD92, MDM2, NPM1, PRICKLE1, SET, ABCB6, POLQ, POLK, POLH, ARTIMIS, MCM6, CD327, CD90 and PARP1. Another set of additional biomarkers useful in the predictions include at least one of H3K27me3, MDM2, NPM1, SET, CD84 and PRICKLE1. Methods of selecting a patient for treatment with an MDM2 inhibitor before or concurrently with chemotherapy are also provided, along with kits and uses.

Abstract: Providing a method of estimating the number of microparticles such as microorganisms in a sample, without performing complicated operations. The method comprises counting by constant flow the number of target microorganisms contained in the sample at a predetermined flow rate, sectioning measurement data obtained as a result of the constant flow counting into a predetermined number of sections by a predetermined unit time for a section, counting the number of sections in which microorganisms are detected and the number of sections in which they are not detected, in the predetermined number of sections; and estimating the number of microorganisms in the sample, by a statistical method from the flow rate of the sample in the constant flow counting step, the predetermined number of sections and the predetermined unit time in the sectioning step, and the number of sections in which microorganisms are detected in the counting step.

Abstract: An analysis chip for determining an efficient anticancer drug or anticancer drug combination for cancer cells, according to an embodiment of the present disclosure, includes a chamber which is a unit for analyzing single cancer cells, and a plurality of valves configured to regulate a fluid to be injected into the chamber, wherein the chamber includes a channel through which a fluid including an anticancer drug and a cell lysis buffer flows, a cell sorting part configured to focus cancer cells flowing along the channel, a cell capturing part configured to focus the cancer cells focused by the cell storing sorting part, and an antibody array configured to capture proteins secreted from the captured cancer cells and intracellular protein through cell lysis.

Abstract: The object of the present invention is to provide an evaluation method capable of accurately determining a metastasis of cancer, the stage of cancer progression, or the malignancy of cancer.

Abstract: The present invention provides a method of producing dye-containing thermosetting resin particles, the method including: dispersing seed particles formed from a thermosetting resin in a dispersion medium; and polymerizing a monomer for thermosetting resin synthesis in the thus obtained dispersion in the presence of a dye and an acid catalyst. By the method of producing dye-containing thermosetting resin particles according to the present invention, dye-containing thermosetting resin particles whose particle size variation coefficient is small at, for example, 8% or less, can be produced without performing a post-treatment such as centrifugation. Therefore, when immunological observation is performed by a fluorescent labeling method using fluorescent dye-containing resin particles produced by the method of producing dye-containing thermosetting resin particles according to the present invention, a high bright spot detection accuracy can be attained.

Abstract: Antigen binding proteins specific for an HLA-A2 restricted Ras peptide are disclosed. The antigen binding proteins encompass antibodies in a variety of forms, including full-length antibodies, substantially intact antibodies, Fab fragments, F(ab?)2 fragments, and single chain Fv fragments. Fusion proteins, such as scFv fusions with immunoglobulin or T-cell receptor domains, and bispecific antibodies incorporating the specificity of the antigen binding region for each peptide are also contemplated by the disclosure. Furthermore, immunoconjugates may include antibodies to which is linked a radioisotope, fluorescent or other detectable marker, cytotoxin, or other molecule are also encompassed by the disclosure. Among other things, immunoconjugates can be used for delivery of an agent to elicit a therapeutic effect or to facilitate an immune effector function.

Abstract: A compact device compact analytical device to perform main steps of analytical procedures comprises a driving part configured to be attached to a stirrer part or a centrifuge part, wherein the stirrer part is configured to mix at least one sample and the centrifuge part is configured to separate a component. Furthermore, an analyzer part is configured to produce analytical data.

Abstract: Provided are methods for detecting chromogranin A by mass spectrometry. In another aspect, provided herein are methods for quantitating chromogranin A by mass spectrometry. In another aspect, provided herein are methods for prognosis of or measuring the size of neuroendocrine tumors by mass spectrometry.

Abstract: In various embodiments various cancer specific antibodies and immunoconjugates are provided. In certain embodiments the antibodies specifically bind and are internalized into a prostate cancer cell, where the antibodies specifically binds cells that express or overexpress a CD46, and where the antibodies specifically bind sushi domain 1 of said CD46 (CD46 CPP1).

Abstract: The present invention provides a modified eukaryotic cell wherein the modified eukaryotic cell is not able to provide an SSN6-like protein that exerts its wildtype function and/or wildtype activity, the amount of SSN6-like protein being present in the modified eukaryotic cell differs from the amount of SSN6-like protein being present in its wildtype form, and/or essentially no SSN6-like protein is present in the modified cell. Additionally, the present invention provides a polynucleotide sequence comprising a modified ssn6-like gene, and a vector comprising said polynucleoptide. Additionally provided is an expression vector comprising a promoter that is repressed in the presence of SSN6-like protein, and a host cell comprising said vectors. The present invention further refers to a method for determining the purity of a composition by using the modified eukaryotic cell, to a method of expressing gene(s) of interest, and eukaryotic cells comprising modified ssn6-like gene.

Abstract: The present disclosure provides processes for describing and quantifying the expression of human programmed death ligand-1 (PD-L1) in tumor tissue sections as detected by immunohistochemical assay using an antibody that specifically binds to PD-L1. The results generated using these processes have a variety of experimental, diagnostic and prognostic applications.

Abstract: Herein disclosed is a method for the normalization of an immunological test, characterized in that the presence of a comparable amount of cells is determined by a sandwich ELISA test in which the capture antibody includes at least one antibody that binds to at least one keratin selected from among keratin 4, 5, 6, 8, 10, 13 and 18 and the detection antibody includes at least one antibody that binds to the selected keratin.

Abstract: A microchannel (1) having a spiral geometry structured with asymmetrical curls (2) that enables separation of metastasis cancer cells rarely found in blood from the blood cells and enrichment thereof, which forces the particles or the cells to focus quicker and where high-quality particle focusing in a wider flow rate range can be performed.

Abstract: The present invention relates to a method for discrimination of p16INK4a overexpressing metaplasias from neoplastic or preneoplastic p16INK4a overexpressing lesions by determination of the level of high risk HPV encoded gene-products such as e.g. HPV E2 and/or HPV E7 molecules in biological samples in the course of cytological testing procedures. The method thus enables for reduction of false positive results in the p16INK4a based detection of anogenital lesions in cytological testing procedures.

Abstract: The present invention relates to methods and compositions for monitoring, diagnosis, prognosis, and determination of treatment regimens in subjects suffering from or suspected of having a renal injury. In particular, the invention relates to using assays that detect one or more markers selected from the group consisting of soluble p-selectin, protein NOV homolog, soluble epidermal growth factor receptor, netrin-4, haptoglobin, heat shock protein beta-1, alpha-1-antitrypsin, leukocyte elastase, soluble tumor necrosis factor receptor superfamily member 6, soluble tumor necrosis factor ligand superfamily member 6, soluble intercellular adhesion molecule 2, active caspase-3, and soluble platelet endothelial cell adhesion molecule as diagnostic and prognostic biomarkers in renal injuries.

Abstract: The present invention provides methods that are for acquiring various types of supplementary information used for diagnosis or treatment of prostate cancer, and that can be implemented in a less-invasive manner at a low cost. Provided are, by measuring the content of prostate specific antigen (PSA) having a ?-N-acetylgalactosamine residue at a non-reducing terminal of a sugar chain in a specimen, and comparing the measured value with a threshold value, (1) a method for estimating whether a Gleason score (primary pattern and secondary pattern) is not less than or less than a prescribed value, (2) a method for estimating whether the pathological stage (pT) is not less than or less than a prescribed value, and (3) a method for acquiring information for assessment indicating diagnosis or treatment should be actively conducted because a GS at gross total removal is expected to be higher than a GS at biopsy.

Abstract: Provided are methods of determining a presence or level of soluble mortalin in a body fluid of a subject, and predicting prognosis of a subject diagnosed with cancer (e.g., solid tumor) by determining the presence or level of soluble mortalin in a body fluid of the subject. Also provided are kits for determining presence and/or level of soluble mortalin in a body fluid of the subject and/or predicting prognosis of a subject diagnosed with cancer, comprising at least two distinct antibodies to mortalin directed against different epitopes of said mortalin.

Abstract: Provided is a method of obtaining an index value used for pathological tissue diagnosis of prostate cancer, which method has low invasiveness and can be performed at a low cost. The method is a method of estimating a Gleason score that represents the malignancy of prostate cancer, which method includes: measuring the content of a prostate-specific antigen having an N-acetylgalactosamine residue at a non-reducing terminal of a sugar chain in a sample; and estimating that the Gleason score is 7 or higher when the thus measured value is larger than a threshold value, or estimating that the Gleason score is 6 or lower when the measured value is smaller than a threshold value. The prostate-specific antigen is preferably quantified by a method including the step of binding a molecule having an affinity for ?-N-acetylgalactosamine residue, such as Wisteria floribunda lectin, soybean agglutinin, Vicia Villosa lectin or an anti-?-N-acetylgalactosamine antibody, to the prostate-specific antigen.

Abstract: The present invention relates to antisense oligonucleotides for modulating the activity of glycine decarboxylase (GLDC). In particular, the present invention relates to antisense oligonucleotides capable of inducing exon skipping of RNA. Also claimed are pharmaceutical compositions, kits and methods of treating cancer and inducing exon-skipping using said antisense oligonucleotides. In addition, a method for aiding the categorising or determining prognosis of a cancer or in selecting a therapeutic strategy for a patient with cancer, based on assessing the level of GLDC nucleic acid, protein or activity in a sample derived from the patient is provided.

Abstract: A method for analyzing an abdominal disease based on a medical image, includes receiving and preprocessing a medical image obtained by photographing an abdominal region of a patient to detect a plurality of analysis candidate regions and setting one of the plurality of analysis candidate regions as a ROI, calculating a nodule grade based on surface unevenness of the ROI, calculating a cellular heterogeneity coefficient based on pixel homogeneity of the ROI, and predicting and outputting an abdominal disease value based on the nodule grade and the cellular heterogeneity coefficient.

Abstract: The invention provides a method of detecting a subject suffering from, or at risk of suffering from, bladder cancer the method comprising i) providing a body fluid sample isolated from a subject; ii) isolating cells from said sample to provide a cell sample; iii) contacting the sample with a specific binding member capable of binding to a minichromosome maintenance (MCM) polypeptide(s); iv) determining the binding of said specific binding member to the cell sample; v) counting those cells in said cell sample which bound to said specific binding member to provide a cell count; vi) determining, based on the cell count, whether the subject has, or is at risk of having, bladder cancer.

Abstract: Some embodiments include an apparatus for processing radio frequency multiplexed cell images such as single-cell images, for example radio frequency multiplexed excitation (FIRE) images. The images can be from a particle analyzer, such as a flow and scanning cytometer or a laser scanning microscope. Some embodiments include an apparatus for displaying radio frequency multiplexed cell images such as FIRE images.

Abstract: The present disclosure is directed, in some embodiments, to methods and compositions of comprising a cell having a non-internalizing receptor, and a nanoparticle surface-modified with a ligand that binds to the non-internalizing receptor.

Abstract: Provided herein are methods and compositions for detecting and characterizing estrogen receptor-negative solid tumor cancers.

Abstract: In one aspect, provided herein is a method comprising: (a) (i) determining cytolytic activity in a tumor from the subject; and/or (ii) determining genetic alterations associated with cytolytic activity in the tumor; and (b) administering an immunotherapeutic agent to the subject if (i) cytolytic activity is detected in the tumor and/or (ii) a genetic alteration associated with induction of cytolytic activity, tumor resistance to cytolytic activity and/or suppression of cytolytic activity is detected in the tumor.

Abstract: The present inventors show that cannibal cells can undergo senescence after entosis in vivo and that the tumor suppressive protein p53 act as a repressor of this phenomenon. They therefore propose new tools to study the molecular pathways involved in the cannibalism process, for example by measuring the expression levels of p53 or splice variants thereof (such as ?133TP53, TP53?, TP53? or ?40TP53), the release of extracellular ATP or purinergic P2Y2 receptor activity. The present inventors also demonstrated that the detection of senescent cannibal cells in breast adenocarcinoma obtained from patients treated with neo-adjuvant therapy positively correlates with good patient's response to treatment. Altogether, these results provide the first evidence that detection of cellular cannibalism and senescence simultaneously in tumors helps for the diagnosis of disease outcomes and for the prediction of treatment efficiency against cancer diseases.

Abstract: A method of detecting cell membrane expression of an MHC molecule in a subject, a method of treating cancer in a subject with an immunotherapeutic agent, and an MHC complex are provided. The method of detecting cell membrane expression of an MHC molecule includes obtaining a tumor cell sample from a subject, and detecting cell membrane expression of the MHC molecule by contacting the tumor cell sample with an antibody targeting the MHC molecule and detecting binding between the MHC molecule and the antibody. The method of treating cancer in a subject with an immunotherapeutic agent includes detecting cell membrane expression of an MHC molecule in the subject and administering a therapeutically effective amount of the immunotherapeutic agent if the level of cell membrane expression of the MHC molecule exceeds a predetermined standard. The complex includes a tumor cell in complex with an antibody or an antigen-binding portion thereof.

Abstract: The present invention relates to methods, kits, and compositions for detecting and/or diagnosing metastatic potential of cancer cells or for evaluating prognosis in a patient with cancer by detection of the protein expression level of an HLA class I molecule and/or the copy number variation of a polynucleotide encoding the HLA class I molecule. The present invention also relates to the use of the protein expression level of an HLA class I molecule and/or the copy number variation of a polynucleotide encoding the HLA class I molecule as a prognosis biomarker and metastasis predictive biomarker of cancer.

Abstract: Compositions comprising a nucleic acid molecule that encodes TB esat-6 proteins are disclosed. Methods of inducing an immune response against TB an individual are disclosed. Method of treating an individual who has been diagnosed with TB are disclosed. Method of preventing TB infection in an individual are disclosed.