Abstract: The instant application relates to methods for determining pancreatic cancer patient outcome and directing treatment to subjects with pancreatic cancer. The present disclosure further provides methods for measuring expression levels of cytokeratin 17 in a subject having pancreatic cancer, such as pancreatic ductal adenocarcinoma, in order to determine the subject's survival rate and clinical outcome.

Abstract: A microscope apparatus includes an illumination optical system that emits activating light and exciting light, an image capturing unit that captures an image formed by an imaging optical system, an image processing unit that carries out image processing using an image capturing result from the image capturing unit, and a controller. The controller provides a plurality of image generation periods and interrupt periods; causes, in the image generation periods, the activated fluorescent material to be irradiated with the exciting light and causes the image capturing unit to capture an image of the fluorescent light from the activated fluorescent material in a plurality of frame periods; and sets an intensity of the exciting light in the interrupt periods to be lower than an intensity in the image generation periods or causes the emission of the exciting light to stop in the interrupt periods.

Abstract: Provided herein are compositions and methods for producing myrcene by culturing genetically modified microbial host cells that express a myrcene synthase and optionally a geranyl pyrophosphate synthase. Also provided herein are isolated nucleic acid molecules that encode myrcene synthase variants derived from the Ocimum species myrcene synthase, which comprise one or more amino acid substitutions that improve in vivo performance of myrcene synthase in genetically modified microbial host cells. Also provided herein are isolated myrcene synthase variants that exhibit an improved activity for converting geranyl diphosphate into myrcene.

Abstract: This disclosure provides microwell capsule array devices. The microwell capsule array devices are generally capable of performing one or more sample preparation operations. Such sample preparation operations may be used as a prelude to one more or more analysis operations. For example, a device of this disclosure can achieve physical partitioning and discrete mixing of samples with unique molecular identifiers within a single unit in preparation for various analysis operations. The device may be useful in a variety of applications and most notably nucleic-acid-based sequencing, detection and quantification of gene expression and single-cell analysis.

Abstract: The present subject matter provides processes and kits for identifying the presence of waste water or human-derived pathogens, particularly those associated with the presence of human fecal matter, in surface or subsurface water sources.

Abstract: This disclosure describes methods, kits, and systems for scoring the immune response to cancer through examination of tissue infiltrating lymphocytes (TILs). Methods of scoring the immune response in cancer using tissue infiltrating lymphocytes include detecting CD3, CD8, CD20, and FoxP3 within the sample and scoring the detection manually or scoring the digital images of the staining with the aid of image analysis and algorithms.

Abstract: Provided is a cell detection method which makes it possible to effectively and accurately perform gene analysis only on target cells. The cell detection method includes a sorting step of obtaining first information derived from cells in a sample solution by using a flow cytometry method and sorting target cells into a container having arrays of wells each having an opening based on the first information, an imaging step of imaging the cells sorted into the container, and a determination step of obtaining second information derived from cells based on the image of the cells captured by the imaging step and determining cells to be analyzed from the sorted cells.

Abstract: The present invention relates to methods for predicting acute severe colitis treatment response. Currently, there is no biomarker of drug response. The present invention provides the first prediction tool for responses to first- and second-line treatments in acute severe ulcerative colitis. Putative mRNA targets of dysregulated microRNAs were identified from patient biopsies. One classifier of fifteen colonic microRNAs plus five biological values at admission were identified with a prediction accuracy of 96.6% for discriminating responders from non-responders to steroids. Using a similar method, 6 and 4 mucosal microRNA-based algorithms were identified to classify responders from non-responders to infliximab and cyclosporine.

Abstract: Compositions and methods for improving plant growth are provided herein. Polynucleotides encoding photosystem I reaction center subunit N (PSAN) proteins, polypeptides encompassing PSAN proteins, and expression constructs for expressing genes of interest whose expression may improve agronomic properties including but not limited to crop yield, biotic and abiotic stress tolerance, and early vigor, plants comprising the polynucleotides, polypeptides, and expression constructs, and methods of producing transgenic plants are also provided.

Abstract: Disclosed is an in vitro method to diagnose or determine the risk of developing a neurodegenerative disease in a subject based on the determination of the methylation pattern in certain regions of mitochondrial DNA from the subject or the determination of the nucleotide at the polymorphic position 16519 in the mitochondrial DNA of the subject. Also, disclosed are nucleic acids suitable for the in vitro method to diagnose or determine the risk of developing a neurodegenerative disease in a subject.

Abstract: The present invention relates to a method, a device, and an apparatus for analyzing the expression of a gene in single cells. Specifically, the present invention relates to: a device for gene expression analysis, characterized by including a support, in which a nucleic acid probe having a test nucleic acid capture sequence and a known sequence, and further containing a cell recognition tag sequence which differs depending on the difference in position on the surface of the support or in the vicinity of the surface thereof, and a common primer sequence having a known sequence is two-dimensionally distributed and immobilized on the surface of the support or in the vicinity of the surface thereof; and a method and an apparatus using the device for gene expression analysis.

Abstract: A method of determining a probability that a human test subject has colorectal cancer as opposed to not having colorectal cancer is disclosed.

Abstract: A data manager determines an appropriate number of clusters for continuous data using unsupervised learning. The data manager selects an appropriate number of clusters based on at least one temporal stability measure between continuous data from at least two time intervals.

Abstract: Methods and devices are provided for simultaneously amplifying a plurality of sample wells for a predetermined amount of amplification, detecting whether amplification has occurred in a first set of the wells, amplifying for an additional amount of amplification and detecting whether amplification has occurred in a second set of the wells. Methods are also provided for analyzing a target nucleic acid sequence using melt curves that were generated in a plurality of amplification cycles.

Abstract: The present disclosure provides methods for increasing drought resistance and heat resistance of a plant. The methods encompass expression of at least one heat shock protein (HSP) from the group consisting of HSP40, HSP60 or HSP70 together with a phosphoenolpyruvate carboxylase (PEPC) comprising an aspartic acid (D) at a position that corresponds to the position 509 of SEQ ID NO: 4, in the plant. In comparison to a plant not manipulated in this manner, the disclosed, genetically-modified, plants display improved drought resistance and heat resistance. Also provided are plants that can be obtained by the method according to the invention, and nucleic acid vectors to be used in the described methods.

Abstract: A method for asymmetric encryption based on a gene chip includes the steps of (a) obtaining original information in text or image or other form and converting the same into a binary code, and (b) preprocessing the binary code to obtain a binary matrix. In (c), an encryption key is obtained, the encryption key comprising a gene expression solution. In (d), the gene expression solution is placed on a gene chip according to an arrangement and correspondence of the binary matrix.

Abstract: An evaluator 21 that evaluates states of cells included in each region of interest of a cell image, and a predictor 22 that performs, in advance, machine learning of a relationship between evaluation results for a specific region of interest within a first cell image obtained by imaging cells before a staining process and regions around the specific region of interest and staining states of cells of the specific region of interest within a second cell image obtained by imaging the same imaging targets as the cells of the first cell image after the staining process are provided. The predictor 22 predicts staining states of cells of a specific region of interest based on evaluation results for the specific region of interest and regions around the specific region of interest among the evaluation results for the third cell image of the cells before the staining process.

Abstract: Disclosed are compositions and methods for enriching a non-host sequence from a host sample. Also disclosed are compositions and methods for detecting a non-host sequence in a host sample. For example, a pathogen can be enriched and detected in a sample taken from a human without knowing what the pathogen is.

Abstract: Deep learning of dental images for national security is described. A computer may receive dental images of a patient from a dental provider. The computer is configured to match dental images to law enforcement databases such as a terrorist database. The process begins with matching a dental image to an anatomy probability dataset and a pathology probability dataset, then correlating it with a patient database to identify a person of interest. With different resolutions each neural network deep learns to probability map and detect different dental object probabilities to authenticate an individual. Further, the dental images will be associated with GPS coordinates to track movements of an individual. The datasets will be provided to e-commerce providers, e-commerce consumers, e-commerce administrators, machine learning entities, government entities and law enforcement entities which may exchange or transfer the data over a communication network such as the internet to locate a person of interest.

Abstract: Identification and use of proteins fluorescently labeled and that undergo a change in fluorescence index upon binding bilirubin are described. Probes are disclosed which are labeled at a cysteine or lysine residue and also probes labeled at both cysteine and lysine with two different fluorophores. These probes are useful for determination of unbound bilirubin levels in a fluid sample.

Abstract: Pre-existing alloreactive memory T cells are a major barrier to the induction of allograft tolerance in organ transplant recipients. The use of Eomesodermin (Eomes) expression in memory T cells to determine the risk of allograft rejection in a subject is described. Also described is the use of Eomes expression in memory T cells of transplant recipients to modify immunosuppressive therapy.

Abstract: Methods of making a three-dimensional matrix of nucleic acids within a cell is provided.

Abstract: In alternative embodiments, provided are products of manufacture, such as assays, chimeric nucleic acids and nucleic acid constructs, recombinant cells, and methods, comprising use of beta3-integrin (ITGB3) promoters operatively linked to a reporter, for drug screening, and in particular, screening for agents that inhibit cancer cell survival and metastasis. In alternative embodiments, compositions and methods as provided herein also can be used to identifying novel pathways that lead to acquired resistance, stemness, and anchorage independent growth; and characterizing distinct populations of cancer cells within a tumor microenvironment.

Abstract: The present invention provides methods, compositions and devices for stabilizing the extracellular nucleic acid population in a cell-containing biological sample using an apoptosis inhibitor, preferably a caspase inhibitor, a hypertonic agent and/or a compound according to formula 1 as defined in the claims.

Abstract: The present invention concerns methods for determining if a dendritic cell is a type 2 dendritic cell or a tolerogenic dendritic cell, methods for determining if a patient undergoing immunotherapy, and/or who has been administered with a vaccine, is developing an immune response oriented either towards a regulatory T cell response or towards an effector type 2 cell response, and methods of determining response to immunotherapy.

Abstract: A representation of a nucleic acid sequence encodes a particular gene having at least one intron. An intron signature value corresponding to the at least one intron is determined based on a first computational function applied to at least one portion of the representation of the nucleic acid sequence corresponding to the at least one intron. A protein signature value is determined, being based on a second computational function applied to a representation of a protein. In a database, an association is formed between the intron and protein signature values. This process is repeated for each of a plurality of nucleic acid sequences. Nucleic acid sequences in the database are ordered based on a sort of corresponding intron signature values. An ordering determined by the sort is used to determine or confirm a role or function of a portion of a given nucleic acid sequence.

Abstract: A method of making a prognosis as to whether a patient having renal cancer is likely to survive in a tumour tissue sample obtained from the patient is provided. The method comprising determining the level of expression for each marker of a panel of markers comprising at least one housekeeping gene selected from the group consisting of ACTB, RPL13A, RPL9, and RPS29 and any combinations thereof and at least one prognostic gene selected from the group consisting of CXCL5, EFNA5, EMCN, G6PC, GFPT2, HIST2H3C, IGFBP1, LAMB3, MMP9, MOCOS, PLG, PRAME, RARRES1, SDPR, SLC6A19, TK1, KDELR3 and TSPAN7 and any combinations thereof, comparing the level of expression of each marker with a predetermined reference level associated with each marker, and determining the differential expression of each marker in the tumour tissue sample based on the expression parameter for each marker to provide a prognosis for renal cancer.

Abstract: A method for detecting a target nucleic acid sequence in a sample in the presence of at least protein capable of binding to single-stranded DNA is provided, comprising contacting said sample with at least one oligonucleotide probe comprising a fluorophore, a quencher and a region complementary to said target nucleic acid sequence. The sequence of the oligonucleotide probe comprises at least 20% RNA nucleotides, modified RNA nucleotides and/or PNA nucleotides.

Abstract: The present disclosure provides micro-array devices for capturing cells in blood and methods of their use. In some aspects, a method for counting cells in a blood sample is provided, the method comprising applying a blood sample onto a CNT device; allowing cells in the blood sample to differentially settle on the CNT device, and identifying and counting cells of preselected type in the blood sample.

Abstract: Disclosed are nucleic acid oligomers, including amplification oligomers, capture probes, and detection probes, for detection of a human papillomavirus (HPV) nucleic acid. Also disclosed are methods of specific nucleic acid amplification and detection using the disclosed oligomers, as well as corresponding reaction mixtures and kits.

Abstract: One variation of a method for interpreting pressures in plants includes: accessing a first image of a first set of sentinel plants in a field; accessing a second image of a second set of sentinel plants in the field, recorded during a first period; interpreting a first pressure of a stressor in the first set based on features extracted from the first image, captured during the first period; interpreting a second pressure in the second set based on features extracted from the second image; deriving a model associating pressure at the first set and pressure at the second set based on the first pressure and the second pressure; interpreting a third pressure in the first set based on features extracted from a third image captured during a second period; and predicting a fourth pressure in the second set during the second period based on the third pressure and the model.

Abstract: The present invention is based on the discovery of genetic polymorphisms that are associated with cardiovascular disorders, particularly acute coronary events such as myocardial infarction and stroke, and genetic polymorphisms that are associated with responsiveness of an individual to treatment of cardiovascular disorders with statin. In particular, the present invention relates to nucleic acid molecules containing the polymorphisms, variant proteins encoded by such nucleic acid molecules, reagents for detecting the polymorphic nucleic acid molecules and proteins, and methods of using the nucleic acid and proteins as well as methods of using reagents for their detection.

Abstract: Compositions and methods are disclosed herein for cloning a synthetic or a semi-synthetic donor genome in a heterologous host cell. In one embodiment, the donor genome can be further modified within a host cell. Modified or unmodified genomes can be further isolated from the host cell and transferred to a recipient cell. Methods disclosed herein can be used to alter donor genomes from intractable donor cells in more tractable host cells.

Abstract: The invention relates to an apparatus for mass-spectrometric analysis and three-dimensional imaging of the surface of a sample, comprising at least one energy source for desorbing and/or ionizing atoms from the surface of a sample, a displacement stage, and a light source. Further, it comprises an interface in order to be able to interchange data with a mass spectrometer such that measurement data can be transmitted from a mass spectrometer to the evaluation unit via the interface such that the chemical composition of the measurement point can be determined by the evaluation unit. The surface of a sample can be captured in three dimensions and the topography of this surface can be determined by the evaluation unit.

Abstract: The present invention concerns subject matter connected to or making use of IgLON5, IgLON5 fragments and variants of IgLON5 and IgLON5-fragments. In particular the present invention relates to a use of a polypeptide comprising one or more sequences of IgLON5, an IgLON5-fragment or a variant thereof for the diagnosis of a disease, in vitro methods for diagnosing such a disease, a polypeptide comprising one or more sequences of IgLON5, an IgLON5-fragment or a variant thereof or a nucleic acid encoding said polypeptide for use in the treatment of a disease, a pharmaceutical composition comprising such polypeptide, a method for treating such a disease, an autoantibody binding to IgLON5, an IgLON5-fragment or a variant thereof, a method for isolating such autoantibody, a medical or diagnostic device comprising such autoantibody or such polypeptide and a test kit for the diagnosis of a disease, which test kit comprises such autoantibody and/or such polypeptide.

Abstract: The present disclosure pertains to a system, a method of using such a system, and a non-transitory computer-readable medium containing instructions to such a system for generating annotated gene fusion data from processing both a patient's DNA and RNA sequence information thereby filtering out weak candidate gene fusions. Thus the annotated gene fusion data contains clinically relevant information and accurate gene fusion detections (low false-positives) for use in clinical and/or R&D settings. The system, method and computer-readable medium allows a user to generate gene fusion data by detecting breakpoints from a patient's DNA-SEQ and RNA-SEQ, creating candidate breakpoint data by combining matching breakpoints from the DNA-SEQ and RNA-SEQ breakpoint data, determining confidence levels of the candidate breakpoint, identifying corresponding gene fusions, and annotating clinically relevant information about the gene fusions.

Abstract: This disclosure relates to methods for determining the quality of polymers, more particularly, polyolefins. The methods involve Raman spectroscopy and artificial intelligence to compute polymer properties and/or features.

Abstract: An antibody preparation suitable for intravenous administration in humans includes IgG, IgA and at least 5% IgM antibodies by weight of the total amount of antibodies. The preparation is prepared from human plasma, has specific complement activating activity, and, in an in vitro assay with human serum suitable to determine the ability of the antibody preparation to activate complement unspecifically, the antibody preparation generates substantially no C5a and/or substantially no C3a. The antibody preparation can have medical uses.

Abstract: Embodiments predict early stage NSCLC recurrence, and include an image acquisition circuit configured to access an image of a region of tissue demonstrating early-stage NSCLC including a plurality of cellular nuclei; a nuclei detecting and segmentation circuit configured to detect a member of the plurality; and classify the member as a tumor infiltrating lymphocyte (TIL) nucleus or non-TIL nucleus; a spatial TIL feature circuit configured to extract spatial TIL features from the plurality, the spatial TIL features including a first subset of features based on the spatial arrangement of TIL nuclei, and a second subset of features based on the spatial relationship between TIL nuclei and non-TIL nuclei; and an NSCLC recurrence classification circuit configured to compute a probability that region will experience recurrence based on the spatial TIL features; and generate a classification of the region as likely or unlikely to experience recurrence based on the probability.

Abstract: This application provides a bead with a covalently attached chemical compound and a covalently attached DNA barcode and methods for using such beads. The bead has many substantially identical copies of the chemical compound and many substantially identical copies of the DNA barcode. The compound consists of one or more chemical monomers, where the DNA barcode takes the form of barcode modules, where each module corresponds to and allows identification of a corresponding chemical monomer. The nucleic acid barcode can have a concatenated structure or an orthogonal structure. Provided are method for sequencing the bead-bound nucleic acid barcode, for cleaving the compound from the bead, and for assessing biological activity of the released compound.

Abstract: An exemplary tissue array, and a method for producing the same, can be provided which can include providing an accepter biological structure(s), providing a donor tissue(s), removing a portion(s) of the donor tissue(s), and removing a portion(s) of the accepter biological structure(s). The removed portion(s) of the accepter biological structure(s) can have a size that is substantially similar to a size of the removed portion(s) of the donor tissue(s). The removed portion(s) of the donor tissue(s) can be inserted into the accepter biological structure(s) at a location substantially corresponding to the removed portion(s) of the accepter biological structure(s).

Abstract: MicroRNA inhibitors as anti-cancer therapeutics are described. The microRNA inhibitors can inhibit microRNA-15a and can mimic the effects of higher dose radiation at lower doses. Other benefits are also described.

Abstract: A method and device for geometrically determining features of a workpiece, having an image processing sensor having a first beam path, the first beam path comprising at least one front optical unit facing the workpiece to be measured, and an optical splitter being mounted on the side of the front optical unit facing away from the workpiece. The optical splitter connects a second beam path to the image processing beam path, a common beam path being formed, and the second beam path being associated with a second optical sensor, the image processing sensor and the second sensor being designed to directly measure the surface of the workpiece. The front optical unit is formed as a sphere and/or has a longitudinal chromatic aberration.

Abstract: The present invention relates to methods and compositions for monitoring, diagnosis, prognosis, and determination of treatment regimens in sepsis patients. In particular, the invention relates to using assays that detect one or more biomarkers selected from the group consisting of Insulin-like growth factor-binding protein 7, Beta-2-glycoprotein 1, Metalloproteinase inhibitor 2, Alpha-1 Antitrypsin, Leukocyte elastase, Serum Amyloid P Component, C-X-C motif chemokine 6, Immunoglobulin A, Immunoglobulin G subclass I, C-C motif chemokine 24, Neutrophil collagenase, Cathepsin D, C-X-C motif chemokine 13, Involucrin, Interleukin-6 receptor subunit beta, Hepatocyte Growth Factor, CXCL-1, -2, -3, Immunoglobulin G subclass II, Metalloproteinase inhibitor 4, C-C motif chemokine 18, Matrilysin, C-X-C motif chemokine 11, and Antileukoproteinase as diagnostic and prognostic biomarker assays of renal injury in the sepsis patient.

Abstract: Methods for diagnosis of tuberculosis are disclosed. In particular, the invention relates to the use of a panel of biomarkers for aiding diagnosis, prognosis, and treatment of tuberculosis. The identified biomarkers can be used to detect active tuberculosis as well as to distinguish active tuberculosis from latent tuberculosis and other pulmonary and infectious diseases, and for monitoring responses to treatment.

Abstract: It is intended to reveal a polynucleotide serving as a novel causative gene of a cancer and, on the basis of this finding, to provide a method for detecting the polynucleotide or a polypeptide encoded thereby, a kit and a primer set for the detection, a method for screening for a substance that inhibits the polypeptide, and a pharmaceutical composition for the treatment of a cancer, containing the inhibiting substance. The detection method of the present invention detects a BRAF fusion protein or a fusion gene encoding the fusion protein, or a PXN or GMDS fusion protein or a fusion gene encoding the fusion protein in a digestive organ-derived sample obtained from a subject.

Abstract: The present invention relates to methods, kits and uses for diagnosing heart failure using miRNA-biomarker from blood.

Abstract: Isolated polynucleotides and polypeptides, and recombinant DNA constructs are useful for conferring improved drought tolerance, and/or for regulating flowering time. Compositions (such as plants or seeds) comprise these recombinant DNA constructs; and methods utilize these recombinant DNA constructs. The recombinant DNA constructs comprise a polynucleotide operably linked to a promoter that is functional in a plant, wherein said polynucleotides encode drought tolerance polypeptides and/or flowering time-regulating polypeptide.

Abstract: Glucose-regulated protein (GRP78) antagonists that block, interfere, and/or inhibit binding of receptor tyrosine kinase orphan receptors (RORs) are described for use as immunotherapy anticancer. These GRP78 antagonists inhibit surface bound GRP78 binding and receptor signaling and are believed to mimic the behavior of anti-angiogenic kringles found in mammalian plasminogen and in receptor tyrosine kinase orphan receptors. These GRP78 antagonist may be free peptide fragments, or peptide fragments covalently fused to blood borne proteins such as albumin or immunoglobins, or modified peptide fragments that a designed to bind to blood or tissue peptides when introduced in vivo into the blood stream of a patient.

Abstract: A novel vaccine that can induce sufficiently high cell-mediated immunity is disclosed. The vaccine of the present invention contains, as an effective component, a polypeptide comprising a tandem repeat structure in which an MHC class I epitope region derived from an antigen protein and a spacer sequence are linked to each other alternately and repeatedly at least three times, or a recombinant vector which comprises a polynucleotide encoding said polypeptide and is capable of expressing said polypeptide in vivo. The spacer sequence is, for example, a sequence generated as an amino acid sequence inevitably encoded by a single base sequence which is designed such that the MHC class I epitope region derived from the antigen protein, an MHC class II epitope region derived from the antigen protein, and at least one higher-order-structure-stabilizing region are encoded by different reading frames in said single base sequence.