Abstract: The present invention relates in some aspects to super-enhancers and related compositions, methods, and agents that are useful for modulating expression of cell type-specific genes that are required for maintenance of cell identity (e.g., embryonic stem cell identity) or maintenance of a disease state (e.g., cancer).

Abstract: A method of detecting the presence of a prostate cancer field defect in a human subject comprising the step of (a) obtaining genomic DNA from the human subject and (b) quantitating methylation in at least one target region selected from the group consisting of CAV1, EVX1, MCF2L, FGF1, NCR2 and WNT2 and EXT1 and SPAG4 target, wherein significant methylation changes indicate the presence of prostate cancer or a prostate cancer field defect, wherein the change is relative to tissue from a second human subject who does not have prostate cancer.

Abstract: The present disclosure provides methods for identifying early stage non-small-cell lung cancer (NSCLC) patients who will have an unfavorable prognosis for the recurrence of lung cancer after surgical resection. The methods are based in part on the discovery of chromosomal copy number abnormalities that can be used for prognostic classification. The methods preferably use fluorescence in situ hybridization with fluorescently labeled nucleic acid probes to hybridize to patient samples to quantify the chromosomal copy number of these genetic loci.

Abstract: A method is described for the diagnosis of rosacea. The method can include a step of measuring the expression of at least one peptide from the galanin family in a sample of biological fluid from a patient. Also described, is a related diagnostic kit.

Abstract: Provided herein are methods of producing erythrocytes from hematopoietic cells, particularly hematopoietic cells from placental perforate in combination with hematopoietic cells from umbilical cord blood, wherein the method results in accelerated expansion and differentiation of the hematopoietic cells to more efficiently produce administrate erythrocytes. Further provided herein is a bioreactor in which hematopoietic cell expansion and differentiation takes place.

Abstract: This disclosure provides methods and compositions for tagging long fragments of a target nucleic acid for sequencing and analyzing the resulting sequence information in order to reduce errors and perform haplotype phasing, for example.

Abstract: The present invention relates to mutants of a parent Trichoderma strain, comprising a polynucleotide encoding a polypeptide and one or more genes selected from the group consisting of a peptaibol synthetase gene, a paracelsin synthetase gene, a first terpene cyclase gene, a second terpene cyclase gene, and a third terpene cyclase gene, wherein one or more of the genes are modified rendering the mutant strain deficient in the production of one or more of the enzymes selected from the group consisting of a peptaibol synthetase, a paracelsin synthetase, a first terpene cyclase, a second terpene cyclase, and a third terpene cyclase compared to the parent Trichoderma strain when cultivated under identical conditions. The present invention also relates to methods of producing a polypeptide in such mutants and methods for producing such mutants.

Abstract: The present invention provides methods and compositions for diagnosing and predicting the occurrence of ischemia. For example, the present invention provides methods and compositions for diagnosing and predicting the risk and cause of transient neurological events (TNE) as ischemic or non-ischemic.

Abstract: Systems and methods are provided for sample processing. A device may be provided, capable of receiving the sample, and performing one or more of a sample preparation, sample assay, and detection step. The device may be capable of performing multiple assays. The device may comprise one or more modules that may be capable of performing one or more of a sample preparation, sample assay, and detection step. The device may be capable of performing the steps using a small volume of sample.

Abstract: This disclosure generally relates to a method, a system and a kit for diagnosing and treating various disease conditions using the gene expression value in a given sample obtained from a subject. This disclosure further relates to selecting the right set of genes as a portfolio of genes for a particular disease. Providing a set of appropriate portfolio of gene for studying the gene expression values and using the values as a diagnostic tool is also disclosed. The gene expression value is further used for intervention by pharmaceuticals as a prediction model for the treatment of the disease. An individual may have a personalized health card that may store the gene expression value for that particular individual. A system may store the data for portability and integrated view of the individual's medical data for effective diagnosis and treatment.

Abstract: A system for monitoring impedance of excitable cells in vitro, which includes a device for monitoring cell-substrate impedance at 20 millisecond resolution, which includes a nonconductive substrate with one or more electrode arrays fabricated in one or more wells, wherein cell attachment on the substrate can result in a detectable change in impedance between electrodes within each electrode array; an impedance analyzer capable of impedance measurement at 20 millisecond time resolution; electronic circuitry that can engage said device and selectively connect said two or more electrode arrays of said device to said impedance analyzer; and a software program that controls said electronic circuitry and records and analyzes data obtained from said impedance analyzer.

Abstract: The present invention provides screening kits, compositions, and diagnostic methods for determining whether a subject has a predisposition to, or likelihood of having, a substance use disorder by determining a nucleic acid methylation profile from a biological sample from the subject, wherein a given profile indicates that the subject has a predisposition to a substance use disorder.

Abstract: This disclosure relates to a method of generating conditionally active biologic proteins from wild type proteins, in particular therapeutic proteins, which are reversibly or irreversibly inactivated at the wild type normal physiological conditions. For example, evolved proteins are virtually inactive at body temperature, but are active at lower temperatures.

Abstract: The present description relates to methods for delivering polypeptide cargos from an extracellular space to the cytosol and/or nucleus of a target eukaryotic cell. The methods involve contacting the cell with the polypeptide cargo in the presence of a peptide shuttle agent at a concentration sufficient to increase the polypeptide cargo's transduction efficiency. Also described here are parameters that may be used in the rational design of such synthetic peptide shuttle agents, peptide shuttle agents that satisfy one or more of these design parameters, as well as methods and compositions relating to the use of the synthetic peptide shuttle agents for delivery of a variety of polypeptide cargos (such as transcription factors, antibodies, CRISPR-associated nucleases and functional genome editing complexes) from an extracellular space to the cytosol and/or nucleus of target eukaryotic cells. Applications and targets for genome-editing NK cells for improved immunotherapy are also described.

Abstract: This disclosure relates to a method of generating conditionally active biologic proteins from wild type proteins, in particular therapeutic proteins, which are reversibly or irreversibly inactivated at the wild type normal physiological conditions. For example, evolved proteins are virtually inactive at body temperature, but are active at lower temperatures.

Abstract: The invention relates to a method for the detection of the occurrence of initiation of replication events in genomic DNA in a eukaryotic cell, involving contacting said eukaryotic cell comprising said genomic DNA with a first nucleotide probe, under conditions enabling in situ hybridization of said first nucleotide probe with a target region in the DNA genome, wherein said target region comprises a nucleic acid sequence which has no identified corresponding annealing RNA in a metabolically active cell and therefore remains RNA-free during transcription and replication of said DNA genome and detecting said first nucleotide probe hybridized to said DNA. Further detection of at least one RNA molecule can be achieved.

Abstract: Systems and methods are provided for sample processing. A device may be provided, capable of receiving the sample, and performing one or more of a sample preparation, sample assay, and detection step. The device may be capable of performing multiple assays. The device may comprise one or more modules that may be capable of performing one or more of a sample preparation, sample assay, and detection step. The device may be capable of performing the steps using a small volume of sample.

Abstract: Methods, apparatuses, and systems for screening, analyzing and selecting microorganisms from complex heterogeneous communities, predicting and identifying functional relationships and interactions thereof, and synthesizing microbial ensembles based thereon are disclosed. Methods for identifying and determining the absolute cell count of microorganism types and strains, along with identifying the network relationships between active microorganisms and environmental parameters, are also disclosed.

Abstract: This invention discloses reagents and methods for increasing specificity and efficiency of RNA-guided genome editing.

Abstract: This disclosure provides Agrobacterium-mediated transformation methods for the oil-producing (oleaginous) yeast Lipomyces sp., as well as yeast produced by the method. Such methods utilize Agrobacterium sp. cells that have a T-DNA binary plasmid, wherein the T-DNA binary plasmid comprises a first nucleic acid molecule encoding a first protein and a second nucleic acid molecule encoding a selective marker that permits growth of transformed Lipomyces sp. cells in selective culture media comprising an antibiotic.