Abstract: The present invention relates to a gene editing system for editing the arylsulfatase A (ARSA) gene, polynucleotides, sgRNA molecules and repair templates which may form parts of the gene editing system, vectors and host cells incorporating said nucleic acid molecules, a pharmaceutical composition, and kits. It also relates to a method of gene editing the arylsulfatase A (ARSA) gene in a cell or a subject, and to a method of treating a disease or disorder associated with functional deficiency of the ARSA enzyme in a subject.

Abstract: Transposase polypeptides and polynucleotides are provided, which have a high activity in mammalian cells. Methods for engineering cells, such as chimeric antigen T-cells, with the transposes are also provided.

Abstract: The present invention relates to RNAi agents, e.g., double stranded RNAi agents, targeting a xanthine dehydrogenase (XDH) gene, and methods of using such double stranded RNAi agents to inhibit expression of an XDH gene and methods of treating subjects having an XDH-associated disease.

Abstract: Compositions and methods for using programmable DNA binding proteins to increase the efficiency and/or specificity of targeted genome modification or to facilitate the detection of specific genomic loci in eukaryotic cells.

Abstract: Provided are a cardiomyocyte preparation, a preparation method therefor and the use of the preparation in treating heart failure. The cardiomyocyte preparation comprises cardiomyocytes and fibroblasts, differentiated from pluripotent stem cells, wherein the concentration of the cardiomyocytes in the cardiomyocyte preparation is 0.75×107-1.0×109 cells/mL, and the content of the cardiomyocytes is higher than 80% while the content of the fibroblasts is not higher than 20%. The cardiomyocyte preparation can improve cardiac ejection fraction and left ventricular fractional shortening, and increase the thickness of the left ventricular inner wall.

Abstract: The field of this invention relates to immunohistochemistry (IHC) and in situ hybridization (ISH) for the targeted detection and mapping of biomolecules (e.g., proteins and miRNAs) in tissues or cells for example, for research use and for clinical use such by pathologists (e.g., biomarker analyses of a resected tumor or tumor biopsy). In particular, the use of mass spectrometric imaging (MSI) as a mode to detect and map the biomolecules in tissues or cells for example. More specifically, the field of this invention relates to photocleavable mass-tag reagents which are attached to probes such as antibodies and nucleic acids and used to achieve multiplex immunohistochemistry and in situ hybridization, with MSI as the mode of detection/readout. Probe types other than antibodies and nucleic acids are also covered in the field of invention, including but not limited to carbohydrate-binding proteins (e.g., lectins), receptors and ligands.

Abstract: The present disclosure relates to the field of plant molecular biology, more particularly to regulation of gene expression in plants.

Abstract: Methods, compositions, and kits are provided herein for CRISPER/Cas-mediated nucleic acid detection or modification.

Abstract: The present invention relates to RNAi agents, e.g., double stranded RNA (dsRNA) agents, targeting the Factor XII (F12) gene. The invention also relates to methods of using such RNAi agents to inhibit expression of an F12 gene and to methods of preventing and treating an F12-associated disorder, e.g., heredity angioedema (HAE), prekallikrein deficiency, malignant essential hypertension, hypertension, end stage renal disease, Fletcher Factor Deficiency, thromboembolic disease, inflammatory disease, or Alzheimer's Disease.

Abstract: Disclosed herein are methods of identifying a cancer patient that will be responsive to treatment with a fibroblast growth factor receptor (FGFR) inhibitor and methods of treating cancer patients. The methods involve evaluating a biological sample from the patient for the presence of one or more FGFR mutants from a FGFR mutant gene panel. Kits and primers for identifying the presence of one or more FGFR mutant genes in a biological sample are also disclosed herein.

Abstract: Methods for proteomic screening on random protein-bead arrays by mass spec is described. Photocleavable mass tags are utilized to code a protein library (bait molecules) displayed on beads randomly arrayed in an array substrate. A library of probes (prey) can be mixed with the protein-bead array to query the array. Because mass spec can detect multiple mass tags, it is possible to rapidly identify all of the interactions resulting from this mixing.

Abstract: Biochemical carriers are provided. Each of the biochemical carriers includes: biochemical molecules having a sequence into which digital data information is encoded; a carrier particle composed of a polymer matrix and in which the biochemical molecules are connected to the surface or inside of the polymer matrix; and an index code introduced into the carrier particle. Also provided is a method for fabricating biochemical carriers. The fabrication method includes: encoding digital data into a sequence of biochemical molecules; synthesizing the biochemical molecules based on the encoded sequence; mixing the biochemical molecules with a photocurable material; curing the mixture to obtain carrier particles including a polymer matrix; and introducing an index code into the carrier particles simultaneously with or separately from the curing. Also provided is a method for restoring digital data from the biochemical carrier.

Abstract: The present invention relates to a method for changing the intercellular mobility of an m RNA of a gene in an organism, comprising: modifying a t RNA-like structure present in the m RNA by mutating the gene from which the m RNA is transcribed, or including the sequence of a t RNA-like structure in the transcribed part of the gene. The method is in particular suited for plants. The intercellular mobility can be between different organs.

Abstract: The present disclosure provides a method for analyzing nucleic acid sequences. The method can comprise determining, by a computer system, a base trace by trimming a Sanger sequencing trace of a plurality of nucleic acid molecules from a sample based on a first target sequence and a second target sequence. Each of the first and second target sequences can be in the plurality of nucleic acid molecules or can be in the complement of sequence of the plurality of nucleic acid molecules.

Abstract: A sorghum seed comprising in its genome at least one polynucleotide encoding a polypeptide having an alanine to tyrosine substitution at position 93 of the sorghum AHAS protein large subunit. The plant has increased resistance to one or more herbicides, for example from the imidazolinone group, as compared to wild-type sorghum plants. The sorghum plant may comprise in its genome, one, two, three or more copies of a polynucleotide encoding a mutated large subunit of sorghum AHAS or a sorghum AHAS polypeptide of the invention. In this context, the sorghum plant may be tolerant to any herbicide capable of inhibiting AHAS enzyme activity. For example, the sorghum plant may be tolerant to herbicides of the imidazolinones type, such as imazethapyr, imazapir, and imazapic or to herbicides of the sulfonylurea group.

Abstract: The present invention provides a non-naturally occurring composition comprising a CRISPR nuclease comprising a sequence having at least 95% identity to the amino acid sequence selected from the group consisting of SEQ ID NOs: 1-8 or a nucleic acid molecule comprising a sequence encoding the CRISPR nuclease.

Abstract: The field of this invention relates to immunohistochemistry (IHC) and in situ hybridization (ISH) for the targeted detection and mapping of biomolecules (e.g., proteins and miRNAs) in tissues or cells for example, for research use and for clinical use such by pathologists (e.g., biomarker analyses of a resected tumor or tumor biopsy). In particular, the use of mass spectrometric imaging (MSI) as a mode to detect and map the biomolecules in tissues or cells for example. More specifically, the field of this invention relates to photocleavable mass-tag reagents which are attached to probes such as antibodies and nucleic acids and used to achieve multiplex immunohistochemistry and in situ hybridization, with MSI as the mode of detection/readout. Probe types other than antibodies and nucleic acids are also covered in the field of invention, including but not limited to carbohydrate-binding proteins (e.g., lectins), receptors and ligands.

Abstract: The disclosure relates to improvements in methods for efficient editing of two or more endogenous tomato genes by insertion of one or more single stranded DNA donor molecules that are not homologous to the insertion sites in the tomato genome.

Abstract: The field of this invention relates to immunohistochemistry (IHC) and in situ hybridization (ISH) for the targeted detection and mapping of biomolecules (e.g., proteins and miRNAs) in tissues or cells for example, for research use and for clinical use such by pathologists (e.g., biomarker analyses of a resected tumor or tumor biopsy). In particular, the use of mass spectrometric imaging (MSI) as a mode to detect and map the biomolecules in tissues or cells for example. More specifically, the field of this invention relates to photocleavable mass-tag reagents which are attached to probes such as antibodies and nucleic acids and used to achieve multiplex immunohistochemistry and in situ hybridization, with MSI as the mode of detection/readout. Probe types other than antibodies and nucleic acids are also covered in the field of invention, including but not limited to carbohydrate-binding proteins (e.g., lectins), receptors and ligands.

Abstract: Methods and kits are described for testing for the presence or absence of any fungus in a sample. Examples of fungi that can be detected include, but are not limited to, those belonging to the genera Candida, Aspergillus and Pneumocystis. The methods include obtaining a sample suspected of containing fungal nucleic acid, including at least one universal region of fungal nucleic acid, and testing for the presence or absence in the sample of the at least one universal region of fungal nucleic acid. Samples may be biological or non-biological.

Abstract: Methods for proteomic screening on random protein-bead arrays by mass spec is described. Photocleavable mass tags are utilized to code a protein library (bait molecules) displayed on beads randomly arrayed in an array substrate. A library of probes (prey) can be mixed with the protein-bead array to query the array. Because mass spec can detect multiple mass tags, it is possible to rapidly identify all of the interactions resulting from this mixing.

Abstract: A method for detecting and characterising a microorganism in a clinical sample includes introducing the clinical sample to a first culture vessel and simultaneously transporting and incubating the clinical sample in a thermally insulated compartment of a sealable container. A test aliquot is removed from the sample and the remainder of the sample is further cultured. DNA is removed from the test aliquot and nucleic acid tests are performed on it to identify the microorganism and to detect the presence or absence of one or more genetic antimicrobial resistance markers in the microorganism. One or more nucleic acid probes or primers are used to perform the nucleic acid tests. It is detected whether or not the probes or primers have hybridised to DNA or the primers have been extended. If a microorganism is identified, then an antimicrobial susceptibility test is performed on the cultured clinical sample.

Abstract: A method for classifying multi-granularity breast cancer genes based on a double self-adaptive neighborhood radius includes large-scale gene locus data are read and normalized, and a data analysis is performed on the large-scale gene loci. An optimum value K is selected by adopting a combination of contour coefficients and a PCA dimensionality reduction visualization, and a model of information granulation is adjusted. A heuristic reduction algorithm is used to implement a multi-granularity attribute reduction of a self-adaptive neighborhood radius based on a cluster center distance and a multi-granularity attribute reduction of a neighborhood radius based on an attribute inclusion degree, and big data for breast cancer genes are classified and predicted by adopting a machine learning classification algorithm based on a SVM support vector machine.

Abstract: The disclosure is directed to an expression vector or a combination of at least two expression vectors for producing a polypeptide of interest, the vector or vectors comprising a polynucleotide encoding a mutated folate receptor as a selectable marker. The disclosure also relates to host cells, selection methods and methods for producing polypeptides with high yield.

Abstract: The disclosure relates to improvements in methods for efficient editing of two or more endogenous soybean genes by insertion of one or more single stranded DNA donor molecules that are not homologous to the insertion sites in the soybean genome.

Abstract: The present invention relates to a nucleic acid construct. The nucleic acid construct includes a nucleic acid molecule configured to silence or reduce the expression of StBEL11 and/or StBEL29 and variants thereof, a 5? DNA promoter sequence, and a 3? terminator sequence, where the first nucleic acid molecule, the promoter sequence, and the terminator sequence are operatively coupled to permit transcription of the first nucleic acid molecule. The present invention is also directed to vectors, host cells, transgenic plants, and transgenic plant seeds, as well as non-transgenic mutant plants, and methods for altering tuber yield in a plant.

Abstract: The field of this invention relates to immunohistochemistry (IHC) and in situ hybridization (ISH) for the targeted detection and mapping of biomolecules (e.g., proteins and miRNAs) in tissues or cells for example, for research use and for clinical use such by pathologists (e.g., biomarker analyses of a resected tumor or tumor biopsy). In particular, the use of mass spectrometric imaging (MSI) as a mode to detect and map the biomolecules in tissues or cells for example. The field of this invention relates to photocleavable mass-tag reagents which are attached to probes such as antibodies and nucleic acids and used to achieve multiplex immunohistochemistry and in situ hybridization, with MSI as the mode of detection/readout, and also encompasses multi-omic MSI procedures, where MSI of photocleavable mass-tag probes is combined with other modes of MSI.

Abstract: Methods for proteomic screening on random protein-bead arrays by mass spec is described. Photocleavable mass tags are utilized to code a protein library (bait molecules) displayed on beads randomly arrayed in an array substrate. A library of probes (prey) can be mixed with the protein-bead array to query the array. Because mass spec can detect multiple mass tags, it is possible to rapidly identify all of the interactions resulting from this mixing.

Abstract: The present disclosure provides methods and systems for amplifying and analyzing nucleic acid samples. The present disclosure provides methods for preparing cDNA and/or DNA molecules ad cDNA and/or DNA libraries using modified reverse transcriptases.

Abstract: The disclosure provides processors that are configured to perform dynamic programming according to an instruction, a method for configuring a processor for dynamic programming according to an instruction and a method of computing a modified Smith Waterman algorithm employing an instruction for configuring a parallel processing unit. In one example, the method for configuring includes: (1) receiving, by execution cores of the processor, an instruction that directs the execution cores to compute a set of recurrence equations employing a matrix, (2) configuring the execution cores, according to the set of recurrence equations, to compute states for elements of the matrix, and (3) storing the computed states for current elements of the matrix in registers of the execution cores, wherein the computed states are determined based on the set of recurrence equations and input data.

Abstract: The present invention generally relates to systems, methods and compositions used for the control of gene expression involving sequence targeting, such as genome perturbation or gene-editing, that may use vector systems related to recombinases and Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and components thereof.

Abstract: Disclosed herein are systems and methods for determining metabolic pathway dynamics using time series multiomics data. In one example, after receiving time series multiomics data comprising time-series metabolomics data associated a metabolic pathway and time-series proteomics data associated with the metabolic pathway, derivatives of the time series multiomics data can be determined. A machine learning model, representing a metabolic pathway dynamics model, can be trained using the time series multiomics data and the derivatives of the time series multiomics data, wherein the metabolic pathway dynamics model relates the time-series metabolomics data and time-series proteomics data to the derivatives of the time series multiomics data. The method can include simulating a virtual strain of the organism using the metabolic pathway dynamics model.

Abstract: Under one aspect, a composition includes a substrate; a first polynucleotide coupled to the substrate; a second polynucleotide hybridized to the first polynucleotide; and a catalyst coupled to a first nucleotide of the second polynucleotide, the catalyst being operable to cause a chemiluminogenic molecule to emit a photon. Under another aspect, a method includes providing a catalyst operable to cause a first chemiluminogenic molecule to emit a photon; providing a substrate; providing a first polynucleotide coupled to the substrate; hybridizing a second polynucleotide to the first polynucleotide; coupling a first quencher to a first nucleotide of the second polynucleotide; and inhibiting, by the first quencher, photon emission by the first chemiluminogenic molecule.

Abstract: Provided herein are methods and compositions for treating cancers, inflammatory diseases, rasopathies, and fibrotic disease involving aberrant Ras superfamily signaling through the binding of compounds to the GTP binding domain of Ras superfamily proteins including, in certain cases, K-Ras and mutants thereof, and a novel method for assaying such compositions.

Abstract: A method of storing information using monomers such as nucleotides is provided including converting a format of information into a plurality of bit sequences of a bit stream with each having a corresponding bit barcode, converting the plurality of bit sequences to a plurality of corresponding oligonucleotide sequences using one bit per base encoding, synthesizing the plurality of corresponding oligonucleotide sequences on a substrate having a plurality of reaction locations, and storing the synthesized plurality of corresponding oligonucleotide sequences.

Abstract: The present teachings provide apparatuses and methods for automated handling of samples, e.g., biological or chemical samples. The apparatuses and the methods of the present teachings allow automated performance of various sample manipulation steps without manual intervention. In a preferred embodiment, the present teachings provide apparatuses and methods for automated enrichment of templated beads produced by PCR.

Abstract: Identifying pathways that are significantly impacted in a given condition is a crucial step in the understanding of the underlying biological phenomena. All approaches currently available for this purpose calculate a p-value that aims to quantify the significance of the involvement of each pathway in the given phenotype. These p-values were previously thought to be independent. Here, we show that this is not the case, and that pathways can affect each other's p-values through a “crosstalk” phenomenon that affects all major categories of existing methods. We describe a novel technique able to detect, quantify, and correct crosstalk effects, as well as identify novel independent functional modules. We assessed this technique on data from four real experiments coming from three phenotypes involving two species.

Abstract: The invention relates to a diagnosis and therapeutic preparation for senile dementia and an application thereof, in particular to an application of ARHGAP11A gene, SPAG7 gene and C16ORF7 gene in preparing a diagnosis and therapeutic preparation for senile dementia. In order to solve the problem that molecular markers of senile dementia are scarce at present, the inventors carried out the high-throughput sequencing on peripheral blood samples of patients with senile dementia and healthy people, selected candidate genes, and confirmed that there was a good correlation between the candidate genes and senile dementia through molecular cell experiments, which laid a foundation for clinical gene diagnosis of senile dementia.

Abstract: A method and a system for performing context-based search. The method is executed by a processing module. The method includes developing a search database, developing a search query, and retrieving at least one context-based data-record from the search database.

Abstract: Described are compositions and methods relating to modified yeast that over-express polyadenylate-binding protein (PAB1). The yeast produces a deceased amount of acetate compared to parental cells. Such yeast is particularly useful for large-scale ethanol production from starch substrates where acetate in an undesirable end product.

Abstract: The present invention provides assays and assay systems for use in spatially encoded biological assays. The invention provides an assay system comprising an assay capable of high levels of multiplexing where reagents are provided to a biological sample in defined spatial patterns; instrumentation capable of controlled delivery of reagents according to the spatial patterns; and a decoding scheme providing a readout that is digital in nature.

Abstract: The sample plate has a principal plane in which a plurality of wells is arranged. The sample plate has a plurality of through-holes each allowing a sampling needle to pass through in a region of the principal plane where the wells are not provided, and positions of the wells and positions of the through-holes are designed such that when two pieces of the sample plates are arranged up and down with a predetermined positional relationship in a state in which respective principal planes are arranged in parallel each other, the through-holes of the sample plate arranged on an upper side is arranged at positions directly above respective wells of the sample plate arranged on a lower side.

Abstract: An image display control system includes a hardware processor that acquires data of a static image of a subject, and data of a dynamic image of the subject including a plurality of frame images, analyzes the dynamic image that is acquired, and creates analysis result data based on an analysis result, and selects, on a basis of a purpose of checking of data, at least one of the data among the data of the static image that is acquired, a part of the data of the dynamic image that is acquired, and the analysis result data that is created.

Abstract: Technology provided herein relates in part to methods, processes, machines and apparatuses for determining sequences of nucleotides for nucleic acid templates in a nucleic acid sample. The technology provide herein also relates in part to methods, processes, machines and apparatuses for counting nucleic acid templates. Nucleic acid templates of a sample are tagged with nonrandom oligonucleotide adapters that include predetermined non-randomly generated sequences. The use of these nonrandom oligonucleotide adapters provides an efficient method to reduce sequencing errors, and increase the sensitivity of detection of low-frequency single nucleotide alterations.

Abstract: Non-parametric transforms such as t-distributed stochastic neighbor embedding (tSNE) are used to analyze multi-parametric data such as data derived from flow cytometry or other particle analysis systems and methods. These transforms may be included for dimensionality reduction and identification of subpopulations (e.g., gating). By nature, non-parametric transforms cannot transform new observations without training a new transformation based on the entire dataset including the new observations. The features described parameterize non-parametric transforms using a neural network thereby allowing a small training dataset to be transformed using non-parametric techniques. The training dataset may then be used to generate an accurate parametric model for assessing additional events in a manner consistent with the initial events.

Abstract: Provided are peptide nucleic acid derivatives targeting a part of the human HIF-1? pre-mRNA. The peptide nucleic acid derivatives potently induce exon skipping to yield splice variants of HIF-1? mRNA in cells, and are useful to treat indications or conditions involving the overexpression of HIF-1?.

Abstract: Provided are methods for determining if a cannabis sample comprises hemp or marijuana, or Cannabis sativa and/or Cannabis indica as well as primers and kits for use in the methods.

Abstract: A nanopore device includes an aperture and an electrode pair. A transimpedance amplifier converts a current signal IS that flows through the nanopore device into a voltage signal VS. The nanopore device measures small particles based on first data obtained by removing a DC component from the voltage signal VS and second data obtained based on the voltage signal VS from which the DC component has not been removed. Furthermore, the nanopore device is capable of monitoring the state of the nanopore device.

Abstract: Techniques to identify a mechanism of action of a compound using network dysregulation are disclosed herein. An example method can include selecting at least a first interaction involving at least a first gene, determining a first n-dimensional probability density of gene expression levels for the first gene and one or more genes in a control state, determining a second n-dimensional probability density of gene expression levels for the first gene and one or more genes following treatment using at least one compound, estimating changes between the first probability density and the second probability density, and determining whether the estimated changes are statistically significant.

Abstract: Provided are isolated polynucleotides at least 80% identical to SEQ ID NOs: 1-479, 813-5173, 8511, 8513, 8515, 8517, 8519, 8521, 8523, 9096-9141 and 9142; and isolated polypeptides at least 80% homologous to an amino acid sequence selected from the group consisting of SEQ ID NOs: 624, 480-623, 625-812, 5174-7015, 7017-7021, 7024, 7026-8510, 8512, 8514, 8516, 8518, 8520, 8522, 8524, 9143-9177, such as the polypeptides set forth in SEQ ID NO:480-812, 5174-8510, 8512, 8514, 8516, 8518, 8520, 8522, 8524, and 9143-9177, nucleic acid constructs comprising same, transgenic cells and plants expressing same and methods of using same for increasing yield, biomass, growth rate, vigor, oil content, fiber yield, fiber quality, nitrogen use efficiency, and/or abiotic stress tolerance of a plant.