Abstract: Provided herein is technology relating to sequencing nucleic acids and particularly, but not exclusively, to methods, compositions, and systems for sequencing a nucleic acid using one or more labels and signal amplitude to distinguish bases.

Abstract: A method for detecting genes sensitive to low-level ionizing radiation and genes detected by the method. More specifically, genes sensitive to low-level ionizing radiation and related to suppressing thymic cancer, discovered in a carcinogenic entity and verified in a normal entity are detected by subjecting a cancerous AKR/J mouse and a normal ICR mouse to low-level radiation. Thymus is collected therefrom, immunogenic and apoptotic genes are classified via microarray processing of the thymus. The genes are amplified and the levels of gene expression are measured. Thus, a gene having a specific reaction to radiation can be accurately detected by preventing the interference of confounding variables.

Abstract: Disclosed are a protein molecular marker Dkk-3 protein associated with age-related muscle atrophy and the use thereof in the diagnosis of age-related muscle atrophy. The expression level of the Dkk-3 protein in amyotrophic cells is significantly higher than that in normal myocytes or tissues, and thus the Dkk-3 protein can be used as an effective marker for the detection of age-related muscle atrophy.

Abstract: The present invention relates to a target gene-detecting device and a method for detecting a target gene. According to an aspect, a target gene-detecting device can be conveniently fabricated at low cost by employing a porous substrate or a method for detecting a target gene allows the pretreatment of a sample, the extraction of a nucleic acid, the amplification of a nucleic acid, and the detection of a target gene to be conducted at high accuracy and specificity in an integral system, with no contamination plausibility and can be thus useful for gene inspection.

Abstract: The disclosure relates to novel particle compositions and methods of making said compositions having applications in nucleic acid analysis, as well as apparatuses and systems for the same.

Abstract: Embodiments may include a method of determining a nucleic acid sequence. The method may include receiving a plurality of DNA fragments. The method may also include concatemerizing a first set of the DNA fragments to obtain a concatemer. The method may include performing single-molecule sequencing of the concatemer to obtain a first sequence of the concatemer. In some embodiments, single-molecule sequencing may be performed using a nanopore, and the method may include passing the concatemer through a nanopore. A first electrical signal may then be detected as the concatemer passes through the nanopore. The first electrical signal may correspond to a first sequence of the concatemer. In addition, the method may include analyzing the first electrical signal to determine the first sequence. Subsequences of the first sequence may be aligned to identify sequences corresponding to each of the first set of the DNA fragments.

Abstract: A nanopore measurement circuit includes a first analog memory configured to store a first electrical value corresponding to a first measurement sample of a nanopore and a second analog memory configured to store a second electrical value corresponding to a second measurement sample of the nanopore. The nanopore measurement circuit also includes a measurement circuitry configured to provide an output indicating a difference between the first electrical value of the first analog memory and the second electrical value of the second analog memory.

Abstract: Disclosed herein include methods and compositions for selectively amplifying and/or extending nucleic acid target molecules in a sample. The methods and compositions can, for example, reduce the amplification and/or extension of undesirable nucleic acid species in the sample, and/or allow selective removal of undesirable nucleic acid species in the sample.

Abstract: The methods described herein, referred to as PCR-Activated Sorting (PAS), allow nucleic acids contained in biological systems to be sorted based on their sequence as detected with nucleic acid amplification techniques, e.g., PCR. The nucleic acids can be free floating or contained within living or nonliving structures, including particles, viruses, and cells. The nucleic acids can include, e.g., DNA or RNA. Systems and devices for use in practicing methods of the invention are also provided.

Abstract: The present disclosure relates to methods for producing recombinant proteins, as well as compositions used in and produced by such methods. Specifically, the present disclosure relates to methods for producing high secreted yields of recombinant proteins, and the compositions provided herein include expression constructs, recombinant vectors, and recombinant host cells that comprise polynucleotide sequences encoding proteins operably linked to recombinant secretion signals that comprise the leader peptide of the ?-mating factor (?MF) of Saccharomyces cerevisiae and a non-?MF signal peptide.

Abstract: A primary object of the present invention is to provide a method for conveniently and accurately testing for pulmonary hypertension. To achieve this object, the present invention provides a method for testing for pulmonary hypertension using as an indicator the concentration of selenoprotein P protein in a sample derived from a subject.

Abstract: Disclosed is an in situ method for detecting spatial proximity relationships between nucleic acid sequences, such as DNA, in a cell. The method includes: providing a sample of one or more cells comprising nucleic acids; fragmenting the nucleic acids present in the cells that leaves 5? overhanging ends; filling in the overhanging ends with at least one labeled nucleotide; joining the filled in end of the fragmented nucleic acids that are in close physical proximity to create one or more end joined nucleic acid fragments having a junction; isolating the one or more end joined nucleic acid fragments using the labeled nucleotide; and determining the sequence at the junction of the one or more end joined nucleic acid fragments.

Abstract: An ultra-sensitive, specific methodology for detecting PIK3CA mutations in biological samples of cancer patients, comprises a combination of allele-specific, asymmetric rapid PCR and melting analysis in a DNA sample from Circulating Tumor Cells, cell-free DNA in plasma/serum, or Formalin-Fixed Paraffin-Embedded tissues. Using the allele-specific primers for hotspot mutations in exons 9 and 20 (E545K and H1047R), detection can enhance amplification of mutant PIK3CA allele sequence, whereas presence of corresponding competitive blocking unlabeled probes for each exon can avoid non-specific amplification of wild-type PIK3CA sequence increasing the sensitivity and the specificity of method. The mutational detection is completed with melting curve analysis of the unlabeled probe and DNA template of the mutant PIK3CA sequence.

Abstract: In cancers such as prostate cancer, the combination of PTEN loss and activation of Myc activates an adaptive stress response that enables tumor cells to escape the stress of massively upregulated protein synthesis. This pro-survival response is mediated by the PERK-phosphorylated eIF2? axis of the UPR adaptive response. Agents that disrupt PERK-eIF2? pathways disrupt the adaptive response and lead to cancer cell death from uncontrolled growth. For example, ISRIB and derivatives may be employed as therapeutic agents to disrupt PERK-mediated adaptive mechanisms. Additionally PTEN loss and activation of Myc provides a diagnostic marker that enables better prognosis and the selection of amenable treatments.

Abstract: Disclosed is a library consisting essentially of a plurality of antigen-binding molecules differing in sequence from each other, wherein an antigen-binding domain in each of the antigen-binding molecules comprises at least one amino acid residue that changes the antigen-binding activity of the antigen-binding molecule depending on ion concentration conditions. Also disclosed are a composition comprising a plurality of polynucleotide molecules each encoding the antigen-binding molecules, a composition comprising a plurality of vectors each comprising the polynucleotide molecules, a method for selecting the antigen-binding molecules, a method for isolating the polynucleotide molecules, a method for producing the antigen-binding molecules, and a pharmaceutical composition comprising any of the antigen-binding molecules.

Abstract: Some embodiments described herein relate to systems and methods operable to combine immunoassay and Total Protein techniques in a single sample run. Some embodiments described herein allow for multiple sequential immunoassays to be performed in the same microfluidic device. Some embodiments described herein relate to stripping reagents operable to remove primary antibodies associated with immunoassays. Such stripping reagents can allow for additional immunoassays and/or Total Protein assays to be performed on the same sample.

Abstract: A system and method for generating a stained image including the steps of obtaining a first image of a key sample section; and processing the first image with a stain learning engine arranged to generate at least one stained image, wherein the at least one stained image represents the key sample section stained with at least one stain.

Abstract: Some embodiments are directed to a process for the diagnosis of systemic lupus erythematosus (SLE) and/or of chronic lymphoid leukaemia (CLL) of a subject who may be suffering therefrom, comprising the in vitro detection of the expression of the fraction of the STIM1 protein located at the cell plasma membrane in a biological sample from human and mice. Some other embodiments are directed to a process for predicting the progression and/or monitoring the progression of CLL and/or of SLE, comprising the in vitro detection of the expression of the fraction of the STIM1 protein located at the cell plasma membrane.

Abstract: Provided is a method of genetically incorporating an L-dihydroxyphenylalanine in a target protein.

Abstract: The present invention provides gene sets the expression of which is important in the diagnosis and/or prognosis of breast cancer.

Abstract: The invention features methods, devices, and kits for predicting the responsiveness of a cancer patient (e.g., a breast cancer patient, such as a grade 1, 2, or 3 breast cancer patient) to anthracycline treatment by determining the expression levels of four chromosomal instability (CIN) genes including HDGF, KIAA0286, RFC4, and MSH6, collectively referred to as CIN4. Patients that have a low CIN4 score benefit from anthracycline treatment compared patients with a high CIN4 score.

Abstract: The present invention provides for methods of epigenetic analysis. In some cases, the methods may include obtaining a sample comprising a nucleic acid sequence. In some cases, the nucleic acid sequence may comprise one or more epigenetic marks. The methods may include performing a sequencing. The methods may include distinguishing a hydroxymethylated base from a methylated base.

Abstract: The present invention relates to methods for detecting and quantifying intact protein-polynucleotide conjugate molecules in various sample matrices. In particular, the methods utilize triplex forming oligonucleotides in combination with protein-specific binding partners to respectively detect the polynucleotide and protein components of the conjugate molecules.

Abstract: The present invention relates to the use of next generation technologies coupled with viability and pathogenicity profiles to determine the threat of microbes in the environment. The invention relates to methods for identifying a pathogenicity and viability profile of microbes from collected samples.

Abstract: The present invention is related to a method for diagnosing Farber's disease in a subject, wherein the method comprises detecting C26 ceramide in a sample from the subject.

Abstract: The present invention relates to a method of controlled competitive exchange of a first agent bound to a metal coordination complex with a competing agent, with selection of the nature of the first agent allowing a tailoring of the binding strength and thereby allowing for a desired level of control for subsequent displacement by the selected competing agent. The method may be employed for release of therapeutic agents, sequestration of larger molecules from a sample, generation of a preferred binding surface and the like.

Abstract: A method of screening for the presence and/or extent of a pathology in a subject, the pathology characterized by an abnormal chromosomal component in a cell of the subject, comprising the steps of: contacting a biological sample comprising cell nuclei from said subject with, one or more distinguishable labeled probes directed to at least one chromosomal sequence that characterizes the abnormality under conditions that promote hybridization of the one or more probes to the at least one sequence, automatically obtaining a representation of the one or more distinguishable labels hybridized to the chromosomal sequences, automatically analyzing the distribution and intensity of binding of the one or more labels in the representation to determine the presence and/or extent of an abnormal chromosomal component; and automatically reporting results of the analysis; wherein the steps are carried out without intervention by a human.

Abstract: To provide a method for quickly and accurately evaluating a condition of skin dryness and a method for efficiently searching a substance to improve dry skin. A method for evaluating a condition of skin dryness, the method comprising measuring the expression levels of AGR2 and/or AGR3 in skin cells collected from subjects.

Abstract: The present disclosure provides affinity tagged heterodimeric polypeptides comprising a hepatitis C virus (HCV) E1 polypeptide and an HCV E2 polypeptide, where one or both of the E1 and E2 polypeptides comprises an affinity tag. The present disclosure provides a method of producing an affinity tagged E1/E2 heterodimer of the present disclosure. The present disclosure provides methods of producing untagged HCV E1/E2 heterodimers. The present disclosure provides HCV E1/E2 heterodimers, compositions comprising same, and methods of inducing an immune response to HCV.

Abstract: A method and system for determining an amount of risk an air pollutant poses to a subject. A risk level is calculated by determining a dosage of the air pollutant, received by the subject over a predetermined period of time, and obtaining historic information about historic dosages of the air pollutant. The risk level is then calculated using the dosage and the historic information to thereby determine a risk level associated with the accumulated deposition of the air pollutant in the portion of the subject's respiratory tract.

Abstract: The present invention relates to a biomarker for predicting susceptibility to an MET inhibitor, and a use thereof, and more specifically, the present invention provides a method for predicting susceptibility to the MET inhibitor. According to the present invention, the present invention has an excellent effect of predicting susceptibility to the MET inhibitor for stomach cancer or lung cancer, and thus the present invention may be usefully employed for treating stomach cancer or lung cancer.

Abstract: The present invention is directed to methods of diagnosing, prognosing, and monitoring cancer in a subject. These methods involves selecting a subject having cancer, and obtaining, from the selected subject, a sample containing exosomal DNA. The presence or absence of one or more mutations in BRAF and/or EGFR is detected in the exosomal DNA sample from the subject, and a diagnosis and/or prognosis of the cancer is given based on the detection of the one or more mutations in BRAF and/or EGFR. The present invention further relates to methods of treating a subject having cancer and/or monitoring a subject response to therapy based on the detection of one or more mutations in BRAF and/or EGFR in the exosomal DNA sample.

Abstract: A method of nucleic acid amplification involving using a first modified primer which provides protection to the amplification product from exonuclease degradation and a second primer. The method provides a double stranded nucleic acid, one strand of which is degraded by a double strand nucleic acid specific exonuclease to form a single stranded nucleic acid, which is protected from exonuclease degradation.

Abstract: Systems and methods are disclosed for receiving one or more electronic slide images associated with a tissue specimen, the tissue specimen being associated with a patient and/or medical case, partitioning a first slide image of the one or more electronic slide images into a plurality of tiles, detecting a plurality of tissue regions of the first slide image and/or plurality of tiles to generate a tissue mask, determining whether any of the plurality of tiles corresponds to non-tissue, removing any of the plurality of tiles that are determined to be non-tissue, determining a prediction, using a machine learning prediction model, for at least one label for the one or more electronic slide images, the machine learning prediction model having been generated by processing a plurality of training images, and outputting the prediction of the trained machine learning prediction model.

Abstract: The invention relates to method for identifying and selecting a subject with increased risk of developing a cardiometabolic disease and optionally, providing a personalized medicine method, which may involve sequencing at least part of a genome of one or more cells in a blood sample of the subject and identifying from said sequencing one or more mutations in one or more somatic mutations.

Abstract: A method, computer system, and a computer program product for compressing at least one delta file for a plurality of genomic data files is provided. The present invention may include receiving the plurality of genomic data files as input. The present invention may also include determining a plurality of rows by traversing the received plurality of genomic data files. The present invention may then include comparing the plurality of rows associated with the traversed plurality of genomic data files. The present invention may further include generating a plurality of resulting delta files based on the compared plurality of rows. The present invention may also include compressing the generated plurality of resulting delta files by utilizing a general purpose file compressor.

Abstract: The present disclosure provides a low cost, high sensitivity, high specificity and rapid diagnostic apparatus and method to detect nucleic acids in a sample at room temperature. As low as tens of copies of nucleic acids can be detected without any additional equipment.

Abstract: The invention provides for a panel for detecting chromosomal abnormalities in a plurality of cells in a cervical sample wherein the panel comprises a plurality of fluorescently labeled probes individually capable of hybridizing to specific chromosomal locations associated with a chromosomal abnormality in patients at risk for a cervical cell disorder. The invention also comprises a fluorescence in situ hybridization (FISH) probe set comprising the plurality of fluorescently labeled probes.

Abstract: The present application relates to K-ras mutations, to polynucleotides encoding mutant K-ras polypeptides, and to methods of identifying K-ras mutations. The present application also relates to methods of diagnosing cancer; and methods and kits for predicting the usefulness of anti-EGFr specific binding agents in the treatment of tumors.

Abstract: Provided herein are methods and compositions for detection of a nucleic acid target in a sample. The methods and compositions use primer directed amplification in conjunction with nucleic acid fragmentation. The methods have high sensitivity even in the presence of a large amount of non-target nucleic acid. Also provided are oligonucleotides and kits useful in the method. Exemplary nucleic acid targets are those with mutant gene sequence such as mutant sequence of the EGFR, APC, TMPRSS2, ERG and ETV1 genes.

Abstract: Provided herein is a system and method for review of forensic report computer files. The method can involve notifying a plurality of service providers of a job to be performed, accepting a bid from a service provider to perform the job, providing the computer file to the service provider, receiving from the service provider a forensic result such as a reviewed file.

Abstract: An automatic service monitor in an information-technology environment performs regular search queries against generated machine data to derive performance measurements. The information technology environment is defined in terms of services provided by entities, and the performance measurements are defined as key performance indicators (KPIs) of the services. Generated machine data used by the search queries pertain to the entities performing the service. Definitional information for the services, entities, and KPIs is administered by a user to control the operation of the service monitor. Various aspects of such definitional information as well as related performance measurement information may be presented in a unified console display tailored to, and organized around, a particular entity. The console display may serve as a central launch point by supporting user interaction to navigate to other specialized monitoring interfaces.

Abstract: It is intended to provide a method for determining a tumor. The method for determining a tumor comprises: (1) treating genomic DNA prepared from a subject tissue or cell with bisulfite (the subject tissue or cell is derived from a patient who is affected by a tumor and is determined as (i) having MSI-H of the tumor in MSI examination and/or no or reduced expression of MLH1 in the tumor in immunohistochemical examination, and (ii) having no mutation in MLH1 in genetic examination); 2) amplifying, by PCR, DNA comprising a portion or the whole of MLH1 promoter region from the bisulfite-treated DNA; 3) subjecting the PCR amplification product to ion exchange chromatography to obtain a detection signal; 4) determining whether or not the peak of the detection signal is a peak indicating highly methylated DNA; and 5) determining the tumor as a tumor derived from a patient without Lynch syndrome when the peak is determined as a peak indicating highly methylated DNA.

Abstract: The cost of data-mining is estimated where data-mining services are delivered via a distributed computing system environment. System requirements are estimated for a particular data-mining task for an input data set having specified properties. Estimating system requirements includes applying a partial learning tool to operate on sample data from the input data set.

Abstract: The present invention relates to a method for detecting cancer, comprising measuring the expression of a polypeptide having a reactivity of binding to an antibody against a CAPRIN-1 protein having an amino acid sequence shown in any one of the even-numbered SEQ ID NOS: 2-30 in the Sequence Listing via an antigen-antibody reaction in a sample separated from a living organism, and, a reagent for detecting a cancer comprising the CAPRIN-1 protein or a fragment thereof, an antibody against the CAPRIN-1 protein or a fragment thereof, or a polynucleotide encoding the CAPRIN-1 protein or a fragment thereof.

Abstract: Gene expression signature predictive of cancer patient response to multi-kinase inhibitor is disclosed. Also disclosed are methods predicting the efficacy of the multi-kinase inhibitor for treating cancer in a patient. Also disclosed are methods for distinguishing responders from non-responders to a multi-kinase inhibitor in treating cancer. Also disclosed are methods for treating a cancer patient with a multi-kinase inhibitor.

Abstract: According to one embodiment, a detection method is a method for detecting a plurality of target nucleic acids in a sample. The method includes (a) preparing a chain-elongation nucleic acid set group, a primer set, and a probe immobilized substrate, (b) obtaining the target nucleic acid and a long-chain nucleic acid group containing a first sub-chain-elongation nucleic acid and a second sub-chain-elongation nucleic acid, (c) obtaining an amplification product group by maintaining the long-chain nucleic acid group and the primer set under amplification conditions, (d) detecting presence/absence and/or an amount of hybridization, and (e) detecting the plurality of target nucleic acids.

Abstract: Early detection of tumors is a major determinant of survival of patients suffering from tumors, including bladder tumors. Members of the BTM or UBTM family can be highly and consistently accumulated in bladder tumor tissue and other tumor tissue, and/or can be accumulated in urine of patients, and thus are markers for bladder and other types of cancer. In certain embodiments, BTMs or UBTMs can accumulate in the urine, and detection of UBTM family members can be an effective diagnostic approach. In some embodiments, quantitative PCR methods have advantages over microarray methods. In other embodiments, detection and quantification of a plurality of BTMs or UBTMs can increase the sensitivity and specificity of detection of bladder cancer, and therefore provides methods for determining the stage and type of bladder cancer. Kits provide easy, convenient ways for carrying out the methods of this invention.

Abstract: A method for generating a reporter cell line comprises culturing a cell line capable of undergoing two or more consecutive stages of differentiation and performing the targeted insertion of two or more secretable reporter genes into the genome of the cultured cell line to form edited cells. One or more first stage inserted secretable reporter genes are placed under control of promoters for genes canonically expressed during the first stage of differentiation, and one or more second stage inserted secretable reporter genes are placed under control of promoters for genes canonically expressed during the second stage of differentiation but not during the first stage of differentiation. Differentiation of the clonally expanded edited cells is then induced to the first stage of differentiation, thus inducing expression of the first stage inserted secretable reporter genes.

Abstract: A method of analyzing a tumor sample comprising: (a) acquiring a library comprising a plurality of tumor members from a tumor sample; (b) contacting the library with a bait set to provide selected members; (c) acquiring a read for a subgenomic interval from a tumor member from said library; (d) aligning said read; and (e) assigning a nucleotide value (e.g., calling a mutation) from said read for the preselected nucleotide position, thereby analyzing said tumor sample.