Abstract: Described herein are efficient methods for preparing a library for use in comprising performing gene targeting or massively parallel reporter assays. The methods comprise performing hybrid capture of a library constant region.

Abstract: A method for amplification of nucleic acids in which substantially use is made of the fact that a pre-defined nucleic acid chain (target sequence) can be multiplied/amplified in the presence of a target sequence-specific activator oligonucleotide. The target sequence-specific activator oligonucleotide causes the separation of re-synthesized complementary primer extension products by strand displacement, so that a new primer oligonucleotide can attach to the respective template strand. The thus formed complex of a primer oligonucleotide and a template strand can initiate a new primer extension reaction. The thus formed primer extension products in turn function as templates, so that an exponential amplification reaction results. Amplification of a particular target sequence takes place more efficiently in case of perfect match complemetary base pair formation between the activator oligonucleotide and the corresponding target sequence.

Abstract: This application provides fluidic devices, such as microfluidic devices, which can be used for the creation and/or manipulation of droplets in droplet-based microfluidic systems, as well as systems and methods for using the same. The microfluidic devices can be used to generate droplets, extract or inject volume to droplets, and/or split droplets. Also provided are methods for generating nucleosomes, and isolated DNA from nucleosomes (or from non-nucleosomes), for example using the disclosed devices.

Abstract: A method for moving a processing vial between locations of an instrument. The method includes the steps of dispensing a fluid into a processing vial with a disposable pipette tip frictionally fitted onto a probe of a pipettor, stripping the disposable pipette tip from the probe of the pipettor, and then engaging a cap in a frictional fit with the probe of the pipettor. While the cap is engaged in a frictional fit with the probe of the pipettor, coupling the cap to the processing vial to form a cap/vial assembly, where the cap seals the processing vial. The pipettor moves the cap/vial assembly from a first location of an instrument to a second location of the instrument. At the second location of the instrument, the cap/vial assembly is ejected from the probe of the pipettor, thereby depositing the cap/vial assembly at the second location.

Abstract: The present invention provides methods, compositions, kits, systems and apparatus that are useful for isolating nucleic acid molecules from a sample. In particular, the methods generally relate to normalizing the concentration of target nucleic acid molecules from a sample. In one aspect, the invention relates to purifying a primer extension product from a primer extension reaction mixture. In some aspects, nucleic acid molecules obtained using the disclosed methods, kits, systems and apparatuses can be used in various downstream processes including nucleic acid sequencing.

Abstract: Compositions, methods and apparatus for diagnosing and/or monitoring a hypoxic condition by measurement of a hypoxia-associated gene signature can be used for diagnosis including early diagnosis, monitoring, making treatment decisions, or management of subjects suspected of having a disease or condition that is associated with a hypoxic condition (e.g., a hypoxic condition). Nucleic acid and protein biomarkers can be used for specifically determining the likelihood of the presence or absence of a hypoxic condition in a subject.

Abstract: The present invention relates to an in vitro method for guiding measures against the propagation of Salmonella and/or against the propagation Campylobacter in an animal flock, the method comprising i.) determining the amount of at least one marker gene being specific for Salmonella or Campylobacter in a test sample and ii.) comparing the amount of said at least one marker gene being specific for Salmonella or Campylobacter determined in the test sample with a control sample, wherein an increase in the amount of said at least one marker gene being specific for Salmonella or Campylobacter in the test sample vs. the control sample by at least a factor of two, indicates the necessity of initiating or enhancing measures against the propagation of Salmonella and/or against the propagation Campylobacter.

Abstract: The present invention relates to bioinformatics methods of in silico validation of circRNA junctions and selection of circRNA junctions for further validation, more particularly detecting sequence reads supporting circRNA junction in a highly computationally efficient manner.

Abstract: The invention provides eukaryotic cell-based screening methods to identify an aptamer that specifically binds a ligand, or a ligand that specifically binds an aptamer, using a polynucleotide cassette for the regulation of the expression of a reporter gene where the polynucleotide cassette contains a riboswitch in the context of a 5? intron-alternative exon-3? intron. The riboswitch comprises an effector region and an aptamer such that when the aptamer binds a ligand, reporter gene expression occurs.

Abstract: Methods of analyzing a biological sample obtained from the feline subject for the presence of two copies of major allele G of SNP A1_212891692 and/or to the concentration of betaine and/or 2-oxoarginine in the sample are disclosed. The methods are used in methods to identify a feline subject that would benefit from a treatment that reduces risk of calcium oxalate stone formation and in methods of treating a feline subject to reduce risk of calcium oxalate stone formation The treatment on comprises administering to the feline subject a composition that comprises an effective amount of one or more of ingredients selected from the group consisting of betaine, green tea, fenugreek and tulsi. Feline food composition that comprise effective amounts of betaine, green tea, fenugreek and tulsi are disclosed.

Abstract: Methods of measuring chimerism in a biological sample use informative copy number variations (CNV) in genetically distinct cell populations. Chimerism describes the co-existence of cells originating from more than one individual. Assessing CNV polymorphisms in genomic DNA provides a useful in-vitro method of measuring chimerism. The accuracy of the methods can be validated using an internal validation step.

Abstract: Methods and systems for detecting allelic imbalance using nucleic acid sequencing are provided.

Abstract: In the present invention, when amplifying a nucleic acid by incorporating at least one primer among a forward primer and reverse primer and/or a probe in an upper critical solution temperature (UCST) particle, or when amplifying a nucleic acid by incorporating at least one primer among the forward primer and reverse primer and/or a probe in a UCST particle and fixing to a hydrogel fine particle, same the primer or probe comprised in the UCST particle can be discharged within a certain temperature range. Accordingly, the formation of primer dimers can be prevented while also achieving excellent PCR amplification efficiency.

Abstract: In certain aspects, the invention disclosed herein relates to the isothermal amplification of probe linkage products to generate specific amplified signals. In some aspects, the invention provides methods, reagents, and kits for carrying out such amplification via the isothermal chain reaction (ICR).

Abstract: This invention relates to imaging, such as by expansion microscopy, labelling, and analyzing biological samples, such as cells and tissues, as well as reagents and kits for doing so.

Abstract: The present invention features compositions and methods for quantifying detection of a target oligonucleotide in a sample in real time. These methods are compatible with target oligonucleotides amplified using a NEAR reaction.

Abstract: The present invention relates to a kit and a method of linear amplification of a least one nucleic acid target in a sample, said method comprising: (a) contacting each target in the sample with a nucleic acid polymerase and a primer comprising a component preventing copying of the primer by the nucleic acid polymerase; and at least one nuclease blocking nucleotide; (b) generating a primer extension product; (c) preventing priming by the 3?-end of the primer extension product, and (d) repeating steps b) and c) at least once.

Abstract: Technical solutions for mapping long nucleic acid sequence reads to a target sequence are provided. A directed graph, representing all or some of a genome and comprising one or more nonlinear topological components, is obtained for an organism having a heterozygous genome. Each nonlinear topological component has an initiating node and a terminal node connected by at least a first branch and a second branch. One of these branches corresponds to the target sequence. The directed graph uses a plurality of sequence reads from a biological sample of the organism. The sequence reads are overlapped by an unrestricted overhang amount, provided there is a minimum consensus region between each two sequence reads. A query sequence, encompassing at least the initiating node or the terminal node of a first nonlinear topological component, is obtained. The directed graph is used to form a mapping of the query sequence to the directed graph.

Abstract: The invention relates to a new method of sequencing a double stranded target polynucleotide. The two strands of the double stranded target polynucleotide are linked by a bridging moiety. The two strands of the target polynucleotide are separated using a polynucleotide binding protein and the target polynucleotide is sequenced using a transmembrane pore.

Abstract: Nucleic acid molecule analysis systems are described. The system may include a nucleic acid molecule attached to a particle with a characteristic dimension. The system may also include an aperture defined by a first electrode, a first insulator, and a second electrode. The aperture may have a characteristic dimension less than the characteristic dimension of the particle. The system may further include a first power supply in electrical communication with the first electrode and the second electrode. In addition, the system may include a second power supply configured to apply an electric field through the aperture. In some embodiments, the aperture may be defined by a first insulator. A portion of the first electrode may extend into the aperture. A portion of the second electrode may extend into the aperture.

Abstract: Described herein are methods, systems, and media for HLA typing an individual from nucleic acid or protein sequences. The methodology disclosed herein represents significant improvements over current methods of HLA typing.

Abstract: The present invention provides methods, compositions and kits for detecting duplicate sequencing reads. In some embodiments, the duplicate sequencing reads are removed.

Abstract: An example of a sequencing kit includes a flow cell, an encapsulation matrix precursor composition, and a radical initiator. The flow cell includes a plurality of chambers and primers attached within each of the plurality of chambers. The encapsulation matrix precursor composition consists of a fluid, a monomer or polymer including a radical generating and chain elongating functional group, a radical source, and a crosslinker. The radical initiator is part of the encapsulation matrix precursor composition or is a separate component.

Abstract: Provided herein are methods and composition for immune repertoire sequencing and single cell barcoding. The methods and compositions can be used to pair any two sequences originating from a single cell, such as heavy and light chain antibody sequences, alpha and beta chain T-cell receptor sequences, or gamma and delta chain T-cell receptor sequences, for antibody and T-cell receptor discovery, disease and immune diagnostics, and low error sequencing.

Abstract: One aspect of the invention is a method for amplifying alpha globin genes HBA1, HBA2 and HBA12 in a single PCR tube to determine an HBA genotype of a subject. This method employs five primers selected to accurate and sensitively identify the HBA1, HBA2, and HBA12, a gene found at a higher frequency in citizens of Saudi Arabia, by accurately annealing to nucleic acids in a biological sample and simultaneously amplifying sequences encoding the alpha globin genes. This invention includes a procedure and required reagents for the amplification of alpha globin genes in a single PCR tube.

Abstract: Chronic activation of the ?-Adrenergic Receptor (?-AR) can have deleterious effects on the heart, and animal models over-expressing the ?-AR develop heart failure. In the classical ?-AR pathway, activation of the receptor results in increased cyclic AMP (cAMP) levels. However, ?-ARs are desensitized in the failing heart and cAMP levels are decreased. Phosphodiesterase 3A (PDE3A) hydrolyzes cAMP in certain subcellular compartments in cardiac myocytes, regulating cAMP levels and subsequent protein kinase A mediated cell signaling. By virtue of being freely diffusable intracellularly and being reduced in failing myocardial tissue, cAMP is reduced in certain important cardiac myocyte subcellular compartments such as the microdomain occupied by phospholamban.

Abstract: Described herein are methods for determining a Caucasian subject's susceptibility to having or developing a complement-mediated disease comprising determining in the Caucasian subject the identity of one or more haplotypes, wherein the presence of one or more of the haplotypes indicates the subject's susceptibility for having or developing a complement-mediated disease.

Abstract: Methods of determining if a subject has an increased risk of poor recovery after suffering a stroke and methods of treating a subject recovering from a stroke. The methods comprise analyzing at least one plasma sample taken from the subject to assess a microRNA (miRNA) profile of the subject and comparing the subject's miRNA profile with a normal miRNA profile, to determine if the subject's miRNA profile is altered compared to a normal miRNA profile. An alteration of the subject's miRNA profile is indicative that the subject has an increased risk of poor recovery after suffering a stroke.

Abstract: Genotyping methods and compositions for selecting patients with cardiovascular disease who will benefit from treatment with HDL-raising or HDL mimicking agent, in particular with a CETP inhibitor/modulator

Abstract: The present inventors identified for the first time a germline genomic alteration that accounts for familial myeloproliferative neoplasms (MPN) and myeloid malignancies. More precisely, they identified a 700 kb germline duplication that predisposes patients to essential thrombocythemia (ET) with a high frequency of evolution to myelofibrosis (MF) secondary myelodysplastic syndromes (MDS) or acute myeloid leukemia (AML). Two out of the 6 duplicated genes (namely ATG2B and GSKIP) have been shown to be overexpressed in hematopoietic progenitors, and this overexpression cooperates with classical mutations in JAK2, MPL and CALR to generate the MPN phenotype. The presence of the 700 kb germline duplication is thus of poor prognosis for a MPN patient. The present invention discloses a method for detecting a predisposition of developing a MPN, as well as a prognostic method for assessing the probability that an ET-suffering patient will develop a myelofibrosis a secondary MDS or an AML.

Abstract: The invention provides compositions and methods for detecting a neoplasia (e.g., pancreatic cancer, lung cancer, colon cancer) in a subject sample (e.g., serum, blood, plasma, tissue). In particular embodiments, the invention provides methods for detecting BNC1 and ADAMTS1 promoter methylation in circulating DNA in serum.

Abstract: Disclosed are: (i) methods for identifying leukemia patients who (or leukemia cells that) do not exhibit an MLL-translocation, rearrangement or MLL-partial tandem duplication but who are nonetheless susceptible to treatment with DOT1L inhibitors; and (ii) methods for treating leukemia patients who (or inhibiting proliferation or inducing apoptosis of leukemia cells that) do not exhibit an MLL-translocation, rearrangement or MLL-partial tandem duplication with DOT1L inhibitors. The patients identified as susceptible and the patients (or cells) treated exhibit elevated expression of a IIOX cluster gene or of a HOX cluster-associated gene. Elevated expression of such genes can be measured, e.g.

Abstract: A system and method for determining a presence of cancer in a test sample from a test subject comprising a set of fragments of deoxyribonucleic acid (DNA). The fragments may be identified through probabilistic analyses or identified when determined to be hypermethylated or hypomethylated. The system generates a test feature vector with a score for each CpG site for use in a trained model. The score is based on a number of the fragments in the test sample that overlap the CpG site. The system inputs the test feature vector into the trained model. The trained model has a function that generates a cancer prediction based on the test feature vector and a set of classification parameters. The cancer prediction for the test sample may include a cancer prediction value for each cancer type that describes a likelihood the test sample is of that particular cancer type.

Abstract: A method and system for determining one or more sources of a cell free deoxyribonucleic acid (cfDNA) test sample from a test subject. The cfDNA test sample contains a plurality of deoxyribonucleic acid (DNA) molecules with numerous CpG sites that may be methylated or unmethylated. A trained deconvolution model comprises a plurality of methylation parameters, including a methylation level at each CpG site for each source, and a function relating a sample vector as input and a source of origin prediction as output. The method generates a test sample vector comprising a site methylation metric relating to DNA molecules from the test sample that are methylated at that CpG site. The method inputs the test sample vector into the trained deconvolution model to generate a source of origin prediction indicating a predicted DNA molecule contribution of each source.

Abstract: This disclosure is directed to the discovery of an improved method to diagnose malignant melanoma of the oral cavity in the dog.

Abstract: The present invention relates to methods of diagnosing melanoma in a subject, the method comprising detecting microRNA expression levels. The present invention also relates to methods of assessing the disease stage of melanoma and/or monitoring said melanoma stage. Also, the present invention relates to selecting a treatment or modifying a treatment based on the diagnosis or stage of melanoma. Further the present invention relates to a system for detecting and diagnosing melanoma in a patient and for determining the disease stage of melanoma.

Abstract: The present invention provides a method for predicting the treatment response of a human gastroesophageal cancer patient, the method comprising: a) measuring the gene expression of at least 3 of the following genes: CDH1, CDK6, COX2, ELOVL5, GATA4, EGFR, TBCEL, FGF7, CDH17, FNBP1, PIP5K1B, TWIST, CD44, MET, CEACAM1, TOX3, GLIPR2, GSTP1, RON, TMEM136, MYB, BRCA2, FGF1, POU5F1, EPR, DPYD, ABL2 and SH3RF1 in a sample obtained from the gastroesophageal tumour of the patient to obtain a sample gene expression profile of at least said genes; and b) making a prediction of the treatment response and/or prognosis of the patient based on the sample gene expression profile. Also provided are related computer-implemented methods and methods of treatment of gastroesophageal cancer.

Abstract: Provided here are methods of assessing prognosis for a patient who has been diagnosed with a type of cancer by measuring TREX2 mRNA expression in a biological sample from the patient, comparing the TREX2 mRNA expression in the biological sample to a reference value, and providing a prognosis based on alterations in the TREX2 mRNA expression and the type of cancer. Also provided here are methods of treating a patient with myelodysplastic syndrome by administering a therapeutically effective amount of a pharmaceutical composition that decreases TREX2 mRNA expression in the patient.

Abstract: Analysis of 13,023 genes in 11 breast and 11 colorectal cancers revealed that individual tumors accumulate an average of ˜90 mutant genes but that only a subset of these contribute to the neoplastic process. Using stringent criteria to delineate this subset, we identified 189 genes (average of 11 per tumor) that were mutated at significant frequency. The vast majority of these genes were not known to be genetically altered in tumors and are predicted to affect a wide range of cellular functions, including transcription, adhesion, and invasion. These data define the genetic landscape of two human cancer types, provide new targets for diagnostic and therapeutic intervention and monitoring.

Abstract: The present invention provides a Lactococcus lactis subspecies lactis isolate WFLU-12 with the accession number of KCTC 13180BP, and a use thereof.

Abstract: The present invention provides a coating agent for leather, the coating agent containing: in terms of solid content ratio, (I) an aqueous urethane resin; (II) a matting agent; and (III) a silicone acryl graft copolymer resin emulsion in which the weight ratio of a polyorganosiloxane represented by a specified formula relative to acrylic ester units or methacrylic ester units is 50:50 to 90:10, and a leather on which a coating by the coating agent for leather is formed. This coating agent for leather has exceptional wear resistance and anti-fouling properties, and a leather on which a coating by the coating agent is formed can maintain a high-quality external appearance and high wear resistance.

Abstract: On molten iron having the P concentration of 2 to 4 mass % and having the Cr concentration of 0.3 to 1.2 mass %, a dechromization treatment is performed by adjusting a basicity (CaO mass %)/(SiO2 mass %) of slag to greater than 0.1 and 1 or less and supplying an oxygen source with a molten iron temperature falling within a range of 1250 to 1500° C. to manufacture molten iron having the P concentration of 1.9 to 3.8 mass % and having the Cr concentration of less than 0.2 mass %.

Abstract: A method for processing a steel plate capable of removing residual strain at a trim edge thereof without causing overheating in areas of the steel plate other than the trim edge is provided. A method of processing a steel plate includes punching a steel plate and disposing heating electrodes in such a way that a trim edge punched in the punching is positioned between electrode surfaces facing each other and then heating a part of the steel plate including the trim edge.

Abstract: A method of strengthening a component made of a metallic material. The method includes subjecting the component to a mechanical grinding process incorporating a relative motion between a tool and the component forming a gradient structure on the surface of the component, resulting in increased tensile strength of the component. A method of strengthening a component made of a TWIP steel. The method includes subjecting the component made of TWIP steel to a mechanical grinding process incorporating a relative motion between a tool and the component forming a gradient structure containing a surface nanolaminate layer, a shear band layer, and an inner deformation twinned layer, resulting in increased tensile strength of the component. A component made of a TWIP steel containing a gradient structure with a surface nanolaminate layer, a shear band layer, and a deformation twinned layer.

Abstract: Provided are a cold-rolled steel sheet and a method for manufacturing same, the steel sheet containing, by weight %, 0.03 to 0.07% of C, 0.3% or less of Si, 2.0 to 3.0% of Mn, 0.01 to 0.10% of Sol.Al, 0.3 to 1.2% of Cr, 0.03 to 0.08% of Ti, 0.01 to 0.05 of Nb, 0.0010 to 0.0050% of B, 0.001-0.10% of P, 0.010% or less of S, 0.010% or less of N, the balance being Fe and other impurities, and having a microstructure comprising 75% or more to less than 87% by area of a transformed structure and 13 to 25% by area of ferrite, wherein the transformed structure includes martensite and bainite, the martensite has an average particle diameter of 2 ?m or less, the bainite has an average particle diameter of 3 ?m or less, the bainite fraction of 3 ?m or more is 5% or less.

Abstract: Provided are: a SOUR-resistant heavy-wall steel plate having excellent low-temperature toughness and post-heat treatment characteristics; and a method for manufacturing the same. The SOUR-resistant heavy-wall steel plate of the present invention comprises: in terms of weight %, 0.02-0.06% of C; 0.5% or less of Si (excluding 0%); 0.8-2.0% of Mn; 0.03% or less of P; 0.003% or less of S; 0.06% or less of Al; 0.01% or less of N; 0.005-0.1% of Nb; 0.005-0.05% of Ti; 0.0005-0.005% of Ca; one or more selected from 0.05-0.5% of Ni, 0.05-0.5% of Cr, 0.02-0.4% of Mo, and 0.005-0.1% of V; and the remainder Fe and unavoidable impurities, wherein the heavy-wall steel plate satisfies relational expressions 1-3, and has a percent ductile fracture of 85% or more in the drop weight tear test (DWTT) at ?20° C.

Abstract: Disclosed herein are system and methods to effectively leach coal ash with hydrochloric acid and separate an insoluble silica product and then selectively precipitate, from the leachate, a number to value-added, strategic, marketable products using a hydroxide reagent. The resulting precipitated products include iron, aluminum, magnesium, calcium, and a mixture of rare earth elements and transition metals. These can be separated as hydroxides or converted to oxides or carbonates. Using hydrochloric acid for leaching and converting the chloride to sodium chloride in the final step results in practically no waste for this process. The silica can be further purified using sodium hydroxide fusion or caustic leach methods and some minor streams from this process are recycled to minimize any waste stream. These systems and methods can be applied to a number of other industrial waste products such as red mud from the aluminum process, slag from steel furnaces, mine tailings, and other metal-bearing waste streams.

Abstract: A method for refining a titanium material, in which oxygen contained in a titanium material made of a pure titanium, a titanium alloy or an intermetallic compound containing titanium as one of main components is removed, the method includes: a first melting step of melting the titanium material under a noble gas atmosphere containing 5 to 70 vol % of hydrogen, thereby introducing hydrogen into a melt of the titanium material; and a second melting step of melting the titanium material into which hydrogen has been introduced in the first melting step under a noble gas atmosphere, thereby removing oxygen contained in the titanium material from the melt of the titanium material together with the hydrogen. Each of the first melting step and the second melting step is carried out at least once.

Abstract: An apparatus for the gasification and vitrification of waste comprises a plasma arc furnace provided with two movable graphite electrodes. The furnace includes an air-cooled bottom electrode adapted for transferring the current through a slag melt. The furnace is entirely sealed and is also provided with gas tight electrode seals adapted to control reducing conditions inside the furnace. An electrical circuit is further provided, which is adapted for switching from transferred io non-transferred modes of heating, thereby allowing the furnace to be restarted in case of slag freezing.

Abstract: A sodium removal method according to the present invention is a method for removing sodium from a sodium-containing solution by precipitating a sodium ion in the sodium-containing solution as a sodium salt, the method including: a sodium precipitating step of precipitating the sodium salt by decreasing a temperature of the sodium-containing solution so that a sodium concentration of the sodium-containing solution exceeds solubility of the sodium salt at said temperature; and a solid-liquid separation step of removing the precipitated sodium salt by solid-liquid separation.