Abstract: A method of evaluating subsurface connectivity, including: extracting biological material from samples obtained from a plurality of hydrocarbon wellbores, the biological material including nucleic acids, proteins, and lipids; determining microbial community structures based on the biological material, which includes determining an abundance of various species included in the samples; generating a reservoir connectivity analysis model, wherein the reservoir connectivity analysis model identifies a connectivity between at least two of the plurality of hydrocarbon wellbores in accordance with similarities in the microbial community structures at a plurality of subsurface locations that establish a path of fluid communication between the at least two of the plurality of hydrocarbon wellbores, wherein the reservoir connectivity analysis model includes a timing of the connectivity based on molecular biology; and generating a subsurface image or visualization, from the reservoir connectivity analysis model, that ind

Abstract: Biomarkers for identifying Johne's disease in cattle are presented herein, as are related methods, uses, agents, and kits comprising same. Methods for treating, detecting, quarantining, and diagnosing Johne's disease in cattle are presented herein.

Abstract: An apparatus includes a housing and an actuator. The housing, which defines a reagent volume that can receive a reagent container, can be removably coupled to a reaction chamber. A delivery portion of the housing defines a delivery path between the reagent volume and the reaction chamber when the housing is coupled to the reaction chamber. The delivery path includes a protrusion such that the delivery path has a discontinuous inner surface. The actuator can be moved to convey a reagent from the reagent container into the reaction chamber via the delivery path.

Abstract: Provided are methods, compositions, devices, and kits for detecting bacteria in a sample. The methods, compositions, devices, and kits are specially useful for diagnosis and prognosis of an individual suspected of having bacterial infection. The methods, compositions, devices, and kits are applicable to a wide variety of areas, for example, medical diagnostics, industries involving bacterial fermentation, dairy and wine industries, prevention of bioterrorism.

Abstract: A bacteria detection device moves a stage on which a detection chip is placed with a membrane filter fixed thereon by a first driving mechanism and a second driving mechanism in front-rear direction and in left-right direction so that an image of an upper surface of the membrane filter to which excitation light from a light emitter aligned with a imaging range by an imaging unit is taken. If bacteria to which a fluorescent label has been bound is captured on the upper surface of the membrane filter, the imaging unit can take an image of the bacteria as luminous points. A controller counts the luminous points in the image taken by the imaging unit so that the bacteria captured on the upper surface of the membrane filter can be detected.

Abstract: The disclosure relates generally to methods for measuring bacteria in biological samples. More particularly, the disclosure relates to methods for measuring bacteria using an aqueous clearance solution.

Abstract: A method of performing antimicrobial susceptibility testing (AST) on a sample uses a reader device that mounts on a mobile phone having a camera. A microtiter plate containing wells preloaded with the bacteria-containing sample, growth medium, and drugs of differing concentrations is loaded into the reader device. The wells are illuminated using an array of illumination sources contained in the reader device. Images of the wells are acquired with the camera of the mobile phone. In one embodiment, the images are transmitted to a separate computing device for processing to classify each well as turbid or not turbid and generating MIC values and a susceptibility characterization for each drug in the panel based on the turbidity classification of the array of wells. The MIC values and the susceptibility characterizations for each drug are transmitted or returned to the mobile phone for display thereon.

Abstract: The present invention provides a method of recovering viable microbial cells from a complex sample, said method comprising: a) providing a sample having a volume of at least 1 ml; b) contacting said sample with a buffer solution and one or more proteases, wherein said buffer solution has a pH of at least pH 6 and less than pH 11, wherein said buffer solution and said one more proteases do not comprise a detergent or a chaotrope, and wherein the buffer solution/protease/sample mixture is non-hypotonic; c) filtering the mixture obtained in step (b) through a filter suitable for retaining microbial cells; and d) recovering the microbial cells retained by the filter in step (c), wherein the recovered microbial cells are viable, and a microbial recovery device for the same.

Abstract: Provided is a compound which accelerates the enzymatic reaction catalyzed by an oxidase. The present invention provides an oxidase reaction accelerating agent comprising a compound represented by formula (I) and a method using the same.

Abstract: An object of the present invention is to provide a blood analysis method and a blood test kit, which are for performing quantitative analysis of components by precisely obtaining a dilution factor.

Abstract: A ribonucleic acid (RNA) reverse transcription amplification method, comprising the steps of reverse transcription of RNA into cDNA and immediate amplification of cDNA, characterized in that the process of reverse transcription of RNA into cDNA is completed during the process that a cDNA amplification reaction system is heated to reach the reaction condition for cDNA amplification. The RNA reverse transcription amplification method can combine the reaction condition for reverse transcription of RNA into cDNA with the reaction condition for cDNA amplification, thereby significantly shorten the time required for RNA reverse transcription amplification. And in the whole process of RNA reverse transcription amplification, there is no need to change the instrument temperature, and thus, it is possible to achieve detection at any time.

Abstract: The invention provides methods for simultaneously amplifying multiple nucleic acid regions of interest in one reaction volume as well as methods for selecting a library of primers for use in such amplification methods. The invention also provides library of primers with desirable characteristics, such as minimal formation of amplified primer dimers or other non-target amplicons.

Abstract: Methodologies for labeling the epigenetic modification 5-hydroxymethyl-cytosine (5hmC) along a DNA molecule, and for imaging this epigenetic modification along a DNA molecule are disclosed. Related compositions and reagents, and methods of preparing same are also disclosed.

Abstract: Automated methods for extracting nucleic acid from one or more tissue samples disposed on slides are disclosed. The methods utilize an automated slide staining apparatus that dispenses a plurality of nucleic acid extraction reagents onto the tissue sample, thus creating an extracted nucleic acid sample. The extracted nucleic acid sample may be used directly in downstream applications such as nucleic acid amplification or sequencing procedures, or may be further purified.

Abstract: The present invention relates to a new method of labelling any target molecules from a plurality of entities, preferably in high throughput regimes, i.e. allowing the analysis of several thousands of entities per run, while preserving the integrity of the single-entity information. This method is based on a tandem molecular barcoding in which all molecular targets are labelled with a first unique barcode which is different for each molecular target from an entity, and with a tag sequence coding the entity from which the molecular target originates. Once this tandem barcoding is performed, the absolute quantification of all molecular targets with a single-entity resolution may be carried out in a single run of next-generation sequencing.

Abstract: Methods and reagents for preparing nucleic acid samples for sequencing are provided. The samples include formalin-fixed (FFPE) samples. The methods comprise contacting a nucleic acid sample with a multimeric barcoding reagent comprising barcode regions linked together and appending barcode sequences to nucleic acid sequences of a target nucleic acid molecule. Methods are also provided that additionally use in-vitro transposition, coupling sequences and/or primer-extension to append barcode sequences to nucleic acid sequences of a target nucleic acid molecule.

Abstract: Reagents and methods for preparing nucleic acid samples for sequencing are provided. The reagents include multimeric barcoding reagents that comprise barcode regions linked together and a cell-binding moiety. The methods comprise contacting a nucleic acid sample comprising cells with a library of multimeric barcoding reagents, wherein each multimeric barcoding reagent comprises barcode regions linked together, and appending barcode sequences of a first multimeric barcoding reagent to sub-sequences of a target nucleic acid of a first cell, and appending barcode sequences of a second multimeric barcoding reagent to sub-sequences of a target nucleic acid of a second cell. Methods are also provided that comprise steps of internalising multimeric barcoding reagents into cells (e.g. by endocytosis) or exposing multimeric barcoding reagents to target nucleic acids by lysing cells or permeabilizing cell membranes.

Abstract: Methods of diagnosing and treating patients afflicted with acne, including diagnosing one as having acne if the individual possesses RT4, RT5, RT7, RT8, RT9, or RT10. Methods for treating acne include administering an effective amount of a drug specifically targeting RT4, RT5, RT7, RT8, RT9, or RT10, such as small molecules, antisense molecules, siRNAs, biologics, antibodies, phages, vaccines, or combination thereof.

Abstract: The invention provides methods for detecting single nucleotide variants in breast cancer, bladder cancer, or colorectal cancer. Additional methods and compositions, such as reaction mixtures and solid supports comprising clonal populations of nucleic acids, are provided.

Abstract: The present disclosure provides a system and method for the detection of rare mutations and copy number variations in cell free polynucleotides. Generally, the systems and methods comprise sample preparation, or the extraction and isolation of cell free polynucleotide sequences from a bodily fluid; subsequent sequencing of cell free polynucleotides by techniques known in the art; and application of bioinformatics tools to detect rare mutations and copy number variations as compared to a reference. The systems and methods also may contain a database or collection of different rare mutations or copy number variation profiles of different diseases, to be used as additional references in aiding detection of rare mutations, copy number variation profiling or general genetic profiling of a disease.

Abstract: A method and system for classifying a target nucleic acid includes exposing, in a test system, one or more capture probes to the target nucleic acid. The one or more capture probes is attached to a surface. A first hybridization condition is established in the test system. A first degree of hybridization of the one or more capture probes with the target nucleic acid under the first hybridization condition is determined. A second hybridization condition in the test system is established. A second degree of hybridization of the one or more capture probes with the target nucleic acid under the second hybridization condition is determined and the target nucleic acid is classified by comparing the first and the second degrees of hybridization.

Abstract: The present invention relates to methods and devices for identifying and quantifying, including low abundance, nucleotide base mutations, insertions, deletions, translocations, splice variants, miRNA variants, alternative transcripts, alternative start sites, alternative coding sequences, alternative non-coding sequences, alternative splicings, exon insertions, exon deletions, intron insertions, or other rearrangement at the genome level and/or methylated nucleotide bases.

Abstract: Disclosed is a method for detecting single nucleotide polymorphism (SNP) using a feature that the 5?-flap endonuclease (FEN) activity of DNA polymerase is inhibited when a probe complementarily binds to the end of a polymerase chain reaction (PCR) product. More specifically, the present invention relates to a novel method wherein it was verified that, when a probe used for a real-time PCR complementarily binds to the end site of a PCR product, the 5?-FEN activity of thermostable DNA polymerase to the probe is inhibited, and thus when such a feature is used to make a design such that an SNP site to be detected is located at the 5?-end site of the probe, the 5?-flap formation is induced according to the allele, thereby allowing effective SNP detection.

Abstract: A polynucleotide comprising a hybrid nucleotide sequence representative of a deletional mutation of the GYPB gene, wherein the hybrid nucleotide sequence representative of a deletional mutation of the GYPB gene has a sequence according to SEQ ID NO 1 or SEQ ID NO 2, or a complementary sequence thereto

Abstract: The present invention provides methods of making and using self-assembled arrays of single polynucleotide molecules for carrying out a variety of large-scale genetic measurements, such as gene expression analysis, gene copy number assessment, and the like. Random arrays used in the invention are “self-assembled” in the sense that they are formed by deposition of polynucleotide molecules onto a surface where they become fixed at random locations. The polynucleotide molecules fixed on the surface are then identified by direct sequence determination of component nucleic acids, such as incorporated probe sequences, or by other decoding schemes. Such identification converts a random array of determinable polynucleotides, and their respective probes into an addressable array of probe sequences.

Abstract: System, including methods, apparatus, compositions, and kits, for making and using a stabilized emulsion. A method of generating a stabilized emulsion is provided. In the method, an aqueous phase may be provided. The aqueous phase may include an effective concentration of one or more skin-forming proteins. An emulsion may be formed. The emulsion may include droplets of a dispersed phase disposed in a continuous phase, with the aqueous phase being the continuous phase or the dispersed phase. The emulsion may be heated to create an interfacial skin between each droplet and the continuous phase, to transform the droplets into capsules.

Abstract: A digital and quantitative PCR (dqPCR) measuring method for a nucleic acid sample is provided, including providing a testing plate having a plurality of reaction wells, so as to perform a dqPCR reaction on the nucleic acid sample. Especially for the nucleic acid sample to be tested having a plurality of nucleic acid targets with different concentration ranges of wide variations, digital PCR and quantitative PCR can be performed simultaneously, so as to quantify the copy number of nucleic acid targets.

Abstract: The present invention relates to a method for amplifying at least three target nucleic acid molecules with reduced primer dimer formation in a multiplex amplification reaction. The method of present invention can inhibit primer dimer formation and hence generation of nonspecific amplification products in an effective manner in a multiplex amplification reaction for at least three target nucleic acid molecules.

Abstract: A method for determining the integrity of the genome of a sample and/or the quality of a library of DNA sequences obtained by deterministic restriction site whole genome amplification can include (a) amplifying the library of DNA sequences to produce first, second, and third PCR products each of a different size from 50 bp to 1000 bp, by PCR using at least one first primer pair, one second primer pair and one third primer pair, the primer pairs each hybridizing to a DNA sequence of the library having a length from 1000 bp to 5000 bp and corresponding to a sequence of the genome located respectively on a first, second and third chromosome arm; (b) detecting the first, second and third PCR products; (c) correlating the presence of the first, second and third PCR products with the integrity of the genome of the sample and/or the quality of the library.

Abstract: Provided herein are methods of capturing a nucleic acid comprising a target oligonucleotide sequence from a library of nucleic acid that include: contacting a library of nucleic acids comprising a nucleic acid comprising a target oligonucleotide sequence with a probe comprising a sequence that is complementary to the target oligonucleotide sequence, wherein the contacting is performed in a tetramethylammonium chloride (TMAC)-based buffer at a temperature of about 60° C. to about 70° C., and the contacting results in the hybridization of the target oligonucleotide sequence to the sequence that is complementary to the target oligonucleotide sequence, to thereby generate a hybridization product; and isolating the hybridization product from nucleic acids in the library that do not comprise the target oligonucleotide sequence. Also provided are compositions useful for performing these methods.

Abstract: Provided herein is a method for analyzing polynucleotides such as genomic DNA. In certain embodiments, the method comprises: (a) treating chromatin isolated from a population of cells with an insertional enzyme complex to produce tagged fragments of genomic DNA; (b) sequencing a portion of the tagged fragments to produce a plurality of sequence reads; and (c) making an epigenetic map of a region of the genome of the cells by mapping information obtained from the sequence reads to the region. A kit for performing the method is also provided.

Abstract: This disclosure provides methods and compositions for sample processing, particularly for sequencing applications. Included within this disclosure are bead compositions, such as diverse libraries of beads attached to large numbers of oligonucleotides containing barcodes. Often, the beads provides herein are degradable. For example, they may contain disulfide bonds that are susceptible to reducing agents. The methods provided herein include methods of making libraries of barcoded beads as well as methods of combining the beads with a sample, such as by using a microfluidic device.

Abstract: Provided herein are methods, compositions, systems, and kits for diagnosing acute rejection of solid organ transplants using at least 5 genes selected from a 10-gene panel.

Abstract: The present invention provides a test method and an evaluation kit for determining the risk of antithyroid drug-induced agranulocytosis. More particularly, it provides a test method for determining the risk of antithyroid drug-induced agranulocytosis, including testing susceptibility polymorphism to antithyroid drug-induced agranulocytosis, and determining the risk of antithyroid drug-induced agranulocytosis, and an evaluation kit for the risk of antithyroid drug-induced agranulocytosis, containing a polynucleotide capable of detecting susceptibility polymorphism to antithyroid drug-induced agranulocytosis.

Abstract: A system and method for determining the genetic data for one or a small set of cells, or from fragmentary DNA, where a limited quantity of genetic data is available, are disclosed. Genetic data for the target individual is acquired and amplified using known methods, and poorly measured base pairs, missing alleles and missing regions are reconstructed using expected similarities between the target genome and the genome of genetically related subjects. In accordance with one embodiment of the invention, incomplete genetic data is acquired from embryonic cells, fetal cells, or cell-free fetal DNA isolated from the mother's blood, and the incomplete genetic data is reconstructed using the more complete genetic data from a larger sample diploid cells from one or both parents, with or without genetic data from haploid cells from one or both parents, and/or genetic data taken from other related individuals.

Abstract: The present invention relates to a method of diagnosing eczema and/or psoriasis, wherein said method differentiates between eczema and psoriasis, and comprises determining the expression of at least two markers in a sample taken from an individual, wherein said at least two markers are selected from CCL27, NOS2, IL36G, KLK13, SOST, NPTX1, PLA2G4D, GDA, IL36A, TGM1, CLEC4G, IL13, TCN1, TMPRSS11D and RHCG, provided that said at least two markers consist of or comprise (a) CCL27 and NOS2; (b) CCL27 and KLK13; (c) IL36G and KLK13; (d) CCL27 and IL36G; (e) NOS2 and IL36G; (f) NOS2 and KLK13; (g) SOST; or (h) NPTX1; and assessing on the basis of the expression of said at least two markers whether the individual is afflicted with eczema and/or psoriasis.

Abstract: Disclosed herein are methods for determining inflammation in subjects. Also disclosed are methods for determining whether a subject has sepsis. The methods include determining methylation of preproinsulin DNA and chromatin target of PRMT1 (CHTOP).

Abstract: An immune response subtype of cancer is associated with DNA damage which allows subjects to be stratified for particular therapies including immune therapies which may be combined with DNA damage therapeutics. A method for predicting responsiveness to an antagonist of an inhibitory immune checkpoint and/or an agonist of a stimulatory immune checkpoint comprises determining the expression level of at least one gene selected from Table 2B, 2A or 1 in a sample from the subject. The determined expression level is used to predict responsiveness to an antagonist of an inhibitory immune checkpoint and/or an agonist of a stimulatory immune checkpoint.

Abstract: The present disclosure relates to a biomarker capable of detecting the genes T3dh (type III alcohol dehydrogenase, CG3425), fbp (fructose 1,6-bisphosphatase, CG31692) and AGL (amylo-alpha-1,6-glucosidase, 4-alpha-glucanotransferase, CG9485), which are involved in the induction and occurrence of aging, obesity and cancer, and thereby determining the progression of aging, determining obesity and diagnosing cancer rapidly, accurately and simply. The biomarker may be used to analyze or diagnose the progression of aging, cancer and obesity in a human, a non-human mammal or an insect individually or collectively.

Abstract: [Problem] To provide: a marker and a kit both for use in the prediction of ovarian cancer prognosis; and a prognosis prediction method. [Solution] A marker and a kit, both for use in the prediction of ovarian cancer prognosis, each of said marker and kit containing a transcript of matrix metalloprotease (MMP) 1 gene; and a method for predicting ovarian cancer prognosis using the marker or the kit, in which the expression level of matrix metalloprotease (MMP) 1 gene in a biological sample collected from a subject is by detecting an ovarian cancer prognosis prediction marker comprising a transcript of matrix metalloprotease (MMP) 1 gene and then obtaining a detection value of the ovarian cancer prognosis prediction marker.

Abstract: Disclosed are methods of selecting a therapy for a cancer patient and methods of treating cancer in the patient. The methods comprise detecting a mutation in one or more genes in a cancer cell from the patient, wherein the one or more genes is selected from the group consisting of PTCD2, TWF1, DEFB134, BBS1, SOX10, APLNR, CD58, COL17A1, CRKL, hsa-mir-101-2, hsa-mir-548s, MAD2L1, MLANA, PSMB5, RNPS1, RPL10A, RPL23, SRP54, TAF3, TAP1, TAP2, TAPBP, TBXAS1, GMIP, OTOA, LAIR1, CLEC1, GPSM3, TRAF1, JAK2, TAPBPL, ICAM1, LILRA1, LILRA3, STAT1, and HLA-F. Also disclosed are methods of screening for one or more genes, the mutation of which confers resistance to T cell-mediated cytolytic activity.

Abstract: Embodiments provide methods and compositions related to determining treatments for colorectal cancer patients by detection and analysis of the expression level of miRNA such as miR-320e in the patients.

Abstract: The present disclosure provides methods of detecting a wnt-?-catenin-mediated cancer and an immunotherapy resistant cancer by detecting the presence of an associated biomarker. Further, methods of threating the wnt-?-catenin-mediated cancer or immunotherapy resistant cancer are provided.

Abstract: A predictive cancer model generates a cancer prediction for an individual of interest by analyzing values of one or more types of features that are derived from cfDNA obtained from the individual. Specifically, cfDNA from the individual is sequenced to generate sequence reads using one or more physical assays, examples of which include a small variant sequencing assay, whole genome sequencing assay, and methylation sequencing assay. The sequence reads of the physical assays are processed through corresponding computational analyses to generate each of small variant features, whole genome features, and methylation features. The values of features can be provided to a predictive cancer model that generates a cancer prediction. In some embodiments, the values of different types of features can be separately provided into different predictive models. Each separate predictive model can output a score that can serve as input into an overall model that outputs the cancer prediction.

Abstract: The invention provides methods, nucleic acids and kits for detecting, or for detecting and distinguishing between or among liver cell proliferative disorders or for detecting, or for detecting and distinguishing between or among colorectal cell proliferative disorders. The invention discloses genomic sequences the methylation patterns of which have utility for the improved detection of and differentiation between said class of disorders, thereby enabling the improved diagnosis and treatment of patients.

Abstract: It is provided a tumor promoting alternative splicing isoform of PACE4, named PACE4-alt CT, analytes specifically binding to PACE4-alt CT, such as antibodies, and use of same for detecting a cancer, such as prostate cancer. It is also provided a method treating a cancer in a patient comprising administering an inhibitor of PACE4-altCT to a patient in need thereof and a kit comprising an analyte specific reagent specifically binding to PACE4-altCT for detecting a cancer.

Abstract: The present invention refers to an in vitro method for identifying patients at risk of suffering from colorectal cancer and/or colorectal adenomas, preferably advanced colorectal adenomas, based on measuring the expression profile or level of some miRNAs, e.g. miR-15b, which are up-regulated or over-expressed in patients suffering from said diseases.

Abstract: Disclosed herein is a method for validation of continuous viral clearance comprising the steps of providing a probe to be validated, spiking the probe in a valid manner, performing viral clearance, sampling the spiked probe and analyzing the sample of the spiked probe of step d).

Abstract: Applicant discloses herein kits for identifying the presence of Zika virus in a sample. In embodiments, these kits comprise reagents disclosed herein. Applicant further provides kits for use in detecting ZIKV in a sample, the kits comprising reagents disclosed herein. In embodiments, kits include primers directed to Zika virus (ZIKV) nucleic acid sequences, the primers capable of hybridizing to ZIKV nucleic acids and to copies of ZIKV nucleic acids (including to cDNA copies of ZIKV nucleic acids). Applicant discloses herein reagents for detecting Zika virus (ZIKV) in a sample, the reagents including one or more nucleic acid primers that are capable of hybridizing to a ZIKV nucleic acid (including to cDNA copies of ZIKV nucleic acids).

Abstract: The invention provides for a portable, self-contained reverse osmosis system of which all necessary components to carry out substrate processing fit within the containment vessel. The invention weighs fewer than 50 pounds, consumes fewer than 250 watts of electricity, and can easily be carried from one location to another. While the invention is capable of processing hundreds of gallons of substrate per day, it can efficiently process as little as one gallon of substrate at a given time.